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Preprint ARTICLE | doi:10.20944/preprints202403.0244.v1

The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa

Nelson Nazzicari, Nicolo Franguelli, Barbara Ferrari, Luciano Pecetti, Paolo Annicchiarico

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: legumes; alfalfa; genomic selection; SNP calling pipeline; autotetraploidy; polyploidy; genome parametrization; SNP subsetting

Online: 5 March 2024 (10:25:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0085.v1

A Concept for Conducting User Studies in Vehicles and Stationary Test Rooms During the COVID-19 Pandemic

Timmy Kantusch, Advan Sinanovic, Stefanie Marker

Subject: Engineering, Automotive Engineering Keywords: user studies; pandemic; COVID-19; hygiene concept

Online: 5 July 2021 (09:59:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1705.v1

MixDeR: A SNP Mixture Deconvolution Workflow for Forensic Genetic Genealogy

Rebecca Mitchell, Michelle Peck, Erin Gorden, Rebecca Just

Subject: Biology And Life Sciences, Other Keywords: mixtures; SNPs; forensic genetic genealogy (FGG); investigative genetic genealogy (IGG); Kintelligence; software

Online: 24 July 2024 (14:45:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0971.v1

AI-Enabled Pipeline for Virus Detection, Validation, and SNP Discovery from Next-Generation Sequencing Data

Abozar Ghorbani, Pietro Hiram Guzzi, Mahsa Rostami

Subject: Biology And Life Sciences, Virology Keywords: virus detection; next-generation sequencing; bioinformatics analysis; SNP discovery; viral genomics; AI-assisted genomics

Online: 14 May 2024 (13:26:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1319.v1

Dysnatremia as a Mortality Marker in Intensive Care Patients with SARS-CoV-2 Infection

Guler Eraslan Doganay, Melek Doganci, Gulsah Yurtseven, Azra Ozanbarci, Abdullah Kahraman, Ozgur Cirik, Fatma Ozturk Yalcin, Seray Hazer, Kerem Ensarioglu

Subject: Medicine And Pharmacology, Other Keywords: COVID-19; Dysnatremia; Hypernatremia; Hyponatremia; Mortality; SARS-CoV-2.

Online: 20 May 2024 (20:15:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1431.v1

Increasing the number of contributors identified by SNP panels

Darrell Ricke

Subject: Biology And Life Sciences, Other Keywords: DNA mixture; single nucleotide polymorphism; mixture analysis; high throughput sequencing; massively parallel sequencing; SNP panels

Online: 26 February 2024 (10:54:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202404.0886.v1

Postprandial Plasma Glucose between 4 and 7.9 Hours May Be a Potential Diagnostic Marker for Diabetes

Yutang Wang, Yan Fang, Christopher L. Aberson, Fadi J. Charchar, Antonio Ceriello

Subject: Biology And Life Sciences, Life Sciences Keywords: postprandial; non-fasting; fasting; glucose; diabetes

Online: 15 April 2024 (04:31:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202112.0238.v1

Genetic Risks and Demographic History of Indigenous Goats of Mongolia Revealed by SNP Genotyping

Alexey Piskunov, Vera Mukhina, Gulnara Svishcheva, Valery Voronkova, Yurii Stolpovsky

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SNP; Mongolian goats; conservational genetics; genotyping

Online: 14 December 2021 (13:25:27 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202408.1349.v1

An Adult Goldenhar Syndrome Patient With a Mosaic Small Su-Pernumerary Marker Chromosome (sSMC) Identified As Ring Chromosome 19

Buse Duru Dikmen, Sarmad Ali, Bin Zhang, M Anwar Iqbal

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Goldenhar Syndrome; small supernumerary marker chromosome (sSMC); mosaic ring chromosome 19; 16p12.2 deletions; chromosomal microarray; comparative genomic hybridization; genetic testing

Online: 20 August 2024 (12:37:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0681.v1

Cancer-associated Systemic Abnormality: A Novel Marker Panel for Early-stage Breast Cancer Characterization

Stefan Schreier, Prapaphan Budchart, Suparerk Borwornpinyo, Lakkana Adireklarpwong, Prakasit Chirappapha, Wannapong Triampo, Panuwat Lertsithichai

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: early-stage breast cancer; circulating tumor cells; rare cells, liquid biopsy; systemic cancer; cytomorphology

Online: 12 February 2024 (11:37:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.2257.v1

Genetic Diversity and Population Structure of Bursaphelenchus xylophilus in Central China based on SNP Markers

Aixia Yang, Xiaolei Ding, Yuan Feng, Tingting Chen, Jianren Ye

Subject: Biology And Life Sciences, Forestry Keywords: Bursaphelenchus xylophilus; SNP; genetic diversity; population differentiation (List three to ten pertinent keywords specific to the article yet reasonably common within the subject discipline.)

Online: 31 May 2023 (13:23:36 CEST)

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Working Paper ARTICLE

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

Tomasz Mamos, Michał Grabowski, Tomasz Rewicz, Jamie Bojko, Domink Strapagiel, Artur Burzyński

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Amphipoda; invasive species; population genetics; miogenome; Ponto-Caspian; SNP

Online: 7 September 2021 (10:56:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1167.v1

Discovery of Novel Potential Prognostic Marker and Targeted Therapy to Overcome Chemotherapy Resistance in an Advanced Stage Wilms’ Tumor

Pongsakorn Choochuen, Natakorn Nokchan, Natthapon Khongcharoen, Wison Laochareonsuk, Komwit Surachat, Thirachit Chotsampancharoen, Thanit Sila, Surasak Sangkhathat

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Wilms’ tumor; Chemotherapy resistance; Biomarkers; Somatic mutation; Targeted therapy; Cancer-driver mutation

Online: 17 April 2024 (15:03:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0092.v1

A Bridge Between the Breath and the Brain: Synchronization of Respiration, a Pupillometric Marker of the Locus Coeruleus, and an EEG Marker of Attentional Control State

Michael Christopher Melnychuk, Ian H. Robertson, Emanuele R.G. Plini, Paul M. Dockree

Subject: Social Sciences, Behavior Sciences Keywords: breath; respiration; synchronization; coupling,; EEG; theta-beta ratio; pranayama; meditation; attention; citta vritti

Online: 6 September 2021 (12:49:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.2134.v2

The Musa Marker Database: a Comprehensive Genomic Resource for the Improvement of the Musaceae Family

Manosh Kumar Biswas, Dhiman Biswas, Ganjun Yi, Guiming Deng

Subject: Biology And Life Sciences, Horticulture Keywords: Microsatellite; SNP; ILP; database; Musa sp.

Online: 15 April 2024 (10:44:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0149.v1

Isolation and Characterization of Analytical Marker Compound from Polyherbal Antigout Remedy

Ayisha Shaukat, Khalid Hussain

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Betulin; palmitoleic acid; NMR; EIMS; fragmentation; polyherbal

Online: 9 January 2023 (07:02:22 CET)

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Preprint REVIEW | doi:10.20944/preprints202403.1084.v1

Unveiling the Significance of LysE in Survival and Virulence of Mycobacterium Tuberculosis: A Comprehensive Review reveals it as a potential Drug Target, Diagnostic Marker, and a Vaccine Candidate

Shilpa Upadhyay, Archana Dhok, Supriya Kashikar, Zahiruddin Syed Quazi, Vinod Agarkar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Lysine exporter; mycobacterium tuberculosis; LysE; transmembrane protein; lysine; arginine

Online: 19 March 2024 (05:12:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.2011.v1

Comparative Analysis of Malaxidinae (Orchidaceae) Plastome: Phylogenetic Relationship and Potential Molecular Marker

Meng-Yao Zeng, Ming-He Li, Jingshan Shi, Jurun Zhao, Ying Zhou, Siren Lan, Zhong-Jian Liu

Subject: Biology And Life Sciences, Plant Sciences Keywords: Malaxidinae; plastid genome; comparative genomics; phylogeny

Online: 26 December 2023 (14:34:08 CET)

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Working Paper ARTICLE

Lipofuscin-Type Pigment as a Marker of Colorectal Cancer

Sónia Carvalho, Isa Carneiro, Rui Henrique, Valery Tuchin, Luís Oliveira

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: optical properties of tissues; tissue spectroscopy; differentiated pigment content; colorectal cancer; optical cancer detection; absorption coefficient; scattering coefficient; scattering anisotropy; light penetration depth

Online: 30 October 2020 (09:02:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0209.v1

Combination Breeding and Marker-Assisted Selection to Develop Late Blight Resistant Potato Cultivars

Mariya P. Beketova, Nadezhda A. Chalaya, Nadezhda M. Zoteyeva, Alena A. Gurina, Mariya A. Kuznetsova, Miles Armstrong, Ingo Hein, Polina E. Drobyazina, Emil E. Khavkin, Еlena V. Rogozina

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Rpi-genes; parental lines; hybrid progeny; dRenSeq; SCAR markers.

Online: 14 October 2021 (08:38:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0178.v1

ALCAM: A Novel Surface Marker on EpCAMlow Circulating Tumor Cells

Harrys Kishore Charles Jacob, Rossana Signorelli, Teresa Maidana Giret, Oliver Umland, Marco Hadisurya, Shweta Lavania, Charles Richard John Lalith, Ashley Nicole Middleton, Belinda Minucci Boone, Ayse Burcu Ergonul, Weiguo Andy Tao, Haleh Amirian, Anton Iliuk, Aliya Mahmood Khan, Robert Alexander Diaz, Daniel Bilbao Cortes, Monica Tulia Garcia-Buitrago

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Biomarkers; Pancreatic Cancer; CTC; Surfaceome; Protemics; Flow Cytometry; ALCAM

Online: 12 July 2022 (09:11:05 CEST)

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Working Paper ARTICLE

p53 Antibodies as a Diagnostic Marker for Cancer: a Metanalysis

Navid Sobhani, Giandomenico Roviello, Alberto D'Angelo, Raheleh Roudi, Praveen Kumar Neeli, Daniele Generali

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Meta-analysis; p53 wild type antibodies; p53 mutant antibodies; cancer survival prognostic factor.

Online: 24 September 2021 (12:46:26 CEST)

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Importance: p53 is an unequivocal tumor suppressor altered in half cancers. The immune system produces systemic p53 autoantibodies (p53 Abs) in many cancer patients. Objective: The focus of this systemic review and meta-analysis is on the prognostic value of p53 Abs expressed in the serum of patients with solid tumors. Data Sources: All the clinical investigations were searched on PubMed, MBase and Cochrane from 1993 reporting the first study until May 2021. Study Selection: Studies were included that met the following criteria: 1) participants with cancer; 2) outcome results expressed in relation to the presence of a p53 antibody; 3) a primary outcome (disease free survival, overall survival or progression free survival) expressed as hazard ratio (HR). The following exclusion criteria were used: 1) insufficient data available to evaluate outcomes; 2) animal studies; 3) studies with less than 10 participants. 1333 potentially relevant articles; studies as duplicates, non-patients studies or reviews were excluded. After viewing the titles and abstracts of the 52 remaining studies, the full texts of 34 studies were retrieved and 12 studies were included in the analysis. Data Extraction and Synthesis: PRISMA guidelines were used for abstracting and assessing data quality and validity by three independent observers. The summary estimates were generated using a fixed-effect model (Mantel–Haenszel method) or a random-effect model (DerSimonian–Laird-method) depending on the absence or presence of heterogeneity (I2). Main Outcome(s) and Measure(s): The primary study outcome was to determine the prognostic value of p53 Abs from a large population size of patients with solid tumors, as determined before data collection. Results: In total 12 clinical studies and of which 2094 patients were included and it was determined that p53-wt Abs expression in the serum significantly correlated with a worse survival of cancer patients (95% CI 1.48 [1.24, 1.77]; p<0.00001). On the contrary, data from literature indicated that there was a potential association between p53-mut Abs antibodies with better survival. Conclusions and Relevance: This is the first meta-analysis proving the diagnostic utility of p53-Abs for cancer patients, predicting a worse outcome. The serum-p53 value (s-p53-value) could be useful for future theranostics.

Working Paper ARTICLE

Inducible Selectable Marker Genes to Improve Aspergillus fumigatus Genetic Manipulation

Clara Baldin, Alexander Kühbacher, Petra Merschak, Luis Enrique Sastré-Velásquez, Beate Abt, Anna-Maria Dietl, Hubertus Haas, Fabio Gsaller

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: dominant selectable marker; Aspergillus fumigatus; inducible marker; hph; ptrA; xylanase promoter; thiamine; hygromycin; pyrithiamine

Online: 24 May 2021 (13:22:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202102.0202.v2

Real-Time Musculoskeletal Kinematics and Dynamics Analysis Using Marker- and IMU-based Solutions in Rehabilitation

Dimitar Stanev, Konstantinos Filip, Dimitrios Bitzas, Sokratis Zouras, Georgios Giarmatzis, Dimitrios Tsaopoulos, Konstantinos Moustakas

Subject: Engineering, Automotive Engineering Keywords: musculoskeletal; kinematics; dynamics; muscle forces; joint reactions; ground reactions; inertial measurement units

Online: 26 February 2021 (12:07:54 CET)

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Working Paper ARTICLE

Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat

Yun Dong Lv, Zhang Chuan Liang, Rui Yv, Juntao Jian, Hui Jian Wu, Peng Xiao Song, Xin Jian Yao, Bo Peng Song, Yuan Ze Zhang, Dejun Han, Jie Dao Sun

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: wheat; plant height; grain traits; Wheat50K; genetic map; QTL

Online: 22 April 2021 (10:20:48 CEST)

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Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main QTLs that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map quantitative trait loci (QTLs) for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as re-combination-rich areas in all chromosomes except chromosome 1B. The middle area of the chro-mosomes was identified as the recombination-barren area. Both the genetic map and the physical map showed a significant correlation when p=0.001, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11mm. A total of 43 QTLs were identified, including 8 QTLs for Plant height(PH), 11 QTLs thousand grain weight(TGW), 15 QTLs for grain length(GL),and 9 QTLs for grain width(GW), which explained 1.36%–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci Qph.nwafu-4B and Qph.nwafu-4D that determined plant height. The explanation rates of phenotypic variation were 7.39%-12.26% and 20.11%-27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43%-6.85% for phenotypic variation, two co-segregating KASP markers were developed, the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43%-6.85%. Three loci that affected the grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2 and Qgl.nwafu-6B, illustrating the explana-tion rates of phenotypic variation as 6.72%-9.59%, 5.62%-7.75%, and 6.68%-10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.

Preprint ARTICLE | doi:10.20944/preprints201904.0321.v1

Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Somayeh Farahani, Mojdeh Maleki, Rahim Mehrabi, Homayoun Kanouni, Reza Talebi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chickpea; genetic diversity; linkage disequilibrium; DArTseq-SNP markers

Online: 29 April 2019 (07:56:52 CEST)

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Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r²≥0.8, while 2961 pairs of markers showed complete LD (r²=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

Preprint ARTICLE | doi:10.20944/preprints202012.0732.v1

Serum Selenium Status as Diagnostic Marker for Prognosis in Liver Transplantation

Safak Gül-Klein, Deana Haxhiraj, Julian Seelig, Annika Kaestner, Julian Hackler, Qian Sun, Nils Lachmann, Johann Pratschke, Moritz Schmelzle, Lutz Schomburg

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: trace element; liver transplantation; selenoprotein P; glutathione peroxidase; hepatitis C virus

Online: 29 December 2020 (15:18:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202402.0334.v1

Genomic Regions and Candidate Genes Affecting Response to Heat Stress with Newcastle Virus Infection in Commercial Layers Chicks Using Chicken 600K SNP Array

Ying Wang, Perot Saelao, Ganrea Chanthavixay, Rodrigo A. Gallardo, Anna Wolc, Janet E. Fulton, Jack C. Dekkers, Susan J. Lamont, Terra R. Kelly, Huaijun Zhou

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Heat stress; GWAS; NDV; chicken; QTL

Online: 6 February 2024 (05:22:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1280.v1

Rice (Oryza sativa L.) Grain Size, Shape, and Weight-Related QTLs Identified using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers

Nkulu Rolly Kabange, Gamenyah Daniel Dzorkpe, Dong-Soo Park, Youngho Kwon, Sais-Beul Lee, So-Myeong Lee, Ju-Won Kang, Seong-Gyu Jang, Ki-Won Oh, Jong-Hee Lee

Subject: Biology And Life Sciences, Plant Sciences Keywords: SNP Chip DNA Marker; GAPIT; GWAS; Genomic Selection; Grain traits; Rice

Online: 20 September 2023 (02:17:56 CEST)

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This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and quantitative trait loci (QTLs) for grain length, co-detected by all GAPIT models on (Chr) 1–3, 5, 7, and 11), were qGL1-1BFSG (AX-95918134, Chr1: 3820526 bp) explains 65.2%–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1BFSG (AX-273945773, Chr1: 5623288 bp) for grain width explains 15.5%–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1Blink, AX-279261704, Chr1: 18023142 bp) and 54.9% (qGT2-1Farm, AX-154787777, Chr2: AX-154787777 bp) of the observed PVE. For t length-to-width ratio, the qLWR2BFSG (AX-274833045, Chr2: 10000097 bp) explains nearly 15.2%–32% of PVE for LWR. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6BFSG, AX-115737727, 28484619 bp) and explains 32.8%–54% of PVE. The qTGW6BFSG QTL coincides with qGW6-1Blink for grain width and explained 32.8%–54% of PVE. Putative Candidate genes pooled from major QTLs for each grain traits have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs.

Preprint ARTICLE | doi:10.20944/preprints202408.0578.v1

Identification of MTA1 as a New Molecular Marker for Canine Urothelial Carcinoma

Gisella Campanelli, Noah Waxner, Nema Parkhomovsky, Chun Kuen Mak, Ji-Hang Yin, Susanne Je-Han Lin, Raphael Vanderstichel, Ching Yang, Anait S Levenson

Subject: Biology And Life Sciences, Life Sciences Keywords: canine urothelial carcinoma; canine cell lines; immunohistochemistry; MTA1; COX2; E-cadherin

Online: 8 August 2024 (08:48:57 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202310.0091.v1

Neutrophil to Lymphocyte Ratio as a Prognostic Marker in Amyotrophic Lateral Sclerosis

Camille Cotet, Hugo Alarcan, Olivier Herault, Philippe Corcia, Patrick Vourc'h, Christian R Andres, Hélène Blasco, Charlotte Veyrat-Durebex

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Amyotrophic lateral sclerosis; neutrophils; lymphocytes; NLR; survival; prognosis

Online: 3 October 2023 (05:55:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1019.v1

Vitamin D Levels as a Marker of Severe SARS-Cov-2 Infection

Lambros Athanassiou, Ifigenia Kostoglou-Athanassiou, Sofia Nikolakopoulou, Alexandra Konstantinou, Olga Mascha, Evangelos Siarkos, Charilaos Samaras, Panagiotis Athanassiou, Yehuda Shoenfeld

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: vitamin D; SARS-CoV-2; outcome; ferritin; d-dimers; fibrinogen

Online: 15 September 2023 (02:40:24 CEST)

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Severe infection from the SARS-CoV-2 virus is associated with various clinical findings, including hematological manifestations. Thrombotic events or a tendency to develop thrombotic events also characterize severe COVID-19 disease and may lead to death. Vitamin D is known to have immunomodulating properties and to enhance the body defense system against invading pathogens and to have immunostimulatory properties as far as the innate immune response is concerned. The aim was to measure 25(OH)D3 levels in patients hospitalized for severe COVID-19 infection, to explore the relationship between 25(OH)D3 and outcome and to investigate the relationship between 25(OH)D3 levels, CRP, ferritin, d-dimers and fibrinogen levels in this cohort. In a cohort of 88 patients hospitalized for severe infection from the SARS-CoV-2 virus and a control group matched for age and sex the levels of 25(OH)D3 were measured. In the same cohort CRP, ferritin, d-dimer and fibrinogen levels were also analyzed. Levels of 25(OH)D3 were 17.36±8.80 ng/ml (mean±SD) as compared with 24.34±10.34 ng/ml, in patients with severe SARS-CoV-2 infection and the control group, respectively, p<0.001 (Student’s t test). The levels of 25(OH)D3 were found to be significantly related to outcome, i.e. survival as opposed to non-survival, as more patients with 25(OH)D3 deficiency (0-10 ng/ml) and insufficiency (10-20 ng/ml) had a fatal outcome as compared with those with vitamin D sufficiency, p<0.001, chi-square test, p<0.001, Fischer’s exact test. Levels of 25(OH)D3 were inversely related to CRP, ferritin, d-dimer and fibrinogen levels, p<0.001, linear regression analysis, beta coefficient of variation, -0.176, -0,160, -0.178, -0.158, respectively. Vitamin D deficiency observed in severe SARS-CoV-2 infection was related to the disease outcome. Increased ferritin levels, and increased thrombotic markers, namely d-dimer and fibrinogen levels were observed in the patients and their concentration was also inversely related to vitamin D. We showed that vitamin D levels were low in hospitalized patients with severe SARS-CoV-2 infection and also inversely related to CRP, ferritin, d-dimer and fibrinogen concentration. It is proposed that vitamin D levels may be an index of severity in the context of SARS-CoV-2 infection.

Preprint REVIEW | doi:10.20944/preprints202211.0160.v1

Chondroitin Sulfate Proteoglycan 4 as a Marker for Aggressive Squamous Cell Carcinoma

Kathryn Chen, Joel Yong, Roland Zauner, Verena Wally, John Whitelock, Mila Sajinovic, Zlatko Kopecki, Kang Liang, Kieran Scott, Albert Sleiman Mellick

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chondroitin sulfate proteoglycan; cutaneous squamous cell carcinoma; head and neck squamous cell carcinoma; cancer biomarker; gene expression.

Online: 9 November 2022 (01:08:57 CET)

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Preprint SHORT NOTE | doi:10.20944/preprints202311.0649.v1

Insights on Ferritin as a Screening and a Diagnostic Marker for Still’s Disease: A Narrative review

Zeal Soni, Samkit Vora, Dev Desai

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Still’s Disease; Ferritin; Arthritis

Online: 9 November 2023 (14:39:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1366.v1

Back Extensor Strength as a Potential Marker of Frailty Using Propensity Score Matching and Machine Learning

Taewook Kim, Gowun Kim, Hee-won Park, Eun-Kyoung Kang, Sora Baek

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: muscle strength; frailty; machine learning

Online: 18 August 2023 (12:40:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0202.v1

Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus Purpureus) Improvement

Ermias Habte, Meki S. Muktar, Asebe Abdena, Jean Hanson, Alieu M. Sartie, Alemayehu Teressa Negawo, Juarez Machado, Franscisco ledo, Chris S. Jones

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Napier grass; elephant grass; EMBRAPA; forage yield; feed quality; marker trait association

Online: 15 February 2020 (15:01:37 CET)

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Preprint REVIEW | doi:10.20944/preprints202001.0370.v1

CCL11 or Eotaxin-1: An Immune Marker for Ageing and Accelerated Ageing in Neuro-psychiatric Disorders

Mariya Ivanovska, Zakee Abdi, Marianna Murdjeva, Danielle Macedo, Annabel Maes, Michael Maes

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: eotaxin; immune marker; neuroinflammation; ageing; neuro-psychiatric disorder

Online: 30 January 2020 (14:42:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0870.v1

Exploration of Novel Genetic Loci Influencing Mercury Accumulation in Maize through a Genome-wide Association Study Utilizing an Enlarged SNP Panel

Jionghao Gao, Jianxin Li, Jihong Zhang, Yan Sun, Xiaolong Ju, Wenlong Li, Haiyang Duan, Zhengjie Xue, Li Sun, Hussian Sahito Javed, Zhiyuan Fu, Xuehai Zhang, Jihua Tang

Subject: Biology And Life Sciences, Plant Sciences Keywords: mercury accumulation; maize tissue; genetic loci; genome-wide association analysis

Online: 11 January 2024 (11:27:58 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202406.0630.v1

Serum Albumin as a Prognostic Marker for Overall Survival in Acute Myeloid Leukemia

Anvay Shah, Ashley Fox, Danielle Bradshaw, Mohammad Mian, Vishrut Shah, Zachery Branham, Mark Dalgetty, Christian Leurinda, Locke Bryan, Anand Jillella, Vamsi Kota

Subject: Medicine And Pharmacology, Hematology Keywords: Keywords; prognostication; albumin; acute myeloid leukemia

Online: 11 June 2024 (08:33:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.2036.v1

Verification of Criterion-Related Validity for Developing a Marker-Less Hand Tracking Device

Ryota Suwabe, Takeshi Saito, Toyohiro Hamaguchi

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: MediaPipe; hand tracking; paralysis estimation

Online: 30 May 2024 (13:13:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.0168.v1

Cancer Screening in Angolan Individuals Using Tumor Marker Tests at Mediag, Luanda-Angola

Edson Kutelela Cassinela, Lourenço Quixari, Silvana da Rocha Silveira, Cruz dos Santos Sebastião, António Armando, Carlos Pinto-Sousa, José Fernando, Manuel Sangombe Epalanga, Euclides Nenga Manuel Sacomboio

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: tumor marker; screening; Angolan population

Online: 4 December 2023 (11:40:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0886.v1

Musashi-1 Is a Novel Immunohistochemical Marker of Neuroendocrine Carcinoma of the Lung

Yu Izaki, Vishwa Jeet Amatya, Takahiro Kambara, Kei Kushitani, Yoshihiro Miyata, Morihito Okada, Yukio Takeshima

Subject: Public Health And Healthcare, Other Keywords: pathological diagnosis; Musashi-1; small cell carcinoma; large cell neuroendocrine carcinoma; lung cancer; surgical specimen; novel marker; immunohistochemistry

Online: 14 November 2023 (10:26:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints201812.0017.v1

Immunohistochemical Study of c-erbB2/HER2 Tumor Marker in Primary Malignant Brain Tumors

Mazaher Ramezani, Shadi Siami, Mansour Rezaei, Sedigheh Khazaei, Masoud Sadeghi

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: primary brain tumor; HER2; immunohistochemistry

Online: 3 December 2018 (09:24:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202105.0089.v1

Social and Behavioral Rhythms as a Marker of Well-being Indicator in Old Adults Living at Home

Mauro Giovanni Carta, Elisa Pintus, Rosanna Zaccheddu, Omar Callia, Giuliana Conti, Cesar Ivan Aviles Gonzalez, Luigi Minerba, Roberto Demontis, Massimiliano Pau, Eleonora Cocco, Maria Petronilla Penna, Goce Kalcev, Stefano Lorrai, Fernanda Velluzzi, Andrea Lovoselli, Marco Monticone, Maria Valeria Massidda, Maria Rita Pinna, Stefano Lorrai, Alberto Cauli, Alessandra Scano, Germano Orrù, Antonio Crisafulli, Sofia Cosentino, Sergio Machado, Dario Fortin, Gian Mario Migliaccio, Gabriele Finco, Giulia Cossu

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Social rhythm; Behavioral rhythm; Well-being; Old adults

Online: 6 May 2021 (14:27:34 CEST)

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Working Paper ARTICLE

Glycan Epitopes on 201B7 Human Induced Pluripotent Stem Cells using R-10G and R-17F Marker Antibodies

Yuko Nagai, Hiromi Nakao, Aya Kojima, Yuka Komatsubara, Yuki Ohta, Nana Kawasaki, Nobuko Kawasaki, Hidenao Toyoda, Toshisuke Kawasaki

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Human induced pluripotent stem cells (hiPSCs); monoclonal antibodies; R-10G; R-17F; keratan sulfate; podocalyxin; keratanase II; endo-β-galactosidase

Online: 9 March 2021 (12:13:56 CET)

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Preprint ARTICLE | doi:10.20944/preprints202102.0605.v1

Molecular Profiles of Prostate Cancer in Men of Middle Eastern Ancestry Identifies Key Differences with Western Populations: A Multiethnic SNP Array Study

Alia Albawardi, Julie Livingstone, Saeeda Al Marzooqi, Kathleen Houlahan, Aktham Adnan Ahmad Awwad, Ramy Abdelsalam, Paul Boutros, Tarek A Bismar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Prostate cancer; Middle Eastern Ancestry; Copy number alteration

Online: 26 February 2021 (10:47:12 CET)

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Background: Our knowledge of prostate cancer (PCa) genomics mainly reflects European (EUR) and Asian (ASN) populations. Our understanding of the influence of Middle Eastern (ME) and African (AFR) ancestry on the mutational profiles of prostate cancer is limited. Design, setting and participants: To characterize genomic differences between ME, EUR, ASN and AFR ancestry, fluorescent in situ hybridization (FISH) studies for NKX3-1 deletions and MYC amplification was carried out on 42 tumors arising in individuals of ME ancestry. These were supplemented by analysis of copy number profiles of 401 tumors of all ancestries. Outcome measurement and statistical analysis: FISH results of NKX3-1 and MYC were assessed in the ME cohort and compared to other ancestries. Gene level copy number aberrations (CNAs) for each sample were statistically compared between ancestry groups. Results and Limitation: NKX3-1 deletions by FISH were observed in 17/42 (17.5%) prostate tumors arising in men of ME ancestry, while MYC amplifications were only observed in 1/42 (0.23%). Using CNAs called from arrays, the incidence of NKX3-1 deletions was significantly lower in ME vs. other ancestries (20% vs. 52%; p = 2.3 x 10-3). No differences in MYC amplifications was noted between the two cohorts using array-based CNAs. Across the genome, tumors arising in men of ME ancestry had fewer CNAs than those of other ancestries (p = 0.014). Additionally, the somatic amplification of 21 specific genes was more frequent in tumors arising in men of ME vs. EUR ancestry (Proportions test; Q < 0.05). Those included amplifications in the glutathione S-transferase family on chromosome 1 (GSTM1, GSTM2, GSTM5) and the IQ Motif Containing family on chromosome 3 (IQCF1, IQCF2, IQCF13, IQCF4, IQCF5, IQCF6). Conclusion: Significant differences in genetic background exists between different ancestries. The lower number of somatic CNAs observed in prostate cancer arising in men of ME ancestry may explain the relatively good prognosis in this population. Larger studies are warranted.

Preprint ARTICLE | doi:10.20944/preprints202311.1187.v1

Evaluation of Urinary L‐FABP as a Tubular Damage Marker in Pediatric Neurogenic Bladder

Joanna Bagińska, Jan Krzysztof Kirejczyk, Agata Korzeniecka-Kozerska

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: neurogenic bladder; L-FABP; proteinuria

Online: 21 November 2023 (10:38:32 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0589.v1

Exploring PTX3 as a Diagnostic and Prognostic Marker in Fetal Inflammatory Response Syndrome in Newborns: A Prospective Study

Bahar Öztelcan Gündüz, Ener Cağrı Dinleyici, Neslihan Ayşe Tekin, Ömer Çolak, Arif Mehmet Akşit

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: PTX3; NEWBORN BABY; FETAL İNFLAMMATORY SYNDROME; SEPSİS; RDS

Online: 8 December 2023 (10:09:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0494.v1

Genetic Diversity and Population Structure of Anopheles funestus in western Kenya Based on Mitochondrial DNA Marker mtDNA-COII

Isaiah Debrah, Kevin O. Ochwedo, Wilfred O. Otambo, Maxwell G. Machani, Edwin O. Magomere, Shirley A. Onyango, Daibin Zhong, Linda Eva Amoah, Andrew Karanja Githeko, Yaw Asare Afrane, Guiyun Yan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Anopheles funestus; western Kenya; mtDNA-COII; genetic diversity; gene flow

Online: 27 January 2023 (06:46:32 CET)

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Working Paper ARTICLE

Detection of Peanut Allergen by Real Time PCR: Looking For the Suitable Detection Marker as Affected by Processing

Africa Sanchiz, Paulina Sánchez-Enciso, Carmen Cuadrado, Rosario Linacero

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Real-time PCR; peanut; food allergen; chloroplast marker; DNA isolation

Online: 16 June 2021 (11:33:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0837.v1

Metabolic Pathway Pairwise-Based Signature as a Potential Non-Invasive Diagnostic Marker in AD patients

Yunwen Feng, Xingyu Chen, Xiaohua Douglas Zhang, Chen Huang

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Alzheimer's Disease; Noninvasive Diagnosis; Metabolic Abnormalities; Biomarker; Peripheral blood; Multi-Machine Learning

Online: 11 May 2023 (09:47:20 CEST)

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Alzheimer's disease (AD) is an incurable neurodegenerative disorder. Early screening, particularly in blood has been regarded as an effective approach for AD diagnosis and prevention. In addition, metabolic dysfunction has been demonstrated to be closely related to AD, which might be reflected in whole blood transcriptome. Hence, we hypothesized that establishment of diagnostic model based on metabolic signatures of blood is a workable strategy. To the end, we initially constructed metabolic pathway pairwise (MPP) signatures to characterize the interplay among metabolic pathways. Then, a series of bioinformatic methodologies, e.g., differential expression analysis, functional enrichment analysis, and network analysis, etc. were used to investigate the molecular mechanism behind AD. Moreover, an unsupervised clustering analysis based on the MPP signature profile via Non-Negative Matrix Factorization (NMF) algorithm was utilized to stratify AD patients. Finally, aimed at distinguishing AD patients from non-AD group, a metabolic pathway-pairwise scoring system (MPPSS) was established using multi-machine learning methods. As a result, many metabolic pathways correlated to AD were disclosed, including oxidative phosphorylation and fatty acid biosynthesis, etc. NMF clustering analysis divided AD patients into two subgroups (S1 and S2), which exhibit distinct activities of metabolism and immunity. Typically, oxidative phosphorylation in S2 exhibits a lower activity than that in S1 and non-AD group, suggesting the patients in S2 might possess a more compromised brain metabolism. Additionally, Immune infiltration analysis showed that the patients in S2 might have phenomena of immune suppression, compared with S1 and non-AD group. These findings indicated that S2 probably have a more severe progression of AD. Finally, MPPSS could achieve an AUC of 0.73 in training dataset, 0.71 in testing dataset and an AUC of 0.82 on weighted average in five external validation datasets. Overall, our study successfully established a novel metabolism-based scoring system for AD diagnosis using blood transcriptome, and provided new insight into the molecular mechanism of metabolic dysfunction implicated in AD.

Preprint ARTICLE | doi:10.3390/sci1020055

Copper-to-Zinc Ratio Correlates with an Inflammatory Marker in Patients with Sickle Cell Disease

Mathias Emokpae, Emmanuel Fatimehin

Subject: Medicine And Pharmacology, Dietetics And Nutrition Keywords: copper; c-reactive protein; inflammation; sickle cell disease; zinc

Online: 18 September 2019 (00:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0533.v1

Improvement of the Classification Algorithms of Postures for Non-Marker Systems of Human Motion Capture

Tatiana Klishkovskaia, Andrey Aksenov

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: exercise classification; motion capture; virtual rehabilitation

Online: 22 November 2018 (04:33:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202408.2276.v1

Corneal Epithelial Wavefront Error as a Novel Objective Biomarker Diagnostic Marker for Epithelial Basement Membrane Dystrophy

Vitus Grauvogl, Wolfgang J. Mayer, Jakob Siedlecki, Niklas Mohr, Martin Dirisamer, Siegfried Georg Priglinger, Stefan Kassumeh, Nikolaus Luft

Subject: Medicine And Pharmacology, Ophthalmology Keywords: Cornea; Dystrophy; Treatment Lasers; Ocular surface

Online: 30 August 2024 (19:20:56 CEST)

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Synopsis Corneal epithelial wavefront error and epithelial thickness variance qualify as highly sensitive and specific biomarkers for epithelial basement membrane dystrophy (EBMD). The biomarkers show a normalization after treatment of EBMD with phototherapeutic keratectomy. Purpose: To gauge the diagnostic value of a novel spectral-domain optical coherence tomography (SD-OCT) based imaging modality for simultaneous morphological (thickness profile) and refractive (optical wavefront) assessment of the corneal epithelial layer in one of the most common but often underdiagnosed corneal dystrophies: epithelial basement membrane dystrophy (EBMD). Methods: In this prospective observational study, a total of 32 eyes of 32 patients diagnosed with EBMD and 32 eyes of 32 healthy control subjects were examined with high-resolution anterior segment SD-OCT (MS-39; CSO, Florence, Italy). Various epithelial thickness and epithelial wavefront derived terms were compared between groups and receiver operating characteristic (ROC) curves were computed to analyze the diagnostic capacity of the respective parameters. A total of 17 of 32 EBMD patients underwent treatment with phototherapeutic keratectomy (PTK) and were followed up for 3 months. Results: Epithelial thickness variance (60.4 ± 56.7 µm versus 7.6 ± 6.1 µm) and interquartile range (11.0±6.9 versus 3.3±1.9 µm) were markedly elevated in EBMD patients as compared with healthy controls (both with p < 0.001). Epithelial wavefront analysis showed a highly statistically significant excess in all examined aberration terms in EBMD patients (all with p < 0.001). Significantly greater areas under the curve (AUC) were yielded by the epithelial wavefront derived parameters (e.g. total epithelial wavefront error: AUC = 0.966; 95% confidence interval (CI) 0.932 – 1) than by the epithelial thickness-derived parameters (e.g., variance: AUC = 0.919; 95% CI 0.848 – 0.990). Conclusion: Corneal epithelial wavefront aberrometry proved valuable as an objective biomarker for EBMD with high sensitivity and specificity. PTK resulted in a reduction of morphological and refractive epithelial irregularities in EBMD.

Preprint BRIEF REPORT | doi:10.20944/preprints202305.2178.v1

Is HSP-27 an Emerging Marker of Good Prognosis in Septic Shock Patients – A Pilot Study

Andrzej Jaroszynski, Rafał Wójtowicz, Ewa Piasek, Wojciech Dąbrowski

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: mortality; sepsis; shock; heat shock protein 27

Online: 31 May 2023 (07:15:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0028.v1

Neck Circumference in Combination with Biochemical Variables as a Surrogate Marker of NAFLD: The FLiO Study

Mariana Elorz, Alberto Benito, Berta Araceli Marin, Nuria Perez del Campo, Jose Ignacio Herrero, Ignacio Monreal, Josep Tur, J. Alfredo Martínez, María Ángeles Zulet, Itziar Abete

Subject: Medicine And Pharmacology, Dietetics And Nutrition Keywords: Anthropometric measurements; fatty liver disease; nutritional intervention; imaging techniques; long-term follow-up; neck-to-height ratio; non-invasive diagnostic methods; neck-to-weight ratio; FLIO study; steatosis markers.

Online: 1 November 2022 (10:04:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202408.0145.v1

The Effect of CKD-495, Eupacidin, and Their Marker Com-pounds on Altered Permeability in the Postoperative Ileus Animal Model

Min-Jae Kim, Zahid Hussain, Young Ju Lee, Hyojin Park

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: ileus; postoperative complications; permeability; natural products

Online: 3 August 2024 (16:08:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.1095.v1

Anti-Müllerian Hormone as Endocrine and Molecular Marker Associated with Reproductive Performance in Holstein Dairy Cows Exposed to Heat Stress

Luis A. Contreras-Méndez, Juan F. Medrano, Milton G. Thomas, R. Mark Enns, Scott E. Speidel, Guillermo Luna-Nevárez, Pedro A. López-Castro, Fernando Rivera-Acuña, Pablo Luna-Nevárez

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: AMH; fertility; Holstein cows; markers; SNPs

Online: 17 November 2023 (08:25:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.0096.v1

Metabolic Fingerprints of Effective Fluoxetine Treatment in the Prefrontal Cortex of Chronically Socially Isolated Rats: Marker Candidates and Predictive Metabolites

Dragana Milutin Filipovic, Julica Inderhees, Alexandra Korda, Predrag Tadić, Markus Schwaninger, Dragoš Inta, Stefan Borgwardt

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: depressive-like behavior; prefrontal cortex; fluoxetine; metabolomics; ROC curve; support vector machine-linear kernel

Online: 1 June 2023 (13:35:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0347.v1

Inactivation of MrPigH in Monascus ruber M7 Results in its Monascus Pigments Increase and Citrinin Decrease with mrpyrG Selection Marker

Li Li, Na Xu, Fusheng Chen

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Monascus ruber; mrpigH; Monascus pigments; citrinin

Online: 19 November 2021 (11:29:21 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202109.0457.v1

Plasmid Curing and Exchange Using a Novel Counter-Selectable Marker Based on Unnatural Amino Acid Incorporation at a Sense Codon

Yusuke Kato

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: counter-selection; unnatural amino acids; pyrrolysyl tRNA synthetase; genetic code expansion; sence codon reassignment; plasmid curing

Online: 27 September 2021 (17:09:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0132.v1

Marker Assisted Selection of Malic-Consuming Saccharomyces cerevisiae Strains for Winemaking. Efficiency and Limits of a QTL’s Driven Breeding Program

Charlotte Vion, Emilien Peltier, Margaux Bernard, Maitena Muro, Philippe Marullo

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Wine yeast; malic acid; pH; breeding; Malo Lactic Fermentation; Marker Assisted Selection

Online: 3 March 2021 (12:43:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.1780.v1

Molecular Mapping To Identify Stable Salinity-Resilient QTLs From the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based 1k-RiCA Genotyping in Rice

Sheikh Maniruzzaman, M. Akhlasur Rahman, Mehfuz Hasan, Golam Golam Rasul, Abul Hossain Molla, Hasina Khatun, KM Md Iftekharuddaula, Salma Akter

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic loci; salt tolerant indica germplasm (Akundi); single nucleotide polymorphisms (SNP); 1k-RiCA; Oryza sativa L.

Online: 25 May 2023 (08:58:09 CEST)

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Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses like salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F2:3) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (boro) rice mega variety and Akundi is a highly salinity tolerant Bangladeshi origin indica rice landrace that is utilized as a donor parent. We report stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used to genotype this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs found unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied Saltol, SKC1, OsSalT and salT locus. Twenty-eight significant digenic/epistatic interactions identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors like Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel and stable QTLs (qSES1, qSL1, qRL1, qSUR1, qSL8, qK8, qK1) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.

Preprint ARTICLE | doi:10.20944/preprints202212.0081.v1

The Use of Low-Density SNP Array for Identification of Interspecific Introgressions of Genetic Material from the Bread Wheat into Homologous Chromosomes of the Durum Wheat

Aleksey Ermolaev, Aleksey Yanovskij, Varvara Korobkova, Gennady Karlov, Mikhail Divashuk

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bread wheat; durum wheat; introgression; homologous chromosomes; SNP microarray; functional enrichment

Online: 5 December 2022 (15:30:20 CET)

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Working Paper ARTICLE

Osteoprotegerin is More Than a Possible Serum Marker in Liver Fibrosis: A Study into Its Function in Human and Murine Liver

Adhyatmika Adhyatmika, Leonie Beljaars, Kurnia Putri, Habibie Habibie, Carian Boorsma, Catharina Reker-Smit, Burak Guney, Axel Haak, Keri Mangnus, Eduard Post, Klaas Poelstra, Kim Ravnskjær, Peter Olinga, Barbro Melgert

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: cirrhosis; TGFβ1; CCl4; resolution; hepatic stellate cells; osteoprotegerin; RANKL; TRAIL

Online: 14 February 2020 (03:28:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202301.0005.v1

NEDD9 Overexpression Causes Hyperproliferation of Luminal Cells and Cooperates with HER2 Oncogene in Tumor Initiation: A Novel Prognostic Marker in Breast Cancer

Marc L. Purazo, Ryan J. Ice, Rahul Shimpi, Mark Hoenerhoff, Elena N. Pugacheva

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: HER2; breast cancer; NEDD9 adaptor protein; hyperplasia; AURKA

Online: 3 January 2023 (06:57:38 CET)

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Working Paper ARTICLE

Comparison of Vitamin D Levels, Bone Metabolic Marker Levels, and Bone Mineral Density among Patients with Thyroid Disease: A Cross-Sectional Study

Masliza Hanuni Mat Ali, Najib Majdi Yaacob, Norhayati Yahaya, Nani Draman, Wan Mohd Izani Wan Mohamed, Mohd Shafie Abdullah, Wan Norlina Wan Azman, Hanim Afzan Ibrahim, Wan Nor Fazila Hafizan Wan Nik, Mafauzy Mohamed, Tuan Salwani Tuan Ismail

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: Hyperthyroid; Hypothyroid; Euthyroid; Vitamin D; Bone Turn Over Markers; Bone Mineral Density

Online: 23 September 2020 (04:52:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0364.v1

Oct4/Sox2 positive breast cancer stem cell-like cells can be detected and targeted by including AURKA and Vimentin in the combinatorial marker profile

Debomita Sengupta, Debanjan Thakur, Elizabeth Mahapatra, Salini Das, Sagar Sen, Arindam Roy, Sutapa Mukherjee

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Oct4; Sox2; AURKA; Vimentin; breast cancer; Alisertib; epithelial to mesenchymal transition; asymmetric cell division; NUMB; stem cell; diagnostics; intervention; chemotherapy

Online: 9 October 2023 (15:14:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.0353.v1

Follicular Fluid Proteomic Analysis of Women Undergoing Assisted Reproduction Suggests Apolipoprotein A1 to Be a Potential Fertility Marker

Csilla Kurdi, János Schmidt, Zoltán Horváth-Szalai, Péter Mauchart, Krisztina Gödöny, Ákos Várnagy, Gábor L Kovács, Tamás Kőszegi

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: assisted reproductive treatment; follicular fluid; proteomics; mass spectrometry; apolipoprotein A1; HDL cholesterol; predictive value

Online: 6 December 2023 (07:44:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.1813.v1

Investigate the Effect of rh-BMP2 on the Healing Process of the Gingival Tissue using Ki-67 Marker

Mansour Chantiri, Toni Zeinoun

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: rh-BMP2; Ki67-Proliferation – Gingival Tissue

Online: 25 May 2023 (14:36:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1645.v1

Quantitative comparison of hand kinematics measured with a markerless commercial head-mounted display and a marker-based motion capture system in stroke survivors.

Antonino Casile, Giulia Fregna, Vittorio Boarini, Chiara Paoluzzi, Fabio Manfredini, Nicola Lamberti, Andrea Baroni, Sofia Straudi

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: markerless system, head-mounted display, stroke, motion analysis, motor recovery, Oculus Quest, Optitrack

Online: 25 July 2023 (08:12:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0147.v1

Whole Genome Alignment Based Development of Molecular Marker for Detecting Leptosphaeria maculans and Leptosphaeria biglobosa, the Causal Agent of Blackleg Disease in Brassicas

Mostari Jahan Ferdous, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Jong-In Park, Hee-Jeong Jung, Hoy-Taek Kim, Ill-Sup Nou

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR

Online: 13 October 2019 (16:08:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0202.v1

Serum C-Reactive Protein to Albumin Ratio as a Reliable Marker of Diabetic Neuropathy in Type 2 Diabetes Mellitus

Gulali Aktas

Subject: Medicine And Pharmacology, Internal Medicine Keywords: type 2 diabetes mellitus; diabetic neuropathy; inflammation; C reactive protein to albumin ratio

Online: 2 June 2023 (12:07:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202201.0211.v1

The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas Reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing

Robert A. Freudenberg, Luisa Wittemeier, Alexander Einhaus, Thomas Baier, Olaf Kruse

Subject: Biology And Life Sciences, Plant Sciences Keywords: microalgae; CRISPR/Cas9; gene editing; spermidine; SPD1; auxotrophy; selectable marker

Online: 14 January 2022 (11:55:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202101.0490.v1

The Cancer Stem Cell Marker CD44 Play Key Roles in Immune Suppression/Evasion, Drug Resistance, Epithelial-Mesenchymal Transition, and Metastasis in Several Human Cancers

Kevin Dzobo, Musalula Sinkala

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: CD44; Cancer Stem Cells; Tumorigenesis; Drug Resistance; Immune Markers; Epithelial to Mesenchymal Transition; Therapeutic Targeting

Online: 25 January 2021 (12:23:49 CET)

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One of the most used markers of cancer stem cells in several cancers, including colorectal cancer and breast cancer, is CD44. CD44 is a glycoprotein that traverses the cell membrane and binds to many ligands including hyaluronan resulting in activation of signaling cascades. Several reports have shown conflicting data on the expression of CD44 and that the expression depends on modes of investigations and subtypes of cancers. In addition, the correlation between CD44 expression and drug resistance, immune infiltration, EMT, metastasis and patients prognosis in several cancer types remains unclear. This study investigated CD44 expression in several cancers and explored its relationship with tumorigenesis using various publicly available databases, including The Cancer Genome Atlas, GEPIA, Oncomine, Genomics of Drug Sensitivity in Cancer and Tumor Immune Estimation Resource. Our analysis reveals that CD44 is differentially expressed in different cancers. CD44 expression is significantly associated with cancer patients’ survival in gastric, pancreatic and colorectal cancers. In addition, CD44 expression is closely linked with immune infiltration and immune suppressive features in pancreatic, colon adenocarcinoma and stomach cancer. High CD44 expression was significantly correlated with the expression of drug resistance-, EMT- and metastasis- linked genes. Tumors expressing high CD44 have higher mutation burden and afflict older patients than tumors expressing low CD44. Cell lines expressing high CD44 are more resistant to anti-cancer drugs compared to those expressing low CD44. Protein-protein interaction investigations and functional enrichment analysis showed that CD44 interacts with gene products related to cell-substrate adhesion, migration, platelet activation, and cellular response to stress. KEGG pathway analysis revealed that these genes play key roles in biological adhesion, cell component organization, locomotion, G-α-signaling and the response to stimulus. Overall, this investigation reveals that CD44 play significant roles in tumorigenesis, can be used as a prognostic biomarker in several cancers and can be therapeutically targeted in cancer therapy.

Preprint ARTICLE | doi:10.20944/preprints201905.0207.v1

Construction of a Single-Nucleotide Polymorphism Marker Based Quantitative Trait Loci Map and Validation of Resistance Loci to Bacterial Wilt (Ralstonia solanacearum) in Tomato

Il Sheob Shin, Jung Ching Hsu, Shu Mei Huang, Jaw Rong Chen, Jaw Fen Wang, Peter Hanson, Roland Schafleitner

Subject: Biology And Life Sciences, Horticulture Keywords: bacterial wilt; Ralstonia solanacearum; genotype-by-sequencing; disease resistance; quantitative trait loci; Solanum lycopersicum

Online: 16 May 2019 (10:35:18 CEST)

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Bacterial wilt (BW), caused by Ralstonia solanacearum is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line ‘Hawaii 7996’ (H7996) is a stable and robust resistance source against various R. solanacearum strains. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1,604 SNP markers with an average distance of 0.82 cM was developed for 188 F9 recombinant inbred lines derived from the cross H7996 × WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I or/and race 3-phylotype II strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC3F3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P < 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P < 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P < 0.01) was confirmed and markers for this QTL have already been made available previously.

Preprint ARTICLE | doi:10.20944/preprints202409.0863.v1

Low Serum Alanine Aminotransferase, a Marker of Sarcopenia and Frailty, is Associated with Shortened Survival of Renal Cell Cancer Patients and Survivors. Retrospective Analysis of 1,830 Patients

Menachem Laufer, Michal Sarfaty, Eyal Jacobi, Edward Itelman, Gad Segal, Maxim Perelman

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Renal Cell Carcinoma; sarcopenia; frailty; alanine aminotransferase; survival; ALT

Online: 11 September 2024 (17:11:07 CEST)

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Background. Sarcopenia is characterized by progressive loss of muscle mass and function. It is often associated with frailty, a syndrome linked to physical disability and shortened survival in various diseases, including cancer patients. Low serum alanine aminotransferase (ALT) values, representing low muscle mass (sarcopenia), is a routine blood test that was shown to be associated with increased frailty and subsequently shortened survival in several cancers. In the current study, we aimed to test the association between low ALT and shorter survival in renal cell carcinoma (RCC) patients and survivors. Methods. This was a retrospective analysis of RCC patients and survivors, both in and out-patients. We defined patients with sarcopenia as those presenting with ALT < 17 IU/L. Results. We identified records of 3,012 patients diagnosed with RCC. The final cohort included 1,830 eligible patients (mean age 65.6 ± 13.3 years, 68% were men) of whom only 179 underwent surgical treatment. Out of the eligible cohort, 811 patients (44.3% ( had ALT < 17 IU/L. The mean ALT value of patients within the low ALT group was 11.79 IU/L while the mean value in the higher ALT level group was 24.44 IU/L (p < 0.001). Patients in the lower ALT group were older (67.9 vs. 63.7 years; p < 0.001) and had lower BMI (26.6 vs. 28; p < 0.001). In addition, patients with low ALT had lower hemoglobin values (12.14 vs. 12.91 g/dL; p < 0.001), higher serum creatinine (1.49 vs. 1.14; p < 0.001) and higher platelets to lymphocytes ratio (178 vs. 156; p < 0.001). In a univariate analysis, low ALT levels were associated with a 72% increase in mortality (95% CI 1.46-2.02, P < 0.001). In a multivariate model controlled for age, male gender, hemoglobin, platelets, LDH, neutrophil to lymphocytes ratio and platelets to lymphocytes ratio, low ALT levels were associated with a 27% increase in mortality (HR = 1.27, 95% CI 1.08 – 1.51; p = 0.005]. Conclusion. Low ALT values, indicative of sarcopenia and frailty, are associated with shortened survival of RCC patients and survivors and could potentially be applied for optimizing individual treatment decisions.

Preprint ARTICLE | doi:10.20944/preprints202306.1654.v1

Serum Level of Cytokeratin 18 (M65) as Prognostic Marker of High Cardiovascular Disease Risk in Non-alcoholic Fatty Liver Disease Individuals

Sabrina Pagano, Stephan J.L. Bakker, Catherine Juillard, Robin P.F. Dullaart, Nicolas Vuilleumier

Subject: Medicine And Pharmacology, Internal Medicine Keywords: Cytokeratin 18; Non-Alcoholic Fatty Liver Disease; Fatty liver index; Framingham risk score; Systematic COronary Risk Evaluation 2

Online: 23 June 2023 (10:36:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202011.0550.v1

Introgression of qDTY1.1 Governing Reproductive Stage Drought Tolerance Into an Elite Rice Variety ‘Pusa Basmati 1’ Through Marker Assisted Backcross Breeding

Gaurav Dhawan, Aruna Kumar, Priyanka Dwivedi, Subbaiyan Gopala Krishnan, Madan Pal, Kunnummal Kurungara Vinod, Mariappan Nagarajan, Prolay Kumar Bhowmick, Haritha Bollinedi, Ranjith Kumar Ellur, Kuram Tirumala Ravi Kiran, Pankaj Kumar, Ashok Kumar Singh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Basmati rice; QTL introgression; near isogenic lines; yield under drought; climate resilience

Online: 20 November 2020 (20:45:02 CET)

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Preprint REVIEW | doi:10.20944/preprints202307.1818.v3

Is modern medicine in need of an overhydration marker in kidney failure? The accuracy of available fluid overload markers and the potential of the new ones.

Barbara Emilia Nikitiuk, Alicja Rydzewska-Rosołowska, Katarzyna Kakareko, Irena Głowińska, Tomasz Hryszko

Subject: Medicine And Pharmacology, Internal Medicine Keywords: fluid status; overhydration; hydration status; renal failure; kidney failure; heart failure; Ca-125; NT-pro-BNP; VEXUS; BIS

Online: 5 October 2023 (14:28:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0716.v1

The Lambousa (Cyprus) Fish Tank in a Quasi-Stable Coastal Area of the Eastern Mediterranean. A Notable Marker for Testing GIA Models

Fabrizio Antonioli, Stefano Furlani, Giorgio Spada, Daniele Melini, Zomenia Zomeni

Subject: Environmental And Earth Sciences, Oceanography Keywords: Fishtanks; GIA; relative sea level; MIS 5.5; Cyprus; Mediterranean Sea

Online: 9 August 2023 (10:28:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1767.v1

Usefulness of Tumor Marker Score for Prediction of Prognosis in Hepatocellular Carcinoma Patients Treated with Atezolizumab plus Bevacizumab: A Multicenter Retrospective Study

Kazunari Tanaka, Kunihiko Tsuji, Atsushi Hiraoka, Toshifumi Tada, Masashi Hirooka, Kazuya Kariyama, Joji Tani, Masanori Atsukawa, Koichi Takaguchi, Ei Itobayashi, Shinya Fukunishi, Toru Ishikawa, Kazuto Tajiri, Hironori Ochi, Hidenori Toyoda, Chikara Ogawa, Takashi Nishimura, Takeshi Hatanaka, Satoru Kakizaki, Noritomo Shimada, Kazuhito Kawata, Atsushi Naganuma, Hisashi Kosaka, Tomomitsu Matono, Hidekatsu Kuroda, Yutaka Yata, Hideko Ohama, Fujimasa Tada, Kazuhiro Nouso, Asahiro Morishita, Akemi Tsutsui, Takuya Nagano, Norio Itokawa, Tomomi Okubo, Taeang Arai, Keisuke Yokohama, Hiroki Nishikawa, Michitaka Imai, Yohei Koizumi, Shinichiro Nakamura, Hiroko Iijima, Masaki Kaibori, Yoichi Hiasa, Takashi Kumada

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: hepatocellular carcinoma; tumor marker; atezolizumab plus bevacizumab; prognosis; predictive model

Online: 26 June 2023 (09:42:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0012.v1

Monitoring Farmed Fish Welfare by Measurement of Cortisol as Stress Marker in Fish Feces by Liquid Chromatography Coupled with Tandem Mass Spectrometry

Vanessa Andrea Meling, Kjetil Berge, David Lausten Knudsen, Per Ola Rønning, Cato Brede

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: aquaculture; fish; salmon; feces; deconjugation; hydrolysis; extraction; chromatography; mass spectrometry; LC-MS/MS

Online: 1 March 2022 (09:36:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202305.0339.v1

Genetic Mapping, Candidate Gene Identification and Marker Validation for Host Plant Resistance to the Race 4 of Fusarium oxysporum f. sp. cubense using Musa acuminata ssp. malaccensis

Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hřibová, Pavla Christelová, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Doležel, Peter Crisp, Allan F. Brown, Guillaume Martin, Nabila Yahiaou, Angelique D’Hont, Lachlan Coin, Rony Swennen, Elizabeth A. B. Aitken

Subject: Biology And Life Sciences, Plant Sciences Keywords: Banana; fine mapping; quantitative trait locus; Musa acuminata ssp. malaccensis; Fusarium wilt; Fusarium oxysporum f. sp. cubense; Tropical Race 4; Subtropical Race 4; marker assisted selection; resistance gene expression; receptor-like kinase; RNAseq

Online: 5 May 2023 (09:51:49 CEST)

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Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on Chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there is a cluster of pattern recognition receptors, namely leucine rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell wall associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant but not in susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus specific resistance to be assessed in a collection of diploid and polyploid banana plants. Out of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4 resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among in the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine-mapping and candidate gene identification will allow characterization of molecular mechanisms underlying TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.

Preprint ARTICLE | doi:10.20944/preprints201806.0261.v1

Searching for Perfect Marker - Differences and Dependencies in Serum Levels of Renalase, KIM-1, MCP-1, Calbindin and GST-Pi in Patients with Diabetes, Glomerulonephritis and Congenital Defects of the Kidney

Natalia Maria Serwin, Magda Wiśniewska, Edyta Skwirczyńska, Karol Serwin, Oskar Wróblewski, Barbara Dołęgowska

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: renalase; KIM-1; calbindin; MCP-1

Online: 15 June 2018 (14:53:54 CEST)

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Diagnosis of kidney diseases has recently become more comprehensive and accurate by using new renal markers. Despite the fact that creatinine and cystatin c have been sufficient in determining kidney function, they did not indicate the exact site of the damage and they were often insufficient in predicting the course of the disease. Aim of the study was to evaluate the potential correlations and differences in levels of six factors related to kidney function and injury: kidney injury molecule-1 (KIM-1), ncalbindin (CALB), glutathione S-transferase Pi (GST-Pi), calbindin and monocyte chemoattractant protein-1 (MCP-1), between renal patients with diabetic nephropathy (DM), congenital defects (CD) of the kidney and glomerulonephritis (GN). Study involved 75 patients: 49 with diabetic nephropathy, 12 with congenital defects and 14 with glomerulonephritis. Levels of renalase was measured using immunoenzymatic tests. Levels of other markers: calbindin, glutathione-S-transferase (GST-pi), interleukin-18 (IL-18), kidney injury molecule-1 (KIM-1) and monocyte chemoattractant protein-1 (MCP-1), were analyzed using Kidney Toxicity-1 Panel and BioPlex system, designed for analyses in urine and optimized by us for serum.From all analyzed markers, only levels of KIM-1 differed significantly between any subgroups, and that was for CD and DM. Renalase correlated significantly negatively with creatinine and positively with all other markers, apart from MCP-1. Obtained results indicate, that serum renalase, KIM-1, calbindin and GST-pi are related to kidney function, with KIM-1 being the most exact, while MCP-1 levels are unrelated to creatinine and glucose levels, does not differ between patients with diabetic nephropathy and other subgroups, and therefore seem to be independent of diabetes. Also, serum-optimized Kidney Toxicity Panel 1 kit for determination of selected markers gave results similar to previous ones and therefore the method can be valuable in determination of analyzed factors.

Preprint ARTICLE | doi:10.20944/preprints201706.0106.v1

Effect of a Particulate and a Putty-Like Tricalcium Phosphate-Based Bone Grafting Material on Bone Formation, Volume Stability and Osteogenic Marker Expression after Bilateral Sinus Floor Augmentation in Humans

Christine Knabe, Doaa Adel-Khattab, Esther Kluk, Rainer Struck, Michael Stiller

Subject: Chemistry And Materials Science, Biomaterials Keywords: Tricalcium phosphate putty scaffold; bioactive ceramics; bone formation, osteogenesis, osteogenic markers, hard tissue histology; immunohistochemical analysis; split-mouth design; sinus floor augmentation; bone grafting materials

Online: 22 June 2017 (18:33:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1870.v1

MYµALBUMIN: A Point-of-Care Medical Device for Determination of Albumin-Creatinine Ratio (uACR) in Random Urine Samples as A Marker of Nephropathy

Nadda Muhamad, Napaporn Yongvises, Tullayakorn Plengsuriyakarn, Wanchai Meesiri, Wanna Chaijaroenkul, Kesara Na-Bangchang

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Albumin; Albumin-Creatinine ratio; Creatinine; Microalbumin; Point-of-Care medical device

Online: 29 April 2024 (10:25:15 CEST)

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Chronic kidney disease (CKD) is a progressive condition that affects more than 10% of the world's population. Monitoring urine albumin and creatinine ratio (µACR) has become the gold standard for nephropathy diagnosis and control. The objective of the present study was to develop a simple, accurate, sensitive, and rapid point-of-care test (PoCT) device - MYμALBUMIN that community healthcare professionals can use in resource-limited facilities and by patients in their own homes for screening the risk and monitoring the progress of CKD. Albumin and creatinine concentrations in urine samples were determined using spectrophotometric dye (tetrabromophenol blue)-binding and colorimetric Jaffe’assay, respectively. Urine samples were diluted with distilled water (1:80) and mixed separately with albumin and creatinine reaction mixture. The creatinine reaction was incubated at room temperature (25oC) for 30 minutes before analysis. Optical density (OD) was measured at the wavelengths of 625 nm (albumin) and 515 nm (creatinine). All calibration curves (2-60 mg/L and 0.25-2 mg/dL for albumin and creatinine) yielded linear relationships with correlation coefficients (r2) of > 0.999. Good accuracy (%DMV < + 2.88%) and precision (%CV < 3.0%) were observed from both the intra- or interday assays for the determination of albumin and creatinine by MYµALBUMIN. The limit of quantification (LOQ) of albumin and creatinine in urine samples determined by MYµALBUMIN and laboratory spectrophotometer were 2 mg/L and 0.1 mg/dL, respectively, using 37.5 μL urine samples. The device was well applied with clinical samples from 13 CKD patients. The median (range) of %DMV of the central (hospital) laboratory method (immune-based assay) was 3.18 (-10.11 to 14.12)%, with a high correlation coefficient (r2 >0.99). In conclusion, MYμALBUMIN showed satisfactory test performance in terms of accuracy, reproducibility, sensitivity, and specificity. The device would have significant economic benefits besides obviously improving clinical decision-making processes.

Preprint ARTICLE | doi:10.20944/preprints202405.1412.v1

Comparison of New Inflammatory Marker Scoring Systems and Conventional Inflammatory Markers in Patients Over 65 Years of Age Admitted to the Intensive Care Unit: A Multicenter Retrospective Cohort Study

Özlem Çakin, Arzu Karaveli, Melike Yüce Aktepe, Ayça Gümüş, Özlem Esra Yildirim

Subject: Medicine And Pharmacology, Internal Medicine Keywords: intensive care unit; inflammatory markers; scoring systems; geriatric patient

Online: 22 May 2024 (15:29:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0042.v1

Seasonal Growth of Zygophyllum dumosum Boiss.: Summer Dormancy is Associated with Loss of the Permissive Epigenetic Marker Dimethyl H3K4 and Extensive Reduction in Proteins Involved in Basic Cell Functions

Janardan Khadka, Narendra Singh Yadav, Gila Granot, Gideon Grafi

Subject: Biology And Life Sciences, Plant Sciences Keywords: epigenetics; H3K9 methylation; H3K4 methylation; DNA methylation; seasonal climate change; summer dormancy; heat shock proteins; ribosomal proteins; Zygophyllum dumosum Boiss

Online: 4 June 2018 (12:49:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1877.v1

Citrullinated Histone H3, a Marker for Neutrophil Extracellular Traps, Is Associated with Poor Prognosis in Cutaneous Squamous Cell Carcinoma Developing in Patients with Recessive Dystrophic Epidermolysis Bullosa

Helene RAGOT, Sonia Gaucher, Mathilde Bonnet des Claustres, Justine Basset, Rose Boudan, Maxime Battistella, Emmanuelle Bourrat, Alain Hovnanian, Matthias Titeux

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: recessive dystrophic epidermolysis bullosa; cutaneous squamous cell carcinoma; citrullinated histone H3

Online: 29 May 2024 (06:57:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0208.v1

Evaluation of Coproporphyrins I and III as an Endogenous Marker for Hepatic Organic Anion Transporting Polypeptides and Multidrug Resistance-Associated Proteins (MRP 2/3) Activity in Animal Models of Nonalcoholic Steatohepatitis Using a Mechanistic Model

Rajeev Kumar, Sagnik Chatterjee, Ravindranath Reddy Gilibili, T Thanga Mariappam, Hong Shen

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Coproporphyrin; Oatps; Mrp; Endogenous biomarker; Modeling and Simulation

Online: 5 September 2023 (03:40:58 CEST)

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Coproporphyrins I and III (CP-I and CP-III) are established as substrates of hepatic sinusoidal organic anion transporting polypeptides (Oatps), multidrug resistance-associated protein 3 (Mrp3), and canalicular transporter Mrp2. We aimed to evaluate the potential of plasma CP-I and CP-III concentrations to indicate functional changes in hepatic transporters in nonalcoholic stea-tohepatitis (NASH) rodent models using modeling and simulation approach. Mechanistic copro-porphyrins (CP-I and CP-III) models in rats and mice were constructed based on metabolism, transport, and elimination pathways in rodents. To parameterize the rat mechanistic model, we measured CP concentrations in plasma, liver, bile, and urine in healthy control Sprague Dawley rats. The mouse mechanistic model was parameterized using published data. The rat and mouse CP models described the steady-state levels of CP-I and CP-III in plasma, liver, and bile. The model recapitulated the observed high plasma CP-III / CP-1 ratio (9- and 3-fold in rats and mice, respec-tively) and elimination pathways of CP-I (>90% via biliary secretion) and CP-III (equal via bile and urine). Rat CP model was further validated with the published rat fistula model. The simulated increased plasma CP-I concentrations (4-fold), resulted from decreased Oatp activity (0.6-fold) and increased Mrp3 activity (3-fold) were comparable to those observed in bile-duct ligated NASH model. Sensitivity analysis revealed that 90% inhibition of Oatp and Mrp2 leads to a 4-fold and 2.5-fold increase in plasma CP-I levels, respectively. Additionally, we demonstrated the utility of the mechanistic CP models in testing hypothesis and understanding the mechanisms of the ob-served plasma CPs disposition in the Oatp knockout (KO) mice, bile-duct ligation NASH mice, and Mrp2 deficient TR- rats. Collectively, using a mechanistic model, we conclude that CP-I is a robust and predictable marker for assessing change in the activity of Oatps and Mrps in animal models. Our analysis suggests that efflux transporters (Mrp2 and Mrp3) can play an important role in the disposition of CP-I along with Oatp transporters in rodents.

Preprint ARTICLE | doi:10.20944/preprints202407.1815.v1

An Integrated Approach Based on Clinical Data Together with Metabolites and Biomarkers for the Assessment of the Postoperative Complications after Cardiac Surgery

Peter Meinarovich, Alisa Pautova, Evgenii Zuev, Ekaterina Sorokina, Ekaterina Chernevskaya, Natalia Beloborodova

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: aromatic microbial metabolites; sepsis-associated metabolites; 4-hydroxyphenyllactic acid; prognostic models; SOFA

Online: 23 July 2024 (16:04:39 CEST)

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Background: Early diagnosis of postoperative complications is an urgent task, allowing timely prescribing of appropriate therapy and reducing the cost of patient treatment. Prognostic models based on various data could help in the early diagnosis of postoperative complications after cardiac surgery. Objectives: The purpose of the study was to determine whether an integrated approach based on clinical data along with metabolites and biomarkers had greater predictive value than the models built on less data. Methods: The study included patients (n=62) admitted for planned cardiac surgery (coronary artery bypass grafting with cardiopulmonary bypass), who were retrospectively divided into two groups depending on the presence (n=26) or absence (n=36) of postoperative complications of all types. Clinical and laboratory data on the first day after surgery were analyzed. Additionally, patients' blood samples were collected before and on the first day after surgery to determine biomarkers (interleukin-6, procalcitonin, NT-proBNP, high-sensitivity troponin T) and metabolites (8 aromatic and 2 dicarboxylic acids were detected using gas chromatography-mass spectrometry). Results: Patients before surgery, compared with healthy donors, differed in the concentration of metabolites (p < 0.05), and had concentrations of a number of biomarkers exceeding the corresponding reference values. Multivariate PLS-DA models, predicting the presence or absence of postoperative complications, were built using clinical data (ROC-AUC=0.71), concentrations of metabolites and biomarkers (ROC-AUC=0.60), and the entire data set (ROC-AUC=0.75). For comparison we built univariate models using the EuroScore2 (ROC-AUC=0.59) and SOFA (ROC-AUC=0.76) scales; concentrations of lactate (ROC-AUC=0.71), the dynamic changes of 4-hydroxyphenyllactic acid (ROC-AUC=0.69), and the sum of three sepsis-associated metabolites (ROC-AUC=0.70). The proposed complex model using entire data set was comparable to the SOFA scale, which confirms the expediency of searching for new predictive models based on a variety of factors.

Preprint REVIEW | doi:10.20944/preprints202406.0540.v1

Whey as an Optimal Substrate for the Development of Functional Products Enriched with Bioactive Peptides

Margarita Saubenova, Yelena Oleinikova, Alexander Rapoport, Sviatoslav Maksimovich, Zhanerke Yermekbay, Elana Khamedova

Subject: Biology And Life Sciences, Food Science And Technology Keywords: functional products; peptides, whey; fermentation; lactic acid bacteria; proteolytic activity.

Online: 10 June 2024 (08:49:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1023.v1

A Contribution to the Integration of International, National and Local Cultural Heritage Protection through a Multilevel Approach to Planning: A Case Study of the Djerdap Area

Ana Niković, Božidar Manić, Nataša Čolić Marković, Nikola Krunić

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Djerdap; Danube; spatial plan; protected area; cultural heritage; multilevel approach

Online: 16 April 2024 (10:27:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1356.v1

Impact of Southerly Surge on Rainfall Pattern Over Java, Bali, West Nusa Tenggara and East Nusa Tenggara during Asian Winter Monsoon and Its Relationship to MJO Condition

Trismidianto Trismidianto, Didi Satiadi, Wendi Harjupa, Ibnu Fathrio, Risyanto Risyanto, Elfira Saufina, Robi Muharsyah, Danang Eko Nuryanto, Fadli Nauval, Dita Fatria Andarini, Anis Purwaningsih, Teguh Harjana, Alfan Sukmana Praja, Adi Witono, Ina Juaeni, Bambang Suhandi

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: Southerly Surge; MJO; Rainfall; Java Island; East Nusa Tenggara

Online: 19 June 2024 (14:10:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1950.v1

A Lightweight and High-Precision Passion Fruit YOLO Detection Model for Deployment in Embedded Devices

Qiyan Sun, Pengbo Li, Chentao He, QiMing Song, Zhicong Luo

Subject: Engineering, Electrical And Electronic Engineering Keywords: passion fruit detection; lightweight; deep learning; knowledge distillation; embedded devices

Online: 29 May 2024 (14:12:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1484.v1

Assessment of SLAM Scanner Accuracy for Outdoor and Indoor Surveying Tasks

Zahra Gharineiat, Fayez Tarsha Kurdi, Krish Henny, Hamish Gray, Aaron Jamieson, Nicholas Reeves

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: SLAM; LiDAR; accuracy assessment; indoor and outdoor; data acquisition

Online: 23 April 2024 (11:59:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.2202.v1

CSA-SA-CRTNN: A Dual-Stream Adaptive Convolutional Cyclic Hybrid Network Combining Attention Mechanisms for EEG Emotion Recognition

Ren Qian, Xin Xiong, Jianhua Zhou, Hongde Yu, Kaiwen Sha

Subject: Biology And Life Sciences, Behavioral Sciences Keywords: EEG; emotion recognition; attention mechanism; Dual-Stream model; adaptive; hybrid network

Online: 29 July 2024 (10:43:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0276.v1

Methylation-GC-MS/FID-Based Glycosidic Linkage Analysis of Unfractionated Polysaccharides in Red Seaweeds

Barinder Bajwa, Xiaohui Xing, Stephanie A. Terry, Robert J. Gruninger, D. Wade Abbott

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: methylation analysis; reductive hydrolysis; whole food fiber; whole cell wall; anhydro sugar; agarose; carrageenan; sulfated galactan; mixed linkage xylan; principal component analysis

Online: 3 April 2024 (10:33:21 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202402.1644.v2

The Impact of an Online Sleep Education Program (Sleep 101) on Sleep Hygiene and Sleep Behavior in College Students

Johanna Schmickler, Rebecca Robbins, Pallas Snider Ziporyn, Stuart Quan

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: sleep hygiene; sleep behavior; college students; sleep education program

Online: 6 March 2024 (04:49:17 CET)

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