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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/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 REVIEW | doi:10.20944/preprints202403.0876.v1

Innovations in Medicine: Exploring ChatGPT's Impact on Rare Disorder Management

Stefania Zampatti, Cristina Peconi, Domenica Megalizzi, Giulia Calvino, Giulia Trastulli, Raffaella Cascella, Claudia Strafella, Carlo Caltagirone, Emiliano Giardina

Subject: Medicine And Pharmacology, Other Keywords: Artificial Intelligence; ChatGPT; Rare Disorders

Online: 15 March 2024 (14:41:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202406.0327.v1

Genomic Landscape of Susceptibility to Severe COVID-19 in the Slovenian Population

Anja Kovanda, Tadeja Lukežič, Aleš Maver, Hana Vokač Križaj, Mojca Čižek Sajko, Julij Šelb, Matija Rijavec, Urška Bidovec-Stojković, Barbara Bitežnik, Boštjan Rituper, Peter Korošec, Borut Peterlin

Subject: Medicine And Pharmacology, Other Keywords: severe COVID-19; severe outcome of SARS-CoV-2 infection; whole-genome sequencing; WGS; genetic susceptibility; rare variants; human rare genomic variants

Online: 6 June 2024 (07:30:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1128.v1

Genetic Factors Contributing to the Pathogenesis of Essential Hypertension in Two African Populations

Kusha Kalideen, Brian Rayner, Raj Ramesar

Subject: Biology And Life Sciences, Other Keywords: essential hypertension; South Africa; Mixed Ancestry; Xhosa; RAAS; AGTR1; AGT; ACE; CYP11B2

Online: 20 February 2024 (09:20:43 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202409.0406.v1

G6PD Potenza: A Novel Pathogenic Variant Broadens the Mutational Landscape in the Italian Population

Claudio Ricciardi Tenore, Eugenia Tulli, Claudia Calo, Roberto Bertozzi, Jessica Evangelista, Giulia Maneri, Martina Rinelli, Francesca Brisighelli, Alessia Perrucci, Elisa De Paolis, Andrea Urbani, Maria De Bonis, Angelo Minucci

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: G6PD Potenza; Sanger Sequencing; G6PD deficiency; RFLP; Italian population

Online: 5 September 2024 (08:20:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0571.v1

Streamlined Two-Step Fragment Analysis PCR and Exome Sequencing of RFC1 for Diagnostic Testing of Suspected CANVAS Patients

Helena Jaklič, Ivana Babič Božović, Borut Peterlin, Anja Kovanda

Subject: Medicine And Pharmacology, Other Keywords: Cerebellar ataxia neuronopathy and vestibular areflexia syndrome (CANVAS); RFC1; genetic testing; genetic diagnostics, ; fluorescent PCR; repeat-primed PCR; repeat-expansion; fragment length analysis

Online: 11 March 2024 (05:36:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202405.0159.v1

The TGFβ Induced MicroRNAome of the Trabecular Meshwork

Chelsey Doyle, Breedge Callaghan, Anton W Roodnat, Lee Armstrong, Karen Lester, David A Simpson, Sarah D. Atkinson, Carl Sheridan, Declan J McKenna, Colin E Willoughby

Subject: Medicine And Pharmacology, Ophthalmology Keywords: glaucoma; primary open-angle glaucoma; POAG; trabecular meshwork; intra-ocular pressure; pseudoexfoliation glaucoma; microRNA; miRNA; transforming growth factor beta; TGFβ ; fibrosis; epigenetics; gene therapy; therapeutics

Online: 3 May 2024 (11:22:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0420.v1

Pirfenidone Reverts Global DNA Hypomethylation, Promoting DNMT1/UHRF/PCNA Coupling Complex in Experimental Hepatocarcinoma

Hipolito Otoniel Miranda-Roblero, Liliana Faridi Saavedra-Salazar, Marina Galicia-Moreno, Scarlet Arceo-Orozco, Fernando Caloca-Camarena, Ana Sandoval-Rodríguez, Jesús García-Bañuelos, Claudia Frias-Gonzalez, Monica Almeida-López, Erika Martínez-López, Juan Armendariz-Borunda, Hugo Christian Monroy-Ramirez

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Hepatocellular carcinoma; DNMT1; DNMT3a; c-Myc; β -catenin

Online: 5 April 2024 (08:39:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201703.0162.v1

Evaluation of the Effects of Airborne Particulate Matter on Bone Marrow-Mesenchymal Stem Cells (BM-MSCs): Cellular, Molecular and Systems Biological Approaches

Muhammad Abu-Elmagd, Mansour A Alghamdi, Magdy Shamy, Mamdouh I Khoder, Max Costa, Mourad Assidi, Roaa Kadam, Haneen Alsehli, Mamdooh Gari, Peter Natesan Pushparaj, Gauthaman Kalamegam, Mohammed Al-Qahtani

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Particulate matter; BM-MSCs; cell proliferation; cell death; qRT-PCR; IPA

Online: 20 March 2017 (16:33:56 CET)

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Preprint REVIEW | doi:10.20944/preprints202406.0329.v1

Are Viruses Taxonomic Units? – A Protein Domain and Loop-Centric Phylogenomic Assessment

Gustavo Caetano-Anollés

Subject: Biology And Life Sciences, Virology Keywords: holobionts; hologenomes; LUCA; origin of viruses; phylogenomic reconstruction; process; protein structure; reductive evolution; superkingdom; syncytins

Online: 6 June 2024 (07:52:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0840.v1

Genetic Architecture of CHD in NICU patients – UMC Ljubljana Experience

Ana Peterlin, Sara Bertok, Karin Writzl, Luca Lovrečić, Aleš Maver, Maruša Debeljak, Gregor Nosan

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: congenital heart disease; chromosomal microarray analysis; next-generation sequencing

Online: 13 May 2024 (12:12:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.0099.v1

Detailed Profiling of the Tumor Microenvironment in Ethnic Breast Cancer, Using Tissue Microarrays and Multiplex Immunofluorescence

Mohamed Zaakouk, Aisling Longworth, Kelly Hunter, Suhaib Jiman, Mervat El-Deftar, Abeer Shaaban

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Tumor microenvironment; Multiplex immunofluorescence; Ethnic breast cancer; Multispectral imaging; TILs; T helper cells; Treg cells; FOXP3; TAMs; B cells

Online: 3 June 2024 (16:07:13 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 REVIEW | doi:10.20944/preprints202404.1075.v1

Genomic Approaches for Drug Repurposing

Kirtan Dave, Meenakshi Sharma, Dahavl Patel, Parmdeep Singh Dhanda, Alpa Yadav, Mukul Jain

Subject: Biology And Life Sciences, Life Sciences Keywords: drug repurposing; genomics; Proteomics; NGS

Online: 17 April 2024 (11:38:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0561.v2

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Sudhakar Bhandare, Opeyemi U. Lawal, Anna Colavecchio, Brigitte Cadieux, Yella Zahirovich-Jovich, Zeyan Zhong, Elizabeth Tompkins, Margot Amitrano, Irena Kukavica-Ibrulj, Brian Boyle, Siyun Wang, Roger C. Levesque, Pascal Delaquis, Michelle Danyluk, Lawrence Goodridge

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Salmonella; bacteriophage; diversity; host specificity; comparative phylogenomics; food safety.

Online: 13 March 2024 (14:07:08 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 REVIEW | doi:10.20944/preprints202407.1479.v1

Diagnosis of Chronic Granulomatous Disease: Strengths and Challenges in the Genomic Era

Conor John O’Donovan, Lay Teng Tan, Mohd Azri Zainal Abidin, Marion Ruth Roderick, Alexandros Grammatikos, Jolanta Bernatoniene

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Inborn errors of immunity (IEI); Chronic granulomatous disease (CGD); NADPH oxidase; Nitroblue tetrazolium (NBT); Dihydrorhodamine (DHR); Genetic testing; Genomic testing; Screening

Online: 18 July 2024 (14:38:08 CEST)

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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 REVIEW | doi:10.20944/preprints202311.1531.v1

Sex Differences in Colon Cancer: Genomic and Non‐Genomic Signaling of Estrogen

Brian Joseph Harvey, Harry Myles Harvey

Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: colon cancer; estrogen; estrogen receptors, sex differences

Online: 23 November 2023 (13:35:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202404.1502.v1

Genomic Profiling and Expression Analysis of BPC Gene Family in Brassica oleracea in Comparison with Arabidopsis

Muhammad Asad Ullah, Akmal Zubair, Aqsa Parvaiz, Inzamam Ul Haq, Hayssam M. Ali, Waleed A. A. Alsakkaf, Mohamed E. Hasan

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: basic pentacysteine; genomic analysis; chromosomal mapping; gene expression

Online: 23 April 2024 (07:29:04 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/preprints202403.0302.v1

IL-10 and IL-1β Serum Levels, Genetic Variants, and Metabolic Syndrome: Insights into Older Adults' Clinical Characteristics

Renata de Souza Freitas, Calliandra Maria De Souza Silva, Caroline Caroline Ferreira Fratelli, Luciano Ramos de Lima, Marina Morato Stival, Silvana Schwerz Funghetto, Izabel Cristina Rodrigues da Silva, Rosângela Vieira de Andrade

Subject: Public Health And Healthcare, Primary Health Care Keywords: Metabolic Syndrome; Interlekine-10; Interlekine-1β ; older population; IL10 rs1800890; IL1B rs1143627

Online: 6 March 2024 (11:09:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202408.2221.v1

Human-Activity-Mediated Gene Flows Are Involved in the Establishment of Magnaporthe oryzae Population Structures: A Population Genomic Analysis

Guohua Duan, Yuchan Liu, Cheng Zheng, Kaihui Yu, Jiahui Xie, Baohua Wang, Huakun Zheng, Wei Tang, Jiandong Bao, Zonghua Wang, Meilian Chen

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Magnaporthe oryzae; population structure; genetic diversity; gene flow

Online: 30 August 2024 (08:36:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.0837.v1

BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata

Sara Ribeiro, Guillaume Chaumet, Karine Alves, Julien Nourikyan, Lei Shi, Jean-Pierre Lavergne, Ivan Mijakovic, Simon de Bernard, Laurent Buffat

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacterial pathogenicity; Genomic metadata analysis; Bioinformatics; Microbiology research; Public health surveillance

Online: 11 July 2024 (00:01:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.0599.v1

A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T Cell Receptor Beta Chain in Equus caballus

Rachele Antonacci, Francesco Giannico, Roberta Moschetti, Angela Pala, Anna Caputi Jambrenghi, Serafina Massari

Subject: Biology And Life Sciences, Life Sciences Keywords: alpha-beta T cell; TRB locus; Perissodactyla; Equus; equine genome; immunogenetics; evolution

Online: 8 August 2024 (08:48:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.0800.v1

Wastewater Genomic Surveillance to Track Infectious Disease-Causing Pathogens in Agadir and Inezgane Cities

Maryem Wardi, Ahmed Belmouden, Mohamed Aghrouch, Abdellah Lotfy, Youssef Idaghdour, Zohra Lemkhente

Subject: Biology And Life Sciences, Virology Keywords: Wastewater-based epidemiology; COVID-19; SARS-CoV-2; Influenza A; Morocco; Genomic surveillance

Online: 13 August 2024 (03:24:22 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 CASE REPORT | doi:10.20944/preprints202312.1095.v2

Genomic Exploration of Pediatric Neurological Diversity: Lessons from Clinical Exome Panel Sequencing

Naresh Tayade, Anjali Krishna A, Gautham Manoj, Akshay Kewat, Rajiv Devulapalli, Somesh Kumar, Sunil K Polipalli, Bipin G Nair, Obul Reddy Bandapalli, Prashanth Suravajhala

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Rare conditions; Neurological disorders; Autism; Arthrogryposis; Bilateral cataract

Online: 7 August 2024 (00:30:58 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 REVIEW | doi:10.20944/preprints201810.0708.v1

Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

Alisha Parveen, Sukank Khurana, Abhishek Kumar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: circular visualization; circos; genomics; next-generation sequencing

Online: 30 October 2018 (07:06:35 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/preprints202404.1794.v1

Genomic Characterization of Carbapenemase-Producing Enterobacter hormaechei, Serratia marcescens, Citrobacter freundii, Providencia stuartii and Morganella morganii Clinical Isolates from Bulgaria

Stefana Sabtcheva, Ivan Stoikov, Ivan N. Ivanov, Deyan Donchev, Magdalena Lesseva, Sylvia Georgieva, Deana Teneva, Elina Dobreva, Iva Christova

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: carbapenemases; NDM-1; VIM-4; VIM-86; OXA-48; horizontal gene transfer; Enterobacter; Serratia; Citrobacter; Providencia; Morganella

Online: 28 April 2024 (08:17:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1579.v1

Combined Genome-Wide Association Studies (GWAS) and Linkage Mapping Identifies Genomic Regions Associated with Seedling Root System Architecture (RSA) under Different Nitrogen Conditions in Wheat (Triticum aestivum L.)

Yulin Jia, Ninglu Xu, Jun Zhang, Kaiming Ren, Jinzhi Wu, Chunping Wang, Ming Huang, Youjun Li

Subject: Biology And Life Sciences, Plant Sciences Keywords: Keywords：Triticum aestivum L; root system architecture; N use efficiency; GWAS; linkage mapping; 660K SNP chip; DArT

Online: 19 July 2024 (08:37:45 CEST)

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The nutrient absorption and utilization efficiency in the roots of seedlings are beneficial for increasing crop yield. Creating marker assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Exploring and identifying the effect of different nitrogen applications on RSA is of great significance for breeding nitrogen efficient wheat varieties. In this study, A total of 243 wheat varieties native to the Yellow and Huai Valley regions of China were utilized for genome-wide association studies (GWAS). Furthermore, a recombinant inbred line (RIL) population of 123 lines derived from the cross between Avocet and Chilero was utilized for linkage examination and confirmation of the hereditary loci distinguished by GWAS. Five RSA traits include the relative number of root tips (RNRT); relative total root length (RTRL); relative total root surface area (RTRS); relative total root volume (RTRV) and relative average root diameter (RARD) where evaluated under two N conditions—normal N (NN) supply and low N (LN)—to characterize the NUE of each accession. GWAS and linkage analysis were performed by integrating data from the wheat 660k single nucleotide polymorphism (SNP) chip and diversity arrays technology (DArT) to identify genetic loci associated with RSA. The results showed that based on the ratio of RSA related traits under two N supply conditions, a total of 598 SNP markers, which are significantly associated with RSA related traits, were detected at 160 genetic loci by GWAS. A total of 10 QTL loci related to RSA were dis-covered and identified by linkage mapping. In which, three significant RSA related Quantitative Trait Locus (QTL) were identified, namely qRtrl-3D, qRnrt-3D, and qRtrl-7D. The study has the potential to enhance the effectiveness of selecting root traits in wheat breeding programs, offering valuable insights into the genetic underpinnings of nitro-gen use efficiency (NUE) in wheat. This could lead to the creation of NUE wheat varieties by implementing focused breeding strategies.

Preprint COMMUNICATION | doi:10.20944/preprints202404.1865.v1

Detection and Characterization of Methylated Circulating Tumor DNAs in Gastric Cancer

Seung Young Seo, Sang Hee Youn, Jin-Han Bae, Sung-Hun Lee, Sun Young Lee

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Gastric cancer; Liquid biopsy; MeDIP; Fragment

Online: 29 April 2024 (10:34:32 CEST)

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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/preprints202402.1069.v1

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

Tania Kartseva, Vladimir Aleksandrov, Ahmad M. Alqudah, Mian Abdur Rehman Arif, Konstantina Kocheva, Dilyana Doneva, Katelina Prokopova, Andreas Börner, Svetlana Misheva

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: association mapping, candidate genes, grain protein content, TKW, grain quality, grain yield, Triticum aestivum L.

Online: 19 February 2024 (15:26:36 CET)

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Preprint REVIEW | doi:10.20944/preprints202407.1052.v1

Targeting Androgen, Thyroid Hormone, and Vitamin A and D Receptors to Treat Prostate Cancer

Brigitte Hantusch, Lukas Kenner, Vesna S Stanulović, Maarten Hoogenkamp, Geoffrey Brown

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Prostate cancer; nuclear hormone receptors; androgen receptor; thyroid hormone receptor; retinoic acid receptor; vitamin D receptor

Online: 12 July 2024 (13:59:33 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/preprints202403.1634.v1

Genomic Insight into the COVID-19 Severity in MAFLD Patients: A Single-Center Prospective Cohort Study

Mykhailo Buchynskyi, Valentyn Oksenych, Iryna Kamyshna, Olena Budarna, Oleksandr Kamyshnyi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: MAFLD; liver disease; SNP; COVID-19; SARS-CoV-2; interferon

Online: 27 March 2024 (15:01:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202007.0336.v3

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils

Arfang Badji, Lewis Machida, Daniel Bomet Kwemoi, Frank Kumi, Dennis Okii, Natasha Mwila, Symphorien Agbahoungba, Angele Ibanda, Astere Bararyenya, Selma Ndapewa Nghituwamhata, Thomas Odong, Peter Wasswa, Mildred Ochwo-Ssemakula, Herbert Talwana, Godfrey Asea, Michael Otim, Samuel Kyamanywa, Patrick Rubaihayo

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Prediction accuracy; Mixed linear and Bayesian models; Machine Learning algorithms; Training set size and composition; Parametric and nonparametric models

Online: 17 September 2020 (05:41:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0192.v1

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Jake Gazeley, Terence Lee, Daniel R Knight, Alexander Shivarev, Cameron Gordon, David Speers, Dylan D Barth, Jelena Maticevic, Meredith Hodge, Paul Armstrong, Paul Knight, Sandra Sjollema, Avram Levy

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Wastewater-based epidemiology; SARS-CoV-2; COVID-19; surveillance system; correlation analysis; genomics

Online: 5 March 2024 (09:07:35 CET)

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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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Preprint REVIEW | doi:10.20944/preprints202405.0592.v1

Progress and Application of Genomic Selection in Sheep and Goat

Linyun Zhang, Yixin Duan, Naiyi Xu, Yongju Zhao

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Goat; Sheep; Genomic Selection; Genetic Evaluation; Accuracy

Online: 9 May 2024 (11:57:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0011.v1

Artificial Intelligence and Machine Learning in Precision and Genomic Medicine

Sameer Quazi

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Machine Learning; Precision Medicine; Genomic Medicine; Therapeutic; Artificial Intelligence

Online: 1 October 2021 (11:41:27 CEST)

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Preprint REVIEW | doi:10.20944/preprints202406.1671.v1

Consent Considerations for Generation and Sharing of Genomic Data

Charles D. Warden

Subject: Public Health And Healthcare, Health Policy And Services Keywords: data sharing, policy, genomics, genetics

Online: 25 June 2024 (09:26:47 CEST)

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Preprint REVIEW | doi:10.20944/preprints202202.0042.v1

Utilizing Genomic Selection for Wheat Population Development and Improvement

Lance F. Merrick, Andrew W. Herr, Karansher S. Sandhu, Dennis N. Lozada, Arron H. Carter

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: plant breeding; two-part strategy; recurrent selection; population improvement; product development; optimization; genetic gain; cross-prediction

Online: 2 February 2022 (18:07:58 CET)

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Working Paper ARTICLE

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Daniele Mercatelli, Federico Manuel Giorgi

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; genomics coronavirus; COVID-19 evolution

Online: 3 July 2020 (09:45:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0184.v1

Carbohydrate Hydrolytic Activity, Antibiotic Resistance and Stress Tolerance of Lacticaseibacillus paracasei BCRC-16100 and Lacticaseibacillus paracasei ZFM54 for Probiotics Using Genomic and Biochemical Approaches

Peter James Icalia Gann, Jimmbeth Zenila P. Fabia, Althea Gay B. Pagurayan, Ma. Joy Theresa Agcaoili, Ryan James J. Pascual, Suerte M. Baranda, Arc Josam J. Racho, Marvielyn P. Olivar, Jayson F. Cariaga, Alvin Domingo, Dionisio S. Bucao, Shirley C. Agrupis

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: probiotics; nutrient digestion; antibiotic resistance; antibacterial activity; whole genome sequence

Online: 2 April 2024 (10:16:40 CEST)

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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/preprints202306.0046.v1

The Future of Newborn Genomic Screening

JOHN David LANTOS

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: ethics; genomics; neonates; outcomes; economics

Online: 1 June 2023 (07:23:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202111.0394.v1

Genomic Designing of Climate Smart Turmeric

Arpitha Shankar

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Turmeric; Climate change; Improved nutrition

Online: 22 November 2021 (13:27:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202109.0441.v1

Genomic Risk Factors for Cervical Cancer

Dhanya Ramachandran, Thilo Dörk

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Cervical cancer; cervical dysplasia, HPV, HLA, GWAS, genetic susceptibility, meta-analysis, SNP, eQTL, Papillomavirus

Online: 24 September 2021 (15:28:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0242.v1

Genomic Fabric Remodeling in Prostate Cancer

Sanda Iacobas, Dumitru A. Iacobas

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: apoptosis; evading apoptosis; expression variability; cancer functional pathway; prostate cancer phenotype; immortality; proliferation; P53 signaling; transcriptomic network

Online: 9 March 2021 (08:44:15 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202408.0010.v1

Genomic Insights into Idiopathic Granulomatous Mastitis through Whole Exome Sequencing: A Case Report of Eight Patients

Seeu Si Ong, Peh Joo Ho, Alexis Jiaying Khng, Benita Kiat Tee Tan, Qing Ting Tan, Ern Yu Tan, Su-Ming Tan, Thomas Choudary Putti, Swee Ho Lim, Ee Ling Serene Tang, Jingmei Li, Mikael Hartman

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: breast pathology; breast abscess; suppurative breast lesion; tuberculous mastitis; breast cancer; mastitis; idiopathic granulomatous mastitis; somatic mutations; pathogenic mutations; whole-exome sequencing

Online: 1 August 2024 (10:59:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0228.v1

Genomic Diversity and Chromosomal Rearrangements in Neisseria Gonorrhoeae and Neisseria Meningitidis

Boris Shaskolskiy, Dmitry Kravtsov, Ilya Kandinov, Ekaterina Dementieva, Dmitry Gryadunov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Neisseria gonorrhoeae; Neisseria meningitidis; whole genome sequencing; chromosomal rearrange-ments; mobile elements

Online: 14 November 2022 (02:11:22 CET)

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Preprint CASE REPORT | doi:10.20944/preprints202404.0136.v1

From Investigating a Case of Cellulitis to Exploring Nosocomial Infection Control of ST1 Legionella pneumophila Using Genomic Approaches

Charlotte Michel, Fedoua Echahidi, Sammy Place, Lorenzo Filippin, Vincent Colombie, Nicolas Yin, Delphine Martiny, Olivier Vandenberg, Denis Piérard, Marie Hallin

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Legionella pneumophila; Legionella pneumophila ST1; WGS; genomic typing; wgMLST; cgMLST; wgSNP; nosocomial; hygiene investigation

Online: 2 April 2024 (07:26:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0043.v1

Genomic Investigation for Potential Therapeutic Use of Abiraterone in the Amazonian Indigenous Population

Jonatas Monteiro Nobre, Marianne R. Fernandes, Jose Oliveira Venancio, Giovanna Gilioli da Costa Nunes, NEY PEREIRA CARNEIRO DOS SANTOS, PAULO PIMENTEL ASSUMPÇÃO, ÂNDREA RIBEIRO-DOS-SANTOS, SIDNEY EMANUEL BATISTA DOS SANTOS, Juliana CARLA GOMES RODRIGUES, Natasha Monte, Rommel M. R. Burbano, João Farias Guerreiro, Kaio Evandro Cardoso Aguiar

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: abiraterone; prostate; amazonian; indigenous; cancer

Online: 1 May 2024 (05:34:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.0713.v1

Genomic Selection for Growth and Wood Traits in Castanopsis hystrix

Weihua Zhang, Ruiyan Wei, Yuanzhen Lin

Subject: Biology And Life Sciences, Plant Sciences Keywords: Castanopsis hystrix; genomic selection; growth trait; wood trait; early selection; SNP

Online: 9 July 2024 (08:45:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0068.v1

Genomic Landscape of Angiosarcoma: A Targeted and Immunotherapy Biomarker Analysis

Andrea Espejo-Freire, Andrew Elliot, Andrew Rosenberg, Philippos Apolinario Costa, Priscila Barreto Coelho, Emily Jonczak, Gina D’Amato, Ty Subhawong, Junaid Arshad, Julio A. Diaz-Perez, W. Michael Korn, Matthew J. Oberley, Daniel Magee, Don Dizon, Margaret von Mehren, Moh'd M. Khushman, Atif Mahmoud Hussein, Kirsten Leu, Jonathan C. Trent

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Angiosarcoma; biomarkers; tumor microenvironment; immunotherapy, next generation sequencing, whole transcriptome sequencing.

Online: 2 July 2021 (15:43:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0089.v1

Genomic Variations and Signatures of Selection in Wuhua Yellow Chicken

Zhuoxian Weng, Yongjie Xu, Weina Li, Jiebo Chen, Ming Zhong, Fusheng Zhong, Bingwang Du, Bin Zhang, Xunhe Huang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Wuhua yellow chicken; whole genome resequencing; heritable variation; selection signal

Online: 7 June 2020 (14:42:23 CEST)

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Preprint REVIEW | doi:10.20944/preprints201906.0178.v1

Evaluation of the Genomic Basis for Alzheimer’s and Parkinson’s Diseases

Pratip Rana, Edian F. Franco, Yug Rao, Khajamoinuddin Syed, Debmalya Barh, Vasco Azevedo, Rommel T. J. Ramos, Preetam Ghosh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Alzheimer's disease; Parkinson's disease; genetics; gene regulatory network; miRNAs

Online: 18 June 2019 (13:07:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1436.v1

Climate Change Impacts on Mediterranean Coral Oculina Patagonica: Reproductive Resilience and Thermal Performance

Tamar Shemesh, Shani Levy, Abigail Einbinder, Itai Kolsky, Jessica Bellworthy, Tali Mass

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Climate Change, Temperate Coral, Reproductive Resilience, Thermal Performance, Bleaching.

Online: 22 May 2024 (12:43:17 CEST)

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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 ARTICLE | doi:10.20944/preprints202204.0255.v1

First Genomic Insights Into The Mandevilla Genus

Fabio Palumbo, Samela Draga, Francesco Scariolo, Gio Batta Sacilotto, Marco Gazzola, Gianni Barcaccia

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome assembly; Apocynaceae; SSR; superbarcoding; flow cytometry; monoterpene indole alkaloids; DNA barcoding; cpDNA; Mandevilla sanderi

Online: 27 April 2022 (10:07:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints202202.0048.v1

Optimizing Plant Breeding Programs For Genomic Selection

Lance F. Merrick, Andrew W. Herr, Karansher S. Sandhu, Dennis N. Lozada, Arron H. Carter

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Plant Breeding; Speed Breeding; Training Population; Field Design; Multi-Environment; Multi-Trait; Deep Learning; High-Throughput Phenotyping; Genetic Gain

Online: 3 February 2022 (10:41:44 CET)

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Preprint REVIEW | doi:10.20944/preprints202103.0209.v1

Genomic Mapping in Detection of Vascular Disorders

Sameer Quazi, Arnaud Capuzzo, Javid Ahmad Malik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic Mapping; Vascular system; Embryogenesis; Vascular disorder; PIk3CA gene

Online: 8 March 2021 (10:43:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0169.v1

Genomic Analysis of the Polyvalent Bacteriophage FP01

Ignacio Vasquez, Julio Retamales, Barbara Parra, James Robeson, Javier Santander

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: polyvalent bacteriophage FP01, Escherichia coli, Salmonella, genome

Online: 12 July 2019 (13:07:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints201812.0156.v1

The Report of Marine Life Genomic Research

Guangyi Fan, Jianwei Chen, Tao Jin, Chengcheng Shi, Xiao Du, He Zhang, Yaolei Zhang, Hanbo Li, Ting Luo, Pengxu Yan, Guang Liu, Xiangqun Chi, Xiaoxuan Tan, Liangwei Li, Guilin Liu, Xiaochuan Liu, Shijie Hao, Kai Han, Xiaoyun Huang, Shuai Sun, Jing Zhou, Mengjun Yu, Lingfeng Meng, Yue Chang, Rui Zhang, Kaiqiang Liu, Mengqi Zhang, Yong Zhao, Chang Li, Jiao Guo, Xinyu Guo, Jiahao Wang, Meiqi Lv, Haoyang Gao, Yujie Liu, Yue Song, Shengjun Wang, Yang Deng, Binjie Ouyang, Jinzhong Lin, Yingjia Yu, lynn Fink, Xianwei Yang, Xun Xu, Xin Liu

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Marine microorganisms, marine fungi, algae, marine plants, marine invertebrates, marine vertebrates, genome, metagenome

Online: 12 December 2018 (15:44:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202407.1356.v1

Comparative Analysis of Comprehensive Genomic Profile in Thymomas and Recurrent Thymomas Reveals Potentially Actionable Mutations for Target Therapies

Filippo Lococo, Elisa De Paolis, Jessica Evangelista, Andrea Dell’Amore, Diana Giannarelli, Marco Chiappetta, Annalisa Campanella, Carolina Sassorossi, Alessandra Cancellieri, Fiorella Calabrese, Emanuele Vita, Angelo Minucci, Emilio Bria, Angelo Castello, Andrea Urbani, Federico Rea, Stefano Margaritora, Giovanni Scambia

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: NGS; recurrent thymoma; surgery; CGP; gene profile; clinical trials

Online: 17 July 2024 (11:00:23 CEST)

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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 REVIEW | doi:10.20944/preprints202403.0424.v1

Genomic Atlas 2.0 Emerging Strategies and Technologies in Advanced Genetic Mapping

Mohammad Odah

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Genomic atlas 2.0; advanced genetic mapping; high-throughput sequencing; long-read sequencing technologies; spatial genomics; CRISPR technologies; integrative genomic mapping

Online: 8 March 2024 (03:57:26 CET)

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Working Paper ARTICLE

Genomic Characterization and Phylogenetic Analysis of SARS-CoV-2 during the early phase of the pandemic in Asia

Jale Moradi, Mohsen Moghoofei, Mohammad Doroudian, Ramin Abiri

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; Phylogenetics; Asia

Online: 15 January 2021 (13:14:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202406.1410.v1

Study Protocol for a Prospective Self-Controlled Trial on Success in Meeting Comprehensive Genomic Profiling Analysis Criteria for Specimens Obtained by Endoscopic Ultrasound-Guided Tissue Acquisition Using a 19G Needle from Primary and Metastatic Lesions

Kotaro Takeshita, Susumu Hijioka, Yoshikuni Nagashio, Hidenobu Hara, Daiki Agarie, Yuki Kawasaki, Tetsuro Takasaki, Shin Yagi, Yuya Hagiwara, Kohei Okamoto, Daiki Yamashige, Soma Fukuda, Masaru Kuwada, Yasuhiro Komori, Mao Okada, Yuta Maruki, Chigusa Morizane, Hideki Ueno, Yasushi Yatabe, Takuji Okusaka

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: endoscopic ultrasound-guided tissue acquisition; comprehensive genomic profiling; pancreatic cancer; metastatic lesion; fine-needle biopsy

Online: 20 June 2024 (13:14:56 CEST)

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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/preprints202306.1828.v1

Genomic Surveillance of Rabies Virus in Georgian Canines

Celeste Huaman, Adrian C. Paskey, Caitlyn Clouse, Austin Feasley, Madeline Rader, Gregory K Rice, Andrea E Luquette, Maren C Fitzpatrick, Hannah M Drumm, Regina Z Cer, Marina Donduashvili, Tamar Buchukuri, Anna Nanava, Christine E Hulseberg, Michael A Washington, Eric D Laing, Francisco Malagon, Kimberly A Bishop-Lilly, Christopher C Broder, Brian C Schaefer

Subject: Biology And Life Sciences, Virology Keywords: Rabies; lyssaviruses; RABV; dog; jackal; canine; neutralization; genomics; next-generation sequencing; phylogeny

Online: 26 June 2023 (14:44:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202304.0326.v1

Recent Advances in the Genomic Resources for Sheep

Shernae A. Woolley, Mazdak Salavati, Emily L. Clark

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Sheep, genome, transcriptome, pangenome, gene editing

Online: 13 April 2023 (14:08:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0016.v2

Retinal Genomic Fabrics Remodeling after Optic Nerve Injury

Pedro Henrique Victorino, Camila Marra, Dumitru Andrei Iacobas, Sanda Iacobas, David C Spray, Rafael Linden, Daniel Adesse, Hilda Petrs-Silva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: glaucoma; retina ganglion cell degeneration; microarray; genes coordination; notch signaling pathway; complement cascade

Online: 23 February 2021 (12:44:20 CET)

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Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the Genomic Fabric Paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers for the expression of each gene 3 independent characteristics: level, variability and correlation with each other gene. Thus, the 17,657 quantified genes our study generated a total of 155,911,310 values to analyze. This represents 8,830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with DiI. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted Protein-Protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among up-regulated genes. Enrichment analysis showed that Complement Cascade and Notch Signaling Pathway, as well as Oxidative Stress and Kit Receptor Pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pair-wise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in Complement Cascade and Notch Signaling Pathway. This deep bioinformatic study provides novel insights beyond the regulation of individual gene expression and discloses changes in the control of expression of Complement Cascade and Notch Signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.

Preprint REVIEW | doi:10.20944/preprints202009.0308.v1

Accelerating Tomato Breeding by Exploiting Genomic Selection Approaches

Elisa Cappetta, Giuseppe Andolfo, Antonio Di Matteo, Amalia Barone, Luigi Frusciante, Maria Raffaella Ercolano

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Tomato; genetic breeding value; training population; genotyping; marker effect; phenotyping; selection schemes

Online: 14 September 2020 (00:08:23 CEST)

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Preprint REVIEW | doi:10.20944/preprints201811.0571.v2

Revisiting Prostate Cancer in India: A Genomic View

Prameesha Perera, Ayam Gupta, Nidhi Shukla, Mamta Nehra, Mukesh Sharma, Sneha Mishra, Vikram Singh Chauhan, Maneesh Kumar Vijay, Suresh Kumar Jatawa, Archana Tiwari, Krishna Mohan Medicherla, Praveen Mathur, Devendra Sharma, Prashanth Suravajhala

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: prostate cancer; prostate-specific antigen; incidence; genomics; next generation sequencing

Online: 3 April 2019 (10:15:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0870.v1

Investigating Cryptosporidium spp. Using Genomic and Proteomic Techniques: Current Progress and Future Directions

Joanna Dąbrowska, Jacek Sroka, Tomasz Cencek

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Cryptosporidium spp.; genomics; proteomics

Online: 13 July 2023 (10:03:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202112.0366.v1

An Integrated Epigenomic and Genomic View on Phyllodes and Phyllodes-Like Breast Tumors

Juergen Hench, Tatjana Vlajnic, Savas Deniz Soysal, Ellen C Obermann, Stephan Frank, Simone Muenst

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: fibroepithelial breast lesions; phyllodes tumors; methylation analysis; copy number alterations; dimension reduction; unsupervised machine learning

Online: 22 December 2021 (12:46:50 CET)

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