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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/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 TECHNICAL NOTE | doi:10.20944/preprints202311.1130.v1

VarChat: The Generative AI Assistant for the Interpretation of Human Genomic Variations

Federica De Paoli, Silvia Berardelli, Ettore Rizzo, Ivan Limongelli, Susanna Zucca

Subject: Computer Science And Mathematics, Software Keywords: Genomics; Variant Interpretation; Generative AI; Genome analysis; Rare Diseases; Bioinformatics

Online: 17 November 2023 (05:24:56 CET)

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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 CONCEPT PAPER | doi:10.20944/preprints202310.0038.v1

Knowledge-Based Prioritization of Genomic Variations: A Quest for Detailed Understanding the Genetic Architecture of Diseases

Ivan Y. Iourov

Subject: Biology And Life Sciences, Life Sciences Keywords: candidate processes; disease; genomic variations; knowledge; medical genomics; ontology; pathways; prioritization; systems analysis; variome

Online: 2 October 2023 (04:26:02 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/preprints202406.0461.v1

Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides

Claudiu N. Lungu, Ionel Mangalagiu, Gabriela Gurau, Mihaela Cezarina Hîncu

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: peripheral artery disease; molecular modeling; docking; angiogenesis; vascular morphogenesis; chimeric protein

Online: 7 June 2024 (07:32:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0987.v1

The Spatiotemporal Surface Velocity Variations and Analysis of Amery Ice Shelf, East Antarctica

Ma yuan Yuan, Zhang Bao Jun, Wang Ze Min, Li Fei, Geng Hong

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: Amery Ice Shelf; Surface velocity variation; AIS thickness; Fast-ice; Ocean temperature

Online: 15 May 2024 (10:28:01 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/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 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 ARTICLE | doi:10.20944/preprints202403.0412.v1

Human Leukocyte Antigen-Allelic Variations May Influence the Age at Cancer Diagnosis in Lynch Syndrome

Lutricia Ndou, Ramadhani Chambuso, Ziyaad Valley-Omar, George Rebello, Paul Goldberg, Adam Boutall, Ursula Algar, Raj Ramesar

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Lynch syndrome; colorectal cancer; germline pathogenic variant MLH1:c.1528C>; T; Human leukocyte antigen (HLA); age at cancer diagnosis; genetic risk modifiers; personalized cancer screening

Online: 7 March 2024 (07:36:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202409.1263.v1

CFD Simulation of Dynamic Temperature Variations Induced by Tunnel Ventilation in a Broiler House

Lak-yeong Choi, Kehinde Favour Daniel, Se-yeon Lee, Chae-rin Lee, Ji-yeon Park, Jinseon Park, and Se-woon Hong

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Poultry heat production; thermal gradients; microclimate; inlet baffles; CFD validation

Online: 17 September 2024 (00:41:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202409.1780.v1

Phenotypic and Genomic Evaluation of ProbioGel (A Probiotic-Infused Cellulose Hydrogel) for Antimicrobial Activity

Alvin Domingo, Abigail Castro, Jayson Cariaga, Francis Gamboa, Aira Cassandra Castro, Aira Nadine Pascua, Jimmbeth Zenila Fabia, Peter James Gann, Bjorn Santos, Shirley Agrupis

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antimicrobial; probiotics; whole genome sequencing; nipa palm

Online: 24 September 2024 (09:06:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.0554.v1

Analysis of Human Papillomavirus 51 (HPV51) Genetic Variations Detected in Women with Cervical Dysplasia

Chiara Giubbi, Chiara Villa, Maria Letizia Di Meo, Illari Sechi, Ruth Chinyere Njoku, Narcisa Muresu, Federica Perdoni, Andrea Fausto Piana, Roberto Pietri, Robert Fruscio, Fabio Landoni, Clementina Elvezia Cocuzza, Marianna Martinelli

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Human Papillomavirus; HPV51; HPV lineage; HPV variants; cervical dysplasia

Online: 5 July 2024 (20:39:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1984.v1

Effect of HVEM/CD160 Variations on the Clear Cell Renal Carcinoma Risk and Overall Survival

Anna Andrzejczak, Bartosz Małkiewicz, Krzysztof Tupikowski, Kuba Ptaszkowski, Tomasz Szydełko, Lidia Karabon

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: HVEM; CD160; clear cell renal cell carcinoma (ccRCC); single nucleotide gene polymorphism (SNP); immunological checkpoint; disease risk; overall survival

Online: 30 May 2024 (09:28:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0147.v1

Examining Chlorophyll Extraction Methods in Sesame Genotypes: Uncovering Leaf Coloration Effects and Anatomy Variations

Muez Berhe Gebremedhin, Jun You, Komivi Dossa, Donghua Li, Rong Zhou, Yanxin Zhang, Linhai Wang

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Carotenoids Content; Chloroplast Ultrastructure; Leaf Disk Positions; Sesamum indicum; SPAD value Index

Online: 3 May 2024 (11:22:26 CEST)

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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/preprints202409.1941.v1

Wound Healing Efficacy of Cellulose Hydrogel on ICR Mice: A Morphoanatomical, Histological and Genomic Study

Abigail Castro, Alvin Domingo, Jayson Cariaga, Francis Gamboa, Aira Cassandra Castro, Aira Nadine Pascua, Jimmbeth Zenila Fabia, Peter James Gann, Bjorn Santos, Shirley Agrupis

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: wound healing; cellulose hydrogel; probiotics; histological assessment

Online: 24 September 2024 (16:57:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0128.v1

The Precipitation Variations in the Qinghai-Xizang (Tibetan) Plateau during 1961-2015

Guoning Wan, Meixue Yang, Zhaochen Liu, Xuejia Wang, Xiaowen Liang

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Precipitation; Tibetan Plateau; trends; temporal-spatial distribution; hydrological cycle;

Online: 29 January 2017 (09:43:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202407.0528.v1

Trophic Level Variations of Heavy Metals in Feathers of Birds from the Awotan Landfill, in Ibadan, Nigeria

Abdulsalam R. Rotimi, Adeola A. Oni, Aina O. Adeogun

Subject: Biology And Life Sciences, Toxicology Keywords: ; bioaccumulation and biomagnification; non-invasive ecological hazard assessment; heavy metals; avian feathers; ecological declination and stress ;

Online: 5 July 2024 (10:50:16 CEST)

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Pollution, urbanization and technological advancements have posed stress on the ecosystem and its matrices. Globally, pollutants are observed in all compartments of ecological communities which affect the integrity of the atmosphere, hydrosphere, lithosphere and biosphere. Xenobiotics bioaccumulate and biomagnify across trophic levels or webs. Heavy metals have been implicated in impacts towards biodiversity and environmental declination. In Nigeria, wastes issues are a cause of concern and landfilling or are waste disposal approaches that cause deleterious effects such as depauperation of diversity and species decline, prompting the non-invasive ecotoxicological hazard assessments. Feathers were used to assess concentration levels of 13 metals (Fe, Mn, Zn, Cu, Co, Cr, Cd, Pb, Ni, Al, B, Se and Hg) using fast atomic absorption spectrophotometer (FAAS), one-way ANOVA was used in comparing variations in mean concentrations across trophic levels, diversity indices and point count methods were used to estimate diversity and abundance. Four avian species were assessed Hirundo aethiopica (insectivore), Streptoptelia senegalensis (granivore), Turdus pelios (omnivore), and Anthus leucophrys. (insectivore). Observed concentrations of important metals like iron were high with the insectivores having the highest concentrations of iron (2.6985 ± 0.1975 ppm) and granivores having the lowest (2.0100 ± 0.3172 ppm). The insectivores had the highest concentrations for cadmium, cobalt and chromium (0.0005 ± 0.0005ppm), nickel (at 00.0012 ± 0.0017 ppm) and least was observed in the granivores (0.0003 ± 0.0006 ppm). Selenium concentrations were quite high in insectivores (0.0775 ± 0.0035 ppm) and lowest in granivores (0.0433 ± 0.0015 ppm) likewise mercury for insectivores (0.0280 ± 0.0010 ppm) and granivores (0.0213 ± 0.0015 ppm). From the study, it is apparent that landfills are sources of pollution and poor management of wastes can affect biota (causing effects such as asymmetry and bioaccumulation) and ecosystem balance. The observation of heavy metals in the feathers serve as good sentinels due to their trophic levels and could be signs for what could be yet to occur. The heavy metal concentrations were significantly different at p < 0.05.

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/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 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/preprints201703.0010.v1

Size Distribution, Seasonal Variations and Sources of Carbonaceous Aerosol in a Typical Industrial City Nanjing in Yangtze River Delta, China

Honglei Wang, Junlin An, Bin Zhu, Lijuan Shen, Qing Duan, Yuanzhe Shi

Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: size distribution; OC; EC; seasonal variation; Yangtze River Delta

Online: 1 March 2017 (16:59:27 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/preprints202407.1401.v1

Diel Variations in Abundance of Microbial Communities in the Pacific Western Subtropical Coastal Waters in Spring: Potential Role of Picoeukaryotes

Patrichka Wei-Yi Chen, Madeline Olivia, Vladimir Mukhanov, Grace Sitorus, Ufimtseva Margarita, Liashko Tatiana, Sakhon Evgenii, Supriyadi Supriyadi, Intan Dwi Puspitasari, Arpita Ghosh, An Yi Tsai

Subject: Environmental And Earth Sciences, Environmental Science Keywords: diel variations; Synechococcus spp.; Prochlorococcus spp.; picoeukaryotes; mixotrophs; nanoflagellate

Online: 17 July 2024 (11:58:12 CEST)

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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 ARTICLE | doi:10.20944/preprints201807.0285.v1

Climatic Variations in Central Italy

Matteo Gentilucci, Maurizio Barbieri, Peter Burt

Subject: Environmental And Earth Sciences, Environmental Science Keywords: climate change; gis; geostatistic; raster math

Online: 16 July 2018 (12:26:24 CEST)

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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/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 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 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/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/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/preprints202407.0870.v1

Bioinformatics Study on Site-Specific Variations of Eotaxin-3, a Key Chemokine in Eosinophilic Esophagitis (EoE)

Deborah Giordano, Antonio D’Acierno, Anna Marabotti, Paola Iovino, Giuseppe Iacomino, Angelo Facchiano

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: eosinophilic esophagitis; protein variants; protein structural analysis; protein modelling; web application

Online: 10 July 2024 (14:07:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1792.v1

Impaired Peripheral Vascular Function Following Ischemic Stroke: Implications for Blood Pressure Variations in the Post-stroke Patient

Gokhan Yilmaz, J. Steven Alexander

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Ischemic Stroke; Blood Pressure; Hypertension; Hypotension; Vasodilation; Vasoconstriction; Peripheral Vessels; Myography; alpha-adrenergic receptors; middle cerebral artery occlusion

Online: 26 June 2024 (05:14:22 CEST)

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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/preprints202405.1866.v1

Diel Variations in Abundance of Microbial Communities in the Coastal Waters of the Subtropical Western Pacific in Spring: Potential Role of Picoeukaryotes

Patrichka Wei-Yi Chen, Madeline Olivia, Vladimir Mukhanov, Grace Sitorus, Ufimtseva Margarita, Liashko Tatiana, Sakhon Evgenii, Supriyadi Supriyadi, Intan Dwi Puspitasari, Arpita Ghosh, An Yi Tsai

Subject: Environmental And Earth Sciences, Ecology Keywords: diel variations; Synechococcus spp.; Prochlorococcus spp.,; picoeukaryotes; mixotrophs; nanoflagellate

Online: 28 May 2024 (14:27:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0067.v2

Modeling Spatial Local Variations in Intermarriage

Albert Esteve, Coro Chasco, Antonio López-Gay

Subject: Social Sciences, Sociology Keywords: Intermarriage; migration; local markets; Poisson model; Probit model; spatial autocorrelation; spatial heterogeneity; Spain

Online: 4 March 2022 (08:43:08 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/preprints202404.0349.v1

Spatial-Temporal Variations of Human Impact on Forest Ecological Functions in the Yellow River Basin from 2004 to 2018

Xiaodi Zhao, Qingjun Wu, Guangyu Wang, Ram P. Sharma, Linyan Feng, Lang Bai

Subject: Social Sciences, Geography, Planning And Development Keywords: Forest ecological function; human activities; spatial-temporal variation; geographic temporal weighted regression

Online: 4 April 2024 (05:34:17 CEST)

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Human activities (e.g., exploitation, utilization, and conservation) exert substantial impact on forest ecological functions (FEF). The human influence on FEF significantly varies across developmental stages, which are attributed to the temporal and spatial in nature. This study evaluates some notable FEF indices (FEFI) in the 448 counties within the Yellow River basin (YRB) using panel data from the Seventh to Ninth National Forest Inventory. Data analysis involves employing the residual trends, geographical and temporal weighted regression. Results indicate that, firstly, the overall forest ecological function in the YRB is moderate to inferior, with superior FEF in counties endowed with more natural forest resources. Afforestation demonstrates a short-term improvement, but its effectiveness diminishes over time. Secondly, the positive spatial correlation is stronger among counties, characterized by both high-high and low-low agglomeration effects. Scattered planting, simple stand structure, and concentrated harvesting of forests at the identical stand ages hinder the formation of complex and large-scale FEF agglomerations. Thirdly, significant spatial-temporal differences exist in the impact of human activities on FEF. In the upper reaches of the basin, increased vegetation coverage through agricultural and forestry production benefited FEF, however, some over-exploitation of forests and grasslands is observed there. In the middle reaches, the economic development, expanding population and the greening activities help to improve FEF effectively, but excessive water using in agricultural production brought more difficulties to FEF improvement. In the lower reaches of the basin, improved wastelands and forest protection positively influence FEF. This study recommends that county governments should prioritize forest management with multi-species and multi-layered complex forests. Each county should define its position in regional development and ecological protection, considering the potential impacts on neighboring regions. This holistic approach promotes more effective integrated regional management.

Preprint ARTICLE | doi:10.20944/preprints202405.0207.v1

H2BFWT Variations in Sperm DNA and Its Correlation to Pregnancy

Houda Amor, Ingolf Juhasz-Böss, Riffat Bibi, Mohamad Eid Hammadeh, Peter Michael Jankowski

Subject: Medicine And Pharmacology, Reproductive Medicine Keywords: Male infertility; sperm DNA; SNPs; H2BFWT; pregnancy; ICSI

Online: 6 May 2024 (08:47:22 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 ARTICLE | doi:10.20944/preprints202404.2016.v1

Variations & Claims in International Construction Contracts (FIDIC) from Statistical Perspective in MENA Region for the Last Decade

Ahmed Mohammed Abdelalim, Mohamed Ramadan Ezz Al Regal, AlJawharah A. AL Nasser, Rawan Alwahaibi, Mohamed Tantawy

Subject: Engineering, Architecture, Building And Construction Keywords: construction industry; international contracts; FIDIC 1999 Red Book; variations; claims; scientometric analysis; statistical analysis; relative importance index (RII); K-means clustering

Online: 1 May 2024 (04:04:08 CEST)

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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 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/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/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/preprints202405.1575.v1

Spatiotemporal Variations of Vegetation and Its Response to Climate Change and Human Activities in Arid Areas—A Case Study of the Shule River Basin, Northwestern China*

Xiaorui He, Luqing Zhang, Yuehan Lu, Linghuan Chai

Subject: Environmental And Earth Sciences, Remote Sensing Keywords: vegetation dynamics; climate change; human activities; arid regions

Online: 23 May 2024 (14:26:30 CEST)

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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 ARTICLE | doi:10.20944/preprints202406.0142.v1

Regional Variations in Urban Trash: Connections between Litter Communities and Place

Randa L Kachef, Michael Chadwick

Subject: Environmental And Earth Sciences, Pollution Keywords: litter; waste management; sustainability; community parameters; litter impact index

Online: 4 June 2024 (08:32:32 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1162.v2

Structural Variations of Prions and Prion-Like Proteins Associated with Neurodegeneration

Carter Sky Christensen, Wenshu Li, Danyang Yu, Henry James Li

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: prions; neurodegeneration; Alzheimer’ s disease; protein homeostasis; aggregation; prion-like proteins; amyloid beta; hyperphosphorylated tau; self replication

Online: 19 December 2023 (09:42:02 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 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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Preprint REVIEW | doi:10.20944/preprints202007.0587.v1

SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence

Sameer Mohammad, Abderrezak Bouchama, Bothina Mohammad Alharbi, Mamoon Rashid, Tanveer Saleem Khatlani, Nusaibah S Gaber, Shuja Shafi Malik

Subject: Biology And Life Sciences, Virology Keywords: Keywords: COVID-19; SARS-CoV-2; SARS-CoV; Accessory Protein; ORF8; ORF8ab

Online: 24 July 2020 (13:51:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints202312.1486.v1

Radiological Anatomy, Variations, and Clinical Significance of Septum Pellucidum: A Mini-Review

Shirom Rajeev Siriwardana, Chamitha Kaveendra Pathirage

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: ; septum pellucidum; cavum septum pellucidum; cavum vergae; cavum veli interpositi

Online: 20 December 2023 (11:01:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202108.0484.v1

Dynamics of Cyanobacterial Global Metabolom in Response to Light and Temperature Variations

Damien Le Moigne, Justine Demay, Anita Reinhardt, Cécile Bernard, Sandra Kim Tiam, Benjamin Marie

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: cyanobacteria; metabolomics; high-resolution mass spectrometry; secondary metabolite induction; culture conditions

Online: 25 August 2021 (10:48:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0578.v1

The Mapping of the Main Functions and Different Variations of YH-DIE

Gilbert Mason, Yuanjue Chou, Springer Pind

Subject: Computer Science And Mathematics, Analysis Keywords: complete Riemannian manifolds; entire solutions; minimal graphs; differential equat; algebraic variety

Online: 26 August 2020 (10:19:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.1759.v1

Sex-Biased Associations of Circulating Ferroptosis Inhibitors with Reduced Lipid Peroxidation and Better Neurocognitive Performance in People with HIV

Harpreet Kaur, Ravi Kumar Alluri, Kunling Wu, Robert C Kalayjian, William S Bush, Frank J Palella, Susan L Koletar, Corrilynn O Hileman, Kristine M Erlandson, Ronald J Ellis, Roger J Bedimo, Babafemi O Taiwo, Katherine K Tassiopoulos, Asha R Kallianpur

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: HIV; ferritin heavy-chain; ferritin light-chain; ferroptosis; lipid peroxidation; iron; oxidative stress; neurocognitive impairment; neurocognitive domains

Online: 24 August 2024 (00:22:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0301.v1

Clinicopathological and Genomic Identification of Breast Cancers with No Impact on Mortality

Salvador Gámez-Casado, Lourdes Rodríguez-Pérez, Cristina Bandera-López, Andrés Mesas-Ruiz, Alicia Campini Bermejo, Marta Bernal-Gómez, Manuel Zalabardo-Aguilar, Julio Calvete-Candenas, Gala Martínez-Bernal, Lidia Atienza-Cuevas, Marcial Garcia-Rojo, Encarnación Benítez-Rodríguez, Bella Pajares-Hachero, María José Bermejo-Pérez, José Manuel Baena-Cañada

Subject: Biology And Life Sciences, Life Sciences Keywords: Low-risk breast cancer; Metastasis; Observational study; Screening

Online: 5 February 2024 (16:30:40 CET)

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