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Preprint ARTICLE | doi:10.20944/preprints202103.0088.v2

A Family Based Whole Exome Sequence Study to Indentify Modifier Genes for Phenotype Heterogeneity Between Severe and Non-Severe Thalassemia Patients

ANUPAM BASU, Dipankar Saha, Prosanto Kumar Chowdhury, , Debashis Pal, Kaustav Nayek, Gispati Chakrabortye, Surupa Basu

Subject: Life Sciences, Biochemistry Keywords: WES; Thalassemia; phenotype

Online: 3 January 2023 (08:28:50 CET)

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Working Paper HYPOTHESIS

Competitive Coherence Generates Qualia in Bacteria and Other Living Systems

Vic Norris

Subject: Biology, Other Keywords: consciousness; qualia; network; bacteria; learning; phenotype

Online: 15 September 2021 (15:58:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0210.v1

Common Connectivity Phenotypes in Rapid Eye Movement Sleep Behavior Disorder and Parkinson’s Disease: The Search for an Intermediate Phenotype

Craig A. Moodie, Kelvin O. Lim, Bryon A. Mueller, Laura S. Hemmy, Michael J. Howell, Paul J. Tuite

Subject: Medicine & Pharmacology, Clinical Neurology Keywords: Parkinson’s; RBD; connectivity; phenotype; classification; network

Online: 18 December 2018 (03:58:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0216.v1

SpainUDP: The Spanish Undiagnosed Rare Diseases Program

Estrella López Martín, Beatriz Martínez-Delgado, Eva Bermejo-Sánchez, Alonso Javier, Manuel Posada

Subject: Medicine & Pharmacology, General Medical Research Keywords: Diagnosis delay; rare diseases; undiagnosed programs; standardized phenotype; phenotype ontologies; whole exome analysis; international data sharing

Online: 13 June 2018 (15:41:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0378.v1

Frequency and Antibiotic Susceptibility Patterns of Streptococcus Agalactiae Strains Isolated from Women in Yaounde, Cameroon

Cécile Ingrid Djuikoue, Paule Dana Djouela Djoulako, Rodrigue Kamga Wouambo, Rosine Yemetio Foutsa, Dorine Ekeu, Teke Apalata

Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: Antibiotic resistance; Colonization; Prevalence; GBS; Resistance phenotype

Online: 22 August 2022 (08:04:16 CEST)

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Group B Streptococcus (GBS), a commensal in the body, causes a wide range of infectious diseases. The colonisation levels of GBS and its resistance profile to antibiotics provide important information useful for orienting prevention strategies. There is little data available on the subject with determination of resistance phenotypes in Cameroon. We therefore aimed to determine the prevalence of colonization, antibiotic resistance, including patterns of inducible resistance to clindamycin of GBS in Yaounde. To achieve this goal, a prospective cross-sectional study with an analytical component was carried out from the 28th June to the 29th August 2020 at the BIOSANTE laboratory and the Yaounde Gynaeco-Obstetrics and Paediatrics hospital. Vaginal swabs and urine were collected on 163 women. This samples were analysed using 5% defibrinated sheep blood agar and chocolate plus polyvitex agar. The isolates were identified using the morphology of the colony, Gram staining, haemolysis, catalase test and latex grouping test. Antibiotic susceptibility testing was done by disk diffusion method following the recommendations of the ACFSM 2019. The double disk diffusion method was used to identify isolates with clindamycin inducible resistance. Our data was analysed by the software SPSS version 2.1. The results obtained showed that the global prevalence of colonization by GBS was 37% (57/163), 40.35% in non-pregnant women and 59.65% in pregnant women. Pregnancy (P-value = 0.019) and gestational age (P-value = 0.025) constituted the risk factors of maternal colonization by GBS. In addition, the strains of GBS were resistant to all antibiotics tested. A D test showcased that 64.7% of GBS were resistant in a constitutive manner to clindamycin. We also note the presence of M phenotypes. As a whole, our results demonstrate that the rate of GBS colonization in this study was similar or higher than those in the previous report in Cameroon. All this indicates that attention should be paid to this bacterium in the monitoring of antimicrobial resistance and in the care of pregnant women and newborns.

Preprint REVIEW | doi:10.20944/preprints202010.0118.v1

From FAANG to Fork: Application of Highly Annotated Genomes to Improve Farmed Animal Production

Emily L Clark, Alan L Archibald, Hans D Daetwyler, Martien AM Groenen, Peter W Harrison, Ross D Houston, Christa Kuehn, Sigbjorn Lien, Daniel J Macqueen, James M Reecy, Diego Robledo, Mick Watson, Christopher K Tuggle, Elisabetta Giuffra

Subject: Keywords: FAANG; farmed animal; genomics; genotype-to-phenotype

Online: 6 October 2020 (10:53:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0034.v1

Phenotype, Genotype and Environment in Architecture Case Study: Traditional Malay House, West Borneo

Indah Kartika Sari, Wiendu Nuryanti, Ikaputra Ikaputra

Subject: Engineering, Biomedical & Chemical Engineering Keywords: the building and the environment; phenotype; genotype

Online: 3 May 2020 (08:10:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202002.0454.v1

Prevalence of Blood Groups in Eastern UP Population

Pradeep Kumar, Vandana Rai

Subject: Keywords: ABO blood groups; antigen; allele frequency; phenotype

Online: 29 February 2020 (08:26:18 CET)

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Preprint REVIEW | doi:10.20944/preprints201807.0089.v1

The Importance of a Multidisciplinary Approach in the Management of a Patient with Type I Gaucher Disease

Miguel-Ángel Torralba-Cabeza, Susana Olivera-González, José-Luis Sierra-Monzón

Subject: Medicine & Pharmacology, Other Keywords: multidisciplinary; Gaucher; genotype/phenotype correlation; genetic counselling

Online: 5 July 2018 (08:51:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0583.v1

A Systematic Review on Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders

Sana Amanat, Teresa Requena, Jose Antonio Lopez-Escamez

Subject: Life Sciences, Genetics Keywords: genetic association studies; extreme phenotype; genetic epidemiology; tinnitus

Online: 24 July 2020 (13:43:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints202208.0316.v1

Type of ANCA may be Superior to Clinical Phenotype in Distinguishing Different Clinical Entities in ANCA-associated Vasculitis

Afroditi Maria Konstantouli, Georgios Lioulios, Asimina Fylaktou, Maria Stangou

Subject: Medicine & Pharmacology, General Medical Research Keywords: ANCA-associated vasculitis; Proteinase 3; Myeloperoxidase; Clinical Phenotype; Outcome

Online: 17 August 2022 (09:58:51 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0160.v2

NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease

Patty J Lee, Philip Blood, Katy Börner, Judith Campisi, Feng Chen, Heike Daldrup-Link, Phil De Jager, Li Ding, Francesca E. Duncan, Oliver Eickelberg, Rong Fan, Toren Finkel, Vesna Garovic, Nils Gehlenborg, Carolyn Glass, Ziv Bar-Joseph, Pragati Katiyar, So-Jin Kim, Melanie Königshoff, George Kuchel, Haesung Lee, Jun H. Lee, Jian Ma, Qin Ma, Simon Melov, Kay Metis, Ana L. Mora, Nicolas Musi, Nicola Neretti, João F. Passos, Irfan Rahman, Juan Carlos Rivera-Mulia, Paul Robson, Mauricio Rojas, Ananda L. Roy, Birgit Schilling, Pixu Shi, Jonathan Silverstein, Vidyani Suryadevera, Jichun Xie, Jinhua Wang, An-Kwok Ian Wong, Laura Niedernhofer

Subject: Life Sciences, Cell & Developmental Biology Keywords: Cellular Senescence Network; Normal Aging; Senescence; Senescence-associated secretory phenotype; SenNet

Online: 15 September 2022 (12:52:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0488.v1

Primary Chemoradiotherapy Treatment (PCRT) for HER2+ and Triple Negative Breast Cancer Patients: A Feasible Combination

Raquel Ciérvide, Angel Montero Luis, Eduardo García-Rico, Mariola Garcia-Aranda, Mercedes Herrero, Jessica Skaarup, Leticia Benasi, Maria Jose Barrera, Estela Vega, Beatriz Rojas, Raquel Bratos, Ana Luna, Manuela Parras, Maria Lopez, Ana Delgado, Paloma Quevedo, Silvia Castilla, Margarita Feyjoo, Ana Higueras, Mario Prieto, Ana Suarez-Gauthier, Lina Garcia-Cañamaque, Nieves Escolán, Beatriz Alvarez, Xin Chen, Rosa Alonso, Mercedes Lopez, Ovidio Hernando, Jeannette Valero, Emilio Sánchez Sahugar, Eva Ciruelos, Carmen Rubio

Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: chemoradiation; preoperative; neoadjuvant; TN/HER-2+ phenotype; pathological response; breast cancer

Online: 29 August 2022 (10:47:34 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0423.v1

Is “Cellular Senescence” a Misnomer?

David Gems, Carina Kern

Subject: Life Sciences, Cell & Developmental Biology Keywords: Aging; cellular senescence; fibroblast; osteoarthritis; remodeling-associated secretory phenotype (RASP); remodeling activation

Online: 27 July 2022 (13:38:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0677.v1

Supervised Analysis for Phenotype Identification: The Case of Heart Failure Ejection Fraction Class

Cristina Lopez, Jose Luis Holgado, Raquel Cortes, Inma Sauri, Antonio Fernandez, Jose Miguel Calderon, Julio Nuñez, Josep Redon

Subject: Medicine & Pharmacology, Allergology Keywords: heart failure, phenotype, left ventricular ejection fraction, primary care, artificial intelligence, supervised analysis

Online: 27 May 2021 (14:08:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0033.v2

Recent Trends of Antibiotic Resistance in Staphylococcus aureus Causing Clinical Mastitis in Dairy Herds in Abruzzo and Molise Regions, Italy

Franca Rossi, Ilaria Del Matto, Maria Antonietta Saletti, Luciano Ricchiuti, Lucio Marino

Subject: Life Sciences, Microbiology Keywords: Staphylococcus aureus; clinical mastitis; antibiotic resistance (AR) prevalence; AR phenotype; AR genotype; recent trend

Online: 22 January 2023 (06:50:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0187.v1

Sample Preservation and Plant Sex Prediction in White Guinea Yam (Dioscorea rotundata Poir.) Seedlings

Asrat Asfaw, Paterne Agre, Chidinma Nwachukwu, Bunmi Olasanmi, Jude Obidiegwu, Emmanuel Nwachukwu, Patrick Adebola, David De Koeyer

Subject: Biology, Plant Sciences Keywords: dioecious; DNA quality; flower type; sample preservation method; sex genotype; sex phenotype; visual assay

Online: 14 February 2020 (04:22:20 CET)

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Preprint REVIEW | doi:10.20944/preprints201809.0185.v1

Towards Individualized Use of Probiotics and Prebiotics for Metabolic Syndrome and Associated Diseases Treatment: Does Pathophysiology-Based Approach Work and Can Anticipated Evidence Be Completed?

Rostyslav Bubnov, Mykola Spivak

Subject: Medicine & Pharmacology, Nutrition Keywords: predictive preventive personalized medicine; Lactobacillus; Bifidobacterium; probiotics, gut microbiota; patient phenotype, individualized medicine; metabolic syndrome

Online: 11 September 2018 (06:00:03 CEST)

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The modification the gut microbiota in metabolic syndrome and associated chronic diseases is among leading tasks of microbiome research and needs for clinical use of probiotics. Evidence lack for the implications for microbiome modification to improve metabolic health in particular when applied impersonalized. Probiotics have tremendous potential in personalized nutrition and medicine to develop healthy diets. The aim was to to conduct comprehensive overview of recent updates of role of microbiota on human health and development of metabolic syndrome and efficacy of microbiota modulation considering specific properties of probiotic strain and particular aspects of metabolic syndrome and patient`s phenotype to fill the gap between probiotic product and individual to facilitate development of individualized / personalized probiotic and prebiotic treatments. We discuss the relevance of using host phenotype-associated biomarkers, those based on imaging and molecular and patrient`s history, reliable and accessible to facilitate person-specific appication of probiotics and prebiotic substances. Microbiome phenotypes can be parameters of predictive medicine to recognize patient`s predispositions and evaluate treatment responses; the number of phenotype markers can be effectively involved to monitor microbiome modulation. The studied strain-dependent properties of probiotic strains are potentially relevant for individualized treatment for gut and distant sites microbiome modulation. The evidence regarding probiotic strains properties can be taken to account via pathophysiology-based approach for most effective individualized treatment via gut, oral and vaginal and other sites microbiome modulation according to phenotype of the patient providing individualized and personalized medical approaches. Preventive potential of probiotics is strong and well-documented. Recommendations for individualized clinical use of probiotics, and for probiotic studies design have been suggested.

Preprint ARTICLE | doi:10.20944/preprints202108.0368.v1

An Investigation of Point Mutations Discovers Novel Genes and Their Corresponding Motifs in Pancreatic Cancer

Amin Ghareyazi, Amir Mohseni, Hamed Dashti, Abdollah Dehzangi, Hamid R. Rabiee, Hamid Alinejad-Rokny

Subject: Life Sciences, Genetics Keywords: pancreatic cancer; cancer subtype identification; somatic point mutations; genotype and phenotype characterization; therapeutic targets; personalized medicine

Online: 17 August 2021 (22:24:57 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0083.v1

Strengthening the Practical Application of Experiments Assessing Maize Drought Tolerance

Qinbin Zhang, Wei Wang

Subject: Biology, Plant Sciences Keywords: drought-tolerance characteristics; maize breeding; maize drought tolerance; molecular markers; phenotype; screening of drought-tolerant plants

Online: 7 April 2020 (10:28:30 CEST)

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Preprint REVIEW | doi:10.20944/preprints201905.0330.v1

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

Elisa Buchberger, Micael Reis, Ting-Hsuan Lu, Nico Posnien

Subject: Biology, Other Keywords: gene expression; gene regulation; evolution; allele specific expression; eQTL; RNAseq; ChIPseq; chromatin; ATACseq; genotype-phenotype map

Online: 28 May 2019 (10:29:26 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: Life Sciences, Biochemistry 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 CONCEPT PAPER | doi:10.20944/preprints202005.0321.v2

Proposed O-GalNAc/Gal Gycosylation Pathways in Blood Group O and Non-O Blood Group Phenotypes During Plasmodium falciparum Infections Driving Evolution

Peter Arend

Subject: Life Sciences, Biochemistry Keywords: trans-species O-glycosylation; trans-species functional bridge; phenotype-specific plasma glycosylation; glycosidic exclusion; ontogenetic Tn formation

Online: 12 January 2021 (12:33:29 CET)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202008.0574.v2

An Engineering Theory of Evolution

Simeon Castle, Claire Grierson, Thomas Gorochowski

Subject: Life Sciences, Biotechnology Keywords: evolution; evotype; engineering theory; genotype-phenotype maps; directed evolution; selection; synthetic biology; bioengineering; evolvability; self-adaptive systems

Online: 9 December 2020 (10:51:51 CET)

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Preprint REVIEW | doi:10.20944/preprints201908.0186.v1

Roles of Extracellular Vesicles (EVs) Carrying HSPs in Cancer Biomarkers, Immune Surveillance, and Immune Evasion

Eman Taha, Kisho Ono, Takanori Eguchi

Subject: Life Sciences, Immunology Keywords: heat shock protein (HSP); extracellular vesicle (EV); exosome; oncosome; immune evasion; resistance-associated secretory phenotype (RASP); EMT; hypoxia; biomarker; liquid biopsy

Online: 17 August 2019 (16:15:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints201912.0386.v1

Exosome Release of Drugs: Coupling with Epithelial-Mesenchymal Transition

Takanori Eguchi, Kisho Ono, Stuart Calderwood, Kuniaki Okamoto

Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: resistance-associated secretory phenotype (RASP); extracellular vesicle (EV); exosome; oncosome; drug resistance; epithelial-mesenchymal transition (EMT); heat shock protein (HSP); cell stress response; hypoxia; acidosis; tumor immunology

Online: 29 December 2019 (13:46:21 CET)

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