166 Works

Data from: \"Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Maria Jose Ruiz Lopez, Tony L. Goldberg, Colin A. Chapman, Patrick A. Omeja, James H. Jones, William M. Switzer, Paul D. Etter, Eric A. Johnson & Nelson Ting
Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus...

Data from: Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: associations with ecological factors, bird behavior and tick infestation

Erica A. Newman, Lars Eisen, Rebecca J. Eisen, Natalia Fedorova, Jeomhee M. Hasty, Charles Vaughn & Robert S. Lane
Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized...

Data from: The Lyme disease pathogen has no effect on the survival of its rodent reservoir host

Maarten J. Voordouw, Shelly Lachish & Marc C. Dolan
Zoonotic pathogens that cause devastating morbidity and mortality in humans may be relatively harmless in their natural reservoir hosts. The tick-borne bacterium Borrelia burgdorferi causes Lyme disease in humans but few studies have investigated whether this pathogen reduces the fitness of its reservoir hosts under natural conditions. We analyzed four years of capture-mark-recapture (CMR) data on a population of white-footed mice, Peromyscus leucopus, to test whether B. burgdorferi and its tick vector affect the survival...

Data from: When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii

Talima Pearson, Heidie M. Hornstra, Jason W. Sahl, Sarah Schaack, James M. Schupp, Stephen M. Beckstrom-Sternberg, Matthew W. O'Neill, Rachael A. Priestley, Mia D. Champion, James S. Beckstrom-Sternberg, Gilbert J. Kersh, James E. Samuel, Robert F. Massung & Paul Keim
Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the...

Data from: Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever

Hao Li, Jie-Ying Bai, Li-Yuan Wang, Lin Zeng, Yan-Sheng Shi, Zheng-Liang Qiu, Hua-Hu Ye, Xiao-Fei Zhang, Qing-Bin Lu, Michael Kosoy, Wei Liu & Wu-Chun Cao
Bartonella quintana is a bacterium that causes a broad spectrum of diseases in humans including trench fever. Humans were previously considered to be the primary, if not the only, reservoir hosts for B. quintana. To identify the animal reservoir and extend our understanding of the ecological and evolutionary history of B. quintana, we examined blood samples from macaques and performed multilocus sequence typing (MLST) analysis. We demonstrated the prevalence of B. quintana infection was common...

Data from: Microbiome sharing between children, livestock and household surfaces in western Kenya

Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Ceclia Noecher, Ohad Manor, Sarah Hilton, Samuel M. Thmbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M. Rabinowitz, Samuel M. Thumbi & Cecilia Noecker
The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we...

Data from: Zoonotic infection of Brazilian primate workers with New World simian foamy virus

Claudia P. Muniz, Liliane T. F. Cavalcante, Hongwei Jia, HaoQiang Zheng, Shaohua Tang, Anderson M. Augusto, Alcides Pissinatti, Luiz P. Fedullo, Andre F. Santos, Marcelo A. Soares & William M. Switzer
Simian foamy viruses (SFVs) are retroviruses present in nearly all nonhuman primates (NHPs), including Old World primates (OWP) and New World primates (NWP). While all confirmed human infections with SFV are from zoonotic transmissions originating from OWP, little is known about the zoonotic transmission potential of NWP SFV. We conducted a longitudinal, prospective study of 56 workers occupationally exposed to NWP in Brazil. Plasma from these workers was tested using Western blot (WB) assays containing...

Additional file 3 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan, Kathryn S. Burch, Christa Caggiano, Brian Hill, Nadav Rakocz, Brunilda Balliu, Christopher T. Denny, Jae Hoon Sul, Noah Zaitlen, Valerie A. Arboleda, Eran Halperin, Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind & Bogdan Pasaniuc
Additional file 3: Table S7. Associations between genetically inferred ancestry and phecodes within ATLAS.

Additional file 6 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan, Kathryn S. Burch, Christa Caggiano, Brian Hill, Nadav Rakocz, Brunilda Balliu, Christopher T. Denny, Jae Hoon Sul, Noah Zaitlen, Valerie A. Arboleda, Eran Halperin, Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind & Bogdan Pasaniuc
Additional file 6: Table S10. Summary of GWAS analyses in ATLAS.

Additional file 8 of Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative

Ruth Johnson, Yi Ding, Vidhya Venkateswaran, Arjun Bhattacharya, Kristin Boulier, Alec Chiu, Sergey Knyazev, Tommer Schwarz, Malika Freund, Lingyu Zhan, Kathryn S. Burch, Christa Caggiano, Brian Hill, Nadav Rakocz, Brunilda Balliu, Christopher T. Denny, Jae Hoon Sul, Noah Zaitlen, Valerie A. Arboleda, Eran Halperin, Sriram Sankararaman, Manish J. Butte, Clara Lajonchere, Daniel H. Geschwind & Bogdan Pasaniuc
Additional file 8: Table S12. Effective sample sizes and effect sizes of correlated phenotypes for chronic nonalcoholic liver disease. Table S13. Role of phecode occurrences for defining cases. Table S14. Summary of methods. Table S15. Comparison of GIA clusters when restricting to unrelated individuals. Table S16. Comparison of genetic ancestry proportions within SIREs when using unrelated individuals.

Additional file 1 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 1: Table S1. Comparison of the Intergrowth-21 and STOPPAM standard charts. Table S2. Quality of studies using Cochrane’s Risk of Bias 2 tool (ROB-2) for randomized trials. Table S3. Risk of Bias assessment by Newcastle scale for cohort studies. Table S4. Prevalence of small for gestational age by gestational age and birthweight. Table S5. Prevalence of small for gestational age when applying the inclusion criteria for each reference chart. Table S6. Sensitivity analysis...

Additional file 5 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 5: Figure S4. Two stage individual participant data meta-analysis on the association between malaria in pregnancy (MIP) and small for gestational age (SGA) using the STOPPAM (SGASTOPPAM) vs. the Intergrowth-21 reference (SGAIG21). uOR: unadjusted odds ratio in panels A and B, aOR: adjusted odds ratio in panels C and D controlling for body mass index, gravidity, gestational age at enrolment, HIV, and hemoglobin level at enrolment. In addition, adjusted for gestational age at...

Additional file 6 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 6: Figure S5. Funnel plots for meta-analysis. The closed dots indicate the observed studies, panel A indicate the trim and fill funnel plot for STOPPAM (P = 0.10) and panel B for Intergrowth-21 reference (P = 0.35). The contour enhanced funnel plot for STOPPAM (panel C) and Intergrowth-21 (panel D) show the distribution of studies in both the small and large p-values contours, hence no publication bias.

The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Abstract Background The prevalence of small for gestational age (SGA) may vary depending on the chosen weight-for-gestational-age reference chart. An individual participant data meta-analysis was conducted to assess the implications of using a local reference (STOPPAM) instead of a universal reference (Intergrowth-21) on the association between malaria in pregnancy and SGA. Methods Individual participant data of 6,236 newborns were pooled from seven conveniently identified studies conducted in Tanzania and Malawi from 2003–2018 with data on...

Cardiac Investigation Trends Among Primary Care Physicians: A Paradigm Shift

Tiffany T. Ni, Fahmeen J. Afgani, Connor T. A. Brenna, Nikita Patel & Elsie T. Nguyen
ObjectiveWhile numerous recent guidelines support coronary computed tomography angiography (CTA) as a first-line test for stable chest pain, it remains underutilized by primary care physicians (PCPs). We aimed to evaluate cardiac investigation ordering practices following education sessions, as well as the total number of downstream tests and time to diagnosis for patients presenting with stable chest pain.MethodsA retrospective chart review was completed for eligible patients assessed at the Women's College Hospital Family Practice Health Centre...

sj-docx-1-arp-10.1177_02750740221128554 - Supplemental material for Resistance or Capitulation? How Discrete Emotions Shape Citizens’ Interactions With the Administrative State

Elizabeth Bell, Julian Christensen & Kristina Jessen Hansen
Supplemental material, sj-docx-1-arp-10.1177_02750740221128554 for Resistance or Capitulation? How Discrete Emotions Shape Citizens’ Interactions With the Administrative State by Elizabeth Bell, Julian Christensen and Kristina Jessen Hansen in The American Review of Public Administration

Supplemental Material - Changes in Harm Perception for E-Cigarettes Among Youth in the United States, 2014–2019

Angella Sandra Namwase, Emmanuel A. Gyimah, Bobbi J. Carothers, Todd B. Combs & Jenine K. Harris
Supplemental Material for Changes in Harm Perception for E-Cigarettes Among Youth in the United States, 2014–2019 by Angella Sandra Namwase, Emmanuel A. Gyimah, Bobbi J. Carothers, Todd B. Combs, and Jenine K. Harris in American Journal of Health Promotion

Changes in Harm Perception for E-Cigarettes Among Youth in the United States, 2014–2019

Angella Sandra Namwase, Emmanuel A. Gyimah, Bobbi J. Carothers, Todd B. Combs & Jenine K. Harris
PurposeTo evaluate the trend of harm perception for e-cigarettes and the trend of the association between harm perception for e-cigarettes and for cigarettes among US youth from 2014 to 2019.Design, setting and subjectsThe National Youth Tobacco Survey is an annual, cross-sectional, school-based survey done among youth selected using three-stage probability sampling.AnalysisData were drawn from the 2014 to 2019 Surveys. A Multinomial logistic regression model was used to assess the association between harm perception for e-cigarettes...

Additional file 3 of Proactive community case management decreased malaria prevalence in rural Madagascar: results from a cluster randomized trial

Rila Ratovoson, Andres Garchitorena, Daouda Kassie, Jemima A. Ravelonarivo, Voahangy Andrianaranjaka, Seheno Razanatsiorimalala, Avotra Razafimandimby, Fanjasoa Rakotomanana, Laurie Ohlstein, Reziky Mangahasimbola, Sandro A. N. Randrianirisoa, Jocelyn Razafindrakoto, Catherine M. Dentinger, John Williamson, Laurent Kapesa, Patrice Piola, Milijaona Randrianarivelojosia, Julie Thwing, Laura C. Steinhardt & Laurence Baril
Additional file 3. Analyses and findings on anemia and PRO-CCM. Table S5. Prevalence of anemia among all women of reproductive age at baseline and endline, by study arm. Table S6. Unadjusted analyses of prevalence of anemia among all women of reproductive age at baseline, using logistic regression models. Table S7. Adjusted analyses of prevalence of anemia among all women of reproductive age at baseline, using logistic regression models.

Additional file 1 of Rationale and guidance for strengthening infection prevention and control measures and antimicrobial stewardship programs in Bangladesh: a study protocol

Md. Golam Dostogir Harun, Md Mahabub Ul Anwar, Shariful Amin Sumon, Md. Zakiul Hassan, Tahrima Mohsin Mohona, Aninda Rahman, Syed Abul Hassan Md Abdullah, Md Saiful Islam, S. Cornelia Kaydos-Daniels & Ashley R. Styczynski
Additional file 1.

Additional file 1 of Rationale and guidance for strengthening infection prevention and control measures and antimicrobial stewardship programs in Bangladesh: a study protocol

Md. Golam Dostogir Harun, Md Mahabub Ul Anwar, Shariful Amin Sumon, Md. Zakiul Hassan, Tahrima Mohsin Mohona, Aninda Rahman, Syed Abul Hassan Md Abdullah, Md Saiful Islam, S. Cornelia Kaydos-Daniels & Ashley R. Styczynski
Additional file 1.

Additional file 4 of The histone deacetylase Cfhos2 is a key epigenetic factor regulating appressorium development and pathogenesis in apple Glomerella leaf spot fungus Colletotrichum fructicola

Mengyu Cao, Zhaohui Zhang, Huanhuan Tian, Wei Yu, Xuemei Zhao, Wenrui Yang, Rong Zhang, Guangyu Sun & Xiaofei Liang
Additional file 4: Table S5. Primers used in this study.

The histone deacetylase Cfhos2 is a key epigenetic factor regulating appressorium development and pathogenesis in apple Glomerella leaf spot fungus Colletotrichum fructicola

Mengyu Cao, Zhaohui Zhang, Huanhuan Tian, Wei Yu, Xuemei Zhao, Wenrui Yang, Rong Zhang, Guangyu Sun & Xiaofei Liang
Abstract Glomerella leaf spot (GLS) is a devastating fungal disease that damages the leaves and fruits and reduces tree vigor of apple (Malus domestica). The pathogen infection mechanism, however, remains elusive. Histone-modifying enzymes, which regulate eukaryotic chromatin conformation and gene expression, are key epigenetic factors controlling fungal development, virulence, and secondary metabolism. To dissect the epigenetic regulation of GLS pathogenesis, we characterized a histone deacetylase gene Cfhos2 in Colletotrichum fructicola, the causing agent of GLS....

Additional file 1 of The histone deacetylase Cfhos2 is a key epigenetic factor regulating appressorium development and pathogenesis in apple Glomerella leaf spot fungus Colletotrichum fructicola

Mengyu Cao, Zhaohui Zhang, Huanhuan Tian, Wei Yu, Xuemei Zhao, Wenrui Yang, Rong Zhang, Guangyu Sun & Xiaofei Liang
Additional file 1: Figure S1. Southern blot and PCR detection of Cfhos2 deletion mutants. Figure S2. Gene deletion mutants of Cfhos3 and Cfhda1 exhibit normal phenotypes in vegetative growth rate, sensitivity to trichostatin A (TSA), and pathogenicity. Figure S3. Deletion of Cfhos3 or Cfhda1 does not affect stress tolerance and appressorium development of Colletotrichum fructicola. Figure S4. Identification of differently expressed gene (DEGs) between WT (1104-6) and Cfhos2 deletion mutant (Δhos2-4) in both apple leaves...

Additional file 1 of The histone deacetylase Cfhos2 is a key epigenetic factor regulating appressorium development and pathogenesis in apple Glomerella leaf spot fungus Colletotrichum fructicola

Mengyu Cao, Zhaohui Zhang, Huanhuan Tian, Wei Yu, Xuemei Zhao, Wenrui Yang, Rong Zhang, Guangyu Sun & Xiaofei Liang
Additional file 1: Figure S1. Southern blot and PCR detection of Cfhos2 deletion mutants. Figure S2. Gene deletion mutants of Cfhos3 and Cfhda1 exhibit normal phenotypes in vegetative growth rate, sensitivity to trichostatin A (TSA), and pathogenicity. Figure S3. Deletion of Cfhos3 or Cfhda1 does not affect stress tolerance and appressorium development of Colletotrichum fructicola. Figure S4. Identification of differently expressed gene (DEGs) between WT (1104-6) and Cfhos2 deletion mutant (Δhos2-4) in both apple leaves...

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