Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)

<p>Abstract</p> <p>Background</p> <p>The level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Avian karyotypes are typified by large variation in chromosome size and the rate of recombination in birds has been shown to be negatively correlated with chromosome size. It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction.</p> <p>Results</p> <p>Here we sequenced 27 autosomal and 12 sex chromosome-linked loci in the white-throated sparrow (<it>Zonotrichia albicollis</it>) to quantify and compare patterns of recombination, linkage disequilibrium (LD), and genetic diversity across the genome of this North American songbird. Genetic diversity on the autosomes varied up to 8-fold, with the lowest diversity observed on the macrochromosomes and the highest diversity on the microchromosomes. Genetic diversity on the sex chromosomes was reduced compared to the autosomes, the most extreme difference being a ~300-fold difference between the W chromosome and the microchromosomes. LD and population structure associated with a common inversion polymorphism (ZAL2/2^m) in this species were found to be atypical compared to other macrochromosomes, and nucleotide diversity within this inversion on the two chromosome arrangements was more similar to that observed on the Z chromosome.</p> <p>Conclusions</p> <p>A negative correlation between nucleotide diversity and autosome size was observed in the white-throated sparrow genome, as well as low levels of diversity on the sex chromosomes comparable to those reported in other birds. The population structure and extended LD associated with the ZAL2/2^mchromosomal polymorphism are exceptional compared to the rest of the white-throated sparrow genome.</p

Does the Proportion of Same-Day and 24-Hour Appointments Impact Patient Satisfaction?

Background: The relationship between open access and patient satisfaction is mixed. Our study is the first to assess the relationship between open access appointment scheduling and patient satisfaction in the Military Health System (MHS). It is also unique in that we examine both same-day and 24-hour access through a relationship with satisfaction. Methods: We conducted a panel time-series analysis with general estimating equations on the Army population of outpatient facilities (N = 32), with 32 364 957 total observations. Our primary independent variables were the proportion of a facility’s appointments within 24 hours and same day from July 2013 to May 2015. Results: We identified that a higher proportion of same-day appointments is associated with increased patient satisfaction with the ability to see their provider when needed. We did not find the same result when examining access within 24 hours. Conclusions: Open access appointment scheduling appears to have a greater impact on patient satisfaction with timeliness of care if that appointment is made the same day the patient presents to the facility. Facilities should consider opening more of their schedule to accommodate same-day appointments. This can result in less costly primary care instead of emergency department usage

Pengembangan Instrumen Pendeteksi Kesulitan Belajar Kimia Kelas X Menggunakan Model Testlet

Penelitian ini bertujuan untuk: (1) menghasilkan instrumen model testlet sebagai instrumen pendeteksi kesulitan belajar kimia peserta didik kelas X SMA sesuai tahapan penelitian pengembangan; (2) menentukan karakteristik butir soal instrumen pendeteksi kesulitan belajar kimia kelas X menggunakan model testlet; (3) mendapatkan profil belajar individu peserta didik. Penelitian ini merupakan penelitian pengembangan model Akker dengan tahapan: preliminary investigation; theoretical embedding; empirical testing; dan documentation, analysis, and reflection on process and outcome. Subjek uji coba yaitu guru kimia SMA di Surakarta; dosen Pendidikan Kimia FKIP UNS Surakarta; peserta didik SMA Negeri 2, SMA Negeri 5, dan SMA Batik 2 Surakarta. Berdasarkan hasil penelitian dapat disimpulkan bahwa: (1) penelitian ini menghasilkan instrumen pendeteksi kesulitan belajar kimia kelas X menggunakan model testlet pada bab Struktur Atom dan Sistem Periodik Unsur yang terdiri dari butir soal dan program analisis datanya; (2) karakteristik butir soal memiliki validitas isi Aiken dengan rentang 0,76-1 yang berarti validitas isi baik; reliabilitas sebesar 0,83 yang berarti reliabilitas tinggi; persentase daya beda soal baik sekali 47,91%, baik 12,5%, cukup 18,75%, jelek 20,83%; persentase tingkat kesukaran soal sukar 4,17%, sedang 50%, mudah 45,83%; dan kunci jawaban 70,83% efektif; (3) profil belajar individu peserta didik dapat memberi laporan yang informatif mengenai kemampuan dan kesulitan belajar kimia peserta didik

ClinicalTrials.gov registration can supplement information in abstracts for systematic reviews: a comparisonstudy.

PMC3689057BACKGROUND: The inclusion of randomized controlled trials (RCTs) reported in conference abstracts in systematic reviews is controversial, partly because study design information and risk of bias is often not fully reported in the abstract. The Association for Research in Vision and Ophthalmology (ARVO) requires trial registration of abstracts submitted for their annual conference as of 2007. Our goal was to assess the feasibility of obtaining study design information critical to systematic reviews, but not typically included in conference abstracts, from the trial registration record. METHODS: We reviewed all conference abstracts presented at the ARVO meetings from 2007 through 2009, and identified 496 RCTs; 154 had a single matching registration record in ClinicalTrials.gov. Two individuals independently extracted information from the abstract and the ClinicalTrials.gov record, including study design, sample size, inclusion criteria, masking, interventions, outcomes, funder, and investigator name and contact information. Discrepancies were resolved by consensus. We assessed the frequencies of reporting variables appearing in the abstract and the trial register and assessed agreement of information reported in both sources. RESULTS: We found a substantial amount of study design information in the ClinicalTrials.gov record that was unavailable in the corresponding conference abstract, including eligibility criteria associated with gender (83%; 128/154); masking or blinding of study participants (53%, 82/154), persons administering treatment (30%, 46/154), and persons measuring the outcomes (40%, 61/154)); and number of study centers (58%; 90/154). Only 34% (52/154) of abstracts explicitly described a primary outcome, but a primary outcome was included in the "Primary Outcome" field in the ClinicalTrials.gov record for 82% (126/154) of studies. One or more study interventions were reported in each abstract, but agreed exactly with those reported in ClinicalTrials.gov only slightly more than half the time (88/154, 56%). We found no contact information for study investigators in the abstract, but this information was available in less than one quarter of ClinicalTrial.gov records (17%; 26/154). CONCLUSION: RCT design information not reported in conference abstracts is often available in the corresponding ClinicalTrials.gov registration record. Sometimes there is conflicting information reported in the two sources and further contact with the trial investigators may still be required.JH Libraries Open Access Fun

Adapting the AHA’s Blood Pressure and Nutrition Management Program into Digestible Teaching Plans for Low-Income Communities

Executive Summary: Adapting the AHA’s blood pressure and nutrition management program into digestible teaching plans for low-income communities According to the American Heart Association (AHA), 46% of American adults have high blood pressure (Whelton et al., 2017). High blood pressure, especially for those above the age of 50, is associated with a higher prevalence of heart disease and a shorter life expectancy. The AHA’s Check Change Control program (CCC), is an evidence based, self-directed blood pressure management guide (American Heart Association, 2021). The CCC program incorporates four lesson topics related to lifestyle changes to manage hypertension. The four topics are: self-monitoring of blood pressure, healthy eating and reducing sodium, exercise, and stress management. Our group’s mission focused on creating educational plans on the first two topics, self-monitoring of blood pressure and healthy eating. Our goal was to provide future educators at an independent senior living facility with a condensed framework of the CCC program that would be more easily understood for an older adult population. Background For our project, we worked alongside a nonprofit organization that provided sustainable housing and services for seniors and families. Our group consisted of eight quarter-five Seattle Pacific University (SPU) nursing students working with a representative from the AHA, our clinical instructor, and a representative from the site to create an educational plan based on a needs assessment of the community. Our primary community was an independent living facility for low-income older adults located south of Seattle, Washington. Based on prior assessments by the community management and AHA, they found a knowledge deficit in blood pressure management and understanding of nutrition. In our site assessments we validated these needs. Residents had limited knowledge of the importance of blood pressure management, had no way to self-monitor, and had limited access to healthy food options. Representatives of the food pantry reported that they had no consistent supplies, relying on internal donations. The pantry consisted primarily of high-sodium prepackaged foods like instant noodles and canned beans. A new addition to the community was a garden; but, for the autumn and winter, fresh vegetables were scarce. In our review of the AHA’s CCC program, we found barriers to its implementation. The document itself was wholly online and utilized many hyperlinks, PowerPoints, and videos. For low-income adults with limited knowledge or access to technology, this program was found to be hard to access by themselves. The complex modules the AHA had prepared were difficult for the residents of the community to use and understand due to the sheer size and depth of the content. For future SPU students who would be implementing the education, the length and depth of the program were also much larger than what was possible to cover within a regular ten-week school quarter. Our group worked to reduce these barriers by condensing the material into weekly teaching activities. Activities We generated a lesson outline to target two main areas of concern within the community as determined by site assessments: blood pressure management, and nutrition, for use by future SPU students. From the CCC program, we curated a five-week outline for nursing students or similar educators to implement over the course of a ten-week school quarter. The first two weeks we focused on blood pressure management, and the second two weeks on nutrition, with a flexible fifth week for review, open activity, or a separate teaching topic. The first week’s topic was blood pressure literacy, measurements, and tracking. This included a review of what blood pressure is, the importance of monitoring, an open discussion of barriers to monitoring, how to accurately check and analyze the readings, and physically getting their blood pressure taken by the educators. The second week’s topic was medications and adherence. The education plan included for students to have a brief check in and review of the content from the previous week, and hold information sessions on specific medications. These information sessions would be private and personalized by being held in a one-on-one manner. The education plan also focuses on identifying potential struggles, assessing a lack of education on their medications such as indications, symptoms, and management, as well as reinforcing adherence. The third week’s topic was nutritional literacy. The education plan includes having students assess the residents’ understanding of what a healthy diet consists of, and then they would provide education on sodium intake with a demonstration of serving sizes. The focus of the fourth week was healthy nutrition options. The education plan included having residents create meals with provided food pages and discuss their choices. The fifth week’s topic would be a flex week, where students and/or residents would pick a topic based on their own community needs assessments. The activities in the education plan include different styles of engagement, including lecture, presentations, PowerPoints, videos, hands-on activities, games, surveys, one-on-one sessions and open discussions, and distribution of educational materials and resources to monitor health effectively. We also have incorporated a weekly survey to assess the effectiveness of our project goals. Outcomes Our project was based on goals and topics organized by facility leadership in collaboration with the AHA. We were tasked with creating teaching materials and educational plans for future SPU Nursing Students to teach the residents during their clinicals. Our lesson outline was provided to agency staff in order to ensure the success of the project goals. Evaluation surveys was provided to the students in the implementation document to allow the students to have sources to use to assess the effectiveness of the teaching plan, activities, and resources. Based on survey responses, adjustments, a weekly focus could be made. Further evaluation of the effectiveness of our plan would be overseen by the AHA representative. For this project we have created a lesson outline at the request of the community manager, using AHA resources along with the assessments by the site management and by our group. This was done in order to aid future SPU Nursing Students in the implementation of our lesson plans for the community. Future nursing students will continue to gather and add information based on their own observations and experiences to ensure the continuity of this project and the health outcomes of the focused community. References American Heart Association (2021) Check. Change. Control. check-change-control-implementation-guide.pdf (heart.org) Whelton, P. K., Carey, R.M., Aronow, W.S., Casey, D.E., Jr., Collins, K.J., Himmelfarb Dennison, C., DePalma, S.M., Gidding, S., Jamerson, K.A., Jones, D.W., MacLaughlin, E.J., Muntner, P., Ovbiagele, B., Smith, S.C., Jr., Spencer, C.C., Stafford, R.S., Taler, S.J., Thomas, R.J., Williams, K.A., Sr., … Wright, J.T., Jr. (2017). ACC/AHA/AAPA/ABC/ACPM/AGS/APhA/ASH/ASPC/NMA/PCNA guideline for the prevention, detection, evaluation, and management of high blood pressure in adults: a report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. Hypertension, 71(6), e13-e115. https://doi.org/10.1161/HYP.000000000000006

Comparison of two multiple-locus variable-number tandem-repeat analysis methods for molecular strain typing of human Brucella melitensis isolates from the Middle East

Brucella species are highly monomorphic, with minimal genetic variation among species, hindering the development of reliable subtyping tools for epidemiologic and phylogenetic analyses. Our objective was to compare two distinct multiple-locus variable-number tandem-repeat analysis (MLVA) subtyping methods on a collection of 101 Brucella melitensis isolates from sporadic human cases of brucellosis in Egypt (n = 83), Qatar (n = 17), and Libya (n = 1). A gel-based MLVA technique, MLVA-15IGM, was compared to an automated capillary electrophoresis-based method, MLVA-15NAU, with each MLVA scheme examining a unique set of variable-number tandem repeats. Both the MLVAIGM and MLVANAU methods were highly discriminatory, resolving 99 and 101 distinct genotypes, respectively, and were able to largely separate genotypes from Egypt and Qatar. The MLVA-15NAU scheme presented higher strain-to-strain diversity in our test population than that observed with the MLVA-15IGM assay. Both schemes were able to genetically correlate some strains originating from the same hospital or region within a country. In addition to comparing the genotyping abilities of these two schemes, we also compared the usability, limitations, and advantages of the two MLVA systems and their applications in the epidemiological genotyping of human B. melitensis strains

Bacillus anthracis in China and its relationship to worldwide lineages

<p>Abstract</p> <p>Background</p> <p>The global pattern of distribution of 1033 <it>B. anthracis </it>isolates has previously been defined by a set of 12 conserved canonical single nucleotide polymorphisms (canSNP). These studies reinforced the presence of three major lineages and 12 sub-lineages and sub-groups of this anthrax-causing pathogen. Isolates that form the A lineage (unlike the B and C lineages) have become widely dispersed throughout the world and form the basis for the geographical disposition of "modern" anthrax. An archival collection of 191 different <it>B. anthracis </it>isolates from China provides a glimpse into the possible role of Chinese trade and commerce in the spread of certain sub-lineages of this pathogen. Canonical single nucleotide polymorphism (canSNP) and multiple locus VNTR analysis (MLVA) typing has been used to examine this archival collection of isolates.</p> <p>Results</p> <p>The canSNP study indicates that there are 5 different sub-lineages/sub-groups in China out of 12 previously described world-wide canSNP genotypes. Three of these canSNP genotypes were only found in the western-most province of China, Xinjiang. These genotypes were A.Br.008/009, a sub-group that is spread across most of Europe and Asia; A.Br.Aust 94, a sub-lineage that is present in Europe and India, and A.Br.Vollum, a lineage that is also present in Europe. The remaining two canSNP genotypes are spread across the whole of China and belong to sub-group A.Br.001/002 and the A.Br.Ames sub-lineage, two closely related genotypes. MLVA typing adds resolution to the isolates in each canSNP genotype and diversity indices for the A.Br.008/009 and A.Br.001/002 sub-groups suggest that these represent older and established clades in China.</p> <p>Conclusion</p> <p><it>B. anthracis </it>isolates were recovered from three canSNP sub-groups (A.Br.008/009, A.Br.Aust94, and A.Br.Vollum) in the western most portion of the large Chinese province of Xinjiang. The city of Kashi in this province appears to have served as a crossroads for not only trade but the movement of diseases such as anthrax along the ancient "silk road". Phylogenetic inference also suggests that the A.Br.Ames sub-lineage, first identified in the original Ames strain isolated from Jim Hogg County, TX, is descended from the A.Br.001/002 sub-group that has a major presence in most of China. These results suggest a genetic discontinuity between the younger Ames sub-lineage in Texas and the large Western North American sub-lineage spread across central Canada and the Dakotas.</p

Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

BACKGROUND: The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. RESULTS: B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10(-5 )per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. CONCLUSION: The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen

Global Genetic Population Structure of Bacillus anthracis

Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064–6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated

HPV-Related Anal Cancer Is Associated With Changes in the Anorectal Microbiome During Cancer Development

BACKGROUND: Squamous cell carcinoma of the anus (SCCA) is a rare gastrointestinal cancer. Factors associated with progression of HPV infection to anal dysplasia and cancer are unclear and screening guidelines and approaches for anal dysplasia are less clear than for cervical dysplasia. One potential contributing factor is the anorectal microbiome. In this study, we aimed to identify differences in anal microbiome composition in the settings of HPV infection, anal dysplasia, and anal cancer in this rare disease. METHODS: Patients were enrolled in two prospective studies. Patients with anal dysplasia were part of a cross-sectional cohort that enrolled women with high-grade lower genital tract dysplasia. Anorectal tumor swabs were prospectively collected from patients with biopsy-confirmed locally advanced SCCA prior to receiving standard-of-care chemoradiotherapy (CRT). Patients with high-grade lower genital tract dysplasia without anal dysplasia were considered high-risk (HR Normal). 16S V4 rRNA Microbiome sequencing was performed for anal swabs. Alpha and Beta Diversity and composition were compared for HR Normal, anal dysplasia, and anal cancer. RESULTS: 60 patients with high-grade lower genital tract dysplasia were initially enrolled. Seven patients had concurrent anal dysplasia and 44 patients were considered HR Normal. Anorectal swabs from 21 patients with localized SCCA were included, sequenced, and analyzed in the study. Analysis of weighted and unweighted UniFrac distances demonstrated significant differences in microbial community composition between anal cancer and HR normal (p CONCLUSION: Although alpha diversity was similar between HR Normal, dysplasia and cancer patients, composition differed significantly between the three groups. Increased anorecta