bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel affinity-based method for the isolation of highly purified extracellular vesicles
Authors: Nakai Wataru , Yoshida Takeshi , Diez Diego , Miyatake Yuji , Nishibu Takahiro , Imawaka Naoko , Naruse Ken , Sadamura Yoshifusa , Hanayama Rikinari 
Published: September 2016

AbstractExtracellular vesicles (EVs) such as exosomes and microvesicles serve as messengers of intercellular network, allowing exchange of cellular components between cells. EVs carry lipids, proteins and RNAs derived from their producing cells and have potential as biomarkers specific to cell types and even cellular states. However, conventional methods (such as ultracentrifugation or polymeric precipitation) for isolating EVs have disadvantages regarding purity and feasibility. Here, we have developed a novel method for EV purification by using Tim4 protein, which specifically binds the phosphatidylserine displayed on the surface of EVs. Because the binding is Ca2+-dependent, intact EVs can be easily released from Tim4 by adding Ca2+ chelators. Tim4 purification, which we have applied to cell conditioned media and biofluids, is capable of yielding EVs of a higher purity than those obtained using conventional methods. The lower contamination found in Tim4-purified EV preparations allows more EV-specific proteins to be detected by mass spectrometry, enabling better characterization and quantification of different EV populations’ proteomes. Tim4 protein can also be used as a powerful tool for quantification of EVs in both ELISA and flow cytometry formats. Thus, the affinity of Tim4 for EVs will find abundant applications in EV studies.
Genome-wide mapping of nucleosome positions in Saccharomyces cerevisiae in response to different nitrogen conditions
Authors: Zhang Peng , Du Guocheng , Zou Huijun , Xie Guangfa , Chen Jian , Shi Zhongping , Zhou Jingwen 
Published: September 2016

AbstractWell-organized chromatin is involved in a number of various transcriptional regulation and gene expression. We used genome-wide mapping of nucleosomes in response to different nitrogen conditions to determine both nucleosome profiles and gene expression events in Saccharomyces cerevisiae. Nitrogen conditions influence general nucleosome profiles and the expression of nitrogen catabolite repression (NCR) sensitive genes. The nucleosome occupancy of TATA-containing genes was higher compared to TATA-less genes. TATA-less genes in high or low nucleosome occupancy, showed a significant change in gene coding regions when shifting cells from glutamine to proline as the sole nitrogen resource. Furthermore, a correlation between the expression of nucleosome occupancy induced NCR sensitive genes or TATA containing genes in NCR sensitive genes and nucleosome prediction were found when cells were cultured in proline or shifting from glutamine to proline as the sole nitrogen source compared to glutamine. These results also showed that variation of nucleosome occupancy accompany with chromatin-dependent transcription factor could influence the expression of a series of genes involved in the specific regulation of nitrogen utilization.
The effects of ordered carbon vacancies on stability and thermo-mechanical properties of V8C7 compared with VC
Authors: Chong XiaoYu , Jiang YeHua , Zhou Rong , Feng Jing 
Published: September 2016

AbstractThe ordered non-stoichiometric V8C7 can form in the VCy carbides by the disorder–order phase transformation. The intrusion of ordered carbon vacancies can affect their stability, mechanical, thermal and electronic properties. The relatively thermodynamic stability and mechanical properties at high temperature for the ordered stoichiometric VC and non-stoichiometric V8C7 are investigated in this paper by first-principle calculations combined with the quasi-harmonic approximation. The difference between the properties of VC and V8C7 can be obtained. We find that the V8C7 is thermodynamic more stable than VC, but has weaker elastic heat resistance than VC. Moreover, the minimum thermal conductivity of VC is a little larger than V8C7 and a simple way is proposed to characterize the anisotropy of lattice thermal conductivity based on the Cahill’s model.
SENP1 Is a Crucial Regulator for Cell Senescence through DeSUMOylation of Bmi1
Authors: Xia Nansong , Cai Juan , Wang Feifei , Dong Baijun , Liu Song , Chen Fengling , Cheng Jinke , Zuo Yong 
Published: September 2016

AbstractCell senescence can limit proliferative potential and prevent tumorigenesis. Bmi1 is a key regulator in cell senescence by suppressing the Ink4a/Arf locus. However, how to regulate Bmi1 activity in cell senescence is largely unknown. Here, we show that SENP1 plays an important role in cell senescence by regulating Bmi1 SUMOylation. Senp1−/− primary MEF cells show resistance to cell senescence induced by passaging or other senescence inducing signals. SENP1 deficiency also reduces oncogene H-RasV12-induced senescence, and enhances H-RasV12-induced cell transformation. We further show that in Senp1−/− MEFs the expression of p19Arf, an important regulator in p53/p21-mediated cell senescence, is markedly reduced. Meanwhile, we demonstrate that SENP1 can specifically de-SUMOylate Bmi1 and thereby decreases the occupancy of Bmi1 on p19Arf promoter leading to decrease of H2AK119 mono-ubiquitination and up-expression of p19Arf. These data reveal a crucial role of SENP1 in regulation of cell senescence as well as cell transformation.
Oligomannan Prebiotic Attenuates Immunological, Clinical and Behavioral Symptoms in Mouse Model of Inflammatory Bowel Disease
Authors: Ferenczi Szilamér , Szegi Krisztián , Winkler Zsuzsanna , Barna Teréz , Kovács Krisztina J. 
Published: September 2016

AbstractInflammatory bowel disease shows increasing prevalence, however its pathomechanism and treatment is not fully resolved. Prebiotics are non-digestible carbohydrates which might provide an alternative to treat inflammatory conditions in the gut due to their positive effects either on the microbiome or through their direct effect on macrophages and mucosa. To test the protective effects of an oligomannan prebiotic, yeast cell wall mannooligosaccharide (MOS) was administered in dextran-sulphate-sodium (DSS)-induced mouse model of acute colitis. MOS reduced DSS-induced clinical- (weight loss, diarrhea) and histological scores (mucosal damage) as well as sickness-related anxiety. DSS treatment resulted in changes in colon microbiome with selective increase of Coliform bacteria. MOS administration attenuated colitis-related increase of Coliforms, normalized colonic muc2 expression and attenuated local expression of proinflammatory cytokines IL-1a, IL1b, IL6, KC, G-CSF and MCP1 as well as toll-like receptor TLR4 and NLRP3 inflammasome. Some of the protective effects of MOS were likely be mediated directly through local macrophages because MOS dose-dependently inhibited IL-1b and G-CSF induction following in vitro DSS challenge and IL1a, IL1b, G-SCF- and IL6 increases after LPS treatment in mouse macrophage cell line RAW264.7. These results highlight oligomannan prebiotics as therapeutic functional food for testing in clinical trials.
Proper hygiene and effective management of livestock as a panacea for agricultural development and increase in Nigeria's gross domestic product (GDP): a review.
Authors: Kwaghe A. V. , Vakuru C. T. , Ndahi M. D. , Abubakar A. , Iwar V. N. , Eze E. 
Published: September 2016

Abstract
Increased livestock production and better food security will naturally follow from proper livestock management practices. Such management practices include the application of appropriate vaccination schedule, biosecurity, feeding regimen, and implementation and sustenance of improved and feasible livestock policies. In meat production, the abattoir needs to be well equipped for antemortem and postmortem procedures, hygienic processing of carcasses, and packaging, to improve the quality and quantity of meat and meat products. In Nigeria, about 90% of the livestock industry (cattle, sheep and goats) is managed extensively (nomadic management system) or semi-intensively (animals are taken out to graze and are brought home with little or no provision at home). These systems are greatly affected by insufficient grazing reserves, lack of cattle routes, and consequently, by conflicts between the livestock farmers and crop farmers due to invasion of livestock into farms during grazing. During the dry season, livestock animals tend to become emaciated due to insufficient food, which leads to health depreciation due to declined immune status, and decline in meat production and reproduction rate. Diseases possess a great challenge to meat and egg production due to illiteracy and lack of resources for proper management of livestock. In the poultry industry, where most of the meat is produced, typically no or only some biosecurity procedures are in place at the commercial farms. The backyard local poultry are kept without any form of care; they tend to scavenge for their food and are prone to all forms of diseases, parasites and predators. The hygienic status and carcass preparation at Nigeria's abattoirs is very poor, which affects the meat industry. In general, livestock production in the country is greatly affected by poor management practices, diseases and poor meat processing strategies, which leads to the production of low-quality meat that can easily decompose, and the spread of food-borne and zoonotic diseases. Livestock policies in the country have not produced the desired economic growth due to their inadequate implementation. Also, the oil boom era relegated agriculture to the background from being the major part of the nation's gross domestic product (GDP). There is need for new strategies and proper implementation of livestock policies - it is recommended to encourage stakeholders to participate and to diversify the industry into manufacturing and not just production. This study was carried out in order to assess state of livestock production, management systems including assessment of livestock policies, and challenges faced by this industry in Nigeria, and to identify the way forward for better livestock production and subsequent increase in the nation's GDP.
PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification
Authors: Chen Xi , Shi Xu , Hilakivi-Clarke Leena , Shajahan-Haq Ayesha N , Clarke Robert , Xuan Jianhua 
Published: September 2016

Abstract

Motivation
Whole genome DNA-sequencing (WGS) of paired tumor and normal samples has enabled the identification of somatic DNA changes in an unprecedented detail. Large-scale identification of somatic structural variations (SVs) for a specific cancer type will deepen our understanding of driver mechanisms in cancer progression. However, the limited number of WGS samples, insufficient read coverage, and the impurity of tumor samples that contain normal and neoplastic cells, limit reliable and accurate detection of somatic SVs.

Results
We present a novel pattern-based probabilistic approach, PSSV, to identify somatic structural variations from WGS data. PSSV features a mixture model with hidden states representing different mutation patterns; PSSV can thus differentiate heterozygous and homozygous SVs in each sample, enabling the identification of those somatic SVs with heterozygous mutations in normal samples and homozygous mutations in tumor samples. Simulation studies demonstrate that PSSV outperforms existing tools. PSSV has been successfully applied to breast cancer data to identify somatic SVs of key factors associated with breast cancer development.

Availability and Implementation
An R package of PSSV is available at http://www.cbil.ece.vt.edu/software.htm.

Supplementary information
Supplementary data are available at Bioinformatics online.
5 Minute Teaching Time Outs: A String of Teaching Pearls
Authors: Patel Silka , Bienstock Jessica , White-Prock Paula , Smith Dora , Burrell Dayna , Chou Betty 
Published: September 2016

BACKGROUND:
Incorporating didactics designed to improve teaching skills into departmental agenda is challenging but necessary. Often lectures take place once a year with little continuing reinforcement. Five Minute Teaching Time Outs (5MTTO) were created to introduce and reinforce important teaching skills to all levels of educators. The goal was to incorporate them into routine departmental activities such as M&M/Grand Rounds.

METHODS:
A multicenter prospective survey was conducted to assess faculty, fellow and resident attitudes towards the 5MTTO. Six-5MTTOs were created to cover a broad range of teaching topics. These were presented over the year at routinely scheduled department meetings. Participants were asked to fill out an anonymous survey at the completion of each 5MTTO.

RESULTS:
On average 45 participants were present at each 5MTTO among the 3 institutions, usually evenly split between faculty/fellows and residents. On average, after each session, participants agreed/strongly agreed that material from the individual 5MTTOs would influence their teaching approach 82–97% of the time. Over 92% of the time participants agreed/strongly agreed that 5 minutes was adequate and over 93% agreed/strongly agreed to having future 5MTTO.

DISCUSSION:
Incorporating teaching skills into departmental activities can be difficult due to time constraints. Regular reinforcement is as important for educators as it is for learners. These 5MTTO are well-received by the department, fit into already scheduled activities and may influence the teaching behaviors of our clinician-educators.
Integrating Basic Science Into a Senior Medical Student Residency Preparation Elective
Authors: Malone Anita , Stein Tamara , Marzano David , Skinner Bethany , Hammoud Maya , Morgan Helen 
Published: September 2016

BACKGROUND:
Increasing medical student residency preparedness is an important current initiative in medical education. Demonstrating knowledge of abdominal and pelvic anatomy is a vital level 1 milestone. Anatomy is typically taught early in medical school, and multiple studies have demonstrated that there is a significant decline in anatomical knowledge throughout medical school. Residency preparation electives are an optimal time for integrating anatomical teaching in relevant clinical and surgical contexts.

METHODS:
In 2014 and 2015, 27 senior medical students matching into OBGYN residency participated in a 4-week Advanced Clinical Skills in OBGYN. Two half-day sessions were dedicated to reviewing pelvic viscera, vasculature and nerve supply, and perineal anatomy using embalmed cadavers. Clinical correlations were emphasized throughout dissection. Two half-days consisted of operative procedures performed on fresh-frozen cadavers. Anatomical knowledge was assessed with pre- and post-course multiple choice assessment. Statistical analysis consisted of paired t tests. Student satisfaction was assessed with a web-based survey.

RESULTS:
Anatomical knowledge scores increased significantly from 64.8% (SD=1.99) to 83.6% (SD=1.63), P<.01. On a 5 point scale (1=Strongly Disagree, 5=Strongly Agree) when asked if the sessions were “relevant to their education” and “made them feel more prepared for residency,” students' average responses were 4.93 and 4.89, respectively.

DISCUSSION:
We need to better prepare senior medical students for obstetrics and gynecology residency. This purposeful and innovative approach to improving preparedness for residency improved anatomical knowledge, with very high student satisfaction ratings.
Residents' Insight on Student Mistreatment: What We Learned From Our First Action Research Cycle
Authors: Galey Hannah , Thompson Amy , Bennett Aurora , Flood-Shaffer Kellie , Wagner Emily 
Published: September 2016

BACKGROUND:
The medical student mistreatment literature focuses on prevalence, risk factors, and mistreatment sources. Studies describe interventions to improve learning culture, however many students continue to report mistreatment. We initiated a project to engage residents to construct knowledge of the mistreatment phenomenon, plan, and evaluate actions to address this problem.

METHODS:
Action research (AR) is a repetitive, cyclical, participatory research process. We used the method of Group Level Assessment (GLA) to organize our first AR cycle. In a group setting, residents responded individually to 22 theoretically-derived prompts. Residents viewed all responses, performed first-cut qualitative analysis, and planned actions from group discussion. Secondary qualitative analysis was performed to understand mistreatment characteristics, contributing factors, responses and outcomes, and interventions.

RESULTS:
Twenty-three residents participated. Factors identified that contributed to student mistreatment included different medical specialty paths, unprepared students, poorly defined expectations, hierarchy, poor communications, and residents' need for patience, time and inspiration to teach. Residents acknowledged both negative and positive outcomes from humiliation, including loss of focus, learner withdrawal, positive resilience traits, motivation to learn, and attention to details. Solutions spanned clinical and educational interventions to needed gains in personal insight and improved behaviors.

DISCUSSION:
Our findings confirm the influence of previously described factors contributing to medical student mistreatment. Most importantly, we gained significant insight into local factors contributing to this phenomenon. Residents are now organizational change-makers, an AR principle. As a result, we are implementing resident-inspired interventions and moving forward with our next AR cycle.
Smart Phone-Based Quick Response (QR) Evaluations for Residents: What Do Faculty Think?
Authors: Debiec Katherine , Sobhani Nasim , Fay Emily , Stephenson-Famy Alyssa , Schiff Melissa 
Published: September 2016

BACKGROUND:
Providing ample, high quality and timely venue-based evaluations of resident performance is a critical mandate of graduate medical education.

METHODS:
We utilized a before and after study design to compare a paper venue-based evaluation tool for procedures to a smart phone QR evaluation tool introduced in July 2014 at the University of Washington OB-GYN Residency Program. Each resident was assigned a QR code for faculty to access the evaluation in a smart-phone based application. Faculty completed a baseline survey evaluating the paper tool and a 6-month follow-up survey evaluating the QR tool. We compared characteristics of the feedback and the evaluation tools using Wilcoxon signed rank test.

RESULTS:
Twenty-three of 40 (58%) eligible teaching faculty 40 completed surveys at 0 and 6 months after introducing the QR tool. More faculty (57.1%) agreed that the QR tool promoted interaction compared to the paper tool (13.0%, P=.0005). More faculty (85.7%) felt comfortable approaching residents with the QR tool compared with paper (34.8%, P=.0019) and more felt that the QR tool (52.4%) helped give feedback for residents (17.4%, P=.0071). Greater percentage of faculty (71.4%) provided feedback within 24 hours with the QR tool compared with paper (17.4%, P=.0005).

DISCUSSION:
Faculty are comfortable utilizing smart phone-based QR technology for resident evaluation and it appears to be associated with more timely feedback.
Development and Validation of Mental Practice as a Training Strategy for Abdominal Hysterectomy
Authors: Salva Catherine , Saab Said , Dayaratna Sandra , Hutton Ellyn , Bastek Jamie 
Published: September 2016

Local Mentor: Lorraine Dugoff, MD

APGO Advisor: Alice R. Goepfert, MD

PURPOSE:
To develop and validate a Mental Practice tool for resident training in abdominal hysterectomy.

BACKGROUND:
Abdominal hysterectomy is a common operation performed by obstetrician-gynecologists. Training opportunities for this procedure are diminishing due to many factors. Mental Practice (the use of mental imagery to rehearse a task symbolically before performance) has been used successfully in sports and music to enhance skill. This strategy demonstrates benefit in existing surgical education literature.

METHODS:
A Mental Practice script was developed by taking expert surgeons through a cognitive walk-through to identify key procedural cues. For validation, resident and attending gynecologic surgeons mentally rehearsed abdominal hysterectomy. Ability to mentally practice this procedure was assessed before and after exposure to the tool. We used a validated 7-point Likert scale questionnaire composed of 8 questions (MIQ: Mental Imagery Questionnaire, 56 points).

EVALUATION:
The study included 16 subjects, with experience ranging from 0 to >100 procedures. Reliability testing of the questionnaire (Cronbach alpha 0.915 before Mental Practice training and 0.933 after) indicated internal consistency. Construct validity was also supported. Significant improvement in MIQ score after use of the tool was shown by residents (39 versus 44; P=.003). Attending scores also improved but not significantly (54 versus 55; P=.066), suggesting a ceiling effect. A linear relationship was evident between the benefit of the tool and experience (P=.051).

DISSEMINATION:
A larger study is planned to determine the effect of mental practice on surgical performance for residents.

REFLECTIVE CRITIQUE:
The tool was most useful for trainees with the least surgical experience.
Interprofessional Education in the Obstetrics and Gynecology Clerkship: Do We Teach Collaboration?
Authors: Justicia-Linde Faye 
Published: September 2016

Local Mentor: Glenna Bett, PhD

APGO Advisors: Jody Steinauer, MD, MAS, and Sonya Erickson, MD

PURPOSE:
To ascertain how obstetrics and gynecology (Ob-Gyn) clerkships incorporate interprofessional education (IPE) into the curriculum and Ob-Gyn clerkship directors' opinions regarding IPE.

BACKGROUND:
The Association of American Medical Colleges (AAMC) identified IPE as a “horizon issue.” Literature review revealed 6 publications regarding IPE focused on the Ob-Gyn clerkship from the United States, Canada and United Kingdom. Most publications on IPE in Ob-Gyn investigated resident and attending perspectives.

METHODS:
The study used an online survey of Ob-Gyn clerkship directors at English-speaking LCME-accredited allopathic medical schools identified through the AAMC's website. Clerkship directors were identified through institutions' websites. The survey contained 16 questions about clerkship structure, if/how IPE activities are conducted, and clerkship director attitudes regarding IPE.

RESULTS:
One hundred fifty-four eligible medical schools were identified; 237 invitations were sent and 84 complete responses received. Seventy-two percent of clerkship directors believed that IPE should be included in the Ob-Gyn clerkship; 25% were unsure, and 4% did not. However, only 54% of Ob-Gyn clerkships incorporated IPE activities, 39% did not, and 7% planned to do so. The most common IPE activities were joint didactic sessions (58%) and interprofessional patient rounds (47%). The main barrier to implementing IPE was difficulty coordinating schedules (78%).

DISCUSSION:
The majority of respondents believed IPE should be included in the Ob-Gyn clerkship and had already done so. This is the first study to address practices and attitudes regarding IPE in the Ob-Gyn clerkship, a strength being its broad reach across LCME-accredited institutions. Potential weaknesses include response biases.