bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antigen Specificity of Type I NKT Cells Is Governed by TCR β-Chain Diversity
Authors: Cameron Garth , Pellicci Daniel G. , Uldrich Adam P. , Besra Gurdyal S. , Illarionov Petr , Williams Spencer J. , La Gruta Nicole L. , Rossjohn Jamie , Godfrey Dale I. 
Published: October 2015

Abstract
NKT cells recognize lipid-based Ags presented by CD1d. Type I NKT cells are often referred to as invariant owing to their mostly invariant TCR α-chain usage (Vα14-Jα18 in mice, Vα24-Jα18 in humans). However, these cells have diverse TCR β-chains, including Vβ8, Vβ7, and Vβ2 in mice and Vβ11 in humans, joined to a range of TCR Dβ and Jβ genes. In this study, we demonstrate that TCR β-chain composition can dramatically influence lipid Ag recognition in an Ag-dependent manner. Namely, the glycolipids α-glucosylceramide and isoglobotrihexosylceramide were preferentially recognized by Vβ7+ NKT cells from mice, whereas the α-galactosylceramide analog OCH, with a truncated sphingosine chain, was preferentially recognized by Vβ8+ NKT cells from mice. We show that the influence of the TCR β-chain is due to a combination of Vβ-, Jβ-, and CDR3β-encoded residues and that these TCRs can recapitulate the selective Ag reactivity in TCR-transduced cell lines. Similar observations were made with human NKT cells where different CDR3β-encoded residues determined Ag preference. These findings indicate that NKT TCR β-chain diversity results in differential and nonhierarchical Ag recognition by these cells, which implies that some Ags can preferentially activate type I NKT cell subsets.
The Best of Both Worlds: Resident Experiences of Urban and Regional Contexts in a Hybrid Pediatrics Residency Program
Authors: Topps Maureen , Ellaway Rachel H. , Baron Tara , Peek Alison 
Published: October 2015

ABSTRACT

Background
The context for specialty residency training in pediatrics has broadened in recent decades to include distributed community sites as well as academic health science centers. Rather than creating parallel, community-only programs, most programs have expanded to include both community and large urban tertiary health center experiences. Despite these changes, there has been relatively little research looking at residents' experiences in these distributed graduate medical education programs.

Objective
A longitudinal case study was undertaken to explore the experiences of residents in a Canadian pediatrics residency program that involved a combination of clinical placements in a large urban tertiary health center and in regional hospitals.

Methods
The study drew on 2 streams of primary data: 1-on-1 interviews with residents at the end of each block rotation and annual focus groups with residents.

Results
A thematic analysis (using grounded theory techniques) of transcripts of the interviews and focus groups identified 6 high-level themes: access to training, quality of learning, patient mix, continuity of care, learner roles, and residents as teachers.

Conclusions
Rather than finding that certain training contexts were “better” than others when comparing residents' experiences of the various training contexts in this pediatrics residency, what emerged was an understanding that the different settings complemented each other. Residents were adamant that this was not a matter of superiority of one context over any other; their experiences in different contexts each made a valuable contribution to the quality of their training.
Patient-Centered Medical Home Knowledge and Attitudes of Residents and Faculty: Certification Is Just the First Step
Authors: El Rayess Fadya , Goldman Roberta , Furey Christopher , Chandran Rabin , Goldberg Arnold R. , Anandarajah Gowri 
Published: October 2015

ABSTRACTBackgroundThe patient-centered medical home (PCMH) is an accepted framework for delivering high-quality primary care, prompting many residencies to transform their practices into PCMHs. Few studies have assessed the impact of these changes on residents' and faculty members' PCMH attitudes, knowledge, and skills. The family medicine program at Brown University achieved Level 3 PCMH accreditation in 2010, with training relying primarily on situated learning through immersion in PCMH practice, supplemented by didactics and a few focused clinical activities.ObjectiveTo assess PCMH knowledge and attitudes after Level 3 PCMH accreditation and to identify additional educational needs.MethodsWe used a qualitative approach, with semistructured, individual interviews with 12 of the program's 13 postgraduate year 3 residents and 17 of 19 core faculty. Questions assessed PCMH knowledge, attitudes, and preparedness for practicing, teaching, and leading within a PCMH. Interviews were analyzed using the immersion/crystallization method.ResultsResidents and faculty generally had positive attitudes toward PCMH. However, many expressed concerns that they lacked specific PCMH knowledge, and felt inadequately prepared to implement PCMH principles into their future practice or teaching. Some exceptions were faculty and resident leaders who were actively involved in the PCMH transformation. Barriers included lack of time and central roles in PCMH activities.ConclusionsPracticing in a certified PCMH training program, with passive PCMH roles and supplemental didactics, appears inadequate in preparing residents and faculty for practice or teaching in a PCMH. Purposeful curricular design and evaluation, with faculty development, may be needed to prepare the future leaders of primary care.
Understanding the Interview and Ranking Behaviors of Unmatched International Medical Students and Graduates in the 2013 Main Residency Match
Authors: Liang Mei , Curtin Laurie S. , Signer Mona M. , Savoia Maria C. 
Published: October 2015

ABSTRACT

Background
Over the past decade, the number of unfilled positions in the National Resident Matching Program (NRMP) Main Residency Match has declined by one-third, while the number of unmatched applicants has grown by more than 50%, largely due to a rise in the number of international medical school students and graduates (IMGs). Although only half of IMG participants historically have matched to a first-year position, the Match experiences of unmatched IMGs have not been studied.

Objective
We examined differences in interview and ranking behaviors between matched and unmatched IMGs participating in the 2013 Match and explored strategic errors made by unmatched IMGs when creating rank order lists.

Methods
Rank order lists of IMGs who failed to match were analyzed in conjunction with their United States Medical Licensing Examination (USMLE) Step 1 scores and responses on the 2013 NRMP Applicant Survey. IMGs were categorized as “strong,” “solid,” “marginal,” or “weak” based on the perceived competitiveness of their USMLE Step 1 scores compared to other IMG applicants who matched in the same specialty. We examined ranking preferences and strategies by Match outcome.

Results
Most unmatched IMGs were categorized as “marginal” or “weak”. However, unmatched IMGs who were non-US citizens presented more competitive USMLE Step 1 scores compared to unmatched IMGs who were US citizens. Unmatched IMGs were more likely than matched IMGs to rank programs at which they did not interview and to rank programs based on their perceived likelihood of matching.

Conclusions
The interview and ranking behaviors of IMGs can have far-reaching consequences on their Match experience and outcomes.
Consensus on Graduate Medical Education Financing: An Analysis of Stakeholder Responses to the House Energy and Commerce Committee's Open Letter
Authors: Harwood Jared L. 
Published: October 2015

ABSTRACT

Background
In December 2014, the Energy and Commerce Committee of the US House of Representatives sent an open letter requesting interested parties to respond to 7 questions on graduate medical education (GME). More than 100 organizations and individuals responded.

Methods
An online search for responses yielded 27 organizations that had published their responses to the committee's open letter. Responses included answers to the 7 questions and additional recommendations. The 27 respondents proposed a total of 80 unique interventions. Each intervention was screened for concordance with those from other organizations, and then categorized as supportive, in opposition, or making no mention. Data were entered into a spreadsheet and rank ordered on the frequency of support.

Results
At the top of the rankings were several interventions with significant support from many respondents.

Conclusions
Given the broader GME constituency represented by the 27 stakeholders in this analysis, the 80 proposed interventions represent a comprehensive inventory of the extant ideas regarding the financing, governance, and oversight of GME. This objective analysis could help both spur productive discussions and form the foundation for a larger public policy deliberation of GME financing.
Role of parents as a protective factor against adolescent athletes’ doping susceptibility
Authors: Blank C , Leichtfried V , Müller D , Schobersberger W 
Published: October 2015

Background. Although literature on sports psychology outlines parental influence in various areas, research has not focused on its potential in the framework of doping.Objective. To assess whether parents’ knowledge about doping effects, and their behaviour and beliefs might act as a protecting factor for Austrian junior (14 - 18 years) elite athletes’ doping susceptibility (DS).Methods. Questionnaires were distributed to 1 818 student athletes and their parents. As well as collecting sociodemographic data, information about current sports activity levels and the former sports careers of parents, the following categories were included: (i) knowledge about effects of doping; (ii) parental behaviour; (iii) parental beliefs about athletes’ skills to become a professional athlete; and (iv) DS.Results. In total 527 data sets were entered for analysis. Current state of knowledge was significantly different between mothers (0.72 (0.2)) and fathers (0.76 (0.2)) (p=0.003). Next to situational variables, only fathers’ behaviour, which was moderated by fathers’ beliefs, was a significant predictor of athletes’ DS.Conclusion. Fathers have the potential of acting as a protective factor for DS in athletes, but only if their level of belief is moderate. Doping prevention strategies should include parents, but need to be careful on the role they are planning to fulfil, with an emphasis on soft skills (e.g. communication). Future research might include variables from sports psychology such as motivational climate, goal orientation and belief in success as possible mediators of the influence of parents on their adolescent children in the sport setting.
Method of preparing emergency medicine residents for giving legal depositions
Authors: Hughes Mary J , Teitelbaum Howard , Clark Michael R , Omondi Paul , Palmer Charles A , Sutton Ron 
Published: October 2015

Abstract
This study was performed to determine if a simulated legal deposition increases emergency medicine (EM) residents' knowledge, self-confidence, and understanding of a legal deposition. This prospective study included a convenience sample of EM 1-3 residents. A knowledge and a self-assessment pretest weregiven, followed by a didactic session moderated by local attorneys, followed by knowledge and a self-assessment posttest. The total time involved was 2 hours. The mean score on the knowledge pretest was 4.5 and 5.25 on the posttest. Using a paried t-test, the authors found this difference to be statistically signifi:cant. (P < 0.01) Using HoteUing's T2 test, the authors compared presimulation and postsimulation self-assessment questions. The results r~vealed that there was a difference between these scores (P < 0.001). Participants in the deposition significantly improved their self-assessment ranking and knowledge inventory test scores by participating in a simulated legal deposition.
Urticaria and angioedema: Diagnostic and treatment considerations
Authors: Kumar Shashi Am , Martin Bryan L 
Published: October 2015

Abstract
Urticaria and angioedema are common-and commonly frustrating-problems for physicians and patients alike. Patients often are in considerable distress with pruritus and uncomfortable lesions. They are frightened about their condition and frustrated when modem medicine cannot pinpoint the cause of the symptoms. Both urticaria and angioedema may be categorized as acute and chronic conditions. The dividing line between acute and chronic forms is relatively arbitrarily set at 6 weeks. A thorough history and physical examination may provide clues to the underlying cause, but in the majority of patients, the cause is rarely identified. One is more likely to discover the cause of acute than of chronic urticaria. A multitude of laboratory tests can be performed, but they often do not provide a diagnosis. It is not appropriate to do a large "screening" battery oflaboratory tests. The dermal mast cells and their mediators playa central role in chronic urticaria. Chronic urticaria may have an autoimmune aspect. Recent evidence reveals that 50% of patients with chronic urticaria have a cutaneous autoimmune disorder mediated by autoantibodies to the high-affinity IgE receptor on mast cells. Biopsy may be necessary and may help with treatment.
Contact dermatitis: Evaluation and treatment
Authors: Martin Bruce G 
Published: October 2015

Abstract
Contact dermatitis is a common condition that can be categorized as irritant dermatitis and allergic contact dermatitis. Although each of these conditions may have a similar presentation, allergic contact dermatitis is immunologically mediated, whereas irritant contact dermatitis is not. Contact dermatitis can be acute, subacute, or chronic, and each of these phases may progress into the next. Almost anysubstance may induce a cutaneous reaction, depending on its concentration, the duration of contact, and the condition of the contacted skin. It is estimated that there are more than 6 million chemicals in the environment; approximately 3000 are potential sensitizers. A careful history may identify the responsible agent. If the contactant is identified and eliminated, the contact dermatitis can be a self-limited,mild condition. H the exposure is not discontinued, a cycle of itching, scratching, and skin disruption occurs, which leads to chronic changes in the skin. The history of presentation, including occupational exposures, and distribution of the rash are important in identifying the offending agent. More severe cases may require more extensive evaluation, possibly including patch testing, to determine the offending agent. This article reviews treatment, including antihistamines, topical and oral steroids, physical measures such as cold water compresses, and the treatment of secondary infection.
Use of Adeno‐Associated and Herpes Simplex Viral Vectors for In Vivo Neuronal Expression in Mice
Authors: Penrod Rachel D. , Wells Audrey M. , Carlezon William A. , Cowan Christopher W. 
Published: October 2015

AbstractAdeno‐associated viruses and the herpes simplex virus are the two most widely used vectors for the in vivo expression of exogenous genes. Advances in the development of these vectors have enabled remarkable temporal and spatial control of gene expression. This unit provides methods for storing, delivering, and verifying expression of adeno‐associated and herpes simplex viruses in the adult mouse brain. It also describes important considerations for experiments using in vivo expression of these viral vectors, including serotype and promoter selection, as well as timing of expression. Additional protocols are provided that describe methods for preliminary experiments to determine the appropriate conditions for in vivo delivery. © 2015 by John Wiley & Sons, Inc.
Transcriptome‐Wide Identification of Pseudouridine Modifications Using Pseudo‐seq
Authors: Carlile Thomas M. , Rojas‐Duran Maria F. , Gilbert Wendy V. 
Published: October 2015

AbstractA diverse array of post‐transcriptional modifications is found in RNA molecules from all domains of life. While the locations of RNA modifications are well characterized in abundant noncoding RNAs, modified sites in less abundant mRNAs are just beginning to be discovered. Recent work has revealed hundreds of previously unknown and dynamically regulated pseudouridines (Ψ) in mRNAs from diverse organisms. This unit describes Pseudo‐seq, an efficient, high‐resolution method for identification of Ψs genome‐wide. This unit includes methods for isolation of RNA from S. cerevisiae, preparation of Pseudo‐seq libraries from RNA samples, and identification of sites of pseudouridylation from the sequencing data. Pseudo‐seq is applicable to any organism or cell type, facilitating rapid identification of novel pseudouridylation events. © 2015 by John Wiley & Sons, Inc.
Laser Microdissection–Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA
Authors: Chandran Divya , Scanlon Michael J. , Ohtsu Kazuhiro , Timmermans Marja C.P. , Schnable Patrick S. , Wildermuth Mary C. 
Published: October 2015

AbstractLaser microdissection of cells allows for isolation of specific cells of interest for downstream analyses including transcriptional profiling. Plant cells present unique challenges for laser microdissection due to their cellulosic cell walls and large vacuoles. Here we present protocols for plant tissue preparation, laser microdissection of select plant cells, and linear amplification of RNA from dissected cells. Linear amplification of RNA from dissected cells allows sufficient RNA for subsequent quantitative analysis by RT‐PCR, microarray, or RNA sequencing. © 2015 by John Wiley & Sons, Inc.
Genome Editing in Human Cells Using CRISPR/Cas Nucleases
Authors: Wyvekens Nicolas , Tsai Shengdar Q. , Joung J. Keith 
Published: October 2015

AbstractThe clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated (Cas) system has been broadly adopted for highly efficient genome editing in a variety of model organisms and human cell types. Unlike previous genome editing technologies such as zinc finger nucleases (ZFNs) and transcription activator−like effector nucleases (TALENs), CRISPR/Cas technology does not require complex protein engineering and can be utilized by any researcher proficient in basic molecular biology and cell culture techniques. This unit describes protocols for design and cloning of vectors expressing single or multiplex gRNAs, for transient transfection of human cell lines, and for quantitation of mutation frequencies by T7 endonuclease I assay. These protocols also include guidance for using two improvements that increase the specificity of CRISPR/Cas nucleases: truncated gRNAs and dimeric RNA‐guided FokI nucleases. © 2015 by John Wiley & Sons, Inc.
A high‐order numerical study of reactive dissolution in an upwelling heterogeneous mantle: 2. Effect of shear deformation
Authors: Baltzell Conroy , Parmentier E. M. , Liang Yan , Tirupathi Seshu 
Published: October 2015

AbstractHigh‐porosity dunite channels produced by orthopyroxene dissolution may provide pathways for orthopyroxene‐undersaturated melt generated in the deep mantle to reach shallower depth without extensive chemical reequilibration with surrounding mantle. Previous studies have considered these high‐porosity channels and melt localization in the presence of a uniform upwelling mantle flow through the process of melt‐rock reaction as well as shear deformation, but not both simultaneously. In this Part 2 of a numerical study of high‐porosity melt and dunite channel formation during reactive dissolution, we considered the effect of shear deformation on channel distribution and channel geometry in an upwelling and viscously compacting mantle column. We formulated a high‐order numerical experiment using conditions similar to those in Part 1, but with an additional prescribed horizontal shearing component in the solid matrix, as could be present in flowing mantle beneath spreading centers. Our focus was to examine orthopyroxene dissolution to determine the behavior of dunite formation and its interaction with melt flow field, by varying the upwelling and shear rate, orthopyroxene solubility gradient, and domain height. Introduction of shearing tilts the developing dunite, causing asymmetry in the orthopyroxene gradient between the dunite channels and the surrounding harzburgite. The downwind gradient is sharp, nearly discontinuous, whereas the upwind gradient is more gradual. For higher shear rates, a wave‐like pattern of alternating high and low‐porosity bands form on the downwind side of the channel. The band spacing increases with increasing shear rate, relative melt flow rate, and orthopyroxene solubility gradient, whereas the band angle is independent of solubility gradient and increases with increasing shear rate and decreasing relative melt flow rate. Such features could be observable in the field and provide evidence for mantle shearing. Standing wave‐like patterns of melt fraction also develop on the downwind side with possible implications for the interpretation of seismic velocities in upwelling mantle.
Southern Bay of Bengal currents and salinity intrusions during the northeast monsoon
Authors: Wijesekera H. W. , Jensen T. G. , Jarosz E. , Teague W. J. , Metzger E. J. , Wang D. W. , Jinadasa S. U. P. , Arulananthan K. , Centurioni L. R. , Fernando H. J. S. 
Published: October 2015

AbstractShipboard velocity and hydrographic profiles collected in December 2013 along with drifter observations, satellite altimetry, global ocean nowcast/forecast products, and coupled model simulations were used to examine the circulation in the southern Bay of Bengal as part of ongoing international research efforts in the region. The observations captured the southward flowing East India Coastal Current (EICC) off southeast India and east of Sri Lanka. The EICC was approximately 100 km wide, with speeds exceeding 1 m s−1 in the upper 75 m. East of the EICC, a subsurface‐intensified 300 km‐wide, northward current was observed, with maximum speeds as high as 1 m s−1 between 50 m and 75 m. The EICC moved low‐salinity water out of the bay and the subsurface northward flow carried high‐salinity water into the bay during typical northeast monsoon conditions during a time period when the central equatorial Indian Ocean was experiencing a westerly wind burst related to the Madden‐Julian Oscillation (MJO) event. While the northward subsurface high‐salinity flow has previously been observed during the southwest monsoon, it was observed during the northeast monsoon. The observations are consistent with northward high‐salinity subsurface flow in numerical model solutions. The analysis suggests that direct forcing along the equator may play a significant role for high‐salinity intrusions east of Sri Lanka.