bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distributional Effects of Crop Insurance Subsidies
Authors: Lusk Jayson L. 
Published: February 2016

AbstractThis article investigates the distributional effects of the subsidized crop insurance program in the United States. An equilibrium displacement model is constructed, linking the supply of disaggregate farm commodities with final consumer food demands. Using state‐specific data on farm commodity production, crop insurance payments, food expenditures, and federal tax payments, the welfare effects of the removal of the premium subsidies for crop insurance are calculated for each state in the United States. Results indicate that the removal of the premium subsidy for crop insurance would have resulted in aggregate net economic benefits of $622, $932, and $522 million in 2012, 2013, and 2014, respectively. The deadweight loss amounts to about 9.6%, 14.4%, and 8.0% of the total crop insurance subsides paid to agricultural producers in 2012, 2013, and 2014, respectively. In aggregate, removal of the premium subsidy for crop insurance reduces farm producer surplus and consumer surplus, with taxpayers being the only aggregate beneficiary. The findings reveal that the costs of such farm policies are often hidden from food consumers in the form of a higher tax burden. On a disaggregate level, there is significant variation in effects of removal of the premium subsidy for crop insurance across states. Agricultural producers in several Western states, such as California, Oregon, and Washington, are projected to benefit from the removal of the premium subsides for crop insurance, whereas producers in the Plains States, such as North Dakota, South Dakota, and Kansas, are projected to be the biggest losers.
Insight Into Resistance Phenotypes of Emergent Non 13-valent Pneumococcal Conjugate Vaccine Type Pneumococci Isolated From Invasive Disease After 13-valent Pneumococcal Conjugate Vaccine Implementation in France
Authors: Janoir Claire , Lepoutre Agnès , Gutmann Laurent , Varon Emmanuelle 
Published: February 2016

Abstract
Background.  In 2010, the pneumococcal 13-valent conjugate vaccine (PCV13), containing 6 additional serotypes including the multidrug-resistant 19A, replaced the PCV7 in France. This study aimed at analyzing trends in antibiotic resistance in invasive pneumococcal disease (IPD) isolates in France after PCV13 introduction.
Methods.  A total of 5243 pneumococci isolated from IPD in 2008–2009 (late PCV7 era) and 2011–2012 (PCV13 era) were studied according to their serotype and antibiotic resistance profile. Multilocus sequence typing analysis was performed on strains of the predominant serotypes (12F and 24F) isolated from young children.
Results.  Overall, the prevalence of antibiotic resistance decreased in France (−21.5% for penicillin from 2008–2009 to 2011–2012), mainly driven by the decline of the 19A serotype. Among non-PCV13 serotypes that concomitantly emerged, serotypes 12F, 24F, 15A, and 35B were consistently associated with resistance to 1 or more antibiotics. In children under 2 years, serotypes 15A, 35B, and 24F accounted together for 37.8% and 31.9% of penicillin-nonsusceptible and erythromycin-resistant isolates, respectively. Chloramphenicol and cotrimoxazole resistance were mainly associated with serotypes 12F and 24F, respectively. Genetic analysis showed that although emergence of serotype 12F pneumococci resulted from the expansion of various pre-existing lineages, increase in serotype 24F was related to the clonal expansion of the ST162 penicillin-susceptible cotrimoxazole-resistant lineage.
Conclusions.  We showed that decline of PCV13-related IPD was associated with a decline in antibiotic resistance in France, but that it likely favored the spread of several resistant nonvaccine serotypes. However, antibiotic resistance does not seem to be the only element that may drive this phenomenon.
Educational Value Units: A Mission-Based Approach to Assigning and Monitoring Faculty Teaching Activities in an Academic Medical Department
Authors: Regan Linda , Jung Julianna , Kelen Gabor D. 
Published: February 2016

Problem
Increasing emphasis on revenue generation could jeopardize the fundamental notion of what it means to be faculty. Despite being a core mission, education is often marginalized in academic medical departments, and expectations of faculty effort in this area are often vague. A potential solution is mission-based budgeting (MBB), which refers to the allocation of resources based on core-mission-related priorities.

Approach
From December 2012 to March 2013, the authors developed an educational value unit (EVU) system (using an MBB approach) to assign and monitor teaching activities related to the core departmental educational mission at the Department of Emergency Medicine, Johns Hopkins Medicine. EVUs were based on learner contact time, with one EVU equal to roughly one hour of in-person time with medical students or residents. Core education faculty vetted the proposed system; educational leaders determined the total EVUs needed and assessed the impact of their equitable distribution among faculty; and faculty members selected preferences and were assigned EVU obligations.

Outcomes
For academic year 2013–2014, 5,896 EVUs were distributed among 54 faculty. At the end of the year, complete EVU data were available for 47 faculty. Of these, only 6 failed to complete their assigned EVU obligations. All core teaching activities were covered, and educational efforts were distributed more equitably across faculty.

Next Steps
The system is being refined, with an emphasis on incorporating learner outcome metrics, refining the teaching grid, incorporating failure to meet EVU obligations into yearly faculty evaluations, and disseminating the system to other departments and institutions.
The Ambulatory Diagnostic and Treatment Center: A Unique Model for Educating Medical Trainees and Providing Expedited Care
Authors: Serrao Richard A. , Orlander Jay D. 
Published: February 2016

In this article, the authors reexamine the Ambulatory Diagnostic and Treatment Center (ADTC) model, which uniquely combines the education of trainees with the care of referred patients at one Veterans Affairs medical center. As an ambulatory clinic with an inpatient mind-set, the ADTC uses a series of closely spaced outpatient appointments that are longer than typical ambulatory visits, offering a VIP-level of evaluation with the patient-centered goal of expedited diagnosis and treatment. Faculty triage patients by weighing factors such as urgency, educational value, complexity, and instability of diseases in conjunction with the resources, availability, and appropriateness of other services within the medical center.
The ADTC’s unique focus on the education of trainees in comparison with other clinical rotations is evident in the ratio of learning to patient care. This intensive training environment expects postgraduate year 2 and 3 internal medicine residents and fourth-year medical students to read, reflect, and review literature daily. This mix of education and care delivery is ripe for reexploration in light of recent calls for curriculum reform amidst headlines exposing delays in veterans’ access to care.
A low-volume, high-intensity clinic like the ADTC can augment the clinical services provided by a busy primary care and subspecialty workforce without losing its emphasis on education. Other academic health centers can learn from this model and adapt its structure in settings where accountable care organizations and education meet.
Intraobserver and Interobserver Reliability of the Oberg-Manske-Tonkin (OMT) Classification: Establishing a Registry on Congenital Upper Limb Differences
Authors: Bae Donald S. , Canizares Maria F. , Miller Patricia E. , Roberts Summer , Vuillermin Carley , Wall Lindley B. , Waters Peter M. , Goldfarb Charles A. 
Published: February 2016

Background:
The purpose of this investigation was to determine the reliability of the Oberg-Manske-Tonkin (OMT) classification system applied to patients enrolled in a prospective, multicenter cohort study of congenital upper limb differences. Our hypothesis was that the OMT classification would exhibit high intraobserver and interobserver reliability and thus would be an appropriate tool for the new Congenital Upper Limb Differences registry.

Methods:
Four pediatric hand surgeons independently reviewed the medical records, clinical photographs, and radiographs of 60 randomly selected patients previously enrolled in the Congenital Upper Limb Differences registry. Patient’s information was summarized and shared electronically (PowerPoint). Each rater classified each congenital anomaly according to the OMT classification system. Responses were recorded using a web-based data capture tool (REDCap). Three weeks later, the surgeons repeated the process. Intraobserver reliability for each rater was assessed using Fleiss’ κ. Interobserver reliability was assessed using percent exact agreement (when all 4 raters were in agreement) as well as Fleiss’ κ.

Results:
Using the OMT classification, intraobserver reliability for the 4 pediatric hand surgeons showed almost perfect agreement, with κ values in the range of 0.89 to 0.93. Interobserver reliability demonstrated substantial agreement, with κ value of 0.79 (95% confidence interval, 0.77-0.82) in the first reading and 0.80 (95% confidence interval, 0.77-0.83) in the second reading. The highest possible agreement (κ=1) was seen for the following diagnoses: congenital dislocation of radial head (OMT I.A.2.v), Madelung deformity (I.A.2.vii), radial polydactyly (I.B.2.iii), triphalangeal thumb (I.B.2.iv), Kirner deformity (I.B.4.vi), and osteochondromatosis (3.B.4.i).

Conclusions:
The OMT classification of congenital upper limb differences exhibits substantial to almost perfect intraobserver and interobserver reliability among pediatric hand surgeons at different institutions. The OMT is therefore well-suited for classification of congenital upper limb anomalies in patients enrolled in a multicenter registry.

Level of Evidence:
Level II—diagnostic.
Trajectories and Prognosis of Older Patients Who Have Prolonged Mechanical Ventilation After High-Risk Surgery
Authors: Nabozny Michael J. , Barnato Amber E. , Rathouz Paul J. , Havlena Jeffrey A. , Kind Amy J. , Ehlenbach William J. , Zhao Qianqian , Ronk Katie , Smith Maureen A. , Greenberg Caprice C. , Schwarze Margaret L. 
Published: February 2016

Objectives:
Surgical patients often receive routine postoperative mechanical ventilation with excellent outcomes. However, older patients who receive prolonged mechanical ventilation may have a significantly different long-term trajectory not fully captured in 30-day postoperative metrics. The objective of this study is to describe patterns of mortality and hospitalization for Medicare beneficiaries 66 years old and older who have major surgery with and without prolonged mechanical ventilation.

Design:
Retrospective cohort study.

Setting:
Hospitals throughout the United States.

Patients:
Five percent random national sample of elderly Medicare beneficiaries (age ≥ 66 yr) who underwent 1 of 227 operations previously defined as high risk during an inpatient stay at an acute care hospital between January 1, 2005, and November 30, 2009.

Interventions:
None.

Measurements and Main Results:
We identified 117,917 episodes for older patients who had high-risk surgery; 4% received prolonged mechanical ventilation during the hospitalization. Patients who received prolonged mechanical ventilation had higher 1-year mortality rate than patients who did not have prolonged ventilation (64% [95% CI, 62–65%] vs 17% [95% CI, 16.4–16.9%]). Thirty-day survivors who received prolonged mechanical ventilation had a 1-year mortality rate of 47% (95% CI, 45–48%). Thirty-day survivors who did not receive prolonged ventilation were more likely to be discharged home than patients who received prolonged ventilation 71% versus 10%. Patients who received prolonged ventilation and were not discharged by postoperative day 30 had a substantially increased 1-year mortality (adjusted hazard ratio, 4.39 [95% CI, 3.29–5.85]) compared with patients discharged home by day 30. Hospitalized 30-day survivors who received prolonged mechanical ventilation and died within 6 months of their index procedure spent the majority of their remaining days hospitalized.

Conclusions:
Older patients who require prolonged mechanical ventilation after high-risk surgery and survive 30 days have a significant 1-year risk of mortality and high burdens of treatment. This difficult trajectory should be considered in surgical decision making and has important implications for surgeons, intensivists, and patients.
Sustained Clostridium tertium Bacteremia in a Nonneutropenic Patient
Authors: Nambiar Puja H. , Belden Katherine A. , Roslund Brian , Silibovsky Randi 
Published: February 2016

Abstract
We report a case of sustained Clostridium tertium bacteremia mimicking an endovascular infection in a nonneutropenic patient with metastatic pancreatic neuroendocrine cancer. Clostridium tertium infection has been increasingly recognized in immunocompromised patients. The significance of this organism in nonneutropenic host, however, is unclear. The diagnosis and treatment can be challenging owing to morphology and antibiotic resistance patterns. Newer rapid identification testing with mass spectrometry enables for early diagnosis and treatment. We discuss the clinical significance of C. tertium as an emerging pathogen with review of the literature.
Using Virtual Patients to Teach Empathy
Authors: Foster Adriana , Chaudhary Neelam , Kim Thomas , Waller Jennifer L. , Wong Joyce , Borish Michael , Cordar Andrew , Lok Benjamin , Buckley Peter F. 
Published: February 2016

Introduction
Physician empathy is a complex phenomenon known to improve illness outcomes; however, few tools are available for deliberate practice of empathy. We used a virtual patient (VP) to teach empathic communication to first-year medical students. We then evaluated students’ verbal empathy in a standardized patient (SP) interaction.

Methods
Seventy medical students, randomly assigned to 3 separate study groups, interacted with (1) a control VP portraying depression, (2) a VP with a backstory simulating patient shadowing, or (3) a VP able to give immediate feedback about empathic communication (empathy-feedback VP). Subsequently, the students interviewed an SP portraying a scenario that included opportunities to express empathy. All SP interviews were recorded and transcribed. The study outcomes were (1) the students’ verbal response to the empathic opportunities presented by the SP, as coded by reliable assessors using the Empathic Communication Coding System, and (2) the students’ responses as coded by the SPs, using a communication checklist.

Results
There were no significant differences in student demographics between groups. The students who interacted with the empathy-feedback VP showed higher empathy in the SP interview than did the students in the backstory VP and the control VP groups [mean (SD) empathy scores coded on a 0–6 scale were 2.91 (0.16) vs. 2.20 (0.22) and 2.27 (0.21), respectively). The difference in scores was significant only for the empathy-feedback VP versus the backstory VP group (P = 0.027). The SPs rated the empathy-feedback and the backstory VP groups significantly higher than the control VP group on offering empathic statements (P < 0.0001), appearing warm and caring (P = 0.015), and forming rapport (P = 0.004).

Conclusions
Feedback on empathy in a VP interaction increased students’ empathy in encounters with SPs, as rated by trained assessors, whereas a simulation of patient shadowing did not. Both VP interventions increased students’ empathy as rated by SPs, compared with the control VP group.
Ophthalmological Assessment of OCT and Electrophysiological Changes in Migraine Patients
Authors: Verroiopoulos George V. , Nitoda Eirini , Ladas Ioannis D. , Brouzas Dimitrios , Antonakaki Dimitra , Moschos Marilita M. 
Published: February 2016

Background:
A cross-sectional study to investigate the morphological and functional changes of the visual pathway taking place in patients with migraine.

Methods:
Fifteen patients (14 female, 1 male) diagnosed with migraine with aura and 23 patients (21 female, 2 male) diagnosed with migraine without aura were compared with 20 healthy volunteers (18 female, 2 male). All the participants underwent optical coherence tomography scan, electroretinogram (ERG), visual evoked potentials, and multifocal electroretinogram (mf-ERG) recording.

Results:
Assessing ERG recordings, no significant differences in mean N1-P1 amplitudes were measured among the groups. The mean visual evoked potentials N80-P100 amplitudes were not significantly different among the three groups (one way analysis of variance: P = 0.075, F = 2.718). No significant difference was found in P100 latency times among groups. The mean retinal response density of mf-ERG in ring 1 was higher in healthy individuals compared with migraineurs, with statistical significance (Kruskal–Wallis analysis of variance and Dunn multiple comparisons test; P < 0.001, mean rank difference = −24.857 and P < 0.001, mean rank difference = −20.9, for migraine with aura-control and migraine without aura-control comparisons, respectively). In migraine with aura subjects, retinal nerve fiber layer thickness in superior and inferior quadrants was significantly decreased compared with healthy individuals, whereas in migraine without aura group, only the superior quadrant was significantly thinner compared with the control group.

Conclusions:
Retinal response density in mfERG of all migraineurs was significantly lessened compared with healthy individuals. There was no significant difference in visual evoked potentials N80-P100 amplitudes or P100 latencies among the groups. Moreover, retinal nerve fiber layer thinning observed in patients with migraine compared with control subjects, appeared statistically significant in some quadrants. The authors may be able to defend the retinal blood flow decrease theory in migraine. The results also indicate that several levels of the visual pathway seem to be affected in migraineurs.
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
Authors: Lees John A. , Vehkala Minna , Välimäki Niko , Harris Simon R. , Chewapreecha Claire , Croucher Nicholas J. , Marttinen Pekka , Davies Mark R. , Steer Andrew C. , Tong Stephen Y. C. , Honkela Antti , Parkhill Julian , Bentley Stephen D. , Corander Jukka 
Published: February 2016

AbstractBacterial genomes vary extensively in terms of both gene content and gene sequence – this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogensStreptococcus pneumoniaeandStreptococcus pyogenes, SEER identifies relevant previously characterised resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness ofS. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.
Predicting protein thermal stability changes upon point mutations using statistical potentials: IntroducingHoTMuSiC
Authors: Pucci Fabrizio , Bourgeas Raphael , Rooman Marianne 
Published: February 2016

AbstractThe accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTmupon point mutations, given the protein structure and, when available, the melting temperatureTmof the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTmvalues of 4.2°C that reduces to 2.9°C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use atsoft.dezyme.com.
Bigger Is Fitter? Quantitative Genetic Decomposition of Selection Reveals an Adaptive Evolutionary Decline of Body Mass in a Wild Rodent Population
Authors: Timothée Bonnet , Peter Wandeler , Glauco Camenisch , Erik Postma 
Published: February 2016

AbstractIn natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions: Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called ‘stasis paradox’ highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e. with a lowpotentialadult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non-causal (i.e. non-genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level thereby enabled us to uncover adaptive evolution in action, and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change.