bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agricultural Landscape and Pesticide Effects on Honey Bee (Hymenoptera: Apidae) Biological Traits
Authors: Alburaki Mohamed , Steckel Sandra J. , Williams Matthew T. , Skinner John A. , Tarpy David R. , Meikle William G. , Adamczyk John , Stewart Scott D. 
Published: March 2017

AbstractSixteen honey bee (Apis mellifera L.) colonies were placed in four different agricultural landscapes to study the effects of agricultural landscape and exposure to pesticides on honey bee health. Colonies were located in three different agricultural areas with varying levels of agricultural intensity (AG areas) and one nonagricultural area (NAG area). Colonies were monitored for their performance and productivity for one year by measuring colony weight changes, brood production, and colony thermoregulation. Palynological and chemical analyses were conducted on the trapped pollen collected from each colony and location. Our results indicate that the landscape’s composition significantly affected honey bee colony performance and development. Colony weight and brood production were significantly greater in AG areas compared to the NAG area. Better colony thermoregulation in AG areas’ colonies was also observed. The quantities of pesticides measured in the trapped pollen were relatively low compared to their acute toxicity. Unexplained queen and colony losses were recorded in the AG areas, while colony losses because of starvation were observed in the NAG area. Our results indicate that landscape with high urban activity enhances honey bee brood production, with no significant effects on colony weight gain. Our study indicates that agricultural crops provide a valuable resource for honey bee colonies, but there is a trade-off with an increased risk of exposure to pesticides.
Entrustment Decisions: Bringing the Patient Into the Assessment Equation
Authors: ten Cate Olle 
Published: March 2017

With the increased interest in the use of entrustable professional activities (EPAs) in undergraduate medical education (UME) and graduate medical education (GME) come questions about the implications for assessment. Entrustment assessment combines the evaluation of learners’ knowledge, skills, and behaviors with the evaluation of their readiness to be entrusted to perform critical patient care responsibilities. Patient safety, then, should be an explicit component of educational assessments. The validity of these assessments in the clinical workplace becomes the validity of the entrustment decisions.
Modern definitions of the validity of educational assessments stress the importance of the purpose of the test and the consequences of the learner’s score. Thus, if the learner is a trainee in a clinical workplace and entrusting her or him to perform an EPA is the focus of the assessment, the validity argument for that assessment should include a patient safety component.
While the decision to allow a learner to practice unsupervised is typically geared toward GME, similar decisions are made in UME regarding learners’ readiness to perform EPAs with indirect supervision (i.e., without a supervisor present in the room). Three articles in this issue address implementing EPAs in UME.
The author of this Commentary discusses the possibility of implementing true entrustment decisions in UME. He argues that bringing the patient into the educational assessment equation is marrying educational and health care responsibilities. Building trust in learners from early on, gradually throughout the continuum of medical education, may reframe our vision on assessment in the workplace.
Prospective Randomized Clinical Trial Investigating the Effect of the Reamer-Irrigator-Aspirator on the Volume of Embolic Load and Respiratory Function During Intramedullary Nailing of Femoral Shaft Fractures
Authors: Hall Jeremy A. , McKee Michael D. , Vicente Milena R. , Morison Zachary A. , Dehghan Niloofar , Schemitsch Christine E. , Kreder Hans J. , Petrisor Brad , Schemitsch Emil H. 
Published: March 2017

Objectives:
We sought to determine whether the use of the Reamer-Irrigator-Aspirator (RIA) device resulted in a decreased amount of fat emboli compared with standard reaming (SR) when performing intramedullary (IM) nailing of femoral shaft fractures.

Design:
Prospective randomized clinical trial.

Setting:
Multi-centered trial, level I trauma centers.

Patients/Participants:
All eligible patients who presented to participating institutions with an isolated femoral shaft fracture amenable to fixation with antegrade IM nailing. Thirty-one patients were enrolled: nine were excluded because of technical difficulties with the transesophageal echocardiogram (TEE) recording. Therefore, the study comprised 22 patients: 11 patients randomized to the SR group and eleven patients randomized to the RIA group.

Intervention:
Antegrade IM nailing of a femoral shaft fracture with standard reamers or the RIA device. All patients were monitored intraoperatively with a continuous TEE to assess embolic events in the right atrium. A radial arterial line was used to monitor blood gases and potential systemic effects of emboli.

Main Outcome Measure:
Duration, size, and severity of emboli as measured by TEE. The operative procedure was divided into 6 distinct stages: preoperative, reduction, guidewire passage, reaming, nail insertion, and postoperative.

Results:
There was no significant difference in emboli between the RIA and SR groups preoperatively, during fracture reduction, guidewire insertion, or postoperatively. Measured with a standardized scoring system, there was a modest reduction in total emboli score in the RIA group during reaming (SR 5.30 [SD; 1.81] vs. RIA 4.05 [SD; 2.19], P = 0.005) and during nail insertion (SR 5.09 [SD; 1.74] vs. RIA 4.25 [SD; 1.89], P = 0.03). We were unable to correlate this reduction with any improvement in physiologic parameters (mean arterial pressure, end-tidal CO2, O2 saturation, pH, paO2, and paCO2).

Conclusions:
This study showed a modest reduction of embolic debris during the reaming and nail insertion segments of the operative procedure. We were unable to correlate this with any change in physiologic parameters.

Level of Evidence:
Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
The Trauma Collaborative Care Study (TCCS)
Authors: Wegener Stephen T. , Pollak Andrew N. , Frey Katherine P. , Hymes Robert A. , Archer Kristin R. , Jones Clifford B. , Seymour Rachel B. , O'Toole Robert V. , Castillo Renan C. , Huang Yanjie , Scharfstein Daniel O. , MacKenzie Ellen J. ,   METRC
Published: March 2017

Summary:
Previous research suggests that the care provided to trauma patients could be improved by including early screening and management of emotional distress and psychological comorbidity. The Trauma Collaborative Care (TCC) program, which is based on the principles of well-established models of collaborative care, was designed to address this gap in trauma center care. This article describes the TCC program and the design of a multicenter study to evaluate its effectiveness for improving patient outcomes after major, high-energy orthopaedic trauma at level 1 trauma centers. The TCC program was evaluated by comparing outcomes of patients treated at 6 intervention sites (n = 481) with 6 trauma centers where care was delivered as usual (control sites, n = 419). Compared with standard treatment alone, it is hypothesized that access to the TCC program plus standard treatment will result in lower rates of poor patient-reported function, depression, and posttraumatic stress disorder.
Physeal and Subphyseal Distraction Osteogenesis in Atrophic-type Congenital Pseudarthrosis of the Tibia: Efficacy and Safety
Authors: Jang Woo Young , Choi Yoon Hyo , Park Moon Seok , Yoo Won Joon , Cho Tae-Joon , Choi In Ho 
Published: March 2017

Purpose:
To examine the efficacy, safety, and clinical outcomes of distraction osteogenesis through the physis (PDO) or through subphyseal osteotomy (SPDO) in patients with atrophic-type congenital pseudarthrosis of tibia with proximal tibial dysplasia.

Methods:
To validate the efficacy and safety of PDO and SPDO, radiographic and clinical parameters were compared between 5 patients who underwent proximal tibial metaphyseal or metadiaphyseal lengthening as a control (group 1) and 7 patients who underwent PDO or SPDO (group 2). Postoperative complication was also compared between the groups.

Results:
A significant difference in terms of healing index (group 1, 83.3±24.7 d/cm; group 2, 35.0±11.1 d/cm; P=0.001) and percentage increase (11.0%±3.7% vs. 23.1%±10.5%, P=0.034) was observed between the 2 groups. According to the Paley classification, group 1 included 1 “problems” case and 3 “obstacles” cases, whereas group 2 included 2 “problems” cases and 1 “obstacles” case. According to the Lascombes classification, group 1 included 2 grade IIIb cases and 3 grade IV cases, whereas group 2 included 6 grade I cases and 1 grade IIa case. Severe complications were significantly higher in group 1 compared with the group 2 (P=0.007).

Conclusions:
This study demonstrated that PDO or SPDO can be effectively and safely performed for tibial lengthening in atrophic-type congenital pseudarthrosis of tibia patients with proximal tibial dysplasia.

Level of Evidence:
Level III.
TWENTY-FIVE–GAUGE PARS PLANA VITRECTOMY IN COMPLEX RETINAL DETACHMENTS ASSOCIATED WITH GIANT RETINAL TEAR
Authors: Kumar Vinod , Kumawat Devesh , Bhari Anju , Chandra Parijat 
Published: March 2017

Purpose:
To study the structural and functional outcomes of 25-gauge pars plana vitrectomy in giant retinal tear–associated retinal detachments.

Methods:
Seventeen eyes of 17 patients with giant retinal tear, who underwent 25-gauge pars plana vitrectomy over a period of 15 months at a tertiary eye care center by a single surgeon, were recruited in this retrospective interventional study.

Results:
Giant retinal tears were mostly traumatic (35.3%) or associated with myopia (35.3%) and occurred in young (mean age 25.7 years) males (94.1%). Most eyes had best-corrected visual acuity ≤20/1,200 (in 82.3%), foveal detachment (in 88.2%), and proliferative vitreoretinopathy ≤Grade B (in 82.3%). The giant retinal tear extent was more than 180° in 29.4% and the fellow eye was involved in 35.2% of eyes. All eyes underwent 25-gauge pars plana vitrectomy with encircling band in 41.1%, perfluorocarbon liquid use in 82.3%, and endotamponade with sulphur hexafluoride (23.6%) or silicone oil (76.4%). At mean follow-up of 10.2 months, reattachment rate was 88.2%. Only 35.2% of eyes achieved final visual acuity ≥20/80 with a cause of poor vision being cataract, secondary glaucoma, macular pucker, and corneal edema.

Conclusion:
Twenty-five–gauge pars plana vitrectomy can achieve excellent attachment rates in eyes with giant retinal tear–associated retinal detachment. It can be as efficient as larger-gauge vitrectomy, at the same time retaining all advantages of smaller-gauge surgery.
Comparison of the Effects of Quetiapine XR and Lithium Monotherapy on Actigraphy-Measured Circadian Parameters in Patients With Bipolar II Depression
Authors: Hwang Jeong Yeon , Choi Jae-Won , Kang Seung-Gul , Hwang Su Hwan , Kim Seog Ju , Lee Yu Jin 
Published: March 2017

Abstract

Purpose/Background
The aim of this study was to evaluate the effects of quetiapine XR and lithium on actigraphy-measured circadian parameters in patients with bipolar II depression.

Methods/Procedures
This was an 8-week, open-label, prospective, randomized comparative study. The assessments included the 17-item Hamilton Depression Rating Scale score and actigraphic measures concerning the previous 7 days, collected at each visit (weeks 0 [baseline], 1, 2, 4, 6, and 8); the actigraphic data were analyzed with a cosinor analysis.

Findings/Results
Medication, time, and the interaction between medication and time were significantly associated with acrophase for the entire group (Ps = 0.003, 0.020, and 0.042, respectively). More specifically, acrophase was significantly delayed at weeks 1 and 6 (Ps = 0.004 and 0.039, respectively) in the quetiapine XR group. The F statistics significantly increased over time for the entire group (P < 0.001), and there was a significant increase in F statistics on weeks 4 and 6 in the quetiapine XR group (Ps = 0.016 and 0.020, respectively) and on weeks 4 and 8 in the lithium group (Ps = 0.001 and 0.016, respectively). In addition, scores on the 17-item Hamilton Depression Rating Scale were significantly associated with the F statistics during 8 weeks for the entire group (P = 0.008).

Implications/Conclusions
Both quetiapine XR and lithium affected several circadian parameters, including peak activity time and robustness of circadian rhythm, but exerted different effects on acrophase in patients with bipolar II depression. In particular, clinical depressive symptoms were associated with robustness of circadian rhythm during the course of the 8-week treatment.
The Normal Adult Human Internal Auditory Canal: A Volumetric Multidetector Computed Tomography Study
Authors: Essbaiheen Fahad , Hegazi Tarek , Rosenbloom Lorne 
Published: March 2017

Objective:
The purpose of this study was to demonstrate that volumetric analysis of multidetector computed tomography (CT) images can be used to calculate the volume of the adult human internal auditory canal (IAC) reproducibly, and to describe the range of normal IAC volumes in the adult population with subgroup analysis of sex, age, and laterality.

Background:
Previous studies of the IAC have typically used measurements in two dimensions or by using casts of cadavers to measure IAC volumes. This study is the first to report the normal ranges of IAC volumes measured by CT.

Methods:
Two hundred eighty-one CT scans were assessed. Of the CT scans that met the inclusion criteria, a software package was used to manually contour the IACs in each subject to calculate the volumes in cubic millimeters. Subgroup analysis of laterality, sex, and age was evaluated. Interobserver agreement was calculated for the first 59 patients (118 canals).

Results:
Two hundred fifty-nine scans (518 canals) met the inclusion criteria. The volumes ranged from 74 to 502 mm3, with no statistically significant difference between left and right (p value = 0.69). In males, the range of volumes measured 74 to 502 mm3 while in females it ranged from 78 to 416 mm3. Males had larger IAC volumes than females (Wilcoxon rank-sum test: S = 14,845.0, p value = 0.01 on the right, and S = 14,646, p value = 0.004 on the left). No correlation was found with age (Spearman: −0.10, p value = 0.09 on the right and −0.04, p value = 0.50 on the left). Excellent interobserver agreement was found.

Conclusion:
IAC volumes of normal adult subjects, measured by CT, were larger in males and not significantly different with respect to age or laterality.
Incidence of Low Seroimmunity to Hepatitis B Virus in Children With Inflammatory Bowel Disease
Authors: Watts Abhishek , Bennett William E. , Molleston Jean P. , Gupta Sandeep K. , Croffie Joseph M. , Waseem Shamaila , McFerron Brian A. , Steiner Steven J. , Kumar Sanjay , Vanderpool Charles P. , Hon Emily C. , Bozic Molly A. , Subbarao Girish C. , Pfefferkorn Marian D. 
Published: March 2017

ABSTRACTObjectives:Patients with inflammatory bowel disease (IBD) often receive immunosuppressive therapy, which may make them vulnerable to infections such as hepatitis B. We hypothesized that hepatitis B virus titers are low in the vaccinated pediatric population with IBD. The aims of our study were to identify the incidence of lower titers of hepatitis B surface antibody (HBsAb) and determine which patient factors may be associated with lower HBsAb titers.Methods:Patients with diagnosis of IBD, ages 5 to 18 years, were prospectively enrolled. Patients were confirmed to have had a full series of hepatitis B vaccination. Quantitative serum HBsAb titers were measured and logistic regression analysis with independent variables of age, sex, race, disease phenotype, surgery, medications and a dependent variable of adequate HBsAb titers (> 10 mIU/mL) was performed.Results:Of the 116 patients enrolled, 57 were boys and 59 were girls. 75 patients had a diagnosis of Crohn disease; 32 had a diagnosis of ulcerative colitis; and 9 patients had been diagnosed as having indeterminate colitis. At the time of the study, 15 patients were taking corticosteroid, 66 on an immunomodulator, and 53 on a biologic. Sixty percent of patients in the 5‐ to 10‐year age group had protective titers versus 22% to 27% in the older groups, P = 0.04. Only 28% of the 116 patients had HBsAb titers of >10m IU/mL. Twenty percent of the patients taking corticosteroids, 27% taking immunomodulators, and 24% taking biologics were found to be seroimmune.Conclusions:Nearly two‐thirds of pediatric patients with IBD have low titers against hepatitis B virus. Titers were highest in the younger patients. No patient‐specific variable, such as the use of immunosuppressants, appeared to influence these low titers.
The physical boundaries of public goods cooperation between surface-attached bacterial cells
Authors: Weigert Michael , Kümmerli Rolf 
Published: March 2017

AbstractBacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa. Using single-cell fluorescent microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 μm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections.
Multi-tissue DNA methylation age predictor in mouse
Authors: Stubbs Thomas M. , Bonder Marc Jan , Stark Anne-Katrien , Krueger Felix ,   Clock Team BI Ageing, von Meyenn Ferdinand , Stegle Oliver , Reik Wolf 
Published: March 2017

AbstractBackgroundDNA-methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this ‘epigenetic clock’ is unique to humans or conserved in the more experimentally tractable mouse.ResultsWe have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. Many CpG sites show significant tissue-independent correlations with age and allowed us to develop a multi-tissue predictor of age in the mouse. Our model, which estimates age based on DNA methylation at 329 unique CpG sites, has a median absolute error of 3.33 weeks, and has similar properties to the recently described human epigenetic clock. Using publicly available datasets, we find that the mouse clock is accurate enough to measure effects on biological age, including in the context of interventions. While females and males show no significant differences in predicted DNA methylation age, ovariectomy results in significant age acceleration in females. Furthermore, we identify significant differences in age-acceleration dependent on the lipid content of the offspring diet.ConclusionsHere we identify and characterize an epigenetic predictor of age in mice, the mouse epigenetic clock. This clock will be instrumental for understanding the biology of ageing and will allow modulation of its ticking rate and resetting the clock in vivo to study the impact on biological age.
Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
Authors: Nguyen Quan H. , Lukowski Samuel W. , Chiu Han Sheng , Senabouth Anne , Bruxner Timothy J. C. , Christ Angelika N. , Palpant Nathan J. , Powell Joseph E. 
Published: March 2017

AbstractHeterogeneity of cell states represented in pluripotent cultures have not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method, and through this identified four subpopulations distinguishable on the basis of their pluripotent state including: a core pluripotent population (48.3%), proliferative (47.8%), early-primed for differentiation (2.8%) and late-primed for differentiation (1.1%). For each subpopulation we were able to identify the genes and pathways that define differences in pluripotent cell states. Our method identified four transcriptionally distinct predictor gene sets comprised of 165 unique genes that denote the specific pluripotency states; and using these sets, we developed a multigenic machine learning prediction method to accurately classify single cells into each of the subpopulations. Compared against a set of established pluripotency markers, our method increases prediction accuracy by 10%, specificity by 20%, and explains a substantially larger proportion of deviance (up to 3-fold) from the prediction model. Finally, we developed an innovative method to predict cells transitioning between subpopulations, and support our conclusions with results from two orthogonal pseudotime trajectory methods.
Phandango: an interactive viewer for bacterial population genomics
Authors: Hadfield James , Croucher Nicholas J. , Goater Richard J , Abudahab Khalil , Aanensen David M , Harris Simon R. 
Published: March 2017

ABSTRACTSummaryFully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.AvailabilityPhandango is a web application freely available for use athttps://jameshadfield.github.io/phandangoand includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub athttps://github.com/jameshadfield/phandangoContactjh22@sanger.ac.uk,sh16@sanger.ac.uk