bluuebunny/crossref_metadata_2025_split huggingface dataset:
The star formation rates of active galactic nuclei host galaxies
Authors: Ellison Sara L. , Teimoorinia Hossen , Rosario David J. , Mendel J. Trevor 
Published: February 2016

Abstract
Using artificial neural network predictions of total infrared luminosities (LIR), we compare the host galaxy star formation rates (SFRs) of ∼21 000 optically selected active galactic nuclei (AGN), 466 low-excitation radio galaxies (LERGs) and 721 mid-IR-selected AGN. SFR offsets (ΔSFR) relative to a sample of star-forming ‘main-sequence’ galaxies (matched in M⋆, z and local environment) are computed for the AGN hosts. Optically selected AGN exhibit a wide range of ΔSFR, with a distribution skewed to low SFRs and a median ΔSFR = −0.06 dex. The LERGs have SFRs that are shifted to even lower values with a median ΔSFR = −0.5 dex. In contrast, mid-IR-selected AGN have, on average, SFRs enhanced by a factor of ∼1.5. We interpret the different distributions of ΔSFR amongst the different AGN classes in the context of the relative contribution of triggering by galaxy mergers. Whereas the LERGs are predominantly fuelled through low accretion rate secular processes which are not accompanied by enhancements in SFR, mergers, which can simultaneously boost SFRs, most frequently lead to powerful, obscured AGN.
Wealth, Health, and Child Development: Evidence from Administrative Data on Swedish Lottery Players *
Authors: Cesarini David , Lindqvist Erik , Östling Robert , Wallace Björn 
Published: February 2016

AbstractWe use administrative data on Swedish lottery players to estimate the causal impact of substantial wealth shocks on players’ own health and their children’s health and developmental outcomes. Our estimation sample is large, virtually free of attrition, and allows us to control for the factors conditional on which the prizes were randomly assigned. In adults, we find no evidence that wealth impacts mortality or health care utilization, with the possible exception of a small reduction in the consumption of mental health drugs. Our estimates allow us to rule out effects on 10-year mortality one sixth as large as the cross-sectional wealth-mortality gradient. In our intergenerational analyses, we find that wealth increases children’s health care utilization in the years following the lottery and may also reduce obesity risk. The effects on most other child outcomes, including drug consumption, scholastic performance, and skills, can usually be bounded to a tight interval around zero. Overall, our findings suggest that in affluent countries with extensive social safety nets, causal effects of wealth are not a major source of the wealth-mortality gradients, nor of the observed relationships between child developmental outcomes and household income.
Value of Gamma‐Glutamyl Transpeptidase for Diagnosis of Biliary Atresia by Correlation With Age
Authors: Chen Xiaoli , Dong Rui , Shen Zhen , Yan Weili , Zheng Shan 
Published: February 2016

ABSTRACTObjectives:The aim of the study was to analyze the value of gamma‐glutamyl transpeptidase (GGT) for distinguishing biliary atresia (BA) from non‐BA for patients suspected of having neonatal obstructive jaundice by correlation with age.Methods:From January 2003 to March 2014, cholangiography and/or surgical exploration were undertaken in 1469 patients with suspicion of having neonatal obstructive jaundice. A total of 1338 patients were diagnosed with BA intraoperatively. Preoperative medical records were compared between BA and non‐BA patients.Results:Preoperative levels of total bilirubin, direct bilirubin, and GGT were significantly higher in the BA group (P < 0.05), whereas the non‐BA group had higher alkaline phosphatase levels (P = 0.0003). The area under the receiver operating characteristic curve of total bilirubin, direct bilirubin, GGT, and alkaline phosphatase was 0.584, 0.614, 0.843, and 0.398, respectively. In all age groups (i: 31–60 days; ii: 61–90 days; iii: 91–120 days; iv: ≥121 days), BA groups had higher GGT levels (in IU/L) (i: 725.3 ± 549.9; ii: 927.0 ± 679.8; iii: 1114.3 ± 823.1; iv: 767.5 ± 666.7). The level of GGT in patients with BA younger than 30 days was 834.2 ± 475.3 IU/L. GGT levels had the highest diagnostic value (0.869) in group ii (61–90 days) and the lowest diagnosis value (0.712) in group iv (≥121 days). At a cutoff of >303 IU/L in group ii (61–90 days), GGT had 82.8% sensitivity and 81.6% specificity for the discrimination of BA.Conclusions:GGT levels contribute to the diagnosis of BA before 120 days. Age must be considered if using GGT levels as a diagnostic test for BA.
Analysis of References on the Plastic Surgery In-Service Training Exam
Authors: Silvestre Jason , Zhang Alicia , Lin Samuel J. 
Published: February 2016

Background:
The Plastic Surgery In-Service Training Exam is a knowledge assessment tool widely used during plastic surgery training in the United States. This study analyzed literature supporting correct answer choices to determine highest yield sources, journal publication lag, and journal impact factors.

Methods:
Digital syllabi of 10 consecutive Plastic Surgery In-Service Training Exam administrations (2006 to 2015) were reviewed. The most-referenced articles, journals, and textbooks were determined. Mean journal impact factor and publication lag were calculated and differences were elucidated by section.

Results:
Two thousand questions and 5386 references were analyzed. From 2006 to 2015, the percentage of journal citations increased, whereas textbook references decreased (p < 0.001). Plastic and Reconstructive Surgery was cited with greatest frequency (38.5 percent), followed by Clinics in Plastic Surgery (5.6 percent), Journal of Hand Surgery (American volume) (5.1 percent), and Annals of Plastic Surgery (3.8 percent). There was a trend toward less publication lag over the study period (p = 0.05), with a mean publication lag of 9.1 ± 9.0 years for all journal articles. Mean journal impact factor was 2.3 ± 4.3 and lowest for the hand and lower extremity section (1.7 ± 2.8; p < 0.001). The highest yield textbooks were elucidated by section.

Conclusion:
Plastic surgery faculty and residents may use these data to facilitate knowledge acquisition during residency.
Evolving Concepts of Keystone Perforator Island Flaps (KPIF): Principles of Perforator Anatomy, Design Modifications, and Extended Clinical Applications
Authors: Mohan Anita T. , Rammos Charalambos K. , Akhavan Arya A. , Martinez Jorys , Wu Peter S. , Moran Steven L. , Sim Franklin H. , Behan Felix , Mardini Samir , Saint-Cyr Michel 
Published: February 2016

Background:
Keystone flaps have demonstrated growing clinical applications in reconstructive surgery in the past decade. This article highlights flap modifications and their versatility for clinical applications and management of complex defects.

Methods:
A retrospective chart review was conducted of consecutive patients undergoing keystone flap reconstruction at the authors’ institution from January of 2012 to December of 2014. Patient demographics, indications, and operative and postoperative details were abstracted.

Results:
Forty-two keystone flaps were performed in 36 patients. Indications included malignant melanoma (n = 14), soft-tissue sarcoma (n = 12), benign pathologic conditions (e.g., exposed hardware, enterocutaneous fistula, tissue necrosis) (n = 6), and nonmelanoma skin cancer (n = 4). Twenty-eight percent received neoadjuvant irradiation, and 70 percent of these were for sarcoma. Locoregional adjunct flaps were performed in eight patients. The deep fascia was nearly completely in a circumferential manner in 18 of 36 patients (50 percent), in 92 percent of the sarcoma reconstructions, and located mainly in the lower extremity. Average defect size was 215 cm2 (range, 4 to 1000 cm2). Average defect size was 474 cm2 and 35.8 cm2 after sarcoma and malignant melanoma resection, respectively. Average flap size was 344 cm2 (range, 5 to 1350 cm2). Ninety percent of cases had flap sizes exceeding the traditional 1:1 ratio. There was no flap loss or partial necrosis. Mean time to mobilization was 1.8 days, and mean hospital length of stay was 6.8 days.

Conclusions:
Keystone flaps offer an excellent versatile tool for reconstructive surgeons. Fundamental principles behind the vascular basis of the keystone flap and its modifications permit their greater utility in complex wounds in the settings of large oncologic resections, irradiation, and trauma.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Human Factors and Quality Improvement in the Emergency Department: Reducing Potential Errors in Blood Collection
Authors: Bashkin Osnat , Caspi Sigalit , Swissa Assaf , Amedi Amitai , Zornano Shai , Stalnikowicz Ruth 
Published: February 2016

Objectives
Adverse events in blood collection procedures such as mismatched or unlabeled samples may have critical implications on patient safety (such as wrong diagnosis and treatments). The current study examined blood collection procedures in an emergency department before and after the application of a human factors approach for improving performance quality and preventing adverse events.

Methods
In the emergency department of a community care hospital, 190 blood collection events were observed in 2 phases: preintervention and postintervention. Two quality measures were tested as follows: quality measure 1, performing all 7 stages in the procedure of blood collection according to protocol, and quality measure 2, performing the stages of the procedure in the correct sequence according to the protocol. In addition, medical staff anonymously answered questionnaires about their procedure for collecting blood.

Results
Analyses of data collected before the intervention revealed only 2 events in which all 7 stages in the protocol of the procedure were performed and only 1 event in which the 7 stages of the procedure were performed in the correct sequence. In 91% of the events, the patient was not fully identified. Based on these findings, we developed an intervention using a human factors approach to improve the quality of performance. Analyses of data collected after the intervention revealed significant differences (t188 = −14.9, ρ < 0.01) in quality measure 1 before (mean [SD], 4.8 [0.6]) and after (mean [SD], 6.4 [0.8]) the intervention was initiated, which implies improvement on efficiency subsequent to the implementation of the intervention. Improvement also appeared in quality measure 2.

Conclusions
This study illustrates the nature of potential errors in blood collection performance, offering a proactive approach to improve the rate of proper performance.
Diffusion Tensor Imaging of Lumbar Nerve Roots
Authors: Manoliu Andrei , Ho Michael , Nanz Daniel , Piccirelli Marco , Dappa Evelyn , Klarhöfer Markus , Del Grande Filippo , Kuhn Felix Pierre 
Published: February 2016

Objectives
The aim of this study was to compare the quality of recently emerged advanced diffusion tensor imaging (DTI) techniques with conventional single-shot echo-planar imaging (EPI) in a functional assessment of lumbar nerve roots.

Materials and Methods
The institutional review board approved the study including 12 healthy volunteers. Diffusion tensor imaging was performed at 3 T (MAGNETOM Skyra; Siemens Healthcare) with b-values of 0 and 700 s/mm2 and an isotropic spatial resolution for subsequent multiplanar reformatting. The nerve roots L2 to S1 were imaged in coronal orientation with readout-segmented EPI (rs-DTI) and selective-excitation EPI (sTX-DTI) with an acquisition time of 5 minutes each, and in axial orientation with single-shot EPI (ss-DTI) with an acquisition time of 12 minutes (scan parameters as in recent literature). Two independent readers qualitatively and quantitatively assessed image quality.

Results
The interobserver reliability ranged from “substantial” to “almost perfect” for all examined parameter and all 3 sequences (κ = 0.70–0.94). Overall image quality was rated higher, and artifact levels were scored lower for rs-DTI and sTX-DTI than for ss-DTI (P = 0.007–0.027), while fractional anisotropy and signal-to-noise ratio values were similar for all sequences (P ≥ 0.306 and P ≥ 0.100, respectively). Contrast-to-noise ratios were significantly higher for rs-DTI and ss-DTI than for sTX-DTI (P = 0.004–0.013).

Conclusions
Despite shorter acquisition times, rs-DTI and sTX-DTI produced images of higher quality with smaller geometrical distortions than the current standard of reference, ss-DTI. Thus, DTI acquisitions in the coronal plane, requiring fewer slices for full coverage of exiting nerve roots, may allow for functional neurography in scan times suitable for routine clinical practice.
Single Breath-Hold T1ρ-Mapping of the Heart for Endogenous Assessment of Myocardial Fibrosis
Authors: van Oorschot Joep W.M. , Visser Fredy , Eikendal Anouk L.M. , Vonken Evert-jan P.A. , Luijten Peter R. , Chamuleau Steven A.J. , Leiner Tim , Zwanenburg Jaco J.M. 
Published: February 2016

ObjectivesIn this study, we propose a method to acquire high spatial-resolution T1ρ-maps, which allows bright and black-blood imaging, in a single breath-hold. To validate this innovative method, the reproducibility was tested in phantoms and volunteers. Lastly, the sensitivity and specificity for infarct detection was compared with the criterion standard late gadolinium enhancement (LGE).MethodsT1ρ-mapping was performed using a T1ρ-prepared balanced steady-state free precession sequence at 1.5 T and 3 T. Five images with increasing spin-lock preparation times (spin-lock = 0, 10, 20, 30, 40 milliseconds, amplitude = 500 Hz) were acquired with an interval of 3 beats. Black-blood imaging was performed using a double inversion pulse sequence. The method was tested in 2 times 10 healthy volunteers at 1.5 and 3 T and in 9 myocardial infarction patients at 1.5 T. T1ρ-maps, and LGE images were scored for presence and extent of myocardial scarring.ResultsPhantom results show that the proposed T1ρ-mapping method gives accurate T1ρ-values. The mean T1ρ-relaxation time of the myocardium in healthy controls was 52.8 ± 1.8 milliseconds at 1.5 T and 46.4 ± 1.8 milliseconds at 3 T. In patients, the T1ρof infarcted myocardium was (82.4 ± 5.2 milliseconds), and the T1ρof remote myocardium was (54.2 ± 2.8 milliseconds;P< 0.0001). Sensitivity of infarct detection on a T1ρ-map was 70%, with a specificity of 94%, compared with LGE.ConclusionsIn this study, we have investigated a method to acquire high spatial-resolution T1ρ-maps of the heart in a single breath-hold. This method proved to be reproducible and had high specificity compared with LGE and can thus be used for the endogenous detection of myocardial fibrosis in patients with ischemic cardiomyopathy.
Succinct Colored de Bruijn Graphs
Authors: Belk Keith , Boucher Christina , Bowe Alexander , Gagie Travis , Morley Paul , Muggli Martin D. , Noyes Noelle R. , Puglisi Simon J. , Raymond Rober 
Published: February 2016

AbstractIqbal et al. (Nature Genetics, 2012) introduced thecolored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at “detecting and genotyping simple and complex genetic variants in an individual or population”. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which require additional information to be succinctly encoded as well as support for non-standard traversal operations. Our data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.
Local joint testing improves power and identifies missing heritability in association studies
Authors: Brown Brielin C. , Price Alkes L. , Patsopoulos Nikolaos A. , Zaitlen Noah 
Published: February 2016

AbstractThere is mounting evidence that complex human phenotypes are highly polygenic, with many loci harboring multiple causal variants, yet most genetic association studies examine each SNP in isolation. While this has lead to the discovery of thousands of disease associations, discovered variants account for only a small fraction of disease heritability. Alternative multi-SNP methods have been proposed, but issues such as multiple testing correction, sensitivity to genotyping error, and optimization for the underlying genetic architectures remain. Here we describe a local joint testing procedure, complete with multiple testing correction, that leverages a genetic phenomenon we call linkage masking wherein linkage disequilibrium between SNPs hides their signal under standard association methods. We show that local joint testing on the original Wellcome Trust Case Control Consortium dataset leads to the discovery of 29% more associated loci that were later found in followup studies containing thousands of additional individuals. These loci double the heritability explained by genome-wide significant associations in the WTCCC dataset, implicating linkage masking as a novel source of missing heritability. Furthermore, we show that local joint testing in acis-eQTL study of the gEUVADIS dataset increases the number of genes discovered by 10.7% over marginal analyses. Our multiple hypothesis correction and joint testing framework are available in a python software package calledjester, available atgithub.com/brielin/Jester.
A Family of Interaction-Adjusted Indices of Community Similarity
Authors: Benedikt Schmidt Thomas Sebastian , Matias Rodrigues João Frederico , von Mering Christian 
Published: February 2016

AbstractInteractions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assess the performance of two specific indices which areTaxa INteraction-Adjusted(TINA, based on taxa co-occurrence networks), andPhylogenetic INteraction-Adjusted(PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity.
Exploiting single-cell quantitative data to map genetic variants having probabilistic effects
Authors: Chuffart Florent , Richard Magali , Jost Daniel , Duplus-Bottin Hélène , Ohya Yoshikazu , Yvert Gaël 
Published: February 2016

ABSTRACTDespite the recent progress in sequencing technologies, genome-wide association studies (GWAS) remain limited by a statistical-power issue: many polymorphisms contribute little to common trait variation and therefore escape detection. The small contribution sometimes corresponds to incomplete penetrance, which may result from probabilistic effects on molecular regulations. In such cases, genetic mapping may benefit from the wealth of data produced by single-cell technologies. We present here the development of a novel genetic mapping method that allows to scan genomes for single-cell Probabilistic Trait Loci that modify the statistical properties of cellular-level quantitative traits. Phenotypic values are acquired on thousands of individual cells, and genetic association is obtained from a multivariate analysis of a matrix of Kantorovich distances. No prior assumption is required on the mode of action of the genetic loci involved and, by exploiting all single-cell values, the method can reveal non-deterministic effects. Using both simulations and yeast experimental datasets, we show that it can detect linkages that are missed by classical genetic mapping. A probabilistic effect of a single SNP on cell shape was detected and validated. The method also detected a novel locus associated with elevated gene expression noise of the yeast galactose regulon. Our results illustrate how single-cell technologies can be exploited to improve the genetic dissection of certain common traits.AUTHOR SUMMARYGenetic association studies are usually conducted on phenotypes measured at the scale of whole tissues or individuals, and not at the scale of individual cells. However, some common traits, such as cancer, can result from a minority of cells that adopted a special behavior. From one individual to another, DNA variants can modify the frequency of such cellular behaviors. The body of one of the individuals then harbours more misbehaving cells and is therefore predisposed to a macroscopic phenotypic change, such as disease. Such genetic effects are probabilistic, they contribute little to trait variation at the macroscopic level and therefore largely escape detection in classical studies. We have developed a novel statistical method that uses single-cell measurements to detect variants of the genome that have non-deterministic effects on cellular traits. The approach is based on a comparison of distributions of single-cell traits. We applied it to colonies of yeast cells and showed that it can detect mutations that change cellular morphology or molecular regulations in a probabilistic manner. This opens the way to study multicellular organisms from a novel angle, by exploiting single-cell technologies to detect genetic variants that predispose to certain diseases or common traits.
Conserved gene clusters in the scrambled plastomes of IRLC legumes (Fabaceae: Trifolieae and Fabeae)
Authors: Sveinsson Saemundur , Cronk Quentin 
Published: February 2016

SummaryThe plastid genome retains several features from its cyanobacterial-like ancestor, one being the co-transcriptional organization of genes into operon-like structures. Some plastid operons have been identified but undoubtedly many more remain undiscovered. Here we utilize the highly variable plastome structure that exists within certain legumes of the inverted repeat lost clade (IRLC) to find conserved gene clusters. These plastomes exhibit an unusually high frequency of translocations and inversions. We analysed the plastomes of 23 legume species and identified 32 locally collinear blocks (LCBs), which are regions within the plastid genomes that occur in different orientation and/or order among the plastid genomes but are themselves free from internal rearrangements. Several represent gene clusters that have previously been recognized as plastid operons. It appears that the number of LCBs has reached saturation in our data set, suggesting that these LCBs are not random, but likely represent legume plastid operons protected from internal rearrangement by functional constraint. Some of the LCBs we identify, such aspsbD/C/Z, are previously known plastid operons. Others, such asrpl32-ndhF-psbA-matK-rbcL-atpB-atpE, may represent novel polycistronic operons in legumes.