bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer vision cracks the leaf code
Authors: Wilf Peter , Zhang Shengping , Chikkerur Sharat , Little Stefan A. , Wing Scott L. , Serre Thomas 
Published: March 2016

SignificanceThe botanical value of angiosperm leaf shape and venation (“leaf architecture”) is well known, but the astounding complexity and variation of leaves have thwarted efforts to access this underused resource. This challenge is central for paleobotany because most angiosperm fossils are isolated, unidentified leaves. We here demonstrate that a computer vision algorithm trained on several thousand images of diverse cleared leaves successfully learns leaf-architectural features, then categorizes novel specimens into natural botanical groups above the species level. The system also produces heat maps to display the locations of numerous novel, informative leaf characters in a visually intuitive way. With assistance from computer vision, the systematic and paleobotanical value of leaves is ready to increase significantly.
Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system
Authors: Elharar Yifat , Roth Ziv , Hecht Nir , Rotkopf Ron , Khalaila Isam , Gur Eyal 
Published: March 2016

Significance
This work describes how a basic regulatory challenge, namely the balancing of two opposing activities of a single enzyme while coordinating these actions with the activity of another enzyme, is addressed in a biological system. In the Pup-proteasome system, the bacterial parallel of the ubiquitin-proteasome system, Pup modification by Dop (deamidase of Pup) is a prerequisite for pupylation by proteasome accessory factor A. Paradoxically, Dop also reverses pupylation through its ability to depupylate substrates. We show that this challenge is resolved posttranslationally by combining substrate discrimination based on molecular weight, and by regulating enzyme levels in response to external stimuli. These findings provide an example of how directionality and coordination of enzyme activities in a single pathway are regulated according to physiological requirements of the cell.
Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses
Authors: Neher Richard A. , Bedford Trevor , Daniels Rodney S. , Russell Colin A. , Shraiman Boris I. 
Published: March 2016

Significance
Humans mount an antibody-mediated immune response against influenza viruses that can be recalled. Nevertheless, individuals can suffer from recurrent influenza infections as viruses can change their antigenic properties by altering their surface glycoproteins. This antigenic evolution requires frequent update of seasonal influenza vaccines. To inform vaccine updates, laboratories that contribute to the World Health Organization Global Influenza Surveillance and Response System assess the antigenic phenotypes of circulating viruses. Based on the relationship of antigenic distance to genetic differences between viruses, we developed a model to interpret measured antigenic data and predict the properties of viruses that have not been characterized antigenically and explore the model’s value in predicting the future composition of influenza virus populations.
EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression
Authors: Lee Nara , Yario Therese A. , Gao Jessica S. , Steitz Joan A. 
Published: March 2016

Significance
In recent years, next-generation sequencing has facilitated the discovery of thousands of nonprotein-coding RNAs (ncRNAs). Some of these ncRNAs have been shown to interact with transcription regulators and may thus form a new class of ncRNAs that function in controlling gene expression. Identifying proteins that interact with this class of ncRNAs will be instrumental in elucidating their poorly understood molecular mode of action. The ncRNA EBV-encoded RNA 2 (EBER2) expressed by the oncogenic Epstein–Barr virus interacts with the cellular transcription factor paired box protein 5 (PAX5) to impact viral gene expression. In this study, we identified additional functionally important protein components of the EBER2–PAX5 complex. Our findings pave the way for investigating whether other transcription-regulating ncRNAs use the same protein components to exert their function.
Estimating Riverwide Abundance of Juvenile Fish Populations: How Much Sampling is Enough?
Authors: Korman Josh , Schick Jody , Mossop Brent 
Published: March 2016

Abstract
Estimating riverwide abundance of juvenile fish populations is challenging because detection probability is typically low and juveniles can be patchily distributed over large areas. We used a hierarchical Bayesian model to estimate the abundance of juvenile steelhead Oncorhynchus mykiss in two rivers in British Columbia over 3 years based on a multigear, two-phase sampling design. These estimates were used to drive a simulation model to evaluate how the precision of abundance estimates varied with the number of single-pass index and mark–recapture sites that were sampled, the proportion of shoreline sampled, and the mean and variation of detection probability and fish density across sites. The extent of variation in fish densities across index sites was the most important factor influencing the precision of river-wide abundance estimates, and increasing the number of index sites was the best approach to reduce variability in abundance estimates. River size, which controls the proportion of habitat sampled for a given level of sampling effort, had a moderate effect on precision, but only when the extent of site-to-site variation in fish density was high. Factors affecting detection probability, such as the number of mark–recapture sites, the mean detection probability, or the extent of variation in detection probability across sites, had much less influence on precision of abundance estimates unless the proportion of river sampled was high. Hierarchical Bayesian models are no substitute for collecting informative data, but they improve our understanding of variance structure, which is critical for providing realistic estimates of uncertainty and designing informative and efficient sampling programs.
Received July 16, 2015; accepted October 7, 2015 Published online March 8, 2016
Impacts of Northern Pike on Stocked Rainbow Trout in Pactola Reservoir, South Dakota
Authors: Scheibel Natalie C. , Dembkowski Daniel J. , Davis Jacob L. , Chipps Steven R. 
Published: March 2016

Abstract
Establishment of nonnative Northern Pike Esox lucius in Pactola Reservoir, South Dakota, has prompted concern among biologists about the influence of this species on the lake's intensively managed salmonid fisheries. Ancedotal information suggests that catch rates of Rainbow Trout Oncorhynchus mykiss have declined while mean size and abundance of Northern Pike has increased, although quantitative information on diet and growth of the Northern Pike population is lacking. To address potential interactions between Northern Pike and Rainbow Trout, we assessed size-dependent predation by Northern Pike on Rainbow Trout and determined the relative energetic contribution of stocked Rainbow Trout to Northern Pike growth using bioenergetics modeling. Stable isotopes combined with traditional diet analyses revealed that smaller Northern Pike (&lt;600 mm TL) consumed primarily centrarchids and Rainbow Smelt Osmerus mordax, and Rainbow Trout contributed less than 10% to their annual energy consumption. In contrast, larger Northern Pike (≥600 mm TL) consumed primarily Rainbow Trout, which accounted for 56% of their annual energy consumption. Combining estimates of Northern Pike predation with production costs of catchable-size Rainbow Trout revealed that annual economic losses ranged from US$15,259 to $24,801 per year. Over its lifespan, an age-10 Northern Pike was estimated to consume ~117 Rainbow Trout worth approximately $340. Thus, Northern Pike predation substantially influences salmonid management initiatives and is likely a primary factor contributing to reduced Rainbow Trout abundance and return to anglers in Pactola Reservoir. Strategies for reducing Northern Pike predation on Rainbow Trout include increasing the size of stocked fish or altering the timing and spatial distribution of stocking events.
Received June 5, 2015; accepted November 2, 2015 Published online March 8, 2016
Remote ischaemic preconditioning shortens QT intervals during exercise in healthy subjects
Authors: Caru Maxime , Lalonde François , Gravel Hugo , Daigle Chantal , Tournoux François , Jacquemet Vincent , Curnier Daniel 
Published: March 2016

AbstractThe protective action of remote ischaemic preconditioning (RIPC) has been demonstrated in the context of surgical interventions in cardiology. Application of RIPC to sports performance has been proposed, but its effect on the electrocardiogram (ECG) during exercise remains unknown. This exploratory study aims to measure the changes in ventricular repolarization observed during exercise following RIPC in healthy subjects. In an experimental randomized crossover study, 17 subjects underwent two bouts of constant load exercise tests at 75% and 115% of gas exchange threshold (GET). Prior to exercise, they were allocated to either control or RIPC intervention with four cycles of 5 min of ischaemia followed by 5 min of reperfusion. ECG was continuously recorded during the protocol. QT and RR intervals were measured every 30 s (on an average tracing of the preceding 10 s). Although the time course of RR intervals did not differ between the two interventions (p = .56 at 75% GET and p = .74 at 115% GET), a significant shortening of QT intervals (measured from Q onset to T end) was observed during exercise (mean ± standard deviation of RIPC vs. control: −32 ± 19 ms at 75% GET (p < .001) and −34 ± 12 ms at 115% GET (p < .001)) as well as during recovery (−21 ± 8 ms at 75% GET (p < .001) and −16 ± 11 ms at 115% GET (p < .001)). This effect was not present at rest. These RIPC‐related changes were clearly identifiable on the QT–RR loops after hysteresis reduction. RIPC therefore induces heart rate‐independent shortening of QT intervals that is revealed during exercise.
A treatment-planning comparison of three beam arrangement strategies for stereotactic body radiation therapy for centrally located lung tumors using volumetric-modulated arc therapy
Authors: Ishii Kentaro , Okada Wataru , Ogino Ryo , Kubo Kazuki , Kishimoto Shun , Nakahara Ryuta , Kawamorita Ryu , Ishii Yoshie , Tada Takuhito , Nakajima Toshifumi 
Published: March 2016

Abstract
The purpose of this study was to determine appropriate beam arrangement for volumetric-modulated arc therapy (VMAT)-based stereotactic body radiation therapy (SBRT) in the treatment of patients with centrally located lung tumors. Fifteen consecutive patients with centrally located lung tumors treated at our institution were enrolled. For each patient, three VMAT plans were generated using two coplanar partial arcs (CP VMAT), two non-coplanar partial arcs (NCP VMAT), and one coplanar full arc (Full VMAT). All plans were designed to deliver 70 Gy in 10 fractions. Target coverage and sparing of organs at risk (OARs) were compared across techniques. PTV coverage was almost identical for all approaches. The whole lung V 10Gy was significantly lower with CP VMAT plans than with NCP VMAT plans, whereas no significant differences in the mean lung dose, V 5Gy , V 20Gy or V 40Gy were observed. Full VMAT increased mean contralateral lung V 5Gy by 12.57% and 9.15% when compared with NCP VMAT and CP VMAT, respectively. Although NCP VMAT plans best achieved the dose–volume constraints for mediastinal OARs, the absolute differences in dose were small when compared with CP VMAT. These results suggest that partial-arc VMAT may be preferable to minimize unnecessary exposure to the contralateral lung, and use of NCP VMAT should be considered when the dose–volume constraints are not achieved by CP VMAT.
Tobacco Smoking Is Not Associated With Accelerated Liver Disease in Human Immunodeficiency Virus-Hepatitis C Coinfection: A Longitudinal Cohort Analysis
Authors: Costiniuk Cecilia T. , Brunet Laurence , Rollet-Kurhajec Kathleen C. , Cooper Curtis L. , Walmsley Sharon L. , Gill M. John , Martel-Laferriere Valérie , Klein Marina B. 
Published: March 2016

Abstract
Background.  Tobacco smoking has been shown to be an independent risk factor for liver fibrosis in hepatitis C virus (HCV) infection in some cross-sectional studies. No longitudinal study has confirmed this relationship, and the effect of tobacco exposure on liver fibrosis in human immunodeficiency virus (HIV)-HCV coinfected individuals is unknown.
Methods.  The study population consisted of participants from the Canadian Co-infection Cohort study (CTN 222), a multicenter longitudinal study of HIV-HCV coinfected individuals from 2003 to 2014. Data were analyzed for all participants who did not have significant fibrosis or end-stage liver disease (ESLD) at baseline. The association between time-updated tobacco exposure (ever vs nonsmokers and pack-years) and progression to significant liver fibrosis (defined as an aspartate-to-platelet ratio index [APRI] ≥1.5) or ESLD was assessed by pooled logistic regression.
Results.  Of 1072 participants included in the study, 978 (91%) had ever smoked, 817 (76%) were current smokers, and 161 (15%) were previous smokers. Tobacco exposure was not associated with accelerated progression to significant liver fibrosis nor with ESLD when comparing ever vs never smokers (odds ratio [OR] = 1.06, 95% confidence interval [CI], 0.43–1.69 and OR = 1.20, 95% CI, 0.21–2.18, respectively) or increases in pack-years smoked (OR = 1.05, 95% CI, 0.97–1.14 and OR = 0.94, 95% CI, 0.83–1.05, respectively). Both time-updated alcohol use in the previous 6 months and presence of detectable HCV ribonucleic acid were associated with APRI score ≥1.5.
Conclusions.  Tobacco exposure does not appear to be associated with accelerated progression of liver disease in this prospective study of HIV-HCV coinfected individuals.
Cell-Based Therapies for Lumbar Discogenic Low Back Pain
Authors: Wu Tao , Song Hai-xin , Dong Yan , Li Jian-hua 
Published: March 2016

Study Design.
A systematic review and single-arm meta-analysis of clinical trials.

Objective.
To assess the efficacy of mesenchymal stem cells or chondrocyte in patients with discogenic low back pain.

Summary of Background Data.
There is no previous review evaluated the efficacy of mesenchymal stem cell or chondrocyte therapy in adults with discogenic low back pain.

Methods.
A comprehensive literature search was conducted on PubMed, Ovid MEDLINE, Ovid EMBASE, EBSCO, and Web of Science from database inception through on September 10th, 2015. We included clinical trials that evaluated stem cells or chondrocyte-based therapy in patients with discogenic back pain. The primary outcomes of interest were pain score and Oswestry Disability Index (ODI). We performed random-effects model meta-analyses to assess net changes in the same outcome variables. Heterogeneity between studies was estimated by I
2 statistic.

Results.
The initial search identified 1393 articles, of which 6 studies were eligible for this review. The pooled mean difference in pain score from baseline to follow-up points was 44.2 points decreased (95% CI: −61.8 to −26.5, P < 0.001, I
2 = 99.4%). Meanwhile, the pooled mean difference in ODI from baseline to follow-up points was 32.2 points decreased (95% CI: −41.6 to −22.9, P < 0.001, I
2 = 99.5%). No related adverse effects were reported by the included studies.

Conclusion.
Cell-based therapy is for patients who have discogenic low back pain associated with improved pain relief and ODI. More stringently designed randomized double-blind clinical trials with appropriately determined sample sizes will be needed to confirm its clinical efficacy and safety.

Level of Evidence: 4
Venous thromboembolism and cardiovascular disease complications in menopausal women using transdermal versus oral estrogen therapy
Authors: Simon James A. , Laliberté François , Duh Mei Sheng , Pilon Dominic , Kahler Kristijan H. , Nyirady Judit , Davis Pamela J. , Lefebvre Patrick 
Published: March 2016

Abstract

Objective:
To evaluate the risk of venous thromboembolism (VTE) and cardiovascular disease (CVD) complications, and assess healthcare costs in menopausal women using an estradiol transdermal system versus oral estrogen therapy (ET).

Methods:
Health insurance claims from 60 self-insured US companies from 1999 to 2011 were analyzed. Women at least 50 years of age, newly initiated on transdermal or oral ET, were included. Cohorts were matched 1:1 based on exact factors and propensity score-matching methods. The incidence rate ratios (IRRs) of CVD complications, as well as VTE and other CVD events separately, were assessed through conditional Poisson models. Cohorts were also compared for healthcare costs using linear regression models to assess per-patient per-month cost differences. Confidence intervals (CIs) and P values were determined using a nonparametric method for cost outcomes.

Results:
From each cohort, 2,551 users were matched to form the study population. A total of 274 transdermal ET users developed CVD complications compared with 316 women in the oral ET cohort (adjusted IRR 0.81; 95% CI, 0.67-0.99). Transdermal ET users also incurred lower adjusted all-cause and VTE/CVD-related healthcare costs relative to oral ET users (all-cause per-patient per-month cost difference [95% CI] = $41 [−34; 137], P = 0.342).

Conclusions:
This large matched-cohort study based on real-world data suggests that women receiving transdermal ET have significantly lower incidences of CVD events compared with those receiving oral ET, and that they also incur lower healthcare costs.
COAGULASE-NEGATIVE STAPHYLOCOCCUS-INDUCED FROSTED BRANCH ANGIITIS AFTER INTRAVITREAL ANTI–VASCULAR ENDOTHELIAL GROWTH FACTOR INJECTION
Authors: Gensure Rebekah H. , Hsu Jason , Federman Jay , Park Carl , Spirn Marc J. 
Published: March 2016

Purpose:
To describe a case of frosted branch angiitis after intravitreal ranibizumab injection.

Methods:
Retrospective chart review.

Results:
A patient with a history of neovascular age-related macular degeneration underwent intravitreal ranibizumab injection and subsequently developed coagulase-negative Staphylococcus endophthalmitis with findings of frosted branch angiitis.

Conclusion:
Endophthalmitis presenting as frosted branch angiitis is a rare complication after intravitreal anti–vascular endothelial growth factor injection. Early recognition is critical to optimize outcomes. To our knowledge, this is the second reported case of frosted branch angiitis as a presentation of endophthalmitis with coagulase-negative Staphylococcus.
Effectiveness of hepatitis B rapid tests toward linkage-to-care: results of a randomized, multicenter study
Authors: Bottero Julie , Boyd Anders , Gozlan Joël , Carrat Fabrice , Lemoine Maud , Rougier Hayette , Varsat Brigitte , Boo Nicolas , Charlois-Ou Cécile , Collignon Anne , Cha Olivier , Campa Pauline , Dhotte Philippe , Girard Pierre-Marie , Lacombe Karine 
Published: March 2016

Objectives
Worldwide, many infected individuals are unaware of their hepatitis B virus (HBV) status. We evaluated the effectiveness of HBV rapid testing in promoting linkage-to-care.

Methods
In 2012, volunteers were recruited from five Parisian centers. Participants were randomized 1 : 1 to receive standard serology (S) or rapid testing (VIKIA-HBsAg/Quick Profile anti-HBsAb) with confirmatory serology (R+S). The primary endpoint was percentage of individuals with appropriate linkage-to-care (nonimmunized individuals starting vaccination or HBsAg-positive individuals receiving medical evaluation). The secondary outcomes were percentage receiving HBV-test results and performance of HBV rapid tests.

Results
In total, 995 individuals were screened. Among the HBV-infection groups included in the primary endpoint (n=409), 20 (4.9%) received appropriate linkage-to-care, with no difference between S and R+S groups (5.7 vs. 4.1%, P=0.5). Two of eight HBsAg-positive participants had a medical visit (1/6 and 1/2 in the S and R+S groups, respectively) and 18/401 (4.5%) nonimmunized participants initiated HBV-vaccination (11/205 and 7/196). Factors that tended to be associated with linkage-to-care were female sex, birth country of high HBV prevalence, and extended medical stay. Test results were not obtained in 4.7% of participants, which was significantly higher in the S arm (P=0.02). Both sensitivity and specificity were 100% for the VIKIA-HBsAg rapid test and 94.4 and 80.8%, respectively, for the anti-HBsAb Quick Profile rapid test.

Conclusion
Despite a higher proportion of participants obtaining their results in the R+S arm and better performance of anti-HBsAb rapid tests than described previously, we found no evidence that HBV screening based initially on rapid tests leads to increased HBV-vaccination rates or medical evaluation. This strategy should be evaluated in more hard-to-reach populations.
Endovascular treatment of symptomatic Budd–Chiari syndrome – in favour of early transjugular intrahepatic portosystemic shunt
Authors: Rosenqvist Kerstin , Sheikhi Reza , Eriksson Lars-Gunnar , Rajani Rupesh , Rorsman Fredrik , Sangfelt Per , Nyman Rickard 
Published: March 2016

Introduction
Treatment of Budd–Chiari syndrome (BCS) has shifted from mainly medical treatment, with surgical shunt and orthotopic liver transplantation (OLT) as rescue, to medical treatment combined with an early endovascular intervention in the past two decades.

Purpose
To assess the safety and efficiency of endovascular treatment of symptomatic patients with BCS and to compare mortality with symptomatic BCS patients in the same region treated with only sporadic endovascular techniques.

Methods
This was a retrospective review of clinical data, treatment and survival in 14 patients diagnosed with BCS and treated with endovascular methods from 2003 to 2015. A national epidemiology study of BCS from 1986 to 2003 was used for comparison.

Results
Thirteen of the 14 patients eventually had transjugular intrahepatic portosystemic shunt (TIPS), four after previous liver vein angioplasty. TIPS were performed with polytetrafluoroethylene-covered stents and technical success was 100%. Calculated preinterventional prognostic indices indicated a high risk of TIPS dysfunction, OLT and death. However, only one patient died and one had an OLT, and the 1- and 2-year primary TIPS-patency was 85 and 67%, respectively. Episodes of de-novo hepatic encephalopathy occurred in three patients. Overall 1- and 5-year transplantation-free survival was 100 and 93% compared with 47 and 28%, respectively, in 1986 to 2003.

Conclusion
TIPS seems to be a safe and effective treatment for symptomatic BCS and there is an obvious improvement in transplantation-free survival compared with conservatory medical treatment. It should, therefore, be considered early, as first-line intervention, in patients with insufficient response to medical treatment.