bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum entanglement of angular momentum states with quantum numbers up to 10,010
Authors: Fickler Robert , Campbell Geoff , Buchler Ben , Lam Ping Koy , Zeilinger Anton 
Published: November 2016

Significance
Challenging quantum mechanical predictions is an important task to better understand the underlying principles of nature and possibly develop novel applications. Quantum entanglement as one of the key features is often investigated in optical experiments to push the known limits from smaller to larger scales, for example by increasing the number of entangled systems, their separation, or dimensionality. In the present study we pursue another route and investigate photons with large quantum numbers. We demonstrate entanglement between a photon with orbital angular momentum quantum numbers up to 10,010 and its partner encoded in polarization. The results show how complex the structure of entangled photons can be and hint at the large information content a single quantum system is able to carry.
Quality Information and Procurement Auction Outcomes: Evidence from a Payment for Ecosystem Services Laboratory Experiment
Authors: Conte Marc N. , Griffin Robert M. 
Published: November 2016

AbstractProcuring agencies in conservation auctions typically have more information about the ecosystem service (ES) quality of conservation actions than landowners and can affect auction outcomes by controlling participants’ access to this information. Our induced‐value laboratory auction experiment explores the impact of sellers’ access to ES‐quality information on auction efficiency when the conservation action choice is endogenous to offer formation. We find that providing ES‐quality information allows sellers to identify and submit higher‐quality conservation actions, an effect that counteracts previously identified efficiency losses from information rents.
Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
Authors: Zakrzewski Martha , Proietti Carla , Ellis Jonathan J , Hasan Shihab , Brion Marie-Jo , Berger Bernard , Krause Lutz 
Published: November 2016

Abstract
Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page.

Availability and Implementation
The web-interface is accessible via http://cgenome.net/calypso/. The software is programmed in Java, PERL and R and the source code is available from Zenodo (https://zenodo.org/record/50931). The software is freely available for non-commercial users.

Supplementary information
Supplementary data are available at Bioinformatics online.
RBPPred: predicting RNA-binding proteins from sequence using SVM
Authors: Zhang Xiaoli , Liu Shiyong 
Published: November 2016

AbstractMotivationDetection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computational prediction is much more efficient than experimental methods and may have guiding significance on the experiment design.ResultsIn this study, we present the RBPPred (an RNA-binding protein predictor), a new method based on the support vector machine, to predict whether a protein binds RNAs, based on a comprehensive feature representation. By integrating the physicochemical properties with the evolutionary information of protein sequences, the new approach RBPPred performed much better than state-of-the-art methods. The results show that RBPPred correctly predicted 83% of 2780 RBPs and 96% out of 7093 non-RBPs with MCC of 0.808 using the 10-fold cross validation. Furthermore, we achieved a sensitivity of 84%, specificity of 97% and MCC of 0.788 on the testing set of human proteome. In addition we tested the capability of RBPPred to identify new RBPs, which further confirmed the practicability and predictability of the method.Availability and ImplementationRBPPred program can be accessed at: http://rnabinding.com/RBPPred.html.Supplementary informationSupplementary data are available at Bioinformatics online.
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data
Authors: Panero Riccardo , Rinaldi Antonio , Memoli Domenico , Nassa Giovanni , Ravo Maria , Rizzo Francesca , Tarallo Roberta , Milanesi Luciano , Weisz Alessandro , Giurato Giorgio 
Published: November 2016

Abstract

Summary
The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT (integrative Small RNA Tool-kit), an automated pipeline to analyze smallRNA-Seq data.

Availability and Implementation
iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington’s Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password)

Supplementary information
Supplementary data are available at Bioinformatics online.
Novel Clinical and Pathologic Findings in a Heartland Virus–Associated Death
Authors: Fill Mary-Margaret A. , Compton Margaret L. , McDonald Edward C. , Moncayo Abelardo C. , Dunn John R. , Schaffner William , Bhatnagar Julu , Zaki Sherif R. , Jones Timothy F. , Shieh Wun-Ju 
Published: November 2016

Abstract
We describe an investigation into a Heartland virus (HRTV)–associated death in Tennessee with novel clinical and pathologic findings. HRTV can cause rapidly fatal, widely disseminated infection with multisystem organ failure in patients without substantial comorbidities. We identified viral antigen in multiple organ tissues where it was not detected previously.
The role of geography in sustainable development
Authors: Qiu Jane 
Published: November 2016

Abstract
China has achieved unprecedented economic growth in the past decades. This has had serious consequences on the environment and public health. The Chinese government now realizes that it is not just the quantity, but the quality of development that matters. It has begun to instigate a series of policies to tackle pollution, increase the proportion of clean energy, and redress the balance between urban and rural development—in a coordinated effort to build a harmonious society.
Building a harmonious world was also the theme of the 33rd International Geographical Congress, which was held in Beijing last August. At the meeting, Bojie Fu, a member of National Science Review’s editorial board, shared a platform with geographers from Australia, China, Canada and France to discuss the challenges of urbanization, the roles of geographers in sustainable development, as well as the importance of food security, safety and diversity.
Dadao Lu
Economic geographer at the Institute of Geography and Natural Resources Research, Chinese Academy of Sciences, Beijing
Jean-Robert Pitte
Historical and cultural geographer at the University of Paris-Sorbonne in Paris, France
Mark Rosenberg
Health geographer at Queen's University in Ontario, Canada
Mark Stafford Smith
Ecologist at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) in Canberra, Australia
Bojie Fu (Chair)
Physical geographer at the Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing; President of Geographical Society of China
Surface brightness correction for compact extended sources observed by the AKARI Far-Infrared Surveyor in the slow-scan mode
Authors: Ueta Toshiya , Tomasino Rachael L. , Takita Satoshi , Izumiura Hideyuki , Shirahata Mai , Fullard Andrew , Yamamura Issei , Matsuura Shuji 
Published: November 2016

Abstract
We present a general surface brightness correction method for compact extended sources imaged in the slow-scan pointed observation mode of the Far-Infrared Surveyor (FIS) aboard the AKARI infrared astronomical satellite. Our method recovers correct surface brightness distribution maps by rescaling archived raw FIS maps using the surface-brightness-dependent inverse FIS response function. The flux of a target source is then automatically corrected for as the simple sum of surface brightnesses within the adopted contour encircling the perimeter of the target (i.e., contour photometry). This correction method is contrasted with the previous aperture photometry method for point sources, which directly corrects for the target flux with a flux-dependent scaling law. The new surface brightness correction scheme is applicable to objects of any shape from unresolved point sources to resolved extended objects, as long as the target is not deemed diffuse, i.e., the total extent of the target source does not exceed too much more than a single FIS scan width of 10΄. The new correction method takes advantage of the well-defined shape (i.e., the scale invariance) of the point spread function, which enables us to adopt a power-law FIS response function. We analyze the point source photometric calibrator data using the FIS AKARI Slow-scan Tool and constrain the parameters of the adopted power-law FIS response function. We conclude that the photometric accuracy of the new correction method is better than 10% error based on comparisons with the expected fluxes of the photometric calibrators, and that resulting fluxes without the present correction method can lead to up to 230% overestimates or down to 50% underestimates.
Corn Yield Loss Estimates Due to Diseases in the United States and Ontario, Canada from 2012 to 2015
Authors: Mueller Daren S. , Wise Kiersten A. , Sisson Adam J. , Allen Tom W. , Bergstrom Gary C. , Bosley D. Bruce , Bradley Carl A. , Broders Kirk D. , Byamukama Emmanuel , Chilvers Martin I. , Collins Alyssa , Faske Travis R. , Friskop Andrew J. , Heiniger Ron W. , Hollier Clayton A. , Hooker David C. , Isakeit Tom , Jackson-Ziems Tamra A. , Jardine Douglas J. , Kelly Heather M. , Kinzer Kasia , Koenning Steve R. , Malvick Dean K. , McMullen Marcia , Meyer Ron F. , Paul Pierce A. , Robertson Alison E. , Roth Gregory W. , Smith Damon L. , Tande Connie A. , Tenuta Albert U. , Vincelli Paul , Warner Fred 
Published: November 2016

Annual decreases in corn yield caused by diseases were estimated by surveying members of the Corn Disease Working Group in 22 corn-producing states in the United States and in Ontario, Canada, from 2012 through 2015. Estimated loss from each disease varied greatly by state and year. In general, foliar diseases such as northern corn leaf blight, gray leaf spot, and Goss's wilt commonly caused the largest estimated yield loss in the northern United States and Ontario during non-drought years. Fusarium stalk rot and plant-parasitic nematodes caused the most estimated loss in the southern-most United States. The estimated mean economic loss due to yield loss by corn diseases in the United States and Ontario from 2012 to 2015 was $76.51 USD per acre. The cost of disease-mitigating strategies is another potential source of profit loss. Results from this survey will provide scientists, breeders, government, and educators with data to help inform and prioritize research, policy, and educational efforts in corn pathology and disease management. Accepted for publication 26 August 2016.
DURATION OF PRONE POSITIONING AFTER MACULAR HOLE SURGERY DETERMINED BY SWEPT-SOURCE OPTICAL COHERENCE TOMOGRAPHY
Authors: Sano Masahiko , Inoue Makoto , Itoh Yuji , Kita Yoshiyuki , Hirota Kazunari , Koto Takashi , Hirakata Akito 
Published: November 2016

Purpose:
To compare the closure rate of macular hole closure and duration of the prone positioning after macular hole (MH) surgery with two protocols for halting the prone positioning.

Methods:
The authors studied 129 eyes of 125 consecutive patients with MH who had undergone vitrectomy. In 60 eyes of 59 patients, the prone positioning was halted after detecting an MH closure in the swept-source optical coherence tomographic images (SS group). In 69 eyes of 66 patients, the prone position was halted by the surgeon's decision (conventional group). The MH closure rate and duration of the prone positioning were compared.

Results:
Clear images of the MH were recorded in the SS group on postoperative Day 1 in 58 eyes (97%). In the SS group, MH closure was detected on postoperative Day 1 in 47 eyes (78%) and Day 2 in 4 eyes (7%). The MH was closed in 58 eyes (97%) in the SS group and 69 eyes (100%) in the conventional group (P = 0.21). None of the eyes had a reopening of the MH. The duration of prone positioning in the SS group was 1.8 ± 2.5 days, which was significantly shorter than that in the conventional group at 8.4 ± 4.2 days (P < 0.0001).

Conclusion:
The SS-OCT protocol can significantly decrease the duration of the prone positioning without a reopening of the MH.
A Comparison of Surgical Treatments for Superior Semicircular Canal Dehiscence: A Systematic Review
Authors: Ziylan Fuat , Kinaci Ahmet , Beynon Andy J. , Kunst Henricus P. M. 
Published: November 2016

Objective:
We investigate the postoperative subjective and objective outcomes of different surgical treatments for superior semicircular canal dehiscence (SSCD): vestibular signs, auditory signs, vestibular evoked myogenic potential test, pure tone audiogram, speech audiogram, or video-nystagmography.

Data Sources:
An electronic search performed in the PubMed, Cochrane Library, and EMBASE databases on 15th of September 2015. A systematic search was conducted. Articles were included if written in English, Dutch, German, or French language.

Study Selection:
Original studies reporting on the pre and postoperative subjective and/or objective outcomes of surgical treatments for superior semicircular canal dehiscence were included.

Data Extraction:
The methodological quality of the studies was independently assessed by two reviewers using a constructed critical appraisal, to assess the directness of evidence and the risk of bias. The results of the pre and postoperative subjective and/or objective outcomes were extracted.

Data Synthesis:
Comparative study was conducted.

Conclusion:
Surgical treatment for SSCD is particularly effective for vestibular symptoms and there is no evidence for improvement of hearing loss after surgical treatment. Since plugging using transmastoid approach had a lower complication rate, lower revision rate, and a shorter hospital stay, this treatment is recommended in high disabled SSCD patients.
Hepatitis C virus infection: opportunities for an earlier detection in primary care
Authors: Lapi Francesco , Capogrosso Sansone Alice , Mantarro Stefania , Simonetti Monica , Tuccori Marco , Blandizzi Corrado , Rossi Alessandro , Corti Giampaolo , Bartoloni Alessandro , Bellia Alfonso , Baiocchi Leonardo , Cricelli Iacopo , Cricelli Claudio 
Published: November 2016

Background/aim
In the era of direct-acting antiviral medications, which can cure the hepatitis C virus (HCV) infection, the actual epidemiology of this condition in the general population is still unclear. We therefore aimed to estimate the prevalence rate of HCV and assess the determinants for incident cases of HCV in primary care in Italy.

Methods
We identified outpatients aged at least 15 years registered in the Italian Health Search IMS Health Longitudinal Patient Database from 1 January 2002 to 30 June 2013. The annual trend of HCV prevalence was estimated. The candidate determinants for the risk of incident HCV infection included geographical area of residence, sex, age, infections by the HIV, hepatitis B virus (HBV), or other forms of hepatitis, and abuse of illicit substances or drugs.

Results
The eligible cohort included 826 300 patients (53.5% women, mean age 48.1±19.1 years). The prevalence rate of HCV increased over the 11-year study period, ranging from 0.24 to 0.50%, with a small increase in men versus women. Patients aged more than 24 years had a higher risk than those aged 14–24 years, with up to a five-fold increase among patients aged 65–74 years. Being resident of Southern/Islands Italy, concurrent diagnosis HBV or HIV, and drug or illicit substance abuse were significant determinants for HCV infection.

Conclusion
Our study shows that the prevalence of HCV in Italy has doubled over the last decade. Patients with certain demographics and clinical characteristics are more prone to be infected by HCV. In this scenario, general practitioners may play a crucial role in screening, early identification, and therapy of high-risk patients.
Neonatal nonimmune hemolytic anemia
Authors: Yaish Hassan M. , Christensen Robert D. , Lemons Richard S. 
Published: November 2016

Purpose of review
As in adults and older children, anemia in newborn infants can be the result of erythropoietic failure, hemorrhage, or hemolysis. When hemolysis is the prime consideration, it can be challenging for physicians caring for neonates to choose from the wide variety of available diagnostic tests. This review describes the authors’ opinions regarding rational, consistent, and cost-effective means of making an exact diagnosis of a neonatal hemolytic condition.

Recent findings
Two recent advances in the diagnosis of neonatal nonimmune hemolytic disorders are highlighted in this review: introduction of flow cytometry-based Eosin-5-maleimide (EMA) uptake as a screening test to identify RBC membrane defects and next-generation sequencing (NGS)-based panels to uncover exact mutations causing hemolysis.

Summary
The availability of newer tools such as EMA and NGS to diagnose specific hemolytic conditions, which might otherwise remain unknown, enables neonatal practitioners not only to identify the exact cause of hemolysis but also to discover novel mutations that can be implicated in the cause of neonatal hemolytic processes.
Telephone Follow-Up by Nurse After Total Knee Arthroplasty
Authors: Szöts Kirsten , Konradsen Hanne , Solgaard Søren , Østergaard Birte 
Published: November 2016

BACKGROUND/PURPOSE:
Because of shorter hospitalizations, patients now have to take responsibility for their recovery period at a very early stage. We evaluated the effects of structured, nurse-managed telephone follow-up (TFU) after discharge from the hospital following total knee arthroplasty (TKA).

METHOD/DESIGN:
The design was a single-center, unblinded, parallel-group randomized clinical trial. The primary outcome was self-reported physical function according to the Western Ontario and McMaster Universities Osteoarthritis (WOMAC) Index. Secondary outcomes were stiffness and pain according to the WOMAC Index; health-related quality of life, measured with the Medical Outcomes Study Short Form (SF-36); general self-efficacy, measured with the General Self-Efficacy Scale; and number of acute visits to the orthopaedic outpatient clinic. In total, 117 patients were randomized to 2 groups: an intervention group receiving TFU 4 and 14 days after discharge in addition to conventional treatment, and a control group receiving conventional treatment. The TFUs were structured by key subjects for health status, as defined by the VIPS model (the Swedish acronym for the concepts of Well-being, Integrity, Prevention, and Safety). The effect was measured 1 and 3 months postsurgery.

RESULTS:
No significant effects on physical function in the disease-specific WOMAC Index were identified. However, significant differences in scores were identified in favor of the intervention group on general self-efficacy (p = .014) and physical function (p = .031), measured with the Medical Outcomes Study Short Form 1 month after TKA, but this effect was not seen at 3 months. A positive improvement in several dimensions of health status and health-related quality of life was identified in favor of the intervention group, but patients who had TFU had more unscheduled visits to the outpatient clinic.

CONCLUSIONS:
Telephone follow-up did not improve physical function compared with conventional treatment, as measured with the WOMAC Index. A short-term effect was identified, improving general self-efficacy and physical function as dimensions of health-related quality of life.
Healthcare Access and PrEP Continuation in San Francisco and Miami After the US PrEP Demo Project
Authors: Doblecki-Lewis Susanne , Liu Albert , Feaster Daniel , Cohen Stephanie E. , Cardenas Gabriel , Bacon Oliver , Andrew Erin , Kolber Michael A. 
Published: November 2016

Background:
Pre-exposure prophylaxis (PrEP) for prevention of HIV infection has demonstrated efficacy in randomized controlled trials and in demonstration projects. For PrEP implementation to result in significant reductions in HIV incidence for men who have sex with men in the United States, sufficient access to PrEP care and continued engagement outside of demonstration projects is required.

Methods:
We report the results of a follow-up survey of 173 former participants from the Miami and San Francisco sites of the US PrEP Demo Project, administered 4–6 months after study completion.

Results:
Survey respondents continued to frequently access medical care and had a high incidence of sexually transmitted infections after completion of the Demo Project, indicating ongoing sexual risk behavior. Interest in continuing PrEP was high with 70.8% indicating that they were “very interested” in continuing PrEP. Among respondents, 39.9% reported continuation of PrEP after completion of the Demo Project, largely through their primary care providers and frequently at low or no cost. Variability in access and engagement was seen, with participants from the San Francisco site, those with medical insurance, and those with a primary care provider at the end of the Demo Project more likely to successfully obtain PrEP medication. Two respondents reported HIV seroconversion in the period between study completion and the follow-up survey.

Conclusions:
Additional effort to increase equitable access to PrEP outside of demonstration projects is needed to realize the potential impact of this evidence-based prevention intervention.