bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous default network activity reflects behavioral variability independent of mind-wandering
Authors: Kucyi Aaron , Esterman Michael , Riley Clay S. , Valera Eve M. 
Published: November 2016

Significance
The brain’s default mode network (DMN) is comprised of regions that are highly active during wakeful rest. In the past 15 y, the DMN has been a target of investigation in thousands of basic and clinical neuroscience studies, yet the fundamental role of this network remains debated and unknown. Some studies suggest that DMN activity increases with self-reported mind-wandering away from the present sensory environment, a state in which task performance tends to be highly unstable. However, we show that DMN activity increases with stable, rather than variable, behavior, independent from increases with mind-wandering. Our work urges reinterpretation of the significance of DMN activity fluctuations in daily life and DMN disruption in disease.
Tetraphenylethene-based highly emissive metallacage as a component of theranostic supramolecular nanoparticles
Authors: Yu Guocan , Cook Timothy R. , Li Yang , Yan Xuzhou , Wu Dan , Shao Li , Shen Jie , Tang Guping , Huang Feihe , Chen Xiaoyuan , Stang Peter J. 
Published: November 2016

Significance
Because of severe side effects, poor specificity, and lack of any ability to track the process of translocation, clinic applications of platinum anticancer drugs are limited. New motifs that combine a targeting ability, diagnostic capabilities, and therapeutic functions are urgently needed. Herein, we use a highly emissive metallacage as a component of theranostic supramolecular nanoparticles. In vitro and in vivo investigations demonstrate the metallacage-loaded nanoparticles (MNPs) are more active and show low systemic activity while also possessing emissive properties that allow for fluorescence imaging. This metallacage provides an excellent nanoplatform on which to develop theranostic anticancer agents, providing a blueprint for the next generation of nanomedicines and the development of noble metal-based–targeted drug delivery systems.
Membrane-bound glycerol dehydrogenase catalyzes oxidation of D-pentonates to 4-keto-D-pentonates, D-fructose to 5-keto-D-fructose, and D-psicose to 5-keto-D-psicose
Authors: Ano Yoshitaka , Hours Roque A , Akakabe Yoshihiko , Kataoka Naoya , Yakushi Toshiharu , Matsushita Kazunobu , Adachi Osao 
Published: November 2016

Abstract
A novel oxidation of D-pentonates to 4-keto-D-pentonates was analyzed with Gluconobacter thailandicus NBRC 3258. D-Pentonate 4-dehydrogenase activity in the membrane fraction was readily inactivated by EDTA and it was reactivated by the addition of PQQ and Ca2+. D-Pentonate 4-dehydrogenase was purified to two different subunits, 80 and 14 kDa. The absorption spectrum of the purified enzyme showed no typical absorbance over the visible regions. The enzyme oxidized D-pentonates to 4-keto-D-pentonates at the optimum pH of 4.0. In addition, the enzyme oxidized D-fructose to 5-keto-D-fructose, D-psicose to 5-keto-D-psicose, including the other polyols such as, glycerol, D-ribitol, D-arabitol, and D-sorbitol. Thus, D-pentonate 4-dehydrogenase was found to be identical with glycerol dehydrogenase (GLDH), a major polyol dehydrogenase in Gluconobacter species. The reaction versatility of quinoprotein GLDH was notified in this study.
Cardiovascular risk factors and hearing impairment
Authors: Pirodda Antonio , Brandolini Cristina , Raimondi Maria Chiara , Pelligra Irene , Strocchi Enrico , Cicero Arrigo F.G. , Rosticci Martina , Borghi Claudio 
Published: November 2016

Background:
In the literature the association between common cardiovascular risk factors and/or major events and inner ear diseases has been widely considered. Despite the controversial related results, a recent review underlines that while a direct and causal correlation between cardiovascular risk factors and hearing impairment is lacking, the former are thought to have an influence on hearing acuity: this should imply some correlation between arterial conditions and inner ear function.

Aims:
Aiming at verifying the reliability of the correlation between arterial conditions and inner ear function, the hearing function of a population with metabolic syndrome and a population without metabolic syndrome were matched.

Methods:
All the examined subjects were enrolled within the Brisighella Heart Study, in order to obtain a detailed knowledge of the cardiovascular and metabolic parameters. 142 subjects were enrolled, including 89 healthy subjects and 53 affected by metabolic syndrome, having ruled out those cases associated with external and/or middle ear pathologies, or unilateral sensorineural hearing loss or with a history of previous ototoxic drugs and ear surgery. Among the examined parameters was arterial stiffness, as evaluated by means of the Vicorder® device with a non-invasive procedure, which had not previously been considered in relation to labyrinthine function.

Results:
The lack of any statistically significant correlation between common cardiovascular risk factors and hearing deterioration, as emerged from the study, has a particular significance.

Conclusions:
The inference from this result is that the relationship between the systemic circulation and inner ear conditions must be more complex than frequently considered.
Force supplementary comparison at SIM (SIM.M.F-S5), compression testing machines calibration, up to 200 kN
Authors: Cárdenas Moctezuma A , Guzmán, J C Torres , Espeleta A Dajer , García L De La Cruz , Mora H Tioli , Granados L 
Published: November 2016

CENAM, through the Force and Pressure Division, organized a comparison on testing machines calibration, in compression mode. The participating laboratories were SIM National Institutes of Metrology from Colombia, Peru and Costa Rica, where CENAM, Mexico was the pilot and reference laboratory. The results obtained by the laboratories are presented in this paper as well as the analysis of compatibility.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Existence of surface energy minimizing partitions of ℝⁿ satisfying volume constraints
Authors: Caraballo David 
Published: November 2016

We give the first proof, with independent smooth normsϕij,\phi _{ij},of the existence of surface energy minimizing partitions ofRn\mathbb {R}^{n}into regions having prescribed volumes. Our existence proof significantly extends that of F. Almgren, who in 1976 gave the first such results for the special case in which eachϕij\phi _{ij}is a scalar multiple of a fixed smoothϕ:\phi :ϕij=cijϕ\phi _{ij}=c_{ij}\phi. Most materials are polycrystalline and do not have surface energy density functions which are scalar multiples of one another, so it is important to extend the theory by removing this restriction, as we have done. We also discuss connections with polycrystalline evolution problems.
fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets
Authors: Madrigal Pedro 
Published: November 2016

Abstract

Summary
Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate reproducibility of biological or technical replicates, and to compare different datasets to identify their potential correlations. Here we present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). We show how this method differs from other measures of correlation, and exemplify how it can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers.

Availability and Implementation
An R/Bioconductor package is available at http://bioconductor.org/packages/fCCAC/.

Supplementary information
Supplementary data are available at Bioinformatics online.
cerebroViz: an R package for anatomical visualization of spatiotemporal brain data
Authors: Bahl Ethan , Koomar Tanner , Michaelson Jacob J 
Published: November 2016

Abstract

Summary
Spatiotemporal transcriptomic profiling has provided valuable insight into the patterning of gene expression throughout the human brain from early fetal development to adulthood. When combined with prior knowledge of a disease’s age at onset and region-specificity, these expression profiles have provided the necessary context to both strengthen putative gene–disease associations and infer new associations. While a wealth of spatiotemporal expression data exists, there are currently no tools available to visualize this data within the anatomical context of the brain, thus limiting the intuitive interpretation of many such findings. We present cerebroViz, an R package to map spatiotemporal brain data to vector graphic diagrams of the human brain. Our tool allows rapid generation of publication-quality figures that highlight spatiotemporal trends in the input data, while striking a balance between usability and customization. cerebroViz is generalizable to any data quantifiable at a brain-regional resolution and currently supports visualization of up to thirty regions of the brain found in databases such as BrainSpan, GTEx and Roadmap Epigenomics.

Availability and Implementation
cerebroViz is freely available through GitHub (https://github.com/ethanbahl/cerebroViz). The tutorial is available at http://ethanbahl.github.io/cerebroViz/

Supplementary information
Supplementary data are available at Bioinformatics online.
LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering
Authors: Specht Alicia T , Li Jun 
Published: November 2016

Abstract

Summary
To construct gene co-expression networks based on single-cell RNA-Sequencing data, we present an algorithm called LEAP, which utilizes the estimated pseudotime of the cells to find gene co-expression that involves time delay.

Availability and Implementation
R package LEAP available on CRAN

Supplementary information
Supplementary data are available at Bioinformatics online.
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks
Authors: Balaur Irina , Mazein Alexander , Saqi Mansoor , Lysenko Artem , Rawlings Christopher J , Auffray Charles 
Published: November 2016

Abstract

Summary
The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing.

Availability and Implementation
The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/. The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework.

Supplementary information
Supplementary data are available at Bioinformatics online.
Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud
Authors: Yang Andrian , Troup Michael , Lin Peijie , Ho Joshua W K 
Published: November 2016

Abstract

Summary
Single-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellization of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq datasets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6–145.4 times faster using Falco than running on a highly optimized standalone computer. Falco also allows users to utilize low-cost spot instances of Amazon Web Services, providing a ∼65% reduction in cost of analysis.

Availability and Implementation
Falco is available via a GNU General Public License at https://github.com/VCCRI/Falco/

Supplementary information
Supplementary data are available at Bioinformatics online.
AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs
Authors: Kochetov Alex V , Allmer Jens , Klimenko Alexandra I , Zuraev Bulat S , Matushkin Yury G , Lashin Sergey A 
Published: November 2016

Abstract

Motivation
Protein synthesis is not a straight forward process and one gene locus can produce many isoforms, for example, by starting mRNA translation from alternative start sites. altORF evaluator (altORFev) predicts alternative open reading frames within eukaryotic mRNA translated by a linear scanning mechanism and its modifications (leaky scanning and reinitiation). The program reveals the efficiently translated altORFs recognized by the majority of 40S ribosomal subunits landing on the 5′-end of an mRNA. This information aids to reveal the functions of eukaryotic genes connected to synthesis of either unknown isoforms of annotated proteins or new unrelated polypeptides.

Availability and Implementation
altORFev is available at http://www.bionet.nsc.ru/AUGWeb/and has been developed in Java 1.8 using the BioJava library; and the Vaadin framework to produce the web service.
Long-term Mortality of Patients With Tuberculous Meningitis in New York City: A Cohort Study
Authors: Vinnard Christopher , King Liza , Munsiff Sonal , Crossa Aldo , Iwata Kentaro , Pasipanodya Jotam , Proops Douglas , Ahuja Shama 
Published: November 2016

Abstract

Background.
Tuberculous meningitis (TBM) is the most devastating clinical presentation of infection with Mycobacterium tuberculosis; delayed initiation of effective antituberculosis therapy is associated with poor treatment outcomes. Our objective was to determine the relationship between drug resistance and 10-year mortality among patients with TBM.

Methods.
We conducted a retrospective cohort study of 324 patients with culture-confirmed TBM, susceptibility results reported for isoniazid and rifampin, and initiation of at least 2 antituberculosis drugs, reported to the tuberculosis registry in New York City between 1 January 1992 and 31 December 2001. Date of death was ascertained by matching the tuberculosis registry with death certificate data for 1992–2012 from the New York Office of Vital Statistics. Human immunodeficiency virus (HIV) status was ascertained by medical records review, matching with the New York City HIV Surveillance registry, and review of cause of death.

Results.
Among 257 TBM patients without rifampin-resistant isolates, isoniazid resistance was associated with mortality after the first 60 days of treatment when controlling for age and HIV infection (adjusted hazard ratio, 1.94 [95% confidence interval, 1.08–3.94]). Death occurred before completion of antituberculosis therapy in 63 of 67 TBM patients (94%) with rifampin-resistant disease.

Conclusions.
Among patients with culture-confirmed TBM, we observed rapid early mortality in patients with rifampin-resistant isolates, and an independent association between isoniazid-resistant isolates and death after 60 days of therapy. These findings support the continued evaluation of rapid diagnostic techniques and the empiric addition of second-line drugs for patients with clinically suspected drug-resistant TBM.
Assessment of the French National Health Insurance Information System as a tool for epidemiological surveillance of malaria
Authors: Delon François , Mayet Aurélie , Thellier Marc , Kendjo Eric , Michel Rémy , Ollivier Lénaïck , Chatellier Gilles , Desjeux Guillaume 
Published: November 2016

Objective: Epidemiological surveillance of malaria in France is based on a hospital laboratory sentinel surveillance network. There is no comprehensive population surveillance. The objective of this study was to assess the ability of the French National Health Insurance Information System to support nationwide malaria surveillance in continental France.
Materials and methods: A case identification algorithm was built in a 2-step process. First, inclusion rules giving priority to sensitivity were defined. Then, based on data description, exclusion rules to increase specificity were applied. To validate our results, we compared them to data from the French National Reference Center for Malaria on case counts, distribution within subgroups, and disease onset date trends.
Results: We built a reusable automatized tool. From July 1, 2013, to June 30, 2014, we identified 4077 incident malaria cases that occurred in continental France. Our algorithm provided data for hospitalized patients, patients treated by private physicians, and outpatients for the entire population. Our results were similar to those of the National Reference Center for Malaria for each of the outcome criteria.
Discussion: We provided a reliable algorithm for implementing epidemiological surveillance of malaria based on the French National Health Insurance Information System. Our method allowed us to work on the entire population living in continental France, including subpopulations poorly covered by existing surveillance methods.
Conclusion: Traditional epidemiological surveillance and the approach presented in this paper are complementary, but a formal validation framework for case identification algorithms is necessary.
Neonectria Canker Found on Spruce and Fir in Swedish Christmas Tree Plantations
Authors: Pettersson Martin , Frampton John , Rönnberg Jonas , Talgø Venche 
Published: November 2016

In May 2015, a Christmas tree disease and pest survey was carried out in southern Sweden. Neonectria canker found on spruce and fir was the most prominent disease problem. Accepted for publication 1 September 2016.
First Report of Boxwood Blight Caused by Calonectria pseudonaviculata in Florida
Authors: Iriarte Fanny , Paret Mathews , Knox Gary , Schubert Tim , Jeyaprakash Ayyamperumal , Davison David 
Published: November 2016

To the authors' knowledge, this is the first report of Boxwood blight in Florida. Accepted for publication 22 September 2016.
Effectiveness of a Low-volume Spray Technology in the Control of Major Strawberry Diseases in Florida
Authors: Cordova Leandro G. , Peres Natalia A. 
Published: November 2016

Florida strawberry production is greatly affected by Botrytis and anthracnose fruit rots (BFR and AFR), caused by Botrytis cinerea and Colletotrichum acutatum, respectively. Fungicide applications are the most effective method for control of both diseases. Traditionally, Florida strawberry growers use sprayers mounted with hydraulic nozzles delivering high flow rates. The objective of this study was to compare the standard hydraulic nozzle (SHN) sprayer with the air-assisted rotary atomizer (AARA). The effects of low volumes on the control of BFR and AFR, the reduction of 25% on fungicide rate, and their operational efficiency were evaluated, and an economic analysis was conducted. Two experiments were conducted (in the 2014-2015 and 2015-2016 seasons) where three treatments were compared: two using the AARA at 25 gal/acre, one of these with 75% of the fungicide rate; and one using the SHN at 100 gal/acre. In the first season, yield, AFR control, and BFR control were similar for all three treatments. In the second, BFR control was similar among all the treatments. However, the AARA treatment had a higher yield than the SHN, with the AARA (75% rate) being more productive. The operational capacity in acres per hour of the AARA was 17% higher than the SHN. Labor and fungicide costs were lower in the AARA treatments. Thus, the technology was shown to be a good fit for Florida growers. Accepted for publication 25 October 2016.
Factors Associated With Nonaccidental Trauma Evaluation Among Patients Below 36 Months Old Presenting With Femur Fractures at a Level-1 Pediatric Trauma Center
Authors: Blatz Allison M. , Gillespie Catherine W. , Katcher Arielle , Matthews Allison , Oetgen Matthew E. 
Published: November 2016

Background:
In 2009, the American Academy of Orthopedic Surgeons published clinical practice guidelines (CPGs) on the treatment of pediatric diaphyseal femur fractures, which recommended a nonaccidental trauma (NAT) evaluation for all patients below 36 months of age. A recent study of these guidelines found <50% clinical compliance with this treatment recommendation. We aimed to identify areas for improvement in compliance with this guideline.

Methods:
A retrospective review was performed of all patients presenting to a single pediatric tertiary care hospital with a diaphyseal femur fracture from January 2007 to June 2013 who were below 36 months old. Medical records were reviewed for documentation of a NAT evaluation, patient characteristics, presence of other fractures or injuries, and hospital of presentation. Radiographs were reviewed for fracture pattern. Statistical analysis was performed to assess for differences overall and before and after CPG publication.

Results:
During the study period, 281 children below 36 months presented with femur fractures; 41% were evaluated for NAT. Overall, the following factors were significantly associated with receipt of a NAT evaluation: younger age (P<0.001), transfer from an outside facility (P=0.027), and identification of another fracture (P=0.004). Before publication of the CPG, nonwhite patients were much more likely to undergo NAT evaluation compared with white patients (43% vs. 19%; P=0.014). After publication of the CPGs, this differential disappeared (43% vs. 47%; P=0.685). Fracture pattern and patient sex did not influence receipt of NAT evaluation.

Conclusions:
We found poor utilization of NAT evaluation for patients below 36 months old presenting with femur fracture. Despite CPG publication, only modest improvements in this evaluation occurred over the study period, with less than half of all patients being evaluated. Younger children, patients transferred from other institutions, and patients presenting with concomitant fractures were more likely to undergo NAT evaluation. Compliance with the CPG may be improved by focusing on older children, patients who initially present to tertiary care centers, and those with an isolated femur fracture.

Level of Evidence:
Level III—retrospective comparative study.