bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macromolecular crowding explains overflow metabolism in cells
Authors: Vazquez Alexei , Oltvai Zoltán N. 
Published: August 2016

AbstractOverflow metabolism is a metabolic phenotype of cells characterized by mixed oxidative phosphorylation (OxPhos) and fermentative glycolysis in the presence of oxygen. Recently, it was proposed that a combination of a protein allocation constraint and a higher proteome fraction cost of energy generation by OxPhos relative to fermentation form the basis of overflow metabolism in the bacterium, Escherichia coli. However, we argue that the existence of a maximum or optimal macromolecular density is another essential requirement. Here we re-evaluate our previous theory of overflow metabolism based on molecular crowding following the proteomic fractions formulation. We show that molecular crowding is a key factor in explaining the switch from OxPhos to overflow metabolism.
Arsenite-loaded nanoparticles inhibit PARP-1 to overcome multidrug resistance in hepatocellular carcinoma cells
Authors: Liu Hanyu , Zhang Zongjun , Chi Xiaoqin , Zhao Zhenghuan , Huang Dengtong , Jin Jianbin , Gao Jinhao 
Published: August 2016

AbstractHepatocellular carcinoma (HCC) is one of the highest incidences in cancers; however, traditional chemotherapy often suffers from low efficiency caused by drug resistance. Herein, we report an arsenite-loaded dual-drug (doxorubicin and arsenic trioxide, i.e., DOX and ATO) nanomedicine system (FeAsOx@SiO2-DOX, Combo NP) with significant drug synergy and pH-triggered drug release for effective treatment of DOX resistant HCC cells (HuH-7/ADM). This nano-formulation Combo NP exhibits the synergistic effect of DNA damage by DOX along with DNA repair interference by ATO, which results in unprecedented killing efficiency on DOX resistant cancer cells. More importantly, we explored the possible mechanism is that the activity of PARP-1 is inhibited by ATO during the treatment of Combo NP, which finally induces apoptosis of HuH-7/ADM cells by poly (ADP-ribosyl) ation suppression and DNA lesions accumulation. This study provides a smart drug delivery strategy to develop a novel synergistic combination therapy for effectively overcome drug- resistant cancer cells.
Mutations in the TMCO3 Gene are Associated with Cornea Guttata and Anterior Polar Cataract
Authors: Chen Peng , Hao Xiaodan , Li Wenfeng , Zhao Xiaowen , Huang Yusen 
Published: August 2016

AbstractThe molecular basis for cornea guttata and anterior polar cataract remains idiopathic in most cases. In this study, our aim was to identify the disease-associated gene in Chinese patients with these conditions. Patients with the conditions from two Chinese families and ten sporadic patients, were investigated. Genome-wide linkage and exome sequencing analyses showed transmembrane and coiled-coil domain 3 (TMCO3) as the disease candidate gene for a coding heterozygous mutation c.41C > T, resulting in a P14L amino acid change that co-segregated with the disease phenotype as discovered in Family A. TMCO3 belongs to the monovalent cation: protein antiporter 2 transporter family, a moderately large group whose members all share a very similar function under normal physiological conditions. The gene is expressed in the human cornea, lens capsule and choroid-retinal pigment epithelium. This study reveals, for the first time, that mutations in TMCO3 are associated with cornea guttata and anterior polar cataract, warranting further investigation into the pathogenesis of this disorder.
Lack of Dependence of Indian Summer Monsoon Rainfall Extremes on Temperature: An Observational Evidence
Authors: Vittal H. , Ghosh Subimal , Karmakar Subhankar , Pathak Amey , Murtugudde Raghu 
Published: August 2016

AbstractThe intensification of precipitation extremes in a warming world has been reported on a global scale and is traditionally explained with the Clausius-Clapeyron (C-C) relation. The relationship is observed to be valid in mid-latitudes; however, the debate persists in tropical monsoon regions, with the extremes of the Indian Summer Monsoon Rainfall (ISMR) being a prime example. Here, we present a comprehensive study on the dependence of ISMR extremes on both the 2 m surface air temperature over India and on the sea surface temperature over the tropical Indian Ocean. Remarkably, the ISMR extremes exhibit no significant association with temperature at either spatial scale: neither aggregated over the entire India/Tropical Indian Ocean area nor at the grid levels. We find that the theoretical C-C relation overestimates the positive changes in precipitation extremes, which is also reflected in the Coupled Model Intercomparison Project 5 (CMIP5) simulations. We emphasize that the changing patterns of extremes over the Indian subcontinent need a scientific re-evaluation, which is possible due to availability of the unique long-termin-situdata. This can aid bias correction of model projections of extremes whose value for climate adaptation can hardly be overemphasized, especially for the developing tropical countries.
Effect of WC/Co coherency phase boundaries on Fracture toughness of the nanocrystalline cemented carbides
Authors: Xie Hongxian , Song Xiaoyan , Yin Fuxing , Zhang Yongguang 
Published: August 2016

AbstractThe effect of coherency WC/Co phase boundaries on the fracture toughness of the nanocrystalline WC-Co cemented carbides is studied by MD simulation method. The simulation results show that the nanocrystalline WC-Co cemented carbides with coherency WC/Co phase boundaries has higher fracture toughness than that without coherency WC/Co phase boundaries. Moreover, the mechanism of why coherency WC/Co phase boundaries can improve the fracture toughness of the nanocrystalline cemented carbides is also investigated. It is found the fact that the separation energy of the coherent WC/Co phase boundary is larger than that of the incoherent WC/Co phase boundaries is the main reason for this excellent mechanical property.
Self-Printing on Graphitic Nanosheets with Metal Borohydride Nanodots for Hydrogen Storage
Authors: Li Yongtao , Ding Xiaoli , Zhang Qingan 
Published: August 2016

AbstractAlthough the synthesis of borohydride nanostructures is sufficiently established for advancement of hydrogen storage, obtaining ultrasmall (sub-10 nm) metal borohydride nanocrystals with excellent dispersibility is extremely challenging because of their high surface energy, exceedingly strong reducibility/hydrophilicity and complicated composition. Here, we demonstrate a mechanical-force-driven self-printing process that enables monodispersed (~6 nm) NaBH4 nanodots to uniformly anchor onto freshly-exfoliated graphitic nanosheets (GNs). Both mechanical-forces and borohydride interaction with GNs stimulate NaBH4 clusters intercalation/absorption into the graphite interlayers acting as a ‘pen’ for writing, which is accomplished by exfoliating GNs with the ‘printed’ borohydrides. These nano-NaBH4@GNs exhibit favorable thermodynamics (decrease in ∆H of ~45%), rapid kinetics (a greater than six-fold increase) and stable de-/re-hydrogenation that retains a high capacity (up to ~5 wt% for NaBH4) compared with those of micro-NaBH4. Our results are helpful in the scalable fabrication of zero-dimensional complex hydrides on two-dimensional supports with enhanced hydrogen storage for potential applications.
Rapid Detection of Cyprinid Herpesvirus 3 in Latently Infected Koi by Recombinase Polymerase Amplification
Authors: Prescott Meagan A. , Reed Aimee N. , Jin Ling , Pastey Manoj K. 
Published: August 2016

Abstract
Since the emergence of cyprinid herpesvirus 3 (CyHV-3), outbreaks have been devastating to Common Carp Cyprinus carpio and koi (a variant of Common Carp), leading to high economic losses. Current diagnostics for detecting CyHV-3 are limited in sensitivity and are further complicated by latency. Here we describe the detection of CyHV-3 by recombinase polymerase amplification (RPA). The RPA assay can detect as low as 10 copies of the CyHV-3 genome by an isothermal reaction and yields results in approximately 20 min. Using the RPA assay, the CyHV-3 genome can be detected in the total DNA of white blood cells isolated from koi latently infected with CyHV-3, while less than 10% of the latently infected koi can be detected by a real-time PCR assay in the total DNA of white blood cells. In addition, RPA products can be detected in a lateral flow device that is cheap and fast and can be used outside of the diagnostic lab. The RPA assay and lateral flow device provide for the rapid, sensitive, and specific amplification of CyHV-3 that with future modifications for field use and validation could lead to enhanced surveillance and early diagnosis of CyHV-3 in the laboratory and field.
Received September 14, 2015; accepted April 9, 2016 Published online August 2, 2016
ReactPRED: a tool to predict and analyze biochemical reactions
Authors: Sivakumar Tadi Venkata , Giri Varun , Park Jin Hwan , Kim Tae Yong , Bhaduri Anirban 
Published: August 2016

Motivation: Biochemical pathways engineering is often used to synthesize or degrade target chemicals. In silico screening of the biochemical transformation space allows predicting feasible reactions, constituting these pathways. Current enabling tools are customized to predict reactions based on pre-defined biochemical transformations or reaction rule sets. Reaction rule sets are usually curated manually and tailored to specific applications. They are not exhaustive. In addition, current systems are incapable of regulating and refining data with an aim to tune specificity and sensitivity. A robust and flexible tool that allows automated reaction rule set creation along with regulated pathway prediction and analyses is a need. ReactPRED aims to address the same.
Results: ReactPRED is an open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. The tool allows automated reaction rule creation from a user defined reaction set. Additionally, reaction rule degree and rule tolerance features allow refinement of predicted data. It is available as a flexible graphical user interface and a console application.
Availability and implementation: ReactPRED is available at: https://sourceforge.net/projects/reactpred/.
Contact: anirban.b@samsung.com or ty76.kim@samsung.com
Supplementary information: Supplementary data are available at Bioinformatics online.
HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Authors: Lee Kyubum , Shin Wonho , Kim Byounggun , Lee Sunwon , Choi Yonghwa , Kim Sunkyu , Jeon Minji , Tan Aik Choon , Kang Jaewoo 
Published: August 2016

Abstract
Summary: We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.
Availability and Implementation: HiPub and detailed user guide are available at http://hipub.korea.ac.kr.
Contact: kangj@korea.ac.kr, aikchoon.tan@ucdenver.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Did high-energy astrophysical sources contribute to Martian atmospheric loss?
Authors: Atri Dimitra 
Published: August 2016

Abstract
Mars is believed to have had a substantial atmosphere in the past. Atmospheric loss led to depressurization and cooling, and is thought to be the primary driving force responsible for the loss of liquid water from its surface. Recently, Mars Atmosphere and Volatile Evolution observations have provided new insight into the physics of atmospheric loss induced by Interplanetary Coronal Mass Ejections and solar wind interacting with the Martian atmosphere. In addition to solar radiation, it is likely that its atmosphere has been exposed to radiation bursts from high-energy astrophysical sources which become highly probable on time-scales of ∼Gy and beyond. These sources are capable of significantly enhancing the rates of photoionization and charged particle-induced ionization in the upper atmosphere. We use Monte Carlo simulations to model the interaction of charged particles and photons from astrophysical sources in the upper Martian atmosphere and discuss its implications on atmospheric loss. Our calculations suggest that the passage of the Solar system though dense interstellar clouds is the most significant contributor to atmospheric loss among the sources considered here.
Outpatient Antibiotic Prescribing Practices for Uncomplicated Urinary Tract Infection in Women in the United States, 2002–2011
Authors: Kobayashi Miwako , Shapiro Daniel J. , Hersh Adam L. , Sanchez Guillermo V. , Hicks Lauri A. 
Published: August 2016

Abstract
Background.  Urinary tract infection (UTI) is one of the most common diagnoses leading to an antibiotic prescription for women seeking ambulatory care. Understanding current national outpatient antibiotic prescribing practices will help ongoing stewardship efforts to optimize antibiotic use; however, information on recent national outpatient antibiotic prescribing trends for UTI is limited.
Methods.  We analyzed the National Ambulatory Medical Care and National Hospital Ambulatory Medical Care Survey datasets from 2002 to 2011. Outpatient visits of women aged ≥18 years with a diagnosis of uncomplicated UTI were included for analysis. We conducted weighted descriptive analyses, examined time trends in antibiotic prescribing, and used multivariable logistic regression to identify patient and provider factors associated with fluoroquinolone prescribing.
Results.  A total of 7111 visits were identified. Eighty percent of visits resulted in an antibiotic prescription; fluoroquinolones were the most frequently prescribed antibiotics throughout the study period (49% overall). Older patients (adjusted odds ratio [AOR] for adults aged ≥70 years = 2.5; 95% confidence interval [CI], 1.6–3.8) and patients treated by internists (AOR = 2.0; 95% CI, 1.1–3.3) were more likely than younger patients and those treated by family practitioners to receive fluoroquinolones. Outpatient visits in the West US Census region were less likely to be associated with fluoroquinolone prescribing (AOR = 0.6; 95% CI, .4–1.0) compared with visits in the Northeast.
Conclusions.  Fluoroquinolones were the most frequently selected antibiotic treatment for uncomplicated UTI in women during the study period. Outpatient antibiotic stewardship initiatives should include efforts to reduce overuse of fluoroquinolones for uncomplicated UTI.
Mutations in the catalytic domain of human β-cardiac myosin that cause early onset hypertrophic cardiomyopathy significantly increase the fundamental parameters that determine ensemble force and velocity
Authors: Adhikari Arjun S. , Kooiker Kristina B. , Liu Chao , Sarkar Saswata S. , Bernstein Daniel , Spudich James A. , Ruppel Kathleen M. 
Published: August 2016

AbstractHypertrophic cardiomyopathy (HCM) is a heritable cardiovascular disorder that affects 1 in 500 people. In infants it can be particularly severe and it is the leading cause of sudden cardiac death in pediatric populations. A high percentage of HCM is attributed to mutations in β-cardiac myosin, the motor protein that powers ventricular contraction. This study reports how two mutations that cause early-onset HCM, D239N and H251N, affect the mechanical output of human β-cardiac myosin at the molecular level. We observe extremely large increases (25% – 95%) in the actin gliding velocity, single molecule intrinsic force, and ATPase activity of the two mutant myosin motors compared to wild type myosin. In contrast to previous studies of HCM-causing mutations in human β-cardiac myosin, these mutations were striking in that they caused changes in biomechanical parameters that were both greater in magnitude and more uniformly consistent with a hyper-contractile phenotype. In addition, S1-S2 binding studies revealed a significant decrease in affinity of the H251N motor for S2, suggesting that this mutation may further increase hyper-contractility by releasing active motors from a sequestered state. This report shows, for the first time, a clear and significant gain in function for all tested molecular biomechanical parameters due to HCM mutations in human β-cardiac myosin.
Advances in the recovery of haplotypes from the metagenome
Authors: Nicholls Samuel M. , Aubrey Wayne , de Grave Kurt , Schietgat Leander , Creevey Christopher J. , Clare Amanda 
Published: August 2016

AbstractHigh-throughput DNA sequencing has enabled us to look beyond consensus reference sequences to the variation observed in sequences within organisms; their haplotypes. Recovery, or assembly of haplotypes has proved computationally difficult and there exist many probabilistic heuristics that attempt to recover the original haplotypes for a single organism of known ploidy. However, existing approaches make simplifications or assumptions that are easily violated when investigating sequence variation within a metagenome.We propose the metahaplome as the set of haplotypes for any particular genomic region of interest within a metagenomic data set and present Hansel and Gretel, a data structure and algorithm that together provide a proof of concept framework for the recovery of true haplotypes from a metagenomic data set. The algorithm performs incremental haplotype recovery, using smoothed Naive Bayes — a simple, efficient and effective method.Hansel and Gretel pose several advantages over existing solutions: the framework is capable of recovering haplotypes from metagenomes, does not require a priori knowledge about the input data, makes no assumptions regarding the distribution of alleles at variant sites, is robust to error, and uses all available evidence from aligned reads, without altering or discarding observed variation. We evaluate our approach using synthetic metahaplomes constructed from sets of real genes and show that up to 99% of SNPs on a haplotype can be correctly recovered from short reads that originate from a metagenomic data set.
RECRUITMENT OF GROUPER BROODSTOCK ON THE BASIS OF SINGLE LOCUS DNA MARKERS
Authors: Rodrigues Kenneth F. , Tani Ahmad Z. , Baharum Syarul N. 
Published: August 2016

AbstractScientific breeding programs are founded on the screening and recruitment of genetically diverse broodstock, with the ultimate aim of developing heterogeneous breeding populations that host a collection of desirable traits. Single locus DNA markers can be applied to facilitate the process of selection as they are species specific, reliable, reproducible and easy to use. This study set forth to develop a library of single locus DNA markers for two commercially cultured species of groupers,Epinephelus fuscoguttatusandE. corallicola. DNA was isolated from one representative specimen of each species and utilized to construct shotgun genomic libraries. DNA sequences derived from the library were selected for the development of 42 and 41 single locus DNA markers forE. fuscoguttatusandE. corallicolarespectively. The markers were then tested against randomly selected specimens obtained from the wild. Genotyping results revealed that the species specific primers demonstrated the ability to distinguish between individuals from the same species into distinct operational taxonomic units (OTUs) on the basis of their differential DNA profiles, thus establishing a basis for selection based on genetic heterogeneity. The findings of this study present a strong case for the application of single locus DNA markers as molecular tools for the selection of broodstock on the basis of genotyping.
Spherical: an iterative workflow for assembling metagenomic datasets
Authors: Hitch Thomas , Creevey Christopher J 
Published: August 2016

AbstractThe consensus emerging from microbiome studies is that they are far more complex than previously thought, requiring deep sequencing. As deep sequenced datasets provide greater coverage than previous datasets, recovering a higher proportion of reads to the assembly is still a challenge. To tackle this issue, we set of to identify if multiple iterations of assembly would allow for otherwise lost contigs to be formed and studied and if so, how successful is such an avenue at improving the current methodology.A simulated metagenomic dataset was initially used to identify if multiple iterations of assembly produce useable contigs or mis-assembled artefacts were produced. Once we had confirmed that the secondary iterations were producing both accurate contigs without a reduction in contig quality we applied this methodology in the form ofSphericalto 3 metagenomic studies.The additional contigs produced by Spherical increased the number of reads aligning to an identified gene by 11–109% compared to the initial iterations assembly. As the size of the dataset increased, as did the amount of data multiple iterations were able to add.AvailabilitySpherical is implemented in Python 2.7 and available for use under a MIT licence agreement at:https://github.com/thh32/Spherical
Improved long read correction for denovoassembly using an FM-index
Authors: Holt James M. , Wang Jeremy R. , Jones Corbin D. , McMillan Leonard 
Published: August 2016

1AbstractLong read sequencing is changing the landscape of genomic research, especiallyde novoassembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging “hybrid” assemblies that use long reads for scaffolding and short reads for accuracy. To this end, we describe a novel application of a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We show that our method efficiently produces significantly higher quality corrected sequence than existing hybrid error-correction methods. We demonstrate the effectiveness of our method compared to state-of-the-art hybrid and long-read onlyde novoassembly methods.
A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data
Authors: Delussu Giovanni , Lianas Luca , Frexia Francesca , Zanetti Gianluigi 
Published: August 2016

AbstractThis work presents a scalable data access layer, called PyEHR, intended for building data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts openEHR formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structures indexing to speed up searches. The persistence is guarantee by a driver layer with a common driver interface. Presently, are implemented the interfaces with two NoSQL DBMS: MongoDB and Elasticsearch. The scalability of PyEHR has been evaluated experimentally through two types of tests, namely constant load and constant number of records, with queries of increasing complexity on a two synthetic datasets of ten millions records each, containing very complex openEHR archetype structures, distributed on up to ten working nodes.