bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of 10-year Risk of Incident Heart Failure in Elderly Hypertensive Population: The ANBP2 Study
Authors: Sahle Berhe W. , Owen Alice J. , Wing Lindon M.H. , Nelson Mark R. , Jennings Garry L.R. , Reid Christopher M. ,   on behalf of the Second Australian National Blood Pressure Study Management Committee
Published: September 2016

Abstract

BACKGROUND
Multivariable risk prediction models consisting of routinely collected measurements can facilitate early detection and slowing of disease progression through pharmacological and nonpharmacological risk factor modifications. This study aims to develop a multivariable risk prediction model for predicting 10-year risk of incident heart failure diagnosis in elderly hypertensive population.

METHODS
The derivation cohort included 6083 participants aged 65 to 84 years at baseline (1995–2001) followed for a median of 10.8 years during and following the Second Australian National Blood Pressure Study (ANBP2). Cox proportional hazards models were used to develop the risk prediction models. Variables were selected using bootstrap resampling method, and Akaike and Bayesian Information Criterion and C-statistics were used to select the parsimonious model. The final model was internally validated using a bootstrapping, and its discrimination and calibration were assessed.

RESULTS
Incident heart failure was diagnosed in 319 (5.2%) participants. The final multivariable model included age, male sex, obesity (body mass index &gt; 30kg/m2), pre-existing cardiovascular disease, average visit-to-visit systolic blood pressure variation, current or past smoking. The model has C-statistics of 0.719 (95% CI: 0.705–0.748) in the derivation cohort, and 0.716 (95% CI: 0.701–0.731) after internal validation (optimism corrected). The goodness-of-fit test showed the model has good overall calibration (χ2 = 1.78, P = 0.94).

CONCLUSION
The risk equation, consisting of variables readily accessible in primary and community care settings, allows reliable prediction of 10-year incident heart failure in elderly hypertensive population. Its application for the prediction of heart failure needs to be studied in the community setting to determine its utility for improving patient management and disease prevention.
Generalized poroviscoelastic model based on effective Biot theory and its application to borehole guided wave analysis
Authors: Liu Xu , Greenhalgh Stewart , Zhou Bing , Heinson Graham 
Published: September 2016

Abstract
A method using modified attenuation factor function is suggested to determine the parameters of the generalized Zener model approximating the attenuation factor function. This method is applied to constitute the poroviscoelastic model based on the effective Biot theory which considers the attenuative solid frame of reservoir. In the poroviscoelastic model, frequency-dependent bulk modulus and shear modulus of solid frame are represented by generalized Zener models. As an application, the borehole logging dispersion equations from Biot theory are extended to include effects from the intrinsic body attenuation in formation media in full-frequency range. The velocity dispersions of borehole guided waves are calculated to investigate the influence from attenuative bore fluid, attenuative solid frame of the formation and impermeable bore wall.
GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey – I. A low-frequency extragalactic catalogue
Authors: Hurley-Walker N , Callingham J R , Hancock P J , Franzen T M O , Hindson L , Kapińska A D , Morgan J , Offringa A R , Wayth R B , Wu C , Zheng Q , Murphy T , Bell M E , Dwarakanath K S , For B , Gaensler B M , Johnston-Hollitt M , Lenc E , Procopio P , Staveley-Smith L , Ekers R , Bowman J D , Briggs F , Cappallo R J , Deshpande A A , Greenhill L , Hazelton B J , Kaplan D L , Lonsdale C J , McWhirter S R , Mitchell D A , Morales M F , Morgan E , Oberoi D , Ord S M , Prabu T , Shankar N Udaya , Srivani K S , Subrahmanyan R , Tingay S J , Webster R L , Williams A , Williams C L 
Published: September 2016

Abstract
Using the Murchison Widefield Array (MWA), the low-frequency Square Kilometre Array precursor located in Western Australia, we have completed the GaLactic and Extragalactic All-sky MWA (GLEAM) survey, and present the resulting extragalactic catalogue, utilizing the first year of observations. The catalogue covers 24 831 square degrees, over declinations south of +30° and Galactic latitudes outside 10° of the Galactic plane, excluding some areas such as the Magellanic Clouds. It contains 307 455 radio sources with 20 separate flux density measurements across 72–231 MHz, selected from a time- and frequency-integrated image centred at 200 MHz, with a resolution of ≈2 arcmin. Over the catalogued region, we estimate that the catalogue is 90 per cent complete at 170 mJy, and 50 per cent complete at 55 mJy, and large areas are complete at even lower flux density levels. Its reliability is 99.97 per cent above the detection threshold of 5σ, which itself is typically 50 mJy. These observations constitute the widest fractional bandwidth and largest sky area survey at radio frequencies to date, and calibrate the low-frequency flux density scale of the southern sky to better than 10 per cent. This paper presents details of the flagging, imaging, mosaicking and source extraction/characterization, as well as estimates of the completeness and reliability. All source measurements and images are available online.1 This is the first in a series of publications describing the GLEAM survey results.
Sex Differences and Drug Dose Influence the Role of the α7 Nicotinic Acetylcholine Receptor in the Mouse Dextran Sodium Sulfate-Induced Colitis Model
Authors: AlSharari Shakir D. , Bagdas Deniz , Akbarali Hamid I. , Lichtman Patraic A. , Raborn Erinn S. , Cabral Guy A. , Carroll F. Ivy , McGee Elizabeth A. , Damaj M. Imad 
Published: September 2016

Abstract

Introduction:
α7 nicotinic acetylcholine receptors (nAChRs) play an important role in vagus nerve-based cholinergic anti-inflammatory effects. This study was designed to assess the role of α7 nAChRs in dextran sodium sulfate (DSS)-induced colitis in male and female mouse. We first compared disease activity and pathogenesis of colitis in α7 knockout and wild-type mice. We then evaluated the effect of several α7 direct and indirect agonists on the severity of disease in the DSS-induced colitis.

Methods:
Male and female adult mice were administered 2.5% DSS solution freely in the drinking water for 7 consecutive days and the colitis severity (disease activity index) was evaluated as well as colon length, colon histology, and levels of tumor necrosis factor-alpha colonic levels.

Results:
Male, but not female, α7 knockout mice displayed a significantly increased colitis severity and higher tumor necrosis factor-alpha levels as compared with their littermate wild-type mice. Moreover, pretreatment with selective α7 ligands PHA-543613, choline, and PNU-120596 decreased colitis severity in male but not female mice. The anti-colitis effects of these α7 compounds dissipated when administered at higher doses.

Conclusions:
Our results suggest the presence of a α7-dependent anti-colitis endogenous tone in male mice. Finally, our results show for the first time that female mice are less sensitive to the anti-colitis activity of α7 agonists. Ovarian hormones may play a key role in the sex difference effect of α7 nAChRs modulation of colitis in the mouse.

Implications:
Our collective results suggest that targeting α7 nAChRs could represent a viable therapeutic approach for intestinal inflammation diseases such as ulcerative colitis with the consideration of sex differences.
Adam Smith, Watch Prices, and the Industrial Revolution *
Authors: Kelly Morgan , Ó Gráda Cormac 
Published: September 2016

AbstractAlthough largely absent from modern accounts of the Industrial Revolution, watches were the first mass-produced consumer durable and were Adam Smith’s preeminent example of technological progress. In fact, Smith makes the notable claim that watch prices may have fallen by up to 95% over the preceding century, a claim that this article attempts to evaluate. We look at changes in the reported value of over 3,200 stolen watches from criminal trials in the Old Bailey in London from 1685 to 1810. Before allowing for quality improvements, we find that the real price of watches in nearly all categories falls steadily by 1.3% a year, equivalent to a fall of 75% over a century, showing that sustained innovation in the production of a highly complex artifact had already appeared in one important sector of the British economy by the early eighteenth century.
Advancing the Measurement of Care Coordination in Pediatric Behavioral Health
Authors: Jorina Maria , Cammaerts Ayesha , Singer Janice , Ozonoff Al , Chan Eugenia , Antonelli Richard , Gurvitz Michelle , Jenkins Kathy 
Published: September 2016

Abstract:

Objective:
To describe the measure review and evaluation process used to identify new measures of care coordination for children with behavioral health needs conducted as part of Massachusetts' Children's Health Insurance Program Reauthorization Act Quality Demonstration Grant.

Method:
The Massachusetts Child Health Quality Coalition identified a shortage of pediatric measures of care coordination in behavioral health. After an extensive literature review, the Measure Development Committee applied the Care Coordination Key Elements Framework (Framework), which was designed as part of the grant work, and used a modified RAND Delphi method to conduct feasibility and validity evaluation and propose the new candidate measures for further rigorous testing.

Results:
Thirty-two measures were evaluated. One existing Healthcare Effectiveness Data and Information Set and 8 newly proposed measures met the criteria for feasibility and reliability. These measures represented each of the key elements contained in the Framework. The measures need further testing to ensure scientific acceptability and wide usability.

Conclusion:
A multipronged methodology was used to propose measures of care coordination in the space of pediatric behavioral health to fill the identified gaps in existing measures.
Managing Incidental Lung Nodules in Patients With a History of Oncologic Disease
Authors: Occhipinti Mariaelena , Heidinger Benedikt H. , Pfannenberg Christina , Munden Reginald F. , Eisenberg Ronald L. , Bankier Alexander A. 
Published: September 2016

Purpose:
The aim of this study was to analyze the impact that a clinical history of an oncologic disease may have on the management decisions for incidentally detected lung nodules on chest computed tomographic (CT) examinations.

Materials and Methods:
An electronic survey was sent to all 796 members of the Society of Thoracic Radiology regarding criteria for the management of incidentally detected lung nodules in oncologic patients, as well as recommendations for nodule follow-up. Nodule characteristics and clinical parameters used by respondents were analyzed. Differences between variables were examined using the χ2 test.

Results:
Of the 796 Society of Thoracic Radiology members, 178 (22.36%) replied. Most respondents were subspecialized in cardiothoracic imaging (92.70%) and practiced in an “academic or teaching hospital setting” (75.28%) with a “dedicated oncology center” (94.03%). “History of oncologic disease” was the most important factor (98.87%) for management decisions. In patients with such a history, respondents most commonly used “experience and common sense” (56.74%) and reported “all incidentally found lung nodules” (65.73%, P<0.0001). “Size” and “shape” were the 2 most important nodule characteristics (33.61% and 27.05%, respectively) used to consider a nodule “clinically relevant,” and “size” (44.07%) was also the most important nodule characteristic prompting recommendation for short-term CT follow-up. Follow-up CT examinations in oncologic patients were recommended by 75.84% of respondents.

Conclusions:
In patients with a history of oncologic disease, radiologists tend to report every detected nodule and to routinely recommend follow-up CT examinations. Although most radiologists rely on “experience and common sense” in managing these nodules, greater standardization of lung nodule management in oncologic patients is needed, ideally through guidelines tailored to this patient population.
Application of the stochastic labeling methods with random-sequence barcodes for simultaneous quantification and sequencing of environmental 16S rRNA genes
Authors: Hoshino Tatsuhiko , Inagaki Fumio 
Published: September 2016

AbstractNext-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5’ end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103to 5.0 × 104copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.
Identification of outcome-related driver mutations in cancer using conditional co-occurrence distributions
Authors: Treviño Victor , Martínez-Ledesma Emmanuel , Tamez-Peña José 
Published: September 2016

AbstractThe methods proposed for the detection of cancer driver mutations are based on the estimation of background mutation rate, impact on protein function, or network influence. Instead, we focus on those influencing patient survival. For this, an approximation of the log-rank test has been systematically applied even though it assumes a large and similar number of patients in both risk groups, which is violated in cancer genomics. Here, we propose VALORATE, a novel algorithm for the estimation of the null distribution for the log-rank test independently of the number of mutations. VALORATE is based on conditional distributions of the co-occurrences between events and mutations. The results using simulations, comparisons with other methods, TCGA and ICGC cancer datasets, and validations, suggests that VALORATE is accurate, fast, and can identify known and novel gene mutations. Our proposal and results may have important implications in cancer biology, in bioinformatics analyses, and ultimately in precision medicine.
kWIP: Thek-mer Weighted Inner Product, ade novoEstimator of Genetic Similarity
Authors: Murray Kevin D. , Webers Christfried , Ong Cheng Soon , Borevitz Justin , Warthmann Norman 
Published: September 2016

AbstractModern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals or samples in an unbiased manner, preferablyde novo. The rapid and unbiased estimation of genetic relatedness has the potential to overcome reference genome bias, to detect mix-ups early, and to verify that biological replicates belong to the same genetic lineage before conclusions are drawn using mislabelled, or misidentified samples.We present thek-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity.kWIPcombines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from theirk-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include detecting sample identity and mix-up, non-obvious genomic variation, and population structure.We show thatkWIPcan reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses.kWIPis written in C++, licensed under the GNU GPL, and is available fromhttps://github.com/kdmurray91/kwip.Author SummaryCurrent analysis of the genetic similarity of samples is overly dependent on alignment to reference genomes, which are often unavailable and in any case can introduce bias. We address this limitation by implementing an efficient alignment free sequence comparison algorithm (kWIP). The fast, unbiased analysiskWIPperforms should be conducted in preliminary stages of any analysis to verify experimental designs and sample metadata, catching catastrophic errors earlier.kWIPextends alignment-free sequence comparison methods by operating directly on sequencing reads.kWIPuses an entropy-weighted inner product overk-mers as a estimator of genetic relatedness. We validatekWIPusing rigorous simulation experiments. We also demonstrate high sensitivity and accuracy even where there is modest divergence between genomes, and/or when sequencing coverage is low. We show high sensitivity in replicate detection, and faithfully reproduce published reports of population structure and stratification of microbiomes. We provide a reproducible workflow for replicating our validation experiments.kWIPis an efficient, open source software package. Our software is well documented and cross platform, and tutorial-style workflows are provided for new users.
Antibiotic susceptibility of bacterial colonies: An assay and experiments withStaphylococcus aureus
Authors: Shao Xinxian , Kim Justin , Jeong Ha Jun , Levin Bruce 
Published: September 2016

AbstractA method is presented to evaluatein vitrothe efficacy of antibiotics to treat bacteria growing as discrete colonies on surfaces and the contribution of the colony structure to the antibiotic susceptibility of bacteria. Using this method, we explored the relative efficacy of six bactericidal and three bacteriostatic antibiotics to inhibit the growth and killStaphylococcus aureuscolonies of different sizes, densities and ages. As measured by the reduction in viable cell density relative to untreated controls, of the bactericidal drugs tested ciprofloxacin and gentamicin were most effective. By this criteria, ampicillin was more effective than oxacillin. Daptomycin and vancomycin were virtually ineffective for treatingS. aureusgrowing as colonies. The bacteriostatic antibiotic tested, tetracycline, linezolid and erythromycin were all able to prevent the growth ofS. aureuscolonies and did so even more effectively than daptomycin, which is highly bactericidal in liquid culture. The results of these experiments and other observations suggest that relative inefficacy of oxacillin, vancomycin and daptomycin to killS. aureusin colonies is due to the density and physiological state of the bacteria rather than the inability of these drugs to penetrate the colonies. The methods developed here are general and can be used to explore the efficacy of antibiotics to treat bacteria growing in biofilms as well as discrete colonies.
Aerobic H2respiration enhances metabolic flexibility of methanotrophic bacteria
Authors: Carere Carlo R. , Hards Kiel , Houghton Karen M. , Power Jean F. , McDonald Ben , Collet Christophe , Gapes Daniel J. , Sparling Richard , Cook Gregory M. , Greening Chris , Stott Matthew B. 
Published: September 2016

AbstractMethanotrophic bacteria are important soil biofilters for the climate-active gas methane. The prevailing opinion is that these bacteria exclusively metabolise single-carbon, and in limited instances, short-chain hydrocarbons for growth. This specialist lifestyle juxtaposes metabolic flexibility, a key strategy for environmental adaptation of microorganisms. Here we show that a methanotrophic bacterium from the phylum Verrucomicrobia oxidises hydrogen gas (H2) during growth and persistence.Methylacidiphilumsp. RTK17.1 expresses a membrane-bound hydrogenase to aerobically respire molecular H2at environmentally significant concentrations. While H2oxidation did not support growth as the sole electron source, it significantly enhanced mixotrophic growth yields under both oxygen-replete and oxygen-limiting conditions and was sustained in non-growing cultures starved for methane. We propose that H2is consumed by this bacterium for mixotrophic growth and persistence in a manner similar to other non-methanotrophic soil microorganisms. We have identified genes encoding oxygen-tolerant uptake hydrogenases in all publicly-available methanotroph genomes, suggesting that H2oxidation serves a general strategy for methanotrophs to remain energised in chemically-limited environments.