bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Total Lung Capacity Determined by Plethysmography With Computed Tomographic Segmentation Using CALIPER
Authors: Matsumoto Andrew J. , Bartholmai Brian J. , Wylam Mark E. 
Published: November 2016

Purpose:
Traditionally, determination of total lung capacity (TLC) by plethysmography (TLCpleth) has been important in the diagnosis of lung diseases. Alternatively, data acquired from computerized tomography (CT) can be utilized to calculate a measure of TLC (TLCCT). The clinical utility of TLCCT is not certain. We sought to determine, in a clinical setting, whether TLCCT correlates with TLCpleth across a range of lung diseases and scanning techniques. In addition, we determined whether TLCCT affects the interpretation of pulmonary function tests.

Subjects and Methods:
Records of 118 of 148 consecutive lung transplant recipients were reviewed and determined to have coinciding pulmonary function tests, including plethysmography as well as volumetric chest CT performed supine during full inspiration. CT images acquired with a wide range of scanning protocols were analyzed using CALIPER, a software program for lung and trachea extraction from a CT volume and volumetric tissue characterization of the lung. Segmentation of the lung was achieved by using completely automated dynamic thresholding and region-growing techniques developed to extract the relatively low-density lung and tracheal anatomy from the CT data set without user intervention.

Results:
TLCpleth and TLCCT were strongly related with a correlation coefficient of 0.88 (P<0.001). The efficacy of the CT-derived measure was not influenced by specific lung diagnoses, age, height, body mass index, or spirometric parameters. TLCCT did not misidentify any diagnosis of restrictive lung disease, nor hyperinflation.

Conclusions:
In a clinical setting, CT segmentation analysis provides a favorable determination of TLC compared with traditional plethysmography. The technique has general applicability across varying CT data acquisition protocols, lung diseases, and patient characteristics. TLCCT may substitute for TLCpleth in pulmonary function interpretation and may be preferable for some patients in whom plethysmography is difficult to perform, such as transplant subjects with severe pulmonary fibrosis.
MEG May Reveal Hidden Population of Spikes in Epilepsy With Porencephalic Cyst/Encephalomalacia
Authors: Kakisaka Yosuke , Wang Zhong I. , Shibata Sumiya , Takahashi Yoko , Mosher John C. , Alexopoulos Andreas V. , Burgess Richard C. 
Published: November 2016

Summary:
Porencephalic cyst/encephalomalacia is often associated with intractable epilepsy. A limited number of studies reported magnetoencephalography's (MEG's) potential to help construct treatment strategy for epilepsies associated with porencephalic cyst/encephalomalacia. The authors present here simultaneous electroencephalography (EEG) and MEG findings in three adult patients with pediatric-onset epilepsy due to porencephalic cyst/encephalomalacia. There were two types of spikes: one type was detected by MEG only (EEG−/MEG+), and the other detected by both EEG and MEG (EEG+/MEG+). Both types were seen in all three cases. The EEG−/MEG+ spikes all formed tight clusters; in contrast, the majority of EEG+/MEG+ spikes formed loose clusters. These data suggest that MEG may be helpful to better identify spike populations in epilepsy patients with porencephalic cyst/encephalomalacia. If hidden spike populations were to be found by MEG, this information would affect the interpretation of patient's pathophysiology and planning of intracranial electrode placement.
Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations
Authors: Bray Marcus S. , Wu Jieying , Reed Benjamin C. , Kretz Cecilia B. , Belli Keaton M. , Simister Rachel L. , Henny Cynthia , Stewart Frank J. , DiChristina Thomas J. , Brandes Jay A. , Fowle David A. , Crowe Sean A. , Glass Jennifer B. 
Published: November 2016

AbstractReactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4oxidation. The balance between Fe(III) reduction, methanogenesis, and methane oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4fluxes to the atmosphere, thereby regulating the capacity for CH4to warm the early Earth under the Faint Young Sun. We studied CH4and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia over three successive transfers (500 days total). Iron reduction, methanogenesis, methane oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4production was observed in the presence of goethite, highlighting the potential for reactive Fe(III)-oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4oxidation, although some incubations displayed CH4-stimulated Fe(III)-reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III)-oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4as a greenhouse gas throughout the first half of Earth history.
Functional transcriptomics in diverse intestinal epithelial cell types reveals robust gut microbial sensitivity of microRNAs in intestinal stem cells
Authors: Peck Bailey C. E. , Mah Amanda T. , Pitman Wendy A. , Ding Shengli , Lund P. Kay , Sethupathy Praveen 
Published: November 2016

ABSTRACTGut microbiota play an important role in regulating the development of the host immune system, metabolic rate, and at times, disease pathogenesis. The factors and mechanisms that mediate communication between microbiota and the intestinal epithelium are poorly understood. We provide novel evidence that microbiota may control intestinal epithelial stem cell (IESC) proliferation in part through microRNAs (miRNAs). We demonstrate that miRNA profiles differ dramatically across functionally distinct cell types of the mouse jejunal intestinal epithelium and that miRNAs respond to microbiota in a highly cell-type specific manner. Importantly, we also show that miRNAs in IESCs are more prominently regulated by microbiota compared to miRNAs in any other intestinal epithelial cell (IEC) subtype. We identify miR-375 as one miRNA that is significantly suppressed by the presence of microbiota in IESCs. Using a novel method to knockdown gene and miRNA expressionex vivoenteroids, we demonstrate that we can knockdown gene expression in Lgr5+IESCs. Furthermore, when we knockdown miR-375 in IESCs, we observe significantly increased proliferative capacity. Understanding the mechanisms by which microbiota regulate miRNA expression in IESCs and other IEC subtypes will elucidate a critical molecular network that controls intestinal homeostasis and, given the heightened interest in miRNA-based therapies, may offer novel therapeutic strategies in the treatment of gastrointestinal diseases associated with altered IESC function.
Structure-based alignment of human caspase recruitment domains provides a framework for understanding their function
Authors: Boyle Joseph P. , Monie Tom 
Published: November 2016

AbstractIntracellular signalling is driven by protein-protein interactions. Members of the Death Domain superfamily mediate protein-protein interactions in both cell death and innate immune signalling pathways. They drive the formation of macromolecular complexes that act as a scaffold for protein recruitment and downstream signal transduction. Death Domain family members have low sequence identity, complicating their identification and predictions of their structure and function. We have taken all known human caspase recruitment domains (CARDs), a subfamily of the Death Domain superfamily, and generated a structure-guided sequence alignment. This alignment has enabled the identification of 14 positions that define the hydrophobic core and present a template for the identification of novel CARD sequences. We identify a conserved salt bridge in over half of all human CARDs and find a subset of CARDs likely to be regulated by tyrosine phosphorylation in their type I interface. Our alignment highlights that the CARDs of NLRC3 and NLRC5 are likely to be pseudodomains that have lost some of their original functionality. Together these studies demonstrate the benefits of structure-guided sequence alignments in understanding protein functionality.
A lottery simulation model for predicting cancer risk based on the strength and abundance of individual mutations
Authors: Wolfe Alexander J , Giangreco Adam 
Published: November 2016

AbstractModels for predicting an individual’s risk of developing cancer are complicated by a lack of well-conserved mutations present in most types of disease. To address this challenge we developed a simple lottery simulation of cancer development based solely on the abundance and relative survival advantage of mutations present within individual stem or progenitor cells. In simulations requiring few mutations or that involve mutations exhibiting a strong survival advantage cancers develop in our simulation in a progressive manner amenable to oncogene-based risk prediction. In contrast, in simulations involving numerous mutations that lack a strong survival advantage, a stochastic process of neutral drift and punctuated equilibrium determines eventual tumour formation. In these situations, the development of cancer is largely attributable to the rate of mutational variability amongst progenitor cells rather than the identity and relative survival advantage of the mutations present at any single time point. These results suggest that measuring rates of stem cell mutational variability represents an important component of predicting an individual’s risk of developing cancer.
Functional constraints on replacing an essential gene with its ancient and modern homologs
Authors: Kacar Betül , Garmendia Eva , Tunçbağ Nurcan , Andersson Dan I. , Hughes Diarmaid 
Published: November 2016

AbstractThe complexity hypothesis posits that network connectivity and protein function are two important determinants of how a gene adapts to and functions in a foreign genome. Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenoustufAgene in theEscherichia coligenome with its extant and ancestral homologs. The extant homologs representedtufvariants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrectedtufsequences dating from 0.7 to 3.6 bya. Our results demonstrate that all of the foreigntufgenes are transferable to theE. coligenome, provided that an additional copy of the EF-Tu gene,tufB, remains present in theE. coligenome. However, when thetufBgene was removed, only the variants obtained from the γ-proteobacterial family (extant and ancestral), supported growth. This demonstrates the limited functional interchangability ofE. coli tufwith its homologs. Our data show a linear correlation between relative bacterial fitness and the evolutionary distance of the extanttufhomologs inserted into theE. coligenome. Our data and analysis also suggest that the functional conservation of protein activity, and its network interactivity, act to constrain the successful transfer of this essential gene into foreign bacteria.
biMM: Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements
Authors: Pirinen Matti , Benner Christian , Marttinen Pekka , Järvelin Marjo-Riitta , Rivas Manuel A. , Ripatti Samuli 
Published: November 2016

AbstractGenetic research utilizes a decomposition of trait variances and covariances into genetic and environmental parts. Our software package biMM is a computationally efficient implementation of a bivariate linear mixed model for settings where hundreds of traits have been measured on partially overlapping sets of individuals.AvailabilityImplementation in R freely available atwww.iki.fi/mpirinen.
The type IVa pilus machinery is pre-installed during cell division
Authors: Carter Tyson , Buensuceso Ryan N.C. , Tammam Stephanie , Lamers Ryan P. , Harvey Hanjeong , Howell P. Lynne , Burrows Lori L. 
Published: November 2016

ABSTRACTType IV pili (T4aP) are ubiquitous microbial appendages used for adherence, twitching motility, DNA uptake, and electron transfer. Many of these functions depend on dynamic assembly and disassembly of the pilus by a megadalton-sized, cell envelope-spanning protein complex located at the poles of rod-shaped bacteria. How the T4aP assembly complex becomes integrated into the cell envelope in the absence of dedicated peptidoglycan (PG) hydrolases is unknown. After ruling out potential involvement of housekeeping PG hydrolases in installation of the T4aP machinery inP. aeruginosa, we discovered that key components of inner (PilMNOP) and outer (PilQ) membrane subcomplexes are recruited to future sites of cell division. Mid-cell recruitment of a fluorescently tagged alignment subcomplex component, mCherry-PilO, depended on PilQ secretin monomers – specifically, their N-terminal PG-binding AMIN domains. PilP, which connects PilO to PilQ, was required for recruitment, while PilM, which is structurally similar to divisome component FtsA, was not. Recruitment preceded secretin oligomerization in the outer membrane, as loss of the PilQ pilotin, PilF, had no effect on localization. These results were confirmed in cells chemically blocked for cell division prior to outer membrane invagination. The hub protein FimV and a component of the Polar Organelle Coordinator complex – PocA – were independently required for mid-cell recruitment of PilO and PilQ. Together, these data reveal an integrated, energy-efficient strategy for the targeting and pre-installation – rather than retrofit – of the T4aP system into nascent poles, without the need for dedicated PG-remodelling enzymes.
SOFIA: an R package for enhancing genetic visualization with Circos
Authors: Diaz-Garcia Luis , Covarrubias-Pazaran Giovanny , Schlautman Brandon , Zalapa Juan 
Published: November 2016

AbstractVisualization of data from any stage of genetic and genomic research is one of the most useful approaches for detecting potential errors, ensuring accuracy and reproducibility, and presentation of the resulting data. Currently software such as Circos, ClicO FS, and RCircos, among others, provide tools for plotting a variety of genetic data types in a concise manner for data exploration and presentation. However, each of the programs have one or more disadvantages that limit their usability in data exploration or construction of publication quality figures, such as inflexibility in formatting and configuration, reduced image quality, lack of potential for automation, or requirements of high-level computational expertise. Therefore, we developed the R package SOFIA, which leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. The advantages of integrating both R and Circos into SOFIA are numerous. R is a very powerful, mid-level programming language widely used among the genetic and genomic research community, while Circos has proven to be a novel software for arranging genomic data to create aesthetical publication quality circular figures. Producing Circos figures in R with SOFIA is simple, requires minimal coding experience, even for complex figures that incorporate high-dimensional genetic information, and allows simultaneous analysis and visual exploration of genomic and genetic data in a single programming environment.
Overcoming evolved resistance to population-suppressing homing-based gene drives
Authors: Marshall John M. , Buchman Anna , Sánchez C. Héctor M. , Akbari Omar S. 
Published: November 2016

AbstractThe use of homing-based gene drive systems to modify or suppress wild populations of a given species has been proposed as a solution to a number of significant ecological and public health related problems, including the control of mosquito-borne diseases. The recent development of a CRISPR-Cas9-based homing system for the suppression ofAnopheles gambiae, the main African malaria vector, is encouraging for this approach; however, with current designs, the slow emergence of homing-resistant alleles is expected to result in suppressed populations rapidly rebounding, as homing-resistant alleles have a significant fitness advantage over functional, population-suppressing homing alleles. To explore this concern, we develop a mathematical model to estimate tolerable rates of homing-resistant allele generation to suppress a wild population of a given size. Our results suggest that, to achieve meaningful population suppression, tolerable rates of resistance allele generation are orders of magnitude smaller than those observed for current designs for CRISPR-Cas9-based homing systems. To remedy this, we propose a homing system architecture in which guide RNAs (gRNAs) are multiplexed, increasing the effective homing rate and decreasing the effective resistant allele generation rate. Modeling results suggest that the size of the population that can be suppressed increases exponentially with the number of multiplexed gRNAs and that, with six multiplexed gRNAs, a mosquito species could potentially be suppressed on a continental scale. We also demonstrate successful multiplexingin vivoinDrosophila melanogasterusing a ribozyme-gRNA-ribozyme (RGR) approach – a strategy that could readily be adapted to engineer stable, homing-based suppression drives in relevant organisms.
The determinants of risk disclosure by banking institutions
Authors: Nahar Shamsun , Azim Mohammad , Jubb Christine 
Published: November 2016

PurposeThe purpose of this paper is to investigate the extent of risk disclosure and the factors determining this for all listed banks in Bangladesh.Design/methodology/approachRelying on a theoretical framework based on agency theory and the creation of a risk disclosure index (RDI) based on International Financial Reporting Standard (IFRS) 7, Basel II: market discipline, and prior literature, hand-collected data from the annual reports of all 30 banks traded on the Dhaka Stock Exchange over 2007-2012, creating 180 bank-year observations, are analysed.FindingsThe study suggests that implementation of IFRS 7 and Basel II: market discipline standards in a non-mandated environment raised the extent of risk disclosure in every category of financial institution risk (market, credit, liquidity, operational and equities). The effect can be attributed to regulatory concerns and voluntary adoption of international disclosure standards in the banking industry in Bangladesh. Specifically, whilst the determinants of disclosure vary across types of risk, the number of risk committees, leverage, company size, the existence of a risk management unit, board size and a Big4 affiliate auditor are significant determinants of at least one category of risk disclosure.Research limitations/implicationsThe source of risk disclosures is limited to listed banks’ annual reports.Practical implicationsThe RDI, developed in this paper, contributes to the literature by: first, quantifying the extent of each of five types of risk disclosure; and second, identifying the factors determining them. Stakeholders, particularly depositors and investors, can use this index to select or monitor their bank of interest.Originality/valueThe RDI was developed according to the most relevant standards – IFRS 7 and Basel II: market discipline, plus prior scholarly literature. This type of benchmarking has not been conducted to date in previous studies. Inferences about risk disclosure are based on archival data derived from all listed banks in a virtually unregulated environment. Further, the study complements the literature by providing support for the applicability of agency theory in investigating the level of risk disclosure by banks.
Collection building trend among the institutes of higher learning in India: a preferential race between print and electronic resources
Authors: Pandita Ramesh , Singh Shivendra 
Published: November 2016

Purpose
The present study aims to assess the resource procurement preferences among the leading academic libraries of the institutes of higher learning across India. The study analyses the amount and percentage of budget spent by the institutions under study during the period 2012-2013, 2013-2014 and 2014-2015 on the procurement of print and electronic resources in their libraries. The study also discusses about concerns with regard to the subscription of e-resources and the reasons for weaning interest among the Indian academicians towards the print resources.

Design/methodology/approach
By and large, the scope of the study is limited to institutes of higher learning across India, but reflects a great deal of relevance to the global higher education practices. The study has been undertaken on the 20 leading institutes each from Universities, Institutes of Management and Institutes of Technology in India, based on the ranking list released by the Ministry of Human Resource Development, Government of India, on 4 April 2016.

Findings
The electronic documents are the dominant forms of present day library procurements in India, with the print struggling to retain its readership. The Institutes of Engineering and Technology and Management have almost similar procurement preferences, spending almost three-fourth of their library budgets on the procurement of e-documents. On average, the University libraries in India have spent 43.54 per cent of their budget on the procurement of print resources and 56.46 per cent of their budget on the procurement of electronic resources during the period of study. Similarly, on average, each Institute of Engineering and Technology has spent 24.04 per cent of their library budget on the procurement of print documents and 75.96 per cent towards the procurement of electronic resources, whereas 27.51 per cent of the library budget by the Institutes of Management in India is being spent on the procurement of print resources and 72.49 per cent towards the procurement of electronic resources.

Originality/value
The study is original and is first of its kind, undertaken on three different category of institutions, based on the national ranking of the country.