bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Analysis of the Intestinal Microbiota in Liver Transplantation
Authors: Kato Karin , Nagao Miki , Miyamoto Kentaro , Oka Kentaro , Takahashi Motomichi , Yamamoto Masaki , Matsumura Yasufumi , Kaido Toshimi , Uemoto Shinji , Ichiyama Satoshi 
Published: March 2017

Background
Increasing evidence suggests that the intestinal microbiota plays an important role in liver diseases. However, the dynamics of the intestinal microbiota during liver transplantation (LT) and its potential role in clinical course remain unknown.

Methods
We prospectively analyzed the intestinal microbiota of 38 patients who underwent LT in Kyoto University Hospital. We characterized the microbial compositions of fecal specimens from LT patients using a metagenomics approach by an Illumina MiSeq platform. We analyzed the diversity of microbiota sequentially from pretransplantation until 2 months after LT and also compared the microbiota during an episode of acute cellular rejection (ACR) and bloodstream infections (BSI) to the microbial composition of time-matched fecal specimens obtained from patients who did not experience ACR or BSI, respectively.

Results
Three hundred twenty fecal specimens were analyzed. Dynamic changes were observed in the microbial composition of LT recipients during the perioperative period. Over the course of LT, the mean diversity index decreased during the first 3 weeks after LT and gradually increased during our observation period. The loss of intestinal microbiota diversity was associated with high Child-Pugh scores, high model for end-stage liver disease scores, ACR, and BSI. At the family level, Bacteroides, Enterobacteriaceae, Streptococcaceae, and Bifidobacteriaceae were increased whereas Enterococcaceae, Lactobacillaceae, Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae were decreased in ACR patients.

Conclusions
The microbiota of LT patients was associated with the severity of liver diseases and the presence of ACR and BSI. These results lay the groundwork for more comprehensive investigations of microbiota characteristics to identify diagnostic markers for transplant health and to guide intervention strategies to improve transplant outcomes.
Network component analysis reveals developmental trajectories of structural connectivity and specific alterations in autism spectrum disorder
Authors: Ball Gareth , Beare Richard , Seal Marc L. 
Published: March 2017

The structural organisation of the brain can be characterised as a hierarchical ensemble of segregated modules linked by densely interconnected hub regions that facilitate distributed functional interactions. Disturbances to this network may be an important marker of abnormal development. Recently, several neurodevelopmental disorders, including autism spectrum disorder (ASD), have been framed as disorders of connectivity but the full nature and timing of these disturbances remain unclear.In this study, we use non-negative matrix factorisation, a data-driven, multivariate approach, to model the structural network architecture of the brain as a set of superposed subnetworks, or network components.In an openly available dataset of 196 subjects scanned between 5 to 85 years we identify a set of robust and reliable subnetworks that develop in tandem with age and reflect both anatomically local and long-range, network hub connections. In a second experiment, we compare network components in a cohort of 51 high-functioning ASD adolescents to a group of age-matched controls. We identify a specific subnetwork representing an increase in local connection strength in the cingulate cortex in ASD (t=3.44, p<0.001).This work highlights possible long-term implications of alterations to the developmental trajectories of specific cortical subnetworks.
Daisy quorum drives for the genetic restoration of wild populations
Authors: Min John , Noble Charleston , Najjar Devora , Esvelt Kevin M. 
Published: March 2017

AbstractAn ideal gene drive system to alter wild populations would 1) exclusively affect organisms within the political boundaries of consenting communities, and 2) be capable of restoring any engineered population to its original genetic state. Here we describe ‘daisy quorum’ drive systems that meet these criteria by combining daisy drive with underdominance. A daisy quorum drive system is predicted to spread through a population until all of its daisy elements have been lost, at which point its fitness becomes frequency-dependent: mostly altered populations become fixed for the desired change, while engineered genes at low frequency are swiftly eliminated by natural selection. The result is an engineered population surrounded by wild-type organisms with limited mixing at the boundary. Releasing large numbers of wild-type organisms or a few bearing a population suppression element can reduce the engineered population below the quorum, triggering elimination of all engineered sequences. In principle, the technology can restore any drive-amenable population carrying engineered genes to wild-type genetics. Daisy quorum systems may enable efficient, community-supported, and genetically reversible ecological engineering.SummaryLocal communities should be able to control their own environments without forcing those choices on others. Ideally, each community could reversibly alter local wild organisms in ways that cannot spread beyond their own boundaries, and any engineered population could be restored to its original genetic state. We've invented a 'daisy quorum' drive system that appears to meet these criteria.“Daisy” refers to a daisy drive, which typically uses a daisy-chain of linked genes to spread a change through a local population while losing links every generation until it stops spreading. “Quorum” reflects the system's ability to “vote” on whether a local population should be altered or not: once all daisy elements are lost, it favors replication by the altered version or the original depending on which is more abundant in the local area. Put together, they result in a change that first spreads through a local population, then either becomes locally prevalent is eliminating, inhibiting mixing at the boundary. All organisms in the target population are altered, but changes are unable to spread much beyond that area due to being greatly outnumbered by wild-type organisms and consequently less able to replicate.We haven't yet performed any experiments involving daisy quorum systems. Rather, we’re describing what we intend to do, including the safeguards we will use and our assessment of risks, in the hope that others will evaluate our plans and tell us if there's anything wrong that we missed. We hope that all researchers working on gene drive systems - and other technologies that could impact the shared environment - will similarly pre-register their plans. Sharing plans can reduce needless duplication, accelerate progress, and make the proposed work safer for everyone.
A homozygous missense mutation inERAL1,encoding a mitochondrial rRNA chaperone, causes Perrault syndrome
Authors: Chatzispyrou Iliana A. , Alders Marielle , Guerrero-Castillo Sergio , Perez Ruben Zapata , Haagmans Martin A. , Mouchiroud Laurent , Koster Janet , Ofman Rob , Baas Frank , Waterham Hans R. , Spelbrink Johannes N. , Auwerx Johan , Mannens Marcel M. , Houtkooper Riekelt H. , Plomp Astrid S. 
Published: March 2017

AbstractPerrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in theERAL1gene (c.707A>T; p.Asn236Ile). Since ERAL1 protein binds to the mitochondrial 12S rRNA and is involved in the assembly of the small mitochondrial ribosomal subunit, the identified variant represented a likely candidate.In silicoanalysis of a 3D model for ERAL1 suggested that the mutated residue hinders protein-substrate interactions, potentially affecting its function. On a molecular basis, PS skin fibroblasts had reduced ERAL1 protein levels. Complexome profiling of the cells showed an overall decrease in the levels of assembled small ribosomal subunit, indicating that theERAL1variant affects mitochondrial ribosome assembly. Moreover, levels of the 12S rRNA were reduced in the patients, and were fully rescued by lentiviral expression of wild type ERAL1. At the physiological level, mitochondrial respiration was markedly decreased in PS fibroblasts, confirming disturbed mitochondrial function. Finally, knockdown of theC. elegans ERAL1homologueE02H1.2almost completely blocked egg production in worms, mimicking the compromised fertility in PS-affected women. Our cross-species data in patient cells and worms support the hypothesis that mutations inERAL1can cause PS and are associated with changes in mitochondrial metabolism.
Whole genome sequences of the raspberry and strawberry pathogensPhytophthora rubiandP. fragariae
Authors: Tabima Javier F. , Kronmiller Brent A. , Press Caroline M. , Tyler Brett M. , Zasada Inga A. , Grünwald Niklaus J. 
Published: March 2017

AbstractPhytophthora rubiandP. fragariaeare two closely related oomycete plant pathogens that exhibit strong morphological and physiological similarities, but are specialized to infect different hosts of economic importance, namely raspberry and strawberry. Here, we report the draft genome sequences of these twoPhytophthoraspecies as a first step towards understanding the genomic processes underlying plant host adaptation in these pathogens.
A mechanistic model for the evolution of multicellularity
Authors: Amado André , Batista Carlos , Campos Paulo R. A. 
Published: March 2017

AbstractThrough a mechanistic approach we investigate the formation of aggregates of variable sizes, accounting mechanisms of aggregation, dissociation, death and reproduction. In our model, cells can produce two metabolites, but the simultaneous production of both metabolites is costly in terms of fitness. Thus, the formation of larger groups can favor the aggregates to evolve to a configuration where division of labor arises. It is assumed that the states of the cells in a group are those that maximizes organismal fitness. In the model it is considered that the groups can grow linearly, forming a chain, or compactly keeping a roughly spherical shape. Starting from a population consisting of single-celled organisms, we observe the formation of groups with variable sizes and usually much larger than two-cell aggregates. Natural selection can favor the formation of large groups, which allows the system to achieve new and larger fitness maxima.
Data-driven modeling of corrosion and scale deposition rate in economizer
Authors: Kumari Amrita , Das S.K. , Srivastava P.K. 
Published: March 2017

Purpose
The aim of this paper is to study the effect of the parametric sensitivity of all critical parameters of feed water and other operating variables on the corrosion rate and oxide scale deposition on economizer tubes of a typical coal-fired 250-MW boiler.

Design/methodology/approach
In this paper, a multilayer perceptron-based artificial neural network (ANN) model has been developed to envisage the corrosion rate and oxide scale deposition rate in economizer tubes of a coal-fired boiler. The neural network architecture has been optimized using an efficient gradient-based network optimization algorithm to minimize the training and testing errors rapidly during simulation runs.

Findings
The parametric sensitivity of all critical parameters of feed water and other operating variables on the corrosion rate and oxide scale deposition activities has been investigated. It has been observed that dissolved oxygen, dissolved copper content, residual hydrazine content and pH of the feed water have a relatively predominant influence on the corrosion rate, whereas dissolved iron content, silica content, pH and temperature of the feed water have a moderately major influence on oxide scale deposition phenomenon. There has been very good agreement between ANN model predictions and the measured values of corrosion rate and oxide scale deposition rate substantiated by the regression fit between these values.

Originality/value
This paper details the development of an alternative model to accurately predict corrosion rate and deposition rate on the inner surface of economizer tubes of a boiler over first principle-based kinetic model.
Debiasing the halo effect in audit decision: evidence from experimental study
Authors: Utami Intiyas , Kusuma Indra Wijaya , Gudono Gudono , Supriyadi Supriyadi 
Published: March 2017

Purpose
The purpose of this paper is to test the existence of the halo effect caused by the presentation of information scope (holistic/specific), which can eventually lead to an inaccurate risk assessment of material misstatement. Empirical evidence is provided to demonstrate that methods of knowledge acquisition (explanatory feedback and self-explanation) are able to mitigate the halo effect.

Design/methodology/approach
This study used an experimental research, which focused on control and experimental groups in order to determine if the halo effect caused by the information scope (holistic/specific) can be mitigated via the explanatory feedback or self-explanation method.

Findings
It was found that auditors who received information from the holistic scope tend to experience the halo effect and eventually, their risk assessments of material misstatement also became less accurate when compared to auditors who received information from the specific scope. The explanatory feedback was found to be effective in mitigating the halo effect. However, the self-explanation knowledge acquisition method was not reliable in mitigating the halo effect.

Research limitations/implications
This research use self-explanation with a manual technique but, in practice, most auditors use audit tools based on computer. Experimental setting with computer to self-explanation cannot held because there is limitation of seminar setting. This research used individual decision; in practice most of audit decision with discussion in audit team.

Practical implications
CPA firms can use explanatory feedback, which comes in the form of managers’ review as a form of knowledge acquisition method as a mitigation strategy for the halo effect.

Social implications
The social implication of this research is the halo effect that can influence the decision in many aspects. Individuals must increase their professional values with many trainings that are useful to mitigating the halo effect.

Originality/value
The outcome of this paper was derived from the first accounting study that relied on learning methods as a mitigation strategy for the halo effect. In other words, this study used explanatory feedback and self-explanation as methods to test the halo effect. Previous literature on mitigating the halo effect had used audit experiences, implying that CPA firms’ intervention was unnecessary. Moreover, such study periods had been much longer, thereby, deteriorating the effectiveness of the research. Previous studies had only used the learning method to increase human capital quality and this was not related to any method as a mean to mitigate individual bias, for example, the halo effect, and an issue that was covered by this study.
The impact of accelerated filing requirements on meeting audit report deadlines
Authors: Farag Magdy 
Published: March 2017

Purpose
The purpose of this study is to examine audit report lags and audit report deadline margins. It specifically examines whether audits of large accelerated filers are completed within a shorter period as compared with regular accelerated filers due to the introduction of new deadline filing requirements by the SEC. The paper also examines whether large accelerated filers have shorter audit report deadline margins.

Design/methodology/approach
Using a sample of 7,129 firm-year observations over the period 2007-2013, an OLS regression model is applied by regressing audit report lags and audit report deadline margins on an indicator variable for large accelerated filers and a set of control variables.

Findings
Results indicate that audits of large accelerated filers have shorter audit report lags as compared with regular accelerated filers. Also, large accelerated filers have shorter audit report deadline margins as compared with regular accelerated filers. These results suggest that even though large accelerated filers’ audits are more complex by nature, auditors of these firms are under more pressure to complete their audits and issue their clients’ audit reports on time.

Research limitations/implications
While the control variables included in the models are all based on established theories and validated in prior research, there may still be some control variables that were excluded from the study’s models. Also, these results cannot be generalized beyond firms that are categorized as large accelerated filers or accelerated filers.

Practical/implications
Public accounting firms should be prepared to devote more resources to large accelerated filers’ clients. Also, regulators might need to reconsider revising the filing deadline requirements for the new category of large accelerated filers by weighing the pros against the cons of these new deadlines, as it appears that auditors of large accelerated filers need more time to complete their audits.

Originality/value
This study uses a new measuring tool in addition to audit report lags, which is the ‘audit report deadline margin’.
Investigating the volume and structure of alcohol consumption in Russian regions
Authors: Kossova Tatiana , Kossova Elena , Sheluntcova Maria 
Published: March 2017

Purpose
The purpose of this paper is to examine macroeconomic factors that are significantly related to consumption of various alcoholic beverages in Russia.

Design/methodology/approach
The authors consider 78 Russian regions for the period from 2008 to 2012. Data were collected from the Federal State Statistics Service of Russia. The authors investigate differences in the volume and structure of consuming absolute alcohol in aggregate, vodka, beer, and wine. Estimating fixed effect panel models enables us to reveal the relationship between alcohol consumption and the set of macroeconomic factors that include economic development of regions and living standards, the effect of unemployment, and the degree of urbanization.

Findings
Alcohol consumption is procyclical in Russia. Two main alcoholic beverages in Russia are vodka and beer. Economic development and urbanization of regions are positively related to consuming alcohol. Unemployment rate affects consumption of different types of alcoholic drinks in a different way. For absolute alcohol, vodka and beer, this relationship is negative. However, it is positive for wine. The effect of unemployment on absolute alcohol and vodka increases over time. For beer, it is remained unchanged. For wine, this effect weakens over time.

Originality/value
To the authors knowledge, the paper is the first one to analyze macro-level factors of consumption of different alcoholic beverages in Russia. Conclusions made on aggregate macroeconomic data add to understanding of drinking patterns in Russia as a country with the large territory and great regional variations. Findings can be used for correcting the alcohol policy at the national and regional level.
Twelve‐week, multicenter, placebo‐controlled, randomized, double‐blind, parallel‐group, comparative phase II/III study of benzoyl peroxide gel in patients with acne vulgaris: A secondary publication
Authors: Kawashima Makoto , Sato Shinichi , Furukawa Fukumi , Matsunaga Kayoko , Akamatsu Hirohiko , Igarashi Atsuyuki , Tsunemi Yuichiro , Hayashi Nobukazu , Yamamoto Yuki , Nagare Toshitaka , Katsuramaki Tsuneo 
Published: March 2017

AbstractA placebo‐controlled, randomized, double‐blind, parallel‐group, comparative, multicenter study was conducted to investigate the efficacy and safety of benzoyl peroxide (BPO) gel, administrated once daily for 12 weeks to Japanese patients with acne vulgaris. Efficacy was evaluated by counting all inflammatory and non‐inflammatory lesions. Safety was evaluated based on adverse events, local skin tolerability scores and laboratory test values. All 609 subjects were randomly assigned to receive the study products (2.5% and 5% BPO and placebo), and 607 subjects were included in the full analysis set, 544 in the per protocol set and 609 in the safety analyses. The median rates of reduction from baseline to the last evaluation of the inflammatory lesion counts, the primary end‐point, in the 2.5% and 5% BPO groups were 72.7% and 75.0%, respectively, and were significantly higher than that in the placebo group (41.7%). No deaths or other serious adverse events were observed. The incidences of adverse events in the 2.5% and 5% BPO groups were 56.4% and 58.8%, respectively; a higher incidence than in the placebo group, but there was no obvious difference between the 2.5% and 5% BPO groups. All adverse events were mild or moderate in severity. Most adverse events did not lead to study product discontinuation. The results suggested that both 2.5% and 5% BPO are useful for the treatment of acne vulgaris.
Immunocompetence in a long‐lived ectothermic vertebrate is temperature dependent but shows no decline in older adults
Authors: Zimmerman Laura M. , Carter Amanda Wilson , Bowden Rachel M. , Vogel Laura A. 
Published: March 2017

Summary

Temperature affects nearly all aspects of the physiology of ectotherms, including their ability to mount an immune response. Typically, the ectothermic vertebrate immune system can respond over a wide range of temperatures, but there is a species‐specific temperature at which responses are strongest, with impaired responses above and below this threshold. In long‐lived ectotherms, ageing could also influence the ability to respond to temperature changes as immunosenecence, the functional decrease in immune function with age, is widely reported.

This study examined the effects of the interaction between temperature and age on B‐cell function in a long‐lived reptile, the red‐eared slider turtle, Trachemys scripta. B cells in this species have previously been shown to have two main functions, phagocytosis and antibody production.

Adult turtles were trapped and blood samples taken. Because sliders grow throughout their lifetime, plastron length was used as a proxy for age. Leucocytes were isolated and used in either an ELISpot assay to examine their ability to produce antibodies spontaneously or when stimulated, or used in a phagocytic assay. The ELISpot and phagocytic assays were conducted over a range of biologically relevant temperatures.

We found no interaction between age and temperature on any measure of B‐cell function. In all cases there was a significant effect of temperature, with impaired function at temperatures below 29 °C, but no impairment of function at higher temperatures. We also found little evidence of immunosenescence in any response.

This study provides insight into the thermal biology of B‐cell function in sliders and provides an interesting connection between immunology, behaviour and ecology in this long‐lived turtle.

A lay summary is available for this article.