bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inadequate seroprotection against hepatitis B virus and one detected case of hepatitis C virus infection among patients with inflammatory bowel disease
Authors: Waszczuk Ewa , Waszczuk Karolina M. , Mulak Agata , Paradowski Leszek 
Published: February 2016

Objectives
The prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections among patients with inflammatory bowel disease (IBD) from central and eastern European countries is unknown. Postvaccination HBV immunity in an immunocompromised host may wane. The aims of the study were as follows: to assess the immune status for HBV and HCV among IBD patients, the level of HBV seroprotection, and to compare the immune status of patients who received mandatory versus recommended HBV vaccination.

Materials and methods
Serological markers of HBV and HCV (anti-HBs, anti-HBc, HBsAg, and anti-HCV) were determined in 147 consecutive IBD patients. An anti-HBs of 10 IU/l or more was considered as immunity to HBV infection.

Results
HBV infection was detected in 21 patients, whereas 11 of them recalled previous HBV vaccination. Sixty-eight noninfected patients had a level of anti-HBs 10 IU/l or more and only 29% reached the cut-off level of 100 IU/l. Among patients vaccinated obligatorily, two patients had previous HBV infection and 15% did not have an adequate seroprotection against HBV. Patients who received a mandatory HBV vaccine more frequently had a protective anti-HBs level than those vaccinated voluntarily (P<0.001). One positive anti-HCV result was found.

Conclusion
A mandatory HBV vaccination significantly increased the number of patients effectively protected against HBV; however, a remarkable number of vaccinated IBD patients had inadequate HBV seroprotection. All IBD patients should be screened for HBV and HCV infections and monitored for anti-HBs titers.
Does Churning in Medicaid Affect Health Care Use?
Authors: Roberts Eric T. , Pollack Craig Evan 
Published: February 2016

Background:
Transitions into and out of Medicaid, termed churning, may disrupt access to and continuity of care. Low-income, working adults who became eligible for Medicaid under the Affordable Care Act are particularly susceptible to income and employment changes that lead to churning.

Objective:
To compare health care use among adults who do and do not churn into and out of Medicaid.

Data:
Longitudinal data from 6 panels of the Medical Expenditure Panel Survey.

Methods:
We used differences-in-differences regression to compare health care use when adults reenrolled in Medicaid following a loss of coverage, to utilization in a control group of continuously enrolled adults.

Outcome Measures:
Emergency department (ED) visits, ED visits resulting in an inpatient admission, and visits to office-based providers.

Results:
During the study period, 264 adults churned into and out of Medicaid and 627 had continuous coverage. Churning adults had an average of approximately 0.05 Medicaid-covered office-based visits per month 4 months before reenrolling in Medicaid, significantly below the rate of approximately 0.20 visits in the control group. Visits to office-based providers did not reach the control group rate until several months after churning adults had resumed Medicaid coverage. Our comparisons found no evidence of significantly elevated ED and inpatient admission rates in the churning group following reenrollment.

Conclusions:
Adults who lose Medicaid tend to defer their use of office-based care to periods when they are insured. Although this suggests that enrollment disruptions lead to suboptimal timing of care, we do not find evidence that adults reenroll in Medicaid with elevated acute care needs.
Brief Report: Relationship Among Viral Load Outcomes in HIV Treatment Interruption Trials
Authors: Treasure Graham C. , Aga Evgenia , Bosch Ronald J. , Mellors John W. , Kuritzkes Daniel R. , Para Michael , Gandhi Rajesh T. , Li Jonathan Z. 
Published: February 2016

Abstract:
Viral load (VL) rebound timing and set point were analyzed in 235 participants undergoing analytic treatment interruption (ATI) in 6 AIDS Clinical Trials Group studies. There was no significant association between rebound timing and ATI VL set point for those who rebounded ≤12 weeks. VL set points were lower in participants with rebound >12 weeks (P < 0.001) and participants treated during early infection (P < 0.001). Pre-antiretroviral therapy VL correlated with set point, though 68% of participants had a set point lower than pre-antiretroviral therapy VL. These results illustrate complex relationships between post-ATI virologic outcomes and the potential presence of biological factors mediating rebound timing and set point.
Noise thermometry at ultra-low temperatures
Authors: Rothfuss D. , Reiser A. , Fleischmann A. , Enss C. 
Published: February 2016

The options for primary thermometry at ultra-low temperatures are rather limited. In practice, most laboratories are using
195
Pt NMR thermometers in the microkelvin range. In recent years, current sensing direct current superconducting quantum interference devices (DC-SQUIDs) have enabled the use of noise thermometry in this temperature range. Such devices have also demonstrated the potential for primary thermometry. One major advantage of noise thermometry is the fact that no driving current is needed to operate the device and thus the heat dissipation within the thermometer can be reduced to a minimum. Ultimately, the intrinsic power dissipation is given by the negligible back action of the readout SQUID. For thermometry in low-temperature experiments, current noise thermometers and magnetic flux fluctuation thermometers have proved to be most suitable. To make use of such thermometers at ultra-low temperatures, we have developed a cross-correlation technique that reduces the amplifier noise contribution to a negligible value. For this, the magnetic flux fluctuations caused by the Brownian motion of the electrons in our noise source are measured inductively by two DC-SQUID magnetometers simultaneously and the signals from these two channels are cross-correlated. Experimentally, we have characterized a thermometer made of a cold-worked high-purity copper cylinder with a diameter of 5 mm and a length of 20 mm for temperatures between 42
μ
K and 0.8 K. For a given temperature, a measuring time below 1 min is sufficient to reach a precision of better than 1%. The extremely low power dissipation in the thermometer allows continuous operation without heating effects.
AC-PCA: simultaneous dimension reduction and adjustment for confounding variation
Authors: Lin Zhixiang , Yang Can , Zhu Ying , Duchi John C. , Fu Yao , Wang Yong , Jiang Bai , Zamanighomi Mahdi , Xu Xuming , Li Mingfeng , Sestan Nenad , Zhao Hongyu , Wong Wing Hung 
Published: February 2016

AbstractDimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biologically or technically originated. In this study, we extend Principal Component Analysis to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding variation. We show that AC-PCA can adjust for a) variations across individual donors present in a human brain exon array dataset, and b) variations of different species in a model organism ENCODE RNA-Seq dataset. Our approach is able to recover the anatomical structure of neocortical regions, and to capture the shared variation among species during embryonic development. For gene selection purposes, we extend AC-PCA with sparsity constraints, and propose and implement an efficient algorithm. The methods developed in this paper can also be applied to more general settings.
PARAQUAT TOLERANCE3 is an E3 ligase and acts as a negative regulator of oxidative stress response
Authors: Luo Chao , Cai Xiao-Teng , Du Jin , Zhao Tao-Lan , Wang Peng-Fei , Zhao Ping-Xia , Liu Rui , Xie Qi , Cao Xiao-Feng , Xiang Cheng-Bin 
Published: February 2016

AbstractOxidative damage could be caused in plant cells when biotic and abiotic stresses are imposed. While the response to oxidative stress is well studied, little is known about how the activated response is switched off when oxidative stress is diminished. By studying Arabidopsis mutantparaquat tolerance3, we identified the genetic locusPARAQUAT TOLERANCE3(PQT3) as a major negative regulator of oxidative stress tolerance.PQT3, encoding an E3 ligase, is rapidly down-regulated by oxidative stress. PQT3 has E3 ubiquitin ligase activity in ubiquitination assay. Subsequently, we identified PRMT4b as a PQT3-interacting protein. By histone methylation, PRMT4b may regulate the expression ofAPX1andGPX1, encoding two key enzymes against oxidative stress. Moreover, PQT3 is able to recognize PRMT4b for targeted degradation via 26S proteasome. Therefore, we have identified PQT3 as an E3 ligase that acts as a negative regulator of activated response to oxidative stress.
Experimental evolution of Escherichia coli harboring an ancient translation protein
Authors: Kaçar Betül , Ge Xueliang , Sanyal Suparna , Gaucher Eric A. 
Published: February 2016

AbstractThe ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes, and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year old inferred ancestral variant oftufB, an essential gene encoding Elongation Factor Tu, and inserted it in a modernEscherichia coligenome in place of the nativetufBgene. While the ancient homolog was not lethal to the cell, it did cause a two-fold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2,000 generations in the laboratory, and examined the adaptive response via fitness assays, whole-genome sequencing, proteomics and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by up-regulation of protein production. We expect that this ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
Benchmarking of product recovery alternatives in reverse logistics
Authors: Sharma S. K. , Mahapatra S.S. , Parappagoudar M.B. 
Published: February 2016

Purpose
– Selection of best product recovery alternative in reverse logistics (RL) has gained great attention in supply chain community. The purpose of this paper is to provide a robust group decision-making tool to select the best product recovery alternative.

Design/methodology/approach
– In this paper, fuzzy values, assigned to various criteria and alternatives by a number of decision makers, are converted into crisp values and then aggregated scores are evaluated. After obtaining experts’ scores, objective and subjective weights of the criteria have been calculated using variance method and analytic hierarchy process, respectively. Then integrated weights of criteria are evaluated using different proportions of the two weights. The superiority and inferiority ranking (SIR) method is then employed to achieve the final ranking of alternatives. An example is presented to demonstrate the methodology.

Findings
– The proposed methodology provides decision makers a systematic, flexible and realistic approach to effectively rank the product recovery alternatives in RL. The alternatives can easily be benchmarked and best recovery strategy can be obtained. The sensitivity analysis carried out by changing different proportion of objective and subjective weights reveals that best ranking alternative never changes and proves the robustness of the methodology. The present benchmarking framework can also be used by decision makers to simplify any problem which encounters multi-attribute decision making and multiple decision makers.

Research limitations/implications
– The proposed methodology should be tested in different situations having varied operational and environmental conditions dealing with different products. A real case study from an industrial set up can help to assess the behavior of the proposed methodology. The presented methodology however can deal with such multi-disciplinary and multi-criteria issues in a simple and structured manner and ease the managers to select the best alternative.

Originality/value
– A novel approach for decision making taking into account both objective and subjective weights for criteria has been proposed to rank the best recovery alternatives in RL. The proposed methodology uses SIR method to prioritize the alternatives. As RL alternative selection is an important issue and involves both technical and managerial criteria as well as multiple decision makers, the proposed robust methodology can provide guidelines for the practicing managers.
Ownership, size, and efficiency: evidence from software companies in India
Authors: Sahoo Bimal Kishore 
Published: February 2016

Purpose– The purpose of this paper is to discuss the trends in relative efficiency of software companies in India during 1999-2008 by applying input-oriented data envelopment analysis (DEA) model. Based upon the PROWESS Database of Centre for Monitoring Indian Economy (CMIE), the efficiencies were estimated for the Indian, multinational and group companies. Also, relationship between efficiency and size is examined.Design/methodology/approach– The study applied DEA to measure relative efficiencies of software companies and two different DEA models, CCR and BCC, were applied to evaluate the relative efficiency of the sample software companies in India. Comparisons of efficiency scores based on ownership were carried out by applying ANOVA andt-statistics.Findings– The mean overall technical efficiency (OTE) of the software industry in India during 1999-2008 was low at 0.477. The mean pure technical efficiency for the industry for the study period was found to be 0.654 suggesting that software firms, on an average, were wasting 35 per cent of their inputs. It was observed that the Indian-owned companies have relatively high OTE score as compared to foreign owned and group owned companies. The mean OTE score of PI companies was found to be greater than the other two categories. In terms of, size it is observed that medium sized companies performance better.Practical implications– Software companies can use DEA to examine their performance against the best performers in the industry. Software industry in India, which is doted by large number of small firms in the lower part of the size pyramid, needs to increase their size to improve their efficiency.Originality/value– Research on measurement of service sector export oriented industry efficiency is limited. This paper is one of the few published studies examined service sector performance. This paper fills the gap in the literature by applying DEA in software industry in India and compares performance in terms of ownership and size.
Objectives priority in university strategy map for resource allocation
Authors: Rahimnia Fariborz , Kargozar Naghmeh 
Published: February 2016

Purpose
– The purpose of this paper is to provide a model for Ferdowsi University of Mashhad (FUM) to prioritize its objectives. This will be achieved by providing strategy map using balanced score card (BSC) method.

Design/methodology/approach
– This research result is based on 21 managers’ opinion about relation among university objectives, gathered by questionnaire. DEMATHEL method which is a structural decision-making model is used to process data in questionnaires and discover casual relationship between university objectives.

Findings
– According to this research result “Having productive competent human resource that are committed to Islamic values and professional ethic” has the highest priority among FUM objectives while “Achieving educating excellence especially in graduate programs and research” has the lowest.

Practical implications
– FUM managers need to focus on their human resources and enhance their competency in order to achieve academic excellence.

Originality/value
– Achieving superiority in university competitive position based on its education and research activities is FUM vision. As a non-profit organization due to resource restriction and environmental circumstances it has to fulfill this goal with higher productivity. BSC as a performance management system will help it to achieve this goal by translating vision into objectives and defining casual relationship between them. This method is rarely studied in the context of universities especially in Iranian universities. This research applied strategy map, one of BSC implementation stages, in a public university in Iran to illustrate series of objectives that leads to mission accomplishment.
Protein Network of the Pseudomonas aeruginosa Denitrification Apparatus
Authors: Borrero-de Acuña José Manuel , Rohde Manfred , Wissing Josef , Jänsch Lothar , Schobert Max , Molinari Gabriella , Timmis Kenneth N. , Jahn Martina , Jahn Dieter 
Published: February 2016

ABSTRACT

Oxidative phosphorylation using multiple-component, membrane-associated protein complexes is the most effective way for a cell to generate energy. Here, we systematically investigated the multiple protein-protein interactions of the denitrification apparatus of the pathogenic bacterium
Pseudomonas aeruginosa
. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO
3−
→ NO
2−
→ NO → N
2
O → N
2
. Genetic experiments suggested that the nitric oxide reductase NorBC and the regulatory protein NosR are the nucleus of the denitrification protein network. We utilized membrane interactomics in combination with electron microscopy colocalization studies to elucidate the corresponding protein-protein interactions. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. The periplasmic nitrous oxide reductase NosZ is linked via NosR. The nitrate transporter NarK2, the nitrate regulatory system NarXL, various nitrite reductase maturation proteins, NirEJMNQ, and the Nos assembly lipoproteins NosFL were also found to be attached. A number of proteins associated with energy generation, including electron-donating dehydrogenases, the complete ATP synthase, almost all enzymes of the tricarboxylic acid (TCA) cycle, and the Sec system of protein transport, among many other proteins, were found to interact with the denitrification proteins. This deduced nitrate respirasome is presumably only one part of an extensive cytoplasmic membrane-anchored protein network connecting cytoplasmic, inner membrane, and periplasmic proteins to mediate key activities occurring at the barrier/interface between the cytoplasm and the external environment.

IMPORTANCE
The processes of cellular energy generation are catalyzed by large multiprotein enzyme complexes. The molecular basis for the interaction of these complexes is poorly understood. We employed membrane interactomics and electron microscopy to determine the protein-protein interactions involved. The well-investigated enzyme complexes of denitrification of the pathogenic bacterium
Pseudomonas aeruginosa
served as a model. Denitrification is one essential step of the universal N cycle and provides the bacterium with an effective alternative to oxygen respiration. This process allows the bacterium to form biofilms, which create low-oxygen habitats and which are a key in the infection mechanism. Our results provide new insights into the molecular basis of respiration, as well as opening a new window into the infection strategies of this pathogen.
Regulation of Growth, Cell Shape, Cell Division, and Gene Expression by Second Messengers (p)ppGpp and Cyclic Di-GMP in Mycobacterium smegmatis
Authors: Gupta Kuldeepkumar Ramnaresh , Baloni Priyanka , Indi Shantinath S. , Chatterji Dipankar 
Published: February 2016

ABSTRACT

The alarmone (p)ppGpp regulates transcription, translation, replication, virulence, lipid synthesis, antibiotic sensitivity, biofilm formation, and other functions in bacteria. Signaling nucleotide cyclic di-GMP (c-di-GMP) regulates biofilm formation, motility, virulence, the cell cycle, and other functions. In
Mycobacterium smegmatis
, both (p)ppGpp and c-di-GMP are synthesized and degraded by bifunctional proteins Rel
Msm
and DcpA, encoded by
rel
Msm
and
dcpA
genes, respectively. We have previously shown that the Δ
rel
Msm
and Δ
dcpA
knockout strains are antibiotic resistant and defective in biofilm formation, show altered cell surface properties, and have reduced levels of glycopeptidolipids and polar lipids in their cell wall (K. R. Gupta, S. Kasetty, and D. Chatterji, Appl Environ Microbiol 81:2571–2578, 2015,
http://dx.doi.org/10.1128/AEM.03999-14
). In this work, we have explored the phenotypes that are affected by both (p)ppGpp and c-di-GMP in mycobacteria. We have shown that both (p)ppGpp and c-di-GMP are needed to maintain the proper growth rate under stress conditions such as carbon deprivation and cold shock. Scanning electron microscopy showed that low levels of these second messengers result in elongated cells, while high levels reduce the cell length and embed the cells in a biofilm-like matrix. Fluorescence microscopy revealed that the elongated Δ
rel
Msm
and Δ
dcpA
cells are multinucleate, while transmission electron microscopy showed that the elongated cells are multiseptate. Gene expression analysis also showed that genes belonging to functional categories such as virulence, detoxification, lipid metabolism, and cell-wall-related processes were differentially expressed. Our results suggests that both (p)ppGpp and c-di-GMP affect some common phenotypes in
M. smegmatis
, thus raising a possibility of cross talk between these two second messengers in mycobacteria.

IMPORTANCE
Our work has expanded the horizon of (p)ppGpp and c-di-GMP signaling in Gram-positive bacteria. We have come across a novel observation that
M. smegmatis
needs (p)ppGpp and c-di-GMP for cold tolerance. We had previously shown that the Δ
rel
Msm
and Δ
dcpA
strains are defective in biofilm formation. In this work, the overproduction of (p)ppGpp and c-di-GMP encased
M. smegmatis
in a biofilm-like matrix, which shows that both (p)ppGpp and c-di-GMP are needed for biofilm formation. The regulation of cell length and cell division by (p)ppGpp was known in mycobacteria, but our work shows that c-di-GMP also affects the cell size and cell division in mycobacteria. This is perhaps the first report of c-di-GMP regulating cell division in mycobacteria.