bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes
Authors: Pookhao Naruekamol , Sohn Michael B. , Li Qike , Jenkins Isaac , Du Ruofei , Jiang Hongmei , An Lingling 
Published: September 2014

AbstractMotivation: With the advance of new sequencing technologies producing massive short reads data, metagenomics is rapidly growing, especially in the fields of environmental biology and medical science. The metagenomic data are not only high dimensional with large number of features and limited number of samples but also complex with a large number of zeros and skewed distribution. Efficient computational and statistical tools are needed to deal with these unique characteristics of metagenomic sequencing data. In metagenomic studies, one main objective is to assess whether and how multiple microbial communities differ under various environmental conditions.Results: We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities. In the functional analysis of metagenomes, the features may refer to the pathways, subsystems, functional roles and so on. In the first stage of the proposed procedure, the informative features are selected using elastic net as reducing the dimension of metagenomic data. In the second stage, the differentially abundant features are detected using generalized linear models with a negative binomial distribution. Compared with other available methods, the proposed approach demonstrates better performance for most of the comprehensive simulation studies. The new method is also applied to two real metagenomic datasets related to human health. Our findings are consistent with those in previous reports.Availability: R code and two example datasets are available at http://cals.arizona.edu/∼anling/software.htmContact: anling@email.arizona.eduSupplementary information: Supplementary file is available at Bioinformatics online.
Tax me if you can! Optimal Nonlinear Income Tax Between Competing Governments*
Authors: Lehmann Etienne , Simula Laurent , Trannoy Alain 
Published: September 2014

AbstractWe investigate how potential tax-driven migrations modify the Mirrlees income tax schedule when two countries play Nash. The social objective is the maximin and preferences are quasi-linear in consumption. Individuals differ both in skills and migration costs, which are continuously distributed. We derive the optimal marginal income tax rates at the equilibrium, extending the Diamond-Saez formula. We show that the level and the slope of the semi-elasticity of migration (on which we lack empirical evidence) are crucial to derive the shape of optimal marginal income tax.
Human Cytomegalovirus Intrahost Evolution–A New Avenue for Understanding and Controlling Herpesvirus Infections
Authors: Renzette Nicholas , Gibson Laura , Jensen Jeffrey D. , Kowalik Timothy F. 
Published: September 2014

AbstractHuman cytomegalovirus (HCMV) is exquisitely adapted to the human host, and much research has focused on its evolution over long timescales spanning millennia. Here, we review recent data exploring the evolution of the virus on much shorter timescales, on the order of days or months. We describe the intrahost genetic diversity of the virus isolated from humans, and how this diversity contributes to HCMV spatiotemporal evolution. We propose mechanisms to explain the high levels of intrahost diversity and discuss how this new information may shed light on HCMV infection and pathogenesis.
Shaheen Ballpoints: a project of the Shaheen Group[1]
Authors: ur Rehman Manqoosh , Azhar Sarwar M. 
Published: September 2014

Subject area
Strategic Management, Strategic Marketing Management.

Study level/applicability
Bachelors, Masters.

Case overview
Shaheen Ballpoints is a project of Shaheen Group of Industries who, apart from manufacturing and marketing writing instruments, are engaged in diversified businesses of sanitary fittings, sanitary tiles, baby diapers and plastic films. Launched in 2001-2002, Shaheen Ballpoints had to compete against established ballpoint pen brands in a growing market. Shaheen Ballpoints believed that by setting out new standards for technology and packaging being used in the writing instruments industry, they would be able to compete with these giants. Shaheen Ballpoints experienced a mega launch of its ballpoint pens range in 2002. The wholesale market of Pakistan welcomed Shaheen Ballpoints quite generously and they paid in advance for their stocks which, generally, was not a norm of the writing instruments industry of Pakistan. However, soon after its launching, Shaheen Ballpoints realized some of the technical and marketing issues in its systems and had to pull all its stock back from the market just after six months of its launch. All the major resellers avoided Shaheen's stocks which was a major setback for the Shaheen Group. They re-launched the ballpoints in early 2004.

Expected learning outcomes
It is expected that the students will be able to understand the: issues associated with using the diversification strategy to grow the business; strategic implications of challenging the established industry norms and practices; and channel relationships within the industry and the need to tune-up the channel relationship strategy according to the varied nature of diversified businesses.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Implementing Federal Health Reform in the States: Who Is Included and Excluded and What Are Their Characteristics?
Authors: Fried Brett , Pintor Jessie Kemmick , Graven Peter , Blewett Lynn A. 
Published: September 2014

ObjectiveTo estimate the characteristics and number of nonelderly adults eligible and ineligible for Affordable Care Act (ACA) expansions.Data Sources and SettingsTwo secondary data sources are used in this analysis: the 2008 Panel of the Survey of Income and Program Participation (SIPP) and the 2009 American Community Survey (ACS).Study DesignWe use multiple imputation to incorporate model‐based uncertainty into the prediction of immigration status into the ACS from the SIPP. Key variables include place of birth, year of entry to the U.S., and health insurance coverage.Data Collection/Extracting MethodsNo primary data are used in this study.Principle FindingsWe estimate that potentially 3.5 million nonelderly adults will be excluded from the ACA Medicaid Expansion and 2 million from the health insurance exchanges because of their immigration status. We also find significant differences in estimates of excluded nonelderly adults across states.ConclusionsOver 15 percent of income‐eligible uninsured nonelderly adults will be potentially excluded from the ACA coverage expansions due to their immigration status. Policy makers must be careful to exclude ineligible nonelderly adults before estimating the impact of the ACA on coverage rates.
A Randomized Controlled Study on the Effects of Acetate‐Free Biofiltration on Organic Anions and Acid‐Base Balance in Hemodialysis Patients
Authors: Sánchez‐Canel Juan J , Hernández‐Jaras Julio , Pons‐Prades Ramón 
Published: September 2014

AbstractMetabolic acidosis correction is achieved by the transfer of bicarbonate and other buffer anions in dialysis. The aim of this study was to evaluate changes in the main anions of intermediary metabolism on standard hemodiafiltration (HDF) and on acetate‐free biofiltration (AFB). A prospective, in‐center, crossover study was carried out with 22 patients on maintenance dialysis. Patients were randomly assigned to start with 12 successive sessions of standard HDF with bicarbonate (34 mmol/L) and acetate dialysate (3 mmol/L) or 12 successive sessions of AFB without base in the dialysate. Acetate increased significantly during the standard HDF session from 0.078 ± 0.062 mmol/L to 0.156 ± 0.128 mmol/L (P < 0.05) and remained unchanged at 0.044 ± 0.034 mmol and 0.055 ± 0.028 mmol/L in AFB modality. Differences in the acetate levels were observed at two hours (P < 0.005), at the end (P < 0.005) and thirty minutes after the session between HDF and AFB (P < 0.05). There were significantly more patients above the normal range in HDF group than AFB group (68.1% vs 4.5% P < 0.005) postdialysis and 30 minutes later. Serum lactate and pyruvate concentrations decreased during the sessions without differences between modalities. Citrate decreased only in the AFB group (P < 0.05). Acetoacetate and betahydroxybutyrate increased in both modalities, but the highest betahydroxybutyrate values were detected in HDF (P < 0.05). The sum of postdialysis unusual measured organic anions (OA) were higher in HDF compared to AFB (P < 0.05). AFB achieves an optimal control of acid–base equilibrium through a bicarbonate substitution fluid. It also prevents hyperacetatemia and restores internal homeostasis with less production of intermediary metabolites.
In Vivo Kinetics of the Uremic Toxin P‐Cresyl Sulfate in Mice With Variable Renal Function
Authors: Ni Jingwei , Zhang Wenli , Zhu Zhengbin , Zhu Jinzhou , Du Run , Jing Yajun , Lu Lin , Zhang Ruiyan 
Published: September 2014

AbstractUremic toxins such as p‐cresyl sulfate (PCS) are associated with increased mortality for chronic kidney disease (CKD) patients, but in vivo PCS toxicity studies are limited due to the lack of a standard animal model. To establish such a model, we measured the pharmacokinetics of PCS in mice with variable renal function. Male Balb/c mice subjected to 5/6 nephrectomy (CRF), unilateral nephrectomy (UNX), or no surgery (controls) were given PCS (po, 50 mg/kg). Blood samples were collected over time and plasma PCS concentrations were measured. Over 4 h, PCS was significantly higher in the plasma of CRF mice (63.28 ± 2.76 mg/L), compared to UNX mice (3.11 ± 0.64 mg/L) and controls (0.39 ± 0.12 mg/L). The PCS half‐life was greatest in CRF mice (12.07 ± 0.12 h), compared to 0.79 ± 0.04 h in UNX mice and 0.48 ± 0.02 h in control mice. However, the potential presence of additional uremic toxins along with PCS in CRF mice and rapid PCS clearance in control mice suggest that the UNX mouse would be a better PCS model to study toxicity.
Effect of DNA Demethylation in Experimental Encapsulating Peritoneal Sclerosis
Authors: Kim Kyung‐Hoon , Ryu Hye‐Myung , Oh Se‐Hyun , Oh Eun‐Joo , Ahn Ji‐Sun , Lee Jong‐Hak , Choi Ji‐Young , Cho Jang‐Hee , Kim Chan‐Duck , Kim Yong‐Lim , Park Sun‐Hee 
Published: September 2014

AbstractEncapsulating peritoneal sclerosis (EPS) involves excessive peritoneal fibrosis in patients on peritoneal dialysis, eventually leading to visceral constriction and bowel obstruction. Few studies have investigated epigenetic mechanisms relating to EPS. Here we evaluated the therapeutic effects of DNA demethylation in experimental EPS. Experimental EPS was induced by intraperitoneal injection of 0.1% chlorhexidine gluconate (CG) and 15% ethanol in non‐uremic male Sprague–Dawley (SD) rats. Rats were divided into three groups: group C (N = 5) with saline injection only, group CG (N = 7) with EPS induction for 4 weeks, and chlorhexidine gluconate and azacytidine (CGA) treated group (N = 7) with EPS induction for 4 weeks and 5'‐azacytidine injection for the last 2 weeks. Morphometric analysis of peritoneum and immunohistochemical staining for type 1 collagen and α‐smooth muscle actin (α‐SMA) were performed. Expressions of transforming growth factor‐β (TGF‐β), fibroblast‐specific protein 1 (FSP1), and DNA methyltransferase 1 (DNMT1) were analyzed by Western blot. Methylation‐specific polymerase chain reaction (PCR) for Ras GTPase activating‐like protein 1 (RASAL1) was performed with measurement of RASAL1 protein expression. Parietal peritoneal thickness and the number of vessels in omental tissue were significantly decreased in group CGA compared to group CG, as were the expressions of type 1 collagen, α‐SMA, TGF‐β, and FSP1. DNMT1 was significantly increased in group CG, and reduced in group CGA. RASAL1 hypermethylation was associated with decreased RASAL1 protein expression in group CG, which was reversed in group CGA. DNA demethylation by 5'‐azacytidine treatment improved pathologic changes of the peritoneum in experimental EPS, and was associated with reversal of increased DNMT1 expression and RASAL1 hypermethylation.
Found in translation? Commentary on a BJP themed issue about animal models in neuropsychiatry research
Authors: Lawrence Andrew J , Cryan John F 
Published: September 2014

This themed issue of Br J Pharmacol is dedicated to the utility and needs of animal models in psychiatry research. The following articles document strengths and weaknesses, indicate areas where better models are sorely needed and provide examples where pharmacological studies may result in mechanistic breakthrough and aid in drug development. In addition, complicating factors both in disease and treatment strategies are canvassed, such as sex differences, genetic and environmental influences. While not exhaustive, the intention was to use a number of exemplars to stimulate discussion around how animal models can aid in improving our understanding and treatment of many devastating conditions.Linked ArticlesThis article is part of a themed section on Animal Models in Psychiatry Research. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-20
Tubulin acetylation promoting potency and absorption efficacy of deacetylase inhibitors
Authors: Mangas‐Sanjuan V , Oláh J , Gonzalez‐Alvarez I , Lehotzky A , Tőkési N , Bermejo M , Ovádi J 
Published: September 2014

Background and PurposeHistone deacetylase 6 (HDAC6) and silent information regulator 2 (SIRT2) control the dynamics of the microtubule network via their deacetylase activities. Tubulin polymerization promoting protein (TPPP/p25) enhances microtubule acetylation by its direct binding to HDAC6. Our objective was to characterize the multiple interactions of the deacetylases and to establish the inhibitory potency and the pharmacokinetic features of the deacetylase inhibitors, trichostatin A (TSA) and AGK2.Experimental ApproachThe interactions of deacetylases with tubulin and TPPP/p25 were quantified by elisa using human recombinant proteins. The effect of inhibitors on the tubulin acetylation was established in HeLa cells transfected with pTPPP and CG‐4 cells expressing TPPP/p25 endogenously by celisa (elisa on cells), Western blot and immunofluorescence microscopy. The pharmacokinetic features of the inhibitors were evaluated by in situ kinetic modelling of their intestinal transport in rats.Key ResultsDeacetylases interact with both tubulin and TPPP/p25, notwithstanding piggy‐back binding of HDAC6 or SIRT2 to the TPPP/p25‐associated tubulin was established. Much higher inhibitory potency for TSA than for AGK2 was detected in both HeLa and CG‐4 cells. Pioneer pharmacokinetic studies revealed passive diffusion and diffusion coupled with secretion for TSA and AGK2 respectively. Both inhibitors exhibited greater permeability than some other well‐established drugs.Conclusions and ImplicationsTPPP/p25‐directed deacetylase inhibition provides mechanisms for the fine control of the dynamics and stability of the microtubule network. Deacetylase inhibitors with chemical structures similar to TSA and AGK2 appear to be excellent candidates for oral drug absorption.
Pre‐bisection of a single skin biopsy does not produce technically inadequate specimens for direct immunofluorescence: a review of 3450 specimens
Authors: Loh Ern , Armstrong April W. , Fung Maxwell A. 
Published: September 2014

BackgroundEvaluation of a potential immunobullous disorder typically requires two pieces of tissue obtained by skin biopsy: one placed in formalin for conventional microscopy and a second placed in a different transport medium suitable for direct immunofluorescence (DIF) testing. Clinical practice in this area is not standardized, with dermatologists either obtaining two biopsies or dividing (pre‐bisecting) a single biopsy. Some DIF specimens are technically inadequate for interpretation of subepidermal imunobullous disorders because the basement membrane zone is not intact, but it is unknown whether pre‐bisecting the tissue increases the risk of compromising the specimen.ObjectiveTo investigate whether technically inadequate DIF specimens are associated with pre‐bisection.MethodsDIF specimens were consecutively sampled from a single referral center and identified as whole (non‐bisected) biopsy specimens or pre‐bisected biopsy specimens. The proportion of inadequate specimens was calculated for both groups.ResultsA total of 3450 specimens were included. The percentage of inadequate specimens was 5.072% (153/3016) for whole (non‐bisected) specimens and 5.299% for pre‐bisected specimens. This difference was not significant (chi square, p = 0.84). The study was sufficiently powered to detect a relative risk of 1.685.ConclusionsPre‐bisection of a single skin biopsy does not significantly increase the risk of a technically inadequate specimen for direct immunofluorescence testing.
Prevention of 5‐hydroxytryptamine2C receptor RNA editing and alternate splicing in C57BL/6 mice activates the hypothalamic‐pituitary‐adrenal axis and alters mood
Authors: Bombail Vincent , Qing Wei , Chapman Karen E. , Holmes Megan C. 
Published: September 2014

AbstractThe 5‐hydroxytryptamine2C (5‐HT)2C receptor is widely implicated in the aetiology of affective and eating disorders as well as regulation of the hypothalamo‐pituitary‐adrenal axis. Signalling through this receptor is regulated by A‐to‐I RNA editing, affecting three amino acids in the protein sequence, with unedited transcripts encoding a receptor (INI) that, in vitro, is hyperactive compared with edited isoforms. Targeted alteration (knock‐in) of the Htr2c gene to generate ‘INI’ mice with no alternate splicing, solely expressing the full‐length unedited isoform, did not produce an overt metabolic phenotype or altered anxiety behaviour, but did display reduced depressive‐like and fear‐associated behaviours. INI mice exhibited a hyperactive hypothalamo‐pituitary‐adrenal axis, with increased nadir plasma corticosterone and corticotrophin‐releasing hormone expression in the hypothalamus but responded normally to chronic stress and showed normal circadian activity and activity in a novel environment. The circadian patterns of 5‐HT2C receptor mRNA and mbii52, a snoRNA known to regulate RNA editing and RNA splicing of 5‐HT2C receptor pre‐mRNA, were altered in INI mice compared with wild‐type control mice. Moreover, levels of 5‐HT1A receptor mRNA were increased in the hippocampus of INI mice. These gene expression changes may underpin the neuroendocrine and behavioural changes observed in INI mice. However, the phenotype of INI mice was not consistent with a globally hyperactive INI receptor encoded by the unedited transcript in the absence of alternate splicing. Hence, the in vivo outcome of RNA editing may be neuronal cell type specific.
Global fire size distribution is driven by human impact and climate
Authors: Hantson Stijn , Pueyo Salvador , Chuvieco Emilio 
Published: September 2014

AbstractAimIn order to understand fire's impacts on vegetation dynamics, it is crucial that the distribution of fire sizes be known. We approached this distribution using a power‐law distribution, which derives from self‐organized criticality theory (SOC). We compute the global spatial variation in the power‐law exponent and determine the main factors that explain its spatial distribution.LocationGlobal, at 2° grid resolution.MethodsWe use satellite‐derivedMODISburned‐area data (MCD45) to obtain global individual fire size data for 2002–2010, grouped together for each 2° grid. A global map of fire size distribution was produced by plotting the exponent of the power law. The drivers of the spatial trends in fire size distribution, including vegetation productivity, precipitation, population density and net income, were analysed using a generalized additive model (GAM).ResultsThe power law gave a good fit for 93% of the global 2° grid cells with important fire activity. A global map of the fire size distribution, as approached by the power law shows strong spatial patterns. These are associated both with climatic variables (precipitation and evapotranspiration) and with anthropogenic variables (cropland cover and population density).Main conclusionsOur results indicate that the global fire size distribution changes over gradients of precipitation and aridity, and that it is strongly influenced by human activity. This information is essential for understanding potential changes in fire sizes as a result of climate change and socioeconomic dynamics. The ability to improveSOCfire models by including these human and climatic factors would benefit fire projections as well as fire management and policy.
Effectiveness of radiotherapy for elderly patients with non‐melanoma skin cancer of the head
Authors: Nguyen Nam P , Ries Tiffany , Vock Jacqueline , Vos Paul , Chi Alexander , Vinh‐Hung Vincent , Thompson Stephen , Desai Anand , Sroka Thomas , Vo Richard A , Gelumbauskas Steve , Hamilton Russell , Karlsson Ulf , Mignault Alan ,   the International Geriatric Radiotherapy Group
Published: September 2014

AimTo assess the effectiveness of conventionally fractionated radiotherapy for local control and cosmesis in elderly patients (age 70 years or older) with non‐melanoma skin cancer of the head.MethodsA retrospective review of 15 patients undergoing definitive radiation (11 patients) or postoperative radiation (4 patients) for squamous cell carcinoma (9 patients) and basal cell carcinoma (6 patients) of the head was undertaken. At each follow‐up visit, a radiation oncology resident and/or medical student was requested to examine the patient's head and neck, and determine the initial location of the cancer without reviewing their medical record.ResultsNo patient developed a loco‐regional recurrence. The residents and medical students were unable to determine the initial location of the cancer because of the skin normalcy.ConclusionConventionally fractionated radiotherapy is effective for local control and provides excellent cosmesis for elderly patients with skin cancer of the head. Geriatr Gerontol Int 2015; 15: 601–605.