bluuebunny/crossref_metadata_2025_split huggingface dataset:
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
Authors: Lun Aaron T.L. , Smyth Gordon K. 
Published: November 2015

Abstract
Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project.
Multiple Cis-acting elements modulate programmed -1 ribosomal frameshifting in Pea enation mosaic virus
Authors: Gao Feng , Simon Anne E. 
Published: November 2015

Abstract
Programmed -1 ribosomal frameshifting (-1 PRF) is used by many positive-strand RNA viruses for translation of required products. Despite extensive studies, it remains unresolved how cis-elements just downstream of the recoding site promote a precise level of frameshifting. The Umbravirus Pea enation mosaic virus RNA2 expresses its RNA polymerase by -1 PRF of the 5′-proximal ORF (p33). Three hairpins located in the vicinity of the recoding site are phylogenetically conserved among Umbraviruses. The central Recoding Stimulatory Element (RSE), located downstream of the p33 termination codon, is a large hairpin with two asymmetric internal loops. Mutational analyses revealed that sequences throughout the RSE and the RSE lower stem (LS) structure are important for frameshifting. SHAPE probing of mutants indicated the presence of higher order structure, and sequences in the LS may also adapt an alternative conformation. Long-distance pairing between the RSE and a 3′ terminal hairpin was less critical when the LS structure was stabilized. A basal level of frameshifting occurring in the absence of the RSE increases to 72% of wild-type when a hairpin upstream of the slippery site is also deleted. These results suggest that suppression of frameshifting may be needed in the absence of an active RSE conformation.
Impact of Genetic Mutations and Health Plan Access to Therapies on Treatment Response and Drug Costs Related to Tyrosine Kinase Inhibitor Treatment Among Patients With Chronic Myelogenous Leukemia
Authors: Jabbour Elias , Makenbaeva Dinara , Lingohr-Smith Melissa , Lin Jay 
Published: November 2015

Objectives:
This study assessed treatment responses and economic consequences of limiting access to the second-generation BCR-ABL1 tyrosine kinase inhibitors (2G-TKI), dasatinib and nilotinib, for treatment of chronic myelogenous leukemia, while taking into account frequencies of genetic mutations that exhibit different sensitivities to the 2G-TKIs.

Methods:
Frequencies of BCR-ABL1 mutations and the impact of mutations on responses to 2G-TKIs were obtained from published literature and used as inputs in a decision analytics model. Complete hematologic response (CHR) and major cytogenetic response (MCyR) were estimated after 12 months of 2G-TKI treatment. Total annual 2G-TKI drug costs per CHR and MCyR were estimated and compared among 3 2G-TKI access scenarios: (1) open access to both 2G-TKIs; (2) access restricted to dasatinib (DASA-only); and (3) access restricted to nilotinib (NILO-only).

Results:
Among a hypothetical cohort of 1000 2G-TKI-treated chronic myelogenous leukemia patients, the percentage of patients with CHR and MCyR were greatest for the open access plan (CHR: 93%, MCyR: 56%), followed by DASA-only (88%, 53%) and NILO-only (67%, 47%). Compared with the 2G-TKI costs per CHR in open access ($120,706/CHR), the costs were 5% higher ($126,753/CHR) in DASA-only and 41% higher ($169,990/CHR) in NILO-only. Likewise, compared with the 2G-TKI costs per MCyR in open access ($198,284/MCyR), the costs were 6% higher ($209,259/MCyR) in DASA-only and 22% higher ($241,515/MCyR) in NILO-only.

Conclusion:
Open access to both 2G-TKIs is associated with improved clinical and economic outcomes: greater treatment response rates (CHR and MCyR) and lower drug costs compared with restricted access to 2G-TKIs.
The Application of the CRASH-CT Prognostic Model for Older Adults With Traumatic Brain Injury: A Population-Based Observational Cohort Study
Authors: Staples John A. , Wang Jin , Mills Brianna , Temkin Nancy , Zaros Mark C. , Jurkovich Gregory J. , Rivara Frederick P. 
Published: November 2015

Objective:
To examine the performance of the Corticosteroid Randomization After Significant Head injury (CRASH) trial prognostic model in older patients with traumatic brain injury.

Setting:
The National Study on Costs and Outcomes of Trauma cohort, established at 69 hospitals in the United States in 2001 and 2002.

Participants:
Adults with traumatic brain injury and an initial Glasgow Coma Scale score of 14 or less.

Design:
The CRASH-CT model predicting death within 14 days was deployed in all patients. Model performance in older patients (aged 65-84 years) was compared with that in younger patients (aged 18-64 years).

Main Measures:
Model discrimination (as defined by the c-statistic) and calibration (as defined by the Hosmer-Lemeshow P value).

Results:
CRASH-CT model discrimination was not significantly different between the older (n = 356; weighted n = 524) and younger patients (n = 981; weighted n = 2602) and was generally adequate (c-statistic 0.83 vs 0.87, respectively; P = .11). CRASH-CT model calibration was adequate for the older patients and inadequate for younger patients (Hosmer-Lemeshow P values .12 and .001, respectively), possibly reflecting differences in sample size. Calibration-in-the-large showed no systematic under- or overprediction in either stratum.

Conclusion:
The CRASH-CT model may be valid for use in a geriatric population.
Feasibility of a Cognitive Behavioral Intervention to Manage Fatigue in Individuals With Traumatic Brain Injury: A Pilot Study
Authors: Raina Ketki D. , Morse Jennifer Q. , Chisholm Denise , Leibold Mary Lou , Shen Jennifer , Whyte Ellen 
Published: November 2015

Objective:
To evaluate the feasibility of conducting a randomized clinical trial of an Internet-based manualized intervention to teach individuals with traumatic brain injury to manage their fatigue.

Setting:
Community dwelling.

Participants:
Forty-one participants randomized to Maximizing Energy (MAX) intervention group (n = 20) and Health Education group (n = 21).

Intervention:
The experimental group (MAX intervention) received an 8-week program that combined education and Problem-Solving Therapy to teach individuals to manage fatigue-related problems. The attention control group received health education.

Measures:
Primary outcome measures pertained to the feasibility of conducting the trial. Secondary outcomes were fatigue impact and fatigue severity assessed at baseline and postintervention.

Results:
Of the 65 participants referred, 41 were enrolled (63% recruitment rate), of which 3 withdrew (92% retention rate). Participants in the experimental and control groups completed their homework 75% and 85% of the time, respectively, and were equally engaged in the sessions. Participants in the experimental group were able to learn and implement the MAX intervention steps. Effect sizes for all measures ranged from small (−0.17) to medium (−0.58) in favor of the intervention group.

Conclusion:
Findings from the study suggest that the MAX intervention is feasible to administer to individuals with post–traumatic brain injury fatigue.
The Nature and Clinical Significance of Preinjury Recall Bias Following Mild Traumatic Brain Injury
Authors: Silverberg Noah D. , Iverson Grant L. , Brubacher Jeffrey R. , Holland Elizabeth , Hoshino Lisa Casagrande , Aquino Angela , Lange Rael T. 
Published: November 2015

Objective:
Patients with mild traumatic brain injury (MTBI) often underestimate their preinjury symptoms. This study aimed to clarify the mechanism underlying this recall bias and its contribution to MTBI outcome.

Setting:
Level I trauma center.

Participants:
Patients with uncomplicated MTBI (N = 88) and orthopedic injury (N = 67).

Design:
Prospective longitudinal.

Main Measures:
Current and retrospective ratings on the British Columbia Postconcussion Symptom Inventory, completed at 6 weeks and 1 year postinjury.

Results:
Preinjury symptom reporting was comparable across groups, static across time, and associated with compensation-seeking. High preinjury symptom reporting was related to high postinjury symptom reporting in the orthopedic injury group but less so in the MTBI group, indicating a stronger positive recall bias in highly symptomatic MTBI patients. Low preinjury symptom reporting was not a risk factor for poor MTBI outcome.

Conclusion:
The recall bias was stronger and more likely clinically significant in MTBI patients with high postinjury symptoms. Multiple mechanisms appear to contribute to recall bias after MTBI, including the reattribution of preexisting symptoms to MTBI as well as processes that are not specific to MTBI (eg, related to compensation-seeking).
MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies
Authors: Madoui Mohammed-Amin , Dossat Carole , d’Agata Léo , van Oeveren Jan , van der Vossen Edwin , Aury Jean-Marc 
Published: November 2015

AbstractBackgroundScaffolding is a crucial step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in continuity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring.ResultsWe present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase continuity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency.ConclusionsMaGuS is a powerful reference-free evaluator of assembly quality and a map-guided scaffolder that is freely available athttps://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the continuity of large and complex genome assemblies.
Islamic social business for sustainable development and subjective wellbeing
Authors: Aydin Necati 
Published: November 2015

Purpose– The purpose of this paper is to report that the social business model has emerged to mitigate the failure of free-market capitalism driven by self-interest in creating social value. It shows how social business contradicts with free-market capitalism while being compatible with Islamic moral economy due to the axiomatic differences between the two economic systems.Design/methodology/approach– The paper follows conceptual, axiomatic and theoretical approach to show how the social business model contradicts with free-market capitalism, but is compatible with Islamic moral economy. The paper provides a theoretical framework for Islamic social business based on an Islamic human and social development perspective. The paper first discusses the failure of free-market capitalism and the emergence of social business in the capitalist system. It then defines Islamic social business and lays out its axiomatic foundation based on the Islamic worldview. It also presents Islamic financial instruments and funds for social business. Finally, it makes a case for sustainable socioeconomic development and subjective well-being within the Islamic development paradigm.Findings– The paper shows that a cosmetic change to capitalism is not sufficient for enabling the social business model to take the main stage in the free-market system. There is a need for a new paradigm of reality, truth, telos and human nature to support social business. Tawhidi paradigm can be such alternative. The paper makes a strong case for social business from an Islamic worldview. Particularly, certain economic axioms within the Tawhidi anthropology, teleology and axiology provide intrinsic causes for pursuing such business model. The multi-dimensional nature of humans from the Tawhidi anthropology sets the intrinsic foundation for social business. Indeed, although the social business model is new to the West, it has been practiced in certain forms in the Muslim world throughout history. Zakat, sadaqah, and qard hasan can be used to support social business in addition to some Islamic banking instruments. The paper suggests that Muslim countries should embrace the social business model for sustainable development and greater subjective well-being.Research limitations/implications– The paper is purely theoretical. Future studies might shed light on the issue through empirical evidence.Practical implications– The paper is likely to enhance the interest in social business in the Muslim world.Social implications– The paper has potential to lead the creation of social value through dissemination of the social business model.Originality/value– The paper contributes the Islamic moral economy doctrine by making a strong case for Islamic social business.
The role of human capital in economic development of the earliest Islamic period
Authors: Sadr Seyed Kazem 
Published: November 2015

Purpose
– The purpose of this paper is to provide explanation for the economic development of the earliest Islamic state. It focuses on the role of human capital as the most important element of this model and focuses on four dimensions of development of human personality in Islam: the incentive structure, rules of behavior, institutions and policies.

Design/methodology/approach
– A review and analysis of the measures and policies that Prophet of Islam and his successors adopted are made to arrive at the underlying economic model of development.

Findings
– The major finding is the role of human capital in the development of the economy at that time.

Originality/value
– The contribution of the paper is to identify the critical role of education and skills for the development of the economy at present.
The diagnostic potential of MPT63‐derived HLA‐A*0201‐restricted CD8+T‐cell epitopes for active pulmonary tuberculosis
Authors: Duan Zhiliang , Li Dezhou , Jia Qingjun , Xu Juanjuan , Chen Xinyu , Xu Zhigang , Liu Huifang , Chen Bokun , Wen Jinsheng 
Published: November 2015

ABSTRACTMPT63 protein is found only in Mycobacterium tuberculosis complex, including M. tuberculosis and M. bovis. Detection of MPT63‐specific IFN‐γ‐secreting T cells could be useful for the diagnosis of tuberculosis (TB) diseases. In the present study, the HLA‐A*0201 restriction of ten predicted MPT63‐derived CD8+T‐cell epitopes was assessed on the basis of T2 cell line and HLA‐A*0201 transgenic mice. The diagnostic potential of immunogenic peptides in active pulmonary TB patients was evaluated using an IFN‐γ enzyme‐linked immunospot assay. It was found that five peptides bound to HLA‐A*0201 with high affinity, whereas the remaining peptides exhibited low affinity for HLA‐A*0201. Five immunogenic peptides (MPT6318–26, MPT6329–37, MPT6320–28, MPT635–14 and MPT6310–19) elicited large numbers of cytotoxic IFN‐γ‐secreting T cells in HLA‐A*0201 transgenic mice. Each of the five immunogenic peptides was recognized by peripheral blood mononuclear cells from 45% to 73% of 40 HLA‐A*0201 positive TB patients. The total diagnostic sensitivity of the five immunogenic peptides was higher than that of a T‐SPOT.TB assay (based on ESAT‐6 and CFP‐10) (93% versus 90%). It is noticeable that the diagnostic sensitivity of the combination of five immunogenic peptides and T‐SPOT.TB assay reached 100%. These MPT63‐derived HLA‐A*0201‐restricted CD8+T‐cell epitopes would likely contribute to the immunological diagnosis of M. tuberculosis infection and may provide the components for designing an effective TB vaccine.
Compensatory life‐history responses of a mesopredator may undermine carnivore management efforts
Authors: Minnie Liaan , Gaylard Angela , Kerley Graham I. H. 
Published: November 2015

Summary

Lethal carnivore management, aimed at reducing carnivore impacts, is a global phenomenon threatening the persistence of many carnivores. Black‐backed jackals Canis mesomelas, the dominant cause of livestock predation in southern Africa, are widely hunted to reduce livestock predation. Despite centuries of lethal management, jackals persist. Smaller canids, like jackals, are highly adaptable and display variable responses to mortality sources, which may affect management outcomes.

The effects of killing carnivores will depend on their behaviour, social organization, reproduction and dispersal patterns. We predicted that hunted jackals will alter demographic and reproductive patterns to compensate for increased mortality. Here, we collected demographic and reproductive information from harvested jackals and compared it between continually hunted (farms) and unmanaged populations (reserves).

The removal of jackals from farms results in a decrease in median age from 5–6 years (reserves) to 2–3 years (farms). Hunting also changed the age structure of jackal populations from a stable population to an expanding population. This may be ascribed to the compensatory immigration of individuals from neighbouring unmanaged areas, suggesting the formation of a source–sink system. Unmanaged areas may act as source populations exporting young, dispersing individuals to hunted areas which may act as sinks. This is likely driven by disruptions in the normal, mutually exclusive territorial system resulting in low densities of conspecifics on farms.

The low density of conspecifics allows younger individuals that would be socially precluded from reproducing to reproduce. Jackals on farms compensated for increased mortality by increasing the pregnancy rate of young individuals and increasing the litter size at younger ages, thereby increasing reproductive output.

Synthesis and applications. The lethal management of predators is the prevailing strategy to reduce livestock predation. However, the highly adaptable nature of jackals and the combination of compensatory mechanisms such as increased reproduction and potential for immigration allow these predators to persist in the face of severe anthropogenic mortality, possibly through the formation of a source–sink system. These compensatory processes will continue to counter population management actions as long as recruitment from unmanaged areas persists.
Rental as A Taste of Freedom: The Decline of Home Ownership amongst Working‐class Youth in Spain during Times of Crisis
Authors: Aramburu Mikel 
Published: November 2015

AbstractOver the past few decades, as the neoliberal project gradually took hold, owning one's home became a widespread practice in Spanish society. However, the prospects of purchasing housing have since been severely reduced due to the bursting of the real estate bubble and the onset of an overwhelming economic crisis. This article analyses how working‐class young people in Catalonia reflect on this phenomenon as they face their own process of moving away from home. It also considers the extent to which the spread of the so‐called ‘culture of ownership' represented an expression of neoliberal culture, and the extent to which the apparent dissolution of the former implies the erosion of the latter. The article concludes that home ownership has undergone a complex resignification in this sector of society, but continues to be an important aspiration insofar as the underlying conditions that originally brought it about continue to exist.
Flavor Chemistry of Cocoa and Cocoa Products—An Overview
Authors: Aprotosoaie Ana Clara , Luca Simon Vlad , Miron Anca 
Published: November 2015

AbstractCocoa originates from beans of the cocoa tree (Theobroma cacao L.) and it is an important commodity in the world and the main ingredient in chocolate manufacture. Its value and quality are related to unique and complex flavors. Bulk cocoas (Forastero type) exhibit strong basic cocoa notes, whereas fine varieties (Criollo, Nacional) show aromatic, floral, or smoother flavor characteristics. About 600 various compounds (alcohols, carboxylic acids, aldehydes, ketones, esters, and pyrazines) have been identified as odor‐active components. The specific cocoa aroma arises from complex biochemical and chemical reactions during the postharvest processing of raw beans, and from many influences of the cocoa genotype, chemical make‐up of raw seeds, environmental conditions, farming practices, processing, and manufacturing stages. There has been much research on cocoa flavor components. However, the relationships between all chemical components that are likely to play a role in cocoa flavor, their sensory properties, and the sources and mechanisms of flavor formation are not fully understood. This paper provides an overview on cocoa flavor from a compositional and a sensory perspective. The nonvolatile and volatile chemical components of cocoa and chocolate flavor, and their sensory properties correlated to the main influences involved in flavor formation, are reviewed.