bluuebunny/crossref_metadata_2025 huggingface dataset:
Reveel: large-scale population genotyping using low-coverage sequencing data
Authors: Huang Lin , Wang Bo , Chen Ruitang , Bercovici Sivan , Batzoglou Serafim
Published: September 2015

Motivation: Population low-coverage whole-genome sequencing is rapidly emerging as a prominent approach for discovering genomic variation and genotyping a cohort. This approach combines substantially lower cost than full-coverage sequencing with whole-genome discovery of low-allele frequency variants, to an extent that is not possible with array genotyping or exome sequencing. However, a challenging computational problem arises of jointly discovering variants and genotyping the entire cohort. Variant discovery and genotyping are relatively straightforward tasks on a single individual that has been sequenced at high coverage, because the inference decomposes into the independent genotyping of each genomic position for which a sufficient number of confidently mapped reads are available. However, in low-coverage population sequencing, the joint inference requires leveraging the complex linkage disequilibrium (LD) patterns in the cohort to compensate for sparse and missing data in each individual. The potentially massive computation time for such inference, as well as the missing data that confound low-frequency allele discovery, need to be overcome for this approach to become practical.

Results: Here, we present Reveel, a novel method for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage. Reveel introduces a novel technique for leveraging LD that deviates from previous Markov-based models, and which is aimed at computational efficiency as well as accuracy in capturing LD patterns present in rare haplotypes. We evaluate Reveel’s performance through extensive simulations as well as real data from the 1000 Genomes Project, and show that it achieves higher accuracy in low-frequency allele discovery and substantially lower computation cost than previous state-of-the-art methods.

Availability and implementation:  http://reveel.stanford.edu/.

Contact: serafim@cs.stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Considering Underrepresented Populations in Work and Family Research
Authors: Agars Mark D. , French Kimberly A.
Published: September 2015

In this chapter we discuss the ways in which work–family researchers can better include underrepresented populations in work–family scholarship. Extant research on five example populations is reviewed: low-income workers; immigrants; lesbian, gay, bisexual, and transgender individuals; single parents; and formerly incarcerated individuals. Methodological challenges are reviewed that contribute to the underrepresentation of such populations in the work–family field. In conclusion, we draw themes common among these populations and present recommendations for expanding work–family research to include more diverse population characteristics.
Conscientiousness
Authors: Jackson Joshua J. , Roberts Brent W.
Published: September 2015

Conscientiousness refers to a broad swath of constructs that reflects the propensity to be self-controlled, responsible to others, hardworking, orderly, and rule abiding. To understand why conscientiousness is one of the best psychological predictors of important outcomes (e.g., longevity; divorce), this chapter provides a broad overview of the trait. First, the Sociogenomic model of personality traits is briefly described as a means to provide a common language to discuss the status of conscientiousness. Next, the hierarchical structure of conscientiousness is described, including a description of common measures used to assess conscientiousness, as well as constructs related to conscientiousness. The development of conscientiousness is then discussed, followed by a review of the predictive ability of conscientiousness. The potential mechanisms driving the development of conscientiousness and the pathways that relate conscientiousness to important outcomes are also examined.
Custom in the Islamic Legal Tradition
Authors: Shabana Ayman
Published: September 2015

This article offers a survey of modern scholarship on the role of custom in the Islamic legal tradition. It begins with a definition of the concept of custom and also the relationship between the two Arabic terms used for custom, ‘urf and ‘ada. The relationship of custom to other terms such as sunna, ‘amal, and istihsan is also explored. The second, and main, part of the article traces the different approaches to the study of custom in Islamic legal studies and examines the development of these approaches. Four themes or debates are identified as the main contexts within which custom has been discussed: the origins of the Sunna of the Prophet and the early development of Islamic law; relationship between theory and practice; sources of Islamic law; and legal change. The article concludes with a summary and suggestions for future research.
Ijtihad
Authors: Emon Anver M.
Published: September 2015

This article examines issues surrounding the historiography of ijtihad within the context of Islamic law. It considers the politics informing debates about whether the “gates” were ever closed, and what “closure” implies about Islamic law. It then discusses calls for the “reopening” of the “gates”, suggesting that such calls seem to reflect more about the conditions of modernity that pose new questions to a tradition with a considerable history, and less about the study of Islamic law. It also reviews the scholarship on ijtihad as a topic of legal theory in the usul al-fiqh genre and in relation to contemporary issues in legal philosophy and interpretation, along with the discourse of ijtihad in the modern period and its significance as a proxy for underlying concerns about epistemology, legal education, and authority. Finally, it outlines new scholarly directions for research on ijtihad.
Islamic Law in South Asia
Authors: Redding Jeff
Published: September 2015

This article examines Islamic law in South Asia as a testament to the wide diversity of both Muslims and non-Muslims in the region. The article discusses several different Islamic trajectories in South Asia, with emphasis on Pakistan, Bangladesh, and India. These different national contexts demonstrate how the practice of Islamic law in South Asia can be of significance for Muslims worldwide, whether in contexts where Muslims comprise an overwhelming majority of a nation’s population (like Pakistan), or where they live along aside a sizeable non-Muslim minority (such as Bangladesh), or where Muslims form a significant minority population (as in India). This article also discusses sectarian diversity in South Asian Islamic law, from historical and contemporary perspectives, and how this sectarian diversity has deeply influenced the development of Islamic law in South Asia. Finally, this article considers sub-national diversity in South Asian Islamic law as a key area of future research.
The Turkish Republic
Authors: Miller Ruth A.
Published: September 2015

This article examines the historical role that Islamic law has played in the Turkish Republic. It first considers multifaceted trends in scholarship on Islamic law in Republican Turkey before turning to the problem, if any, that Islamic law poses in the country with respect to the constitution and constitutional law. It then traces the formality of Islamic law in Turkey to the legacy of the Ottoman Empire and the persistent rejection or repudiation of Islamic law by the Turkish parliament and judiciary as part of the country’s secularism and republicanism. It also analyzes distinctive Republican interpretations of Islamic law and concludes by highlighting the dynamic presence of ?eriat in Turkey’s political and legal landscape.
Protest and Institutional Change
Authors: Aleman Jose
Published: September 2015

This article studies how social protest contributes to institutional reforms in both new and established democracies. It evaluates the effects of social protest on changes in the protection of workers’ rights, women’s political rights, and the ability of other branches of government to constrain chief executives. Three important findings emerge in this regard: (1) strikes promote workers’ rights, (2) general strikes advance women’s political rights in the presence of an independent judiciary, and (3) antigovernment demonstrations constrain executives, while riots empower them when the government is cohesive. Regarding the mechanisms behind these changes, the analysis reveals that whereas the effects of strikes on workers’ rights are not institutionally mediated, general strikes can affect women’s political rights indirectly through the institution of an independent judiciary. Antigovernment demonstrations and riots can likewise affect executive constraints indirectly, through the behavior of actors in other branches of government.
Mysticism and Reform in Catholic Theology between 1600 and 1800
Authors: Lehner Ulrich L. , O'Brien William P.
Published: September 2015

These introductory remarks focus on themes not covered in the handbook—the Council of Trent’s focus on a universal call to holiness, the effect of parish missions on popular faith, and practical reforms such as the founding of seminaries and improving the moral life of the clergy. Moreover, Trent’s support for positive theology is outlined, as well as Catholic attempts to defend traditional Trinitarian theology against the anti-Trinitarianism that arose during the Protestant Reformation. Finally, this introduction considers the rise of Catholic mysticism, particularly in Spain and France; and discusses its contra-authoritarian character, the significant influence of female mystics, and the Quietist controversy.
Diversity of Ralstonia solanacearum Strains on the Andaman Islands in India
Authors: Sakthivel K. , Gautam R. K. , Kumar K. , Dam Roy S. , Kumar A. , Devendrakumar C. , Vibhuti M. , Neelam S. , Vinatzer B. A.
Published: September 2015

Fourteen Ralstonia solanacearum strains from solanaceous vegetables on the Andaman Islands, India, were characterized using a polyphasic approach. The strains wilted their respective hosts within 1 to 3 weeks postinoculation. Virulence assays on tomato (Solanum lycopersicum), brinjal (eggplant; S. melongena), and chili pepper (Capsicum annuum) revealed that all strains were infective on all three hosts. However, tomato was more susceptible than eggplant and chili pepper. Strains were identified as R. solanacearum based on carbon substrate utilization profiling with Biolog similarity coefficients >0.82. Species identity was further confirmed by 16S ribosomal RNA and recN gene sequence analysis. Intraspecific identification of strains revealed the presence of race 1 biovar 3 and race 1 biovar 4. Both biovars wilted plants with similar aggressiveness. All strains were identified as phylotype I, and multilocus sequence typing revealed that the strains belong to a small number of clonal complexes that also comprise strains from mainland India, especially West Bengal state and Kerala.
Incidence of Wheat streak mosaic virus, Triticum mosaic virus, and Wheat mosaic virus in Wheat Curl Mites Recovered from Maturing Winter Wheat Spikes
Authors: Byamukama E. , Tatineni S. , Hein G. , McMechan J. , Wegulo S. N.
Published: September 2015

Wheat curl mites (WCM; Aceria tosichella) transmit Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and Wheat mosaic virus (WMoV) to wheat (Triticum aestivum L.) in the Great Plains region of the United States. These viruses can be detected in single, double, or triple combinations in leaf samples. Information on incidence of viruses in WCM at the end of the growing season is scant. The availability of this information can enhance our knowledge of the epidemiology of WCM-transmitted viruses. This research was conducted to determine the frequency of occurrence of WSMV, TriMV, and WMoV in WCM populations on field-collected maturing wheat spikes and to determine differences in WCM densities in three geographical regions (southeast, west-central, and panhandle) in Nebraska. Maturing wheat spikes were collected from 83 fields across Nebraska in 2011 and 2012. The spikes were placed in proximity to wheat seedlings (three- to four-leaf stage) in WCM-proof cages in a growth chamber and on sticky tape. WCM that moved off the drying wheat spikes in cages infested the wheat seedlings. WCM that moved off wheat spikes placed on sticky tape were trapped on the tape and were counted under a dissecting microscope. At 28 days after infestation, the wheat plants were tested for the presence of WSMV, TriMV, or WMoV using enzyme-linked immunosorbent assay and multiplex polymerase chain reaction. WSMV was the most predominant virus detected in wheat seedlings infested with WCM from field-collected spikes. Double (TriMV+WSMV or WMoV+WSMV) or triple (TriMV+ WMoV +WSMV) virus detections were more frequent (47%) than single detections (5%) of TriMV or WSMV. Overall, 81% of the wheat seedlings infested with WCM tested positive for at least one virus. No significant association (P > 0.05) was found between regions for WCM trapped on tape. These results suggest that WCM present on mature wheat spikes harbor multiple wheat viruses and may explain high virus incidence when direct movement of WCM into emerging winter wheat occurs in the fall.
Dissecting the Genetic Architecture of Leaf Rust Resistance in Wheat by QTL Meta-Analysis
Authors: Soriano Jose Miguel , Royo Conxita
Published: September 2015

Leaf rust is an important disease that causes significant yield losses in wheat. Many studies have reported the identification of quantitative trait loci (QTL) controlling leaf rust resistance; therefore, QTL meta-analysis has become a useful tool for identifying consensus QTL and refining QTL positions among them. In this study, QTL meta-analysis was conducted using reported results on the number, position, and effects of QTL for leaf rust resistance in bread and durum wheat. Investigation of 14 leaf rust resistance traits from 19 studies involving 20 mapping populations and 33 different parental lines provided information for 144 unique QTL that were projected onto the Wheat Composite 2004 reference map. In total, 35 meta-QTL for leaf rust resistance traits were identified in 17 wheat chromosomes and 13 QTL remained as unique QTL. The results will facilitate further work on the cloning of QTL for pyramiding minor- and partial-effect resistance genes to develop varieties with durable resistance to leaf rust.
Altered Mitochondrial Dynamics Contributes to Propofol-induced Cell Death in Human Stem Cell–derived Neurons
Authors: Twaroski Danielle M. , Yan Yasheng , Zaja Ivan , Clark Eric , Bosnjak Zeljko J. , Bai Xiaowen
Published: September 2015

AbstractAbstract

In supratherapeutic doses, propofol increased mitochondrial fission; key proteins involved in fission were increased. Suppression of these proteins mitigated the increases in mitochondrial fission and reduced toxicity. Propofol accelerated mitochondrial permeability transition pore (mPTP) opening; blockade of fission rescued the mPTP opening time. The data indicate that propofol, when administered in supratherapeutic concentrations, may induce neurotoxicity via a mitochondria fission and mPTP pathway.

Background

Studies in developing animals have shown that anesthetic agents can lead to neuronal cell death and learning disabilities when administered early in life. Development of human embryonic stem cell–derived neurons has provided a valuable tool for understanding the effects of anesthetics on developing human neurons. Unbalanced mitochondrial fusion and fission lead to various pathological conditions including neurodegeneration. The aim of this study was to dissect the role of mitochondrial dynamics in propofol-induced neurotoxicity.

Methods

Terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate in situ nick-end labeling staining was used to assess cell death in human embryonic stem cell–derived neurons. Mitochondrial fission was assessed using TOM20 staining and electron microscopy. Expression of mitochondrial fission-related proteins was assessed by Western blot, and confocal microscopy was used to assess opening time of the mitochondrial permeability transition pore (mPTP).

Results

Exposure to 6 h of 20 μg/ml propofol increased cell death from 3.18 ± 0.17% in the control-treated group to 9.6 ± 0.95% and led to detrimental increases in mitochondrial fission (n = 5 coverslips per group) accompanied by increased expression of activated dynamin-related protein 1 and cyclin-dependent kinase 1, key proteins responsible for mitochondrial fission. Propofol exposure also induced earlier opening of the mPTP from 118.9 ± 3.1 s in the control-treated group to 73.3 ± 1.6 s. Pretreatment of the cells with mdivi-1, a mitochondrial fission blocker rescued the propofol-induced toxicity, mitochondrial fission, and mPTP opening time (n = 75 cells per group). Inhibiting cyclin-dependent kinase 1 attenuated the increase in cell death and fission and the increase in expression of activated dynamin-related protein 1.

Conclusion

These data demonstrate for the first time that propofol-induced neurotoxicity occurs through a mitochondrial fission/mPTP-mediated pathway.
Preoperative Surgical Risk Predictions Are Not Meaningfully Improved by Including the Surgical Apgar Score
Authors: Terekhov Maxim A. , Ehrenfeld Jesse M. , Wanderer Jonathan P.
Published: September 2015

AbstractAbstract

Both the Risk Quantification Index and Present-On-Admission Risk predicted mortality well. Adding the Surgical Apgar Score did not substantively improve predictions.

Background

Estimating surgical risk is critical for perioperative decision making and risk stratification. Current risk-adjustment measures do not integrate dynamic clinical parameters along with baseline patient characteristics, which may allow a more accurate prediction of surgical risk. The goal of this study was to determine whether the preoperative Risk Quantification Index (RQI) and Present-On-Admission Risk (POARisk) models would be improved by including the intraoperative Surgical Apgar Score (SAS).

Methods

The authors identified adult patients admitted after noncardiac surgery. The RQI and POARisk were calculated using published methodologies, and model performance was compared with and without the SAS. Relative quality was measured using Akaike and Bayesian information criteria. Calibration was compared by the Brier score. Discrimination was compared by the area under the receiver operating curves (AUROCs) using a bootstrapping procedure for bias correction.

Results

SAS alone was a statistically significant predictor of both 30-day mortality and in-hospital mortality (P < 0.0001). The RQI had excellent discrimination with an AUROC of 0.8433, which increased to 0.8529 with the addition of the SAS. The POARisk had excellent discrimination with an AUROC of 0.8608, which increased to 0.8645 by including the SAS. Similarly, overall performance and relative quality increased.

Conclusions

While AUROC values increased, the RQI and POARisk preoperative risk models were not meaningfully improved by adding intraoperative risk using the SAS. In addition to the estimated blood loss, lowest heart rate, and lowest mean arterial pressure, other dynamic clinical parameters from the patient’s intraoperative course may need to be combined with procedural risk estimate models to improve risk stratification.
Relationships Between Severity of Deformity and Impingement in Slipped Capital Femoral Epiphysis
Authors: Jones Carly E. , Cooper Anthony P. , Doucette Jonathan , Buchan Lawrence L. , Wilson David R. , Mulpuri Kishore , d’Entremont Agnes G.
Published: September 2015

Background:

In situ pinning, a low-risk treatment for slipped capital femoral epiphysis (SCFE), leaves the slipped femoral head in place and may reduce range of motion (ROM) and cause impingement. It is unclear when a more complex surgery should be considered, because the relationships between severity, slip stability, remodeling, impingement, and ROM are unknown. Research questions:

(1) Do more severe acute SCFE deformities (no bony remodeling) result in a greater loss of flexion ROM?

(2) Does the presence or location of impingement on the pelvis vary with severity of acute SCFE deformity?

Methods:

We developed a 3D geometric model of acute SCFE deformity from 1 computed tomography scan of a normal adolescent hip. Ethics board approval was obtained from our institution. Bone models were created from the segmented pelvis, epiphysis, and subphyseal femur.

In total, 3721 SCFE deformities were simulated by combining posterior and inferior slips in the axial and coronal planes, respectively. Southwick angles were estimated from a frog-leg lateral projection. Deformities were divided into mild (0 to 30 degrees), moderate (30 to 60 degrees), and severe (≥60 degrees) Southwick groups. Each joint was flexed in combination with internal/external rotation until contact occurred. A total of 121 ROM trials, with different degrees of internal/external rotation (0 to 90 degrees at 1.5-degree steps) were performed for each deformity.

Results:

In total, 3355 simulated SCFE deformities (363 could not be rotated out of impingement) were analyzed.

Increasing slip severity reduced flexion ROM across the range of internal/external rotation. Contact occurred for most mild deformities, and for all moderate and severe deformities in at least 1 ROM trial. Impingement was observed mainly on the anterosuperior aspect of the acetabulum.

Conclusions:

Increasing slip severity in acute SCFE reduced flexion and increased incidence of impingement, primarily occurring on the anterosuperior aspect of the acetabulum. The impingement patterns observed are consistent with damaged cartilage locations seen in clinical literature.

Clinical Relevance:

In this experimental model, moderate and severe acute slips in SCFE lead to reduced ROM and impingement with the acetabulum. This suggests that in situ pinning may result in impingement of moderate and severe acute SCFE slips.
Polyethylene Glycol– or Sodium Picosulphate–Based Laxatives Before Colonoscopy in Children
Authors: Vejzovic Vedrana , Wennick Anne , Idvall Ewa , Agardh Daniel , Bramhagen Ann‐Cathrine
Published: September 2015

Objectives:

The purpose of this randomised study was to compare the quality of bowel cleansing using either polyethylene glycol (PEG) or sodium picosulphate (NaPico) (primary outcome) in relation to the tolerability and acceptance of these laxatives among children and their caregivers (secondary outcome).

Methods:

The study was a randomised controlled trial that was conducted as an investigator‐blinded study within the Department of Paediatrics of Skåne University Hospital in Malmö, Sweden. A total of 72 children (10–18 years of age) were randomly placed into 1 of 2 groups (PEG or NaPico). The Ottawa Bowel Preparation Quality Score was used to evaluate the quality of bowel cleansing. A total of 2 different questionnaires were used to evaluate both the acceptability and tolerability of the laxatives.

Results:

In total, 71 children completed the bowel cleansing. Of these 71 cleanses, 67 protocols were analysed according to the Ottawa Bowel Preparation Quality Score. No significant difference in bowel cleansing quality was detected between the 2 groups. Rates of acceptability and tolerability were significantly higher in the NaPico group than in the PEG group.

Conclusions:

In the present study, both laxatives were found to be satisfactory in terms of aiding the performance of an uncomplicated and successful colonoscopy. NaPico was, however, more tolerable to the children than PEG, and both, the children and their caregivers, were more accepting of NaPico than of PEG. Consequently, NaPico can be recommended as the option for bowel cleansing in children ages 10 years and older.
From Theory to Practice: Implementation of a Resource Allocation Model in Health Departments
Authors: Yaylali Emine , Farnham Paul G. , Schneider Karen L. , Landers Stewart J. , Kouzouian Oskian , Lasry Arielle , Purcell David W. , Green Timothy A. , Sansom Stephanie L.
Published: September 2015

Objective:

To develop a resource allocation model to optimize health departments' Centers for Disease Control and Prevention (CDC)–funded HIV prevention budgets to prevent the most new cases of HIV infection and to evaluate the model's implementation in 4 health departments.

Design, Settings, and Participants:

We developed a linear programming model combined with a Bernoulli process model that allocated a fixed budget among HIV prevention interventions and risk subpopulations to maximize the number of new infections prevented. The model, which required epidemiologic, behavioral, budgetary, and programmatic data, was implemented in health departments in Philadelphia, Chicago, Alabama, and Nebraska.

Main Outcome Measures:

The optimal allocation of funds, the site-specific cost per case of HIV infection prevented rankings by intervention, and the expected number of HIV cases prevented.

Results:

The model suggested allocating funds to HIV testing and continuum-of-care interventions in all 4 health departments. The most cost-effective intervention for all sites was HIV testing in nonclinical settings for men who have sex with men, and the least cost-effective interventions were behavioral interventions for HIV-negative persons. The pilot sites required 3 to 4 months of technical assistance to develop data inputs and generate and interpret the results. Although the sites found the model easy to use in providing quantitative evidence for allocating HIV prevention resources, they criticized the exclusion of structural interventions and the use of the model to allocate only CDC funds.

Conclusions:

Resource allocation models have the potential to improve the allocation of limited HIV prevention resources and can be used as a decision-making guide for state and local health departments. Using such models may require substantial staff time and technical assistance. These model results emphasize the allocation of CDC funds toward testing and continuum-of-care interventions and populations at highest risk of HIV transmission.
Dynamic footprint of sequestration in the molecular fluctuations of osteopontin
Authors: Lenton S. , Seydel T. , Nylander T. , Holt C. , Härtlein M. , Teixeira S. , Zaccai G.
Published: September 2015

The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core–shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering. The effects of sequestration are quantified on the nanosecond– ångström resolution by elastic incoherent neutron scattering. The molecular fluctuations of the free phosphopeptide are in agreement with a highly flexible protein. An increased resilience to diffusive motions of OPN is corroborated by molecular fluctuations similar to those observed for globular proteins, yet retaining conformational flexibilities. The results bring insight into the modulation of the activity of OPN and phosphopeptides with a role in the control of biomineralization. The quantification of such effects provides an important handle for the future design of new peptides based on the dynamics–activity relationship.
Life history of the most complete fossil primate skeleton: exploring growth models forDarwinius
Authors: López-Torres Sergi , Schillaci Michael A. , Silcox Mary T.
Published: September 2015

Darwiniusis an adapoid primate from the Eocene of Germany, and its only known specimen represents the most complete fossil primate ever found. Its describers hypothesized a close relationship to Anthropoidea, and using aSaimirimodel estimated its age at death. This study reconstructs the ancestral permanent dental eruption sequences for basal Euprimates, Haplorhini, Anthropoidea, and stem and crown Strepsirrhini. The results show that the ancestral sequences for the basal euprimate, haplorhine and stem strepsirrhine are identical, and similar to that ofDarwinius. However,Darwiniusdiffers from anthropoids by exhibiting early development of the lower third molars relative to the lower third and fourth premolars. The eruption of the lower second premolar marks the point of interruption of the sequence inDarwinius. The anthropoidSaimirias a model is therefore problematic because it exhibits a delayed eruption of P2. Here, an alternative strepsirrhine model based onEulemurandVareciais presented. Our proposed model shows an older age at death than previously suggested (1.05–1.14 years), while the range for adult weight is entirely below the range proposed previously. This alternative model is more consistent with hypotheses supporting a stronger relationship between adapoids and strepsirrhines.
Mycobacterium saopaulense sp. nov., a rapidly growing mycobacterium closely related to members of the Mycobacterium chelonae–Mycobacterium abscessus group
Authors: Nogueira Christiane Lourenço , Whipps Christopher M. , Matsumoto Cristianne Kayoko , Chimara Erica , Droz Sara , Tortoli Enrico , de Freitas Denise , Cnockaert Margo , Palomino Juan Carlos , Martin Anandi , Vandamme Peter , Leão Sylvia Cardoso
Published: September 2015

Five isolates of non-pigmented, rapidly growing mycobacteria were isolated from three patients and, in an earlier study, from zebrafish. Phenotypic and molecular tests confirmed that these isolates belong to the Mycobacterium chelonae–Mycobacterium abscessus group, but they could not be confidently assigned to any known species of this group. Phenotypic analysis and biochemical tests were not helpful for distinguishing these isolates from other members of the M. chelonae–M. abscessus group. The isolates presented higher drug resistance in comparison with other members of the group, showing susceptibility only to clarithromycin. The five isolates showed a unique PCR restriction analysis pattern of the hsp65 gene, 100 % similarity in 16S rRNA gene and hsp65 sequences and 1–2 nt differences in rpoB and internal transcribed spacer (ITS) sequences. Phylogenetic analysis of a concatenated dataset including 16S rRNA gene, hsp65, and rpoB sequences from type strains of more closely related species placed the five isolates together, as a distinct lineage from previously described species, suggesting a sister relationship to a group consisting of M. chelonae, Mycobacterium salmoniphilum, Mycobacterium franklinii and Mycobacterium immunogenum. DNA–DNA hybridization values >70 % confirmed that the five isolates belong to the same species, while values < 70 % between one of the isolates and the type strains of M. chelonae and M. abscessus confirmed that the isolates belong to a distinct species. The polyphasic characterization of these isolates, supported by DNA–DNA hybridization results, demonstrated that they share characteristics with M. chelonae–M. abscessus members, but constitute a different species, for which the name Mycobacterium saopaulense sp. nov. is proposed. The type strain is EPM 10906T ( = CCUG 66554T = LMG 28586T = INCQS 0733T).
Efficient Integrative Multi-SNP Association Analysis using Deterministic Approximation of Posteriors
Authors: Wen Xiaoquan , Lee Yeji , Luca Francesca , Pique-Regi Roger
Published: September 2015

With the increasing availability of functional genomic data,1–3incorporating genomic annotations into genetic association analysis has become a standard procedure. However, the existing methods often lack rigor and/or computational efficiency and consequently do not maximize the utility of functional annotations. In this paper, we propose a rigorous inference procedure to perform integrative association analysis incorporating genomic annotations for both traditional GWAS and emerging molecular QTL mapping studies. In particular, we propose an algorithm, named “Deterministic Approximation of Posteriors” (DAP), which enables highly efficient and accurate joint enrichment analysis and identification of multiple causal variants. We use a series of simulation studies to highlight the power and computational efficiency of our proposed approach and further demonstrate it by analyzing the cross-population eQTL data from the GEUVADIS project and the multi-tissue eQTL data from the GTEx project. In particular, we find that genetic variants predicted to disrupt transcription factor binding sites are enriched incis-eQTLs across all tissues. Moreover, the enrichment estimates obtained across the tissues are correlated with the cell types for which the annotations are derived.
Variable separation method for nonlinear time fractional biological population model
Authors: Zhang Sheng , Cai Bin , Xu Bo
Published: September 2015

Purpose

– The purpose of this paper is to analytically solve the (2+1)-dimensional nonlinear time fractional biological population model in the Caputo sense.

Design/methodology/approach

– The paper uses the variable separation method and the properties of Gamma function to construct exact solutions of the time fractional biological population model.

Findings

– New variable separation solutions are obtained, from which some known solutions are recovered as special cases.

Originality/value

– Solving fractional biological population model by the variable separation method and the properties of Gamma function is original. It is shown that the method presented in this paper can be also used for some other nonlinear fractional partial differential equations arising in sciences and engineering.
Cosine expansion based differential quadrature algorithm for numerical simulation of two dimensional hyperbolic equations with variable coefficients
Authors: Verma Anjali , Jiwari Ram
Published: September 2015

Purpose

– The purpose of this paper is to present the computational modeling of second-order two-dimensional nonlinear hyperbolic equations by using cosine expansion-based differential quadrature method (CDQM).

Design/methodology/approach

– The CDQM reduced the equations into a system of second-order differential equations. The obtained system is solved by RK4 method by converting into a system of first ordinary differential equations.

Findings

– The computed numerical results are compared with the results presented by other workers (Mohantyet al., 1996; Mohanty, 2004) and it is found that the present numerical technique gives better results than the others. Second, the proposed algorithm gives good accuracy by using very less grid point and less computation cost as comparison to other numerical methods such as finite difference methods, finite elements methods, etc.

Originality/value

– The author extends CDQM proposed in (Korkmaz and Dağ, 2009b) for two-dimensional nonlinear hyperbolic partial differential equations. This work is new for two-dimensional nonlinear hyperbolic partial differential equations.
Unsteady flow of variable viscosity Cu-water and Al2O3-water nanofluids in a porous pipe with buoyancy force
Authors: Khamis Sara , Makinde Daniel Oluwole , Nkansah-Gyekye Yaw
Published: September 2015

Purpose

– The purpose of this paper is to investigate the combined effects of buoyancy force and variable viscosity on unsteady flow and heat transfer of water-based nanofluid containing copper and alumina as nanoparticles through a porous pipe.

Design/methodology/approach

– Using the Boussinesq and boundary-layer approximations with Buongiorno nanofluid model. The governing nonlinear partial differential equations for the continuity, momentum and energy balance are formulated. The equations obtained are solved numerically using a semi-discretization finite difference method (know) as method of line coupled with Runge-Kutta-Fehlberg integration scheme.

Findings

– Numerical results for the skin-friction, heat transfer and for the velocity and temperature profiles are obtained. The results show that with suction, Cu-water produces higher skin friction and heat transfer rate than Al2O3-water. Both nanofluids velocity and temperature increase with a decrease in viscosity and an increase in buoyancy force intensity.

Practical implications

– Buoyancy-driven flow and heat transfer in porous geometries has many significant applications in industrial and engineering such as, electrical and microelectronic equipments, solar-collectors, geothermal engineering, petroleum reservoirs, thermal buildings insulation. This work provides very important information for researchers on this subject.

Originality/value

– This paper illustrates the effects of buoyancy force and temperature dependent on heat transfer and fluid flow problem using Cu-water and Al2O3-water nanofluids in a porous pipe.
Developing a quality management system implementation process for a medical device manufacturer
Authors: Gadotti Martins Eduardo , Pinheiro de Lima Edson , Gouvea da Costa Sergio E.
Published: September 2015

Purpose

– The purpose of this paper is to develop and test a quality management system (QMS) implementation process for a medical devices manufacturer, which are covered by ISO 13485:2007 and RDC No. 59:2000 and based on operations strategy content definitions.

Design/methodology/approach

– The research strategy is based on the Cambridge approach which is supported by action research techniques for producing “application” processes. This research strategy is also known as the “Process Approach” or “the Engineering Approach” and was developed in the mid-1990s by researchers from the “Institute for Manufacturing” (IFM/University of Cambridge).

Findings

– The results reveal how real conditions “shape” implementation, indicating solutions for integrating procedures for performance and control indicators that represent manufacturing strategy objectives. The regulatory framework and the manufacturing environment offer these real conditions. The operations strategy that is underlying implementation shows how to reconcile regulation and strategy through its content.

Research limitations/implications

– The developed process can be improved by increasing the number of test cases until they bring no new contributions for its evolution. However, because it is a long-term and complex implementation process, the present research was concluded with a full understanding of process development.

Practical implications

– The QMS implementation process based on the Cambridge Engineering approach creates several opportunities for discussing QMS design requirements, but also in testing procedures for quality policy deployment. Learning by doing is a practical contribution of the process as a participative component effectively applied in different moments at the mentioned workshops – WSH. The logical organization of the QMS implementation process shows causalities among manufacturing strategy, QMS and performance measurements, creating strategic coherence among the connected elements.

Originality/value

– Although many studies had approached the QMS implementation, few of them actually addressed the system integration with the business strategic objectives. None of the studies to date related the implementation to the ISO 13485:2003 and the RDC No. 59.
Physicochemical properties of radiographic contrast media, potential nephrotoxicity and prophylaxis
Authors: Hogstrom Barry , Ikei Nobuhiro
Published: September 2015

Contrast induced nephropathy (CIN) remains a controversial topic. The clinical relevance of changes in laboratory parameters has been challenged; some authors have even suggested that CIN simply reflects natural fluctuations. Other areas of controversy include the pathophysiology of CIN, effectiveness of prophylactic approaches and differences in nephrotoxicity between individual contrast media (CM). The aim of this review is to summarize the current understanding of laboratory findings and explore its relationship to CM toxicity.
Effects of parental infidelity and interparental conflict on relational ethics between adult children and parents: a contextual perspective
Authors: Schmidt Alexandra E. , Green Mary S. , Prouty Anne M.
Published: September 2015

Little research within the couple and family therapy field has specifically addressed the influence of infidelity on members of the family outside the couple sub‐system. The purpose of this exploratory quantitative study was to utilize the lens of contextual therapy to explore the influence of parental infidelity and interparental conflict on adult children's (N = 703) reports of vertical relational ethics, including subscales measuring trust and justice, loyalty, and entitlement. Results from multiple regression analyses demonstrated that both higher levels of interparental conflict and the occurrence of parental infidelity were associated with lower levels of vertical relational ethics, which often takes the form of decreased trust in family members and increased potential for loyalty conflicts. Implications for addressing relational dynamics related to parental infidelity through systemic family therapy, as well as recommendations for future research, are discussed.

Practitioner points

Therapeutic assessment should include questions about influence of transgenerational patterns of infidelity and conflict between partners on parenting experiences.

Acknowledge young and adult children who feel caught in a split loyalty between parents and how they cope with these loyalty conflicts.

Engage clients in dialogue concerning how to restore the balance of offering and receiving care, support, and connection within family's unique cultural context.
Sustaining change following multisystemic therapy: caregiver's perspectives
Authors: Kaur Pinder , Pote Helen , Fox Simone , Paradisopoulos Daphne A.
Published: September 2015

Multisystemic therapy (MST) is an empirically supported intervention for young people presenting with antisocial behaviour. This study explored the process of sustaining positive outcomes following MST from caregiver perspectives. Semi‐structured interviews were carried out 5–21 months post‐MST with 12 caregivers. A grounded theory methodology was used to analyse the data. Caregivers in this study identified the following themes as contributing to sustaining change; improvements in their relationship with their child, shifting how they viewed difficulties and solutions and feeling personally strengthened and resilient. The therapeutic alliance in MST was described as important in initiating these changes. Clinical implications and how the themes from this study fit into the existing model of change in MST are discussed.

Practitioner points

Caregivers validated the therapeutic alliance as key to the MST approach.

Experiencing a positive therapeutic alliance was also identified as important in improving relationships within the family even after therapy was completed.

Positive experiences of MST developed caregivers’ experiences of feeling more resilient in the face of later difficulties helping sustain positive outcomes.
Bulimia nervosa in adolescents: a new therapeutic frontier
Authors: Hurst Kim , Read Shelly , Holtham Tiegan
Published: September 2015

Enhanced cognitive behaviour therapy (CBT‐E) is the first‐line treatment for bulimia nervosa (BN) in adulthood. There is limited evidence for therapies for children and adolescents with BN; however family‐based treatment (FBT) is being increasingly used. This case study contrasts the delivery of FBT with an augmented version (CBT‐E) in two adolescents presenting with BN. In both cases, the adolescents achieved remission from BN symptoms, (cessation of bingeing and compensatory behaviour) at the end of treatment. The families reported that FBT provided a platform for them to work together and view BN as a family issue, rather than leaving the onus on the young person to recover independently. The addition of CBT‐E strategies assisted with managing cognitions associated with bodyweight and shape concerns and appeared to be useful in a more complex presentation with comorbidities. Future research should examine the effectiveness of augmenting CBT‐E strategies to FBT using larger samples and more rigorous research designs.

Practitioner points

Involving families in the treatment of adolescent BN is both effective and acceptable to young people and their families.

Two promising treatment approaches, FBT‐BN and CBT‐E, can effectively be combined to provide a therapy which has the strengths of both modalities alone.

Adolescents with comorbidities or complex presentations may benefit most from combining the two modalities to develop additional skills and strategies.
Governmentality and the ‘Selling’ of School Surveillance Devices
Authors: Hope Andrew
Published: September 2015

In late modernity there has been a massive growth in ‘new’ surveillance devices situated within schools. This paper explores the reasons behind this proliferation, considering the role of key protagonists and the promises made regarding these technologies. It is suggested that there is strong connection between notions of neoliberal governmentality ( Foucault, 2008 ; Gane, 2012 ) and arguments relating to increased security, improved efficiency, the desirability of techno-surveillance devices and desensitization to pervasive monitoring. In particular, it is maintained that the devolution of state power, the marketization of education, increased responsibilization and the nature of observation in the viewer society all help to explain the emergence of ‘surveillance schools’. It is concluded that failure to recognize these new dynamics may result in schools quietly, subtly becoming experimental labs and then junkyards for our surveillance futures.
Cuminaldehyde as the Major Component of Cuminum cyminum, a Natural Aldehyde with Inhibitory Effect on Alpha‐Synuclein Fibrillation and Cytotoxicity
Authors: Morshedi Dina , Aliakbari Farhang , Tayaranian‐Marvian Amir , Fassihi Afshin , Pan‐Montojo Francisco , Pérez‐Sánchez Horacio
Published: September 2015

Fibrillation of alpha‐synuclein (α‐SN) is a critical process in the pathophysiology of several neurodegenerative diseases, especially Parkinson's disease. Application of bioactive inhibitory compounds from herbal extracts is a potential therapeutic approach for this cytotoxic process. Here, we investigated the inhibitory effects of the Iranian Cuminum cyminum essential oil on the fibrillation of α‐SN. Analysis of different fractions from the total extract identified cuminaldehyde as the active compound involved in the antifibrillation activity. In comparison with baicalein, a well‐known inhibitor of α‐SN fibrillation, cuminaldehyde showed the same activity in some aspects and a different activity on other parameters influencing α‐SN fibrillation. The presence of spermidine, an α‐SN fibrillation inducer, dominantly enforced the inhibitory effects of cuminaldehyde even more intensively than baicalein. Furthermore, the results from experiments using preformed fibrils and monobromobimane‐labeled monomeric protein also suggest that cuminaldehyde prevents α‐SN fibrillation even in the presence of seeds, having no disaggregating impact on the preformed fibrils. Structural studies showed that cuminaldehyde stalls protein assembly into β‐structural fibrils, which might be achieved by the interaction with amine groups through its aldehyde group as a Schiff base reaction. This assumption was supported by FITC labeling efficiency assay. In addition, cytotoxicity assays on PC12 cells showed that cuminaldehyde is a nontoxic compound, treatment with cuminaldehyde throughout α‐SN fibrillation showed no toxic effects on the cells. Taken together, these results show for the first time that the small abundant natural compound, cuminaldehyde, can modulate α‐SN fibrillation. Hence, suggesting that such natural active aldehyde could have potential therapeutic applications.