bluuebunny/crossref_metadata_2025_split huggingface dataset:
MuClone: Somatic mutation detection and classification through probabilistic integration of clonal population structure
Authors: Dorri Fatemeh , Jewell Sean , Bouchard-Côté Alexandre , Shah Sohrab P. 
Published: September 2017

AbstractAccurate detection and classification of somatic single nucleotide variants (SNVs) is important in defining the clonal composition of human cancers. Existing tools are prone to miss low prevalence mutations and methods for classification of mutations into clonal groups across the whole genome are underdeveloped. Increasing interest in deciphering clonal population dynamics over multiple samples in time or anatomic space from the same patient is resulting in whole genome sequence (WGS) data from phylogenetically related samples. With the access to this data, we posited that injecting clonal structure information into the inference of mutations from multiple samples would improve mutation detection.We developed MuClone: a novel statistical framework for simultaneous detection and classification of mutations across multiple tumour samples of a patient from whole genome or exome sequencing data. The key advance lies in incorporating prior knowledge about the cellular prevalences of clones to improve the performance of detecting mutations, particularly low prevalence mutations. We evaluated MuClone through synthetic and real data from spatially sampled ovarian cancers. Results support the hypothesis that clonal information improves sensitivity in detecting somatic mutations without compromising specificity. In addition, MuClone classifies mutations across whole genomes of multiple samples into biologically meaningful groups, providing additional phylogenetic insights and enhancing the study of WGS-derived clonal dynamics.
Failure analysis of the left waterwall tube of boiler furnace in the steam power plant based on thickness changes and pressure
Authors: Drastiawati Novi Sukma , Agustin H.C. Kis 
Published: September 2017

Purpose
The purpose of this paper is to analyze the failure of the left waterwall tube of a boiler furnace in the steam power plant which led to cracks and rupture. Macro visual observation showed the rupture like a fish mouth with slag adhering at the outer surface of the tube. Magnetite as a protective layer was peeled off. Changes in the thickness were analyzed through dimensional measurement. In this research, an analysis to find the cause and determine the fracture mechanism is presented.

Design/methodology/approach
A physical analysis was performed through visual observation of changes in the thickness. Micro visual testing with a metallography test provided the data required to measure the change of grain size. The mechanical analysis used Von Mises criteria and API 530 standard and provided the pressure limits data.

Findings
The thickness of the tube decreased at the peak curvature of the tube. The smallest thickness at the peak curvature of the tube was 0.108 inches. The working pressure was 40.74 percent from permit limits with Von Mises calculations. The percentage of pressure calculated by the API standard was 48.42 percent from permit limits. Larger crystal grains occurred only in the nearby area of the oxide layer and at the end of the crack tip. It indicated that part of the inner surface had a relatively high temperature and plastic deformation occurred because of the pressure from inside the tube. Combining all these factors ruptured the tube at this location because the cross-section could not hold up the pressure.

Originality/value
The analysis of this discussion focuses on the combined effect of those factors causing the ability to decrease stress being received. It restricts the tube from holding up the stress and furthermore it will generate fractures.
Stakeholder Corporate Social Responsibility Orientation Congruence, Entrepreneurial Orientation and Environmental Performance of Chinese Small and Medium‐sized Enterprises
Authors: Tang Zhi , Tang Jintong 
Published: September 2017

AbstractStakeholder studies have discovered that strong stakeholder corporate social responsibility (CSR) orientation can motivate firms to engage better in environmental activities. However, when multiple stakeholders are involved, strong yet incongruent stakeholder pressure may not lead to improved environmental performance. The authors integrate complexity science with stakeholder management theory to address this issue. Using a sample of 149 Chinese small and medium‐sized enterprises, they find that the average stakeholder's CSR orientation improves environmental strengths, but generates an inverted U‐shaped relationship with environmental concerns. Further, results indicate that the congruence in stakeholders’ CSR orientation enhances this inverted U‐shaped relationship, and that the moderating impact of congruence is weaker when entrepreneurial orientation is higher.
‘Rules that apply in times of crisis’: time, agency, and norm‐remaking during Nepal's People's War
Authors: Zharkevich Ina 
Published: September 2017

AbstractThis article explores how people in the former Maoist heartland of Nepal adopted previously transgressive norms and practices during the decade of the People's War (1996‐2006). By examining the rise in practices of beef‐eating and inter‐caste commensality, this article suggests that the temporal dimension of wartime ‘when different rules apply’ was crucial in making people accept new ideas and break established norms on a scale atypical for the ‘normal’ times of peace. Analysing the agency of Maoist activists, who self‐consciously tried to implement a project of radical social transformation, and those people who were caught in the midst of the Maoist transformative endeavour, this article argues that the contours of the ‘new society’ emerged not only due to revolutionaries’ intentional actions but also because of the ‘exceptional’ nature of wartime, which forced people to radically re‐create their daily lives. By transgressing social norms, ‘ordinary’ people did not deliberately undermine the normative order, but rather responded to the constraints of wartime, when people's agency and ethical choices were mostly driven by the need to secure the survival of their families and ensure the continuity of life itself.
Financialization of Housing in Brazil: New Frontiers
Authors: Pereira Alvaro Luis Dos Santos 
Published: September 2017

AbstractThe financialization of housing has been increasingly identified as an important driver of social and economic change in contemporary capitalism. Focusing on the Brazilian context, this article considers the extent to which recent changes in housing regulations, policies and markets confirm or challenge narratives about the financialization of housing in the international academic debate. I argue that while many of the trends stressed in the literature are apparent, more extreme processes of financialization within the Brazilian housing sector remain limited––not only because of institutional and regulatory constraints, path dependence or political resistance, but also because of fundamental structural conditions of Brazil's position as a peripheral economy. Three different but mutually reinforcing processes are scrutinized in order to evaluate the financialization of housing and its limits in Brazil: the re‐regulation of the real estate financial sector initiated in the 1990s; the changing funding patterns among real estate companies since the mid‐2000s; and the increasing commodification of housing induced by a large‐scale and heavily subsidized housing program launched in 2009.
Fetal head position and perineal distension associated with the use of the BD Odon Device™ in operative vaginal birth: a simulation study
Authors: O'Brien SM , Winter C , Burden CA , Boulvain M , Draycott TJ , Crofts JF 
Published: September 2017

ObjectiveTo investigate (1) the placement of the BD Odon Device on the model fetal head and (2) perineal distention during simulated operative vaginal births conducted with the BD Odon Device.DesignObservational simulation study.SettingNorth Bristol NHS Trust, UK.Population or sampleFour hundred and forty simulated operative vaginal births.MethodsThree bespoke fetal mannequins were developed to represent (1) bi‐parietal diameter of the 50th centile at term, (2) bi‐parietal diameter at the 5th centile at term, and (3) 50th centile head with 2 cm of caput. Siting of the BD Odon Device on model heads was determined before and after 400 simulated operative vaginal births. Variables were analysed to determine their effect on device siting and movement during birth. The fetal mannequins were placed inside a maternal mannequin and the BD Odon Device was placed around the fetal head as per the instructions for use. The location of the air cuff was determined before and after the head was delivered. Perineal distension was determined by recording maximum perineal distention during a simulated operative vaginal birth using the same procedure, as well as scenarios employing an inappropriately non‐deflated air cuff (for the BD Odon Device), the Kiwi ventouse and non‐rotational forceps.Main outcome measuresSite and displacement during birth of the BD Odon Device on a model head. Maximal perineal distension during birth.ResultsThe BD Odon Device was reliably sited in a standard over the fetal head position (approximately 40 mm above the fetal chin) for all stations, head sizes and positions with no significant displacement. In occipito‐posterior births, compared with occipito‐anterior or transverse, the BD Odon Device routinely sited further down the fetal head (toward the chin). The BD Odon Device was not associated with more perineal distension compared with forceps or Kiwi ventouse (respectively 21, 26 and 21 mm at posterior fourchette).ConclusionsThe BD Odon Device reliably sited over a safe area of the fetal head in 400 simulated births representative of clinical practice. The BD Odon Device generates similar levels of perineal distension compared with Kiwi ventouse when used correctly.Tweetable abstractLocation of the BD Odon Device on a fetal head in simulation
Spending per Medicare Beneficiary Is Higher in Hospital‐Owned Small‐ and Medium‐Sized Physician Practices
Authors: Pesko Michael F. , Ryan Andrew M. , Shortell Stephen M. , Copeland Kennon R. , Ramsay Patricia P. , Sun Xuming , Mendelsohn Jayme L. , Rittenhouse Diane R. , Casalino Lawrence P. 
Published: September 2017

ObjectiveTo examine the relationship of physician versus hospital ownership of small‐ and medium‐sized practices with spending and utilization of care.Data Source/Study Setting/Data CollectionSurvey data for 1,045 primary care‐based practices of 1–19 physicians linked to Medicare claims data for 2008 for 282,372 beneficiaries attributed to the 3,010 physicians in these practices.Study DesignWe used generalized linear models to estimate the associations between practice characteristics and outcomes (emergency department visits, index admissions, readmissions, and spending).Principal FindingsBeneficiaries linked to hospital‐owned practices had 7.3 percent more emergency department visits and 6.4 percent higher total spending compared to beneficiaries linked to physician‐owned practices.ConclusionsPhysician practices are increasingly being purchased by hospitals. This may result in higher total spending on care.
Estimating Input Complementarities with Unobserved Heterogeneity: Evidence from Ethiopia
Authors: Abay Kibrom A. , Berhane Guush , Taffesse Alemayehu Seyoum , Abay Kibrewossen , Koru Bethelhem 
Published: September 2017

AbstractThe level of technology adoption is often characterised as low in Africa. Recent evidence, however, points to the coexistence of substantial heterogeneity across farm households and the lack of a suitable mix of inputs for farmers to take advantage of input complementarities. We use a random coefficients multivariate probit model to quantify the complementarities between agricultural inputs and alternative forms of unobserved heterogeneity effects in modeling farmers' technology adoption decisions. The empirical analysis reveals that, conditional on various types of unobserved heterogeneity effects, farmers' technology adoption decisions exhibit strong complementarity for some inputs. The analysis also reveals substantial unobserved heterogeneity effects. We show that ignoring these behavioural features (unobserved heterogeneity and input complementarity) has important implications in quantifying the effect of some policy interventions that are meant to facilitate technology adoption. In particular, ignoring these features leads to significant overestimation of the effectiveness of extension services.
Forecasting the Probability of Future Groundwater Levels Declining Below Specified Low Thresholds in the Conterminous U.S.
Authors: Dudley Robert W. , Hodgkins Glenn A. , Dickinson Jesse E. 
Published: September 2017

AbstractWe present a logistic regression approach for forecasting the probability of future groundwater levels declining or maintaining below specific groundwater‐level thresholds. We tested our approach on 102 groundwater wells in different climatic regions and aquifers of the United States that are part of the U.S. Geological Survey Groundwater Climate Response Network. We evaluated the importance of current groundwater levels, precipitation, streamflow, seasonal variability, Palmer Drought Severity Index, and atmosphere/ocean indices for developing the logistic regression equations. Several diagnostics of model fit were used to evaluate the regression equations, including testing of autocorrelation of residuals, goodness‐of‐fit metrics, and bootstrap validation testing. The probabilistic predictions were most successful at wells with high persistence (low month‐to‐month variability) in their groundwater records and at wells where the groundwater level remained below the defined low threshold for sustained periods (generally three months or longer). The model fit was weakest at wells with strong seasonal variability in levels and with shorter duration low‐threshold events. We identified challenges in deriving probabilistic‐forecasting models and possible approaches for addressing those challenges.
Effects of short‐term add‐on ezetimibe to statin treatment on expression of adipokines and inflammatory markers in diabetic and dyslipidemic patients
Authors: Guimarães Elizandra Silva , Cerda Alvaro , Dorea Egidio Lima , Bernik Marcia Martins Silveira , Gusukuma Maria Cecilia , Pinto Gelba Almeida , Fajardo Cristina Moreno , Hirata Mario Hiroyuki , Hirata Rosario Dominguez Crespo 
Published: September 2017

SummaryAimThe influence of short‐term add‐on ezetimibe to simvastatin treatment on expression of adipokines and inflammatory markers was investigated in diabetic and nondiabetic patients with hypercholesterolemia.MethodHypercholesterolemic nondiabetic (HC, n = 37) and diabetic (DM, n = 47) patients were treated with simvastatin (SV, 10 or 20 mg/d/8‐wk) and then SV plus ezetimibe (SV + EZ, 10 mg each/d/4 wk). Serum lipids, glycemic profile, and inflammatory markers (hsCRP, adiponectin, resistin, VCAM‐1, and ICAM‐1) were evaluated before and after the add‐on ezetimibe therapy. mRNA expression of ADIPOR1, ADIPOR2, RETN, VCAM1, and ICAM1 was measured by real‐time PCR in peripheral blood mononuclear cells (PBMC).ResultsSerum concentrations of LDL and HDL cholesterol, and adiponectin were higher in HC than DM patients (P < .05). The add‐on ezetimibe therapy reduced total and LDL cholesterol, apoB and adiponectin serum levels in HC and DM groups, and resistin in HC subjects (P < .05). DM patients showed higher expression of ADIPOR1, ADIPOR2, RETN, and VCAM1 in PBMC than subjects in HC group, before and after add‐on ezetimibe therapy (P < .05). PBMC RETN mRNA expression was reduced by add‐on ezetimibe therapy in HC individuals (P < .05), but not in DM subjects.ConclusionShort‐term add‐on ezetimibe to simvastatin treatment suppressing effects on hypercholesterolemia and adiponectinemia is independent of the diabetes status. Resistin serum levels and leukocyte mRNA expression are influenced by add‐on ezetimibe to statin treatment.
National clinical practice guidelines for allergen immunotherapy: An international assessment applying AGREE‐II
Authors: Larenas‐Linnemann D. E. S. , Antolín‐Amérigo D. , Parisi C. , Nakonechna A. , Luna‐Pech J. A. , Wedi B. , Davila I. , Gómez M. , Levin M. , Ortega Martell J. A. , Klimek L. , Rosario N. , Muraro A. M. , Agache I. , Bousquet J. , Sheikh A. ,   EAACI International Societies Council, Pfaar O. 
Published: September 2017

AbstractBackgroundSince 1988, numerous allergen immunotherapy guidelines (AIT‐GLs) have been developed by national and international organizations to guide physicians in AIT. Even so, AIT is still severely underused.ObjectiveTo evaluate AIT‐GLs with AGREE‐II, developed in 2010 by McMaster University methodologists to comprehensively evaluate GL quality.MethodsAllergist, from different continents, knowledgeable in AIT and AGREE‐II trained were selected into the project team. The project received methodologists’ guidance. AIT‐GLs in any language were sought from 1980 to 2016; AIT‐GLs were AGREE II‐evaluated by at least 2 team members, independently; discrepancies were resolved in a second round, by team discussion or methodologists’ consulting.ResultsWe found 31 AIT‐GLs (15 post‐2010), ranging from local consensus reports to international position papers (EAACI, AAAAI‐ACAAI, WAO). Pre‐2010 GLs scored 1.6‐4.6 (23%‐67%) and post‐2010 GLs scored 2.1‐6 (30%‐86%), on a 7‐point Likert scale. The highest scores went to: German‐Austrian‐Swiss (6.0), Mexican (5.1), and the AAAAI/ACAAI AIT‐GL (4.7). These were also the only 3 GLs that received “yes” of both evaluators to the item: “I would recommend this GL for use.” The domains of “Stakeholder involvement” and “Rigor of Development” only scored 3/7, and “Applicability” scored the lowest. Strikingly, newer GLs only scored clearly better in “Editorial independence” and “Global evaluation.”ConclusionsIn AIT‐GLs, there is still a lot of room for improvement, especially in domains crucial for the dissemination. For some GLs, the “Scientific rigor” domain flawed. When resources are limited, transculturizing a high‐quality GL might be preferable over developing a GL from zero. Our study and AGREE‐II could help to select the best candidate.Clinical ImplicationsWe here evaluate allergen immunotherapy guideline (AIT‐GL) quality. Only high‐quality AIT‐GLs should be consulted for AIT management decisions. In low‐resource settings, transculturization of these is preferred over developing low‐quality guidelines.
Preterm and term‐equivalent age general movements and 1‐year neurodevelopmental outcomes for infants born before 30 weeks' gestation
Authors: Olsen Joy E , Allinson Leesa G , Doyle Lex W , Brown Nisha C , Lee Katherine J , Eeles Abbey L , Cheong Jeanie L Y , Spittle Alicia J 
Published: September 2017

AimTo examine the associations between Prechtl's General Movements Assessment (GMA), conducted from birth to term‐equivalent age, and neurodevelopmental outcomes at 12 months corrected age, in infants born very preterm.MethodOne hundred and thirty‐seven infants born before 30 weeks' gestation had serial GMA (categorized as ‘normal’ or ‘abnormal’) before term and at term‐equivalent age. At 12 months corrected age, neurodevelopment was assessed using the Alberta Infant Motor Scale (AIMS); Neurological, Sensory, Motor, Developmental Assessment (NSMDA); and Touwen Infant Neurological Examination (TINE). The relationships between GMA at four time points and 12‐month neurodevelopmental assessments were examined using regression models.ResultsAbnormal GMA at all time points were associated with worse continuous scores on the AIMS, NSMDA, and TINE (p<0.05). Abnormal GMA before term and at term‐equivalent age were associated with increased odds of mild–severe dysfunction on the NSMDA (odds ratio [OR] 4.26, 95% confidence interval [CI] 1.55–11.71, p<0.01; and OR 4.16, 95% CI 1.55–11.17, p<0.01 respectively) and abnormal GMA before term with increased odds of suboptimal–abnormal motor function on the TINE (OR 2.75, 95% CI 1.10–6.85, p=0.03).InterpretationAbnormal GMA before term and at term‐equivalent age were associated with worse neurodevelopment at 12 months corrected age in children born very preterm.What this paper adds

Abnormal general movements before term predict developmental deficits at 1 year in infants born very preterm.

General Movements Assessment before term identifies at‐risk infants born very preterm.
Estimating winter survival of winter wheat by simulations of plant frost tolerance
Authors: Bergjord Olsen A. K. , Persson T. , de Wit A. , Nkurunziza L. , Sindhøj E. , Eckersten H. 
Published: September 2017

AbstractBased on soil temperature, snow depth and the grown cultivar's maximum attainable level of frost tolerance (LT50c), the FROSTOL model simulates development of frost tolerance (LT50) and winter damage, thereby enabling risk calculations for winter wheat survival. To explore the accuracy of this model, four winter wheat cultivars were sown in a field experiment in Uppsala, Sweden in 2013 and 2014. The LT50 was determined by tests of frost tolerance in November, and the cultivars’ LT50c was estimated. Further, recorded winter survival from 20 winter wheat field variety trials in Sweden and Norway was collected from two winter seasons with substantial winter damages. FROSTOL simulations were run for selected cultivars at each location. According to percentage of winter damage, the cultivar survival was classified as “survived,” “intermediate” or “killed.” Mean correspondence between recorded and simulated class of winter survival was 75% and 37% for the locations in Sweden and Norway, respectively. Stress factors that were not accounted for in FROSTOL might explain the poorer accuracy at the Norwegian locations. The accuracy was poorest for cultivars with intermediate LT50c levels. When low temperature was the main cause of damage, as at the Swedish locations, the model accuracy was satisfying.
Preliminary studies on the use of pertussis toxin for the modulation of intravaginal SIV transmission in rhesus macaques
Authors: Ortiz Kristina , Sampathkumar Rebecca S. , Ansari Aftab A. , Byrareddy Siddappa N. 
Published: September 2017

AbstractBackgroundPertussis toxin (PTX) blocks GPCR signaling resulting in the inhibition of chemotaxis/cell adhesion. It was reasoned that inhibition of cell trafficking may be an approach to prevent HIV/SIV transmission.MethodsIn this study, PTX in HEC gel was applied to the vaginal wall of monkeys that were then challenged intravaginally with SIVmac251.ResultsResults of these studies showed that 2 of 4 animals were resistant to infection. Furthermore, infection was correlated with a marked increase in the plasma and cervicovaginal lavage levels of select chemokines and cytokines.ConclusionsResults from this preliminary feasibility study dictate that further studies that include a larger number of animals are required to optimize this protocol and establish the efficacy of this approach. In addition, such future studies will provide important information on the role of specific chemokines that play a role in lymphocyte trafficking within the genital tract and serve as additional therapeutic targets.