bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential transcript usage from RNA-seq data: isoform pre-filtering improves performance of count-based methods
Authors: Soneson Charlotte , Matthes Katarina L. , Nowicka Malgorzata , Law Charity W. , Robinson Mark D. 
Published: August 2015

AbstractLarge-scale sequencing of cDNA (RNA-seq) has been a boon to the quantitative analysis of transcriptomes. A notable application is the detection of changes in transcript usage between experimental conditions. For example, discovery of pathological alternative splicing may allow the development of new treatments or better management of patients. From an analysis perspective, there are several ways to approach RNA-seq data to unravel differential transcript usage, such as annotation-based exon-level counting, differential analysis of the ‘percent spliced in’ measure or quantitative analysis of assembled transcripts. The goal of this research is to compare and contrast current state-of-the-art methods, as well as to suggest improvements to commonly used workflows.We assess the performance of representative workflows using synthetic data and explore the effect of using non-standard counting bin definitions as input to a state-of-the-art inference engine (DEXSeq). Although the canonical counting provided the best results overall, several non-canonical approaches were as good or better in specific aspects and most counting approaches outperformed the evaluated event- and assembly-based methods. We show that an incomplete annotation catalog can have a detrimental effect on the ability to detect differential transcript usage in transcriptomes with few isoforms per gene and that isoform-level pre-filtering can considerably improve false discovery rate (FDR) control.Count-based methods generally perform well in detection of differential transcript usage. Controlling the FDR at the imposed threshold is difficult, mainly in complex organisms, but can be improved by pre-filtering of the annotation catalog.
Crystals of the Arp2/3 complex in two new space groups with structural information about actin-related protein 2 and potential WASP binding sites
Authors: Jurgenson Christopher T. , Pollard Thomas D. 
Published: August 2015

Co-crystals of the bovine Arp2/3 complex with the CA motif from N-WASP in two new space groups were analyzed by X-ray diffraction. The crystals in the orthorhombic space groupP212121contained one complex per asymmetric unit, with unit-cell parametersa= 105.48,b= 156.71,c= 177.84 Å, and diffracted to 3.9 Å resolution. The crystals in the tetragonal space groupP41contained two complexes per asymmetric unit, with unit-cell parametersa=b= 149.93,c = 265.91 Å, and diffracted to 5.0 Å resolution. The electron-density maps of both new crystal forms had densities for small segments of subdomains 1 and 2 of Arp2. Both maps had density at the binding site on Arp3 for the C-terminal EWE tripeptide from N-WASP and a binding site proposed for the C motif of N-WASP in the barbed-end groove of Arp2. The map from the tetragonal crystal form had density near the barbed end of Arp3 that may correspond to the C helix of N-WASP. The noise levels and the low resolution of the maps made the assignment of specific molecular structures for any of these CA peptides impossible.
Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase
Authors: Serrano-Posada Hugo , Centeno-Leija Sara , Rojas-Trejo Sonia , Stojanoff Vivian , Rodríguez-Sanoja Romina , Rudiño-Piñera Enrique , Sánchez Sergio 
Published: August 2015

Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg2+(LrdC-Mg2+) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg2+–PPi). Crystals of native LrdC-Mg2+diffracted to 2.50 Å resolution and belonged to the trigonal space groupP3221, with unit-cell parametersa = b = 107.1,c= 89.2 Å. Crystals of the LrdC-Mg2+–PPicomplex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space groupP3221. Crystals of the LrdC-Mg2+–PPicomplex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space groupP21, with unit-cell parametersa= 49.9,b= 104.1,c= 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.
Understanding trust
&
commitment of individual saving customers in Islamic banking
Authors: Sumaedi Sik , Juniarti Rosa P , Bakti I Gede Mahatma Yuda 
Published: August 2015

Purpose
– This paper aims to examine the relationship among trust, commitment and ego involvement and their impacts on word-of-mouth communication (WOM) for individual saving customers in Islamic banking.

Design/methodology/approach
– The conceptual model and the hypotheses are formulated based on trust and commitment theory, organizational commitment theory, social judgment theory and the results of previous empirical studies on buyer–seller marketing relationship in business-to-customer (B2C) markets. Quantitative research methodology was performed to examine the model and the hypotheses. The data were collected using survey with questionnaire. The respondents of the survey are 100 Islamic banking individual saving customers. Multiple regression analysis was used to test the proposed model and the hypotheses.

Findings
– The research results show that affective commitment has a positive and significant impact on WOM, while normative commitment and calculative commitment have no significant impact on WOM. Ego involvement has a positive and significant impact on trust, normative commitment, calculative commitment and affective commitment. However, trust does not have a significant impact on calculative commitment, normative commitment and affective commitment.

Research limitations/implications
– This research was only conducted in one Islamic bank in Indonesia. The data collection using the convenience sampling method as well as the use of a small sample size caused the limitation of the research results in representing across the retail customer of the bank. This study can be replicated with a larger sample size and by involving more Islamic banks to examine the stability of the findings.

Practical implications
– The research results indicate that ego involvement has an important role in shaping trust and commitment of Islamic banking individual saving customers. Given this, the managements of Islamic banks need to ensure that the banks they have managed are relevant, important and appropriate with the values espoused by their individual customers.

Originality/value
– This study is important because of the limited literature which discusses relationship marketing in the context of Islamic banking. Furthermore, this research has a novelty on the inclusion of ego involvement in explaining trust and commitment. The use of commitment as a multi-attribute construct also enriches the literature on buyer–seller marketing relationship in B2C markets due to the limited literature that addresses commitment as a multi-attribute construct.
Determining value in a complex service setting
Authors: Plewa Carolin , Sweeney Jillian C. , Michayluk David 
Published: August 2015

Purpose– The purpose of this paper is to capture the richness of customer perceived value by determining its benefit and cost dimensions in a complex service setting. Perceived value is argued as equivalent to value-in-use; that is value that emerges for or is created by the customer.Design/methodology/approach– A series of in-depth interviews was conducted with a diverse group of clients of financial planning services as well as with financial planners in Australia.Findings– Six benefit and four cost dimensions of complex service are identified, namely expertise, education, motivation, support, relationship and convenience benefits, as well as monetary, time and effort, emotional and lifestyle costs. The results also indicate proposed outcomes of these dimensions, along with relevant moderators, leading to a broad conceptual framework for future empirical validation.Originality/value– This study contributes to the sparse conceptual development of value perceptions, or value-in-use, in a complex service context. In particular, the authors identify the benefit and cost dimensions, specifically addressing aspects of value that are linked to the long-term relationship between provider and customer. The authors also develop a conceptual model of value, including both outcomes and situational moderators of the various value dimensions. Finally, the conceptualization of perceived value is discussed with respect to the value co-creation literature.
Determinants of Private Long‐Term Care Insurance Purchase in Response to the Partnership Program
Authors: Lin Haizhen , Prince Jeffrey T. 
Published: August 2015

ObjectiveTo assess three possible determinants of individuals' response in their private insurance purchases to the availability of the Partnership for Long‐Term Care (PLTC) insurance program: bequest motives, financial literacy, and program awareness.Data SourcesThe health and retirement study (HRS) merged with data on states' implementation of the PLTC program.Study DesignIndividual‐level decision on private long‐term care insurance is regressed on whether the PLTC program is being implemented for a given state‐year, asset dummies, policy determinant variable, two‐way and three‐way interactions of these variables, and other controls, using fixed effects panel regression.Data Extraction MethodsAnalysis used a sample between 50 and 69 years of age from 2002 to 2010, resulting in 12,695 unique individuals with a total of 39,151 observations.Principal FindingsWe find mild evidence that intent to bequest influences individual purchase of insurance. We also find that program awareness is necessary for response, while financial literacy notably increases responsiveness.ConclusionsIncreasing response to the PLTC program among the middle class (the stated target group) requires increased efforts to create awareness of the program's existence and increased education about the program's benefits, and more generally, about long‐term care risks and needs.
Three‐dimensional in vitro measurements of tooth wear using fluoridated dentifrices
Authors: Al‐Mashhadani A , Plygkos I , Bozec L , Rodriguez JM 
Published: August 2015

AbstractBackgroundThe aim of this study was to compare differences in wear of human enamel and dentine in vitro using a 3D measurement method comparing silica versus non‐silica containing fluoridated dentifrices (Colgate Total™ [CT] or Fluor Protector Gel™ [FPG]).MethodsMounted native enamel (n = 36) and polished dentine (n = 36) samples were subjected to 10 wear cycles. Each cycle consisted of: (1) 1 hour remineralization in artificial saliva (AS); (2) 10 minute erosion (0.3% citric acid; pH = 2.8); (3) 2 minute toothbrush abrasion in AS (G1, control) or a slurry of 3:1 by weight of AS:dentifrice (G2 = CT; G3 = FPG) under a load of 2 N. Each group contained 12 enamel and 12 dentine samples. Paired pre‐ and post‐wear scans made with a contacting scanner were digitally superimposed using ball bearings as datum.ResultsMean and (SD) enamel wear was G1 = 21.9 μm (6.4); G2 = 15.2 μm (2.8); G3 = 16.9 μm (3.2). Enamel wear was not different between dentifrices (p = 0.99). Both dentifrices resulted in less enamel wear compared to the control (p < 0.05). Dentine wear was G1 = 41.3 μm (8.1); G2 = 29.1 μm (4.4); G3 = 22.1 μm (3.5). Differences in measurements were observed between dentifrices and control (p < 0.05) and between dentifrices (p = 0.014) with FPG showing less dentine wear than CT.ConclusionsFPG offered protection against erosive/abrasive tooth wear in dentine compared to CT. FPG did not offer such protective effect on enamel wear.
Efficacy of on‐demand treatment in reducing morbidity in patients with hereditary angioedema due to C1 inhibitor deficiency
Authors: Zanichelli A. , Mansi M. , Azin G. M. , Wu M. A. , Periti G. , Casazza G. , Vacchini R. , Suffritti C. , Cicardi M. 
Published: August 2015

AbstractBackgroundAngioedema due to hereditary deficiency of C1 inhibitor causes temporarily disability. Guidelines recommend early on‐demand treatment of attacks to reduce morbidity. In this prospective observational study, we evaluated the efficacy of on‐demand approach.MethodsFrom January 2009 to August 2014, data on attacks and treatments were collected from 227 patients from our centre in Milan.ResultsA total of 4244 attacks were reported; 50% were treated with approved therapies (pdC1‐INH or icatibant), 15% were with tranexamic acid, and 35% were not treated. Attack locations were peripheral cutaneous (46%), abdominal (34%), multiple (12%), facial (5%) and laryngeal (3%). Attack severities were moderate (48%), mild (28%) and severe (24%). Median attack duration (data available for 2393 attacks) with approved therapies was 10 h, significantly shorter than without treatment (45 h) or with tranexamic acid (38 h). Most of the treatments were self‐administered: 93% with icatibant and 59% with pd‐C1‐INH. Median attack duration with icatibant was 8 and 11.5 h with pd‐C1 INH. Median time from onset of symptoms to drug administration was 1 h with icatibant and 2 h with pd‐C1INH and median time from drug administration to complete resolution was 5.5 and 8 h, respectively. Second treatment was required in 12.7% of icatibant‐treated attacks and in 1.9% of pdC1‐INH‐treated attacks.ConclusionThis study provides evidence that on‐demand treatment is effective in reducing disease‐related morbidity. The use of on‐demand treatment in Italy has increased up to 50% of attacks in the last years, reflecting a better adherence to international guidelines.
Epicutaneous immunotherapy with a hypoallergenic Bet v 1 suppresses allergic asthma in a murine model
Authors: Siebeneicher S. , Reuter S. , Wangorsch A. , Krause M. , Foetisch K. , Heinz A. , Naito S. , Reuter A. , Taube C. , Vieths S. , Scheurer S. , Toda M. 
Published: August 2015

AbstractBackgroundDue to reduced allergic potency, hypoallergenic variants have been suggested as safer and potentially more efficacious alternative to the corresponding wild‐type allergens in allergen‐specific immunotherapy. Here, we aimed at investigating the efficacy of recombinant Bet v 1B2, a hypoallergenic folding variant of Bet v 1, in epicutaneous immunotherapy to suppress asthmatic features using a murine model of birch pollen allergy.Methods and ResultsBefore, or after sensitization with rBet v 1 plus ALUMW and intranasal challenges with birch pollen extract, BALB/c mice received epicutaneous immunization (EPI) with rBet v 1, or rBet v 1B2 on their depilated back. Prophylactic EPI with rBet v 1B2, but not with rBet v 1, suppressed serum levels of Bet v 1‐specific IgE antibodies and reduced the number of eosinophils and the concentrations of Th2 cytokines in bronchoalveolar lavage. In an established allergic condition, serum levels of Bet v 1‐specific IgE antibodies were similar between PBS‐treated control mice and EPI‐treated mice. However, therapeutic EPI with rBet v 1B2, but not with rBet v 1, significantly suppressed the development of airway inflammation and lung function impairment.ConclusionThis study is the first to show the effect of therapeutic EPI with a recombinant form of a hypoallergenic folding variant on the suppression of asthmatic features. Our results suggest that rBet v 1B2 along with its reduced IgE‐binding capacity could be a preferred therapeutic allergen than wild‐type rBet v 1 in epicutaneous immunotherapy of birch pollen‐induced allergic asthma, in particular due to a lower risk of allergic side effect.
Determinants of anterior chamber depth in a large Caucasian population and agreement between intra‐ocular lens Master and Pentacam measurements of this variable
Authors: Fernández‐Vigo José Ignacio , Fernández‐Vigo José Ángel , Macarro‐Merino Ana , Fernández‐Pérez Cristina , Martínez‐de‐la‐Casa Jose Maria , García‐Feijoó Julian 
Published: August 2015

AbstractPurposeTo establish the main determinants of anterior chamber depth (ACD) in Caucasian subjects and examine agreement between IOL Master® (Carl Zeiss, Meditec) and Pentacam® (Oculus Inc.) ACD measurements.MethodsIn a cross‐sectional study, 1006 right eyes of 1006 healthy subjects were subjected to a general ophthalmologic examination using the Pentacam®, IOLMaster® and OCT RTVue® (Optovue Inc.). The variables recorded were age, sex, intra‐ocular pressure, spherical refractive error, axial length (AL), central corneal thickness, corneal diameter, iris thickness, and anterior chamber depth, volume and angle (ACA). The effects of these variables on ACD were analysed by multivariate linear regression.ResultsMean age was 49.1 years (range 18–84); 61% were women. In 98.3% of the eyes, ACD could be measured using the IOL Master and in 98% the Pentacam was used to give mean depths of 3.30 ± 0.42 mm and 3.35 ± 0.43 mm, respectively, for the two instruments. Agreement between these devices was high. In men, ACD was 0.13 mm on average deeper than in women (p < 0.001). ACD was correlated with ACA, AL, corneal diameter, spherical refractive error and age (p < 0.001). Five variables – age, sex, spherical error, corneal diameter and ACA – were able to explain 74.1% of the variation produced in ACD (R2 = 0.741; p < 0.001), among which age emerged as the main determinant (partial R2 = 0.279; p < 0.001).ConclusionsAge, sex, spherical error, corneal diameter and ACA correlate highly with ACD and together serve to explain much of its variation. When used to measure ACD, the IOLMaster and Pentacam show excellent agreement.
Alcohol consumption is higher among left‐behind Chinese children whose parents leave rural areas to work
Authors: Jiang Shan , Chu Jie , Li Cuicui , Medina Alexis , Hu Qiongwei , Liu Jing , Zhou Chengchao 
Published: August 2015

AbstractAimOver the past few decades, a large number of rural residents have migrated to cities in China and left their children behind. This study estimated how many 10‐ to 14‐year‐old children in rural Anhui drank alcohol and examined the association between parental migration and children's alcohol use.MethodsA cross‐sectional study was conducted in six cities in Anhui between July and August 2012. All participants had lived in the study villages for at least six months during the previous year and were interviewed face‐to‐face using a standardised questionnaire.ResultsMore than half (57%) of the 1367 subjects were left‐behind children, 43% lived with both parents and 9.6% currently drank alcohol. When we controlled for other variables, the rate of alcohol use was statistically higher among left‐behind children if both parents had migrated (14.0%) than among children living with both parents (7.8%) (p = 0.002). Boys, children with siblings and those with a poorer academic performance were more likely to drink.ConclusionChildren in rural China were more likely to drink if both their parents had migrated in search of work. School‐based interventions could help to reduce alcohol use among rural left‐behind children, especially boys.
Respiratory illness contributed significantly to morbidity in children born extremely premature or with extremely low birthweights in 1999–2000
Authors: Skromme Kaia , Leversen Katrine Tyborg , Eide Geir Egil , Markestad Trond , Halvorsen Thomas 
Published: August 2015

AbstractAimThis study investigated respiratory morbidity and risk factors during the first five years of life after extremely preterm birth.MethodsPaediatric assessments and parental questionnaires were obtained at two and five years of age in this national prospective cohort of 372 Norwegian children born during 1999–2000 at a gestational age of <28 weeks or birthweight <1,000 grams.ResultsPaediatric assessments were obtained for 100% and 82% of the children at two and five years of age and completed questionnaires for 71% and 76%, respectively. Total readmission rates decreased from 49 to 14% at one to five years, and readmissions for respiratory causes fell from 31 to 3%. Bronchopulmonary dysplasia (BPD) or gestational age was not associated with readmissions for respiratory causes in multiple logistic regression models. However, both BPD and gestational age ≤25 weeks was associated with wheezing during the first year and the use of asthma medication during the first two years. BPD was associated with asthma medication between three and five years but not significantly at five years.ConclusionRespiratory morbidity decreased during the first five years of life but was still more common than expected. It was unrelated to BPD and gestational age at five years of age.
Differences in the ARID‐1 alpha expressions in squamous and adenosquamous carcinomas of uterine cervix
Authors: Solakoglu Kahraman Dudu , Diniz Gulden , Sayhan Sevil , Ayaz Duygu , Uncel Melek , Karadeniz Tugba , Akman Tulay , Ozdemir Aykut 
Published: August 2015

AT‐rich interactive domain 1A (ARID1A) is a tumor suppressor gene involved in chromatin remodeling which encodes ARID1A (BAF250a) protein. Recent studies have shown the loss of ARID1A expression in several types of tumors. This retrospective study was designed to evaluate the differences in tissue expressions of ARID1A in a spectrum of cervical neoplasms. Cervical intraepithelial neoplasms, invasive squamous or adenosquamous carcinomas were identified in 100 patients recently diagnosed as cervical neoplasms based on pathology databases. In this series, there were 29 low‐ and 29 high‐grade cervical intraepithelial neoplasms, 27 squamous cell carcinomas, and 15 adenosquamous carcinomas. Mean age of the patients was 47.8 ± 13 years (20–80 years). It was determined that the expression of ARID1A was statistically significantly down‐regulated in adenosquamous carcinomas when compared with non‐invasive or invasive squamous cell carcinomas (p = 0.015). Lower levels of the ARID1A expression were detected in cases with adenosquamous carcinomas (60%), low‐ or high‐grade squamous intraepithelial lesion (SIL) (31%), and squamous cell carcinomas (18.5%). Our findings have demonstrated the presence of a correlation between ARID1A expression and adenomatous differentiation of uterine squamous cell carcinomas. Therefore, ARID1A gene may suggestively have a role in the pathogenesis of cervical adenosquamous carcinomas.
Loss of B cell regulatory function is associated with delayed healing in patients with tibia fracture
Authors: Yang Shufeng , Ding Wei , Feng Dapeng , Gong Haiyang , Zhu Dongmei , Chen Bin , Chen Jianmin 
Published: August 2015

The process of bone regeneration after fracture is a complex and well‐orchestrated process usually requiring 3–12 weeks. A subset of patients, however, exhibit delayed healing time and even incomplete restoration of the normal bone structure. Although the precise mechanism is unknown, studies have shown that smurf1 may play a role during the process. Here, we sought to determine the involvement of the immune system in impaired bone healing. We found that immediately after fracture, the B‐cell composition was shifted toward increased frequency of plasmablasts and decreased frequency of naïve B cells, reflecting higher inflammatory status. The percentage of CD19+CD24+CD38+ regulatory B cells was also upregulated in response to bone fracture. The production of IL‐10, a pivotal cytokine in regulatory B‐cell function, was upregulated in all patients. Interestingly, the increase in IL‐10 production was only sustained throughout the healing course in normal healing patients but not in delayed healing patients. Rather, delayed healing patients downregulated B‐cell IL‐10 secretion early and had reduced level of regulatory B‐cell activity. Together, these data revealed a role of regulatory B cells in the endogenous bone regeneration process and an alternation in B‐cell‐mediated regulation in delayed healing patients.