bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering of Circular Consensus Sequences: Accurate Error Correction and Assembly of Single Molecule Real-Time Reads from Multiplexed Amplicon Libraries
Authors: Francis Felix , Dumas Michael D. , Davis Scott B. , Wisser Randall J. 
Published: December 2017

BACKGROUNDTargeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical challenge for research and applications using HTS data, especially from long-read platforms, is errors arising from technological limits and bioinformatic algorithms.RESULTSA single molecule real-time (SMRT) sequencing-error correction and assembly pipeline, C3S-LAA, was developed for libraries of pooled amplicons. By uniquely leveraging the structure of SMRT sequence data (comprised of multiple low quality subreads from which higher quality circular consensus sequences are formed) to cluster raw reads, C3S-LAA produced accurate consensus sequences and assemblies of overlapping amplicons from single sample and multiplexed libraries. In contrast, despite read depths in excess of 100X per amplicon, the standard long amplicon analysis module from Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences. A bootstrap analysis showed that the C3S-LAA pipeline per se was effective at removing bioinformatic sources of error, but in rare cases a read depth of nearly 400X was not sufficient to overcome minor but systematic errors inherent to amplification or sequencing.CONCLUSIONSC3S-LAA uses a novel processing algorithm for SMRT amplicon-sequence data that produces accurate consensus sequences and local sequence assemblies. The community standard long amplicon analysis module from Pacific Biosciences is prone to substantial errors that raise concerns about findings based on this pipeline. The method developed here removed this confounding bioinformatics source of error, allowing for the identification of limited instances of errors due to DNA amplification or sequencing.
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome
Authors: Semick Stephen A. , Collado-Torres Leonardo , Markunas Christina A. , Shin Joo Heon , Deep-Soboslay Amy , Tao Ran , Bierut Laura J. , Maher Brion S. , Johnson Eric O. , Hyde Thomas M. , Weinberger Daniel R. , Hancock Dana B. , Kleinman Joel E. , Jaffe Andrew E. 
Published: December 2017

AbstractCigarette smoking during pregnancy is a major public health concern. While there are well-described consequences in early child development, there is very little known about the effects of maternal smoking on human cortical biology during prenatal life. We therefore performed a genome-wide differential gene expression analysis using RNA sequencing (RNA-seq) on prenatal (N=33; 16 smoking-exposed) as well as adult (N=207; 57 active smokers) human post-mortem prefrontal cortices. Smoking exposure during the prenatal period was directly associated with differential expression of 14 genes; in contrast, during adulthood, despite a much larger sample size, only 2 genes showed significant differential expression (FDR<10%). Moreover, 1,315 genes showed significantly different exposure effects between maternal smoking during pregnancy and direct exposure in adulthood (FDR<10%) – these differences were largely driven by prenatal differences that were enriched for pathways previously implicated in addiction and synaptic function. Furthermore, prenatal and age-dependent differentially expressed genes were enriched for genes implicated in non-syndromic autism spectrum disorder (ASD) and were differentially expressed as a set between patients with ASD and controls in post-mortem cortical regions. These results underscore the enhanced sensitivity to the biological effect of smoking exposure in the developing brain and offer novel insight into the effects of maternal smoking during pregnancy on the prenatal human brain. They also begin to address the relationship between in utero exposure to smoking and the heightened risks for the subsequent development of neuropsychiatric disorders.One Sentence SummaryMaternal smoking during pregnancy alters the expression of genes within the developing human cortex and these changes are enriched for genes implicated in neuropsychiatric disorders.
Characterization of the bHLH Family of Transcriptional Regulators in the ACOELS. roscoffensisand their Putative Role in Neurogenesis
Authors: Perea-Atienza E , Sprecher S.G. , Martínez P 
Published: December 2017

ABSTRACTBackgroundThe basic Helix loop helix (bHLH) family of transcription factors is one of the largest superfamilies of regulatory transcription factors and are widely used in eukaryotic organisms. They play an essential role in a range of metabolic, physiological, and developmental processes, including the development of the nervous system (NS). These transcription factors have been studied in many metazoans, especially in vertebrates but also in early branching metazoan clades such as the cnidarians and sponges. However, currently very little is known about their expression in the most basally branching bilaterian group, the xenacoelomorphs. Recently, our laboratory has characterized the full complement of bHLH in the genome of two members of the Xenacoelomorpha, the xenoturbellidXenoturbella bockiand the acoelSymsagittifera roscoffensis. Understanding the patterns of bHLH gene expression in members of this phylum (in space and time) provides critical new insights into the conserved roles of the bHLH and their putative specificities in this group. Our focus is on deciphering the specific roles that these genes have in the process of neurogenesis.ResultsHere, we analyze the developmental expression of the whole complement of bHLH genes identified in the acoelS. roscoffensis.Based on their expression patterns several members of bHLH class A appear to have specific conserved roles in neurogenesis, while other class A genes (as well as members of other classes) have likely taken on more generalized functions. All gene expression patterns are described in embryos and early juveniles.ConclusionOur results suggest that the main roles of the bHLH genes ofS. roscoffensisare evolutionarily conserved, with a specific subset dedicated to patterning the nervous system: SrAscA, SrAscB, SrHes/Hey, SrNscl, SrSrebp, SrE12/E47 and SrOlig.
Dialogue as a source of positive emotions during cross-border post-acquisition socio-cultural integration
Authors: Harikkala-Laihinen Riikka , Hassett Mélanie , Raitis Johanna , Nummela Niina 
Published: December 2017

PurposeThe purpose of this paper is to analyse how dialogue can be used to promote post-acquisition socio-cultural integration. Specifically, it addresses questions regarding when and how companies can utilise dialogue to generate positivity regarding socio-cultural integration.Design/methodology/approachA single case study approach was adopted owing to its suitability for creating in-depth understanding in the context of socio-cultural integration. Primary data were collected via interviews, an employee satisfaction survey, and participant observation. Secondary data were obtained from the case company’s internal materials, such as strategies, integration workflows, and employee magazines. Analysis methods included descriptive statistics and thematic qualitative analysis.FindingsThe findings suggest that dialogue can be used to create positivity regarding socio-cultural integration throughout the stages of unfreezing, moving, and refreezing by actively engaging employees in voicing, listening, respecting, and suspending. It is proposed that cultural conflict during post-acquisition socio-cultural integration can be overcome through the generation of positivity; dialogue enables the collective management of emotions during post-acquisition integration by offering a platform for creating positivity and social cohesion; and due to its collaborative and engaging nature, dialogue provides an especially effective means of communication for overcoming cross-cultural conflict.Originality/valueTo the authors’ knowledge, this is the first attempt to showcase dialogue as a specific means of communication for creating positivity during cross-border socio-cultural integration. This study reached beyond comparative cultural research to offer views on positivity, emotion during socio-cultural integration, and dialogue as means for overcoming cross-cultural conflict.
Fracture analysis of a three-dimensional functionally graded beam
Authors: Rizov Victor 
Published: December 2017

Purpose
The purpose of this paper is to carry out a delamination fracture analysis of the three-dimensional functionally graded split cantilever beam (SCB) configuration.

Design/methodology/approach
The fracture behaviour was studied analytically in terms of the strain energy release rate by applying methods of linear elastic fracture mechanics. It was assumed that the material is functionally graded along the beam width, height and length. The strain energy release rate was derived by analysing the stress and strain state in the beam cross-sections ahead and behind the crack front. An additional analysis of the strain energy release rate was performed by considering the beam strain energy for verification.

Findings
The influence of material gradient along the beam width, height and length on the delamination fracture behaviour was investigated. The effect of crack length was analysed too. The analytical approach developed is very useful for parametric fracture investigations. The results obtained in the present study can be applied for optimisation of three-dimensional functionally graded beam systems in their design with respect to delamination fracture behaviour.

Originality/value
An analytical approach for studying the delamination fracture in the SCB configuration that is functionally graded along the beam width, height and length was developed.
Distribution of accumulated irrecoverable hysteretic energy in MDOF structures
Authors: Tu Bing Bing , Zhao Dong 
Published: December 2017

Purpose
The study of the character of structural hysteretic energy under earthquake is an essential foundation for energy-based seismic design and evaluation method. The purpose of this paper is to explore the distribution law of the accumulative irrecoverable hysteretic energy for MDOF structures, a formula of the accumulated irrecoverable hysteretic energy ratio along the layers is derived.

Design/methodology/approach
The procedure is based on the energy balance principle and the concept of the equivalent single-degree-of-freedom system. Furthermore, sensitivity analysis is carried out for 16 working conditions, considering all these possibilities of local failure or damage. And then the sensitivity influencing rule is obtained and the proposed formula is simplified.

Findings
Finally, the validation of the proposed formula is investigated through comparisons with the nonlinear time-history analysis results.

Originality/value
The proposed formula can be effectively to estimate the distribution of the hysteretic energy under a given ground motion.
An Empirical Evaluation of Investment Income under the Equity Method of Accounting
Authors: Lai Cheng , Wu Jingjing , Mo Caihua , Zhou Hua 
Published: December 2017

AbstractThis study investigates the valuation implications of equity method earnings among Chinese listed firms, which are often perceived by the Chinese business press of employing the equity method to avoid reported losses. Our results show that firms with declining core earnings are more likely to have equity method investments than firms with increasing core earnings. Also, firms with lower core earnings report higher equity method earnings. Moreover, equity method earnings do not improve earnings persistence but are found to be relevant. Investors act as if they naively fixate on equity method earnings. A portfolio constructed on the basis of core earnings and equity method earnings generates a hedged return of 8%.
Marital Conflict Predicts Mother‐to‐Infant Adrenocortical Transmission
Authors: Hibel Leah C. , Mercado Evelyn 
Published: December 2017

Employing an experimental design, mother‐to‐infant transmission of stress was examined. Mothers (N = 117) were randomized to either have a positive or conflictual discussion with their marital partners, after which infants (age = 6 months) participated in a fear and frustration task. Saliva samples were collected to assess maternal cortisol responses to the discussion and infant cortisol responses to the challenge task. Results indicate maternal cortisol reactivity and recovery to the conflict (but not positive) discussion predicted infant cortisol reactivity to the infant challenge. Mothers’ positive affect during the discussion buffered, and intrusion during the free‐play potentiated, mother‐to‐infant adrenocortical transmission. These findings advance our understanding of the social and contextual regulation of adrenocortical activity in early childhood.
The attitudes of Turkish nurses towards the employment of internationally educated nurses
Authors: Harmanci Seren A.K. , Eskin Bacaksiz F. , Yildirim A. 
Published: December 2017

AimTo define the attitudes of nurses working in public hospitals towards the employment of internationally educated nurses.BackgroundThe employment of internationally educated nurses is expected to be an important strategy for solving the nursing shortage in Turkey and many other countries.MethodsThis descriptive and cross‐sectional study was conducted with nurses working in seven public university hospitals in different geographical regions of Turkey in September 2015. The data were collected from 1061 nurses in these hospitals using a self‐report questionnaire. Data analysis was performed using descriptive statistics, t‐test and the Mann–Whitney U test.ResultsThe participants generally did not have positive attitudes towards the employment of internationally educated nurses citing the possibility of experiencing cultural and professional difficulties. They also indicated that the employment of internationally educated nurses is not a real solution for the nursing shortage unless working conditions for nurses are improved. However, younger nurses have more positive attitudes towards employment of internationally educated nurses than older ones.Implications for nursing policyDefining the attitudes of the nurses working in clinical fields towards the employment of internationally educated nurses is an important issue, because it provides data for reviewing the existing policies and evaluating the possible issues that require attention during implementation of these policies. Policymakers may focus on both creating better working environment conditions and helping both the native and internationally educated nurses during the recruiting process.
Integration of hepatitis B virus S gene impacts on hepatitis B surface antigen levels in patients with antiviral therapy
Authors: Hu Bobin , Wang Rongming , Fu Jiaxin , Su Minghua , Du Man , Liu Yu , Li Huijiao , Wang Huiwen , Lu Fengmin , Jiang Jianning 
Published: December 2017

AbstractBackground and AimThe aim of this study is to investigate the impact of hepatitis B virus (HBV) S gene integration on serum hepatitis B surface antigen (HBsAg) levels in chronic hepatitis B with long‐term nucleos(t)ide analogue (NUC) therapy.MethodsChronic hepatitis B patients who performed liver biopsy at baseline and treated with long‐term NUC therapy were recruited. The integration of HBV S gene in baseline liver biopsy specimen was detected by Alu polymerase chain reaction method. Serum HBsAg levels were measured at baseline and the second year and the fourth year after NUC therapy by Roche reagent, respectively. Serum HBsAg levels between HBV S gene integrated group and nonintegrated group were compared and analyzed.ResultsSeventy patients were eligible for this study. Among them, 11 (15.7%) were found to have HBV S gene integration in their baseline liver biopsy specimens. Similar significant decrease of HBsAg levels was found in both integrated and nonintegrated groups (2.63vs2.65 log IU/mL,P = 0.478) after the first 2 years of NUC therapy. Thereafter, the decrease of HBsAg level from 2 to 4 years after therapy was largely unchanged in integrated group as compared with that of nonintegrated group (0.1vs2.53 log IU/mL,P = 0.002), with statistical difference.ConclusionsSerum HBsAg could be originated from the expression of the integrated HBV S gene in patients with S gene integration, which implicated the limitations when regarding HBsAg as a surrogate biomarker of covalently closed circular DNA activity and as an indicator of safe NUC discontinuation.
Dysphagia severity is related to the amplitude of distal contractile integral in patients with Jackhammer esophagus
Authors: Kristo I. , Schwameis K. , Paireder M. , Jomrich G. , Kainz A. , Schoppmann S. F. 
Published: December 2017

AbstractBackgroundDysphagia and non‐cardiac chest pain are common symptoms associated with a novel hypercontractile disorder, namely Jackhammer esophagus (JE). The aim of this study was to explore these symptoms in patients with JE and to elucidate associations with disease defining metrics, crucial for subsequent therapies.MethodsAll consecutive patients, who were referred between January 2014 and December 2016 and fulfilled the criteria for JE were included in this study. Exclusion criteria were opioid intake, previous gastrointestinal surgery, mechanical esophageal obstruction and diseases explaining their symptoms.Key ResultsOf 2205 examined subjects, thirty patients (females: n = 17, 56.7%) with a median age of 58 (51.6‐64.9) years were finally enrolled. Dysphagia was noted in 53.3% (n = 16), whereas non‐cardiac chest pain was specified within 40% (n = 12) with symptom duration of up to 10 years. Perception of dysphagia (P = .03) and presence of both symptoms (P = .008) increased to the end of the study period. Dysphagia was significantly associated with distal contractile integral (DCI) scores of all (P = .023), hypercontractile (P = .011) and maximum DCI swallows (P = .008). Symptoms duration influenced hypercontractile DCI scores (P = .015, r = .438) and significantly correlated with the intensity of perceived dysphagia (P = .01, r = .585). Presence of non‐cardiac chest pain was not associated with any of these metrics.Conclusions & InterferencesThe DCI mediates dysphagia in patients with JE. Duration of symptoms affected hypercontractile DCI scores and aggravated perception of dysphagia indicating a progressive character of disease.
Cardiorespiratory events in infants with gastroesophageal reflux symptoms: Is there any association?
Authors: Cresi F. , Martinelli D. , Maggiora E. , Locatelli E. , Liguori S. A. , Baldassarre M. E. , Cocchi E. , Bertino E. , Coscia A. 
Published: December 2017

AbstractBackgroundCardiorespiratory (CR) events (apnea, bradycardia, oxygen desaturation) and gastroesophageal reflux (GER) symptoms often coexist in infants admitted to Neonatal Intensive Care Unit, leading to over‐prescription of drugs and delayed discharge. We aimed to evaluate the relationships between CR and GER events.MethodsThe temporal associations between CR and GER events were analyzed in symptomatic infants who underwent synchronized CR and pH‐impedance monitoring. The symptom association probability (SAP) index was used to identify infants with a significant number of temporal associations. Gastroesophageal reflux characteristics and the chronological sequence of CR and GER events occurring within 30 seconds of each other were evaluated according to SAP index.Key ResultsOf the 66 infants enrolled, aged 29 (18‐45) days, 58 had CR events during monitoring. From these 58 patients, a total of 1331 CR events and 5239 GER (24% acidic) were detected. The SAP index was positive in seven (12%) infants. These infants had greater GER frequency, duration, and proximal extent (P < .05). The number of temporal associations was 10 times greater in the positive SAP group. Gastroesophageal reflux events preceded CR events in 83% of these associations. These GER events had a higher proximal extent (P = .004), but showed no differences in pH values.Conclusions & InferencesThe simultaneous evaluation of CR and GER events could be useful to identify infants with severe GER and significant temporal associations between these events. Treatment of GER could be indicated in these infants, but as the GER events involved are mainly non‐acidic, empirical treatment with antacids is, often, inappropriate.
Pengaruh Budaya dan Lokasi Terhadap Persepsi dan Penggunaan Telefon Bimbit di Tempat-Tempat Awam: Satu Analisis Perbandingan Antara Beberapa Negara
Authors: Amir Hushin Siti Harnani , Mustafa Hasrina , Omar Bahiyah 
Published: December 2017

This study aims to compare the level of perception of using mobile phones at public places among users of four different countries; Malaysia, Indonesia, China and Iran from the perspective of Social Interaction Theory. A survey was conducted on 100 university students from each country that makes up a sample of 400 respondents. The findings of the study show 1) a significant difference in the perception of mobile phone and SMS usage in public places among respondents from different countries. Unlike Malaysian, Indonesian and Chinese respondents, the results of the study show that Iranian respondents are not too disturbed by the usage of mobile phones at public places. 2) The study also finds that Malaysian and Indonesian respondents seldom use mobile phone in public places, and that Chinese respondents often use mobile phone in public transport (i.e: bus). Meanwhile, Iranian respondents use mobile phone the most in four identified places – the supermarket, bus, pedestrian walkway and restaurant. 3) Most of the respondents in each category, however, prefer to use mobile phone – for making calls and SMS – in multi focused gathering compared to fully focused ones. The study concludes that cultural and geographical factors exert significant influence on the usage and perception of using mobile phone at public places.
Antimicrobial Activity of Dalbavancin against Staphylococcus aureus with Decreased Susceptibility to Glycopeptides, Daptomycin, and/or Linezolid from U.S. Medical Centers
Authors: Sader Helio S. , Mendes Rodrigo E. , Duncan Leonard R. , Pfaller Michael A. , Flamm Robert K. 
Published: December 2017

ABSTRACT

Dalbavancin activity was assessed against a large collection of
Staphylococcus aureus
isolates (
n
= 59,903), including isolates with decreased susceptibility to vancomycin (MIC, ≥2 mg/liter;
n
= 1,141), daptomycin (MIC, ≥2 mg/liter;
n
= 48), telavancin (MIC, ≥0.12 mg/liter;
n
= 52), teicoplanin (MIC, ≥4 mg/liter;
n
= 143), and/or linezolid (MIC, ≥8 mg/liter;
n
= 25). Dalbavancin displayed susceptibility rates ranging from 90.4% (isolates with telavancin MIC ≥0.12 mg/liter) to 100.0% (linezolid-resistant isolates) and lower MIC values than the comparators against these resistant subsets.