bluuebunny/crossref_metadata_2025 huggingface dataset:
Luteolin Ameliorates Experimental Chronic Pancreatitis Induced by Trinitrobenzenesulfonic Acid in Rats
Authors: Yu Qiang , Zhu Jianhong , Sheng Xiaolei , Xu Limin , Hu Kewei , Chen Guilian , Wu Wei , Cai Wei , Chen Weichang , Yin Guojian
Published: March 2018

Objectives

The purpose of this study is to assess the effect and possible mechanism of luteolin on chronic pancreatitis (CP).

Methods

Trinitrobenzenesulfonic acid–induced CP was used as CP models in vivo. After the intervention of luteolin for 28 days, chronic pancreatic injury was assessed by serum hydroxyproline and pancreatic histology. α-Smooth muscle actin (α-SMA) expression was performed to detect the activation of pancreatic stellate cells (PSCs). Pancreatic stellate cells were also isolated and cultured in vitro, and the effect of luteolin on PSCs was evaluated. Transforming growth factor β (TGF-β1) signaling and its regulated mRNA expression was tested by Western blot and quantitative real-time polymerase chain reaction, respectively.

Results

The protective role of luteolin on CP was confirmed by increased pancreas/body weight ratio, decreased pancreas hydroxyproline level, and reduced fibrosis. α-SMA expressions in PSCs were significantly decreased both in vitro and in vivo after the management of luteolin. Pancreas TGF-β1 expression was significantly decreased by luteolin. Luteolin inhibited the proliferation and activation of PSCs in a dose-dependent manner.

Conclusions

Luteolin played a protective role in CP in many aspects, partly by regulating release of inflammatory cytokines through TGF-β1 signaling pathway.
Development and Feasibility of an Interactive Smartphone App for Early Assessment and Management of Symptoms Following Pancreaticoduodenectomy
Authors: Gustavell Tina , Langius-Eklöf Ann , Wengström Yvonne , Segersvärd Ralf , Sundberg Kay
Published: March 2018

Background

Patients who have undergone pancreaticoduodenectomy because of pancreatic cancer experience distressing symptoms and unmet supportive care needs after discharge. To meet these needs, we have developed a mobile health app (Interaktor) for daily assessment of symptoms and access to self-care advice that includes a risk assessment model for alerts with real-time interactions with professionals.

Objective

The study aim was to develop and test a version of the Interaktor app adapted for patients who have undergone pancreaticoduodenectomy.

Methods

The app was developed and tested for feasibility in 6 patients during 4 weeks. One nurse monitored and responded to alerts. Logged data from the app were collected, and all participants were interviewed about their experiences.

Results

Adherence to reporting daily was 84%. Alerts were generated in 41% of the reports. The patients felt reassured and cared for and received support for symptom management. The app was easy to use, had relevant content, and had few technical problems, although suggestions for improvement were given.

Conclusions

The daily reporting of symptoms and having access to a nurse in real time in the case of an alarming symptom seem to enhance symptom management and render a feeling of security in patients. Some modifications of the app are needed before use in a larger sample.

Implications for Practice

Daily reporting of symptoms after pancreaticoduodenectomy enhances symptom management, self-care, and participation without being a burden to patients, indicating that mobile health can be used in clinical practice by patients with poor prognosis who experience severe symptoms.
Accredited Health Department Partnerships to Improve Health: An Analysis of Community Health Assessments and Improvement Plans
Authors: Kronstadt Jessica , Chime Chinecherem , Bhattacharya Bulbul , Pettenati Nicole
Published: March 2018

Context:

The Public Health Accreditation Board (PHAB) Standards & Measures require the development and updating of collaborative community health assessments (CHAs) and community health improvement plans (CHIPs).

Objective:

The goal of this study was to analyze the CHAs and CHIPs of PHAB-accredited health departments to identify the types of partners engaged, as well as the objectives selected to measure progress toward improving community health.

Design:

The study team extracted and coded data from documents from 158 CHA/CHIP processes submitted as part of the accreditation process. Extracted data included population size, health department type, data sources, and types of partner organizations. Health outcome objectives were categorized by Healthy People 2020 Leading Health Indicator (LHI), as well as by the 7 broad areas in the PHAB reaccreditation framework for population health outcomes reporting.

Participants:

Participants included health departments accredited between 2013 and 2016 that submitted CHAs and CHIPs to PHAB, including 138 CHAs/CHIPs from local health departments and 20 from state health departments.

Results:

All the CHAs/CHIPs documented collaboration with a broad array of partners, with hospitals and health care cited most frequently (99.0%). Other common partners included nonprofit service organizations, education, business, and faith-based organizations. Small health departments more frequently listed many partner types, including law enforcement and education, compared with large health departments. The majority of documents (88.6%) explicitly reference Healthy People 2020 goals, with most addressing the LHIs nutrition/obesity/physical activity and access to health services. The most common broad areas from PHAB's reaccreditation framework were preventive health care and individual behavior.

Conclusions:

This study demonstrates the range of partners accredited health departments engage with to collaborate on improving their communities' health as well as the objectives used to measure community health improvement. This illustrates the collaborative nature in which accredited health departments tackle community priorities.
Benefits and Perceptions of Public Health Accreditation Among Health Departments Not Yet Applying
Authors: Heffernan Megan , Kennedy Mallory , Siegfried Alexa , Meit Michael
Published: March 2018

Objective:

To identify the benefits and perceptions among health departments not yet participating in the public health accreditation program implemented by the Public Health Accreditation Board (PHAB).

Design:

Quantitative and qualitative data were gathered via Web-based surveys of health departments that had not yet applied for PHAB accreditation (nonapplicants) and health departments that had been accredited for 1 year.

Participants:

Respondents from 150 nonapplicant health departments and 57 health departments that had been accredited for 1 year.

Results:

The majority of nonapplicant health departments are reportedly conducting a community health assessment (CHA), community health improvement plan (CHIP), and health department strategic plan—3 documents that are required to be in place before applying for PHAB accreditation. To develop these documents, most nonapplicants are reportedly referencing PHAB requirements. The most commonly reported perceived benefits of accreditation among health departments that planned to or were undecided about applying for accreditation were as follows: increased awareness of strengths and weaknesses, stimulated quality improvement (QI) and performance improvement activities, and increased awareness of/focus on QI. Nonapplicants that planned to apply reported a higher level of these perceived benefits. Compared with health departments that had been accredited for 1 year, nonapplicants were more likely to report that their staff had no or limited QI knowledge or familiarity.

Conclusions:

The PHAB accreditation program has influenced the broader public health field—not solely health departments that have undergone accreditation. Regardless of their intent to apply for accreditation, nonapplicant health departments are reportedly referencing PHAB guidelines for developing the CHA, CHIP, and health department strategic plan. Health departments may experience benefits associated with accreditation prior to their formal involvement in the PHAB accreditation process. The most common challenge for health departments applying for accreditation is identifying the time and resources to dedicate to the process.
Interpersonal Skills Among Fourth- and Fifth-Year Medical Students
Authors: Morel Alexandre , Hardouin Jean-Benoit , Pottier Pierre
Published: March 2018

Objective

The aim of this study was to validate a French version of the standardized patient satisfaction questionnaire (SPSQ), an interpersonal skills assessment form, originally published in English, destined to be completed by SPs and used as a validated tool for the evaluation of communication skills of French medical students, during ambulatory care consultations.

Methods

During the academic year, fourth- and fifth-year medical students participated in mock ambulatory care consultations. The French SPSQ was completed by 16 SPs who performed scenarios written by professors of medicine. Validity evidence for test content, response process, internal structure, and relation to other variables was determined by calculating the Cronbach α coefficient, the Loevinger H index (response coherence), intraclass coefficients, the differences between fourth- and fifth-year students and by using item correlations as well as the correlation with an independent validated assessment form. G theory was used to identify the sources of variations in the mean of SPSQ.

Results

Four hundred thirty-three students were evaluated for a period of 2 months and participated in a total of 1703 mock consultations. The Cronbach α coefficient (0.94) was superior to that of the English SPSQ. The Loevinger H index was good ranging from 0.65 to 0.70. The reproducibility among external observers (intraclass correlation coefficient = 0.67) and between external observers and the SPs (intraclass correlation coefficient = 0.79 and 0.78, respectively) was satisfactory. Results of the French SPSQ were positively and significantly correlated to the scores obtained via an independent, validated, questionnaire (R = 0.72) and showed a significant difference between fourth- and fifth-year students' scores (P < 0.0001). G coefficients were estimated at 0.64 and 0.52 for year 4 and year 5, respectively.

Conclusions

Validity evidence supports the use of French-version SPSQ scores to screen for students experiencing difficulty with communication.
Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel
Authors: Rew Vanessa , Mook Piers , Trienekens Suzan , Baker Kate S. , Dallman Timothy J. , Jenkins Claire , Crook Paul D. , Thomson Nicholas R.
Published: March 2018

In December 2013, Public Health England (PHE) observed an increase in the number of cases of Shigella sonnei linked to the Orthodox Jewish Community (OJC). Ultimately, 52 cases of S. sonnei phage type (PT) P and PT7 were notified between November 2013 and July 2014. Whole-genome sequencing (WGS) was performed on a HiSeq 2500 platform (Illumina) on isolates of S. sonnei submitted to PHE during the investigation. Quality trimmed sequence reads were mapped to a reference genome using BWA-MEM, and single-nucleotide polymorphisms (SNPs) were identified using GATK2. Analysis of the core genome SNP positions (>90 % consensus, minimum depth 10×, MQ≥30) revealed that isolates linked to the outbreak could be categorized as members of distinct monophyletic clusters (MPCs) representing concurrent regional outbreaks occurring in the OJCs across the United Kingdom. A dated phylogeny predicted the date of the most recent common ancestor of the MPCs to be approximately 3.1 years previously [95 % highest posterior density (HPD), 2.4–3.4]. Isolates of S. sonnei from cases from the OJCs in Israel included in the phylogeny, branched from nodes basal to the UK OJC outbreak clusters, indicating they were ancestral to the UK OJC isolates, and that the UK isolates represented multiple importations of S. sonnei into the UK population from Israel. The level of discrimination exhibited by WGS facilitated the identification of clusters of isolates within the closely related bacterial populations circulating in the OJC that may be linked to a unique point sources or transmission routes, thus enabling a more appropriate public health response and targeted interventions.
Attempts to implement CRISPR/Cas9 for genome editing in the oomycetePhytophthora infestans
Authors: van den Hoogen Johan , Govers Francine
Published: March 2018

Few techniques have revolutionized the molecular biology field as much as genome editing using CRISPR/Cas9. Recently, a CRISPR/Cas9 system has been developed for the oomycetePhytophthora sojae, and since then it has been employed in two otherPhytophthoraspp. Here, we report our progress on efforts to establish the system in the potato late blight pathogenPhytophthora infestans. Using the original constructs as developed forP. sojae, we did not obtain any transformants displaying a mutagenized target gene. We made several modifications to the CRISPR/Cas9 system to pinpoint the reason for failure and also explored the delivery of pre-assembled ribonucleoprotein complexes. With this report we summarize an extensive experimental effort pursuing the application of a CRISPR/Cas9 system for targeted mutagenesis inP. infestansand we conclude with suggestions for future directions.
Evolution of theD. melanogasterchromatin landscape and its associated proteins
Authors: Parey Elise , Crombach Anton
Published: March 2018

In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins inDrosophilacells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit flyD. melanogasterchromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the emergence of the different chromatin types. Our results indicate that the two euchromatic types, YELLOW and RED, were one single activating type that split early in eukaryotic history. Next, we provide evidence that GREEN-associated proteins are involved in a centromere drive and expanded in a lineage-specific way inD. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
Single cell transcriptome profiling of mouse and hESC-derived pancreatic progenitors
Authors: Krentz Nicole A. J. , Lee Michelle , Xu Eric E. , Sasaki Shugo , Lynn Francis C.
Published: March 2018

Human embryonic stem cells (hESCs) are a potential unlimited source of insulin-producing β-cells for diabetes treatment. A greater understanding of how β-cells form during embryonic development will improve current hESC differentiation protocols. As β-cells are formed from NEUROG3-expressing endocrine progenitors, this study focused on characterizing the single-cell transcriptomes of mouse and hESC-derived endocrine progenitors. To do this, 7,223 E15.5 and 6,852 E18.5 single cells were isolated fromNeurog3-Cre; Rosa26mT/mGembryos, allowing for enrichment of endocrine progenitors (yellow; tdTomato + EGFP) and endocrine cells (green; EGFP). From aNEUROG3-2A-eGFPCyT49 hESC reporter line (N5-5), 4,497 hESC-derived endocrine progenitor cells were sequenced. Differential expression analysis reveals enrichment of markers that are consistent with progenitor, endocrine, or novel cell-state populations. This study characterizes the single-cell transcriptomes of mouse and hESC-derived endocrine progenitors and serves as a resource (https://lynnlab.shinyapps.io/embryonic_pancreas/) for improving the formation of functional β-like cells from hESCs.
Systematic Elucidation and Validation of OncoProtein-Centric Molecular Interaction Maps
Authors: Broyde Joshua , Simpson David R. , Murray Diana , Giorgi Federico M. , Lachmann Alexander , Jackson Peter K. , Sweet-Cordero E. Alejandro , Honig Barry , Califano Andrea
Published: March 2018

The largely incomplete and tissue-independent nature of cancer pathways represents a key limitation to the ability to elucidate mechanistic determinants of cancer phenotypes and to predict adaptive response to targeted therapy. To address these challenges, we propose replacing canonical cancer pathways with a more accurate, comprehensive, and context-specific architecture – dubbed a Protein-Centric molecular interaction Map (PC-Map) – representing modulators, effectors, and cognate binding-partners of any oncoprotein of interest. To reconstruct these complex molecular architecturesde novo, we introduce a novel OncoSig algorithm. Validation of a lung adenocarcinoma specific (LUAD) KRAS-centric PC-Map recapitulated known KRAS biology and, more critically, identified a novel repertoire of proteins eliciting synthetic lethality in KRASG12DLUAD organoid cultures. Showing the generalizable nature of the algorithm, we elucidated PC-Maps for ten recurrently mutated oncoproteins, including KRAS, in distinct tumor contexts. This revealed a highly context-specific nature of cancer’s regulatory and signaling architectures to an unprecedented degree of resolution.
Chronic environmentally relevant levels of Simvastatin induces non-monotonic responses in Zebrafish (Danio rerio)
Authors: Barros Susana , Montes Rosa , Quintana José Benito , Rodil Rosario , André Ana , Capitão Ana , Soares Joana , Santos Miguel M. , Neuparth Teresa
Published: March 2018

Simvastatin (SIM), a hypocholesterolaemic compound, is among the most prescribed pharmaceuticals for cardiovascular disease prevention worldwide. Several studies have shown that acute exposure to SIM is able to produce multiple adverse effects in aquatic organisms. However, uncertainties still remain regarding the chronic effects of SIM in aquatic ecosystems. Therefore, the present study aimed to investigate the effects of SIM in the model freshwater teleost zebrafish (Danio rerio) following a chronic exposure (90 days) to environmentally relevant concentrations ranging from 8 ng/L to 1000 ng/L. This study used a multi-parametric approach integrating distinct ecological-relevant endpoints, i.e. survival, growth, reproduction and embryonic development, with biochemical markers (cholesterol and triglycerides). Furthermore, Real Time PCR was used to analyse the transcription levels of key genes involved in the mevalonate pathway (hmgcra, cyp51, and dhcr7). Globally, SIM induced several non-monotonic dose-responses; embryonic development, biochemical and molecular markers, were significantly impacted in the low-intermediate concentrations, 40 ng/L and 200 ng/L, whereas no effects were recorded for the highest tested SIM levels (1000 ng/L). Taken together, these findings expand our understanding of statins effects in teleost’s, demonstrating significant impacts at environmentally relevant concentrations. The findings highlight the importance of addressing the effects of chemicals under chronic low-level concentrations.

Graphical abstract

Highlights

Several uncertainties exist regarding simvastatin mode of action in non-target organisms

This work integrates D. rerio multi-level responses after long-term exposure to simvastatin

Simvastatin impacted cholesterol/triglycerides levels and transcript levels of genes related to mevalonate pathway.

Parental exposure to simvastatin induced offspring embryonic malformations.

Embryonic abnormalities, biochemical and molecular data did follow a non-monotonic curve.
Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study
Authors: Dai Jiaan , Yu Fengchao , Li Ning , Yu Weichuan
Published: March 2018

Motivation

Analyzing tandem mass spectrometry data to recognize peptides in a sample is the fundamental task in computational proteomics. Traditional peptide identification algorithms perform well when identifying unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Recently, Chick et al., 2015 and Yu et al., 2016 proposed the spectrum-based and tag-based open search methods, respectively, to identify peptides with PTMs. While the performance of these two methods is promising, the identification results vary greatly with respect to the quality of tandem mass spectra and the number of PTMs in peptides. This motivates us to systematically study the relationship between the performance of open search methods and quality parameters of tandem mass spectrum data, as well as the number of PTMs in peptides.

Results

Through large-scale simulations, we obtain the performance trend when simulated tandem mass spectra are of different quality. We propose an analytical model to describe the relationship between the probability of obtaining correct identifications and the spectrum quality as well as the number of PTMs. Based on the analytical model, we can quantitatively describe the necessary condition to effectively apply open search methods.

Availability

Source codes of the simulation are available at http://bioinformatics.ust.hk/PST.html.

Contact

boningli@ust.hk or eeyu@ust.hk

Supplementary information

Supplementary data are available at Bioinformatics online.
Minimally invasive deep-brain imaging through a 50 μm-core multimode fibre
Authors: Vasquez-Lopez Sebastian A. , Koren Vadim , Plöschner Martin , Padamsey Zahid , Čižmár Tomáš , Emptage Nigel J.
Published: March 2018

Achieving optical access to deep-brain structures represents an important step towards the goal of understanding the mammalian central nervous system. The complex refractive index distribution within brain tissue introduces severe aberrations to long-distance light propagation thereby prohibiting image reconstruction using currently available non-invasive techniques. In an attempt to overcome this challenge endoscopic approaches have been adopted, principally in the form of fibre bundles or GRIN-lens based endoscopes. Unfortunately, these approaches create substantial mechanical lesions of the tissue precipitating neuropathological responses that include inflammation and gliosis. Together, lesions and the associated neuropathology may compromise neural circuit performance. By replacing Fourier-based image relay with a holographic approach, we have been able to reduce the volume of tissue lesion by more than 100-fold, while preserving diffraction-limited imaging performance. Here we demonstrate high-resolution fluorescence imaging of neuronal structures, dendrites and synaptic specialisations, in deep-brain regions of living mice. These results represent a major breakthrough in the compromise between high-resolution imaging and tissue damage, heralding new possibilities for deep-brain imaging in vivo.
C. elegansavoidance ofPseudomonas: thioredoxin shapes the sensory response to bacterially produced nitric oxide
Authors: Hao Yingsong , Yang Wenxing , Ren Jing , Hall Qi , Zhang Yun , Kaplan Joshua M.
Published: March 2018

We show thatC. elegansavoids a bacterial pathogenPseudomonas aeruginosa(PA14) by detecting PA14-produced nitric oxide (NO). PA14 mutants deficient for NO production fail to elicit avoidance and NO donors repel worms. PA14 and NO avoidance are mediated by the ASJ chemosensory neurons, which respond to NO with intracellular calcium rises. PA14 avoidance and NO-evoked calcium responses require receptor guanylate cyclases (DAF-11 and GCY-27), and cyclic nucleotide gated ion channels (TAX-2 and -4). ASJ exhibits calcium increases at both the onset and removal of NO. These NO-evoked ON and OFF calcium transients are affected by a redox sensing protein, TRX-1/thioredoxin. TRX-1’s trans-nitrosylation activity inhibits the ON transient whereas TRX-1’s de-nitrosylation activity promotes the OFF transient. Thus,C. elegansexploits bacterially produced NO as a cue to mediate avoidance and TRX-1 functions as an NO-sensor that endows ASJ with a bi-phasic response to NO exposure.
Network-Based Biomarkers Enable Cross-Disease Biomarker Discovery
Authors: Haider Syed , Yao Cindy Q. , Sabine Vicky S. , Grzadkowski Michal , Stimper Vincent , Starmans Maud H.W. , Wang Jianxin , Nguyen Francis , Moon Nathalie C. , Lin Xihui , Drake Camilla , Crozier Cheryl A. , Brookes Cassandra L. , van de Velde Cornelis J.H. , Hasenburg Annette , Kieback Dirk G. , Markopoulos Christos J. , Dirix Luc Y. , Seynaeve Caroline , Rea Daniel W. , Kasprzyk Arek , Lambin Philippe , Lio Pietro , Bartlett John M.S. , Boutros Paul C.
Published: March 2018

Biomarkers lie at the heart of precision medicine, biodiversity monitoring, agricultural pathogen detection, amongst others. Surprisingly, while rapid genomic profiling is becoming ubiquitous, the development of biomarkers almost always involves the application of bespoke techniques that cannot be directly applied to other datasets. There is an urgent need for a systematic methodology to create biologically-interpretable molecular models that robustly predict key phenotypes. We therefore created SIMMS: an algorithm that fragments pathways into functional modules and uses these to predict phenotypes. We applied SIMMS to multiple data-types across four diseases, and in each it reproducibly identified subtypes, made superior predictions to the best bespoke approaches, and identified known and novel signaling nodes. To demonstrate its ability on a new dataset, we measured 33 genes/nodes of the PIK3CA pathway in 1,734 FFPE breast tumours and created a four-subnetwork prediction model. This model significantly out-performed existing clinically-used molecular tests in an independent 1,742-patient validation cohort. SIMMS is generic and can work with any molecular data or biological network, and is freely available at:https://cran.r-project.org/web/packages/SIMMS.
A method for faster purification of serine proteinases fromBothrops alternatusandBothrops moojenisnake venoms
Authors: Heleno M.A.G. , Santos L.D. , Ferreira R.S. , Barraviera B
Published: March 2018

Snake venoms are important sources of substances with a variety of pharmacological activities. Among the different proteins present in these venoms, snake venom serine proteinases (SVSPs) have important effects on the hemostatic system that influence the hemodynamic properties of blood.Bothropsgenus snakes presented their venom richly composed of SVSPs thrombin-like, and the isolation of these enzymes is of great interest. In 1994, the Center for the Study of Venoms and Venomous Animals (CEVAP) - UNESP standardized the fibrin sealant derived from snake venom, replacing the bovine thrombin by gyroxin thrombin-like enzyme fromCrotalus durissus terrificus(Rattlesnake) and human plasma fibrinogen by buffaloes cryoprecipitate. Despite chromatographic techniques for the purification of gyroxin be well grounded in the literature, that income is considered low. Thus, in addition to gyroxin, other thrombin-like enzymes could be employed in the composition of the new fibrin sealant after being standardized to the purifying and chromatographic performance and widely evaluated for biological activities. Therefore, it is extremely important that in our lab is deployed, standardized and validated a method for the chromatographic purification of other thrombin-like enzymes such as found in Bothrops snake venoms. Thus a two-step chromatographic procedure was developed to routinely purify serine proteinases fromBothrops alternatusandB. moojenisnakes venoms to provide new enzymes for improving the CEVAP’s heterologous fibrin sealant.
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews
Authors: Crisan Anamaria , Munzner Tamara , Gardy Jennifer L.
Published: March 2018

Adjutant is an open-source, interactive, and R-based application to support mining PubMed for a systematic or a literature review. Given a PubMed-compatible search query, Adjutant downloads the relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support.

Availability and Implementation

Adjutant is implemented in R, using Shiny, and is available athttps://github.com/amcrisan/Adjutant
Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
Authors: McGurk Michael P. , Barbash Daniel A.
Published: March 2018

Eukaryotic genomes are replete with repeated sequences in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequences. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites. The best available population resources, short-read DNA sequences, are often considered to be of limited utility for analyzing repetitive DNA due to the challenge of mapping individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt that demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. By analyzing 85 genomes from five populations ofDrosophila melanogaster, we discover that TEs commonly form tandem dimers. Our results further suggest that insertion site preference is the major mechanism by which dimers arise and that, consequently, dimers form rapidly during periods of active transposition. This abundance of TE dimers has the potential to provide source material for future expansion into satellite arrays, and we discover one such copy number expansion of the DNA transposonhoboto approximately 16 tandem copies in a single line. The very process that defines TEs—transposition—thus regularly generates sequences from which new satellites can arise.
4-(4-Chlorophenyl)-1,2,3-selenadiazole
Authors: Ravichandran K. , Ranjith S. , Sankari S. , Beemarao M. , Ponnuswamy M. N.
Published: March 2018

In the title compound, C8H5ClN2Se, the dihedral angle between the planes of the selenadiazole and chlorophenyl rings is 16.6 (2)°. In the crystal, the packing of the molecules is consolidated by weak C—H...N hydrogen bonds, which generate [001] chains, and π–π stacking interactions are observed between the phenyl and selenadiazole rings, with a centroid–centroid distance of 3.884 (2) Å. There is also a short Se...Cl contact of 3.468 (1) Å
Abnormal mortgage delinquencies as housing crisis early symptoms
Authors: Parnes Dror
Published: March 2018

Purpose

The purpose of this paper is to analyze the differences between the actual mortgage prompt and late payments and their respective expected measures from 2004 to 2010 to spot early symptoms of housing crisis.

Design/methodology/approach

This paper explores these discrepancies across the entire US market and along various delinquency lengths of 30, 60 and 90 days. This paper constructs a Bayesian forecasting model that relies on prior distributional properties of diverse time horizons.

Findings

Abnormal mortgage delinquency rates are identified in real time and can be served as early symptoms for housing crisis.

Practical implications

The statistical scheme proposed in this paper can function as a valuable predictive tool for lending institutions, bank audit companies, regulatory bodies and real estate professional investors who examine changes in economic settings and trends in short sale leads.

Social implications

The abnormal mortgage delinquencies can serve as indicators of changes in economic fundamentals and early signs of a mounting housing crisis.

Originality/value

This paper presents a unique statistical technique in the context of mortgage delinquencies.
Religious aspects in psychiatry and psychotherapy
Authors: Schwarz Silke
Published: March 2018

Purpose

The purpose of this paper is to explore the role of religion in psychiatry and psychotherapy and it introduces a context-oriented approach to religion.

Design/methodology/approach

The paper opted for a selective literature review to highlight significant issues with regard to mainstream psychology.

Findings

It provides a short summary on the historical neglect and exclusion from clinical practice and shows how religion was integrated into the mainstream of psychotherapy and psychiatry. A quantitative and universalistic approach to religion is dominant. The widespread approach to religious coping by Pargament is presented as well as related findings with regard to religion and mental health.

Research limitations/implications

The paper includes implications for the development of a context-oriented inclusion of religion and encourages for associated empirical research.

Originality/value

With a critical inclusion of contexts, professionals may stay alerted to the issue that health and disorders are not ontological facts but contain moral codes of a current society. It takes the social context and unequal power relations as the starting point for a partisan cooperation with the affected persons.
The marginalization of religion in end of life care: signs of microaggression?
Authors: Pentaris Panagiotis
Published: March 2018

Purpose

Service users very often interpret and respond to their experiences of death, dying and bereavement through a religious or spiritual lens. However, recent trends in religion and belief have influenced how professionals respond to indicators such as faith. Since the post-war years in Britain, and due to the transfer of services from church to state, as well as the change in the religious landscape, language has largely secularized. When people start addressing religion and belief again, they lack the appropriate literacy to do so, this is termed religious literacy by Dinham (2015). The purpose of this paper is to explore how professionals in end of life (EOL) care respond to service users’ religious and spiritual indicators, through the lens of religious literacy.

Design/methodology/approach

The paper draws from an ethnographic study undertaken across hospices in England, UK. In this study, healthcare professionals (HCPs) were observed for one calendar year.

Findings

Results show that lack of religious literacy on the part of HCPs may lead to subtle and unintentional microaggression. Three types of indications of microinvalidation have been noted: verbal, non-verbal and environmental.

Originality/value

This paper innovates in offering a first-hand phenomenological interpretation of observations in the field. The research data capture visually the impact of lack of religious literacy, an achievement which adds to the dialogue about service user rights in EOL care.
Impact of financial inclusion on poverty alleviation through cooperative banks
Authors: Lal Tarsem
Published: March 2018

Purpose

The purpose of this paper is to examine the impact of financial inclusion on poverty alleviation through cooperative banks.

Design/methodology/approach

In order to fulfil the objectives of the study, primary data were collected from 540 beneficiaries of cooperative banks operating in three northern states of India, i.e., J&K, Himachal Pradesh (HP) and Punjab using purposive sampling during July-December 2015. The technique of factor analysis had been used for summarisation of the total data into minimum factors. For checking the validity and reliability of the data, the second-order CFA was performed. Statistical techniques like one-way ANOVA, t-test and SEM were used for data analysis.

Findings

The study results reveal that financial inclusion through cooperative banks has a direct and significant impact on poverty alleviation. The study highlights that access to basic financial services such as savings, loans, insurance, credit, etc., through financial inclusion has generated a positive impact on the lives of the poor and help them to come out of the clutches of poverty.

Research limitations/implications

The study was conducted amidst few limitations. First, the in-depth analysis of the study is restricted to three northern states only because of limited resources and time availability. Second, the study is limited to the perception of financial inclusion beneficiaries only, which, in future, could be carried further on the perception of other stakeholders such as bank officials, business correspondents, village panchayats, etc.

Originality/value

The study makes contribution towards the financial inclusion literature relating to poverty alleviation and fulfils the research gap to some extent by assessing the impact of financial inclusion on poverty alleviation through cooperative banks. This paper can help the policymakers and other stakeholders of cooperative banks in promoting banking habits among poor rural households both at the national and international level.
Exploring the mediating role of social capital in the relationship between financial intermediation and financial inclusion in rural Uganda
Authors: Bongomin George Okello Candiya , Munene John C. , Ntayi Joseph Mpeera , Malinga Charles Akol
Published: March 2018

Purpose

The purpose of this paper is to establish the mediating role of social capital in the relationship between financial intermediation and financial inclusion in rural Uganda.

Design/methodology/approach

The current study used cross-sectional research design and a semi-structured questionnaire was used to collect data for this study. The study applied structural equation modeling through bootstrap approach in AMOS to establish the mediating role of social capital in the relationship between financial intermediation and financial inclusion.

Findings

The results indicated that social capital significantly mediates the relationship between financial intermediation and financial inclusion in rural Uganda. Therefore, it can be deduced that social capital among the poor play an important role in promoting financial intermediation for improved financial inclusion in rural Uganda.

Research limitations/implications

Although the sample was large, it may not be generalized to other segments of the population. Data were collected from only poor households located in rural Uganda. Besides, the study was cross-sectional, thus, limiting efforts in investigating certain characteristics of the sample over time. Perhaps future studies could adopt the use of longitudinal research design.

Practical implications

Financial institutions such as banks should rely on social capital as a substitute for physical collateral in order to promote financial inclusion, especially among the poor in rural Uganda.

Originality/value

This study provides empirical evidence on phenomenon not studied in rural areas in Sub-Saharan Africa where the poor use social capital embedded in customs and norms for doing business. The results highlight the importance of social capital in mediating the relationship between financial intermediation and financial inclusion of the poor in rural Uganda.
Factors influencing farmer’s perceptions and behavior toward pesticide use in Malaysia
Authors: Ali Jamal , Yusof Norhafezah , Abd. Aziz Fadzli Shah
Published: March 2018

Purpose

The purpose of this paper is to examine the factors believed to influence the behavior of 1,042 rice farmers in Malaysia regarding the overuse of pesticides. Frequent overuse of pesticide will have an impact on human health and the environment, which lead to greater expenditure on health care.

Design/methodology/approach

The theoretical models of compliance behavior tested include the basic deterrence model, which focuses on the enforcement of regulation as a key determinant of compliance. The models integrate economic theory with theories of social behavior to account for motivations expected, influencing individuals’ decisions on whether to follow the regulation on using pesticides.

Findings

Significance tests reported that the information regarding the danger of using pesticides, the perception toward the impact on the environment and the expected impact on health influences the compliance behavior of using pesticides.

Research limitations/implications

These findings highlight the necessity for the policy makers to design an effective program which gives more information and provide training related to the risk and the safe handling of pesticides.

Practical implications

The farmers who receive information and training related to handling of pesticides become more cautious in the use of pesticides. Countries involved in agriculture and the use of pesticides widely by their farmers need to emphasize continuous training and periodic information dissemination.

Social implications

The implication drawn is rice farmers should be encouraged to practice new methods in rice planting, especially in the integrated pest management method.

Originality/value

These research findings suggest that the overuse of pesticides in the rice farming continues to be an important problem.
Performance analysis of high-stiffness bearing composited by hydrostatic cavities and tilting pads with preload
Authors: Chen Runlin , Wang Jianlei , Yuan XiaoYang , Li Longlong , Cui Yahui
Published: March 2018

Purpose

To meet the high stiffness requirement of bearings used in high-precision spindles, this paper aims to propose a novel kind of bearing composited by hydrostatic cavities and tilting pads with preload.

Design/methodology/approach

Cavities are cut on the oil seal surface of a hybrid bearing, in which the tilting pads are set up. The load of the bearing is carried by the hydrostatic cavities and tilting pads. The structural features of this compound bearing and the controlling variables of the main stiffness coefficient are presented. Two basic design principles are proposed on the basis of equal machining clearance (EMC) and equal installation clearance (EIC).

Findings

The theoretical analysis indicates that the stiffness of compound bearings under the EMC condition increases to infinity monotonously when the preload coefficient of the tilting pad tends to 1, while the stiffness under the EIC condition has a peak value. Therefore, a synthetic design principle is proposed by synthetically using the above-mentioned two principles. The applicable range of the three principles is discussed through an example.

Originality/value

The study about technological combination of hydrostatic cavity and tilting pad in this paper can provide suggestions for the design of a high-stiffness bearing in a precision spindle.
Online condition monitoring of misaligned meshing gears using wear debris and oil quality sensors
Authors: Kumar Paras , Hirani Harish , Agrawal Atul Kumar
Published: March 2018

Purpose

This paper aims to investigate the effect of misalignment on wear of spur gears and on oil degradation using online sensors.

Design/methodology/approach

The misalignment effect on gears is created through a self-alignment bearing, and is measured using laser alignment system. Several online sensors such as Fe-concentration sensor, moisture sensor, oil condition sensor, oil temperature sensor and metallic particle sensor are installed in the gear test rig to monitor lubricant quality and wear debris in real time to assess gearbox failure.

Findings

Offset and angular misalignments are detected in both vertical and horizontal planes. The failure of misaligned gear is observed at both the ends and on both the surfaces of the gear teeth. Larger-size ferrous and non-ferrous particles are traced by metallic particle sensor due to gear and seal wear caused by misalignment. Scanning electron microscope (SEM) images examine chuck, spherical and flat platelet particles, and confirm the presence of fatigue (pitting) and adhesion (scuffing) wear mechanism. Energy-dispersive X-ray spectroscopy analysis of SEM particles traces carbon (C) and iron (Fe) elements due to gear failure.

Originality/value

Gear misalignment is one of the major causes of gearbox failure and the lubricant analysis is as important as wear debris analysis. A reliable online gearbox condition monitoring system is developed by integrating wear and oil analyses for misaligned spur gear pair in contact.
A general performance calculation model of journal bearing using unified coordinate system
Authors: Zhu Aibin , Wu Hongling , Yang Yulei , He Shengli
Published: March 2018

Purpose

Because of the various geometric descriptions of different bearing types, performance calculation of journal bearing is complicated, and is difficult in traditional model. This paper aims to simplify the calculation of the journal bearing performance, and to reduce the workload.

Design/methodology/approach

On the basis of previous research, a general performance calculation model of journal bearing is proposed in this paper. Eccentricity ratio and attitude angle of axis to each pad are calculated by coordinates of spindle center and each pad center by establishing the unified coordinate system. The surface deformation of journal bearing is taken into consideration, and a correction value is added to the dimensionless oil film thickness.

Findings

The performance calculation results of various fix-pad and tilting-pad journal bearings match the results of the existing references very well, revealing the validity of the model. The general model can greatly reduce programming workload, and increase adaptability to different bearings.

Originality/value

Geometric descriptions of both fix-pad and tilting-pad journal bearings are unified in this model, which can be applied to both standard and non-standard journal bearings with different preload ratios. In addition, due to the unification of different bearings types, this model is more conducive to performance comparison among different bearing types, and promotes the development of new structural forms for journal bearings.