bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune Modulation of Allergic Asthma by Early Pharmacological Inhibition of RIP2
Authors: Miller Madelyn H. , Shehat Michael G. , Tigno-Aranjuez Justine T. 
Published: June 2020

AbstractExposure to house dust mite (HDM) is highly associated with the development of allergic asthma. The adaptive immune response to HDM is largely T helper cell type 2 (Th2) dominant and a number of innate immune receptors have been identified which recognize HDM to initiate a Th2 response. Nucleotide-binding Oligomerization Domain-containing Protein 2 (NOD2) is a cytosolic sensor of peptidoglycan which is important for Th2 polarization. NOD2 mediates its signaling through its downstream effector kinase, Receptor-interacting Serine/Threonine Protein Kinase 2 (RIP2). We have previously shown that RIP2 is important in promoting HDM-associated allergic airway inflammation and Th2 immunity. In particular, we demonstrated that the effects of RIP2 were important early in the HDM response, likely within airway epithelial cells. However, the consequences of inhibiting RIP2 during this critical period has not yet been examined. In this study, we pharmacologically inhibited RIP2 activity during the initial exposure to allergen in an acute HDM model of asthma and determined the effect on the subsequent development of allergic airway disease. We show that early inhibition of RIP2 was sufficient to reduce lung histopathology and local airway inflammation while skewing the immune response from Th2 towards Th1. Using a chronic HDM asthma model, we demonstrate that inhibition of RIP2, despite attenuating airway inflammation and airway remodeling, was insufficient to reduce airway hyperresponsiveness. These data demonstrate the potential of pharmacological targeting of this kinase in asthma and support further development and optimization of RIP2 targeted therapies.
Changes to zonular tension alters the subcellular distribution of AQP5 in regions of influx and efflux of water in the rat lens
Authors: Petrova Rosica S , Bavana Nandini , Zhao Rusin , Schey Kevin L , Donaldson Paul J 
Published: June 2020

ABSTRACTPurposeThe lens utilizes circulating fluxes of ions and water that enter the lens at both poles and exit at the equator to maintain its optical properties. We have mapped the subcellular distribution of the lens aquaporins (AQP0, 1, & 5) in these water influx and efflux zones and investigated how their membrane location is affected by changes in tension applied to the lens by the zonules.MethodsImmunohistochemistry using AQP antibodies was performed on axial sections obtained from rat lenses that had been removed from the eye and then fixed, or were fixedin situto maintain zonular tension. Zonular tension was pharmacologically modulated by applying either tropicamide (increased), or pilocarpine (decreased). AQP labelling was visualized using confocal microscopy.ResultsModulation of zonular tension had no effect on AQP1 or AQP0 labelling in either the water efflux, or influx zones. In contrast, AQP5 labelling changed from membranous to cytoplasmic in response to both mechanical and pharmacologically induced reductions in zonular tension in both the efflux zone, and anterior (but not posterior) influx zone associated with the lens sutures.ConclusionsAltering zonular tension dynamically regulates the membrane trafficking of AQP5 in the efflux and anterior influx zones to potentially change the magnitude of circulating water fluxes in the lens.
HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
Authors: Solares Edwin A. , Tao Yuan , Long Anthony D. , Gaut Brandon S. 
Published: June 2020

ABSTRACTBackgroundDespite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.ResultsHere we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490Mb, a mosquito (Anopheles funestus; 200Mb) and the Thorny Skate (Amblyraja radiata; 2,650 Mb).ConclusionsHapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~84%. The improvements for mosquito scaffolding were similar to that of Chardonnay (from 61% to 86%), but even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on another published method for identifying secondary contigs, with generally superior results for HapSolo.
Depressive symptoms and single nucleotide polymorphisms predict clinical recurrence of inflammatory bowel disease
Authors: Ulrich Jordi Sebastian Bruno , Lang Brian Matthew , Auschra Bianca , von Känel Roland , Biedermann Luc , Greuter Thomas , Schreiner Philipp , Rogler Gerhard , Krupka Niklas , Sulz Michael Christian , Misselwitz Benjamin , Begré Stefan 
Published: June 2020

AbstractBackground and AimsInflammatory bowel disease (IBD) patients are at high risk for depression. We examined interrelations between genetic risk factors for depression, depressive symptoms and IBD flares.MethodsIn 1973 patients (1137 Crohn’s disease, 836 ulcerative colitis) of the Swiss IBD cohort study (SIBDC), 62 single nucleotide polymorphisms (SNPs) preselected for associations with depression, stress, pain and smoking were screened for cross-sectional associations with depression (hospital anxiety and depression subscale for depression, HADS-D≥11). Logistic regression and Cox proportional hazards models were built to test for effects of depressive symptoms on disease course and genetic risk factors on depression and disease course. As endpoints we used active disease (CDAI≥150 or MTWAI≥10) and two published composite flare definitions: FNCE: physician reported flare, non-response to therapy, new complication or extraintestinal manifestation and AFFSST: active disease, physician reported flare, fistula, stenosis and new systemic therapy.ResultsDepressive symptoms were a strong risk factor for disease related endpoints including active disease (adjusted hazard ratio, aHR: 3.25, p<0.001), AFFSST (aHR: 1.62, p<0.001) and FNCE (aHR: 1.35, p=0.019). Rs588765’s TC alleles and rs2522833’s C allele were associated with depressive symptoms at baseline (odds ratio, OR: 0.43, q=0.050 and OR: 1.73, q=0.059, respectively). Rs588765-TC remained protective regarding presence of depression (aHR: 0.67, p=0.035) and was associated with fewer active disease states (aHR: 0.72, p=0.045) during follow-up.ConclusionsIn IBD, genetics, depressive symptoms and inflammatory activity are intimately related: Depressive symptoms were a predictor of clinical deterioration and rs588765-TC was protective for depression and high IBD activity.FundingThis work was supported by the Swiss National Science Foundation (SNSF).
Cochlear implant-related speech processing may diminish the advantage of exposure to infant-directed speech
Authors: Arjmandi Meisam K. , Houston Derek , Wang Yuanyuan , Dilley Laura C. 
Published: June 2020

ABSTRACTCaregivers modify their speech when talking to infants, a specific type of speech known as infant-directed speech (IDS). This speaking style facilitates language learning compared to adult-directed speech (ADS) in infants with normal hearing (NH). While infants with NH and those with cochlear implants (CIs) prefer listening to IDS over ADS, it is yet unknown how CI speech processing may affect the acoustic distinctiveness between ADS and IDS, as well as the degree of intelligibility of these. This study analyzed speech of seven female adult talkers to investigate the effects of simulated CI speech processing on (1) acoustic distinctiveness between ADS and IDS, (2) estimates of intelligibility of caregivers’ speech in ADS and IDS, and (3) individual differences in caregivers’ ADS-to-IDS modification and speech intelligibility. Results suggest that CI speech processing is substantially detrimental to the acoustic distinctiveness between ADS and IDS, as well as to the intelligibility benefit derived from ADS-to-IDS modifications. Moreover, the observed considerable variability across individual talkers in acoustic implementation of ADS-to-IDS modification and speech intelligibility was significantly reduced due to CI speech processing. The findings are discussed in the context of the link between IDS and language learning in infants with CIs.
A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes
Authors: Rodriguez-Manzano Jesus , Malpartida-Cardenas Kenny , Moser Nicolas , Pennisi Ivana , Cavuto Matthew , Miglietta Luca , Moniri Ahmad , Penn Rebecca , Satta Giovanni , Randell Paul , Davies Frances , Bolt Frances , Barclay Wendy , Holmes Alison , Georgiou Pantelis 
Published: June 2020

AbstractThe COVID-19 pandemic is a global health emergency characterized by the high rate of transmission and ongoing increase of cases globally. Rapid point-of-care (PoC) diagnostics to detect the causative virus, SARS-CoV-2, are urgently needed to identify and isolate patients, contain its spread and guide clinical management. In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. The developed LAMP assay was tested on a real-time benchtop instrument (RT-qLAMP) showing a lower limit of detection of 10 RNA copies per reaction. It was validated against 183 clinical samples including 127 positive samples (screened by the CDC RT-qPCR assay). Results showed 90.55% sensitivity and 100% specificity when compared to RT-qPCR and average positive detection times of 15.45 ± 4.43 min. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 ± 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Paired with a smartphone for results visualization and geo-localization, this portable diagnostic platform with secure cloud connectivity will enable real-time case identification and epidemiological surveillance.One Sentence SummaryWe demonstrate isothermal detection of SARS-CoV-2 in under 20 minutes from extracted RNA samples with a handheld Lab-on-Chip platform.
Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data
Authors: Stewart Robert , Broadbent Matthew 
Published: June 2020

AbstractThe lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.
Epidemiological investigation of the first 135 COVID-19 cases in Brunei: Implications for surveillance, control, and travel restrictions
Authors: Wong Justin , Chaw Liling , Koh Wee Chian , Alikhan Mohammad Fathi , Jamaludin Sirajul Adli , Wan Wen Patricia POH , Naing Lin 
Published: June 2020

AbstractBackgroundStudies on the early introduction of SARS-CoV-2 in a naïve population have important epidemic control implications. We report findings from the epidemiological investigation of the initial 135 COVID-19 cases in Brunei and describe the impact of control measures and travel restrictions.MethodsEpidemiological and clinical information were obtained for all confirmed COVID-19 cases in Brunei, whose symptom onset was from March 9 to April 5, 2020 (covering the initial 5 weeks of the epidemic). Transmission-related measures such as reproduction number (R), incubation period, serial interval were estimated. Time-varying R was calculated to assess the effectiveness of control measures.ResultsA total of 135 cases were detected, of which 53 (39.3%) were imported. The median age was 36 years (range = 0.5 to 72). 41 (30.4%) and 13 (9.6%) were presymptomatic and asymptomatic cases respectively. The median incubation period was 5 days (IQR = 5, range = 1 to 11), and the mean serial interval was 5.39 days (sd = 4.47; 95% CI: 4.25, 6.53). R0 was between 3.88 and 5.96, and the doubling time was 1.3 days. By the 13th day of the epidemic, the Rt was under one (Rt = 0.91; 95% credible interval: 0.62, 1.32) and the epidemic was under control.ConclusionEpidemic control was achieved through a combination of public health measures, with emphasis on a test-isolate-trace approach supplemented by travel restrictions and moderate physical distancing measures but no actual lockdown. To maintain suppression, regular and ongoing testing of high-risk groups can supplement the existing surveillance program.
A global analysis of song frequency in passerines provides no support for the acoustic adaptation hypothesis but suggests a role for sexual selection
Authors: Mikula Peter , Valcu Mihai , Brumm Henrik , Bulla Martin , Forstmeier Wolfgang , Petrusková Tereza , Kempenaers Bart , Albrecht Tomáš 
Published: June 2020

AbstractMany animals use acoustic signals for communication, implying that the properties of these signals can be under strong selection. The acoustic adaptation hypothesis predicts that species living in dense habitats emit lower-frequency sounds than those in open areas, because low-frequency sounds generally propagate further in denser vegetation. Signal frequency may also be under sexual selection, because it correlates with body size and lower-frequency sounds are perceived as more intimidating. Here, we evaluate these hypotheses by analysing variation in peak song frequency across 5,085 passerine species (Passeriformes). A phylogenetically-informed analysis revealed that song frequency decreases with increasing body mass and with male-biased sexual size dimorphism. However, we found no support for the predicted relationship between frequency and habitat. Our results suggest that the global variation in passerine song frequency is mostly driven by natural and sexual selection causing evolutionary shifts in body size rather than by habitat-related selection on sound propagation.Statement of authorshipTA and PM conceived and designed the study with input from all authors. TA and BK coordinated the study. PM collected the song data. MV performed the statistical analyses with input from WF. MB made the figures with help from MV and PM. TP and HB provided bioacoustic expertise. PM drafted the first version of the manuscript. TA, BK and PM revised and finalized the manuscript with input from all authors.Data availability statementThe data used in this study were collected from publicly available databases. All data and computer code used to generate the results, as well as supplementary figures and tables will be freely available athttps://osf.io/fa9ky/.
Investigations for partial denture casting by fused deposition modelling-assisted chemical vapour smoothing
Authors: Singh Gurpartap , Singh Rupinder , Bal S.S. 
Published: June 2020

Purpose
The purpose of this study is to investigate dimensional accuracy (Δd), surface roughness (Ra) and micro hardness (HV) of partial dentures (PD) prepared with synergic combination of fused deposition modelling (FDM) assisted chemical vapour smoothing (CVS) patterns and conventional dental casting (DC) from multi-factor optimization view point.

Design/methodology/approach
The master pattern for PD was prepared with acrylonitrile butadiene styrene (ABS) thermoplastic on FDM set-up (one of the low cost additive manufacturing process) followed by CVS process. The final PD as functional prototypes was casted with nickel–chromium-based (Ni-Cr) alloy by varying Ni% (Z). The other input parameters were powder to water ratio P/W (X) and pH value (Y) of water used.

Findings
The results of this study suggest that for controlling the Δd and Ra of the PD, most important factor is X, followed by Z. For hardness of PD, the most important factor is Z. But from overall optimization viewpoint, the best settings are X-100/12, Y-10 and Z-61% (in Ni-Cr alloy). Further, based upon X-bar chart (for HV), the FDM-assisted DC process used for preparation of PD is statistically controlled.

Originality/value
This study highlights that PD prepared with X-100/12, Y-10 and Z-61% gives overall better results from multi-factor optimization view point. Finally, X-bar chart has been plotted to understand the statistical nature of the synergic combination of FDM, CVS and DC.
Addressing treatment capacity of uninsured adults with co-occurring disorders
Authors: Gruber Kenneth J. , Poole Kelly Jay , Graves Kelly N. , Richburg Antonia Monk 
Published: June 2020

Purpose
The purpose of this paper is to report on the success of an initiative involving the transformation of a group of small substance use treatment only or mental health treatment only provider agencies serving uninsured adults into providers of co-occurring disorder treatment.

Design/methodology/approach
The paper uses a case study narrative to describe the initiative and the transformation of the participant agencies from being providers of mental health or substance use treatment to providers of co-occurring disorders.

Findings
Six agencies serving uninsured adults expanded their scope of patient treatment services to include the capacity to treat adults with co-occurring disorders. This was achieved with modest support funding from a local foundation. The initiative has been ongoing for five years.

Practical implications
The outcome of this initiative demonstrates the financial and practical feasibility of improving and expanding treatment services to low-resourced patient populations. The participating agencies were able to improve their capacity to treat patients with substance use or mental health issues that previously they were not prepared to treat and thus increased their ability to provide integrated care.

Originality/value
The initiative described here shows that the treatment of concomitant substance use and mental health disorders is within the range of many small-scale treatment providers, if provided the leadership and support. Delivery of effective treatments to populations experiencing co-occurring disorders that are underserved and undertreated are achievable in community-based clinical practices. This has implications for developing treatment capacity outside of hospital settings to enable treatment of co-occurring disorders to become more accessible.
Green Banking: a road map for adoption
Authors: Bukhari Syed Asim Ali , Hashim Fathyah , Amran Azlan 
Published: June 2020

PurposeThe purpose of this study is to propose Green Banking best practices for the adoption of this business construct based on the dimensions of environment, social and governance (ESG). This paper proposes a number of green practices under the ESG dimensions that can be adopted by individual banks at any stage of Green Banking adoption. It provides tactics for implementing this business construct that can serve as a tool for regulatory authorities forming Green Banking guidelines or policies for adoption. Such research has not been undertaken up until now.Design/methodology/approachThe Green Banking adoption model is based on the concept of human ecology in which the inter-dependency and inter-connectivity of the variables impacting the phenomenon of environmental sustainability. These influencing variables are, in turn, connected with the natural environment. In the proposed model, the variables of ESG are inter-connected and impacting the natural environment as well. The proposed best practices have been derived from the Green Banking practices of the global industry leaders and Green Banking regulations of developed and developing countries. It can be beneficial to the stakeholders, as it proposes a step-by-step guide to Green Banking adoption that can be followed either sequentially or in parallel by the banks.FindingsGreen Banking adoption can be achieved by banks through implementing certain practices in either sequential or parallel manner. The adoption process depends on the various external and internal environmental dependencies. The Green Banking adoption practices can be broken down in three areas, i.e. ESG, allowing the construct optimal depth of coverage and complexity.Originality/valueThe literature on Green Banking is steadily increasing but a lack of research exists in the area of Green Banking adoption. Currently, limited literature exists that can provide the banking industry or the regulatory authorities with a framework or guideline to adopt Green Banking.