bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Authors: Rizzetto Simone , Eltahla Auda A. , Lin Peijie , Bull Rowena , Lloyd Andrew R. , Ho Joshua W. K. , Venturi Vanessa , Luciani Fabio 
Published: October 2017

AbstractSingle cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% − 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
The drinking water contaminant dibromoacetonitrile delays G1-S transition and suppresses Chk1 activation at broken replication forks
Authors: Caspari Thomas , Dyer James , Fenner Nathalie , Dunn Christian , Freeman Chris 
Published: October 2017

AbstractChlorination of drinking water protects humans from water-born pathogens, but it also produces low concentrations of dibromoacetonitrile (DBAN), a common disinfectant by-product found in many water supply systems. DBAN is not mutagenic but causes DNA breaks and elevates sister chromatid exchange in mammalian cells. The WHO issued guidelines for DBAN after it was linked with cancer of the liver and stomach in rodents. How this haloacetonitrile promotes malignant cell transformation is unknown. Using fission yeast as a model, we report here that DBAN delays G1-S transition. DBAN does not hinder ongoing DNA replication, but specifically blocks the serine 345 phosphorylation of the DNA damage checkpoint kinase Chk1 by Rad3 (ATR) at broken replication forks. DBAN is particularly damaging for cells with defects in the lagging-strand DNA polymerase delta. This sensitivity can be explained by the dependency of pol delta mutants on Chk1 activation for survival. We conclude that DBAN targets a process or protein that acts at the start of S phase and is required for Chk1 phosphorylation. Taken together, DBAN may precipitate cancer by perturbing S phase and by blocking the Chk1-dependent response to replication fork damage.
DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient
Authors: Emilson Caroline E. , Thompson Dean G. , Venier Lisa A. , Porter Teresita M. , Swystun Tom , Chartrand Derek , Capell Scott , Hajibabaei Mehrdad 
Published: October 2017

AbstractCost-effective, ecologically relevant, sensitive, and standardized indicators are requisites of biomonitoring. DNA metabarcoding of macroinvertebrate communities is a potentially transformative biomonitoring technique that can reduce cost and time constraints while providing information-rich, high resolution taxonomic data for the assessment of watershed condition. Here, we assess the utility of DNA metabarcoding to provide aquatic indicator data for evaluation of forested watershed condition across Canadian eastern boreal watersheds, subject to natural variation and low-intensity harvest management. We do this by comparing the similarity of DNA metabarcoding and morphologically derived macroinvertebrate metrics (i.e. richness, % Ephemeroptera, Plecoptera and Trichoptera, % chironomid), and the ability of DNA metabarcoding and morphological metrics to detect key gradients in stream condition linked to forested watershed features. Our results show consistency between methods, where common DNA metabarcoding and morphological macroinvertebrate metrics are positively correlated and indicate the same key gradients in stream condition (i.e. dissolved oxygen, and dissolved organic carbon, total nitrogen and conductivity) linked to watershed size and shifts in forest composition across watersheds. Our study demonstrates the potential usefulness of macroinvertebrate DNA metabarcoding to future application in broad-scale biomonitoring of watershed condition across environmental gradients.
Effects of 1950 MHz radiofrequency electromagnetic fields on Aβ processing in human neuroblastoma and mouse hippocampal neuronal cells
Authors: Park Jeongyeon , Kwon Jong Hwa , Kim Nam , Song Kiwon 
Published: October 2017

AbstractAlzheimer’s disease (AD) is a neurodegenerative disease leading to progressive loss of memory and other cognitive functions. One of the well-known pathological markers of AD is the accumulation of amyloid-beta protein (Aβ), and its plaques, in the brain. Recent studies using Tg-5XFAD mice as a model of AD have reported that exposure to radiofrequency electromagnetic fields (RF-EMF) from cellular phones reduced Aβ plaques in the brain and showed beneficial effects on AD. In this study, we examined whether exposure to 1950 MHz RF-EMF affects Aβ processing in neural cells. We exposed HT22 mouse hippocampal neuronal cells and SH-SY5Y human neuroblastoma cells to RF-EMF (SAR 6 W/kg) for 2 h per day for 3 days, and analyzed the mRNA and protein expression of the key genes related to Aβ processing. When exposed to RF-EMF, mRNA levels of APP, BACE1, ADAM10 and PSEN1 were decreased in HT22, but the mRNA level of APP was not changed in SH-SY5Y cells. The protein expression of APP and BACE1, as well as the secreted Aβ peptide, was not significantly different between RF-EMF–exposed 7w-PSML, HT22 and SH-SY5Y cells and the unexposed controls. These observations suggest that RF-EMF exposure may not have a significant physiological effect on Aβ processing of neural cells in the short term. However, considering that we only exposed HT22 and SH-SY5Y cells to RF-EMF for 2 h per day for 3 days, we cannot exclude the possibility that 1950 MHz RF-EMF induces physiological change in Aβ processing with long-term and continuous exposure.
On Backreaction in Newtonian cosmology
Authors: Buchert Thomas 
Published: October 2017

Abstract
We clarify that a result recently stated by Kaiser is contained in a theorem of Buchert and Ehlers that is widely known for its main result: that there is no global kinematical backreaction in Newtonian cosmology. Kaiser cites this paper, re-derives parts of the theorem, but incompletely restates its content. He makes further claims, which cannot be proven beyond the limited context of Newtonian cosmology. We also discuss recent papers of Rácz et al. and Roukema, who claim the existence of global backreaction within the Newtonian framework.
Descemet Membrane Endothelial Transfer: Ultimate Outcome
Authors: Birbal Rénuka S. , Parker Jack , Dirisamer Martin , Janićijević Ana , Baydoun Lamis , Dapena Isabel , Melles Gerrit R. J. 
Published: October 2017

Purpose:
To evaluate the clinical outcome of 16 eyes undergoing Descemet membrane endothelial transfer (DMET).

Methods:
In this retrospective cohort study, a consecutive series of 16 eyes from 16 patients was evaluated after subtotal detachment of the Descemet graft after a Descemet membrane endothelial keratoplasty procedure (n = 8) or intended DMET (n = 8) for either Fuchs endothelial dystrophy (n = 10) or bullous keratopathy (BK; n = 6).

Results:
All 8 Descemet membrane endothelial keratoplasty procedures were complicated by subtotal detachment of the donor graft. The remaining 8 eyes that underwent a DMET procedure were uneventful and no postoperative complications occurred, except 1 eye with BK that experienced a postoperative wound leak. Throughout all postoperative time points, the partially attached status of all Descemet grafts was maintained. Although all eyes operated on for Fuchs endothelial dystrophy showed initial central corneal clearance, no eye operated for BK demonstrated any degree of corneal deturgescence. Ultimately, all 16 corneas decompensated and 15 of the 16 patients elected retransplantation, while 1 patient declined further surgery for health reasons. Retransplantation was performed on average 10.3 (±7.4) months (range, 3–31 mo) postoperatively.

Conclusions:
Ultimately, regardless of the etiology of endothelial dysfunction, DMET fails to provide satisfactory results in the long term; durable corneal clearance may therefore require the presence of a nearly completely attached Descemet graft.
Drying characteristics and quality evaluation of dehydrated catfish (Clarias gariepinus)
Authors: Otolowo Dupe Temilade , Olapade Abiodun Adekunle , Oladele Samouel Olugbenga , Egbuna Felix 
Published: October 2017

Purpose
Fresh catfish (Clarias gariepinus) is highly perishable. This paper aims to investigate the drying characteristics and quality of body-mass dehydrated catfish to determine the effective dehydration parameters for preservation.

Design/methodology/approach
Brine concentration (3-9 per cent), brining time (30-90 min) and drying temperature (90-130°C) interacted using the response surface methodology. Preliminary experiments were conducted to select treatments. Moisture content and ratio and drying rate were determined and fitted into five thin-layer drying models; the goodness of fit was evaluated by average grade ranking of the regression parameters. Proximate compositions and microbial load of dehydrated catfish were determined using standard methods.

Findings
Treatments with 110°C gave initial higher drying rate (0.034-0.043 kg H2O/kg solid/h) and shorter drying time (20-21 h). Drying occurred at two falling rate periods. Midilli model ranked first in fitting the drying data. It explained up to 99.6-99.7 per cent of the total variations in the independent variables with low values of error terms; RMSE was 0.02131-0.01794 and χ2 was 0.00037-0.00043, indicating good predictive quality. Processing parameters positively and significantly (p < 0.05) influenced the proximate compositions of dehydrated catfish. Treatment: 6 per cent brine, 90 min and 110°C presented the most effective dehydration parameters for quality preservation of body-mass catfish.

Practical implications
The dehydration technique used in this study could enhance nutritive quality and storage stability of body-mass dehydrated catfish that could serve as a useful and convenient tool for commercial application.

Social implications
Hygienically processed dehydrated catfish of good quality could be used as a source of nutrients to ameliorate malnutrition and reduce post-harvest losses of catfish.

Originality/value
The effective processing parameters established is an important step to harness the high nutrients and economic values embedded in catfish.
Using enterprise social networks as a knowledge management tool in higher education
Authors: Corcoran Niall , Duane Aidan 
Published: October 2017

Purpose
The management of organisational knowledge and the promotion of staff knowledge sharing are largely neglected in higher education institutions. The purpose of this study is to examine how enterprise social networks can enable staff knowledge sharing in communities of practice in that context.

Design/methodology/approach
The study is framed as an Action Research project, covering three cycles over a 12-month period. During the Diagnosing phase, a conceptual model was developed for empirical testing. Data were collected through 30 semi-structured interviews and a number of focus groups. This was supplemented by content analysis and reflective journaling.

Findings
The findings support the conceptual model and provide insight into the antecedents necessary for the creation of an enterprise social network-enabled knowledge-sharing environment, the motivators for and barriers to participation, and the perceived organisational and individual benefits of increased staff knowledge-sharing activity.

Research limitations/implications
As the study has a higher education focus, all of the findings may not be generalizable to other types of organisation. Further development of the conceptual model and testing in other contextual settings will yield greater generalizability.

Practical implications
A number of findings have practical implications for the management of higher education institutions, such as the evidence of a divide between faculty and other staff. In general, the study findings provide an opportunity for educationalists to better understand the scope and impact of employing social media platforms for knowledge sharing.

Originality/value
This paper adds to the growing body of work on organisational implementations of social media, and should be of interest to practitioners and researchers undertaking similar projects.
A plasmid‐borne Rap‐Phr system regulates sporulation of Bacillus thuringiensis in insect larvae
Authors: Fazion Fernanda , Perchat Stéphane , Buisson Christophe , Vilas‐Bôas Gislayne , Lereclus Didier 
Published: October 2017

SummaryThe entomopathogen Bacillus thuringiensis species harbours numerous plasmids essentially studied for their involvement in pathogenicity, as Cry‐plasmids. The life cycle of B. thuringiensis in the insect host is regulated by the sequential activation of quorum sensing systems to kill, survive and sporulate. In this study, we characterize a new quorum sensing system belonging to the Rap‐Phr family. The Rap8‐Phr8 system is borne by the pHT8_1 plasmid, a small cryptic plasmid from the B. thuringiensis var. kurstaki HD73 strain. Our results demonstrate that the Rap8 protein inhibits sporulation and biofilm formation through the Spo0A pathway. The Rap8 activity is inhibited by the mature Phr8 heptapeptide YAHGKDI. The key residues specific for the Rap phosphatase activity are conserved in Rap8 suggesting a common mode of action. Interestingly, we show that the Rap8‐Phr8 system is specifically required for regulating sporulation of B. thuringiensis in insect larvae. This system may allow the bacteria to exert a tight control of the sporulation process in the host cadaver for optimizing the multiplication, the survival and the dissemination of the bacteria. Thus, our results suggest that pHT8_1 provides advantages for adaptation and evolution of B. thuringiensis in its ecological niche.
The Association of Health Reform and Infant Health: Evidence from Massachusetts
Authors: Boudreaux Michel H. , Dagher Rada K. , Lorch Scott A. 
Published: October 2017

ObjectiveTo estimate whether the incidence of low birthweight and rates of infant mortality were associated with Massachusetts health reform in the overall population and for subgroups that are at higher risk for poor health outcomes.Data SourcesIndividual‐level data on birthweight were obtained from the National Center for Health Statistics detailed natality files, and aggregated county‐level mortality rates were generated from linked birth–death files. We used restricted versions of each file that had intact state and substate geographic identifiers.Research DesignWe employed a quasi‐experimental difference‐in‐differences design.Principal ResultsWe found small and statistically nonsignificant associations between the reform and the incidence of low birthweight and infant mortality rates. Results were consistent across a number of subgroups and were robust to alternative comparison groups and alternative modeling assumptions.ConclusionsWe found no evidence that the Massachusetts reform was associated with improvements in individual low birthweights or county‐level infant mortality rates, despite increasing health insurance coverage rates for adult women of child‐bearing age. Because our mortality analysis was ecological, we are not able to draw conclusions about how an individual‐level health insurance intervention for uninsured pregnant women would affect the mortality outcomes of their infants.
The induction of cashmere shedding via cyclophosphamide injection
Authors: Chen Qian , Cong Yu‐yan , Li Xue‐jian , Zhang Rui‐yang 
Published: October 2017

AbstractThe aim of this study was to investigate the effects of cyclophosphamide (CPA) on cashmere shedding in cashmere goats. Thirty‐two castrated Liaoning cashmere goats were randomly allotted to four groups, with eight replicates in each group. The four groups were injected intravenously with CPA doses of 0, 15, 20 and 25 mg/kg body weight, respectively. Feed intake, body weight, body temperature, and sphygmus were recorded and the erythrocyte count, leukocyte count, hemoglobin content, and cashmere yield and length were determined. CPA has no significant effect on feed intake, body weight, body temperature, or sphygmus of cashmere goats. It was found that CPA significantly decreased the erythrocyte count and hemoglobin content in cashmere goats on the days immediately following injection, but the effects on erythrocytes diminished within 6 days, with hemoglobin content returning to normal within 10 days. Cashmere fiber began to shed on about day 10 after injection with CPA. CPA had no significant effect on cashmere length but significantly increased cashmere yield. The results indicate that CPA can induce cashmere shedding and achieve the purpose of concentrated defleecing. A dose of 20 mg/kg body weight is preferable for hair removal and regrowth in cashmere goats.
Chronic treatment with novel nanoformulated micelles of rapamycin, Rapatar, protects diabetic heart against ischaemia/reperfusion injury
Authors: Samidurai Arun , Salloum Fadi N , Durrant David , Chernova Olga B , Kukreja Rakesh C , Das Anindita 
Published: October 2017

Background and PurposeEnhanced mammalian target of rapamycin (mTOR) signalling contributes to the pathogenesis of diabetes and plays a critical role in myocardial ischaemia/reperfusion (I/R) injury. Rapatar is a novel nanoformulated micellar of rapamycin, a putative inhibitor of mTOR that has been rationally designed to increase water solubility of rapamycin to facilitate p.o. administration and enhance bioavailability. We examined the effect of Rapatar on the metabolic status and protection against myocardial I/R injury in type 2 diabetic mice.Experimental ApproachAdult male db/db mice were treated daily for 10 weeks with Rapatar (0.75 mg·kg−1·day−1, p.o.) or vehicle. Isolated hearts were connected to a Langendorff perfusion system and subjected to global ischaemia (30 min) and reperfusion (1 h).Key ResultsRapatar reduced fasting plasma glucose and triglyceride levels, prevented the gain in body weight and also improved glucose tolerance and insulin sensitivity in db/db mice compared with control. Cardiac function was improved following Rapatar treatment in db/db mice. Myocardial infarct size was reduced in Rapatar‐treated mice with improved post‐ischaemic rate–force product. Western blot analyses demonstrated a significant inhibition of phosphorylation of ribosomal protein S6 (downstream target of mTORC1), but not Akt (Ser473, target of mTORC2) following chronic treatment with Rapatar. Rapatar also induced phosphorylation of AMPK, STAT3, ERK1/2 and glycogen synthase kinase 3β, without interfering with phosphorylation of p38.Conclusion and implicationsOur studies indicate that chronic treatment with Rapatar improves metabolic status and cardiac function with a reduction of infarct size following myocardial I/R injury in diabetic mice.
Congenital anomalies and the severity of impairments for cerebral palsy
Authors: Jystad Kjersti P , Strand Kristin M , Bjellmo Solveig , Lydersen Stian , Klungsöyr KARI , Stoknes Magne , Skranes Jon , Andersen Guro L , Vik Torstein 
Published: October 2017

AimTo study the prevalence of congenital anomalies among children with cerebral palsy (CP) born at term or late preterm, and if CP subtypes and clinical manifestations differ between children with and without congenital anomalies.MethodThis was a cross‐sectional study using data from the Cerebral Palsy Register of Norway and the Medical Birth Registry of Norway. All children with congenital CP born at and later than 34 weeks’ gestation in Norway from 1999 to 2009 were included. Anomalies were classified according to the European Surveillance of Congenital Anomalies classification guidelines. Groups were compared using Fisher's exact test, Kruskal–Wallis test, and the Mann–Whitney U test.ResultsAmong 685 children with CP, 169 (25%) had a congenital anomaly; 125 within the central nervous system. Spastic bilateral CP was more prevalent in children with anomalies (42%) than in children without (34%; p=0.011). Children with anomalies less frequently had low Apgar scores (p<0.001), but more often had severe limitations in gross‐ and fine‐motor function, speech impairments, epilepsy, severe vision, and hearing impairments than children without anomalies (p<0.03).InterpretationAlthough children with CP and anomalies had low Apgar scores less frequently, they had more severe limitations in motor function and more associated problems than children with CP without anomalies.What this paper adds

One in four children with cerebral palsy (CP) born at term or late preterm has a congenital anomaly.

The added value of neuroimaging to detect central nervous system anomalies in children with CP.

Children with anomalies have more severe motor impairments.

More severe clinical manifestations are not explained by perinatal complications as indicated by low Apgar scores.
Type 2 diabetes in young adults in Central Auckland: demography and complications
Authors: Beig Junaid , Khanolkar Manish , Cundy Tim 
Published: October 2017

AbstractBackgroundType 2 diabetes (T2D) in young adults is associated with a high risk of diabetes complications.AimsTo investigated the demography and the emergence of complications of young adults with T2D in the central Auckland region where there has been substantial immigration.MethodsIn total, 310 young adults with T2D (<40 years) were registered with the Auckland Diabetes Centre in 2015. We documented demographic, anthropometric and metabolic variables and prevalence and the emergence of complications.ResultsThree demographic groups accounted for 243 participants (78%): 135 (44%) were migrants of Asian or Pacific Island origin, diagnosed a median 9 years after migration at a mean age of 28 ± 6 years; 88 (29%) were New Zealand‐born Pāsifika descent, with a high prevalence of morbid obesity and 37 (12%) had major mental illness or intellectual disability. At diagnosis, the median HbA1c was 80 mmol/mol, and in 28%, it was ≥100 mmol/mol. A median 6 years after diagnosis, 56% had some degree of retinopathy, with the prevalence related both to the duration of diabetes and glycaemic control (P = 0.001). Forty‐four percent of subjects had abnormal albuminuria at diagnosis (12% with macroalbuminuria). Increased albuminuria was strongly associated with obesity (P = 0.002). The development of CKD stages 4–5 was related both to the severity of retinopathy and degree of albuminuria at diagnosis (P = 0.0001). Major cardiovascular events were related to the severity of retinopathy at diagnosis (P = 0.0001).ConclusionsNew migrants, New Zealand‐born Pāsifika and patients with mental illness or an intellectual disability comprise the bulk of young onset T2D. The disease is aggressive, and by the age of 40, patients are already developing advanced complications.