bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunnel engineering to accelerate product release for better biomass-degrading abilities in lignocellulolytic enzymes
Authors: Lu Zhenghui , Li Xinzhi , Zhang Rui , Yi Li , Ma Yanhe , Zhang Guimin 
Published: November 2019

Abstract
Background
For enzymes with buried active sites, transporting substrates/products ligands between active sites and bulk solvent via access tunnels is a key step in the catalytic cycle of these enzymes. Thus, tunnel engineering is becoming a powerful strategy to refine the catalytic properties of these enzymes. The tunnel-like structures have been described in enzymes catalyzing bulky substrates like glycosyl hydrolases, while it is still uncertain whether these structures involved in ligands exchange. Till so far, no studies have been reported on the application of tunnel engineering strategy for optimizing properties of enzymes catalyzing biopolymers.

Results
In this study, xylanase S7-xyl (PDB: 2UWF) with a deep active cleft was chosen as a study model to evaluate the functionalities of tunnel-like structures on the properties of biopolymer-degrading enzymes. Three tunnel-like structures in S7-xyl were identified and simultaneously reshaped through multi-sites saturated mutagenesis; the most advantageous mutant 254RL1 (V207N/Q238S/W241R) exhibited 340% increase in specific activity compared to S7-xyl. Deconvolution analysis revealed that all three mutations contributed synergistically to the improved activity of 254RL1. Enzymatic characterization showed that larger end products were released in 254RL1, while substrate binding and structural stability were not changed. Dissection of the structural alterations revealed that both the tun_1 and tun_2 in 254RL1 have larger bottleneck radius and shorter length than those of S7-xyl, suggesting that these tunnel-like structures may function as products transportation pathways. Attributed to the improved catalytic efficiency, 254RL1 represents a superior accessory enzyme to enhance the hydrolysis efficiency of cellulase towards different pretreated lignocellulose materials. In addition, tunnel engineering strategy was also successfully applied to improve the catalytic activities of three other xylanases including xylanase NG27-xyl from Bacillus sp. strain NG-27, TSAA1-xyl from Geobacillus sp. TSAA1 and N165-xyl from Bacillus sp. N16-5, with 80%, 20% and 170% increase in specific activity, respectively.

Conclusions
This study represents a pilot study of engineering and functional verification of tunnel-like structures in enzymes catalyzing biopolymer. The specific activities of four xylanases with buried active sites were successfully improved by tunnel engineering. It is highly likely that tunnel reshaping can be used to engineer better biomass-degrading abilities in other lignocellulolytic enzymes with buried active sites.
A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage
Authors: Southworth Jade , Grace C. Alastair , Marron Alan O. , Fatima Nazeefa , Carr Martin 
Published: November 2019

AbstractBackgroundUnicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellateMonosiga brevicollisrevealed the presence of only three families of LTR retrotransposons, all of which appeared to be active.Salpingoeca rosettais the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans.ResultsScreening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present inS. rosettashow the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.ConclusionsS. rosettaincreases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, theS. rosettafamilies show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
Clinical validation of the Lumipulse G cerebrospinal fluid assays for routine diagnosis of Alzheimer’s disease
Authors: Leitão Maria João , Silva-Spínola Anuschka , Santana Isabel , Olmedo Veronica , Nadal Alicia , Le Bastard Nathalie , Baldeiras Inês 
Published: November 2019

Abstract
Background
Ongoing efforts within the Alzheimer’s disease (AD) field have focused on improving the intra- and inter-laboratory variability for cerebrospinal fluid (CSF) biomarkers. Fully automated assays offer the possibility to eliminate sample manipulation steps and are expected to contribute to this improvement. Recently, fully automated chemiluminescence enzyme immunoassays for the quantification of all four AD biomarkers in CSF became available. The aims of this study were to (i) evaluate the analytical performance of the Lumipulse G β-Amyloid 1-42 (restandardized to Certified Reference Materials), β-Amyloid 1-40, total Tau, and pTau 181 assays on the fully automated LUMIPULSE G600II; (ii) compare CSF biomarker results of the Lumipulse G assays with the established manual ELISA assays (INNOTEST®) from the same company (Fujirebio); and (iii) establish cut-off values and the clinical performance of the Lumipulse G assays for AD diagnosis.

Methods
Intra- and inter-assay variation was assessed in CSF samples with low, medium, and high concentrations of each parameter. Method comparison and clinical evaluation were performed on 40 neurological controls (NC) and 80 patients with a diagnosis of probable AD supported by a follow-up ≥ 3 years and/or positive amyloid PET imaging. A small validation cohort of 10 NC and 20 AD patients was also included to validate the cut-off values obtained on the training cohort.

Results
The maximal observed intra-assay and inter-assay coefficients of variation (CVs) were 3.25% and 5.50%, respectively. Method comparisons revealed correlation coefficients ranging from 0.89 (for Aβ40) to 0.98 (for t-Tau), with those for Aβ42 (0.93) and p-Tau (0.94) in-between. ROC curve analysis showed area under the curve values consistently above 0.85 for individual biomarkers other than Aβ40, and with the Aβ42/40, Aβ42/t-Tau, and Aβ42/p-Tau ratios outperforming Aβ42. Validation of the cut-off values in the independent cohort showed a sensitivity ranging from 75 to 95% and a specificity of 100%. The overall percentage of agreement between Lumipulse and INNOTEST was very high (> 87.5%).

Conclusions
The Lumipulse G assays show a very good analytical performance that makes them well-suited for CSF clinical routine measurements. The good clinical concordance between the Lumipulse G and INNOTEST assays facilitates the implementation of the new method in routine practice.
Human astrovirus infection associated with encephalitis in an immunocompetent child: a case report
Authors: Koukou Georgia , Niendorf Sandra , Hornei Britt , Schlump Jan-U , Jenke Andreas C. , Jacobsen Sonja 
Published: November 2019

Abstract
Background
Until today, classic human astroviruses have not been associated with central nervous system infections in immunocompetent patients.

Case presentation
A 16-month-old Caucasian girl presented with repetitive generalized seizures with a 4-day history of watery diarrhea, which had already gradually improved. Initially, the prolonged seizures ceased after systemic midazolam treatment and were thought to be fever associated. However, her mental status remained altered, and after seizure recurrence, she was transferred to our pediatric intensive care unit. Seizure control was achieved by a combination of high-dose levetiracetam and phenobarbital, but she remained unconscious. An electroencephalogram at this time revealed generalized high voltage theta activity. All laboratory analyses, including extended blood and cerebrospinal fluid analyses, and a brain magnetic resonance imaging were normal.
On day 4, the child gradually became conscious, but was very agitated and not able to walk. Since an electroencephalogram at this time still revealed generalized high voltage theta activity, although she had not received sedative medications for 72 hours, she was diagnosed as having encephalopathy. At that time, results of diagnostic testing of the stool sample were positive for classic astrovirus infection, and we decided to analyze the initially obtained cerebrospinal fluid for astrovirus as well. Cerebrospinal fluid was also found positive for human astrovirus. Sequencing analysis revealed a classic astrovirus genotype 1 with exactly the same nucleotide sequence as in the feces. Clinically, the child gradually improved and was discharged on day 9.

Conclusions
Whereas the new human astrovirus subtypes have been recently associated with central nervous system infection, this is the first case of encephalitis in an immunocompetent child due to classic human astrovirus. Considering that classic human astroviruses are the third most common etiological agents of viral gastroenteritis in children, we believe that human astroviruses as causative agents for central nervous system infections should be considered more often, especially in children and infants with preceding gastroenteritis.
Two functional variants at 6p21.1 were associated with lean mass
Authors: Pei Yu-Fang , Hu Wen-Zhu , Yang Xiao-Lin , Wei Xin-Tong , Feng Gui-Juan , Zhang Hong , Shen Hui , Tian Qing , Deng Hong-Wen , Zhang Lei 
Published: November 2019

AbstractBackgroundLow lean body mass is the most important predictor of sarcopenia with strong genetic background. The aim of this study was to uncover genetic factors underlying lean mass development.Materials and methodsWe performed a genome-wide association study (GWAS) of fat-adjusted leg lean mass in the Framingham Heart Study (FHS,N = 6587), and replicated in the Women’s Health Initiative–African American sub-sample (WHI-AA,N = 847) and the Kansas City Osteoporosis Study (KCOS,N = 2219). We also cross-validated significant variants in the publicly available body mass index (BMI) summary results (N~ 700,000). We then performed a series of functional investigations on the identified variants.ResultsFour correlated SNPs at 6p21.1 were identified at the genome-wide significance (GWS,α = 5.0 × 10−8) level in the discovery FHS sample (rs551145, rs524533, rs571770, and rs545970,p = 3.40–9.77 × 10−9), and were successfully replicated in both the WHI-AA and the KCOS samples (one-sidedp = 1.61 × 10−3–0.04). They were further cross-validated by the large-scale BMI summary results (p = 7.0–9.8 × 10−3). Cis-eQTL analyses associated these SNPs with theNFKBIEgene expression. Electrophoresis mobility shift assay (EMSA) in mouse C2C12 myoblast cells implied that rs524533 and rs571770 were bound to an unknown transcription factor in an allelic specific manner, while rs551145 and rs545970 did not. Dual-luciferase reporter assay revealed that both rs524533 and rs571770 downregulated luciferase expression by repressing promoter activity. Moreover, the regulation pattern was allelic specific, strengthening the evidence towards their differential regulatory effects.ConclusionsThrough a large-scale GWAS followed by a series of functional investigations, we identified 2 correlated functional variants at 6p21.1 associated with leg lean mass. Our findings not only enhanced our understanding of molecular basis of lean mass development but also provided useful candidate genes for further functional studies.
Implementation strategies to improve preconception and antenatal care for tobacco smoking, alcohol consumption and weight management: a systematic review protocol
Authors: Doherty Emma , Kingsland Melanie , Wolfenden Luke , Wiggers John , Dray Julia , Hollis Jenna , Elliott Elizabeth J. , Daly Justine B. , Bailey Kylie A. , Attia John , Hunter Mandy , Symonds Ian , Tully Belinda , Tremain Danika , Hodder Rebecca K. 
Published: November 2019

Abstract
Background
Despite existing best practice care recommendations for addressing tobacco smoking, alcohol consumption and weight management in preconception and antenatal care, such recommendations are often not implemented into routine practice. Effective strategies that target known barriers to implementation are key to reducing this evidence to practice gap. The aim of this review is to synthesise the evidence on the effectiveness of implementation strategies in improving the provision of preconception and antenatal care for these modifiable risk factors.

Methods
Randomised and non-randomised study designs will be eligible for inclusion if they have a parallel control group. We will include studies that either compare an implementation strategy to usual practice or compare two or more strategies. Participants may include any health service providing preconception or antenatal care to women and/or the health professionals working within such a service. The primary outcome will be any measure of the effectiveness of implementation strategies to improve preconception and/or antenatal care for tobacco smoking, alcohol consumption and/or weight management (including care to improve nutrition and/or physical activity). Secondary outcomes will include the effect of the implementation strategy on women’s modifiable risk factors, estimates of absolute costs or cost-effectiveness and any reported unintentional consequences. Eligible studies will be identified via searching Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, Maternity and Infant Care, CINAHL, ProQuest Dissertations and Theses and other sources (e.g. contacting experts in the field). Study selection, data extraction and risk of bias will be assessed independently by two review authors and differences resolved by a third reviewer. If data permits, we will conduct fixed-effects or random-effects meta-analysis where appropriate. If studies do not report the same outcome or there is significant heterogeneity, results will be summarised narratively.

Discussion
This review will identify which implementation strategies are effective in improving the routine provision of preconception and antenatal care for tobacco smoking, alcohol consumption and weight management. Such a review will be of interest to service providers, policy makers and implementation researchers seeking to improve women’s modifiable risk factors in preconception and antenatal care settings.

Systematic review registration
PROSPERO CRD42019131691
We Can Quit2 (WCQ2): a community-based intervention on smoking cessation for women living in disadvantaged areas of Ireland—study protocol for a pilot cluster randomised controlled trial
Authors: Hayes Catherine , Ciblis Aurelia , Darker Catherine , Dougall Nadine , Vance Joanne , O’Connell Nicola , Dobbie Fiona , Loudon Kirsty , Burke Emma , Devane Declan , Bauld Linda 
Published: November 2019

Abstract
Background
Tobacco use is the leading cause of preventable death in Ireland with almost 6000 smokers dying each year from smoking-related diseases. The ‘We Can Quit2’ (WCQ2) study is a pilot pragmatic two-arm, parallel-group, cluster randomised trial that aims to explore the feasibility and acceptability of trial processes including recruitment and to estimate parameters to inform sample size estimates needed for an effectiveness trial. This future trial will assess the effectiveness of a community-based smoking cessation intervention for women living in disadvantaged areas on short- and medium-term cessation rates.

Methods/design
Four matched pairs of districts (eight clusters) selected by area level of deprivation, geographical proximity, and eligibility for free medical services will be randomised to receive either WCQ (behavioural support + access to Nicotine Replacement Therapy (NRT)) delivered over 12 weeks by trained Community Facilitators (CFs) or to a form of usual care, a one-to-one smoking cessation service delivered by Smoking Cessation Officers from Ireland’s national health service, the Health Service Executive (HSE). Within each cluster, 24–25 women will be recruited (97 per arm; 194 in total) in 4 phases with consent obtained prior to cluster randomisation. The outcome measures will assess feasibility and acceptability of trial processes, including randomisation. Outcome data for a future definitive intervention (biochemically validated smoking abstinence) will be collected at end of programme (12 weeks) and at 6 months. WCQ2 has an embedded process evaluation using both qualitative and quantitative methods. This will be conducted (semi-structured client and CF interviews, intervention delivery checklist, and diary) to explore acceptability of trial processes, intervention fidelity, trial context, and implementation. Trial processes will be assessed against domains of the PRECIS-2 wheel to inform a future definitive trial design.

Discussion
Data from this pilot trial will inform the design and sample size for a full cluster randomised trial to determine the effectiveness of an intervention tailored to disadvantaged women in improving smoking cessation rates. It will provide transferable learning on the systems and implementation strategies needed to support effective design of future pragmatic community-based trials which address health promotion interventions for women in disadvantaged communities.

Trial registration
Concurrent to publication. Controlled trials ISRCTN74721694.
The Optimal Cut-off of BIPSS in Differential Diagnosis of ACTH-dependent Cushing’s Syndrome: Is Stimulation Necessary?
Authors: Chen Shi , Chen Kang , Wang Shirui , Zhu Huijuan , Lu Lin , Zhang Xiaobo , Tong Anli , Pan Hui , Wang Renzhi , Lu Zhaolin 
Published: November 2019

AbstractContextsBilateral inferior petrosal sinus sampling (BIPSS) can differentiate Cushing’s disease (CD) and ectopic adrenocorticotropin (ACTH) syndrome (EAS). The traditional cutoff of inferior petrosal sinus to peripheral (IPS:P) ACTH gradient was 2 before stimulation and 3 after stimulation, which yielded unsatisfactory sensitivity in some studies.ObjectivesTo determine the optimal cutoff in BIPSS before or after desmopressin stimulation and to evaluate the necessity of stimulation.Design and SettingSingle-center retrospective study (2011–2018) along with meta-analysis.Patients226 CD and 24 EAS patients with confirmed diagnosis who underwent BIPSS with desmopressin stimulation.ResultsIn the meta-analysis of 25 studies with 1249 CD and 152 EAS patients, the traditional cutoff yielded sensitivity of 86% and 97% and specificity of 98% and 100% before and after stimulation, respectively. We then analyzed the data from our center. With the traditional cutoff, the sensitivity was 87.2% (197/226) and 96.5% (218/226) before and after stimulation, and specificity was both 100% (25/25), which were close to the results of meta-analysis. Receiver operating characteristic analysis revealed that the optimal cutoff was 1.4 before stimulation and 2.8 after stimulation. With the new cutoff, the sensitivity was 94.7% (214/226) and 97.8% (221/226) while the specificity remained 100% (25/25) before and after stimulation. Among the 7 CD patients (7/226; 3.1%) for whom stimulation was necessary to get correct diagnosis, none has a pituitary lesion &gt;6 mm by magnetic resonance imaging, and their sampling lateralization rate (P = .007) and peak ACTH level at dominant inferior petrosal sinus (P = .011) were lower than those among CD patients with IPS:P &gt;1.4 before stimulation.ConclusionsThe optimal cutoff for IPS:P in BIPSS is different from the commonly-used one. The optimal cutoff value can yield satisfactory accuracy even without stimulation, and stimulation may be unnecessary for those with pituitary adenoma &gt;6 mm.
Gnrh3 Regulates PGC Proliferation and Sex Differentiation in Developing Zebrafish
Authors: Feng Ke , Cui Xuefan , Song Yanlong , Tao Binbin , Chen Ji , Wang Jing , Liu Shaojun , Sun Yonghua , Zhu Zuoyan , Trudeau Vance L , Hu Wei 
Published: November 2019

AbstractGonadotropin-releasing hormone (Gnrh) plays important roles in reproduction by stimulating luteinizing hormone release, and subsequently ovulation and sperm release, ultimately controlling reproduction in many species. Here we report on a new role for this decapeptide. Surprisingly, Gnrh3-null zebrafish generated by CRISPR/Cas9 exhibited a male-biased sex ratio. After the dome stage, the number of primordial germ cells (PGCs) in gnrh3-/- fish was lower than that in wild-type, an effect that was partially rescued by gnrh3 overexpression. A terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) analysis revealed no detectable apoptosis of PGCs in gnrh3-/- embryos. Proliferating PGCs could be detected in wild-type embryos, while there was no detectable signal in gnrh3-/- embryos. Compared with wild type, the phosphorylation of AKT was not significantly different in gnrh3-/- embryos, but the phosphorylation of ERK1/2 decreased significantly. Treatment with a Gnrh analog (Alarelin) induced ERK1/2 phosphorylation and increased PGC numbers in both wild-type and gnrh3-/- embryos, and this was blocked by the MEK inhibitor PD0325901. The relative expression of sox9a, amh, and cyp11b were significantly upregulated, while cyp19a1a was significantly downregulated at 18 days post-fertilization in gnrh3-/- zebrafish. Taken together, these results indicate that Gnrh3 plays an important role in early sex differentiation by regulating the proliferation of PGCs through a MAPK-dependent path.
Neuroeducation:An Approach to Brain Plasticity in Learning
Authors: Sousa Léa Barbosa de , Sá Ingrid Soraya De Oliveira , Oliveira Ana Rebeca Soares Maia de , Carvalho Maria das Graças De , Teixeira Marlene Menezes de Souza 
Published: November 2019

Neuroscience is a field of science that studies the central nervous system (CNS) as well as its relations with the human body. It is intricately implicated in the different fields of knowledge, directly interfering in linguistics, the arts, medicine, among others. Neuropsychology, in turn, deals with the study of the relationship between cognition, behavior and CNS activities, both under normal and pathological conditions. This study aims to discuss aspects of neuroscience in order to clarify aspects related to how the brain learns and how it behaves in the learning process, so that the quality of pedagogical intervention can be reached. Keywords: Neuroeducation, Neuroscience, Learning.