bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asp30 of Aspergillus oryzae cutinase CutL1 is involved in the ionic interaction with fungal hydrophobin RolA
Authors: Terauchi Yuki , Kim Yoon-Kyung , Tanaka Takumi , Nanatani Kei , Takahashi Toru , Abe Keietsu 
Published: May 2017

Abstract
Aspergillus oryzae hydrophobin RolA adheres to the biodegradable polyester polybutylene succinate-co-adipate (PBSA) and promotes PBSA degradation by interacting with A. oryzae polyesterase CutL1 and recruiting it to the PBSA surface. In our previous studies, we found that positively charged amino acid residues (H32, K34) of RolA and negatively charged residues (E31, D142, D171) of CutL1 are important for the cooperative ionic interaction between RolA and CutL1, but some other charged residues in the triple mutant CutL1-E31S/D142S/D171S are also involved. In the present study, on the basis of the 3D-structure of CutL1, we hypothesized that D30 is also involved in the CutL1–RolA interaction. We substituted D30 with serine and performed kinetic analysis of the interaction between wild-type RolA and the single mutant CutL1-D30S or quadruple mutant CutL1-D30S/E31S/D142S/D171S by using quartz crystal microbalance. Our results indicate that D30 is a novel residue involved in the ionic interaction between RolA and CutL1.
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
Authors: Del Carratore Francesco , Jankevics Andris , Eisinga Rob , Heskes Tom , Hong Fangxin , Breitling Rainer 
Published: May 2017

AbstractMotivationThe Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable.ResultsWe implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P-value estimation methods have been replaced by exact methods, providing faster and more accurate results.Availability and implementationRankProd 2.0 is available at Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html) and as part of the mzMatch pipeline (http://www.mzmatch.sourceforge.net).Supplementary informationSupplementary data are available at Bioinformatics online.
Epidural Neostigmine versus Fentanyl to Decrease Bupivacaine Use in Patient-controlled Epidural Analgesia during Labor
Authors: Booth Jessica L. , Ross Vernon H. , Nelson Kenneth E. , Harris Lynnette , Eisenach James C. , Pan Peter H. 
Published: May 2017

Abstract

Background
The addition of opioids to epidural local anesthetic reduces local anesthetic consumption by 20% but at the expense of side effects and time spent for regulatory compliance paperwork. Epidural neostigmine also reduces local anesthetic use. The authors hypothesized that epidural bupivacaine with neostigmine would decrease total hourly bupivacaine use compared with epidural bupivacaine with fentanyl for patient-controlled epidural analgesia.

Methods
A total of 215 American Society of Anesthesiologists physical status II, laboring parturients requesting labor epidural analgesia consented to the study and were randomized to receive 0.125% bupivacaine with the addition of either fentanyl (2 μg/ml) or neostigmine (2, 4, or 8 μg/ml). The primary outcome was total hourly local anesthetic consumption, defined as total patient-controlled epidural analgesia use and top-ups (expressed as milliliters of 0.125% bupivacaine) divided by the infusion duration. A priori analysis determined a group size of 35 was needed to have 80% power at α = 0.05 to detect a 20% difference in the primary outcome.

Results
Of 215 subjects consented, 151 patients were evaluable. Demographics, maternal and fetal outcomes, and labor characteristics were similar among groups. Total hourly local anesthetic consumption did not differ among groups (P = 0.55). The total median hourly bupivacaine consumption in the fentanyl group was 16.0 ml/h compared with 15.3, 14.6, and 16.2 ml/h in the 2, 4, and 8 μg/ml neostigmine groups, respectively (P = 0.55).

Conclusions
The data do not support any difference in bupivacaine requirements for labor patient-controlled epidural analgesia whether patients receive epidural bupivacaine with 2 to 8 μg/ml neostigmine or epidural bupivacaine with 2 μg/ml fentanyl.
Nodular Sclerodermatous Chronic Cutaneous Graft-Versus-Host Disease (GvHD): A New Clinicopathological Variant of Cutaneous Sclerodermatous GvHD Resembling Nodular/Keloidal Scleroderma
Authors: Prieto-Torres Lucía , Boggio Francesca , Gruber-Wackernagel Alexandra , Cerroni Lorenzo 
Published: May 2017

Abstract:
Cutaneous chronic graft-versus-host disease (GvHD) has a broad spectrum of clinicopathological presentations, the most common ones being poikiloderma, lichen planus–like eruptions, lichen sclerosus–like lesions, morphea-like plaques, and deep sclerosis. New forms of chronic cutaneous GvHD with different clinicopathological characteristics have been described, most of them mimicking cutaneous manifestations of autoimmune diseases. We report the case of a 35-year-old man who underwent allogenic stem cell transplantation for a therapy-associated acute myeloid leukemia and developed an acute GvHD with involvement of skin and gastrointestinal tract. He subsequently presented with chronic sclerodermatous cutaneous GvHD, followed by the appearance of indurated erythematous papules and plaques located on his back, resembling the nodular/keloidal form of cutaneous scleroderma on both clinical and histopathological grounds. This peculiar clinicopathologic presentation of chronic cutaneous GvHD was never described previously.
Annular Lichenoid Dermatitis (of Youth): Report of a Case With Lichen Planus-Like Features
Authors: Cesinaro Anna M. 
Published: May 2017

Abstract:
Annular lichenoid dermatitis of youth (ALDY), a dermatosis with peculiar clinical and pathological features, represents still a debated entity, given its similarity, among others, with mycosis fungoides. A case of ALDY in a 50-year-old male patient is reported. Clinically, the patient presented an oval scleroderma-like plaque on the right flank. Histology and immunohistochemistry showed the classic appearance described in ALDY. T-cell receptor rearrangement was absent. Interestingly, a focus consistent with lichen planus was observed. The lesion resolved with topical steroids and at a follow-up of 24 months no recurrence has been registered. The case described herein supports the hypothesis that ALDY is a reactive lichenoid dermatosis, closely related to lichen planus.
Favorable Outcomes Using an eHealth Approach to Promote Physical Activity and Nutrition Among Young African American Women
Authors: Staffileno Beth A. , Tangney Christy C. , Fogg Louis 
Published: May 2017

Background:
Internet and mobile devices are widely used and provide alternative approaches for promoting healthy lifestyles, yet less information is available describing outcomes of these approaches when used with young African American (AA) women at risk for developing hypertension.

Objective:
In this study, we evaluated a Web-based, culturally relevant lifestyle change intervention targeting AA women (referred to as the eHealth study).

Methods:
African American women, aged 18 to 45 years, with untreated prehypertension and Internet access were eligible for a 12-week study that incorporated social cognitive theory strategies. Participants were randomized to (1) lifestyle physical activity (PA) or (2) Dietary Approaches to Stop Hypertension (DASH) online education modules.

Results:
The 14 DASH and 12 PA participant attributes were similar at baseline. The DASH participants had a significant change in total DASH score (P = .001) and large effect sizes for DASH components (vegetables, 0.84; nonfat dairy, 0.71; fruit, 0.62). The PA participants had a favorable change (+39%) in pedometer steps (P = .055). With respect to weight change, a large effect size was observed for PA (0.84) and smaller for DASH participants (0.18). Seventy-one percent of DASH and 48% of PA participants completed program activities, corresponding to a moderate difference in program engagement between groups (d = 0.58).

Conclusion:
Our eHealth platform provides an alternative approach for reaching young AA women and was successful with respect to improving PA and dietary behaviors. Furthermore, the eHealth approach has the potential as a powerful program for changing health behaviors for other at-risk populations.
A Survey of Genome Editing Activity for 16 Cpf1 orthologs
Authors: Zetsche Bernd , Strecker Jonathan , Abudayyeh Omar O. , Gootenberg Jonathan S. , Scott David A. , Zhang Feng 
Published: May 2017

SummaryThe recently discovered class 2 CRISPR-Cas endonuclease Cpf1 offers several advantages over Cas9, including the ability to process its own array and requirement for just a single RNA guide. These attributes make Cpf1 promising for many genome engineering applications. To further expand the suite of Cpf1 tools available, we tested 16 Cpf1 orthologs for activity in eukaryotic cells. Four of these new enzymes demonstrated targeted activity, one of which, fromMoraxella bovoculiAAX11_00205 (Mb3Cpf1), exhibited robust indel formation. We also show that Mb3Cpf1 displays some tolerance for a shortened PAM (TTN versus the canonical Cpf1 PAM TTTV). The addition of these enzymes to the genome editing toolbox will further expand the utility of this powerful technology.
The N-terminal domain of ALS-linked TDP-43 assembles without misfolding
Authors: Tsoi Phoebe S. , Choi Kyoungjae J. , Leonard Paul G. , Sizovs Antons , Moosa Mahdi Muhammad , MacKenzie Kevin R. , Ferreon Josephine C. , Ferreon Allan Chris M. 
Published: May 2017

AbstractTDP-43 forms inclusions in several neurodegenerative diseases, and both its N- and C-terminal domains are implicated in this process. We show that the folded TDP-43 N-terminal domain oligomerizes under physiological conditions and propose that, in full-length TDP-43, association between folded N-terminal domains enhances the propensity of the intrinsically unfolded C-terminal domains to drive pathological aggregation.
Pathway crosstalk enables cells to interpret TGF-β duration
Authors: Zhang Jingyu , Tian Xiao-Jun , Chen Yi-Jiun , Wang Weikang , Watkins Simon , Xing Jianhua 
Published: May 2017

AbstractThe detection and transmission of the temporal quality of intracellular and extracellular signals is an essential cellular mechanism. It remains largely unexplored how cells interpret the duration information of a stimulus. In this paper, through an integrated quantitative and computational approach we demonstrate that crosstalk among multiple TGF-β activated pathways forms a relay from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. This transaction is smoothed and accelerated by another temporal switch from elevated cytosolic GSK3 enzymatic activity to reduced nuclear GSK3 enzymatic activity. The intertwined network places SNAIL1 as a key integrator of information from TGF-β signaling subsequently distributed through upstream divergent pathways; essentially cells generate a transient or sustained expression of SNAIL1 depending on TGF-β duration. Other signaling pathways may use similar network structure to encode duration information.
Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode
Authors: Nguyen Son Hoang , Duarte Tania , Coin Lachlan J. M. , Cao Minh Duc 
Published: May 2017

AbstractMotivationThe recently introduced barcoding protocol to Oxford Nanopore sequencing has increased the versatility of the technology. Several bioinformatic tools have been developed to demultiplex the barcoded reads, but none of them support the streaming analysis. This limits the use of pooled sequencing in real-time applications, which is one of the main advantages of the technology.ResultsWe introduced npBarcode, an open source and cross platform tool for barcode demultiplex in streaming fashion. npBarcode can be seamlessly integrated into a streaming analysis pipeline. The tool also provides a friendly graphical user interface through npReader, allowing the real-time visual monitoring of the sequencing progress of barcoded samples. We show that npBarcode achieves comparable accuracies to the other alternatives.AvailabilitynpBarcode is bundled in Japsa - a Java tools kit for genome analysis, and is freely available athttps://github.com/hsnguyen/npBarcode.
Deep Phenotyping: Deep Learning for Temporal Phenotype/Genotype Classification
Authors: Namin Sarah Taghavi , Esmaeilzadeh Mohammad , Najafi Mohammad , Brown Tim B. , Borevitz Justin O. 
Published: May 2017

AbstractHigh resolution and high throughput, genotype to phenotype studies in plants are underway to accelerate breeding of climate ready crops. Complex developmental phenotypes are observed by imaging a variety of accessions in different environment conditions, however extracting the genetically heritable traits is challenging. In the recent years, deep learning techniques and in particular Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs) and Long-Short Term Memories (LSTMs), have shown great success in visual data recognition, classification, and sequence learning tasks. In this paper, we proposed a CNN-LSTM framework for plant classification of various genotypes. Here, we exploit the power of deep CNNs for joint feature and classifier learning, within an automatic phenotyping scheme for genotype classification. Further, plant growth variation over time is also important in phenotyping their dynamic behavior. This was fed into the deep learning framework using LSTMs to model these temporal cues for different plant accessions. We generated a replicated dataset of four accessions of Arabidopsis and carried out automated phenotyping experiments. The results provide evidence of the benefits of our approach over using traditional hand-crafted image analysis features and other genotype classification frameworks. We also demonstrate that temporal information further improves the performance of the phenotype classification system.
A cell culture platform forcryptosporidiumthat enables long-term cultivation and new tools for the systematic investigation of its biology
Authors: Miller Christopher N. , Jossé Lyne , Brown Ian , Blakeman Ben , Povey Jane , Yiangou Lyto , Price Mark , Cinatl Jindrich , Xue Wei-Feng , Michaelis Martin , Tsaousis Anastasios D. 
Published: May 2017

AbstractCryptosporidiumparasites are a major cause of diarrhoea that pose a particular threat to children in developing areas and immunocompromised individuals. Curative therapies and vaccines are lacking. Currently,Cryptosporidiumoocysts for research must be freshly produced in animals and cannot be long-term stored. Here, we show that COLO-680N cells infected with two differentCryptosporidium parvumstrains (Moredun, Iowa) produce sufficient infectious oocysts to infect subsequent cultures. Oocyst identity was confirmed by specific staining (Crypt-a-glo, Vicia Villosa lectin, Sporo-glo), PCR-based amplification ofCryptosporidium-specific genes, lipidomics fingerprinting, and atomic force microscopy (AFM). Antibody-stained oocysts produced unstained oocysts confirming production of novel oocysts. Infected cultures could be cryoconserved and continued to produce infectious oocysts after resuscitation. Transmission electron microscopy identified all keyCryptosporidiumlife cycle stages. Infected cultures produced thick-walled (primarily involved inCryptosporidiumtransmission between organisms) and thin-walled oocysts (important forCryptosporidiumpropagation within a host/tissue) as indicated by DAPI staining (only thin-walled oocysts are permeable to DAPI staining, thus allowing visualisation of sporozoites) and AFM. In conclusion, we present a novel, easy-to-handle cell culture system that enables the propagation, cryopreservation and detailed investigation ofCryptosporidiumat a laboratory scale. Its availability will accelerate research onCryptosporidiumand the development of anti-Cryptosporidiumdrugs.
Aubergine and piRNAs repress the proto-oncogeneCblfor germline stem cell self-renewal
Authors: Rojas-Ríos Patricia , Chartier Aymeric , Simonelig Martine 
Published: May 2017

AbstractPIWI proteins have essential roles in germ cells and stem cell lineages. InDrosophila, Piwi is required in somatic niche cells and germline stem cells (GSCs) for GSC self-renewal and differentiation. Whether and how other PIWI proteins are involved in GSC biology remains unknown. Here, we show that Aubergine (Aub), another PIWI protein, is intrinsically required in GSCs for their self-renewal and differentiation. Aub loading with piRNAs is essential for these functions. The major role of Aub is in self-renewal and depends on mRNA regulation. We identify theCblproto-oncogene, a regulator of mammalian hematopoietic stem cells, as a novel GSC differentiation factor. Aub repressesCblmRNA translation for GSC self-renewal, and does so through recruitment of the CCR4-NOT complex. This study reveals the role of piRNAs and PIWI proteins in translational repression for stem cell homeostasis and highlights piRNAs as major post-transcriptional regulators in key developmental decisions.
Challenging deprivation of liberty: advocating for your rights
Authors: O’Kane Niall , Hall Ian , Eyeoyibo Mo 
Published: May 2017

Purpose
The purpose of this paper is to review a case of a man with a mild learning disability and autistic spectrum disorder who successfully appealed against a Deprivation of Liberty Safeguards authorisation under English law.

Design/methodology/approach
The authors wanted to identify the factors contributing to the individual’s deprivation of liberty and subsequent successful appeal. The authors examined the accounts from the experts involved on each side of the case including different views on the person’s capacity to make certain decisions. The authors examined several of the individual’s psychological and psychiatric assessments. The authors interviewed the individual on two occasions: once during the appeals process, and following his successful appeal.

Findings
The authors identified several reasons as to why the individual was successful in appealing against the Deprivation of Liberty Safeguards. First, the individual was able to seek legal support to appeal independently. Second, experts involved on each side of the case had differing opinions regarding capacity to make certain decisions. Third, the indication for the Deprivation of Liberty Safeguards was subsequently declared not valid. Finally, the authors found that the quality of life and psychological well-being for the individual improved following removal of restrictions.

Practical implications
The authors highlight the wider issues relating to an individuals’ rights to challenge authorisations in the Court of Protection as well as to future considerations and directions of the Deprivation of Liberty Safeguards legislation in light of evolving case law.

Social implications
The authors highlight the importance of empowering patients in matters relating to their care and treatment, as well as protecting their human rights, dignity and autonomy.

Originality/value
The authors examine the barriers to challenging Deprivation of Liberty Safeguards authorisation and the ever-evolving Deprivation of Liberty Safeguards process.
Social networking, identity and sexual behaviour of undergraduate students in Nigerian universities
Authors: Nwagwu Williams Ezinwa 
Published: May 2017

Purpose
The purpose of this study was to examine how the identity of undergraduates who use social networking sites in selected Nigerian universities influences the prediction of their sexual behaviour.

Design/methodology/approach
A questionnaire survey was used to collect data from 388 students from three public universities in Nigeria.

Findings
Sex and age exerted sufficient influence on the youth’s sexual behaviour, but the identity variables seemed only to increase the tendency of younger males to form intimate relationship with partners. Specifically, young males who maintain high level of social relationships have a high tendency of developing intimate relationship with partners.

Research limitations/implications
This study that deployed identity variables provides wide-ranging information on how identity moderates sexual behaviour in the presence of traditional predictors of demographic characteristics and social networking.

Practical implications
This study demonstrates that identity has a very strong influence of the predictive power of sex and age on sexual behaviour.

Originality/value
This study is the first that examined sexual behaviour, identity and social networking together.
Why should I pay for e-books?
Authors: Zhang Min , Zhu Mingxing , Liu Xiaotong , Yang Jun 
Published: May 2017

Purpose
Because mobile phones offer a new, affordable and easy-to-use portal to reading material, mobile reading is emerging as the most ultra-modern reading approach. From the perspective of mobile reading service providers, knowledge of customer purchase, and consumption behaviour is critical for their survival and success. This paper aims to provide insights into the factors that influence the purchase e-books.

Design/methodology/approach
Following means-end chain theory, the prospect theory and elaboration likelihood model, a structural equation model is proposed to investigate and identify key factors that drive the purchase intention of experienced mobile readers. In the theoretical model, utilitarian value (UV) and hedonic value (HV) are supposed as formative second-order constructs formed by related payoff.

Findings
Both UV and HV are positively associated with readers’ purchase intention. However, there are no big differences between these two path coefficients. People seem to perceive relatively low payment risk although perceived risk could still negatively affect purchase intention. As a predictor of purchase intention, UV is less important when risk perception increases or when involvement (IV) decreases. Furthermore, this study illustrates that uniqueness and convenience (CV) are significant components of UV, whereas curiosity and flow are components of HV.

Practical implications
Mobile reading providers should highlight the professional and specificity of app such as beautiful cover, page setup that similar to real books and so on. Readers should be allowed to post real-time reviews and communicate with others to improve their sense of satisfaction, participation and belonging. The payment process should be concise and simple through which readers can save their purchase time and effort. Mobile reading service providers should provide trustworthy payment approaches, especially third-party platform and guarantee the CV and safety of payment activity.

Originality value
By focusing on the impacts of relationships among UV, HV, perceived risk and IV to purchase intention, this paper not only provides a theoretical understanding of mobile reading purchase behaviour but also offers practical insights to reading material manufactures and app developers for promoting such a process.