bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Methylprednisolone on Pain Management in Total Knee or Hip Arthroplasty
Authors: Liu Guoming , Gong Min , Wang Youcui , Xiang Zhou 
Published: March 2018

Background:
Total joint arthroplasty (TJA) has been reported to be a successful strategy for patients with advanced osteoarthritis; however, early postoperative pain has become an unresolved issue. Perioperative methylprednisolone (MP) administration in TJA is an important and controversial topic. This study was conducted to assess the efficacy and safety of MP for pain management after total knee or hip arthroplasty (TKA/THA).

Materials and Methods:
PubMed, Embase, and the Cochrane Library were searched for randomized controlled trials comparing MP versus placebo for patients undergoing TKA/THA. Related indicators that reflected the efficacy and safety for pain management were evaluated by meta-analysis.

Results:
Six randomized controlled trials involving a total of 350 patients met the inclusion criteria. The outcomes showed that intravenous MP significantly reduced pain scores at 6 and 24 hours during activity after TKA and THA but local use of MP had no clear benefit in reducing pain scores compared with the control group. There was no significant difference in VAS at 24 hours at rest and 48 hours during activity after TKA and THA. In addition, MP was associated with a reduction of morphine consumption at 24 hours after TKA. Furthermore, patients receiving MP had an obvious inflammatory control and improving postoperative nausea and vomiting and the use of MP was not associated with a significant increase in the risk of complications. There was no significant difference in the range of knee motion and length of hospital stay in both groups.

Conclusions:
This study showed that intravenous MP significantly alleviated early postoperative pain and the incidence of postoperative nausea and vomiting after TKA and THA. For safety, intravenous MP as a promising strategy in rapid recovery to TJA.
Effects of Underrunning Water Bathing and Immersion Tub Bathing on Vital Signs of Newborn Infants
Authors: Ar Işıl , Gözen Duygu 
Published: March 2018

Background:
Newborn infants are susceptible to hypothermia during bathing due to environmental conditions.

Purpose:
This study examined the effects of 2 common newborn bathing methods used in Turkey, underrunning water bathing (URWB) and immersion tub bathing (ITB), on infant heart rate (HR), oxygen saturation, and body temperature.

Methods:
In this randomized controlled study, 44 newborns were allocated to the ITB group and 36 newborns to the URWB group. Body temperature, HR, and oxygen saturation values of the newborns were compared between groups every hour during 4 hours before the bath to evaluate infants' vital sign stability. All measurements were compared at 10, 20, 40, and 60 minutes after the bath too.

Results:
No statistically significant differences were found in vital signs performed prior to bathing as compared with after bathing; however, changes in oxygen saturation at 20 minutes after the bath were significantly higher in the ITB group (P < .05).

Conclusion:
Although both bathing methods decreased overall infant body temperature, ITB positively affected newborn oxygen saturation and HR to a greater degree compared with URWB.

Implications for Practice:
ITB facilitated maintenance of oxygen saturation and HR during the bath and should be preferred for newborn infants to feel more relaxed.

Implications for Research:
These findings indicate a need for additional studies with larger sample sizes to further evaluate the effect of different bathing methods on newborn comfort.
Controlling false discoveries in Bayesian gene networks with lasso regression p-values
Authors: Wang Lingfei , Michoel Tom 
Published: March 2018

AbstractMotivationBayesian networks can represent directed gene regulations and therefore are favored over co-expression networks. However, hardly any Bayesian network study concerns the false discovery control (FDC) of network edges, leading to low accuracies due to systematic biases from inconsistent false discovery levels in the same study.ResultsWe design four empirical tests to examine the FDC of Bayesian networks from three p-value based lasso regression variable selections — two existing and one we originate. Our method, lassopv, computes p-values for the critical regularization strength at which a predictor starts to contribute to lasso regression. Using null and Geuvadis datasets, we find that lassopv obtains optimal FDC in Bayesian gene networks, whilst existing methods have defective p-values. The FDC concept and tests extend to most network inference scenarios and will guide the design and improvement of new and existing methods. Our novel variable selection method with lasso regression also allows FDC on other datasets and questions, even beyond network inference and computational biology.AvailabilityLassopv is implemented in R and freely available at https://github.com/lingfeiwang/lassopv and https://cran.r-project.org/package=lassopv.ContactLingfei.Wang@roslin.ed.ac.ukSupplementary informationSupplementary data are available at Bioinformatics online.
System Biology Modeling with Compositional Microbiome Data Reveals Personalized Gut Microbial Dynamics and Keystone Species
Authors: Li Chenhao , Tucker-Kellogg Lisa , Nagarajan Niranjan 
Published: March 2018

AbstractA growing body of literature points to the important roles that different microbial communities play in diverse natural environments and the human body. The dynamics of these communities is driven by a range of microbial interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood, making it hard to predict the response of the community to different perturbations. With the increasing availability of high-throughput sequencing based community composition data, it is now conceivable to directly learn models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is however affected by several experimental limitations, particularly the compositional nature of sequencing data. We present a new computational approach (BEEM) that addresses this key limitation in the inference of generalised Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference in an expectation maximization like algorithm (BEEM). Surprisingly, BEEM outperforms state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM’s application to previously inaccessible public datasets (due to the lack of biomass data) allowed us for the first time to analyse microbial communities in the human gut on a per individual basis, revealing personalised dynamics and keystone species.
PGP-UK: a research and citizen science hybrid project in support of personalized medicine
Authors:   PGP-UK Consortium, Beck Stephan , Berner Alison M , Bignell Graham , Bond Maggie , Callanan Martin J , Chervova Olga , Conde Lucia , Corpas Manuel , Ecker Simone , Elliott Hannah R , Fioramonti Silvana A , Flanagan Adrienne M , Gaentzsch Ricarda , Graham David , Gribbin Deirdre , Guerra-Assunção José Afonso , Hamoudi Rifat , Harding Vincent , Harrison Paul L , Herrero Javier , Hofmann Jana , Jones Erica , Khan Saif , Kaye Jane , Kerr Polly , Libertini Emanuele , McCormack Laura , Moghul Ismail , Pontikos Nikolas , Rajanayagam Sharmini , Rana Kirti , Semega-Janneh Momodou , Smith Colin P , Strom Louise , Umur Sevgi , Webster Amy P , Wint Karen , Wood John N 
Published: March 2018

AbstractMolecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited ten participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes. Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.
Hampered motility promotes the evolution of wrinkly phenotype in Bacillus subtilis
Authors: Richter Anne , Hölscher Theresa , Pausch Patrick , Sehrt Tim , Brockhaus Franziska , Bange Gert , Kovács Ákos T. 
Published: March 2018

SummarySelection for a certain trait in microbes depends on the genetic background of the strain and the selection pressure of the environmental conditions acting on the cells. In contrast to the sessile state in the biofilm, various bacterial cells employ flagellum-dependent motility under planktonic conditions suggesting that the two phenotypes are mutually exclusive. However, flagellum dependent motility facilitates the prompt establishment of floating biofilms on the air-medium interface, called pellicles. Previously, pellicles of B. subtilis were shown to be preferably established by motile cells, causing a reduced fitness of non-motile derivatives in the presence of the wild type strain. Here, we show that lack of fully assembled flagella promotes the evolution of matrix overproducers that can be distinguished by the characteristic wrinkled colony morphotype. The wrinkly phenotype is associated with amino acid substitutions in the master repressor of biofilm-related genes, SinR. By analyzing one of the mutations, we show that it alters the tetramerization and DNA binding properties of SinR, allowing an increased expression of the operon responsible for exopolysaccharide production. Finally, we demonstrate that the wrinkly phenotype is advantageous when cells lack flagella, but not in the wild type background.Graphical AbstractAbbreviated SummaryDuring biofilm establishment at the air-liquid interface, Bacillus subtilis evolves matrix overproducers with a wrinkly colony phenotype (WS). This is caused by mutations in the regulator SinR which alter its dimerization and DNA interaction properties. The matrix overproducers appear mostly in a non-motile mutant where they possess a competitive advantage for biofilm formation, which is not present in the wild type background.
Ecological and evolutionary consequences of viral plasticity
Authors: Choua Melinda , Bonachela Juan A. 
Published: March 2018

AbstractViruses can infect any organism. Because viruses use the host machinery to replicate, their performance depends on the host physiological state. For bacteriophages, this host-viral performance link has been characterized empirically and with intracellular theories. Such theories are too detailed to be included in models that study host-phage interactions in the long term, which hinders our understanding of systems that range from pathogens infecting gut bacteria to marine phage shaping present and future oceans. Here, we combined data and models to study the short- and long-term consequences that host physiology has on bacteriophage performance. We compiled data showing the dependence of lytic-phage traits on host growth rate (viral phenotypic “plasticity”) to deduce simple expressions representing such plasticity. We included these expressions in a standard host-phage model, to understand how viral plasticity can break the expected evolutionary trade-off between infection time and viral offspring number. Furthermore, viral plasticity influences dramatically dynamic scenarios (e.g. sudden nutrient pulses or host starvation). We show that the effect of plasticity on offspring number, not generation time, drives the phage ecological and evolutionary dynamics. Standard models do not account for this plasticity, which handicaps their predictability in realistic environments. Our results highlight the importance of viral plasticity to unravel host-phage interactions, and the need of laboratory and field experiments to characterize viral plastic responses across systems.
A thermo-responsive plasmid for biconditional protein expression
Authors: Lermant Agathe , Magnanon Alicia , Silvain Alexandra , Lubrano Paul , Lhuissier Marie , Dury Camille , Follenfant Maryne , Guiot Zoe , Christien Gaëtan , Coudert Pauline , Arvor Antoine , Sportich Maxime , Vuillaume Gabrielle , Delettre Nicolas , Henry Julie , Lafon Eliott , Lhernould Thomas , Richard Fanny , Ismail Alexandre 
Published: March 2018

AbstractHere we develop a temperature sensitive expression vector that allows the selective production of distinct proteins over different temperature ranges with a single plasmid. We use theE. colicold shock translational control system (the cspA 5’Untranslated Transcribed Region - UTR) to drive the expression of a desired protein below a certain temperature threshold, and the lambda phage pL/cI857 transcriptional repressor system to drive the expression of a different protein above a certain temperature threshold. In this developmental work we use the chromogenic reporter proteins amilCP (blue chromoprotein) and monomeric red fluorescent protein (mRFP) to assess the function of the thermo-sensitive regulatory sequences over the desired temperature ranges. Our results show temperature dependent response of the cold shock regulatory sequence. However, our sequence design for the heat shock regulatory sequence did not give the intended result. The integration of these two temperature sensitive elements into a single plasmid awaits the re-design of the heat shock sequence.
PRY-1/AXIN signaling regulates lipid metabolism inCaenorhabditis elegans
Authors: Ranawade Ayush , Mallick Avijit , Gupta Bhagwati P 
Published: March 2018

SUMMARYThe nematodeCaenorhabditis elegansis a leading animal model to study how signaling pathway components function in conserved biological processes. Here, we describe the role of an Axin family member,pry-1, in lipid metabolism. As a central component of the canonical Wnt signaling pathway,pry-1acts as a scaffold to multiprotein destruction complex that negatively regulates the expression of Wnt target genes. A genome-wide transcriptome profiling ofpry-1mutant revealed genes associated with aging and lipid metabolism such as vitellogenins (yolk lipoproteins), fatty acid desaturases, lipases, and fatty acid transporters. Consistent with this we found thatpry-1is crucial for the normal adult lifespan and maintenance of lipid levels. Knock-downs ofvitgenes inpry-1mutant background restored lipid levels, suggesting that Vitellogenins contribute to PRY-1 function in lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomics analysis provided evidence that the fatty acid synthesis is reduced inpry-1mutants. In agreement with this an exogenous supply of oleic acid restored depleted lipids in somatic tissues of worms. Overall, our findings demonstrate that PRY-1/Axin signaling is essential for lipid metabolism and involves regulation of yolk proteins.
Low dose resveratrol promotes hypertrophy in wildtype skeletal muscle and reduces damage in skeletal muscle of exercised mdx mice
Authors: Woodman KG , Coles CA , Toulson SL , Knight M , McDonagh M , Lamandé SR , White JD 
Published: March 2018

AbstractDuchenne muscular dystrophy (DMD) is a progressive and fatal neuromuscular disorder for which there is no treatment. Therapies to restore dystrophin deficiency are not ready for clinical use and long-term efficiency is yet to be established. Therefore, there is a need to develop alternative strategies to treat DMD. Resveratrol is a nutraceutical with anti-inflammatory properties and previous studies have shown that high doses can benefit mdx mice. We treated 4-week-old mdx and wildtype mice with low-dose resveratrol (5mg/kg bodyweight/day) for 15 weeks. A voluntary exercise protocol was added to test if low dose resveratrol could reduce exercise-induced damage. We showed that resveratrol promoted skeletal muscle hypertrophy in the wildtype mice. There was no change in markers of pathology in the mdx mice; however, the low-dose resveratrol reduced exercised induced damage. Gene expression of immune cell markers such as CD86, CD163 and PCNA was reduced; however signalling targets associated with resveratrol’s mechanism of action of action including SIRT1 and NF-κB were unchanged. In conclusion, low-dose resveratrol was not effective in reducing disease pathology; however, its ability to promote hypertrophy in wildtype skeletal muscle could have direct applications to the livestock industry or in sports medicine.
DSeg: A dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures
Authors: Zhang Hanqing , Söderholm Niklas , Sandblad Linda , Wiklund Krister , Andersson Magnus 
Published: March 2018

AbstractMotivationQuantitative image analysis of growing filamentous fungi and prokaryotes are important to detect and evaluate morphological effects of growth conditions, compounds and mutations. However, analysis of time-series image data is often limited by the ability of the algorithms to accurately segment structures that are complicated or if an organism is within a crowded population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data as well as single images to find multiple filamentous structures e.g., filamentous prokaryotes, yeasts and molds using a dynamic segmentation approach. DSeg automatically segments and analyzes objects, includes drift correction, and outputs statistical data such as persistence length, growth rate and growth direction.Availability and implementationDSeg is a free open-source program written in MATLAB. DSeg can be downloaded as a package from https://sourceforge.net/projects/dseg-software.Contactmagnus.andersson@umu.se and hanqing.zhang@umu.seSupplementary informationSupplementary data are available at online.
Cystinosin regulates kidney inflammation through its interaction with galectin-3
Authors: Lobry Tatiana , Miller Roy , Nevo Nathalie , Rocca Celine J. , Zhang Jinzhong , Catz Sergio D. , Moore Fiona , Bailleux Anne , Guerrera Ida Chiara , Gubler Marie-Claire , Wilson Cheung W. , Mak Robert H. , Montier Tristan , Antignac Corinne , Cherqui Stephanie 
Published: March 2018

AbstractInflammation is implicated in the pathogenesis of many disorders. Here, we show that cystinosin, protein defective in the lysosomal storage disorder cystinosis, is a critical regulator of galectin-3 during inflammation. Cystinosis is a lysosomal storage disorder and despite ubiquitous expression of cystinosin, kidney is the primary organ to be impacted by the disease. Here, we show that cystinosin interacts with galectin-3 and enhances its lysosomal localization and degradation. Galectin-3 is also found overexpressed in the kidney of the mouse model of cystinosis,Ctns-/-mice. Absence of galectin-3 inCtns-/-mice led to a better renal function and structure, and decreased macrophage/monocyte infiltration in the kidney. Finally, galectin-3 interacts with a protein implicated in the recruitment of monocytes and macrophages during inflammation, Monocyte Chemoattractant Protein-1 (MCP1), that was found increased in the serum ofCtns-/-mice. These findings highlight a new role of cystinosin and galectin-3 interaction in inflammation, providing a mechanistic explanation for kidney disease pathogenesis in cystinosis, which may lead to the identification of new drug targets to delay its progression.
Comparing methanol-glucose and dimethyl-sulfoxide based extender for milt cryopreservation of brown trout (Salmo trutta)
Authors: Nusbaumer David , Marques da Cunha Lucas , Wedekind Claus 
Published: March 2018

AbstractThe potential importance of sperm cryopreservation for aquaculture and conservation management seems still undervalued, probably because the available protocols often lead to reduced fertilization success. We experimentally compared the effectiveness of two different freezing extenders for cryopreservation of brown trout (Salmo trutta) semen, controlling for possible male and female effects. The methanol-glucose based extender that we tested was significantly more effective than a common dimethyl-sulfoxide based extender (a commercial cryopreservation kit). We then studied the effectiveness of the methanol-glucose based extender at different sperm-egg ratios and found no significant differences in fertilization ability of fresh and cryopreserved milt at a sperm-egg ratio of at least 110,000:1. We conclude that brown trout sperm cryopreserved with this extender can be used even at low sperm-egg ratios without significant effects on fertilization rates.
Intronic non-coding RNAs within ribosomal protein coding genes can regulate biogenesis of yeast ribosome
Authors: Pande Akshara , Sharma Rani , Iyengar Bharat Ravi , Scaria Vinod , Pillai Beena , Brahmachari Samir K 
Published: March 2018

AbstractThe genome of the budding yeast (Saccharomyces cerevisiae) has selectively retained introns in ribosomal protein coding genes. The function of these introns has remained elusive in spite of experimental evidence that they are required for the fitness of yeast. Here, we computationally predict novel small RNAs that arise from the intronic regions of ribosomal protein (RP) coding genes in Saccharomyces cerevisiae. Further, we experimentally validated the presence of seven intronic small RNAs (isRNAs). Computational predictions suggest that these isRNAs potentially bind to the ribosomal DNA (rDNA) locus or the corresponding rRNAs. Several isRNA candidates can also interact with transcripts of transcription factors and small nucleolar RNAs (snoRNAs) involved in the regulation of rRNA expression. We propose that the isRNAs derived from intronic regions of ribosomal protein coding genes may regulate the biogenesis of the ribosome through a feed-forward loop, ensuring the coordinated regulation of the RNA and protein components of the ribosomal machinery. Ribosome biogenesis and activity are fine-tuned to the conditions in the cell by integrating nutritional signals, stress response and growth to ensure optimal fitness. The enigmatic introns of ribosomal proteins may prove to be a novel and vital link in this regulatory balancing act.