bluuebunny/crossref_metadata_2025 huggingface dataset:
tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks
Authors: Spurney Ryan J. , Van den Broeck Lisa , Clark Natalie M. , Fisher Adam P. , de Luis Balaguer Maria A. , Sozzani Rosangela
Published: October 2019

Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA‐sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user‐friendly platform that can process raw RNA‐sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree‐based pipeline, rtp‐star. We obtained time‐course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp‐star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild‐type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell‐type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non‐bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.
Evaluation of riboflavin photochemical treatment for inactivation of HCT116 tumor cells mixed in simulative intraoperative salvage blood
Authors: Yu Yang , Yang Lu , He Chunyu , Tai Shengfei , Ma Chunya , Yang Tianxin , Wang Deqing
Published: October 2019

BACKGROUND

Radiation and filtration have achieved satisfactory results in inactivation or removal of tumor cells mixed in salvage blood, but some drawbacks remain. This study evaluated the inactivation on HCT116 cells mixed in simulative salvage blood by riboflavin photochemical treatment.

METHODS

HCT116 cells were added to the whole blood to simulate contaminated salvaged blood. The mixed blood was added with riboflavin of 50 μmol/L final concentration and illuminated by ultraviolet light. The samples were divided into control group and Experimental Groups 1 (18 J/cm2), 2 (23.4 J/cm2), and 3 (28.8 J/cm2). An autotransfusion system (Cell Saver Elite, Haemonetics) was used to simulate the intraoperative blood salvage procedure to deal with whole blood. The apoptosis rate and tumorigenicity of HCT116 cells and the superimposed damage to red blood cells (RBCs) were evaluated.

RESULTS

The apoptosis rates of HCT116 in Experimental Groups 1, 2, and 3 were much higher than that in the control group. Tumor growth was found in the control group, but no tumor growth was found in the three experimental groups. The hemolysis rates in the three experimental groups were significantly higher than that in the control group, but much lower than the quality standard of RBCs at the end of preservation. The concentration of adenosine triphosphate in RBCs was comparable in the control and experimental groups.

CONCLUSION

Riboflavin at a 50 μmol/L final concentration and 18 J/cm2 ultraviolet illumination can effectively inactivate HCT116 cells in salvaged blood, with minimum damage to the structure and function of RBCs, and the main quality indexes of salvaged RBCs were within the standard range.
Allogeneic platelet‐rich plasma (PRP) is superior to platelets or plasma alone in stimulating fibroblast proliferation and migration, angiogenesis, and chemotaxis as relevant processes for wound healing
Authors: van der Bijl Ivo , Vlig Marcel , Middelkoop Esther , de Korte Dirk
Published: October 2019

BACKGROUND

Platelet‐rich plasma (PRP) is frequently used in the treatment of acute and chronic wounds. One of the major problems concerning the use of PRP is the absence of a well‐characterized and standardized product, which leads to a high variety in study outcomes. Therefore, more studies on the composition and standardization of PRP in wound healing are needed.

STUDY DESIGN AND METHODS

Platelet concentrates derived from healthy blood donors were made in plasma (PC‐plasma) or platelet additive solution (PC‐PAS). The effects of PC‐plasma, PC‐PAS, and plasma were then tested on proliferation, differentiation, and migration of fibroblasts, as well as sprouting of endothelial cells in fibrin gels and chemotaxis of white blood cells (WBCs).

RESULTS

PC‐plasma stimulates the migration and proliferation of human dermal fibroblasts more than plasma or platelets alone. Furthermore, platelet factors decrease the expression of α‐smooth muscle actin in dermal fibroblast cultures. PC‐plasma also stimulates sprouting of endothelial cells. Finally, PC‐plasma also acts as a strong chemoattractant for WBCs.

CONCLUSIONS

Allogeneic PC‐plasma has beneficial effects on various aspects of wound healing in vitro and is superior to plasma or platelets alone. PC‐plasma is an attractive candidate for further in vivo evaluation.
Shipping cost and development of the landlocked developing countries: Panel evidence from the common correlated effects approach
Authors: Pham Ngoc Thien Anh , Sim Nicholas
Published: October 2019

We estimate the impact of shipping cost on development for landlocked developing countries (LLDCs). Since container trade is important to them, we construct a country‐specific measure of shipping cost, called HarpexCost, which combines the global cost of container shipping with information on how exposed to container shipping each LLDC is. We employ the common correlated effects (CCE) estimator of Pesaran (Econometrica, 2006; 55: 967) to first estimate the impact of HarpexCost on the LLDCs’ development, and then recover the actual impact of shipping cost from these estimates. Overall, we observe that shipping cost has large negative effects on the LLDCs. Building upon these results, we provide new estimates on the cost of landlockedness and how trade benefits their development.
Antimicrobial activity of thyme oil, oregano oil, thymol and carvacrol against sensitive and resistant microbial isolates from dogs with otitis externa
Authors: Sim Jowenna Xiao Feng , Khazandi Manouchehr , Chan Wei Yee , Trott Darren J. , Deo Permal
Published: October 2019

Background

Multidrug‐resistant pathogens present a major global challenge in antimicrobial therapy and frequently complicate otitis externa in dogs.

Hypothesis/Objectives

In vitro efficacy of oregano oil, thyme oil and their main phenolic constituents against bacterial and fungal isolates associated with canine otitis externa were investigated. It was hypothesized that the main phenolic components would have greater antimicrobial activity compared to the relative essential oil.

Methods and materials

Antimicrobial susceptibility testing was performed using broth microdilution with spot‐plating technique to determine minimum inhibitory and bactericidal/fungicidal concentrations (MICs, MBCs and MFCs). A time–kill kinetics assay was performed to confirm the bactericidal and fungicidal activity of the oils and their phenolic constituents. One hundred bacterial and fungal isolates, including meticillin‐susceptible Staphylococcus pseudintermedius (n = 10), meticillin‐resistant S. pseudintermedius (n = 10), β‐haemolytic Streptococcus spp. (n = 20), Pseudomonas aeruginosa (n = 20; including 10 isolates resistant to one or two antimicrobials), Proteus mirabilis (n = 20) and Malassezia pachydermatis (n = 20) from dogs with otitis externa were used.

Results

Oregano oil, thyme oil, carvacrol and thymol exhibited antibacterial activity against all bacterial and fungal isolates tested. MIC90 values ranged from 0.015 to 0.03% (146–292 μg/mL) for the Gram‐positive bacteria and P. mirabilis. For P. aeruginosa and M. pachydermatis, MIC90 values ranged from 0.09 to 0.25% (800–2,292 μg/mL).

Conclusions and clinical significance

Oregano oil, thyme oil, carvacrol and thymol showed good in vitro bactericidal and fungicidal activity against 100 isolates from dogs with otitis externa, including some highly drug‐resistant isolates. These essential oils and their main phenolic constituents have the potential to be further investigated in vivo for the treatment of canine otitis externa.
Local and transient inhibition of p21 expression ameliorates age‐related delayed wound healing
Authors: Jiang Dongsheng , de Vries Juliane C. , Muschhammer Jana , Schatz Susanne , Ye Haifeng , Hein Tabea , Fidan Miray , Romanov Vasily S. , Rinkevich Yuval , Scharffetter‐Kochanek Karin
Published: October 2019

Nonhealing chronic wounds in the constantly growing elderly population represent a major public health problem with high socioeconomic burden. Yet, the underlying mechanism of age‐related impairment of wound healing remains elusive. Here, we show that the number of dermal cells expressing cyclin‐dependent kinase inhibitor p21 was elevated upon skin injury, particularly in aged population, in both man and mouse. The nuclear expression of p21 in activated wound fibroblasts delayed the onset of the proliferation phase of wound healing in a p53‐independent manner. Further, the local and transient inhibition of p21 expression by in vivo delivered p21‐targeting siRNA ameliorated the delayed wound healing in aged mice. Our results suggest that the increased number of p21+ wound fibroblasts enforces the age‐related compromised healing, and targeting p21 creates potential clinical avenues to promote wound healing in aged population.
Chemical constituent analysis of the Babassu (Orbignya phalerata Mart.) mesocarp
Authors: Batista de Farias Gabriela , Da Silva Rodrigues Jean Lucas , De Sousa Ribeiro Maria Nilce , Oliveira Magalhães Lyege , Ferreira Antonio Gilberto , Lima Maria Da Paz
Published: October 2019

The Babassu nut (Orbignya phalerata Mart.) mesocarp is traditionally transformed to flour and consumed in some Brazilian areas for its attributed medicinal activity; however, its chemical properties remain to be elucidated. The present work aimed at analyzing the babassu mesocarp phytochemical constituents. Babassu nut samples were collected in the Brazilian Amazon, and their mesocarps were prepared and macerated in different solvents. The chromatographic fractionation of selected methanol extracts yielded three fractions, A-5, A-6, and B-1 that were characterized with high resolution methods. Fraction A-5 was characterized through GC/MS as a fatty acid mixture with predominance of eicosanoic (38.67 %) and 11-octadecanoic (21.71  %) acids. Fraction A-6 was characterized by the presence of three phytosteroids (32.02 %), sesquiterpene (nerolidol; 24.89 %), and diterpene (17-acetoxy-19-kauranal; 15.17 %). The 1H and 13C NMR spectra on fraction A-6 showed characteristic chemical shifts for its compounds. Compound B-1 was identified as ergostanol-3-benzoate based on NMR experiments in one and two dimensions. These results constitute the first identification of babassu mesocarp chemical constituents in 1 and 2-dimensions, paving the way to understanding its role in popular medicine.
Effects of Swirl on the Stabilization of Non-Premixed Oxygen-Enriched Flames Above Coaxial Injectors
Authors: Degeneve A. , Mirat C. , Caudal J. , Vicquelin R. , Schuller T.
Published: October 2019

An experimental study is carried out to analyze the effects of swirl on the structure and stabilization of methane non-premixed oxygen-enriched flames above a coaxial injector in which the two streams are eventually swirled. The mean position of the flame and the liftoff height above the injector lips are investigated with OH* chemiluminescence images. The oxygen enrichment, the momentum flux ratio between the two coflows, the swirl level inside the central jet, and the swirl level in the annular jet are varied over a large range of operating conditions. It is found that, in the absence of swirl in the central stream, the flame is always attached to the lips of the internal injection tube. As the inner swirl level increases, the flame front located at the lips of the internal injection tube disappears. When the annular swirl level is high enough to create a central recirculating bubble, the flame detaches from the nozzle rim and remains lifted at a finite distance above the injector. Increasing the oxygen concentration shifts this transition to smaller momentum flux ratios and smaller annular swirl levels. The liftoff distance can be finely tuned and depends on the inner and outer swirl levels, and on the momentum flux ratio between the two coaxial streams. It is shown that this feature depends neither on the confinement of the injector nor on the thermal stress exerted by the hot burnt gases on the injector back plane. About 1000 configurations were investigated that could be classified into only four distinct stabilization modes, in which the flame structure was shown to follow a similar pathway when the momentum flux ratio between the two streams, the swirl level in the central and external streams, and the quarl angle of the annular stream are varied. It is finally shown how these limits are altered when the oxygen concentration in the annular oxidizer stream is varied from air to oxygen-enriched operation.
Multiobjective Design Optimization of a Biconcave Mobile-Bearing Lumbar Total Artificial Disk Considering Spinal Kinematics, Facet Joint Loading, and Metal-on-Polyethylene Contact Mechanics
Authors: Zhou Chaochao , Willing Ryan
Published: October 2019

Total disk arthroplasty (TDA) using an artificial disk (AD) is an attractive surgical technique for the treatment of spinal disorders, since it can maintain or restore spinal motion (unlike interbody fusion). However, adverse surgical outcomes of contemporary lumbar TDAs have been reported. We previously proposed a new mobile-bearing AD design concept featuring a biconcave ultrahigh-molecular-weight polyethylene (UHMWPE) mobile core. The objective of this study was to develop an artificial neural network (NN) based multiobjective optimization framework to refine the biconcave-core AD design considering multiple TDA performance metrics, simultaneously. We hypothesized that there is a tradeoff relationship between the performance metrics in terms of range of motion (ROM), facet joint force (FJF), and polyethylene contact pressure (PCP). By searching the resulting three-dimensional (3D) Pareto frontier after multiobjective optimization, it was found that there was a “best-tradeoff” AD design, which could balance all the three metrics, without excessively sacrificing each metric. However, for each single-objective optimum AD design, only one metric was optimal, and distinct sacrifices were observed in the other two metrics. For a commercially available biconvex-core AD design, the metrics were even worse than the poorest outcomes of the single-objective optimum AD designs. Therefore, multiobjective design optimization could be useful for achieving native lumbar segment biomechanics and minimal PCPs, as well as for improving the existing lumbar motion-preserving surgical treatments.
Deep Friction Massage in the Management of Patellar Tendinopathy in Athletes: Short-Term Clinical Outcomes
Authors: Chaves Paula , Simões Daniela , Paço Maria , Silva Sandra , Pinho Francisco , Duarte José Alberto , Ribeiro Fernando
Published: October 2019

Context: Deep friction massage (DFM) is often used in the treatment of tendinopathies; however, the pressure applied may vary and interfere with the obtained results. Objective: To assess whether the immediate effects of DFM on pain (pain intensity and time to onset of analgesia) and muscle strength are dependent on the pressure applied during the DFM application in athletes with patellar tendinopathy. Design: Randomized, controlled, cross-over trial. Setting: University research laboratory (institutional). Participants: Ten athletes with diagnosis of unilateral patellar tendinopathy (age 27.90 [5.24] y). Interventions: All participants attended 4 sessions, 3 treatment sessions with DFM applied with different pressures (the mean pressure—previously determined for each participant—and the mean pressure ± 25%) and a control session, each of which was separated by 48 hours. Main Outcome Measures: Pain (intensity upon palpation and time to onset of analgesia), and muscle strength of knee extensors were assessed before and immediately after each session. Results: Pain intensity changed significantly over time (F1,9 = 52.364; P < .001; ) and among sessions (F3,27 = 82.588; P < .001; ), with a significant interaction for group × time (F3,27 = 19.841; P < .001; ). The knee extensors strength did not change significantly over time (F1,9 = 2.240; P = .17; ), nor a significant interaction for session × time was observed (F3,27 = 3.276; P = .07; ). Regardless of the pressure applied, the time to onset of analgesia was not significantly different (F2,18 = 1.026; P > .05; ). Conclusion: It was shown that DFM induces an immediate reduction in pain intensity upon palpation, regardless of the pressure performed. Notwithstanding, the reader should take into account the small sample size and the caution needed in the results’ interpretation.
LGP2 binds to PACT to regulate RIG-I– and MDA5-mediated antiviral responses
Authors: Sanchez David Raul Y. , Combredet Chantal , Najburg Valérie , Millot Gael A. , Beauclair Guillaume , Schwikowski Benno , Léger Thibaut , Camadro Jean-Michel , Jacob Yves , Bellalou Jacques , Jouvenet Nolwenn , Tangy Frédéric , Komarova Anastassia V.
Published: October 2019

The interaction between LGP2 and a component of the RNA-silencing machinery enables coordination of innate immune responses.
Association of
TRAF1/C5
Locus Polymorphisms with Epilepsy and Clinical Traits in Mexican Patients with Neurocysticercosis
Authors: Villegas Marcela , Sciutto Edda , Rosetti Marcos , Fleury Agnes , Fragoso Gladis
Published: October 2019

Neurocysticercosis is caused by the establishment of
Taenia solium
cysts in the central nervous system. Murine cysticercosis by
Taenia crassiceps
is a useful model of cysticercosis in which the complement component 5 (C5) has been linked to infection resistance/permissiveness.
Tripartite Regulation of the
glpFKD
Operon Involved in Glycerol Catabolism by GylR, Crp, and SigF in Mycobacterium smegmatis
Authors: Bong Hyun-Ju , Ko Eon-Min , Song Su-Yeon , Ko In-Jeong , Oh Jeong-Il
Published: October 2019

Using genetic approaches, we first revealed that glycerol is catabolized through the glycolytic pathway after conversion to dihydroxyacetone phosphate in two sequential reactions catalyzed by glycerol kinase (GlpK) and flavin adenine dinucleotide (FAD)-containing glycerol-3-phosphate dehydrogenase (GlpD) in
M. smegmatis
. Our study also revealed that in addition to the GylR transcriptional activator that mediates the induction of the
glpFKD
operon by glycerol, the operon is regulated by SigF and Crp, which reflect the cellular energy state and cAMP level, respectively.
Vesicular Stomatitis Virus Transcription Is Inhibited by TRIM69 in the Interferon-Induced Antiviral State
Authors: Kueck Tonya , Bloyet Louis-Marie , Cassella Elena , Zang Trinity , Schmidt Fabian , Brusic Vesna , Tekes Gergely , Pornillos Owen , Whelan Sean P. J. , Bieniasz Paul D.
Published: October 2019

Interferons are important antiviral cytokines that work by inducing hundreds of host genes whose products inhibit the replication of many viruses. While the antiviral activity of interferon has long been known, the identities and mechanisms of action of most interferon-induced antiviral proteins remain to be discovered. We identified gene products that are important for the antiviral activity of interferon against vesicular stomatitis virus (VSV), a model virus that whose genome consists of a single RNA molecule with negative-sense polarity. We found that a particular antiviral protein, TRIM69, functions by a previously undescribed molecular mechanism. Specifically, TRIM69 interacts with and inhibits the function of a particular phosphoprotein (P) component of the viral transcription machinery, preventing the synthesis of viral messenger RNAs.
Impact of major depression on cardiovascular outcomes for individuals with hypertension: prospective survival analysis in UK Biobank
Authors: Graham Nicholas , Ward Joey , Mackay Daniel , Pell J P , Cavanagh Jonathan , Padmanabhan Sandosh , Smith Daniel J
Published: October 2019

Objectives

To assess whether a history of major depressive disorder (MDD) in middle-aged individuals with hypertension influences first-onset cardiovascular disease outcomes.

Design

Prospective cohort survival analysis using Cox proportional hazards regression with a median follow-up of 63 months (702 902 person-years). Four mutually exclusive groups were compared: hypertension only (n=56 035), MDD only (n=15 098), comorbid hypertension plus MDD (n=12 929) and an unaffected (no hypertension, no MDD) comparison group (n=50 798).

Setting

UK Biobank.

Participants

UK Biobank participants without cardiovascular disease aged 39–70 who completed psychiatric questions relating International Classification of Diseases-10 Revision (ICD-10) diagnostic criteria on a touchscreen questionnaire at baseline interview in 2006–2010 (n=134 860).

Primary and secondary outcome measures

First-onset adverse cardiovascular outcomes leading to hospital admission or death (ICD-10 codes I20–I259, I60–69 and G45–G46), adjusted in a stepwise manner for sociodemographic, health and lifestyle features. Secondary analyses were performed looking specifically at stroke outcomes (ICD-10 codes I60–69 and G45–G46) and in gender-separated models.

Results

Relative to controls, adjusted HRs for adverse cardiovascular outcomes were increased for the hypertension only group (HR 1.36, 95% CI 1.22 to 1.52) and were higher still for the comorbid hypertension plus MDD group (HR 1.66, 95% CI 1.45 to 1.9). HRs for the comorbid hypertension plus MDD group were significantly raised compared with hypertension alone (HR 1.22, 95% CI 1.1 to 1.35). Interaction measured using relative excess risk due to interaction (RERI) and likelihood ratios (LRs) were identified at baseline (RERI 0.563, 95% CI 0.189 to 0.938; LR p=0.0116) but not maintained during the follow-up.

Limitations

Possible selection bias in UK Biobank and inability to assess for levels of medication adherence.

Conclusions

Comorbid hypertension and MDD conferred greater hazard than hypertension alone for adverse cardiovascular outcomes, although evidence of interaction between hypertension and MDD was inconsistent over time. Future cardiovascular risk prediction tools may benefit from the inclusion of questions about prior history of depressive disorders.
Benefits and harms of lower blood pressure treatment targets: systematic review and meta-analysis of randomised placebo-controlled trials
Authors: Brunström Mattias , Carlberg Bo
Published: October 2019

Objectives

To assess the effect of antihypertensive treatment in the 130–140 mm Hg systolic blood pressure range.

Design

Systematic review and meta-analysis.

Information sources

PubMed, CDSR and DARE were searched for the systematic reviews, which were manually browsed for clinical trials. PubMed and Cochrane Central Register of Controlled Trials were searched for trials directly in February 2018.

Eligibility criteria

Randomised double-blind trials with ≥1000 patient-years of follow-up, comparing any antihypertensive agent against placebo.

Data extraction and risk of bias

Two reviewers extracted study-level data, and assessed risk of bias using Cochrane Collaborations risk of bias assessment tool, independently.

Main outcomes and measures

Primary outcomes were all-cause mortality, major cardiovascular events and discontinuation due to adverse events. Secondary outcomes were cardiovascular mortality, myocardial infarction, stroke, heart failure, hypotension-related adverse events and renal impairment.

Results

Eighteen trials, including 92 567 participants (34% women, mean age 63 years), fulfilled the inclusion criteria. Primary preventive antihypertensive treatment was associated with a neutral effect on all-cause mortality (relative risk 1.00, 95% CI 0.95 to 1.06) and major cardiovascular events (1.01, 0.96 to 1.06), but an increased risk of discontinuation due to adverse events (1.23, 1.03 to 1.47). None of the secondary efficacy outcomes were significantly reduced, but the risk of hypotension-related adverse events increased with treatment (1.71, 1.32 to 2.22). In coronary artery disease secondary prevention, antihypertensive treatment was associated with reduced risk of all-cause mortality (0.91, 0.83 to 0.99) and major cardiovascular events (0.85, 0.77 to 0.94), but doubled the risk of adverse events leading to discontinuation (2.05, 1.62 to 2.61).

Conclusion

Primary preventive blood pressure lowering in the 130–140 mm Hg systolic blood pressure range adds no cardiovascular benefit, but increases the risk of adverse events. In the secondary prevention, benefits should be weighed against harms.

PROSPERO registration number

CRD42018088642.
Proposals on Kaplan–Meier plots in medical research and a survey of stakeholder views: KMunicate
Authors: Morris Tim P , Jarvis Christopher I , Cragg William , Phillips Patrick P J , Choodari-Oskooei Babak , Sydes Matthew R
Published: October 2019

Objectives

To examine reactions to the proposed improvements to standard Kaplan–Meier plots, the standard way to present time-to-event data, and to understand which (if any) facilitated better depiction of (1) the state of patients over time, and (2) uncertainty over time in the estimates of survival.

Design

A survey of stakeholders’ opinions on the proposals.

Setting

A web-based survey, open to international participation, for those with an interest in visualisation of time-to-event data.

Participants

1174 people participated in the survey over a 6-week period. Participation was global (although primarily Europe and North America) and represented a wide range of researchers (primarily statisticians and clinicians).

Main outcome measures

Two outcome measures were of principal importance: (1) participants’ opinions of each proposal compared with a ‘standard’ Kaplan–Meier plot; and (2) participants’ overall ranking of the proposals (including the standard).

Results

Most proposals were more popular than the standard Kaplan–Meier plot. The most popular proposals in the two categories, respectively, were an extended table beneath the plot depicting the numbers at risk, censored and having experienced an event at periodic timepoints, and CIs around each Kaplan–Meier curve.

Conclusions

This study produced a high response number, reflecting the importance of graphics for time-to-event data. Those producing and publishing Kaplan–Meier plots—both authors and journals—should, as a starting point, consider using the combination of the two favoured proposals.
Intracytoplasmic sperm injection (ICSI) versus conventional in vitro fertilisation (IVF) in couples with non-severe male infertility (NSMI-ICSI): protocol for a multicentre randomised controlled trial
Authors: Zheng Danni , Zeng Lin , Yang Rui , Lian Ying , Zhu Yi-Min , Liang Xiaoyan , Tang Li , Wang Huichun , Cao Yunxia , Hao Guimin , Liu Jianqiao , Zhao Junli , Wang Rui , Mol Ben Willem , Li Rong , Huang He-Feng , Qiao Jie
Published: October 2019

Introduction

Intracytoplasmic sperm injection (ICSI), originally introduced as add-on to in vitro fertilisation (IVF) for couples with severe male infertility, is in current clinical practice also used in couples with mild male or even unexplained infertility. However, ICSI has involved unresolved concerns regarding the selection and damage to gametes and the health conditions of the offspring, and it is also labour intensive and therefore more expensive than conventional IVF. High-quality well-powered randomised clinical trials (RCTs) comparing ICSI and IVF are lacking.

Methods and analysis

We propose a multicentre, open-label RCT in 10 reproductive medical centres across China. We will study couples with non-severe male infertility (defined as a semen concentrate 5–15×106/mL or sperm with a progressive motility 10%–32%) scheduled for their first or second ICSI or IVF cycle, as low fertility rate after fertilisation are more frequent in this population, which could lead to controversy about ICSI or conventional IVF for fertilisation. On the day of oocyte retrieval, eligible participants are after informed consent be randomised to undergo either ICSI or conventional IVF in a 1:1 treatment ratio. Other standard assisted reproductive treatments are similar and parallel between two groups. Our primary outcome is ongoing pregnancy leading to live birth after the first cycle with embryo transfer. To demonstrate or refute a difference of 7% between ICSI and conventional IVF, we need to include 2346 women (1173 in each intervention arm). In addition, we will follow-up neonatal outcomes after delivery to identify the influence of ICSI on offspring.

Ethics and dissemination

Ethical approval was obtained from Peking University Third Hospital medical science research ethics committee. The findings will be disseminated to the public through conference presentations and peer-reviewed scientific journals.

Trial registration number

ClinicalTrials.gov registry (NCT03298633).
Evidence map of pancreatic surgery: protocol for a living systematic review and meta-analysis
Authors: Probst Pascal , Hüttner Felix J , Meydan Ömer , Kalkum Eva , Kretschmer Rüdiger , Jensen Katrin , Kenngott Hannes G , Mihaljevic André L , Hackert Thilo , Büchler Markus W , Diener Markus K
Published: October 2019

Introduction

Pancreatic surgery is a large and complex field of research. Several evidence gaps exist for specific diseases or surgical procedures. An overview on existing knowledge is needed to plan and prioritise future research. The aim of this project is to create a systematic and living evidence map of pancreatic surgery.

Methods and analysis

A systematic literature search in MEDLINE (via PubMed), Web of Science and Cochrane Central Register of Controlled Trials will be performed searching for all randomised controlled trials (RCT) and systematic reviews (SR) on pancreatic surgery. RCT and SR will be grouped in research topics. Baseline and outcome data from RCT will be extracted, presented and effect sizes meta-analysed. Data from SR will be used to identify evidence gaps. A freely accessible web-based evidence map in the format of a mind map will be created. The evidence map and meta-analyses will be updated periodically.

Dissemination

After completion of the project, a permanently updated evidence map of pancreatic surgery will be available to patients, physicians, researchers and funding bodies viawww.evidencemap.surgery. Its use will allow clinical decision-making based on primary data and prioritisation of future research endeavours.

PROSPERO registration number

CRD42019133444.
Publicly available apps for cancer survivors: a scoping review
Authors: Adam Rosalind , McMichael Drew , Powell Daniel , Murchie Peter
Published: October 2019

Objectives

To review the nature and scope of apps targeting individuals living with and beyond cancer.

Design

Scoping review, searching the two largest app stores, Google Play and Apple’s App store. App descriptions were exported verbatim, and summarised descriptively, thematically and by content coding.

Results

We included 151 apps targeting individuals living with and beyond cancer. Most targeted all cancer types (n=89, 58.9%) or breast cancer (n=22, 14.6%) and originated in the USA (n=68, 45.0%). The country of origin was unclear for 31 (20.5%) apps. Most apps were developed by commercial companies/private individuals (n=64, 43%) or non-profit organisations (n=30, 19.9%) and marketed apps in terms of fighting metaphors, navigating a journey and becoming empowered to take control.

App content could be summarised under five main categories: (1) imparting information about cancer; (2) planning and organising cancer care; (3) interacting with others (including others affected by cancer and healthcare professionals); (4) enacting management strategies and adjusting to life with or beyond cancer and (5) getting feedback about cancer management, for example, by sharing self-monitoring reports with professionals. We found some apps describing ‘cures’ for cancer or selling products, such as alkaline waters to cancer survivors.

Conclusions

Apps are currently available via on-line stores that cover a large spectrum of cancer survivorship activities. The effects of such apps on clinical consultations, patient work/burden and clinical outcomes merit further attention. Most apps are developed by commercial organisations, and promises of empowerment in the ‘fight’ against cancer are tempered by the potential for exaggerated claims and exploitation.
Using commercial ELISAs to assess humoral response in sows repeatedly vaccinated with modified live porcine reproductive and respiratory syndrome virus
Authors: Díaz Ivan , Genís‐Jorquera Blanca , Martín‐Valls Gerard E , Mateu Enric
Published: October 2019

Background

Sows in breeding herds are often mass vaccinated against porcine reproductive and respiratory syndrome (PRRS) every few months using modified live vaccines (MLV). Field veterinarians repeatedly report that multiple vaccinated sows test negative in ELISA. Obviously, this creates uncertainty when assessing the compliance of vaccination and the status of sows.

Methods

In the present study, four commercial ELISAs were used to assess the serological PRRS status in gilts and sows of three farms that were PRRS MLV vaccinated every four months. Animals were tested before vaccination (BV) and postvaccination (PV). Total and neutralising antibodies and cell‐mediated responses were also measured in animals that yielded negative results in all ELISAs.

Results

The proportion of seronegative animals BV varied depending on the farm and the ELISA used. When samples were analysed using only one ELISA, a substantial number of negative results obtained BV remained as negative afterwards. Five animals were negative BV and PV with all the examined ELISAs. Those animals also yielded negative results in all the other immunological assays.

Conclusion

Our findings suggest that the use of ELISA for monitoring multiple PRRS MLV vaccinated sows is very limited due to the variability of the humoral responses and the moderate agreement between tests.
Production ofBrucella melitensisOmp16 protein fused to the human interleukin 2 inLactococcus lactisMG1363 toward developing aLactococcus-based vaccine against brucellosis
Authors: Rezaei Marzieh , Rabbani Khorasgani Mohammad , Zarkesh Esfahani Sayyed Hamid , Emamzadeh Rahman , Abtahi Hamid
Published: October 2019

The use of the food-grade bacterium Lactococcus lactis as a new cell factory is a promising alternative expression system for producing a desired protein. The Omp16-IL2 fusion protein antigen was cloned, expressed, and purified in this study. The Omp16-IL2 fusion gene was designed and cloned in pGH plasmid with appropriate restriction sites and subcloned in pAMJ2008 expression vector digested with the same enzymes. The purified recombinant constructed pAMJ-rOmp-IL2 was introduced into L. lactis subsp. cremoris MG1363 by electrotransformation. Finally, the expression and purification of Omp16-IL2 fusion protein was investigated. This study reports the construction of a recombinant L. lactis expressing the Omp16-IL2 fusion protein as an oral Lactococcus-based vaccine, as compared with commonly used live attenuated vaccines, for future studies against brucellosis.
Parallel Architecture of Reconfigurable Hardware for Massive Output Active Noise Control
Authors: Mendez Diego , Arevalo David , Patino Diego , Gerlein Eduardo , Quintana Ricardo
Published: October 2019

Filtered-x Least Mean Squares (FxLMS) is an algorithm commonly used for Active Noise Control (ANC) systems in order to cancel undesired acoustic waves from a sound source. There is a small number of hardware designs reported in the literature, that in turn only use one reference signal, one error signal and one output control signal. In this paper, it is proposed a 3-dimensional hardware-based version of the widely used FxLMS algorithm, using one reference microphone, 18 error microphones, one output and a FIR filter of 400[Formula: see text] order. The FxLMS algorithm was implemented in a Xilinx Artix 7 FPGA running at 25 MHz, which allowed to update the filter coefficients in 32.44[Formula: see text] s. The main idea behind this work is to propose a pipelined parallelized architecture to achieve processing times faster than real time for the filter coefficients update. The main contribution of this work is not the ANC technique itself, but rather the proposed hardware implementation that utilizes integer arithmetic, which provided an acceptable error when benchmarked with a software implementation. This parallel system allows a scalable implementation as an advantage of using FPGA without compromising the computational cost and, consequently, the latency.
Supervised Learning Methods in Classifying Organized Behavior in Tweet Collections
Authors: Beğenilmiş Erdem , Uskudarli Susan
Published: October 2019

The successful use of social media to manipulate public opinion via bots and hired individuals to spread (mis)information to unsuspecting users reached alarming levels due to the manipulations during the 2016 US elections and the Brexit deliberations in the UK. Fake interaction such as “liking” and “retweeting” are staged to foster trust in the posts of bots and individuals, which makes it difficult for individuals to detect the posts that are part of greater schemes. We propose an approach based on supervised learning to classify collections of tweets as “organized” when they inhabit premeditated intent and as “organic” otherwise. Features related to users and posting behavior are used to train the classifiers using 851 data sets totaling above 270 million tweets. Further classifiers are trained to assess the effectiveness of the selected features. The random forest algorithm persistently yielded the best results with scores greater than 95% for both accuracy and f-measure. For comparison purposes, unsupervised learning methods were used to cluster the same data sets. The Gaussian Mixture Model clustered [organized vs organic] data set with 99% agreement with the labels. The success of using only behavioral features to detect organized behavior is encouraging.
Parameter Setting for Deep Neural Networks Using Swarm Intelligence on Phishing Websites Classification
Authors: Vrbančič Grega , Fister Iztok , Podgorelec Vili
Published: October 2019

Over the past years, the application of deep neural networks in a wide range of areas is noticeably increasing. While many state-of-the-art deep neural networks are providing the performance comparable or in some cases even superior to humans, major challenges such as parameter settings for learning deep neural networks and construction of deep learning architectures still exist. The implications of those challenges have a significant impact on how a deep neural network is going to perform on a specific task. With the proposed method, presented in this paper, we are addressing the problem of parameter setting for a deep neural network utilizing swarm intelligence algorithms. In our experiments, we applied the proposed method variants to the classification task for distinguishing between phishing and legitimate websites. The performance of the proposed method is evaluated and compared against four different phishing datasets, two of which we prepared on our own. The results, obtained from the conducted empirical experiments, have proven the proposed approach to be very promising. By utilizing the proposed swarm intelligence based methods, we were able to statistically significantly improve the predictive performance when compared to the manually tuned deep neural network. In general, the improvement of classification accuracy ranges from 2.5% to 3.8%, while the improvement of F1-score reached even 24% on one of the datasets.
Width of the Whitehead double of a nontrivial knot
Authors: Guo Qilong , Li Zhenkun
Published: October 2019

In this paper, we prove that [Formula: see text], where [Formula: see text] is the width of a knot and [Formula: see text] is the Whitehead double of a nontrivial knot [Formula: see text].
ELECTROCHEMICAL, DFT AND MD SIMULATION INVESTIGATIONS OF THE CORROSION INHIBITION PROPERTIES OF HETEROCYCLIC SULFIDE DERIVATIVES FOR MILD STEEL IN ACIDIC MEDIUM
Authors: BENMAHAMMED IMENE , DOUADI TAHAR , ISSAADI SAIFI , DAOUD DJAMEL , CHAFAA SALAH
Published: October 2019

The study of the corrosion inhibition of mild steel in acid medium 1 M HCl by the Schiff base compounds named {4,4′-Bis(pyrrole-2-carboxaldehyde) diphenyl diimino sulfide (L1) and 4,4′-Bis(thiophene-2-carboxaldehyde) diphenyl diimino sulfide (L2)} was carried out using various techniques: weight loss measurements, polarization curves, electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The influence of the concentration, immersion time and temperature was examined and the mode of adsorption of these inhibitors on the surface of the metal was highlighted by assigning the appropriate isotherm. The experimental results indicate that these compounds are effective corrosion inhibitors and the inhibitory competence rises with increasing inhibitor concentration. The adsorption of these compounds on the mild steel surface obeys the isotherm of Langmuir. The correlation between the molecular structures and the inhibitory properties of the compounds studied was performed using the Density Functional Theory (DFT) method. Furthermore, molecular dynamics (MD) simulation has been taken into account. The results indicate that the adsorption energy of L1 was less than L2, which is in accordance with the experimentally determined inhibition effect.
Weighted p-regular kernels for reproducing kernel Hilbert spaces and Mercer Theorem
Authors: Agud L. , Calabuig J. M. , Sánchez Pérez E. A.
Published: October 2019

Let [Formula: see text] be a finite measure space and consider a Banach function space [Formula: see text]. Motivated by some previous papers and current applications, we provide a general framework for representing reproducing kernel Hilbert spaces as subsets of Köthe–Bochner (vector-valued) function spaces. We analyze operator-valued kernels [Formula: see text] that define integration maps [Formula: see text] between Köthe–Bochner spaces of Hilbert-valued functions [Formula: see text] We show a reduction procedure which allows to find a factorization of the corresponding kernel operator through weighted Bochner spaces [Formula: see text] and [Formula: see text] — where [Formula: see text] — under the assumption of [Formula: see text]-concavity of [Formula: see text] Equivalently, a new kernel obtained by multiplying [Formula: see text] by scalar functions can be given in such a way that the kernel operator is defined from [Formula: see text] to [Formula: see text] in a natural way. As an application, we prove a new version of Mercer Theorem for matrix-valued weighted kernels.
The Cauchy problem for a two-dimensional generalized Kadomtsev–Petviashvili-I equation in anisotropic Sobolev spaces
Authors: Yan Wei , Li Yongsheng , Huang Jianhua , Duan Jinqiao
Published: October 2019

The goal of this paper is three-fold. First, we prove that the Cauchy problem for a generalized KP-I equation [Formula: see text] is locally well-posed in the anisotropic Sobolev spaces [Formula: see text] with [Formula: see text] and [Formula: see text]. Second, we prove that the Cauchy problem is globally well-posed in [Formula: see text] with [Formula: see text] if [Formula: see text]. Finally, we show that the Cauchy problem is globally well-posed in [Formula: see text] with [Formula: see text] if [Formula: see text] Our result improves the result of Saut and Tzvetkov [The Cauchy problem for the fifth order KP equations, J. Math. Pures Appl. 79 (2000) 307–338] and Li and Xiao [Well-posedness of the fifth order Kadomtsev–Petviashvili-I equation in anisotropic Sobolev spaces with nonnegative indices, J. Math. Pures Appl. 90 (2008) 338–352].
Model Predictive Control for Stable Walking Using the Divergent Component of Motion with Footstep Location and Yaw Adaptation
Authors: Griffin Robert J. , Leonessa Alexander
Published: October 2019

This paper presents an extension of previous model predictive control (MPC) schemes for dynamic walking to the stabilization of the time-varying divergent component-of-motion (DCM). In order to address the control authority limitations caused by fixed footholds, the step positions and rotations are treated as control inputs, allowing the generation and execution of stable walking motions, both at high speeds and in the face of disturbances. The use of the time-varying DCM allows consideration of height changes on the DCM dynamics, improving the robustness of the controller over varying terrain. Footstep rotation is included to allow for better modeling of the adjustment effects on reachability for stability and navigation of complex environments. This is done by formulating a quadratically constrained mixed-integer quadratic program (MIQCQP), which, when combined with the use of the time-varying DCM to account for the effects of height changes and use of angular momentum, improves the capabilities of MPC strategies for bipedal walking. While the MIQCQP cannot be solved at the desired control frequency, a method for compensating for the DCM dynamics between solves is presented. Simulation results of fast walking over flat ground and navigating varying-height terrain is presented with the ESCHER humanoid. This is combined with experiments that recover from a variety pushes, which demonstrate the effectiveness of this approach.
Purely chromatic and hyper chromatic lattices
Authors: Pawar Madhukar M. , Wadile Amit S.
Published: October 2019

We introduce the concepts of a hyper chromatic, a critically chromatic and a purely chromatic lattice. We obtain some characterizations for purely chromatic and hyper chromatic dismantlable lattices. We prove relationships between the chromatic number of two lattices and their linear sum, vertical sum and adjunct.
The Psychology of Workplace Mentoring Relationships
Authors: Eby Lillian T. , Robertson Melissa M.
Published: October 2019

Workplace mentoring relationships have been advanced as critical to employee development. However, mentoring research has tended to find small to moderate effects of mentoring on protégé and mentor outcomes and considerable heterogeneity in effect sizes. These findings underscore the need to better understand the psychology of mentoring relationships in order to maximize the benefits of mentoring for mentors, protégés, and organizations. In this article, after briefly reviewing established research on workplace mentoring relationships, we introduce five relationship science theories from outside organizational psychology and organizational behavior that provide new insight into the psychology of workplace mentoring: attachment theory, interdependence theory, self-expansion theory, Rhodes’ model of formal youth mentoring, and the working alliance. We then discuss several unique features of workplace mentoring that should be considered when applying these relationship science theories and introduce provocative ideas for future research. We conclude by discussing practical implications for mentors, protégés, and organizations.