bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic review of randomized controlled trials of the Wenyang Huoxue method in treating diabetic peripheral neuropathy
Authors: Deng Zhiyuan , Wang Manjia , Fan Yao-hua , Huang Ruilin , Rao Yawen , Mai Xurong , Liu Min 
Published: October 2019

Abstract

Objective:
To assess the efficacy and safety of the Wenyang Huoxue method for patients with diabetic peripheral neuropathy.

Methods:
A systematic literature search was performed using 7 databases: PUBMED, EMBASE, the Chinese National Knowledge Infrastructure, Wanfang, Chinese BioMedical, and the VIP Chinese Science and Technique Journals. The publication time was from the start of each database up to November 2018. Review Manager 5.3 software was used for assessing potential bias, data synthesis, and the subgroup analysis. Begg and Egger tests were used to assess funnel plot symmetries using Stata 14.0 software. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) system was used to assess the quality of evidence.

Results:
A total of 22 trials involving 1835 participants were eligible. There were significant differences in a total effective rate between the Wenyang Huoxue method combined with Western medicine and Western medicine alone (RR = 1.33, 95% CI 1.26–1.41; P < .00001). As for the sensory conduction velocity (SCV) of the peroneal nerve, the Wenyang Huoxue method combined with Western medicine compared with Western medicine alone had a significant increase (weighted mean difference [WMD] = 5.00, 95% CI 3.42–6.57; P < .00001). Also, the Wenyang Huoxue method combined with Western medicine had significant increases in motor conduction velocity (MCV) of the peroneal nerve (WMD = 4.48, 95% CI 3.78–5.19; P < .00001), tibial nerve SCV (WMD = 3.47, 95% CI 2.66–4.28; P < .00001), tibial nerve MCV (4.87, 95% CI 3.21–6.53; P < .00001), median nerve SCV (WMD = 3.78, 95% CI 3.07–4.50; P < .00001), and median nerve MCV (WMD = 4.50, 95% CI 3.40–5.59; P < .00001). However, the effect of the Wenyang Huoxue method on fasting blood glucose, 2-h postprandial blood glucose, and glycosylated hemoglobin was not statistically significant. Egger's test results showed that there was no publication bias (P = .0008), but the trim and filling method showed steady results. An influence analysis showed that no single study affected the overall result. The GRADE quality of the evidence was low to moderate across the different outcomes.

Conclusion:
Despite of the apparently positive findings, the quality of GRADE is not high, suggesting that the Wenyang Huoxue method can improve nerve conduction velocity to a certain extent, but more rigorous literature is needed to support this evidence.
Effect of anticoagulation therapy in older patients with chronic kidney disease and atrial fibrillation
Authors: He Wenfeng , Zhang Hao , Zhu Wengen , Xue Zhengbiao 
Published: October 2019

Abstract

Background:
The role of anticoagulation therapy for stroke prevention in older atrial fibrillation (AF) patients with chronic kidney disease (CKD) remains unclear. Therefore, we conducted a meta-analysis to explore the efficacy and safety of anticoagulation therapy in this population.

Methods:
The Cochrane Library, PubMed, and Embase databases were systematically searched for studies reporting the effect of anticoagulation therapy in older patients with AF and CKD. The risk ratios (RRs) and 95% confidence intervals (CIs) were regarded as the risk estimates. A random-effects model selected was to evaluate the treatment outcomes. The presentations were based on the Preferred Reporting Items for reporting systematic reviews and meta-analyses statement.

Results:
A total of 7 studies with 24,794 older patients with AF and CKD were included. The follow-up of the included studies ranged from 0.9 to 9.0 years. In older patients with no dialysis, compared with nonanticoagulants, anticoagulants reduced the risk of all-cause death (RR 0.66, 95% CI 0.54–0.79), but had comparable risks of ischemic stroke/transient ischemic attack (TIA, RR 0.91, 95% CI 0.46–1.79) and bleeding (RR 1.17, 95% CI 0.86–1.60). In older patients with dialysis, compared with nonanticoagulants, anticoagulants increased the risk of bleeding (RR 1.37, 95% CI 1.09–1.74), but had similar risks of ischemic stroke/TIA (RR 1.18, 95% CI 0.88–1.58) and death (RR 0.87, 95% CI 0.60–1.27).

Conclusion:
Compared with nonanticoagulation, anticoagulation therapy is associated with a reduced risk of death in older AF patients with nondialysis, but an increased risk of bleeding in older patients with dialysis.
An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
Authors: Bowling Sarah , Sritharan Duluxan , Osorio Fernando G. , Nguyen Maximilian , Cheung Priscilla , Rodriguez-Fraticelli Alejo , Patel Sachin , Fujiwara Yuko , Li Bin E. , Orkin Stuart H. , Hormoz Sahand , Camargo Fernando D. 
Published: October 2019

AbstractTracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Particularly in the context of stem cell biology, analysis of single cell lineages in their native state has elucidated novel fates and highlighted heterogeneity of function. Coupling of such ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures based on in vivo stem cell function without a need for markers or cell sorting.
An elusive endosymbiont: DoesWolbachiaoccur naturally inAedes aegypti?
Authors: Ross Perran A. , Callahan Ashley G. , Yang Qiong , Jasper Moshe , Arif A. K. M. , Noor Afizah A. , Nazni W. A. , Hoffmann Ary A. 
Published: October 2019

AbstractWolbachiaare maternally-inherited endosymbiotic bacteria found within many insect species.Aedesmosquitoes experimentally infected withWolbachiaare being released into the field forAedes-borne disease control. TheseWolbachiainfections induce cytoplasmic incompatibility which is used to suppress populations through incompatible matings or replace populations through the reproductive advantage provided by this mechanism. However the presence of naturally-occurringWolbachiain target populations could interfere with both population replacement and suppression programs depending on the compatibility patterns between strains.Aedes aegyptiwere thought to not harborWolbachianaturally but several recent studies have detectedWolbachiain natural populations of this mosquito. We therefore review the evidence for naturalWolbachiainfections inAe. aegyptito date and discuss limitations of these studies. We draw on research from other mosquito species to outline the potential implications of naturalWolbachiainfections inAe. aegyptifor disease control. To validate previous reports, we obtained a laboratory population ofAe. aegyptifrom New Mexico, USA, that harbors a naturalWolbachiainfection, and we conducted field surveys in Kuala Lumpur, Malaysia where a naturalWolbachiainfection has also been reported. However, we were unable to detectWolbachiainfection in both the laboratory and field populations. Because the presence of naturally-occurringWolbachiainAe. aegypticould have profound implications forWolbachia-based disease control programs, it is important to continue to accurately assess theWolbachiastatus of targetAedespopulations.
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
Authors: Gómez-de-Mariscal Estibaliz , García-López-de-Haro Carlos , Ouyang Wei , Donati Laurène , Lundberg Emma , Unser Michael , Muñoz-Barrutia Arrate , Sage Daniel 
Published: October 2019

ABSTRACTDeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learn ing (DL) models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained DL models (BioImage Model Zoo). Hence, non-experts can easily perform common image processing tasks in life-science research with DL-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state-of-the-art solutions and it is equipped with utility tools for developers to include new models. Very recently, several train ing frameworks have adopted the deepImageJ format to deploy their work in one of the most used software in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of DL models in life-sciences applications and bioimage informatics.
The evolution of competitive ability for essential resources
Authors: Bernhardt Joey R. , Kratina Pavel , Pereira Aaron , Tamminen Manu , Thomas Mridul K. , Narwani Anita 
Published: October 2019

AbstractCompetition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species’ minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species’ competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposedChlamydomonas reinhardtiifor approximately 285 generations to seven environments in chemostats which differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.
An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses
Authors: Radhakrishnan Guru V. , Keller Jean , Rich Melanie K. , Vernié Tatiana , Mbadinga Mbaginda Duchesse L. , Vigneron Nicolas , Cottret Ludovic , San Clemente Hélène , Libourel Cyril , Cheema Jitender , Linde Anna-Malin , Eklund D. Magnus , Cheng Shifeng , Wong Gane KS , Lagercrantz Ulf , Li Fay-Wei , Oldroyd Giles E. D. , Delaux Pierre-Marc 
Published: October 2019

ABSTRACTPlants are the foundation of terrestrial ecosystems and their colonization of land was facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Through analysis of 271 transcriptomes and 122 plant genomes, we demonstrate that the common symbiosis signalling pathway controlling the association with arbuscular mycorrhizal fungi and with nitrogen-fixing bacteria specifically co-evolved with intracellular endosymbioses, including ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. In contrast, species forming exclusively extracellular symbioses like ectomycorrhizae or associations with cyanobacteria have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million years of plant diversification.
A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas
Authors: Siegle Joshua H. , Jia Xiaoxuan , Durand Séverine , Gale Sam , Bennett Corbett , Graddis Nile , Heller Greggory , Ramirez Tamina K. , Choi Hannah , Luviano Jennifer A. , Groblewski Peter A. , Ahmed Ruweida , Arkhipov Anton , Bernard Amy , Billeh Yazan N. , Brown Dillan , Buice Michael A. , Cain Nicolas , Caldejon Shiella , Casal Linzy , Cho Andrew , Chvilicek Maggie , Cox Timothy C. , Dai Kael , Denman Daniel J. , de Vries Saskia E. J. , Dietzman Roald , Esposito Luke , Farrell Colin , Feng David , Galbraith John , Garrett Marina , Gelfand Emily C. , Hancock Nicole , Harris Julie A. , Howard Robert , Hu Brian , Hytnen Ross , Iyer Ramakrishnan , Jessett Erika , Johnson Katelyn , Kato India , Kiggins Justin , Lambert Sophie , Lecoq Jerome , Ledochowitsch Peter , Lee Jung Hoon , Leon Arielle , Li Yang , Liang Elizabeth , Long Fuhui , Mace Kyla , Melchior Jose , Millman Daniel , Mollenkopf Tyler , Nayan Chelsea , Ng Lydia , Ngo Kiet , Nguyen Thuyahn , Nicovich Philip R. , North Kat , Ocker Gabriel Koch , Ollerenshaw Doug , Oliver Michael , Pachitariu Marius , Perkins Jed , Reding Melissa , Reid David , Robertson Miranda , Ronellenfitch Kara , Seid Sam , Slaughterbeck Cliff , Stoecklin Michelle , Sullivan David , Sutton Ben , Swapp Jackie , Thompson Carol , Turner Kristen , Wakeman Wayne , Whitesell Jennifer D. , Williams Derric , Williford Ali , Young Rob , Zeng Hongkui , Naylor Sarah , Phillips John W. , Reid R. Clay , Mihalas Stefan , Olsen Shawn R. , Koch Christof 
Published: October 2019

AbstractThe mammalian visual system, from retina to neocortex, has been extensively studied at both anatomical and functional levels. Anatomy indicates the cortico-thalamic system is hierarchical, but characterization of cellular-level functional interactions across multiple levels of this hierarchy is lacking, partially due to the challenge of simultaneously recording activity across numerous regions. Here, we describe a large, open dataset (part of theAllen Brain Observatory) that surveys spiking from units in six cortical and two thalamic regions responding to a battery of visual stimuli. Using spike cross-correlation analysis, we find that inter-area functional connectivity mirrors the anatomical hierarchy from theAllen Mouse Brain Connectivity Atlas. Classical functional measures of hierarchy, including visual response latency, receptive field size, phase-locking to a drifting grating stimulus, and autocorrelation timescale are all correlated with the anatomical hierarchy. Moreover, recordings during a visual task support the behavioral relevance of hierarchical processing. Overall, this dataset and the hierarchy we describe provide a foundation for understanding coding and dynamics in the mouse cortico-thalamic visual system.
Evaluation of nutraceuticals including vitamin B12and xenobiotic degradation capacity ofPleurotusspecies
Authors: Patel Yashvant , Vishwakarma Sanjay Kumar , Sunita Kumari 
Published: October 2019

AbstractDiverse edaphic zone (namely: usar, wastelands, forest area, wetlands, flood prone area and fertile lands) were identified in the eastern part of Uttar Pradesh and collected species ofPleurotusfor present study. A total of 39 purified isolates were evaluated for the presence of neutraceuticals like proteins, carbohydrates, phenolic and vitamin B12along with xenobiotic dye degradation capacity for textile dyes (MG and BPB) and production of laccase enzyme simultaneously. Isolate no. 06, appeared most distant in dendrogram having two major clusters, which also showed highest MG degradation capacity, however, other isolates also showed excellent degradation of BPB; and the laccase activity was found in the range of 4.03 to 19.13 IU/ml of crude enzyme extract from mycelia. All the isolates used in the present study, were also mounted for their genetic diversity analysis through RAPD. Diversity study revealed gene frequency from 0.012 to 0.987 and the average gene diversity for all RAPD loci were 0.244. The Shannon Information Index was 0.397. The unbiased genetic similarity among all pairs of isolates was 0.36 to 0.93 with a mean of 0.64. Significant genetic diversity, nutraceuticals and laccase enzyme availability and dye degradation capacity within the studied genusPleurotuswas found, which makes necessary to carry out a selection process in each one for superior selection not only for human being but also many aquatic as well as other terrestrial flora and fauna. Present investigation suggest that due to wide range of variation within species, the adaptation of strains to different edaphic zones must be taken into account in selection processes.
SapTrap assembly ofC. elegansMosSCI transgene vectors
Authors: Fan Xintao , De Henau Sasha , Feinstein Julia , Miller Stephanie I. , Han Bingjie , Frøkjær-Jensen Christian , Griffin Erik E. 
Published: October 2019

AbstractThe Mos1-mediated Single-Copy Insertion (MosSCI) method is widely used to establish stableCaenorhabditis eleganstransgenic strains. Cloning MosSCI targeting plasmids can be cumbersome because it requires assembling multiple genetic elements including a promoter, a 3’UTR and gene fragments. Recently, Schwartz and Jorgensen developed the SapTrap method for the one-step assembly of plasmids containing components of the CRISPR/Cas9 system forC. elegans(Schwartz and Jorgensen 2016 Genetics, 202:1277-1288). Here, we report on the adaptation of the SapTrap method for the efficient and modular assembly of a promoter, 3’UTR and either 2 or 3 gene fragments in a MosSCI targeting vector in a single reaction. We generated a toolkit that includes several fluorescent tags, components of the ePDZ/LOV optogenetic system and regulatory elements that control gene expression in theC. elegansgermline. As a proof of principle, we generated a collection of strains that fluorescently label the endoplasmic reticulum and mitochondria in the hermaphrodite germline and that enable the light-stimulated recruitment of mitochondria to centrosomes in the one-cell worm embryo. The method described here offers a flexible and efficient method for assembly of custom MosSCI targeting vectors.
Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)
Authors: Wang Xi , Bernhardsson Carolina , Ingvarsson Pär K. 
Published: October 2019

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses inP. abiesin an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity ofP.abiesis low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe inP. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
Physical activity and risk of lung cancer: a two-sample Mendelian randomization study
Authors: Baumeister Sebastian E , Leitzmann Michael F , Bahls Martin , Meisinger Christa , Amos Christopher I , Hung Rayjean J ,   Cancer in Lung of the International Lung Cancer Consortium (TRICL-ILCCO),   Lung Cancer Cohort Consortium (LC3), Teumer Alexander , Baurecht Hansjörg 
Published: October 2019

AbstractObservational studies have suggested that physical activity might lower the risk of lung cancer in former and current smokers but not in never smokers. Using genetic instruments for self-reported and accelerometer-measured physical activity traits implemented through two-sample Mendelian randomization (MR), we sought to strengthen the evidence for causality. We used 18 genome-wide significant (P < 5×10−8) single nucleotide polymorphisms (SNPs) for self-reported moderate-to-vigorous physical activity and seven SNPs for accelerometer-measured (‘average acceleration’) physical activity from up to 377,234 UK Biobank participants and evaluated these in relation to risk using 29,266 lung cancer cases (including 11,273 adenocarcinomas, 7,426 squamous cell and 2,664 small cell cases) and 56,450 controls. The MR analysis suggested no effect of self-reported physical activity (odds ratio (OR) [95% confidence interval (CI)] = 0.67 [0.42-1.05], P-value = 0.081, Q-value = 0.243) and accelerometer-measured activity (OR [95% CI] = 0.98 [0.93-1.03], P-value = 0.372,Q-value = 0.562) on lung cancer. There was no evidence for associations of physical activity with histologic types and lung cancer in ever and never smokers. Replication analysis using genetic instruments from a different genome-wide study and sensitivity analysis to address potential pleiotropic effects led to no substantive change in estimates. These findings do not support a protective relationship between physical activity and the risk of lung cancer.SignificanceThe present study provides little evidence that recommending physical activity would help to prevent lung cancer.