bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sero-Prevalence and Risk Factor ofPeste Des Petits Ruminantsin Sheep and Goats of Ethiopia: Systematic Review and Meta-Analysis
Authors: Yizengaw Liuel , Molla Wassie , Temesgen Wudu 
Published: April 2021

AbstractBackgroundPeste des petits ruminant (PPR) is the most common prevalent viral disease of sheep and goats that impacts productivity and international animal trade in the world and also in Ethiopia. Despite the huge economic consequences related toPPR, little is known about the sero-prevalence of this disease at the country levels. The objective of this systematic review and meta-analysis was to estimate a single-group summary for sero-prevalence ofPPRdisease in small ruminants of Ethiopia and assess the potential risk factor to contribute the sero-prevalence estimate.MethodologyArticle onPPRin sheep and goats were searched in PubMed, Web of Science, Google Scholar, reference lists and African online source of articles that had been conducted between 1994 to 2020 and using inclusion and exclusion criteria with restricted to those studies published in English language.ResultsA total of 13 published papers containing 46 district level studies were included for analyses. The single-group summary ofPPRdisease sero-prevalence in small ruminant was estimated to be 27.71% (95 % CI: 21.46 - 33.96). Overall, the estimated pooled sero-prevalence at country level in sheep was 33.56% (95% CI: 18.72–48.41) and in goats 25.14% (95% CI: 15.68–34.59). Significant heterogeneity (I2> 80%) was noted in all pooled estimates. The visual inspection of the funnel plot demonstrated the presence of possible publication bias which could be associated with the small number of studies and longtime interval.ConclusionsThis quantitative review showed that the pooled sero-prevalence to be high and regional prevalence estimates ofPPRpresented here will be useful in raising awareness and advocating the Governments to engage in initiativesPPRcontrol and prevention.
Automated Raman micro-spectroscopy of epithelial cells for the high-throughput classification
Authors: O’Dwyer Kevin , Domijan Katarina , Dignam Adam , Butler Marion , Hennelly Bryan M. 
Published: April 2021

AbstractRaman micro-spectroscopy is a powerful technique for the identification and classification of cancer cells and tissues. In recent years, the application of Raman spectroscopy to detect bladder, cervical, and oral cytological samples has been reported to have an accuracy that is greater than standard pathology. However, despite being entirely non-invasive and relatively inexpensive, the slow recording time, and lack of reproducibility, have prevented the clinical adoption of the technology. Here we present an automated Raman cytology system that can facilitate high-throughput screening and improve reproducibility. The proposed system is designed to be integrated directly into the standard pathology clinic, taking into account their methodologies and consumables. The system employs image processing algorithms and integrated hardware/software architectures in order to achieve automation and is tested using the ThinPrep standard, including the use of glass slides, and a number of bladder cancer cell lines. The entire automation process is implemented using the open source Micro-Manager platform, and is made freely available. We believe this code can be readily integrated into existing commercial Raman micro-spectrometers.
Coagulation disorders in patients with severe hemophagocytic lymphohistiocytosis
Authors: Valade Sandrine , Joly Bérangère S. , Veyradier Agnès , Fadlallah Jehane , Zafrani Lara , Lemiale Virginie , Launois Amélie , Stepanian Alain , Galicier Lionel , Fieschi Claire , Mirouse Adrien , Tudesq Jean Jacques , Lepretre Anne-Claire , Azoulay Elie , Darmon Michael , Mariotte Eric 
Published: April 2021

AbstractBackgroundCoagulation disorders are common in patients with hemophagocytic lymphohistiocytosis (HLH), associated with an increased risk of bleeding and death. We aim to investigate coagulation disorders and their outcome implications in critically ill patients with HLH.MethodsWe prospectively evaluated 47 critically ill patients with HLH (median age of 54 years [42-67]) between April 2015 and December 2018. Coagulation assessments were performed at day 1. Abnormal standard coagulation was defined as prothrombin time (PT) <50% and/or fibrinogen <2g/L. HLH aetiology was mostly ascribed to haematological malignancies (74% of patients).ResultsCoagulation disorders and severe bleeding events were frequent, occurring in 30 (64%) and 11 (23%) patients respectively. At day 1, median fibrinogen level was 2·65g/L [1.61-5.66]. Fibrinolytic activity was high as suggested by increased median levels of D-dimers, fibrin monomers, PAI-1 (plasminogen activator inhibitor) and tPA (tissue plasminogen activator). Forty-one (91%) patients had a decreased ADAMTS13 activity (A Disintegrin-like And Metalloproteinase with ThromboSpondin type 1 repeats, member 13). By multivariable analysis, the occurrence of a severe bleeding (OR 3.215 [1.194-8.653], p=0·021) and SOFA score (Sepsis-Related Organ Failure Assessment) at day 1 (OR 1.305 per point [1.146-1.485], p<0·001) were independently associated with hospital mortality. No early biological marker was associated with severe bleeding.ConclusionsHyperfibrinolysis may be the primary mechanism responsible for hypofibrinogenemia and may also participate in ADAMTS13 degradation. Targeting the plasmin system appears as a promising approach in severe HLH-related coagulation disorders.
Optimized Protocol for Cyanobacterial 16S rRNA Analysis in Danube Delta Lakes
Authors: Moza Maria Iasmina , Postolache Carmen 
Published: April 2021

AbstractMolecular biology protocols have been more and more accessible to researchers for ecological investigations, however, these protocols always require optimization steps for the analysis of specific types of samples. The purpose of this study was to optimize a molecular protocol for the analysis of cyanobacterial 16S rRNA in Danube Delta shallows lakes. In this regard, several commercial DNA extraction kits were tested in comparison with potassium ethyl xanthogenate extraction method on different matrices. The obtained DNA was further used for 16S rRNA PCR optimization. Finally, an optimized protocol is proposed for the molecular analysis of cyanobacteria group in freshwater samples. The best DNA extraction method was the potassium xanthogenate extraction from dried cyanobacterial biomass. A dynamic in total genomic eDNA was observed, reflecting the seasonal difference in phytoplankton biomass from the studied lakes. The PCR protocol optimized by us can be successfully applied for the identification of a broad range of cyanobacterial genetic markers.
Memes: an R interface to the MEME Suite
Authors: Nystrom Spencer L. , McKay Daniel J. 
Published: April 2021

AbstractIdentification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we presentmemes, an R package which provides a seamless R interface to the MEME Suite.memesprovides a novel “data aware” interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools,memesleverages existing R/Bioconductor data structures to store the complex, multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally,memesprovides data visualization capabilities to facilitate communication of results.memesis available as a Bioconductor package athttps://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.
Computational investigation reveals that the mutant strains of SARS-CoV2 are highly infectious than wildtype
Authors: Kumar Rakesh , Kumar Rahul , Goel Harsh , Tanwar Pranay 
Published: April 2021

ABSTRACTRemarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains, thus enable the virus to rule the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, the mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. Therefore, in this study various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were carried and elucidated the protein structure and dynamics using molecular dynamics (MD) approach. MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed through protein-protein docking and observed that MTs showed high binding affinities than WT. Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.
PINAWeb: A web-based tool for the comparison of Protein-Protein Interaction Networks Aligners
Authors: Alcalá A. , Riera G. , García I. , Alberich R. , Llabrés M. 
Published: April 2021

AbstractMotivationSeveral protein-protein interaction networks (PPIN) aligners have been developed during the last 15 years. One of their goals is to help the functional annotation of proteins and the prediction of protein-protein interactions. A correct aligner must preserve the network’s topology as well as the biological coherence. However, this is a trade-off that is hard to achieve. In addition, most aligners require a considerable effort to use in practice and many researchers must choose an aligner without the opportunity to previously compare the performance of different aligners.ResultsWe developed PINAWeb, a user-friendly web-based tool to obtain and compare the results produced by the aligners: AligNet, HubAlign, L-GRAAL, PINALOG and SPINAL. PPINs can be uploaded either from the STRING database or from a user database. The source code of PINAWeb is freely available on GitHub to enable researchers to add other aligners, network databases or alignment score metrics. In addition, PINAWeb provides a report with the analysis for every alignment in terms of topological and functional information scores, as well as the visualization of the alignments’ comparison (agreement/differences) when more than one aligner are considered.Availabilityhttps://bioinfo.uib.es/~recerca/PINAWeb
Protein Charge Neutralization is the Proximate Driver Dynamically Tuning a Nanoscale Bragg Reflector
Authors: Levenson Robert , Malady Brandon , Lee Tyler , Sabeh Yahya Al , Kohl Phillip , Li Youli , Morse Daniel E. 
Published: April 2021

AbstractReflectin is a cationic, block copolymeric protein that mediates the dynamic fine-tuning of color and brightness of light reflected from nanostructured Bragg reflectors in iridocyte skin cells of squids. In vivo, neuronally activated phosphorylation of reflectin triggers its assembly, driving osmotic dehydration of the membrane-bounded Bragg lamellae containing the protein to simultaneously shrink the lamellar thickness and spacing while increasing its refractive index contrast, thus tuning the wavelength and increasing the brightness of reflectance. In vitro, we show that reduction in repulsive net charge of the purified, recombinant reflectin – either (for the first time) by generalized anionic screening with salt, or by pH titration - drives a finely tuned, precisely calibrated increase in size of the resulting multimeric assemblies. The calculated effects of phosphorylation in vivo are consistent with these effects observed in vitro. X-ray scattering analyses confirm the sphericity, size and low polydispersity of the assemblies. Precise proportionality between assembly size and charge-neutralization is enabled by the demonstrated rapid dynamic arrest of multimer growth. The resulting stability of reflectin assemblies with time ensures reciprocally precise control of the particle number concentration, thereby encoding a precise calibration between the extent of neuronal signaling, osmotic pressure, and the resulting optical changes. The results presented here strongly suggest that it is charge neutralization, rather than any change in aromatic content, that is the proximate driver of assembly, fine-tuning a colligative property-based nanostructured biological machine. A physical mechanism is proposed.
Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions
Authors: Grencewicz Dennis , Romigh Todd , Thacker Stetson , Abbas Ata , Jaini Ritika , Luse Donal , Eng Charis 
Published: April 2021

ABSTRACTGermline mutation ofPTENis causally observed in Cowden syndrome (CS) and is one of the most common genetic causes of autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are found to bePTEN-mutation negative. Reassessment ofPTENpromoter regulation may help explain abnormalPTENdosage, as only the minimal promoter and coding regions are currently included in diagnosticPTENmutation analysis. We reanalyzed the architecture of thePTENpromoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional TSRs at −2052 and −1907 basepairs from the start of PTEN, thus redefining thePTENpromoter and extending thePTEN5’UTR. The upstream TSRs described are active in cancer cell lines and human cancer and normal tissue. Further, these TSRs can produce novelPTENtranscripts due to the introduction of new splice sites. Evaluation of transcription factor binding specific to the upstream TSRs shows overrepresentation of TFs involved in inflammatory processes. Together, these data suggest that potentially clinically relevant promoter variants upstream of the known promoter may be overlooked in indivduals consideredPTENgermline mutation-negative and may also explain lack of PTEN expression in sporadic neoplasias withoutPTENsomatic structural defects.
Image-based Motion Artifact Reduction on Liver Dynamic Contrast Enhanced MRI
Authors: Wu Yunan , Liu Junchi , White Gregory M , Deng Jie 
Published: April 2021

AbstractLiver MRI images often suffer degraded quality from ghosting or blurring artifact caused by patient respiratory or bulk motion. In this study, we developed a two-stage deep learning model to reduce motion artifact on dynamic contrast enhanced (DCE) liver MRIs. The stage-I network utilized a deep residual network with a densely connected multi-resolution block (DRN-DCMB) network to remove the majority of motion artifacts. The stage-II network applied the perceptual loss to preserve image structural features by updating the parameters of the stage-I network via backpropagation. The stage-I network was trained using small image patches simulated with five types of motion, i.e., rotational, sinusoidal, random, elastic deformation and through-plane, to mimic actual liver motion patterns. The stage-II network training used full-size images with the same types of motion as the stage-I network. The motion reduction deep learning model was testing using simulated motion images and images with real motion artifacts. The resulted images after two-stage processing demonstrated substantially reduced motion artifacts while preserved anatomic details without image blurriness. This model outperformed existing methods of motion reduction artifact on liver DCE-MRI.
The genetic population structure of Lake Tanganyika’sLatesspecies flock, an endemic radiation of pelagic top predators
Authors: Rick Jessica A. , Junker Julian , Kimirei Ismael A. , Sweke Emmanuel A. , Mosille Julieth B. , Dinkel Christian , Mwaiko Salome , Seehausen Ole , Wagner Catherine E. 
Published: April 2021

AbstractUnderstanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemicLatesspecies of Lake Tanganyika(Lates stappersii, L. microlepis, L. mariaeandL. angustifrons)using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST= 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure withinL. mariae,with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis,andL. angustifrons).Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species—particularly that ofL. mariae—which may be important for conservation and management of this culturally and economically important clade of fish.
PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum
Authors: Zhou Yadi , Sukul Abhijit , Mishler-Elmore John W. , Faik Ahmed , Held Michael A. 
Published: April 2021

AbstractGlobal gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such asHordeum vulgare(barley) andSorghum bicolor(sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available athttps://plantnexus.ohio.edu/.
Blebs Promote Cell Survival by Assembling Oncogenic Signaling Hubs
Authors: Weems Andrew D. , Welf Erik S. , Driscoll Meghan K. , Zhou Felix , Mazloom-Farsibaf Hanieh , Chang Bo-Jui , Murali Vasanth S. , Gihana Gabriel M. , Weiss Byron G. , Chi Joseph , Rajendran Divya , Dean Kevin M. , Fiolka Reto , Danuser Gaudenz 
Published: April 2021

AbstractMost human cells require anchorage for survival. Cell-substrate adhesion activates diverse signaling pathways, without which cells undergo anoikis – a form of programmed cell death1. Acquisition of anoikis resistance is a pivotal step in cancer disease progression, as metastasizing cancer cells often lose firm attachment to surrounding tissue2–5. In these poorly attached states, cells adopt rounded morphologies and form small hemispherical plasma membrane protrusions called blebs6–13. Bleb function has been thoroughly investigated in the context of amoeboid migration but is far less examined in other scenarios14–19. Here we show by quantitative subcellular 3D imaging and manipulation of cell morphological states that blebbing triggers the formation of plasma membrane-proximal signaling hubs that confer anoikis resistance. Specifically, we discovered in melanoma cells that blebbing generates plasma membrane contours, which recruit curvature-sensing septin proteins as scaffolds for constitutively active mutant NRAS and effectors. These signaling hubs activate ERK and PI3K – canonical promoters of pro-survival pathways. Inhibition of blebs or septins has little effect on the survival of well-adhered cells, but in detached cells causes NRAS mislocalization, reduced MAPK and PI3K activity, and ultimately, death. This unveils an unanticipated morphological requirement for mutant NRAS to operate as an effective oncoprotein. Moreover, we find that though some BRAF mutant melanoma do not rely on this survival pathway in a basal state, BRAF/MEK inhibition strongly sensitizes them to both bleb and septin inhibition. Importantly, we demonstrate that fibroblasts engineered to sustain blebbing acquire the same anoikis resistance as cancer cells even without harboring oncogenic mutations. These data define a role for blebs as potent signaling organelles capable of integrating myriad cellular information flows into concerted cellular responses, in this case granting robust anoikis resistance.
A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis
Authors: Capece Marina , Tessari Anna , Mills Joseph , Rampioni Vinciguerra Gian Luca , Lin Chenyu , McElwain Bryan K , Miles Wayne O. , Coppola Vincenzo , Palmieri Dario , Croce Carlo M. 
Published: April 2021

AbstractThe OsTIR1/auxin-inducible degron (AID) system allows “on demand” selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. This new tool paves the way to studying the differential roles that target proteins may have in specific phases of the cell cycle.
Microglial ablation does not affect opioid-induced hyperalgesia in rodents
Authors: Liu Xin , Liu Bo-Long , Yang Qing , Zhou Xiangfu , Tang Shao-Jun 
Published: April 2021

AbstractOpioids are the frontline analgesics in pain management. However, chronic use of opioid analgesics causes paradoxical pain that contributes to the decrease of their efficacy in pain control and the escalation of dose in long-term management of pain. The underling pathogenic mechanism is not well understood. Microglia have been commonly thought to play a critical role in the expression of opioid-induced hyperalgesia (OIH) in animal models. We performed microglial ablation experiments using either a genetic (CD11b-diphtheria toxin receptor transgenic mouse) or pharmacological (colony-stimulating factor 1 receptor inhibitor PLX5622) approaches. Surprisingly, ablating microglia using these specific and effective approaches did not cause detectable impairment in the expression of hyperalgesia induced by morphine. We confirmed this conclusion with behavioral test of mechanical and thermal hyperalgesia, in male and female mice, and with different species (mouse and rat). These findings raise caution about the widely assumed contribution of microglia to the development of OIH.