bluuebunny/crossref_metadata_2025_split huggingface dataset:
PCV2 aggravated SS2 infection directly showed from differentially expressed proteome of PK15 cells
Authors: Jimin Tan , Qi Xiao , Xingguang Li , Hongjie Fan , Kongwang He 
Published: February 2020

ABSTRACTPCV2 and SS2 were clinically two major pathogens in pigs and they were zoonotic pathogens. There was extensive cellular tropism for both PCV2 and SS2, as well as, PK15 cells was PCV2 infection mainly cell model. It was found that when PCV2 infected PK15 cells before at the MOI=0.1, SS2 could cause more damage to PK15 cells. ITRAQ labeling proteomic technology was used to explore the differentially expressed proteome of PCV2 and SS2 single infection and co-infection in PK15 cells. The results showed that there were total 4736 proteins distinct changed in this infection models for PK15 cells. PCV2 aggravated SS2 infection were showed directly in the big amount of differentially expressed proteins like AGO3, OSBPL1A, ALB, RIC8A, UBL4A, INTS5 and so on. For the KEGG pathway analysis, it indicated that PCV2 mainly induced the proteins lessen though a series of disease pathway like metabolic pathways, huntington’s disease, insulin signaling pathways, long-term depression, etc. to make cell at a state of compensation. PCV2 before infection made the cells was on the chopping block. Contemporary, SS2 induced the proteins of PK15 rapidly changing, including pathways like spliceosome, endoplasmic reticulum, tight junction, actin cytoskeleton and some involved in parasitic infections pathways like ECM-receptor interaction, Leishmaniasis, Toxoplasmosis and so on. Simultaneously, PCV2 and SS2 existed common ground that they influence PK15 cell by some virulence factor interacted with cytomembrane, influenced the function of ribosome and tRNA. The role of SS2 in the co-infection like a cook chopper.
Ecdysone steroid hormone remote controls intestinal stem cell fate decisions via thePPARγ-homologEip75BinDrosophila
Authors: Zipper Lisa , Jassmann Denise , Burgmer Sofie , Görlich Bastian , Reiff Tobias 
Published: February 2020

AbstractDevelopmental studies revealed fundamental principles on how organ size and function is achieved, but less is known about organ adaptation to new physiological demands. In fruit flies, juvenile hormone (JH) induces intestinal stem cell (ISC) driven absorptive epithelial expansion balancing energy uptake with increased energy demands of pregnancy. Here, we show 20-Hydroxy-Ecdysone (20HE)-signaling controlling organ homeostasis with physiological and pathological implications. Upon mating, 20HE titer in ovaries and hemolymph are increased and act on nearby midgut progenitors inducingEcdysone-induced-protein-75B (Eip75B). Strikingly, thePPARγ-homologueEip75Bdrives ISC daughter cells towards absorptive enterocyte lineage ensuring epithelial growth. To our knowledge, this is the first time a systemic hormone is shown to direct local stem cell fate decisions. Given the protective, but mechanistically unclear role of steroid hormones in female colorectal cancer patients, our findings suggest a tumor-suppressive role for steroidal signaling by promoting postmitotic fate when local signaling is deteriorated.
Transparent and flexible ECoG electrode arrays based on silver nanowire networks for neural recordings
Authors: Neto Joana P. , Costa Adriana , Vaz Pinto Joana , Marques–Smith André , Costa Júlio , Martins Rodrigo , Fortunato Elvira , Kampff Adam R. , Barquinha Pedro 
Published: February 2020

ABSTRACTThis work explored hybrid films of silver nanowires (AgNWs) with indium-zinc oxide (IZO) for developing high-performance and low-cost electrocorticography (ECoG) electrodes. The transparent hybrid films achieved a sheet resistance of 6 Ω/sq enabling electrodes with 500 μm diameter to reach an impedance of 20 kΩ at 1 kHz and a charge storage capacity of 3.2 mC/cm2, an improvement in properties over IZO electrodes, whose performance is on par with the classical tin doped indium oxide (ITO). Characterization of light-induced artifacts was performed showing that light intensities <14 mW/mm2elicit minimal electrical potential variation, which falls within the magnitude of baseline noise. The validation of electrodes in vivo was achieved by recording electrical neural activity from the surface of rat cortex under anaesthesia. Moreover, the presence of the hybrid films did not cause distortion of light during fluorescence microscopy. This study highlighted the capabilities of the hybrid structure of AgNWs with IZO, that can be fabricated with industrially-established processes at low cost, to be used for transparent ECoG electrodes, offering a new way to record neural electrical activity on a large and fast scale with direct visualization of neurons.
A streamlined workflow for automated cryo focused ion beam milling
Authors: Tacke Sebastian , Erdmann Philipp , Wang Zhexin , Klumpe Sven , Grange Michael , Plitzko Jürgen M. , Raunser Stefan 
Published: February 2020

AbstractCryo-electron tomography is an emerging technique to study the cellular architecture and the structure of proteins at high resolutionin situ. Most biological specimens are too thick to be directly investigated and are therefore thinned by milling with a focused ion beam under cryogenic conditions. This procedure is prone to frost and amorphous ice depositions which makes it a tedious process, leading to suboptimal results especially when larger batches are milled. Here, we present new hardware that overcomes the current limitations. We developed a new glove box and a high vacuum cryo transfer system and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. This tremendously reduces the ice depositions during transfer and milling, and simplifies the handling of the sample. In addition, we tested a new software application that automates the key milling steps. Together, these improvements allow for high-quality, high-throughput cryo-FIB milling.
Neutral auditory words immediately followed by painful electric shock show reduced next-day recollection
Authors: Norton Caroline M. , Ibinson James W. , Pcola Samantha J. , Popov Vencislav , Tremel Joshua J. , Reder Lynne M. , Fiez Julie A. , Vogt Keith M. 
Published: February 2020

AbstractIn this study, we investigated the effect of experimentally delivered acute pain on explicit and implicit memory. Twenty-five subjects participated in experimental sessions on consecutive days. The first session involved a categorization task intended to induce incidental memory encoding. There were two conditions, presented in randomized order, in which subjects listened to a series of words, which was repeated three times. In one condition, one-third of the word items were immediately followed by a painful electrical shock and these pain-paired items were presented unpredictably. In the other condition, all word items were not associated with pain. Response times over these repeated presentations were assessed for differences. Explicit memory was tested the following day, employing a Remember-Know assessment of word recognition, with no shocks employed. Recollection was significantly reduced for pain-paired words, as the proportion of correct Remember responses (out of total correct responses) was significantly lower. There were no significant reductions in memory for non-pain items that followed painful stimulation after a period of several seconds. Consistent with the experience of pain consuming working memory resources, we theorize that painful shocks interrupt memory encoding for the immediately preceding experimental items, due to a shift in attention away from the word item.
Normalizing and denoising protein expression data from droplet-based single cell profiling
Authors: Mulè Matthew P. , Martins Andrew J. , Tsang John S. 
Published: February 2020

AbstractMultimodal single-cell protein and transcriptomic profiling (e.g. CITE-seq) holds promise for comprehensive dissection of cellular heterogeneity, yet protein counts measured by oligo-conjugated-antibody can have substantial noise that masks biological variations. Here we integrated experiments and computational analysis to reveal two major noise sources: protein-specific noise from unbound antibodies and cell-specific noise captured by the shared variance of isotype controls and background protein counts. We provide an open source R package (dsb) to denoise and normalize CITE-seq data based on these findings. (https://cran.r-project.org/web/packages/dsb/index.html).
Whole Slide Preview Image Segmentation and Setup for Digital Pathology Scanners
Authors: Hosseini Mahdi S. , Lee Dohyoung , Gershanik Daniel , Lee Dongwoon , Damaskinos Savvas , Plataniotis Konstantinos N. 
Published: February 2020

AbstractThe problem of tissue finding is of special interest in automating WSI scanners where it decomposes the preview image of tissue glass slides into a simplified and abstract level of localization and identification to setup WSI scanner for high-resolution scan. Prior to such scanning, a preview image is captured to calibrate the scanner’s parameters. Scan parameters such as focus depth and scan region are determined using a tissue finding software package. This paper introduces a series of pipelines (e.g. binary mask segmentation, tissue/artifact classification, region-of-interest allocation) to automate tissue preview segmentation in both brightfield and darkfield microscopy.
Knockdown of CSNK2β suppresses MDA-MB231 cells growth, induces apoptosis, inhibits migration and invasion
Authors: Lal Karna Shibendra Kumar , Lone Bilal Ahmad , Ahmad Faiz , Shahi Nerina , Pokharel Yuba Raj 
Published: February 2020

AbstractBreast cancer is most common cancer among women worldwide and among different types of breast cancer treatment of triple-negative breast cancer is major challenge, thus identification of specific drivers is required for targeted therapies of this malignancy. The aim of the present study is to elucidate the effects of silencing of CSNK2β gene by small interfering RNA (siRNA) on proliferation, cell cycle and apoptosis in breast carcinoma MDA MB-231 cells. Silencing of CSNK2β in MDA-MB-231(a triple negative cell line) cells resulted in decreased cell viability and colony formation. Cell cycle analysis showed that silencing of CSNK2β arrested MDA MB-231 cells in G2/M phase. We demonstrated that silencing of CSNK2β promoted nuclear condensation and augmented intracellular ROS production. Furthermore, Silencing of CSNK2β in MDA-MB 231 cells modulated the apoptotic machinery- BAX, Bcl-xL and caspase 3; autophagy machinary-Beclin-1 and LC3-1; and inhibited the vital markers (p-ERK, c-Myc, NF-κB, E2F1, PCNA, p38-α) associated with cell proliferation and DNA replication pathways. In addition, Knocking down of CSNK2 β also affected the migration potential of MDA-MB231 as observed in the wound healing and transwell migration assays. Together, our study suggests that CSNK2β silencing may offer future therapeutic target in triple negative breast cancer.
Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing
Authors: Silvestre-Ryan Jordi , Holmes Ian 
Published: February 2020

AbstractNanopore technology allows for direct sequencing of individual DNA duplexes. However, its higher error rate compared to other sequencing methods has limited its application in situations where deep coverage is unavailable, such as detection of rare variants or characterization of highly polymorphic samples. In principle, 2X coverage is available even for single duplexes, using Oxford Nanopore Technologies’ 1D2protocol or related methods which sequence both strands of the duplex consecutively. Using both strands should improve accuracy; however, most neural network basecaller architectures are designed to operate on single strands. We have developed a general approach for improving accuracy of 1D2and related protocols by finding the consensus of two neural network basecallers, by combining a constrained profile-profile alignment with a heuristic variant of beam search. When run on a basecalling neural network we trained, our consensus algorithm improves median basecall accuracy from 86.2% (for single-read decoding) to 92.1% (for pair decoding). Our software can readily be adapted to work with the output of other basecallers, such as the recently released Bonito basecaller. Although Bonito operates only on individual strands and was not designed to leverage the 1D2protocol, our method lifts its median accuracy from 93.3% to 97.7%, more than halving the median error rate. This surpasses the maximum accuracy achievable with Guppy, an alternate basecaller which was designed to include pair decoding of 1D2reads. Our software PoreOver, including both our neural network basecaller and our consensus pair decoder (which can be separably applied to improve other basecallers), is implemented in Python 3 and C++11 and is freely available athttps://github.com/jordisr/poreover.
Using Major Depression Polygenic Risk Scores to Explore the Depressive Symptom Continuum
Authors: Jermy Bradley S , Hagenaars Saskia P , Glanville Kylie P , Coleman Jonathan RI , Howard David M , Breen Gerome , Vassos Evangelos , Lewis Cathryn M 
Published: February 2020

AbstractBackgroundIt is not clear whether major depression (MD) is a categorical disorder or if depressive symptoms exist on a continuum based on severity. Observational studies comparing sub-threshold and clinical depression suggest MD is continuous, but many do not explore the full continuum and are yet to consider genetics as a risk factor. This study sought to understand if polygenic risk for MD could provide insight into the continuous nature of MD.MethodsFactor analysis on symptom-level data from the UK Biobank (N=148,957) was used to derive continuous depression phenotypes which were tested for association with polygenic risk scores for a categorical definition of MD (N=119,692).ResultsConfirmatory factor analysis showed a five-factor hierarchical model, incorporating 15 of the original 18 items, produced good fit to the observed covariance matrix (CFI = 0.992, TLI = 0.99, RMSEA = 0.038, SRMR = 0.031). MD PRS associated with each factor score (standardised ß range: 0.057 – 0.064) and the association remained when the sample was stratified into case- and control-only subsets. The case-only subset had an increased association compared to controls for all factors, shown via a significant interaction between lifetime MD diagnosis and MD PRS (p-value range: 2.28×10−3- 4.56×10−7).ConclusionsAn association between MD PRS and a continuous phenotype of depressive symptoms in case- and control-only subsets provides support against a purely categorical phenotype; indicating further insights into MD can be obtained when this within-group variation is considered. The stronger association within cases suggests this variation may be of particular importance.
X-ray and solution structures of human beta-2 glycoprotein I reveal a new mechanism of autoantibody recognition
Authors: Ruben Eliza , Planer William , Chinnaraj Mathivanan , Chen Zhiwei , Zuo Xiaobing , Pengo Vittorio , Filippis Vincenzo De , Alluri Ravi K. , McCrae Keith R. , Macor Paolo , Tedesco Francesco , Pozzi Nicola 
Published: February 2020

AbstractVenous and arterial thromboses in patients suffering from the autoimmune disorder Antiphospholipid Syndrome (APS) are caused by the presence of antiphospholipid antibodies (aPL). Emerging evidence indicates that autoantibodies targeting the epitope R39-R43 in the N-terminal domain, Domain I (DI), of β2-glycoprotein I (β2GPI) are among the most pathogenic aPL in patients with APS. How such autoantibodies engage β2GPI at the molecular level remains incompletely understood. Here, we have used X-ray crystallography, single-molecule FRET, and small-angle X-ray scattering to demonstrate that, in the free form, under physiological pH and salt concentrations, human recombinant β2GPI adopts an elongated, flexible conformation in which DI is exposed to the solvent, thus available for autoantibody recognition. Consistent with this structural model, binding and mutagenesis studies revealed that the elongated form interacts with a pathogenic anti-DI antibody in solution, without the need of phospholipids. Furthermore, complex formation was affected neither by the neighboring domains, nor by the presence of the linkers, nor by the glycosylations. Since the pathogenic autoantibody requires residues R39 and R43 for optimal binding, these findings challenge longstanding postulates in the field envisioning β2GPI adopting immunologic inert conformations featuring inaccessibility of the epitope R39-R43 in DI and support an alternative model whereby the preferential binding of anti-DI antibodies towards phospholipid-bound β2GPI arises from the ability of the pre-existing elongated form to bind to the membranes and then oligomerize, processes that are likely to be supported by protein conformational changes. Interfering with these steps may limit the pathogenic effects of anti-DI antibodies in APS patients.SignificanceIn the autoimmune disorder called Antiphospholipid Syndrome (APS), the presence of autoantibodies targeting the plasma glycoprotein beta-2 glycoprotein I (β2GPI) is associated with arterial and venous thrombosis as well as pregnancy complications. Understanding how β2GPI becomes immunogenic and how autoantibodies in complex with β2GPI cause the blood to clot remains a top priority in the field. By elucidating the structural architecture of β2GPI free in solution, our studies challenge longstanding postulates in the field and shed new light on the pathogenic mechanisms of APS that may help the development of new diagnostics and therapeutic approaches.
Purple bacteria as added-value protein ingredient in shrimp feed:Litopenaeus vannameigrowth performance, and tolerance againstVibrioand ammonia stress
Authors: Alloul Abbas , Wille Mathieu , Lucenti Piergiorgio , Bossier Peter , Van Stappen Gilbert , Vlaeminck Siegfried E. 
Published: February 2020

AbstractPurple non-sulfur bacteria (PNSB) biomass is an emerging alternative protein source, yet research of PNSB as added-value protein ingredient is limited. This research aimed to study the use of PNSB as protein source for shrimp and investigate the shrimp’s tolerance againstVibrioand ammonia stress. A 28-day shrimp feeding trial was performed withRhodopseudomonas palustris, Rhodobacter capsulatusand a mixed PNSB culture. PNSB contained in feed (5-10% protein substitution) resulted in 5-26% higher individual weights, better feed conversions ratios (1.2-1.7) compared to commercial feed (1.7) and tolerance against ammonia. In parallel, the effect of PNSB on the growth ofVibriopathogens was testedin vitro.The speciesRps. palustris, Rb. capsulatus, Rb. sphaeroides, Rhodospirillum rubrumandAfifella marinasuppressed the growth ofVibrio parahaemolyticusTW01 andV. campbelliiLMG 21363. Overall, this study demonstrated the potential of PNSB as nutritious feed ingredient for shrimp. This can contribute to circular economy, as PNSB enable resource recovery from wastewater.Abstract FigureGraphical abstractHighlightsPurple non-sulfur bacteria (PNSB) enhance the growth performance of shrimpPNSB-fed shrimp has better feed conversion ratio, growth rate and weight gainShrimp fed withRhodopseudomonasare more resistance against ammonia stressFreeze-dried and live PNSB inhibitVibriopathogensin vitro
Three-dimensional synaptic organization of the human hippocampal CA1 field
Authors: Montero-Crespo Marta , Domínguez-Álvaro Marta , Rondón-Carrillo Patricia , Alonso-Nanclares Lidia , DeFelipe Javier , Blázquez-Llorca Lidia 
Published: February 2020

AbstractThe hippocampal CA1 field integrates a wide variety of subcortical and cortical inputs, but its synaptic organization in humans is still unknown due to the difficulties involved studying the human brain via electron microscope techniques. However, we have shown that the 3D reconstruction method using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) can be applied to study in detail the synaptic organization of the human brain obtained from autopsies, yielding excellent results. Using this technology, 24,752 synapses were fully reconstructed in CA1, revealing that most of them were excitatory, targeting dendritic spines and displaying a macular shape, regardless of the layer examined. However, remarkable differences were observed between layers. These data constitute the first extensive description of the synaptic organization of the neuropil of the human CA1 region.
The occurrence of tarsal injuries in male mice of C57BL/6N substrains in multiple international mouse facilities
Authors: Herbert Eleanor , Stewart Michelle , Hutchison Marie , Flenniken Ann M. , Qu Dawei , Nutter Lauryl M. J. , McKerlie Colin , Hobson Liane , Kick Brenda , Lyons Bonnie , Wiegand Jean-Paul , Doty Rosalinda , Aguilar-Pimentel Juan Antonio , Hrabe de Angelis Martin , Dickinson Mary , Seavitt John , White Jacqueline K. , Scudamore Cheryl L , Wells Sara 
Published: February 2020

AbstractDislocation in hindlimb tarsals are being observed at a low, but persistent frequency in adult male mice from C57BL/6N substrains. Clinical signs included a sudden onset of mild to severe unilateral or bilateral tarsal abduction, swelling, abnormal hindlimb morphology and lameness. Contraction of digits and gait abnormalities were noted in multiple cases. Radiographical and histological examination revealed caudal dislocation of the calcaneus and partial dislocation of the calcaneoquartal (calcaneous-tarsal bone IV) joint. The detection, frequency, and cause of this pathology in five large mouse production and phenotyping centres (MRC Harwell, UK; The Jackson Laboratory, USA; The Centre for Phenogenomics, Canada; German Mouse Clinic, Germany; Baylor College of Medicine, USA) are discussed.