bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role ofCNC1gene in TDP-43 aggregation-induced oxidative stress-mediated cell death inS. cerevisiaemodel of ALS
Authors: Bharathi Vidhya , Girdhar Amandeep , Patel Basant K 
Published: March 2020

ABSTRACTTDP-43 is a multi-functional ribonucleoprotein that is also found deposited as hyper-phosphorylated and ubiquitinated TDP-43 inclusions in the brain and spinal cord of the patients of the motor neuron diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Till date, how the cell death ensues is not fully deciphered although several molecular mechanisms of the TDP-43 toxicity such as impairments of endocytosis and chromatin remodelling, mis-regulations of autophagy and proteasome function, mis-localization to the mitochondria and generation of oxidative stress etc., have been proposed. A predominantly nuclear protein, Cyclin C, can regulate the oxidative stress response by affecting the transcription of stress response genes and also by translocation to the cytoplasm for the activation of the mitochondrial fragmentation-dependent cell death pathway. Using the well-established yeast model of TDP-43 aggregation and toxicity, we examined here whether upon TDP-43 aggregation, the cell survival depends on the presence of theCNC1gene that encodes Cyclin C protein or other genes that encode proteins that function in conjunction with Cyclin C, such as theDNM1, FIS1andMED13genes. We found that the TDP-43 toxicity is significantly reduced in the yeast deleted for theCNC1orDNM1genes. Importantly, the rescue of TDP-43 toxicity in these yeast deletion backgrounds required the presence of functional mitochondria. Also, the deletion ofYBH3gene, which encodes for a protein involved in the mitochondria-dependent apoptosis, also reduced the TDP-43 toxicity. Furthermore, Cyclin C-YFP was observed to localize from the nucleus to the cytoplasm in response to the TDP-43 co-expression. Also, this cytoplasmic localization of Cyclin C was prevented by the addition of an anti-oxidant molecule, N-acetyl-cysteine. Taken together, our data suggest that Cyclin C, Dnm1 and Ybh3 proteins are important in mediating the TDP-43-induced oxidative stress-mediated cell death in theS. cerevisiaemodel.
Simultaneous monitoring of the same animals with PIT-tags and sensor nodes causes no system interference
Authors: Ripperger Simon P , Duda Niklas , Kölpin Alexander , Carter Gerald G 
Published: March 2020

AbstractRecent technological advances have multiplied the variety of biologgers used in wildlife research, particularly with small-bodied animals. Passive integrated transponders (PIT) have been used for decades to log visits of tagged animals at reader-equipped artificial feeders or roost boxes. More recently, novel miniaturized sensor nodes can collect data on social encounters among tagged individuals in any location. Combining these systems allows researchers to gather high-resolution tracking data on certain individuals from their long-term PIT-tagged animal populations. However, there can be a risk of interference among tracking systems. Here we tested whether placing an additional biologging sensor on top of a PIT-tag might attenuate the magnetic field reaching the PIT-tag and in turn hamper reading success of the radio-frequency identification (RFID) reader. We also evaluated data transmission by a digital sensor node in the presence of a magnetic field created by the RFID-antenna. The combination of this RFID-system and wireless biologging sensors works without error, suggesting that the simultaneous use of PIT-tags and other digital biologgers, e.g. miniaturized GPS-loggers, should also work together properly when communication channels do not overlap. The combination of long-term monitoring with PIT tags and short-term tracking with biologging sensor nodes creates exciting new opportunities to gather rich social data from individuals not present at RFID reader stations.
Automated search of stimulation targets with closed-loop transcranial magnetic stimulation
Authors: Tervo Aino E. , Metsomaa Johanna , Nieminen Jaakko O. , Sarvas Jukka , Ilmoniemi Risto J. 
Published: March 2020

AbstractTranscranial magnetic stimulation (TMS) protocols often include a manual search of an optimal location and orientation of the coil or peak stimulating electric field to elicit motor responses in a target muscle. This target search is laborious, and the result is user-dependent. Here, we present a closed-loop search method that utilizes automatic electronic adjustment of the stimulation based on the previous responses. The electronic adjustment is achieved by multi-locus TMS, and the adaptive guiding of the stimulation is based on the principles of Bayesian optimization to minimize the number of stimuli (and time) needed in the search. We compared our target-search method with other methods, such as systematic sampling in a predefined cortical grid. Validation experiments on five healthy volunteers and further offline simulations showed that our adaptively guided search method needs only a relatively small number of stimuli to provide outcomes with good accuracy and precision. The automated method enables fast and user-independent optimization of stimulation parameters in research and clinical applications of TMS.
Semantic Segmentation of HeLa Cells: An Objective Comparison between one Traditional Algorithm and Three Deep-Learning Architectures
Authors: Karabağ Cefa , Jones Martin L. , Peddie Christopher J. , Weston Anne E. , Collinson Lucy M. , Reyes-Aldasoro Constantino Carlos 
Published: March 2020

AbstractIn this work, images of a HeLa cancer cell were semantically segmented with one traditional image-processing algorithm and three deep learning architectures: VGG16, ResNet18 and Inception-ResNet-v2. Three hundred slices, each 2000 × 2000 pixels, of a HeLa Cell were acquired with Serial Block Face Scanning Electron Microscopy. The deep learning architectures were pre-trained with ImageNet and then fine-tuned with transfer learning. The image-processing algorithm followed a pipeline of several traditional steps like edge detection, dilation and morphological operators. The algorithms were compared by measuring pixel-based segmentation accuracy and Jaccard index against a labelled ground truth. The results indicated a superior performance of the traditional algorithm (Accuracy = 99%, Jaccard = 93%) over the deep learning architectures: VGG16 (93%, 90%), ResNet18 (94%, 88%), Inception-ResNet-v2 (94%, 89%).
Phosphine: an eco-friendly alternative for management of wheat storage insects
Authors: Arora Sumitra , Stanley J. , Srivastava C. 
Published: March 2020

ABSTRACTMethyl bromide (MB) fumigant has been phased out in many countries honouring ‘Montreal Protocol’. Reports on phosphine fumigant efficacy under different ecological zones in India are scanty. Field fumigation trials were conducted on 5 Metric Tons of wheat stacks per replication of a treatment for testing phosphine efficacy against laboratory cultured and resident population ofTribolium castanium,Sitophilus oryzae, andRhyzopertha dominica. The trials were organized in triplicate including control at two locations with varying climate locations namely, Pithoragarh and Delhi using conventional 56% tablet (2 and 3 tablet/MT) and 77.5% granular (1.0 and 1.5 g phosphine/m3) formulations of Aluminium phosphide (AlP) for 7 and 10-days exposure periods for each dosage. Phosphine concentration was monitored every 24 hours till end of the exposure periods. Insect mortality of laboratory culture and resident infestation was observed as 100% in both the exposure periods using all dosages of phosphine. No emergence of insects was observed till 60 days after treatment at both the locations, indicating mortality of all available life stages of insects during the exposure periods. Minimum effective phosphine concentration for controlling all life stages ofS. oryzae,R. dominicaandT castaneumwas observed 500-600 ppm for 7-days exposure at 25°-27°C and humidity 38-45%, at 1.5 g phosphine/m3. Hence, phosphine can be an effective alternative to methyl bromide fumigant for wheat stored grain insects at different climatic conditions.
ACTB and GAPDH proteins appear at multiple positions of SDS-PAGE and may not be suitable for serving as reference genes for the protein level determination in such techniques as Western blotting
Authors: He Yan , Zhang Ju , Qu Jiayuan , Zellmer Lucas , Zhao Yan , Liu Siqi , Huang Hai , Liao Dezhong Joshua 
Published: March 2020

AbstractMost human genes can produce multiple protein isoforms that should appear at multiple positions of polyacrylamide gel electrophoresis (PAGE) with sodium dodecyl sulfate (SDS), but most published results of Western blotting show only one protein. We performed SDS-PAGE of proteins from several human cell lines, isolated the proteins at the 72-, 55-, 48-, 40-, and 26-kD positions, and used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although ACTB and GAPDH are 41.7-kD and 36-kD proteins, respectively, LC-MS/MS identified peptides of ACTB and GAPDH at all of these SDS-PAGE positions, making us wonder whether they produce some unknown protein isoforms. The NCBI (National Center for Biotechnology Information, USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one non-coding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatic analysis identified a 17.6-kD isoform encoded by the non-coding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with great similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to ACTB. These data collectively disqualify GAPDH and ACTB from serving as the reference genes for determination of the protein level in such techniques as Western blotting, a leading role these two genes have been playing for decades in the biomedical research.
Epizootic of highly pathogenic H7N3 Avian Influenza in an ecologic reserve in Mexico
Authors: Navarro-López Roberto , Solís-Hernández Mario , Márquez-Ruiz Miguel A. , Rosas-Téllez Abel , Guichard-Romero Carlos A. , Cartas-Heredia Gerardo de J. , Morales-Espinosa Romeo , Valdez-Gómez Héctor E. , Afonso Claudio L. 
Published: March 2020

SummaryThis report includes a 2015 epizootic of highly pathogenic H7N3 avian influenza virus among captive and wild birds at “El Zapotal” ecologic reserve, located in the state of Chiapas, Mexico. Epidemiological control measures were implemented to prevent virus dissemination. The infection with the highly pathogenic H7N3 virus was detected predominantly among Plain Chachalaca (Ortalis vetula), with occasional detections in a White-fronted Parrot (Amazona albifrons) and a single Clay-colored Thrush (Turdus grayi). Here, we describe the characteristics of the outbreak environment, the surveillance strategy, the biosecurity measures, and the evaluation of the site, including external farms. These actions, timely implemented by the veterinary authorities, helped to contain the outbreak beyond the ecologic reserve. This contingency showed the importance of developing a more complete analysis of the existing risks and the challenges to implement minimal biosecurity measures in these facilities.
NORMA-The network makeup artist: a web tool for network annotation visualization
Authors: Koutrouli Mikaela , Karatzas Evangelos , Papanikolopoulou Katerina , Pavlopoulos Georgios A. 
Published: March 2020

AbstractNORMA is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g. Gene Ontology/Pathway enrichment or clustering results) can be uploaded and visualized in a network either as colored pie-chart nodes or as color-filled convex hulls in a Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are:i)the network,ii)the communities or annotations andiii)node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at:http://bib.fleming.gr:3838/NORMAorhttp://genomics-lab.fleming.gr:3838/NORMA. Code is available at:https://github.com/PavlopoulosLab/NORMA
Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry
Authors: Zhang Fangfei , Yu Shaoyang , Wu Lirong , Zang Zelin , Yi Xiao , Zhu Jiang , Lu Cong , Sun Ping , Sun Yaoting , Selvarajan Sathiyamoorthy , Chen Lirong , Teng Xiaodong , Zhao Yongfu , Wang Guangzhi , Xiao Junhong , Huang Shiang , Kon Oi Lian , Iyer N. Gopalakrishna , Li Stan Z. , Luan Zhongzhi , Guo Tiannan 
Published: March 2020

AbstractA novel approach for phenotype prediction is developed for mass spectrometric data. First, the data-independent acquisition (DIA) mass spectrometric data is converted into a novel file format called “DIA tensor” (DIAT) which contains all the peptide precursors and fragments information and can be used for convenient DIA visualization. The DIAT format is fed directly into a deep neural network to predict phenotypes without the need to identify peptides or proteins. We applied this strategy to a collection of 102 hepatocellular carcinoma samples and achieved an accuracy of 96.8% in classifying malignant from benign samples. We further applied refined model to 492 samples of thyroid nodules to predict thyroid cancer; and achieved a predictive accuracy of 91.7% in an independent cohort of 216 test samples. In conclusion, DIA tensor enables facile 2D visualization of DIA proteomics data as well as being a new approach for phenotype prediction directly from DIA-MS data.
Model-based design and analysis of life table experiments for insect vectors
Authors: Erguler Kamil , Demirok Murat Can , Gunay Filiz , Petrić Mina , Kavran Mihaela , Petrić Dušan Veljko , Alten Bulent 
Published: March 2020

AbstractLife tables help identify physiological differences in distinct development stages and detect potential vulnerabilities for conservation and control. However, cataloguing mortality, development, and fecundity by following each individual could be challenging in insects due to interweaving generations and development stages.Here, we propose to use age- and stage-structured population dynamics modelling to help derive life table characteristics from the observed dynamics of reared populations. We examine a hypothetical case, a simulated population with known life parameters, and two experimental cases, observations of the population dynamics of the mosquito vectorsCulex quinquefasciatusandCulex pipiens, to demonstrate that model-based inference can correctly identify life parameters from longitudinal observations. The analysis reveals not only the differential physiological behaviour of distinct development stages, but also identifies the degree to which each parameter can be inferred from the data.The methods introduced constitute a model-based approach to identifying life table characteristics from incomplete longitudinal data, and help to improve the design of life table experiments. The approach is readily applicable to the development of climate- and environment-driven population dynamics models for important vectors of disease.
ProminTools: Shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
Authors: Skeffington Alastair W , Donath Andreas 
Published: March 2020

AbstractBiominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpetLottia gigantea.
Time of Day Dependent Effects of Contractile Activity on the Phase of the Skeletal Muscle Clock
Authors: Kemler Denise , Wolff Christopher A. , Esser Karyn A. 
Published: March 2020

ABSTRACTExercise has been proposed to be a zeitgeber for the muscle circadian clock mechanism. However, this is not well defined and it is unknown if exercise timing induces directional shifts of the muscle clock. Our purpose herein was to assess the effect of one bout of treadmill exercise on skeletal muscle clock phase changes. We subjected PERIOD2::LUCIFERASE mice (n=30F) to one 60-minute treadmill exercise bout at three times of day. Exercise at ZT5, 5h after lights on, induced a phase advance (1.4±0.53h; p=0.038), whereas exercise at ZT11, 1h before lights off, induced a phase delay (−0.95±0.43h; p=0.0315). Exercise at ZT17, middle of the dark phase, did not alter muscle clock phase. Exercise induces diverse systemic changes so we developed anin-vitromodel system to examine effects of contractile activity on muscle clock phase. Contractions applied at peak or troughBmal1expression induced significant phase delays (applied at peak: 1.3±0.02h; p=0.0425; applied at trough: 1.8±0.02h, p=0.0074). Contractions applied during the transition from peak to troughBmal1expression induced a phase advance (1.8±0.03h; p=0.0265). Lastly, contractions at different times of day resulted in differential changes of core-clock gene expression demonstrating an exercise and clock interaction, providing insight into potential mechanisms exercise-induced phase shifts. These data demonstrate that muscle contractions, as part of exercise, are sufficient to shift muscle circadian clock phase, likely through changes in core-clock gene expression. Additionally, our findings that exercise induces directional muscle clock phase changes confirms exercise is a bone fide environmental time cue for skeletal muscle.
Modification of forests by people means only 40% of remaining forests have high ecosystem integrity
Authors: Grantham H.S. , Duncan A. , Evans T. D. , Jones K. , Beyer H. , Schuster R. , Walston J. , Ray J. , Robinson J. , Callow M. , Clements T. , Costa H.M. , DeGemmis A. , Elsen P.R. , Ervin J. , Franco P. , Goldman E. , Goetz S. , Hansen A. , Hofsvang E. , Jantz P. , Jupiter S. , Kang A. , Langhammer P. , Laurance W.F. , Lieberman S. , Linkie M. , Malhi Y. , Maxwell S. , Mendez M. , Mittermeier R. , Murray N. , Possingham H. , Radachowsky J. , Samper C. , Silverman J. , Shapiro A. , Strassburg B. , Stevens T. , Stokes E. , Taylor R. , Tear T. , Tizard R. , Venter O. , Visconti P. , Wang S. , Watson J.E.M. 
Published: March 2020

AbstractMany global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remains poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate the first globally-consistent, continuous index of forest condition as determined by degree of anthropogenic modification. Globally, only 17.4 million km2of forest (40.5%) have high landscape level integrity (mostly found in Canada, Russia, the Amazon, Central Africa and New Guinea) and only 27% of this area is found in nationally-designated protected areas. Of the forest in protected areas, only 56% has high landscape level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.
miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems
Authors: Kern Fabian , Fehlmann Tobias , Solomon Jeffrey , Schwed Louisa , Backes Christina , Meese Eckart , Keller Andreas 
Published: March 2020

AbstractGene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs.Here, we present miEAA 2.0, supporting miRNA input fromHomo sapiens, Mus musculus, andRattus norvegicus. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miR-Base miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualisations such as heatmaps and running sum curves with background distributions. Lastly, additional methods to correct for multiple hypothesis testing were implemented. We demonstrate the new features using case studies for human kidney cancer and mouse samples. The tool is freely accessible at:https://www.ccb.uni-saarland.de/mieaa2.