bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings
Authors: Rathore Akanksha , Sharma Ananth , Sharma Nitika , Torney Colin J. , Guttal Vishwesha 
Published: January 2020

AbstractVideo recordings of animals are used for many areas of research such as collective movement, animal space-use, animal censuses and behavioural neuroscience. They provide us with behavioural data at scales and resolutions not possible with manual observations. Many automated methods are being developed to extract data from these high-resolution videos. However, the task of animal detection and tracking for videos taken in natural settings remains challenging due to heterogeneous environments.We present an open-source end-to-end pipeline calledMulti-Object Tracking in Heterogenous environments (MOTHe), a python-based application that uses a basic convolutional neural network for object detection. MOTHe allows researchers with minimal coding experience to track multiple animals in their natural habitats. It identifies animals even when individuals are stationary or partially camouflaged.MOTHe has a command-line-based interface with one command for each action, for example, finding animals in an image and tracking each individual. Parameters used by the algorithm are well described in a configuration file along with example values for different types of tracking scenario. MOTHe doesn’t require any sophisticated infrastructure and can be run on basic desktop computing units.We demonstrate MOTHe on six video clips from two species in their natural habitat - wasp colonies on their nests (up to 12 individuals per colony) and antelope herds in four different types of habitats (up to 156 individuals in a herd). Using MOTHe, we are able to detect and track all individuals in these animal group videos. MOTHe’s computing time on a personal computer with 4 GB RAM and i5 processor is 5 minutes for a 30-second long ultra-HD (4K resolution) video recorded at 30 frames per second.MOTHe is available as an open-source repository with a detailed user guide and demonstrations at Github (https://github.com/tee-lab/MOTHe).
Functional MRI Investigation on Paradigmatic and Syntagmatic Lexical Semantic Processing
Authors: Ying Songsheng , Ploux Sabine 
Published: January 2020

AbstractThe word embeddings related to paradigmatic and syntagmatic axes are applied in an fMRI encoding experiment to explore human brain’s activity pattern during story listening. This study proposes the construction of paradigmatic and syntagmatic semantic embeddings respectively by transforming WordNet-alike knowledge bases and subtracting paradigmatic information from a statistical word embedding. It evaluates the semantic embeddings by leveraging word-pair proximity ranking tasks and contrasts voxel encoding models trained with the two types of semantic features to reveal the brain’s spatial pattern for semantic processing. Results indicate that in listening comprehension, paradigmatic and syntagmatic semantic operations both recruit inferior (ITG) and middle temporal gyri (MTG), angular gyrus, superior parietal lobule (SPL), inferior frontal gyrus. A non-continuous voxel line is found in MTG with a predominance of paradigmatic processing. The ITG, middle occipital gyrus and the surrounding primary and associative visual areas are more engaged by syntagmatic processing. The comparison of two semantic axes’ brain map does not suggest a neuroanatomical segregation for paradigmatic and syntagmatic processing. The complex yet regular contrast pattern starting from temporal pole, along MTG to SPL necessitates further investigation.
Efficient replacement of long DNA fragments via non-homologous end joining at non-doding regions
Authors: Gu Shan-Ye , Li Jia , Cao Jian-Bin , Bu Ji-Wen , Ren Yong-Gang , Du Wen-Jie , Chen Zhe-Cong , Xu Chu-Fan , Wang Min-Cang , Jiang Lai , Huang Cheng , Du Jiu-Lin 
Published: January 2020

AbstractGenomic DNA replacement for achieving sophisticated genetic manipulation is implemented currently through homogenous recombination/homology-dependent repair (HR/HDR). Here we report an efficient DNA fragment replacement method that is mediated by non-homologous end joining (NHEJ)-dependent DNA repair at two sites of CRISPR/Cas9-induced double-strand breaks at non-coding genomic regions flanking the exons of targeted genes. We demonstrated this method by generating three conditional alleles and two reporter lines of zebrafish. Functional assays of the conditional alleles proved that the genomic sequence between two insertedloxPsites was deleted by the Cre recombinase, and the phenotype after Cre-induced excision was comparable to previously reported mutants or morphants. Furthermore, combining double-fluorescence expression donor vectors, we showed that the efficiency of this NHEJ-mediated DNA replacement was around 3 times larger than that of HR/HDR-mediated approach. Our method provides a feasible strategy for genomic DNA replacement in zebrafish, which can be applicable for other organisms as well.
Size-Based Dominance Hierarchy In One Of Two Sympatric Cryptic Pacific Skinks (Emoia imparAndEmoia Cyanura)
Authors: Hallsten Mary “Molly” 
Published: January 2020

AbstractEmoia imparandEmoia cyanuraare two morphologically cryptic Pacific skinks that have different preferred thermal micro-habitats but similar geographic range and overlap. Previously individuals have been noted to display a size-based dominance hierarchy at favored basking sites, though this behavior was not specified between species. I found that only one of the two species,E. impar, naturally presents this size-based dominance hierarchy in areas of high population density. Neither species exhibit the hierarchy in low population density areas. No evidence was found to suggest that the presence of this hierarchy allows one species to exclude the other.
Cancer-associated fibroblast compositions change with breast-cancer progression linking S100A4 and PDPN ratios with clinical outcome
Authors: Friedman Gil , Levi-Galibov Oshrat , David Eyal , Bornstein Chamutal , Giladi Amir , Dadiani Maya , Mayo Avi , Halperin Coral , Pevsner-Fischer Meirav , Lavon Hagar , Nevo Reinat , Stein Yaniv , Ali H. Raza , Caldas Carlos , Nili-Gal-Yam Einav , Alon Uri , Amit Ido , Scherz-Shouval Ruth 
Published: January 2020

AbstractTumors are supported by cancer-associated fibroblasts (CAFs). CAFs are heterogeneous and carry out distinct cancer-associated functions. Understanding the full repertoire of CAFs and their dynamic changes could improve the precision of cancer treatment. CAFs are usually analyzed at a single time-point using specific markers, and it is therefore unclear whether CAFs display plasticity as tumors evolve. Here, we analyze thousands of CAFs using index and transcriptional single-cell sorting, at several time-points along breast tumor progression in mice, uncovering distinct subpopulations. Strikingly, the transcriptional programs of these subpopulations change over time and in metastases, transitioning from an immune-regulatory program to wound healing and antigen-presentation programs, indicating that CAFs and their functions are dynamic. Two main CAF subpopulations are also found in human breast tumors, where their ratio is associated with disease outcome across subtypes, and is particularly correlated with BRCA mutations in triple-negative breast cancer. These findings indicate that the repertoire of CAFs changes over time in breast cancer progression, with direct clinical implications.
Apolipoprotein E4 disrupts the neuroprotective action of sortilin in neuronal lipid metabolism and endocannabinoid signaling
Authors: Asaro Antonino , Carlo-Spiewok Anne-Sophie , Malik Anna R. , Rothe Michael , Schipke Carola G. , Peters Oliver , Heeren Joerg , Willnow Thomas E. 
Published: January 2020

ABSTRACTINTRODUCTIONApoE is a carrier for brain lipids and the most important genetic risk factor for Alzheimer’s disease (AD). ApoE binds the receptor sortilin which mediates uptake of apoE-bound cargo into neurons. The significance of this uptake route for brain lipid homeostasis and AD risk seen with apoE4, but not apoE3, remains unresolved.METHODSCombining neurolipidomics in patient specimens with functional studies in mouse models, we interrogated apoE isoform-specific functions for sortilin in brain lipid metabolism and AD.RESULTSSortilin directs uptake and conversion of polyunsaturated fatty acids into endocannabinoids, lipid-based neurotransmitters that act through nuclear receptors to sustain neuroprotective gene expression in the brain. This sortilin function requires apoE3, but is disrupted by binding of apoE4, impairing endocannabinoid signaling and increasing amyloidogenic processing.DISCUSSIONWe uncovered the significance of neuronal apoE receptor sortilin in facilitating neuroprotective actions of brain lipids, and its relevance for AD risk seen with apoE4.
Deletion of MOrpholino Binding Sites (DeMOBS) to Assess Specificity of Morphant Phenotypes
Authors: Cunningham Carlee MacPherson , Bellipanni Gianfranco , Habas Raymond , Balciunas Darius 
Published: January 2020

AbstractTwo complimentary approaches are widely used to study gene function in zebrafish: induction of genetic mutations, usually using targeted nucleases such as CRISPR/Cas9, and suppression of gene expression, typically using Morpholino oligomers. Neither method is perfect. Morpholinos (MOs) sometimes produce off-target or toxicity-related effects that can be mistaken for true phenotypes. Conversely, genetic mutants can be subject to compensation, or may fail to yield a null phenotype due to leakiness. When discrepancy between mutant and morpholino-induced (morphant) phenotypes is observed, experimental validation of such phenotypes becomes very labor intensive. We have developed a simple genetic method to differentiate between genuine morphant phenotypes and those produced due to off-target effects. We speculated that indels within 5’ untranslated regions would be unlikely to have a significant negative effect on gene expression. Mutations induced within a MO target site would result in a Morpholino-refractive allele thus suppressing true MO phenotypes whilst non-specific phenotypes would remain. We tested this hypothesis on one gene with an exclusively zygotic function,tbx5a, and one gene with strong maternal effect,ctnnb2. We found that indels within the Morpholino binding site are indeed able to suppress both zygotic and maternal morphant phenotypes. We also observed that the ability of such indels to suppress Morpholino phenotypes does depend on the size and the location of the deletion. Nonetheless, mutating the morpholino binding sites in both maternal and zygotic genes can ascertain the specificity of morphant phenotypes.
Germ plasm localisation dynamics mark distinct phases of transcriptional and post-transcriptional regulation control in primordial germ cells
Authors: D’Orazio Fabio M. , Balwierz Piotr , Guo Yixuan , Hernández-Rodríguez Benjamín , Jasiulewicz Aleksandra , Vaquerizas Juan M. , Cairns Bradley , Lenhard Boris , Müller Ferenc 
Published: January 2020

SUMMARYIn many animal models, primordial germ cell (PGC) development depends on maternally-deposited germ plasm to avoid somatic cell fate. Here, we show that PGCs respond to regulatory information from the germ plasm in two distinct phases and mechanisms in zebrafish. We show that PGCs commence zygotic genome activation together with the rest of the embryo with no demonstrable differences in transcriptional and chromatin accessibility levels. Thus, cytoplasmic germ plasm determinants only affect post-transcriptional stabilisation of RNAs to diverge transcriptome from somatic cells, which, unexpectedly, also activate germ cell-specific genes. Perinuclear relocalisation of germ plasm is coupled to dramatic divergence in chromatin opening and transcriptome from somatic cells characterised by PGC-specific chromatin topology. Furthermore, we reveal Tdrd7, regulator of germ plasm localisation, as crucial determinant of germ fate acquisition.
URMAP, an ultra-fast read mapper
Authors: Edgar Robert C. 
Published: January 2020

AbstractMapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA and Bowtie2 with comparable accuracy on a benchmark test using simulated paired 150nt reads of a well-studied human genome. Software is freely available athttps://drive5.com/urmap.
Ubiquitin Ligase MARCH5 Regulates Apoptosis through Mediation of Stress-Induced and NOXA-Dependent MCL1 Degradation
Authors: Arai Seiji , Chen Sen , Xie Lisha , Balk Steven P. 
Published: January 2020

AbstractMCL1 has critical antiapoptotic functions and its levels are tightly regulated by ubiquitylation and degradation, but mechanisms that drive this degradation, particularly in solid tumors, remain to be established. We show here in prostate cancer cells that increased NOXA, mediated by activation of an integrated stress response, drives the degradation of MCL1, and identify the mitochondria-associated ubiquitin ligase MARCH5 as the primary mediator of this NOXA-dependent MCL1 degradation. Therapies that enhance MARCH5-mediated MCL1 degradation markedly enhance apoptosis in response to a BH3 mimetic agent targeting BCLXL, which may provide for a broadly effective therapy in solid tumors. Conversely, increased MCL1 in response to MARCH5 loss does not sensitize to BH3 mimetic drugs targeting MCL1, but instead also sensitizes to BCLXL inhibition, revealing a codependence between MARCH5 and MCL1 that may also be exploited in tumors withMARCH5genomic loss.
Reward-driven enhancements in motor control are robust to TMS manipulation
Authors: Codol Olivier , Galea Joseph M. , Jalali Roya , Holland Peter J. 
Published: January 2020

AbstractA wealth of evidence describes the strong positive impact that reward has on motor control at the behavioural level. However, surprisingly little is known regarding the neural mechanisms which underpin these effects, beyond a reliance on the dopaminergic system. In recent work, we developed a task that enabled the dissociation of the selection and execution components of an upper limb reaching movement. Our results demonstrated that both selection and execution are concommitently enhanced by immediate reward availability. Here, we investigate what the neural underpinnings of each component may be. To this end, we disrupted activity of the ventromedial prefrontal cortex and supplementary motor area using continuous theta-burst transcranial magnetic stimulation (cTBS) in a within-participant design (N=23). Both cortical areas are involved in reward processing and motor control, and we hypothesised that disruption of their activity would result in disruption of the reward-driven effects on action selection and execution, respectively. To increase statistical power, participants were pre-selected based on their sensitivity to reward in the reaching task. While reward did lead to enhanced perforance during the cTBS sessions and a control sham session, cTBS was ineffective in altering these effects. These results may provide evidence that other areas, such as the primary motor cortex or the premotor area, may drive the reward-based enhancements of motor performance.
Accelerating Prediction of Chemical Shift of Protein Structures on GPUs
Authors: Wright Eric , Ferrato Mauricio , Bryer Alex , Searles Robert , Perilla Juan , Chandrasekaran Sunita 
Published: January 2020

AbstractExperimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that the code refactoring and acceleration brought down the time taken of the software running on an NVIDIA V100 GPU to 46.71 seconds for our largest dataset of 11.3M atoms. We use OpenACC, a directive-based programming model for porting the application to a heterogeneous system consisting of x86 processors and NVIDIA GPUs. Finally, we demonstrate the feasibility of our approach in systems of increasing complexity ranging from 100K to 11.3M atoms.Author summary
The peptide sensor motif stabilizes the outward-facing conformation of TmrAB
Authors: Millan Cinthia R. , Francis Martina , Thompson Valery F. , Thaker Tarjani M. , Tomasiak Thomas M. 
Published: January 2020

ABSTRACTThe ATP binding cassette (ABC) family of transporters move diverse small molecules across membranes in nearly all organisms. Transport activity requires conformational switching between inward-facing and outward-facing states driven by ATP-dependent dimerization of two nucleotide binding domains (NBDs). The allosteric mechanism that connects ATP binding and hydrolysis in the NBDs to conformational changes in a substrate binding site in the transmembrane domains (TMDs) presents an unresolved question. Here we use sequence coevolution analyses together with biochemical characterization to investigate the role of a highly conserved motif called the peptide sensor in coordinating domain rearrangements in the heterodimeric peptide exporter fromThermus thermophilus, TmrAB. Mutations in the peptide sensor motif alter ATP hydrolysis rates as well as substrate release. Disulfide crosslinking, evolutionary trace, and evolutionary coupling analysis reveal that these effects likely destabilize a network between the peptide sensor motif and the Q-loop and X-loop, two known allosteric elements in the NBDs. We further find that disruption of this network in TmrA versus TmrB has different functional consequences, hinting at an intrinsic asymmetry in heterodimeric ABC transporters extending beyond that of the NBDs. These results support a mechanism in which the peptide sensor motifs help coordinate the transition of TmrAB to an outward open conformation, and each half of the transporter likely plays a different role in the conformational cycle of TmrAB.
sgRNA level is a major factor affecting CRISPRi knockdown efficiency in K562 cells
Authors: Wang Y. , Xie Y. , Dong Z. C. , Jiang X. J. , Gong P. , Lu J. , Wan F. 
Published: January 2020

AbstractTo determine how nuclease deactivated Cas9 (dCas9) or sgRNA expression level affects the knockdown efficiency of CRISPRi, K562 cell clones expressing KRAB-dCas9 protein either with the inducible Tet-on system or with the constitutive SFFV promotor were created by lentiviral transduction, and single clones were selected by fluorescence-activated cell sorting (FACS) for further study. Six genes with various expression levels were targeted using lentiviral sgRNA from two libraries in four cell clones with various KRAB-dCas9 expression levels. We determined the knockdown efficiency and the expression level of the dCas9 protein /sgRNA level by flow cytometry. The cell clone with the highest KRAB-dCas9 expression level achieved effective CRISPRi knockdown, and is statistically different from other clones, indicating enough KRAB-dCas9 expression might be a prerequisite for CRISPRi. Utilizing this clone, we modified the expression level of sgRNA by adopting different multiplicity of infection (MOI)in lentiviral transduction and found that the knockdown efficiency was neither affected by the target gene expression level nor does it correlate with KRAB-dCas9 level, which remained relatively constant (CV=2.2%) across knockdown experiments. 74.72%, 72.28%, 39.08% knockdown ofmmadhc, rpia, znf148genes were achieved, and the knockdown efficiency correlated well with the sgRNA expression level. Linear regression modeling of the data revealed that the knockdown efficiency is significantly affected by both KRAB-dCas9 and sgRNA level, and the sgRNA level has a greater impact, based on the standardized coefficient (0.525 for KRAB-dCas9, 0.981 for sgRNA), indicating that sgRNA level is a major factor affecting CRISPRi efficiency.
A broad and potent H1-specific human monoclonal antibody produced in plants prevents influenza virus infection and transmission in guinea pigs
Authors: Park Jun-Gyu , Ye Chengjin , Piepenbrink Michael S. , Nogales Aitor , Wang Haifeng , Shuen Michael , Meyers Ashley J. , Martinez-Sobrido Luis , Kobie James J. 
Published: January 2020

AbstractAlthough seasonal influenza vaccines block most predominant influenza types and subtypes, humans still remain vulnerable to waves of seasonal and new potential pandemic influenza viruses for which no immunity may exist because of viral antigenic drift and/or shift, respectively. Previously, we have described a human monoclonal antibody (hMAb), KPF1, which was produced in human embryonic kidney 293T cells (KPF1-HEK) with broad and potent neutralizing activity against H1N1 influenza A viruses (IAV)in vitro, and prophylactic and therapeutic activitiesin vivo. In this study, we produced hMAb KPF1 in tobacco plants (KPF1-Antx) and demonstrate how the plant-produced KPF1-Antx hMAb possesses similar biological activity compared with the mammalian produced KPF1-HEK hMAb. KPF1-Antx hMAb shows broad binding to recombinant HA proteins and H1N1 IAV, including A/California/04/2009 (pH1N1)in vitro, that are comparable to those observed with KPF1-HEK hMAb. Importantly, prophylactic administration of KPF1-Antx hMAb to guinea pigs prevented pH1N1 infection and transmission in both prophylactic and therapeutic experiments, substantiating its clinical potential to prevent and treat H1N1 infections. Collectively, this study demonstrates, for the first time, that plant-produced influenza hMAbs have similarin vitroandin vivobiological properties to those produced in mammalian cells. Because of the many advantages of plant-produced hMAbs, such as rapid batch production, low cost, and the absence of mammalian cell products, they represent an alternative strategy for the production of immunotherapeutics for the treatment of influenza viral infections, including emerging seasonal and/or pandemic strains.
Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells
Authors: Park Seongjin , Prévost Karine , Heideman Emily M. , Carrier Marie-Claude , Reyer Matthew A. , Liu Wei , Massé Eric , Fei Jingyi 
Published: January 2020

AbstractRNA binding proteins play myriad roles in controlling and regulating RNAs and RNA-mediated functions, often through simultaneous binding to other cellular factors. In bacteria, the RNA chaperone Hfq modulates post-transcriptional gene regulation. Absence of Hfq leads to the loss of fitness and compromises the virulence of bacterial pathogens. Using live-cell super-resolution imaging, we are able to distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA binding activity. Particularly, the distal face of Hfq contributes mostly to the mRNA bindingin vivo. In addition, binding of Hfq to these mRNAs can recruit RNase E to promote turnover of these mRNAs in an sRNA-independent manner, providing one mechanism to release Hfq from the pre-bound mRNAs. Finally, our data indicate that sRNAs, once expressed, can either co-occupy Hfq with the mRNA or displace the mRNA from Hfq, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Our data collectively demonstrate that Hfq dynamically changes its interactions with different RNAs in response to changes in cellular conditions.