bluuebunny/crossref_metadata_2025_split huggingface dataset:
Back to the Future: Whole Blood Resuscitation of the Severely Injured Trauma Patient
Authors: McCoy Christopher Cameron , Brenner Megan , Duchesne Juan , Roberts Derek , Ferrada Paula , Horer Tal , Kauvar David , Khan Mansoor , Kirkpatrick Andrew , Ordonez Carlos , Perreira Bruno , Priouzram Artai , Cotton Bryan A. 
Published: October 2020

ABSTRACT
Following advances in blood typing and storage, whole blood transfusion became available for the treatment of casualties during World War I. While substantially utilized during World War II and the Korean War, whole blood transfusion declined during the Vietnam War as civilian centers transitioned to blood component therapies. Little evidence supported this shift, and recent conflicts in Iraq and Afghanistan have renewed interest in military and civilian applications of whole blood transfusion. Within the past two decades, civilian trauma centers have begun to study transfusion protocols based upon cold-stored, low anti-A/B titer type O whole blood for the treatment of severely injured civilian trauma patients. Early data suggests equivalent or improved resuscitation and hemostatic markers with whole blood transfusion when compared to balanced blood component therapy. Additional studies are taking place to define the optimal way to utilize low-titer type O whole blood in both prehospital and trauma center resuscitation of bleeding patients.
Behaviour of two species of psittacine birds at wild bird feeding sites in Australia
Authors: Plant Michelle R. , Vankan Dianne , Baxter Gregory , Hall Evelyn , Phalen David 
Published: October 2020

AbstractThis study investigated how Crimson RosellasPlatycercus elegans(CR) and Australian King-ParrotsAlisterus scapularis(AKP) used provisioned seed at two public bird feeding sites in Australia. A total of 197 CR and 72 AKP were trapped and colour-banded. Observational data was collected every 10mins between 08:00-16:00 for three consecutive days during autumn and spring. Foraging effort was described using five metrics that quantified the birds’ visiting frequency and foraging duration over each day and observation period. Seed selection (over 5mins) and intake (over 10mins) were determined, and the energy intake was calculated. Total counts and population estimates were calculated for each species. Individual, species, seasonal and geographic variation in the use of provisioned seed was demonstrated by the metric summaries and Restricted Maximum Likelihood Modelling. Both species fed as part of large mixed species flocks that would not naturally congregate together to forage. Overall, CR were found to have higher foraging effort and feed in greater numbers than AKP, but a spectrum of use was observed for both species. Individuals were observed using the provisioned seed between 0-3 days/observation period. When birds used the provisioned seed, they were found to make between 1-8 visits/day, with most lasting 10-30mins. Few daily durations lasted longer than 50mins. Within a 10-minute interval, it was possible for a CR and AKP to obtain between 1.73-62.91% and 6.84-88.54% of their daily energy requirements, respectively. In a visit, either species could fill their crop and meet most, if not all, of their daily energy requirements. A small percentage of birds (6.5%) were found to use the feeding sites daily and for long durations (up to 160mins). It is likely that a proportion of the birds using the provisioned seed at both sites were dependent on the food source and would be at risk if the seed supply were suddenly reduced. The study also provided evidence that wild bird feeding provided an advantage to one or more species, as well as evidence that the food source did not affect the study species’ seasonal dispersal patterns or juveniles’ ability to forage on natural food sources.
Magnetoencephalographic Signatures of Conscious Processing Before Birth
Authors: Moser Julia , Schleger Franziska , Weiss Magdalene , Sippel Katrin , Semeia Lorenzo , Preissl Hubert 
Published: October 2020

AbstractThe concept of fetal consciousness is a widely discussed topic. In this study, we applied a hierarchical rule learning paradigm to investigate the possibility of fetal conscious processing during the last trimester of pregnancy. We used fetal magnetoencephalography, to assess fetal brain activity in 56 healthy fetuses between gestational week 25 and 40, during an auditory oddball paradigm containing first- and second-order regularities. The comparison of fetal brain responses towards standard and deviant tones revealed that the investigated fetuses show signs of hierarchical rule learning, and thus the formation of a memory trace for the second-order regularity. This ability develops over the course of the last trimester of gestation, in accordance with processes in physiological brain development and was only reliably present in fetuses older than week 35 of gestation. Analysis of fetal autonomic nervous system activity replicates findings in newborns, showing importance of activity state for cognitive processes. On the whole, our results support the assumption that fetuses in the last weeks of gestation are capable of consciously processing stimuli that reach them from outside the womb.
Accurate Prediction of Breast Cancer Survival through Coherent Voting Networks with Gene Expression Profiling
Authors: Pellegrini Marco 
Published: October 2020

ABSTRACTWe describe a novel machine learning methodology which we call Coherent Voting Network (CVN) and we demonstrate its usefulness by building a 5-years prognostic predictor for post-surgery breast cancer patients based on CVNs. Coherent Voting Network (CVN) is a supervised learning paradigm designed explicitly to uncover non-linear, combinatorial patterns in complex data, within a statistical robust framework. Breast Cancer patients after surgery may receive several types of post-surgery adjuvant therapeutic regimen (endocrine, radio- or chemo-therapy, and combinations thereof) aiming at reducing relapse and the formation of metastases, and thus favouring log term survival. We wish to predict the outcome of adjuvant therapy using just small molecular fingerprints (mRNA) of the patient’s transcriptome. Our aim is to have simultaneously high scores for PPV (positive predictive value) and NPV (negative predictive value) as these are important indices for the final clinical applications of the predictor. A Training-validate-test protocol is applied onto CVN built on patient data from the Metabric Consortium (about 2000 patients). For the testing pool of 82 lymph node positive patients we obtain PPV 0.77 and NPV 0.78 (Odds Ratio 11.50); for the pool of 61 lymph node negative patients we obtain PPV 0.68 and NPV 0.88 (Odds Ratio 16.07). Improved results are obtained on some specific sub-types of BC. For the testing pool of 16 TNBC patients we obtain PPV 1.0 and NPV 0.83 (Odds Ratio 45.00). For the testing pool of 18 HER2+ patients we obtain PPV 0.91 and NPV 1.0 (Odds Ratio 40.00). For the testing pool of 41 Luminal B patients we obtain PPV 0.75 and NPV 0.95 (Odds Ratio 60.00). Effectiveness of the selected fingerprints is confirmed also on several independent data sets (for a total of 601 patients) from the NCBI Gene Expression Omnibus (GEO).
BC-store: a program for mgiseq barcode sets analysis
Authors: Bulusheva Irina , Belova Vera , Nikashin Boris , Korostin Dmitriy 
Published: October 2020

AbstractHere we present the devised BC-store – a program for analyzing and selecting sets of barcodes for sequencing on platforms manufactured by MGI Tech (China). The app is available as an open source in Python3 and as a desktop version. The application allows analyzing the compatibility of barcodes on a single lane of a flow cell in a set in the case of equal and arbitrary fractions. In addition, with the help of this tool barcodes can be added to an existing set with custom share options. In this paper we describe how BC-store works for different tasks and consider the effectiveness of using BC-store in sequence lab routine tasks.Author summaryThe performance of modern NGS machines allows considerable amount of data to be obtained which exceed the data required for one specific sample. To pool multiple samples on a single lane of the flow cell, barcoding is used – adapters carrying a unique nucleotide sequence are introduced by ligation [1]. Adapters are sequenced from their specific primers. Their sequences are used for demultiplexing the sequencing results for individual fastq files by programs like zebracall [2] or bcl2fastq [3]. The task of selecting the adapters for a set is similar to sequencing low diversity libraries [4]: if all adapters on the lane have the same nucleotide during this sequencing cycle, the quality of its reading drops dramatically. Therefore, manufacturers recommend grouping the adapters by sets. However, the sets offered by MGI Tech [5] are far from routine practice, as they do not allow for non-equimolar sample pooling by default, and they have other disadvantages (more on them later in the text). To overcome these problems, we created the BC-store program, which allows analyzing the sets of MGI Tech barcodes entered by the user to be further used in sequencing. This tool also provides the opportunity to vary the number of simultaneously sequenced samples, to use reagents more efficiently, and, as a result, to correctly distribute reads across samples, which helps to increase both the quality of sequencing and the level of data interpretation.
5-amino levulinic acid inhibits SARS-CoV-2 infection in vitro
Authors: Sakurai Yasuteru , Ngwe Tun Mya Myat , Kurosaki Yohei , Sakura Takaya , Inaoka Daniel Ken , Fujine Kiyotaka , Kita Kiyoshi , Morita Kouichi , Yasuda Jiro 
Published: October 2020

AbstractThe current COVID-19 pandemic requires urgent development of effective therapeutics. 5-amino levulinic acid (5-ALA) is a naturally synthesized amino acid and has been used for multiple purposes including as an anticancer therapy and as a dietary supplement due to its high bioavailability. In this study, we demonstrated that 5-ALA treatment potently inhibited infection of SARS-CoV-2, a causative agent of COVID-19. The antiviral effects could be detected in both human and non-human cells, without significant cytotoxicity. Therefore, 5-ALA is a candidate as an oral antiviral drug for COVID-19.
Modulating Intra-Nuclear LC3 with Small Molecules Rescues Cells from a Docetaxel-Induced Phenotype
Authors: Rosenberg Daniel P. , Kolla Likhitha , Heo David S. , Cassio Emily E. , Veenstra Matthew J. , Vakaki Marianna , Zhang Jibo , Anyetei-Anum Cyril , Allison Lizabeth A. , Buchser William J. 
Published: October 2020

AbstractNucleus-associated autophagy has been described as a cellular metabolic response by which nuclear material is actively degraded. This degradation occurs after stress, such as nuclear damage or the onset of tumorigenesis. Here we describe a nucleus-associated autophagic process distinct from other forms of selective autophagy in human cell lines. We found that although nuclear localization of MAP1LC3B (LC3) is not dependent on particular nuclear importins, knockdown of nuclear importins, which causes nuclear stress, can induce a nuclear autophagic response. Our characterization of this autophagic phenomenon was facilitated by chemical modulation of the process via two compounds discovered previously in a high content analysis. These small molecules bidirectionally regulate nuclear LC3 in human renal, pancreatic, and bladder cell lines. One molecule (NSC31762 orDTEP)enhancesnuclear LC3 puncta and increases lysosomal targeting of LC3. This compound also decreases the nuclear envelope protein LaminB1. Another molecule (NSC279895 orDIHI)reducesthe nuclear localization of LC3. Finally, we applied these chemical tools in the setting of mitotic-disruptor induced nuclear stress. The compound DIHI, shown to reduce nuclear autophagic puncta, diminished the mitotic disruptor effect. These new tools will allow for deeper exploration of nucleus-associated autophagies, and could serve as proof-of-principle in guiding new therapies for diseases involving nuclear stress.
Microtissue geometry and cell-generated forces drive patterning of liver progenitor cell differentiation in 3D
Authors: Berg Ian C. , Mohagheghian Erfan , Habing Krista , Wang Ning , Underhill Gregory H. 
Published: October 2020

AbstractTowards understanding the impact of mechanical signaling on progenitor cell differentiation in three dimensional (3D) microenvironments, we implemented a hydrogel based microwell platform to produce arrays of multicellular microtissues in constrained geometries, which cause distinct profiles of mechanical signals. We applied this to a model liver development system to investigate the impact of geometry and stress on early liver progenitor cell fate. We fabricated 3D liver progenitor cell microtissues of varied geometries, including cylinder and toroid, and used image segmentation to track individual single cell fate. We observed patterning of hepatocytic makers to the outer shell of the microtissues, except at the inner diameter surface of the toroids. Biliary markers were distributed throughout the interior regions and was increased in toroid tissues compared to cylinder tissues. Finite element models of predicted stress distributions demonstrated that cell-cell tension correlated with hepatocytic fate, while compression correlated with decreased hepatocytic and increased biliary fate. This combined approach integrating microfabrication, imaging and analysis, and mechanical modeling demonstrate of how microtissue geometry can drive patterning of mechanical stresses that regulate cell differentiation trajectories. It also can serve as a platform for the further investigation of signaling mechanisms in the liver and other systems.
Phosphorylation triggers presynaptic phase separation of Liprin-α3 to control active zone structure
Authors: Emperador-Melero Javier , Wong Man Yan , Wang Shan Shan H. , de Nola Giovanni , Kirchhausen Tom , Kaeser Pascal S. 
Published: October 2020

AbstractLiquid-liquid phase separation enables the assembly of membrane-less subcellular compartments, but testing its biological functions has been difficult. The presynaptic active zone, protein machinery in nerve terminals that defines sites for neurotransmitter release, may be organized through phase separation. Here, we discover that the active zone protein Liprin-α3 rapidly and reversibly undergoes phase separation upon phosphorylation by PKC at a single site. RIM and Munc13 are co-recruited to membrane-attached condensates, and phospho-specific antibodies establish Liprin-α3 phosphorylation in vivo. At synapses of newly generated Liprin-α2/α3 double knockout mice, RIM, Munc13 and the pool of releasable vesicles were reduced. Re-expression of Liprin-α3 restored these defects, but mutating the Liprin-α3 phosphorylation site to abolish phase condensation prevented rescue. Finally, PKC activation acutely increased RIM, Munc13 and neurotransmitter release, which depended on the presence of phosphorylatable Liprin-α3. We conclude that Liprin-α3 phosphorylation rapidly triggers presynaptic phase separation to modulate active zone structure and function.
Prevalence and Associated Factors of Agricultural Technology Adoption and Teff Productivity in Basso Liben District, East Gojjame Zone, North west Ethiopia
Authors: Elemineh Demelash Abewa , Merie Hayimero Edmealem , Kassa Mulusew 
Published: October 2020

AbstractTeff productivity and Teff technology adoption in Ethiopia is low and it requiring immediate attention for policymakers and decision-makers. This study was conducted to identify the determinant factors that affect Teff technology adoption and Teff productivity in Basso Liben district, East Gojjam Zone, Northwest Ethiopia. A cross-sectional study design was conducted among 190 households. Multivariable linear and logistic regressions were employed to identify the factors associated with Teff production and Teff technology adoption respectively. Of a total of 190 households considered in the study, 77.9% were Teff technology adopter. Household head gender (male) (OR=7.644), family size (OR=1.149), age of household head (OR=0.873), row planting (use)(OR=257.2), credit access (yes)(OR=3.141), manure(use)(OR=0.042) were significance associated with Teff technology adoption in the study area. Age of household head (β= 0.079), Education level (primary)(β= −0.612), total land holding (β= 5.107), annual income(β=0.0051), extension service (no)(β= −0.635), row planting (yes) (β= 1.409), organic fertilizer (no)(β= −0.946) were significance associated with teff production in the study area. In this study, a low prevalence of agricultural technology adoption and Teff production and various associated agricultural technology adoption and Teff production factors have been identified in the study area. Thus, the concerned stockholders should intervene in agricultural technology adoption and Teff production via different extension service and by considering household size, community-based household head education, and efficient use landholding in hectare.
SARS-CoV-2 replication triggers an MDA-5-dependent interferon production which is unable to efficiently control replication
Authors: Antoine Rebendenne , Valadão Ana Luiza Chaves , Marine Tauziet , Ghizlane Maarifi , Boris Bonaventure , Rémi Planès , Joe McKellar , Sébastien Nisole , Mary Arnaud-Arnould , Olivier Moncorgé , Caroline Goujon 
Published: October 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third highly pathogenic coronavirus to spill over to humans in less than 20 years, after SARS-CoV-1 in 2002-2003 and Middle East respiratory syndrome (MERS)-CoV in 2012. SARS-CoV-2 is the etiologic agent of coronavirus disease 19 (COVID-19), which ranges from mild respiratory symptoms to severe lung injury and death in the most severe cases. The COVID-19 pandemic is currently a major health issue worldwide. Immune dysregulation characterized by altered innate cytokine responses is thought to contribute to the pathology of COVID-19 patients, which is a testimony of the fundamental role of the innate immune response against SARS-CoV-2. Here, we further characterized the host cell antiviral response against SARS-CoV-2 by using primary human airway epithelia and immortalized model cell lines. We mainly focused on the type I and III interferon (IFN) responses, which lead to the establishment of an antiviral state through the expression of IFN-stimulated genes (ISGs). Our results demonstrate that both primary airway epithelial cells and model cell lines elicit a robust immune response characterized by a strong induction of type I and III IFN through the detection of viral pathogen molecular patterns (PAMPs) by melanoma differentiation associated gene (MDA)-5. However, despite the high levels of type I and III IFNs produced in response to SARS-CoV-2 infection, the IFN response was unable to control viral replication, whereas IFN pre-treatment strongly inhibited viral replication andde novoproduction of infectious virions. Taken together, these results highlight the complex and ambiguous interplay between viral replication and the timing of IFN responses.
Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations and NMR Experiments
Authors: Zhang Zhengyue , Vögele Jennifer , Mráziková Klaudia , Kruse Holger , Cang Xiaohui , Wöhnert Jens , Krepl Miroslav , Šponer Jiří 
Published: October 2020

AbstractPhosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single non-bridging oxygen of the phosphate is replaced with a sulphur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present Molecular Dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the Neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn; an H-bond, an anion-π interaction and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulphur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases dispersion component of the anion-π stacking. The sulphur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulphur parameters and provide suggestions for improving the force-field performance.
Characterization of spatial dynamics of fMRI data in white matter using diffusion-informed white matter harmonics
Authors: Behjat Hamid , Aganj Iman , Abramian David , Eklund Anders , Westin Carl-Fredrik 
Published: October 2020

ABSTRACTIn this work, we leverage the Laplacian eigenbasis of voxelwise white matter (WM) graphs derived from diffusion-weighted MRI data, dubbedWM harmonics, to characterize the spatial structure of WM fMRI data. Our motivation for such a characterization is based on studies that show WM fMRI data exhibit a spatial correlational anisotropy that coincides with underlying fiber patterns. By quantifying the energy content of WM fMRI data associated with subsets of WM harmonics across multiple spectral bands, we show that the data exhibits notable subtle spatial modulations under functional load that are not manifested during rest. WM harmonics provide a novel means to study the spatial dynamics of WM fMRI data, in such way that the analysis is informed by the underlying anatomical structure.
Striking parallels between dorsoventral patterning inDrosophilaandGryllusreveal a complex evolutionary history behind a model gene regulatory network
Authors: Pechmann Matthias , Kenny Nathan James , Pott Laura , Heger Peter , Chen Yen-Ta , Buchta Thomas , Özüak Orhan , Lynch Jeremy , Roth Siegfried 
Published: October 2020

AbstractDorsoventral pattering relies on Toll and BMP signalling in all insects studied so far, with variations in the relative contributions of both pathways.Drosophilaand the beetleTriboliumshare extensive dependence on Toll, while representatives of more distantly related lineages like the waspNasoniaand bugOncopeltusrely more strongly on BMP signalling. Here, we show that in the cricketGryllus bimaculatus, an evolutionarily distant outgroup, Toll has, like inDrosophila, a direct patterning role for the ventral half of the embryo. In addition Toll polarizes BMP signalling, although this does not involve the conserved BMP inhibitor Sog/Chordin. Finally, Toll activation relies on ovarian patterning mechanisms with striking similarity toDrosophila.Our data suggest two surprising hypotheses: 1) that Toll’s patterning function inGryllusandDrosophilais the result of convergent evolution or 2) aDrosophila-likesystem arose early in insect evolution, and was extensively altered in multiple independent lineages.