bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non-human primate in vitro functional assay for the early evaluation of TB vaccine candidates
Authors: Tanner Rachel , White Andrew D. , Boot Charelle , Sombroek Claudia C. , O’Shea Matthew K. , Wright Daniel , Hoogkamer Emily , Bitencourt Julia , Harris Stephanie A. , Sarfas Charlotte , Wittenberg Rachel , Satti Iman , Fletcher Helen A. , Verreck Frank A. W. , Sharpe Sally A. , McShane Helen 
Published: January 2021

AbstractWe present a non-human primate mycobacterial growth inhibition assay (MGIA) using in vitro blood or cell co-culture with the aim of refining and expediting early tuberculosis vaccine testing. We have taken steps to optimise the assay using cryopreserved peripheral blood mononuclear cells, transfer it to end-user institutes, and assess technical and biological validity. Increasing cell concentration or mycobacterial input and co-culturing in static 48-well plates compared with rotating tubes improved intra-assay repeatability and sensitivity. Standardisation and harmonisation efforts resulted in high consistency agreements, with repeatability and intermediate precision <10% coefficient of variation (CV) and inter-site reproducibility <20% CV; although some systematic differences were observed. As proof-of-concept, we demonstrated ability to detect a BCG vaccine-induced improvement in growth inhibition in macaque samples, and a correlation between MGIA outcome and measures of protection from in vivo disease development following challenge with either intradermal BCG or aerosol/endobronchial Mycobacterium tuberculosis (M.tb) at a group and individual animal level.
Gendered movement ecology and landscape use in Hadza hunter-gatherers
Authors: Wood Brian M. , Harris Jacob A. , Raichlen David A. , Pontzer Herman , Sayre Katherine , Sancilio Amelia , Berbesque Colette , Crittenden Alyssa N. , Mabulla Audax , McElreath Richard , Cashdan Elizabeth , Jones James Holland 
Published: January 2021

AbstractUnderstanding how gendered economic roles structure space use is critical to evolutionary models of foraging behaviour, social organization and cognition. Here, we examine hunter-gatherer spatial behaviour on a very large scale, using GPS devices worn by Hadza foragers to record 2,078 person-days of movement. Theory in movement ecology suggests that the density and mobility of targeted foods should predict spatial behaviour and that strong gender differences should arise in a hunter-gatherer context. As predicted, we find that men walked further per day, explored more land, followed more sinuous paths and were more likely to be alone. These data are consistent with the ecology of male- and female-targeted foods and suggest that male landscape use is more navigationally challenging in this hunter-gatherer context. Comparisons of Hadza space use with space use data available for non-human primates suggest that the sexual division of labour likely co-evolved with increased sex differences in spatial behaviour and landscape use.
Probing valley population imbalance in transition metal dichalcogenides via temperature-dependent second harmonic generation imaging
Authors: Mouchliadis Leonidas , Psilodimitrakopoulos Sotiris , Maragkakis George Miltos , Demeridou Ioanna , Kourmoulakis George , Lemonis Andreas , Kioseoglou George , Stratakis Emmanuel 
Published: January 2021

AbstractDegenerate minima in momentum space—valleys—provide an additional degree of freedom that can be used for information transport and storage. Notably, such minima naturally exist in the band structure of transition metal dichalcogenides (TMDs). When these atomically thin crystals interact with intense laser light, the second harmonic generated (SHG) field inherits special characteristics that reflect not only the broken inversion symmetry in real space but also the valley anisotropy in reciprocal space. The latter is present whenever there exists a valley population imbalance (VPI) between the two valleys and affects the polarization state of the detected SHG. In this work, it is shown that the temperature-induced change of the SHG intensity dependence on the excitation field polarization is a fingerprint of VPI in TMDs. In particular, pixel-by-pixel VPI mapping based on polarization-resolved raster-scanning imaging microscopy was performed inside a cryostat to generate the SHG contrast in the presence of VPI from every point of a TMD flake. The generated contrast is marked by rotation of the SHG intensity polar diagrams at low temperatures and is attributed to the VPI-induced SHG.
Facilely synthesized nitrogen-doped reduced graphene oxide functionalized with copper ions as electrocatalyst for oxygen reduction
Authors: Garino Nadia , Zeng Juqin , Castellino Micaela , Sacco Adriano , Risplendi Francesca , Fiorentin Michele Re , Bejtka Katarzyna , Chiodoni Angelica , Salomon Damien , Segura-Ruiz Jaime , Pirri Candido F. , Cicero Giancarlo 
Published: January 2021

AbstractNitrogen-doped reduced graphene oxide is successfully synthesized and functionalized with hydroxylated copper ions via one-pot microwave-assisted route. The presence of cationic Cu coordinated to the graphene layer is fully elucidated through a set of experimental characterizations and theoretical calculations. Thanks to the presence of these hydroxyl-coordinated Cu2+ active sites, the proposed material shows good electrocatalytic performance for the oxygen reduction reaction, as evidenced by an electron transfer number of almost 4 and by high onset and half-wave potentials of 0.91 V and 0.78 V vs. the reversible hydrogen electrode, respectively. In addition, the N-doped Cu-functionalized graphene displays a superior current retention with respect to a commercial Pt/C catalyst during the stability test, implying its potential implementation in high-performance fuel cells and metal-air batteries.
Privacy protections to encourage use of health-relevant digital data in a learning health system
Authors: McGraw Deven , Mandl Kenneth D. 
Published: January 2021

AbstractThe National Academy of Medicine has long advocated for a “learning healthcare system” that produces constantly updated reference data during the care process. Moving toward a rapid learning system to solve intractable problems in health demands a balance between protecting patients and making data available to improve health and health care. Public concerns in the U.S. about privacy and the potential for unethical or harmful uses of this data, if not proactively addressed, could upset this balance. New federal laws prioritize sharing health data, including with patient digital tools. U.S. health privacy laws do not cover data collected by many consumer digital technologies and have not been updated to address concerns about the entry of large technology companies into health care. Further, there is increasing recognition that many classes of data not traditionally considered to be healthcare-related, for example consumer credit histories, are indeed predictive of health status and outcomes. We propose a multi-pronged approach to protecting health-relevant data while promoting and supporting beneficial uses and disclosures to improve health and health care for individuals and populations. Such protections should apply to entities collecting health-relevant data regardless of whether they are covered by federal health privacy laws. We focus largely on privacy but also address protections against harms as a critical component of a comprehensive approach to governing health-relevant data. U.S. policymakers and regulators should consider these recommendations in crafting privacy bills and rules. However, our recommendations also can inform best practices even in the absence of new federal requirements.
Digital oximetry biomarkers for assessing respiratory function: standards of measurement, physiological interpretation, and clinical use
Authors: Levy Jeremy , Álvarez Daniel , Rosenberg Aviv A. , Alexandrovich Alexandra , del Campo Félix , Behar Joachim A. 
Published: January 2021

AbstractPulse oximetry is routinely used to non-invasively monitor oxygen saturation levels. A low oxygen level in the blood means low oxygen in the tissues, which can ultimately lead to organ failure. Yet, contrary to heart rate variability measures, a field which has seen the development of stable standards and advanced toolboxes and software, no such standards and open tools exist for continuous oxygen saturation time series variability analysis. The primary objective of this research was to identify, implement and validate key digital oximetry biomarkers (OBMs) for the purpose of creating a standard and associated reference toolbox for continuous oximetry time series analysis. We review the sleep medicine literature to identify clinically relevant OBMs. We implement these biomarkers and demonstrate their clinical value within the context of obstructive sleep apnea (OSA) diagnosis on a total of n = 3806 individual polysomnography recordings totaling 26,686 h of continuous data. A total of 44 digital oximetry biomarkers were implemented. Reference ranges for each biomarker are provided for individuals with mild, moderate, and severe OSA and for non-OSA recordings. Linear regression analysis between biomarkers and the apnea hypopnea index (AHI) showed a high correlation, which reached $$\overline R ^2 = 0.82$$

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. The resulting python OBM toolbox, denoted “pobm”, was contributed to the open software PhysioZoo (physiozoo.org). Studying the variability of the continuous oxygen saturation time series using pbom may provide information on the underlying physiological control systems and enhance our understanding of the manifestations and etiology of diseases, with emphasis on respiratory diseases.
A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation
Authors: Scheffen Marieke , Marchal Daniel G. , Beneyton Thomas , Schuller Sandra K. , Klose Melanie , Diehl Christoph , Lehmann Jessica , Pfister Pascal , Carrillo Martina , He Hai , Aslan Selçuk , Cortina Niña S. , Claus Peter , Bollschweiler Daniel , Baret Jean-Christophe , Schuller Jan M. , Zarzycki Jan , Bar-Even Arren , Erb Tobias J. 
Published: January 2021

AbstractThe capture of CO2 by carboxylases is key to sustainable biocatalysis and a carbon-neutral bio-economy, yet currently limited to few naturally existing enzymes. Here, we developed glycolyl-CoA carboxylase (GCC), a new-to-nature enzyme, by combining rational design, high-throughput microfluidics and microplate screens. During this process, GCC’s catalytic efficiency improved by three orders of magnitude to match the properties of natural CO2-fixing enzymes. We verified our active-site redesign with an atomic-resolution, 1.96-Å cryo-electron microscopy structure and engineered two more enzymes that, together with GCC, form a carboxylation module for the conversion of glycolate (C2) to glycerate (C3). We demonstrate how this module can be interfaced with natural photorespiration, ethylene glycol conversion and synthetic CO2 fixation. Based on stoichiometrical calculations, GCC is predicted to increase the carbon efficiency of all of these processes by up to 150% while reducing their theoretical energy demand, showcasing how expanding the solution space of natural metabolism provides new opportunities for biotechnology and agriculture.
Single-cell fluidic force microscopy reveals stress-dependent molecular interactions in yeast mating
Authors: Mathelié-Guinlet Marion , Viela Felipe , Dehullu Jérôme , Filimonava Sviatlana , Rauceo Jason M. , Lipke Peter N. , Dufrêne Yves F. 
Published: January 2021

AbstractSexual agglutinins of the budding yeast Saccharomyces cerevisiae are proteins mediating cell aggregation during mating. Complementary agglutinins expressed by cells of opposite mating types “a” and “α” bind together to promote agglutination and facilitate fusion of haploid cells. By means of an innovative single-cell manipulation assay combining fluidic force microscopy with force spectroscopy, we unravel the strength of single specific bonds between a- and α-agglutinins (~100 pN) which require pheromone induction. Prolonged cell–cell contact strongly increases adhesion between mating cells, likely resulting from an increased expression of agglutinins. In addition, we highlight the critical role of disulfide bonds of the a-agglutinin and of histidine residue H273 of α-agglutinin. Most interestingly, we find that mechanical tension enhances the interaction strength, pointing to a model where physical stress induces conformational changes in the agglutinins, from a weak-binding folded state, to a strong-binding extended state. Our single-cell technology shows promises for understanding and controlling the complex mechanism of yeast sexuality.
miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1
Authors: Kato Mitsuo , Abdollahi Maryam , Tunduguru Ragadeepthi , Tsark Walter , Chen Zhuo , Wu Xiwei , Wang Jinhui , Chen Zhen Bouman , Lin Feng-Mao , Lanting Linda , Wang Mei , Huss Janice , Fueger Patrick T , Chan David , Natarajan Rama 
Published: January 2021

AbstractDiabetic kidney disease (DKD) is a major complication of diabetes. Expression of members of the microRNA (miRNA) miR-379 cluster is increased in DKD. miR-379, the most upstream 5′-miRNA in the cluster, functions in endoplasmic reticulum (ER) stress by targeting EDEM3. However, the in vivo functions of miR-379 remain unclear. We created miR-379 knockout (KO) mice using CRISPR-Cas9 nickase and dual guide RNA technique and characterized their phenotype in diabetes. We screened for miR-379 targets in renal mesangial cells from WT vs. miR-379KO mice using AGO2-immunopreciptation and CLASH (cross-linking, ligation, sequencing hybrids) and identified the redox protein thioredoxin and mitochondrial fission-1 protein. miR-379KO mice were protected from features of DKD as well as body weight loss associated with mitochondrial dysfunction, ER- and oxidative stress. These results reveal a role for miR-379 in DKD and metabolic processes via reducing adaptive mitophagy. Strategies targeting miR-379 could offer therapeutic options for DKD.
A single day of TGF-β1 exposure activates chondrogenic and hypertrophic differentiation pathways in bone marrow-derived stromal cells
Authors: Futrega Kathryn , Robey Pamela G. , Klein Travis J. , Crawford Ross W. , Doran Michael R. 
Published: January 2021

AbstractVirtually all bone marrow-derived stromal cell (BMSC) chondrogenic induction cultures include greater than 2 weeks exposure to transforming growth factor-β (TGF-β), but fail to generate cartilage-like tissue suitable for joint repair. Herein we used a micro-pellet model (5 × 103 BMSC each) to determine the duration of TGF-β1 exposure required to initiate differentiation machinery, and to characterize the role of intrinsic programming. We found that a single day of TGF-β1 exposure was sufficient to trigger BMSC chondrogenic differentiation and tissue formation, similar to 21 days of TGF-β1 exposure. Despite cessation of TGF-β1 exposure following 24 hours, intrinsic programming mediated further chondrogenic and hypertrophic BMSC differentiation. These important behaviors are obfuscated by diffusion gradients and heterogeneity in commonly used macro-pellet models (2 × 105 BMSC each). Use of more homogenous micro-pellet models will enable identification of the critical differentiation cues required, likely in the first 24-hours, to generate high quality cartilage-like tissue from BMSC.
Identification of PIM1 substrates reveals a role for NDRG1 phosphorylation in prostate cancer cellular migration and invasion
Authors: Ledet Russell J. , Ruff Sophie E. , Wang Yu , Nayak Shruti , Schneider Jeffrey A. , Ueberheide Beatrix , Logan Susan K. , Garabedian Michael J. 
Published: January 2021

AbstractPIM1 is a serine/threonine kinase that promotes and maintains prostate tumorigenesis. While PIM1 protein levels are elevated in prostate cancer relative to local disease, the mechanisms by which PIM1 contributes to oncogenesis have not been fully elucidated. Here, we performed a direct, unbiased chemical genetic screen to identify PIM1 substrates in prostate cancer cells. The PIM1 substrates we identified were involved in a variety of oncogenic processes, and included N-Myc Downstream-Regulated Gene 1 (NDRG1), which has reported roles in suppressing cancer cell invasion and metastasis. NDRG1 is phosphorylated by PIM1 at serine 330 (pS330), and the level of NDRG1 pS330 is associated higher grade prostate tumors. We have shown that PIM1 phosphorylation of NDRG1 at S330 reduced its stability, nuclear localization, and interaction with AR, resulting in enhanced cell migration and invasion.
Structural insights into photoactivation of plant Cryptochrome-2
Authors: Palayam Malathy , Ganapathy Jagadeesan , Guercio Angelica M. , Tal Lior , Deck Samuel L. , Shabek Nitzan 
Published: January 2021

AbstractCryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.
Fast automated detection of COVID-19 from medical images using convolutional neural networks
Authors: Liang Shuang , Liu Huixiang , Gu Yu , Guo Xiuhua , Li Hongjun , Li Li , Wu Zhiyuan , Liu Mengyang , Tao Lixin 
Published: January 2021

AbstractCoronavirus disease 2019 (COVID-19) is a global pandemic posing significant health risks. The diagnostic test sensitivity of COVID-19 is limited due to irregularities in specimen handling. We propose a deep learning framework that identifies COVID-19 from medical images as an auxiliary testing method to improve diagnostic sensitivity. We use pseudo-coloring methods and a platform for annotating X-ray and computed tomography images to train the convolutional neural network, which achieves a performance similar to that of experts and provides high scores for multiple statistical indices (F1 scores > 96.72% (0.9307, 0.9890) and specificity >99.33% (0.9792, 1.0000)). Heatmaps are used to visualize the salient features extracted by the neural network. The neural network-based regression provides strong correlations between the lesion areas in the images and five clinical indicators, resulting in high accuracy of the classification framework. The proposed method represents a potential computer-aided diagnosis method for COVID-19 in clinical practice.
Rate volatility and asymmetric segregation diversify mutation burden in cells with mutator alleles
Authors: Dowsett Ian T. , Sneeden Jessica L. , Olson Branden J. , McKay-Fleisch Jill , McAuley Emma , Kennedy Scott R. , Herr Alan J. 
Published: January 2021

AbstractMutations that compromise mismatch repair (MMR) or DNA polymerase ε or δ exonuclease domains produce mutator phenotypes capable of fueling cancer evolution. Here, we investigate how combined defects in these pathways expands genetic heterogeneity in cells of the budding yeast, Saccharomyces cerevisiae, using a single-cell resolution approach that tallies all mutations arising from individual divisions. The distribution of replication errors present in mother cells after the initial S-phase was broader than expected for a single uniform mutation rate across all cell divisions, consistent with volatility of the mutator phenotype. The number of mismatches that then segregated to the mother and daughter cells co-varied, suggesting that each division is governed by a different underlying genome-wide mutation rate. The distribution of mutations that individual cells inherit after the second S-phase is further broadened by the sequential actions of semiconservative replication and mitotic segregation of chromosomes. Modeling suggests that this asymmetric segregation may diversify mutation burden in mutator-driven tumors.
A framework for identifying the recent origins of mobile antibiotic resistance genes
Authors: Ebmeyer Stefan , Kristiansson Erik , Larsson D. G. Joakim 
Published: January 2021

AbstractSince the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome.
Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome
Authors: Hontani Yusaku , Baloban Mikhail , Escobar Francisco Velazquez , Jansen Swetta A. , Shcherbakova Daria M. , Weißenborn Jörn , Kloz Miroslav , Mroginski Maria Andrea , Verkhusha Vladislav V. , Kennis John T. M. 
Published: January 2021

AbstractNear-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.