bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of integration of brain networks after sleep deprivation relates to the worsening of cognitive functions
Authors: Matteo Pesoli , Rosaria Rucco , Marianna Liparoti , Anna Lardone , Giula D’Aurizio , Roberta Minino , Emahnuel Troisi Lopez , Antonella Paccone , Carmine Granata , Giuseppe Sorrentino , Laura Mandolesi , Pierpaolo Sorrentino 
Published: July 2020

AbstractThe topology of brain networks changes according to environmental demands and can be described within the framework of graph theory. We hypothesized that 24-hours long sleep deprivation (SD) causes functional rearrangements of the brain topology so as to impair optimal communication, and that such rearrangements relate to the performance in specific cognitive tasks, namely the ones specifically requiring attention. Thirty-two young men underwent resting-state MEG recording and assessments of attention and switching abilities before and after SD. We found loss of integration of brain network and a worsening of attention but not of switching abilities. These results show that brain network changes due to SD affect switching abilities, worsened attention and induce large-scale rearrangements in the functional networks.
Acute Demyelinating Encephalomyelitis (ADEM) in COVID-19 infection: A Case Series
Authors: McCuddy Micheala , Kelkar Praful , Zhao Yu , Wicklund David 
Published: July 2020

AbstractObjectiveTo report three patients infected with COVID-19 with severe respiratory syndrome requiring intubation, who developed acute demyelinating encephalomyelitis (ADEM).MethodPatient data were obtained from medical records from the North Memorial Health Hospital, Robbinsdale, MN, USAResultsThree patients (two men and one woman, aged 38 - 63) presented with fatigue, cough and fever leading to development of acute respiratory distress syndrome secondary to COVID-19 infection requiring intubation and ventilatory support. Two patients were unresponsive, one with strong eye deviation to the left and the third patient had severe diffuse weakness. MRI in all patients showed findings consistent with ADEM. CSF showed elevated protein in all patients with normal cell count and no evidence of infection, including negative COVID-19 PCR. All three of the patients received Convalescent plasma therapy for COVID-19. All patients were treated with intravenous corticosteroids and improved, although two responded minimally. Two patients treated with IVIG showed no further improvement.ConclusionNeurological complications from COVID-19 are being rapidly recognized. Our three cases highlight the occurrence of ADEM as a postinfectious/immune mediated complication of COVID-19 infection, which may be responsive to corticosteroid treatment. Early recognition of this complication and treatment is important to avoid long term complications.
A systematic review uncovers a wide-gap between COVID-19 in humans and animal models
Authors: Ehaideb Salleh N. , Abdullah Mashan L. , Abuyassin Bisher , Bouchama Abderrezak 
Published: July 2020

AbstractBackgroundAnimal models of COVID-19 have been rapidly reported after the start of the pandemic. We aimed to assess whether the newly created models reproduce the full spectrum of humans COVID-19.MethodsWe searched the Medline, as well as BioRxiv and MedRxiv preprint servers for original research published in English from January 1, to May 20, 2020. We used the search terms “COVID-19” OR “SARS-CoV-2” AND, “animal models”, “hamsters”, “nonhuman primates”, “macaques”, “rodent”, “mice”, “rats”, “ferrets”, “rabbits”, “cats”, and “dogs”. Inclusion criteria were the establishment of animal models of COVID-19 as an endpoint. Other inclusion criteria were assessment of prophylaxis, therapies, or vaccines, using animal models of COVID-19.Findings13 peer-reviewed studies and 14 preprints met inclusion criteria. The animals used were nonhuman primates (n=13), mice (n=7), ferrets (n=4), hamsters (n=4), and cats (n=1). All animals supported high viral replication in the upper and lower respiratory tract associated with mild clinical manifestations, lung pathology and full recovery. Older animals displayed relatively more severe illness than the younger ones. No animal models developed hypoxemic respiratory failure, multiple organ dysfunction, culminating in death. All species elicited a specific IgG antibodies response to the spike proteins, which were protective against a second exposure. Transient systemic inflammation was observed occasionally in Rhesus macaques, hamsters, and mice. Notably, none of the animals unveiled cytokine storm or coagulopathy.ConclusionsMost of the animal models of COVID-19 recapitulated mild pattern of human COVID-19 with full recovery phenotype. No severe illness associated with mortality was observed, suggesting a wide gap between COVID-19 in humans and animal models.FundingThere was no funding source for this study.
Seroprevalence of SARS-CoV-2 antibodies in an entirely PCR-sampled and quarantined community after a COVID-19 outbreak - the CoNAN study
Authors: Weis Sebastian , Scherag André , Baier Michael , Kiehntopf Michael , Kamradt Thomas , Kolanos Steffi , Ankert Juliane , Glöckner Stefan , Makarewicz Oliwia , Hagel Stefan , Bahrs Christina , Kimmig Aurelia , Proquitté Hans , Guerra Joel , Löffler Bettina , Pletz Mathias W. ,   CoNAN study group.
Published: July 2020

ABSTRACTBackgroundDue to the substantial proportion of asymptomatic and mild courses many SARS-CoV-2 infections remain unreported. Therefore, assessment of seroprevalence may detect the real burden of disease. We aimed at determining and characterizing the rate of SARS-CoV-2 infections and the resulting immunity in a defined population.MethodsCoNAN is a population-based cohort study in the previously quarantined community Neustadt-am-Rennsteig, Germany six weeks after a SARS-CoV-2 outbreak with 49 cases identified by PCR screening of all 883 inhabitants. The primary objective of the study was to assess SARS-CoV-2 antibody seroconversion rate using six different IgG detecting immunoassays. Secondary objectives of the study were: i.) to determine the rate of seroconversion in children; ii.) to determine potential risk factors for symptomatic vs. asymptomatic Covid19 courses; iii.) to investigate the rate of virus persistence.FindingsWe enrolled 626 participants (71% of the community population). All actual SARS-CoV-2 PCR tests were negative; while a total of 8·4% (52 of 620 tested) had antibodies against SARS-CoV-2 in at least two independent tests. Twenty of the antibody positive participants had previously a positive SARS-CoV-2 PCR. On the contrary, of those 38 participants with SARS-CoV-2 infection, only 20 (52·6%) were antibody positive.InterpretationSeveral antibody tests conducted six weeks after an outbreak of SARS-CoV-2 did not detect all previously PCR-positive tested individuals. Cautious evaluation of antibody testing strategies to assess immunity against the infection is warranted.FundingCoNAN was funded by the Thuringian Ministry for Economic Affairs, Science and Digital Society (TMWWDG).
Ferroportin 3 is a dual-targeted mitochondrial/chloroplast iron exporter necessary for iron homeostasis in Arabidopsis
Authors: Kim Leah J. , Tsuyuki Kaitlyn M. , Hu Fengling , Park Emily Y. , Zhang Jingwen , Iraheta Jennifer Gallegos , Chia Ju-Chen , Huang Rong , Tucker Avery E. , Clyne Madeline , Castellano Claire , Kim Angie , Chung Daniel D. , DaVeiga Christopher T. , Parsons Elizabeth M. , Vatamaniuk Olena K. , Jeong Jeeyon 
Published: July 2020

ABSTRACTMitochondria and chloroplasts are organelles with high iron demand that are particularly susceptible to iron-induced oxidative stress. Despite the necessity of strict iron regulation in these organelles, much remains unknown about mitochondrial and chloroplast iron transport in plants. Here, we propose that Arabidopsis Ferroportin 3 (FPN3) is an iron exporter dual-targeted to mitochondria and chloroplasts.FPN3is expressed in shoots regardless of iron conditions, but its transcripts accumulate under iron deficiency in roots.fpn3mutants cannot grow as well as wild type under iron-deficient conditions and shoot iron levels are reduced infpn3mutants compared to wild type. ICP-MS measurements show that iron levels in the mitochondria and chloroplasts are increased relative to wild type, consistent with the proposed role of FPN3 as a mitochondrial/plastid iron exporter. In iron deficientfpn3mutants, abnormal mitochondrial ultrastructure was observed, whereas chloroplast ultrastructure was not affected, implying that FPN3 plays a critical role in the mitochondria. Overall, our study suggests that FPN3 is essential for optimal iron homeostasis.Significance statementIron homeostasis must be tightly controlled in the mitochondria and chloroplasts, but iron trafficking in these organelles is not fully understood. Our work suggests that FPN3 is an iron exporter required for maintaining proper iron levels in mitochondria and chloroplasts. Furthermore, FPN3 is necessary for the optimal growth and normal mitochondrial ultrastructure under iron deficiency. This study reveals the physiological role of FPN3 and advances our understanding of iron regulation in mitochondria and chloroplasts.
Retinoic acid fluctuation activates an uneven, direction-dependent network-wide robustness response in early embryogenesis
Authors: Parihar Madhur , Bendelac-Kapon Liat , Gur Michal , Abbou Tali , Belorkar Abha , Achanta Sirisha , Kinberg Keren , Vadigepalli Rajanikanth , Fainsod Abraham 
Published: July 2020

ABSTRACTRobustness is a feature of regulatory pathways to ensure signal consistency in light of environmental changes or genetic polymorphisms. The retinoic acid (RA) pathway, is a central developmental and tissue homeostasis regulatory signal, strongly dependent on nutritional sources of retinoids and affected by environmental chemicals. This pathway is characterized by multiple proteins or enzymes capable of performing each step and their integration into a self-regulating network. We studied RA network robustness by transient physiological RA signaling disturbances followed by kinetic transcriptomic analysis of the recovery during embryogenesis. The RA metabolic network was identified as the main regulated module to achieve signaling robustness using an unbiased pattern analysis. We describe the network-wide responses to RA signal manipulation and found the feedback autoregulation to be sensitive to the direction of the RA perturbation: RA knockdown exhibited an upper response limit, whereas RA addition had a minimal feedback-activation threshold. Surprisingly, our robustness response analysis suggests that the RA metabolic network regulation exhibits a multi-objective optimization, known as Pareto optimization, characterized by trade-offs between competing functionalities. We observe that efficient robustness to increasing RA is accompanied by worsening robustness to reduced RA levels and vice versa. This direction-dependent trade-off in the network-wide feedback response, results in an uneven robustness capacity of the RA network during early embryogenesis, likely a significant contributor to the manifestation of developmental defects.
Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria
Authors: Popa Alexandra , Genger Jakob-Wendelin , Nicholson Michael , Penz Thomas , Schmid Daniela , Aberle Stephan W. , Agerer Benedikt , Lercher Alexander , Endler Lukas , Colaço Henrique , Smyth Mark , Schuster Michael , Grau Miguel , Martinez Francisco , Pich Oriol , Borena Wegene , Pawelka Erich , Keszei Zsofia , Senekowitsch Martin , Laine Jan , Aberle Judith H. , Redlberger-Fritz Monika , Karolyi Mario , Zoufaly Alexander , Maritschnik Sabine , Borkovec Martin , Hufnagl Peter , Nairz Manfred , Weiss Günter , Wolfinger Michael T. , von Laer Dorothee , Superti-Furga Giulio , Lopez-Bigas Nuria , Puchhammer-Stöckl Elisabeth , Allerberger Franz , Michor Franziska , Bock Christoph , Bergthaler Andreas 
Published: July 2020

AbstractSuperspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations.Graphical Abstract
Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
Authors: Salvy Pierre , Hatzimanikatis Vassily 
Published: July 2020

AbstractThe sequential rather than simultaneous consumption of carbohydrates in bacteria such asE. coli, a phenomenon termed diauxie, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth, thus giving the bacterium a competitive advantage. Currently, computational techniques used in industrial biotechnology fall short of explaining the intracellular dynamics underlying diauxic behavior, in particular at a proteome level.Some hypotheses postulate that diauxie is due to limitations in the catalytic capacity of bacterial cells. We developed a robust iterative dynamic method based on expression- and thermodynamically enabled flux models (dETFL) to simulate the temporal evolution of carbohydrate consumption and cellular growth. The dETFL method couples gene expression and metabolic networks at the genome scale, and successfully predicts the preferential uptake of glucose over lactose inE. colicultures grown on a mixture of carbohydrates. The observed diauxic behavior in the simulated cellular states suggests that the observed diauxic behavior is supported by a switch in the content of the proteome in response to fluctuations in the availability of extracellular carbon sources. We are able to model both the proteome allocation and the proteomic switch latency induced by different types of cultures.Our models suggest that the diauxic behavior of the cell is the result of the evolutionary objective of maximization of the specific growth of the cell. We propose that genetic regulatory networks, such as thelacoperon inE. coli, are the biological implementation of a robust control system to ensure optimal growth.
Application of Digital Colorimeter for Preliminary Characterization of Gold Nanoparticle Swarms Produced byTermitomyces heimiiUsing a novel Bioinspired Microfluidics Assay
Authors: Dabolkar Sujata , Kamat Nandkumar M. 
Published: July 2020

ABSTRACTIn our laboratory work extending over several years we have successfully studied the biogeochemical role of termite mounds and their occupants the termites and the exosymbiont fungus-Termitomyces. Fungi appear to be promising for large scale production of nanoparticles (NPs) as these are simpler to grow both in laboratory and at industrial scale. This paper reports a novel microfluidic based assay system to detect Gold bioreduction capacity of different tissues in tissue based and cell free environment. Using sterile microtest wells, different tissues such as umbo, pileus, lamellae, stipe context, stipe epicutis, pseudorrhiza context, pseudorrhiza epicutis ofTermitomyces heimiimature fruitbodies were tested with 200μl chloroauric acid (one mM) and after an interval of 5, 10, 15, 30, 45, 60, 120 min and 12, 24 and 48 hours. The results in terms production of distinct nanoparticles were directly visualized microscopically and using mobile based digital colorimeter. Membrane filtered sterile water soluble extracts (SWSE) from the same tissues were similarly screened. The results manifested by mono and polydisperse GNPs and microparticles of mixed size groups demonstrated that cell free system can be potentially useful for bioinspired fabrication of GNPs. Further work in this direction is in progress using severaltermitomycespure cultures.
The Aging Brain and Executive Functions Revisited: Implications from Meta-Analytic and Functional-Connectivity Evidence
Authors: Heckner Marisa K. , Cieslik Edna C. , Eickhoff Simon B. , Camilleri Julia A. , Hoffstaedter Felix , Langner Robert 
Published: July 2020

AbstractHealthy aging is associated with changes in cognitive performance including executive functions (EFs) and their associated brain activation patterns. However, it has remained unclear which EF-related brain regions are affected consistently, because the results of pertinent neuroimaging studies and earlier meta-analyses vary considerably. We, therefore, conducted new rigorous meta-analyses of published age differences in EF-related brain activity. Out of a larger set of regions associated with EFs, only left inferior frontal junction (IFJ) and left anterior cuneus/precuneus (aC/PrC) were found to show consistent age differences. To further characterize these two age-sensitive regions, we performed seed-based resting-state functional connectivity (RS-FC) analyses using fMRI data from a large adult sample with a wide age range. We also assessed associations of the two regions’ whole-brain RS-FC patterns with age and EF performance. Although functional profiling and RS-FC analyses point towards a domain-general role of left IFJ in EFs, the pattern of individual study contributions to the meta-analytic results suggests process-specific modulations by age. Our analyses further indicate that left aC/PrC is recruited differently by older (compared to younger) adults during EF tasks, potentially reflecting inefficiencies in switching the attentional focus. Overall, our findings question earlier meta-analytic results and suggest a larger heterogeneity of age-related differences in brain activity associated with EFs. Hence, they encourage future research that pays greater attention to replicability, investigates age-related differences in deactivation, and focuses on more narrowly defined EF subprocesses, combining multiple behavioral assessments with multi-modal imaging.Highlights- Healthy aging is linked to deterioration in executive functions (EFs)- ALE meta-analyses examined consistent age differences in brain activity linked to EFs- In a larger set of EF regions, only left IFJ and (pre)cuneus were sensitive to age- Advanced age was linked to weaker functional coupling within EF-related networks- Our findings question earlier meta-analytic findings
Red seaweed (Asparagopsis taxiformis)supplementation reduces enteric methane by over 80 percent in beef steers
Authors: Roque B.M. , Venegas M. , Kinley R. , deNys R. , Neoh T. L. , Duarte T.L. , Yang X. , Salwen J. K. , Kebreab E. 
Published: July 2020

AbstractThe red macroalgae (seaweed)Asparagopsis spp.has shown to reduce ruminant enteric methane (CH4) production up to 99%in vitro.The objective of this study was to determine the effect ofAsparagopsis taxiformison CH4production (g/day per animal), CH4yield (g CH4/kg dry matter intake (DMI)), average daily gain (ADG), feed conversion efficiency (FCE), and carcass and meat quality in growing beef steers. Twenty-one Angus-Hereford beef steers were randomly allocated to one of three treatment groups: 0% (Control), 0.25% (Low Dose; LD), and 0.5% (High Dose; HD)A. taxiformisinclusion based on organic matter intake. Steers were fed 3 diets: high, medium, and low forage total mixed ration (TMR) representing typical life-stage diets of growing beef steers. The LD and HD treatments over 147 days reduced enteric CH4yield 45 and 68%, respectively; however, there was an interaction between TMR type and the magnitude of CH4yield reduction. Supplementing the low forage TMR reduced CH4yield 69.8% (P<0.001) for LD and 80% (P<0.001) for HD treatment. Hydrogen (H2) yield (g H2/DMI) increased significantly (P<0.001) 336 and 590% compared to Control for the LD and HD treatments, respectively. No differences were found in carbon dioxide (CO2) yield (g CO2/DMI), ADG, carcass quality, strip loin proximate analysis and shear force, or consumer taste preferences. DMI tended (P= 0.08) to decrease 8% in steers in LD treatment but significantly (P= 0.002) reduced 14% in steers in HD treatment. Conversely, FCE tended to increase 7% in steers in LD treatment (P= 0.06) and increased 14% in steers in HD (P< 0.01) treatment compared to Control. The persistent reduction of CH4byA. taxiformissupplementation suggests that this is a viable feed additive to significantly decrease the carbon footprint of ruminant livestock and potentially increase production efficiency.
Computational approaches towards reducing contamination in single-cell RNA-seq data
Authors: Yousefi Siamak , Chen Hao , Ingels Jesse F. , McCarty Melinda S. , Centeno Arthur G. , Chintalapudi Sumana , Mulligan Megan K. , Williams Pete A. , John Simon J. , Jones Bryan W. , Jablonski Monica M. , Hollingsworth T J. , Geisert Eldon E. , Lu Lu , Williams Robert W. 
Published: July 2020

SUMMARYSingle cell RNA sequencing has enabled quantification of single cells and identification of different cell types and subtypes as well as cell functions in different tissues. Single cell RNA sequence analyses assume acquired RNAs correspond to cells, however, RNAs from contamination within the input data are also captured by these assays. The sequencing of background contamination as well as unwanted cells making their way to the final assay Potentially confound the correct biological interpretation of single cell transcriptomic data. Here we demonstrate two approaches to deal with background contamination as well as profiling of unwanted cells in the assays. We use three real-life datasets of whole-cell capture and nucleotide single-cell captures generated by Fluidigm and 10x technologies and show that these methods reduce the effect of contamination, strengthen clustering of cells and improves biological interpretation.
Positivity effect in aging: Evidence for the primacy of positive responses to emotional ambiguity
Authors: Petro Nathan M. , Basyouni Ruby , Neta Maital 
Published: July 2020

AbstractOlder compared to younger adults show greater amygdala activity to positive emotions, and are more likely to interpret emotionally ambiguous stimuli (e.g., surprised faces) as positive. While some evidence suggests this positivity effect results from a relatively slow, top-down mechanism, others suggest it emerges from early, bottom-up processing. The amygdala is a key node in rapid, bottom-up processing and patterns of amygdala activity over time (e.g., habituation) can shed light on the mechanisms underlying the positivity effect. Younger and older adults passively viewed neutral and surprised faces in an MRI. Only in older adults, we found that amygdala habituation was associated with the tendency to interpret surprised faces as positive or negative (valence bias), where a more positive bias was associated with greater habituation. Interestingly, although a positive bias in younger adults was associated with slower reaction times, consistent with an initial negativity hypothesis in younger adults, older adults showed faster ratings of positivity. Together, we propose that there may be a switch to a primacy of positivity in aging.