bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic Hemodialysis Patients have better outcomes with COVID-19 - a retrospective cohort study
Authors: Naaraayan Ashutossh , Nimkar Abhishek , Hasan Amrah , Pant Sushil , Durdevic Momcilo , Elenius Henrik , Suarez Corina Nava , Basak Prasanta , Lakshmi Kameswari , Mandel Michael , Jesmajian Stephen 
Published: July 2020

AbstractIntroductionSeveral comorbid conditions, have been identified as risk factors in patients with COVID-19. However, there is a dearth of data describing the impact of COVID-19 infection in patients with end-stage renal disease on hemodialysis (ESRD-HD).MethodsThis retrospective case series analyzed 362 adult patients consecutively hospitalized with confirmed COVID-19 illness between March 12, 2020 and May 13, 2020, at a teaching hospital in the New York City metropolitan area. Primary outcome was severe pneumonia as defined by the World Health Organization. Secondary outcomes were: 1) the Combined Outcome of Acute respiratory distress syndrome or in-hospital Death (COAD), and 2) the need for High-levels of Oxygen supplementation (HiO2).ResultsPatients with ESRD-HD had lower odds for poor outcomes including severe pneumonia [Odds Ratio (OR) 0.4, Confidence Interval (CI) (0.2–0.9) p=.04], HiO2 [OR 0.3, CI (0.1– 0.8) p=.02] and COAD [OR 0.4, CI (0.2–1.05) p=.06], when compared to patients without ESRD. In contrast, higher odds for severe pneumonia, COAD and HiO2 were seen with advancing age. African-Americans were over-represented in the hospitalized patient cohort, when compared to their representation in the community (35% vs 18%). Hispanics had higher odds for severe-illness and HiO2 when compared to Caucasians.ConclusionsPatients with ESRD-HD had a milder course of illness with a lower likelihood of severe pneumonia and a lesser need for aggressive oxygen supplementation when compared to patients not on chronic dialysis. This “protective effect” might have a pathophysiologic basis and needs to be further explored.
Use of finger length ratio as a marker for knee osteoarthritis: A case-control study of 2,456 patients
Authors: Magu Dukhum , Aggarwal Aditya , Behera Prateek , Khurana Ankit 
Published: July 2020

AbstractBackgroundIn the human hand, the index and ring finger present a considerable variation in their relative lengths and the ratio of their lengths (2D:4D ratio). This ratio is associated with a variety of behavioral and physiological traits possibly linked to variation in sex hormones levels. Previous studies have revealed inconsistent results while assessing the association of 2D:4D ratio as a risk factor for occurrence of knee osteoarthritis (KOA). This study was designed as a prospective observational study to analyze this association using a better methodology.MethodsPatients were enrolled into KOA group (1396 patients) and non-KOA group (1060 patients) based on ACR criteria for OA knee. Knee and hand radiographs of all patients enrolled were assessed. The 2D:4D length ratio was calculated for phalanges, metacarpal bones and for the combined (metacarpal & phalanx) finger lengths on radiographs and visual finger lengths. The finger patterns were classified and assessment was done between these ratios and finger pattern types for occurrence and severity of KOA.ResultsA lower 2D:4D ratio in an individual was associated with an increased chance of KOA and a dose response relationship was found between radiographic grading of KOA and 2D:4D ratio.ConclusionBased on the findings of this study one can predict the risk of developing KOA using this simple technique which can be used as a screening tool whereby preventive intervention can be started if someone presents early with a low 2D:4D finger length ratio.KEY MESSAGESEvaluation of finger patterns reveals an association with osteoartritis knee (KOA)Low 2D:4D ratio and Type 3 finger pattern is associated with increased KOA riskLow 2D:4D ratio has as positive correlation to radiographic severity of KOAPreventive interventons can be initiated for those with at risk finger pattern
Excess deaths in Spain during the first year of the COVID–19 pandemic outbreak from age/sex–adjusted death rates
Authors: Martín-Olalla José María 
Published: July 2020

ObjectivesAssess the impact of the illness designated COVID–19 during the first year of pandemic outbreak in Spain through age/sex–specific death rates.Study designAge/sex–specific weeekly deaths in Spain were retrieved from Eurostat. Spanish resident population was obtained from the National Statistics Office.MethodsGeneralized linear Poisson regressions were used to compute the contrafactual expected rates after one year (52 weeks or 364 days) of the pandemic onset. From this one–year age/sex–specific and age/sex–adjusted mortality excess rates were deduced.ResultsFor the past continued 13 years one–year age/sex–adjusted death rates had not been as high as the rate observed on February 28th, 2021.The excess death rate was estimated as 1.790×10−3 (95 % confidence interval, 1.773×10−3 to 1.808×10−3; P−score = 20.2 % and z−score = 11.4) with an unbiased standard deviation of the residuals equal to 157×10−6. This made 84 849 excess deaths (84 008 to 85 690). Sex disaggregation resulted in 44 887 (44 470 to 45 303) male excess deaths and 39 947 (39 524 to 40 371) female excess deaths.ConclusionWith 73 571 COVID–19 deaths and 9772 COVID–19 suspected deaths that occurred in nursing homes during the spring of 2020 it is only 1496 excess deaths (1.8 %, a z−score of 0.2) that remains unattributed.The infection rate during the first year of the pandemic is estimated in 16 % of population after comparing the ENE–COVID seroprevalence, the excess deaths at the end of the spring 2020 and the excess deaths at the end of the first year of the pandemic.
The biphasic and age-dependent impact of Klotho on hallmarks of aging and skeletal muscle function
Authors: Pius Abish , Clemens Zachary , Sivakumar Sruthi , Sahu Amrita , Shinde Sunita , Mamiya Hikaru , Luketich Nathaniel , Cui Jian , Hoeck Joerg D. , Kreuz Sebastian , Franti Michael , Barchowsky Aaron , Ambrosio Fabrisia 
Published: July 2020

ABSTRACTAging is accompanied by a disrupted information flow, which results from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders such as skeletal muscle wasting, or sarcopenia. To estimate the growing “disorderliness” of the aging muscle system, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Although the most prominent structural and functional alterations were observed in the oldest old mice (27-29 months), we found that the escalating network entropy reached an inflection point at old age (22-24 months). To probe the potential for restoration of molecular “order” and reversal of the sarcopenic phenotype, we overexpressed the longevity protein, α-Klotho. Klotho overexpression modulated genes representing all hallmarks of aging in both old and oldest-old mice. However, whereas Klotho improved strength in old mice, intervention failed to induce a benefit beyond the entropic tipping point.
Soil N2O emission potential falls along a denitrification phenotype gradient linked to differences in microbiome, rainfall and carbon availability
Authors: Highton Matthew P. , Bakken Lars R. , Dörsch Peter , Wakelin Steve , de Klein Cecile A. M. , Molstad Lars , Morales Sergio E. 
Published: July 2020

AbstractSoil denitrification produces the potent greenhouse gas nitrous oxide (N2O) and by further reduction of N2O, the harmless inert gas N2. N2O emission is determined by rate and timing of the N2O producing and reducing steps which are sensitive to a series of proximal and distal regulators such as pH and microbial community composition. Microbial community associations to N2O emission potential (N2O/(N2O+N2)) are commonly entangled with pH leaving the true role of community composition unclear. Here, we leverage a set of soil microbiomes strongly linked to rainfall above pH to test the hypothesis that microbiome vs. N2O emission potential (N2O/(N2O+N2)) correlations will be maintained across alternative distal drivers. N2O emission potential (N2O/(N2O+N2)) and denitrification gas (NO, N2O, N2) kinetics were assessed by automated gas chromatography while community composition was assessed by 16S rRNA gene sequencing and qPCR ofnosZIandIIgenes. Analyses revealed a sustained correlation between microbiome and N2O emission potential (N2O/(N2O+N2)) in the absence of a pH effect. Further, a continuum of gas accumulation phenotypes linked to NO accumulation and sensitive to carbon addition are identified. Separate phenotypes carried out N2O production and reduction steps more concurrently or sequentially and thus determined N2O accumulation and emission potential (N2O/(N2O+N2)). Concurrent N2O producing/reducing soils typically contained NO accumulation to a low steady state, while carbon addition manipulations which increased NO accumulation also increased sequentiality of N2O production/reduction and thus emission potential (N2O/(N2O+N2)). These features may indicate a conserved NO inhibitory mechanism across multiple effectors (rainfall, community composition, carbon availability).HighlightsN2O emission potential is linked to microbiome changes associated with rainfall, but not to pH.Sequential vs. concurrent denitrification phenotypes differing in NO and N2O accumulation are identified.High N2O accumulation is associated with increased NO accumulation.Sequentiality of N2O production/reduction determines soil N2O emission potential.Sequentiality of N2O reduction was susceptible to manipulation via carbon addition.
De novo protein design by deep network hallucination
Authors: Anishchenko Ivan , Chidyausiku Tamuka M. , Ovchinnikov Sergey , Pellock Samuel J. , Baker David 
Published: July 2020

AbstractThere has been considerable recent progress in protein structure prediction using deep neural networks to infer distance constraints from amino acid residue co-evolution1–3. We investigated whether the information captured by such networks is sufficiently rich to generate new folded proteins with sequences unrelated to those of the naturally occuring proteins used in training the models. We generated random amino acid sequences, and input them into the trRosetta structure prediction network to predict starting distance maps, which as expected are quite featureless. We then carried out Monte Carlo sampling in amino acid sequence space, optimizing the contrast (KL-divergence) between the distance distributions predicted by the network and the background distribution. Optimization from different random starting points resulted in a wide range of proteins with diverse sequences and all alpha, all beta sheet, and mixed alpha-beta structures. We obtained synthetic genes encoding 129 of these network hallucinated sequences, expressed and purified the proteins in E coli, and found that 27 folded to monomeric stable structures with circular dichroism spectra consistent with the hallucinated structures. Thus deep networks trained to predict native protein structures from their sequences can be inverted to design new proteins, and such networks and methods should contribute, alongside traditional physically based models, to the de novo design of proteins with new functions.
Ecological aspects of sandfly fauna (Diptera: Psychodidae, Phlebotominae) of Sumidouro District, State of Rio de Janeiro, Brazil
Authors: Alves João Ricardo Carreira , Carmo Cleber Nascimento do , Menezes Rodrigo Caldas , Luís Vilela Mauricio , dos Santos-Mallet Jacenir Reis 
Published: July 2020

AbstractAiming to compare and update the sand fly fauna of Portão de Pedra site, Sumidouro District, Rio de Janeiro State, Brazil, and considering the environmental changes occurred, the biology and ecology of the local sandfly species were examined five years later as a complementary study carried. Captures were made in the cave, surroundings of cave and forest of the region, from 6 p.m. to 6 a.m. 2 3 2 3 sandflies of eigth species of theLutzomyiawere captured:L. gasparviannai, L. edwardsi, L. tupynambai, L. hirsuta, L. whitmani, L. migonei, L. intermedia, Lutzomyia. sp and one species of theBrumptomyiaKind:B. brumpti. In 2009 and 2010 were collected 1756 samples from ten species of the former genus and two of the second.L. gasparviannaiwas predominant, in the three collection sites, in both periods. Five species implicated as vector ofLeishmania:L. intermedia, L. whitmani, L. migonei, L. hirsutaandL. davisihave been collected in the area. Poisson regression and ANOVA were used to perform statistical analysis of species most relevant. The record ofL. intermediaand a case of American tegumentary leishmaniasis are relevant to public health of municipality and of state of Rio de Janeiro.
Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites
Authors: Walter Jean-Charles , Rech Jérôme , Walliser Nils-Ole , Dorignac Jérôme , Geniet Frédéric , Palmeri John , Parmeggiani Andrea , Bouet Jean-Yves 
Published: July 2020

AbstractBacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation have recently been shown to belong to a new class of CTP-dependent molecular switches. Strikingly, CTP binding and hydrolysis was shown to induce a conformational change enabling ParB dimers to switch between an open and a closed conformation. This latter conformation clamps ParB dimers on DNA molecules, allowing their diffusion in one dimension along the DNA. It has been proposed that this novel sliding property may explain the spreading capability of ParB over more than 10-Kb fromparScentromere sites where ParB is specifically loaded. Here, we modeled such a mechanism as a typical reaction-diffusion system and compared this ‘Clamping & sliding’ model to the ParB DNA binding pattern from high-resolution ChIP-sequencing data. We found that this mechanism cannot account for all thein vivocharacteristics, especially the long range of ParB binding to DNA. In particular, it predicts a strong effect from the presence of a roadblock on the ParB binding pattern that is not observed in ChIP-seq. Moreover, the rapid assembly kinetics observedin vivoafter the duplication ofparSsites is not easily explained by this mechanism. We propose that ‘Clamping & sliding’ might explain the ParB spreading pattern at short distances fromparSbut that another mechanism must apply for ParB recruitment at larger genomic distances.
Nasal respiration is necessary for the emergence of ketamine-induced high frequency network oscillations and behavioral hyperactivity in freely moving rats
Authors: Wróbel Jacek , Średniawa Władysław , Bernatowicz Gabriela , Zygierewicz Jaroslaw , Wójcik Daniel K , Whittington Miles Adrian , Hunt Mark Jeremy 
Published: July 2020

AbstractChanges in oscillatory activity are widely reported after subanesthetic ketamine, however their mechanisms of generation are unclear. Here, we tested the hypothesis that nasal respiration underlies the emergence of high-frequency oscillations (130-180 Hz, HFO) and behavioral activation after ketamine in freely moving rats. We found ketamine 20 mg/kg provoked “fast” theta sniffing in rodents which correlated with increased locomotor activity and HFO power in the OB. Bursts of ketamine-dependent HFO were coupled to “fast” theta frequency sniffing. Theta coupling of HFO bursts were also found in the prefrontal cortex and ventral striatum which, although of smaller amplitude, were in phase with OB activity. Haloperidol 1 mg/kg pretreatment prevented ketamine-dependent increases in fast sniffing and instead HFO coupling to slower basal respiration. Consistent with ketamine-dependent HFO being driven by nasal respiration, unilateral naris blockade led to an ipsilateral reduction in ketamine-dependent HFO power compared to the control side. Bilateral nares blockade reduced ketamine-induced hyperactivity and HFO power and frequency. In conclusion, nasal entrainment of ketamine-dependent HFO across cortical and subcortical regions at theta frequencies represents a mechanism of orchestrated neural activity across distinct brain regions. The dense divergent connectivity of the olfactory system serves to broadcast this HFO to limbic areas.
Precise characterization of somatic complex structural variations from paired long-read sequencing data with nanomonsv
Authors: Shiraishi Yuichi , Koya Junji , Chiba Kenichi , Okada Ai , Arai Yasuhito , Saito Yuki , Shibata Tatsuhiro , Kataoka Keisuke 
Published: July 2020

AbstractWe present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5’ truncations, internal inversions, as well as source sites for 3’ transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.
Signatures of optimal codon usage predict metabolic ecology in budding yeasts
Authors: LaBella Abigail Leavitt , Opulente Dana A. , Steenwyk Jacob , Hittinger Chris Todd , Rokas Antonis 
Published: July 2020

ABSTRACTReverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically-relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in theGALpathway is positively correlated with quantitative growth on galactose, suggesting thatGALcodon optimization reflects increased capacity to grow on galactose. Optimal codon usage in theGALpathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage ofGALgenes is greater than 85% of all genes in the major human pathogenCandida albicans(CUG-Ser1 clade) and greater than 75% of genes in the dairy yeastKluyveromyces lactis(family Saccharomycetaceae). We further find a correlation between optimization in the thiamine biosynthesis andGALpathways. As a result, optimal codon usage in thiamine biosynthesis genes is also associated with dairy ecological niches in Saccharomycetaceae, which may reflect competition with co-occurring microbes for extracellular thiamine. This work highlights the potential of codon optimization as a tool for gaining insights into the metabolic ecology of microbial eukaryotes. Doing so may be especially illuminating for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.
Orally Administered Exosomes Alleviate Mouse Contact Dermatitis through Delivering miRNA-150 to Antigen-Primed Macrophages Targeted by Exosome-Surface Antibody Light Chains
Authors: Nazimek Katarzyna , Bryniarski Krzysztof , Ptak Wlodzimierz , Kormelink Tom Groot , Askenase Philip W. 
Published: July 2020

AbstractWe previously discovered suppressor T cell-derived, antigen (Ag)-specific exosomes inhibiting mouse hapten-induced contact sensitivity effector T cells by targeting antigen-presenting cells (APCs). These suppressive exosomes acted Ag-specifically due to a coating of antibody free light chains (FLC) from Ag-activated B1a cells. Current studies aimed at determining if similar immune tolerance could be induced in cutaneous delayed-type hypersensitivity (DTH) to the protein Ag (ovalbumin, OVA). Intravenous administration of a high dose of OVA-coupled, syngeneic erythrocytes induced CD3+CD8+suppressor T cells producing suppressive, miRNA-150-carrying exosomes, also coated with B1a cell-derived, OVA-specific FLC. Simultaneously, OVA-immunized B1a cells produced exosome subpopulation, originally coated with Ag-specific FLC, that could be rendered suppressive by in vitro association with miRNA-150. Importantly, miRNA-150-carrying exosomes from both suppressor T cells and B1a cells efficiently induced prolonged DTH suppression after single systemic administration into actively immunized mice, with the strongest effect observed after oral administration. Current studies also showed that OVA-specific FLC on suppressive exosomes bind OVA peptides, suggesting that exosome-coating FLC target APCs by binding to Ag-major histocompatibility complexes. This renders APCs able to inhibit DTH effector T cells. Thus, our studies described a novel immune tolerance mechanism mediated by FLC-coated, Ag-specific, miRNA-150-carrying exosomes that are particularly effective after oral administration.
Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings
Authors: Sip Viktor , Scholly Julia , Guye Maxime , Bartolomei Fabrice , Jirsa Viktor 
Published: July 2020

AbstractIntracranial electroencephalography is a standard tool in clinical evaluation of patients with focal epilepsy. Various early electrographic seizure patterns differing in frequency, amplitude, and waveform of the oscillations are observed. The pattern most common in the areas of seizure propagation is the so-called theta-alpha activity (TAA), whose defining features are oscillations in theθ–αrange and gradually increasing amplitude. A deeper understanding of the mechanism underlying the generation of the TAA pattern is however lacking. In this work we evaluate the hypothesis that the TAA patterns are caused by seizures spreading across the cortex. To do so, we perform simulations of seizure dynamics on detailed patient-derived cortical surfaces using the spreading seizure model as well as reference models with one or two homogeneous sources. We then detect the occurrences of the TAA patterns both in the simulated stereo-electroencephalographic signals and in the signals of recorded epileptic seizures from a cohort of fifty patients, and we compare the features of the groups of detected TAA patterns to assess the plausibility of the different models. Our results show that spreading seizure hypothesis is qualitatively consistent with the evidence available in the seizure recordings, and it can explain the features of the detected TAA groups best among the examined models.