julilili42/papers huggingface dataset:
Contextual and Parenting Factors Contribute to Shorter Sleep Among Hispanic/Latinx Compared to Non-Hispanic White Infants
2020-09-11

Abstract Background Sleep is an important aspect of child development and health. Disparities in childhood sleep have been observed as early as infancy, but little is known about the factors contributing to them. Purpose The objective of this study was to examine whether intrinsic, contextual, and parenting factors contribute to differences in sleep duration between Hispanic/Latinx and non-Hispanic white infants at 6 months of age. Methods We analyzed data of 119 Hispanic/Latinx and 146 non-Hispanic white infants in Rise &amp; SHINE, a prospective birth cohort study of mother–infant dyads. Mothers reported their infant’s sleep patterns using the Brief Infant Sleep Questionnaire at 6 months. Mothers also completed surveys measuring intrinsic (sex, gestational length, and birth weight), contextual (cultural, environmental, and familial), and parenting (behaviors and practices) factors. We used multivariable linear and logistic regression analyses to examine the contributing effects of these clusters of variables on the association between racial/ethnic background and infant sleep duration. Results Hispanic/Latinx infants slept 38 min less than white infants at 6 months (β: −0.63 [95% confidence interval: −1.07, −0.19]) and were nearly three times more likely to not meet the minimum sleep recommendation. The differences persisted after adjustment for intrinsic factors but were attenuated after additional adjustment for contextual and parenting factors, especially having a foreign-born mother and later bedtime. Conclusions The results of this study demonstrate that differences in sleep duration among Hispanic/Latinx infants compared to their white counterparts are present as early as 6 months of age and that context and parenting matter.
Estimating the Risk of Outbreaks of COVID-19 Associated with Shore Leave by Merchant Ship Crews: Simulation Studies for a Case Country
2020-09-11

Abstract Aim We aimed to estimate the risk of COVID-19 outbreaks in a case study COVID-free destination country, associated with shore leave for merchant ship crews. Methods A stochastic version of the SEIR model CovidSIM v1.1, designed specifically for COVID-19 was utilised. It was populated with parameters for SARS-CoV-2 transmission, shipping characteristics, and plausible control measures. Results When no control interventions were in place, an outbreak of COVID-19 in our case study destination country (New Zealand; NZ) was estimated to occur after a median time of 23 days (assuming a global average for source country incidence of 2.66 new infections per 1000 population per week, a crew of 20, a voyage length of 10 days, 1 day of shore leave both in NZ and abroad, and 108 port visits by international merchant ships per week). For this example the uncertainty around when outbreaks occur is wide (an outbreak occurs with 95% probability between 1 and 124 days). The combined use of a PCR test on arrival, self-reporting of symptoms with contact tracing, and mask use during shore leave, increased this median time to 1.0 year (14 days to 5.4 years). Scenario analyses found that onboard infection chains could persist for well over 4 weeks even with crews of only 5 members. Conclusion Introduction of SARS-CoV-2 through shore leave from international shipping crews is likely, even after long voyages. The risk can be substantially mitigated by control measures such as PCR testing and mask use.
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
2020-09-11

<ns4:p>The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training &amp; Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.</ns4:p>
Unique and distinct identities and functions of leaf phloem cells revealed by single cell transcriptomics
2020-09-11

A bstract The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ≥19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.
Radiography in high mass X-ray binaries
2020-09-12

Context. In high mass X-ray binaries, an accreting compact object orbits a high mass star, which loses mass through a dense and inhomogeneous wind. Aims. Using the compact object as an X-ray backlight, the time variability of the absorbing column density in the wind can be exploited in order to shed light on the micro-structure of the wind and obtain unbiased stellar mass-loss rates for high mass stars. Methods. We developed a simplified representation of the stellar wind where all the matter is gathered in spherical “clumps” that are radially advected away from the star. This model enables us to explore the connections between the stochastic properties of the wind and the variability of the column density for a comprehensive set of parameters related to the orbit and to the wind micro-structure, such as the size of the clumps and their individual mass. In particular, we focus on the evolution with the orbital phase of the standard deviation of the column density and of the characteristic duration of enhanced absorption episodes. Using the porosity length, we derive analytical predictions and compare them to the standard deviations and coherence time scales that were obtained. Results. We identified the favorable systems and orbital phases to determine the wind micro-structure. The coherence time scale of the column density is shown to be the self-crossing time of a single clump in front of the compact object. We thus provide a procedure to get accurate measurements of the size and of the mass of the clumps, purely based on the observable time variability of the column density. Conclusions. The coherence time scale grants direct access to the size of the clumps, while their mass can be deduced separately from the amplitude of the variability. We further show how monitoring the variability at superior conjunctions can probe the onset of the clump-forming region above the stellar photosphere. If the high column density variations in some high mass X-ray binaries are due to unaccreted clumps which are passing by the line-of-sight, this would require high mass clumps to reproduce the observed peak-to-peak amplitude and coherence time scales. These clump properties are marginally compatible with the ones derived from radiative-hydrodynamics simulations. Alternatively, the following components could contribute to the variability of the column density: larger orbital scale structures produced by a mechanism that has yet to be identified or a dense environment in the immediate vicinity of the accretor, such as an accretion disk, an outflow, or a spherical shell surrounding the magnetosphere of the accreting neutron star.
Transcript Levels of Aldo-Keto Reductase Family 1 Subfamily C (AKR1C) Are Increased in Prostate Tissue of Patients with Type 2 Diabetes
2020-09-12

Aldo-keto reductase family 1 (AKR1) enzymes play a crucial role in diabetic complications. Since type 2 diabetes (T2D) is associated with cancer progression, we investigated the impact of diabetes on AKR1 gene expression in the context of prostate cancer (PCa) development. In this study, we analyzed benign (BEN) prostate and PCa tissue of patients with and without T2D. Furthermore, to replicate hyperglycemia in vitro, we treated the prostate adenocarcinoma cell line PC3 with increasing glucose concentrations. Gene expression was quantified using real-time qPCR. In the prostate tissue of patients with T2D, AKR1C1 and AKR1C2 transcripts were higher compared to samples of patients without diabetes. In PC3 cells, high glucose treatment induced the gene expression levels of AKR1C1, C2, and C3. Furthermore, both in human tissue and in PC3 cells, the transcript levels of AKR1C1, C2, and C3 showed positive associations with oncogenes, which are involved in proliferation processes and HIF1α and NFκB pathways. These results indicate that in the prostate glands of patients with T2D, hyperglycemia could play a pivotal role by inducing the expression of AKR1C1, C2, and C3. The higher transcript level of AKR1C was furthermore associated with upregulated HIF1α and NFκB pathways, which are major drivers of PCa carcinogenesis.
Transplantation of a latissimus dorsi flap after nearly 6 hr of extracorporal perfusion: A case report
2020-09-12

Abstract Prolonged ischemia of tissues inevitably leads to their necrosis. This is especially relevant in the case of transplantation or replantation. In such situations, reperfusion in a timely manner might not be possible due to transportation times or other unforeseen complications. Therefore, a readily available and simple method to oxygenate the tissue and thus widen the time frame to reperfusion seems desirable. Here, we present the case of extracorporal perfusion of a latissimus dorsi (LD) flap that was successfully transplanted after nearly 6 hr of ischemia. A 41‐year‐old patient suffered multiple injuries including complete severance of the popliteal artery requiring emergency bypass. After stabilization of the patient and subsequent debridement, a LD flap was performed for soft tissue coverage. However, there was an acute occlusion of the bypass during flap inset. To salvage the free flap, a one‐way extracorporal perfusion of the flap with heparinized isotonic saline solution was performed for a total of 5 hr and 47 min. The flap survived with minimal tip necrosis. This case report describes the application of a simple extracorporal perfusion technique for salvage of a free flap over a prolonged ischemia time and discusses the relevant literature. Due to its ease and quickness of application as well as ubiquitous availability, it might serve as a valuable tool in cases of acute problems with the recipient vessels or other incidents where several hours of ischemia time are to be anticipated.
Preliminary results of the first lithic raw material survey in the piedmont zones of Kazakhstan
2020-09-12

The study of raw materials focuses on different aspects of hominin behaviour such as mobility strategies, land-use patterns and raw material transfer. They were comprehensively studied in the Palaeolithic of Europe and Africa. However, systematic studies of raw material sourcing have not been undertaken for the Palaeolithic of Kazakhstan, such surveys being embedded in reconnaissance works aimed at discovering new Palaeolithic sites. Our study presents preliminary results of the first lithic raw material survey in Kazakhstan. The study is based on outcrop surveying, collecting and sampling of potential sources of raw materials, and on a substantial literature review. The current study distinguishes the geographic patterns of land-use and their correlation with the lithic assemblages from stratified sites. Here, we describe primary and secondary sources of raw materials, and compare them macroscopically with the assemblages of stone tools. The survey results show a heterogeneous distribution of raw materials throughout the study regions. Macroscopic observations of lithic assemblages, and data extracted from literature suggest that hominins primarily selected locally occurring raw materials. Additionally, regional difference in the utilisation of a particular type of raw material which can be observed through the macroscopic examination of the lithic collections are confirmed by survey results.
Neural encoding of socially adjusted value during competitive and hazardous foraging
2020-09-12

In group foraging organisms, optimizing the conflicting demands of competitive food loss and safety is critical. We demonstrate that humans select competition avoidant and risk diluting strategies during foraging depending on socially adjusted value. We formulate a mathematically grounded quantification of socially adjusted value in foraging environments and show using multivariate fMRI analyses that socially adjusted value is encoded by mid-cingulate and ventromedial prefrontal cortices, regions that integrate value and action signals.
Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation
2020-09-13

The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).
Utilizing minicomputer technology for low-cost photorefraction: a feasibility study
2020-09-13

Eccentric photorefraction is an objective technique to determine the refractive errors of the eye. To address the rise in prevalence of visual impairment, especially in rural areas, a minicomputer-based low-cost infrared photorefractor was developed using off-the-shelf hardware components. Clinical validation revealed that the developed infrared photorefractor demonstrated a linear working range between +4.0 D and −6.0 D at 50 cm. Further, measurement of astigmatism from human eye showed absolute error for cylinder of 0.3 D and high correlation for axis assessment. To conclude, feasibility was shown for a low-cost, portable and low-power driven stand-alone device to objectively determine refractive errors, showing potential for screening applications. The developed photorefractor creates a new avenue for telemedicine for ophthalmic measurements.
Altered Spatial Composition of the Immune Cell Repertoire in the Bone Marrow Stem Cell Niche in Myelodysplastic Syndromes and Secondary Acute Myeloid Leukemia
2020-09-13

Purpose: Myelodysplastic syndromes (MDS) are caused by a stem cell failure, but the relationship between immune dysregulation and the course of disease has not yet been analyzed in detail. Experimental design: To get insights into the pathophysiologic and clinical relevance of the histotopography of immune cell subpopulations in this process, the immune cell infiltrate with focus on its spatial distribution was determined by multispectral imaging (MSI) in 147 bone marrow biopsies from MDS or secondary acute myeloid leukemia (sAML) patients and healthy controls (HC). In addition, the data were correlated to genetic alterations and clinical features of these patients including therapy response. Results: A high inter-tumoral heterogeneity in the frequency and spatial distribution of CD3+CD8+, CD3+CD8-, CD3+FOXP3+ T cell subsets, MUM1p+CD3- post-germinal B/plasma cells and CD34+ blasts was found in MDS and sAML samples. In HC only few B cells/plasma cells, but no T cell subpopulations were detected in the proximity to CD34+ blasts. In contrast, the frequency of these lymphocytes was increased in proximity to CD34+ blasts in both MDS and sAML independent of the karyotype, genetic alterations frequently detected in MDS, clinical risk stratification systems or treatment response to hypomethylating agents. Furthermore, an increased frequency of CD3+CD8+ T cells and MUM1p+ CD3- B cells was found in responders to epigenetic drugs. Conclusions: Thus, we conclude that (i) T cell subsets do not belong to the normal stem cell niche, (ii) the presence of T and B cell subpopulations not directly affect the course of MDS, (iii) lymphocytes in the proximity to CD34+ blasts might indicate defective stem cell properties and (iv) the number of lymphocytes is a predictor of therapy response to hypomethylating agents.
Two unequally redundant "helper" immune receptor families mediate Arabidopsis thaliana intracellular "sensor" immune receptor functions
2020-09-14

Plant nucleotide-binding (NB) leucine-rich repeat (LRR) receptor (NLR) proteins function as intracellular immune receptors that perceive the presence of pathogen-derived virulence proteins (effectors) to induce immune responses. The 2 major types of plant NLRs that "sense" pathogen effectors differ in their N-terminal domains: these are Toll/interleukin-1 receptor resistance (TIR) domain-containing NLRs (TNLs) and coiled-coil (CC) domain-containing NLRs (CNLs). In many angiosperms, the RESISTANCE TO POWDERY MILDEW 8 (RPW8)-CC domain containing NLR (RNL) subclass of CNLs is encoded by 2 gene families, ACTIVATED DISEASE RESISTANCE 1 (ADR1) and N REQUIREMENT GENE 1 (NRG1), that act as "helper" NLRs during multiple sensor NLR-mediated immune responses. Despite their important role in sensor NLR-mediated immunity, knowledge of the specific, redundant, and synergistic functions of helper RNLs is limited. We demonstrate that the ADR1 and NRG1 families act in an unequally redundant manner in basal resistance, effector-triggered immunity (ETI) and regulation of defense gene expression. We define RNL redundancy in ETI conferred by some TNLs and in basal resistance against virulent pathogens. We demonstrate that, in Arabidopsis thaliana, the 2 RNL families contribute specific functions in ETI initiated by specific CNLs and TNLs. Time-resolved whole genome expression profiling revealed that RNLs and "classical" CNLs trigger similar transcriptome changes, suggesting that RNLs act like other CNLs to mediate ETI downstream of sensor NLR activation. Together, our genetic data confirm that RNLs contribute to basal resistance, are fully required for TNL signaling, and can also support defense activation during CNL-mediated ETI.
The Combined Algae Test for the Evaluation of Mixture Toxicity in Environmental Samples
2020-09-14

Abstract The combined algae test is a 96-well plate-based algal toxicity assay with the green algae Raphidocelis subcapitata that combines inhibition of 24-h population growth rate with inhibition of photosynthesis detected after 2 and 24 h with pulse-amplitude modulated (PAM) fluorometry using a Maxi-Imaging PAM. The combined algae test has been in use for more than a decade but has had limitations due to incompatibilities of the measurements of the 2 biological endpoints on the same microtiter plates. These limitations could be overcome by increasing growth rates and doubling times on black, clear-bottom 96-well plates by application of dichromatic red/blue light-emitting diode illumination. Different robotic dosing approaches and additional data evaluation methods helped to further expand the applicability domain of the assay. The combined algae test differentiates between nonspecifically acting compounds and photosynthesis inhibitors, such as photosystem II (PSII) herbicides. The PSII herbicides acted immediately on photosynthesis and showed growth rate inhibition at higher concentrations. If growth was a similar or more sensitive endpoint than photosynthesis inhibition, this was an indication that the tested chemical acted nonspecifically or that a mixture or a water sample was dominated by chemicals other than PSII herbicides acting on algal growth. We fingerprinted the effects of 45 chemicals on photosynthesis inhibition and growth rate and related the effects of the single compounds to designed mixtures of these chemicals detected in water samples and to the effects directly measured in water samples. Most of the observed effects in the water samples could be explained by known photosystem II inhibitors such as triazines and phenylurea herbicides. The improved setup of the combined algae test gave results consistent with those of the previous method but has lower costs, higher throughput, and higher precision. Environ Toxicol Chem 2020;39:2496–2508. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Abstract The combined algae test (CAT) allows cost-efficient high-throughput monitoring of chemicals and water samples for their algae toxicity with a diagnostic component to differentiate between the mixture effects of photosynthesis inhibitors and other chemicals.