Miracle-dz/UniFAR-FTUs huggingface dataset:
Remdesivir for the treatment of patients in hospital with COVID-19 in Canada: a randomized controlled trial

Background: The role of remdesivir in the treatment of patients in hospital with COVID-19 remains ill defined in a global context. The World Health Organization Solidarity randomized controlled trial (RCT) evaluated remdesivir in patients across many countries, with Canada enrolling patients using an expanded data collection format in the Canadian Treatments for COVID-19 (CATCO) trial. We report on the Canadian findings, with additional demographics, characteristics and clinical outcomes, to explore the potential for differential effects across different health care systems. Methods: We performed an open-label, pragmatic RCT in Canadian hospitals, in conjunction with the Solidarity trial. We randomized patients to 10 days of remdesivir (200 mg intravenously [IV] on day 0, followed by 100 mg IV daily), plus standard care, or standard care alone. The primary outcome was in-hospital mortality. Secondary outcomes included changes in clinical severity, oxygen- and ventilator-free days (at 28 d), incidence of new oxygen or mechanical ventilation use, duration of hospital stay, and adverse event rates. We performed a priori subgroup analyses according to duration of symptoms before enrolment, age, sex and severity of symptoms on presentation. Results: Across 52 Canadian hospitals, we randomized 1282 patients between Aug. 14, 2020, and Apr. 1, 2021, to remdesivir (n = 634) or standard of care (n = 648). Of these, 15 withdrew consent or were still in hospital, for a total sample of 1267 patients. Among patients assigned to receive remdesivir, in-hospital mortality was 18.7%, compared with 22.6% in the standard-of-care arm (relative risk [RR] 0.83 (95% confidence interval [CI] 0.67 to 1.03), and 60-day mortality was 24.8% and 28.2%, respectively (95% CI 0.72 to 1.07). For patients not mechanically ventilated at baseline, the need for mechanical ventilation was 8.0% in those assigned remdesivir, and 15.0% in those receiving standard of care (RR 0.53, 95% CI 0.38 to 0.75). Mean oxygen-free and ventilator-free days at day 28 were 15.9 (± standard deviation [SD] 10.5) and 21.4 (± SD 11.3) in those receiving remdesivir and 14.2 (± SD 11) and 19.5 (± SD 12.3) in those receiving standard of care (p = 0.006 and 0.007, respectively). There was no difference in safety events of new dialysis, change in creatinine, or new hepatic dysfunction between the 2 groups. Interpretation: Remdesivir, when compared with standard of care, has a modest but significant effect on outcomes important to patients and health systems, such as the need for mechanical ventilation. Trial registration: ClinicalTrials.gov, no. NCT04330690.
Antelope Jackrabbit (Lepus alleni) Habitat Characteristics in a Former Rangeland

ABSTRACT Semi-desert grasslands in the southwestern United States have undergone significant ecological changes as a result of anthropogenic activities beginning in the 1800s. As efforts to restore semi-desert grasslands continue, importance should be placed on understanding the habitat requirements of species, and their relationships with other plants and animals. We examined habitat characteristics of antelope jackrabbits (Lepus alleni Mearns 1890) at Buenos Aires National Wildlife Refuge in south-central Arizona. We examined antelope jackrabbit habitat in relation to endangered Pima pineapple cacti (Coryphantha scheeri Kuntz var. robustispina Schott) and available freshwater sources. Dominant vegetation type and cover were measured at 247 points in antelope jackrabbit home ranges between October 2015 and December 2015. Additionally, we documented the proximity of antelope jackrabbit locations to Pima pineapple cacti and available water sources to determine whether antelope jackrabbits have a spatial relationship with this endangered cactus or water availability.Antelope jackrabbits did not select for habitat based on the vegetation characteristics we measured, proximity to Pima pineapple cacti or based on water availability (P > 0.05). Some jackrabbit species have indicated habitat structure preferences, and while antelope jackrabbits are most commonly associated with tropic-subtropic savannas, our study did not show that antelope jackrabbits select for specific vegetation types or a specific vegetation density, nor native grasses over non-native grasses. Antelope jackrabbits may encounter and eat Pima pineapple cactus opportunistically, as opposed to selecting habitat where Pima pineapple cactus occur. Additionally, antelope jackrabbits did not choose habitat based on the location of freshwater sources which may be because they do not need to drink water to survive and instead get their water needs from their food. Little information exists on how antelope jackrabbits select habitat. This study concluded that there is no relation between vegetation factors previously thought to influence antelope jackrabbit habitat selection and habitat use. Future studies based on larger-scale variables, like topography or predator pressure, may help in understanding the factors that influence how this species uses man-altered landscapes.
Nipah virus from bats - another potential pandemic? Risk mapping the impact of anthropogenic and climate change on the transmission of Nipah virus infection to humans.

Henipavirus infection (NiV), a fatal disease transmitted by bats has caused human death and disease in India and Bangladesh. With an average case fatality rate of more than 70%, NiV has the potential to cause widespread outbreaks that can have a devastating impact on human health. Spillover of NiV from bats to humans is influenced by several factors mainly human behaviour and human interaction with bats. Climatic conditions and habitat destruction influence the shedding of the virus and the transmission of the disease to humans. Limited research has been conducted on the factors driving these spillover events. As the world has recently witnessed the devastating impact of the COVID-19 global pandemic, a forewarning of spillover events will enable the adoption of adequate measures to prevent and control future outbreaks. Our study maps the likely changing distribution of NiV reservoir Pteropus medius bat species using future climate and landuse change predictions. We use existing data to predict which districts within India and Bangladesh have increased risk of spillover of NiV in the future. We use Species Distribution Modelling to predict the likely change in the distribution of P. medius under different future scenarios and the concurrent increase in the risk of NiV spillover events. We focus on the influence of anthropogenic changes in different socioeconomic scenarios to predict future spillover events. We consider climate and social goals set by the International Panel on Climate Change (IPPC) to create accurate predictions of regions at risk of NiV spillovers. We find that the risk of NiV spillover events in India and Bangladesh will likely increase. More districts are predicted to be at risk of NiV spillovers under the high population growth and persistent environmental degradation scenario than under moderate population growth and medium challenges to achieve climate goals. This highlights the significance of population growth and climate change when considering disease outbreaks and public health. Our findings will enable the authorities in the predicted spillover regions to take public health measures to prevent and control NiV outbreaks.
The Lothian Diary Project: sociolinguistic methods during the COVID-19 lockdown

Abstract The Lothian Diary Project is an interdisciplinary effort to collect self-recorded audio or video diaries of people’s experiences of COVID-19 in and around Edinburgh, Scotland. In this paper we describe how the project emerged from a desire to support community members. The diaries have been disseminated through public events, a website, an oral history project, and engagement with policymakers. The data collection method encouraged the participation of people with disabilities, racialized individuals, immigrants, and low-proficiency English/Scots speakers, all of whom are more likely to be negatively affected by COVID-19. This is of interest to sociolinguists, given that these groups have been under-represented in previous studies of linguistic variation in Edinburgh. We detail our programme of partnering with local charities to help ensure that digitally disadvantaged groups and their caregivers are represented. Accompanying survey and demographic data means that this self-recorded speech can be used to complement existing Edinburgh speech corpora. Additional sociolinguistic goals include a narrative analysis and a stylistic analysis, to characterize how different people engage creatively with the act of creating a COVID-19 diary, especially as compared to vlogs and other video diaries.
Finite Element Analysis of Stress Relaxation in a Flange Seal System

The stress relaxation properties of steel 35CrMoA and 40MnB have been measured by tensile stress relaxation tests under 400 ℃. Using the finite element analysis software ANSYS,the development of stress relaxation behavior in the flange sealing system of a floating head heat exchanger were analyzed.In the analysis,the flange sealing system consists of the bolts,two flanges and two gaskets,which is a typical nonlinear system.
3D Registration of the Point Cloud Data Using Parameter Adaptive Super4PCS Algorithm in Medical Image Analysis

In this article, we use the parameter-adaptive Super4PCS algorithm to achieve high-precision registration of medical point clouds. First, generate the corresponding point cloud from the biological data (CT, MRI) to be registered. Then analyze the characteristics of the point cloud to be registered, and use it to adaptively set the parameters of Super4PCS, and finally perform point cloud registration. We compare the performance of six different algorithms with their accuracy and robustness. The accuracy, robustness of our method are the best. At the same time, no parameter input is required which is very convenient for medical workers. Experiments on medical models demonstrate the efficiency and robustness of our algorithm.
Global stability and resolvent analyses of laminar boundary-layer flow interacting with viscoelastic patches

Abstract The attenuation of two-dimensional boundary-layer instabilities by a finite-length, viscoelastic patch is investigated by means of global linear stability theory. First, the modal stability properties of the coupled problem are assessed, revealing unstable fluid-elastic travelling-wave flutter modes. Second, the Tollmien–Schlichting instabilities over a rigid wall are characterised via the analysis of the fluid resolvent operator in order to determine a baseline for the fluid-structural analysis. To investigate the effect of the elastic patch on the growth of these flow instabilities, we first consider the linear frequency response of the coupled fluid-elastic system to the dominant rigid-wall forcing modes. In the frequency range of Tollmien–Schlichting waves, the energetic flow amplification is clearly reduced. However, an amplification is observed for higher frequencies, associated with travelling-wave flutter. This increased complexity requires the analysis of the coupled fluid-structural resolvent operator; the optimal, coupled, resolvent modes confirm the attenuation of the Tollmien–Schlichting instabilities, while also being able to capture the amplification at the higher frequencies. Finally, a decomposition of the fluid-structural response is proposed to reveal the wave cancellation mechanism responsible for the attenuation of the Tollmien–Schlichting waves. The viscoelastic patch, excited by the incoming rigid-wall wave, provokes a fluid-elastic wave that is out-of-phase with the former, thus reducing its amplitude.
MEASURING CONSUMER INVOLVEMENT: A TEST OF THE AUTOMOBILE INVOLVEMENT SCALE

This study empirically investigated consumer involvement with a product class. Data was collected from 178 vehicle buyers. Reliability and factor analyses investigated the structure of the Bloch (1981) instrument and the dimensions underlying involvement. In terms of replication, the results suggest the reduced-item version of the instrument previously proposed by Shimp and Sharma (1983) is reliable and is a less excessive measurement instrument. Similar dimensions underlying involvement with the product class are reported here. The study extends previous work by obtaining similar results in a different cultural setting, producing findings from a more relevant sample, applying an additional method of data collection, and suggesting that the underlying dimensions may be temporally stable.
Median Filter Helps Lymph Node Segmentation in Deep Learning via PET/CT

Pathological lymph node segmentation plays a vital role in clinical practice. Yet it is still a challenging problem owing to low contrast to surrounding structures on images. In this paper, we investigate the problem whether the classical median filter helps lymph node segmentation in deep learning via PET/CT. Specifically, we design a median filter layer and integrate it into two types of deep convolution neural networks: SegNet and DeepLabv3+, which takes the encoder and decoder structure that has the advantage to segment objects in a multi-scale way. Meanwhile, we adopt three various objective functions, which are cross entropy loss, generalized Dice loss and focal loss, to study which is the best choice for pathological lymph node segmentation with median filter. Four-fold cross validation has been done on 63 volumes containing 214 malignant lymph nodes, and the experiments demonstrate that median filter could help improve the lymph segmentation performance with cross entropy as loss function, which has 3% and 2% improvements with SegNet and 4% and 3% improvements with DeepLabv3+ in terms of Sensitivity and Dice Similarity Coefficient (DSC).
Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots

Meristems are stem cells niches that support the formation of all plant organs and are either set during embryogenesis and maintained throughout the plant life or specified de novo, post-embryonically. The embryo-derived root apical meristem is organized around a group of infrequently dividing cells, the quiescent centre, that maintains the stem cells, organizes growth along two axes and owing to its resistance to 3ic stress can replace damaged stem cells. In most cases, lateral roots post-embryonically branch off the primary and establish a new root meristem which organization is identical to the primary root one. The cellular and molecular processes underpinning the emergence of new stem cell niches are not well known. Here, we characterize the de novo establishment of the root apical meristem in lateral roots. While the position of the new stem cell niche is set early during morphogenesis, its cellular layout, unique gene expression profile and mitotic quiescence are only acquired after emergence concomitant to the establishment of two diverging growth axis. Our results show that the intertwined attributes of the mature root stem cell niche are progressively acquired during lateral root formation, and support a model in which the position of the stem cell niche emerges from the establishment of diverging growth axis. Highlight Analyze of the ontogeny of the quiescent center during lateral root ontogeny reveal its late formation and supports that its emergence results from the establishment of two diverging growth axis.
The Predictive Value of Individual Electric Field Modeling for Transcranial Alternating Current Stimulation Induced Brain Modulation

There is considerable individual variability in the reported effectiveness of non-invasive brain stimulation. This variability has often been ascribed to differences in the neuroanatomy and resulting differences in the induced electric field inside the brain. In this study, we addressed the question whether individual differences in the induced electric field can predict the neurophysiological and behavioral consequences of gamma band tACS. In a within-subject experiment, bi-hemispheric gamma band tACS and sham stimulation was applied in alternating blocks to the participants’ superior temporal lobe, while task-evoked auditory brain activity was measured with concurrent functional magnetic resonance imaging (fMRI) and a dichotic listening task. Gamma tACS was applied with different interhemispheric phase lags. In a recent study, we could show that anti-phase tACS (180° interhemispheric phase lag), but not in-phase tACS (0° interhemispheric phase lag), selectively modulates interhemispheric brain connectivity. Using a T1 structural image of each participant’s brain, an individual simulation of the induced electric field was computed. From these simulations, we derived two predictor variables: maximal strength (average of the 10,000 voxels with largest electric field values) and precision of the electric field (spatial correlation between the electric field and the task evoked brain activity during sham stimulation). We found considerable variability in the individual strength and precision of the electric fields. Importantly, the strength of the electric field over the right hemisphere predicted individual differences of tACS induced brain connectivity changes. Moreover, we found in both hemispheres a statistical trend for the effect of electric field strength on tACS induced BOLD signal changes. In contrast, the precision of the electric field did not predict any neurophysiological measure. Further, neither strength, nor precision predicted interhemispheric integration. In conclusion, we found evidence for the dose-response relationship between individual differences in electric fields and tACS induced activity and connectivity changes in concurrent fMRI. However, the fact that this relationship was stronger in the right hemisphere suggests that the relationship between the electric field parameters, neurophysiology, and behavior may be more complex for bi-hemispheric tACS.
Mechanically Optimize T Cells Activation by Spiky Nanomotors

T cell activation is vital for immune response initiation and modulation. Except for the strength of the interaction between T cell receptors (TCR) and peptides on major histocompatibility complex molecules (MHC), mechanical force, mediated by professional mechanosensitive ion channels, contributes to activating T cells. The intrinsic characteristic of synthetic micro/nanomotors that convert diverse energy sources into physical movement and force, opening up new possibilities for T cell regulation. In this work, Pd/Au nanomotors with spiky morphology were fabricated, and in the presence of low concentrations of hydrogen peroxide fuel, the motors exhibited continuous locomotion in the cellular biological environment. Physical cues (force and pressure) generated by the dynamic performance are sensed by mechanosensitive ion channels of T cells and trigger Ca2+ influx and subsequent activation. The successful demonstration that mechanical signals generated in the bio microenvironment can potentiate T cells activation, represents a potential approach for cell-based cancer immunotherapy.
Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics

The heart has been the center of numerous transcriptomic studies in the past decade. Even though our knowledge of the key organ in our cardiovascular system has significantly increased over the last years, it is still not fully understood yet. In recent years, extensive efforts were made to understand the genetic and transcriptomic contribution to cardiac function and failure in more detail. The advent of Next Generation Sequencing (NGS) technologies has brought many discoveries but it is unable to comprehend the finely orchestrated interactions between and within the various cell types of the heart. With the emergence of single-cell sequencing more than 10 years ago, researchers gained a valuable new tool to enable the exploration of new subpopulations of cells, cell-cell interactions, and integration of multi-omic approaches at a single-cell resolution. Despite this innovation, it is essential to make an informed choice regarding the appropriate technique for transcriptomic studies, especially when working with myocardial tissue. Here, we provide a primer for researchers interested in transcriptomics using NGS technologies.
The Lineage Differentiation and Dynamic Heterogeneity of Thymic Epithelial Cells During Thymus Organogenesis

Although much progress has been made recently in revealing the heterogeneity of the thymic stromal components, the molecular programs of cell lineage divergency and temporal dynamics of thymic epithelial cell (TEC) development are largely elusive. Here, we constructed a single-cell transcriptional landscape of non-hematopoietic cells from mouse thymus spanning embryonic to adult stages, producing transcriptomes of 30,959 TECs. We resolved the transcriptional heterogeneity of developing TECs and highlighted the molecular nature of early TEC lineage determination and cortico-medullary thymic epithelial cell lineage divergency. We further characterized the differentiation dynamics of TECs by clarification of molecularly distinct cell states in the thymus developing trajectory. We also identified a population of Bpifa1+ Plet1+ mTECs that was preserved during thymus organogenesis and highly expressed tissue-resident adult stem cell markers. Finally, we highlighted the expression of Aire-dependent tissue-restricted antigens mainly in Aire+ Csn2+ mTECs and Spink5+ Dmkn+ mTECs in postnatal thymus. Overall, our data provided a comprehensive characterization of cell lineage differentiation, maturation, and temporal dynamics of thymic epithelial cells during thymus organogenesis.
Aeromonas sobria Serine Protease Degrades Several Protein Components of Tight Junctions and Assists Bacterial Translocation Across the T84 Monolayer

Aeromonas sobria is a Gram-negative pathogen that causes food-borne illness. In immunocompromised patients and the elderly, A. sobria opportunistically leads to severe extraintestinal diseases including sepsis, peritonitis, and meningitis. If A. sobria that infects the intestinal tract causes such an extraintestinal infection, the pathogen must pass through the intestinal epithelial barrier. In our earlier study using intestinal cultured cells (T84 cells), we observed that an A. sobria strain with higher A. sobria serine protease (ASP) production caused a marked level of bacterial translocation across the T84 intestinal epithelial monolayer. Herein, we investigated the effect of ASP on tight junctions (TJs) in T84 cells. We observed that ASP acts on TJs and causes the destruction of ZO-1, ZO-2, ZO-3, and claudin-7 (i.e., some of the protein components constituting TJs), especially in the strains with high ASP productivity. Based on the present results together with those of our earlier study, we propose that ASP may cause a disruption of the barrier function of the intestinal epithelium as a whole due to the destruction of TJs (in addition to the destruction of adherens junctions) and that ASP may assist invasion of the pathogens from the intestinal epithelium into deep sites in the human body.