Miracle-dz/UniFAR-FTUs huggingface dataset:
Awareness, knowledge, attitude and practice towards measures for prevention of the spread of COVID-19 in the Ugandans: A nationwide online cross-sectional Survey

Background The world is facing the Coronavirus pandemic which is highly infectious. A number of measures have been put in place to prevent its spread among the population. However, for these preventive measures to be effective, the population requires an appropriate and sufficient knowledge. Thus, a survey was conducted with the aim of assessing the awareness, knowledge, attitude and practices towards measures for prevention of the spread of Covid-19 amongst Ugandans. Methods This was a cross-sectional study conducted during the lockdown in Uganda. An online questionnaire and a snowballing approach was used for participant recruitment of 18 years above literate Ugandans. Data collection was done from 6th to 15th April 2020 during which 1763 people participated. We analyzed all data using STATA 14.2, applying appropriate statistical tests. Results Out of 1763 participants, 97.6% were aware of the current pandemic. 83.9% of participants had a good knowledge score (21.8/27), 72.4% had a good attitude and 85.3% were practicing measures to prevent the spread of the Coronavirus disease. The ordered logistic regression showed that being a Health worker was significantly associated with a high knowledge (aOR:6 (3.32-10.93); a good attitude (aOR:2.5(1.68-3.8)]) and good practice (aOR:2.9 (1.95-4.2). On contrary, being a driver, business entrepreneur and a security personnel were found to have less rate in awareness, knowledge, attitude and practice. Conclusions Ugandans had a good overall awareness, knowledge, attitude and practice. However, there is still a gap of knowledge, attitude and practice among drivers, business entrepreneur and security personnel. There is a need to mobilize the population in the country to have the same degree of awareness and knowledge which will have an impact on attitude and practice to prevent spread of COVID-19.
Hemolymph cell types of the mussel Mytilus galloprovincialis

Two types of circulating hemocytes were identified in Mytilus galloprovincialis hemolymph: hyalinocytes and granulocytes. The hyalinocytes are agranular cells and show a central nucleus surrounded by relatively small cytoplasm. The granulocytes are larger than hyalinocytes and have smaller nuclei. Three classes of granulocytes (acidophilic granulocytes, basophilic granulocytes and granulocytes containing both types of granules) were distinguished based on staining properties of their cytoplasmic granules. At the ultrastructural level, the hyahnocytes show characteristics of undifferentiated cells. The granulocytes are more differentiated and have membrane-limited cytoplasmic granules. Some granulocytes contain only small granules; others have numerous large granules and some of them contain a mix of granule sizes. Density grad~ent centnfugation allowed the separation of acidophilic granulocytes from the other types. Immunocharacterization demonstrated that the granulocytes are an antigenically heterogeneous population.
Post-exercise Endothelium-Dependent Vasodilation Is Dependent on Training Status

The effect of training status on post-exercise flow-mediated dilation (FMD) is not well characterized. We tested the hypothesis that the more trained the subjects, the lower the reduction in FMD after an acute bout of aerobic exercise. Forty-seven men (mean ± SD, age: 20.1 ± 1.2 years, body mass: 75.5 ± 5.1 kg, height 178.1 ± 5.4 cm) were divided into five groups with different training characteristics (sedentary, two different groups of active subjects, two different groups of well-trained subjects – runners and weightlifters). Brachial artery FMD (blood pressure cuff placed around the arm distal to the probe with the proximal border adjacent to the medial epicondyle; 5 min at a pressure of 220 mmHg) was assessed before and during 3 min immediately after a bout of cycling exercise at a relative intensity of 170 bpm [(physical work capacity (PWC170)]. At baseline, a progressive increase in FMD was observed in the participants with the higher training status, if the training remained moderate. Indeed, FMD was reduced in runners and weightlifters compared to those who were moderately trained. After PWC170, FMD did not significantly change in sedentary and highly trained runners, significantly increased in the two groups of active subjects but significantly decreased in highly trained weightlifters. These results showed that endothelium-dependent vasodilation evaluated using brachial FMD is maintained or improved following acute aerobic exercise in moderately trained participants, but not in well-trained participants, especially if they are engaged in resistance training.
Intravital Multiphoton Microscopy of the Ocular Surface: Alterations in Conventional Dendritic Cell Morphology and Kinetics in Dry Eye Disease

Dry eye disease (DED) is a multifactorial disease of the ocular surface, characterized by loss of tear film homeostasis and ocular symptoms, in which neurosensory abnormalities have recently been shown to play an etiological role. Although the role of inflammation has been widely studied in DED, the kinetics of immune cells of the ocular surface in this complex disease are hereto unclear. Herein, we utilized intravital multiphoton imaging on transgenic mice to investigate the 3D morphology and kinetics of conventional dendritic cells (cDCs) and the role of ocular surface sensory nerves in regulating them in both the naïve state and experimental DED. Mice with DED had significantly lower tear secretion (p < 0.01), greater corneal fluorescein staining (p < 0.001), and higher cDC density in the ocular surface (p < 0.05), compared to naïve mice. cDCs in DED mice showed morphological alterations in the limbus, exhibiting smaller surface area (p < 0.001) and volume (p < 0.001) compared to naïve mice. Furthermore, corneal cDCs showed greater sphericity in DED mice compared to naïve mice (p < 0.01). In addition, limbal cDCs displayed significantly increased migratory kinetics in DED, including mean track speed, 3D instantaneous velocity, track length, and displacement, compared to naïve mice (all p < 0.05). In mice with DED, cDCs showed a higher meandering index in the limbus compared to central cornea (p < 0.05). In DED, cDCs were less frequently found in contact with nerves in the limbus, peripheral, and central cornea (p < 0.05). cDCs in contact with nerves demonstrated a larger surface area (p < 0.001) and volume (p < 0.001), however, they exhibited less sphericity (p < 0.05) as compared to cDCs not in contact with nerves in naïve mice. Importantly, cDCs in contact with nerves during DED had a decreased track length, displacement, mean track speed, and 3D instantaneous velocity compared to those not in contact with nerves (all p < 0.05). Taken together, we present in vivo evidence of altered cDC kinetics and 3D morphology in DED. Furthermore, apparent neuronal contact significantly alters cDC kinetics and morphological characteristics, suggesting that ocular surface nerves may play a direct role in mediating immune responses in DED.
The Application of Nanopore Sequencing Technology to the Study of Dinoflagellates: A Proof of Concept Study for Rapid Sequence-Based Discrimination of Potentially Harmful Algae

Harmful algal blooms (HABs) are a naturally occurring global phenomena that have the potential to impact fisheries, leisure and ecosystems, as well as posing a significant hazard to animal and human health. There is significant interest in the development and application of methodologies to study all aspects of the causative organisms and toxins associated with these events. This paper reports the first application of nanopore sequencing technology for the detection of eukaryotic harmful algal bloom organisms. The MinION sequencing platform from Oxford Nanopore technologies provides long read sequencing capabilities in a compact, low cost, and portable format. In this study we used the MinION to sequence long-range PCR amplicons from multiple dinoflagellate species with a focus on the genus Alexandrium. Primers applicable to a wide range of dinoflagellates were selected, meaning that although the study was primarily focused on Alexandrium the applicability to three additional genera of toxic algae, namely; Gonyaulax, Prorocentrum, and Lingulodinium was also demonstrated. The amplicon generated here spanned approximately 3 kb of the rDNA cassette, including most of the 18S, the complete ITS1, 5.8S, ITS2 and regions D1 and D2 of the 28S. The inclusion of barcode genes as well as highly conserved regions resulted in identification of organisms to the species level. The analysis of reference cultures resulted in over 99% of all sequences being attributed to the correct species with an average identity above 95% from a reference list of over 200 species (see Supplementary Material 1). The use of mock community analysis within environmental samples highlighted that complex matrices did not prevent the ability to distinguish between phylogenetically similar species. Successful identification of causative organisms in environmental samples during natural toxic events further highlighted the potential of the assay. This study proves the suitability of nanopore sequencing technology for taxonomic identification of harmful algal bloom organisms and acquisition of data relevant to the World Health Organisations “one health” approach to marine monitoring.
Genomic Selection Using Pedigree and Marker-by-Environment Interaction for Barley Seed Quality Traits From Two Commercial Breeding Programs

With the current advances in the development of low-cost high-density array-based DNA marker technologies, cereal breeding programs are increasingly relying on genomic selection as a tool to accelerate the rate of genetic gain in seed quality traits. Different sources of genetic information are being explored, with the most prevalent being combined additive information from marker and pedigree-based data, and their interaction with the environment. In this, there has been mixed evidence on the performance of use of these data. This study undertook an extensive analysis of 907 elite winter barley (Hordeum vulgare L.) lines across multiple environments from two breeding companies. Six genomic prediction models were evaluated to demonstrate the effect of using pedigree and marker information individually and in combination, as well their interactions with the environment. Each model was evaluated using three cross-validation schemes that allows the prediction of newly developed lines (lines that have not been evaluated in any environment), prediction of new or unobserved years, and prediction of newly developed lines in unobserved years. The results showed that the best prediction model depends on the cross-validation scheme employed. In predicting newly developed lines in known environments, marker information had no advantage to pedigree information. Predictions in this scenario also benefited from including genotype-by-environment interaction in the models. However, when predicting lines and years not observed previously, marker information was superior to pedigree data. Nonetheless, such scenarios did not benefit from the addition of genotype-by-environment interaction. A combination of pedigree-based and marker-based information produced a similar or only marginal improvement in prediction ability. It was also discovered that combining populations from the different breeding programs to increase training population size had no advantage in prediction.
USP5 Promotes Metastasis in Non-Small Cell Lung Cancer by Inducing Epithelial-Mesenchymal Transition via Wnt/β-Catenin Pathway

Ubiquitin-specific protease 5 (USP5) is a deubiquitinating enzyme that functions as an oncoprotein in a variety of human cancers. However, the expression and role of USP5 in the metastasis of non-small cell lung cancer (NSCLC) have not been addressed. In this study, we examined the expression and prognostic significance of USP5 in NSCLC. The results revealed that USP5 was overexpressed and correlated with metastasis and overall survival in NSCLC tissues. A further in vitro study revealed that the levels of USP5 protein in NSCLC cells were associated with epithelial–mesenchymal transition (EMT) markers. Furthermore, USP5 overexpression significantly enhanced, whereas USP5 silencing significantly decreased the expression of EMT proteins and migration and invasion of NSCLC cells. In addition, the results from western blotting demonstrated that USP5 regulated EMT via the Wnt/β-catenin signaling pathway. Further immunohistochemical analysis revealed that USP5 was significantly associated with the expression of β-catenin and EMT markers in NSCLC tissues. Overall, USP5 upregulation is associated with tumor metastasis and poor prognosis in patients with NSCLC. USP5 promotes EMT and the invasion and migration of NSCLC cells. Therefore, USP5 may serve as a novel prognostic biomarker and provide a potential target for the treatment of metastasis in NSCLC.
Dependence of behavioral and neocortical seizures on brain pH and oxygen levels in a rat model of term birth asphyxia

Birth asphyxia (BA) is a pathologic condition that arises from severe perinatal hypoxia and hypercapnia. Recovery following BA is often associated with seizures which may exacerbate the ensuing hypoxic-ischemic encephalopathy (HIE). Drugs used to treat post-BA seizures are often ineffective and there are concerns over their safety. Therefore, novel seizure-suppressing therapies are urgently needed. Most rodent models of BA-induced seizures are based on exposing neonatal rats or mice to hypoxia (or hypoxia-ischemia), and overlook the fact that the hypercapnic acidosis linked to asphyxia has brain-sparing effects by suppressing neuronal excitability and enhancing cerebral blood flow. Thus, the aim of the present study was to investigate the dependence of asphyxia-induced seizures on brain pH and oxygen (Po2) levels in a rodent model of term BA based on postnatal day 11-12 rat pups. Cortical activity and electrographic seizures were recorded in freely-behaving animals using epidural electrodes. Simultaneous measurements of cortical local field potentials as well as intracortical pH and Po2 were made using microelectrodes and microsensors in urethane-anesthesized animals. The pups were exposed either to steady asphyxia (duration 15 min; with ambient air containing 5 % O2 plus 20 % CO2) or to intermittent asphyxia (30 min; with repetitive 5 min steps from 9 % to 5 % O2 at constant 20 % CO2). Both protocols led to acidemia (blood pH
Temporal signal and the phylodynamic threshold of SARS-CoV-2

The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real-time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates. For example, before the phylodynamic threshold is reached, genomic variation is so low that even large amounts of genome sequences may be insufficient to estimate the virus’s evolutionary rate and the time scale of an outbreak. We collected genome sequences of SARS-CoV-2 from public databases at 8 different points in time and conducted a range of tests of temporal signal to determine if and when the phylodynamic threshold was reached, and the range of inferences that could be reliably drawn from these data. Our results indicate that by February 2nd 2020, estimates of evolutionary rates and time scales had become possible. Analyses of subsequent data sets, that included between 47 to 122 genomes, converged at an evolutionary rate of about 1.1×10−3 subs/site/year and a time of origin of around late November 2019. Our study provides guidelines to assess the phylodynamic threshold and demonstrates that establishing this threshold constitutes a fundamental step for understanding the power and limitations of early data in outbreak genome surveillance.
Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase – mcrA) and methanotrophic (particulate methane monooxygenase – pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4 cycling in this region.
Impact of referencing scheme on decoding performance of LFP-based brain-machine interface

Objective. There has recently been an increasing interest in local field potential (LFP) for brain-machine interface (BMI) applications due to its desirable properties (signal stability and low bandwidth). LFP is typically recorded with respect to a single unipolar reference which is susceptible to common noise. Several referencing schemes have been proposed to eliminate the common noise, such as bipolar reference, current source density (CSD), and common average reference (CAR). However, to date, there have not been any studies to investigate the impact of these referencing schemes on decoding performance of LFP-based BMIs. Approach. To address this issue, we comprehensively examined the impact of different referencing schemes and LFP features on the performance of hand kinematic decoding using a deep learning method. We used LFPs chronically recorded from the motor cortex area of a monkey while performing reaching tasks. Main results. Experimental results revealed that local motor potential (LMP) emerged as the most informative feature regardless of the referencing schemes. Using LMP as the feature, CAR was found to yield consistently better decoding performance than other referencing schemes over long-term recording sessions. Significance. Overall, our results suggest the potential use of LMP coupled with CAR for enhancing the decoding performance of LFP-based BMIs.
Deep barriers, shallow divergences: reduced phylogeographical structure in the collared pika (Mammalia: Lagomorpha: Ochotona collaris)

Pikas (Ochotona spp.) are alpine specialists that show considerable morphological and genetic variation structured along latitudinal and elevational gradients. Recent studies of North American and Asian pikas have uncovered phylogeographical partitioning among separate mountain ranges and drainages, driven by Quaternary climate fluctuations. We tested the prediction that collared pikas (O. collaris) exhibit lower genetic diversity and less structure than other species of pika due to lower long‐term habitat stability.
δ‐Aminolevulinate Dehydratase from Rat Harderian Gland Purification and Properties

δ-Aminolevulinate dehydratase which catalyzes the second step in the biosynthesis of protoporphyrin has been purified from Harderian gland homogenates of normal rats. The enzyme preparation has a specific activity of 860 units per mg of protein at 37°, and about a 150-fold purification from the crude extract has been achieved. The purified material appears to be homogeneous in starch gel and polyacrylamide gel disc electrophoretic studies. Partially purified enzyme preparations have an absolute requirement for cysteine or analogous thiol reagents. Effect of anions and cations is discussed.
Dynamics of regional distribution: the core and satellite species hypothesis

A new concept is introduced to analyse species' regional distributions and to relate the pattern of distributions to niche relations. Several sets of data indicate that average local abundance is positively correlated with regional distribution, i.e. the fraction of patchily distributed population sites occupied by the species. This observation is not consistent with the assumptions of a model of regional distribution introduced by Levins. A corrected model is now presented, in which the probability of local extinction is a decreasing function of distribution, and a stochastic version of the new model is analysed. If stochastic variation in the rates of local extinction and/or colonization is sufficiently large, species tend to fall into two distinct types, termed the "core" and the "satellite" species. The former are regionally common and locally abundant, and relatively well spaced-out in niche space, while opposite attributes characterize satellite species. This dichotomy, if it exists, provides null hypotheses to test theories about community structure, and it may help to construct better structured theories. Testing the core-satellite hypothesis and its connection to the r-K theory and to Raunkiaer's "law of frequency" are discussed.
Fat partitioning in British Friesian cows: the influence of physiological state on dissected body composition

Summary The influence of physiological state (pregnant, lactating, dry) on body composition and fat partitioning in Friesian cows has been examined. A total of 20 cows, four per physiological state, were slaughtered and their left half carcasses dissected into individual muscles, bones and fat depots. All body parts, including the internal organs and fat depots, were weighed at slaughter. Muscle tissue and the internal organs showed some weight changes, consistent with a redistribution of tissue towards the udder and gut, and mobilization of muscle, but the major changes in weight associated with changing physiological state occurred in total body fat. Intermuscular fat made the greatest absolute contribution to changing fat weight, but subcutaneous fat showed the greatest proportional change with changing physiological state. The order of depletion of fat depots during fat loss was approximately the reverse of the order of development found during developmental growth. The distribution of subcutaneous fat between seven defined regions of the carcass was not affected by differences in total fatness in different physiological states. This, and the high correlation found between fat depth and total body fatness, confirms the view that measures of subcutaneous fat depth, e.g. by ultrasonics, should be useful predictors of the energy status of cows in varying physiological states.