Miracle-dz/UniFAR-FTUs huggingface dataset:
The spectre of biogeographical regionalization

A biogeographical regionalization is a hierarchical system that categorizes geographical areas in terms of their biotas. I provide a general protocol to undertake biogeographical regionalizations, that consists of seven steps: (1) defining the study area; (2) assembling distributional data; (3) identifying natural areas; (4) discovering area relationships; (5) defining boundaries/transition zones; (6) regionalization and (7) area nomenclature. Natural biogeographical units are useful for people undertaking different types of analyses, like macroecologists, evolutionary biologists, systematists and conservationists. Biogeographical regionalizations may help biogeographers communicate more effectively between themselves and discover opportunities to work on common problems, contributing to the development of a truly integrative biogeography.
Higher temperatures worsen the effects of mutations on protein stability

Understanding whether and how temperature increases alter the effects of mutations on protein stability is crucial for understanding the limits to thermal adaptation by organisms. Currently, it is generally assumed that the stability effects of mutations are independent of temperature. Yet, mutations should become increasingly destabilizing as temperature rises due to the increase in the energy of atoms. Here, by performing an extensive computational analysis on the essential enzyme adenylate kinase in prokaryotes, we show, for the first time, that mutations become more destabilizing with temperature both across and within species. Consistent with these findings, we find that substitution rates of prokaryotes decrease nonlinearly with temperature. Our results suggest that life on Earth likely originated in a moderately thermophilic and thermally fluctuating environment, and indicate that global warming should decrease the per-generation rate of molecular evolution of prokaryotes.
Programmed Cell Death Ligand (PD-L)-1 Contributes to the Regulation of CD4+ T Effector and Regulatory T Cells in Cutaneous Leishmaniasis

Cutaneous Leishmaniasis (CL) affects up to one million people every year and treatments are costly and toxic. The regulation of the host immune response is complex and the knowledge of how CD4+ T cells are activated and maintained during Leishmania infection is still limited. Current therapies aim to target programmed cell death (PD)-1 and programmed cell death ligand (PD-L)-1 in order to boost T cell activity. However, the role of the PD-1/PD-L1 axis during Leishmania infection is still unclear. In this study, we found that patients with active and post-treatment CL displayed different subsets of CD4+PD-1+ T cells. Accordingly, L. major-infected mice upregulated PD-1 on activated CD4+ T effector cells and PD-L1 on resident macrophages and infiltrating monocytes at the site of infection. L. major-infected Pdl1−/− mice expressed lower levels of MHCII and higher levels of CD206 on macrophages and monocytes and, more importantly, the lack of PD-L1 contributed to a reduced frequency of CD4+Ly6Chi T effector cells and an increase of CD4+Foxp3+ regulatory T cells at the site of infection and in draining lymph nodes. Additionally, the lack of PD-L1 was associated with lower production of IL-27 by infiltrating monocytes and lower levels of the Th1 cytokines IFN-γ and TNF-α produced by CD4+ T effector cells. Pdl1−/− mice initially exhibited larger lesions despite having a similar parasite load. Our results describe for the first time how the interruption of the PD-1/PD-L1 axis influences the immune response against CL and suggests that this axis regulates the balance between CD4+Ly6Chi T effector cells and CD4+Foxp3+ regulatory T cells.
PROBLÈMES D’ASYMPTOTIQUE EN TEMPS

We study the Maxwell-Landau-Lifshitz system without exchange energy. First, we prove an L(Lloc) estimate for the linear wave equation and apply this local energy estimate to obtain a bound on the curl of the electromagnetic field, uniformly in time and locally in space. Next, we prove strong convergence results, when the time t tends to ∞ or when when the speed of light tends to ∞ (which corresponds to the quasi-stationary approximation). Finally, we establish a stability result with respect to the damping parameter of the Landau-Lifshitz equation.
Neurophysiological coding of statistical and deterministic rule information

Humans are capable of acquiring multiple types of information presented in the same visual information stream. It has been suggested that at least two parallel learning processes are important during learning of sequential patterns – statistical learning and rule-based learning. Yet, the neurophysiological underpinnings of these parallel learning mechanisms in visual sequences are not fully understood. To differentiate between the simultaneous mechanisms at the single trial level, we apply a temporal EEG signal decomposition approach together with sLORETA source localization method to delineate whether distinct statistical and rule-based learning codes can be distinguished in EEG data and can be related to distinct functional neuroanatomical structures. We demonstrate that concomitant but distinct aspects of information coded in the N2 time window play a role in these mechanisms: mismatch detection and response control underlie statistical learning and rule-based learning, respectively, albeit with different levels of time-sensitivity. Moreover, the effects of the two learning mechanisms in the different temporally decomposed clusters of neural activity also differed from each other in neural sources. Importantly, the right inferior frontal cortex (BA44) was specifically implicated in statistical learning, confirming its role in the acquisition of transitional probabilities. In contrast, rule-based learning was associated with the prefrontal gyrus (BA6). The results show how simultaneous learning mechanisms operate at the neurophysiological level and are orchestrated by distinct prefrontal cortical areas. The current findings deepen our understanding on the mechanisms how humans are capable of learning multiple types of information from the same stimulus stream in a parallel fashion.
Immersive virtual reality alters selection of head-trunk coordination strategies in young children

Developing coordinated motor control is essential for competent interactions with the surrounding world and requires a balanced multisensory integration. This integration can be challenged under altered sensory feedback, as is the case for vision in immersive virtual reality (VR). While recent works suggest that a virtual sensory environment alters visuomotor integration in healthy adults, little is known about the effects on younger individuals. Here, we assessed the development of head-trunk coordination in children aged 6 to 10 years and young adults using an immersive flight simulator and a virtual joint angle reproduction task. Contrarily to previous results, when vision was decoupled from the steering body part, only older children and adults displayed a joint (‘en-bloc’) head-torso operation mode. Our results reveal that immersive VR affects the coordination strategy in younger children and highlight the immaturity of postural control through the inability to implement a simplified coordination strategy. These findings have implications for pediatric applications of immersive VR, and reveal its usability as an investigation tool for sensorimotor maturation.
Genetic variability and selection criteria of some sunflower genotypes under different pollination methods

To determinate self-compatible genotypes for increasing autogamy yielded, the ten sunflower genotypes were sown under four pollination methods i.e., open-, self-, hand- and sib-pollinations in a randomized complete block design replicated thrice at Kafr-El-Hamam Agricultural research Station, Sharkia Governorate, Agricultural Research Center, Egypt during 2018 and 2019 summer seasons. Significant variation existed for different pollination treatments, genotypes and their interactions for all studied traits. Among the treatments, open pollination followed by sibbing one was regarded as the best pollination treatment for head diameter, number of filled seeds per head, percentage of seed setting , kernel to hull ratio, seed mass per plant, seed yield per fed and seed oil content. Autogamy studies revealed that ‘L120’ followed by ‘L92’ and ‘L880’ recorded higher proportion of autogamy and self-compatibility. Preferred improvement of seed mass per plant may be achieved through selecting genotypes having the largest head diameter, bigger number of filled seeds per head, the highest proportion of seed setting and the heaviest seed, kernel and hull mass as proven by high phenotypic and genotypic coefficient of variation and high heritability coupled with high genetic advance (as % of mean) as well as correlation and path analyses at both phenotypic and genotypic levels.
Human Vulnerability to Landslides

Landslides pose a devastating threat to human health, killing thousands of people annually. Human vulnerability is a crucial element of landslide risk reduction, yet up until now, all methods for estimating the human consequences of landslides rely on subjective, expert judgment. Furthermore, these methods do not explore the underlying causes of mortality or inform strategies to reduce landslide risk. In light of these issues, we develop a data‐driven tool to estimate an individual's probability of death based on landslide intensity, which can be used directly in landslide risk assessment. We find that between inundation depths of approximately 1–6 m, human behavior is the primary driver of mortality. Landslide vulnerability is strongly correlated with the economic development of a region, but landslide losses are not stratified by gender and age to the degree of other natural hazards. We observe that relatively simple actions, such as moving to an upper floor or a prepared refuge space, increase the odds of survival by up to a factor of 12. Additionally, community‐scale hazard awareness programs and training for citizen first responders offer a potent means to maximize survival rates in landslides.
Prescribing medicinal cannabis

SUMMARY The Australian Federal Government legalised access to medicinal cannabis in 2016 More than 100 different cannabis products are now available to prescribe. Most are oral preparations (oils) or capsules containing delta-9-tetrahydrocannabinol or cannabidiol. Dried-flower products are also available As most products are unregistered drugs, prescribing requires approval under the Therapeutic Goods Administration Special Access Scheme-B or Authorised Prescriber Scheme Special Access Scheme Category B applications can be made online, with approval usually being given within 24–48 hours. However, supply chain problems may delay dispensing by the pharmacy By the end of 2019, over 28,000 prescribing approvals had been issued to patients, involving more than 1400 doctors, mostly GPs. More than 70,000 approvals are projected by the end of 2020 Most prescriptions are for chronic non-cancer pain, anxiety, cancer-related symptoms, epilepsy and other neurological disorders. However, the evidence supporting some indications is limited Many doctors are cautious about prescribing cannabis. While serious adverse events are rare, there are legitimate concerns around driving, cognitive impairment and drug dependence with products containing delta-9-tetrahydrocannabinol. Cannabidiol-only products pose fewer risks
Distribution of Body Fluid in Reticulated Python, Broghammerus reticulatus (Schneider, 1801), During Subcutaneous Administration with Ringer's Acetate Solution

Alterations of the distribution of body fluid were studied in Reticulated Python, Broghammerus reticulatus, (Schneider, 1801), which were subcutaneously injected with 20 ml per kg body weight of Ringer's acetate (RA) solution. The distribution of body fluid was observed by monitoring plasma volume (PV), blood volume (BV), extracellular fluid (ECF) and intracellular fluid (ICF) volumes including total body water (TBW) and water turnover (WTO) rate prior to treatment and treatment periods. The Reticulated Python erythrocyte as a representative of a cell model was performed in vitro to determine intracellular sodium (Na+) and potassium (K+) ion concentrations including the mean corpuscular fragility (MCF) index during fluid loading. The results demonstrated that the PV, BV, ECF and TBW significantly increased at 60 minutes after administration of RA solution, while as ICF volume, WTO rate, and Na+ and K+ concentrations were not significantly disturbed. The Na+ and K+ concentrations in erythrocytes were higher in ICF than in the plasma in both pretreatment and treatment periods. MCF index showed that 0.26% of NaCl solution caused erythrocyte to be lysed. This study suggests that only ECF volume was increased during fluid loading with RA solution in the Reticulated Python. However, the ICF volume was not disturbed with such treatment due to high resistance of erythrocyte membrane to water permeability.
Seed infusion with liquid microbial consortia for improving germination and vigour in blackgram [Vigna mungo (L.) Hepper]

Blackgram seeds soaked in the liquid cultures viz., Rhizobium @ 1: 50 dilution for 3 h or phosphobacteria @ 1:50 dilution for 4 h or PPFM @ 1:100 dilution for 3 h have showed the increased germination and vigour. Among the cultures, PPFM performed better with the population of 3 x 104 cfu g-1 of seed during three months storage. Also, increased seed vigour was found in the seed infusion treatment with microbial consortia viz., Rhizobium @1:50 dilution + PPFM @1:100 dilution (1:1) for 3 h with the populations of 3 x 104 and 2 x 104 cfu g-1 of seed respectively. In addition, the seed infusion with PPFM liquid culture @ 1:100 dilution for 3 h followed by polymer coating @ 5 ml kg-1 or carbendazim treatment @ 2 g kg-1 or polymer coating @ 5 ml kg-1 + carbendazim treatment @ 2 g kg-1 of seed have recorded the increased germination and vigour. However, the reduction in bioinoculants population was noticed when the seeds treated with carbendazim fungicide. Nevertheless, the minimum population of 1 x 104 cfu g-1 of seed was recorded in the fungicide treated seeds.
Multi-Unit Transformers for Neural Machine Translation

Transformer models achieve remarkable success in Neural Machine Translation. Many efforts have been devoted to deepening the Transformer by stacking several units (i.e., a combination of Multihead Attentions and FFN) in a cascade, while the investigation over multiple parallel units draws little attention. In this paper, we propose the Multi-Unit Transformers (MUTE), which aim to promote the expressiveness of the Transformer by introducing diverse and complementary units. Specifically, we use several parallel units and show that modeling with multiple units improves model performance and introduces diversity. Further, to better leverage the advantage of the multi-unit setting, we design biased module and sequential dependency that guide and encourage complementariness among different units. Experimental results on three machine translation tasks, the NIST Chinese-to-English, WMT'14 English-to-German and WMT'18 Chinese-to-English, show that the MUTE models significantly outperform the Transformer-Base, by up to +1.52, +1.90 and +1.10 BLEU points, with only a mild drop in inference speed (about 3.1%). In addition, our methods also surpass the Transformer-Big model, with only 54\% of its parameters. These results demonstrate the effectiveness of the MUTE, as well as its efficiency in both the inference process and parameter usage.
Incidence and economic burden of sarcoidosis in years 2011-2015 in Silesian voivodeship, Poland

Background: Sarcoidosis is a rare, chronic systemic disease. Earlier data (2006-2010) suggest that the incidence of pulmonary sarcoidosis in Silesian voivodeship increased, however there is no current data on other clinical forms of the disease. Objectives: The aim of presented study was an analysis of the actual epidemiological situation of sarcoidosis with simultaneous estimation of treatment cost financed from public funds. Methods: Epidemiological descriptive study concerned registered cases of sarcoidosis diagnosed in adult inhabitants of the Silesian voivodeship in years 2011-2015. Secondary epidemiological data on the main diagnosis and co-morbidity were obtained from the National Health Fund (NFZ) database in Katowice. Territorial and temporal variability of standardized incidence rates were analysed with simultaneous estimation of treatment costs reimbursed from the state budget. Results: Pulmonary sarcoidosis was the most frequently registered clinical form of such disease in the Silesian voivodeship (65% of total cases). The highest number of cases was diagnosed in the age 35–54 years, frequently in men than in women. Significantly decrease of the standardized incidence of sarcoidosis noticed between 2011 and 2015 is related with observed lower number of total cases of pulmonary disease. Observed territorial variability of the sarcoidosis incidence requires future, well-planned studies. The annual average direct cost of sarcoidosis treatment is high and exceed 538 EUR per patient. Conclusions: It was confirmed that sarcoidosis in the Silesian Voivodeship is a rare disease, however reimbursed direct costs of treatment remains very high. (Sarcoidosis Vasc Diffuse Lung Dis 2020; 37 (1): 43-52)
Probabilistic Numeric Convolutional Neural Networks

Continuous input signals like images and time series that are irregularly sampled or have missing values are challenging for existing deep learning methods. Coherently defined feature representations must depend on the values in unobserved regions of the input. Drawing from the work in probabilistic numerics, we propose Probabilistic Numeric Convolutional Neural Networks which represent features as Gaussian processes (GPs), providing a probabilistic description of discretization error. We then define a convolutional layer as the evolution of a PDE defined on this GP, followed by a nonlinearity. This approach also naturally admits steerable equivariant convolutions under e.g. the rotation group. In experiments we show that our approach yields a $3\times$ reduction of error from the previous state of the art on the SuperPixel-MNIST dataset and competitive performance on the medical time series dataset PhysioNet2012.
A stain on iron therapy

SUMMARY Iron staining is an unwanted and in some cases permanent adverse effect of intravenous iron administration. Cosmetically unacceptable staining may cause distress and have psychological implications for the patient There should be a suitable indication for parenteral iron therapy. Patients must be advised of the risk of harm and give their informed consent before receiving parenteral iron Strategies to minimise the risks of staining with intravenous iron include appropriate cannulation and close monitoring of the infusion. Stop the infusion if there are signs of extravasation Laser therapy may be a treatment option in cases of persistent discolouration due to iron staining
Comparison of Selected Blood Parameters of Captive Eastern Indigo Snakes (Drymarchon couperi) Housed Indoors vs. Outdoors in Central Florida, USA

Abstract Eastern indigo snakes (Drymarchon couperi) have unique physiological features that are still not well understood. The objective of this study was to evaluate the effects of indoor vs. outdoor housing on plasma biochemistry analytes of eastern indigo snakes. Thirty-two captive eastern indigo snakes were divided into two groups: one group was housed indoors and the other group was housed outdoors in central Florida, USA. Packed cell volume and several plasma biochemistry analytes were evaluated: sodium, potassium, chloride, total magnesium, ionized magnesium, total calcium, ionized calcium, phosphorus, pH, glucose, uric acid, glutamate dehydrogenase, aspartate aminotransferase, creatinine kinase, total protein, protein gel electrophoresis, albumin (bromocresol method), cholesterol, calcidiol, and calcitriol. Significant differences were seen in plasma total calcium and calcidiol concentrations between indoor and outdoor female groups. Significant differences were also seen in packed cell volume and plasma total calcium and calcidiol concentrations between male and female eastern indigo snakes. All of the eastern indigo snakes in this study had markedly elevated plasma total calcium concentrations, similar to previous reports by others.
Cancer Genomics in the Era of Checkpoint Inhibition: Biomarkers to Predict Tumor Response to Checkpoint Inhibition Therapy

With their ground-breaking clinical success, immune checkpoint inhibitors (ICIs) have opened a new chapter in cancer treatment; however, not all patients have a response to ICI treatment. Current approaches to maximizing the efficacy of ICI treatment include combining it with conventional cancer treatments and identifying biomarkers that accurately predict tumor responses to ICI agents. This mini-review introduces genomic determinants of ICI efficacy and directions for future immunogenomic studies in the era of checkpoint inhibition.
An absence of temporal filling-in at the physiological blind-spot

Visual objects that extend across physiological blind spots seem to encapsulate the extent of blindness, due to a process commonly referred to as a perceptual filling-in of spatial vision. It is unclear if temporal perception is similar, so we examined temporal relationships governing causality perception across the blind spot. We found the human brain does not allow for the time an object should take to traverse the blind-spot when engaging in a causal interaction. We also used electroencephalogram (EEG), to examine temporal signatures of elements flickering on and off in tandem, or in counter-phase. At a control site, we found more brain activity was entrained at the duty cycle by flicker relative to counter-phase changes, whereas these conditions were indistinguishable about blind spots. Our data suggest a common pool of neurons might encode temporal properties on either side of physiological blind-spots. This would explain the absence of any allowance for the extent of blindness in causality perception, and the weakened differences between temporal representations of flicker and counter-phased changes about the blind spot. Overall, our data suggest that, unlike spatial vision, there is no temporal filling-in for perceptual representations about physiological blind spots.
Computational and experimental analyses of mitotic chromosome formation pathways in fission yeast

Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long S. pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin density enrichment. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.