Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative epidemiology of citrus tristeza in Cuba and citrus sudden death in Brazil

Citrus Sudden Death (CSD) is a disease of unknown etiology, reported only in Brazil. Due to similarities between the epidemiology of CSD in Brazil and Citrus Tristeza (CT) in other countries, this work aimed to compare CSD and CT in Cuba. Besides testing the hypothesis of shared epidemiological patterns, the data generated can be used to carry out control strategies if CSD breaks out in Cuba. Seven epidemic data sets were statistically compared for each disease by analyzing their progress in time and the dependence among symptomatic or infected plants at two levels of spatial scale. CSD and CT epidemics could not be differentiated based on mean progress rate, area under disease progress curves, proportion of aggregated sequences (Ordinary runs test), index of Dispersion (D) or both parameters, log (A) and b, of the binary power law model. The progress rate of both diseases varied from low (0.0003/month) to very high (0.045/month). The proportion of aggregated sequences was low (<0.16) and D, log(A) and b values indicated aggregation in groups of 4 to 16 plants for both diseases. These results suggest that measures currently used for CT eradication and management in Cuba may be applied in case of an eventual introduction of CSD in that country.
Effects of pre-existing morbidities on occurrence of death among COVID-19 disease patients: A systematic review and meta-analysis

Abstract Background: Coronavirus disease 2019 (COVID-19), most hectic pandemic of the era, is increasing exponentially and taking thousands of lives, worldwide. Objective: This study aimed to assess the prevalence of pre-existing morbidities among COVID-19 infected patients and their mortality risks against each type of pre-existing morbidity categories. Design: Systematic review and meta-analysis Data sources: Medline, Web of Science, Scopus, and CINAHL databases were searched using the following keywords: (COVID-19 or 2019-nCoV or Coronavirus or SARS-CoV-2) AND (Comorbidity or Morbidity) AND (Mortality or Death or Died) up to May 01, 2020. Further searches were conducted using the reference list of the selected studies, renowned pre-print servers (e.g., medRxiv, bioRixv, SSRN), and relevant journal websites. Eligibility criteria: Studies written in the English language included if those were conducted among COVID-19 patients with and without comorbidities and presented survivor vs. non-survivor counts or hazard/odds of deaths or survivors against types of pre-existing morbidities. Methods: Comorbidities reported in the selected studies were grouped into eight categories. The pooled likelihoods of deaths in each category were estimated using a fixed or random-effect model, based on the heterogeneity assessment. Publication bias was assessed by visual inspection of the funnel plot asymmetry and Egger regression test. Trim and Fill method was used if there any publication bias was found. Results: A total of 42 studies included in this study comprised of 39,398 samples. The most common pre-existing morbidities in COVID-19 infected patients were hypertension (36.5%), cardiovascular disease (11.9%), and diabetes (22.0%). The higher likelihood of deaths was found among COVID-19 patients who had pre-existing cardiovascular system diseases (OR: 3.32, 95% CI: 2.79-3.95), immune and metabolic disorders (OR: 2.39, 95% CI: 2.00-2.85), respiratory diseases (OR: 2.02, 95% CI: 1.80-2.26), cerebrovascular system diseases (OR: 4.12, 95% CI: 3.04-5.58), any types of cancers (OR: 2.22, 95% CI: 1.63-3.03), renal (OR: 3.02, 95% CI: 2.60-3.52), and liver system diseases (OR: 1.44, 95% CI: 1.21-1.71). Conclusions: This study provides evidence of a higher likelihood of deaths among COVID-19 patients against morbidity categories. These findings could potentially help healthcare providers to sort out the most endangered COVID-19 patients by comorbidities, take precautionary measures during hospitalization, assess susceptibility to death, and prioritize their treatment, which could potentially reduce the number of fatalities in COVID-19 disease.
DNA methylation mediates the effect of cocaine use on HIV severity

Background Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population. Methods We analyzed 1435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation. Results More frequent cocaine use was significantly associated with a higher VACS index ( β = 1.00, p = 2.7E−04), and cocaine use increased the risk of 10-year mortality (hazard ratio = 1.10, p = 0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3–29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response ( IFIT3 , IFITM1 , NLRC5 , PLSCR1 , PARP9 ) and HIV progression ( CX3CR1 , MX1 ). Conclusions We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna

The rapid developments in the next-generation sequencing methods in the recent years have provided a wealth of information on the community structures and functions of endophytic bacteria. However, the assembly processes of these communities in different plant tissues are still currently poorly understood, especially in wild plants in natural settings. The aim of this study was to compare the composition of endophytic bacterial communities in leaves and roots of arcto-alpine pioneer plant Oxyria digyna, and investigate, how plant tissue (leaf or root) or plant origin affect the community assembly. To address this, we planted micropropagated O. digyna plants with low bacterial load (bait plants) in experimental site with native O. digyna population, in the Low Arctic. The endophytic bacterial community structures in the leaves and roots of the bait plants were analyzed after one growing season and one year in the field, and compared to those of the wild plants growing at the same site. 16S rRNA gene targeted sequencing revealed that endophytic communities in the roots were more diverse than in the leaves, and the diversity in the bait plants increased in the field, and was highest in the wild plants. Both tissue type and plant group had strong impact on the endophytic bacterial community structures. Firmicutes were highly abundant in the leaf communities of both plant types. Proteobacteria and Bacteroidetes were more abundant in the roots, albeit with different relative abundances in different plant groups. The community structures in the bait plants changed in the field over time, and increasingly resembled the wild plant endophytic communities. This was due to the changes in the relative abundances of several bacterial taxa, as well as species acquisition in the field, but with no species turnover. Several OTUs that were acquired by the bait plants in the field and represent phosphate solubilizing and diazotrophic bacterial taxa, suggesting major role in nutrient acquisition of these bacteria for this nonmycorrhizal plant, thriving in the nutrient poor arctic soils.
Training Positive Rumination in Expressive Writing to Enhance Psychological Adjustment and Working Memory Updating for Maladaptive Ruminators

Rumination is associated with psychological adjustment and working memory (WM) capacity. Studies have shown that psychological interventions can reduce negative rumination and improve psychological adjustment and WM capacity. The present study investigated the effect of positive rumination training in expressive writing on psychological adjustment and WM updating capacity. Within an experimental design, positive rumination was manipulated for 10 participants who were maladaptive ruminators in an experiment using a 5-week training compared to the control group with nine participants. Results revealed significant enhancement of psychological adjustment and the response time (RT) of WM updating in the experimental group but not in the control group. The two groups did not show significant difference of all the variables in pretest. However, the experimental group showed significantly better outcomes than the control group in posttest. The results suggest that positive rumination training in expressive writing is effective and rumination has a causal influence on WM updating capacity.
Intention-Related Natural Language Grounding via Object Affordance Detection and Intention Semantic Extraction

Similar to specific natural language instructions, intention-related natural language queries also play an essential role in our daily life communication. Inspired by the psychology term “affordance” and its applications in Human-Robot interaction, we propose an object affordance-based natural language visual grounding architecture to ground intention-related natural language queries. Formally, we first present an attention-based multi-visual features fusion network to detect object affordances from RGB images. While fusing deep visual features extracted from a pre-trained CNN model with deep texture features encoded by a deep texture encoding network, the presented object affordance detection network takes into account the interaction of the multi-visual features, and reserves the complementary nature of the different features by integrating attention weights learned from sparse representations of the multi-visual features. We train and validate the attention-based object affordance recognition network on a self-built dataset in which a large number of images originate from MSCOCO and ImageNet. Moreover, we introduce an intention semantic extraction module to extract intention semantics from intention-related natural language queries. Finally, we ground intention-related natural language queries by integrating the detected object affordances with the extracted intention semantics. We conduct extensive experiments to validate the performance of the object affordance detection network and the intention-related natural language queries grounding architecture.
Spatiotemporal Modulation of Flavonoid Metabolism in Blueberries

Blueberries are distinguished by their purple-blue fruit color, which develops during ripening and is derived from a characteristic composition of flavonoid-derived anthocyanin pigments. The production of anthocyanins is confined to fruit skin, leaving the colorless fruit flesh devoid of these compounds. By linking accumulation patterns of phenolic metabolites with gene transcription in Northern Highbush (Vaccinium corymbosum) and Rabbiteye (Vaccinium virgatum) blueberry, we investigated factors limiting anthocyanin production in berry flesh. We find that flavonoid production was generally lower in fruit flesh compared with skin and concentrations further declined during maturation. A common set of structural genes was identified across both species, indicating that tissue-specific flavonoid biosynthesis was dependent on co-expression of multiple pathway genes and limited by the phenylpropanoid pathway in combination with CHS, F3H, and ANS as potential pathway bottlenecks. While metabolite concentrations were comparable between the blueberry genotypes when fully ripe, the anthocyanin composition was distinct and depended on the degree of hydroxylation/methoxylation of the anthocyanidin moiety in combination with genotype-specific glycosylation patterns. Co-correlation analysis of phenolic metabolites with pathway structural genes revealed characteristic isoforms of O-methyltransferases and UDP-glucose:flavonoid-3-O-glycosyltransferase that were likely to modulate anthocyanin composition. Finally, we identified candidate transcriptional regulators that were co-expressed with structural genes, including the activators MYBA, MYBPA1, and bHLH2 together with the repressor MYBC2, which suggested an interdependent role in anthocyanin regulation.
Near-Death Experience Memories Include More Episodic Components Than Flashbulb Memories

Memories of near-death experiences (NDEs) are recalled as “realer” than memories of other real or imagined events. Given their rich phenomenology, emotionality and consequentiality, it was hypothesized that they could meet some aspects of the definition of flashbulb memories. We aimed to identify and compare the episodic and non-episodic information provided in verbal recollections of NDE, flashbulb, and control autobiographical memories. The phenomenological characteristics and centrality of the memories were also compared. Twenty-five participants who had lived a NDE in a life-threatening situation were interviewed and completed the Memory Characteristics Questionnaires as well as the Centrality of Event Scale for their NDE, a flashbulb and another autobiographical memory used as control. Overall, transcribed NDE verbal recollections included a higher overall amount of details and more internal/episodic information than control autobiographical and flashbulb memories. Moreover, flashbulb memories were associated to a lower intensity of feelings while remembering and a lower personal importance, and are less reactivated and less susceptible to be remembered from a first person perspective compared to NDE and control autobiographical memories. Finally, NDE memories are the most central memories to experiencers’ identity, followed by control autobiographical and then by flashbulb memories. These findings corroborate previous studies highlighting the impact and uniqueness of NDE memories.
Phylogenetic relationships of three genera of Erpobdellidae (Hirudinoidea), with a description of a new genus, Motobdella, and species, Motobdella sedonensis

A new genus, Motobdella, is recognized for Erpobdella montezumaDavies, Singhal, and Blinn, 1985. In addition, a new species for this genus, Motobdella sedonensis, is described. Morphological characters that include the presence of crop caeca, number and size of the eyes, arrangement of the eyes, arrangement of ovisacs, position of the gonopore, structure and size of the sensilla, coloration, and position of the anus distinguish this new genus from Erpobdella and Nephelopsis. DNA fingerprinting methods were used to examine the phylogenetic relationships of these genera and corroborated the morphological data supporting the evolution of this genus with two distinct species. Resume : Un nouveau genre, Motobdella, est cree et il contient l'espece Erpobdella montezumaDavies, Singhal et Blinn, 1985. On trouvera ici une description d'une nouvelle espece qui appartient aussi a ce genre, Motobdella sedonensis. Les caracteristiques morphologiques qui distinguent le nouveau genre d'Erpobdella et de Nephelopsis sont la presence de caecums au jabot, le nombre et la taille des yeux, leur disposition, la disposition de l'ovisac, la position du gonopore, la structure des sensilles, de meme que la taille, la coloration et la position de l'anus. Des methodes de cartographie des oligonucleotides d'ADN ont ete utilisees pour examiner les relations phylogenetiques de ces genres et elles confirment les donnees morphologiques qui demontrent l'evolution de ce genre en deux especes distinctes.
Nitrogen from Legume Cover Crops for No‐Tillage Corn1

Determination de la quantite d'azote fixee biologiquement fournie a Zea mays, par une plante de couverture: Vicia vilosa, V. grandiflora et Trifolium incarnatum. Comparaison avec un couvert de residus de mais seulement et un couvert de seigle
Air Distribution in a Fully-Closed Higher Plant Growth Chamber Impacts Crop Performance of Hydroponically-Grown Lettuce

The MELiSSA Pilot Plant (MPP) is testing in terrestrial conditions regenerative life support technologies for human exploration in Space. One of its components is a controlled Higher Plant Chamber (HPC) accommodating hydroponic plant cultures. It consists of a 9 m3 single closed growth chamber providing adequate environmental conditions for growing plants, enabling the production of food, water and oxygen for the crew. A critical aspect for a reliable HPC performance is to achieve homogeneous air distribution. The initial experiment carried out in the MPP with lettuce as salad crop, showed uneven plant growth throughout the HPC, which was attributed to inadequate air distribution due to non-homogeneous air velocity profile along the inlet-vents. After a detailed computational fluid dynamics (CFD) analysis, the heating, ventilation, and air conditioning subsystem of the HPC was upgraded and a new experiment was carried out in optimized air flow conditions. Nine-day seedlings of lettuce cultivar “Grand Rapids” were transplanted into the HPC and harvested at the end of the growing cycle, where shoot fresh weight, dry biomass, and shoot mineral composition were analyzed. During the experiment, the environmental control system performed remarkably well based on the biometric measurements as well as the mineral composition leading to a vast homogeneous growth. Overall, the results demonstrated the beneficial effect of an adequate air distribution system in HPCs and the effectiveness of CFD-analysis to design properly the gas distribution. The obtained results are of high relevance for life support systems in space involving plants growth.
A Physiology-Based Pharmacokinetic Framework to Support Drug Development and Dose Precision During Therapeutic Hypothermia in Neonates

Therapeutic hypothermia (TH) is standard treatment for neonates (≥36 weeks) with perinatal asphyxia (PA) and hypoxic–ischemic encephalopathy. TH reduces mortality and neurodevelopmental disability due to reduced metabolic rate and decreased neuronal apoptosis. Since both hypothermia and PA influence physiology, they are expected to alter pharmacokinetics (PK). Tools for personalized dosing in this setting are lacking. A neonatal hypothermia physiology-based PK (PBPK) framework would enable precision dosing in the clinic. In this literature review, the stepwise approach, benefits and challenges to develop such a PBPK framework are covered. It hereby contributes to explore the impact of non-maturational PK covariates. First, the current evidence as well as knowledge gaps on the impact of PA and TH on drug absorption, distribution, metabolism and excretion in neonates is summarized. While reduced renal drug elimination is well-documented in neonates with PA undergoing hypothermia, knowledge of the impact on drug metabolism is limited. Second, a multidisciplinary approach to develop a neonatal hypothermia PBPK framework is presented. Insights on the effect of hypothermia on hepatic drug elimination can partly be generated from in vitro (human/animal) profiling of hepatic drug metabolizing enzymes and transporters. Also, endogenous biomarkers may be evaluated as surrogate for metabolic activity. To distinguish the impact of PA versus hypothermia on drug metabolism, in vivo neonatal animal data are needed. The conventional pig is a well-established model for PA and the neonatal Göttingen minipig should be further explored for PA under hypothermia conditions, as it is the most commonly used pig strain in nonclinical drug development. Finally, a strategy is proposed for establishing and fine-tuning compound-specific PBPK models for this application. Besides improvement of clinical exposure predictions of drugs used during hypothermia, the developed PBPK models can be applied in drug development. Add-on pharmacotherapies to further improve outcome in neonates undergoing hypothermia are under investigation, all in need for dosing guidance. Furthermore, the hypothermia PBPK framework can be used to develop temperature-driven PBPK models for other populations or indications. The applicability of the proposed workflow and the challenges in the development of the PBPK framework are illustrated for midazolam as model drug.
Mating behaviour of the corn stalk borer Sesamia nonagrioides

The mating behaviour of the corn stalk borer Sesamia nonagrioides (Lef.) [Lepidoptera: Noctuidae] was studied under laboratory conditions at 25 ± 1 ° C, 65 ± 5 % r.h. and 16:8 (L:D) regime. The females began calling during the first scotophase following emergence, the peak of calling occurred during the second scotophase and thereafter decreased. Maximum calling was observed between the fourth and sixth hour of the scotophase. The calling pattern varied with age. During the first and second scotophase most of the females were calling continuously, while during the third and fourth scotophase periodic calling was observed. The mean onset of calling was advanced and the mean length of calling per day was increased slightly as the female became older. Females held for 72 h in continuous darkness exhibited an endogenous circadian rhythm of calling. Matings began during the first scotophase following emergence and the peak of mating was observed during the second scotophase. Mated females did not remate. Few males mated more than once during the following scotophases.
Changing Trend in Vitamin D Status from 2008 to 2016: An Experience from a Tertiary Care Institute in North India

Background: Serum 25-hydroxyvitamin D (25(OH)D) assays have become readily available in India over the past decade. A large number of cross-sectional studies have been performed on the vitamin D status and the prevalence of vitamin D deficiency (VDD) in India. However, seasonal and long-term trends in serum 25(OH)D levels have been reported less frequently. Aim: To determine the seasonal and year-wise variation in vitamin D status at a tertiary care hospital in north India. Materials and Methods: Using hospital records, the data on serum 25(OH)D assays performed in its endocrinology laboratory between 2008 and 2016 were obtained. For analysis of seasonal trends, the months of a year were divided into following seasons: March to June (summer season), July to October (rainy season), and November to February (winter season). VDD was defined as serum 25(OH)D concentration ង ng/mL. Results: A total of 26,339 assays of serum 25(OH)D were analyzed in the study. The year-wise assay numbers increased steadily from 2008 to peak in the year 2012, followed by a decline and a second smaller peak in the year 2016. The mean serum 25(OH)D concentration increased from 19.1 ± 16.4 ng/mL in 2008 to 21.7 ± 17.1 ng/mL in 2016 (P = 0.02). Between 2008 and 2016, the prevalence of VDD decreased from 71.9% to 54.3% in females, and from 56.7% to 52.1% in males. The levels in rainy season were significantly higher as compared to winters and summers (P < 0.05 for both). Hypervitaminosis D (serum 25(OH)D >100 ng/mL) and vitamin D toxicity (serum 25(OH)D >150 ng/mL) were seen in 319 (1.2%) and 27 (0.1%) assays, respectively. Conclusions: This study provides data on seasonal and year-wise trends in vitamin D status over a long period of time at a tertiary care hospital in north India. A long-term trend toward improving vitamin D status, especially in females, was noted in the study. The prevalence of VDD was found to decrease in the analyzed samples during the study period.