Miracle-dz/UniFAR-FTUs huggingface dataset:
Riboregulation in the Major Gastric Pathogen Helicobacter pylori

Helicobacter pylori is a Gram-negative bacterial pathogen that colonizes the stomach of about half of the human population worldwide. Infection by H. pylori is generally acquired during childhood and this bacterium rapidly establishes a persistent colonization. H. pylori causes chronic gastritis that, in some cases, progresses into peptic ulcer disease or adenocarcinoma that is responsible for about 800,000 deaths in the world every year. H. pylori has evolved efficient adaptive strategies to colonize the stomach, a particularly hostile acidic environment. Few transcriptional regulators are encoded by the small H. pylori genome and post-transcriptional regulation has been proposed as a major level of control of gene expression in this pathogen. The transcriptome and transcription start sites (TSSs) of H. pylori strain 26695 have been defined at the genome level. This revealed the existence of a total of 1,907 TSSs among which more than 900 TSSs for non-coding RNAs (ncRNAs) including 60 validated small RNAs (sRNAs) and abundant anti-sense RNAs, few of which have been experimentally validated. An RNA degradosome was shown to play a central role in the control of mRNA and antisense RNA decay in H. pylori. Riboregulation, genetic regulation by RNA, has also been revealed and depends both on antisense RNAs and small RNAs. Known examples will be presented in this review. Antisense RNA regulation was reported for some virulence factors and for several type I toxin antitoxin systems, one of which controls the morphological transition of H. pylori spiral shape to round coccoids. Interestingly, the few documented cases of small RNA-based regulation suggest that their mechanisms do not follow the same rules that were well established in the model organism Escherichia coli. First, the genome of H. pylori encodes none of the two well-described RNA chaperones, Hfq and ProQ that are important for riboregulation in several organisms. Second, some of the reported small RNAs target, through “rheostat”-like mechanisms, repeat-rich stretches in the 5′-untranslated region of genes encoding important virulence factors. In conclusion, there are still many unanswered questions about the extent and underlying mechanisms of riboregulation in H. pylori but recent publications highlighted original mechanisms making this important pathogen an interesting study model.
Routine Hematological Parameters May Be Predictors of COVID-19 Severity

To date, coronavirus disease 2019 (COVID-19) has affected over 100 million people globally. COVID-19 can present with a variety of different symptoms leading to manifestation of disease ranging from mild cases to a life-threatening condition requiring critical care-level support. At present, a rapid prediction of disease severity and critical care requirement in COVID-19 patients, in early stages of disease, remains an unmet challenge. Therefore, we assessed whether parameters from a routine clinical hematology workup, at the time of hospital admission, can be valuable predictors of COVID-19 severity and the requirement for critical care. Hematological data from the day of hospital admission (day of positive COVID-19 test) for patients with severe COVID-19 disease (requiring critical care during illness) and patients with non-severe disease (not requiring critical care) were acquired. The data were amalgamated and cleaned and modeling was performed. Using a decision tree model, we demonstrated that routine clinical hematology parameters are important predictors of COVID-19 severity. This proof-of-concept study shows that a combination of activated partial thromboplastin time, white cell count-to-neutrophil ratio, and platelet count can predict subsequent severity of COVID-19 with high sensitivity and specificity (area under ROC 0.9956) at the time of the patient's hospital admission. These data, pending further validation, indicate that a decision tree model with hematological parameters could potentially form the basis for a rapid risk stratification tool that predicts COVID-19 severity in hospitalized patients.
H3K4me3 Histone ChIP-Seq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil Dysfunction in HIV-Infected Individuals

Peripheral neutrophils in HIV-infected individuals are characterized by impairment of chemotaxis, phagocytosis, bactericidal activity, and oxidative burst ability regardless of whether patients are receiving antiretroviral therapy or not. Neutrophil dysfunction leads not only to increased susceptibility to opportunistic infections but also to tissue damage through the release of reactive oxygen species (ROS), proteases, and other potentially harmful effector molecules contributing to AIDS progression. In this study, we demonstrated high levels of histone H3 lysine K4 trimethylated (H3K4me3) and dysregulation of DNA transcription in circulating neutrophils of HIV-infected subjects. This dysregulation was accompanied by a deficient response of neutrophils to LPS, impaired cytokine/chemokine/growth factor synthesis, and increased apoptosis. Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis revealed that the most spectacular abnormalities were observed in the exons, introns, and promoter-TSS regions. Bioinformatic analysis of Gene Ontology, including biological processes, molecular function, and cellular components, demonstrated that the main changes were related to the genes responsible for cell activation, cytokine production, adhesive molecule expression, histone remodeling via upregulation of methyltransferase process, and downregulation of NF-κB transcription factor in canonical pathways. Abnormalities within H3K4me3 implicated LPS-mediated NF-κB canonical activation pathway that was a result of low amounts of κB DNA sites within histone H3K4me3, low NF-κB (p65 RelA) and TLR4 mRNA expression, and reduced free NF-κB (p65 RelA) accumulation in the nucleus. Genome-wide survey of H3K4me3 provided evidence that chromatin modifications lead to an impairment within the canonical NF-κB cell activation pathway causing the neutrophil dysfunction observed in HIV-infected individuals.
Economically Feasible Wood Biopreservation Platform in Lannea coromandelica (Houtt.) Merr. Against Wood Rotting Fungus Through Bio-Prospecting Weed Extracts

As an alternative to synthetic preservatives, the use of plant-based, environmentally sustainable preservatives for wood protection has tremendous potential. The current research analyzed the dimensional stability and longevity of Lannea coromandelica wood using weed extracts viz. Lantana camara L. and Ageratum conyzoides L. , respectively. Petroleum ether (PE) and methanolic weed extracts were used to treat wood blocks (5 cm × 2.5 cm × 2.5 cm) at varying concentrations ranging from 0.25 to 2.00%. The PE extract of A. conyzoides resulted in maximum swelling (tangential plane, 6.30%) at 2.00%, volumetric swelling coefficient (13.17%) at 1.50%, and volumetric shrinkage coefficient (7.71%) at 1.00% concentration, while maximum shrinkage (tangential plane, 4.10%) in methanol (M) extract was observed. In L. camara methanolic extract (1.00%), maximum anti-shrink efficiency (37.01%) was recorded. In vitro mycelial growth of the wood-rotting fungus was completely inhibited by PE extract from both weeds. However, the methanolic extract of A. conyzoides resulted in maximal inhibition (75.93%) at a concentration of 2.00%. Also, PE extract (2.00%) of A. conyzoides reduced the fungal colonization to 50%, as compared with control. The lowest weight loss (decay test, 12 weeks) was observed at a 2.00% concentration of L. camara PE extract. The present research highlighted that both A. conyzoides and L. camara could be used as an environmentally sustainable wood preservative substitute that will encourage the utilization of L. coromandelica in wood-based industries.
Prevalence and Correlation Analysis of Soil-Transmitted Helminths Infections and Treatment Coverage for Preschool and School Aged Children in Kenya: Secondary Analysis of the National School Based Deworming Program Data

Background: Soil-transmitted helminths (STH) are among the most common parasitic infections globally, disproportionately affecting children. Treatment of STH in Kenya is often targeted at preschool (PSAC) and school aged (SAC) children delivered through annual mass drug administration (MDA) in primary schools. Understanding group-specific prevalence and dynamics between treatment and coverage is critical for continued treatment success. This study aims to provide detailed information on group-specific infection prevalence and relative reductions (RR), and their relationships with treatment coverage over time. Additionally, it aims to quantify the correlation between the observed school level infection prevalence and treatment coverage. Methods: Secondary analysis of existing data collected between 2012 and 2018 by the monitoring and evaluation (M&E) program of the National School-Based Deworming (NSBD) program was used. The M&E program conducted surveys utilizing cross-sectional study design, at four survey time points, in a nationally-representative sample of schoolchildren across counties in Kenya. In each participating school, the program randomly sampled 108 children per school, of both groups. Infection prevalence was estimated using binomial regression, RR in prevalence using multivariable mixed effects model, statistical correlations using structural equation modeling, and change-point-analysis using the binary segmentation algorithm. Results: Overall, STH prevalence for PSAC was 33.7, 20.2, 19.0, and 17.9% during Year 1 (Y1), Year 3 (Y3), Year 5 (Y5), and Year 6 (Y6) surveys, respectively with an overall RR of 46.9% (p = 0.001) from Y1 to Y6. Similarly, overall STH prevalence for SAC was 33.6, 18.4, 14.7, and 12.5% during Y1, Y3, Y5, and Y6 surveys, respectively with an overall RR of 62.6% (p < 0.001). An overall (all time points) significant but very weak negative correlation was found between treatment coverage and undifferentiated STH prevalence (r = −0.144, p = 0.002) among PSAC but not in SAC. Further, we observed inter-county heterogeneity variation in infection prevalence, RR, as well as correlations. Conclusion: The analysis showed that after six rounds of MDA, prevalence of STH has significantly declined among both groups of children, however not to a point where it is not a public health problem (below 1%). The analysis, additionally established an overall significant but weak negative correlation between treatment coverage and prevalence, indicating that the current treatment coverage might not be sufficient to drive the overall STH prevalence to below 1%. These findings will allow STH control programs in Kenya to make decisions that will accelerate the attainment of STH elimination as a public health problem.
Influence of Regional Erosion and Sedimentary Loading on Fault Activities in Active Fold-Thrust Belts: Insights From Discrete Element Simulation and the Southern and Central Longmen Shan Fold-Thrust Belt

Four groups of discrete element models (DEMs) were set-up to simulate and analyze the influence of regional erosion and sedimentary loading on the formation and spatial-temporal evolution of faults in the southern and central Longmen Shan (LMS) active fold-thrust belt. The interior characteristics of faults in the southern and central LMS fold-thrust belt were also evaluated during the interaction of tectonic processes and surface processes according to the stress-strain analysis from DEM results. The results showed that synkinematic erosion promoted the reactivation of pre-existing faults in thrust wedges and also retarded the formation and development of new incipient faults in the pre-wedge regions. Meanwhile, synkinematic sedimentation also delayed the development of new incipient faults in the pre-wedge regions by promoting the development of thrust faults in the front of thrust wedges, causing these thrust wedges in supercritical stages with relatively narrow wedge lengths. According to these DEM results, we infer that: 1) The characteristics of erosion and sedimentation in the central and southern LMS have important influences on the activities of large faults which are extended into the deep detachment layer; 2) Besides differential erosion, the differential sedimentary loading may also be one of the important factors for the along-strike differential evolution of the LMS fold-thrust belt. This kind of differential deposition may lead to differential fault activity and uplift in the interior thrust wedge and pre-wedge region in the central and southern LMS; 3) Compared to the northern LMS, the central LMS and southern LMS is more conducive to the occurrence of earthquakes, because of synkinematic sedimentation (such as the growth of Chengdu plain) has a greater blocking effect on the stress propagation and strain convergence on the fault planes of front faults of an active thrust wedge.
DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren’s Syndrome

Primary Sjögren’s syndrome (pSS) is an autoimmune inflammatory disease with profound clinical heterogeneity, where excessive activation of the type I interferon (IFN) system is considered one of the key mechanisms in disease pathogenesis. Here we present a DNA methylation-based IFN system activation score (DNAm IFN score) and investigate its potential associations with sub-phenotypes of pSS. The study comprised 100 Swedish patients with pSS and 587 Swedish controls. For replication, 48 patients with pSS from Stavanger, Norway, were included. IFN scores were calculated from DNA methylation levels at the IFN-induced genes RSAD2, IFIT1 and IFI44L. A high DNAm IFN score, defined as > meancontrols +2SDcontrols (IFN score >4.4), was observed in 59% of pSS patients and in 4% of controls (p=1.3x10-35). Patients with a high DNAm IFN score were on average seven years younger at symptom onset (p=0.017) and at diagnosis (p=3x10-3). The DNAm IFN score levels were significantly higher in pSS positive for both SSA and SSB antibodies compared to SSA/SSB negative patients (pdiscovery=1.9x10-8, preplication=7.8x10-4). In patients positive for both SSA subtypes Ro52 and Ro60, an increased score was identified compared to single positive patients (p=0.022). Analyzing the discovery and replication cohorts together, elevated DNAm IFN scores were observed in pSS with hypergammaglobulinemia (p=2x10-8) and low C4 (p=1.5x10-3) compared to patients without these manifestations. Patients < 70 years with ongoing lymphoma at DNA sampling or lymphoma at follow-up (n=7), presented an increased DNAm IFN score compared to pSS without lymphoma (p=0.025). In conclusion, the DNAm-based IFN score is a promising alternative to mRNA-based scores for identification of patients with activation of the IFN system and may be applied for patient stratification guiding treatment decisions, monitoring and inclusion in clinical trials.
The Effect of Forest Management on the Avifauna of a Brazilian Dry Forest

The conversion of tropical habitats has dramatic implications on biodiversity and represents one of the greatest conservation challenges of our time. Seasonally Dry Tropical Forests (SDTF), which are disjointly distributed throughout the Neotropics, are especially susceptible to human activities. The Caatinga Dry Forest, located in the semi-arid interior of northeastern Brazil, represents not only the largest and most biologically diverse nucleus of SDTF, but also the world’s most densely populated semi-arid region, with ever-growing pressure on its natural resources. To prevent illegal logging, conservation agencies looked at forest management, where an area is divided in smaller stands which are gradually logged and allowed to regrow for a period of time, when a new cutting cycle should reinitiate. The impacts of these management schemes on biodiversity, however, remain largely untested. We conducted standardized avian surveys to evaluate the effects of forest management on the avian community at a 1,670 ha privately owned property located on the Chapada do Araripe, northeastern Brazil. This area was divided in 22 forest stands, half of which had already been logged at the time of our sampling, creating a gradient of logged and natural forests and an 11-yr chrono-sequence of forest regeneration. Our results show that logged areas present fewer individuals, fewer species, and different avian assemblages than unlogged forests. Such differences are mostly driven by forest-dependent species, which were overwhelmingly affected by forest management. Our results show that although logged forests tend to recover its height after a decade, they do not recover the originally forest cover, measured by the Normalized Difference Vegetation Index. Likewise, decade-long recovering stands continue to show lower species richness, lower bird abundance, and different avian composition than unlogged forests. We identified a set of bird species that are more affected by forest management (ecological losers) and a group of birds that apparently benefit from the referred changes in land use (ecological winners). We conclude that completely managing an entire area may cause the extirpation of several forest-dependent species. We therefore suggest keeping logged and unlogged plots intermingled, to avoid local extinctions and the complete modification of the original avifauna.
Muscle Architectural and Functional Adaptations Following 12-Weeks of Stretching in Adolescent Female Athletes

This study examined the effects of high-volume static stretching training on gastrocnemius muscle architecture, ankle angle and jump height in 21 female adolescent volleyball players. Static stretching of the plantar flexors of one leg (STR) was performed five times/week for 12 weeks, in addition to volleyball training, with the contra-lateral leg used as control (CON). Total duration of stretching per session increased from 540 s (week 1) to 900 s (week 12). At baseline, week 12 and after 3 weeks of detraining, muscle architecture at the middle and the distal part of both gastrocnemius heads (medialis and lateralis) and ankle angle were examined at rest and at maximum dorsiflexion. At the same time-points gastrocnemius cross-sectional area (CSA) was also assessed, while jumping height was measured at baseline and week 12. Following intervention, ankle dorsiflexion increased in both legs with a greater increase in STR than CON (22 ± 20% vs. 8 ± 17%, p < 0.001). Fascicle length at the middle part of gastrocnemius medialis increased only in the STR, at rest (6 ± 7%, p = 0.006) and at maximum dorsiflexion (11 ± 7%, p < 0.001). Fascicle length at maximum dorsiflexion also increased at the distal part of gastrocnemius lateralis of STR (15 ± 13%, p < 0.001). A greater increase in CSA (23 ± 14% vs. 13 ± 14%, p < 0.001) and in one-leg jumping height (27 ± 30% vs. 17 ± 23%, p < 0.001) was found in STR than CON. Changes in ankle angle, fascicle length and CSA were maintained following detraining. High-volume stretching training for 12 weeks results in ankle dorsiflexion, fascicle length and muscle cross sectional area increases in adolescent female volleyball players. These adaptations may partly explain improvements in jump performance.
Do Histories of Painful Life Experiences Affect the Expression of Empathy Among Young Adults? An Electroencephalography Study

Previous research suggests that prior experience of pain affects the expression of empathy. However, most of these studies attended to physical pain despite evidence indicating that other forms of pain may also affect brain activity and emotional states in similar ways. To address this limitation, we compared empathic responses of 33 participants, some of whom had experienced a personal loss, across three conditions: observing strangers in physical pain, psychological pain, and a non-painful condition. We also examined the effect of presence of prior painful experience on empathic reactions. In addition, we examined the stimulation type, prior experience, and ERPs in the early Late Positive Potential (300–550 ms), late Late Positive Potential (550–800 ms), and very late Late Positive Potential (VLLPP; 800–1,050 ms) time windows. Behavioral data indicated that participants who had personally experienced a loss scored significantly higher on perspective taking in the psychological-pain condition. ERP results also indicated significantly lower intensity in Fp2, an electrode in the prefrontal region, within VLLPP time window for participants experiencing a loss in the psychological-pain condition. The results of both behavioral and ERP analysis indicated that prior experience of psychological pain is related to cognitive empathy, but not affective empathy. The implication of these findings for research on empathy, for the study of psychological pain, and the moderating influence of prior painful experiences are discussed.
Children With Autism Spectrum Disorder Can Attribute False Beliefs in a Spontaneous-Response Preferential-Looking Task

An established body of literature indicates that children with autism spectrum disorder (ASD) have difficulty understanding figurative language due to a deficit in theory of mind, or the ability to consider the beliefs of other people. Children with ASD tend to similarly fail traditional theory of mind tasks, which assess their ability to represent false beliefs. Our claim is, however, that these tasks involve cognitive processing demands that might mask false belief understanding because they require elicited responses. We examined whether children with ASD demonstrate false-belief understanding when tested with a spontaneous-response false belief task that measures children’s eye gaze durations. The two child participant groups were composed of 20 males with ASD (aged 3–9 years) and 20 typically developing males (aged 2–5 years) who were individually matched according to verbal mental age. Children with ASD and typically developing children listened to a change-of-location story accompanied by a book with matching and non-matching pictures. The final page showed the character searching for her object in a location that was either consistent or inconsistent with her belief. Both groups of children looked reliably longer at the belief-consistent picture, regardless of whether the character’s belief was true or false, though children with ASD were slower to do so. We suggest that a spontaneous-response assessment technique can potentially reveal figurative language comprehension in children with ASD in future research.