Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and validation of key biomarkers based on RNA methylation genes in sepsis

Background RNA methylation is closely involved in immune regulation, but its role in sepsis remains unknown. Here, we aim to investigate the role of RNA methylation-associated genes (RMGs) in classifying and diagnosing of sepsis. Methods Five types of RMGs (m1A, m5C, m6Am, m7G and Ψ) were used to identify sepsis subgroups based on gene expression profile data obtained from the GEO database (GSE57065, GSE65682, and GSE95233). Unsupervised clustering analysis was used to identify distinct RNA modification subtypes. The CIBERSORT, WGCNA, GO and KEGG analysis were performed to explore immune infiltration pattern and biological function of each cluster. RF, SVM, XGB, and GLM algorithm were applied to identify the diagnostic RMGs in sepsis. Finally, the expression levels of the five key RMGs were verified by collecting PBMCs from septic patients using qRT-PCR, and their diagnostic efficacy for sepsis was verified in combination with clinical data using ROC analysis. Results Sepsis was divided into three subtypes (cluster 1 to 3). Cluster 1 highly expressed NSUN7 and TRMT6, with the characteristic of neutrophil activation and upregulation of MAPK signaling pathways. Cluster 2 highly expressed NSUN3, and was featured by the regulation of mRNA stability and amino acid metabolism. NSUN5 and NSUN6 were upregulated in cluster 3 which was involved in ribonucleoprotein complex biogenesis and carbohydrate metabolism pathways. In addition, we identified that five RMGs (NSUN7, NOP2, PUS1, PUS3 and FTO) could function as biomarkers for clinic diagnose of sepsis. For validation, we determined that the relative expressions of NSUN7, NOP2, PUS1 and PUS3 were upregulated, while FTO was downregulated in septic patients. The area under the ROC curve (AUC) of NSUN7, NOP2, PUS1, PUS3 and FTO was 0.828, 0.707, 0.846, 0.834 and 0.976, respectively. Conclusions Our study uncovered that dysregulation of RNA methylation genes (m1A, m5C, m6Am, m7G and Ψ) was closely involved in the pathogenesis of sepsis, providing new insights into the classification of sepsis endotypes. We also revealed that five hub RMGs could function as novel diagnostic biomarkers and potential targets for treatment.
Effect of Plant Extracts Addition on the Physico-Chemical and Sensory Properties of Biscuits

Biscuits are one of the most consumed bakery products that contain a high content of fat, sugar, and different additives that may cause various health problems. This has led to an increased focus on enriching bakery products with plant extracts to improve their nutritional and sensory properties. The objective of the current work was to investigate the effect of replacing wheat flour with plant extracts such as blueberry and cranberry (at concentrations of 3%, 6%, and 9%) and compare with control biscuits regarding the physico-chemical and color parameters. In addition, sensory analysis was conducted to determine the consumer acceptability of the enriched biscuits. The enrichment of biscuits with blueberry powder significantly increased the moisture content and decreased pH values (p < 0.05). Similarly, cranberry-enriched biscuits had a significantly higher moisture content, water activity, and decreased pH values compared to control samples (p < 0.05). On the other hand, enrichment of biscuits with either blueberry or cranberry powder significantly decreased lightness (L*), yellowness (b*), chroma value (C*), and h-value (h) but increased the redness values (a* value) of samples (p < 0.05). Our results showed that with increasing concentrations of plant extract addition in biscuits, the sensory attributes such as odor and taste were significantly improved. The results of the study suggest that the addition of plant extracts to biscuits improved their physico-chemical and sensory properties.
Elucidating the Potential of Biochar-Bentonite Composite and Kaolinite-Based Seed Balls for the Remediation of Coal Mining Impacted Heavy Metals Contaminated Soil

Globally, open-pit coal mining is associated with severe land use impact and the contamination of soil and water resources with heavy metals. Thus, in growing economies like India, where coal is a significant energy source, the heavy metals contamination of soil and water become ubiquitous. This study uses a unique remediation approach by developing biochar-bentonite-based seed balls encapsulating Shorgham grass seeds at their core for application in the contaminated soil. The seed ball was developed by using the bentonite biochar composite in varying weight fractions of 0.5–5% with respect to the kaolinite, whose fractions in the seed ball also varied at one, three, and five parts. The seed balls were applied to the pots containing 3 kg of heavy-metals-contaminated soil for a pot-culture study in a polyhouse for a period of four months. Initial soil analysis results indicated that the mine soil samples showed poor nutrient and organic matter content and were contaminated with heavy metals such as Ni, Zn, Cr, and Cd. Post-pot-culture soil analysis results indicated that the application of seed balls containing five fractions of biochar composite with its combination with three and five-weight fractions of kaolinite showed substantial improvement in the pH, available nutrients, organic matter content, soil enzymes, and overall soil fertility index compared to the controlled study and other cases. The same combination of seed balls also significantly reduced the plant-available fractions of Ni, Zn, Cr, and Cd in the soil, indicating the stabilization of heavy metals within the soil matrix. Also, the application of seed balls substantially improved the plant physiology and reduced the release of stress hormones within the plant cells, indicating improvement in the plant’s biotic and abiotic stress factors. Thus, the application of seed balls in heavy metals contaminated soils, particularly over a large stretch of land, could be a low-cost and viable remediation technique.
Consistent metagenome-derived metrics verify and define bacterial species boundaries

Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. We compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity, and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of non-synonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, estimates for homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full length 16S rRNA genes were least useful because they were under-recovered from metagenomes, but many ribosomal proteins displayed both high metagenomic recoverability and species-discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.
Respiratory management and outcomes in high-risk preterm infants with development of a population outcome dashboard

Introduction Bronchopulmonary dysplasia (BPD) is associated with adverse long-term respiratory and neurodevelopmental outcomes. No recent studies examined the changing respiratory management and outcomes, particularly severe BPD, across a whole population. Purpose Evaluate the temporal trends in the respiratory management and outcomes of preterm infants born below 32 weeks gestational age and develop an individualised dashboard of the incidence of neonatal outcome. Methods Using the National Neonatal Research Database, we determined changes in respiratory management, BPD rates, postdischarge respiratory support and mortality in 83 463 preterm infants in England and Wales from 2010 to 2020. Results Between 2010 and 2020, antenatal corticosteroids use increased (88%–93%, p<0.0001) and neonatal surfactant use decreased (65%–60%, p<0.0001). Postnatal corticosteroid use increased, especially dexamethasone (4%–6%, p<0.0001). More recently, hydrocortisone and budesonide use increased from 2% in 2017 to 4% and 3%, respectively, in 2020 (p<0.0001). Over the study period, mortality decreased (10.1%–8.5%), with increases in BPD (28%–33%), severe BPD (12%–17%), composite BPD/death (35%–39%) and composite severe BPD/death (21%–24%) (all p<0.0001). Overall, 11 684 infants required postdischarge respiratory support, increasing from 13% to 17% (p<0.0001), with 1843 infants requiring respiratory pressure support at discharge. A population dashboard (https://premoutcome.github.io/) depicting the incidence of mortality and respiratory outcomes, based on gestation, sex and birthweight centile, was developed. Conclusion More preterm infants are surviving with worse respiratory outcomes, particularly severe BPD requiring postdischarge respiratory support. Ultimately, these survivors will develop chronic respiratory diseases requiring greater healthcare resources.
A Cluster Randomised Control Trial of an SMS-Based Intervention to Promote Antenatal Health amongst Pregnant Women in a Remote, Highland Region of Vietnam

Although Vietnam has achieved significant improvements in maternal, newborn, and children’s health, outcomes for ethnic minorities living in remote mountainous areas continue to lag. Interventions that leverage the extensive mobile networks in the country have been proposed as a way to overcome some of these challenges. A cluster randomised controlled trial (cRCT) was conducted to assess the effectiveness of an intervention comprising tailored SMS messages for promoting antenatal care knowledge and behaviours amongst ethnic minority (EM) pregnant women. The cRCT was implemented across eight intervention communes (640 women) and four control communes (315 women) in Northern Vietnam. Maternal health-related knowledge and behaviour outcomes and self-rated health status were assessed through questionnaires administered pre- and post-intervention. Difference-in-difference and logistic regression analysis found that the intervention group showed significant improvements in awareness about the danger signs of pregnancy and the importance of nutritional supplements. Significant improvements were seen in antenatal care-seeking behaviours and the intake of nutritional supplements. Mobile messaging-based behaviour change interventions can significantly improve maternal health-related knowledge and care-seeking amongst women residing in marginalised, hard-to-reach populations.
Typhoons and Lower Birth Weight in the Philippines

Do typhoons impact birth weights of infants exposed to a typhoon while in utero? This research exploits the exogeneity and randomness of typhoons in the Philippines to estimate the impact of typhoon exposure as determined by wind speed on birth weights. Using four waves of the Demographic and Health Survey (DHS) data from the Philippines combined with temperature, precipitation, and rainfall data from the Philippines, I can empirically estimate the impact of a 1 m/s increase in wind speed on birth weights. I find that for certain subgroups of the population, specifically children born to mothers with primary education or less, typhoon exposure in the year of birth and more specifically the quarter of birth, has a negative and statistically significant effect on birth weights. Since birth weights are common indicators of overall infant health as well as predictors of later life outcomes, these findings are important for policymakers. Policy implications of this study include shifting the focus of campaigns directed to focus on the importance of health and nutrition in the later stages of pregnancy, and also focusing on the needs of pregnant women in post-typhoon aid and relief efforts.
Prevalence of impaired renal function among rural and urban populations: findings of a cross-sectional study in Malawi [version 1; peer review: 1 approved, 2 approved with reservations]

: Sub-Saharan Africa faces region-specific risk factors for Background chronic kidney disease (CKD), such as nephrotoxic herbal medicines, antiretroviral therapy and infections, in addition to hypertension and diabetes. However, large epidemiological studies from this area are scarce. : In a cross-sectional survey of non-communicable diseases, we Methods conducted a prevalence sub-study of CKD in two Malawian populations. Study participants (N=5264) of 18 years of age and above were recruited and data on demographics and CKD risk factors were collected. Glomerular filtration rate was estimated (eGFR) using the CKD-EPI equation. : The prevalence of eGFR<60ml/min/1.73m was 1.4% (95% CI 1.1 Results – 1.7%) and eGFR<90ml/min/1.73m was 20.6% (95% CI 19.5 – 21.7%). The rural area had higher age-standardized prevalence of both eGFR<60ml/min/1.73m , at 1.8% (95% CI 1.4 – 2.3) and eGFR <90 ml/min/1.73m², at 21.1% (95% CI 19.9 – 22.3), than urban
Decoupling Gating from Linearity

ReLU neural-networks have been in the focus of many recent theoretical works, trying to explain their empirical success. Nonetheless, there is still a gap between current theoretical results and empirical observations, even in the case of shallow (one hidden-layer) networks. For example, in the task of memorizing a random sample of size $m$ and dimension $d$, the best theoretical result requires the size of the network to be $\tilde{\Omega}(\frac{m^2}{d})$, while empirically a network of size slightly larger than $\frac{m}{d}$ is sufficient. To bridge this gap, we turn to study a simplified model for ReLU networks. We observe that a ReLU neuron is a product of a linear function with a gate (the latter determines whether the neuron is active or not), where both share a jointly trained weight vector. In this spirit, we introduce the Gated Linear Unit (GaLU), which simply decouples the linearity from the gating by assigning different vectors for each role. We show that GaLU networks allow us to get optimization and generalization results that are much stronger than those available for ReLU networks. Specifically, we show a memorization result for networks of size $\tilde{\Omega}(\frac{m}{d})$, and improved generalization bounds. Finally, we show that in some scenarios, GaLU networks behave similarly to ReLU networks, hence proving to be a good choice of a simplified model.
Neural Specialization for English and Arabic Print in Early Readers

Abstract Learning to read requires the specialization of a region in the left fusiform gyrus known as the visual word form area (VWFA). This region, which initially responds to faces and objects, develops specificity for print over a long trajectory of instruction and practice. VWFA neurons may be primed for print because of their pre-literate tuning properties, becoming specialized through top-down feedback mechanisms during learning. However, much of what is known about the VWFA comes from studies of Western orthographies, whose alphabets share common visual characteristics. Far less is known about the development of the VWFA for Arabic, which is a complex orthography and is significantly more difficult to achieve fluency in in reading. In the current study, electroencephalography responses were collected from first grade children in the United Arab Emirates learning to read in both English and Arabic. Children viewed words and false font strings in English and Arabic while performing a vigilance task. The P1 and N1 responses to all stimulus categories were quantified in two occipital and two parietal electrodes as well as the alpha band signal across all four electrodes of interest. Analysis revealed a significantly stronger N1 response to English compared to Arabic and decreased alpha power to Arabic compared to English. These findings suggest a fundamental difference in neural plasticity for these two distinct orthographies, even when instruction is concurrent. Future work is needed to determine whether VWFA specialization for Arabic takes longer than more well-studied orthographies and if differences in reading instruction approaches help accelerate this process.
Unified Modeling and Reasoning in Outdoor and Indoor Spaces

In recent years, indoor spatial data management has started to attract attention partly due to the increasing use of receptor devices (e.g., RFID readers, and wireless sensor networks) in both outdoor and indoor spaces. Applications that employ these devices are expected to span uniformly and supply seamless functionality in both outdoor and indoor spaces. What makes this impossible is the current absence of a unified account of these two types of spaces both in terms of modeling and reasoning about the models. This paper reviews and extends a recent unified model of outdoor and indoor spaces and receptor deployments in these spaces. The extended model enables modelers to capture various information pieces from the physical world. On top of the extended model, this paper hones the route observability concept, derives its powerful, bounded information-theoretic function, and demonstrates its usefulness in enhancing the reading environment. Additionally, this paper establishes a conclusive relation between a route observability and the uncertainty in tracking moving objects. The extended model enables incorporating receptor data through a probabilistic trajectory-to-route translator. This translator first facilitates the tracking of moving objects enabling the search for them to be optimized, and second permits performing high-level reasoning about points of potential traffic (over)load in outdoor and indoor spaces, so-called bottleneck points. A functional analysis illustrates the behavior of the route observability function. An experimental evaluation follows to corroborate the competitive accuracy of the translator, the high quality of the inference, and the sensibleness of the reasoning, when applied to synthetic data, and to uncleansed, real-world data obtained from tracking RFID-tagged flight baggage.
Post-traumatic complex regional pain syndrome : clinical features and epidemiology Mini-review

Complex Regional Pain Syndrome (CRPS) is a chronic pain condition that occurs after a tissue injury (fractures, sprain, surgery) of the upper or lower extremities. A clear pathophysiological mechanism has not been established yet and different patterns are considered to play a role in the genesis of the disease. The diagnosis is made by different diagnosis criteria and a gold standard has not been established yet. Incidence of CRPS is unclear and large prospective studies on the incidence and prevalence of CRPS are scarce. The aim of this review is to give an overview on the prevalent data regarding this chronic syndrome.
Physical Activity in Women with Endometriosis: Less or More Compared with a Healthy Control?

Background: Endometriosis, i.e., endometrial-like tissue outside the uterus, is a chronic inflammatory condition affecting physical functioning. However, the specific levels of physical activity (PA) in the context of endometriosis and different disease symptoms remain unclear. Methods: This multi-center, cross-sectional study compared PA levels and influencing factors in endometriosis patients and non-endometriosis patients. Data were collected through questionnaires. Endometriosis was surgically confirmed. A statistical analysis was performed with appropriate tests. Results: The study included 460 women with endometriosis and 460 age-matched women without this condition. The two groups did not differ significantly in terms of age, education level, or stable partnership. Women with endometriosis exhibited lower PA levels, practicing fewer hours of sports weekly and climbing fewer stairs daily compared to the control group. These differences remained significant after controlling for confounding factors. Factors such as endometriosis, current dysmenorrhea, and depression were associated with decreased PA. Conclusions: These findings suggest that women with endometriosis engage in less PA compared to those without this condition. These results highlight the need for interventions to promote increased PA in endometriosis patients and harness the associated health benefits. Further research is warranted to explore the underlying mechanisms and develop tailored exercise therapies for this population.
NEW PHOTOGRAMMETRIC TECHNIQUES USED IN THE 2003 MARS EXPLORATION ROVER MISSION

The 2003 Mars Exploration Rover (MER) mission rovers, Spirit and Opportunity, have been exploring the Martian surface for more than two years (as of February 2006). During the mission, our team has routinely performed topographic mapping and rover localization to support strategic and tactical traverse planning as well as various scientific investigations. Topographic maps and localization data have been provided to MER mission scientists and engineers through a web-based GIS. This paper presents new photogrammetric techniques that are being used for the latest mapping- and localization-related activities. Among them is a bundle adjustment-based rover localization technology that has corrected wheel slippage, IMU (Inertial Measurement Unit) drift and other navigation errors as large as 10.5% in the Husband Hill area of the Gusev Crater landing site (Spirit) and 21% in Eagle Crater at the Meridiani Planum landing site (Opportunity). Detailed 3D terrain models of major features, such as Endurance Crater and Larry’s Lookout, have been generated using multi-site or single-site panoramic stereo images. These models are being used as important data for geological analysis of craters and stratigraphy. Special products such as a north-facing slope map and a solar energy map have been generated to aid in choosing north-facing slopes where the Spirit rover can capture more solar energy during the upcoming winter season. Comparison of bundle-adjusted rover locations with those seen from orbital images is also being conducted to verify the bundle adjustment results.
Zebrafish as a robust preclinical platform for screening plant-derived drugs with anticonvulsant properties—a review

Traditionally, selected plant sources have been explored for medicines to treat convulsions. This continues today, especially in countries with low-income rates and poor medical systems. However, in the low-income countries, plant extracts and isolated drugs are in high demand due to their good safety profiles. Preclinical studies on animal models of seizures/epilepsy have revealed the anticonvulsant and/or antiepileptogenic properties of, at least some, herb preparations or plant metabolites. Still, there is a significant number of plants known in traditional medicine that exert anticonvulsant activity but have not been evaluated on animal models. Zebrafish is recognized as a suitable in vivo model of epilepsy research and is increasingly used as a screening platform. In this review, the results of selected preclinical studies are summarized to provide credible information for the future development of effective screening methods for plant-derived antiseizure/antiepileptic therapeutics using zebrafish models. We compared zebrafish vs. rodent data to show the translational value of the former in epilepsy research. We also surveyed caveats in methodology. Finally, we proposed a pipeline for screening new anticonvulsant plant-derived drugs in zebrafish (“from tank to bedside and back again”).