Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions of the Streptococcus pneumoniae Toxin-Antitoxin RelBE Proteins with Their Target DNA

Type II bacterial toxin-antitoxin (TA) systems are found in most bacteria, archaea, and mobile genetic elements. TAs are usually found as a bi-cistronic operon composed of an unstable antitoxin and a stable toxin that targets crucial cellular functions like DNA supercoiling, cell-wall synthesis or mRNA translation. The type II RelBE system encoded by the pathogen Streptococcus pneumoniae is highly conserved among different strains and participates in biofilm formation and response to oxidative stress. Here, we have analyzed the participation of the RelB antitoxin and the RelB:RelE protein complex in the self-regulation of the pneumococcal relBE operon. RelB acted as a weak repressor, whereas RelE performed the role of a co-repressor. By DNA footprinting experiments, we show that the proteins bind to a region that encompasses two palindromic sequences that are located around the −10 sequences of the single promoter that directs the synthesis of the relBE mRNA. High-resolution footprinting assays showed the distribution of bases whose deoxyriboses are protected by the bound proteins, demonstrating that RelB and RelB:RelE contacted the DNA backbone on one face of the DNA helix and that these interactions extended beyond the palindromic sequences. Our findings suggest that the binding of the RelBE proteins to its DNA target would lead to direct inhibition of the binding of the host RNA polymerase to the relBE promoter.
Identification of Vulnerable Populations and Areas at Higher Risk of COVID-19-Related Mortality during the Early Stage of the Epidemic in the United States

We characterized vulnerable populations located in areas at higher risk of COVID-19-related mortality and low critical healthcare capacity during the early stage of the epidemic in the United States. We analyze data obtained from a Johns Hopkins University COVID-19 database to assess the county-level spatial variation of COVID-19-related mortality risk during the early stage of the epidemic in relation to health determinants and health infrastructure. Overall, we identified highly populated and polluted areas, regional air hub areas, race minorities (non-white population), and Hispanic or Latino population with an increased risk of COVID-19-related death during the first phase of the epidemic. The 10 highest COVID-19 mortality risk areas in highly populated counties had on average a lower proportion of white population (48.0%) and higher proportions of black population (18.7%) and other races (33.3%) compared to the national averages of 83.0%, 9.1%, and 7.9%, respectively. The Hispanic and Latino population proportion was higher in these 10 counties (29.3%, compared to the national average of 9.3%). Counties with major air hubs had a 31% increase in mortality risk compared to counties with no airport connectivity. Sixty-eight percent of the counties with high COVID-19-related mortality risk also had lower critical care capacity than the national average. The disparity in health and environmental risk factors might have exacerbated the COVID-19-related mortality risk in vulnerable groups during the early stage of the epidemic.
Tractography for Subcortical Resection of Gliomas Is Highly Accurate for Motor and Language Function: ioMRI-Based Elastic Fusion Disproves the Severity of Brain Shift

Simple Summary Tractography enables the visualization of eloquent white matter pathways. Inaccuracies due to brain shift might occur intraoperatively. The aim of this study was to evaluate the impact of intraoperative magnetic resonance imaging (MRI)-based elastic fusion on preoperative tractography for subcortical resection of gliomas. We confirmed the high accuracy of tractography during the whole course of surgery. Abstract When using preoperative tractography intraoperatively, inaccuracies due to brain shift might occur. Intraoperative tractography is rarely performed. Elastic fusion (EF) is a tool developed to compensate for brain shift, gravity, and tissue resection based on intraoperative images. Our hypothesis was that preoperative tractography is accurate and adjustments of tractography by intraoperative magnetic resonance imaging (ioMRI)-based EF (IBEF) compensate for brain shift. Between February 2018 and June 2019, 78 patients underwent eloquent (46 motor, 32 language) glioma resection in our department using intraoperative MRI. Mean distances between the resection cavity and tractography were analyzed and correlated with clinical outcomes. The mean ± standard deviation (range) distance after the application of IBEF was 5.0 ± 2.9 mm (0–10 mm) in patients without surgery-related motor deficits compared with 1.1 ± 1.6 mm (0–5 mm) in patients who showed new permanent surgery-related motor deficits postoperatively (p < 0.001). For language, the distance was 0.7 ± 1.2 mm (0–2 mm) in patients with new permanent deficits compared with 3.1 ± 4.5 mm (0–14 mm) in patients without new permanent surgery-related language deficits (p = 0.541). Preoperative tractography corrected by IBEF for subcortical resection of gliomas is highly accurate. However, at least for such subcortical anatomy, the severity of brain shift was considerably overestimated in the past.
Telehealth Interventions to Support Self-Management in Stroke Survivors: A Systematic Review

Telehealth (TH) intervention is a method to optimize self-management (SM) support in stroke survivors. Objectives of this study included identifying the TH-SM intervention’s focus and SM support components, the TH delivery type, and the TH-SM support effects on stroke survivors. Five databases were searched for the years 2005–2020 to identify TH-SM support interventions for stroke survivors. Randomized controlled trials and quasi-experimental, one-group re-post study designs were included. Ten studies were reviewed. TH-SM support focused on post-stroke depression, obesity management, participation, functional mobility, and activities of daily living. The TH delivery type most used in selected studies was messaging. Regarding the SM support components, the education component was used in all studies, and psychological support and lifestyle advice and support were used in 8 out of 10 studies. TH-SM intervention had positive effects in terms of goal achievement for SM behavior, emotional state, and mobility of clinical outcomes, and TH acceptance in stroke survivors. Although the TH-SM-supported intervention effects were not found consistently in all outcomes, this review discovered a positive effect on various SM-related outcomes. In addition, TH delivery types and SM support components showed the possibility of various options to be considered for intervention. Therefore, we suggest that TH-SM supported intervention is a positive alternative for SM support in stroke survivors.
Impact of COVID-19 Pandemic on Serum Vitamin D Level among Infants and Toddlers: An Interrupted Time Series Analysis and before-and-after Comparison

Background: During the coronavirus disease 2019 (COVID-19) pandemic, the implementation of social distancing and home confinement measures may elevate the risk of vitamin D deficiency particularly for infants. This study aimed to quantify changes in vitamin D level among infants and toddlers in Hong Kong after the COVID-19 outbreak. Methods: We recruited 303 infants and toddlers aged 2–24 months by stratified random sampling from 1 June 2019 to November 30, 2020. Regression models were used to estimate the effect of time on infants’ serum 25-hydroxyvitamin D (25(OH)D) level overall and by age groups before and after the outbreak. Interrupted time series (ITS) analysis was performed to examine the sustained effect of COVID-19 on their serum 25(OH)D level. Results: The ITS results showed no immediate reduction in serum 25(OH)D level among infants, but a decreasing trend was observed in the subsequent months post-outbreak at a monthly decline rate of −6.32 nmol/L. When analyzed by age group, the magnitude of post-outbreak reduction in 25(OH)D was stronger among younger infants (aged 2–6 months). Conclusion: Guidelines and recommendations should be given to pregnant women and mothers to ensure sufficient vitamin D level in their infants during the COVID-19 period.
Recent Advances in Chemical Sensors Using Porphyrin-Carbon Nanostructure Hybrid Materials

Porphyrins and carbon nanomaterials are among the most widely investigated and applied compounds, both offering multiple options to modulate their optical, electronic and magnetic properties by easy and well-established synthetic manipulations. Individually, they play a leading role in the development of efficient and robust chemical sensors, where they detect a plethora of analytes of practical relevance. But even more interesting, the merging of the peculiar features of these single components into hybrid nanostructures results in novel materials with amplified sensing properties exploitable in different application fields, covering the areas of health, food, environment and so on. In this contribution, we focused on recent examples reported in literature illustrating the integration of different carbon materials (i.e., graphene, nanotubes and carbon dots) and (metallo)porphyrins in heterostructures exploited in chemical sensors operating in liquid as well as gaseous phase, with particular focus on research performed in the last four years.
Molecular Phylogeny of Endophytic Fungi from Rattan (Calamus castaneus Griff.) Spines and Their Antagonistic Activities against Plant Pathogenic Fungi

Calamus castaneus is a common rattan palm species in the tropical forests of Peninsular Malaysia and is noticeable by the yellow-based spines that cover the stems. This study aimed to determine the prevalence of fungal endophytes within C. castaneus spines and whether they inhibit the growth of fungal pathogens. Twenty-one genera with 40 species of fungal endophytes were isolated and identified from rattan palm spines. Based on molecular identification, the most common isolates recovered from the spines were Colletotrichum (n = 19) and Diaporthe spp. (n = 18), followed by Phyllosticta spp. , Xylaria sp. , Trichoderma spp. , Helminthosporium spp. , Penicillium spp. , Fusarium spp. , Neopestalotiopsis spp. , Arthrinium sp. , Cyphellophora sp. , Cladosporium spp. , Curvularia sp. , Bionectria sp. , and Acremonium spp. Non-sporulating fungi were also identified, namely Nemania primolutea, Pidoplitchkoviella terricola, Muyocopron laterale, Acrocalymma fici, Acrocalymma medicaginis, and Endomelanconiopsis endophytica. The isolation of these endophytes showed that the spines harbor endophytic fungi. Most of the fungal endophytes inhibited the growth of several plant pathogenic fungi, with 68% of the interactions resulting in mutual inhibition, producing a clear inhibition zone of <2 mm. Our findings demonstrate the potential of the fungal endophytes from C. castaneus spines as biocontrol agents.
Histone Epigenetic Signatures in Embryonic Limb Interdigital Cells Fated to Die

During limb formation in vertebrates with free digits, the interdigital mesoderm is eliminated by a massive degeneration process that involves apoptosis and cell senescence. The degradation process is preceded by intense DNA damage in zones located close to methylated DNA, accompanied by the activation of the DNA repair response. In this study, we show that trimethylated histone 3 (H3K4me3, H3K9me3, and H3K27me3) overlaps with zones positive for 5mC in the nuclei of interdigital cells. This pattern contrasts with the widespread distribution of acetylated histones (H3K9ac and H4ac) and the histone variant H3.3 throughout the nucleoplasm. Consistent with the intense labeling of acetylated histones, the histone deacetylase genes Hdac1, Hdac2, Hdac3, and Hdac8, and at a more reduced level, Hdac10, are expressed in the interdigits. Furthermore, local treatments with the histone deacetylase inhibitor trichostatin A, which promotes an open chromatin state, induces massive cell death and transcriptional changes reminiscent of, but preceding, the physiological process of interdigit remodeling. Together, these findings suggest that the epigenetic profile of the interdigital mesoderm contributes to the sensitivity to DNA damage that precedes apoptosis during tissue regression.
Review of Design Considerations for Brain-on-a-Chip Models

In recent years, the need for sophisticated human in vitro models for integrative biology has motivated the development of organ-on-a-chip platforms. Organ-on-a-chip devices are engineered to mimic the mechanical, biochemical and physiological properties of human organs; however, there are many important considerations when selecting or designing an appropriate device for investigating a specific scientific question. Building microfluidic Brain-on-a-Chip (BoC) models from the ground-up will allow for research questions to be answered more thoroughly in the brain research field, but the design of these devices requires several choices to be made throughout the design development phase. These considerations include the cell types, extracellular matrix (ECM) material(s), and perfusion/flow considerations. Choices made early in the design cycle will dictate the limitations of the device and influence the end-point results such as the permeability of the endothelial cell monolayer, and the expression of cell type-specific markers. To better understand why the engineering aspects of a microfluidic BoC need to be influenced by the desired biological environment, recent progress in microfluidic BoC technology is compared. This review focuses on perfusable blood–brain barrier (BBB) and neurovascular unit (NVU) models with discussions about the chip architecture, the ECM used, and how they relate to the in vivo human brain. With increased knowledge on how to make informed choices when selecting or designing BoC models, the scientific community will benefit from shorter development phases and platforms curated for their application.
Silicon Enhances Plant Resistance of Rice against Submergence Stress

Flooding is an important natural disaster limiting rice production. Silicon (Si) has been shown to have an important role in alleviating varied environmental stress. However, very few studies have investigated the effects and mechanisms of Si in alleviating flood stress in rice. In the present study, wild type rice (cv. Oochikara, WT) and Si-defective mutant (lsi1) were chosen to examine the impacts of Si application on plant growth, photosynthesis, cell structure, and antioxidant enzyme activity of rice exposed to submergence stress at tillering stage. Our results showed that Si application improved root morphological traits, and increased Si uptake and plant biomass of WT under submergence stress, but non-significantly influenced lsi1 mutant. Under submergence stress, leaf photosynthesis of WT was significantly inhibited, and Si application had no significant effects on photosynthetic rate, transpiration rate, stomatal conductance, and intercellular carbon dioxide concentration for both of WT and lsi1 mutant, but the photochemical quenching of WT was increased and the integrity of cell structure was improved. In addition, Si application significantly reduced malondialdehyde concentration and increased the activity of peroxidase and catalase in WT leaves under submergence stress. These results suggested that Si could increase rice plant resistance against submergence stress by improving root morphological traits and chloroplast ultrastructure and enhancing antioxidant defense.
Modeling of Vaccination and Contact Tracing as Tools to Control the COVID-19 Outbreak in Spain

We developed an agent-based stochastic model, based on P Systems methodology, to decipher the effects of vaccination and contact tracing on the control of COVID-19 outbreak at population level under different control measures (social distancing, mask wearing and hand hygiene) and epidemiological scenarios. Our findings suggest that without the application of protection social measures, 56.1% of the Spanish population would contract the disease with a mortality of 0.4%. Assuming that 20% of the population was protected by vaccination by the end of the summer of 2021, it would be expected that 45% of the population would contract the disease and 0.3% of the population would die. However, both of these percentages are significantly lower when social measures were adopted, being the best results when social measures are in place and 40% of contacts traced. Our model shows that if 40% of the population can be vaccinated, even without social control measures, the percentage of people who die or recover from infection would fall from 0.41% and 56.1% to 0.16% and 33.5%, respectively compared with an unvaccinated population. When social control measures were applied in concert with vaccination the percentage of people who die or recover from infection diminishes until 0.10% and 14.5%, after vaccinating 40% of the population. Vaccination alone can be crucial in controlling this disease, but it is necessary to vaccinate a significant part of the population and to back this up with social control measures.
Recent Advances and Applications of Passive Harmonic RFID Systems: A Review

Harmonic Radio Frequency Identification (RFID) systems have attracted significant interest over the last decade as it provides many benefits over the conventional RFID systems. Harmonic RFID is desired over conventional RFID systems due to reduced self-jamming, location accuracy from dual frequency, and higher phase noise immunity. In a harmonic RFID system, the tag receives instructions from the reader at an RF carrier frequency and replies back at the harmonic of the RF frequency. A nonlinear element consuming very low power at the tag is required to generate the harmonic carrier for the battery-less system. In this review article, a detailed contrast between conventional and harmonic RFID systems is presented. This is followed by different circuit design techniques to generate harmonics and integration techniques to form a fully operable passive harmonic RFID tag. Also, a wide range of applications, especially sensor integration with harmonic RFID’s, along with the future trends are presented.
Design of Experiment on Concrete Mechanical Properties Prediction: A Critical Review

Concrete mix design and the determination of concrete performance are not merely engineering studies, but also mathematical and statistical endeavors. The study of concrete mechanical properties involves a myriad of factors, including, but not limited to, the amount of each constituent material and its proportion, the type and dosage of chemical additives, and the inclusion of different waste materials. The number of factors and combinations make it difficult, or outright impossible, to formulate an expression of concrete performance through sheer experimentation. Hence, design of experiment has become a part of studies, involving concrete with material addition or replacement. This paper reviewed common design of experimental methods, implemented by past studies, which looked into the analysis of concrete performance. Several analysis methods were employed to optimize data collection and data analysis, such as analysis of variance (ANOVA), regression, Taguchi method, Response Surface Methodology, and Artificial Neural Network. It can be concluded that the use of statistical analysis is helpful for concrete material research, and all the reviewed designs of experimental methods are helpful in simplifying the work and saving time, while providing accurate prediction of concrete mechanical performance.
Methodology for Estimating Digestion and Passage Kinetics of Forages

The nutritive value of a feedstuff is determined by its content of chemical entities and their transformations to nutrients required by the animal. Digestive transformations are determined by intrinsic attributes of the forage and by their interactions with the kinetic processes of digestion. Quantitative expressions of the kinetics of digestion and passage are needed to Po.ore precisely estimate the quantity and composition of nutrients digested from forages and their subsequent efficiency of utilization by the animal. The objective of this chapter is to review methodology for estimating parameters describing the kinetics of physical and chemical digestion in ruminants. The kinetic processes of primary concern are: 1) flow of digesta through segments of the ruminant's digestive system, several of which involve fermentative digestion; and 2) digestion of specific entities in the forage. Recent reviews of this subject by Allen and Mertens (1987), Sauvant and Ramangasovina (1991), and Mertens (l993a,b) have emphasized deterministic, age-independent kinetics of this flow and digestion. This review will additionally emphasize age-dependent models of digestion and passage of fragments derived from mastication during ingestion and rumination. The need to simultaneously consider the fragmentation process has been emphasized by Sauvant and Ramangasovina (1991).
Modeling Between-Subject Variability in Subcutaneous Absorption of a Fast-Acting Insulin Analogue by a Nonlinear Mixed Effects Approach

Despite the great progress made in insulin preparation and titration, many patients with diabetes are still experiencing dangerous fluctuations in their blood glucose levels. This is mainly due to the large between- and within-subject variability, which considerably hampers insulin therapy, leading to defective dosing and timing of the administration process. In this work, we present a nonlinear mixed effects model describing the between-subject variability observed in the subcutaneous absorption of fast-acting insulin. A set of 14 different models was identified on a large and frequently-sampled database of lispro pharmacokinetic data, collected from 116 subjects with type 1 diabetes. The tested models were compared, and the best one was selected on the basis of the ability to fit the data, the precision of the estimated parameters, and parsimony criteria. The selected model was able to accurately describe the typical trend of plasma insulin kinetics, as well as the between-subject variability present in the absorption process, which was found to be related to the subject’s body mass index. The model provided a deeper understanding of the insulin absorption process and can be incorporated into simulation platforms to test and develop new open- and closed-loop treatment strategies, allowing a step forward toward personalized insulin therapy.