Miracle-dz/UniFAR-FTUs huggingface dataset:
The Potential of Lung Epithelium Specific Proteins as Biomarkers for COVID-19-Associated Lung Injury

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection was first reported in Wuhan, China, and was declared a pandemic by the World Health Organization (WHO) on 20 March 2020. The respiratory system is the major organ system affected by COVID-19. Numerous studies have found lung abnormalities in patients with COVID-19, including shortness of breath, respiratory failure, and acute respiratory distress syndrome. The identification of lung-specific biomarkers that are easily measurable in serum would be valuable for both clinicians and patients with such conditions. This review is focused on the pneumoproteins and their potential to serve as biomarkers for COVID-19-associated lung injury, including Krebs von den Lungen-6 (KL-6), surfactant proteins (SP-A, SP-B, SP-C, SP-D), and Clara cell secretory protein (CC16). The current findings indicate the aforementioned pneumoproteins may reflect the severity of pulmonary manifestations and could serve as potential biomarkers in COVID-19-related lung injury.
Catenin Alpha 2 May Be a Biomarker or Potential Drug Target in Psychiatric Disorders with Perseverative Negative Thinking

AlphaN-catenin gene CTNNA2 has been implicated in intrauterine brain development, as well as in several psychiatric disorders and cardiovascular diseases. Our present aim was to investigate CTNNA2 gene-wide associations of single-nucleotide polymorphisms (SNPs) with psychiatric and cardiovascular risk factors to test the potential mediating role of rumination, a perseverative negative thinking phenotype in these associations. Linear mixed regression models were run by FaST-LMM within a sample of 795 individuals from the Budakalasz Health Examination Survey. The psychiatric outcome variables were rumination and its subtypes, and ten Brief Symptom Inventory (BSI) scores including, e.g., obsessive-compulsive, depression, anxiety, hostility, phobic anxiety, and paranoid ideation. Cardiovascular outcome variables were BMI and the Framingham risk scores for cardiovascular disease, coronary heart disease, myocardial infarction, and stroke. We found nominally significant CTNNA2 associations for every phenotype. Rumination totally mediated the associations of CTNNA2 rs17019243 with eight out of ten BSI scores, but none with Framingham scores or BMI. Our results suggest that CTNNA2 genetics may serve as biomarkers, and increasing the expression or function of CTNNA2 protein may be a potential new therapeutic approach in psychiatric disorders with perseverative negative thinking including, e.g., depression. Generally, an antiruminative agent could be a transdiagnostic and preventive psychopharmacon.
Permeation Challenges of Drugs for Treatment of Neurological Tuberculosis and HIV and the Application of Magneto-Electric Nanoparticle Drug Delivery Systems

The anatomical structure of the brain at the blood–brain barrier (BBB) creates a limitation for the movement of drugs into the central nervous system (CNS). Drug delivery facilitated by magneto-electric nanoparticles (MENs) is a relatively new non-invasive approach for the delivery of drugs into the CNS. These nanoparticles (NPs) can create localized transient changes in the permeability of the cells of the BBB by inducing electroporation. MENs can be applied to deliver antiretrovirals and antibiotics towards the treatment of human immunodeficiency virus (HIV) and tuberculosis (TB) infections in the CNS. This review focuses on the drug permeation challenges and reviews the application of MENs for drug delivery for these diseases. We conclude that MENs are promising systems for effective CNS drug delivery and treatment for these diseases, however, further pre-clinical and clinical studies are required to achieve translation of this approach to the clinic.
AimR Adopts Preexisting Dimer Conformations for Specific Target Recognition in Lysis-Lysogeny Decisions of Bacillus Phage phi3T

A bacteriophage switches between lytic and lysogenic life cycles. The AimR-AimP-AimX communication system is responsible for phage lysis-lysogeny decisions during the infection of Bacillus subtilis. AimX is a regulator biasing phage lysis, AimR is a transcription factor activating AimX expression, and AimP is an arbitrium peptide that determines phage lysogeny by deactivating AimR. A strain-specific mechanism for the lysis-lysogeny decisions is proposed in SPbeta and phi3T phages. That is, the arbitrium peptide of the SPbeta phage stabilizes the SPbeta AimR (spAimR) dimer, whereas the phi3T-derived peptide disassembles the phi3T AimR (phAimR) dimer into a monomer. Here, we find that phAimR does not undergo dimer-to-monomer conversion upon arbitrium peptide binding. Gel-filtration, static light scattering (SLS) and analytical ultracentrifugation (AUC) results show that phAimR is dimeric regardless of the presence of arbitrium peptide. Small-angle X-ray scattering (SAXS) reveals that the arbitrium peptide binding makes an extended dimeric conformation. Single-molecule fluorescence resonance energy transfer (smFRET) analysis reveals that the phAimR dimer fluctuates among two distinct conformational states, and each preexisting state is selectively recognized by the arbitrium peptide or the target DNA, respectively. Collectively, our biophysical characterization of the phAimR dynamics underlying specific target recognition provides new mechanistic insights into understanding lysis-lysogeny decisions in Bacillus phage phi3T.
Factors Affecting the Necessity of Tracheostomy in Patients with Deep Neck Infection

Deep neck infection (DNI) is a serious disease that can lead to airway obstruction, and some patients require a tracheostomy to protect the airway instead of intubation. However, no previous study has explored risk factors associated with the need for a tracheostomy in patients with DNI. This article investigates the risk factors for the need for tracheostomy in patients with DNI. Between September 2016 and February 2020, 403 subjects with DNI were enrolled. Clinical findings and critical deep neck spaces associated with a need for tracheostomy in patients with DNI were assessed. In univariate and multivariate analysis, older age (≥65 years old) (OR = 2.450, 95% CI: 1.163–5.161, p = 0.018), multiple spaces involved (≥3 spaces) (OR = 4.490, 95% CI: 2.153–9.360, p = 0.001), and the presence of mediastinitis (OR = 14.800, 95% CI: 5.097–42.972, p < 0.001) were independent risk factors associated with tracheostomy in patients with DNI. Among the 44 patients with DNI that required tracheostomy, ≥50% of patients had involvement of the parapharyngeal or retropharyngeal space (72.72% and 50.00%, respectively). Streptococcus constellatus (25.00%) was the most common pathogen in patients with DNI who required tracheostomy. In conclusion, requiring a tracheostomy was associated with a severe clinical presentation of DNI. Older age (≥65 years old), multiple spaces (≥3 spaces), and presence of mediastinitis were significant risk factors associated with tracheostomy in patients with DNI. The parapharyngeal and retropharyngeal spaces were the most commonly involved, and Streptococcus constellatus was the most common pathogen in the patients with DNI that required tracheostomy.
Non-Invasive Hemodynamics Monitoring System Based on Electrocardiography via Deep Convolutional Autoencoder

This study evaluates cardiovascular and cerebral hemodynamics systems by only using non-invasive electrocardiography (ECG) signals. The Massachusetts General Hospital/Marquette Foundation (MGH/MF) and Cerebral Hemodynamic Autoregulatory Information System Database (CHARIS DB) from the PhysioNet database are used for cardiovascular and cerebral hemodynamics, respectively. For cardiovascular hemodynamics, the ECG is used for generating the arterial blood pressure (ABP), central venous pressure (CVP), and pulmonary arterial pressure (PAP). Meanwhile, for cerebral hemodynamics, the ECG is utilized for the intracranial pressure (ICP) generator. A deep convolutional autoencoder system is applied for this study. The cross-validation method with Pearson’s linear correlation (R), root mean squared error (RMSE), and mean absolute error (MAE) are measured for the evaluations. Initially, the ECG is used to generate the cardiovascular waveform. For the ABP system—the systolic blood pressure (SBP) and diastolic blood pressures (DBP)—the R evaluations are 0.894 ± 0.004 and 0.881 ± 0.005, respectively. The MAE evaluations for SBP and DBP are, respectively, 6.645 ± 0.353 mmHg and 3.210 ± 0.104 mmHg. Furthermore, for the PAP system—the systolic and diastolic pressures—the R evaluations are 0.864 ± 0.003 mmHg and 0.817 ± 0.006 mmHg, respectively. The MAE evaluations for systolic and diastolic pressures are, respectively, 3.847 ± 0.136 mmHg and 2.964 ± 0.181 mmHg. Meanwhile, the mean CVP evaluations are 0.916 ± 0.001, 2.220 ± 0.039 mmHg, and 1.329 ± 0.036 mmHg, respectively, for R, RMSE, and MAE. For the mean ICP evaluation in cerebral hemodynamics, the R and MAE evaluations are 0.914 ± 0.003 and 2.404 ± 0.043 mmHg, respectively. This study, as a proof of concept, concludes that the non-invasive cardiovascular and cerebral hemodynamics systems can be potentially investigated by only using the ECG signal.
Extended Adhesion-Sparing Liver Eversion during Kasai Portoenterostomy for Infants with Biliary Atresia

Background: Despite the fact that Kasai portoenterostomy (KPE) is the primary treatment for biliary atresia (BA), liver transplantation (LT) remains the ultimate surgery for two-thirds of these patients. Their true survival rate with the native liver reflects the original KPE and the burden of post-operative complications. We report an original modification of the adhesion-sparing liver eversion (ASLE) technique during KPE that facilitates the total native hepatectomy at time of transplantation. Methods: All consecutive patients with BA who underwent KPE at our department and subsequent LT at Paediatric Liver Transplant Centre at Papa Giovanni XXIII Hospital between 2010–2018 were retrospectively enrolled. All patients underwent ASLE during KPE. Patients’ demographic data, type of KPE, total transplant time (TTT), hepatectomy time (HT), intra-operative packed red blood cells and plasma transfusions, intra- and post-operative complications were noted. Results: 44 patients were enrolled. Median TTT and HT were 337 and 57 min, respectively. The median volume of packed red blood cell transfusion was 95 mL. No patients presented bowel perforation during the procedure or in the short post-operative course. No mortality after LT was recorded. Conclusions: In addition to the well-known advantages of the standard liver eversion technique, ASLE reduces the formation of intra-abdominal adhesions, lowering significantly the risk of bowel perforation and bleeding when liver transplantation is performed for failure of KPE.
Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (Eint(BSSE)) was determined using a supramolecular approach. The Eint(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.
Association between Domperidone Administered via Feeding Tube and Feeding Success in Critically Ill Patients with Enteral Feeding Intolerance

One nutritional challenge in critically ill patients is enteral feeding intolerance (EFI), but current prokinetic agents have uncertain efficacy and safety profiles. We conducted a longitudinal, single-center, retrospective study to evaluate the efficacy and safety of domperidone administered via the feeding tube versus intravenous (IV) metoclopramide among adult patients with EFI. The primary outcome was feeding success, defined as the proportion of patients with average percentage of daily protein prescription >80% of the target dose. The secondary outcomes were safety endpoints. Among 28,814 intensive care unit (ICU) admissions, 552 patients with EFI were included, 38 receiving IV metoclopramide and 514 receiving tube feeding domperidone. The proportion of feeding success in patients receiving tube feeding domperidone and IV metoclopramide was 42.02% and 21.05%, respectively. After 1:2 matching (IV metoclopramide to tube feeding domperidone), the proportion of feeding success was 40.79% in patients receiving tube feeding domperidone. Basically, after matching, there were no differences in any safety endpoints (mortality and length of stay during ICU and hospitalization, organ-support-treatment free days) or adverse events (recurrence of EFI, electrolyte disturbance, abdominal and other symptoms) between the two groups (p > 0.05). A logistic regression analysis in the matched cohort indicated that domperidone administered via the feeding tube was independently associated with feeding success. We found that tube feeding domperidone was efficient in increasing enteral nutrition delivery performance among critically ill adult patients with EFI.
Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction

Fast kinetic experiments with dramatically improved time resolution have contributed significantly to understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpin, contact formation, and overall collapse of the peptide chain. Interpretation of experimental results through application of a simple statistical mechanical model was key to this understanding. Atomistic description of all events observed in the experimental findings was challenging. Recent advancements in theory, more sophisticated algorithms, and a true long-term trajectory made way for an atomically detailed description of kinetics, examining folding pathways, validating experimental results, and reporting new findings for a wide range of molecular processes in biophysical chemistry. This review describes how optimum dimensionality reduction theory can construct a simplified coarse-grained model with low dimensionality involving a kinetic matrix that captures novel insights into folding pathways. A set of metastable states derived from molecular dynamics analysis generate an optimally reduced dimensionality rate matrix following transition pathway analysis. Analysis of the actual long-term simulation trajectory extracts a relaxation time directly comparable to the experimental results and confirms the validity of the combined approach. The application of the theory is discussed and illustrated using several examples of helix <==> coil transition pathways. This paper focuses primarily on a combined approach of time-resolved experiments and long-term molecular dynamics simulation from our ongoing work.
Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.
Comparison of Methods for Determination of Carbon in Calcareous Soils

ABSTRACT The global cycle of carbon (C) has raised attention in recent decades due to the great increase in carbon dioxide levels (CO2) levels in the atmosphere and its influence on climate change. Calcareous soils represent a significant fraction of the areas with potential for agriculture and have differential attributes, such as high calcium contents, magnesium, carbonates, and pH values. These attributes have been ignored in analytical procedures despite these characteristics, resulting in an overestimation or underestimation of the soil carbon. Several methods have been proposed for determining the soil carbon contents, however, studies evaluating the analytical procedures of C quantification methods, considering the soil characteristics, such as the calcareous soils, are needed, in order to improve their accuracy. Therefore, the objective of this work was to evaluate and compare methods for C determination and to propose adjustments in the methodology for calcareous soil analysis. The Yeomans and Bremner (YB) was the most efficient method for quantification of organic C among the wet oxidation methods. On the other hand, the Donagemma (WB) method underestimated the organic carbon contents. The results showed that the samples must be macerated and pretreated with a hydrochloric acid solution for the use of CHNS-O, in order to eliminate carbonates in the form of nodules and concretions.
Towards Intraoperative Quantification of Atrial Fibrosis Using Light-Scattering Spectroscopy and Convolutional Neural Networks

Light-scattering spectroscopy (LSS) is an established optical approach for characterization of biological tissues. Here, we investigated the capabilities of LSS and convolutional neural networks (CNNs) to quantitatively characterize the composition and arrangement of cardiac tissues. We assembled tissue constructs from fixed myocardium and the aortic wall with a thickness similar to that of the atrial free wall. The aortic sections represented fibrotic tissue. Depth, volume fraction, and arrangement of these fibrotic insets were varied. We gathered spectra with wavelengths from 500–1100 nm from the constructs at multiple locations relative to a light source. We used single and combinations of two spectra for training of CNNs. With independently measured spectra, we assessed the accuracy of the CNNs for the classification of tissue constructs from single spectra and combined spectra. Combined spectra, including the spectra from fibers distal from the illumination fiber, typically yielded the highest accuracy. The maximal classification accuracy of the depth detection, volume fraction, and permutated arrangements was (mean ± standard deviation (stddev)) 88.97 ± 2.49%, 76.33 ± 1.51%, and 84.25 ± 1.88%, respectively. Our studies demonstrate the reliability of quantitative characterization of tissue composition and arrangements using a combination of LSS and CNNs. The potential clinical applications of the developed approach include intraoperative quantification and mapping of atrial fibrosis, as well as the assessment of ablation lesions.
Elemental Composition and Cell Mass Quantification of Cultured Thraustochytrids Unveil Their Large Contribution to Marine Carbon Pool

The element stoichiometry of bacteria has received considerable attention because of their significant role in marine ecosystems. However, relatively little is known about the composition of major structural elements of the unicellular heterotrophic protists—thraustochytrids, despite their widely recognized contribution to marine nutrient cycling. Here, we analyze the cell volume and elemental C, N, H, and S cell content of seven cultured thraustochytrids, isolated from different marine habitats, in the exponential and stationary growth phases. We further derive the relationships between the cell volume and elemental C and N content of the cultured thraustochytrids. The cell volumes varied significantly (p < 0.001) among the isolates, with median values of 96.9 and 212.5 μm3 in the exponential and stationary phases, respectively. Our results showed a significantly higher percentage of C (64.0 to 67.5) and H (9.9 to 13.2) but a lower percentage of N (1.86 to 2.16) and S (0.34 to 0.91) in the stationary phase, along with marked variations of C and N fractions among isolates in the exponential phase. The cell C (5.7 to 203.7 pg) and N (0.65 to 6.1 pg) content exhibited a significant (p < 0.001) linear relationship with the cell volume (27.7 to 510 μm3). On further analysis of the relationship across the two growth phases, we found the equation (cell C (pg) = 0.356 × cell volume (μm3) + 20.922) for stationary phase cells more appropriate for C estimation of natural thraustochytrids. This study provides the first experimental evidence of higher cell C density than the current estimate and relatively larger C contribution of thraustochytrids than bacteria to the marine organic pool.