Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations and their relation to the development and progression of various complex diseases. Improved data-analytical tools are needed to exploit all information from these biological datasets, taking into account the peculiarities of microbiome data, i.e., compositional, heterogeneous and sparse nature of these datasets. The possibility of predicting host-phenotypes based on taxonomy-informed feature selection to establish an association between microbiome and predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights into the development of models that can be used to predict outputs, such as classification and prediction in microbiology, infer host phenotypes to predict diseases and use microbial communities to stratify patients by their characterization of state-specific microbial signatures. Here we review the state-of-the-art ML methods and respective software applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on the application of ML in microbiome studies related to association and clinical use for diagnostics, prognostics, and therapeutics. Although the data presented here is more related to the bacterial community, many algorithms could be applied in general, regardless of the feature type. This literature and software review covering this broad topic is aligned with the scoping review methodology. The manual identification of data sources has been complemented with: (1) automated publication search through digital libraries of the three major publishers using natural language processing (NLP) Toolkit, and (2) an automated identification of relevant software repositories on GitHub and ranking of the related research papers relying on learning to rank approach.
Synthesis and characterization of well‐defined block and statistical copolymers based on lauryl methacrylate and 2‐(acetoacetoxy)ethyl methacrylate using RAFT‐controlled radical polymerization

Four well-defined diblock copolymers and one statistical copolymer based on lauryl methacrylate (LauMA) and 2-(acetoacetoxy)ethyl methacrylate (AEMA) were prepared using reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers were characterized in terms of molecular weights, polydispersity indices (ranging between 1.12 and 1.23) and compositions by size exclusion chromatography and 1H NMR spectroscopy, respectively. The preparation of the block copolymers was accomplished following a two-step methodology: First, well-defined LauMA homopolymers were prepared by RAFT using cumyl dithiobenzoate as the chain transfer agent (CTA). Kinetic studies revealed that the polymerization of LauMA followed first-order kinetics demonstrating the “livingness” of the RAFT process. The pLauMAs were subsequently used as macro-CTA for the polymerization of AEMA. The glass transition (Tg) and decomposition temperatures (ranging between 200 and 300 °C) of the copolymers were determined using differential scanning calorimetry and thermal gravimetric analysis, respectively. The Tgs of the LauMA homopolymers were found to be around −53 °C. Block copolymers exhibited two Tgs suggesting microphase separation in the bulk whereas the statistical copolymer presented a single Tg as expected. Furthermore, the micellization behavior of pLauMA-b-pAEMA block copolymers was investigated in n-hexane, a selective solvent for the LauMA block, using dynamic light scattering. pLauMA-b-pAEMA block copolymers formed spherical micelles in dilute hexane solutions with hydrodynamic diameters ranging between 30 and 50 nm. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5442–5451, 2008
Association Between AGT M235T and Left Ventricular Mass in Vietnamese Patients Diagnosed With Essential Hypertension

Background: Increasing left ventricular mass in hypertensive patients is an independent prognostic marker for adverse cardiovascular outcomes. Genetic factors have been shown to critically affect left ventricular mass. AGT M235T is one of the genetic polymorphisms that may influence left ventricular mass due to its pivotal role in the regulation of plasma angiotensinogen level as well as hypertension pathophysiology in Asian populations. Currently, how M235T affects left ventricular mass is not well-described in Vietnamese hypertensive patients. This study aimed to investigate the association between M235T and left ventricular mass in Vietnamese patients diagnosed with essential hypertension. Materials and Methods: AGT M235T genotyping and 2D echocardiography were performed on 187 Vietnamese subjects with essential hypertension. All the ultrasound parameters were obtained to calculate the left ventricular mass index according to the American Society of Echocardiography and the European Association of Cardiovascular Imaging 2015 guidelines. Other clinical characteristics were also recorded, including age, gender, duration of hypertension, hypertensive treatment, lifestyle, renal function, fasting plasma glucose, and lipid profile. Results: MT and TT genotypes were determined in 30 and 157 subjects, respectively. AGT M235T genotype, duration of hypertension, body mass index, and ejection fraction statistically affected the left ventricular mass index, which was significantly greater in TT compared to MT carriers after adjusting for confounding factors. Conclusion: The TT genotype of AGT M23T was associated with greater left ventricular mass in Vietnamese patients diagnosed with essential hypertension.
Serum Amyloid A in Inflammatory Rheumatic Diseases: A Compendious Review of a Renowned Biomarker

Serum amyloid A (SAA) is an acute phase protein with a significant importance for patients with inflammatory rheumatic diseases (IRD). The central role of SAA in pathogenesis of IRD has been confirmed by recent discoveries, including its involvement in the activation of the inflammasome cascade and recruitment of interleukin 17 producing T helper cells. Clinical utility of SAA in IRD was originally evaluated nearly half a century ago. From the first findings, it was clear that SAA could be used for evaluating disease severity and monitoring disease activity in patients with rheumatoid arthritis and secondary amyloidosis. However, cost-effective and more easily applicable markers, such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), overwhelmed its use in clinical practice. In the light of emerging evidences, SAA has been discerned as a more sensitive biomarker in a wide spectrum of IRD, especially in case of subclinical inflammation. Furthermore, a growing number of studies are confirming the advantages of SAA over many other biomarkers in predicting and monitoring response to biological immunotherapy in IRD patients. Arising scientific discoveries regarding the role of SAA, as well as delineating SAA and its isoforms as the most sensitive biomarkers in various IRD by recently developing proteomic techniques are encouraging the revival of its clinical use. Finally, the most recent findings have shown that SAA is a biomarker of severe Coronavirus disease 2019 (COVID-19). The aim of this review is to discuss the SAA-involving immune system network with emphasis on mechanisms relevant for IRD, as well as usefulness of SAA as a biomarker in various IRD. Therefore, over a hundred original papers were collected through an extensive PubMed and Scopus databases search. These recently arising insights will hopefully lead to a better management of IRD patients and might even inspire the development of new therapeutic strategies with SAA as a target.
Case Report: A Novel Synonymous ARPC1B Gene Mutation Causes a Syndrome of Combined Immunodeficiency, Asthma, and Allergy With Significant Intrafamilial Clinical Heterogeneity

Recently, a novel syndrome of combined immune deficiency, infections, allergy, and inflammation has been attributed to mutations in the gene encoding actin-related protein 2/3 complex subunit 1B (ARPC1B), which is a key molecule driving the dynamics of the cytoskeleton. Homozygous mutations in the ARPC1B gene have been found to result in the disruption of the protein structure and cause an autosomal recessive syndrome of combined immune deficiency, impaired T-cell migration and proliferation, increased levels of immunoglobulin E (IgE) and immunoglobulin A (IgA), and thrombocytopenia. To date, only a few individuals have been diagnosed with the ARPC1B deficiency syndrome worldwide. In this case series, we report the wide spectrum of phenotype in 3 siblings of a consanguineous family from Afghanistan with a novel homozygous synonymous pathogenic variant c.783G>A, p. (Ala261Ala) of the ARPC1B gene that causes a similar syndrome but no thrombocytopenia. Targeted RNA studies demonstrated that the variant affects the splicing process of mRNA, resulting in a marked reduction of the levels of primary (normal) RNA transcript of the ARPC1B gene in the affected patients and likely premature termination from the abnormally spliced mRNA. The next generation sequencing (NGS) studies facilitated the diagnosis of this rare combined immunodeficiency and led to the decision to treat the affected patients with hematopoietic cell transplant (HCT) from an human leukocyte antigen (HLA)-matched healthy sibling.
The Roles of Envelope Glycoprotein M in the Life Cycle of Some Alphaherpesviruses

The envelope glycoprotein M (gM), a surface virion component conserved among alphaherpesviruses, is a multiple-transmembrane domain-containing glycoprotein with a complex N-linked oligosaccharide. The gM mediates a diverse range of functions during the viral life cycle. In this review, we summarize the biological features of gM, including its characterization and function in some specicial alphaherpesviruses. gM modulates the virus-induced membrane fusion during virus invasion, transports other proteins to the appropriate intracellular membranes for primary and secondary envelopment during virion assembly, and promotes egress of the virus. The gM can interact with various viral and cellular components, and the focus of recent research has also been on interactions related to gM. And we will discuss how gM participates in the life cycle of alphaherpesviruses.
Natural Melanin-Based Nanoparticles With Combined Chemo/Photothermal/Photodynamic Effect Induce Immunogenic Cell Death (ICD) on Tumor

Melanin, as a natural product, has been used as an extraordinary ingredient for nanomedicine due to its great biocompatibility and light responsive property. In this study, polydopamine (PDA), an analog of melanin, was extracted from dopamine and encapsulated with doxorubicin (DOX). The as-prepared nanoparticles (NPs) with good stability, great biosafety and high near infrared (NIR) responsive property ameliorated the cell uptake of DOX in OS-RC-2/ADR cells, exhibited synergistic chemo/photothermal (PTT)/photodynamic (PDT) effects, induced the release of damage associated molecular patterns (DAMPs), and finally, led to immunogenic cell death (ICD). In general, it was suggested that PDA-DOX NPs with NIR irradiation could serve as a promising agent for tumor therapy.
The Relationship Between Selected Load-Velocity Profile Parameters and 50 m Front Crawl Swimming Performance

The purpose of the present study was to establish relationships between sprint front crawl performance and a swimming load-velocity profile. Fourteen male national-level swimmers performed 50 m front crawl and semi-tethered swimming with three progressive loads. The 50 m performance was recorded with a multi-camera system, with which two-dimensional head displacement and the beginning of each arm-stroke motion were quantified. Forward velocity (V50m), stroke length (SL) and frequency (SF) were quantified for each cycle, and the mean value of all cycles, excluding the first and last cycles, was used for the analysis. From the semi-tethered swimming test, the mean velocity during three stroke cycles in mid-pool was calculated and plotted as a function of the external load, and a linear regression line expressing the relationship between the load and velocity was established for each swimmer. The intercepts between the established line and the axes of the plot were defined as theoretical maximum velocity (V0) and load (L0). Large to very large correlations were observed between V50m and all variables derived from the load-velocity profiling; L0 (R = 0.632, p = 0.015), L0 normalized by body mass (R = 0.743, p = 0.002), V0 (R = 0.698, p = 0.006), and the slope (R = 0.541, p < 0.046). No significant relationships of SL and SL with V50m and the load-velocity variables were observed, suggesting that each swimmer has his own strategy to achieve the highest swimming velocity. The findings suggest that load-velocity profiling can be used to assess swimming-specific strength and velocity capabilities related to sprint front crawl performance.
Treatment of in vitro-Matured Bovine Oocytes With Tauroursodeoxycholic Acid Modulates the Oxidative Stress Signaling Pathway

In several species, oocyte and embryo competence are improved by the addition of endoplasmic reticulum (ER) stress inhibitors to in vitro maturation (IVM) medium and/or in vitro culture (IVC) medium. This study aimed to evaluate the effects of three concentrations of tauroursodeoxycholic acid (TUDCA; 50, 200, and 1,000 μM), a chemical chaperone for relieving ER stress, during IVM of bovine cumulus–oocyte complexes (COCs) for 24 h. Treated oocytes were analyzed for nuclear maturation, reactive oxygen species (ROS) production, mitochondrial activity, and abundance of target transcripts. In addition, the number of pronuclei in oocytes was evaluated after 18–20 h of insemination, and the rates of blastocyst and hatched blastocyst formation were evaluated after 7 and 8/9 days of culture, respectively. We further evaluated the transcript abundance of embryonic quality markers. Our findings showed that supplementation of IVM medium with 200 μM of TUDCA decreased ROS production and increased abundance of transcripts related to antioxidant activity in oocytes (CAT, GPX1, and HMOX1) and embryos (GPX1 and PRDX3). Interestingly, high concentration of TUDCA (1,000 μM) was toxic to oocytes, reducing the nuclear maturation rate, decreasing mitochondrial activity, and increasing the abundance of ER stress (HSPA5) and cellular apoptosis (CASP3 and CD40) related transcripts. The results of this study suggest that treatment with 200 μM of TUDCA is associated with a greater resistance to oxidative stress and indirectly with ER stress relief in bovine oocytes.
The Pathology of Morphine-Inhibited Nerve Repair and Morphine-Induced Nerve Damage Is Mediated via Endoplasmic Reticulum Stress

Objective The aim of the present study was to observe the pathological damage in the cerebral cortex of rats under acute morphine exposure (AME) and different durations of morphine dependence (MD), explore whether endoplasmic reticulum stress (ERS) is involved in the damage process, and assess the effect of morphine exposure on the proliferation and differentiation of newborn neurons. Methods Rat models of AME and different durations of MD were established. Pathological changes in cortical neurons were assessed by hematoxylin and eosin (H&E) and thionine staining. The expression of nuclear receptor-related factor 1 (NURR1) and that of the ERS-related proteins glucose-regulated protein 78 (GRP78), p-eIF2α, activating transcription factor 6 (ATF6), and CHOP in cortical neurons was assessed by immunohistochemistry. Double immunofluorescence labeling was used to observe the expression of Ki-67. Results H&E and thionine staining revealed that AME resulted in pyknotic changes in cortical neurons. With prolonged morphine exposure, the number of pyknotic neurons was significantly increased, the protein expression of Ki-67 and NURR1 was significantly decreased, and the protein levels of GRP78, p-eIF2α, ATF6, and CHOP showed marked dynamic changes. Conclusion AME and different durations of MD caused varying degrees of pathological changes in the cortex. Furthermore, the dynamic changes observed in ERS-related protein expression suggested that ERS may be associated with cortical injury. Different durations of MD inhibited the proliferation, differentiation, and migration of newborn neurons, which may affect the nerve repair process after injury.
Deacetylation of HSC70-4 Promotes Bombyx mori Nucleopolyhedrovirus Proliferation via Proteasome-Mediated Nuclear Import

Silkworm (Bombyx mori) is a model organism with great agricultural economic value that plays a crucial role in biological studies. B. mori nucleopolyhedrovirus (BmNPV) is a major viral pathogen found in silkworms, which leads to huge silk loss annually. In a recent lysine acetylome of silkworm infected with BmNPV, we focused on the heat shock cognate protein 70-4 (HSC70-4) lysine acetylation change due to the consequent nuclear accumulation and viral structure assembly. In this study, the genome replication, proliferation, and production of budded viruses (BVs) were arrested by HSP/HSC70 inhibitor treatment. However, HSC70-4 overexpression enhanced BmNPV reproduction. Furthermore, site-direct mutagenesis for acetylated mimic (K/Q) or deacetylated mimic (K/R) mutants of HSC70-4 demonstrated that lysine 77 (K77) deacetylation promotes HSC70-4 stability, viral DNA duplication, and HSC70-4 nuclear entry upon BmNPV challenge, and the nuclear propulsion of HSC70-4 after viral stimulus might be dependent on the interaction with the carboxyl terminus of HSC70-interacting protein (CHIP, an E3 ubiquitin ligase), followed by ubiquitin-proteasome system assistance. In this study, single lysine 77 deacetylation of HSC70-4 was deemed a part of the locomotive pathway for facilitating BmNPV proliferation and provided novel insights into the antiviral strategic development.
The Circulation of Ancient Animal Resources Across the Yellow River Basin: A Preliminary Bayesian Re-evaluation of Sr Isotope Data From the Early Neolithic to the Western Zhou Dynasty

Many questions still remain regarding the acquisition and circulation of ancient domesticated animals across the Yellow River Basin, one of the key areas for the development of complex societies in ancient China. Here, we re-evaluate previously published strontium isotope data (87Sr/86Sr, n = 167) from tooth enamel of domesticated animals at 10 archaeological sites in the Yellow River Basin to shed new light on the transition between the Neolithic (7000–5000 BCE) and the Western Zhou Dynasty (1046–771 BCE). The results show that from the Late Neolithic to the Western Zhou Dynasty, some domesticated animals, mostly cattle and sheep, were increasingly sourced from non-local areas. We employed Bayesian methods to define an isoscape of bioavailable Sr for the Yellow River Basin and to show the considerable diversity in the origins of non-local domesticated animals, some of which may have come from locations hundreds of kilometers away from the site as early as the Late Neolithic. The increasingly variable 87Sr/86Sr ratios of domesticated animals from the Neolithic to the Western Zhou Dynasty are consistent with that of associated human remains, and also match the archaeological and zooarchaeological evidence for increased circulation of animal products in the Yellow River Basin. Therefore, we infer that local economies increasingly incorporated non-local animals as part of wider circulation networks that emerged with the development of complex societies since the Late Neolithic.
Vestibular Thresholds: A Review of Advances and Challenges in Clinical Applications

Vestibular disorders pose a substantial burden on the healthcare system due to a high prevalence and the severity of symptoms. Currently, a large portion of patients experiencing vestibular symptoms receive an ambiguous diagnosis or one that is based solely on history, unconfirmed by any objective measures. As patients primarily experience perceptual symptoms (e.g., dizziness), recent studies have investigated the use of vestibular perceptual thresholds, a quantitative measure of vestibular perception, in clinical populations. This review provides an overview of vestibular perceptual thresholds and the current literature assessing use in clinical populations as a potential diagnostic tool. Patients with peripheral and central vestibular pathologies, including bilateral vestibulopathy and vestibular migraine, show characteristic changes in vestibular thresholds. Vestibular perceptual thresholds have also been found to detect subtle, sub-clinical declines in vestibular function in asymptomatic older adults, suggesting a potential use of vestibular thresholds to augment or complement existing diagnostic methods in multiple populations. Vestibular thresholds are a reliable, sensitive, and specific assay of vestibular precision, however, continued research is needed to better understand the possible applications and limitations, especially with regard to the diagnosis of vestibular disorders.
Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System

Polyhydroxyalkanoates (PHAs) are the biopolymer of choice if we look for a substitute of petroleum-based non-biodegradable plastics. Microbial production of PHAs as carbon reserves has been studied for decades and PHAs are gaining attention for a wide range of applications in various fields. Still, their uneconomical production is the major concern largely attributed to high cost of organic substrates for PHA producing heterotrophic bacteria. Therefore, microalgae/cyanobacteria, being photoautotrophic, prove to have an edge over heterotrophic bacteria. They have minimal metabolic requirements, such as inorganic nutrients (CO2, N, P, etc.) and light, and they can survive under adverse environmental conditions. PHA production under photoautotrophic conditions has been reported from cyanobacteria, the only candidate among prokaryotes, and few of the eukaryotic microalgae. However, an efficient cultivation system is still required for photoautotrophic PHA production to overcome the limitations associated with (1) stringent management of closed photobioreactors and (2) optimization of monoculture in open pond culture. Thus, a hybrid system is a necessity, involving the participation of microalgae/cyanobacteria and bacteria, i.e., both photoautotrophic and heterotrophic components having mutual interactive benefits for each other under different cultivation regime, e.g., mixotrophic, successive two modules, consortium based, etc. Along with this, further strategies like optimization of culture conditions (N, P, light exposure, CO2 dynamics, etc.), bioengineering, efficient downstream processes, and the application of mathematical/network modeling of metabolic pathways to improve PHA production are the key areas discussed here. Conclusively, this review aims to critically analyze cyanobacteria as PHA producers and proposes economically sustainable production of PHA from microbial autotrophs and heterotrophs in “hybrid biological system. ”