Miracle-dz/UniFAR-FTUs huggingface dataset:
Phototheranostics Using Erythrocyte-Based Particles

There has been a recent increase in the development of delivery systems based on red blood cells (RBCs) for light-mediated imaging and therapeutic applications. These constructs are able to take advantage of the immune evasion properties of the RBC, while the addition of an optical cargo allows the particles to be activated by light for a number of promising applications. Here, we review some of the common fabrication methods to engineer these constructs. We also present some of the current light-based applications with potential for clinical translation, and offer some insight into future directions in this exciting field.
Exploration of Alternative Splicing Events in Mesenchymal Stem Cells from Human Induced Pluripotent Stem Cells

Although comparative genome-wide transcriptomic analysis has provided insight into the biology of human induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs), the distinct alternative splicing (AS) signatures of iMSCs remain elusive. Here, we performed Illumina RNA sequencing analysis to characterize AS events in iMSCs compared with tissue-derived MSCs. A total of 4586 differentially expressed genes (|FC| > 2) were identified between iMSCs and umbilical cord blood-derived MSCs (UCB-MSCs), including 2169 upregulated and 2417 downregulated genes. Of these, 164 differentially spliced events (BF > 20) in 112 genes were identified between iMSCs and UCB-MSCs. The predominant type of AS found in iMSCs was skipped exons (43.3%), followed by retained introns (19.5%), alternative 3′ (15.2%) and 5′ (12.8%) splice sites, and mutually exclusive exons (9.1%). Functional enrichment analysis showed that the differentially spliced genes (|FC| > 2 and BF > 20) were mainly enriched in functions associated with focal adhesion, extracellular exosomes, extracellular matrix organization, cell adhesion, and actin binding. Splice isoforms of selected genes including TRPT1, CNN2, and AP1G2, identified in sashimi plots, were further validated by RT-PCR analysis. This study provides valuable insight into the biology of iMSCs and the translation of mechanistic understanding of iMSCs into therapeutic applications.
A Study of Older Adults’ Mental Health across 33 Countries during the COVID-19 Pandemic

Despite older adults’ extremely high vulnerability to COVID-19 complications and death, few studies have examined how personal characteristics and the COVID-19 pandemic have impacted the mental health of older adults at the global level. The purpose of this study was to examine the relationships among demographics, COVID-19 life impacts, and depression and anxiety in adults aged 60 and older from 33 countries. A sample of 823 older adults aged 60–94 and residing in 33 countries completed a 10-min online survey following recruitment from mailing lists and social media. Being separated from and having conflicts with loved ones predicted both anxiety and depression, as did residing in a country with higher income. Getting medical treatment for severe symptoms of COVID-19 and having decreased work responsibilities predicted depression, but adjustment to working from home and younger age predicted both depression and anxiety. Participants from Europe and Central Asia reported higher depression than those from all other regions and higher anxiety than those from Latin America and the Caribbean. The COVID-19 pandemic has had serious deleterious effects on the mental health of older adults worldwide. The current findings have direct implications for mental health services that may be delivered to older adults to help facilitate healthy psychological adjustment.
Genetic Variants of Alcohol Metabolizing Enzymes and Alcohol-Related Liver Cirrhosis Risk

Alcohol-related liver disease (ARLD) is a major public health issue caused by excessive alcohol consumption. ARLD encompasses a wide range of chronic liver lesions, alcohol-related liver cirrhosis being the most severe and harmful state. Variations in the genes encoding the enzymes, which play an active role in ethanol metabolism, might influence alcohol exposure and hence be considered as risk factors of developing cirrhosis. We conducted a case-control study in which 164 alcohol-related liver cirrhosis patients and 272 healthy controls were genotyped for the following functional single nucleotide variations (SNVs): ADH1B gene, rs1229984, rs1041969, rs6413413, and rs2066702; ADH1C gene, rs35385902, rs283413, rs34195308, rs1693482, and rs35719513; CYP2E1 gene, rs3813867. Furthermore, copy number variations (CNVs) for ADH1A, ADH1B, ADH1C, and CYP2E1 genes were analyzed. A significant protective association with the risk of developing alcohol-related liver cirrhosis was observed between the mutant alleles of SNVs ADH1B rs1229984 (Pc value = 0.037) and ADH1C rs283413 (Pc value = 0.037). We identified CNVs in all genes studied, ADH1A gene deletions being more common in alcohol-related liver cirrhosis patients than in control subjects, although the association lost statistical significance after multivariate analyses. Our findings support that susceptibility to alcohol-related liver cirrhosis is related to variations in alcohol metabolism genes.
Diverse Immunological Factors Influencing Pathogenesis in Patients with COVID-19: A Review on Viral Dissemination, Immunotherapeutic Options to Counter Cytokine Storm and Inflammatory Responses

The pathogenesis of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still not fully unraveled. Though preventive vaccines and treatment methods are out on the market, a specific cure for the disease has not been discovered. Recent investigations and research studies primarily focus on the immunopathology of the disease. A healthy immune system responds immediately after viral entry, causing immediate viral annihilation and recovery. However, an impaired immune system causes extensive systemic damage due to an unregulated immune response characterized by the hypersecretion of chemokines and cytokines. The elevated levels of cytokine or hypercytokinemia leads to acute respiratory distress syndrome (ARDS) along with multiple organ damage. Moreover, the immune response against SARS-CoV-2 has been linked with race, gender, and age; hence, this viral infection’s outcome differs among the patients. Many therapeutic strategies focusing on immunomodulation have been tested out to assuage the cytokine storm in patients with severe COVID-19. A thorough understanding of the diverse signaling pathways triggered by the SARS-CoV-2 virus is essential before contemplating relief measures. This present review explains the interrelationships of hyperinflammatory response or cytokine storm with organ damage and the disease severity. Furthermore, we have thrown light on the diverse mechanisms and risk factors that influence pathogenesis and the molecular pathways that lead to severe SARS-CoV-2 infection and multiple organ damage. Recognition of altered pathways of a dysregulated immune system can be a loophole to identify potential target markers. Identifying biomarkers in the dysregulated pathway can aid in better clinical management for patients with severe COVID-19 disease. A special focus has also been given to potent inhibitors of proinflammatory cytokines, immunomodulatory and immunotherapeutic options to ameliorate cytokine storm and inflammatory responses in patients affected with COVID-19.
Bodyweight Measures and Lifestyle Habits in Individuals with Multiple Sclerosis and Moderate to Severe Disability

Multiple sclerosis (MS) is a chronic disease marked by progressive disability and decreased mobility over time. We studied whether individuals with MS of higher disability levels will be more overweight/obese as a result of their immobility and/or recurrent steroid treatments. In a prospective study, 130 individuals with MS and significant disability were classified according to the Expanded Disability Status Scale (EDSS) score as belonging to four groups: EDSS 3.0–4.0 (n = 31, 24%), EDSS 4.5–5.5 (n = 24, 18%), EDSS = 6.0 (n = 44, 34%) and EDSS ≥ 6.5 (n = 31, 24%). Medical history, body mass index (BMI), waist circumference and the level of engagement in physical activity were obtained. The mean ± standard error age was 55.8 ± 0.5 years, disease duration 18.2 ± 1.0 years and EDSS score 5.5 ± 0.1. Disease duration, the number of steroid courses per disease duration, weight, BMI and physical activity did not differ according to the four disability groups. The mean waist circumference increased significantly with increased severity of EDSS, p = 0.03. Increased disability in individuals with MS was not correlated with disease duration, lifestyle habits or overweight/obesity. However, increased disability was associated with central obesity.
Reactive and Proactive Adaptation of Cognitive and Motor Neural Signals during Performance of a Stop-Change Task

The ability to inhibit or suppress unwanted or inappropriate actions, is an essential component of executive function and cognitive health. The immense selective pressure placed on maintaining inhibitory control processes is exemplified by the relatively small number of instances in which these systems completely fail in the average person’s daily life. Although mistakes and errors do inevitably occur, inhibitory control systems not only ensure that this number is low, but have also adapted behavioral strategies to minimize future failures. The ability of our brains to adapt our behavior and appropriately engage proper motor responses is traditionally depicted as the primary domain of frontal brain areas, despite evidence to the fact that numerous other brain areas contribute. Using the stop-signal task as a common ground for comparison, we review a large body of literature investigating inhibitory control processes across frontal, temporal, and midbrain structures, focusing on our recent work in rodents, in an effort to understand how the brain biases action selection and adapts to the experience of conflict.
Bowel Wall Thickening on Computed Tomography in Children: A Novel Method of Measurement and Its Clinical Significance

Purpose The clinical implications of bowel wall thickening (BWT) on abdominal computed tomography (CT) among children are unknown. We aimed to suggest a new method for measuring BWT and determining its clinical significance in children. Methods We retrospectively analyzed 423 patients with acute abdomen who underwent abdominal CT; 262 were classified into the BWT group. For this group, the pediatric radiologist described the maximal bowel wall thickness (MT), normal bowel wall thickness (mm) (NT), and their ratios for each segment of the bowel wall. Results In the thickened bowel walls, the thickness differed significantly between the small bowel (6.83±2.14 mm; mean±standard deviation) and the colon (8.56±3.46 mm; p<0.001). The ratios of MT to NT in the small bowel (6.09±3.17) and the colon (7.58±3.70) were also significantly different (p<0.001). In the BWT group, 35 of 53 patients had positive fecal polymerase chain reaction results; 6 patients infected with viruses predominantly had BWT in the small intestine, while the terminal ileum and the colon were predominantly affected in 29 patients with bacterial infections. In the initially undiagnosed 158 patients with BWT, the symptoms improved spontaneously without progression to chronic gastrointestinal disease. Conclusion This study provides a clinical reference value for BWT in the small intestine and colon using a new method in children. The BWT on abdominal CT in children might indicate nonspecific findings that can be observed and followed up without additional evaluation, unlike in adults.
Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination

Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in AtENO2 mutation (eno2−) was earlier than that of wild type (WT) in Arabidopsis thaliana. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including ARF family, TIR1, INVC, RR19, TUDOR2, GA3OX2, PXMT1, and TGA1. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the AtENO2 regulation for seed germination.
Antibiotic Resistance and Virulence Gene Patterns Associated with Avian Pathogenic Escherichia coli (APEC) from Broiler Chickens in Qatar

Avian Pathogenic Escherichia coli (APEC) is the contributing agent behind the avian infectious disease colibacillosis, which causes substantial fatalities in poultry industries that has a significant impact on the economy and food safety. Several virulence genes have been shown to be concomitant with the extraintestinal survival of APEC. This study investigates the antibiotic resistance patterns and APEC-associated virulence genes content in Escherichia coli isolated from non-healthy and healthy broiler chickens from a commercial poultry farm in Qatar. A total of 158 E. coli strains were isolated from 47 chickens from five different organs (air sac, cloacal, kidney, liver, and trachea). Based on genetic criteria, 65% were APEC strains containing five or more virulence genes, and 34% were non-pathogenic E. coli (NPEC) strains. The genes ompT, hlyF, iroN, tsh, vat, iss, cvi/cva, and iucD were significantly prevalent in all APEC strains. E. coli isolates showed 96% resistance to at least one of the 18 antibiotics, with high resistance to ampicillin, cephalothin, ciprofloxacin, tetracycline, and fosfomycin. Our findings indicate high antibiotic resistance prevalence in non-healthy and healthy chicken carcasses. Such resistant E. coli can spread to humans. Hence, special programs are required to monitor the use of antibiotics in chicken production in Qatar.
Resource Misallocation and Energy-Related Pollution

Developing countries face the conflict between economic development and environmental protection. Resource misallocation will not only affect the effectiveness of economic development, but also have environmental impacts. Based on two large-scale enterprise databases in China, this paper measured the level of enterprise resource allocation, and further used empirical research methods to investigate the environmental impact of enterprise resource misallocation and specific mechanisms. The results show that the low efficiency of resource allocation will harm the quality of China’s environment. Further investigation, resource misallocation is accompanied by an increase in total energy input, a decrease in the labor-to-energy ratio and the capital-to-energy ratio, and a loss of energy efficiency, which in turn affects the environmental performance of enterprises. China is the largest developing country in the world, and research on China’s environmental and economic issues is important. The conclusions of this paper can provide experience and suggestions for other developing countries to improve environmental quality and promote sustainable development from the perspective of resource misallocation.
The Power of Stress: The Telo-Hormesis Hypothesis

Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.
Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning

Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person’s variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.
On the Thermal Models for Resistive Random Access Memory Circuit Simulation

Resistive Random Access Memories (RRAMs) are based on resistive switching (RS) operation and exhibit a set of technological features that make them ideal candidates for applications related to non-volatile memories, neuromorphic computing and hardware cryptography. For the full industrial development of these devices different simulation tools and compact models are needed in order to allow computer-aided design, both at the device and circuit levels. Most of the different RRAM models presented so far in the literature deal with temperature effects since the physical mechanisms behind RS are thermally activated; therefore, an exhaustive description of these effects is essential. As far as we know, no revision papers on thermal models have been published yet; and that is why we deal with this issue here. Using the heat equation as the starting point, we describe the details of its numerical solution for a conventional RRAM structure and, later on, present models of different complexity to integrate thermal effects in complete compact models that account for the kinetics of the chemical reactions behind resistive switching and the current calculation. In particular, we have accounted for different conductive filament geometries, operation regimes, filament lateral heat losses, the use of several temperatures to characterize each conductive filament, among other issues. A 3D numerical solution of the heat equation within a complete RRAM simulator was also taken into account. A general memristor model is also formulated accounting for temperature as one of the state variables to describe electron device operation. In addition, to widen the view from different perspectives, we deal with a thermal model contextualized within the quantum point contact formalism. In this manner, the temperature can be accounted for the description of quantum effects in the RRAM charge transport mechanisms. Finally, the thermometry of conducting filaments and the corresponding models considering different dielectric materials are tackled in depth.
Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs

Simple Summary The cloacal anatomy is unique because the fecal, urinary, and reproductive tracts converge into one orifice. Therefore, sampling for microbiome research can be difficult in birds, especially in agricultural production settings where it may not be feasible to sample the intestines, and cloacal swabs are often used. There is a need to evaluate laboratory methods for 16S rRNA sequencing in cloacal swab samples to ensure reproducible and trustworthy downstream results. We compared four DNA extraction methods from two commercially available magnetic-based DNA extraction kits. Mock communities and negative controls were included for each method and subjected to 16S rRNA sequencing. While extraction quality and yield differed between each extraction method, overall sequencing results were not affected, including alpha and beta diversity. Positive and negative controls are an important aspect of microbiome science and our findings lend guidance to future microbiome research in poultry. Abstract As the applications of microbiome science in agriculture expand, laboratory methods should be constantly evaluated to ensure optimization and reliability of downstream results. Most animal microbiome research uses fecal samples or rectal swabs for profiling the gut bacterial community; however, in birds, this is difficult given the unique anatomy of the cloaca where the fecal, urinary, and reproductive tracts converge into one orifice. Therefore, avian gut microbiomes are usually sampled from cloacal swabs, creating a need to evaluate sample preparation methods to optimize 16S sequencing. We compared four different DNA extraction methods from two commercially available kits on cloacal swabs from 10 adult commercial laying hens and included mock communities and negative controls, which were then subjected to 16S rRNA amplicon sequencing. Extracted DNA yield and quality, diversity analyses, and contaminants were assessed. Differences in DNA quality and quantity were observed, and all methods needed further purification for optimal sequencing, suggesting contaminants due to cloacal contents, method reagents, and/or environmental factors. However, no differences were observed in alpha or beta diversity between methods. Importantly, multiple bacterial contaminants were detected in each mock community and negative control, indicating the prevalence of laboratory and handling contamination as well as method-specific reagent contamination. We found that although the extraction methods resulted in different extraction quality and yield, overall sequencing results were not affected, and we did not identify any method that would be an inappropriate choice in extracting DNA from cloacal swabs for 16S rRNA sequencing. Overall, our results highlight the need for careful consideration of positive and negative controls in addition to DNA isolation method and lend guidance to future microbiome research in poultry.