Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Systems Biology of Alfalfa – Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop

Medicago sativa (also known as alfalfa), a forage legume, is widely cultivated due to its high yield and high-value hay crop production. Infectious diseases are a major threat to the crops, owing to huge economic losses to the agriculture industry, worldwide. The protein-protein interactions (PPIs) between the pathogens and their hosts play a critical role in understanding the molecular basis of pathogenesis. Pseudomonas syringae pv. syringae ALF3 suppresses the plant’s innate immune response by secreting type III effector proteins into the host cell, causing bacterial stem blight in alfalfa. The alfalfa-P. syringae system has little information available for PPIs. Thus, to understand the infection mechanism, we elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two computational approaches: interolog-based and domain-based method. A total of ∼14 M putative PPIs were predicted between 50,629 alfalfa proteins and 2,932 P. syringae proteins by combining these approaches. Additionally, ∼0.7 M consensus PPIs were also predicted. The functional analysis revealed that P. syringae proteins are highly involved in nucleotide binding activity (GO:0000166), intracellular organelle (GO:0043229), and translation (GO:0006412) while alfalfa proteins are involved in cellular response to chemical stimulus (GO:0070887), oxidoreductase activity (GO:0016614), and Golgi apparatus (GO:0005794). According to subcellular localization predictions, most of the pathogen proteins targeted host proteins within the cytoplasm and nucleus. In addition, we discovered a slew of new virulence effectors in the predicted HPIs. The current research describes an integrated approach for deciphering genome-scale host-pathogen PPIs between alfalfa and P. syringae, allowing the researchers to better understand the pathogen’s infection mechanism and develop pathogen-resistant lines.
Chemical Composition of Fresh Leaves Headspace Aroma and Essential Oils of Four Coriander Cultivars

Aroma is one of the key food characteristics determining consumers’ perception and acceptability of products. Coriandrum sativum L. is an aromatic herb commonly used as a food additive and taste enhancer. Besides the culinary applications, coriander is also used in traditional medicine, cosmetics, and the food industry. In this study, we aimed to determine aroma composition of fresh chopped leaves and essential oils extracted from the leaves of four coriander cultivars. The essential oils were extracted from the fresh leaves using steam distillation and volatile aroma components were collected from the headspace by solid phase micro extraction technique. Analyses were carried out by gas chromatography-mass spectrometry. Free radical scavenging activity of essential oils was determined by using 2,2-diphenyl-1-picrylhydrazyl assay. The essential oils were also investigated for their anti-microbial potential. The aroma of freshly chopped coriander leaves was characterized by thirteen compounds, including six aldehydes, four alcohols, one ester and one hydrocarbon. The essential oils were comprised of twenty-seven compounds, where (E)-2-decenal, decanal, (E)-2-dodecenal and (E)-2-tetradecenal were the main components in all cultivars. Free radical scavenging activity of the essential oil samples was in the range of 6–15%. The essential oils of Desi and Hybrid cultivars exhibited least minimum inhibitory concentration (MIC) against all tested bacterial strains. Fresh green leaves of the Desi and Peshawari cultivars were found to be the richest in six carbon chain length alcohols and acetates, which are important constituents of the aroma giving a characteristic odor referred to as the “green note. ” The Hybrid cultivar showed the highest free radical scavenging activity, bearing the highest amount of antioxidants. The study revealed that the fresh leaves HS aroma of Desi and Hybrid cultivars were different, however, their essential oils possessed almost similar chemistry and anti-bacterial activity.
Good Performance of the Chinese Version of Mini Social Cognition and Emotional Assessment in the Early Diagnosis of Behavioral Variant Frontotemporal Dementia

Social cognition impairment has been recognized as an early and characteristic change in behavioral variant frontotemporal dementia (bvFTD). The Mini Social Cognition and Emotional Assessment (mini-SEA) is a clinical tool to rapidly evaluate social cognition. In this study, we explored the diagnostic value of social cognition by assessing the Chinese version of the mini-SEA and other standard neuropsychological tests in 22 patients with mild bvFTD, 26 patients with mild Alzheimer's disease (AD), including mild cognitive impairment (MCI) and mild dementia, and 30 control subjects. The discriminatory powers of these tests were evaluated and compared using the receiver operating characteristic curve (ROC). The mini-SEA scores of the bvFTD patients were significantly lower than those of the controls (Z = –6.850, adjusted P < 0.001) and AD patients (Z = –3.737, adjusted P = 0.001). ROC analysis showed that the mini-SEA had a high discriminatory power for differentiating bvFTD from the controls, with an area under the curve (AUC) value of 0.989 (95% CI = 0.905-1.000, P < 0.001). The AUC value of the mini-SEA for differentiating bvFTD from AD was 0.899 (95% CI = 0.777-0.967, P < 0.001), higher than that of the Auditory Verbal Learning Test Delayed Recall (AUC = 0.793), Boston Naming Test (AUC = 0.685) or Frontal Assessment Battery (AUC = 0.691). The Chinese version of mini-SEA is a good clinical tool for the early diagnosis of bvFTD, and has a high sensitivity and specificity to discriminate bvFTD from AD.
Fecal Microbiota Transplantation (FMT) as an Adjunctive Therapy for Depression—Case Report

Depression is a debilitating disorder, and at least one third of patients do not respond to therapy. Associations between gut microbiota and depression have been observed in recent years, opening novel treatment avenues. Here, we present the first two patients with major depressive disorder ever treated with fecal microbiota transplantation as add-on therapy. Both improved their depressive symptoms 4 weeks after the transplantation. Effects lasted up to 8 weeks in one patient. Gastrointestinal symptoms, constipation in particular, were reflected in microbiome changes and improved in one patient. This report suggests further FMT studies in depression could be worth pursuing and adds to awareness as well as safety assurance, both crucial in determining the potential of FMT in depression treatment.
Interactive Modeling and Visualization of Virtual Urban Spaces

In this overview paper the main techniques used in procedural modelling of architecture (buildings, facades) are described. This is a relat ively new and wide interdisciplinary field, which is growing very quickly, mainly in the last t en years. We discuss important publications focused on procedural techniques like L systems or shape grammars and their usability in procedural architecture creation. Then, we introduc e essential articles on procedural modelling of cities and we also include ideas from papers specialized in generation of buildings, facades, architectural structures and re lated city components. Finally, we focus on interesting computer vision techniques in architect ure reconstruction and their connection to formal languages. Our aim is to demonstrate that th e procedural city modelling needs to integrate specially modified computer vision algori thms in order to achieve a higher degree of realism and a wider acceptance in various profes sional application areas.
Mathematical Model of Ultrasound Attenuation With Skull Thickness for Transcranial-Focused Ultrasound

Transcranial-focused ultrasound (tFUS) has potential for both neuromodulation and neuroimaging. Due to the influence of head tissue, especially the skull, its attenuation is a key issue affecting precise focusing. The objective of the present study was to construct a mathematical model of ultrasound attenuation inclusive of skull thickness. First, combined with real skull phantom experiments and simulation experiments, tFUS attenuation of different head tissues was investigated. Furthermore, based on the system identification method, a mathematical model of ultrasound attenuation was constructed taking skull thickness into account. Finally, the performance of the mathematical model was tested, and its potential applications were investigated. For different head tissues, including scalp, skull, and brain tissue, the skull was found to be the biggest influencing factor for ultrasound attenuation, the attenuation caused by it being 4.70 times and 7.06 times that of attenuation caused by the brain and scalp, respectively. Consistent with the results of both the simulation and phantom experiments, the attenuation of the mathematical model increased as the skull thickness increased. The average error of the mathematical model was 1.87% in the phantom experiment. In addition, the experimental results show that the devised mathematical model is suitable for different initial pressures and different skulls with correlation coefficients higher than 0.99. Both simulation and phantom experiments validated the effectiveness of the proposed mathematical model. It can be concluded from this experiment that the proposed mathematical model can accurately calculate the tFUS attenuation and can significantly contribute to further research and application of tFUS.
Maternal Pre-pregnancy Body Mass Index Categories and Infant Birth Outcomes: A Population-Based Study of 9 Million Mother–Infant Pairs

Background and Aims Infant adverse birth outcomes have been suggested to contribute to neonatal morbidity and mortality and may cause long-term health consequences. Although evidence suggests maternal prepregnancy body mass index (BMI) categories associate with some birth outcomes, there is no consensus on these associations. We aimed to examine the associations of maternal prepregnancy BMI categories with a wide range of adverse birth outcomes. Methods Data were from a population-based retrospective cohort study of 9,282,486 eligible mother–infant pairs in the U.S. between 2016 and 2018. Maternal prepregnancy BMI was classified as: underweight (<18.5 kg/m2); normal weight (18.5–24.9 kg/m2); overweight (25.0–29.9 kg/m2); obesity grade 1 (30–34.9 kg/m2); obesity grade 2 (35.0–39.9 kg/m2); and obesity grade 3 (≥40 kg/m2). A total of six birth outcomes of the newborn included preterm birth, low birthweight, macrosomia, small for gestational age (SGA), large for gestational age (LGA), and low Apgar score (5-min score <7). Results Maternal prepregnancy overweight and obesity increased the likelihood of infant preterm birth, with odds ratios (ORs) (95% CIs) of 1.04 (1.04–1.05) for overweight, 1.18 (1.17–1.19) for obesity grade 1, 1.31 (1.29–1.32) for obesity grade 2, and 1.47 (1.45–1.48) for obesity grade 3, and also for prepregnancy underweight (OR = 1.32, 95% CI = 1.30–1.34) after adjusting for all potential covariates. Prepregnancy overweight and obesity were associated with higher odds of macrosomia, with ORs (95% CIs) of 1.53 (1.52–1.54) for overweight, 1.92 (1.90–1.93) for obesity grade 1, 2.33 (2.31–2.35) for obesity grade 2, and 2.87 (2.84–2.90) for obesity grade 3. Prepregnancy overweight and obesity was associated with higher odds of LGA, with ORs (95% CIs) of 1.58 (1.57–1.59) for overweight, 2.05 (2.03–2.06) for obesity grade 1, 2.54 (2.52–2.56) for obesity grade 2, and 3.17 (3.14–3.21) for obesity grade 3. Prepregnancy overweight and obesity were also associated with higher odds of low Apgar score, with ORs (95% CIs) of 1.12 (1.11–1.14) for overweight, 1.21 (1.19–1.23) for obesity grade 1, 1.34 (1.31–1.36) for obesity grade 2, and 1.55 (1.51–1.58) for obesity grade 3. Conclusion Our findings suggest maintaining or obtaining a healthy body weight for prepregnancy women could substantially reduce the likelihood of important infant adverse birth outcomes.
ACE and ACE2 Gene Variants Are Associated With Severe Outcomes of COVID-19 in Men

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, affecting more than 219 countries and causing the death of more than 5 million people worldwide. The genetic background represents a factor that predisposes the way the host responds to SARS-CoV-2 infection. In this sense, genetic variants of ACE and ACE2 could explain the observed interindividual variability to COVID-19 outcomes. In order to improve the understanding of how genetic variants of ACE and ACE2 are involved in the severity of COVID-19, we included a total of 481 individuals who showed clinical manifestations of COVID-19 and were diagnosed by reverse transcription PCR (RT-PCR). Genomic DNA was extracted from peripheral blood and saliva samples. ACE insertion/deletion polymorphism was evaluated by the high-resolution melting method; ACE single-nucleotide polymorphism (SNP) (rs4344) and ACE2 SNPs (rs2285666 and rs2074192) were genotyped using TaqMan probes. We assessed the association of ACE and ACE2 polymorphisms with disease severity using logistic regression analysis adjusted by age, sex, hypertension, type 2 diabetes, and obesity. The severity of the illness in our study population was divided as 31% mild, 26% severe, and 43% critical illness; additionally, 18% of individuals died, of whom 54% were male. Our results showed in the codominant model a contribution of ACE2 gene rs2285666 T/T genotype to critical outcome [odds ratio (OR) = 1.83; 95%CI = 1.01–3.29; p = 0.04] and to require oxygen supplementation (OR = 1.76; 95%CI = 1.01–3.04; p = 0.04), in addition to a strong association of the T allele of this variant to develop critical illness in male individuals (OR = 1.81; 95%CI = 1.10–2.98; p = 0.02). We suggest that the T allele of rs2285666 represents a risk factor for severe and critical outcomes of COVID-19, especially for men, regardless of age, hypertension, obesity, and type 2 diabetes.
Chinese Versus United States Workplace Ageism as GATE-ism: Generation, Age, Tenure, Experience

Ageism is a pan-cultural problem, and correspondingly, increased research attention worldwide has focused on how a person’s age drives prejudice against them. Nevertheless, recent work argues that chronological age alone is a limited predictor of prejudice—particularly in the workplace, where age conflates intertwined elements (e.g., life stage and work experience), and across cultures, in which the nature of ageism can substantially differ. A recent organizational behavior (GATE) framework advocates for extending beyond numerical age alone, focusing instead on prejudice arising from workers’ perceived Generation (birth cohort), Age (life stage), Tenure (time with organization), and Experience (accumulated skillset over time). In addition to clarifying the multifaceted nature of workplace ageism, GATE helps uncover potential cultural ageism differences. Using the United States and China as focal Western and Eastern prototypes, the current paper compares Eastern and Western cultures through a GATE Lens. Eastern and Western cultures adopt different perceptions of generations (e.g., United States “Boomers,” versus Chinese “Cultural Revolution” generation), elder life stages (United States warm-but-incompetent older adults, versus Eastern pragmatic elder resource concerns), organizational tenure expectations (Western job-hopping, versus Eastern filial-piety-based loyalty), and desired experience levels (shaped different by higher Eastern frequency of mandatory retirement practices and family business ventures). Moreover, existing research offers clues for how workplace GATE-ism likely differs between cultures, but more research is needed. Future research should adopt a nuanced GATE conception of “age”-ism, toward enhanced ageism understanding and the ability to utilize a globally aging workforce.
Determinants and Variations of COVID-19 Vaccine Uptake and Responses Among Minority Ethnic Groups in Amsterdam, the Netherlands

The outbreak of the deadly novel coronavirus disease (COVID-19) has disrupted life worldwide in an unprecedented manner. Over the period, scientific breakthroughs have resulted in the rollout of many vaccination programmes to protect against the disease, reduce the fear and ease public health restrictions for lives to return to some normalcy. The aim of this study was to identify the factors responsible for COVID-19 vaccine acceptance or vaccine hesitancy and to develop a framework to improve vaccine uptake in the Ghanaian-Dutch, Afro and Hindustani Surinamese-Dutch communities in Amsterdam. Using a mixed method approach, this community-based cross-sectional survey recruited 160 respondents consisting of 57 Ghanaian-Dutch, 54 Afro Surinamese-Dutch and 49 Hindustani-Dutch residents in Amsterdam. Our findings showed that the choice of a vaccine as well as the likelihood of self-reported willingness to receive a vaccine is highly dependent on vaccine efficacy and safety. Available evidence of high vaccine effectiveness and safety could encourage about 41.3% of the respondents to accept the vaccine. Additionally, 69.6% of the respondents indicated their willingness to accept the vaccine when vaccine passports are made mandatory by the government. Other major factors that could drive the likelihood of accepting the COVID-19 vaccine include travel requirement for vaccination (28.3%), the safety/probability of only minor side effects (26.1%) and recommendation by family and friends (15.2%). The study therefore provides systematic evidence of factors associated with individual preferences toward COVID-19 vaccination. It demonstrates that the needs of each community are unique and specific interventional efforts are urgently needed to address concerns likely to be associated with vaccine hesitancy.
Trained Immunity: An Overview and the Impact on COVID-19

Effectively treating infectious diseases often requires a multi-step approach to target different components involved in disease pathogenesis. Similarly, the COVID-19 pandemic has become a global health crisis that requires a comprehensive understanding of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) infection to develop effective therapeutics. One potential strategy to instill greater immune protection against COVID-19 is boosting the innate immune system. This boosting, termed trained immunity, employs immune system modulators to train innate immune cells to produce an enhanced, non-specific immune response upon reactivation following exposure to pathogens, a process that has been studied in the context of in vitro and in vivo clinical studies prior to the COVID-19 pandemic. Evaluation of the underlying pathways that are essential to inducing protective trained immunity will provide insight into identifying potential therapeutic targets that may alleviate the COVID-19 crisis. Here we review multiple immune training agents, including Bacillus Calmette-Guérin (BCG), β-glucan, and lipopolysaccharide (LPS), and the two most popular cell types involved in trained immunity, monocytes and natural killer (NK) cells, and compare the signaling pathways involved in innate immunity. Additionally, we discuss COVID-19 trained immunity clinical trials, emphasizing the potential of trained immunity to fight SARS-CoV-2 infection. Understanding the mechanisms by which training agents activate innate immune cells to reprogram immune responses may prove beneficial in developing preventive and therapeutic targets against COVID-19.
Secreted Autotransporter Toxin (Sat) Mediates Innate Immune System Evasion

Several strategies are used by Escherichia coli to evade the host innate immune system in the blood, such as the cleavage of complement system proteins by secreted proteases. Members of the Serine Proteases Autotransporters of Enterobacteriaceae (SPATE) family have been described as presenting proteolytic effects against complement proteins. Among the SPATE-encoding genes sat (secreted autotransporter toxin) has been detected in high frequencies among strains of E. coli isolated from bacteremia. Sat has been characterized for its cytotoxic action, but the possible immunomodulatory effects of Sat have not been investigated. Therefore, this study aimed to evaluate the proteolytic effects of Sat on complement proteins and the role in pathogenesis of BSI caused by extraintestinal E. coli (ExPEC). E. coli EC071 was selected as a Sat-producing ExPEC strain. Whole-genome sequencing showed that sat sequences of EC071 and uropathogenic E. coli CFT073 present 99% identity. EC071 was shown to be resistant to the bactericidal activity of normal human serum (NHS). Purified native Sat was used in proteolytic assays with proteins of the complement system and, except for C1q, all tested substrates were cleaved by Sat in a dose and time-dependent manner. Moreover, E. coli DH5α survived in NHS pre-incubated with Sat. EC071-derivative strains harboring sat knockout and in trans complementations producing either active or non-active Sat were tested in a murine sepsis model. Lethality was reduced by 50% when mice were inoculated with the sat mutant strain. The complemented strain producing active Sat partially restored the effect caused by the wild-type strain. The results presented in this study show that Sat presents immunomodulatory effects by cleaving several proteins of the three complement system pathways. Therefore, Sat plays an important role in the establishment of bloodstream infections and sepsis.
Experience of Managing Countertransference Through Self-Guided Imagery in Meditation Among Healthcare Professionals

Introduction As a part of the therapeutic relationship, a significant, well-established predictor of outcomes in psychiatric healthcare, healthcare professionals' emotional reactions to patients may affect treatment outcomes. Aim The aim of our study was to explore and describe healthcare professionals' experiences with managing countertransference using skills from a training program on self-guided imagery in meditation (SIM). Method Following an exploratory descriptive design, we conducted qualitative interviews with 10 healthcare professionals who care for patients with mental illness and subjected the collected data to thematic content analysis. Results Participants reported that SIM had helped them to manage countertransference and had prompted changes that we categorized into three themes: managing personal vulnerability, setting clearer boundaries, and practicing self-care. Conclusion The results suggest that by cultivating wellbeing and dealing with unresolved inner conflicts, SIM can help healthcare professionals to manage countertransference.