Miracle-dz/UniFAR-FTUs huggingface dataset:
A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients

COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.
An adaptive compromise - Conflicting evolutionary pressures on arthropod-borne Zika virus dinucleotide composition in mammalian hosts and mosquito vectors

Most vertebrate RNA viruses show pervasive suppression of CpG and UpA dinucleotides, closely resembling the dinucleotide composition of host cell transcriptomes. In contrast, CpG suppression is absent in both invertebrate mRNA and RNA viruses that exclusively infect arthropods. Arthropod-borne (arbo) viruses are transmitted between vertebrate hosts by invertebrate vectors and thus encounter potentially conflicting evolutionary pressures in the different cytoplasmic environments. Using a newly developed Zika virus (ZIKV) model, we have investigated how demands for CpG suppression in vertebrate cells can be reconciled with potentially quite different compositional requirements in invertebrates, and how this affects ZIKV replication and transmission. Mutant viruses with synonymously elevated CpG or UpA dinucleotide frequencies showed attenuated replication in vertebrate cell lines, which was rescued by knockout of the zinc-finger antiviral protein (ZAP). Conversely, in mosquito cells, ZIKV mutants with elevated CpG dinucleotide frequencies showed substantially enhanced replication compared to wildtype. Host-driven effects on virus replication attenuation and enhancement were even more apparent in mouse and mosquito models. Infections with CpG-or UpA-high ZIKV mutants in mice did not cause typical ZIKV-induced tissue damage and completely protected mice during subsequent challenge with wildtype virus, which demonstrates their potential as live-attenuated vaccines. In contrast, the CpG-high mutants displayed enhanced replication in Aedes aegypti mosquitoes and a larger proportion of mosquitoes carried infectious virus in their saliva. These findings show that mosquito cells are also capable of discriminating RNA based on dinucleotide composition. However, the evolutionary pressure on the CpG dinucleotides of viral genomes in arthropod vectors directly opposes the pressure present in vertebrate host cells, which provides evidence that an adaptive compromise is required for arbovirus transmission. This suggests that the genome composition of arthropod-borne flaviviruses is crucial to maintain the balance between high-level replication in the vertebrate host and persistent replication in the mosquito vector.
Initial and final state effects in the ESCA spectra of cadmium and silver oxides

The factors which influence chemical shifts are examined in order to elucidate the cause of the anomalous chemical shifts for Cd and Ag oxides. The effects of extra‐atomic relaxation are accounted for using a procedure employing experimental Auger and binding energies. Atomic partial ionic charges for some simple Cd, Ag, and Zn compounds are calculated from experimental binding energies using a model which includes the effects of lattice potentials and extra‐atomic relaxation. Inclusion of extra‐atomic relaxation effects did not have a drastic effect on the relative ionicities computed for these selected compounds. However, for CdO, a large extra‐atomic relaxation energy contribution reduces the binding energy by 0.5 eV more than is predicted from nearest neighbor electronegativity arguments.
The Role of Root Morphology and Pulling Direction in Pullout Resistance of Alfalfa Roots

There is a growing consensus on soil conservation by mechanics of plant root system. In order to further study how root system exerts its mechanical properties during soil reinforcing process and which morphological indicator is suitable for reflecting pullout resistance, in-situ vertical pullout test (VPT) and 45° oblique pullout test (OPT) were performed on alfalfa (Medicago sativa L.) roots in the loess area. The results showed that the failure mode of alfalfa roots was pulling out in this study. The peak pullout resistance of the roots increased with root diameter, root length and root surface area, and power law relationships were observed between the pullout resistance and the morphological indices: root diameter, root length and root surface area. The maximum gray relational degree of the morphological indices was 0.841 (VPT) and 0.849 (OPT) for root surface area, suggesting that root surface area was a more significant root morphological index affecting root pullout resistance than root diameter and root length, and was more suitable for characterizing the difference in peak pullout resistance of roots with different size. The index could be used to validate the methods for predicting root pullout capacity. The value of peak pullout resistance was 17.2 ± 2.3 N in VPT test and 28.2 ± 3.8 N (mean ± SE) in OPT test, and a significant difference was observed between the two tests, which showed that the pulling direction significantly affected the peak pullout resistance of alfalfa roots. Vertical pullout test, giving the safety margin, was suggested to determine root pullout resistance for estimate of root reinforcement.
Addressing Pain for a Proper Rehabilitation Process in Patients With Severe Disorders of Consciousness

Consciousness constitutes a fundamental prerequisite in the individual appraisal and experience of pain. In the same way, a person needs to be able to report on pain perception. Patients who suffered a severe brain injury with disorders of consciousness (DOC) represent a spectrum of pathologies affecting patients' capacity to interact with the external world. In these patients, the most relevant aspects in response to pain are physiologic and behavioral. The treatments and management of pain are challenging issues in these patients, arising serious ethical concerns and bringing emotional load among medical staff, caregivers, and relatives. In this review, we report the importance of having a correct pain management in DOC patients, to individuate the best pharmacological treatment that can make the difference in detecting a behavioral response, indicative of a change in the level of consciousness, and in planning a more effective rehabilitative approach.
Disentangling the Association of Corn Root Mycobiome With Plant Productivity and the Importance of Soil Physicochemical Balance in Shaping Their Relationship

Soil bacteria and fungi are integral parts of healthy ecosystem functioning in production agriculture. The effects of fungal abundance and diversity on crop productivity is poorly understood. We sampled 10 corn farms at the V10 growth stage across southwestern Ontario, Canada, using aerial infrared imaging to identify zones of low and high productive corn plants. Roots and soils were sampled from low and high yield zones and soil physical and chemical properties were measured in conjunction with assessment of the root mycobiome communities using Illumina MiSeq sequencing of 4 rRNA amplicons. Higher crop yields were associated with sites having greater fungal phylogenetic diversity and Fisher's α diversity. Indicator species associated with high and low yield sites within a farm could be identified but there were no shared fungal indicators of productivity differences across farms. Communities largely varied across locations despite crop genetics, demonstrating a major influence of soil texture and chemistry in shaping the mycobiome in a site-specific manner. Across all 4 primers, roots from high-yielding sites shared 35 major OTUs including Penicillium spp. , Trichoderma, Chalara fungorum, and Gibellulopsis. Low-yielding sites shared 31 OTUs including Fusarium spp. , Pythium, Setophoma terrestris, and Neonectria. Soil physical and chemical parameters that contributed to broad scale differences in yield and mycobiome diversity included: %clay, %sand, %phosphorus saturation, cation exchange capacity, aluminum, pH, iron, potassium, %moisture, organic matter, and chlorine. The results show the importance of physicochemical balance in shaping the relationship between root mycobiome and plant productivity.
Development and Validation of the Knowledge and Attitude Scale Toward COVID-19 Pandemic Breaking Transmission Chain (KA-C) Among Iranian Population

Objectives: We aimed to develop a scale and evaluate this scale's validity and reliability to measure factors affecting people's knowledge and attitudes toward the pandemic breaking transmission chain. Methods: This exploratory mixed-method study was carried out in two phases: (1) item generation using literature reviews and interviews and, (2) item reduction by psychometric assessments of the developed scale. The face, content, construct (exploratory and confirmatory factor analysis), convergent, and discriminant validity of the scale were assessed in the Iranian population (n = 500) from March to June 2020. The Composite Reliability (CR) and the internal consistency correlation coefficient were estimated. Results: The Knowledge and Attitude Scale Toward COVID-19 Pandemic Breaking Transmission Chain (KA-C) among the Iranian population included 18 items. Two factors with a whole variance of 66.05% were identified by exploratory factor analysis. Factors were labeled as “health literacy” and “home health empowerment. ” The confirmatory factor analysis showed the goodness of fit. The CR of the scale for first and second factors were 0.965 and 0.833 receptively. The scale's internal consistency correlation coefficient was acceptable (Cronbach's alpha = 0.960 and 0.823, average interitem correlation = 0.643 and 0.635, McDonald's omega = 0.963 and 0.829, for the first and second factor, receptively). Conclusion: The KA-C scale can be exerted to screen the people's knowledge and attitude about the COVID-19 pandemic breaking the transmission chain as a valid and reliable scale for further policymaking, health care providers, and for a multi-dimensional psychosocial assessment of the pandemic period.
Beating Rate Variability of Isolated Mammal Sinoatrial Node Tissue: Insight Into Its Contribution to Heart Rate Variability

Background Because of the complexity of the interaction between the internal pacemaker mechanisms, cell interconnected signals, and interaction with other body systems, study of the role of individual systems must be performed under in vivo and in situ conditions. The in situ approach is valuable when exploring the mechanisms that govern the beating rate and rhythm of the sinoatrial node (SAN), the heart’s primary pacemaker. SAN beating rate changes on a beat-to-beat basis. However, to date, there are no standard methods and tools for beating rate variability (BRV) analysis from electrograms (EGMs) collected from different mammals, and there is no centralized public database with such recordings. Methods We used EGM recordings obtained from control SAN tissues of rabbits (n = 9) and mice (n = 30) and from mouse SAN tissues (n = 6) that were exposed to drug intervention. The data were harnessed to develop a beat detector to derive the beat-to-beat interval time series from EGM recordings. We adapted BRV measures from heart rate variability and reported their range for rabbit and mouse. Results The beat detector algorithm performed with 99% accuracy, sensitivity, and positive predictive value on the test (mouse) and validation (rabbit and mouse) sets. Differences in the frequency band cutoff were found between BRV of SAN tissue vs. heart rate variability (HRV) of in vivo recordings. A significant reduction in power spectrum density existed in the high frequency band, and a relative increase was seen in the low and very low frequency bands. In isolated SAN, the larger animal had a slower beating rate but with lower BRV, which contrasted the phenomena reported for in vivo analysis. Thus, the non-linear inverse relationship between the average HR and HRV is not maintained under in situ conditions. The beat detector, BRV measures, and databases were contributed to the open-source PhysioZoo software (available at: https://physiozoo.com/). Conclusion Our approach will enable standardization and reproducibility of BRV analysis in mammals. Different trends were found between beating rate and BRV or HRV in isolated SAN tissue vs. recordings collected under in vivo conditions, respectively, implying a complex interaction between the SAN and the autonomic nervous system in determining HRV in vivo.
Adipose Tissue Macrophage Polarization in Healthy and Unhealthy Obesity

Over 650 million adults are obese (body mass index ≥ 30 kg/m2) worldwide. Obesity is commonly associated with several comorbidities, including cardiovascular disease and type II diabetes. However, compiled estimates suggest that from 5 to 40% of obese individuals do not experience metabolic or cardiovascular complications. The existence of the metabolically unhealthy obese (MUO) and the metabolically healthy obese (MHO) phenotypes suggests that underlying differences exist in both tissues and overall systemic function. Macrophage accumulation in white adipose tissue (AT) in obesity is typically associated with insulin resistance. However, as plastic cells, macrophages respond to stimuli in their microenvironments, altering their polarization between pro- and anti-inflammatory phenotypes, depending on the state of their surroundings. The dichotomous nature of MHO and MUO clinical phenotypes suggests that differences in white AT function dictate local inflammatory responses by driving changes in macrophage subtypes. As obesity requires extensive AT expansion, we posit that remodeling capacity with adipose expansion potentiates favorable macrophage profiles in MHO as compared with MUO individuals. In this review, we discuss how differences in adipogenesis, AT extracellular matrix deposition and breakdown, and AT angiogenesis perpetuate altered AT macrophage profiles in MUO compared with MHO. We discuss how non-autonomous effects of remote organ systems, including the liver, gastrointestinal tract, and cardiovascular system, interact with white adipose favorably in MHO. Preferential AT macrophage profiles in MHO stem from sustained AT function and improved overall fitness and systemic health.
Trends in Haptic Communication of Human-Human Dyads: Toward Natural Human-Robot Co-manipulation

In this paper, we analyze and report on observable trends in human-human dyads performing collaborative manipulation (co-manipulation) tasks with an extended object (object with significant length). We present a detailed analysis relating trends in interaction forces and torques with other metrics and propose that these trends could provide a way of improving communication and efficiency for human-robot dyads. We find that the motion of the co-manipulated object has a measurable oscillatory component. We confirm that haptic feedback alone represents a sufficient communication channel for co-manipulation tasks, however we find that the loss of visual and auditory channels has a significant effect on interaction torque and velocity. The main objective of this paper is to lay the essential groundwork in defining principles of co-manipulation between human dyads. We propose that these principles could enable effective and intuitive human-robot collaborative manipulation in future co-manipulation research.
Epidemiology of Bovine Tuberculosis and Its Zoonotic Implication in Addis Ababa Milkshed, Central Ethiopia

Bovine tuberculosis (bTB) continues to be one of the most widely distributed chronic infectious diseases of zoonotic importance, which causes a significant economic loss in animal production. A cross-sectional study was conducted to estimate the prevalence of bTB and its associated risk factors and type the Mycobacterium bovis isolated in central Ethiopia. A total of 65 dairy farms and 654 cattle were tested for bTB using a single intradermal comparative cervical tuberculin (SICCT) test. Data on farm management, animal-related characteristics, and the owner's knowledge of the zoonotic importance of bTB were collected using a structured questionnaire. In addition, a total of 16 animals from different farms were identified for postmortem examination. Lowenstein Jensen (LJ) culture was also conducted, and spoligotyping was used to type the M. bovis strains isolated. Chi-square test and logistic regression models were used to analyze the herd- and animal-level risk factors. Herd- and animal-level prevalence rates of bTB were 58.5% (95% CI: 46.2%−69.2%) and 39.3% (95% CI: 35.5%−43.5%), respectively. At the herd level, poor farm management was the predictor for bTB positivity (p < 0.05). Animal breed, poor BCS, farm type, and poor farm management conditions were significant predictors of bTB positivity (p < 0.05) at an individual animal level. All animals identified for postmortem examination were found to have gross TB-like lesions. A total of 14 M. bovis strains were identified from 12 animals that were positive for LJ culture. The strain with the largest number of clusters (five isolates) was SB1176, followed by SB0134 (three isolates), SB0192 (two isolates), and SB2233 (two isolates), and two new strains, each consisting of only one isolate. The majority (58.5%) of the respondents did not know the zoonotic importance of bTB. The result of this study showed a high prevalence of bTB in the Addis Ababa milkshed and a low level of consciousness of the owners on its transmission to humans. Therefore, the launching of acceptable control measures of bTB and the creation of public awareness about its zoonotic transmission and prevention measures are required.
Predicting Therapeutic Response in Pediatric Ulcerative Colitis—A Journey Towards Precision Medicine

Ulcerative colitis (UC) is a disabling disease, characterized by chronic inflammation of the colon, with a rising prevalence worldwide in the pediatric age group. Although UC presents in children with varying severity, disease extent, and comorbidities, initial treatment is essentially uniform, consisting of 5-aminosalicylate drugs with corticosteroid induction for those with moderately to severely active disease. With the advent of anti-tumor necrosis factor (TNF) biologic therapy and several new biologics and small-molecule drugs for UC, precision medicine approaches to treatment are needed to more rapidly achieve sustained remission, restore quality of life, normalize development, and limit exposure to toxic corticosteroids in children with UC. Here, we review available data on clinical, biochemical, histopathologic, and molecular predictors of treatment response in UC. We also address known predictors and special treatment considerations in specific relevant scenarios such as very-early-onset UC, acute severe UC, ileal pouch anal anastomosis, and UC with concomitant primary sclerosing cholangitis. The review concludes with a prediction of how machine learning will integrate multimodal patient data to bring precision medicine to the bedside of children with UC in the future.
The Comprehensive Analyses of Genomic Variations and Assessment of TMB and PD-L1 Expression in Chinese Lung Adenosquamous Carcinoma

The poor prognosis and fewer treatment option is a current clinical challenge for patients with lung adenosquamous carcinoma (ASC). The previous studies reported that tumor mutational burden (TMB, numbers of mutation per Megabase) is a predictor of clinical response in trials of multiple cancer types, while fewer studies assessed the relationship between TMB level and clinical features and outcomes of lung ASC. Herein, the present study enrolled Chinese patients with lung ASC. DNA was extracted from formalin-fixed paraffin-embedded tumor samples and subjected to next generation sequencing (NGS), and the 457 cancer related genes were evaluated. The results demonstrated that 95 unique genes with somatic variations were identified in the enrolled patients. The top three of high frequency gene mutations were TP53, EGFR, PIK3CA with rates of 62% (13 cases), 48% (10 cases), and 14% (3 cases), respectively. We identified TMB value was significantly correlated with pathological stages (p < 0.05) and invasion of lymph node (p < 0.05). However, TMB value was not significantly correlated to other clinicopathologic indexes, for examples, age, sex, smoking history, tumor size, as well as TP53 and EGFR mutations in lung ASC. Moreover, TMB value was associated with the overall survival (p < 0.01), but not with the relapse-free survival (p = 0.23). In conclusion, this study indicated that lung ASC with high TMB might be associated with the invasion of lymph node and short overall survival. Immunotherapy might be a promising treatment option for lung ASC patients with high TMB.
Parental Involvement and Life Satisfaction in Early Adolescence

Early adolescence is a developmental stage that comprises some basic interactional processes with parents, which can be described as gaining autonomy while maintaining relatedness. Studying how maternal and paternal involvement influence the life satisfaction of sons and daughters during early adolescence is especially important while seeking to understand the challenges of this developmental stage. In this paper, we investigate the differential effects of maternal and paternal involvement, as assessed by sons and daughters, on their life satisfaction during early adolescence. We use a unique survey conducted in Chile, The National Survey on Student Trajectories and Transitions, focusing on a subsample of 497 early adolescents attending 5th to 8th grade (60% female, M age = 12.42, SD = 1.18). Our findings indicate that both paternal and maternal involvement are positively correlated with the life satisfaction of adolescents. We also find that the gender of adolescents moderates the effect of maternal involvement, so daughters (but not sons) who deemed the involvement of their mothers to be more positive reported greater life satisfaction. More positive paternal involvement correlates with greater life satisfaction for sons and daughters. We discuss some mechanisms that might bring about these differences.