Miracle-dz/UniFAR-FTUs huggingface dataset:
The Chimeric Antigen Receptor Detection Toolkit

Chimeric antigen receptor-T (CAR-T) cell therapy is a promising frontier of immunoengineering and cancer immunotherapy. Methods that detect, quantify, track, and visualize the CAR, have catalyzed the rapid advancement of CAR-T cell therapy from preclinical models to clinical adoption. For instance, CAR-staining/labeling agents have enabled flow cytometry analysis, imaging applications, cell sorting, and high-dimensional clinical profiling. Molecular assays, such as quantitative polymerase chain reaction, integration site analysis, and RNA-sequencing, have characterized CAR transduction, expression, and in vivo CAR-T cell expansion kinetics. In vitro visualization methods, including confocal and total internal reflection fluorescence microscopy, have captured the molecular details underlying CAR immunological synapse formation, signaling, and cytotoxicity. In vivo tracking methods, including two-photon microscopy, bioluminescence imaging, and positron emission tomography scanning, have monitored CAR-T cell biodistribution across blood, tissue, and tumor. Here, we review the plethora of CAR detection methods, which can operate at the genomic, transcriptomic, proteomic, and organismal levels. For each method, we discuss: (1) what it measures; (2) how it works; (3) its scientific and clinical importance; (4) relevant examples of its use; (5) specific protocols for CAR detection; and (6) its strengths and weaknesses. Finally, we consider current scientific and clinical needs in order to provide future perspectives for improved CAR detection.
Online Information of Vaccines: Information Quality, Not Only Privacy, Is an Ethical Responsibility of Search Engines

The fact that Internet companies may record our personal data and track our online behavior for commercial or political purpose has emphasized aspects related to online privacy. This has also led to the development of search engines that promise no tracking and privacy. Search engines also have a major role in spreading low-quality health information such as that of anti-vaccine websites. This study investigates the relationship between search engines' approach to privacy and the scientific quality of the information they return. We analyzed the first 30 webpages returned searching “vaccines autism” in English, Spanish, Italian, and French. The results show that not only “alternative” search engines (Duckduckgo, Ecosia, Qwant, Swisscows, and Mojeek) but also other commercial engines (Bing, Yahoo) often return more anti-vaccine pages (10–53%) than Google.com (0%). Some localized versions of Google, however, returned more anti-vaccine webpages (up to 10%) than Google.com. Health information returned by search engines has an impact on public health and, specifically, in the acceptance of vaccines. The issue of information quality when seeking information for making health-related decisions also impact the ethical aspect represented by the right to an informed consent. Our study suggests that designing a search engine that is privacy savvy and avoids issues with filter bubbles that can result from user-tracking is necessary but insufficient; instead, mechanisms should be developed to test search engines from the perspective of information quality (particularly for health-related webpages) before they can be deemed trustworthy providers of public health information.
Mathematical Modeling of Growth and Paclitaxel Biosynthesis in Corylus avellana Cell Culture Responding to Fungal Elicitors Using Multilayer Perceptron-Genetic Algorithm

Paclitaxel is the top-selling anticancer medicine in the world. In vitro culture of Corylus avellana has been made known as a promising and inexpensive strategy for producing paclitaxel. Fungal elicitors have been named as the most efficient strategy for enhancing the biosynthesis of secondary metabolites in plant cell culture. In this study, endophytic fungal strain HEF17 was isolated from C. avellana and identified as Camarosporomyces flavigenus. C. avellana cell suspension culture (CSC) elicited with cell extract (CE) and culture filtrate (CF) derived from strain HEF17, either individually or combined treatment, in mid and late log phase was processed for modeling and optimizing growth and paclitaxel biosynthesis regarding CE and CF concentration levels, elicitor adding day, and CSC harvesting time using multilayer perceptron-genetic algorithm (MLP-GA). The results displayed higher accuracy of MLP-GA models (0.89–0.95) than regression models (0.56–0.85). The great accordance between the predicted and observed values of output variables (dry weight, intracellular, extracellular and total yield of paclitaxel, and also extracellular paclitaxel portion) for both training and testing subsets supported the excellent performance of developed MLP-GA models. MLP-GA method presented a promising tool for selecting the optimal conditions for maximum paclitaxel biosynthesis. An Excel® estimator, HCC-paclitaxel, was designed based on MLP-GA model as an easy-to-use tool for predicting paclitaxel biosynthesis in C. avellana CSC responding to fungal elicitors.
New Plasmodium vivax Genomes From the China-Myanmar Border

Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS.
Study of Milkability and Its Relation With Milk Yield and Somatic Cell in Mediterranean Italian Water Buffalo

Milkability is defined as the ability of an animal to give a regular, complete, and rapid milk secretion by the mammary gland in response to a proper milking technique. The aim of the present study was to investigate the relationship of milkability pattern with milk yield and somatic cell score in buffaloes. Milk yield and milkability can be observed through the milk flow profiles recorded by an electronic milkmeter (Lactocorder). A total of 2,288 milk flow curves of Mediterranean Italian buffaloes were used for one-way analysis of variance, and eight milk emission patterns were studied. The most represented milk flow curve was type 3 (27.32%), followed by type 6 (17.79%) characterized by a very long plateau phase. The less represented curve was type 1 (4.41%) characterized by long lag time and low peak flow rate. According to analysis of variance, milk yield ranged from 2.21 to 5.22 kg per milking for types 1 and 6, respectively, whereas the peak flow rate was minimum (0.50 kg/min) and maximum (1.73 kg/min) for types 1 and 4, respectively. The total milking time was on average 11.29 ± 3.68 min; lag time and milk emission time averaged 2.19 ± 2.34 min and 4.30 ± 2.33 min, respectively. The 12.5% (n = 286) of total curves were classified as bimodal and 60 of these were found in type 4. Based on literature, type 4 curves are representative of very short teat canals and very high milk flow. Average somatic cell score was 3.63 ± 1.67 units, with maximum least-squares mean found for type 1 and minimum for type 6. Buffaloes showing curves of type 5 and 6 were characterized by the greatest milk yield at milking, lowest somatic cell score, and lowest milking time. Results of the present study evidenced that such traits could be used in the dairy buffaloes as indicators to improve udder health and milkability.
Measuring Magnetic Field With Atacama Large Millimeter/Submillimeter Array

The article discusses the use of magnetic bremsstrahlung at short radio wavelengths for measuring solar magnetic fields. The polarization and brightness spectra observed at millimeter wavelengths can be used to deduce the vertical component of the chromospheric magnetic field both in the quit Sun and in active regions. State-of-the-art three-dimensional (3D) radiative magnetohydrodynamic (R-MHD) simulations of the quiet solar atmosphere were used to synthesize observational deliverables at the wavelengths of the Atacama Large Millimeter/Submillimeter Array (ALMA) and to test the applicability of the method. The article provides selected observational examples of the successful application of the method and presents an overview of the recent developments and potential of the magnetic field measurements with ALMA.
IMPACT OF ORGANIC AND INORGANIC MANAGEMENT AND PLANT-BASED PRODUCTS ON PLANT-PARASITIC AND MICROBIVOROUS NEMATODE COMMUNITIES

Application of poultry and cattle manures, inorganic fertilizer in the form of urea and neem-based urea-coating agent 'Nimin' and biopesticide 'Suneem G' significantly reduced populations of Meloidogyne incognita and other plant-parasitic nematodes and their symptoms on the plant and increased the populations of microbivorous nematodes. Enhanced growth of tomato in treated soil was directly correlated with the suppression of plant-parasitic nematode populations. Higher dosages resulted in greater effects.
Care for Critical Ill Patients With COVID-19: Establishment of a Temporary Intensive Care Unit in an Isolated Hospital

The current global spread of COVID-19, a highly contagious disease, has challenged healthcare systems, and placed immense burdens on medical staff globally. With a sharp increase in the number of newly confirmed cases and the rapid progression of the disease into a critically ill state, overstretched critical care units have had to contend with a shortage of beds, specialist personnel, and medical resources. Temporary intensive care units (ICUs) were therefore set up in isolated hospitals to provide the required standardized care for all severe cases. The current paper describes the authors' experience of setting up and managing such an ICU in Wuhan, Hubei Province, China, from the identification of critically ill COVID-19 patients through to the arranging and equipping of the unit, providing training and protection for staff, and standardizing all aspects of care.
Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls

Genomic selection in modern farming demands sufficient semen production in young bulls. Factors affecting semen quality and production capacity in young bulls are not well understood; DNA methylation, a complicated phenomenon in sperm cells, is one such factors. In this study, fresh and frozen-thawed semen samples from the same Norwegian Red (NR) bulls at both 14 and 17 months of age were examined for sperm chromatin integrity parameters, ATP content, viability, and motility. Furthermore, reduced representation bisulfite libraries constructed according to two protocols, the Ovation® RRBS Methyl-Seq System (Ovation method) and a previously optimized gel-free method and were sequenced to study the sperm DNA methylome in frozen-thawed semen samples. Sperm quality analyses indicated that sperm concentration, total motility and progressivity in fresh semen from 17 months old NR bulls were significantly higher compared to individuals at 14 months of age. The percentage of DNA fragmented sperm cells significantly decreased in both fresh and frozen-thawed semen samples in bulls with increasing age. Libraries from the Ovation method exhibited a greater percentage of read loss and shorter read size following trimming. Downstream analyses for reads obtained from the gel-free method revealed similar global sperm DNA methylation but differentially methylated regions (DMRs) between 14- and 17 months old NR bulls. The majority of identified DMRs were hypomethylated in 14 months old bulls. Most of the identified DMRs (69%) exhibited a less than 10% methylation difference while only 1.5% of DMRs exceeded a 25% methylation difference. Pathway analysis showed that genes annotated with DMRs having low methylation differences (less than 10%) and DMRs having between 10 and 25% methylation differences, could be associated with important hormonal signaling and sperm function relevant pathways, respectively. The current research shows that RRBS in parallel with routine sperm quality analyses could be informative in reproductive capacity of young NR bulls. Although global sperm DNA methylation levels in 14 and 17 months old NR bulls were similar, regions with low and varying levels of DNA methylation differences can be identified and linked with important sperm function and hormonal pathways.
Randomized Clinical Trial: Bergamot Citrus and Wild Cardoon Reduce Liver Steatosis and Body Weight in Non-diabetic Individuals Aged Over 50 Years

Background: Non-alcoholic fatty liver disease is the most common cause of liver-related morbidity and mortality in the world. However, no effective pharmacological treatment for this condition has been found. Purpose: This study evaluated the effect of a nutraceutical containing bioactive components from Bergamot citrus and wild cardoon as a treatment for individuals with fatty liver disease. The primary outcome measure was the change in liver fat content. Methods: A total of 102 patients with liver steatosis were enrolled in a double-blind placebo controlled clinical trial. The intervention group received a nutraceutical containing a Bergamot polyphenol fraction and Cynara Cardunculus extract, 300 mg/day for 12 weeks. The control group received a placebo daily. Liver fat content, by transient elastography, serum transaminases, lipids and glucose were measured at the baseline and the end of the study. Results: We found a greater liver fat content reduction in the participants taking the nutraceutical rather than placebo (−48.2 ± 39 vs. −26.9 ± 43 dB/m, p = 0.02); The percentage CAP score reduction was statistically significant in those with android obesity, overweight/obesity as well as in women. However, after adjustment for weight change, the percentage CAP score reduction was statistically significant only in those over 50 years (44 vs. 78% in placebo and nutraceutical, respectively, p = 0.007). Conclusions: This specific nutraceutical containing bioactive components from Bergamot and wild cardoon reduced the liver fat content during 12 weeks in individuals with liver steatosis over 50 years. If confirmed, this nutraceutical could become the cornerstone treatment of patients affected by liver steatosis. Clinical Trial Registration: www.isrctn. com, identifier ISRCTN12833814.
Tumor Microenvironment in Ovarian Cancer: Function and Therapeutic Strategy

Ovarian cancer is one of the leading causes of death in patients with gynecological malignancy. Despite optimal cytoreductive surgery and platinum-based chemotherapy, ovarian cancer disseminates and relapses frequently, with poor prognosis. Hence, it is urgent to find new targeted therapies for ovarian cancer. Recently, the tumor microenvironment has been reported to play a vital role in the tumorigenesis of ovarian cancer, especially with discoveries from genome-, transcriptome- and proteome-wide studies; thus tumor microenvironment may present potential therapeutic target for ovarian cancer. Here, we review the interactions between the tumor microenvironment and ovarian cancer and various therapies targeting the tumor environment.
Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits

Understanding how the gut microbiome and short-chain fatty acids (SCFAs) affect finishing weight is beneficial to improve meat production in the meat rabbit industry. In this study, we identified 15 OTUs and 23 microbial species associated with finishing weight using 16S rRNA gene and metagenomic sequencing analysis, respectively. Among these, butyrate-producing bacteria of the family Ruminococcaceae were positively associated with finishing weight, whereas the microbial taxa related to intestinal damage and inflammation showed opposite effects. Furthermore, interactions of these microbial taxa were firstly found to be associated with finishing weight. Gut microbial functional capacity analysis revealed that CAZymes, such as galactosidase, xylanase, and glucosidase, could significantly affect finishing weight, given their roles in regulating nutrient digestibility. GOs related to the metabolism of several carbohydrates and amino acids also showed important effects on finishing weight. Additionally, both KOs and KEGG pathways related to the membrane transportation system and involved in aminoacyl-tRNA biosynthesis and butanoate metabolism could act as key factors in modulating finishing weight. Importantly, gut microbiome explained nearly 11% of the variation in finishing weight, and our findings revealed that a subset of metagenomic species could act as predictors of finishing weight. SCFAs levels, especially butyrate level, had critical impacts on finishing weight, and several finishing weight-associated species were potentially contributed to the shift in butyrate level. Thus, our results should give deep insights into how gut microbiome and SCFAs influence finishing weight of meat rabbits and provide essential knowledge for improving finishing weight by manipulating gut microbiome.
Effects of Revegetation on Soil Physical and Chemical Properties in Solar Photovoltaic Infrastructure

Solar photovoltaic (PV) technology is being deployed at an unprecedented rate. However, utility-scale solar energy development is land intensive and its large-scale installation can have negative impacts on the environment. In particular, solar energy infrastructure can require extensive landscape modification that transforms soil ecological functions, thereby impacting hydrologic, vegetative, and carbon dynamics. However, reintroducing native vegetation to solar PV sites may be a means of restoring their soils. To this end, we investigated critical soil physical and chemical parameters at a revegetated photovoltaic array and an adjacent reference grassland in Colorado, United States. Seven years after revegetation, we found that carbon and nitrogen remained lower in the PV soil than in the reference soil and contained a greater fraction of coarse particles. We also found that the PV modules introduced heterogeneity in the soil moisture distribution, with precipitation accumulating along the lower edges of panels. The redistribution of soil moisture by panel arrays could potentially be used in concert with planting strategies to maximize plant growth or minimize soil erosion, and should be considered when evaluating the potential to co-locate vegetation with solar infrastructure.
Social Cognition in Children With Non-specific Intellectual Disabilities: An Exploratory Study

Social cognitive abilities – notably, Theory of Mind (ToM) and social information processing (SIP) – are key skills for the development of social competence and adjustment. By understanding affective and cognitive mental states and processing social information correctly, children will be able to enact prosocial behaviors, to interact with peers and adults adaptively, and to be socially included. As social adjustment and inclusion are major issues for children with intellectual disabilities (IDs), the present study aimed to explore their social cognitive profile by combining cluster analysis of both ToM and SIP competence, and to investigate the structure of relations between these skills in children with IDs. Seventy-eight elementary school children with non-specific IDs were recruited. They had a chronological age ranging from 4 years and 8 months to 12 years and 6 months and presented a preschool developmental age. Performance-based measures were administered to assess ToM and SIP abilities. Questionnaires were completed by the children’s parents to evaluate the children’s social competence and adjustment and their risk of developing externalizing or internalizing behaviors. Exploratory analysis highlighted strengths and weaknesses in the social cognitive profiles of these children with IDs. It also emphasized that the understanding of affective and cognitive mental states was used differently when facing appropriate vs. inappropriate social behaviors. The present study leads to a better understanding of the socio-emotional profile of children with IDs and offers some suggestions on how to implement effective interventions.
Carbon footprint of milk production under smallholder dairying in Anand district of Western India: a cradle-to-farm gate life cycle assessment

In recent years, the concept of life cycle assessment (LCA) has proven to be useful because of its potential to assess the integral environmental impacts of agricultural products. Developing countries such as India are good candidates for LCA research because of the large contribution of smallholder dairy system to the production of agricultural products such as milk. Therefore, the aim of the present study was to explore the carbon footprint of milk production under the multi-functional smallholder dairy system in Anand district of Gujarat state, western India. A cradle-to-farm gate LCA was performed by covering 60 smallholder dairy farms within 12 geographically distinct villages of the district. The average farm size was 4.0 animals per farm, and the average number of each category of animal was 2.5 lactating cows, 1.4 lactating buffaloes, 1.8 replacement cows, 1.6 replacement buffaloes, 2.0 retired cows, 1.3 retired buffaloes and 1.0 ox per farm. The emissions of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) on CO2-equivalent (CO2-eq) basis from feed production, enteric fermentation and manure management were allocated to fat- and protein-corrected milk (FPCM) on the basis of mass balance, price and digestibility. Emissions of CO2, CH4 and N2O from cattle contributed 11.0%, 75.4% and 13.6%, respectively, to the total greenhouse gas (GHG) emissions. The contribution of CO2, CH4 and N2O from buffalo was 8.2%, 80.5% and 11.3%, respectively, to the total GHG emissions of farms. The average carbon footprint (CF) of cow milk was 2.3, 1.9 and 2.0 kg CO2-eq/kg FPCM on mass, economic and digestibility basis, respectively, whereas for buffalo, milk CF was 3.0, 2.5 and 2.7 kg CO2-eq/kg FPCM, respectively. On the basis of digestibility allocation, emissions from retired (>10 years of age and incapable of or ceased producing milk) cows and buffaloes were 1571.3 and 2556.1 kg CO2-eq/retirement year, respectively. Overall, the CF of milk production under the smallholder dairy system in Anand district was 2.2 kg CO2-eq/kg FPCM, which reduced to 1.7 kg CO2-eq/kg FPCM when milk, manure, finance and insurance were considered as economic functions of the smallholder system. The CF was lower by 65% and 22% for cow and buffalo milk, respectively, than were the estimates of FAO for southern Asia, and this was mainly attributed to difference in the sources of GHG emissions, manure management systems, feed digestibility and milk production data used by FAO.