Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in Grain Zinc and Iron Concentrations, Grain Yield and Associated Traits of Biofortified Bread Wheat Genotypes in Nepal

Wheat (Triticum aestivum L.) is one of the major staples in Nepal providing the bulk of food calories and at least 30% of Fe and Zn intake and 20% of dietary energy and protein consumption; thus, it is essential to improve its nutritional quality. To select high-yielding genotypes with elevated grain zinc and iron concentration, the sixth, seventh, eighth, and ninth HarvestPlus Yield Trials (HPYTs) were conducted across diverse locations in Nepal for four consecutive years: 2015–16, 2016–17, 2017–18, and 2018–19, using 47 biofortified and 3 non-biofortified CIMMYT-bred, bread wheat genotypes: Baj#1, Kachu#1, and WK1204 (local check). Genotypic and spatial variations were found in agro-morphological traits; grain yield and its components; and the grain zinc and iron concentration of tested genotypes. Grain zinc concentration was highest in Khumaltar and lowest in Kabre. Likewise, grain iron concentration was highest in Doti and lowest in Surkhet. Most of the biofortified genotypes were superior for grain yield and for grain zinc and iron concentration to the non-biofortified checks. Combined analyses across environments showed moderate to high heritability for both Zn (0.48–0.81) and Fe (0.46–0.79) except a low heritability for Fe observed for 7th HPYT (0.15). Grain yield was positively correlated with the number of tillers per m2, while negatively correlated with days to heading and maturity, grain iron, grain weight per spike, and thousand grain weight. The grain zinc and iron concentration were positively correlated, suggesting that the simultaneous improvement of both micronutrients is possible through wheat breeding. Extensive testing of CIMMYT derived high Zn wheat lines in Nepal led to the release of five biofortified wheat varieties in 2020 with superior yield, better disease resistance, and 30–40% increased grain Zn and adaptable to a range of wheat growing regions in the country – from the hotter lowland, or Terai, regions to the dryer mid- and high-elevation areas.
Bioink Formulation and Machine Learning-Empowered Bioprinting Optimization

Bioprinting enables the fabrication of complex, heterogeneous tissues through robotically-controlled placement of cells and biomaterials. It has been rapidly developing into a powerful and versatile tool for tissue engineering. Recent advances in bioprinting modalities and biofabrication strategies as well as new materials and chemistries have led to improved mimicry and development of physiologically relevant tissue architectures constituted with multiple cell types and heterogeneous spatial material properties. Machine learning (ML) has been applied to accelerate these processes. It is a new paradigm for bioprinting. In this review, we explore current trends in bioink formulation and how ML has been used to accelerate optimization and enable real-time error detection as well as to reduce the iterative steps necessary for bioink formulation. We examined how rheometric properties, including shear storage, loss moduli, viscosity, shear-thinning property of biomaterials affect the printability of a bioink. Furthermore, we scrutinized the interplays between yield shear stress and the printability of a bioink. Moreover, we systematically surveyed the application of ML in precision in situ surgical site bioprinting, closed-loop AI printing, and post-printing optimization.
COVID-19 Vaccination Uptake Among a Nationwide Sample of People Living With HIV During the Early Phase of Vaccine Rollout in China

People living with HIV (PLWH), if infected with Coronavirus Disease 2019 (COVID-19), had an increased risk of mortality compared to people without HIV infection. They are considered as a priority group to receive COVID-19 vaccination. This cross-sectional online survey investigated the prevalence of and factors associated with COVID-19 vaccination uptake among 2740 PLWH aged 18–65 years in eight Chinese metropolitan cities between January and February 2021. As validated by requesting participants to send an image of receipt hiding personal identification, 6.2% of PLWH had taken up COVID-19 vaccination. Participants living in cities where individuals could make an appointment to receive COVID-19 vaccination reported significantly higher uptake than those living in cities without such allowance (11.0 vs. 2.9%, p < 0.001). Being a member of priority groups to receive vaccination, concerning about the side effects of COVID-19 vaccination and its interaction with HIV treatment, and exposing to information on the Internet/social media supporting PLWH to receive COVID-19 vaccination were significantly associated with COVID-19 vaccination uptake in both groups of participants. Receiving advice from the staff of community-based organizations supporting COVID-19 vaccination was associated with higher uptake among participants living in cities where individuals could make an appointment to receive such vaccination, while a shortage in COVID-19 vaccine supply was associated with a lower uptake among participants living in other cities. Our findings presented a snapshot of COVID-19 vaccination uptake among PLWH in the early phase of vaccine rollout in China. It provided a knowledge basis to formulate interventions promoting COVID-19 vaccination for PLWH.
Characterization of the B-Cell Epitopes of Echinococcus granulosus Histones H4 and H2A Recognized by Sera From Patients With Liver Cysts

Cystic echinococcosis (CE) is a zoonotic disease worldwide distributed, caused by the cestode Echinococcus granulosus sensu lato (E. granulosus), with an incidence rate of 50/100,000 person/year and a high prevalence in humans of 5-10%. Serology has variable sensitivity and specificity and low predictive values. Antigens used are from the hydatid fluid and recombinant antigens have not demonstrated superiority over hydatid fluid. A cell line called EGPE was obtained from E. granulosus sensu lato G1 strain from bovine liver. Serum from CE patients recognizes protein extracts from EGPE cells with higher sensitivity than protein extracts from hydatid fluid. In the present study, EGPE cell protein extracts and supernatants from cell colonies were eluted from a protein G affinity column performed with sera from 11 CE patients. LC-MS/MS proteomic analysis of the eluted proteins identified four E. granulosus histones: one histone H4 in the cell extract and supernatant, one histone H2A only in the cell extract, and two histones H2A only in the supernatant. This differential distribution of histones could reflect different parasite viability stages regarding their role in gene transcription and silencing and could interact with host cells. Bioinformatics tools characterized the linear and conformational epitopes involved in antibody recognition. The three-dimensional structure of each histone was obtained by molecular modeling and validated by molecular dynamics simulation and PCR confirmed the presence of the epitopes in the parasite genome. The three histones H2A were very different and had a less conserved sequence than the histone H4. Comparison of the histones of E. granulosus with those of other organisms showed exclusive regions for E. granulosus. Since histones play a role in the host-parasite relationship they could be good candidates to improve the predictive value of serology in CE.
Development and Validation of the Breast Cancer Scale QLICP-BR V2.0 Based on Classical Test Theory and Generalizability Theory

Objective The aim of this study was to develop and validate the breast cancer scale among the system of quality-of-life instruments for cancer patients (QLICP-BR V2.0). Methods Programmed decision procedures and theories on instrument development were applied to develop QLICP-BR V2.0. A total of 246 breast cancer inpatients were investigated using QLICP-BR V2.0 from hospital admission until discharge. The reliability, validity, and responsiveness of the QLICP-BR V2.0 scale were evaluated by using the classical test theory combined with the generalizability theory (GT), including correlation analysis, multi-trait scaling analysis, factor analyses, t-tests, and also multivariate generalizability theory analysis. Results The test–retest reliability of the total scale is 0.79, the Cronbach coefficient is 0.85, and the intra-class correlations coefficient is 0.88. The item–domain correlation analysis showed that the correlation coefficient between items and their own domain is greater than that with other domains except of item GSO4. The exploratory factor analysis showed that three principal components are obtained in the specific module. The outcome of the factor analysis coincides substantially with our theoretical conception. The score difference of each domain of the scale and the total scale before and after treatment is statistically significant (P < 0.05), with the standardized response mean of the total scale being 0.61. According to GT, the generalization coefficient of the scores in the 5 domains is between 0.626 and 0.768, and the reliability index is between 0.557 and 0.695. Conclusion QLICP-BR V2.0 exhibited reasonable degrees of validity, reliability, and responsiveness according to classical test and the generalizability theory. The number of items in the scale is appropriate.
Oral Administration of a Shigella 2aT32-Based Vaccine Expressing UreB-HspA Fusion Antigen With and Without Parenteral rUreB-HspA Boost Confers Protection Against Helicobacter pylori in Mice Model

Helicobacter pylori (H. pylori) is a gram-negative pathogen classified as a class I carcinogen. The H. pylori urease B subunit (UreB) and heat shock protein A (HspA) are two important vaccine candidate antigens. In this study, we evaluated the immunogenicity and immunoprotective effect of the attenuated Shigella vector vaccine SH02 expressing the UreB-HspA fusion protein of H. pylori in a mouse model. Oral SH02 with or without subcutaneous injection of rUreB-HspA induced antigen-specific serum IgG, mucosal sIgA, and T cells immune response. Subcutaneous injection of the candidate antigen rUreB-HspA enhanced the level of serum antigen-specific IgG antibodies (p < 0.0001) and the levels of IgG1/IgG2a/IgG2b subtypes. In addition, injection boost also increased the proportion of spleen antigen-specific CD4+CD154+ T cells (p < 0.001), and the proportion of CD4+CD154+ T cells that secrete IFN-γ and IL-17A. Following the H. pylori challenge, the levels of H. pylori colonization in the two experimental groups (Groups A and B) significantly reduced compared with the control group (p < 0.001), indicating that the candidate vaccine yielded a preventive effect of anti-H.pylori infection. Compared with the non-subcutaneous booster injection group (Group A), the subcutaneous booster injection group (Group B) exhibited less gastric inflammation, but there was no significant difference in the level of colonization (p > 0.05). These results lay a foundation for the development of a vaccine against H. pylori and the optimization of immunization methods and procedures to prevent H. pylori infection.
NGLY1 Deficiency Zebrafish Model Manifests Abnormalities of the Nervous and Musculoskeletal Systems

Background: NGLY1 is an enigmatic enzyme with multiple functions across a wide range of species. In humans, pathogenic genetic variants in NGLY1 are linked to a variable phenotype of global neurological dysfunction, abnormal tear production, and liver disease presenting the rare autosomal recessive disorder N-glycanase deficiency. We have ascertained four NGLY1 deficiency patients who were found to carry a homozygous nonsense variant (c.1294G > T, p.Glu432*) in NGLY1. Methods: We created an ngly1 deficiency zebrafish model and studied the nervous and musculoskeletal (MSK) systems to further characterize the phenotypes and pathophysiology of the disease. Results: Nervous system morphology analysis has shown significant loss of axon fibers in the peripheral nervous system. In addition, we found muscle structure abnormality of the mutant fish. Locomotion behavior analysis has shown hypersensitivity of the larval ngly1 (−/−) fish during stress conditions. Conclusion: This first reported NGLY1 deficiency zebrafish model might add to our understanding of NGLY1 role in the development of the nervous and MSK systems. Moreover, it might elucidate the natural history of the disease and be used as a platform for the development of novel therapies.
Relationship Between Ovary Size and Anti-Müllerian Hormone Levels in Holstein–Friesian Cows

The aim of this study was to verify the association between ovarian size and blood AMH levels in HF cows. Sixty multiparous HF cows from three herds were included in this study. The data required for calculating the ovarian volume included the “major axis (length),” “minor axis (width),” and “thickness” of the ovary. All ultrasonography (US) images were acquired at the outermost ends/poles of both the ovaries and of the follicles (>8 mm) and corpus luteum (CL); concomitantly, the blood was sampled from the jugular or coccygeal vein. Based on the ovarian images of each cow, the following ovarian size patterns were calculated using an image analysis software: (1) total area of both the left and right ovaries, (2) individual size of the large ovary, and (3) individual size of the small ovary. For each ovary area pattern, two properties were assessed: (A) presence of follicles (>8 mm) and CL, which may not secret AMH, in the ovaries and (B) absence of follicles (>8 mm) and CL in the ovaries. Serum AMH levels were measured using enzyme-linked immunosorbent assay. The correlation between ovary size and serum AMH levels was measured in terms of the aforementioned patterns and was evaluated statistically. The results of our preliminary study with ovaries from slaughter-house cows (n = 22) revealed that the “thickness” of the ovary was not necessary for estimating ovarian volume and that length and width were sufficient. A strong correlation was observed among ovarian length, width, and thickness (r > 0.96). No significant difference was observed (p > 0.05) in the mean ages or parities among the three herds. Among the ovary sizes measured in this study, the highest correlation was found between the total size of an individual large ovary (including follicular and luteal size) and AMH levels (r = 0.387, p = 0.002). This is the first study to demonstrate the correlation between total size of individual large ovaries and serum AMH levels in HF cows. US observations of the ovaries will allow for estimation of differences in AMH levels and help predict ovarian activity and superovulation performance of cows.
Causal Effects of Circulating Cytokines on the Risk of Psoriasis Vulgaris: A Mendelian Randomization Study

Background: Psoriasis vulgaris is an inflammatory skin disease. Observational studies have shown associations between circulating cytokine levels and psoriasis vulgaris. But the causal relationship between circulating cytokine and psoriasis vulgaris remains elusive. Methods: To assess the causal effects of cytokine levels on the risk of psoriasis vulgaris and vice versa, we performed a two-sample Mendelian randomization (MR) study by using the inverse-variance weighted (IVW), weighted median, and Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) in genome-wide association summary statistics of 41 circulating cytokines in up to 8,293 individuals and psoriasis vulgaris in 399,883 individuals. Results: We identified that increasing RANTES level induced an elevated risk of psoriasis vulgaris in IVW (β = 0.33, S.E. = 0.12, p = 0.006). This causal effect showed consistency across the weighted median (β = 0.35, S.E. = 0.15, p = 0.022) and MR-PRESSO method (β = 0.33, S.E. = 0.11, p = 0.028). Conclusions: Our results suggest a potential causal effect of elevated RANTES concentration on the increased risk of psoriasis vulgaris.
A Mouse Model of Ulcerative Cutaneous Leishmaniasis by Leishmania (Viannia) panamensis to Investigate Infection, Pathogenesis, Immunity, and Therapeutics

A mouse model of cutaneous leishmaniasis (CL) by Leishmania (Viannia) panamensis (L(V)p) that reproduces the characteristics of the human disease remains elusive. Here we report the development of a CL model that uses a mouse-adapted L(V)p isolate to reproducibly induce a dermal disease with a remarkable similarity to human CL. BALB/c mice infected intradermally in the ear with 105 stationary UA-946 L(V)p promastigotes develop a progressive cutaneous disease that exhibits the typical ulcerated lesions with indurated borders observed in CL patients. Although most of parasites in the inoculum die within the first week of infection, the survivors vigorously multiply at the infection site during the following weeks, paralleling disease appearance and aggravation. Regional lymphadenopathy as well as lymphatic dissemination of parasites to draining lymph nodes (dLN) was evidenced early after infection. Viable parasites were also isolated from spleen at later timepoints indicating systemic parasitic dissemination, but, strikingly, no signs of systemic disease were observed. Increasing numbers of myeloid cells and T lymphocytes producing IFNγ and IL-4 were observed in the dLN as disease progressed. A mixed adaptive L(V)p-specific T cell-mediated response was induced, since ex vivo recall experiments using dLN cells and splenocytes revealed the production of type 1 (IFNγ, IL-2), type 2 (IL-4, IL-13), regulatory (IL-10), and inflammatory (GM-CSF, IL-3) cytokines. Humoral adaptive response was characterized by early production of IgG1- followed by IgG2a-type of L(V)p-specific antibodies. IFNγ/IL-4 and IgG2a/IgG1 ratios indicated that the initial non-protective Th2 response was redirected toward a protective Th1 response. In situ studies revealed a profuse recruitment of myeloid cells and of IFNγ- and IL-4-producing T lymphocytes to the site of infection, and the typical histopathological changes induced by dermotropic Leishmania species. Evidence that this model is suitable to investigate pharmacological and immunomodulatory interventions, as well as for antigen discovery and vaccine development, is also presented. Altogether, these results support the validity and utility of this novel mouse model to study the pathogenesis, immunity, and therapeutics of L(V)p infections.
Modeling the Behavioral Response of Dentists to COVID-19 and Assessing the Perceived Impacts of Pandemic on Operative Dentistry Practices in Pakistan

COVID-19 pandemic has affected dentistry in unprecedented ways. This study investigates the perceived effects of the pandemic on operative dentistry procedures and dentistry profession in Pakistan and the factors that determine the behavioral changes among dentists to adapt to the “new normal. ” A Capability Opportunity Motivation-Behavioral model (COM-B) was utilized to investigate the factors that determine the behavior of dentists in Punjab, Pakistan to adhere to COVID-19 standard operating procedures (SOPs). Using social media, an online questionnaire was sent to operative dentistry professionals in Pakistan, and 312 responses were received. 81.4% of the respondents believed that the COVID-19 pandemic has severely affected the level of care provided to the patients, 66% were extremely worried about the risk of contagion during clinical practices, and more than 75% of the respondents opined that the pandemic has led to an increased emphasis on disinfection and oral hygiene instructions. The multiple regression model suggests that the behavior of Pakistani dentists to adhere to the COVID-19 SOPs is significantly affected by their Capabilities (β = 0.358) and Opportunities (β = 0.494). The study concluded that dentists in Punjab, Pakistan are concerned about the risk of contagion and report a serious concern about consequences such as financial loss and inappropriate care of patients. The current study results can feed the policymaking in Pakistan and other developing countries. Facilities and training to improve dentists' opportunities and capabilities can improve their ability to cope with the COVID-19 challenges.
Real-World Impact of Switching From Insulin Glargine (Lantus®) to Basaglar® and Potential Cost Saving in a Large Public Healthcare System in Saudi Arabia

Background The advent of Basaglar®, which is a biosimilar insulin glargine formulation for Lantus® has brought hope that it will result in similar outcomes and lower costs. However, some health practitioners raised some concerns about the therapeutic equivalence of this new biosimilar. Therefore, we aimed to examine the clinical and financial impact of switching from Lantus® to Basaglar®. Methods This was a single–center retrospective chart review study of adult patients (e.g., ≥18 years) with diabetes mellitus (DM) who were treated with insulin glargine (Lantus®) for at least 12 months and then switched to Basaglar® for another 12 months. The potential cost savings for the years 2018 to 2021 and the cost avoidance for 2022 were estimated using different conversion ratios between the two insulin glargine products (Basaglar® and Lantus®) and acquisition prices. Results One–hundred patients with DM who were previously treated with Lantus® and switched to Basaglar® were retrospectively recruited. About two–thirds of the patients (68%) had type 2 DM, and the male and female patients were equally represented. The mean glycated hemoglobin (A1C) at baseline was 9, and the mean difference in the A1C levels before and after switching to Basaglar® was not significant (0.18, p-value = 0.503, 95% CI [−0.36–0.72]). Although the difference in the total daily insulin units between Lantus® and Basaglar® was not significant, the difference was leaning toward statistical significance despite the small sample size (−1.88, P-value = 0.25, 95% CI [−5.15–1.38]). Switching from Lantus® to Basaglar® could have led to significant cost savings that would range from approximately 1.77 to 23.7 million United States Dollars (USD) for the years 2018 to 2021 assuming an equal conversion ratio. However, those cost savings might not be realized if the switching to Basaglar® required higher daily insulin units, and the difference in the public tender acquisition price between Lantus® and Basaglar® is less than 15%. Conclusion Basaglar® and potentially other biosimilar insulin glargine products can lead to significant cost savings without compromising the quality of care. However, their acquisition prices should be discounted.