Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-reactivities and cross-neutralization of different envelope glycoproteins E2 antibodies against different genotypes of classical swine fever virus

Classical swine fever (CSF) is a highly contagious swine disease caused by the classical swine fever virus (CSFV), wreaking havoc on global swine production. The virus is divided into three genotypes, each comprising 4–7 sub-genotypes. The major envelope glycoprotein E2 of CSFV plays an essential role in cell attachment, eliciting immune responses, and vaccine development. In this study, to study the cross-reaction and cross-neutralizing activities of antibodies against different genotypes (G) of E2 glycoproteins, ectodomains of G1.1, G2.1, G2.1d, and G3.4 CSFV E2 glycoproteins from a mammalian cell expression system were generated. The cross-reactivities of a panel of immunofluorescence assay-characterized serum derived from pigs with/without a commercial live attenuated G1.1 vaccination against different genotypes of E2 glycoproteins were detected by ELISA. Our result showed that serum against the LPCV cross-reacted with all genotypes of E2 glycoproteins. To evaluate cross-neutralizing activities, hyperimmune serum from different CSFV E2 glycoprotein-immunized mice was also generated. The result showed that mice anti-E2 hyperimmune serum exhibited better neutralizing abilities against homologous CSFV than heterogeneous viruses. In conclusion, the results provide information on the cross-reactivity of antibodies against different genogroups of CSFV E2 glycoproteins and suggest the importance of developing multi-covalent subunit vaccines for the complete protection of CSF.
Intrinsic Bayesian Estimation of Vector Autoregression Impulse Responses

We propose an information-theoretic alternative to the conventional Bayesian posterior mean estimator of impulse responses in vector autoregression (VAR) models. The proposed estimator is based on the intrinsic entropy loss function, which is invariant to nonlinear transformations of parameters. Consequently, intrinsic estimation of impulse responses is equivalent to that of VAR parameters. The Bayesian estimator under the entropy loss involves a frequentist expectation of regressors. We propose Markov chain Monte Carlo algorithms to simulate the posterior of the frequentist expectation of regressors and compute the Bayesian estimates. We estimate the VAR impulse responses in two applications.
Mouse all-cone retina models of Cav1.4 synaptopathy

The voltage-gated calcium channel, Cav1.4 is localized to photoreceptor ribbon synapses and functions both in molecular organization of the synapse and in regulating release of synaptic vesicles. Mutations in Cav1.4 subunits typically present as either incomplete congenital stationary night blindness or a progressive cone-rod dystrophy in humans. We developed a cone-rich mammalian model system to further study how different Cav1.4 mutations affect cones. RPE65 R91W KI; Nrl KO “Conefull” mice were crossed to Cav1.4 α1F or α2δ4 KO mice to generate the “Conefull:α1F KO” and “Conefull:α2δ4 KO” lines. Animals were assessed using a visually guided water maze, electroretinogram (ERG), optical coherence tomography (OCT), and histology. Mice of both sexes and up to six-months of age were used. Conefull: α1F KO mice could not navigate the visually guided water maze, had no b-wave in the ERG, and the developing all-cone outer nuclear layer reorganized into rosettes at the time of eye opening with degeneration progressing to 30% loss by 2-months of age. In comparison, the Conefull: α2δ4 KO mice successfully navigated the visually guided water maze, had a reduced amplitude b-wave ERG, and the development of the all-cone outer nuclear layer appeared normal although progressive degeneration with 10% loss by 2-months of age was observed. In summary, new disease models for studying congenital synaptic diseases due to loss of Cav1.4 function have been created.
Analysis of adoption of conservation agriculture practices in southern Africa: mixed-methods approach

In southern Africa, conservation agriculture (CA) has been promoted to address low agricultural productivity, food insecurity, and land degradation. However, despite significant experimental evidence on the agronomic and economic benefits of CA and large scale investments by the donor community and national governments, adoption rates among smallholders remain below expectation. The main objective of this research project was thus to investigate why previous efforts and investments to scale CA technologies and practices in southern Africa have not led to widespread adoption. The paper applies a multivariate probit model and other methods to survey data from 4,373 households and 278 focus groups to identify the drivers and barriers of CA adoption in Malawi, Zambia, and Zimbabwe. The results show that declining soil fertility is a major constraint to maize production in Zambia and Malawi, and drought/heat is more pronounced in Zimbabwe. We also find gaps between (a) awareness and adoption, (b) training and adoption, and (c) demonstration and adoption rates of CA practices in all three countries. The gaps are much bigger between awareness and adoption and much smaller between hosting demonstration and adoption, suggesting that much of the awareness of CA practices has not translated to greater adoption. Training and demonstrations are better conduits to enhance adoption than mere awareness creation. Therefore, demonstrating the applications and benefits of CA practices is critical for promoting CA practices in all countries. Besides, greater adoption of CA practices requires enhancing farmers’ access to inputs, addressing drudgery associated with CA implementation, enhancing farmers’ technical know-how, and enacting and enforcing community bylaws regarding livestock grazing and wildfires. The paper concludes by discussing the implications for policy and investments in CA promotion.
Digital capital and belonging in universities: quantifying social inequalities in the Philippines

This study examines social inequalities in Philippine universities that were exacerbated during the COVID-19 pandemic. A quantitative approach using a national sample of 677 university students was utilized to measure the mediating role of digital capital on social inequalities associated with belonging to academic spaces. For the purpose of determining direct and indirect impacts, structural equation modeling (SEM) was employed. Sociodemographic (i.e., gender, age, type of residence, and family income) and educational (i.e., type of university, year in the university, and excellence criterion) characteristics were the direct predictors that were examined as exogenous variables for both digital capital and belonging. Results indicate that type of residence (β=0.200, p<0.05), family income (β=0.220, p <0.001), and excellence criterion (β=0.271, p <0.01) are major determinants of digital capital. The model also shows that belonging is significantly predicted by age (β=0.087, p <0.05), family income (β=-0.207, p <0.001), and digital capital (β=0.576, p <0.001). Lastly, the findings reveal that the impacts of type of residence (β=0.116, p <0.05), family income (β=0.127, p <0.001), and excellence criterion (β=0.156, p <0.001) on belonging are successfully mediated by digital capital. These results suggest that there are indeed differences in students’ abilities to accumulate digital capital and that digital capital enhances the sense of belonging to and together in academic spaces for certain groups.
An anti-cancer surveillance by the interplay between interferon-beta and retinoblastoma protein RB1

Interferon-beta (IFN-β), an extracellular cytokine that initiates signaling pathways for gene regulation, has been demonstrated to function as a tumor suppressor protein through lentiviral gene transduction. In this article, I review the relevant previous works and propose a cell cycle-based, tumor suppressor protein-mediated mechanism of anti-cancer surveillance. IFN-β induces a tumor cell cycle alteration that leads to S phase accumulation, senescence entry, and a loss of tumorigenicity in solid tumor cells. IFN-β does not show a significant cell cycle effect in their normal counterparts. Retinoblastoma protein RB1, another tumor suppressor protein, tightly controls the cell cycle and differentiation of normal cells, preventing them from being significantly impacted by the IFN-β effect. The interplay between IFN-β and RB1 acts as a mechanism of cell cycle-based, tumor suppressor protein-mediated anti-cancer surveillance that can selectively suppress solid tumor or proliferating transformed cells from the loss of control leading to cancer. This mechanism has important implications for the treatment of solid tumors.
Animate monitoring is not uniform: implications for the animate monitoring hypothesis

The animate monitoring hypothesis (AMH) purports that humans evolved specialized mechanisms that prioritize attention to animates over inanimates. Importantly, the hypothesis emphasizes that any animate—an entity that can move on its own—should take priority in attention. While many experiments have found general support for this hypothesis, there have yet been no systematic investigations into whether the type of animate matters for animate monitoring. In the present research we addressed this issue across three experiments. In Experiment 1, participants (N = 53) searched for an animate or inanimate entity in a search task, and the animate was either a mammal or a non-mammal (e.g., bird, reptile, insect). Mammals were found significantly faster than inanimates, replicating the basic AMH finding. However, they were also found significantly faster than non-mammals, who were not found faster than inanimates. Two additional experiments were conducted to probe for differences among types of non-mammals using an inattentional blindness task. Experiment 2 (N = 171) compared detection of mammals, insects, and inanimates, and Experiment 3 (N = 174) compared birds and herpetofauna (reptiles and amphibians). In Experiment 2, mammals were spontaneously detected at significantly higher rates than insects, who were detected at only slightly higher rates than the inanimates. Furthermore, when participants did not consciously identify the target, they nonetheless could correctly guess the higher level category of the target (living vs. nonliving thing) for the mammals and the inanimates, but could not do so for the insects. We also found in Experiment 3 that reptiles and birds were spontaneously detected at rates similar to the mammals, but like insects they were not identified as living things at rates greater than chance when they were not consciously detected. These results do not support a strong claim that all animates are prioritized in attention, but they do call for a more nuanced view. As such, they open a new window into the nature of animate monitoring, which have implications for theories of its origin.
Construction of an interferon regulatory factors-related risk model for predicting prognosis, immune microenvironment and immunotherapy in clear cell renal cell carcinoma

Background Interferon regulatory factors (IRFs) played complex and essential roles in progression, prognosis, and immune microenvironment in clear cell renal cell carcinoma (ccRCC). The purpose of this study was to construct a novel IRFs-related risk model to predict prognosis, tumor microenvironment (TME) and immunotherapy response in ccRCC. Methods Multi-omics analysis of IRFs in ccRCC was performed based on bulk RNA sequencing and single cell RNA sequencing data. According to the expression profiles of IRFs, the ccRCC samples were clustered by non-negative matrix factorization (NMF) algorithm. Then, least absolute shrinkage and selection operator (LASSO) and Cox regression analyses were applied to construct a risk model to predict prognosis, immune cells infiltration, immunotherapy response and targeted drug sensitivity in ccRCC. Furthermore, a nomogram comprising the risk model and clinical characteristics was established. Results Two molecular subtypes with different prognosis, clinical characteristics and infiltration levels of immune cells were identified in ccRCC. The IRFs-related risk model was developed as an independent prognostic indicator in the TCGA-KIRC cohort and validated in the E-MTAB-1980 cohort. The overall survival of patients in the low-risk group was better than that in the high-risk group. The risk model was superior to clinical characteristics and the ClearCode34 model in predicting the prognosis. In addition, a nomogram was developed to improve the clinical utility of the risk model. Moreover, the high-risk group had higher infiltration levels of CD8+ T cell, macrophages, T follicular helper cells and T helper (Th1) cells and activity score of type I IFN response but lower infiltration levels of mast cells and activity score of type II IFN response. Cancer immunity cycle showed that the immune activity score of most steps was remarkably higher in the high-risk group. TIDE scores indicated that patients in the low-risk group were more likely responsive to immunotherapy. Patients in different risk groups showed diverse drug sensitivity to axitinib, sorafenib, gefitinib, erlotinib, dasatinib and rapamycin. Conclusions In brief, a robust and effective risk model was developed to predict prognosis, TME characteristics and responses to immunotherapy and targeted drugs in ccRCC, which might provide new insights into personalized and precise therapeutic strategies.
Short exposure to photo-oxidative damage triggers molecular signals indicative of early retinal degeneration

Introduction Age-related macular degeneration (AMD) is the leading cause of blindness in the developed world, currently affecting over 350 billion people globally. For the most prevalent late-stage form of this disease, atrophic AMD, there are no available prevention strategies or treatments, in part due to inherent difficulties in early-stage diagnosis. Photo-oxidative damage is a well-established model for studying inflammatory and cell death features that occur in late-stage atrophic AMD, however to date has not been investigated as a potential model for studying early features of disease onset. Therefore, in this study we aimed to determine if short exposure to photo-oxidative damage could be used to induce early retinal molecular changes and advance this as a potential model for studying early-stage AMD. Methods C57BL/6J mice were exposed to 1, 3, 6, 12, or 24h photo-oxidative damage (PD) using 100k lux bright white light. Mice were compared to dim-reared (DR) healthy controls as well as mice which had undergone long periods of photo-oxidative damage (3d and 5d-PD) as known timepoints for inducing late-stage retinal degeneration pathologies. Cell death and retinal inflammation were measured using immunohistochemistry and qRT-PCR. To identify retinal molecular changes, retinal lysates were sent for RNA sequencing, following which bioinformatics analyses including differential expression and pathway analyses were performed. Finally, to investigate modulations in gene regulation as a consequence of degeneration, microRNA (miRNA) expression patterns were quantified using qRT-PCR and visualized using in situ hybridization. Results Short exposure to photo-oxidative damage (1-24h-PD) induced early molecular changes in the retina, with progressive downregulation of homeostatic pathways including metabolism, transport and phototransduction observed across this time-course. Inflammatory pathway upregulation was observed from 3h-PD, preceding observable levels of microglia/macrophage activation which was noted from 6h-PD, as well as significant photoreceptor row loss from 24h-PD. Further rapid and dynamic movement of inflammatory regulator miRNA, miR-124-3p and miR-155-5p, was visualized in the retina in response to degeneration. Conclusion These results support the use of short exposure to photo-oxidative damage as a model of early AMD and suggest that early inflammatory changes in the retina may contribute to pathological features of AMD progression including immune cell activation and photoreceptor cell death. We suggest that early intervention of these inflammatory pathways by targeting miRNA such as miR-124-3p and miR-155-5p or their target genes may prevent progression into late-stage pathology.
Improvement in the ideal range of vault after implantable collamer lens implantation: a new vault prediction formula

Background To derive and validate a novel vault prediction formula to improve the predictability and safety of implantable collamer lens (ICL) implantation. Methods Thirty-five patients (61 eyes) with previous posterior chamber intraocular lens implantation were included. Various parameters, such as horizontal-visible iris diameter (HVID), photopic pupil diameter (PPD), axial length (AL), white-to-white (WTW), anterior chamber width (ACW), angle-to-angle (ATA), crystalline lens rise (CLR), anterior chamber depth (ACD), horizontal sulcus-to-sulcus (HSTS), and ciliary sulcus angle (CSA) were measured. Vault was measured at 3 months after surgery using CASIA2 anterior segment optical coherence tomography. The formula was derived using multiple linear regression analysis and named as WH formula. It was validated in 65 patients (118 eyes) to determine the percentage of the ideal postoperative vault range and to compare the differences between the WH formula and the NK, KS, and STAAR formulas. Results Final ICL size, ATA, CSA, and CLR were included in the prediction formula model (adjusted R2 = 0.67, p < 0.001). The achieved vault 1 month after the surgery was 556.19 μm ± 166.98 μm in the validation group, and the ideal vault range was 200–800 μm (92%). The difference between the achieved vault and that predicted using the WH formula was not statistically significant (p = 0.165), whereas the difference between the achieved vault and that predicted using the NK and KS formulas was statistically significant (p < 0.001 and p < 0.001, respectively). The 95% agreement limit range of the achieved vault and the vault predicted using the WH formula was narrower than those predicted using the NK and KS formulas (−295.20–258.82 μm). Conclusion This study combined the results of optical coherence tomography and ultrasound biomicroscopy measurements of the anterior segment of the eye and incorporated ciliary sulcus morphology quantification into the prediction formula. The study derived a prediction formula for vault by combining ICL size, ATA, and CLR. The derived formula was found to be superior to the currently available formulas.
Prevalence of hepatitis B infection and its associated factors among pregnant mothers attending antenatal care at public hospitals at Hararghe, Eastern Ethiopia

Background Hepatitis B infection is one of the world's most serious public health problems, causing significant morbidity and mortality. More than 2 billion individuals around the world have been infected with the hepatitis B virus (HBV), and approximately 400 million people are chronically infected with the virus, with more than a million dying each year from hepatitis B virus-related liver disease. A newborn infant whose mother is positive for both HBsAg and HBeAg has a 90% chance of developing chronic infection by the age of 6. Its infectivity is a 100 times that of the human immunodeficiency virus, but it receives little attention in public health. Therefore, this study was conducted to assess the prevalence of hepatitis B infection and its associated factors among pregnant mothers attending antenatal care at public hospitals in west Hararghe, eastern Ethiopia 2020. Method This institution-based cross-sectional study was conducted on 300 pregnant mothers selected by systematic random sampling from September to December 2020. Data were collected by face-to-face interview using a pretested structured questionnaire. A blood sample was collected and tested for hepatitis B surface antigen using the enzyme-linked immunosorbent assay test method. Data were entered into EpiData version 3.1 and exported to Statistical Package for the Social Science version 22 for analysis. Bivariate and multivariable logistic regressions were used to assess the association between outcome and predictor variables. P-value <0.05 was considered to be statistically significant. Results The overall seroprevalence of hepatitis B virus infection was 8% [95% confidence interval (CI): 5.3–11.0] among pregnant mothers. History of tonsillectomy [adjusted odd ratio (AOR) = 5.7; 95% CI: 1.3–23.9], tattoo (AOR = 4.3; 95% CI: 1.1, 17.0), having multiple sexual partners (AOR = 10.8; 95% CI: 2.5, 45.9), and history of contact with jaundiced patients (AOR = 5.6; 95% CI: 1.2, 25.7) were factors associated with the seroprevalence of hepatitis B virus infection among pregnant mothers. Conclusion The hepatitis B virus was highly prevalent. A history of tonsillectomy, tattooing, having multiple partners, and contact with jaundiced patients were factors associated with hepatitis B virus infection. To reduce HBV transmissions, the government should increase HBV vaccination coverage. All newborns should receive the hepatitis B vaccine as soon as possible after birth. It is also recommended that all pregnant women have HBsAg testing and antiviral prophylaxis to reduce the risk of transmission from mother to child. Hospitals, districts, regional health bureaus, and medical professionals should also educate pregnant women about hepatitis B virus transmission and prevention, both in the hospital and in the community, with a focus on modifiable risk factors.
Serological analysis of allergic components of house dust mite provides more insight in epidemiological characteristics and clinical symptom development in North China

Background House dust mite (HDM) is the most common airborne source causing complex allergy symptoms. There are geographic differences in the allergen molecule sensitization profiles. Serological testing with allergen components may provide more clues for diagnosis and clinical management. Objective This study aims to investigate the sensitization profile of eight HDM allergen components in a large number of patients enrolled in the clinic and to analyze the relation of gender, age, and clinical symptoms in North China. Methods The 548 serum samples of HDM-allergic patients (ImmunoCAP® d1 or d2 IgE ≥0.35) were collected in Beijing City and divided in four different age groups and three allergic symptoms. The specific IgE of HDM allergenic components, Der p 1/Der f 1, Der p 2/Der f 2, Der p 7, Der p 10, Der p 21, and Der p 23, was measured using the micro-arrayed allergen test kit developed by Hangzhou Zheda Dixun Biological Gene Engineering Co., Ltd. The new system was validated by comparing to single-component Der p 1, Der p 2, and Der p 23 tests by ImmunoCAP in 39 sera. The epidemiological study of these IgE profiles and the relation to age and clinical phenotypes were analyzed. Results A greater proportion of male patients was in the younger age groups, while more female patients were in the adult groups. Both the sIgE levels and the positive rates (approximately 60%) against Der p 1/Der f 1 and Der p 2/Der f 2 were higher than for the Der p 7, Der p 10, and Der p 21 components (below 25%). The Der f 1 and Der p 2 positive rates were higher in 2–12-year-old children. The Der p 2 and Der f 2 IgE levels and positive rates were higher in the allergic rhinitis group. The positive rates of Der p 10 increased significantly with age. Der p 21 is relevant in allergic dermatitis symptom, while Der p 23 contributes to asthma development. Conclusion HDM groups 1 and 2 were the major sensitizing allergens, with group 2 being the most important component relevant to respiratory symptoms in North China. The Der p 10 sensitization tends to increase with age. Der p 21 and Der p 23 might be associated with the development of allergic skin disease and asthma, respectively. Multiple allergen sensitizations increased the risk of allergic asthma.