Miracle-dz/UniFAR-FTUs huggingface dataset:
MALE STERILITY 3 encodes a plant homeodomain‐finger protein for male fertility in soybean

Abstract Male‐sterile plants are used in hybrid breeding to improve yield in soybean (Glycine max (L.) Merr. ). Developing the capability to alter fertility under different environmental conditions could broaden germplasm resources and simplify hybrid production. However, molecular mechanisms potentially underlying such a system in soybean were unclear. Here, using positional cloning, we identified a gene, MALE STERILITY 3 (MS3), which encodes a nuclear‐localized protein containing a plant homeodomain (PHD)‐finger domain. A spontaneous mutation in ms3 causing premature termination of MS3 translation and partial loss of the PHD‐finger. Transgenetic analysis indicated that MS3 knockout resulted in nonfunctional pollen and no self‐pollinated pods, and RNA‐seq analysis revealed that MS3 affects the expression of genes associated with carbohydrate metabolism. Strikingly, the fertility of mutant ms3 can restore under long‐d conditions. The mutant could thus be used to create a new, more stable photoperiod‐sensitive genic male sterility line for two‐line hybrid seed production, with significant impact on hybrid breeding and production.
Recombinant human Hsp110-gp100 chaperone complex vaccine is nontoxic and induces response in advanced stage melanoma patients

Supplemental Digital Content is available in the text. Heat shock proteins (hsp) are intracellular chaperones that possess extracellular immunostimulatory properties when complexed with antigens. A recombinant Hsp110-gp100 chaperone complex vaccine showed an antitumor response and prolonged survival in murine melanoma. A phase Ib dose-escalation study of a recombinant human Hsp110-gp100 vaccine in advanced-stage melanoma patients was performed to evaluate toxicity, immunostimulatory potential and clinical response. Patients with pretreated, unresectable stage IIIB/C/IV melanoma received the chaperone complex vaccine in a dose-escalation protocol; three vaccinations over a 43-day-period. Tumor response, clinical toxicity and immune response were measured. Ten patients (eight female, median age 70 years) were enrolled and two patients had grade 1 adverse events; minor skin rash, hyperhidrosis and fever (no grade 2 or higher adverse events). Median progression-free survival was longer for lower vaccine doses as compared to the maximum dose of 180 mcg (4.5 vs. 2.9 months; P = 0.018). The lowest dose patients (30 and 60 mcg) had clinical tumor responses (one partial response, one stable disease). CD8+ T cell interferon-γ responses to gp100 were greater in the clinically responding patients. A pattern of B cell responses to vaccination was not observed. Regulatory T cell populations and co-stimulatory molecules including cytotoxic T-lymphocyte-associated protein 4 and PD-1 appeared to differ in responders versus nonresponders. A fully recombinant human Hsp110-gp100 chaperone complex vaccine had minimal toxicity, measurable tumor responses at lower doses and produced peripheral CD8+ T cell activation in patients with advanced, pretreated melanoma. Combination with currently available immunotherapies may augment clinical responses.
Polyproline Peptide Aggregation with Klebsiella pneumoniae Extracellular Polysaccharides Exposes Biofilm Associated Bacteria

Klebsiella pneumoniae bacterial infections are a major threat to human health as mortality rates are steadily on the rise. A defining characteristic of K. pneumoniae is the robust polysaccharide capsule that aids in resistance to the human immune system. ABSTRACT Klebsiella pneumoniae produces a thick capsule layer composed of extracellular polysaccharides protecting the bacterial cells from clearance by innate host immunity during infection. Here we characterize the interactions of a structurally diverse set of host defense peptides with K. pneumoniae extracellular polysaccharides. Remarkably, we found that all host defense peptides were active against a diverse set of K. pneumoniae strains, including hypermucoviscous strains with extensive capsule production, and aggregated with extracted capsule. Interestingly, the polyproline peptide bac7 (1-35), was the most potent antimicrobial and induced the most capsule aggregation. In addition to capsule aggregation, we found that bac7 (1-35) could also disrupt pre-formed hypermucoviscous K. pneumoniae biofilm. Further analysis using scanning electron microscopy revealed the biofilm matrix of a hypermucoviscous strain is removed by bac7 (1-35) exposing associated bacterial cells. This is the first description of a host defense peptide interacting with capsular and biofilm extracellular polysaccharides to expose cells from a K. pneumoniae biofilm matrix and suggests that features of polyproline peptides may be uniquely suited for extracellular polysaccharide interactions. IMPORTANCE Klebsiella pneumoniae bacterial infections are a major threat to human health as mortality rates are steadily on the rise. A defining characteristic of K. pneumoniae is the robust polysaccharide capsule that aids in resistance to the human immune system. We have previously discovered that a synthetic peptide could aggregate with capsule polysaccharides and disrupt the capsule of K. pneumoniae. Here we describe that host defense peptides also aggregate with capsule produced from hypermucoviscous K. pneumoniae, revealing this mechanism is shared by natural peptides. We found the polyproline peptide bac7 (1-35) had the greatest antimicrobial activity and caused the most capsule aggregation. Interestingly, bac7 (1-35) also removed the biofilm matrix of hypermucoviscous K. pneumoniae exposing the associated bacterial cells. This is the first description of a polyproline peptide interacting with capsular and biofilm polysaccharides to expose cells from a K. pneumoniae biofilm matrix.
ExceS-A: an exon-centric split aligner

Abstract Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat-based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.
Hepatitis delta coinfection in persons with HIV: misdiagnosis and disease burden in Italy

ABSTRACT Hepatitis Delta virus (HDV) causes severe liver disease. Due to similarities in transmission routes, persons living with HIV (PLWH) are at risk of HDV infection. This analysis investigates the prevalence and the long-term clinical outcome of people with HDV in a large cohort of PLWH. We retrieved HBsAg ± anti-HDV positive PLWH enrolled from 1997 to 2015 in the multicentre, prospective ICONA study. The primary endpoint was a composite clinical outcome (CCO = having experienced ≥1 of the following: Fib4 score >3.25; diagnosis of cirrhosis; decompensation; hepatocellular carcinoma or liver-related death). Kaplan–Meier curves and unweighted and weighted Cox regression models were used for data analysis. Less than half of HBsAg positive patients had been tested for anti-HDV in clinical practice. After testing stored sera, among 617 HBV/HIV cases, 115 (19%) were anti-HDV positive; 405 (65%) HBV monoinfected; 99 (16%) undeterminate. The prevalence declined over the observation period. HDV patients were more often males, intravenous drug users, HCV coinfected. After a median of 26 months, 55/115 (48%) developed CCO among HDV+; 98/403 (24%) among HBV monoinfected; 18/99 (18%) in HDV unknown (p < 0.001). After controlling for geographical region, alcohol consumption, CD4 count, anti-HCV status and IFN-based therapies, the association with HDV retained statistical significance [HR = 1.67 (1.15, 2.95; p = 0.025)]. HDV infection among PLWH is underdiagnosed, although HDV entails an high risk of liver disease progression. Because effective drugs to treat HDV are now available, it is even more crucial to identify PLWH at an early stage of liver disease.
Experimental demonstration of improved magnetorelaxometry imaging performance using optimized coil configurations

Abstract Background Magnetorelaxometry imaging is an experimental imaging technique capable of reconstructing magnetic nanoparticle distributions inside a volume noninvasively and with high specificity. Thus, magnetorelaxometry imaging is a promising candidate for monitoring a number of therapeutical approaches that employ magnetic nanoparticles, such as magnetic drug targeting and magnetic hyperthermia, to guarantee their safety and efficacy. Prior to a potential clinical application of this imaging modality, it is necessary to optimize magnetorelaxometry imaging systems to produce reliable imaging results and to maximize the reconstruction accuracy of the magnetic nanoparticle distributions. Multiple optimization approaches were already applied throughout a number of simulation studies, all of which yielded increased imaging qualities compared to intuitively designed measurement setups. Purpose None of these simulative approaches was conducted in practice such that it still remains unclear if the theoretical results are achievable in an experimental setting. In this study, we demonstrate the technical feasibility and the increased reconstruction accuracy of optimized coil configurations in two distinct magnetorelaxometry setups. Methods The electromagnetic coil positions and radii of a cuboidal as well as a cylindrical magnetorelaxometry imaging setup are optimized by minimizing the system matrix condition numbers of their corresponding linear forward models. The optimized coil configurations are manufactured alongside with two regular coil grids. Magnetorelaxometry measurements of three cuboidal and four cylindrical magnetic nanoparticle phantoms are conducted, and the resulting reconstruction qualities of the optimized and the regular coil configurations are compared. Results The computed condition numbers of the optimized coil configurations are approximately one order of magnitude lower compared to the regular coil grids. The reconstruction results show that for both setups, every phantom is recovered more accurately by the optimized coil configurations compared to the regular coil grids. Additionally, the optimized coil configurations yield better signal qualities. Conclusions The presented experimental study provides a proof of the practicality and the efficacy of optimizing magnetorelaxometry imaging systems with respect to the condition numbers of their system matrices, previously only demonstrated in simulations. From the promising results of our study, we infer that the minimization of the system matrix condition number will also enable the practical optimization of other design parameters of magnetorelaxometry imaging setups (e.g., sensor configuration, coil currents, etc.) in order to improve the achievable reconstruction qualities even further, eventually paving the way towards clinical application of this imaging modality.
Disparities in smoking prevalence and associations with mental health and substance use disorders in underserved communities across the United States

Smoking contributes to the top 3 deadliest cancers, cancers of the lung, colon, and pancreas, which account for nearly 40% of all cancer‐related deaths in the United States. Despite historicly low smoking rates, substantial disparities remain among people with mental health conditions and substance use disorders (SUDs).
Hair removal in dermoscopy images using variational autoencoders

In recent years, melanoma is rising at a faster rate compared to other cancers. Although it is the most serious type of skin cancer, the diagnosis at early stages makes it curable. Dermoscopy is a reliable medical technique used to detect melanoma by using a dermoscope to examine the skin. In the last few decades, digital imaging devices have made great progress which allowed capturing and storing high‐quality images from these examinations. The stored images are now being standardized and used for the automatic detection of melanoma. However, when the hair covers the skin, this makes the task challenging. Therefore, it is important to eliminate the hair to get accurate results.
Predictors of Mortality in Individuals with Dementia in the National Alzheimer's Coordinating Center.

BACKGROUND Dementia is one of the top causes of death worldwide, but individuals with dementia and their caregivers report that knowing what to expect, including regarding approaching end of life, is an unmet need. OBJECTIVE To identify predictors of death in individuals with Alzheimer disease (AD) dementia, Lewy body dementia (LBD), vascular dementia, and frontotemporal dementia. METHODS The study used data from National Alzheimer's Coordinating Center participants with dementia and an etiologic diagnosis of AD, Lewy body disease, frontotemporal lobar degeneration (FTLD, with or without motor neuron disease), or vascular dementia. Analyses included median survival across dementia types and predictors of death at 5 years based on baseline demographics and clinical measure performance. Five-year survival probability tables were stratified by predictor values. RESULTS Individuals with AD had the longest survival (median 6 years), followed by FTLD (5 years), and vascular dementia and LBD (each 4 years). The strongest predictors of death for the full cohort were dementia type (higher risk with non-AD dementias), sex (higher risk with male sex), and race and ethnicity (higher risk with white and non-Hispanic participants). Age was associated with higher mortality risk across the non-Alzheimer dementias; other significant associations included worse cognitive status (FTLD, LBD) and more depression (LBD). CONCLUSION Results can help clinicians counsel individuals with dementia and families regarding average dementia trajectories; findings regarding individual risk factors can aid individualizing expectations. Further research is needed to investigate drivers of mortality in the non-AD dementias to improve counseling and help identify potentially modifiable factors.
Flotillin 2 Facilitates the Infection of a Plant Virus in the Gut of Insect Vector

Plant viral diseases are a major threat to world agriculture. The transmission of 80% of plant viruses requires vector insects, and 54% of vector-borne plant viruses are persistent-circulative viruses, which must overcome the barriers of gut cells with the help of proteins on the cell surface. ABSTRACT Most plant viruses require insect vectors for transmission. One of the key steps for the transmission of persistent-circulative plant viruses is overcoming the gut barrier to enter epithelial cells. To date, little has been known about viral cofactors in gut epithelial cells of insect vectors. Here, we identified flotillin 2 as a plasma membrane protein that facilitates the infection of rice stripe virus (RSV) in its vector, the small brown planthopper. Flotillin 2 displayed a prominent plasma membrane location in midgut epithelial cells. The nucleocapsid protein of RSV and flotillin 2 colocalized on gut microvilli, and a nanomolar affinity existed between the two proteins. Knockout of flotillin 2 impeded the entry of virions into epithelial cells, resulting in a 57% reduction of RSV levels in planthoppers. The knockout of flotillin 2 decreased disease incidence in rice plants fed by viruliferous planthoppers from 40% to 11.7%. Furthermore, flotillin 2 mediated the infection of southern rice black-streaked dwarf virus in its vector, the white-backed planthopper. This work implies the potential of flotillin 2 as a target for controlling the transmission of rice stripe disease. IMPORTANCE Plant viral diseases are a major threat to world agriculture. The transmission of 80% of plant viruses requires vector insects, and 54% of vector-borne plant viruses are persistent-circulative viruses, which must overcome the barriers of gut cells with the help of proteins on the cell surface. Here, we identified flotillin 2 as a membrane protein that mediates the cell entry of rice stripe virus in its vector insect, small brown planthopper. Flotillin 2 displays a prominent cellular membrane location in midgut cells and can specifically bind to virions. The loss of flotillin 2 impedes the entry of virions into the midgut cells of vector insects and substantially suppresses viral transmission to rice. Therefore, flotillin 2 may be a promising target gene for manipulation in vector insects to control the transmission of rice stripe disease and perhaps that of other rice virus diseases in the future.
Analysis of Informative Content on Cerebral Palsy Presented in Brazilian-Portuguese YouTube Videos

Abstract Aims: To describe the characteristics of the most accessed YouTube videos in Brazilian-Portuguese on cerebral palsy (CP), and to analyze content of informational videos about this topic. Methods: This was a cross-sectional study. Searching on YouTube website was conducted by two independent examiners between November and December 2019, using the keywords “Paralisia Cerebral” sorted by videos’ number of views. Videos that did not present content related to CP or duplicate videos were excluded. The interaction parameters and content characteristics of the included videos were extracted. To access the trustworthiness and quality of informational videos, the modified Discern checklist and the Global Quality Score was used. Results: Following the eligibility criteria 90 videos were included. Fifty-three (53) were classified as experiential videos and 37 as informational videos. Informational videos presented multi-topics about different aspects of CP. This group of videos presented moderate trustworthiness due to the lack of scientific evidence content. Informational videos had good quality and generally good flow. Conclusion: YouTube presented a large number of videos about CP in Brazilian-Portuguese. Informational videos are useful for patients and healthcare providers; however, it is necessary to included information about scientific evidence, as a strategy to facilitate and promote knowledge translation.
Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices

We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. ABSTRACT Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage. IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.
Synchrophasors-Assisted IPII-Based Intelligent Relaying for Transmission Lines Including UPFC

Abstract This paper proposes a synchrophasors-assisted intelligent relaying scheme for transmission lines compensated by Unified Power Flow Controller (UPFC). The algorithm uses a new relaying signal termed as imaginary part of integrated impedance (IPII). The synchronized phasor measurements at both ends of the transmission line are used to extract voltage and current phasors from instantaneous voltage and current signals. The voltage and current phasors are utilized to derive IPII of each phase. Further, IPII of each phase is used as input to a data-mining model termed as decision tree (DT) which provides the final relaying decision. The proposed algorithm is validated on real-time digital simulator (RTDS) platform, and the results obtained indicate that the proposed scheme is both dependable and secure in protecting transmission system compensated by UPFC.
Predictive power of a body shape index and traditional anthropometric indicators for cardiovascular disease: a cohort study in rural Xinjiang, China

Abstract Background A body shape index (ABSI) has been proven to be related to a population’s CVD incidence. However, the application of this indicator has produced different results. Aim This study aimed to evaluate the applicability of the ABSI in predicting the incidence of CVD in rural Xinjiang, China, and compare it with waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR), and body mass index (BMI). Subjects and methods 5375 people aged 18 years or older were included in the study. We used the Cox proportional hazard model to evaluate the relationship between WC, WHR, WHtR, BMI, and ABSI and the incidence of CVD, the area under the curve (AUC) to evaluate the predictive power of each anthropometric index for the incidence of CVD, and restricted cubic splines are used to analyse the trend relationship between anthropometric indicators and the incidence of CVD. Results After multivariate adjustment, standardised WC, WHR, WHtR, BMI, and ABSI all positively correlated with the incidence of CVD. WC had the highest HR (95% CI) value, 1.64 (1.51–1.78), and AUC (95% CI) value, 0.7743 (0.7537–0.7949). ABSI had the lowest HR (95% CI) value, 1.21(1.10–1.32), and AUC (95% CI) value, 0.7419 (0.7208–0.7630). In the sex-specific sensitivity analysis, the predictive ability of traditional anthropometric indicators for the incidence of CVD is higher than that of ABSI. Conclusions In the rural areas of Xinjiang, the traditional anthropometric indicators of WC had better ability to predict the incidence of CVD than ABSI.