Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of robust precipitation changes across crop production areas in the 21st century

Significance Using 21st century climate model projections we show that for many crop-producing regions, average precipitation will change by more than the long-term natural variability, even under a low-emission scenario. However, emissions compatible with the Paris Agreement can significantly reduce cropped land affected. We identify the regions where adaptation measures are most needed. A warming climate will affect regional precipitation and hence food supply. However, only a few regions around the world are currently undergoing precipitation changes that can be attributed to climate change. Knowing when such changes are projected to emerge outside natural variability—the time of emergence (TOE)—is critical for taking effective adaptation measures. Using ensemble climate projections, we determine the TOE of regional precipitation changes globally and in particular for the growing areas of four major crops. We find relatively early (<2040) emergence of precipitation trends for all four crops. Reduced (increased) precipitation trends encompass 1–14% (3–31%) of global production of maize, wheat, rice, and soybean. Comparing results for RCP8.5 and RCP2.6 clearly shows that emissions compatible with the Paris Agreement result in far less cropped land experiencing novel climates. However, the existence of a TOE, even under the lowest emission scenario, and a small probability for early emergence emphasize the urgent need for adaptation measures. We also show how both the urgency of adaptation and the extent of mitigation vary geographically.
Model‐based analysis of therapeutic efficacy of blonanserin and risperidone in schizophrenia patients and effects on prolactin: A randomized double‐blind study

This study examined randomized controlled trial data for blonanserin and risperidone in Chinese schizophrenia patients (N = 264). Data related to historical changes in the Positive and Negative Syndrome Scale (PANSS) were used to successfully construct a longitudinal Emax model. Results: (a) The efficacy of the two drugs was similar after week 8, showing a small difference in PANSS reduction. (b) Using the model, we predicted that each 5‐point increase in the baseline FPOS (positive score in PANSS five‐factor subscales) leads to a decrease in the PANSS total scores at week 8 for 2 points in patients administered blonanserin. (c) The effect of blonanserin on prolactin (PRL) elevation was less. The model was used to predict that prolactin elevations in patients administered risperidone were 2.41‐fold of those in patients administered blonanserin. (d) Model quantitation showed that gender is a risk factor for prolactin elevation. Prolactin elevations in female patients were 2.95‐fold of the value in male patients administered the same drug. The model demonstrated Blonanserin has similar antischizophrenic efficacy and less serum prolactin rising compared to risperidone in Chinese patients.
Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin

Channelrhodopsins (ChRs) are light-gated transmembrane cation channels which are widely used for optogenetic technology. Replacing glutamate located at the central gate of the ion channel with positively charged amino acid residues will reverse ion selectivity and allow anion conduction. The structures and properties of the ion channel, the transport of chloride, and potential of mean force (PMF) of the chimera protein (C1C2) and its mutants, EK-TC, ER-TC and iChloC, were investigated by molecular dynamics simulation. The results show that the five-fold mutation in E122Q-E129R-E140S-D195N-T198C (iChloC) increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC, and results in an expanded ion channel pore size and decreased steric resistance. The iChloC mutant was also found to have a higher affinity for chloride ions and, based on surface electrostatic potential analysis, provides a favorable electrostatic environment for anion conduction. The PMF free energy curves revealed that high affinity Cl− binding sites are generated near the central gate of the three mutant proteins. The energy barriers for the EK-TC and ER-TC were found to be much higher than that of iChloC. The results suggest that the transmembrane ion channel of iChloC protein is better at facilitating the capture and transport of chloride ions.
Prevalence and Work-Related Factors Associated with Lower Back Musculoskeletal Disorders in Female Shellfish Gatherers in Saubara, Bahia-Brazil

Lower back musculoskeletal disorders (MSDs) are an important public health problem and the leading cause of disability worldwide, but with yet unknown prevalence among shellfish gatherers. To investigate the prevalence and work-related factors associated with lower back MSD in a population of female shellfish gatherers, an epidemiological cross-sectional study was carried out in Saubara, Bahia-Brazil, in 2013. The Brazilian version of the Job Content Questionnaire (JCQ) and the Nordic Musculoskeletal Questionnaire (NMQ), in addition to a questionnaire containing the physical demands adapted to the artisanal work, were applied to a random sample of 209 female shellfish gatherers. The prevalence of lower back MSD was 72.7%. Using multivariate logistic regression, the shellfish gatherers who had worked for more than 26 years in the activity showed a prevalence of 1.22 (95% CI: 1.04–1.44) times higher compared to those unexposed. Lower back MSD was 1.24 (95% CI: 1.08–1.42) times higher among those more exposed to work sitting with trunk flexion. Those performed manual handling and muscle force with the arms had a prevalence ratio of 1.18 (95% CI: 1.01–1.39). These results show the need for greater awareness of health and social welfare factors impacting workers in small-scale fisheries and will promote the elaboration of health care policies for this occupational class.
Diffuse large B‐cell lymphoma: 2019 update on diagnosis, risk stratification, and treatment

Diffuse large B‐cell lymphoma (DLBCL) is the most common type of aggressive non‐Hodgkin lymphoma originating from the germinal center, and it represents a heterogeneous group of diseases with variable outcomes that are differentially characterized by clinical features, cell of origin (COO), molecular features, and most recently, frequently recurring mutations.
Effective La-Na Co-Doped TiO2 Nano-Particles for Dye Adsorption: Synthesis, Characterization and Study on Adsorption Kinetics

The mesoporous La-Na co-doped TiO2 nanoparticles (NPs) have been synthesized by non-aqueous, solvent-controlled, sol-gel route. The substitutional doping of large sized Na+1 and La+3 at Ti4+ is confirmed by X-ray diffraction (XRD) and further supported by Transmission Electron Microscopy (TEM) and X-ray Photo-electron Spectroscopy (XPS). The consequent increase in adsorbed hydroxyl groups at surface of La-Na co-doped TiO2 results in decrease in pHIEP, which makes nanoparticle surface more prone to cationic methylene blue (MB) dye adsorption. The MB dye removal was examined by different metal doping, pH, contact time, NPs dose, initial dye concentration and temperature. Maximum dye removal percentage was achieved at pH 7.0. The kinetic analysis suggests adsorption dynamics is best described by pseudo second-order kinetic model. Langmuir adsorption isotherm studies revealed endothermic monolayer adsorption of Methylene Blue dye.
Hydraulic Traits Emerge as Relevant Determinants of Growth Patterns in Wild Olive Genotypes Under Water Stress

The hydraulic traits of plants, or the efficiency of water transport throughout the plant hydraulic system, could help to anticipate the impact of climate change and improve crop productivity. However, the mechanisms explaining the role of hydraulic traits on plant photosynthesis and thus, plant growth and yield, are just beginning to emerge. We conducted an experiment to identify differences in growth patterns at leaf, root and whole plant level among four wild olive genotypes and to determine whether hydraulic traits may help to explain such differences through their effect on photosynthesis. We estimated the relative growth rate (RGR), and its components, leaf gas exchange and hydraulic traits both at the leaf and whole-plant level in the olive genotypes over a full year. Photosynthetic capacity parameters were also measured. We observed different responses to water stress in the RGRs of the genotypes studied being best explained by changes in the net CO2 assimilation rate (NAR). Further, net photosynthesis, closely related to NAR, was mainly determined by hydraulic traits, both at leaf and whole-plant levels. This was mediated through the effects of hydraulic traits on stomatal conductance. We observed a decrease in leaf area: sapwood area and leaf area: root area ratios in water-stressed plants, which was more evident in the olive genotype Olea europaea subsp. guanchica (GUA8), whose RGR was less affected by water deficit than the other olive genotypes. In addition, at the leaf level, GUA8 water-stressed plants presented a better photosynthetic capacity due to a higher mesophyll conductance to CO2 and a higher foliar N. We conclude that hydraulic allometry adjustments of whole plant and leaf physiological response were well coordinated, buffering the water stress experienced by GUA8 plants. In turn, this explained their higher relative growth rates compared to the rest of the genotypes under water-stress conditions.
Heterologous prime-boost vaccination protects from EBV antigen expressing lymphomas.

The Epstein Barr virus (EBV) is one of the predominant tumor viruses in humans, but so far no therapeutic or prophylactic vaccination against this transforming pathogen is available. We demonstrated that heterologous prime-boost vaccination with the nuclear antigen 1 of EBV (EBNA1) either targeted to the DEC205 receptor on dendritic cells or expressed from a recombinant modified vaccinia virus Ankara (MVA) vector improved priming of antigen-specific CD4+ T-cell help. This help supported the expansion and maintenance of EBNA1 specific CD8+ T cells that are most efficiently primed by recombinant adenoviruses that encode EBNA1. These combined CD4+ and CD8+ T-cell responses protected from EBNA1 expressing T and B cell lymphomas, including lymphoproliferations that emerge spontaneously after EBNA1 expression. In particular the heterologous EBNA1-expressing adenovirus, boosted by EBNA1-encoding MVA vaccination, demonstrated protection as prophylactic and therapeutic treatment of the respective lymphoma challenges. Therefore, we suggest that such heterologous prime-boost vaccinations should be further explored for clinical development against EBV-associated malignancies as well as symptomatic primary EBV infection.
Why is sterility virulence most common in sexually transmitted infections? Examining the role of epidemiology

Sterility virulence, or the reduction in host fecundity due to infection, occurs in many host–pathogen systems. Notably, sterility virulence is more common for sexually transmitted infections (STIs) than for directly transmitted pathogens, while other forms of virulence tend to be limited in STIs. This has led to the suggestion that sterility virulence may have an adaptive explanation. By focusing upon finite population models, we show that the observed patterns of sterility virulence can be explained by consideration of the epidemiological differences between STIs and directly transmitted pathogens. In particular, when pathogen transmission is predominantly density invariant (as for STIs), and mortality is density dependent, sterility virulence can be favored by demographic stochasticity, whereas if pathogen transmission is predominantly density dependent, as is common for most directly transmitted pathogens, sterility virulence is disfavored. We show these conclusions can hold even if there is a weak selective advantage to sterilizing.
A Review and Hypothesized Model of the Mechanisms That Underpin the Relationship Between Inflammation and Cognition in the Elderly

Age is associated with increased risk for several disorders including dementias, cardiovascular disease, atherosclerosis, obesity, and diabetes. Age is also associated with cognitive decline particularly in cognitive domains associated with memory and processing speed. With increasing life expectancies in many countries, the number of people experiencing age-associated cognitive impairment is increasing and therefore from both economic and social terms the amelioration or slowing of cognitive aging is an important target for future research. However, the biological causes of age associated cognitive decline are not yet, well understood. In the current review, we outline the role of inflammation in cognitive aging and describe the role of several inflammatory processes, including inflamm-aging, vascular inflammation, and neuroinflammation which have both direct effect on brain function and indirect effects on brain function via changes in cardiovascular function.
Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences

In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.
The complete structure of the human TFIIH core complex

Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
Growth and breastfeeding of preterm infants receiving neonatal tele homecare compared to hospital-based care

Objective Neonatal tele-homecare implies that parents of clinically stable preterm infants can manage tube feeding and establishment of oral feeding in the home. Support is provided from the neonatal intensive care unit (NICU) through a telehealth service. The aim of this study was to compare growth and breastfeeding rates amongst infants being managed in the NICU (conventional care) and by neonatal tele-homecare. Methods A total of 96 preterm infants with tube feeding requirements participated in the observational study of neonatal tele-homecare. Retrospective data in 278 preterm infants receiving standard care in the same neonatal intensive care unit prior to implementation of neonatal tele-homecare were used for comparison. Rates of breastfeeding and growth were monitored during neonatal tele-homecare. Infant weights were converted to standard deviation weight-for-age z-scores based on a reference. Results There was no significant difference in rates of exclusive breastfeeding between the neonatal tele-homecare infants and the controls. Among the very preterm singleton infants more neonatal tele-homecare infants were exclusively breastfed at discharge compared to the controls (p=0.02). There was no difference in median weight for age z-scores at discharge. Conclusion The breastfeeding rates in infants receiving neonatal tele-homecare at time of discharge were higher compared to historical controls. Growth rates remained the same amongst groups. This study demonstrates that neonatal tele-homecare may be an appropriate model of care for the management of preterm infants outside of the hospital environment; with the added benefit of higher rates of breastfeeding at time of discharge.
RTX Toxins Ambush Immunity’s First Cellular Responders

The repeats-in-toxin (RTX) family represents a unique class of bacterial exoproteins. The first family members described were toxins from Gram-negative bacterial pathogens; however, additional members included exoproteins with diverse functions. Our review focuses on well-characterized RTX family toxins from Aggregatibacter actinomycetemcomitans (LtxA), Mannheimia haemolytica (LktA), Bordetella pertussis (CyaA), uropathogenic Escherichia coli (HlyA), and Actinobacillus pleuropneumoniae (ApxIIIA), as well as the studies that have honed in on a single host cell receptor for RTX toxin interactions, the β2 integrins. The β2 integrin family is composed of heterodimeric members with four unique alpha subunits and a single beta subunit. β2 integrins are only found on leukocytes, including neutrophils and monocytes, the first responders to inflammation following bacterial infection. The LtxA, LktA, HlyA, and ApxIIIA toxins target the shared beta subunit, thereby targeting all types of leukocytes. Specific β2 integrin family domains are required for the RTX toxin’s cytotoxic activity and are summarized here. Research examining the domains of the RTX toxins required for cytotoxic and hemolytic activity is also summarized. RTX toxins attack and kill phagocytic immune cells expressing a single integrin family, providing an obvious advantage to the pathogen. The critical question that remains, can the specificity of the RTX-β2 integrin interaction be therapeutically targeted?
Improved prediction of brain age using multimodal neuroimaging data

Brain age prediction based on imaging data and machine learning (ML) methods has great potential to provide insights into the development of cognition and mental disorders. Though different ML models have been proposed, a systematic comparison of ML models in combination with imaging features derived from different modalities is still needed. In this study, we evaluate the prediction performance of 36 combinations of imaging features and ML models including deep learning. We utilize single and multimodal brain imaging data including MRI, DTI, and rs‐fMRI from a large data set with 839 subjects. Our study is a follow‐up to the initial work (Liang et al., 2019. Human Brain Mapping) to investigate different analytic strategies to combine data from MRI, DTI, and rs‐fMRI with the goal to improve brain age prediction accuracy. Additionally, the traditional approach to predicting the brain age gap has been shown to have a systematic bias. The potential nonlinear relationship between the brain age gap and chronological age has not been thoroughly tested. Here we propose a new method to correct the systematic bias of brain age gap by taking gender, chronological age, and their interactions into consideration. As the true brain age is unknown and may deviate from chronological age, we further examine whether various levels of behavioral performance across subjects predict their brain age estimated from neuroimaging data. This is an important step to quantify the practical implication of brain age prediction. Our findings are helpful to advance the practice of optimizing different analytic methodologies in brain age prediction.
Genotoxic Effects of Tributyltin and Triphenyltin Isothiocyanates, Cognate RXR Ligands: Comparison in Human Breast Carcinoma MCF 7 and MDA-MB-231 Cells

The cytotoxicity of two recently synthesized triorganotin isothiocyanate derivatives, nuclear retinoid X receptor ligands, was tested and compared in estrogen-receptor-positive MCF 7 and -negative MDA-MB-231 human breast carcinoma cell lines. A 48 h MTT assay indicated that tributyltin isothiocyanate (TBT-ITC) is more cytotoxic than triphenyltin isothiocyanate (TPT-ITC) in MCF 7 cells, and the same trend was observed in the MDA-MB-231 cell line. A comet assay revealed the presence of both crosslinks and increasing DNA damage levels after the 17 h treatment with both derivatives. Differences in cytotoxicity of TBT-ITC and TPT-ITC detected by FDA staining correspond to the MTT data, communicating more pronounced effects in MCF 7 than in the MDA-MB-231 cell line. Both derivatives were found to cause apoptosis, as shown by the mitochondrial membrane potential (MMP) depolarization and caspase-3/7 activation. The onset of caspase activation correlated with MMP dissipation and the total cytotoxicity more than with the amount of active caspases. In conclusion, our data suggest that the DNA damage induced by TBT-ITC and TPT-ITC treatment could underlie their cytotoxicity in the cell lines studied.
Effective Medium Method for Chloride Diffusion Coefficient of Mature Fly Ash Cement Paste

The chloride diffusion coefficient of concrete plays an essential role in the durability assessment and design of concrete structures built in chloride-laden environments. The purpose of this paper is to present an effective medium method (EMM) for evaluating the chloride diffusion coefficient of mature fly ash cement paste. In this method, a numerical method is used to estimate the degrees of hydration of cement and fly ash. Fly ash cement paste is then modeled as a two-phase composite material, composed of a solid phase and a pore space. By introducing the percolation theory, the EMM is modified to derive the chloride diffusion coefficient of fly ash cement paste in an analytical manner. To verify the EMM, a chloride diffusion test of fly ash cement paste at a curing age of up to 540 days is conducted. It is shown that, within a reasonable fly ash content, a larger fly ash content and/or curing age results in a smaller chloride diffusion coefficient. The chloride diffusion coefficient decreases with a decreasing water/binder ratio. Finally, the validity of the EMM is verified with experimental results.