A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle.

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle.

The intramuscular fat (IMF) content of beef determined the meat quality, and the market value of beef varies with different breeds. To provide some new approaches for improving meat quality and cattle breed improvement, 24-month-old Qinchuan cattle (Q, n = 6), Nanyang cattle (N, n = 6), and Japanese black cattle (J, n = 6) were selected. IMF content of the J group (16.92 ± 1.08%) is remarkably higher than that of indigenous Chinese cattle (Q, 13.38 ± 1.08%, and N, 12.35 ± 1.22%). Monounsaturated fatty acids and polyunsaturated fatty acids in the J group are higher than the Q and creatine, lysine, and glutamine are the three most abundant amino acids in beef, which contribute to the flavor formation. Similarly, IMF content-related genes were enriched in four vital KEGG pathways, including fatty acid metabolism, biosynthesis of unsaturated fatty acids, fatty acid elongation, and insulin resistance. Moreover, weighted genes coexpression network analysis (WGCNA) revealed that ITGB1 is the critical gene associated with the IMF content. This study compares transcriptome and metabolome of local and high-IMF cattle breeds, providing data for native cattle breeding and improvement of beef quality.

Experimental determination and QSAR analysis of the rate constants for SO5•- reactions with aromatic micropollutants in water.

S(IV)-based systems used for advanced oxidation processes (AOPs) have been constructed for the degradation of organic contaminants via oxysulfur radicals, including SO3•-, SO4•-, and SO5•-. Although SO5•- is proposed as an active species in AOPs processes, research on the reactivity of SO5•- has remained unclear. In this work, 53 target aromatic micropollutants (AMPs), including 13 phenols, 27 amines, and 13 PPCPs were selected to determine the second-order reaction rate constants for SO5•- using the competitive kinetics method, in which the [Formula: see text] values, observed at pH 4 ranged from (2.44 ± 0.00) × 105 M-1 s-1 to (4.41 ± 0.28) × 107 M-1 s-1. Quantitative structure-activity relationship (QSAR) models for the oxidation of AMPs by SO5•- were developed based on 40 [Formula: see text] values of amines and phenols, and their molecular descriptors, using the stepwise multiple linear regression method. This comprehensive model exhibited the excellent goodness-of-fit (Radj2 = 0.802), robustness (QLOO2 = 0.749), and predictability (Qext2 = 0.656), and the one-electron oxidation potential (Eox), energy of the highest occupied molecular orbital energy (EHOMO), and most positive net atomic charge on the carbon atoms (qC+) were considered the most influential descriptors for the comprehensive model, indicating that SO5•- oxidizes pollutants via single electron transfer reaction and exhibits a strong oxidation capacity, especially for pollutants containing electron-donating groups. Moreover, the [Formula: see text] values of 13 PPCPs were predicted using this comprehensive model, which suggested the practical application significance of the QSAR model. This study emphasizes the direct oxidation capacity of SO5•-, which is important to evaluate and simulate AOPs based on S(IV).

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle.

A genome-wide association study (GWAS) is an effective tool for identifying the dominant genes of complex economic traits in livestock by statistical analysis of genotype data and measured phenotype data. In this study, we rigorously measured 14 body conformation traits in 254 Qinchuan cattle, comprising body weight (BW), body height (BOH), back height (BAH), buttock height (BUH), chest depth (CD), chest width (CW), hip cross height (HCH), body length (BL), hip width (HW), rump length (RL), pin bone width (PBW), chest girth (CG), abdomen circumference (AG), and calf circumference (CC). After quality control, 281,889 SNPs were generated for GWAS with different traits. A total of 250 suggestive SNPs (p < 3.54 × 10-6) were screened and 37 candidate genes were annotated. Furthermore, we performed a linkage disequilibrium analysis of SNP loci and considered published studies, identifying the eight genes (ADAMTS17, ALDH1A3, CHSY1, MAGEL2, MEF2A, SYNM, CNTNAP5, and CTNNA3) most likely to be involved in growth traits. This study provides new insights into the regulatory mechanisms of bovine body size development, which can be very useful in the development of management and breeding strategies.

ComparePD: Improving protein-DNA complex model comparison with hydrogen bond energy-based metrics.

Computational modeling of protein-DNA complex structures has important implications in biomedical applications such as structure-based, computer aided drug design. A key step in developing methods for accurate modeling of protein-DNA complexes is similarity assessment between models and their reference complex structures. Existing methods primarily rely on distance-based metrics and generally do not consider important functional features of the complexes, such as interface hydrogen bonds that are critical to specific protein-DNA interactions. Here, we present a new scoring function, ComparePD, which takes interface hydrogen bond energy and strength into account besides the distance-based metrics for accurate similarity measure of protein-DNA complexes. ComparePD was tested on two datasets of computational models of protein-DNA complexes generated using docking (classified as easy, intermediate, and difficult cases) and homology modeling methods. The results were compared with PDDockQ, a modified version of DockQ tailored for protein-DNA complexes, as well as the metrics employed by the community-wide experiment CAPRI (Critical Assessment of PRedicted Interactions). We demonstrated that ComparePD provides an improved similarity measure over PDDockQ and the CAPRI classification method by considering both conformational similarity and functional importance of the complex interface. ComparePD identified more meaningful models as compared to PDDockQ for all the cases having different top models between ComparePD and PDDockQ except for one intermediate docking case.

Molecular Oxygen Activation by Citric Acid Boosted Pyrite-Photo-Fenton Process for Degradation of PPCPs in Water.

Pyrite has been used in photo-Fenton reactions for the degradation of pollutants, but the application of photo-Fenton processes with extra H2O2 in real water/wastewater treatment has still been limited by the economic cost of H2O2 and artificial light sources. Herein, citric acid (CA) and simulated/natural sunlight are used to develop a pyrite-based photo-Fenton system (pyrite-CA-light) in situ generating H2O2 through the enhanced activation of molecular oxygen. The degradation of pharmaceuticals and personal care products (PPCPs), especially acetaminophen (APAP) as the main target pollutant, in the pyrite-CA-light system was investigated. The effects of influencing factors such as various organic acids, APAP concentration, pH, pyrite dosage, CA concentration and co-existing anions (HCO3-, Cl-, NO3-, SO42- and H2PO4-) were examined. At a pyrite dosage of 0.1 g L-1, CA concentration of 0.6 mM and an initial pH of 6.0, the degradation efficiency of APAP (30 µM) was 99.1% within 30 min under the irradiation of xenon lamp (70 W, λ ≥ 350 nm). Almost the same high efficiency of APAP degradation (93.9%) in the system was achieved under natural sunlight irradiation (ca. 650 W m-2). The scavenging experiments revealed that the dominant active species for degrading APAP was hydroxyl radical (HO•). Moreover, a quantitative structural-activity relationship (QSAR) model for pseudo-first-order rate constants (kobs) was established with a high significance (R2 = 0.932, p = 0.001) by using three descriptors: octanol-water partition coefficient (logKow), dissociation constant (pKa) and highest occupied molecular orbital (HOMO). This work provides an innovative strategy of the photo-Fenton process for the degradation of PPCPs using natural minerals and ordinary carboxylic acid under sunlight.

Effect of Co-Existing Cations and Anions on the Adsorption of Antibiotics on Iron-Containing Minerals.

The adsorption of antibiotics on minerals is an important process in their environment behavior. The adsorption behavior of antibiotics on iron-containing minerals and the effect of co-existing cations and anions were studied in this work. Magnetite, hematite, goethite and kaolin were selected as the representative minerals and characterized by SEM, XRD and BET. A total of eight antibiotics, including three quinolones, three sulfonamides and two mycins were chosen as the research targets. Results showed a higher adsorption amount of quinolones than that of sulfonamides and mycins on the surface of iron-containing minerals in most mineral systems. The adsorption isotherms of quinolones can be well fitted using the Freundlich models. The effects of five cations and five anions on the adsorption of quinolones were investigated, among which Mg2+, Ca2+, HCO3- and H2PO4- mainly showed significant inhibition on the adsorption, while the effects of K+, Na+, NH4+, Cl-, NO3- and SO42- showed less. Natural surface water samples were also collected and used as media to investigate the adsorption behavior of quinolones on iron-containing minerals. The buffering capacity of the natural water kept the reaction solution at circumneutral conditions, and the adsorption amount was mostly promoted in the goethite system (from 0.56~0.78 µmol/g to 0.52~1.43 µmol/g), but was inhibited in the other systems (magnetite: from 1.13~1.33 µmol/g to 0.45~0.76 µmol/g; hematite: from 0.52~0.65 µmol/g to 0.02~0.18 µmol/g; kaolin: from 1.98~1.99 µmol/g to 0.90~1.40 µmol/g). The results in this work help to further understand the transportation and fate of antibiotics in an aqueous environment.

Aquatic photochemistry of Cu(II) in the presence of As(III): Mechanistic insights from Cu(III) production and As(III) oxidation under neutral pH conditions.

Surface complexation between arsenite (As(III)) and colloidal metal hydroxides plays an important role not only in the immobilization and oxidation of As(III) but also in the cycle of the metal and the fate of their ligands. However, the photochemical processes between Cu(II) and As(III) are not sufficiently understood. In this work, the photooxidation of As(III) in the presence of Cu(II) under neutral pH conditions was investigated in water containing 200 µM Cu(II) and 5 µM As(III) under simulated solar irradiation consisting of UVB light. The results confirmed the complexation between As(III) and Cu(II) hydroxides, and the photooxidation of As(III) is attributed to the ligand-to-metal charge transfer (LMCT) process and Cu(III) oxidation. The light-induced LMCT process results in simultaneous As(III) oxidation and Cu(II) reduction, then produced Cu(I) undergoes autooxidation with O2 to produce O2•⁻ and H2O2, and further the Cu(I)-Fenton reaction produces Cu(III) that can oxidize As(III) efficiently (kCu(III)+As(III) = 1.02 × 109 M-1 s-1). The contributions from each pathway (ρrCu(II)-As(III)+hv = 0.62, ρrCu(III)+As(III) = 0.38) were obtained using kinetic analysis and simulation. Sunlight experiments showed that the pH range of As(III) oxidation could be extended to weak acidic conditions in downstream water from acid mine drainage (AMD). This work helps to understand the environmental chemistry of Cu(II) and As(III) regarding their interaction and photo-induced redox reactions.

Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.

Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).

Spatial analysis of tuberculosis treatment outcomes in Shanghai: implications for tuberculosis control.

OBJECTIVES: Tuberculosis (TB) treatment outcomes are a key indicator in the assessment of TB control programs. We aimed to identify spatial factors associated with TB treatment outcomes, and to provide additional insights into TB control from a geographical perspective. METHODS: We collected data from the electronic TB surveillance system in Shanghai, China and included pulmonary TB patients registered from January 1, 2009 to December 31, 2016. We examined the associations of physical accessibility to hospitals, an autoregression term, and random hospital effects with treatment outcomes in logistic regression models after adjusting for demographic, clinical, and treatment factors. RESULTS: Of the 53,475 pulmonary TB patients, 49,002 (91.6%) had successful treatment outcomes. The success rate increased from 89.3% in 2009 to 94.4% in 2016. The successful treatment outcome rate varied among hospitals from 78.6% to 97.8%, and there were 12 spatial clusters of poor treatment outcomes during the 8-year study period. The best-fit model incorporated spatial factors. Both the random hospital effects and autoregression terms had significant impacts on TB treatment outcomes, ranking 6th and 10th, respectively, in terms of statistical importance among 14 factors. The number of bus stations around the home was the least important variable in the model. CONCLUSIONS: Spatial autocorrelation and hospital effects were associated with TB treatment outcomes in Shanghai. In highly-integrated cities like Shanghai, physical accessibility was not related to treatment outcomes. Governments need to pay more attention to the mobility of patients and different success rates of treatment among hospitals.

Comparison of porcine milk microRNA expression in milk exosomes versus whole swine milk and prediction of target genes.

Milk exosomal microRNAs (miRNAs) are important for postnatal growth and immune system maturation in newborn mammals. The functional hypothesis of milk exosomal miRNAs and their potential bioavailability in milk to newborn mammals were investigated. Briefly, 37 exosomal miRNAs were upregulated compared to miRNAs found outside the exosomes. Among these miRNAs, ssc-miR-193a-3p expression was upregulated 1467.35 times, while ssc-miR-423-5p, ssc-miR-551a, ssc-miR-138, ssc-miR-1 and ssc-miR-124a were highly concentrated and upregulated 13.58-30.06 times. Moreover, these miRNAs appeared to be relevant for cell development and basic physiological processes of the immune system. Following the analysis of target gene prediction and related signalling pathways, 9262 target genes were mainly concentrated in three signalling pathways: metabolic pathways, pathways in cancer, and phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signalling pathways. Among 9262 target genes, more than 20 miRNAs were enriched in exosomes, such as methyl CpG binding protein 2 (MECP2) and glycogen synthase 1 (GYS1). After determining the miRNA localization-, distribution- and function-related metabolism, we found that these exosomes were specifically concentrated miRNA target genes and they were interrelated with cell development and basic cell functions, such as metabolism and immunity. It is speculated that miRNAs in milk can influence offspring via milk exosomes.

Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.

Hydrogen bonds play important roles in protein folding and protein-ligand interactions, particularly in specific protein-DNA recognition. However, the distributions of hydrogen bonds, especially hydrogen bond energy (HBE) in different types of protein-ligand complexes, is unknown. Here we performed a comparative analysis of hydrogen bonds among three non-redundant datasets of protein-protein, protein-peptide, and protein-DNA complexes. Besides comparing the number of hydrogen bonds in terms of types and locations, we investigated the distributions of HBE. Our results indicate that while there is no significant difference of hydrogen bonds within protein chains among the three types of complexes, interfacial hydrogen bonds are significantly more prevalent in protein-DNA complexes. More importantly, the interfacial hydrogen bonds in protein-DNA complexes displayed a unique energy distribution of strong and weak hydrogen bonds whereas majority of the interfacial hydrogen bonds in protein-protein and protein-peptide complexes are of predominantly high strength with low energy. Moreover, there is a significant difference in the energy distributions of minor groove hydrogen bonds between protein-DNA complexes with different binding specificity. Highly specific protein-DNA complexes contain more strong hydrogen bonds in the minor groove than multi-specific complexes, suggesting important role of minor groove in specific protein-DNA recognition. These results can help better understand protein-DNA interactions and have important implications in improving quality assessments of protein-DNA complex models.

Single-cell sequencing reveals the new existence form of dermal papilla cells in the hair follicle regeneration of cashmere goats.

The problem of human hair loss has caused widespread concern, however, such research is difficult because the periodicity is not obvious and the deeper levels knowledge of dermal papilla (DP) stem cells' differentiation are limited. Here, cashmere goats which have obvious periodicity of hair follicles were used, based on unbiased scRNA sequencing, we constructed DP cell lineage differentiation trajectory and revealed the key genes, signals and functions involved in cell fate decisions. And then we revealed the molecular landscape of hair follicle on regeneration. Revealed that DP cells differentiate into four intermediate cell states at different periodicity: Intermediate-cell-10 showed important functions in the growth and maintenance of cashmere; intermediate-cell-1 acting on apoptosis and cashmere shedding; intermediate-cell-0 initiated new follicular cycles, the migration of hair follicles and the occurrence of cashmere; and intermediate-cell-15 are suggested to be DP progenitor cells. In general, we provide new insights for hair regrowth. At the same time, it provides a new research ideas, directions and molecular landscape for the mechanism of dermal papilla cells.

Bone mesenchymal stem cell-derived extracellular vesicles inhibit DAPK1-mediated inflammation by delivering miR-191 to macrophages.

Alveolar macrophage activation and apoptosis are vital contributors to sepsis-associated acute lung injury (ALI). However, the mechanisms of alveolar macrophage activation are yet to be clarified. Death-associated protein kinase 1 (DAPK1) is one of the potential candidates that play crucial roles in regulating alveolar macrophage inflammation. Herein, we found that primary human bone mesenchymal stem cell (BMSC)-derived extracellular vesicles (EVs) antagonize LPS-induced inflammation in the THP-1 human macrophage-like cell line. Mechanistically, LPS stimulation elevates the expression of DAPK1 and the inflammation markers in THP-1 cells, while BMSC-derived EVs inhibit the expression of DAPK1 and inflammation through delivering miR-191, which can target the 3'-UTR of the DAPK1 mRNA and therefore suppress its translation. The importance of DAPK1 in the activation of THP-1 is also stressed in this study. Our findings provide evidence that BMSC-derived EVs regulate the alveolar macrophage inflammation and highlight BMSC-derived EVs as a potential vehicle to deliver biomacromolecules to macrophages.

Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes.

Insertions and deletions (Indels) represent one of the major variation types in the human genome and have been implicated in diseases including cancer. To study the features of somatic indels in different cancer genomes, we investigated the indels from two large samples of cancer types: invasive breast carcinoma (BRCA) and lung adenocarcinoma (LUAD). Besides mapping somatic indels in both coding and untranslated regions (UTRs) from the cancer whole exome sequences, we investigated the overlap between these indels and transcription factor binding sites (TFBSs), the key elements for regulation of gene expression that have been found in both coding and non-coding sequences. Compared to the germline indels in healthy genomes, somatic indels contain more coding indels with higher than expected frame-shift (FS) indels in cancer genomes. LUAD has a higher ratio of deletions and higher coding and FS indel rates than BRCA. More importantly, these somatic indels in cancer genomes tend to locate in sequences with important functions, which can affect the core secondary structures of proteins and have a bigger overlap with predicted TFBSs in coding regions than the germline indels. The somatic CDS indels are also enriched in highly conserved nucleotides when compared with germline CDS indels.

MicroRNA-mRNA Regulatory Networking Fine-Tunes Polyunsaturated Fatty Acid Synthesis and Metabolism in the Inner Mongolia Cashmere Goat.

Fatty acid composition is an important aspect of meat quality in ruminants. Improving the beneficial fatty acid level in cashmere goat meat is important to its economic value. To investigate microRNAs (miRNAs) and mRNAs that regulate or coregulate polyunsaturated fatty acid (PUFA) synthesis and metabolism in the Inner Mongolia cashmere goat, we used longissimus dorsi muscle (WLM) and biceps femoris muscle (WBM) for transcript-level sequencing. RT-qPCR was used to evaluate the expression of mRNAs and miRNAs associated with PUFA synthesis and metabolism. The total PUFA content in the WBM was significantly higher than that in the WLM (P < 0.05). Our study is the first to systematically report miRNAs in cashmere goat meat. At the mRNA level, 20,375 genes were identified. ACSL1, CD36 and TECRL were at the center of a gene regulatory network and contributed significantly to the accumulation and metabolic regulation of fatty acids. At the miRNA level, 426 known miRNAs and 30 novel miRNAs were identified. KEGG analysis revealed that the miRNA target genes were involved mainly in the PPAR signaling pathway. The mRNA-miRNA coregulation analysis showed that ACSL1 was negatively targeted by nine miRNAs: chi-miR-10a-5p, chi-miR-10b-5p, chi-miR-130b-5p, chi-miR-15a-5p_R-1, chi-miR-15b-5p, chi-miR-16a-5p, chi-miR-16b-5p, chi-miR-181c-5p_R+1, and chi-miR-26b-5p. Finally, we speculated that the simultaneous silencing of ACSL1 by one or more of these nine miRNAs through PPAR signaling led to low ACSL1 expression in the WLM and, ultimately to high PUFA content in the WBM. Our study helps elucidate the metabolic regulation of fatty acids in Inner Mongolia cashmere goats.

A comparative study of protein-ssDNA interactions.

Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.

Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data.

BACKGROUND: Insertion and deletion (indel) is one of the major variation types in human genomes. Accurate annotation of indels is of paramount importance in genetic variation analysis and investigation of their roles in human diseases. Previous studies revealed a high number of false positives from existing indel calling methods, which limits downstream analyses of the effects of indels on both healthy and disease genomes. In this study, we evaluated seven commonly used general indel calling programs for germline indels and four somatic indel calling programs through comparative analysis to investigate their common features and differences and to explore ways to improve indel annotation accuracy. METHODS: In our comparative analysis, we adopted a more stringent evaluation approach by considering both the indel positions and the indel types (insertion or deletion sequences) between the samples and the reference set. In addition, we applied an efficient way to use a benchmark for improved performance comparisons for the general indel calling programs RESULTS: We found that germline indels in healthy genomes derived by combining several indel calling tools could help remove a large number of false positive indels from individual programs without compromising the number of true positives. The performance comparisons of somatic indel calling programs are more complicated due to the lack of a reliable and comprehensive benchmark. Nevertheless our results revealed large variations among the programs and among cancer types. CONCLUSIONS: While more accurate indel calling programs are needed, we found that the performance for germline indel annotations can be improved by combining the results from several programs. In addition, well-designed benchmarks for both germline and somatic indels are key in program development and evaluations.

Mechanisms of enhanced hexavalent chromium removal from groundwater by sodium carboxymethyl cellulose stabilized zerovalent iron nanoparticles.

Chromium (Cr) contamination poses serious threats to the environment and human health. Thus, batch and column experiments were performed to investigate hexavalent chromium [Cr (VI)] removal from solution and porous media using nanoscale zerovalent iron nanoparticles (NZVI) stabilized by sodium carboxymethyl cellulose (CMC). Batch experiments indicated that the mass ratio of Fe/CMC = 1, the presence of 150-200 mg L-1 CMC and lower ionic strength led to optimum Cr (VI) removal in aqueous solution. Column experiments demonstrated that Cr (VI) removal was enhanced with decreasing solution pH and increasing CMC-NZVI concentration. The presence of CMC can increase Cr (VI) removal by NZVI in both aqueous solution and porous media by complexation precipitation of Cr (VI) compounds and better dispersion of NZVI. X-ray photoelectron spectroscopy (XPS) analysis revealed that an appropriate amount of CMC supported the redox reaction of Cr (VI) and NZVI. The removal of Cr (VI) through columns was 20.8% and 88.5% under no additional CMC and optimized CMC content, respectively. However, Cr (VI) removal decreased to 64.6% under excessive CMC content. The CMC modified NZVI nanoparticles were characterized by XRD, XPS and TEM techniques. These findings imply that CMC can be used as an effective stabilizer on NZVI which can in turn be applied for the efficient removal of Cr (VI) from industrial wastewater and groundwater.

Incidence of pulmonary tuberculosis in Chinese adults with type 2 diabetes: a retrospective cohort study in Shanghai.

To estimate the incidence of pulmonary tuberculosis (PTB) in Chinese diabetes patients and to evaluate the effect of blood glucose on PTB risk, a retrospective cohort study was built based on the diabetes management system in Shanghai and included 240,692 adults aged 35 or above. Incidences of PTB in all diabetes patients and by subgroups were calculated and compared. Multivariable Cox regression models with restricted cubic splines were used to evaluate the association of fasting plasma glucose (FPG) with the risk of PTB. A total of 439 incident PTB cases were identified in the cohort after an average of 3.83 years of follow-up. The overall PTB incidence rate was 51.3/100,000 in diabetes patients, and annual incidence remained higher than that in general population. The PTB incidence rate of diabetes patients was higher in men than in women (86.2 vs. 22.1 per 100,000) and was highest in patients with body mass index (BMI) < 18.5 kg/m2 (215.2/100,000) or FPG ≥ 10 mmol/L (143.2/100,000). Our results suggest that the risk of tuberculosis may be greater at higher levels of FPG in diabetes patients of normal weight. Specific tuberculosis screening strategies for different characteristic diabetes population should be provided to prevent and control tuberculosis in China.