An Automated Approach for Identifying Erroneous IS-A Relations in SNOMED CT.

SNOMED CT is the most comprehensive clinical terminology employed worldwide and enhancing its accuracy is of utmost importance. In this work, we introduce an automated approach to identifying erroneous IS-A relations in SNOMED CT. We first extract linked concept-pairs from which we generate Term Difference Pairs (TDPs) that contain differences between the concepts. Given a TDP, if the reversed TDP also exists and the number of linked-pairs generating this TDP is less than those generating the reversed TDP, then we suggest the former linked-pairs as potentially erroneous IS-A relations. We applied this approach to the Clinical finding and Procedure subhierarchies of the 2022 March US Edition of SNOMED CT, and obtained 52 potentially erroneous IS-A relations and a candidate list of 48 linked-pairs. A domain expert confirmed 41 out of 52 (78.8%) are valid and identified 26 erroneous IS-A relations out of 48 linked-pairs demonstrating the effectiveness of the approach.

A radiomics model of contrast-enhanced computed tomography for predicting post-acute pancreatitis diabetes mellitus.

Background: Diabetes mellitus can occur after acute pancreatitis (AP), but the accurate quantitative methods to predict post-acute pancreatitis diabetes mellitus (PPDM-A) are lacking. This retrospective study aimed to establish a radiomics model based on contrast-enhanced computed tomography (CECT) for predicting PPDM-A. Methods: A total of 374 patients with first-episode AP were retrospectively enrolled from two tertiary referral centers. There were 224 patients in the training cohort, 56 in the internal validation cohort, and 94 in the external validation cohort, and there were 86, 22, and 27 patients with PPDM-A in these cohorts, respectively. The clinical characteristics were collected from the hospital information system. A total of 2,398 radiomics features, including shape-based features, first-order histogram features, high order textural features, and transformed features, were extracted from the arterial- and venous-phase CECT images. Intraclass correlation coefficients were used to assess the intraobserver reliability and interobserver agreement. Random forest-based recursive feature elimination, collinearity analysis, and least absolute shrinkage and selection operator (LASSO) were used for selecting the final features. Three classification methods [eXtreme Gradient Boosting (XGBoost), Adaptive Boosting, and Decision Tree] were used to build three models and performances of the three models were compared. Each of the three classification methods were used to establish the clinical model, radiomics model, and combined model for predicting PPDM-A, resulting in a total of nine classifiers. The predictive performances of the models were evaluated by the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1-score. Results: Eleven radiomics features were selected after a reproducibility test and dimensionality reduction. Among the three classification methods, the XGBoost classifier showed better and more consistent performances. The AUC of the XGBoost's radiomics model to predict PPDM-A in the training, internal, and external cohorts was good (0.964, 0.901, and 0.857, respectively). The AUC of the XGBoost's combined model to predict PPDM-A in the training, internal, and external cohorts was good (0.980, 0.901, and 0.882, respectively). The AUC of the XGBoost's clinical model to predict PPDM-A in the training, internal, and external cohorts did not perform well (0.685, 0.733, and 0.619, respectively). In the external validation cohort, the AUC of the XGBoost's radiomics model was significantly higher than that of the clinical model (0.857 vs. 0.619, P<0.001), but there was no significant difference between the combined and radiomics models (0.882 vs. 0.857, P=0.317). Conclusions: The radiomics model based on CECT performs well and can be used as an early quantitative method to predict the occurrence of PPDM-A.

TMEM120B strengthens breast cancer cell stemness and accelerates chemotherapy resistance via ß1-integrin/FAK-TAZ-mTOR signaling axis by binding to MYH9.

BACKGROUND: Breast cancer stem cell (CSC) expansion results in tumor progression and chemoresistance; however, the modulation of CSC pluripotency remains unexplored. Transmembrane protein 120B (TMEM120B) is a newly discovered protein expressed in human tissues, especially in malignant tissues; however, its role in CSC expansion has not been studied. This study aimed to determine the role of TMEM120B in transcriptional coactivator with PDZ-binding motif (TAZ)-mediated CSC expansion and chemotherapy resistance. METHODS: Both bioinformatics analysis and immunohistochemistry assays were performed to examine expression patterns of TMEM120B in lung, breast, gastric, colon, and ovarian cancers. Clinicopathological factors and overall survival were also evaluated. Next, colony formation assay, MTT assay, EdU assay, transwell assay, wound healing assay, flow cytometric analysis, sphere formation assay, western blotting analysis, mouse xenograft model analysis, RNA-sequencing assay, immunofluorescence assay, and reverse transcriptase-polymerase chain reaction were performed to investigate the effect of TMEM120B interaction on proliferation, invasion, stemness, chemotherapy sensitivity, and integrin/FAK/TAZ/mTOR activation. Further, liquid chromatography-tandem mass spectrometry analysis, GST pull-down assay, and immunoprecipitation assays were performed to evaluate the interactions between TMEM120B, myosin heavy chain 9 (MYH9), and CUL9. RESULTS: TMEM120B expression was elevated in lung, breast, gastric, colon, and ovarian cancers. TMEM120B expression positively correlated with advanced TNM stage, lymph node metastasis, and poor prognosis. Overexpression of TMEM120B promoted breast cancer cell proliferation, invasion, and stemness by activating TAZ-mTOR signaling. TMEM120B directly bound to the coil-coil domain of MYH9, which accelerated the assembly of focal adhesions (FAs) and facilitated the translocation of TAZ. Furthermore, TMEM120B stabilized MYH9 by preventing its degradation by CUL9 in a ubiquitin-dependent manner. Overexpression of TMEM120B enhanced resistance to docetaxel and doxorubicin. Conversely, overexpression of TMEM120B-∆CCD delayed the formation of FAs, suppressed TAZ-mTOR signaling, and abrogated chemotherapy resistance. TMEM120B expression was elevated in breast cancer patients with poor treatment outcomes (Miller/Payne grades 1-2) than in those with better outcomes (Miller/Payne grades 3-5). CONCLUSIONS: Our study reveals that TMEM120B bound to and stabilized MYH9 by preventing its degradation. This interaction activated the ß1-integrin/FAK-TAZ-mTOR signaling axis, maintaining stemness and accelerating chemotherapy resistance.

Buoyancy-Driven Dissolution Instability in a Horizontal Hele-Shaw Cell.

The dissolution of minerals within rock fractures is fundamental to many geological processes. Previous research on fracture dissolution has highlighted the significant role of buoyancy-driven convection leading to dissolution instability. Yet, the pore-scale mechanisms underlying this instability are poorly understood primarily due to the challenges in experimentally determining flow velocity and concentration fields. Here, we integrate pore-scale simulations with theoretical analysis to delve into the dissolution instability prompted by buoyancy-driven convection in a radial horizontal geometry. Initially, we develop a pore-scale modeling approach incorporating gravitational effects, subsequently validating it through experiments. We then employ pore-scale numerical simulations to elucidate the 3D intricacies of flow-dissolution dynamics. Our findings reveal that a simple criterion can delineate the condition for the onset of buoyancy-driven dissolution instability. If the characteristic length falls below a critical threshold, dissolution remains stable. Conversely, exceeding this threshold leads to two distinct regimes: the unstable regime of the confined domain affected by the initial aperture and the unstable regime of the semi-infinite domain independent of the initial aperture where the instability is no longer influenced by the lower boundary. We demonstrate that the pore-scale mechanism for this instability is due to the concentration boundary layer attaining a gravitationally unstable critical thickness. Through theoretical analysis of this layer and the time scales of diffusion and advection, we establish a theoretical model to predict where the dissolution instability occurs. This model aligns closely with our numerical simulations and experimental data across diverse conditions. Our work improves the understanding of buoyancy-driven dissolution instability in radial horizontal geometry. It is also of practical significance in understanding cavity formation in karst hydrology and preventing leaks in geological CO2 storage.

Intravoxel incoherent motion diffusion-weighted imaging for evaluating the pancreatic perfusion in cirrhotic patients.

PURPOSE: To assess the characteristics of pancreatic perfusion in normal pancreas versus cirrhotic patients using intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI). METHODS: A total of 67 cirrhotic patients and 33 healthy subjects underwent IVIM on a 3.0 T MRI scanner. Diffusion coefficient (ADCslow), pseudo-diffusion coefficient (ADCfast), and perfusion fraction (f) were calculated based on the bi-exponential model. The pancreatic IVIM-derived parameters were then compared. In the cirrhotic group, the relationship was analyzed between IVIM-derived pancreatic parameters and different classes of hepatic function as determined by the Child-Pugh classification. Also, the pancreatic IVIM-derived parameters were compared among different classes of cirrhosis as determined by the Child-Pugh classification. RESULTS: The f value of the pancreas in cirrhotic patients was significantly lower than that in normal subjects (p = 0.01). In the cirrhotic group, the f value of the pancreas decreased with the increase of the Child-Pugh classification (R = - 0.49, p = 0.00). The f value of the pancreas was significantly higher in Child-Pugh class A patients than in class B and C patients (p = 0.02, 0.00, respectively), whereas there was no significant difference between class B and C patients (p = 0.16). CONCLUSION: The IVIM-derived perfusion-related parameter (f value) could be helpful for the evaluation of pancreatic perfusion in liver cirrhosis. Our data also suggest that the blood perfusion decrease in the pancreas is present in liver cirrhosis, and the pancreatic perfusion tends to decrease with the increasing severity of hepatic function. TRIAL REGISTRATION: Trial registration number is 2021-ky-68 and date of registration for prospectively registered trials is February 23, 2022.

Simple and field-adapted species identification of biological specimens combining multiplex multienzyme isothermal rapid amplification, lateral flow dipsticks, and universal primers for initial rapid screening without standard PCR laboratory.

Species identification of biological specimens can provide the valuable clues and accelerate the speed of prosecution material processing for forensic investigation, especially when the case scene is inaccessible and the physical evidence is cumbersome. Thus, establishing a rapid, simple, and field-adapted species identification method is crucial for forensic scientists, particularly as first-line technology at the crime scene for initial rapid screening. In this study, we established a new field-adapted species identification method by combining multiplex multienzyme isothermal rapid amplification (MIRA), lateral flow dipstick (LFD) system, and universal primers. Universal primers targeting COX I and COX II genes were used in multiplex MIRA-LFD system for seven species identification, and a dedicated MIRA-LFD system primer targeting CYT B gene was used to detect the human material. DNA extraction was performed by collecting DNA directly from the centrifuged supernatant. Our study found that the entire amplification process took only 15 min at 37 °C and the results of LFDs could be visually observed after 10 min. The detection sensitivity of human material could reach 10 pg, which is equivalent to the detection of single cell. Different common animal samples mixed at the ratio of 1 ng:1 ng, 10 ng:1 ng, and 1 ng:10 ng could be detected successfully. Furthermore, the damaged and degraded samples could also be detected. Therefore, the convenient, feasible, and rapid approach for species identification is suitable for popularization as first-line technology at the crime scene for initial rapid screening and provides a great convenient for forensic application.

Ectoine Globally Hypomethylates DNA in Skin Cells and Suppresses Cancer Proliferation.

Epigenetic modifications, mainly aberrant DNA methylation, have been shown to silence the expression of genes involved in epigenetic diseases, including cancer suppression genes. Almost all conventional cancer therapeutic agents, such as the DNA hypomethylation drug 5-aza-2-deoxycytidine, have insurmountable side effects. To investigate the role of the well-known DNA protectant (ectoine) in skin cell DNA methylation and cancer cell proliferation, comprehensive methylome sequence analysis, 5-methyl cytosine (5mC) analysis, proliferation and tumorigenicity assays, and DNA epigenetic modifications-related gene analysis were performed. The results showed that extended ectoine treatment globally hypomethylated DNA in skin cells, especially in the CpG island (CGIs) element, and 5mC percentage was significantly reduced. Moreover, ectoine mildly inhibited skin cell proliferation and did not induce tumorigenicity in HaCaT cells injected into athymic nude mice. HaCaT cells treated with ectoine for 24 weeks modulated the mRNA expression levels of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Hdac1, Hdac2, Kdm3a, Mettl3, Mettl14, Snrpn, and Mest. Overall, ectoine mildly demethylates DNA in skin cells, modulates the expression of epigenetic modification-related genes, and reduces cell proliferation. This evidence suggests that ectoine is a potential anti-aging agent that prevents DNA hypermethylation and subsequently activates cancer-suppressing genes.

Identification of the High-Affinity Potassium Transporter Gene Family (HKT) in Brassica U-Triangle Species and Its Potential Roles in Abiotic Stress in Brassica napus L.

Members of the high-affinity potassium transporter (HKT) protein family regulate the uptake and homeostasis of sodium and potassium ions, but little research describes their roles in response to abiotic stresses in rapeseed (Brassica napus L.). In this study, we identified and characterized a total of 36 HKT genes from the species comprising the triangle of U model (U-triangle species): B. rapa, B. nigra, B. oleracea, B. juncea, B. napus, and B. carinata. We analyzed the phylogenetic relationships, gene structures, motif compositions, and chromosomal distributions of the HKT family members of rapeseed. Based on their phylogenetic relationships and assemblage of functional domains, we classified the HKT members into four subgroups, HKT1;1 to HKT1;4. Analysis of the nonsynonymous substitutions (Ka), synonymous substitutions (Ks), and the Ka/Ks ratios of HKT gene pairs suggested that these genes have experienced strong purifying selective pressure after duplication, with their evolutionary relationships supporting the U-triangle theory. Furthermore, the expression profiles of BnaHKT genes varies among potassium, phytohormone and heavy-metal treatment. Their repression provides resistance to heavy-metal stress, possibly by limiting uptake. Our results systematically reveal the characteristics of HKT family proteins and their encoding genes in six Brassica species and lay a foundation for further exploration of the role of HKT family genes in heavy-metal tolerance.

In Situ Interfacial Polymerized Arginine-Doped Polydopamine Thin-Film Nanocomposite Membranes for High-Separation and Antifouling Reverse Osmosis.

In this work, we synthesized polydopamine nanoparticles (PDNPs-M, M = I, II, III, and IV) with uniform particle sizes but varying l-arginine (Arg) contents (0%, 0.53%, 3.73%, and 6.62%) through a one-pot synthesis approach. Thin-film nanocomposite (TFN) membranes were fabricated via in situ interfacial polymerization (IP). The effects of the PDNPs-M chemical structure on the IP process and the consequent impacts on the structure and properties of the polyamide (PA) selective layer were investigated. The hydrophilicity and dispersibility of PDNPs-M exhibited an upward trend with the Arg content. Furthermore, Arg doping contributes to a denser and smoother PA layer. Among the TFC and TFN membranes, TFN-PDNPs-IV exhibited a water permeability of 3.89 L·m-2·h-1·bar-1 (55.1% higher than that of TFC-0) with a NaCl rejection rate of 98.8%, signifying superior water/salt selectivity. Additionally, TFN-PDNPs-IV exhibited regular pressure stability, commendable acid/alkali stability, and enhanced antifouling properties. These findings highlight the significant impact of nanoparticle hydrophilic functional groups on the structural and functional attributes of TFN membranes, offering a promising approach for developing advanced reverse osmosis membranes.

Post-marketing safety surveillance for both CRM197 and TT carrier proteins PCV13 in Jiangsu, China.

Background: This study is to evaluate the safety of two kinds of PCV13 carriers by monitoring the occurrence of adverse event following immunization (AEFI) after the launch of two kinds of PCV13 carriers in Jiangsu Province, China. Methods: The AEFI Information System (CNAEFIS) of mainland China was used to monitor the incidence and classification of adverse reactions of the CRM197-carrier protein PCV13 and TT-carrier protein PCV13 vaccines. Results: There was no statistical difference between the cumulative reported incidence of AEFI between the two vaccines from 2020 to 2022 (χ2 = 1.991, p < 0.158). 96.62% of the AEFIs were classified as common reactions; rare reactions and coincidental events only accounted for 2.99 and 0.39% of all the AEFI cases, respectively. Redness (2.6 cm-5 cm) is the commonest symptom at the injection site for both vaccines. More than 97% of AEFIs occurred between 30 min and 3 days after administration for both types of PCV13. Conclusion: Both vaccines perform well in terms of safety. We did not identify any new/unexpected safety concern from the NAEFISS during a 4 years timespan.

Low-dose atorvastatin protects skeletal muscle mitochondria in high-fat diet-fed mice with mitochondrial autophagy inhibition and fusion enhancement.

Despite the great clinical benefits of statins in cardiovascular diseases, their widespread use may lead to adverse muscle reactions associated with mitochondrial dysfunction. Some studies have demonstrated that statins provide substantial improvement to skeletal muscle health in mice. Our previous study found that oral treatment with atorvastatin (Ator, 3 mg/kg) protected myocardial mitochondria in high-fat diet (HFD)-fed mice. Therefore, this study aimed to explore the influence of low-dose Ator (3 mg/kg) on mitochondria in skeletal muscle under cholesterol overload. Male C57BL/6J mice were fed a HFD for 18 weeks and orally administered Ator (3 mg/kg) during the last 12 weeks. Ator treatment had no effects on elevated serum cholesterol and glucose levels in HFD-fed mice. Serum creatine kinase levels and the cross-sectional area of muscle cells were not affected by HFD feeding or Ator treatment. Increased expression of PINK1-LC3 II (activated mitophagy), MFN2 (fusion), and PGC-1α (biogenesis) proteins was induced in the skeletal muscles of HFD-fed mice. Treatment with Ator inhibited PINK1 and LC3 II protein expression, but further promoted MFN1, MFN2, and OPA1 expression. The impairments in mitochondrial quality and morphology in HFD-fed mice were attenuated by treatment with Ator. Furthermore, Ator treatment enhanced glucose oxidation capacity and restored ATP production in the skeletal muscles of HFD-fed mice. The study reveals that low-dose Ator has a protective effect on muscle mitochondria in mice, likely through inhibiting mitophagy and enhancing mitochondrial fusion. This suggests that skeletal muscle mitochondria may be one of low-dose Ator-mediated protective targets.

Evaluation of vaccination status of children with special health care needs in Suzhou, China, 2020-2022: A retrospective survey study.

Children with special health care needs (CSHCNs) are at an increased risk of vaccine-preventable infections (VPDs), but they also face the dilemma of vaccine hesitancy. We obtained information on pediatric visits from the Referral and Assessment Information System for Vaccination (RAISV) and information on vaccination from the Jiangsu Province Immunization Information System (JSIIS). We followed the occurrence of Adverse Events Following Immunization (AEFIs) and VPDs by actively calling and querying the China Information System for Disease Control and Prevention (CISDCP). The Poisson test was used to compare the incidence of AEFIs between groups. A total of 5,037 children who visited a vaccination assessment clinic were followed-up in this study. The majority were children with developmental anomalies (28.5%), certain conditions originating in the perinatal period (12.1%), and nervous system disorders (9.0%). Most CSHCNs (66.9%) were advised to have all vaccines according to routine practice, 29.0% were advised to have partial vaccination, and 4.1% were advised to delay all vaccines and wait for future assessment. A total of 201 (4.0%) CSHCNs were not vaccinated, although they were assessed to be eligible for vaccination. By querying the immunization planning module in CISDCP, we observed 55 AEFI cases, which amounted to an incidence rate of 1.2 per 1,000, and the occurrence of abnormal reactions was not significantly different compared with the general population. The vaccination program following the designed workflow for CSHCNs was safe and could be recommended in other areas.

ZNF500 abolishes breast cancer proliferation and sensitizes chemotherapy by stabilizing P53 via competing with MDM2.

Zinc finger protein 500 (ZNF500) has an unknown expression pattern and biological function in human tissues. Our study revealed that the ZNF500 mRNA and protein levels were higher in breast cancer tissues than those in their normal counterparts. However, ZNF500 expression was negatively correlated with advanced TNM stage (p = 0.018), positive lymph node metastasis (p = 0.014), and a poor prognosis (p < 0.001). ZNF500 overexpression abolished in vivo and in vitro breast cancer cell proliferation by activating the p53-p21-E2F4 signaling axis and directly interacting with p53 via its C2H2 domain. This may prevent ubiquitination of p53 in a manner that is competitive to MDM2, thus stabilizing p53. When ZNF500-∆C2H2 was overexpressed, the suppressed proliferation of breast cancer cells was neutralized in vitro and in vivo. In human breast cancer tissues, ZNF500 expression was positively correlated with p53 (p = 0.022) and E2F4 (p = 0.004) expression. ZNF500 expression was significantly lower in patients with Miller/Payne Grade 1-2 than in those with Miller/Payne Grade 3-5 (p = 0.012). ZNF500 suppresses breast cancer cell proliferation and sensitizes cells to chemotherapy.

Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus.

Yellow-seed trait is a desirable breeding characteristic of rapeseed (Brassica napus) that could greatly improve seed oil yield and quality. However, the underlying mechanisms controlling this phenotype in B. napus plants are difficult to discern because of their complexity. Here, we assemble high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821). Combining in-depth fine mapping of a quantitative trait locus (QTL) for seed color with other omics data reveal BnA09MYB47a, encoding an R2R3-MYB-type transcription factor, as the causal gene of a major QTL controlling the yellow-seed trait. Functional studies show that sequence variation of BnA09MYB47a underlies the functional divergence between the yellow- and black-seeded B. napus. The black-seed allele BnA09MYB47aZY821, but not the yellow-seed allele BnA09MYB47aGH06, promotes flavonoid biosynthesis by directly activating the expression of BnTT18. Our discovery suggests a possible approach to breeding B. napus for improved commercial value and facilitates flavonoid biosynthesis studies in Brassica crops.

Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases.

Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)-caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively-are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.

Using Twitter-Based Data for Sexual Violence Research: Scoping Review.

BACKGROUND: Scholars have used data from in-person interviews, administrative systems, and surveys for sexual violence research. Using Twitter as a data source for examining the nature of sexual violence is a relatively new and underexplored area of study. OBJECTIVE: We aimed to perform a scoping review of the current literature on using Twitter data for researching sexual violence, elaborate on the validity of the methods, and discuss the implications and limitations of existing studies. METHODS: We performed a literature search in the following 6 databases: APA PsycInfo (Ovid), Scopus, PubMed, International Bibliography of Social Sciences (ProQuest), Criminal Justice Abstracts (EBSCO), and Communications Abstracts (EBSCO), in April 2022. The initial search identified 3759 articles that were imported into Covidence. Seven independent reviewers screened these articles following 2 steps: (1) title and abstract screening, and (2) full-text screening. The inclusion criteria were as follows: (1) empirical research, (2) focus on sexual violence, (3) analysis of Twitter data (ie, tweets or Twitter metadata), and (4) text in English. Finally, we selected 121 articles that met the inclusion criteria and coded these articles. RESULTS: We coded and presented the 121 articles using Twitter-based data for sexual violence research. About 70% (89/121, 73.6%) of the articles were published in peer-reviewed journals after 2018. The reviewed articles collectively analyzed about 79.6 million tweets. The primary approaches to using Twitter as a data source were content text analysis (112/121, 92.5%) and sentiment analysis (31/121, 25.6%). Hashtags (103/121, 85.1%) were the most prominent metadata feature, followed by tweet time and date, retweets, replies, URLs, and geotags. More than a third of the articles (51/121, 42.1%) used the application programming interface to collect Twitter data. Data analyses included qualitative thematic analysis, machine learning (eg, sentiment analysis, supervised machine learning, unsupervised machine learning, and social network analysis), and quantitative analysis. Only 10.7% (13/121) of the studies discussed ethical considerations. CONCLUSIONS: We described the current state of using Twitter data for sexual violence research, developed a new taxonomy describing Twitter as a data source, and evaluated the methodologies. Research recommendations include the following: development of methods for data collection and analysis, in-depth discussions about ethical norms, exploration of specific aspects of sexual violence on Twitter, examination of tweets in multiple languages, and decontextualization of Twitter data. This review demonstrates the potential of using Twitter data in sexual violence research.

cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA.

Cell-free DNA (cfDNA) in blood, viewed as a surrogate for tumor biopsy, has many clinical applications, including diagnosing cancer, guiding cancer treatment and monitoring treatment response. All these applications depend on an indispensable, yet underdeveloped task: detecting somatic mutations from cfDNA. The task is challenging because of the low tumor fraction in cfDNA. Recently, we developed the computational method cfSNV, the first method that comprehensively considers the properties of cfDNA for the sensitive detection of mutations from cfDNA. cfSNV vastly outperformed the conventional methods that were developed primarily for calling mutations from solid tumor tissues. cfSNV can accurately detect mutations in cfDNA even with medium-coverage (e.g., ≥200×) sequencing, which makes whole-exome sequencing (WES) of cfDNA a viable option for various clinical utilities. Here, we present a user-friendly cfSNV package that exhibits fast computation and convenient user options. We also built a Docker image of it, which is designed to enable researchers and clinicians with a limited computational background to easily carry out analyses on both high-performance computing platforms and local computers. Mutation calling from a standard preprocessed WES dataset (~250× and ~70 million base pair target size) can be carried out in 3 h on a server with eight virtual CPUs and 32 GB of random access memory.

Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L.

Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.