Sequence-based Structural B-cell Epitope Prediction by Using Two Layer SVM Model and Association Rule Features

Background:

Immune reaction is the most important defense mechanism for destroying invading pathogens in our body, and the epitope is the position of the antigen–antibody interaction on pathogenic proteins.

Objective:

The majority of epitopes are structural; however, the existing sequence-based predicting websites still have several methods to improve the predicting performance. Therefore, in this study, we used SVM as a machine learning tool to predict the epitope-based on protein sequences.

Methods:

Firstly, we built five SVM models in the first layer according to five features, including binary composition, position-specific scoring matrix, secondary structure, accessible surface area, and association rule, and then chose the patterns that exhibited the best performance in each model. Secondly, using the confidence score of the first-layer models as the input value for the SVM model in the second layer, that SVM model was integrated into the first-layer SVM models for improving the predicting accuracy.

Results:

The final prediction model was able to achieve up to 63% accuracy in predicting epitope results, and the predicting performance was better than that achieved by the existing predicting websites.

Conclusion:

Finally, a case study using a two-subunit cytochrome c oxidase of Paracoccus denitrificans was tested, achieving an accuracy of up to 66%.

Urban-rural disparity of preventive healthcare utilisation among children under the universal health insurance coverage in Taiwan: a national birth cohort analysis

OBJECTIVE

In the context of universal health insurance coverage, this study aimed to determine whether urban-rural inequality still exists in preventive health care (PHC) amongst children in Taiwan.

STUDY DESIGN

Prospective cohort study.

METHODS

A total of 184,117 mothers and their children born in 2009 were identified as the study cohort. The number of children born in urban, satellite and rural areas was 40,176, 57,565 and 86,805, respectively. All children were followed for 7 years, before which a total of seven times PHC were provided by Taiwan's National Health Insurance (NHI) programme. Ordinal logistic regression models were used to associate urbanisation level with the frequency of PHC utilisation. Stratified analyses were further performed in accordance with the children's birth weight and the mothers' birthplace.

RESULTS

Children from satellite areas had higher utilisation for the first four scheduled PHC visits. Children living in urban areas received more PHC for the fifth and sixth scheduled visits. Compared with those from rural areas, children in satellite areas exhibited a small but significant increase in odds in PHC utilisation, with a covariate-adjusted odds ratio (aOR) of 1.04 and 95% confidence interval (CI) of 1.02-1.06. By contrast, no significant difference was observed between rural and urban areas (aOR = 1.01). Further stratified analyses suggest more evident urban-rural difference in PHC utilisation amongst children with low birth weight and foreign-born mothers.

CONCLUSIONS

Given a universal health insurance coverage and embedded mechanisms in increasing the availability of healthcare resources in Taiwan, a slight urban-rural difference is observed in PHC utilisation amongst children. Hence, sociodemographic inequality in utilisation of PHC still exists. This issue should be addressed through policy intervention.

iStable 2.0: Predicting protein thermal stability changes by integrating various characteristic modules

Protein mutations can lead to structural changes that affect protein function and result in disease occurrence. In protein engineering, drug design or and optimization industries, mutations are often used to improve protein stability or to change protein properties while maintaining stability. To provide possible candidates for novel protein design, several computational tools for predicting protein stability changes have been developed. Although many prediction tools are available, each tool employs different algorithms and features. This can produce conflicting prediction results that make it difficult for users to decide upon the correct protein design. Therefore, this study proposes an integrated prediction tool, iStable 2.0, which integrates 11 sequence-based and structure-based prediction tools by machine learning and adds protein sequence information as features. Three coding modules are designed for the system, an Online Server Module, a Stand-alone Module and a Sequence Coding Module, to improve the prediction performance of the previous version of the system. The final integrated structure-based classification model has a higher Matthews correlation coefficient than that of the single prediction tool (0.708 vs 0.547, respectively), and the Pearson correlation coefficient of the regression model likewise improves from 0.669 to 0.714. The sequence-based model not only successfully integrates off-the-shelf predictors but also improves the Matthews correlation coefficient of the best single prediction tool by at least 0.161, which is better than the individual structure-based prediction tools. In addition, both the Sequence Coding Module and the Stand-alone Module maintain performance with only a 5% decrease of the Matthews correlation coefficient when the integrated online tools are unavailable. iStable 2.0 is available at http://ncblab.nchu.edu.tw/iStable2.

[Several issues worthy of reference and discussion of 2019 edition of the European Association for the Study of the Liver guideline for drug-induced liver injury]

The 2019 European Association for the Study of the Liver (EASL) Clinical Practice Guidelines (hereinafter referred to as the EASL Guidelines) extracted the required evidence from detailed research materials, and rigorously graded and condensed the varying strengths of evidence into 32 recommendations and 14 statements (recommendations and reminders) for drug-induced Liver Injury (DILI). This guideline has important reference values for helping clinicians to further improve their understanding of DILI and the level of clinical diagnosis, treatment and prevention; however, there are still several issues worthy of further discussion.

Context-dependent activation of SIRT3 is necessary for anchorage-independent survival and metastasis of ovarian cancer cells

Tumor cells must alter their antioxidant capacity for maximal metastatic potential. Yet the antioxidant adaptations required for ovarian cancer transcoelomic metastasis, which is the passive dissemination of cells in the peritoneal cavity, remain largely unexplored. Somewhat contradicting the need for oxidant scavenging are previous observations that expression of SIRT3, a nutrient stress sensor and regulator of mitochondrial antioxidant defenses, is often suppressed in many primary tumors. We have discovered that this mitochondrial deacetylase is specifically upregulated in a context-dependent manner in cancer cells. SIRT3 activity and expression transiently increased following ovarian cancer cell detachment and in tumor cells derived from malignant ascites of high-grade serous adenocarcinoma patients. Mechanistically, SIRT3 prevents mitochondrial superoxide surges in detached cells by regulating the manganese superoxide dismutase (SOD2). This mitochondrial stress response is under dual regulation by SIRT3. SIRT3 rapidly increases SOD2 activity as an early adaptation to cellular detachment, which is followed by SIRT3-dependent increases in SOD2 mRNA during sustained anchorage-independence. In addition, SIRT3 inhibits glycolytic capacity in anchorage-independent cells thereby contributing to metabolic changes in response to detachment. While manipulation of SIRT3 expression has few deleterious effects on cancer cells in attached conditions, SIRT3 upregulation and SIRT3-mediated oxidant scavenging are required for anoikis resistance in vitro following matrix detachment, and both SIRT3 and SOD2 are necessary for colonization of the peritoneal cavity in vivo. Our results highlight the novel context-specific, pro-metastatic role of SIRT3 in ovarian cancer.

Expression and prognostic significance of melatonin receptor MT1 in patients with gastric adenocarcinoma

Melatonin receptor type 1 (MTNR1A or MT1) is known to play an important role in cancer progression; however, its prognostic value for resected gastric adenocarcinoma (RGA) is unknown. In this study, we examined the potential of MT1 as a prognostic biomarker for RGA. The expression of the MT1 was evaluated in 67 patients with RGA by immunohistochemistry, and the relationship between MT1 levels and RGA prognosis was analyzed by Chi-square test, multivariate Cox regression, Kaplan-Meier method, and log-rank test. High MT1 expression was associated with a poor survival rate (29.0%, p=0.002) and the occurrence of metastasis (62.9%, p=0.004). Kaplan-Meier survival analysis and log rank tests revealed that patients with high expression of the MT1 had significantly shorter median overall survival compared to those with low expression (33.0 vs. 65.0 months, respectively; p=0.02). Multivariate Cox analysis indicated that the calculated death risk (hazard ratio [HR]) in patients with high expression levels of the MT1 increased to 2.68 (95% confidence interval [CI] 1.21-5.94, p=0.015), which was higher compared to those with low levels. HR of death was also high in patients with advanced T stage (2.51; 95 % CI 1.00-6.26, p=0.049) and metastasis (5.02; 95% CI 1.94-13.03, p=0.001). Our results showed that high MT1 expression in primary gastric adenocarcinoma tissues was associated with the occurrence of metastasis and poor prognosis. It may have prognostic significance as a potential biomarker in patients with RGA.

[Investigation of treatment and analysis of prognostic risk on enterocutaneous fistula in China: a multicenter prospective study]

Objective: To investigate the diagnosis and treatment for enterocutaneous fistula (ECF) in China, and to explore the prognostic factors of ECF. Methods: A multi-center cross-sectional study was conducted based on the Registration System of Chinese Gastrointestinal Fistula and Intra-Abdominal Infections to collect the clinical data of ECF patients from 54 medical centers in 22 provinces/municipalities from January 1, 2018 to December 31, 2018. The clinical data included patient gender, age, length of hospital stay, intensive care unit (ICU) admission, underlying diseases, primary diseases, direct causes of ECF, location and type of ECF, complications, treatment and outcomes. All medical records were carefully filled in by the attending physicians, and then re-examined by more than two specialists. The diagnosis of ECF was based on the clinical manifestations, laboratory/imaging findings and intraoperative exploration. Results: A total of 1521 patients with ECF were enrolled, including 1099 males and 422 females, with a median age of 55 years. The top three primary diseases of ECF were malignant tumors in 626 cases (41.2%, including 540 gastrointestinal tumors, accounting for 86.3% of malignant tumors), gastrointestinal ulcers and perforations in 202 cases (13.3%), and trauma in 157 cases (10.3%). The direct causes of ECF were mainly surgical operation in 1194 cases (78.5%), followed by trauma in 156 (10.3%), spontaneous fistula due to Crohn's disease in 92 (6.0%), radiation intestinal injury in 41 (2.7%), severe pancreatitis in 20 (1.3%), endoscopic treatment in 13 (0.9%) and 5 cases (0.3%) of unknown reasons. All the patients were divided into three groups: 1350 cases (88.7%) with simple ECF, 150 (9.9%) with multiple ECF, and 21 (1.4%) with combined internal fistula. Among the patients with simple ECF, 438 cases (28.8%) were jejuno-ileal fistula, 313 (20.6%) colon fistula, 170 (11.2%) rectal fistula, 111 (7.3%) duodenal fistula, 76 (5.0%) ileocecal fistula, 65 (4.3%) ileocolic anastomotic fistula, 55 (3.6%) duodenal stump fistula, 36 (2.4%) gastrointestinal anastomotic fistula, 36 (2.4%) esophagogastric/esophagojejunal anastomotic fistula, 29 (1.9%) gastric fistula and 21 (1.4%) cholangiopancreatiointestinal. Among all the simple ECF patients, 991 were tubular fistula and 359 were labial fistula. A total of 1146 patients finished the treatment, of whom 1061 (92.6%) were healed (586 by surgery and 475 self-healing) and 85 (7.4%) died. A total of 1043 patients (91.0%) received nutritional support therapy, and 77 (6.7%) received fistuloclysis. Infectious source control procedures were applied to 1042 patients, including 711 (62.0%) with active lavage and drainage and 331 (28.9%) with passive drainage. Among them, 841 patients (73.4%) underwent minimally invasive procedures of infectious source control (replacement of drainage tube through sinus tract, puncture drainage, etc.), 201 (17.5%) underwent laparotomy drainage, while 104 (9.1%) did not undergo any drainage measures. A total of 610 patients (53.2%) received definitive operation, 24 patients died within postoperative 30-day with mortality of 3.9% (24/610), 69 (11.3%) developed surgical site infection (SSI), and 24 (3.9%) had a relapse of fistula. The highest cure rate was achieved in ileocecal fistula (100%), followed by rectal fistula (96.2%, 128/133) and duodenal stump fistula (95.7%,44/46). The highest mortality was found in combined internal fistula (3/12) and no death in ileocecal fistula. Univariate prognostic analysis showed that primary diseases as Crohn's disease (χ(2)=6.570, P=0.010) and appendicitis/appendiceal abscess (P=0.012), intestinal fistula combining with internal fistula (χ(2)=5.460, P=0.019), multiple ECF (χ(2)=7.135, P=0.008), esophagogastric / esophagojejunal anastomotic fistula (χ(2)=9.501, P=0.002), ECF at ileocecal junction (P=0.012), non-drainage/passive drainage before the diagnosis of intestinal fistula (χ(2)=9.688, P=0.008), non-drainage/passive drainage after the diagnosis of intestinal fistula (χ(2)=9.711, P=0.008), complicating with multiple organ dysfunction syndrome (MODS) (χ(2)=179.699, P<0.001), sepsis (χ(2)=211.851, P<0.001), hemorrhage (χ(2)=85.300, P<0.001), pulmonary infection (χ(2)=60.096, P<0.001), catheter-associated infection (χ(2)=10.617, P=0.001) and malnutrition (χ(2)=21.199, P<0.001) were associated with mortality. Multivariate prognostic analysis cofirmed that sepsis (OR=7.103, 95%CI:3.694-13.657, P<0.001), complicating with MODS (OR=5.018, 95%CI:2.170-11.604, P<0.001), and hemorrhage (OR=4.703, 95%CI: 2.300-9.618, P<0.001) were independent risk factors of the death for ECF patients. Meanwhile, active lavage and drainage after the definite ECF diagnosis was the protective factor (OR=0.223, 95%CI: 0.067-0.745, P=0.015). Conclusions: The overall mortality of ECF is still high. Surgical operation is the most common cause of ECF. Complications e.g. sepsis, MODS, hemorrhage, and catheter-associated infection, are the main causes of death. Active lavage and drainage is important to improve the prognosis of ECF.

ERK Regulates HIF1α-Mediated Platinum Resistance by Directly Targeting PHD2 in Ovarian Cancer

PURPOSE

Up to 80% of patients with ovarian cancer develop platinum resistance over time to platinum-based chemotherapy. Increased HIF1α level is an important mechanism governing platinum resistance in platinum-resistant ovarian cancer (PROC). However, the mechanism regulating HIF1α stability in PROC remains largely unknown. Here, we elucidate the mechanism of HIF1α stability regulation in PROC and explore therapeutic approaches to overcome cisplatin resistance in ovarian cancer.

EXPERIMENTAL DESIGN

We first used a quantitative high-throughput combinational screen (qHTCS) to identify novel drugs that could resensitize PROC cells to cisplatin. Next, we evaluated the combination efficacy of inhibitors of HIF1α (YC-1), ERK (selumetinib), and TGFβ1 (SB431542) with platinum drugs by in vitro and in vivo experiments. Moreover, a novel TGFβ1/ERK/PHD2-mediated pathway regulating HIF1α stability in PROC was discovered.

RESULTS

YC-1 and selumetinib resensitized PROC cells to cisplatin. Next, the prolyl hydroxylase domain-containing protein 2 (PHD2) was shown to be a direct substrate of ERK. Phosphorylation of PHD2 by ERK prevents its binding to HIF1α, thus inhibiting HIF1α hydroxylation and degradation-increasing HIF1α stability. Significantly, ERK/PHD2 signaling in PROC cells is dependent on TGFβ1, promoting platinum resistance by stabilizing HIF1α. Inhibition of TGFβ1 by SB431542, ERK by selumetinib, or HIF1α by YC-1 efficiently overcame platinum resistance both in vitro and in vivo. The results from clinical samples confirm activation of the ERK/PHD2/HIF1α axis in patients with PROC, correlating highly with poor prognoses for patients.

CONCLUSIONS

HIF1α stabilization is regulated by TGFβ1/ERK/PHD2 axis in PROC. Hence, inhibiting TGFβ1, ERK, or HIF1α is potential strategy for treating patients with PROC.

The Cdk2-c-Myc-miR-571 Axis Regulates DNA Replication and Genomic Stability by Targeting Geminin

DNA rereplication leads to genomic instability and has been implicated in the pathology of a variety of human cancers. Eukaryotic DNA replication is tightly controlled to ensure it occurs only once during each cell cycle. Geminin is a critical component of this control, it prevents DNA rereplication from occurring during S, G₂, and early M phases by preventing MCM helicases from forming prereplication complexes. Geminin is targeted for degradation by the anaphase-promoting complex (APC/C) from anaphase through G₁-phase, however, accumulating evidence indicates that Geminin is downregulated in late S-phase due to an unknown mechanism. Here, we used a high-throughput screen to identify miRNAs that can induce excess DNA replication and found that miR-571 could reduce the protein level of Geminin in late S-phase independent of the APC/C. Furthermore, miR-571 regulated efficient DNA replication and S-phase cell-cycle progression. Strikingly, c-Myc suppressed miR-571 expression by binding directly to the miR-571 promoter. At the beginning of S-phase, Cdk2 phosphorylated c-Myc at Serine 62, promoting its association with the miR-571 promoter region. Collectively, we identify miR-571 as the first miRNA that prevents aberrant DNA replication and the Cdk2-c-Myc-miR-571 axis as a new pathway for regulating DNA replication, cell cycle, and genomic stability in cancer cells. SIGNIFICANCE: These findings identify a novel regulatory mechanism that is critical for maintaining genome integrity by regulating DNA replication and cell-cycle progression.

Conservation region finding for influenza A viruses by machine learning methods of N-linked glycosylation sites and B-cell epitopes

Influenza type A, a serious infectious disease of the human respiratory tract, poses an enormous threat to human health worldwide. It leads to high mortality rates in poultry, pigs, and humans. The primary target identity regions for the human immune system are hemagglutinin (HA) and neuraminidase (NA), two surface proteins of the influenza A virus. Research and development of vaccines is highly complex because the influenza A virus evolves rapidly. This study focused on three genetic features of viral surface proteins: ribonucleic acid (RNA) sequence conservation, linear B-cell epitopes, and N-linked glycosylation. On the basis of these three properties, we analyzed 12,832 HA and 9487 NA protein sequences, which we retrieved from the influenza virus database. We classified the viral surface protein sequences into the 18 HA and 11 NA subtypes that have been identified thus far. Using available analytic tools, we searched for the representative strain of each virus subtype. Furthermore, using machine learning methods, we looked for conservation regions with sequences showing linear B-cell epitopes and N-linked glycosylation. Compared to the prediction of the Immune Epitope Database (IEDB) antibody neutralization response (i.e., screening of antibody sequence regions), in this study, the virus sequence coverage was large and accurate and contained N-linked glycosylation sites. The results of this study proved that we can use the machine learning-based prediction method to solve the problem of vaccine invalidation that occurred during the rapid evolution of the influenza A virus and also as a prevaccine assessment. In addition, the screening fragments can be used as a universal influenza vaccine design reference in the future.

EAT-Rice: A predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches

T-DNA activation-tagging technology is widely used to study rice gene functions. When T-DNA inserts into genome, the flanking gene expression may be altered using CaMV 35S enhancer, but the affected genes still need to be validated by biological experiment. We have developed the EAT-Rice platform to predict the flanking gene expression of T-DNA insertion site in rice mutants. The three kinds of DNA sequences including UPS1K, DISTANCE, and MIDDLE were retrieved to encode and build a forecast model of two-layer machine learning. In the first-layer models, the features nucleotide context (N-gram), cis-regulatory elements (Motif), nucleotide physicochemical properties (NPC), and CG-island (CGI) were used to build SVM models by analysing the concealed information embedded within the three kinds of sequences. Logistic regression was used to estimate the probability of gene activation which as feature-encoding weighting within first-layer model. In the second-layer models, the NaiveBayesUpdateable algorithm was used to integrate these first layer-models, and the system performance was 88.33% on 5-fold cross-validation, and 79.17% on independent-testing finally. In the three kinds of sequences, the model constructed by Middle had the best contribution to the system for identifying the activated genes. The EAT-Rice system provided better performance and gene expression prediction at further distances when compared to the TRIM database. An online server based on EAT-rice is available at http://predictor.nchu.edu.tw/EAT-Rice.

[Clinical effect and safety of pegylated interferon-α-2b injection (Y shape, 40 kD) in treatment of HBeAg-positive chronic hepatitis B patients]

Objective: To investigate the clinical effect and safety of long-acting pegylated interferon-α-2b (Peg-IFN-α-2b) (Y shape, 40 kD) injection (180 μg/week) in the treatment of HBeAg-positive chronic hepatitis B (CHB) patients, with standard-dose Peg-IFN-α-2a as positive control. Methods: This study was a multicenter, randomized, open-label, and positive-controlled phase III clinical trial. Eligible HBeAg-positive CHB patients were screened out and randomized to Peg-IFN-α-2b (Y shape, 40 kD) trial group and Peg-IFN-α-2a control group at a ratio of 2:1. The course of treatment was 48 weeks and the patients were followed up for 24 weeks after drug withdrawal. Plasma samples were collected at screening, baseline, and 12, 24, 36, 48, 60, and 72 weeks for centralized detection. COBAS® Ampliprep/COBAS® TaqMan® HBV Test was used to measure HBV DNA level by quantitative real-time PCR. Electrochemiluminescence immunoassay with Elecsys kit was used to measure HBV markers (HBsAg, anti-HBs, HBeAg, anti-HBe). Adverse events were recorded in detail. The primary outcome measure was HBeAg seroconversion rate after the 24-week follow-up, and non-inferiority was also tested. The difference in HBeAg seroconversion rate after treatment between the trial group and the control group and two-sided confidence interval (CI) were calculated, and non-inferiority was demonstrated if the lower limit of 95% CI was > -10%. The t-test, chi-square test, or rank sum test was used according to the types and features of data. Results: A total of 855 HBeAg-positive CHB patients were enrolled and 820 of them received treatment (538 in the trial group and 282 in the control group). The data of the full analysis set showed that HBeAg seroconversion rate at week 72 was 27.32% in the trial group and 22.70% in the control group with a rate difference of 4.63% (95% CI -1.54% to 10.80%, P = 0.1493). The data of the per-protocol set showed that HBeAg seroconversion rate at week 72 was 30.75% in the trial group and 27.14% in the control group with a rate difference of 3.61% (95% CI -3.87% to 11.09%, P = 0.3436). 95% CI met the non-inferiority criteria, and the trial group was non-inferior to the control group. The two groups had similar incidence rates of adverse events, serious adverse events, and common adverse events. Conclusion: In Peg-IFN-α regimen for HBeAg-positive CHB patients, the new drug Peg-IFN-α-2b (Y shape, 40 kD) has comparable effect and safety to the control drug Peg-IFN-α-2a.

[Experimental study of silybin-phospholipid complex intervention on amiodarone-induced fatty liver in mice]

Objective: To probe into the mechanism and interventional effects of silybin-phospholipid complex on amiodarone-induced steatosis in mice. Methods: Eight-week-old male C57BL/6 mice were divided into three groups (5 mice in each group): a control group (WT) with normal diet, a model group with amiodarone 150mg/kg/d by oral gavage (AM), and an intervention group on amiodarone 150mg/kg/d combined with silybin-phospholipid complex(AM+SILIPHOS. All mice were fed their assigned diet for one week. Then, one week later, serum alanine aminotransferase, aspartate aminotransferase, triglyceride, total cholesterol and high-density lipoprotein were detected of each group. A liver pathological change was observed by oil red O and H&E staining. Ultrastructural pathological changes of hepatocytes were observed to evaluate the intervention effect by transmission electron microscopy. RT-q PCR was used to detect the expression of peroxisome proliferator-activated receptor alpha and its regulated lipid metabolism genes CPTI, CPTII, Acot1, Acot2, ACOX, Cyp4a10 and Cyp4a14 in liver tissues. Intra-group comparison was done by paired t-test. One-way ANOVA was used for comparison between groups and semi-quantitative data were tested using Mann-Whitney U test. Results: Oil Red O and H&E staining results of liver tissue in the intervention group showed that intrahepatic steatosis was significantly reduced when compared to model group. Transmission electron microscopy showed that the model group had pyknotic nuclei, mitochondrial swelling, structural damage, and lysosomal degradation whereas the intervention group had hepatic nucleus without pyknosis, reduced mitochondrial swelling and slight structural damage than that of model group. RT-q PCR results showed that the expression of peroxisome proliferator-activated receptor alpha, CPTI, CPTII, Acot1, Acot2, ACOX, Cyp4a10 and Cyp4a14 were increased in the model group but the expression of CPTI, Cyp4a14, Acot1 and peroxisome proliferator-activated receptor alpha were decreased in the intervention group (P < 0.05). Conclusion: Silybin-phospholipid complex can alleviate amiodarone-induced steatosis, and its mechanism may play a role in protecting mitochondrial function and regulating fatty acid metabolism. Thus, silybin-phospholipid complex has potential intervention effect on amiodarone-induced fatty liver.

MADS-Box Gene Classification in Angiosperms by Clustering and Machine Learning Approaches

The MADS-box gene family is an important transcription factor family involved in floral organogenesis. The previously proposed ABCDE model suggests that different floral organ identities are controlled by various combinations of classes of MADS-box genes. The five-class ABCDE model cannot cover all the species of angiosperms, especially the orchid. Thus, we developed a two-stage approach for MADS-box gene classification to advance the study of floral organogenesis of angiosperms. First, eight classes of reference datasets (A, AGL6, B12, B34, BPI, C, D, and E) were curated and clustered by phylogenetic analysis and unsupervised learning, and they were confirmed by the literature. Second, feature selection and multiple prediction models were curated according to sequence similarity and the characteristics of the MADS-box gene domain using support vector machines. Compared with the BindN and COILS features, the local BLAST model yielded the best accuracy. For performance evaluation, the accuracy of Phalaenopsis aphrodite MADS-box gene classification was 93.3%, which is higher than 86.7% of our previous classification prediction tool, iMADS. Phylogenetic tree construction – the most common method for gene classification yields classification errors and is time-consuming for analysis of massive, multi-species, or incomplete sequences. In this regard, our new system can also confirm the classification errors of all the random selection that were incorrectly classified by phylogenetic tree analysis. Our model constitutes a reliable and efficient MADS-box gene classification system for angiosperms.

Removal of sulfonamides from wastewater in the UV/TiO2 system: effects of pH and salinity on photodegradation and mineralization

The effects of salinity on the photodegradation and mineralization of sulfonamides in the UV/TiO₂ system were investigated. The goals of this study were to analyze the effects of pH and salinity on the sulfonamide concentration and total organic carbon (TOC) during the removal of sulfonamides in a UV/TiO₂ system. Four sulfonamides - sulfadiazine (SDZ), sulfamethizole (SFZ), sulfamethoxazole (SMX) and sulfathiazole (STZ) - were selected as parent compounds. The photodegradation and mineralization rates of sulfonamides in the UV/TiO₂ system satisfy pseudo-first-order kinetics. Direct photolysis degraded sulfonamides but sulfonamides cannot be mineralized. The photodegradation and mineralization rate constants in all experiments followed the order pH 5 > pH 7 > pH 9. At pH 5, the mineralization rate constants of SMX, SFZ, SDZ and STZ were 0.015, 0.009, 0.012 and 0.011 min^-1, respectively. The addition of NaCl inhibited the mineralization of the four tested sulfonamides more than it inhibited their photodegradation. The inhibitory effect of chloride ions on the removal of sulfonamides in the UV/TiO₂ system was attributed to the scavenging by chloride ions of hydroxyl radicals (HO•) and holes and the much lower reactivity of chlorine radicals thus formed, even though the chlorine radicals were more abundant than HO•.

KStable: A Computational Method for Predicting Protein Thermal Stability Changes by K-Star with Regular-mRMR Feature Selection

Thermostability is a protein property that impacts many types of studies, including protein activity enhancement, protein structure determination, and drug development. However, most computational tools designed to predict protein thermostability require tertiary structure data as input. The few tools that are dependent only on the primary structure of a protein to predict its thermostability have one or more of the following problems: a slow execution speed, an inability to make large-scale mutation predictions, and the absence of temperature and pH as input parameters. Therefore, we developed a computational tool, named KStable, that is sequence-based, computationally rapid, and includes temperature and pH values to predict changes in the thermostability of a protein upon the introduction of a mutation at a single site. KStable was trained using basis features and minimal redundancy–maximal relevance (mRMR) features, and 58 classifiers were subsequently tested. To find the representative features, a regular-mRMR method was developed. When KStable was evaluated with an independent test set, it achieved an accuracy of 0.708.

DHS (trans-4,4'-dihydroxystilbene) suppresses DNA replication and tumor growth by inhibiting RRM2 (ribonucleotide reductase regulatory subunit M2)

DNA replication machinery is responsible for accurate and efficient duplication of the chromosome. Since inhibition of DNA replication can lead to replication fork stalling, resulting in DNA damage and apoptotic death, inhibitors of DNA replication are commonly used in cancer chemotherapy. Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the biosynthesis of deoxyribonucleoside triphosphates (dNTPs) that are essential for DNA replication and DNA damage repair. Gemcitabine, a nucleotide analog that inhibits RNR, has been used to treat various cancers. However, patients often develop resistance to this drug during treatment. Thus, new drugs that inhibit RNR are needed to be developed. In this study, we identified a synthetic analog of resveratrol (3,5,4’-trihydroxy-trans-stilbene), termed DHS (trans-4,4’-dihydroxystilbene), that acts as a potent inhibitor of DNA replication. Molecular docking analysis identified the RRM2 (ribonucleotide reductase regulatory subunit M2) of RNR as a direct target of DHS. At the molecular level, DHS induced cyclin F-mediated down-regulation of RRM2 by the proteasome. Thus, treatment of cells with DHS reduced RNR activity and consequently decreased synthesis of dNTPs with concomitant inhibition of DNA replication, arrest of cells at S-phase, DNA damage, and finally apoptosis. In mouse models of tumor xenografts, DHS was efficacious against pancreatic, ovarian, and colorectal cancer cells. Moreover, DHS overcame both gemcitabine resistance in pancreatic cancer and cisplatin resistance in ovarian cancer. Thus, DHS is a novel anti-cancer agent that targets RRM2 with therapeutic potential either alone or in combination with other agents to arrest cancer development.

Foreign body in the thoracic spine due to a nail gun penetrating injury: A case report

RATIONALE

Spinal cord injuries could be catastrophic because they may result in severe neurovascular complications. Here, we present a case of thoracic spine-penetrating injury by a nail-gun.

PATIENT CONCERNS

A 60-year-old male presented to our emergency department with complaints of progressive right chest pain for 1 week that was preceded by back pain. He had a medical history of hypertension and denied any trauma history. He had alert consciousness and stable vital signs. He was a carpenter. Upon physical and neurological examination, no obvious wounds or vesicle formation were noted, and the patient was neurologically intact.

DIAGNOSIS

Laboratory test results showed abnormally elevated D-dimer levels. Electrocardiography showed normal sinus rhythm. Chest radiography showed no mediastinal widening. Chest computed tomography was performed. The formal radiology report indicated a foreign body in the T4-5 spinal cord and upper back.

INTERVENTIONS

A neurosurgeon was consulted with suggestion of operation. We performed T4-5 laminectomy and foreign body removal. The foreign body, stuck to the spinal cord with dural rupture, was removed and found to be a 5 cm-long broken nail.

OUTCOMES

The pain resolved immediately post operation.

LESSONS

Surgical removal of the foreign body is recommended if neurovascular complications or cerebrospinal fluid (CSF) leak is detected. Obtaining the patient's complete history, including occupation, might be helpful in determining the diagnosis. Careful interpretation of diagnostic imaging is necessary for avoiding medical disputes. Even in the absence of wounds and ecchymosis, trauma-related injury should be considered.

A survival case of intravenous paraquat intoxication: A case report

RATIONALE

Paraquat, an agent highly toxic to humans and animals, is a widely used herbicide and also commonly used for suicide attempts in Taiwan. The most common route of intoxication is oral ingestion, and parenteral poisoning is respectively rare.

PATIENT CONCERNS

A 39-year-old illicit abuser of heroin and amphetamine injected 0.5 mL of 24% paraquat directly into his right cephalic vein due to hallucination. The patient was brought to our emergency department for management 4 hours after injection. He was fully conscious and had normal vital signs. Systemic review showed mild dyspnea, abdominal pain and right wrist pain over the injection site. The only abnormal physical finding was erythema over the injection site and epigastric tenderness.

DIAGNOSIS

Laboratory investigations, including complete blood count, liver and renal function, and electrolytes initially yielded normal results. Urinalysis showed normal findings except a positive urine paraquat test (4+). The initial plasma paraquat concentration was 0.51 μg/mL.

INTERVENTIONS

He was admitted to the intensive care unit and underwent one session of charcoal hemoperfusion therapy. Acute kidney injury developed on the fourth day after intoxication, with the level of serum creatinine rising rapidly from 0.96 to 4.57 mg/dL and the daily urine output decreased noticeably from > 2000 to 900 mL. The serum creatinine level improved gradually with adequate fluid supplementation.

OUTCOMES

The patient was discharged 13 days later in a stable condition.

LESSONS

Intravenous paraquat intoxication is rare. Patients who suffer from intravenous intoxication may not directly suffer from mucosal irritation, but the clinical onset of systemic effects is more immediate and lethal. The prognosis of paraquat poisoning is determined by the time of poisoning and the plasma paraquat concentration before treatment. Proudfoot's curve provides a simple method of predicting the survival rate. The most effective mode of management is extracorporeal therapy, and immunosuppressive or antioxidant therapies have shown insufficient evidence of benefit.

DUOXA1-mediated ROS production promotes cisplatin resistance by activating ATR-Chk1 pathway in ovarian cancer

The acquisition of resistance is a major obstacle to the clinical use of platinum drugs for ovarian cancer treatment. Increase of DNA damage response is one of major mechanisms contributing to platinum-resistance. However, how DNA damage response is regulated in platinum-resistant ovarian cancer cells remains unclear. Using quantitative high throughput combinational screen (qHTCS) and RNA-sequencing (RNA-seq), we show that dual oxidase maturation factor 1 (DUOXA1) is overexpressed in platinum-resistant ovarian cancer cells, resulting in over production of reactive oxygen species (ROS). Elevated ROS level sustains the activation of ATR-Chk1 pathway, leading to resistance to cisplatin in ovarian cancer cells. Moreover, using qHTCS we identified two Chk1 inhibitors (PF-477736 and AZD7762) that re-sensitize resistant cells to cisplatin. Blocking this novel pathway by inhibiting ROS, DUOXA1, ATR or Chk1 effectively overcomes cisplatin resistance in vitro and in vivo. Significantly, the clinical studies also confirm the activation of ATR and DOUXA1 in ovarian cancer patients, and elevated DOUXA1 or ATR-Chk1 pathway correlates with poor prognosis. Taken together, our findings not only reveal a novel mechanism regulating cisplatin resistance, but also provide multiple combinational strategies to overcome platinum-resistance in ovarian cancer.

Autocrine activation of JAK2 by IL-11 promotes platinum drug resistance

Antineoplastic platinum agents are used in first-line treatment of ovarian cancer, but treatment failure frequently results from platinum drug resistance. Emerging observations suggest a role of reactive oxygen species (ROS) in the resistance of cancer drugs including platinum drugs. However, the molecular link between ROS and cellular survival pathway is poorly understood. Using quantitative high-throughput combinational screen (qHTCS) and genomic sequencing, we show that in platinum-resistant ovarian cancer elevated ROS levels sustain high level of IL-11 by stimulating FRA1-mediated IL-11 expression and increased IL-11 causes resistance to platinum drugs by constitutively activating JAK2-STAT5 via an autocrine mechanism. Inhibition of JAK2 by LY2784544 or IL-11 by anti-IL-11 antibody overcomes the platinum resistance in vitro or in vivo. Significantly, clinic studies also confirm the activated IL-11-JAK2 pathway in platinum-resistant ovarian cancer patients, which highly correlates with poor prognosis. These findings not only identify a novel ROS-IL-11-JAK2-mediated platinum resistance mechanism but also provide a new strategy for using LY2784544- or IL-11-mediated immunotherapy to treat platinum-resistant ovarian cancer.

Source identification and ecological impact evaluation of PAHs in urban river sediments: A case study in Taiwan

The Love River and Ho-Jin River, two major urban rivers in Kaohsiung City, Taiwan, are moderately to heavily polluted because different types of improperly treated wastewaters are discharged into the rivers. In this study, sediment and river water samples were collected from two rivers to investigate the river water quality and accumulation of polycyclic aromatic hydrocarbons (PAHs) in sediments. The spatial distribution, composition, and source appointment of PAHs of the sediments were examined. The impacts of PAHs on ecological system were assessed using toxic equivalence quotient (TEQ) of potentially carcinogenic PAHs (TEQ^carc) and sediment quality guidelines. The average PAHs concentrations ranged from 2161 ng/g in Love River sediment to 160 ng/g in Ho-Jin River sediment. This could be due to the fact that Love River Basin had much higher population density and pyrolytic activities. High-ring PAHs (4-6 rings) contributed to 59-90% of the total PAHs concentrations. Benzo(a)pyrene (BaP) had the highest toxic equivalence quotient (up to 188 ng TEQ/g). Moreover, the downstream sediments contained higher TEQ of total TPHs than midstream and upstream sediment samples. The PAHs were adsorbed onto the fine particles with high organic content. Results from diagnostic ratio analyses indicate that the PAHs in two urban river sediments might originate from oil/coal combustion, traffic-related emissions, and waste combustion (pyrogenic activities). Future pollution prevention and management should target the various industries, incinerators, and transportation emission in this region to reduce the PAHs pollution.

NMR-based metabolomics for the environmental assessment of Kaohsiung Harbor sediments exemplified by a marine amphipod (Hyalella azteca)

Inflow of wastewater from upstream causes a large flux of pollutants to enter Kaohsiung Harbor in Taiwan daily. To reveal the ecological risk posed by Kaohsiung Harbor sediments, an ecological metabolomic approach was employed to investigate environmental factors pertinent to the physiological regulation of the marine amphipod Hyalella azteca. The amphipods were exposed to sediments collected from different stream inlets of the Love River (LR), Canon River (CR), Jen-Gen River (JR), and Salt River (SR). Harbor entrance 1 (E1) was selected as a reference site. After 10-day exposure, metabolomic analysis of the Hyalella azteca revealed differences between two groups: {E1, LR, CR} and {JR, SR}. The metabolic pathways identified in the two groups of amphipods were significantly different. The results demonstrated that NMR-based metabolomics can be effectively used to characterize metabolic response related to sediment from polluted areas.

[Efficacy and safety of pegylated interferon α-2b injection (Y shape, 40 kD) in treatment of patients with genotype 1/6 chronic hepatitis C]

Objective: To investigate the efficacy and safety of the new investigational drug pegylated interferon α-2b (Peg-IFN-α-2b) (Y shape, 40 kD) injection (180 µg/week) combined with ribavirin in the treatment of patients with genotype 1/6 chronic hepatitis C (CHC), with standard-dose Peg-IFN-α-2a combined with ribavirin as a positive control. Methods: A multicenter, randomized, open-label, and positive-controlled phase III clinical trial was performed. Eligible patients with genotype 1/6 CHC were screened out and randomly divided into Peg-IFN-α-2b(Y shape, 40kD) group and Peg-IFN-α-2a group at a ratio of 2:1. The patients in both groups were given oral ribavirin for 48 weeks in addition and then followed up for 24 weeks after drug withdrawal. Abbott Real Time HCV Genotype II was used to determine HCV genotype, and Cobas TaqMan quantitative real-time PCR was used to measure HCV RNA level at 0, 4, 12, 24, 48, and 72 weeks. Adverse events were recorded in detail. The primary efficacy endpoint was sustained virological response (SVR), and a non-inferiority test was also performed. Results: A total of 561 patients with genotype 1/6 CHC were enrolled, among whom 529 received treatment; 90.9% of these patients had genotype 1 CHC. The data of the full analysis set showed that SVR rate was 69.80% (95% CI 65.00%-74.60%) in the trial group and 74.16% (95% CI 67.73%-80.59%) in the control group (P = 0.297 0). The data of the per protocol set (PPS) showed that SVR rate was 80.63% (95% CI 76.04%-85.23%) in the trial group and 81.33% (95% CI 75.10%-87.57%) in the control group (P = 0.849 8), and the 95% CI of rate difference conformed to the non-inferiority standard. The analysis of the PPS population showed that of all subjects, 47.9% achieved rapid virologic response, with a positive predictive value of 93.8%. The incidence rate of adverse events was 96.30% in the trial group and 94.94% in the control group, and the incidence rate of serious adverse events was 5.13% in the trail group and 5.06% in the control group. Conclusion: In the regimen of Peg-IFN-α combined with ribavirin for the treatment of genotype 1/6 CHC, the new investigational drug Peg-IFN-α-2b(Y shape, 40 kD) has comparable clinical effect and safety to the control drug Peg-IFN-α-2a.

Predicting human protein subcellular localization by heterogeneous and comprehensive approaches

Drug development and investigation of protein function both require an understanding of protein subcellular localization. We developed a system, REALoc, that can predict the subcellular localization of singleplex and multiplex proteins in humans. This system, based on comprehensive strategy, consists of two heterogeneous systematic frameworks that integrate one-to-one and many-to-many machine learning methods and use sequence-based features, including amino acid composition, surface accessibility, weighted sign aa index, and sequence similarity profile, as well as gene ontology function-based features. REALoc can be used to predict localization to six subcellular compartments (cell membrane, cytoplasm, endoplasmic reticulum/Golgi, mitochondrion, nucleus, and extracellular). REALoc yielded a 75.3% absolute true success rate during five-fold cross-validation and a 57.1% absolute true success rate in an independent database test, which was >10% higher than six other prediction systems. Lastly, we analyzed the effects of Vote and GANN models on singleplex and multiplex localization prediction efficacy. REALoc is freely available at http://predictor.nchu.edu.tw/REALoc.