Salmonellosis outbreaks linked to eggs at 2 gimbap restaurants in the Republic of Korea.

Objectives: Salmonellosis outbreaks occurred at 2 restaurants 2 days apart, and an epidemiological investigation was conducted to determine whether the outbreaks were connected. Methods: Case studies were conducted for both outbreaks. Stool samples were collected from individuals, and food samples were collected from the restaurants. Pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing analyses were performed on outbreak-related Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) isolates. Traceback investigations were also conducted for the ingredients from gimbap restaurants A and B. Results: In total, 106 people from gimbap restaurant A and 5 from gimbap restaurant B met the case definition. Salmonella Enteritidis was detected in samples from 2 food handlers, 22 patients, and 1 food (iceberg lettuce) at gimbap restaurant A and from 1 patient at gimbap restaurant B. According to PFGE, all isolates were identified as SEGX01.089. The molecular typing of all isolates showed the same pattern, and the genetic distance was close according to phylogenetic analysis. Eggs were the only food ingredient that was supplied to both gimbap restaurants. Conclusion: The outbreaks were caused by Salmonella Enteritidis, and the source of infections was suspected to be contaminated eggs. To prevent foodborne outbreaks of Salmonella, restaurants should heat eggs sufficiently, and egg farms need to establish management systems that prevent Salmonella infections.

Intra-articular injection of stigmasterol-loaded nanoparticles reduce pain and inhibit the inflammation and joint destruction in osteoarthritis rat model: A pilot study.

Stigmasterol, a plant-derived sterol, sharing structural similarity with cholesterol, has demonstrated anti-osteoarthritis (OA) properties, attributed to its antioxidant and anti-inflammatory capabilities. Given that OA often arises in weight bearing or overused joints, prolonged localized treatment effectively targets inflammatory aspects of the disease. This research explored the impact of stigmasterol-loaded nanoparticles delivered via intra-articular injections in an OA rat model. Employing mesoporous silica nanomaterials (MSNs) combined with ß-cyclodextrin (ß-CD) as a vehicle, stigmasterol was loaded in conjunction with tannic acid, forming stigmasterol/ß-CD-MSNs to facilitate a sustained stigmasterol release. The study employed RAW 264.7 cells to examine the in vitro cytotoxicity and anti-inflammatory effect of stigmasterol/ß-CD-MSNs. For in vivo experimentation, we used healthy control rats and monosodium iodoacetate (MIA)-induced OA rats, separated into five groups, varying the injection substances. In vitro findings indicated that stigmasterol/ß-CD-MSNs suppressed the mRNA expression of key pro-inflammatory mediators such as interleukin-6, tumor necrosis factor-α, and matrix metalloproteinase-3 in a dose-dependent manner. In vivo experiments revealed a substantial decrease in the mRNA levels of pro-inflammatory factors in the stigmasterol(50 µg)/ß-CD-MSN group compared to the others. Macroscopic, radiographic, and histological evaluations established that intra-articular injections of stigmasterol/ß-CD-MSNs inhibited cartilage degeneration and subchondral bone deterioration. Therefore, in a chemically induced OA rat model, intra-articular stigmasterol delivery was associated with reduction in both local and systemic inflammatory responses, alongside a slowdown in joint degradation and arthritic progression.

Species Profiles and Antimicrobial Resistance of Non-aureus Staphylococci Isolated from Healthy Broilers, Farm Environments, and Farm Workers.

Non-aureus staphylococci (NAS), particularly antimicrobial-resistant NAS, have a substantial impact on human and animal health. In the current study, we investigated (1) the species profiles of NAS isolates collected from healthy broilers, farm environments, and farm workers in Korea, (2) the occurrence of antimicrobial-resistant NAS isolates, especially methicillin resistance, and (3) the genetic factors involved in the methicillin and fluoroquinolone resistance. In total, 216 NAS isolates of 16 different species were collected from healthy broilers (n=178), broiler farm environments (n=18), and farm workers (n=20) of 20 different broiler farms. The two most dominant broiler-associated NAS species were Staphylococcus agnetis (23.6%) and Staphylococcus xylosus (22.9%). Six NAS isolates were mecA-positive carrying staphylococcal cassette chromosome mec (SCCmec) II (n=1), SCCmec IV (n=1), SCCmec V (n=2), or non-typeable SCCmec element (n=2). While two mecA-positive Staphylococcus epidermidis isolates from farm workers had SCCmec II and IV, a mecA-positive S. epidermidis isolate from broiler and a Staphylococcus haemolyticus isolate farm environment carried SCCmec V. The occurrence of multidrug resistance was observed in 48.1% (104/216 isolates) of NAS isolates with high resistance rates to ß-lactams (>40%) and fusidic acid (59.7%). Fluoroquinolone resistance was confirmed in 59 NAS isolates (27.3%), and diverse mutations in the quinolone resistance determining regions of gyrA, gyrB, parC, and parE were identified. These findings suggest that NAS in broiler farms may have a potential role in the acquisition, amplification, and transmission of antimicrobial resistance.

CCIDB: a manually curated cell-cell interaction database with cell context information.

Cell-cell interaction (CCI) is a crucial event in the development and function of multicellular organisms. The development of CCI databases is beneficial for researchers who want to analyze single-cell sequencing data or study CCI through molecular experiments. CCIs are known to act differently according to cellular and biological contexts such as cell types, gene mutations or disease status; however, previous CCI databases do not completely provide this contextual information pertaining to CCIs. We constructed a cell-cell interaction database (CCIDB) containing the biological and clinical contexts involved in each interaction. To build a database of cellular and tissue contexts, we collected 38 types of context features, which were categorized into seven categories, including 'interaction', 'cell type', 'cofactor', 'effector', 'phenotype', 'pathology' and 'reference'. CCIs were manually retrieved from 272 studies published recently (less than 6 years ago). In the current version of CCIDB, 520 CCIs and their 38 context features have been manually collected and curated by biodata engineers. We suggest that CCIDB is a manually curated CCI resource that is highly useful, especially for analyzing context-dependent alterations in CCIs. Database URL https://ccidb.sysmed.kr/.

Association between interleukin 12B and interleukin 23R gene polymorphisms and systemic lupus erythematosus: a meta-analysis.

OBJECTIVE: To determine whether polymorphisms of interleukin 12B (IL12B) and IL23 receptor genes (IL23R) confer susceptibility to systemic lupus erythematosus (SLE). METHODS: A meta-analysis was conducted to analyze the associations between SLE and IL12B rs3212227 and rs17860508 and IL23R rs7517847, rs10489629, rs10889677, rs1004819, rs11209026, rs11209032, rs1343151, and rs1884444 polymorphisms using allele contrast, dominant, recessive, heterozygote, and homozygote models. Ten studies involving 1989 patients with SLE and 2394 controls were considered for the meta-analysis. RESULTS: The meta-analysis using the homozygote model revealed that IL23R rs10889677 was significantly associated with SLE susceptibility in the overall population (AA vs. CC) (odds ratio = 0.70, 95% confidence interval = 0.50-0.98) but not in the Asian population. Other polymorphisms of IL12B and IL23R were not significantly associated with SLE protection. CONCLUSIONS: These findings suggest that the IL23R rs10889677 polymorphism confers SLE susceptibility to individuals of certain ethnicities. (Research Registry number: 1268).

Management of facial nerve schwannoma: when is the timing for surgery.

PURPOSE: Although the estimated prevalence is extremely low, facial nerve schwannoma (FNS) is the most common primary tumor of the facial nerve (FN). In the present study, the outcome of surgical management in 18 patients with FNS was analyzed and an appropriate time for surgery was proposed. MATERIALS AND METHODS: A total of 18 patients with FNS who underwent surgical management by a single surgeon from 1999 to 2018 were retrospectively analyzed. RESULTS: Among the 18 patients, five had no facial paralysis before surgery. Near-total removal was performed in three cases, and two cases were managed with decompression. In 13 cases with various degree of preoperative facial palsy, nerve continuity was lost during surgery. FN was reconstructed using cable graft in ten cases, direct anastomosis in one case, and facial-hypoglossal nerve transfer in one case. Facial reanimation surgery without FN reconstruction was performed in one case due to a long-standing facial paralysis before surgery. Preoperative House-Brackmann (H-B) grade in all patients was significantly worse as tumor size increased. The correlation was not observed between the duration and severity of preoperative facial palsy. Analysis of 12 patients who underwent FN reconstruction revealed that all patients with good preoperative facial function (H-B grade II-III) recovered to H-B grade III after surgery (7/7, 100%). However, patients with poor preoperative facial function (H-B grade IV or worse) had only a 40% (2/5) chance of improving to grade III after surgery. Preoperative tumor size and duration of facial palsy did not affect postoperative final facial function. CONCLUSION: We suggest that H-B grade III facial palsy is the best time for surgical intervention, regardless of the tumor size or duration of facial palsy.

Prevalence of chronic obstructive pulmonary disease in patients with rheumatoid arthritis: A cross-sectional study.

OBJECTIVE: Rheumatoid arthritis (RA) and chronic obstructive pulmonary disease (COPD) are both chronic inflammatory diseases; the prevalence of COPD in RA patients is known to be high. However, the prevalence of both RA and COPD differs according to sex; the relationship between RA and COPD may also vary according to sex. Therefore, we investigated the prevalence of COPD and its association in patients with RA in Korea by sex. METHODS: We conducted a nationwide cross-sectional study using data from the Korea National Health and Nutrition Examination Survey. A total of 12 417 men and 15 878 women were included. In this study, RA was defined as physician diagnosed or currently under RA treatment. COPD was defined based on spirometry results, chronic symptoms, and smoking history. Multivariable logistic regression models were employed and we calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for COPD prevalence in patients with RA. RESULTS: The prevalence of COPD was 15.5% in men with RA, 3.5% in women with RA, 7.8% in men without RA, and 2.2% in women without RA. After adjustment for potential confounding variables, including smoking status, RA was significantly associated with COPD in men (OR 2.16, 95% CI 1.06-4.40), but not in women (OR 1.58, 95% CI 0.81-3.10). CONCLUSIONS: In Korea, the prevalence of COPD was high in patients with RA of both sexes; RA and COPD was significantly likely to be associated in men, but not in women.

Low expression of mitofusin 1 is associated with mitochondrial dysfunction and apoptosis in porcine somatic cell nuclear transfer embryos.

Mitochondria are necessary for the transition from oocyte to embryo and for early embryonic development. Mitofusin 1 is the main mediator of mitochondrial fusion and homeostasis. We investigated Mitofusin 1 expression levels in porcine somatic cell nuclear transfer (SCNT) embryos. The rate of blastocyst formation in SCNT embryos was reduced significantly compared with that of parthenogenetic activation embryos. SCNT embryos showed significantly decreased Mitofusin 1 expression and mitochondrial membrane potential, while exhibiting increased reactive oxygen species and apoptosis. Mitochondrial functional changes were observed in the SCNT embryos and may be correlated with low levels of Mitofusin 1 to negatively affect development.

Clinical Performance Evaluation of a Personal Sound Amplification Product vs a Basic Hearing Aid and a Premium Hearing Aid.

Importance: Hearing loss is a highly prevalent condition with multiple negative associated outcomes, yet few persons with hearing loss have hearing aids (HAs). Personal sound amplification products (PSAPs) could be an alternative low-cost solution to HAs, but data are lacking on the performance of PSAPs. Objective: To evaluate the clinical efficacy of a PSAP by comparing its performance with that of a basic HA and a premium HA in participants with mild, moderate, and moderately severe hearing impairment. Design, Setting, and Participants: A prospective, single-institution cohort study was performed with a total of 56 participants, including 19 with mild hearing loss, 20 with moderate hearing loss, and 17 with moderately severe hearing loss. All participants underwent 4 clinical hearing tests with each of the PSAP, basic HA, and premium HA, and all completed an evaluative questionnaire. Interventions: All hearing devices (PSAP, basic HA, and premium HA) were applied by a clinician to prevent bias and order effects; participants were blinded to the device in use, and sequence of devices was randomized. Main Outcomes and Measures: The study used the Korean version of the hearing in noise test, the speech intelligibility in noise test, listening effort measurement using a dual-task paradigm, pupillometry, and a self-rating questionnaire regarding sound quality and preference. These tests were administered under the following 4 hearing conditions: unaided hearing, use of PSAP, use of basic HA, and use of premium HA. Results: The study included 56 participants with a mean age of 56 years (interquartile range, 48-59 years); 29 (52%) were women. In the mild and moderate hearing loss groups, there was no meaningful difference between PSAP, basic HA, and premium HA for speech perception (Cohen d = 0.06-1.05), sound quality (Cohen d = 0.06-0.71), listening effort (Cohen d = 0.10-0.92), and user preference (PSAP, 41%; basic HA, 28%; premium HA, 31%). However, for the patients with moderately severe hearing loss, the premium HA had better performance across most tests (Cohen d = 0.60-1.59), and 70% of participants preferred to use the premium HA. Conclusions and Relevance: The results indicate that basic and premium HAs were not superior to the PSAP in patients with mild to moderate hearing impairment, which suggests that PSAPs might be used as an alternative to HAs in these patient populations. However, if hearing loss is more severe, then HAs, especially premium HAs, should be considered as an option to manage hearing loss.

Quantification of Thiopurine Nucleotides in Erythrocytes and Clinical Application to Pediatric Acute Lymphoblastic Leukemia.

BACKGROUND: Concentrations of 6-thioguanine (6TG) nucleotides and 6-methylmercaptopurine (6MMP) nucleotides in RBCs were measured using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This assay was validated for clinical use and was applied to blood samples from patients taking mercaptopurine (6MP). METHODS: RBCs were hemolyzed and deproteinized using perchloric acid, followed by heating for the hydrolysis of nucleotides, and the resultant base was measured using LC-MS/MS. Precision, recovery, linearity, matrix effect, and limit of quantification was validated for clinical application. Our results were compared with another institution's established LC-MS/MS assay. We measured the concentrations of 6TG and 6MMP in RBCs of pediatric patients with acute lymphoblastic leukemia (ALL), and the clinical impact of those metabolites was investigated. RESULTS: The imprecision coefficient of variations of 6TG and 6MMP were 5.7%-8.1%, and the bias was within 5%. Lower limits of quantification were set at 54 ng/mL for 6TG and 1036 ng/mL for 6MMP. Correlation coefficients for 6TG and 6MMP were 0.997 and 1.0 in a comparison study. For clinical proof-of-concept, 74 blood samples were collected from 37 pediatric ALL patients receiving maintenance therapy. Concentration of 6TG ranged from 16.1 to 880 pmol/8 × 10 RBCs and that of 6MMP from 55 to 20,937 pmol/8 × 10 RBCs. The 6MP metabolites were not correlated with WBC or absolute neutrophil count. On the other hand, the higher 6MMP level was associated with elevated alanine aminotransferase and aspartate aminotransferase. CONCLUSIONS: In this study, an assay for the quantification of 6TG and 6MMP in RBCs was established and applied to pediatric ALL patients. Interindividual variability in 6MP metabolite concentrations was considerable and associated with elevation of liver enzymes, which may be useful in the clinical monitoring of 6MP maintenance therapy in pediatric ALL patients.

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model.

Mechanistic models are essential to deepen the understanding of complex diseases at the molecular level. Nowadays, high-throughput molecular and phenotypic characterizations are possible, but the integration of such data with prior knowledge on signaling pathways is limited by the availability of scalable computational methods. Here, we present a computational framework for the parameterization of large-scale mechanistic models and its application to the prediction of drug response of cancer cell lines from exome and transcriptome sequencing data. This framework is over 104 times faster than state-of-the-art methods, which enables modeling at previously infeasible scales. By applying the framework to a model describing major cancer-associated pathways (>1,200 species and >2,600 reactions), we could predict the effect of drug combinations from single drug data. This is the first integration of high-throughput datasets using large-scale mechanistic models. We anticipate this to be the starting point for development of more comprehensive models allowing a deeper mechanistic insight.

Effect of Cytochalasin B Treatment on the Improvement of Survival Rate in Vitrified Pig Oocyte.

To improve survival rates of vitrified pig oocytes, the treatment of cytoskeletal stabilizer on an appropriate time is one of the possible approaches. However, the exact treatment timing and effect of cytoskeletal stabilizer such as cytochalasin B (CB) is not well known during oocyte vitrification procedures. Thus, the present study was conducted to determine optimal treatment timing of CB during vitrification and warming procedures. In experiment 1, the survival rates of the post-warming pig oocytes were analyzed by fluorescein diacetate (FDA) assays with 4 classifications. In results, post-warming oocytes showed significantly (p<0.05) decreased number of alive oocytes (31.8% vs. 86.4%) compared to fresh control. In detail, the significant difference (p<0.05) was found only in strong fluorescence (18.2% vs. 70.5%) not in intermediate fluorescence groups (13.6% vs. 15.9%). In experiment 2, CB was treated before (CB-Vitri) and after (Vitri-CB) vitrification. In results, group of Vitri-CB showed significantly (p<0.05) higher (91.6%) survival rates compared to group of CB-Vitri (83.7%), significantly (p<0.05) and comparable with group of Vitri Control (88.7%) by morphological inspection. In FDA assay results, group of Vitri-CB showed significantly (p<0.05) higher (44.2%) survival rates compared to groups of CB-Vitri (36.7%) and Vitri Control (35.1%). In conclusion, the increased survival rates of post-warming pig oocyte treated with Vitri-CB method are firstly described here. The main finding of present study is that the CB treatment during recovery could be helpful to refresh the post-warming pig oocyte resulting its improved survival rates.

Clinical Outcomes of Standard Triple Therapy Plus Probiotics or Concomitant Therapy for Helicobacter pylori Infection.

BACKGROUND/AIMS: The efficacy of standard triple therapy (STT) in treating Helicobacter pylori infection has decreased. Many investigators have attempted to increase the eradication rate. We investigated the outcomes of concomitant therapy (CT) and STT combined with probiotics (STP) as a first-line treatment for H. pylori infection. METHODS: We reviewed the medical records of 361 patients who received either STP (n=286) or CT (n=75). The STP group received STT combined with a probiotic preparation for 1 week. The CT group received STT and metronidazole for 1 week. RESULTS: The intention-to-treat and per-protocol eradication rates were 83.6% (95% confidence interval [CI], 79.0 to 87.7) and 87.1% (95% CI, 81.2 to 89.7) in the STP group and 86.7% (95% CI, 78.7 to 93.3) and 91.4% (95% CI, 83.6 to 97.1) in the CT group (p=0.512 and p=0.324), respectively. The frequency of adverse effects was higher in the CT group (28.2%) than in the STP group (12.8%) (p=0.002). CONCLUSIONS: STP and CT are encouragingly efficacious as first-line treatments for H. pylori infection. Therefore, adding probiotics to STT may be a feasible option to avoid side effects.

Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions.

p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. It functions as a tetramer, where each component dimer binds to a decameric DNA region known as a response element. We identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. We start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. When combined, they give rise to three types of p53 binding sites. We find that probabilistic and alignment-based assessments of cross-species conservation show no strong evidence of differential conservation between types of binding sites. In contrast, functional analysis of the genes most proximal to the binding sites provides strong bioinformatic evidence of functional differentiation between the three types of binding sites. Our results are consistent with recent structural data identifying two conformations of the L1 loop in the DNA binding domain, suggesting that they reflect biologically meaningful groups imposed by the p53 protein structure.

NDRG2 Expression Decreases Tumor-Induced Osteoclast Differentiation by Down-regulating ICAM1 in Breast Cancer Cells.

Bone matrix is properly maintained by osteoclasts and osteoblasts. In the tumor microenvironment, osteoclasts are increasingly differentiated by the various ligands and cytokines secreted from the metastasized cancer cells at the bone metastasis niche. The activated osteoclasts generate osteolytic lesions. For this reason, studies focusing on the differentiation of osteoclasts are important to reduce bone destruction by tumor metastasis. The N-myc downstream-regulated gene 2 (NDRG2) has been known to contribute to the suppression of tumor growth and metastasis, but the precise role of NDRG2 in osteoclast differentiation induced by cancer cells has not been elucidated. In this study, we demonstrate that NDRG2 expression in breast cancer cells has an inhibitory effect on osteoclast differentiation. RAW 264.7 cells, which are monocytic preosteoclast cells, treated with the conditioned media (CM) of murine breast cancer cells (4T1) expressing NDRG2 are less differentiated into the multinucleated osteoclast-like cells than those treated with the CM of 4T1-WT or 4T1-mock cells. Interestingly, 4T1 cells stably expressing NDRG2 showed a decreased mRNA and protein level of intercellular adhesion molecule 1 (ICAM1), which is known to enhance osteoclast maturation. Osteoclast differentiation was also reduced by ICAM1 knockdown in 4T1 cells. In addition, blocking the interaction between soluble ICAM1 and ICAM1 receptors significantly decreased osteoclastogenesis of RAW 264.7 cells in the tumor environment. Collectively, these results suggest that the reduction of ICAM1 expression by NDRG2 in breast cancer cells decreases osteoclast differentiation, and demonstrate that excessive bone resorption could be inhibited via ICAM1 down-regulation by NDRG2 expression.

Moxifloxacin-containing triple therapy after non-bismuth quadruple therapy failure for Helicobacter pylori infection.

AIM: To assess the efficacy of moxifloxacin-containing triple therapy after non-bismuth quadruple therapy failure for Helicobacter pylori (H. pylori) eradication. METHODS: Between January 2010 and December 2012, we screened individuals who were prescribed non-bismuth quadruple therapy for H. pylori eradication. Among them, a total of 98 patients who failed non-bismuth quadruple therapy received 1-wk or 2-wk moxifloxacin-containing triple therapy (400 mg moxifloxacin once daily, and 20 mg of rabeprazole and 1 g of amoxicillin twice daily). H. pylori status was evaluated using the (13)C-urea breath test 4 wk later, after treatment completion. The eradication rates were determined by intention-to-treat and per-protocol analyses. RESULTS: In total, 60 and 38 patients received 1-wk and 2-wk moxifloxacin-containing triple therapy, respectively. The intention-to-treat and per-protocol eradication rates were 56.7% (95%CI: 45.0-70.0) and 59.6% (95%CI: 46.6-71.7) in the 1-wk group and 76.3% (95%CI: 63.2-89.5) and 80.6% (95%CI: 66.7-91.9) in the 2-wk group (P = 0.048 and 0.036, respectively). All groups had good compliance (95% vs 94.9%). Neither group showed serious adverse events, and the proportions of patients experiencing mild side effects were not significantly different (21.1% vs 13.9%). Clinical factors such as age, sex, alcohol and smoking habits, comorbidities, and presence of gastric or duodenal ulcer did not influence the eradication therapy efficacy. The efficacy of second-line eradication therapy did not differ significantly according to the first-line regimen. CONCLUSION: Two-week moxifloxacin-containing triple therapy showed better efficacy than a 1-wk regimen after non-bismuth quadruple therapy failure.

Inhibition of osteoclast differentiation by overexpression of NDRG2 in monocytes.

N-Myc downstream-regulated gene 2 (NDRG2), a member of the NDRG family of differentiation-related genes, has been characterized as a regulator of dendritic cell differentiation from monocytes, CD34(+) progenitor cells, and myelomonocytic leukemic cells. In this study, we show that NDRG2 overexpression inhibits the differentiation of U937 cells into osteoclasts in response to stimulation with a combination of macrophage colony-stimulating factor (M-CSF) and soluble receptor activator of NF-κB ligand (RANKL). U937 cells stably expressing NDRG2 are unable to differentiate into multinucleated osteoclast-like cells and display reduced tartrate-resistant acid phosphatase (TRAP) activity and resorption pit formation. Furthermore, NDRG2 expression significantly suppresses the expression of genes that are crucial for the proliferation, survival, differentiation, and function of osteoclasts, including c-Fos, Atp6v0d2, RANK, and OSCAR. The activation of ERK1/2 and p38 is also inhibited by NDRG2 expression during osteoclastogenesis, and the inhibition of osteoclastogenesis by NDRG2 correlates with the down-regulation of the expression of the transcription factor PU.1. Taken together, our results suggest that the expression of NDRG2 potentially inhibits osteoclast differentiation and plays a role in modulating the signal transduction pathway responsible for osteoclastogenesis.

Efficacy of 7-Day and 14-Day Bismuth-Containing Quadruple Therapy and 7-Day and 14-Day Moxifloxacin-Based Triple Therapy as Second-Line Eradication for Helicobacter pylori Infection.

BACKGROUND/AIMS: Bismuth-containing quadruple and moxifloxacin-based triple regimens are recommended as second-line therapy for Helicobacter pylori infection. The aim of this study was to compare the efficacy of each regimen. METHODS: From August 2004 to October 2012, a total of 949 patients (mean age, 54.32±12.08 years; male, 49.4%) who failed H. pylori eradication with a standard triple regimen were included. Patients treated with a bismuth-containing quadruple regimen for 7 and 14 days were designated as 7-BMT and 14-BMT, respectively, and those treated with a moxifloxacin-based triple regimen for 7 and 14 days were designated as 7-MA and 14-MA, respectively. H. pylori eradication was confirmed using the (13)C-urea breath test, rapid urease test or histology. RESULTS: The eradication rates by 7-BMT, 14-BMT, 7-MA, and 14-MA were 66.4% (290/437), 71.1% (113/159), 53.1% (51/96), and 73.5% (189/257), respectively, by intention-to-treat analysis (ITT) and 76.5% (284/371), 83.8% (109/130), 55.6% (50/90), and 80.6% (187/232), respectively, by per-protocol analysis (PP). The eradication rates were higher in 14-BMT than 7-BMT by the ITT and PP analyses (p=0.277 and p=0.082, respectively). The 14-BMT and 14-MA treatments showed similar efficacies by ITT and PP (p=0.583 and p=0.443, respectively). CONCLUSIONS: The 7-BMT, 14-BMT, and 14-MA treatments showed similar and suboptimal efficacies. In both regimens, extending the duration of treatment may be reasonable considering the high level of antibiotic resistance in Korea.

Models incorporating chromatin modification data identify functionally important p53 binding sites.

Genome-wide prediction of transcription factor binding sites is notoriously difficult. We have developed and applied a logistic regression approach for prediction of binding sites for the p53 transcription factor that incorporates sequence information and chromatin modification data. We tested this by comparison of predicted sites with known binding sites defined by chromatin immunoprecipitation (ChIP), by the location of predictions relative to genes, by the function of nearby genes and by analysis of gene expression data after p53 activation. We compared the predictions made by our novel model with predictions based only on matches to a sequence position weight matrix (PWM). In whole genome assays, the fraction of known sites identified by the two models was similar, suggesting that there was little to be gained from including chromatin modification data. In contrast, there were highly significant and biologically relevant differences between the two models in the location of the predicted binding sites relative to genes, in the function of nearby genes and in the responsiveness of nearby genes to p53 activation. We propose that these contradictory results can be explained by PWM and ChIP data reflecting primarily biophysical properties of protein-DNA interactions, whereas chromatin modification data capture biologically important functional information.