Pathogen and Surrogate Survival in Relation to Fecal Indicator Bacteria in Freshwater Mesocosms.

The microbial quality of agricultural water for fresh produce production is determined by the presence of the fecal indicator bacterium (FIB) Escherichia coli, despite poor correlations with pathogen presence. Additional FIB, such as enterococci, have been utilized for assessing water quality. The study objective was to determine the survival times (first time to detect zero or censored) of FIB (E. coli and enterococci), surrogates (Listeria innocua, Listeria seeligeri, Salmonella enterica serovar Typhimurium, and PRD1), and pathogens (four strains each of pathogenic E. coli and Listeria monocytogenes and five Salmonella serovars) simultaneously inoculated in freshwater mesocosms exposed to diel and seasonal variations. Six separate mesocosm experiments were conducted for ≤28 days each season, with samples (sediment/water) collected each day for the first 7 days and weekly thereafter. Microorganisms survived significantly longer in sediment than in water (hazard ratio [HR] for water/sediment is 2.2; 95% confidence interval [CI], 1.79 to 2.71). Also, FIB E. coli survived significantly longer than FIB enterococcus (HR for enterococci/E. coli is 12.9 [95% CI, 8.18 to 20.37]) after adjusting for the sediment/water and lake/river effects. Differences in the area under the curve (calculated from log CFU or PFU over time) were used to assess pathogen and surrogate survival in relation to FIB. Despite sample type (sediment/water) and seasonal influences, survival rates of pathogenic Salmonella serovars were similar to those of FIB E. coli, and survival rates of L. monocytogenes and pathogenic E. coli were similar to those of FIB enterococci. Further investigation of microbial survival in water and sediment is needed to determine which surrogates are best suited to assess pathogen survival in agricultural water used in irrigation water for fresh produce. IMPORTANCE Contamination of fresh produce via agricultural water is well established. This research demonstrates that survival of fecal indicator bacteria, pathogenic microorganisms, and other bacterial and viral surrogates in freshwater differs by sample type (sediment/water) and season. Our work highlights potential risks associated with pathogen accumulation and survival in sediment and the possibility for resuspension and contamination of agricultural water used in fresh produce production. Specifically, a greater microbial persistence in sediments than in water over time was observed, along with differences in survival among microorganisms in relation to the fecal indicator bacteria E. coli and enterococci. Previous studies compared data among microbial groups in different environments. Conversely, fecal indicator bacteria, surrogates, and pathogenic microorganisms were assessed within the same water and sediment mesocosms in the present study during four seasons, better representing the agricultural aquatic environment. These data should be considered when agricultural microbial water quality criteria in fresh produce operations are being determined.

One-year urinary and sexual outcome trajectories among prostate cancer patients treated by radical prostatectomy: a prospective study.

BACKGROUND: To examine one-year trajectories of urinary and sexual outcomes, and correlates of these trajectories, among prostate cancer patients treated by radical prostatectomy (RP). METHODS: Study participants were recruited from 2011 to 2014 at two US institutions. Self-reported urinary and sexual outcomes were measured at baseline before surgery, and 5 weeks, 6 months and 12 months after surgery, using the modified Expanded Prostate Cancer Index Composite-50 (EPIC-50). Changes in EPIC-50 scores from baseline were categorized as improved (beyond baseline), maintained, or impaired (below baseline), using previously-reported minimum clinically important differences. RESULTS: Of the 426 eligible participants who completed the baseline survey, 395 provided data on at least one EPIC-50 sub-scale at 5 weeks and 12 months, and were analyzed. Although all mean EPIC-50 scores declined markedly 5 weeks after surgery and then recovered to near (incontinence-related outcomes) or below (sexual outcomes) baseline levels by 12 months post-surgery, some men experienced improvement beyond their baseline levels on each sub-scale (3.3-51% depending on the sub-scale). Having benign prostatic hyperplasia (BPH) at baseline (prostate size ≥ 40 g; an International Prostate Symptom Index Score ≥ 8; or using BPH medications) was associated with post-surgical improvements in voiding dysfunction-related bother at 5 weeks (OR = 3.9, 95% CI: 2.1-7.2) and 12 months (OR = 3.3, 95% CI: 2.0-5.7); and in sexual bother at 5 weeks (OR = 5.7, 95% CI:1.7-19.3) and 12 months (OR = 3.0, 95% CI: 1.2-7.1). CONCLUSIONS: Our findings provide additional support for considering baseline BPH symptoms when selecting the best therapy for early-stage prostate cancer.

Levels and patterns of self-reported and objectively-measured free-living physical activity among prostate cancer survivors: A prospective cohort study.

BACKGROUND: No prior study has measured or compared self-reported and objectively measured physical activity trajectories in prostate cancer survivors before and after treatment. METHODS: Clinically localized prostate cancer patients treated with radical prostatectomy were recruited between 2011 and 2014. Of the 350 participants enrolled at the main site, 310 provided self-reported physical activity at baseline before radical prostatectomy, and 5 weeks, 6 months, and 12 months after radical prostatectomy. A subset of participants (n = 81) provided objectively measured physical activity at all study time points by wearing an accelerometer for 7 days each. Changes in activity over time were compared using Friedman's test. Agreement between self-reported and objective measures was evaluated using Spearman's rank correlation coefficient. RESULTS: Self-reported moderate-to-vigorous physical activity was high at baseline (median, 32.1 min/day), followed by a decline at 5 weeks (median, 15.0 min/day) and a recovery at 6 and 12 months (median, 32.1-47.1 min/day). In contrast, objectively measured moderate-to-vigorous physical activity was low at all 4 time points (median, 0.0-5.2 min/day), with no overall change across study assessments (global P = .29). Self-reported moderate-to-vigorous physical activity tended to be more closely related to objectively measured light-intensity physical activity (ρ = 0.29-0.42) than to objectively measured moderate-to-vigorous physical activity (ρ = 0.07-0.27, P = .009-.32). CONCLUSIONS: In our population of prostate cancer survivors with critically low moderate-to-vigorous physical activity levels, self-reported measures greatly overestimated moderate-to-vigorous physical activity and may have been more reflective of light-intensity physical activity. Because cancer survivor guidelines are derived from self-reported data, our findings may imply that intensities of physical activity below moderate, such as light intensity, still have health benefits.

Pre-diagnosis body mass index, physical activity and ovarian cancer mortality.

BACKGROUND: Ovarian cancer is the deadliest gynecologic malignancy, yet the effects on survival of modifiable pre-diagnosis lifestyle factors, such as obesity and physical activity, remain largely unexplored. Our objective was to evaluate the effect of pre-diagnosis BMI and physical activity on ovarian cancer mortality using prospectively collected data. METHODS: Data on women who developed ovarian cancer after enrollment into the NIH-AARP Diet and Health Study were analyzed. Cancer incidence was ascertained through linkage state cancer registries and consisted of 741 cases of epithelial ovarian cancer. RESULTS: Higher pre-diagnosis BMI was associated with increased overall and ovarian cancer-specific mortality. Comparing women with BMI 25-29.9, 30-34.9 and ≥ 35 to normal weight women, the HRs of overall mortality were 1.18 (95%CI 0.96-1.45), 1.05 (0.82-1.36) and 1.59 (1.14-2.18, p-trend = 0.02). The findings were similar for ovarian cancer-specific mortality comparing women with BMI ≥ 35 to normal weight women (BMI <25) with a HR of 1.47 (95%CI 1.03-2.09, p-trend 0.08). Pre-diagnosis physical activity was not associated with mortality, with HRs for overall mortality of 1.06 (95%CI 0.79-1.43), 0.94 (0.72-1.23), 0.98 (0.76-1.25), and 0.98 (0.75-1.28, p-trend = 0.91), comparing women who engaged in vigorous physical activity 1-3 times/month, 1-2 times/week, 3-4 times/week and 5 times/week, respectively, with those who never/rarely engaged in such activity. CONCLUSIONS: Women who were obese before developing ovarian cancer had increased mortality than those who were normal weight, but physical activity before diagnosis was not associated with mortality in this study population. These results suggest that maintaining a healthy weight is a powerful preventative tool.

Factors predicting intolerance to definitive conventional radiotherapy in geriatric patients.

PURPOSE: Although radiotherapy can be administered with a relatively low therapeutic burden, many elderly patients do not complete radiotherapy. In order to predict intolerance during radiotherapy, this study retrospectively analyzed the frequency of and risk factors for radiotherapy interruption among geriatric patients. METHODS: From September 2009 to December 2016, 353 patients aged ≥70 years received definitive radiotherapy with a conventionally fractionated schedule. "Total interruption" included completion of ≤90% of a planned radiotherapy, temporary discontinuation, and treatment-related mortality within 2 months. "Early-phase incompletion" and "mid-phase incompletion" represented completion of ≤50 and ≤80% of a planned radiotherapy, respectively. RESULTS: The median age of patients was 74 years. Early- and mid-phase incompletions and total interruption occurred in 4.2, 9.3, and 19.3% of patients, respectively. Total interruption occurred frequently in cancers involving the thorax (27.4%), head and neck (23.1%), abdomen (20.0%), pelvis (17.4%), and breast/extremity (8.1%). The Eastern Cooperative Oncology Group (ECOG) performance score (P = 0.004 and 0.002), serum albumin level (P = 0.016 and 0.002), and the expected 5­year survival (P = 0.033 and 0.034) were significant factors for mid-phase incompletion and total interruption. Age ≥ 75 years (P = 0.008), concurrent chemotherapy (P = 0.017), and the extent of radiation field (P = 0.027) were factors associated with total interruption. CONCLUSION: Overall, 19.3% of the elderly patients showed treatment intolerance during conventional radiotherapy. Serum albumin level and ECOG performance score should be considered as surrogate markers for radiotherapy interruption prior to the decision regarding definite conventional radiotherapy.

Mixed methods analysis of eighteen worksite policies, programs, and environments for physical activity.

BACKGROUND: This study examined whether specific worksite supports for physical activity (PA) were associated with total and domain-specific PA. METHODS: A cross-sectional, telephone-based study was conducted in four Missouri, USA, metropolitan areas in 2012 and 2013. Outcome variables included total PA and sub-domains (leisure, work, travel) measured using the International Physical Activity Questionnaire. Logistic regression determined odds of meeting PA recommendations, given access to and use of 18 unique PA worksite supports. A subsample of 119 participants also wore hip accelerometry for seven consecutive days and maintained a wear-time diary. Access to worksite supports were associated with odds of meeting objective moderate and vigorous (MV) PA above 150 min per week. RESULTS: Among 2013 survey participants, meeting PA recommendations while performing work-related tasks was significantly associated with several supports (e.g., walking maps, stair prompts), as was meeting recommendations during travel (e.g., flextime for PA, incentives for public transportation, walking/bicycling to work). Access to 11 worksite supports increased odds of meeting PA recommendations through leisure-time PA; five supports were associated with total PA. There were significant differences between access to and use of supports. Using objective MVPA, access to worksite challenges and bike storage were significantly associated with five and three times greater odds of meeting 150 min of MVPA per week, respectively. CONCLUSIONS: Worksite wellness plans are increasing across the US and employers are eager for evidence-based supports for increasing PA. This study provides insights into the utility of multiple worksite supports for PA to increase odds that employees meet PA recommendations.

Identification of Factors Affecting Fecal Pollution in Beaver Lake Reservoir.

Standard methods for the evaluation of recreational water quality rely on generic bacterial indicators such as . However, does not provide enough information to determine fecal source or public health risk. The stsudy objective was to determine factors influencing the presence of and host-specific markers (HSM) from upstream to downstream in Beaver Lake Reservoir (BLR). From February 2014 to September 2015, 420 base flow and rain event samples were collected from seven sites-two sites from streams (White River [WR] and War Eagle Creek) draining into BLR and five sites from within BLR. Each sample was analyzed for and by quantitative polymerase chain reaction for HSM related to human, bovine, and poultry. The data indicate that overall levels of were significantly greater in the WR and significantly lower at the most downstream sampling location in BLR. is more likely present during spring (adjusted odds ratio [aOR] = 1.86), at the WR sampling site (aOR = 3.39), or during a rain event (aOR = 2.73). Moreover, the HSM HumM2 is more likely present (aOR = 1.99) when is present. These same factors were associated with concentrations >126 most probable number 100 mL (aOR = 2.76-12.48), except the poultry marker CL was more likely associated (aOR = 3.81) than HumM2. This study revealed that both seasonal and locational factors are important variables for fecal pollution in BLR. Moreover, these same factors may apply to fecal pollution in manmade reservoirs within similar types of watersheds across the United States, as well as internationally.

Covariance adjustment for batch effect in gene expression data.

Batch bias has been found in many microarray gene expression studies that involve multiple batches of samples. A serious batch effect can alter not only the distribution of individual genes but also the inter-gene relationships. Even though some efforts have been made to remove such bias, there has been relatively less development on a multivariate approach, mainly because of the analytical difficulty due to the high-dimensional nature of gene expression data. We propose a multivariate batch adjustment method that effectively eliminates inter-gene batch effects. The proposed method utilizes high-dimensional sparse covariance estimation based on a factor model and a hard thresholding. Another important aspect of the proposed method is that if it is known that one of the batches is produced in a superior condition, the other batches can be adjusted so that they resemble the target batch. We study high-dimensional asymptotic properties of the proposed estimator and compare the performance of the proposed method with some popular existing methods with simulated data and gene expression data sets.

Predictors of high score patient-reported barriers to controlling cancer pain: a preliminary report.

PURPOSE: Pain is one of the most common and devastating symptoms in cancer patients, and misunderstandings on the patient's part can cause major obstacles in pain management. METHOD: We evaluated factors associated with patient's high barrier score to managing cancer-associated pain by having 201 patients complete the Korean Barriers Questionnaire II, the Brief Pain Inventory--Korean, the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30, and the Korean Beck Depression Inventory. The Pain Management Index (PMI) was also assessed. RESULTS: The patients were from nine oncology clinics in university hospitals and a veterans' hospital in South Korea. The median pain score (0-10 scale) was 4, with a median percentage of pain improvement during the last 24 h of 70 %. A total of 150 patients (75 %) received strong opioids, and 177 (88 %) achieved adequate analgesia (positive PMI). Mean scores ± SD for the Barriers Questionnaire II ranged from 1.5 ± 1 to 2.8 ± 1.1, with the harmful effects subscale the highest. In the multiple regression model, depression was significantly associated with total barrier score to pain management (p < 0.0001). Pain reduction was significantly associated with the fatalism subscale. CONCLUSIONS: Depression was associated with high barrier score in patients with cancer pain. Management of cancer pain should include screening for depression, and management of depression could reduce patient-reported barriers to pain management.

Effectiveness of high-dose three-dimensional conformal radiotherapy in hepatocellular carcinoma with portal vein thrombosis.

OBJECTIVE: To evaluate the treatment outcome of three-dimensional conformal radiotherapy in hepatocellular carcinoma patients with portal vein thrombosis, concerning survival and treatment response of thrombosis. METHODS: Forty-five patients with hepatocellular carcinoma who had portal vein thrombosis treated from March 2005 to March 2011 were the subjects of this study. The median total dose was 61.2 Gy (range 38-65 Gy). A daily radiation dose of 1.8-2.5 Gy was administered at a frequency of five fractions per week. The clinical target volume included portal vein thrombosis with or without primary tumour with clinical consideration. RESULTS: Three of the 45 patients (6.7%) showed complete remission of portal vein thrombosis, 25 patients (55.6%) showed partial response, 14 patients (31%) had stable disease and 3 patients (6.7%) had progressive disease. The median and the 1-year survival rate of the responders (complete remission + progressive disease) were 16.7 months and 63.7%, respectively, and those of the non-responders were 8 months and 28.2%, respectively (P= 0.003). A univariate analysis revealed that thrombosis response, Eastern Cooperative Oncology Group performance status, maximum tumour size, tumour bilaterality, Cancer of the Liver Italian Program stage, Okuda stage, hepatic arterial infusion, hepatitis B 'e' antigen and hepatitis C antibody were statistically significant prognostic factors affecting survival. In a multivariate analysis, thrombosis response, Cancer of the Liver Italian Program stage and Okuda stage were found to be statistically significant. No clinically significant radiation-induced liver disease was noted. One grade 3 late complication (duodenal ulcer) was reported. CONCLUSIONS: High-dose three-dimensional conformal radiotherapy yielded a response rate of 62.3%. It is a safe and effective treatment prolonging the survival of hepatocellular carcinoma patients with portal vein thrombosis.

The extent and serial pattern of interfractional variation in patients with whole pelvic irradiation: a study using a kilovoltage orthogonal on-board imager.

The purpose of this study is to assess the extent and serial pattern of setup error of conventional fractionated whole pelvic irradiation using a kilovoltage on-board imager. The daily on-board images of 69 patients were matched with the digitally reconstructed radiographs of simulation on the basis of pelvic bony structure. The shifts along x- (lateral), y- (longitudinal), and z- (vertical) axes, and the 3D vector, were measured. The shift between an origin of the first fraction and each fraction (Δshift(1st)) and the shift between an isocenter of simulation and each fraction (Δshift(Sim)) were calculated. To evaluate serial changes, the shifts of each fraction were classified into four consecutive sessions, and an ANOVA and chi-square test were used. The systematic error of the Δshift(Sim) and Δshift(1st) were 2.72 and 1.43 mm along the x-axis, 2.98 and 1.28 mm along the y-axis, and 4.26 and 2.39 mm along the z-axis, respectively. The Δshift(Sim) and Δshift(1st) ≥ 5 mm of the 3D vector occurred in 54.3% and 23.1%, respectively. The recommended margins to cover setup error in case of using Δshift(1st) were 3.81, 3.54, and 6.01 mm along x-, y-, and z-axes, whereas those using Δshift(Sim) were 6.39, 6.95, and 9.95 mm, respectively. With the passage of time, the Δshift(1st) ≥ 5 mm of 3D vector and along any axis in supine setup increased from 14.1% for first session to 22.5% for fourth session (p=0.027) and from 10.8% to 18.5% (p = 0.034), respectively. In prone setup, first session was better than others in the Δshift(1st) ≥ 5 mm of 3D vector and along any axis. It is expected that the correction using the on-board images on the first fraction improves geometrical uncertainties and reduces the margin for target coverage. Daily continuous OBI follow-up during conventional fractionated pelvic irradiation can increase the reproducibility and be more effective in the late period.

Relationship between ATP Bioluminescence Measurements and Microbial Assessments in Studies Conducted in Food Establishments: A Systematic Literature Review and Meta-Analysis.

ABSTRACT: Adherence to proper environmental cleaning practices is critical in food establishments. To validate cleanliness, cleaning practices should be routinely monitored, preferably by a rapid, reliable, and cost-effective method. The aim of this study was to determine whether a correlation exists between ATP bioluminescence measurements and selected microbial assessments in studies conducted in food establishments. A systematic literature review and meta-analysis was conducted using the principles of preferred reporting items for systematic reviews and meta-analyses. Twelve online databases and search engines were selected for the review. Peer-reviewed articles published in English between January 2000 and July 2020 were included in the search. From a total of 19 eligible studies, 3 that included Pearson correlation coefficients (r) between ATP bioluminescence measurements and microbial assessments were used for the meta-analysis calculations. Only the fixed-effect model produced a strong correlation because one value dominated the estimates: r = 0.9339 (0.9278, 0.9399). In contrast, both the random effects model, 0.2978 (0.24, 0.3471), and the mixed effects model, r = 0.3162 (-0.0387, 0.6711), indicated a weak relationship between ATP bioluminescence and microbial assessments, with no evidence of a strong correlation. The meta-analysis results indicated no sufficient evidence of a strong correlation between ATP bioluminescence measurements and microbial assessments when applied within food establishments. This lack of evidence for a strong correlation between the results of these two monitoring tools suggests that food establishments cannot depend on only one method. Yet, with immediate feedback and quantification of organic soiling, ATP bioluminescence could be an effective monitoring tool to use in food establishments.

Treatment outcomes of patients with involved resection margin after rectal cancer surgery: A nationwide population-based cohort study in South Korea.

BACKGROUND: The involvement of resection margins after rectal cancer surgery by malignant tumors is a negative prognostic factor. Therefore, it is important to analyze treatment outcomes and establish adjuvant therapy. METHODS: The Health Insurance Review and Assessment Service collects data from medical institutions in South Korea. We reviewed the database of this prospectively collected cohort for patients who underwent curative resection for rectal cancer. RESULTS: Of the 5,620 patients, 113 (2.0%) were diagnosed with resection margin involvement after surgery. The resection margins of patients with mid-rectal cancer, pathologic stage III, mucinous/signet ring cell carcinoma, and undergoing emergency surgery were more frequently involved. Neoadjuvant chemoradiotherapy was a significant preventive factor for resection margin involvement (odds ratio = 0.53; 95% confidence interval [CI], 0.32-0.87; p = 0.012). The OS of patients with adjuvant treatment was better than that of patients without adjuvant treatment (5-year overall survival [OS]: 62.8% vs. 46.3%, p = 0.02). The administration of chemoradiotherapy was also significantly associated with better OS (hazard ratio = 0.36; 95% CI, 0.17-0.77; p = 0.009). CONCLUSION: Efforts to acquire wider resection margins are necessary for patients with mid-rectal cancer, pathologic stage III, mucinous/signet ring cell carcinoma, and emergency surgery. Neoadjuvant chemoradiotherapy was a significant preventive factor for involved resection margin. Patients with resection margin involvement showed better OS after adjuvant treatment than those without adjuvant treatment. The adjuvant chemoradiotherapy was helpful to prevent the worse prognosis of these patients.

Waldenstrom macroglobulinemia with CD5+ expression presented as cryoglobulinemic glomerulonephropathy: a case report.

Waldenstrom macroglobulinemia (WM) is a B-cell lymphoproliferative disorder associated with bone marrow involvement of lymphoplasmacytic lymphoma (LPL) and an IgM monoclonal gammopathy. Generally B-lymphocytes in LPL do not express CD5 that is important for differential diagnosis of B-cell lymphoproliferative disorders. In WM, various renal diseases and type I cryoglobulinemia are well described separately, but cryoglobulinemic glomerulonephropathy is very rarely reported. A 61-yr-old woman complained of generalized edema, cyanosis of the extremities in cold weather, visual disturbance, and pancytopenia. Bone marrow and renal biopsy showed CD5+ expressing B-cells and cryoglobulinemic glomerulonephropathy. With the diagnosis of WM, she received cyclophosphamide, doxorubicin, vincristine and prednisolone chemotherapy and got complete remission. Here, we report a rare case of WM associated with unusual expression of CD5+ B-lymphocytes and cryoglobulinemic glomerulonephropathy, and emphasize the importance of the clinical features in differentiating CD5+ B-cell lymphoproliferative disorders.

An Improved Animal Model of Multiple Myeloma Bone Disease.

Multiple myeloma (MM) is a plasma cell malignancy that causes an accumulation of terminally differentiated monoclonal plasma cells in the bone marrow, accompanied by multiple myeloma bone disease (MMBD). MM animal models have been developed and enable to interrogate the mechanism of MM tumorigenesis. However, these models demonstrate little or no evidence of MMBD. We try to establish the MMBD model with severe bone lesions and easily accessible MM progression. 1 × 106 luciferase-expressing 5TGM1 cells were injected into 8-12 week-old NOD SCID gamma mouse (NSG) and C57BL/KaLwRij mouse via the tail vein. Myeloma progression was assessed weekly via in vivo bioluminescence (BL) imaging using IVIS-200. The spine and femur/tibia were extracted and scanned by the micro-computer tomography for bone histo-morphometric analyses at the postmortem. The median survivals were 56 days in NSG while 44.5 days in C57BL/KaLwRij agreed with the BL imaging results. Histomorphic and DEXA analyses demonstrated that NSG mice have severe bone resorption that occurred at the lumbar spine but no significance at the femur compared to C57BL/KaLwRij mice. Based on these, we conclude that the systemic 5TGM1 injected NSG mouse slowly progresses myeloma and develops more severe MMBD than the C57BL/KaLwRij model.

Reduction of Norovirus Surrogates Alone and in Association with Bacteria on Leaf Lettuce and Tomatoes During Application of Aqueous Ozone.

Retail foodservice establishments (FSE) frequently utilize washes with sanitizing agents during fresh produce preparation. This study evaluated the efficacy of ozonated water on the inactivation of viruses, bacteria, and viruses in association with bacteria on produce surfaces. Boston bibb lettuce (BB) and cherry tomatoes were spot inoculated with viruses (murine norovirus (MNV) and MS2 bacteriophage), bacteria (Enterobacter cloacae and Bacillus cereus), or MNV associated with E. cloacae or B. cereus. Following inoculation, produce was held at 4 °C for 90 min (virus, virus + bacteria) or 24 h (virus, bacteria) prior to treatment. A batch wash ozone sanitation system (BWOSS) was prepared with ice (3-5 °C) and 0.5 ppm initial ozone concentration or no ozone. Produce samples were treated for 40 min with an ozonated water (0.86-0.99 ppm) or water-only wash with samples taken every 10 min. Samples were processed for microbial recovery, and plaque forming units (PFU) and colony forming units remaining on the produce were determined. Although microbial reductions of 99 to 99.99% were achieved during ozone treatments, few statistically significant differences (P > 0.1) were detected when comparing the ozonated water to water-only wash. Notably, a significant difference (P = 0.009) in log reduction of MNV + bacteria and MNV alone on BB was observed after 40 min ozonated water wash. Specifically, MNV with B. cereus achieved a 1-log greater reduction (2.60 log PFU/ml) compared to MNV alone (1.63 log PFU/ml). Overall, washing produce in ozonated water did not significantly increase microbial inactivation compared to water alone under the conditions presented here. Variables impacting ozone wash effectiveness should be considered when implementing produce wash sanitation systems within FSE.

In Vitro Fecal Fermentation Patterns of Arabinoxylan from Rice Bran on Fecal Microbiota from Normal-Weight and Overweight/Obese Subjects.

Arabinoxylan (AX) is a structural polysaccharide found in wheat, rice and other cereal grains. Diets high in AX-containing fiber may promote gut health in obesity through prebiotic function. Thus, the impact of soluble AX isolated from rice bran fiber on human gut microbiota phylogenetic composition and short-chain fatty acid (SCFA) production patterns from normal-weight and overweight/obese subjects was investigated through in vitro fecal fermentation. Results showed that rice bran arabinoxylan modified the microbiota in fecal samples from both weight classes compared to control, significantly increasing Collinsella, Blautia and Bifidobacterium, and decreasing Sutterella, Bilophila and Parabacteroides. Rice bran AX also significantly increased total and individual SCFA contents (p < 0.05). This study suggests that rice bran AX may beneficially impact gut health in obesity through prebiotic activities.

Clinical characteristics of rectal cancer patients with neoadjuvant chemoradiotherapy: a nationwide population-based cohort study in South Korea.

PURPOSE: Neoadjuvant chemoradiotherapy has been accepted as a standard treatment for stage II-III rectal cancer. This study aimed to evaluate the clinical characteristics of patients who underwent neoadjuvant chemoradiotherapy for rectal cancer and effects on overall survival (OS) of neoadjuvant chemoradiotherapy in South Korea. METHODS: Patients who underwent curative resection for rectal cancer from 2014 to 2016 were retrospectively reviewed from the database of the National Quality Assessment program in South Korea. Patients were categorized into the upfront surgery group and neoadjuvant chemoradiotherapy group. We evaluated factors associated with the administration of neoadjuvant chemoradiotherapy and its effects on OS. Inverse probability of treatment weighting was performed to account for baseline differences between subgroups. RESULTS: A total of 6,141 patients were categorized into the upfront surgery group (n = 4,237) and neoadjuvant chemoradiotherapy group (n = 1,904). The neoadjuvant chemoradiotherapy was more frequently administered to male, midrectal cancer, and younger patients. In the neoadjuvant chemoradiotherapy group, old age, underweight, and pathologic stage were significant risk factors of OS, and male sex, the level of tumor and clinical stages were not associated with OS. After adjustment, the OS of the neoadjuvant chemoradiotherapy group followed the OS of the upfront surgery group of the same pathologic stage. CONCLUSION: Male sex and the level of tumor were not related to the OS of rectal cancer patients with neoadjuvant chemoradiotherapy. The OS of patients who underwent neoadjuvant chemoradiotherapy was decided by their pathologic stages regardless of clinical stages.

Soil microbial diversity in organic and non-organic pasture systems.

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0-15 cm in July and August from 2017-2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson's index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use.

Despite the wide application of next-generation sequencing, Sanger sequencing still plays a necessary role in clinical laboratories. However, recent developments in the field of bioinformatics have focused mostly on next-generation sequencing, while tools for Sanger sequencing have shown little progress. In this study, SnackVar (https://github.com/Young-gonKim/SnackVar, last accessed June 22, 2020), a novel graphical user interface-based software for Sanger sequencing, was developed. All types of variants, including heterozygous insertion/deletion variants, can be identified by SnackVar with minimal user effort. The featured reference sequences of all of the genes are prestored in SnackVar, allowing for detected variants to be precisely described based on coding DNA references according to the nomenclature of the Human Genome Variation Society. Among 88 previously reported variants from four insertion/deletion-rich genes (BRCA1, APC, CALR, and CEBPA), the result of SnackVar agreed with reported results in 87 variants [98.9% (93.0%; 99.9%)]. The cause of one incorrect variant calling was proven to be erroneous base callings from poor-quality trace files. Compared with commercial software, SnackVar required less than one-half of the time taken for the analysis of a selected set of test cases. We expect SnackVar to be a cost-effective option for clinical laboratories performing Sanger sequencing.