Examining DNA breathing with pyDNA-EPBD.

MOTIVATION: The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others. RESULTS: We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm. AVAILABILITY AND IMPLEMENTATION: pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.

Increased risk of stress urinary incontinence surgery after hysterectomy for benign indication-a population-based cohort study.

BACKGROUND: Hysterectomy is a common procedure used to treat different gynecologic conditions. The association between hysterectomy for benign indication and stress urinary incontinence has previously been established. Stress urinary incontinence can be treated surgically, and options have improved after introduction of the midurethral sling procedure in 1998. OBJECTIVE: This study aimed to estimate the risk of stress urinary incontinence surgery after hysterectomy for benign indication. STUDY DESIGN: The study was carried out as a matched register-based cohort study including Danish women born from 1947 to 2000. Women who underwent hysterectomy for benign indication were matched to nonhysterectomized women in a 1:5 ratio on the basis of age and calendar year of hysterectomy. The risk of stress urinary incontinence surgery after hysterectomy was estimated. We adjusted for income, educational level, and parity. The risk of stress urinary incontinence surgery was further estimated in a subcohort excluding all vaginal hysterectomies. The joint effect of hysterectomy and parity was estimated in the main cohort, and the joint effect of hysterectomy and vaginal birth or cesarean delivery on stress urinary incontinence surgery was explored in a subgroup of women who only had 1 mode of delivery. All analyses were made using the Cox proportional hazards model. RESULTS: We included 83,370 women who underwent hysterectomy and 413,969 reference women. The overall risk of stress urinary incontinence surgery was more than doubled for women who underwent hysterectomy (adjusted hazard ratio, 2.6; 95% confidence interval, 2.4-2.8). The adjusted hazard ratio decreased slightly to 2.4 (95% confidence interval, 2.3-2.6) when excluding all vaginal hysterectomies. We found a trend of increasing risk of stress urinary incontinence surgery with increased parity among both women who underwent hysterectomy and the reference group. In the subgroup of women who only had 1 mode of delivery, we found the risk of stress urinary incontinence surgery to be particularly increased for women with a history of ≥1 vaginal births. The hazard ratio was 15.1 (95% confidence interval, 10.3-22.1) for women with a history of 1 vaginal birth who underwent hysterectomy, whereas the hazard ratio for women in the reference group with 1 vaginal birth was 5.1 (95% confidence interval, 3.8-8.1). Overall, women who underwent hysterectomy had a 3 times higher risk of stress urinary incontinence surgery than the reference group, irrespective of the number of vaginal births. CONCLUSION: This study indicates, in accordance with previous studies, that hysterectomy increases the risk of subsequent stress urinary incontinence surgery. Women should be informed and gynecologists include this knowledge in decision-making. Further precautions should be taken when treating parous women, particularly those with a history of ≥1 vaginal births.

Effect of Yoga and Mediational Influence of Fatigue on Walking, Physical Activity, and Quality of Life Among Cancer Survivors.

BACKGROUND: Cancer-related fatigue (CRF) negatively affects survivors' walking, engagement in physical activity (PA), and quality of life (QoL). Yoga is an effective therapy for treating CRF; however, evidence from large clinical trials regarding how reducing CRF through yoga influences CRF's interference with survivors' walking, engagement in PA, and QoL is not available. We examined the effects of yoga and the mediational influence of CRF on CRF's interference with walking, PA, and QoL among cancer survivors in a multicenter phase III randomized controlled trial. PATIENTS AND METHODS: Cancer survivors (n=410) with insomnia 2 to 24 months posttreatment were randomized to a 4-week yoga intervention-Yoga for Cancer Survivors (YOCAS)-or standard care. A symptom inventory was used to assess how much CRF interfered with survivors' walking, PA, and QoL. The Multidimensional Fatigue Symptom Inventory-Short Form was used to assess CRF. Two-tailed t tests and analyses of covariance were used to examine within-group and between-group differences. Path analysis was used to evaluate mediational relationships between CRF and changes in CRF's interference with walking, PA, and QoL among survivors. RESULTS: Compared with standard care controls, YOCAS participants reported significant improvements in CRF's interference with walking, PA, and QoL at postintervention (all effect size = -0.33; all P≤.05). Improvements in CRF resulting from yoga accounted for significant proportions of the improvements in walking (44%), PA (53%), and QoL (45%; all P≤.05). CONCLUSIONS: A significant proportion (44%-53%) of the YOCAS effect on CRF's interference with walking, PA, and QoL was due to improvements in CRF among cancer survivors. Yoga should be introduced and included as a treatment option for survivors experiencing fatigue. By reducing fatigue, survivors further improve their walking, engagement in PA, and QoL.

Cervical cancer after the Manchester procedure: a nationwide cohort study.

INTRODUCTION AND HYPOTHESIS: The Manchester procedure is a successful operation to treat uterine prolapse. However, the influence on cervical cancer remains unknown. We hypothesized a lower risk of cervical cancer after the Manchester procedure. METHODS: We included all Danish women undergoing the Manchester procedure during 1977-2018 (N = 23,935). Women undergoing anterior colporrhaphy (N = 51,008) were included as references due to comparable health-seeking behaviors. The study cohort is as previously described. We assessed the risk of cervical cancer mortality after the Manchester procedure versus anterior colporrhaphy using cumulated incidence plots and Cox hazard regressions. We applied Fisher's exact test to compare the distribution of histological subtypes after the operations. RESULTS: Generally, few women were diagnosed with cervical cancer (0.1% after Manchester procedure and 0.2% after anterior colporrhaphy). After the Manchester procedure, the risk of cervical cancer was reduced (HR 0.60 [95% CI 0.39-0.94]). Furthermore, we found a slightly reduced risk of overall death (HR 0.96 [95% 0.94-0.99]), but no association regarding death due to cervical cancer (HR 0.66 [95% 0.34-1.25]). The distribution of histological subtypes was not changed. CONCLUSIONS: Women undergoing the Manchester procedure are at lower risk of being diagnosed with cervical cancer, while the risk of cancer specific mortality is unchanged compared to women undergoing anterior colporrhaphy. Based on this study, we cannot recommend that women exit ordinary screening programs for human papillomavirus/cervical dysplasia after a Manchester procedure.

[Nutrition and adipose tissue distribution in low cardiovascular risk individuals, depending on the central obesity].

The low cardiovascular risk group according to SCORE in relation to the clinical and laboratory characteristics of patients is very heterogeneous, which leads to the presence of a residual risk of cardiovascular events. This category may include individuals with a family history of cardiovascular disease at a young age, with abdominal obesity (AO), endothelial dysfunction, and high levels of triglyceride-rich lipoproteins. In this regard, an active search is underway for new metabolic markers within the low cardiovascular risk group. The purpose of the study was to compare the nutrition, the adipose tissue distribution in low cardiovascular risk individuals, depending on the AO. Material and methods. The study included 86 healthy low risk (SCORE<1%) patients (mean age 42.6±2 years), who were divided into 2 groups: with AO [waist circumference (WC) >=94 cm in men and >=80 cm in women] - 44 patients (32% of men) and without AO - 42 patients (38% of men). The body composition was carried out using the bioimpedance analyzer. The distribution of ectopic fat deposits in the liver, pancreas and epicardial region was studied using ultrasound methods. A frequency questionnaire (Diet Risk Score) was used to assess nutrition. Results. In low risk patients with AO, signs of unhealthy diet are statistically significantly more common (in 52 in the main group vs 2% in the control group, p<0.01), ectopic deposition of adipose tissue in the liver (53 vs 9%, p<0.001), pancreas (56% in the main group, absent in the control group, p<0.001), epicardia l region (the epicardial fat thickness median is 4.24 mm in the main group vs 2.15 mm in the control group) compared with a control group. Conclusion. The low cardiovascular risk group is very heterogeneous. One of the markers of heterogeneity is central obesity - a marker of unhealthy diet, subclinical ectopic fat deposition and hypertriglyceridemia. Patients with AO of the low cardiovascular risk group require a more thorough examination with the obligatory determination of waist circumference, ultrasound assessment of the liver and pancreas parenchyma, and determination of the epicardial fat thickness. Using a short nutrition questionnaire allows you to quickly identify signs of unhealthy diet and discuss them with the patient.

Bacteremia With Anaerobic Bacteria and Association With Colorectal Cancer: A Population-based Cohort Study.

BACKGROUND: There is a well-described association between bacteremia with bovis group streptococci or Clostridium septicum and an increased probability of a colorectal cancer (CRC) diagnosis. We wanted to investigate the existence of a similar association between CRC and bacteremia with other bacteria belonging to the gut microbiota.. METHODS: A population based cohort study in a population about 2 million people including 45 774 bacteremia episodes and 231 387 blood culture negative cases was performed in the Region of Southern Denmark and Region Zealand from 2007-2016. Episodes of bacteremia were combined with the Danish central register for CRC. We performed Cox's regression analysis with hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS: The study results confirmed previous findings of an increased risk of a CRC diagnosis after bacteremia with the bovis group streptococci (risk within a year: 4.3%; HR [95% CI]: 8.46 [3.51-20.4]) or C. septicum (20.8%; 76.2 [42.0-138]). Furthermore, Bacteroides ovatus (6.7%; 20.3 [5.04-81.8]), Bacteroides uniformis (5.4%; 16.2 [4.02-65.7]), Clostridium tertium (3.6 %; 13.9 [1.96-99.4]), Fusobacterium spp. (excluding F. necrophorum) (3.0 %; 8.51 [2.73-26.5]), and Gram-positive anaerobic cocci (3.6 %; 10.9 [4.50-26.3]) were also associated with an increased risk of a CRC diagnosis compared to patients with negative blood cultures (0.4%). CONCLUSIONS: Bacteremia with specific gut microbiota anaerobic bacteria is associated with a high risk of a diagnosis of CRC, indicating the need for colorectal workup. Importantly, this strategy also holds the possible additional benefit of detecting adenomas or other premalignant conditions, which were not included in the present study.

Pelvic organ prolapse following hysterectomy on benign indication: a nationwide, nulliparous cohort study.

BACKGROUND: Hysterectomy is commonly performed and may increase the risk of pelvic organ prolapse. Previous studies in parous women have shown an increased risk of pelvic organ prolapse surgery after hysterectomy. Parity is a strong risk factor for pelvic organ prolapse and may confuse the true relation between hysterectomy and pelvic organ prolapse. OBJECTIVE: This study aimed to investigate whether hysterectomy performed for benign conditions other than pelvic organ prolapse leads to an increased risk of pelvic organ prolapse surgery in a cohort of nulliparous women. STUDY DESIGN: We conducted a historical matched cohort study based on a nationwide population of nulliparous women born in 1947 to 2000 and living in Denmark during 1977 to 2018 (N=549,197). The data were obtained from the Danish Civil Registration System, the Danish National Patient Registry, the Fertility Register, and Statistics Denmark. Women who had a hysterectomy performed in 1977 to 2018 were included in the study (n=9535). For each of these women we randomly retrieved five nonhysterectomized women matched on age and calendar year to constitute the reference group (n=47,370). Cox proportional hazard regression analyses were performed to compare the risk of pelvic organ prolapse surgery in the 2 groups of women. RESULTS: The study included 56,905 women whom we observed for up to 42 years, entailing 809,435 person-years in risk. Overall, 9535 women who underwent a hysterectomy were matched individually with 47,370 reference women. Subsequently, a total of 29 women (30.4%) who underwent a hysterectomy and 85 reference women (17.9%) had a pelvic organ prolapse surgery performed, corresponding to incidence rates of 20.5 and 12.7 per 100,000 risk years, respectively. In addition, the risk of pelvic organ prolapse surgery increased by 60% in women who underwent a hysterectomy compared with women in the reference group (crude hazard ratio, 1.6; 95% confidence interval, 1.0-2.5; P=.04; adjusted hazard ratio, 1.6; 95% confidence interval, 1.0-2.5; P=.04). After the exclusion of women who underwent vaginal hysterectomy and their matches, the results were significantly the same (crude hazard ratio, 1.5; 95% confidence interval, 1.0-2.4; P=.05). Furthermore, we found higher rates of pelvic organ prolapse surgery in women who had a subtotal hysterectomy, total hysterectomy, or vaginal and laparoscopic-assisted vaginal hysterectomies than in women in the reference group. CONCLUSION: Hysterectomy increased the risk of pelvic organ prolapse surgery for nulliparous women by 60%. Previous studies of multiparous women have similarly shown an increased risk of prolapse after hysterectomy. As the most common risk factor for pelvic organ prolapse-vaginal birth-was not included and women were >72 years of age in this study, the numbers of pelvic organ prolapse surgeries were low. Despite the low absolute risk of pelvic organ prolapse surgery in nulliparous women, they were important in investigating the association between hysterectomy and pelvic organ prolapse, excluding vaginal birth, which is the most common risk factor for pelvic organ prolapse. As this cohort study of nulliparous women found an increased risk of pelvic organ prolapse surgery after hysterectomy, it is implied that the uterus per se protects against pelvic organ prolapse. As such, gynecologists should be aware of the risks associated with hysterectomy, and alternative uterus-sparing treatments should be considered when possible. Furthermore, women should be informed about the risks before being offered a hysterectomy.

Endometrial cancer after the Manchester procedure: a nationwide cohort study.

INTRODUCTION AND HYPOTHESIS: We aimed to investigate whether the Manchester procedure affects the risk and prognosis of endometrial cancer. METHODS: All Danish residents have a personal number permitting linkage of nationwide registers on the individual level enabling epidemiological studies with lifelong follow-up. We performed a nationwide historical cohort study including Danish women born before 2000 undergoing the Manchester procedure (N = 23,935) during 1977-2018. We included women undergoing anterior colporrhaphy as a reference group (N = 51,008) because of comparable inclination to consult a doctor and clinical similarities. Main outcomes were the number of women diagnosed with endometrial cancer, the stage of endometrial cancer at time of diagnosis, and cancer-specific and overall mortality. We followed the cohort until endometrial cancer/death/emigration/hysterectomy/31 December 2018. We performed chi-square test for trend to compare the diagnostic stage and Cox regressions to analyze the risk of endometrial cancer and mortality. The models were adjusted for age, calendar year, income level, and parity. RESULTS: During follow-up (median 13 years), 271 (1.13%) women were diagnosed with endometrial cancer after the Manchester procedure and 520 (1.05%) after anterior colporrhaphy. The adjusted hazard ratio (HR) for endometrial cancer was 1.00 [95% confidence interval (CI) 0.86-1.16]. No difference in stage of cancer was found (p = 0.18) nor when stratifying for calendar year. The HR for cancer-specific mortality and overall mortality after the Manchester procedure was 0.87 (95% CI 0.65-1.16) and 0.93 (95% CI 0.77-1.12), respectively. CONCLUSIONS: The Manchester procedure does not affect the risk or prognosis of endometrial cancer.

A Low-Cost, High-Precision Vehicle Navigation System for Deep Urban Multipath Environment Using TDCP Measurements.

In this study, we developed a low-cost, high-precision vehicle navigation system for deep urban multipath environments using time-differenced carrier phase (TDCP) measurements. Although many studies are being conducted to navigate autonomous vehicles using the global positioning system (GPS), it is difficult to obtain accurate navigation solutions due to multipath errors in urban environments. Low-cost GPS receivers that determine the solution based on pseudorange measurements are vulnerable to multipath errors. We used carrier phase measurements that are more robust for multipath errors. Without correction information from reference stations, the limited information of a low-cost, single-frequency receiver makes it difficult to quickly and accurately determine integer ambiguity of carrier phase measurements. We used TDCP measurements to eliminate the need to determine integer ambiguity that is time-invariant and we combined TDCP-based GPS with an inertial navigation system to overcome deep urban multipath environments. Furthermore, we considered a cycle slip algorithm for its accuracy and a multi-constellation navigation system for its availability. The results of dynamic field tests in a deep urban area indicated that it could achieve horizontal accuracy of at the submeter level.

Depressive symptoms, professional quality of life and turnover intention in Korean nurses.

AIM: The purpose of this study was to identify the effects of depressive symptoms and professional quality of life on turnover intention. BACKGROUND: The high turnover rate of nurses is a critical healthcare issue globally. INTRODUCTION: Nurses often experience depressive symptoms and compassion fatigue due to the efforts of patient care. The impact of such psychological health issues on turnover intention needs to be confirmed. METHODS: Participants were 10 163 female nurses who completed an online or mobile survey using the Korea Nurses' Health Study. To identify the influencing factors on the turnover intention of nurses, descriptive statistics, spearman's correlation coefficients and multivariable ordinal logistic regression were performed. RESULTS: The turnover intention increased by about 2.81-4.60 times when depressive symptom was moderate or more, 1.14 times when secondary traumatic stress disorder was moderate or more, and 1.54 times when burnout was moderate or more. When compassion satisfaction was moderate or high, the turnover intention decreased by 0.72 and 0.52 times. DISCUSSION: Korean nurses demonstrated high levels of depressive symptoms, secondary traumatic stress and burnout, while demonstrating lower levels of compassion satisfaction. The results of this study demonstrate that depressive symptoms, secondary traumatic stress, burnout and compassion satisfaction affect turnover intention. CONCLUSIONS: To reduce nurses' turnover intention, it is necessary to reduce depressive symptoms and enhance the quality of professional life. IMPLICATIONS FOR NURSING AND HEALTH POLICY: Hospital managers need to maintain adequate nurse-to-patient ratios and provide nurses with a supportive work environment. Also, health policymakers need to identify factors affecting hospital nurses' turnover intention and provide strategies to address them. These conditions may reduce the excessive workload placed on nurses, thereby preventing depression and burnout and improving nurses' quality of work-life.

DETECTION OF AN ARENAVIRUS IN A GROUP OF CAPTIVE WAGLER'S PIT VIPERS (TROPIDOLAEMUS WAGLERI).

A group of eight Wagler's pit vipers (Tropidolaemus wagleri) from a private collection died with respiratory signs within 6 mo of one another. The group consisted of an adult breeding pair that was wild caught and six offspring from this pair. Four of the dead snakes were submitted for gross and histopathology. Signs of bacterial pneumonia were detected in all four examined snakes. No inclusion bodies suggestive of viral infection were found in any of the examined tissues. Polymerase chain reactions for the detection of ferla-, adeno-, reo-, and nidoviruses were all negative, but reptarenaviruses closely related to viruses previously described in boa constrictors (Boa constrictor) with inclusion body disease were detected in two of the four snakes. This is the first description of reptarenaviruses in viperid snakes. The pathogenic role of the virus in illness is unknown.

The severity of periodontitis and metabolic syndrome in Korean population: The Dong-gu study.

OBJECTIVES: We assessed the association between periodontal disease status and metabolic syndrome (MetS) and its individual components in Korean adults over 50 years old. MATERIAL AND METHODS: In the Dong-gu study, 5078 men and women aged over 50 years were included. They underwent a questionnaire survey, physical assessment, biochemical assessment and periodontal assessment. The percentages of sites with periodontal probing depth ≥4 mm, and clinical attachment loss ≥4 mm were recorded for each participant. Periodontal disease was also classified by the Centers for Disease Control and Prevention/American Academy of Periodontology definition of periodontitis and the American Academy of Periodontology definition (1999). MetS was defined by the 2009 guidelines of the International Diabetes Federation. This study used multivariate negative binominal regression analysis to assess the association between the severity of periodontitis and MetS, after age, smoking habits, alcohol consumption and physical activity related factors were adjusted for. RESULTS: Prevalence of MetS was 32.3%, 36.2% and 45.9% among men with no or mild, moderate and severe periodontitis, respectively. The severity of periodontitis was positively associated with the prevalent MetS in men but not in women. In men, severe periodontitis showed a higher risk of MetS than those with no or mild periodontitis (relative risk 1.43, 95% confidence interval 1.17-1.73) after adjusting for confounders. Periodontal probing depth was positively associated with the prevalence of MetS in both genders. In the analysis separated by individual MetS components, periodontitis severity was positively associated with hypertriglyceridemia and low high-density lipoprotein cholesterol in men, while positively associated with low high-density lipoprotein cholesterol and abdominal obesity in women. CONCLUSION: Increasing the severity of periodontitis was associated with the risk of prevalent MetS in Korean adults. This result confirmed that periodontal inflammation might be a contributive factor of MetS.

Binge eating disorder and depressive symptoms among females of child-bearing age: the Korea Nurses' Health Study.

BACKGROUND: Most studies regarding the relationship between binge eating disorder (BED) and depression have targeted obese populations. However, nurses, particularly female nurses, are one of the vocations that face these issues due to various reasons including high stress and shift work. This study investigated the prevalence of BED and the correlation between BED and severity of self-reported depressive symptoms among female nurses in South Korea. METHODS: Participants were 7,267 female nurses, of which 502 had symptoms of BED. Using the propensity score matching (PSM) technique, 502 nurses with BED and 502 without BED were included in the analyses. Data were analyzed using descriptive statistics, Spearman's correlation, and multivariable ordinal logistic regression analysis. RESULTS: The proportion of binge eating disorder was 6.90% among the nurses, and 81.3% of nurses displayed some levels of depressive symptoms. Multivariable ordinal logistic regression analysis revealed that age (40 years old and older), alcohol consumption (frequent drinkers), self-rated health, sleep problems, and stress were associated with self-reported depression symptoms. Overall, after adjusting for confounders, nurses with BED had 1.80 times the risk (95% CI = [1.41-2.30]; p-value < 0.001) of experiencing a greater severity of self-reported depression symptoms. CONCLUSIONS: Korean female nurse showed a higher prevalence of both binge eating disorder and depressive symptoms, and the association between the two factors was proven in the study. Therefore, hospital management and health policy makers should be alarmed and agreed on both examining nurses on such problems and providing organized and systematic assistance.

DETECTION OF OPHIDIOMYCES OPHIODIICOLA IN TWO CAPTIVE BOCOURT WATER SNAKES ( SUBSESSOR BOCOURTI) AND ONE CAPTIVE PUEBLAN MILK SNAKE ( LAMPROPELTIS TRIANGULUM CAMPBELLI).

Two captive Bocourt water snakes ( Subsessor bocourti) presented with chronic white skin lesions on their heads; Ophidiomyces ophiodiicola was identified by culture and polymerase chain reaction (PCR) in skin scrapings from both snakes. Histopathology performed in one Bocourt water snake revealed fungal hyphae in epidermal structures of lesions. One Pueblan milk snake ( Lampropeltis triangulum campbelli) from the same zoologic institution presented with yellow crusts and white blisters on its body, from which O. ophiodiicola was identified by culture and PCR. Two of the three snakes apparently recovered from lesions after multiple natural sheds, whereas the third snake died. This is the first report of O. ophiodiicola infection in Bocourt water snakes and in a Pueblan milk snake, as well as the first report of O. ophiodiicola in France.

Impact of appropriate empirical antibiotic treatment on recurrence and mortality in patients with bacteraemia: a population-based cohort study.

BACKGROUND: Data on the impact of empirical antibiotic treatment (EAT) on patient outcome in a population-based setting are sparse. We assessed the association between EAT and the risk of recurrence within one year, short-term- (2-30 days) and long-term (31-365 days) mortality in a Danish cohort of bacteraemia patients. METHODS: A cohort study including all patients hospitalized with incident bacteraemia during 2007-2008 in the Copenhagen City and County areas and the North Denmark Region. EAT was defined as the antibiotic treatment given at the 1st notification of a positive blood culture. The definition of recurrence took account of pathogen species, site of infection, and time frame and was not restricted to homologous pathogens. The vital status was determined through the civil registration system. Association estimates between EAT and the outcomes were estimated by Cox and logistic regression models. RESULTS: In 6483 eligible patients, 712 (11%) had a recurrent episode. A total of 3778 (58%) patients received appropriate EAT, 1290 (20%) received inappropriate EAT, while EAT status was unrecorded for 1415 (22%) patients. The 2-30 day mortality was 15.1%, 17.4% and 19.2% in patients receiving appropriate EAT, inappropriate EAT, and unknown EAT, respectively. Among patients alive on day 30, the 31-365 day mortality was 22.3% in patients given appropriate EAT compared to 30.7% in those given inappropriate EAT. Inappropriate EAT was independently associated with recurrence (HR 1.25; 95% CI = 1.03-1.52) and long-term mortality (OR 1.35; 95% CI = 1.10-1.60), but not with short-term mortality (OR 0.85; 95% CI = 0.70-1.02) after bacteraemia. CONCLUSIONS: Our data indicate that appropriate EAT is associated with reduced incidence of recurrence and lower long-term mortality following bacteraemia.

DETECTION OF INTRANUCLEAR COCCIDIOSIS IN TORTOISES IN EUROPE AND CHINA.

Intranuclear coccidiosis of tortoises (TINC) has been described in association with systemic disease in various species of tortoises. TINC has been detected in numerous tortoises from the United States, but there are only a few reports from tropical tortoises in Germany and no reports from Asia. Using a real-time polymerase chain reaction assay, samples from 1,011 tortoises were screened for the presence of TINC. Samples originated from animals kept in captivity in Europe and in China. Coccidia were detected in a total of 27 chelonians (2.7%), including the first description of TINC in a marginated tortoise ( Testudo marginata ), Hermann's tortoise ( Testudo hermanni ), African spurred tortoise (Centrochelys sulcata), and yellow-footed tortoise (Chelonoidis denticulatus). The highest percentage of positive animals was found in radiated tortoises ( Astrochelys radiata ). Although the percentage of positive animals was relatively low, this study demonstrates the global distribution of TINC in captive chelonians as well as expanding the known host range for these pathogens.

The role of structural parameters in DNA cyclization.

BACKGROUND: The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization. RESULTS: We calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data. CONCLUSIONS: Our data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.

Activation of Autophagy by Everolimus Confers Hepatoprotection Against Ischemia-Reperfusion Injury.

As the criteria for liver donation have been extended to include marginal donors, liver grafts are becoming particularly vulnerable to hepatic ischemia-reperfusion injury (IRI). However, no specific measures have been validated to ameliorate hepatic IRI. In this article, we explored whether everolimus has protective effects against hepatic IRI in relation with autophagy. The effects of everolimus were investigated in both in vitro and in vivo hepatic IRI models. Mouse hepatocyte AML12 cells and BALB/c mice were utilized for the establishment of each model. In the IRI-induced AML12 cells, everolimus treatment increased the expressions of autophagic markers (microtubule-associated protein 1 light chain 3 and p62) and decreased pro-apoptotic proteins (cleaved caspase 3 and cleaved poly-ADP ribose polymerase). The blockage of autophagy, using either bafilomycin A1 or si-autophagy-related protein 5, abrogated these anti-apoptosis effects of everolimus. Subsequently, everolimus administration to the hepatic IRI-induced mice provided hepatoprotective effects in terms of (1) decreasing the expressions of pro-apoptotic proteins, (2) inhibiting the release of pro-inflammatory cytokines (IL-6 and tumor necrosis factor-α), (3) reducing elevated liver enzymes (aspartate transaminase, alanine transaminase, and ammonia), and (4) restoring liver histopathology. These findings suggest that everolimus protects the liver against hepatic IRI by way of activating autophagy, and thus could be a potential therapeutic agent for hepatic IRI.

The NLSY Kinship Links: Using the NLSY79 and NLSY-Children Data to Conduct Genetically-Informed and Family-Oriented Research.

The National Longitudinal Survey of Youth datasets (NLSY79; NLSY-Children/Young Adults; NLSY97) have extensive family pedigree information contained within them. These data sources are based on probability sampling, a longitudinal design, and a cross-generational and within-family data structure, with hundreds of phenotypes relevant to behavior genetic (BG) researchers, as well as to other developmental and family researchers. These datasets provide a unique and powerful source of information for BG researchers. But much of the information required for biometrical modeling has been hidden, and has required substantial programming effort to uncover-until recently. Our research team has spent over 20 years developing kinship links to genetically inform biometrical modeling. In the most recent release of kinship links from two of the NLSY datasets, the direct kinship indicators included in the 2006 surveys allowed successful and unambiguous linking of over 94 % of the potential pairs. In this paper, we provide details for research teams interested in using the NLSY data portfolio to conduct BG (and other family-oriented) research.