A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Implementing Clinical Guidelines for the Treatment of Psychosis: The Frontline Leaders' Point of View. A Qualitative Study.

Background: Despite the large amount of leadership and implementation theories and recommendations, healthcare services continue to struggle with efficiently incorporating new knowledge. The questioning of conventional leadership approaches in healthcare organizations prompted us to investigate how frontline leaders comprehend their own implementation intentions and actions, and how these intentions and actions may impact the implementation of clinical guidelines in mental healthcare in Norway. Methods: Employing a theory-driven qualitative design, we conducted nine semi-structured interviews with frontline leaders who had recently led implementation of clinical guidelines for the treatment of psychosis in mental health. We employed Systematic Text Condensation, informed by Normalization Process Theory, to structure and analyze the data and used fidelity scales to measure the degree of implementation and distinguish between leaders' levels of success in implementation. Results: Frontline leaders in units that achieved high success in implementation described their intentions and actions differently, from those with less success. The former group's actions aligned more closely with the constructs of the Normalization Process Theory compared to the latter group when describing their actions. Frontline leaders leading units with a high degree of implementation success describe relation-orientation, trust, and providing adaptive space for staff members to take initiative. In contrast, those leading units with less implementation success describe more control and guidance of co-operators and place more emphasize on information and knowledge. Conclusion: Differences in how frontline leaders describe their actions and intentions to achieve clinical guideline implementation suggest that the leadership approach of these frontline leaders is an important factor to consider when planning and conducting implementation. To better understand the implementation process, it is important to pay attention to how frontline leaders customize their leadership approaches to the dynamics of complex organizations, and how they interact with their team and superiors.

Complement gene mutations in children with C3 glomerulopathy: do they affect the response to mycophenolate mofetil?

BACKGROUND: C3 glomerulopathy (C3G) is a complement-mediated disease. Although genetic studies are not required for diagnosis, they are valuable for treatment planning and prognosis prediction. The aim of this study is to investigate the clinical phenotypes, kidney survival, and response to mycophenolate mofetil (MMF) treatment in pediatric C3G patients with and without mutations in complement-related genes. METHODS: Sixty pediatric C3G patients were included, divided into two groups based on complement-related gene mutations. Demographic and clinical-pathological findings, treatment modalities, and outcome data were compared, and Kaplan-Meier analysis was performed for kidney survival. RESULTS: Out of the 60 patients, 17 had mutations. The most common mutation was in the CFH gene (47%). The mean age at diagnosis was higher in the group with mutation (12.9 ± 3.6 vs. 11.2 ± 4.1 years, p = 0.039). While the patients without mutation most frequently presented with nephritic syndrome (44.2%), the mutation group was most likely to have asymptomatic urinary abnormalities (47.1%, p = 0.043). Serum parameters and histopathological characteristics were similar, but hypoalbuminemia was more common in patients without mutation. During 45-month follow-up,10 patients progressed to chronic kidney disease stage 5 (CKD5), with 4 having genetic mutation. The time to develop CKD5 was longer in the mutation group but not significant. MMF treatment had no effect on progression in either group. CONCLUSIONS: This study is the largest pediatric C3G study examining the relationship between genotype and phenotype. We showed that the mutation group often presented with asymptomatic urinary abnormalities, was diagnosed relatively late but was not different from the without mutation group in terms of MMF treatment response and kidney survival.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Individual variation of the percentage of Y-chromosome bearing sperm content in human ejaculates.

The study aimed to determine the variation of Y-chromosome-bearing sperm content among individual ejaculates. A real-time polymerase chain reaction (qPCR) with unique primers was developed and used to calculate the percentage of Y-chromosome-bearing sperm in individual ejaculates from 50 randomly selected men. There was a significant difference in the overall mean ± SD between the proportion of Y-chromosome-bearing sperm and X-chromosome-bearing sperm (45.36 ± 7.88 vs. 54.42 ± 7.88). Of the 50 ejaculates, 17 had more than, and 14 had less than the 99% confidence interval of the mean of the Y-chromosome-bearing sperm (45.58 ± 2.87). These results suggest that the inconsistency in sperm-based sex-selection outcomes appears to be a function of differences in the ejaculates and highlights the need for further study in environmental and genetic factors contributing to X or Y bearing spermatozoan instability.Abbreviations: qPCR: real-time polymerase chain reaction; ROS: reactive oxygen species; DTT: dithiothreitol; SRY: sex-determining region Y.

Urinary oxalate to creatinine ratios in healthy Turkish schoolchildren.

AIM: we aimed to establish reference values for urinary oxalate to creatinine ratios in healthy children aged 6-15 years and to investigate the relationship between their nutritional habits and oxalate excretion. MATERIALS AND METHODS: Random urine specimens from 953 healthy children aged 6-15 years were obtained and analyzed for oxalate and creatinine. Additionally, a 24-h dietary recall form was prepared and given to them. The ingredient composition of the diet was calculated. The children were divided into three groups according to age: Group I (69 years, n = 353), Group II (10-12 years, n = 335), and Group III (13-15 years, n = 265). RESULTS: The 95th percentile of the oxalate to creatinine ratio for subjects aged 6-9, 10-12, and 13-15 years were 0.048, 0.042, and 0.042 mg/mg, respectively. The oxalate to creatinine ratio was significantly higher in Group 1 than in Group 2 and Group 3. Urinary oxalate excretion was positively correlated with increased protein intake and negatively correlated with age. A significant positive correlation was determined between urinary oxalate excretion and the proline, serine, protein, and glycine content of diet. Dietary proline intake showed a positive correlation with the urine oxalate to creatinine ratio and was found to be an independent predictor for urinary oxalate. CONCLUSIONS: These data lend support to the idea that every country should have its own normal reference values to determine the underlying metabolic risk factor for kidney stone disease since regional variation in the dietary intake of proteins and other nutrients can affect normal urinary excretion of oxalate.

Are there possible associations between MnSOD and GPx1 gene variants for laryngeal cancer risk or disease progression?

Laryngeal squamous cell carcinoma (LSCC) is a multifaceted and genomically complex disease and cellular and preclinical studies have demystified wide ranging molecular mechanisms which underpin its development and progression and resistance against wide ranging molecular therapeutics. Oxidative stress is a widely studied molecular mechanism and reportedly involved in carcinogenesis. Increasingly it is being realized that accumulation of Reactive Oxygen Species (ROS) activates defensive mechanism to counteract oxidative stress induced damage. Manganese superoxide dismutase (MnSOD) and glutathione peroxidase (GPx) are important members of defensive machinery. We investigated whether the polymorphisms of MnSOD (Ala-9Val, rs4880) and GPx1 (Pro198Leu, rs1050450) are associated with LSCC and also evaluated possible interactions between these polymorphisms and various lifestyle factors or pathological features of patients. For this purpose, 67 LSCC patients and 73 healty controls were enrolled. Molecular assessment of MnSOD and GPx1 variants were determined with polymerase chain reaction-restriction fragment length polymorphism techniques. We found that the frequency of both heterozygous PL genotype and P allele was considerably higher in patients with advanced tumor stage (T3/T4) than in those with early tumor stage (T1/T2) (OR= 5.106; 95% CI=1.372-19.004; p<0.001, OR=5.787; 95% CI =1.564-21.414; p<0.001 respectively). Although the frequency of ValVal/LL combine genotype was significantly decreased (OR=0.204, 95% CI=0.055-0.760; p=0.021), the frequency of ValAla/PL combine genotypes was higher in patients with stage T3/T4 than in those patients with stage T1/T2 (p=0.027). Consequently, we have concluded that variants of GPx1 and MnSOD should not be considered as a risk factor of LSCC, only may be accepted as a prognostic markers. Use of new technologies such as metabolomics and deep DNA sequencing will prove to be helpful in developing a deeper knowledge related to how cancer cell metabolism adapts and provides a buffer against increased oxidative stress.

Frequency of embryo multinucleation detected by time-lapse system and its impact on pregnancy outcome.

OBJECTIVE: To compare the detection rate of multinucleation with the time-lapse system and conventional control timing proposed by European Society of Human Reproduction and Embryology (ESHRE) consensus and evaluate its impact on pregnancy rates. DESIGN: Retrospective study. SETTING: A private IVF center. PATIENT(S): A total of 686 embryos from 511 intracytoplasmic sperm injection (ICSI) cycles. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): A time-lapse system was used to acquire embryo images until ET; the stored data were reviewed for the presence and persistence of multinucleation. The detection rate of multinucleation was compared with ESHRE/ALPHA consensus-proposed embryo evaluating times (23 ± 1, 26 ± 1, 44 ± 1 hours). Morphokinetic characteristics of multinucleated embryos and the effect of multinucleation on pregnancy rate were researched. RESULT(S): Multinucleation was detected in 159 embryos of 145 ICSI cycles. Using ESHRE/ALPHA consensus embryo evaluating times, only 44 (27.6%) out of 159 multinucleated embryos could be identified. In cycles with multinucleated ETs compared with cycles with no multinucleated embryos, clinical pregnancy rates (respectively, 23.4 vs. 44) and implantation rates (respectively, 23.3 vs. 43.6) were significantly lower. Time to 2-cell, 4-cell, and 6-cell stage was significantly longer in multinucleated embryos. Patient age (odds ratio [OR], 0.95; confidence interval [CI], 0.92-0.98) and presence of multinucleation (OR, 0.37; CI, 0.24-0.56) were the only significant predictors of clinical pregnancy rate. CONCLUSION(S): The time-lapse monitoring system seems to be a valuable tool to identify all cases with multinucleation. We conclude that the detection of multinucleation by time-lapse monitoring is associated with lower implantation and clinical pregnancy rates.

Possible Risk Factors for Acute Stress Disorder and Post-Traumatic Stress Disorder After an Industrial Explosion.

INTRODUCTION: There have been deaths and injuries after an explosion which happened in an industrial region in Ankara in February 2011. The aim of this study was to determine the prevalence of acute stress disorder (ASD) and posttraumatic stress disorder (PTSD), and to determine the variables which can be the risk factors for PTSD. METHODS: In this study, we included a total of 197 subjects who were present at the factory building and at the four offices nearby when the disaster occurred. All the participants were assessed one month after the explosion and 157 of them were reassessed six months after the explosion. Socio-demographic information forms were given and the Clinician-Administered PTSD Scale (CAPS) was administered to the participants one month after the explosion. Psychiatric assessments were done using the structured clinical interview for DSM-IV axis-I disorders (SCID-I). The CAPS was re-applied six month after the disaster. RESULTS: At the first-month assessments, ASD was detected in 37.1% of participants and PTSD in 13.7%, whereas PTSD was observed in 16.6% of subjects at the sixth month of the accident. According to the first month data, having any psychiatric disorder before the incident, physical injury, acquaintances among the dead and the injured people, being involved in the incident and seeing dead people were detected as the risk factors for PTSD. At the sixth month assessment, physical injury, acquaintances among the dead and the injured, being involved in the incident were seen as risk factors for PTSD. CONCLUSION: ASD and PTSD can be seen after an explosion. Having a previous psychiatric disorder and being directly affected by trauma and being injured are the risk factors for PTSD. This study implies that preventive mental health care services should include the management of current psychiatric condition and employee safety issues.

Serum omentin 1 level is associated with coronary artery disease and its severity in postmenopausal women.

We evaluated whether serum omentin levels are associated with coronary artery disease (CAD) and its severity among postmenopausal women. We enrolled 193 consecutive postmenopausal women who had undergone coronary angiography for suspected stable CAD. The study population was divided into 2 groups based on the results of coronary angiography (CAD group, n=110 and control group, n=83). Omentin 1 levels were measured and disease severity was assessed using the SYNTAX score (SS) in the CAD group. Those patients with angiographic CAD had significantly decreased omentin 1 levels, compared to those without CAD (247.5+127.4 vs 506+246 ng/mL, P<.001). After adjusting for cardiovascular risk factors, a decreased omentin 1 level was found to be an independent predictor of both angiographic CAD and a high SS. Our data indicate that a decreased omentin 1 level is associated with CAD and its severity among postmenopausal women.

Spontaneous resolution of paraparesis because of acute spontaneous thoracolumbar epidural hematoma.

BACKGROUND: Symptomatic spontaneous spinal epidural hematoma(SSEH) is an uncommon cause of cord compression that commonly is considered an indication for emergent surgical decompression. We aimed to investigate a patient with a SSEH that completely resolved clinically and radiographically, without surgical treatment. The patient presented three days after the sudden onset of back pain, numbness, and weakness. Magnetic Resonance Imaging (MRI) revealed a posterior thoracolumbar epidural hematoma extending from the level of T10 to L2 with significant cord compression. Decompression was recommended but he refused surgery and was managed conservatively. One month later weakness totally recovered and hematoma was absent on MRI.

Are increased carotid artery pulsatility and resistance indexes early signs of vascular abnormalities in young obese males?

PURPOSE: To provide insight into the factors by which obesity in itself may directly lead to early arterial damage, we aimed to determine early sonographic markers of obesity-related vascular dysfunction in young obese males. METHODS: Thirty-five young obese males and 23 age-matched healthy male volunteers were recruited into the study. Common carotid artery pulsatility index and resistance index were calculated from blood flow velocities curves obtained by pulsed Doppler ultrasonography. RESULTS: The mean pulsatility index, resistance index, body mass index, waist circumference, systolic and diastolic blood pressure, homeostasis model assessment for insulin resistance, plasma fasting glucose, insulin, C-peptide, triglycerides, low-density lipoprotein cholesterol, and high-sensitivity C-reactive protein were statistically higher in obese subjects than in healthy controls. CONCLUSIONS: Our results suggest that depressed vessel compliance and increased vascular resistance are features of young, obese, normotensive subjects independently of and in addition to cardiovascular risk factors. As changes in arterial wall properties may be incipient in young obese subjects, future studies will be required to demonstrate whether early intervention such as diet and exercise in this population can improve vascular functions.

Increased endothelial microparticles in obese and overweight children.

BACKGROUND: Obesity in children increases the risk of atherosclerosis. Endothelial dysfunction is an important factor in the pathogenesis of atherosclerosis, and endothelial microparticles (EMPs) are considered as markers of endothelial dysfunction. In this study, we aimed to evaluate circulating EMPs in obese and overweight children and to disclose the measure of obesity with the strongest relation with circulating microparticles and carotid atherosclerosis. METHODS: This prospective study included 55 obese and overweight children and 23 healthy controls. Insulin resistance was studied. Both in vivo and in vitro human umbilical vein endothelial cell evaluations were used for the study. Circulating EMPs (CD144 and CD146) were measured by flow cytometry. The carotid artery intima-media thickness (cIMT) and left ventricular mass index (LVMI) were measured using ultrasound and echocardiography, respectively. Study groups were compared for anthropometric measurement, insulin resistance, circulating EMP, cIMT, and LVMI. The relationship among overweight, obesity, and circulating EMPs were investigated. RESULTS: Blood pressure, CD144+EMP levels, and LVMI were statistically higher in the patients group than in the control group. The multiple logistic regression analysis and the backward elimination method showed that CD144+EMP and systolic blood pressure had a linear relationship with overweight and obesity. CONCLUSION: Our results suggest that endothelial damage starts in the early stage of childhood obesity and that obese and overweight children have increased circulating CD144+EMPs, showing that endothelial dysfunction and increased CD144+EMPs may be related to obesity.

Increased iron and oxidative stress are separately related to cognitive decline in elderly.

AIM: The aim of this study is to examine the relation between body iron, oxidative stress and cognitive function in elderly. METHODS: Eighty-seven elderly residents from nursing homes were the subjects of our study. Cognitive status was screened by the Mini-Mental State Examination (MMSE). Of the 87 eligible subjects, 46 patients who obtained 24 or fewer points on the MMSE scale were considered as subjects with cognitive dysfunction. The control group consisted of 41 subjects who obtained more than 24 points on the MMSE. Routine biochemical analyses, parameters of iron metabolism, malondialdehyde (MDA) and glutathione peroxidase (GSH-Px) were determined in all subjects. RESULTS: There were statistically significant increases in serum iron, transferrin saturation, ferritin and MDA levels; whereas there was a statistically significant decrease in serum GSH-Px enzyme activity and serum sodium levels in subjects with cognitive dysfunction. A significant negative correlation was found between serum iron, transferrin saturation, ferritin and MMSE score. There was a negative correlation between MMSE score and serum MDA; however, a positive significant correlation was found between MMSE score and both GSH-Px enzyme activity and serum sodium. CONCLUSION: Our study provides evidence of increased markers of iron deposition and oxidative stress in patients with cognitive dysfunction. It seems likely that these markers negatively affect the MMSE score. Interestingly, we did not find any correlation between the markers of iron deposition and oxidative stress. Future studies will be required to demonstrate whether diminishing iron and oxidative stress will enhance MMSE score and thereby ameliorate cognitive impairment.

Current concepts in the treatment of epidermolysis bullosa acquisita.

INTRODUCTION: Long-term remission in EBA patients is difficult to achieve. Patients who are resistant or develop side effects to conventional immunosuppressive therapy (CIST) have been treated with several other agents. AREAS COVERED: This review focuses on the clinical outcome in patients treated with a single drug or combination, and determines if long-term remission can be induced. Data on 71 patients was analyzed. There are no controlled trials. The regimens used included dapsone, colchicine, mesalazine, cyclosporine, mycophenolic acid, intravenous immunoglobulin, rituximab, daclizumab, extracorporeal photochemotherapy, and plasmapheresis. An algorithm on treating a patient has been presented. EXPERT OPINION: The use of CIST, especially in wide spread and recalcitrant patients, usually does not produce a prolonged clinical remission and can have hazardous side effects. Intravenous immunoglobulin, rituximab and immunoadsorption have been successfully used in some, but the benefits from their use may require additional studies. The immediate future holds much promise for the development of a specific ELISA which may facilitate the early diagnosis of EBA. As the population ages, it is likely that the number of patients will increase and newer biological agents may emerge that may have a better clinical outcome. One of the challenges is to produce "targeted therapies".

The vasoactive intestinal polypeptide (VIP) levels at the patients with ankylosing spondylitis and its association with inflammation markers.

Vasoactive intestinal polypeptide (VIP) is a neuropeptide from secretin/glukagon family. Recently, the importance of VIP is becoming more evident, and it is thought that VIP is playing an important regulatory role between neuroendocrine-immune-gastrointestinal systems. In this study, we have tried to evaluate the potential role of VIP in patients with ankylosing spondylitis (AS). In this study, 40 patients (30 male and 10 female) with AS and 40 healthy controls were included. X-ray examinations and scoring of sacroiliac joints of the patients with AS were done according to 1984 Modified New York Criteria for AS. All patients have been assessed with Bath Ankylosing Spondylitis Disease Activity Index. Platelet counts were significantly higher in study group (P < 0.05) in contrast to levels of the hemoglobin. The mean VIP levels were 4.2 ± 1.8 (pg/mL) for study group and 2.8 ± 0.8 (pg/mL) for controls. These results were statistically significant (P < 0.05). There was not any correlation between plasma VIP levels with CRP, ESR, Hb, BASDAI results and radiological scoring of the patients (P > 0.05) in contrast to our expectations. However, platelet counts and VIP levels were correlated significantly (P = 0.03). Our data demonstrate that VIP tended to be high in patients with AS when compared with healthy subjects and correlated with platelet counts significantly, for the first time at the literature. According to this study, VIP may have potential role in the pathogenesis of AS, and it is a potential candidate for many kinds of therapies.

Circulating endothelial microparticles in children with Henoch-Schönlein purpura; preliminary results.

The aim of this study was to investigate the levels of circulating endothelial microparticles (EMPs) in children with HSP and to determine whether there was a difference between patients with nephritis and those without nephritis. Twenty patients with HSP aged between 2.5 and 15 and 10 age-and sex-matched healthy controls were enrolled in the study. The HSP group was divided into two groups, including patients with nephritis (n = 9) and those without nephritis (n = 11). In all groups, circulating EMPs were enumerated by flow cytometry, after staining platelet-free plasma with PE-conjugated anti-CD144. At the same time, human umbilical vein endothelial cells (HUVEC) were incubated with the platelet-free plasma of patients with HSP and that of the control group. Then, circulating EMPs were counted in HUVEC supernatant incubated with the platelet-free plasma of patients and control groups, after staining the supernatant with PE-conjugated anti-CD146. Circulating EMPs were significantly higher in both the active and the remission period of the patient groups compared with the control subjects. In the patient group, there were no statistically significant differences in the level of circulating EMPs between patients with nephritis and those without nephritis. Both CD144 and 146+EMP in patients with HSP nephritis in the active period were substantially higher than in those remissions. CD144+EMP in the active period were substantially higher than in the remission period in patients without nephritis. We detected that circulating EMPs increased in patients with HSP in both active and remission periods. Although clinical and laboratory findings return to normal in the remission period, the increased circulating EMPs may show that the subclinical inflammatory process is continuous. We think that circulating EMPs could be used as a surrogate marker for subclinical inflammation in HSP.

Association between cancer and immunosuppressive therapy--analysis of selected studies in pemphigus and pemphigoid.

OBJECTIVE: To determine whether there is an association between the use of immunosuppressive agents (ISAs) and cancer in patients with pemphigus and pemphigoid-rare, potentially fatal diseases of the skin and mucous membranes, often requiring long-term use of ISAs. DATA SOURCE: Literature was accessed through PubMed (all years available), using the search terms cancer, immunosuppressive agents, pemphigoid, and pemphigus. STUDY SELECTION AND DATA EXTRACTION: A retrospective review of the literature was conducted. Inclusion criteria for studies were: (1) English language, (2) diagnosis of pemphigus and/or pemphigoid based on histology and immunopathology, (3) more than 10 patients evaluated, (4) investigators had a high index of suspicion of cancer and patients were monitored for it, (5) follow-up information was provided for at least 1 year after initiation of therapy, and (6) absence of diagnosis of cancer before initiation of an ISA. Case reports were not included in the analysis. DATA SYNTHESIS: A total of 929 patients diagnosed with either pemphigus or pemphigoid in 17 studies were identified. Patients were divided into 2 groups. Group A comprised patients treated with azathioprine, cyclophosphamide, cyclosporine, or mycophenolate mofetil in combination with prednisone. In Group A, 22 cases of cancer were reported in 21 of the 218 patients (9.6%). Group B comprised patients treated with systemic corticosteroids only. In this group, cancer was reported in 11 of the 711 patients (1.5%). In this study there was no control group (untreated patients) and the sample sizes were small. CONCLUSIONS: Preliminary data suggest a possible association between the use of azathioprine, cyclophosphamide, and cyclosporine and increased susceptibility to cancer in patients with pemphigus and pemphigoid.