Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and param-eters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.

Objective: To investigate the sex-related differences in single-task performance through motor torque, cognitive tasks and walking speed, and the combined dual-task costs (DTCs) considering both motor and cognitive performance in young adults. Methods: Sixty-seven non-athletic subjects 37 females and 30 males were enrolled. The study measured their knee extension muscle torque using an isokinetic strength dynamometer and their walking speed using the one step app. these assessments were performed both with and without a cognitive task, and the DTCs were calculated. Results: The females exhibited significantly larger motor performance dual task effect through (torque-DTC, speed-DTC) compared with males while exhibiting smaller cognitive dual task effect with muscle torque and speed. Conclusion Deterioration in motor performance during muscle force production and speed during dual tasks was large in females compared to males, whereas males experience a decline in cognitive ability when performing dual tasks compared with females.

BACKGROUND: It is still unclear the ideal vitamin D dosage once the deficiency and insufficiency is treated. Once deficiency was corrected we prospectively treated patients with 2,000 IU of vitamin D3 to check whether this dosage is enough to keep them above the 30 ng/mL of 25-hydroxy-vitamin D (25[OH]D). METHODS: One hundred and thirty-five Saudi Arabian men and women treatment naïve for the vitamin D deficiency and insufficiency were part of this study. History and clinical examination were done to rule out any metabolic bone disease. Weight and height was taken to calculate the body mass index (BMI). Patients who were vitamin D deficient (≥30 ng/mL), a standard treatment of 50,000 IU of vitamin D3 weekly for 3 months, a blood test for the vitamin D levels at the end of 3 months, maintenance dose of 2,000 IU of vitamin D3 for 3 months and a third blood sample after 3 months. RESULTS: The data for 128 patients was available for analysis. The average age was 44.95±12.97 years with the mean BMI of 29.60±2.59 kg/m2. The baseline 25(OH)D level was 13.16±3.30 ng/mL. The increase in the level of 25(OH)D on 50,000 IU weekly was significant from 13.16±3.3 ng/mL to 36.97±4.67 ng/mL (P < 0.001) and then 2,000 IU daily for next 3 months, the level of 25(OH)D dropped top 20.38±5.42 ng/mL (P < 0.001). CONCLUSIONS: Our study indicates that the maintenance dose of 2,000 IU of vitamin D is not enough for patients to keep the 25(OH)D levels above 30 ng/mL.
Body Mass Index ; Bone Diseases, Metabolic ; Calcifediol ; Cholecalciferol ; Dietary Supplements ; Female ; Hematologic Tests ; Humans ; Male ; Prospective Studies ; Vitamin D Deficiency ; Vitamin D* ; Vitamins*

PURPOSE: Augmentation cystoplasty (AC) is a surgical procedure used in adults and children with refractory bladder dysfunction, including a small bladder capacity and inadequate bladder compliance, and in whom conservative and medical treatment has failed. This study was aimed to determine the long-term outcomes of AC in children. METHODS: A retrospective analysis was conducted of 42 patients (31 males; mean age, 14.2±6.2 years) who underwent AC for neurogenic and nonneurogenic bladder dysfunction, with a median 12.0±1.5 years of follow-up. All patients underwent AC using the ileum with or without continent reconstruction. Pre-AC, concurrent, and post-AC procedures and complications were analyzed. Patients who underwent ureterocystoplasty, were lost to follow-up, or had less than 10 years of follow-up were excluded. The primary outcomes were the complication and continence rates, the post-AC linear rate of height and weight gain, and renal function. The Student t-test was used to evaluate between-group differences and the paired t-test was used to evaluate longitudinal changes in measured variables. RESULTS: Renal function was stable or improved in 32 of 42 patients (76.2%), with a post-AC continence rate of 88.1%. Thirty patients (71.4%) required 72 procedures post-AC. There was no statistically significant difference in the mean percentile of height (P=0. 212) or weight (P=0.142) of patients in the pre- and post-AC periods. No cases of bladder perforation or malignancy were detected. CONCLUSIONS: We consider AC to be a safe and effective procedure that does not negatively affect future physical growth, while achieving a good rate of stable renal function. Patients need long-term follow-up to address long-term complications.
Adult ; Child ; Compliance ; Follow-Up Studies* ; Humans ; Ileum ; Lost to Follow-Up ; Male ; Retrospective Studies ; Urinary Bladder Calculi ; Urinary Bladder* ; Weight Gain

Background: In patients with suspected pulmonary embolism (PE), the literature suggests the overuse of computerized tomography pulmonary angiography (CTPA) and underuse of clinical decision rules before imaging request. This study determined the potential for avoidable CTPA using the modified Wells score (mWS) and D-dimer assay in patients with suspected PE. Methods: This hospital-based retrospective study analyzed the clinical data of 661 consecutive patients with suspected PE who underwent CTPA in the emergency department of a tertiary hospital for the use of a clinical prediction rule (mWS) and D-dimer assay. The score was calculated retrospectively from the available data in the files of patients who did not have a documented clinical prediction rule. Overuse (avoidable) CTPA was defined as D-dimer negativity and PE unlikely for this study. Results: Of 661 patients’ data examined, clinical prediction rules were documented in 15 (2.3%).In total, 422 patients (63.8%) had required information on modified Wells criteria and D-dimer assays and were included for further analysis. PE on CTPA was present in 22 (5.21%) of PE unlikely (mWS ≤4) and 1 (0.24%) of D-dimer negative patients. Thirty patients (7.11%) met the avoidable CTPA (DD negative+PE unlikely) criteria, and it was significantly associated with dyspnea. The value of sensitivity of avoidable CTPA was 100%, whereas the positive predictive value was 90.3%. Conclusion Underutilization of clinical prediction rules before prescribing CTPA is common in emergency departments. Therefore, a mandatory policy should be implemented regarding the evaluation of avoidable CTPA imaging to reduce CTPA overuse.

Studies demonstrate that there is a dearth of literature published in the local context regarding competencies in nursing informatics in Saudi Arabia. This study employs mixed method design (specifically, a sequential explanatory approach) in documenting the nursing informatics competencies of nurses. A total population was used for the quantitative aspect and purposive sampling was used for the qualitative. There were 295 nurses as respondents. This study commenced with the approval of the Ethics Review Board of the University of Hail. The study was conducted from October 2016 to March 2017 at King Khalid Hospital, Kingdom of SaudiArabia. The results show that nurses are competent in computer literacy (3.38), informatics management (3.49), and informatics literacy (3.27). Nationality and area of assignment proved to be significant in relation to nurses’ competencies. Three themes and six subthemes emerged which included: (a) uncertainty, with the subthemes of diffident and reticent; (b) uncovering the meaning of technology, with the subthemes of value for patients and technology for nurses; and, (c) streamlining Continuing Nursing Education, with the subthemes of competency perspective and the missing link. Nurses acknowledged the significance of nursing informatics in promoting safety and quality care to the patient. However, there can be improvement in the impact of the results of this study by focusing on what the nurses consider as contributory factor in the full achievement of competence in nursing informatics.
Computer Literacy ; Nursing Informatics

Objective: To develop a set of quality indicators (QIs) tailored to improve the care provided to children with juvenile idiopathic arthritis (JIA) in countries across the Asia-Pacific region. Methods: An adaptation of the Research and Development Corporation (RAND)/University of California, Los Angeles (UCLA) Appropriateness Method (RAM) was used. An initial set of 32 QIs was developed after a systematic search of the literature. These were presented to members of a Delphi panel composed of pediatric rheumatologists and other relevant stakeholders from the Asia Pacific League of Associations for Rheumatology Pediatric Special Interest Group (APLAR-Pediatric SIG). After each round, the mean scores for validity and reliability, level of disagreement, and median absolute deviation from the mean were calculated. Results: The panelists were presented with 32 QIs in two rounds of voting, resulting in the formulation of a final set of 22 QIs for JIA. These QIs are categorized within six domains of care, including access to care, clinical assessment, medications and medication monitoring, screening for comorbidities, counseling, and self-efficacy and satisfaction with care. Conclusion These QIs have been developed to evaluate and improve the quality of care provided to children with JIA, aiming to enhance health outcomes and ensure that healthcare services are tailored to the unique needs of this patient population.

Aims: The coronavirus disease 2019 (COVID-19) is a contagious respiratory disease. The massive use of antibiotics during COVID-19 treatment induced the problem of antibiotic resistance among different strains of microbiome. The current study was conducted to evaluate the level of antibiotic resistance among pathogenic and microbiome bacteria isolated from the blood and upper respiratory tract of COVID-19 patients and its correlation with the case fatality rate in each patient. Methodology and results: COVID-19 patients were diagnosed using real-time reverse transcription-polymerase chain reaction (RT-PCR) technique. Swabs and blood samples were collected from each patient to isolate bacteria and every isolate identification was performed using the bioMérieux VITEK® 2 system. The case fatality rate among the study group was 50% for patients whose isolates were highly antibiotic-resistant. Blood culture was positive in 2.5% compared to nasal swab culture in 65%. Results of nasal swab culture revealed growth of Gram-positive bacteria isolated from 17.1% of patients, Gram-negative isolates were found in 9.75% and fungal isolates formed 9.75%. Most of the isolates were reflective of normal microbiomes; unfortunately, isolates were 100% resistant to penicillins, cephalosporins, azithromycin and amoxicillin-clavulanate. On the other hand, isolates were 100% sensitive to daptomycin. Conclusion, significance and impact of study Results were alarming and there is a need to take measures to prevent the increase in bacterial resistance to antibiotics and limit the excessive use of it. It is crucial to monitor the rise in fungal infections among patients and consider it a risk factor for increasing the case fatality rate.

Leishmaniasis is an infectious disease with various clinical manifestations. We studied the therapeutic effects of Elettaria cardamomum essential oil (ECEO) against Leishmania major infection. In vitro effects of ECEO against L. major were examined by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and macrophage assays. Nitric oxide (NO) production, infection inhibition in macrophages, and the apoptotic activity of ECEO in treated parasites were also measured. By calculating the 50% cytotoxic concentrations (CC50), we studied the cytotoxicity effects of ECEO on human macrophage cells (THP-1). The efficacy of ECEO for improving cutaneous leishmaniasis (CL) lesions in mice (BALB/c) was determined by evaluating the size of lesions and the number of amastigotes before and after four weeks of treatment. The effects of ECEO on liver and kidney function in the tested mice were also evaluated. ECEO dose-dependently (p<0.001) inhibited the viability and the mean number of promastigotes and amastigote forms of L. tropica. Four weeks of treatment with ECEO at the doses of 2.5 and 5 mg/kg/ day significantly (p<0.001) improved the CL lesions and reduced the number of parasites in the infected mice. ECEO significantly increased NO production, apoptosis induction, and infection rate in parasites. The CC50 value for ECEO and MA was 303.4 µg/mL and 835.2 µg/mL, respectively. In the mice receiving ECEO at the doses of 2.5 and 5 mg/kg/day for 28 days, no significant change was reported between the serum level of liver enzymes and kidney factors when compared with the control group. ECEO displayed promising efficacy in parasite reduction in vitro and in the animal model. ECEO can thus be used as an alternative medicine to treat CL.

Objective: To investigate the effect of Opuntia humifusa aqueous extract on gastric ulcers. Methods: An ethanol-induced model was used to examine the protective effect of Opuntia humifusa against gastric ulcers. The gastric ulcer index was evaluated via clinical observation and image analysis. Various inflammatory indicators were determined by RT-PCR and Western blotting assays. Results: The gastric ulcer index was reduced to 8% in the group treated with Opuntia humifusa aqueous extract compared with that in the control group. RT-PCR analysis revealed that MUC5AC expression was reduced to 39% in the control group compared with the non-treated group, whereas the omeprazole and Opuntia humifusa aqueous extract-treated groups increased the expression to 95% and 79%, respectively. Moreover, the expressions of various cytokines including TNF-α, IL-1β, and IL-6 were increased in the control group, while decreasing in Opuntia humifusa aqueous extract-treated group. Opuntia humifusa aqueous extract also suppressed the expressions of iNOS, COX-2, and its transcription factor NF-κB and increased mucus content considerably as compared to the control group. Conclusions: These results suggest that Opuntia humifusa aqueous extract is suitable as an alternative remedy for gastric ulcer treatment.