Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

Universal pre-mixing dry-film stickers capable of retrofitting existing microfluidics.

Integrating microfluidic mixers into lab-on-a-chip devices remains challenging yet important for numerous applications including dilutions, extractions, addition of reagents or drugs, and particle synthesis. High-efficiency mixers utilize large or intricate geometries that are difficult to manufacture and co-implement with lab-on-a-chip processes, leading to cumbersome two-chip solutions. We present a universal dry-film microfluidic mixing sticker that can retrofit pre-existing microfluidics and maintain high mixing performance over a range of Reynolds numbers and input mixing ratios. To attach our pre-mixing sticker module, remove the backing material and press the sticker onto an existing microfluidic/substrate. Our innovation centers around the multilayer use of laser-cut commercially available silicone-adhesive-coated polymer sheets as microfluidic layers to create geometrically complex, easy to assemble designs that can be adhered to a variety of surfaces, namely, existing microfluidic devices. Our approach enabled us to assemble the traditional yet difficult to manufacture "F-mixer" in minutes and conceptually extend this design to create a novel space-saving spiral F-mixer. Computational fluid dynamic simulations and experimental results confirmed that both designs maintained high performance for 0.1 < Re < 10 and disparate input mixing ratios of 1:10. We tested the integration of our system by using the pre-mixer to fluorescently tag proteins encapsulated in an existing microfluidic. When integrated with another microfluidic, our pre-mixing sticker successfully combined primary and secondary antibodies to fluorescently tag micropatterned proteins with high spatial uniformity, unlike a traditional pre-mixing "T-mixer" sticker. Given the ease of this technology, we anticipate numerous applications for point-of-care devices, microphysiological-systems-on-a-chip, and microfluidic-based biomedical research.

Designing schedule configuration of a hybrid appointment system for a two-stage outpatient clinic with multiple servers.

Even though several clinics serve patients in more than one stage (e.g., visit nurse and then visit doctor) and employ multiple providers in each stage, most of the previous work on appointment system design considers a simplified single-stage single-server clinic. Motivated by a real-life clinic setting, this paper aims to determine the schedule configuration of a hybrid appointment system (i.e., the number of pre-booking and same-day time slots reserved for a physician along with their positions in the schedule) for a two-stage multi-server clinic. A stochastic optimization model is developed to obtain a schedule configuration that minimizes the expected total cost - a weighted sum of excessive patient waiting time, resource idle time, resource overtime, and denied appointment requests. Owing to its computational complexity, we estimate the expected total cost using the sample average approximation method. The proposed model is verified and validated using small test instances and subject matter experts. A case study of a family medicine clinic in Pennsylvania is used to illustrate the proposed approach. The schedule generated by the proposed model results in a significantly lower expected cost compared to the approximated single-stage system's best schedule configuration and clinic's existing configuration. Further, sensitivity analysis is conducted to assess the impacts of no-show rate, service time variation, and cost ratios on the schedule configuration. Our findings demonstrate that the schedule configuration is sensitive to changes in the average no-show rate and cost ratios but is not significantly impacted by service time variation. Several managerial insights are also drawn from our analysis. Finally, we provide directions for future research that also highlights the potential to use the revenue management approach to address the problem under study.

Perceived functional impairment and spirituality/religiosity as predictors of depression in a Sri Lankan spinal cord injury patient population.

STUDY DESIGN: Cross-sectional, questionnaire-based study. OBJECTIVES: To test the hypothesis that self-perceived functional impairment and religiosity/spirituality (S/R) predict depression among traumatic spinal cord injury (SCI) patients in Sri Lanka. SETTING: Ragama Rheumatology and Rehabilitation Hospital, Ragama, Sri Lanka. METHODS: The Spinal Cord Independence Measure, Benefit Through Spirituality/Religiosity Scale, Sheehan Disability Inventory and Beck Depression Inventory-II (BDI-II) were administered to 61 consenting in-patients with traumatic SCI between June and July 2014. A linear regression model on BDI-II score was developed to examine the impact of self-perceived functional impairment and S/R activities on psychiatric outcomes in context of various sociodemographic variables. RESULTS: Psychiatric consequences of SCI were reflected in a 41% prevalence of depression. Thirty-six percent (R2=0.36) of the variance in BDI-II scores (F(5, 55)=6.07, P<0.001) was explained by the regression model. Functional impairment (ß=0.54, t(55)=4.73, P<0.001) and perceived benefit through S/R activities (ß=-0.31, t(55)=-2.55, P<0.05) emerged as the strongest predictors for depression severity. CONCLUSIONS: Perceived functional impairment in work, social and family domains predicted depressive symptomatology among SCI inpatients in Sri Lanka, while perceived benefit through S/R protected against depression. The findings emphasize the need for rehabilitative programming to support patients' S/R activities and mental wellbeing, promoting reintegration into their community roles.

Association of ethnicity with antipsychotic dosage using STRUCTURE analysis.

Several studies have examined whether ethnicity as an independent factor can influence the individual's dosage of antipsychotics. However, there has been inconsistency in the results of these studies, particularly between white and non-white populations. This retrospective study tests the hypothesis of different dosing of antipsychotics in white Europeans vs. non-white Europeans considering both the self-reported ethnicity and the geographical ancestry calculated using 196 DNA markers.We collected self-reported ethnicity and DNA samples from 209 schizophrenia patients. We tested the association between self-reported and genetically-determined ethnicity with the chlorpromazine equivalent dose of each antipsychotic prescribed at the time of the assessment.We did not find any significant difference between self-reported white European -ethnicity and chlorpromazine equivalent doses (p=0.972). Furthermore, when we considered the geographical ancestry determined by the 196 SNPs, we could not find any correlation between the European ancestry and chlorpromazine equivalent dose.Our preliminary analysis shows that there is no evidence that different ethnic groups receive different dose of antipsychotics.

A comparative study on effective cell disruption methods for lipid extraction from microalgae.

AIMS: To compare effective cell disruption methods for lipid extraction from fresh water microalgae. METHODS AND RESULTS: Chlorella sp., Nostoc sp. and Tolypothrix sp. were isolated from fresh water ponds in and around Gandhigram, Dindigul District, Tamilnadu, India, and used for lipid extraction. Different methods, including autoclaving, bead beating, microwave, sonication and a 10% NaCl solution treatments, were tested to identify the most effective cell disruption method. The total lipids from three microalgal species were extracted using a mixture of chloroform and methanol. Fatty acid composition was detected by gas chromatography (GC). Nostoc sp. and Tolypothrix sp. showed higher oleic acid content of 13.27 mg g(-1) dw and 17.75 mg g(-1) dw, respectively, whereas Chlorella sp. had high linoleic acid content of 17.61 mg g(-1) dw when the cells were disrupted using the sonication method. CONCLUSIONS: Finally, the sonication method was found to be the most applicable and efficient method of lipid extraction from microalgae. The highest lipid content was extracted from Chlorella sp. SIGNIFICANCE AND IMPACT OF THE STUDY: In biodiesel production from microalgae, lipid extraction is a crucial step and important as cell disruption comes in this step. Therefore, the appropriate cell disruption method and device is a key to increase the lipid extraction efficiency.

Intravenous anti-obsessive agents: a review.

Oral antidepressants are currently the first-line pharmacotherapy for obsessive-compulsive disorder (OCD), but response rates can often be low and with delayed onset of therapeutic action. Some reports have suggested that intravenous (i.v.) anti-obsessive agents may have faster onset of action and greater efficacy. A Medline search was conducted for all reports pertaining to the use of i.v. antidepressants for OCD. Search terms included: 'intravenous', 'clomipramine', 'selective serotonin reuptake inhibitor', 'tricyclic', 'citalopram', 'sertraline', 'paroxetine', 'fluvoxamine', 'SSRIs' and 'intravenous antidepressants'. Relevant articles mainly investigated clomipramine (CMI) with one open trial examining citalopram. Intravenous agents appear to be well-tolerated, particularly in those who have failed oral agents, and may act more rapidly to produce initial clinical response, although this advantage is often lost over time. Preliminary evidence suggests subgroups of patients with severe treatment-refractory OCD may benefit from i.v. anti-obsessive agents, CMI and citalopram. Larger, controlled trials are needed for more definitive conclusions.

Turner syndrome diagnosed in northeastern Malaysia.

INTRODUCTION: Turner syndrome affects about one in 2,000 live-born females, and the wide range of somatic features indicates that a number of different X-located genes are responsible for the complete phenotype. This retrospective study highlights the Turner syndrome cases confirmed through cytogenetic analysis at the Human Genome Centre of Universiti Sains Malaysia, from 2001 to 2006. METHODS: Lymphocyte cultures were set up using peripheral blood samples, chromosomes were prepared, G-banded, karyotyped and analysed in accordance to guidelines from the International System for Human Cytogenetic Nomenclature. RESULTS: The various karyotype patterns observed were 45,X; 46,X,i, (Xq); 45,X/45,X,+mar; 45,X/46,X,i,(Xq) and 45,X/46,XY. The mean age of our patients with Turner syndrome was 21 years, and the most common clinical features encountered in all these patients were short stature (100 percent), primary amenorrhoea (85.7 percent), absence of secondary sexual characteristics (57.1 percent), scanty pubic and axillary hair (50 percent), webbed neck (42.9 percent), wide carrying angle (42.9 percent), rudimentary uterus with bilateral streak ovaries (42.9 percent), underdeveloped breasts (35.7 percent) and wide-spaced nipples (21.4 percent). CONCLUSION: Even though there is no causal therapy for Turner syndrome, management and treatment are possible for malformations and conditions associated with it. In addition, counselling of the parents and of the patients themselves are necessary. Hence, establishing an early diagnosis, educating and increasing awareness among doctors, and if possible, a prenatal diagnosis, will help in early intervention, genetic counselling and in improving the quality of life in these patients.

Symptom-onset dosing with citalopram in the treatment of premenstrual dysphoric disorder (PMDD): a case series.

The efficacy and tolerability of symptom-onset dosing with citalopram in the treatment of premenstrual dysphoric disorder (PMDD) was evaluated in an open trial. Eight outpatients, aged 18-45 years and diagnosed with PMDD, were treated with 10-20 mg of citalopram from the start of premenstrual symptoms until the onset of menses. Primary efficacy variables were the premenstrual tension scale (PMTS-O) and the clinical global impression of improvement (CGI). Treatment was associated with significant improvement in PMDD symptoms (p < 0.001).

Celastrus paniculatus seed oil and organic extracts attenuate hydrogen peroxide- and glutamate-induced injury in embryonic rat forebrain neuronal cells.

Seed oil of Celastrus paniculatus Willd. (CP) has been reported to improve memory and the methanolic extract (ME) of CP was shown to exhibit free-radical-scavenging properties and anti-oxidant effects in human non-immortalized fibroblasts. In the present study, we have investigated the free-radical-scavenging capacity of CP seed oil (CPO) and two extracts, an ethanolic extract (EE) and a ME. CPO and EE showed dose-dependent, free-radical-scavenging capacity, but to a lesser degree than observed for ME. Oxidative stress involves the generation of free radicals and free radical scavenging is one of the mechanisms of neuroprotection. We therefore investigated the effects of CPO, ME, and EE for protection against hydrogen peroxide (H(2)O(2))- and glutamate-induced neurotoxicity in embryonic rat forebrain neuronal cells (FBNC). Pre-treatment of neuronal cells with CPO dose-dependently attenuated H(2)O(2)-induced neuronal death. Pre-treatment with ME and EE partially attenuated H(2)O(2)-induced toxicity, but these extracts were less effective than CPO for neuronal survival. In H(2)O(2)-treated cells, cellular superoxide dismutase (SOD) activity was unaffected, but catalase activity was decreased and levels of malondialdehyde (MDA) were increased. Pre-treatment with CPO, ME, or EE increased catalase activity and decreased MDA levels significantly. Also, CPO pre-treatment attenuated glutamate-induced neuronal death dose-dependently. The activity of cellular acetylcholinesterase (AChE) was not affected by CPO, ME, or EE, suggesting that the neuroprotection offered by CPO was independent of changes in AChE activity. Taken together, the data suggest that CPO, ME, and EE protected neuronal cells against H(2)O(2)-induced toxicity in part by virtue of their antioxidant properties, and their ability to induce antioxidant enzymes. However, CPO, which exhibited the least antioxidant properties, was the most effective in preventing neuronal cells against H(2)O(2)- and glutamate-induced toxicities. Thus, in addition to free-radical scavenging attributes, the mechanism of CP seed component (CP-C) neuroprotection must be elucidated.

Evaluation of the LightCycler Staphylococcus M GRADE kits on positive blood cultures that contained gram-positive cocci in clusters.

We evaluated the Roche LightCycler Staphylococcus M(GRADE) kits to differentiate between Staphylococcus aureus and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing S. aureus), the assay was 100% sensitive and 98.44% specific for S. aureus and 100% sensitive and specific for coagulase-negative staphylococci.

Involvement of nitric oxide in neurodegeneration: a study on the experimental models of Parkinson's disease.

The present study was undertaken to explore involvement of nitric oxide (NO) in the experimental models of Parkinson's disease. Neurodegeneration was induced by unilateral injections of 6-hydroxydopamine (6-OHDA) or lipopolysaccharide (LPS) in the right striatum. Lesions were functionally evaluated by amphetamine-induced asymmetrical behaviour and by decrease in the tyrosine hydroxylase (TH) immunostaining. An induction in the expression of iNOS and augmentation in nitrite content was observed in both the models. The extent of increase in iNOS expression was, however, different but the elevation in the nitrite content was comparable in both the models. The increase in iNOS expression inversely correlated with the tyrosine hydroxylase (TH) immunolabeling. Animals pretreated with a NOS inhibitor, N(G)-nitro-L-arginine methyl ester (L-NAME), exhibited complete protection against amphetamine induced rotations in both the models. Thus, augmented NO availability subsequent to iNOS induction seems to play an important role in the initial phase of neurodegeneration.

Sertraline in generalized anxiety disorder: efficacy in treating the psychic and somatic anxiety factors.

OBJECTIVE: The objective was to study the efficacy of sertraline on symptoms of psychic and somatic anxiety in patients suffering from moderate-to-severe generalized anxiety disorder (GAD). METHOD: Out-patients with DSM-IV GAD were randomized to 12 weeks of double-blind treatment with placebo. The psychic and somatic anxiety factors of the Hamilton Anxiety Rating Scale (HAM-A) and the Quality of Life, Enjoyment, and Satisfaction Questionnaire were analyzed. RESULTS: Treatment with sertraline resulted in significantly greater last observation carried forward (LOCF)-endpoint improvement than placebo on both the HAM-A psychic and somatic anxiety factors. At LOCF-endpoint, all items on the HAM-A psychic factor were more improved on sertraline than placebo, as were three of seven items on the somatic factor. Reduction of secondary depressive symptoms was more correlated with endpoint improvement in quality of life than either psychic- or somatic anxiety. CONCLUSION: Sertraline treatment demonstrated efficacy for both the psychic and somatic anxiety symptoms of GAD.

The emergence of methicillin-resistant Staphylococcus aureus in the community.

Infections with methicillin-resistant Staphylococcus aureus (MRSA), long endemic in hospitals and nursing homes, are now being reported in the community as well. While we await further epidemiological and microbiological study of this emerging pathogen, current clinical practice requires a reconsideration of the empiric use of beta-lactam agents for the seriously ill patient with a gram-positive infection.

What's new in antibiotics?

Antibiotics are important agents in dermatologic practice. New drugs have expanded the therapeutic approach to uncomplicated skin infections and complicated infections involving deeper soft tissue or infections that require surgical intervention. This article reviews new antibiotics of dermatologic importance, including daptomycin (cyclic lipopeptide), linezolid (oxazolidinone), quinupristin-dalfopristin (streptogramins), moxifloxacin and gatifloxacin (fluoroquinolones), and dalbavancin and oritavancin, which are presently under investigation.

Emphysematous urinoma in a renal transplant patient.

Urinary infection is a common complication after kidney transplantation. In some instances, especially with Escherichia coli infections, there is formation and collection of gas in the parenchyma and collecting system of the kidney, giving rise to the condition of emphysematous pyelonephritis. Such a process could occur in collections of urine (urinoma) secondary to ureteric leak in the transplant kidney. This process has not been described so far. In this report, we describe the first case of an infected urinoma with an interesting radiologic finding, a so-called emphysematous urinoma.

Posttraumatic stress symptoms and salivary cortisol levels.

OBJECTIVE: This study assessed the relationship between posttraumatic stress symptoms and salivary cortisol levels after a severe ice storm. METHOD: Posttraumatic stress symptoms (Impact of Event Scale scores) and salivary cortisol levels were determined in 115 victims of an ice storm and in 27 healthy comparison subjects 1 month and approximately 1 year after the ice storm. RESULTS: One month after the storm, Impact of Event Scale scores for the victims (mean=20.31, SD=15.23) exceeded those of the comparison subjects (mean=5.30, SD=9.78) but were reduced approximately 1 year later (mean=14.01, SD=13.68). A quadratic relation was found to exist between Impact of Event Scale scores and cortisol levels. CONCLUSIONS: One month after the storm, cortisol levels were found to be elevated among the victims but were diminished among those with the highest Impact of Event Scale scores. This relationship was found not to exist approximately 1 year later.

Clinical guidelines for the treatment of depressive disorders. IV. Medications and other biological treatments.

BACKGROUND: The Canadian Psychiatric Association and the Canadian Network for Mood and Anxiety Treatments partnered to produce clinical guidelines for psychiatrists for the treatment of depressive disorders. METHODS: A standard guidelines development process was followed. Relevant literature was identified using a computerized Medline search supplemented by review of bibliographies. Operational criteria were used to rate the quality of scientific evidence, and the line of treatment recommendations included consensus clinical opinion. This section, "Medications and Other Biological Treatments," is 1 of 7 articles that were drafted and reviewed by clinicians. Revised drafts underwent national and international expert peer review. RESULTS: Evidence-based recommendations are presented for 1) choosing an antidepressant, based on efficacy, tolerability, and safety; 2) the optimal use of antidepressants, including augmentation, combination, and switching strategies; 3) maintenance treatment; and 4) electroconvulsive therapy (ECT), light therapy, and additional somatic treatments. Evidence from metaanalyses is presented first, followed by conclusions from randomized controlled trials (RCTs) and, if appropriate, open-label data. CONCLUSIONS: There is significant evidence to support the role of selective serotonin reuptake inhibitors (SSRIs), novel agents, and classic agents in the treatment of major depressive disorder (MDD). There is also evidence to support the use of somatic treatments, including ECT and light therapy, for some patients with MDD. There is limited evidence for the use of specific medications to treat subtypes of MDD. There is emerging evidence to support augmentation and combination strategies for patients previously nonresponsive to medication.