CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

BACKGROUND

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

RESULTS

Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.

CONCLUSIONS

Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Participatory asset mapping and photovoice interviews to scope cultural and community resources to reduce alcohol harm in Chitwan, Nepal

AIMS

To scope the breadth of existing cultural and community assets and how alcohol drinkers and community health workers perceived them in relation to reducing alcohol-related harm.

METHODS

The study was conducted in Chitwan, south-central Nepal, which has considerable alcohol problems. Participatory asset mapping was conducted using field notes, photography, and through engaging with communities to explore how community assets affect alcohol consumption. Semi-structured photovoice interviews were conducted with harmful/hazardous drinkers (AUDIT score 8 to 19) and community health workers. Purposive and snowball sampling were used to recruit participants. During interviews, participants used their photographs to reflect on how community assets influenced alcohol use. Thematic framework analysis was used to analyse the data.

RESULTS

We recruited 12 harmful/hazardous drinkers (3 females) and 6 health workers (2 females). The mean AUDIT score of the former was 12.17 (SD ±2.86). Thematic analysis of the photovoice interviews produced three themes: 'influences and impact of families and communities'; 'culture and spirituality'; and 'nature and the environment'. The community mapping produced five assets that promoted alcohol consumption: (1) availability; (2) advertising; (3) negative attitudes towards users; (4) festivals/gatherings; and (5) illiteracy/poverty. Six assets that discouraged consumption were: (1) legislation restricting use; (2) community organisations; (3) cultural/spiritual sites; (4) healthcare facilities; (5) family and communities; and (6) women's community groups. Those from certain ethnic groups consumed more alcohol, experienced more family discord, or felt stigmatised due to their drinking. Assets 'festivals/gatherings' and 'negative attitudes toward users' and the theme 'family and communities' concerned with relationships and community activities were perceived to both promote and reduce alcohol use.

CONCLUSIONS

This study provides new insight into a variety of cultural and community assets that promote and reduce alcohol use. The study identifies new possibilities to build on visual participatory and arts-based methods that have potential to be effectively implemented at scale.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

One Sentence Summary

Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

Microplastics in environment: global concern, challenges, and controlling measures

Plastic pollution in various forms has emerged as the most severe environmental threat. Small plastic chunks, such as microplastics and nanoplastics derived from primary and secondary sources, are a major concern worldwide due to their adverse effects on the environment and public health. Several years have been spent developing robust spectroscopic techniques that should be considered top-notch; however, researchers are still trying to find efficient and straightforward methods for the analysis of microplastics but have yet to develop a viable solution. Because of the small size of these degraded plastics, they have been found in various species, from human brains to blood and digestive systems. Several pollution-controlling methods have been tested in recent years, and these methods are prominent and need to be developed. Bacterial degradation, sunlight-driven photocatalyst, fuels, and biodegradable plastics could be game-changers in future research on plastic pollution control. However, recent fledgling steps in controlling methods appear insufficient due to widespread contamination. As a result, proper regulation of environmental microplastics is a significant challenge, and the most equitable way to manage plastic pollution. Therefore, this paper discusses the current state of microplastics, some novel and well-known identification techniques, strategies for overcoming microplastic effects, and needed solutions to mitigate this planetary pollution. This review article, we believe, will fill a void in the field of plastic identification and pollution mitigation research.

Surface acoustic wave assisted depinning of magnetic domain walls

We investigate the effects of high frequency strain on the depinning of magnetic domain walls in perpendicular anisotropy materials. Micron wide stripes of [Co(0.3 nm)/Pt(0.6 nm)]₅are patterned between a pair of identical inter-digital transducers that generate high frequency (114.8 MHz) standing surface acoustic waves. We use magneto-optical Kerr effect microscopy to characterize the thermally-assisted depinning of domain walls at defect sites within the strips. Our results show that the excitation of the domain walls with surface acoustic waves results in an increase in their depinning probabilities by approximately a factor of 10. Our data are consistent with a model in which the magnetoelastic anisotropies induced by the acoustic waves modulate the energy barriers that pin the domain walls. These results suggest an alternative route to domain wall depinning in thin films and nanostructures and are relevant to the development of racetrack memories, where domain wall pinning can result in reduced velocities and non-deterministic motion.

The Band-Gap Studies of Short-Period CdO/MgO Superlattices

Trends in the behavior of band gaps in short-period superlattices (SLs) composed of CdO and MgO layers were analyzed experimentally and theoretically for several thicknesses of CdO sublayers. The optical properties of the SLs were investigated by means of transmittance measurements at room temperature in the wavelength range 200-700 nm. The direct band gap of {CdO/MgO} SLs were tuned from 2.6 to 6 eV by varying the thickness of CdO from 1 to 12 monolayers while maintaining the same MgO layer thickness of 4 monolayers. Obtained values of direct and indirect band gaps are higher than those theoretically calculated by an ab initio method, but follow the same trend. X-ray measurements confirmed the presence of a rock salt structure in the SLs. Two oriented structures (111 and 100) grown on c- and r-oriented sapphire substrates were obtained. The measured lattice parameters increase with CdO layer thickness, and the experimental data are in agreement with the calculated results. This new kind of SL structure may be suitable for use in visible, UV and deep UV optoelectronics, especially because the energy gap can be precisely controlled over a wide range by modulating the sublayer thickness in the superlattices.

Neuroanatomy and behavior in mice with a haploinsufficiency of AT-rich interactive domain 1B (ARID1B) throughout development

BACKGROUND

One of the causal mechanisms underlying neurodevelopmental disorders (NDDs) is chromatin modification and the genes that regulate chromatin. AT-rich interactive domain 1B (ARID1B), a chromatin modifier, has been linked to autism spectrum disorder and to affect rare and inherited genetic variation in a broad set of NDDs.

METHODS

A novel preclinical mouse model of Arid1b deficiency was created and validated to characterize and define neuroanatomical, behavioral and transcriptional phenotypes. Neuroanatomy was assessed ex vivo in adult animals and in vivo longitudinally from birth to adulthood. Behavioral testing was also performed throughout development and tested all aspects of motor, learning, sociability, repetitive behaviors, seizure susceptibility, and general milestones delays.

RESULTS

We validated decreased Arid1b mRNA and protein in Arid1b+/- mice, with signatures of increased axonal and synaptic gene expression, decreased transcriptional regulator and RNA processing expression in adult Arid1b+/- cerebellum. During neonatal development, Arid1b+/- mice exhibited robust impairments in ultrasonic vocalizations (USVs) and metrics of developmental growth. In addition, a striking sex effect was observed neuroanatomically throughout development. Behaviorally, as adults, Arid1b+/- mice showed low motor skills in open field exploration and normal three-chambered approach. Arid1b+/- mice had learning and memory deficits in novel object recognition but not in visual discrimination and reversal touchscreen tasks. Social interactions in the male-female social dyad with USVs revealed social deficits on some but not all parameters. No repetitive behaviors were observed. Brains of adult Arid1b+/- mice had a smaller cerebellum and a larger hippocampus and corpus callosum. The corpus callosum increase seen here contrasts previous reports which highlight losses in corpus callosum volume in mice and humans.

LIMITATIONS

The behavior and neuroimaging analyses were done on separate cohorts of mice, which did not allow a direct correlation between the imaging and behavioral findings, and the transcriptomic analysis was exploratory, with no validation of altered expression beyond Arid1b.

CONCLUSIONS

This study represents a full validation and investigation of a novel model of Arid1b+/- haploinsufficiency throughout development and highlights the importance of examining both sexes throughout development in NDDs.

Plant growth-promoting endophytic bacteria augment growth and salinity tolerance in rice plants

Salt stress negatively affects growth and development of plants. However, it is hypothesized that plant growth-promoting endophytic bacteria can greatly alleviate the adverse effects of salinity and can promote growth and development of plants. In the present research, we aimed to isolate endophytic bacteria from halotolerant plants and evaluate their capacity for promoting crop plant growth. The bacterial endophytes were isolated from selected plants inhabiting sand dunes at Pohang beach, screened for plant growth-promoting traits and applied to rice seedlings under salt stress (NaCl; 150 mm). Out of 59 endophytic bacterial isolates, only six isolates, i.e. Curtobacterium oceanosedimentum SAK1, Curtobacterium luteum SAK2, Enterobacter ludwigii SAK5, Bacillus cereus SA1, Micrococcus yunnanensis SA2, Enterobacter tabaci SA3, resulted in a significant increase in the growth of Waito-C rice. The cultural filtrates of bacterial endophytes were tested for phytohormones, including indole-3-acetic acid, gibberellins and organic acids. Inoculation of the selected strains considerably reduced the amount of endogenous ABA in rice plants under NaCl stress, however, they increased GSH and sugar content. Similarly, these strains augmented the expression of flavin monooxygenase (OsYUCCA1) and auxin efflux carrier (OsPIN1) genes under salt stress. In conclusion, the pragmatic application of the above selected bacterial strains alleviated the adverse effects of NaCl stress and enhanced rice growth attributes by producing various phytohormones.

Effect of Yarcha Gumba (O sinensis) on Male Reproductive System in Rat

The present study was undertaken to assess the aphrodisiac effect of O sinensis. It was a pre-clinical experimental case-control study performed in the Department of Pharmacology, RG Kar Medical College, Kolkata, India; from February 2019 to March 2019 using Wister rat model. One group of rats was given the test drug suspension (10mg/kg body weight) and the control group animals received the same volume of vehicle devoid of drug orally for 10 days. Sexual behaviour of individual rats was studied on 9th day of treatment with oestrogenized female Wister rats. On 10th day of treatment the animals were sacrificed by decapitation. After collection of blood sera from each animal; serum LH, FSH, testosterone and nitric oxide were assessed. Histological assessment of testes was done. Improved sexual behaviour, hypertrophy of Leydig cells, significant increase in serum LH (1.248 vs. 1.448mIU/ml), FSH (0.324 vs. 0.413mIU/ml) testosterone (3.120 vs. 4.498ng/ml) and nitric oxide (0.01757 vs. 0.02690nM/ml) were noted. Elevated NO titre in animals treated with O sinensis extract might be the cause of good erection capacity and increased libido in them. Nevertheless, result of the present study points that the active principle of O sinensis also acts on LHRH receptors present in pituitary gonadotrophs evidenced by significant increase in serum LH and FSH and indicating great aphrodisiac property.

Antibacterial activities of the extracts, fractions and isolated compounds from Canarium patentinervium Miq. against bacterial clinical isolates

Background

Canarium patentinervium leaves are used by the local indigenous people of Malaysia for wound healing. The current study is undertaken to screen the comprehensive antibacterial activity of the leaves and barks extracts, fractions and isolated compounds from this plant. Bioassay guided fractionation was also undertaken to deeply evaluate the antibacterial activity of the water fraction of the leaves extract. This is to provide preliminary scientific evidence to the ethnopharmacology usage of this plant by investigating antibacterial properties of the plant and its isolated constituents.

Methods

Bio-assay guided fractionation and subsequent isolation of compounds using open column chromatography. The antibacterial activity against gram positive and gram negative ATCC strain and resistant clinical strains were evaluated using microtiter broth dilution method to determine minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and time-kill assay. The chemical structure of the isolated compounds from the water fraction of the ethanol extract of leaves was elucidated using Nuclear Magnetic Resonance (NMR).

Results

The ethanol extract of the leaves and barks showed antimicrobial activity against all four ATCC and eight clinical isolates. The ethanol extract of the leaves and the corresponding water fraction had good activity against MRSA S. aureus. (MIC: 250 μg/ml) and had bactericidal effect on eight of the clinical strains (MSSA,MRSA, oxacillin-resistant CONS, oxacillin-sensitive CONS, Enterococcus faecalis, Klebsiela species, Kleb pneumoniae ESBL and Candida parapsilosis). Further phytochemical investigation of the water fraction of the crude ethanol extract of leaves afforded compound 7 (hyperin) and compound 8 (cynaroside) that had bactericidal activity against tested bacterial species (MIC 50 μg/ml and 100 μg/ml). The two compounds were isolated from this genus for the first time.

Conclusions

These results may provide a rational support for the traditional use of Canarium patentinervium Miq. in infections and wound healing, since the antimicrobial compounds isolated were also present in the leaves extract.

Translational outcomes in a full gene deletion of ubiquitin protein ligase E3A rat model of Angelman syndrome

Angelman syndrome (AS) is a rare neurodevelopmental disorder characterized by developmental delay, impaired communication, motor deficits and ataxia, intellectual disabilities, microcephaly, and seizures. The genetic cause of AS is the loss of expression of UBE3A (ubiquitin protein ligase E6-AP) in the brain, typically due to a deletion of the maternal 15q11-q13 region. Previous studies have been performed using a mouse model with a deletion of a single exon of Ube3a. Since three splice variants of Ube3a exist, this has led to a lack of consistent reports and the theory that perhaps not all mouse studies were assessing the effects of an absence of all functional UBE3A. Herein, we report the generation and functional characterization of a novel model of Angelman syndrome by deleting the entire Ube3a gene in the rat. We validated that this resulted in the first comprehensive gene deletion rodent model. Ultrasonic vocalizations from newborn Ube3am-/p+ were reduced in the maternal inherited deletion group with no observable change in the Ube3am+/p- paternal transmission cohort. We also discovered Ube3am-/p+ exhibited delayed reflex development, motor deficits in rearing and fine motor skills, aberrant social communication, and impaired touchscreen learning and memory in young adults. These behavioral deficits were large in effect size and easily apparent in the larger rodent species. Low social communication was detected using a playback task that is unique to rats. Structural imaging illustrated decreased brain volume in Ube3am-/p+ and a variety of intriguing neuroanatomical phenotypes while Ube3am+/p- did not exhibit altered neuroanatomy. Our report identifies, for the first time, unique AS relevant functional phenotypes and anatomical markers as preclinical outcomes to test various strategies for gene and molecular therapies in AS.

Diagnostic diversities of Clear Fluid encountered during Fine needle aspiration cytology with an analysis of various variables

Background: Incidental finding of clear fluid during fine needle aspiration (FNA) is not rare in day to day practice of cytology. Though clear in appearance, cells obtained from it may yield a diverse diagnosis ranging from an inconclusive opinion to a malignant lesion. So, clear fluid is not non-significant always; lack of proper processing and examination may prove fatal to a patient. Aim: To evaluate the diverse diagnosis of clear fluid. Materials and methods: During a period of three years, hundred and seven cases which yielded clear fluid during FNAC from different parts of the body were studied. Direct and indirect smears (wherever applicable) was prepared, stained and examined microscopically. Results: Of these 107 cases of clear fluid, Male: Female ratio was 1: 1.6. Maximum cases - 55 (51.40%) was found in the age group 21 to 40 years. Trunk held the most number of lesions - 54 cases (50.46%). FNA results were interpreted as inconclusive in 19 cases (17.76%), benign in 84 cases (78.50%), suspicious in 01 case (0.93%) and malignant in 03 cases (2.80%). Epidermal cyst was the most common benign lesion - 16 cases (14.95%). Malignant lesions found were papillary carcinoma of thyroid, carcinoma of breast and metastatic squamous cell carcinoma – one case each. Conclusion: Our study emphasizes on the importance of proper examination of clear fluid as it may prove helpful in an undiagnosed case of malignancy and it may also improvise the learning of young pathologists. Bangladesh Journal of Medical Science Vol.18(4) 2019 p.753-755

Effectiveness of daily rinsing of alfalfa sprouts with aqueous chlorine dioxide and ozonated water on the growth of Listeria monocytogenes during sprouting

Alfalfa sprouts have been implicated in multiple foodborne disease outbreaks. This study evaluated the growth of Listeria monocytogenes during sprouting of alfalfa seeds and the effectiveness of daily chlorine dioxide & ozone rinsing in controlling the growth. Alfalfa seeds inoculated with L. monocytogenes were sprouted for 5 days (25°C) with a daily aqueous ClO₂ (3 ppm, 10 min) or ozone water (2 ppm, 5 min) rinse. Neither treatment significantly reduced the growth of L. monocytogenes on sprouting alfalfa seeds. The initial level of L. monocytogenes was 3·44 ± 0·27, which increased to c. 7·0 log CFU per g following 3 days of sprouting. There was no significant difference in the bacterial population between the treatment schemes. Bacterial distribution in roots (7·63 ± 0·511 log CFU per g), stems (7·51 ± 0·511 log CFU per g) and leaves (7·41 ± 0·511 log CFU per g) were similar after 5 days. Spent sanitizers had significantly lower levels of bacterial populations compared to the spent distilled water control. The results indicated that sprouting process provides a favourable condition for the growth of L. monocytogenes and the sanitizer treatment alone may not be able to reduce food safety risks. SIGNIFICANCE AND IMPACT OF THE STUDY: Sprouts are high-risk foods. Consumption of raw sprouts is frequently associated with foodborne disease outbreaks. Optimum sprouting procedure involves soaking seeds in water followed by daily water rinsing to maintain a moist environment that is also favourable for the growth of pathogenic micro-organisms. The present study emphasized the potential food safety risks during sprouting and the effect of applying daily sanitizer rinsing in the place of water rinsing to reduce those risks. The finding of this study may be useful in the development of pre-harvest and post-harvest risk management strategies.

Neutrophil-lymphocyte Ratio and C-reactive Protein Level in Patients with Major Depressive Disorder Before and After Pharmacotherapy

BACKGROUND

Neutrophil-lymphocyte ratio (NLR) and C-reactive protein (CRP) level are useful biomarkers of inflammation. This study aimed to assess NLR and CRP level in patients with major depressive disorder before and after pharmacotherapy to determine whether NLR or CRP could be used as biomarkers of severity of major depression and whether there was any sex difference.

METHODOLOGY

Patients with major depression who received no pharmacotherapy 1 month prior to the study were included. Their haemoglobin, total white blood cell count, neutrophil and lymphocyte counts, NLR, and CRP levels were evaluated at baseline and 12 weeks post pharmacotherapy, as were the Montgomery Asberg Rating Scale for Depression, the Scale for Impact of Suicidality Management and Assessment and Planning of Care (SIS-MAP), and the Clinical Global Impression Scale - Severity.

RESULTS

24 male and 26 female patients were included. At 12 weeks after pharmacotherapy, males had a higher haemoglobin level (p = 0.025), higher total white blood cell count (p = 0.018), and lower percentage of neutrophils (p = 0.019) than females. There was no sex difference in NLR or CRP. From baseline to 12 weeks, males had no significant change in any blood parameter, but females had a significantly greater increase in the percentage of neutrophils (p = 0.0001) and decrease in the percentage of lymphocytes (p = 0.012), resulting in a significantly increased NLR (p = 0.001). Both males and females had significant improvement on all 3 scales (p < 0.001). At 12 weeks, in males, the increase in NLR positively correlated with CRP as well as the Montgomery-Asberg Depression Rating Scale and the SIS-MAP, but not the Clinical Global Impression-Severity Scale. In females, the increase in NLR did not correlate with CRP or any of the scales.

CONCLUSION

In female patients, the NLR increased in response to antidepressant therapy while CRP remained unchanged. This indicated that inflammation has a role in the pathogenesis of major depression.

Invasion of alien plant species and their impact on different ecosystems of Panchase Area, Nepal

The aggressiveness of invasive alien plant species has been amidst the changing climate, which has necessitated further research in this area. The impact of invasive alien plant species in the Panchase area of Nepal was assessed through the forest resource assessment and other methodologies such as, household survey, group discussion, direct field observation, participatory cluster mapping, quadrat sampling, laboratory analysis, and GIS mapping. A total of nine major invasive species, in which Ageratum houstonianum and Ageratina adenophora were found spread throughout the ecosystem. The invasion was fueled by anthropogenic disturbances such as leaving the agricultural lands, fallow and degradation of habitat. As a consequence, native species such as Artemisia indica and Urtica dioica were outcompeted mostly in the fringes of fallow lands, agricultural lands and in the disturbed sites. The intrusion was, however, less in the forest area, implying that community-managed dense canopy forests are less susceptible to invasion and routine management can offset the negative effects of invasion. Even though many negative consequences of the invasion were observed in the study sites, the possibility of the economically exploiting the biomass of invasive alien plant species for generating income locally was noticed.Banko Janakari, Vol. 27, No. 1, page: 31-42

Lessons from the CAGI-4 Hopkins clinical panel challenge

The CAGI-4 Hopkins clinical panel challenge was an attempt to assess state-of-the-art methods for clinical phenotype prediction from DNA sequence. Participants were provided with exonic sequences of 83 genes for 106 patients from the Johns Hopkins DNA Diagnostic Laboratory. Five groups participated in the challenge, predicting both the probability that each patient had each of the 14 possible classes of disease, as well as one or more causal variants. In cases where the Hopkins laboratory reported a variant, at least one predictor correctly identified the disease class in 36 of the 43 patients (84%). Even in cases where the Hopkins laboratory did not find a variant, at least one predictor correctly identified the class in 39 of the 63 patients (62%). Each prediction group correctly diagnosed at least one patient that was not successfully diagnosed by any other group. We discuss the causal variant predictions by different groups and their implications for further development of methods to assess variants of unknown significance. Our results suggest that clinically relevant variants may be missed when physicians order small panels targeted on a specific phenotype. We also quantify the false-positive rate of DNA-guided analysis in the absence of prior phenotypic indication.

Oleanolic acid from antifilarial triterpene saponins of Dipterocarpus zeylanicus induces oxidative stress and apoptosis in filarial parasite Setaria digitata in vitro

Absence of a drug that kills adult filarial parasites remains the major challenge in eliminating human lymphatic filariasis (LF); the second leading cause of long-term and permanent disability. Thus, the discovery of novel antifilarial natural products with potent adulticidal activity is an urgent need. In the present study, methanol extracts of leaves, bark and winged seeds of Dipterocarpus zeylanicus (Dipterocarpaceae) were investigated for macro and microfilaricidal activity. Two antifilarial triterpene saponins were isolated from winged seed extracts by bioactivity guided chromatographic separation and identified using Nuclear Magnetic Resonance and mass spectroscopic analysis as oleanolic acid 3-O-β-D- glucopyranoside (1) (IC50 = 20.54 μM for adult worms, 19.71 μM for microfilariae ) and oleanolic acid 3-O-α-L-arabinopyranoside (2) (IC50 = 29.02 μM for adult worms, 25.99 μM for microfilariae). Acid hydrolysis of both compounds yielded oleanolic acid (3) which was non or least toxic to human peripheral blood mono nuclear cells (Selectivity index = >10) while retaining similar macrofilaricidal (IC50 = 38.4 μM) and microfilaricidal (IC50 = 35.6 μM) activities. In adult female worms treated with 50 and 100 μM doses of oleanolic acid, condensation of nuclear DNA, apoptotic body formation and tissue damage was observed by using Hoechst 33342 staining, TUNEL assay and Hematoxylin and Eosin staining respectively. A dose dependent increase in caspase 3/CED3 activity and decrease in total protein content were also observed in these parasites. A dose dependant DNA fragmentation was observed in adult parasites and microfilariae. Decreased levels of reduced glutathione (GSH) and elevated levels of glutathione S transferase (GST), superoxide dismutase (SOD) and reactive oxygen species (ROS) were also observed in parasites treated with oleanolic acid indicating an oxidative stress mediated apoptotic event. Compound 3/oleanolic acid was thus identified as a potent and safe antifilarial compound in vitro.

The Epidemiology of Chronic Venous Diseases

Objective:

To review the prevalence of and risk factors for varicose veins, chronic venous insufficiency (CVI) and venous leg ulcers.

Data sources:

MEDLINE was searched for the terms prevalence and varicose veins, chronic venous insufficiency, or venous leg ulcers.

Study selection:

The extant world literature (1966–1999) with a minimum of an available English abstract was collected. Ninety-nine studies were reviewed.

Data extraction:

Data were extracted on prevalence of diseases of the veins in the lower limb, age and gender of the subject populations, and other risk factors for those diseases examined by the original researchers.

Data synthesis:

The two most prominent risk factors for venous disease are increasing age and female gender. Additional risk factors for venous disease with at least some documentation in the literature include dietary patterns, obesity, physical activity, standing occupations, constrictive clothing, connective tissue laxity, and hormonal differences, including pregnancy. Family history is also a prominent risk factor, suggesting a genetic component.

Conclusions:

Varicose veins are found more commonly in women, and with increased age. The increase with age is linear, suggesting a constant incidence and cumulative prevalence. CVI is also more common in women and increases with age, but data are limited. Venous leg ulcers are much less common than varicose veins or CVI and show less of a female preponderance, but increase exponentially with age, suggesting a true increasing incidence with age.

Acute Pulmonary Embolism after Cesarean Section

Pregnancy is a well-known state of hypercoagubality, increasing the risk of venous thromboembolism (VTE). It is more common with cesarean delivery than vaginal delivery. Pulmonary Embolism (PE) is under diagnosed during pregnancy and postpartum period as majority of signs and symptoms of PE are non-specific. We describe a case of 35-yearold obese female who suffered a syncopal attack following caesarean delivery and was diagnosed to have pulmonary embolism. A high index of suspicion is required for the timely diagnosis and treatment of PE as most of the signs and symptoms of PE are nonspecific. It is important to consider VTE prophylaxis especially in patients with risk factors.

Evaluation of Phytochemical Screening and Anti Inflammatory Activity of Leaves and Stem of Mikania scandens (L.) Wild

Background:

The greatest disadvantage in the presently available potent synthetic anti-inflammatory drugs lies in their toxicity and reappearance of symptoms after discontinuation. Hence, people are returning to the natural products with the hope of safety and security. Several species of Mikania have been reported to have anti-inflammatory properties.

Aim:

The present study aims to assess the anti-inflammatory activity of the ethanolic extract of the leaves and stem of Mikania scandensin vivo and in vitro.

Materials and Methods:

The in vitro bioassay consisted of assaying the effect of the extracts against denaturation of protein (egg albumin) and measuring the absorbance. In vivo anti-inflammatory activity was checked by measuring the percentage inhibition of carrageenan-induced rat paw edema after oral administration of the extracts to male Wistar rats.

Results:

The plant extracts revealed the presence of tannins, alkaloids, steroids and flavonoids in both the leaf and stem extracts. The in vitro study of leaf extracts of M. scandens demonstrated that at 16000 μg/ml concentration a better anti-inflammatory activity was exhibited which is more than the stem extracts. Similarly in the in vivo study, carrageenan induced inflammation was significantly antagonized by M. scandens leaf extract, with inhibition of 50% at 1000 mg/kg.

Conclusion:

The ethanolic extract of both leaf and stem of M. scandens showed potent anti-inflammatory activity. In comparison the leaf extract found to be more potent in both the conditions in vivo and in vitro, comparing with the standard drug diclofenac sodium and traditional control rumalaya perhaps due to the presence of phytochemicals like alkaloids and flavonoids in the plant.

Stenotrophomonas, Mycobacterium, and Streptomyces in home dust and air: associations with moldiness and other home/family characteristics

Respiratory illnesses have been linked to children's exposures to water-damaged homes. Therefore, understanding the microbiome in water-damaged homes is critical to preventing these illnesses. Few studies have quantified bacterial contamination, especially specific species, in water-damaged homes. We collected air and dust samples in twenty-one low-mold homes and twenty-one high-mold homes. The concentrations of three bacteria/genera, Stenotrophomonas maltophilia, Streptomyces sp., and Mycobacterium sp., were measured in air and dust samples using quantitative PCR (QPCR). The concentrations of the bacteria measured in the air samples were not associated with any specific home characteristic based on multiple regression models. However, higher concentrations of S. maltophilia in the dust samples were associated with water damage, that is, with higher floor surface moisture and higher concentrations of moisture-related mold species. The concentrations of Streptomyces and Mycobacterium sp. had similar patterns and may be partially determined by human and animal occupants and outdoor sources of these bacteria.

Airborne fungal cell fragments in homes in relation to total fungal biomass

Fungal exposure may induce respiratory symptoms. The causative agents are compounds in the fungal cell wall. Fragments of microbes may be present in air samples but are not measurable using conventional spore counting or by the determination of viable organisms. This study assesses the proportion of fungal cell biomass and endotoxin in different particle size fractions in air samples from homes. Air samples were collected from 15 homes using a cyclone sampler, collecting particles in three aerodynamic size fractions: <1.0, 1.0-1.8, and >1.8 μm. N-Acetylhexosaminidase (NAHA) was determined as a marker of fungal cell biomass. Endotoxin was determined using the Limulus amebocyte lysate method. NAHA and endotoxin in the size range <1.0 μm comprised up to 63% (mean 22.7%) and 96.3% (mean 22.6%) of the total concentrations, respectively. There were significant relationships between the amounts of NAHA and endotoxin in the total amount and in the size fraction >1.8 μm but not in the smaller fractions. The results demonstrate significant amounts of fungal cell biomass and endotoxin in particles <1.0 μm. Homes with reported mold damage had a lower concentration of NAHA in particles <1.0 μm than homes without mold damage. To assess airborne exposure for diagnostic and preventive purposes, measurement techniques that include this fraction should be considered.

Lateral sinus thrombosis and haemorrhagic ischemic stroke with protein S deficiency in a young

Stroke or cerebro-vascular disease is one of the most important causes of high morbidity and mortality throughout the world. Stroke in young individuals poses a major problem as these individuals are the earning members of the family. Ischemic strokes are increasingly being attributed to causes other than athero-thrombotic disease. Protein S deficiency is a disorder with increased risk of venous thrombosis. Our patient, 19 years old lady presented with haemorrhagic venous infarction in right temporo-occipito-parietal region with right sided lateral sinus thrombosis.

The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized)

Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data that can be meaningfully compared to simulations are required. According to standard mutational ϕ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by ϕ analysis also occurs for acyl phosphatase [Pandit, A. D., Jha, A., Freed, K. F. & Sosnick, T. R., (2006). Small proteins fold through transition states with native-like topologies. J. Mol. Biol.361, 755-770], ubiquitin [Sosnick, T. R., Dothager, R. S. & Krantz, B. A., (2004). Differences in the folding transition state of ubiquitin indicated by ϕ and ψ analyses. Proc. Natl Acad. Sci. USA 101, 17377-17382] and BdpA [Baxa, M., Freed, K. F. & Sosnick, T. R., (2008). Quantifying the structural requirements of the folding transition state of protein A and other systems. J. Mol. Biol.381, 1362-1381]. The carboxy-terminal hairpin in the transition state of Protein L is found to be nonnative, a significant result that agrees with our Protein Data Bank-based backbone sampling and all-atom simulations. The nonnative character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states.

Histological changes of placentas associated with intra-uterine growth restriction of fetuses: a case control study

Placenta is the maternal-fetal contact zone. The placentas of "idiopathic" intra-uterine growth restriction (IUGR) babies may hold the key to the etiology of growth restriction. The present study primarily aimed at evaluating the structural peculiarities of IUGR placenta. The study was conducted on 35 IUGR and 25 control placentas. Placental tissues were processed for routine histological studies, to determine numbers of syncytial knots in villi and X-cells in the basal plate. Light microscopy suggested that syncytiotrophoblastic lining was more degenerated and number of syncytial knots increased in IUGR placentas than that of the control placentas. X cells were present in both the cases, though more in IUGR. Intravillous and perivillous fibrin depositions were markedly increased in IUGR; also there were more hypovascular/avascular villi and large areas of infarction. Cumulative effects of several placental injuries, e.g. poor perfusion, presence of increased number of X-cells, increased fibrin deposition; etc for a sufficient time were likely cause of IUGR.

A study on evalution of antidepressant effect of imipramine adjunct with Aswagandha and Bramhi

Depressive disorders increase the risks of self-harm or even suicide in patients. Indigenous drugs are being tried to treat such patient along with conventional antidepressant drugs. This study was planned to investigate the antidepressant action of Ashwagandha and Bramhi and also to confirm its efficacy in the behavioural despair animal model of depression. Normal saline as control (5 ml/kg), Imipramine as standard (16, 32, 64 mg/ kg) and Ashwagandha (50, 100, 150 mg/kg), Bramhi (20, 40, 80 mg/kg) as test drugs were introduced to the albino rats weighing between 200-250 gm for 2 weeks, 1 hr before electric shock in Learned helplessness test (LHT) and swimming in Forced swimming test (FST). Effects of individual drugs as well as their combination were evaluated. Avoidance response, escape failure and immobility period in case of Imipramine and Ashwagandha showed highly significant (p < 0.01) result on individual use. There was no significant result in case of Bramhi used alone except in escape failure and immobility period (FST), where at higher doses it showed significant (p < 0.01) result. But combination of Bramhi and Ashwagandha in low doses with low dose of Imipramine gave a highly significant result (p < 0.01) in all the parameters. Ashwagandha had significant antidepressant action, but Bramhi had not when used alone. Combination of these two indigenous drug with Imipramine showed high efficacy in animal model.

3α-Dimethylamino-20-(N-methylacetamido)pregn-5-ene

The title compond, C₂₆H₄₄N₂O, is an steroidal alkaloid isolated from the medicinally important plant Sarcococca saligna. The mol­ecule consists of four fused rings (A–D), having chair, half-chair, chair and envelope conformations, respectively. The dimethyl­amino group is axially oriented on ring A, whereas the (N-methyl­acetamido)­ethyl group is attached equatorially on ring D. The crystal structure is stabilized only by van der Waals forces.

Attitude of medical students about different teaching aids used in lectures in anatomy

Nowadays medical teachers use different audiovisual (AV) aids of teaching in their classes to make the subject more interesting and understandable. To assess the impact of three common lecture delivery methods, viz Blackboard (BB), Transparency and Over Head Projector (OHP) and Powerpoint Presentation (PP), a questionnaire based study was carried out among first year MBBS students of R.G.Kar Medical College, Kolkata. One hundred fouty students of academic session 2010-2011 were exposed to different aids of teaching, viz. Black Board (BB), Over Head Projector (OHP), power point presentation (PP) for ten months. They were taught Anatomy by different teachers who used all the three AV aids in their lectures. Then they were asked to respond to a questionnaire regarding these three AV aids of teaching. The students preferred Black Board teaching over OHP and result was statistically significant (p value < 0.0001). BB teaching was also preferred over PP presentations (p < 0.02). But in comparison to OHP, students preferred PP though the difference is not statistically significant (p < 0.10). Most of the students still prefer Black Board teaching to other modern AV aids like OHP and PP. For better understanding of a subject by students and improvement of their performance, a teacher should match the lectures with preferred AV aids and use the AV aids prudently.

A study on habit of preservation of prescriptions by pregnant women in India

Irrational use of medicine is very common in developing countries like India. Drug or medicine use during pregnancy is an important event for both mother and child. Thalidomide disaster showed the adverse effects of drugs on the unborn child. Knowledge about use of medicines can play a crucial role in rational drug use. Prescription is an important tool to assess the past clinical condition of patients and the use of medicines for them. The present study explored the habit of preservation of previous prescriptions in the pregnant women of villages of Wardha District of Maharashtra state of India. This is an observational cross sectional survey using predesigned, precoded and pretested questionnaire. This study showed an interesting habit of these women. 81% of pregnant women have a habit of preservation of prescription as an important document. It was clear that with increasing level of formal education there is a definite increase in habit of preservation of prescription among the pregnant women in rural areas of India.

Influence of spontaneous calcium events on cell-cycle progression in embryonal carcinoma and adult stem cells

Spontaneous Ca(2+) events have been observed in diverse stem cell lines, including carcinoma and mesenchymal stem cells. Interestingly, during cell cycle progression, cells exhibit Ca(2+) transients during the G(1) to S transition, suggesting that these oscillations may play a role in cell cycle progression. We aimed to study the influence of promoting and blocking calcium oscillations in cell proliferation and cell cycle progression, both in neural progenitor and undifferentiated cells. We also identified which calcium stores are required for maintaining these oscillations. Both in neural progenitor and undifferentiated cells calcium oscillations were restricted to the G1/S transition, suggesting a role for these events in progression of the cell cycle. Maintenance of the oscillations required calcium influx only through inositol 1,4,5-triphosphate receptors (IP(3)Rs) and L-type channels in undifferentiated cells, while neural progenitor cells also utilized ryanodine-sensitive stores. Interestingly, promoting calcium oscillations through IP(3)R agonists increased both proliferation and levels of cell cycle regulators such as cyclins A and E. Conversely, blocking calcium events with IP(3)R antagonists had the opposite effect in both undifferentiated and neural progenitor cells. This suggests that calcium events created by IP(3)Rs may be involved in cell cycle progression and proliferation, possibly due to regulation of cyclin levels, both in undifferentiated cells and in neural progenitor cells.

Ubiquitin-mediated activation of TAK1 and IKK

Transforming growth factor beta activated kinase-1 (TAK1), a member of the mitogen-activated protein kinase kinase kinase family, has emerged as a key regulator of signal transduction cascades leading to the activation of the transcription factors nuclear factor-kappa B (NF-kappaB) and activator protein-1 (AP-1). Stimulation of cells with cytokines and microbial pathogens results in the activation of TAK1, which subsequently activates the I-kappa B kinase complex (IKK) and mitogen-activated protein (MAP) kinases, culminating in the activation of NF-kappaB and AP-1, respectively. Recent studies have shown that polyubiquitination of signalling proteins through lysine (Lys)-63-linked polyubiquitin chains plays an important role in the activation of TAK1 and IKK. Unlike Lys-48-linked polyubiquitination, which normally targets proteins for degradation by the proteasome, Lys-63-linked polyubiquitin chains act as scaffolds to assemble protein kinase complexes and mediate their activation through proteasome-independent mechanisms. The concept of ubiquitin-mediated activation of protein kinases is supported by the discoveries of ubiquitination and deubiquitination enzymes as well as ubiquitin-binding proteins that function upstream of TAK1 and IKK. Recent biochemical and genetic studies provide further insights into the mechanism and function of ubiquitin signalling and these advances will be the focus of this review.

Gauze packing of open surgical wounds: empirical or evidence-based practice?

INTRODUCTION

Most surgical wounds are closed primarily, but some are allowed to heal by secondary intention. This usually involves repeated packing and dressing of the raw wound surfaces. Although the long-term care of such wounds has devolved to the care of nurses in the community or out-patient setting, the initial wound dressing or cavity packing is done by the surgeon in the operating theatre. Many surgeons are unaware of the growth of the discipline of wound care, and still use traditional soaked gauze for dressing and packing open surgical wounds and cavities.

RESULTS

This review summarises the some of the modern alternatives available and the evidence--or the lack of it--for their use in both the acute and chronic setting.

Relationship between indoor and outdoor bio-aerosols collected with a button inhalable aerosol sampler in urban homes

This field study investigated the relationship between indoor and outdoor concentrations of airborne actinomycetes, fungal spores, and pollen. Air samples were collected for 24 h with a button inhalable aerosol sampler inside and outside of six single-family homes located in the Cincinnati area (overall, 15 pairs of samples were taken in each home). The measurements were conducted during three seasons - spring and fall 2004, and winter 2005. The concentration of culturable actinomycetes was mostly below the detection limit. The median indoor/outdoor ratio (I/O) for actinomycetes was the highest: 2.857. The indoor of fungal and pollen concentrations followed the outdoor concentrations while indoor levels were mostly lower than the outdoor ones. The I/O ratio of total fungal spores (median=0.345) in six homes was greater than that of pollen grains (median=0.025). The low I/O ratios obtained for pollen during the peak ambient pollination season (spring) suggest that only a small fraction penetrated from outdoor to indoor environment. This is attributed to the larger size of pollen grains. Higher indoor concentration levels and variability in the I/O ratio observed for airborne fungi may be associated with indoor sources and/or higher outdoor-to-indoor penetration of fungal spores compared to pollen grains. Practical Implication This study addresses the relationship between indoor and outdoor concentrations of three different types of bio-aerosols, namely actinomycetes, fungal spores, and pollen grains. The results show that actinomycetes are rare in indoor and outdoor air in Midwest, USA. Exposure to pollen occurs mainly in the outdoor air even during peak pollen season. Unexpectedly high fungal spore concentrations were measured outdoors during winter. The presented pilot database on the inhalable levels of indoor and outdoor bio-aerosols can help apportion and better characterize the inhalation exposure to these bio-aerosols. Furthermore, the data can be incorporated into existing models to quantify the penetration of biological particles into indoor environments from outdoors.

Evaluation of ionic air purifiers for reducing aerosol exposure in confined indoor spaces

Numerous techniques have been developed over the years for reducing aerosol exposure in indoor air environments. Among indoor air purifiers of different types, ionic emitters have gained increasing attention and are presently used for removing dust particles, aeroallergens and airborne microorganisms from indoor air. In this study, five ionic air purifiers (two wearable and three stationary) that produce unipolar air ions were evaluated with respect to their ability to reduce aerosol exposure in confined indoor spaces. The concentration decay of respirable particles of different properties was monitored in real time inside the breathing zone of a human manikin, which was placed in a relatively small (2.6 m3) walk-in chamber during the operation of an ionic air purifier in calm air and under mixing air condition. The particle removal efficiency as a function of particle size was determined using the data collected with a size-selective optical particle counter. The removal efficiency of the more powerful of the two wearable ionic purifiers reached about 50% after 15 min and almost 100% after 1.5 h of continuous operation in the chamber under calm air conditions. In the absence of external ventilation, air mixing, especially vigorous one (900 CFM), enhanced the air cleaning effect. Similar results were obtained when the manikin was placed inside a partial enclosure that simulated an aircraft seating configuration. All three stationary ionic air purifiers tested in this study were found capable of reducing the aerosol concentration in a confined indoor space. The most powerful stationary unit demonstrated an extremely high particle removal efficiency that increased sharply to almost 90% within 5-6 min, reaching about 100% within 10-12 min for all particle sizes (0.3-3 microm) tested in the chamber. For the units of the same emission rate, the data suggest that the ion polarity per se (negative vs. positive) does not affect the performance but the ion emission rate does. The effects of particle size (within the tested range) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria) as well as the effects of the manikin's body temperature and its breathing on the ionic purifier performance were either small or insignificant. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when used inside confined spaces with a relatively high surface-to-volume ratio.

PRACTICAL IMPLICATIONS

Ionic air purifiers have become increasingly popular for removing dust particles, aeroallergens and airborne microorganisms from indoor air in various settings. While the indoor air cleaning effect, resulting from unipolar and bipolar ion emission, has been tested by several investigators, there are still controversial claims (favorable and unfavorable) about the performance of commercially available ionic air purifiers. Among the five tested ionic air purifiers (two wearable and three stationary) producing unipolar air ions, the units with a higher ion emission rate provided higher particle removal efficiency. The ion polarity (negative vs. positive), the particle size (0.3-3 microm) and properties (NaCl, PSL, Pseudomonas fluorescens bacteria), as well as the body temperature and breathing did not considerable affected the ionization-driven particle removal. The data suggest that the unipolar ionic air purifiers are particularly efficient in reducing aerosol exposure in the breathing zone when they are used inside confined spaces with a relatively high surface-to-volume ratio (such as automobile cabins, aircraft seating areas, bathrooms, cellular offices, small residential rooms, and animal confinements). Based on our experiments, we proposed that purifiers with a very high ion emission rate be operated in an intermittent mode if used indoors for extended time periods. As the particles migrate to and deposit on indoor surfaces during the operation of ionic air purifiers, some excessive surface contamination may occur, which introduces the need of periodic cleaning these surfaces.

Incidence of allergenically significant fungal aerosol in a rural bakery of West Bengal, India

The frequency of fungal spores in the air of three different sections of a rural bakery was analyzed using a Burkard personal slide sampler and Andersen two stage viable sampler. In average concentration of spores (No./m3) was 228-26770/m3 and concentration of viable colony forming units (CFU/m3) was 65-2061 CFU/m3. Dominant fungus species both culturable and nonculturable, were species of Aspergillus and Penicillium, Cladosporium sp., Aspergillus niger, Aspergillus flavus, Aspergillus fumigatus, Cladosporium cladosporioides, Penicillium citrinum and Alternaria alternata. Seasonal variations in the spore concentrations were clearly observed in case of some fungi. Total culturable mould concentration of different bakery sections sometimes exceeded the acceptable limit for a healthy indoor environment. Antigenic extracts prepared from some dominant culturable fungi showed high level of allergenicity in skin prick tests indicating that they could be responsible for allergic respiratory dysfunction of bakery workers.

Kinetic characterization of rat brain type IIA sodium channel alpha-subunit stably expressed in a somatic cell line

1. The rat brain type IIA Na+ channel alpha-subunit was stably expressed in Chinese hamster ovary (CHO) cells. Current through the expressed Na+ channels was studied using the whole-cell configuration of the patch clamp technique. The transient Na+ current was sensitive to TTX and showed a bell-shaped peak current vs. membrane potential relation. 2. Na+ current inactivation was better described by the sum of two exponentials in the potential range -30 to + 40 mV, with a dominating fast component and a small slower component. 3. The steady-state inactivation, h infinity, was related to potential by a Boltzmann distribution, underlying three states of the inactivation gate. 4. Recovery of the channels from inactivation at different potentials in the range -70 to -120 mV were characterized by an initial delay which decreased with hyperpolarization. The time course was well fitted by the sum of two exponentials. In this case the slower exponential was the major component, and both time constants decreased with hyperpolarization. 5. For a working description of the Na+ channel inactivation in this preparation, with a minimal deviation from the Hodgkin-Huxley model, a three-state scheme of the form O<-->I1<-->I2 was proposed, replacing the original two-state scheme of the Hodgkin-Huxley model, and the rate constants are reported. 6. The instantaneous current-voltage relationship showed marked deviation from linearity and was satisfactorily fitted by the constant-field equation. 7. The time course of activation was described by an m chi model. However, the best-fitted value of chi varied with the membrane potential and had a mean value of 2. 8. Effective gating charge was determined to be 4.7e from the slope of the activation plot, plotted on a logarithmic scale. 9. The rate constants of activation, alpha m and beta m, were determined. Their functional dependence on the membrane potential was investigated.