Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes

Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster. Limited overlap among the lists of discovered genes makes it difficult to determine which, if any, exhibit truly rhythmic patterns of expression. We reanalyzed data from all five reports and found two sources for the observed discrepancies, the use of different expression pattern detection algorithms and underlying variation among the datasets. To improve upon the methods originally employed, we developed a new analysis that involves compilation of all existing data, application of identical transformation and standardization procedures followed by ANOVA-based statistical prescreening, and three separate classes of post hoc analysis: cross-correlation to various cycling waveforms, autocorrelation, and a previously described fast Fourier transform–based technique [1–3]. Permutation-based statistical tests were used to derive significance measures for all post hoc tests. We find application of our method, most significantly the ANOVA prescreening procedure, significantly reduces the false discovery rate relative to that observed among the results of the original five reports while maintaining desirable statistical power. We identify a set of 81 cycling transcripts previously found in one or more of the original reports as well as a novel set of 133 transcripts not found in any of the original studies. We introduce a novel analysis method that compensates for variability observed among the original five Drosophila circadian array reports. Based on the statistical fidelity of our meta-analysis results, and the results of our initial validation experiments (quantitative RT-PCR), we predict many of our newly found genes to be bona fide cyclers, and suggest that they may lead to new insights into the pathways through which clock mechanisms regulate behavioral rhythms

Design and operational parameters of dol nets operated in Bhayander Estuary, Maharashtra

Bhayander estuary is a very sensitive ecosystem due to the disposal of industrial effluents and heavy load due to urbanisation, but still it hold stand firmly as the breeding and nursery ground for many commercially important species of Maharashtra and the dol net fishery in this region provides a source of livelihood to the traditional fishermen. The overall size of dol net operated in this estuary varied from 12 to 14 m and the numbers of dol nets/vessel varied from one to three. The mesh size of the dol nets varied between 8 to 160 mm across its different parts from cod end towards mouth of the net. The average number of fishing days of single-day dol netters per month varied from 12 to 16 days. Maximum distance of dol net station was 1.4 km from the landing jetty and mean distance travelled by dol netters was 0.8 km. The present study highlights the detail structural design and the operational parameters of the dol net operated in this estuary

Brain health measurement: a scoping review

Objectives Preservation of brain health is an urgent priority for the world’s ageing population. The evidence base for brain health optimisation strategies is rapidly expanding, but clear recommendations have been limited by heterogeneity in measurement of brain health outcomes. We performed a scoping review to systematically evaluate brain health measurement in the scientific literature to date, informing development of a core outcome set. Design Scoping review. Data sources Medline, APA PsycArticles and Embase were searched through until 25 January 2023. Eligibility criteria for selecting studies Studies were included if they described brain health evaluation methods in sufficient detail in human adults and were in English language. Data extraction and synthesis Two reviewers independently screened titles, abstracts and full texts for inclusion and extracted data using Covidence software. Results From 6987 articles identified by the search, 727 studies met inclusion criteria. Study publication increased by 22 times in the last decade. Cohort study was the most common study design (n=609, 84%). 479 unique methods of measuring brain health were identified, comprising imaging, cognitive, mental health, biological and clinical categories. Seven of the top 10 most frequently used brain health measurement methods were imaging based, including structural imaging of grey matter and hippocampal volumes and white matter hyperintensities. Cognitive tests such as the trail making test accounted for 286 (59.7%) of all brain health measurement methods. Conclusions The scientific literature surrounding brain health has increased exponentially, yet measurement methods are highly heterogeneous across studies which may explain the lack of clinical translation. Future studies should aim to develop a selected group of measures that should be included in all brain health studies to aid interstudy comparison (core outcome set), and broaden from the current focus on neuroimaging outcomes to include a range of outcomes

New Record of Ariomma brevimanum (Klunzinger, 1884) (Perciformes: Ariommatidae) from Indian Waters

Nine specimens (584–670 mm standard length) of Ariomma brevimanum (Klunzinger 1884) were collected from the Cochin Fishing Harbour (south-eastern Arabian Sea) in 2016. Morphometric and meristic parameters, along with the DNA barcoding confirmed the identity of the specimens. The majority of the proportional morphometric measurement and meristic counts were concurrent with the previous description of A. brevimanus: body elongated (depth at first dorsal and second dorsal fin origin was about 22.8–25.2% and 22.0–22.7%of the standard length respectively); first dorsal fin with XI spine and second dorsal fin with I spine and 15 rays; anal fin with II spine and 15 rays; pectoral fin with 22–24 rays; scales large, cycloid, thin and deciduous; lateral line with 52–55 pored scales; pre-dorsal scale patch extending to about the hind margin of the eye; pre-opercular margin angular; horizontal eye diameter 18–22% of head length; gill rakers, 30–32 on first gill arch. In the present study, the partial sequences of the mitochondrial COI gene of A. brevimanum were generated. The analysis using the sequences of the COI gene produced a phylogenetic tree considering the maximum likelihood tree showed distinct clustering among species of Ariomma and revealed an identical phylogenetic relationship. The present study represents the first record for Indian waters, as well as the south-eastern Arabian Sea record of this species

Catch composition and discards in set bagnets of Karanja Estuary, Raigad, Maharashtra

Dol netting is one of the major fishing methods used mainly by traditional fishermen of Maharashtra. Study of catch composition of dol nets operated in Karanja Estuary of Raigad district, Maharashtra was carried out during September 2016 - May 2017. A total of ten single-day dol-netters were selected for the purpose of this study. Fortnightly on-board sampling and questionnaire-based sampling were carried out to fulfil the objectives of the study. The number of fishing days per month ranged from 12-16 due to tide-based restrictions. Dol net catch comprised 50 species of fin fishes, 3 species of elasmobranchs, 13 species of shrimps, 10 species of crabs, 5 species of cephalopods, 2 species of jellyfish, 4 species of sea snakes, 1 species of lobster and 2 species of stomatopods. Major catch composition of dol nets recorded during the study included Acetes indicus, Arius maculatus, Charybdis callianassa , Chrysaora Caliparea, Coilia dussumieri , Harpadon nehereus , Lepturacanthus savala , Miyakella nepa, Mystus gulio and Parapenaeopsis sculptilis. Significant discards such as jellyfishes, juveniles of several fishes and plastics were recorded in the dol nets operated in the Karanja estuar

Biometry, length-weight and length-length relationships of flathead sillago Sillaginopsis panijus (Hamilton, 1822) (Perciformes: Sillaginidae) from the north-western Bay of Bengal

Biometry, length-weight relationships (LWRs) and length-length relationships (LLRs) of Sillaginopsis panijus (Hamilton, 1822) were investigated in the Indian coast of north-western Bay of Bengal. Altogether 622 specimens were collected between August 2018 and September 2019 from landings by trawls (30-35 mm mesh size), gillnets (15-55 mm mesh size) and shore seines (7-15 mm bag mesh size). The total length and weight of the specimens ranged from 7.8-40.3 cm and 2.9-506 g, respectively. The LWR established was W=0.0048 L3.059 for males, W=0.0032 L3.185 for females and W=0.0047 L3.0645 for indeterminates, indicating positive allometric growth pattern. All the LWRs were highly significant (p<0.001, r2≥0.977). The highest coefficient of correlation (r) was observed for total length against fork length (0.999) and lowest for head length against eye diameter (0.951). The fin formula was expressed as D1 X, D2 I + 24-28, P 17-22, V I + 5, A II + 25-27, GR 2-3/6-9. The study provides the first detailed account of the biometric relationships of S. panijus in the north-western Bay of Bengal, which can be used as baseline information for subsequent biological and population based studies in the region

Relationship between fish and otolith dimensions of flathead sillago Sillaginopsis panijus (Hamilton, 1822) (Perciformes: Sillaginidae) in the north-western Bay of Bengal

The present study established the fish body and otolith dimension relationships of flathead sillago Sillaginopsis panijus (Hamilton, 1822), to assist the interpretation of growth. A total of 413 specimens were collected fortnightly from September 2018 to August 2019 off north-western Bay of Bengal. The samples ranged between 142–394 mm in total length and16-413.1 g in total weight. With fish growth, positive correlation was observed between the fish and otolith morphometric parameters. The highest coefficient of determination (R2) was observed between total length and otolith weight (R2=0.9198), followed by otolith weight and otolith width (R2=0.896). These results provide baseline information on the dimensional relationship between fish length and otolith size of this species in Indian waters, which will be helpful in future study on the food and feeding habits, growth and stock structure. Keywords: Coefficient of determination, Correlation, Growth rings, Life history, Morphometry, Sagitt

Beneficial Role of Antioxidant Secondary Metabolites from Medicinal Plants in Maintaining Oral Health.

Plant-derived phytochemicals have been touted as viable substitutes in a variety of diseases. All over the world, dentists have turned to natural remedies for dental cure due to the negative possessions of certain antibacterial mediators used in dentistry. Antimicrobial and other drugs are currently in use, but they show some side effects. Since ancient times, antioxidant EOs have been used for different ailments and have grown in popularity over time. Several in vitro, in vivo, and clinical trials have shown the safety and effectiveness of antioxidant essential oils (EOs) in oral health obtained from medicinal plants. The current review of literature provides a summary of secondary metabolites, more specifically EOs from 20 most commonly used medicinal plants and their applications in maintaining oral health. Dental caries and periodontal diseases are the most common and preventable global infectious diseases, with diseases of the oral cavity being considered major diseases affecting a person&#39;s health. Several clinical studies have shown a connection between oral diseases and oral microbiota. This review discusses the role of antioxidant secondary metabolites in inhibiting the growth of oral pathogens and reducing the formation of dental plaque, and as well as reducing the symptoms of oral diseases. This review article contributes a basic outline of essential oils and their healing actions

Validation of a self-esteem inventory among bachelor-level students of a medical college in Kathmandu, Nepal

Background The necessity of self-esteem is often discussed and taught but measurements of self-esteem are lacking in Nepal and a locally validated tool is a needed to measure self-esteem among Nepalese people. The aim of this study was to assess the reliability, validity and factorial structure of the Self Esteem Inventory (SEI). Methods A total of 560 undergraduate students participated in the study. Explorative factor analysis was conducted to examine the underlying structure of the SEI. Concurrent validity evidence was gathered by correlating the Self Esteem Inventory with the established Rosenberg Self Esteem Scale (RSES). Results The factor analysis suggested a four-factor solution labelled as Childhood and Family Background, Likeability, Wealth and Financial Background, and Purpose Needs. The SEI showed an overall internal consistency (? = 0.75) with a coefficient alpha of range 0.52–0.71 for the subscales and found a low correlation of the SEI with the Rosenberg Self-Esteem Scale (r=0.368). Conclusion This study provides psychometric properties of 15 items retained from 56 on the original self-esteem scale, developed for the context of Nepal. The SEI is a valid and reliable measure that can be used to study self-esteem

Role of random biopsies in surveillance of dysplasia in ulcerative colitis patients with high risk of colorectal cancer

Background/AimsRecent data suggest that the incidence of ulcerative colitis (UC) related colorectal cancer (CRC) in India is similar to that of West. The optimum method for surveillance is still a debate. Surveillance with random biopsies has been the standard of care, but is a tedious process. We therefore undertook this study to assess the yield of random biopsy in dysplasia surveillance.MethodsBetween March 2014 and July 2015, patients of UC attending the Inflammatory Bowel Disease clinic at the All India Institute of Medical Sciences with high risk factors for CRC like duration of disease >15 years and pancolitis, family history of CRC, primary sclerosing cholangitis underwent surveillance colonoscopy for dysplasia. Four quadrant random biopsies at 10 cm intervals were taken (33 biopsies). Two pathologists examined specimens for dysplasia, and the yield of dysplasia was calculated.ResultsTwenty-eight patients were included. Twenty-six of these had pancolitis with a duration of disease greater than 15 years, and two patients had associated primary sclerosing cholangis. No patient had a family history of CRC. The mean age at onset of disease was 28.89±8.73 years and the duration of disease was 19.00±8.78 years. Eighteen patients (64.28%) were males. A total of 924 biopsies were taken. None of the biopsies revealed any evidence of dysplasia, and 7/924 (0.7%) were indefinite for dysplasia.ConclusionsRandom biopsy for surveillance in longstanding extensive colitis has a low yield for dysplasia and does not suffice for screening. Newer techniques such as chromoendoscopy-guided biopsies need greater adoption