An Estimating Equations Approach for Modelling Kappa

Agreement between raters for binary outcome data is typically assessed using the kappa coefficient. There has been considerable recent work extending logistic regression to provide summary estimates of interrater agreement adjusted for covariates predictive of the marginal probability of classification by each rater. We propose an estimating equations approach which can also be used to identify covariates predictive of kappa. Models may include an arbitrary and variable number of raters per subject and yet do not require any stringent parametric assumptions. Examples used to illustrate this procedure include an investigation of factors affecting agreement between primary and proxy respondents from a case‐control study and a study of the effects of gender and zygosity on twin concordance for smoking history.     

Design,synthesis, molecular modeling and biological evaluation of novel Benzoxazole-Benzamide conjugates via a 2-Thioacetamido linker as potential anti-proliferative agents,VEGFR-2 inhibitors and apoptotic inducers

A novel series of 2-thioacetamide linked benzoxazole-benzamide conjugates 1–15 was designed as potential inhibitors of the vascular endothelial growth factor receptor-2 (VEGFR-2). The prepared compounds were evaluated for their potential antitumor activity and their corresponding selective cytotoxicity was estimated using normal human fibroblast (WI-38) cells. Compounds 1, 9–12 and 15 showed good selectivity and displayed excellent cytotoxic activity against both HCT-116 and MCF-7 cancer cell lines compared to sorafenib, used as a reference compound. Furthermore, compounds 1 and 11 showed potent VEGFR-2 inhibitory activity. The cell cycle progression assay showed that 1 and 11 induced cell cycle arrest at G2/M phase, with a concomitant increase in the pre-G1 cell population. Further pharmacological studies showed that 1 and 11 induced apoptosis and inhibited the expression of the anti-apoptotic Bcl-2 and Bcl-xL proteins in both cell lines. Therefore, compounds 1 and 11 might serve as promising candidates for future anticancer therapy development.     

Effectiveness of a monthly schedule of follow-up for the treatment of uncomplicated severe acute malnutrition in Sokoto,Nigeria: A cluster randomized crossover trial

BackgroundCommunity-based management of severe acute malnutrition (SAM) involves weekly or biweekly outpatient clinic visits for clinical surveillance and distribution of therapeutic foods. Distance to outpatient clinics and high opportunity costs for caregivers can represent major barriers to access. Reducing the frequency of outpatient visits while providing training to caregivers to recognize clinical danger signs at home between outpatient visits may increase acceptability, coverage, and public health impact of SAM treatment. We investigated the effectiveness of monthly clinic visits compared to the standard weekly follow-up in the outpatient treatment of uncomplicated SAM in northwestern Nigeria.Methods and findingsWe conducted a cluster randomized crossover trial to test the noninferiority of nutritional recovery in children with uncomplicated SAM receiving monthly follow-up compared to the standard weekly schedule. From January 2018 to November 2019, 3,945 children aged 6 to 59 months were enrolled at 10 health centers (5 assigned to monthly follow-up and 5 assigned to weekly follow-up) in Sokoto, Nigeria. In total, 96% of children (n = 1,976 in the monthly follow-up group and 1,802 in the weekly follow-up group) were followed until program discharge, and 91% (n = 1,873 in the monthly follow-up group and 1,721 in the weekly follow-up group) were followed to 3 months postdischarge. The mean age at admission was 15.8 months (standard deviation [SD] 7.1), 2,097/3,945 (53.2%) were girls, and the mean midupper arm circumference (MUAC) at admission was 105.8 mm (SD 6.0). In a modified intention-to-treat analysis, the primary outcome of nutritional recovery, defined as having MUAC ≥125 mm on 2 consecutive visits, was analyzed using generalized linear models, with generalized estimating equations to account for clustering. Nutritional recovery was lower in the monthly follow-up group compared to the weekly group (1,036/1,976, 52.4% versus 1,059/1,802, 58.8%; risk difference: −6.8%), and noninferiority was not demonstrated (lower bound of the confidence interval [CI] was −11.5%, lower than the noninferiority margin of 10%). The proportion of children defaulting was lower in the monthly group than in the weekly group (109/1,976, 5.5% versus 151/1,802, 8.4%, p = 0.03). Three months postdischarge, children in the monthly group were less likely to relapse compared to those in the weekly group (58/976, 5.9% versus 78/1,005, 7.8%, p = 0.03), but cumulative mortality at 3 months postdischarge was higher in the monthly group (159/1,873, 8.5% versus 106/1,721, 6.2%, p < 0.001). Study results may depend on context-specific factors including baseline level of care and the clinical status of children presenting to health centers, and, thus, generalizability of these results may be limited.ConclusionsWhere feasible, a weekly schedule of clinic visits should be preferred to maintain effectiveness of SAM treatment. Where geographic coverage of programs is low or frequent travel to outpatient clinics is difficult or impossible, a monthly schedule of visits may provide an alternative model to deliver treatment to those in need. Modifications to the outpatient follow-up schedule, for example, weekly clinic visits until initial weight gain has been achieved followed by monthly visits, could increase the effectiveness of the model and add flexibility for program delivery.Trial registrationClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT03140904","term_id":"NCT03140904"}}NCT03140904.

Matt D.T. Hitchings and colleagues investigate the effectiveness of a monthly schedule of follow-up for the management of uncomplicated severe acute malnutrition in children aged 6-59 months in Nigeria.     

Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta

Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up < 1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.     

High-yield isolation, expansion, and differentiation of murine bone marrow-derived mesenchymal stem cells using fibrin microbeads (FMB)

Transplantation of adult mesenchymal stem cells (MSCs) could provide a basis for tissue regeneration. MSCs are typically isolated from bone marrow (BM) based on their preferential adherence to plastic, although with low efficiency in terms of yield and purity. Extensive expansion is needed to reach a significant number of MSCs for any application. Fibrin microbeads (FMB) were designed to attach mesenchymal cells and to provide a matrix for their expansion. The current study was aimed at isolating a high yield of purified BM-derived mouse MSCs based on their preferential adherence and proliferation on FMB in suspension cultures. MSCs could be downloaded to plastics or further expanded on FMB. The yield of MSCs obtained by the FMB isolation technique was about one order of magnitude higher than that achieved by plastic adherence, suggesting that these cells are more abundant than previously reported. FMB-isolated cells were classified as MSCs by their fibroblastic morphology, self-renewal ability, and expression profile of their surface antigens, as examined by flow cytometry and immunostaining. In cell culture, the isolated MSCs could be induced to differentiate into three different mesodermal lineages, as demonstrated by histochemical stains and by RT-PCR analyses of tissue-specific genes. MSCs were also able to differentiate into osteocytes while still cultured on FMB. Our results suggest that FMB might serve as an efficient platform for the isolation, expansion, and differentiation of mouse BM-derived MSCs to be subsequently implanted for tissue regeneration.     

Calpain from rat intestinal epithelial cells: Age-dependent dynamics during cell differentiation

Micromolar and millimolar Ca²⁺-requiring neutral protease (calpain I and calpain II) along with their endogenous inhibitor calpastatin were isolated and partially purified from the same preparation of rat intestinal epithelial cells. Calpain I and II were partially purified by 1300 and 900-fold with 57 and 53 per cent yield, respectively. The optimum assay conditions revealed pH 7.5, 20 min incubation at 25° C and 0.24% casein substrate for both calpains. The optimum calcium concentration obtained for calpain I and II were 25 M and 4 mM, respectively. Distribution of rat intestinal epithelial cells calpain I and II along with calpastatin during cell differentiation stages in weanling to senescence age were studied. Calpain I in weanling rats was in an increasing order from villus to crypt regions. Adult rats indicated well expressed consistent calpain I throughout the differentiation stages. Whereas, significant lowering towards crypt region cells were evident in old rats. Calpain II in weanling and adult rats was found to be consistent throughout the differentiation stages. Old animals revealed an increasing trend from villus to crypt region with insignificant activity present in upper villus cells. Concomitantly, different concentrations of calpastatin were observed throughout the differentiation stages in all the age groups. Moreover, the levels of calpains exceeded that of calpastatin in most of the epithelial cell populations during developmental stages. In addition to casein, intestinal epithelial cell membranes were found to be equally good substrates for calpains. Proteolytic susceptibility of weanling, adult and old rat membrane proteins varied significantly all along the ageing process in rats. Simultaneous age-dependent calpastatin response were also evident. Taken together the results obtained provided strong evidence that calpain plays significant role in rat intestinal cell differentiation and ageing process with calpastatin as its specific regulatory protein.Abbreviations DEAE-cellulose O-(Diethylaminoethyl)-cellulose - EDTA Ethylene Diamine Tetra Acetic Acid - Tris Tris (hydroxymethyl) amino methane - KH₂PO₄ potassium dihydrogen orthophosphate - Na₂HPO₄ disodium hydrogen phosphate - CaCl₂ Calcium Chloride - TCA Trichloroacetic Acid - PMSF Phenylmethylsulfonyl Fluoride     

Molecular cloning, sequence and structural analysis of dehairing Mn(2+) dependent alkaline serine protease (MASPT) of Bacillus pumilus TMS55

Leather industries release a large amount of pollution-causing chemicals which creates one of the major industrial pollutions. The development of enzyme based processes as a potent alternative to pollution-causing chemicals is useful to overcome this issue. Proteases are enzymes which have extensive applications in leather processing and in several bioremediation processes due to their high alkaline protease activity and dehairing efficacy. In the present study, we report cloning, characterization of a Mn2+ dependent alkaline serine protease gene (MASPT) of Bacillus pumilus TMS55. The gene encoding the protease from B. pumilus TMS55 was cloned and its nucleotide sequence was determined. This gene has an open reading frame (ORF) of 1,149 bp that encodes a polypeptide of 383 amino acid residues. Our analysis showed that this polypeptide is composed of 29 residues N-terminal signal peptide, a propeptide of 79 residues and a mature protein of 275 amino acids. We performed bioinformatics analysis to compare MASPT enzyme with other proteases. Homology modeling was employed to model three dimensional structure for MASPT. Structural analysis showed that MASPT structure is composed of nine α-helices and nine β-strands. It has 3 catalytic residues and 14 metal binding residues. Docking analysis showed that residues S223, A260, N263, T328 and S329 interact with Mn2+. This study allows initial inferences about the structure of the protease and will allow the rational design of its derivatives for structure-function studies and also for further improvement of the enzyme.     

Termites Improve the Horizontal Movement of Carbonized Particles: A Step towards Sustainable Utilization of Biochar

Soil amendments containing carbonized materials increase the soil carbon reservoir, influence plant productivity, and, ultimately, help to clean the environment. There is data on the effect of such additions on soil physicochemical properties or plant growth, but few studies have focused on how these carbonized materials are distributed by termite species in the soil ecosystem. It is the first comprehensive study of the transportation of biochar (BC) by termite species under tropical environmental conditions in Pakistan. The present study was carried out to test the hypothesis that if termite species I) were involved in the distribution of biochar particles II) if yes, then how far these particles were transported during the study period (10 days) and III) check their preference between the enriched BC (EBC) and non-enriched BC. BC was enriched with the cattle slurry after its pyrolysis in the study. The results showed that EBC particles were significantly more widely distributed than non-enriched BC particles, but both types of BC were transported more than 4 cm (ring 4) within 10 days (at the end of the experiment). The current study also revealed that EBC was easily attached to the setae, cuticle, and legs of termites, implying that it could potentially be transported over a greater distance. Furthermore, transportation of EBC over larger distances indicated a potential preference of termite species between the EBC and BC particles. During the study, however, the preference among the termite species was also observed. Under the prevailing study conditions, the Coptotermes heimi and Heteroterme indicola species transported the EBC further than Microtermes obesi and Odontotermes obesus. These findings revealed that transportation preferences were observed among the four termite species. In conclusion, the current study found that termites were involved in the distribution of BC particles, with a preference for EBC and that these have the potential to transport BC particles more than 4 cm within 10 days. Furthermore, two species Coptotermes heimi and Heteroterme indicola may be more suitable candidates for EBC transpiration in Pakistani soils. It was necessary to conduct additional research into the effect of temperature on the transportation process.     

Effectiveness of a brief group behavioural intervention on psychological distress in young adolescent Syrian refugees: A randomised controlled trial

BackgroundMillions of young adolescents in low- and middle-income countries (LMICs) affected by humanitarian crises experience elevated rates of poor mental health. There is a need for scalable programs that can improve the mental health of young adolescents. This study evaluated the effectiveness of a nonspecialist delivered group-based intervention (Early Adolescent Skills for Emotions (EASE)) to improve young adolescents’ mental health.Methods and findingsIn this single-blind, parallel, controlled trial, Syrian refugees aged 10 to 14 years in Jordan were identified through screening of psychological distress as defined by scores ≥15 on the Paediatric Symptom Scale. Participants were randomised to either EASE or enhanced usual care (EUC) involving referral to local psychosocial services (on a 1:1.6 ratio). Participants were aware of treatment allocation but assessors were blinded. Primary outcomes were scores on the Paediatric Symptom Checklist (PSC; internalising, externalising, and attentional difficulty scales) assessed at week 0, 9 weeks, and 3 months after treatment (primary outcome time point). It was hypothesised that EASE would result in greater reductions on internalising symptoms than EUC. Secondary outcomes were depression, posttraumatic stress, well-being, functioning, school belongingness, and caregivers’ parenting and mental health. Between June 2019 and January 2020, 1,842 young adolescent refugees were screened for eligibility on the basis of psychological distress. There were 520 adolescents (28.2%) who screened positive, of whom 471 (90.6%) agreed to enter the trial. Overall, 185 were assigned to EASE and 286 to EUC, and 169 and 254 were retained at 3 months for EASE and EUC, respectively. Intent-to-treat analyses indicated that at 3 months, EASE resulted in greater reduction on the PSC-internalising scale than EUC (estimated mean difference 0.69, 95% CI 0.19 to 1.19; p = 0.007; effect size, 0.38) but there were no differences for PSC-externalising (estimated mean difference 0.24, 95% CI −0.43 to 0.91; p = 0.49; effect size, −0.10), PSC-attentional problem (estimated mean difference −0.01, 95% CI −0.51 to 0.54; p = 0.97; effect size, −0.01) scores, or on depression, posttraumatic stress, well-being, functioning, or school belongingness. Relative to EUC, caregivers in EASE had less psychological distress (estimated mean difference 1.95, 95% CI 0.71 to 3.19; p = 0.002) and inconsistent disciplinary parenting (mean difference 1.54, 95% CI 1.03 to 2.05; p < 0.001). Secondary analyses that (a) focused on adolescents with probable internalising disorders; (b) completed the 3-month assessment; and (c) controlled for trauma exposure did not alter the primary results. Mediation analysis indicated that for caregivers in the EASE condition, reduction in inconsistent disciplinary parenting was associated with reduced attentional (β = 0.11, SE 0.07; 95% CI 0.003, 0.274) and internalising (β = 0.11, SE 0.07; 95% CI 0.003, 0.274) problems in their children. No adverse events were attributable to the intervention. A limitation was that EUC was not matched to EASE in terms of facilitator attention or group involvement.ConclusionsEASE led to reduced internalising problems in young refugee adolescents and was associated with reduced distress and less inconsistent disciplinary parenting in caregivers. This intervention has the potential as a scalable intervention to mitigate young adolescents’ emotional difficulties in LMIC.Trial registrationProspectively registered at Australian and New Zealand Clinical Trials Registry: ACTRN12619000341123.

In a randomized controlled trial, Richard A. Bryant and colleagues study the effectiveness of the Early Adolescent Skills for Emotions (EASE) intervention to improve the mental health of Syrian refugees aged 10-14 years living in Jordan.