OBJECTIVE: Communities are important settings for health promotion and prevention. The community readiness assessment offers a structured approach to assess resources and opportunities to tackle a health problem within a community. The assessment relies on semi-structured interviews with key informants from the communities. A number of 4-6 key informant interviews are recommended in the literature. However, it is unclear whether this is sufficient to obtain a valid representation of the respective community. This study analysed whether increasing the number of key informants from 4-6 to 12-15 alters the results of the community readiness assessment. RESULTS: A total of 55 community readiness interviews were carried out in 4 communities. Overall, the community readiness scores showed little variation after having interviewed 10 key informants in a community. However, even after completing 10 interviews in a community, key informants were still able to identify up to 6 new information items regarding community efforts for physical activity promotion among the elderly, contact and communication channel for informing or approaching the target group, or barriers to participation.

OBJECTIVES: Gastric cancer (GC) is a multifactorial disease and the fifth most frequent diagnosed cancer worldwide. It accounts for one third of cancer-related mortalities. Geospatial analysis using geographical information systems (GIS) can provide an efficient solution to identify spatial disparities associated with GC. As such, GIS enables policymakers to control cancer in a better way and identify the regions where interventions are needed. This study aims to publish a comprehensive dataset, which was applied to conduct a spatial analysis of GC patients in the city of Mashhad, Iran. DATA DESCRIPTION: We provide a personal geodatabase, a Microsoft Access database that can store, query, and manage both spatial and non-spatial data, which contains four feature classes. "Male_Stomach_Cancer_Patients" and "Female_Stomach_Cancer_Patients" are point feature classes, which show the age and geographical location of 1156 GC cancer patients diagnosed between 2014 and 2017. "Air_Polution_Mashhad" is another point feature class that reveals the amount of six air pollutants, which was taken from Mashhad Environmental Pollutants Monitoring Center between 2017 and 2018. Finally, "Stomach_Cancer_and_Risk_Factors" is a polygon feature class of neighborhood division of Mashhad, consisting of contributor risk factors including dietary habits, smoking, alcohol use, body mass index and population by age groups for all 165 city neighborhoods.

OBJECTIVES: To assess the appropriateness of the statistical methodology used in a recent meta-analysis investigating the effect of maternity waiting homes (MWHs) on perinatal mortality in Sub-Saharan Africa. RESULTS: A recent meta-analysis published in BMC Research Notes used a fixed-effect model to generate an unadjusted summary estimate of the effectiveness of MWHs in reducing perinatal mortality in Africa using ten observational studies (pooled odds ratio 0.15, 95% confidence interval 0.14-0.17). The authors concluded that MWHs reduce perinatal mortality by over 80% and should be incorporated into routine maternal health care services. In the present article, we illustrate that due to the contextual and methodological heterogeneity present in existing studies, the authors' conclusions about the effectiveness of MWHs in reducing perinatal mortality were likely overstated. Additionally, we argue that because of the selection bias and confounding inherent in observational studies, unadjusted pooled estimates provide little causal evidence for effectiveness. Additional studies with robust designs are required before an appropriately designed meta-analysis can be conducted; until then, the ability to draw causal inferences regarding the effectiveness of MWHs in reducing perinatal mortality is limited.

OBJECTIVE: The most common histopathologic malignant and benign nodules are Adenocarcinoma and Granuloma, respectively, which have different standards of care. In this paper, we propose an automatic framework for the diagnosis of the Adenocarcinomas and the Granulomas in the CT scans of the chest from a private dataset. We use the radiomic features of the nodules and the attached vessel tortuosity for the diagnosis. The private dataset includes 22 CTs for each nodule type, i.e., adenocarcinoma and granuloma. The dataset contains the CTs of the non-smoker patients who are between 30 and 60 years old. To automatically segment the delineated nodule area and the attached vessels area, we apply a morphological-based approach. For distinguishing the malignancy of the segmented nodule, two texture features of the nodule, the curvature Mean and the number of the attached vessels are extracted. RESULTS: We compare our framework with the state-of-the-art feature selection methods for differentiating Adenocarcinomas from Granulomas. These methods employ only the shape features of the nodule, the texture features of the nodule, or the torsion features of the attached vessels along with the radiomic features of the nodule. The accuracy of our framework is improved by considering the four selected features.

OBJECTIVE: Nosocomial infections (NIs) are known as one of the remarkable problems in all countries. This study is aimed to estimate the prevalence rate of nosocomial bacterial agents with antimicrobial susceptibility pattern in hospitalized patients. This study was conducted from April 2017 to September 2018, on 4029 hospitalized patients. We set out to recognize the commonest bacterial infections and antimicrobial susceptibility patterns of nosocomial infection. RESULTS: Of the 4029 patients, 509 (12.6%) of them were culture positive. Of these Escherichia coli (E. coli) (98.3%) and Staphylococcus epidermidis (S. epidermidis) (37.5%) were the most abundant bacterial identified in the urinary tract and bloodstream cultures respectively, Moreover, Acinetobacter spp. (100%) and Pseudomonas aeruginosa (22.2%) were the most abundant organisms detected in the respiratory system. According to susceptibility testing results, 370 (80.5%) and 264 (57.3%) in Gram-negatives and 44 (91.7%) and 35 (72.9%) in gram positives isolated strains were classified as multidrug-resistant (MDR) and extensive drug-resistant (XDR) strain respectively. On account of the high prevalence of MDR and XDR bacterial species, there is a pressing need for the expansion of new strategies on antibiotic supervision and infection control to introduce new guideline on empirical antibiotic therapy.

OBJECTIVE: In 2018, we conducted a retrospective survey using the medical records of 484 patients with type 2 diabetes. The observed value of coronary heart disease (CHD) incidence after 5 years and the predicted value by the JJ risk engine as of 2013 were compared and verified using the discrimination and calibration values. RESULTS: Among the total cases analyzed, the C-statistic was 0.588, and the calibration was p < 0.05; thus, the JJ risk engine could not correctly predict the risk of CHD. However, in the group expected to have a low frequency of hypoglycemia, the C-statistic was 0.646; the predictability of the JJ risk engine was relatively accurate. Therefore, it is difficult to accurately predict the complication rate of patients using the JJ risk engine based on the diabetes treatment policy after the Kumamoto Declaration 2013. The JJ risk engine has several input items (variables), and it is difficult to satisfy them all unless the environment is well-equipped with testing facilities, such as a university hospital. Therefore, it is necessary to create a new risk engine that requires fewer input items than the JJ risk engine and is applicable to several patients.

OBJECTIVE: Tuberculosis (TB) is a major cause of morbidity and mortality globally. Despite efforts to eliminate TB in Thailand, the incidence rate has declined slowly. This study aimed to identify the incidence and risk factors of unsuccessful pulmonary TB treatment (failed, died and loss-to- follow up) in a community hospital in Chachoengsao Province, Thailand from 1st January 2013 to 31st December 2019. RESULTS: A total of 487 patients were eligible for the study. The incidence of unsuccessful treatment was 21.67/100 population person year. Risk factors of unsuccessful pulmonary TB treatment were unemployment (adjusted hazard ratio (AHR) 3.12, 95%CI 1.41-6.86), HIV co-infection (AHR 2.85, 95%CI 1.25-6.46), previous history of TB (AHR 2.00, 95%CI 1.04-3.81), positive sputum AFB at the end of the intensive phase (AHR 5.66, 95%CI 2.33-13.74), and sputum AFB was not performed at the end of the intensive phase (AHR 18.40, 95%CI 9.85-34.35). This study can be utilized to improve prevention and intervention of TB treatment by strengthening public health system on treatment quality especially TB patient monitoring tools or methods easy for accessing to patients in communities.

OBJECTIVE: Prompt diagnosis of Helicobacter pylori infection is essential for proper treatment and eradication of the pathogen because prolonged infection could lead to gastric cancer. Sensitive and cost effective diagnostic methods are key to guiding treatment options that will reduce mortality. This study was aimed at detecting H. pylori from biopsies of peptic ulcer patients. Real-time PCR using TaqMan and EvaGreen assays targeting 16S rRNA and ureA genes were used to detect H. pylori DNA extracted from 40 biopsy samples comprising 20 biopsies obtained from the antrum and 20 from the corpus of 20 patients undergoing endoscopy for duodenal ulcer investigation in Lagos, Nigeria. RESULTS: H. pylori was detected in 80% of the biopsy samples by combined cycle threshold (Ct) and melting temperature (Tm) values. Mean Ct value for ureA gene ranged from 21.40 to 37.53 and 22.71 to 35.44 for 16SrRNA gene. Average melting temperatures (Tm) of 81.57 and 82.90 °C among amplicons of ureA and 16S rRNA were observed respectively. H. pylori DNA was generally detected in biopsies collected from antrum and corpus. Real-time PCR in the diagnosis of H. pylori can be considered a simple, low cost and efficient alternative or addition to the gold standard.

OBJECTIVE: The purpose of this study was to compare the charges and payments associated with bone marrow aspiration and biopsies performed by hematology/oncology specialists versus interventional radiology specialists at Bassett Medical Center located in a rural area of New York State. Charges pertained to what the hospital charged for the procedure and payment refers to the reimbursement the hospital received. Our secondary objectives were to compare specimen quality by procedure and to determine whether body mass index was associated with which specialist performed the procedure. RESULTS: The median charge was significantly higher in the interventional radiology group ($5254 USD) compared to the hematology/oncology group ($413 USD), p < 0.0001. Median payments were also higher in the interventional radiology ($1392 USD) compared to the hematology/oncology group ($1109 USD), p < 0.0001. Adequacy of the samples obtained by either profession was similar. Disease process was not associated with adequacy of the sample. There was no statistically significant difference in the proportion of males and females in the respective groups or in the mean age. However, the patients' in the interventional radiology group had a significantly higher mean BMI (34.3) compared to those in the hematology/oncology group (28.6), p = 0.0014.

OBJECTIVE: Necrotizing enterocolitis (NEC) is the most frequent life-threatening gastrointestinal disease experienced by premature infants in neonatal intensive care units all over the world. The objective of the present study was to take advantage of RNA-Seq data from the analysis of intestinal specimens of preterm infants diagnosed with NEC. Function enrichments with Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used to analyse previous data in order to identify biological and functional processes, which could provide more insight into the pathogenesis of NEC in infants. RESULTS: Gene set enrichment analysis indicated that the most significant biological pathways over-represented in NEC neonates were closely associated with innate immune functions. One of the striking observations was the highly modulated expression of inflammatory genes related to the IL-17 pathway including such as pro-inflammatory cytokines (CXCL8), chemokines (CXCL5 and CXCL10) and antimicrobials (DEF5A, DEF6A, LCN2, NOS2) in the intestine of neonates diagnosed with NEC. Interestingly, the increase in IL-17 expression appeared to be under the IL-17F form, as reported in Crohn's disease, another inflammatory bowel disease. Further investigation is thus still needed to determine the precise role of IL-17F and its downstream targets in NEC.

OBJECTIVE: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. RESULTS: One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.

OBJECTIVE: Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. RESULTS: In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.

OBJECTIVE: The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. RESULTS: Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.

Erratum in BMC Res Notes. 2021 Jul 12;14(1):268.

OBJECTIVES: Agarwood is the aromatic heartwood formed upon wounding of Aquilaria trees either naturally formed due to physical wound sustained from natural phenomena followed by microbial infection, or artificially induced using different inoculation methods. Different induction methods produce agarwoods with different aromas which have impacts on their commercial values. In lieu of elucidating the molecular mechanisms of agarwood formation under different treatment conditions, the transcriptome profiles of trunk tissues from healthy A. malaccensis tree, and naturally and artificially induced trees were obtained. DATA DESCRIPTION: The transcriptome of trunk tissues from healthy A. malaccensis, and naturally and artificially induced trees were sequenced using Illumina HiSeq™ 4000 platform which resulted in a total of 38.4 Gb clean reads with Q30 rate of at least 91%. The transcriptome consists of 85,986 unigenes containing 1305 bases on average which were annotated against several databases. From this, 44,654 unigenes were mapped to 290 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. These transcriptome data represent considerable contribution towards Aquilaria transcriptome data and enhance current knowledge in comprehending the molecular mechanisms underlying agarwood formation in Aquilaria spp.

OBJECTIVES: The research aimed to determine the prevalence and associated factors of uncontrolled hyperlipidemia among Thai patients with the disease and Clinical ASCVD. RESULTS: A total of 1,527 Thai diabetic patients with a history of ASCVD were included in the study. Uncontrolled hyperlipidemia was detected among 1,216 patients (79.6%; 95% CI 77.6-81.7). The independent factors associated with uncontrolled hyperlipidemia included being female (adjusted odds ratio (AORs); 1.5, 95% CI 1.2-2.0), using thiazolidinedione (AORs; 1.7, 95% CI 1.1-2.7), community hospital (AORs; 4.3, 95% CI 1.0-18.0) and BMI level at 18.5-22.9 kg/m2 (AORs; 2.2, 95% CI 1.2-4.0), 23.0-24.9 kg/m2 (AORs; 1.8 95% CI 0.9-3.3), 25.0-29.9 kg/m2 (AORs; 2.3 95% CI 1.3-4.3) and ≥ 30 kg/m2 (AORs; 2.5 95% CI 1.3-4.9).

OBJECTIVE: CD4 Lymphocyte Count (CD4) is a major predictor of HIV progression to AIDS. Exploring the factors affecting CD4 levels may assist healthcare staff and patients in management and monitoring of health cares. This retrospective cohort study aimed to explore factors associated with CD4 cell counts at the time of diagnosis in HIV patients using Poisson, Generalized Poisson, and Negative Binomial regression models. RESULTS: Out of 4402 HIV patients diagnosis in Iran from 1987 to 2016, 3030 (68.8%) were males, and the mean age was 34.8 ± 10.4 years. The results indicate that the Negative Binomial model outperformed the other models in terms of AIC, log-likelihood and RMSE criteria. In this model, factors include sex, age, clinical stage and Tuberculosis (TB) co-infection were significantly associated with CD4 count (P < 0.05). CONCLUSION: Given the effect of age, sex, clinical stage and stage of HIV on CD4 count of the patients, adopting policies and strategies to increase awareness and encourage people to seek early HIV testing and care is advantageous.

OBJECTIVES: To reduce the spread of the infection, especially during aerosol generating procedures, we invented "The Cupola", a shield that creates a mechanical barrier around the patient's head and body. With this pilot study we aimed to assess the effectiveness of an additional layer of protection (The Cupola) developed for providers working in the oropharyngeal region. RESULTS: The mean number of 0.3 μm particles with no Cupola was 3777 (SD: ± 556), with The Cupola was 2068 (SD: ± 1468) and with the Cupola and Drape was 2031 (SD: ± 1108) (p < 0.015). The mean number of 0.5 μm airborne particles with no Cupola was 65 (SD: ± 7), with The Cupola was 29 (SD: ± 28) and with the Cupola and Drape was 28 (SD: ± 23) (p < 0.05). Results showed a significant reduction of aerosols generated during simulated dental procedures when the Cupola was used. The Cupola offers an extra layer of protection in addition to the recommended personal protective equipment.

OBJECTIVE: Different studies with adolescents address the difficulty they have to adhere to oral dental treatments. Therefore, better understanding the processes involved in adherence to treatment in this population is necessary. The aim of this study was to investigate the factors that influence adherence to dental treatment in socially underprivileged adolescents in primary care. RESULTS: Non-adherence to treatment showed high rate in the studied sample (49.5%). Family income (p = 0.039) and number of individuals in the family (p = 0.003) were associated with non-adherence to dental treatment. It is concluded that the adolescents' social vulnerability condition resulted in situations that are incompatible with adherence, which hinders dental treatment and health service planning.

OBJECTIVE: Diversion of less urgent emergency medical services (EMS) callers to alternative primary care (PC) is much debated. Using data from the EMACROSS survey of respiratory ED patients, we aimed to characterize self-referred EMS patients, compare these with non-EMS patients, and assess scope and acceptability of a potential redirection to alternative PC. RESULTS: Of n = 292 self-referred patients, n = 99 were transported by EMS. Compared to non-EMS patients, these were older, triaged more urgently and arrived out-of-hours more frequently. The share of chronically and severely ill patients was greater. Out-of-hours ED visit, presence of a chronic pulmonary condition as well as a hospital diagnosis of respiratory failure were identified as determinants of EMS utilization in a logistic model, while consultation for access and quality motives as well as migrant status decreased the probability. EMS-transported lower urgency outpatients visiting during regular physicians' hours were defined as potential PC cases and evaluated descriptively (n = 9). As a third was medically complex and potentially less suitable for PC, redirection potential could be estimated at only 6% of EMS cases. This would be reduced to 2% if considering patients' judgment concerning the appropriate setting. Overall, the scope for PC diversion of respiratory EMS patients seems limited.

OBJECTIVE: Intellectual Disability (ID) represents a neuropsychiatric disorder, which its etiopathogenesis remains insufficiently understood. Mutations in the Aristaless Related Homeobox gene (ARX) have been identified to cause syndromic and nonsyndromic (NS-ID). The most recurrent mutation of this gene is a duplication of 24pb, c.428-451dup. Epidemiological and genetic studies about ID in the Moroccan population remain very scarce, and none study is carried out on the ARX gene. This work aimed to study c.428-451dup (24 bp) mutation in the exon 2 of the ARX gene in 118 males' Moroccan patients with milder NS-ID to evaluate if the gene screening is a good tool for identifying NS-ID. RESULTS: Our mutational analysis did not show any dup(24pb) in our patients. This is because based on findings from previous studies that found ARX mutations in 70% of families with NS-ID, and in most cases, 1.5-6.1% of individuals with NS-ID have this duplication. Since 1/118 = 0.0084 (0.84%) is not much different from 1.5%, then it is reasonable that this could a sample size artifact. A complete screening of the entire ARX gene, including the five exons, should be fulfilled. Further investigations are required to confirm these results.

OBJECTIVES: Universal stool banks provide stool to physicians for use in treating recurrent Clostridioides difficile infection via fecal microbiota transplantation. Stool donors providing the material are rigorously screened for diseases and disorders with a potential microbiome etiology, and they are likely healthier than the controls in most microbiome datasets. 16S rRNA sequencing was performed on samples from a selection of stool donors at a large stool bank, OpenBiome, to characterize their gut microbial community and to compare samples across different timepoints and sequencing runs. DATA DESCRIPTION: 16S rRNA sequencing was performed on 200 samples derived from 170 unique stool donations from 86 unique donors. Samples were sequenced on 11 different sequencing runs. We are making this data available because rigorously screened, likely very healthy stool donors may be useful for characterizing and understanding microbial community differences across different populations and will help shed light into the how the microbiome community promotes health and disease.

OBJECTIVES: The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is one of the major public health concerns as colistin is the last-resort antibiotic for treating infections caused by multidrug-resistant Gram-negative bacteria. We aimed to determine the prevalence of the prototype widespread colistin resistance genes (mcr-1 and mcr-2) among commensal and pathogenic Escherichia coli strains isolated from food-producing and companion animals in Iran. RESULTS: A total of 607 E. coli isolates which were previously collected from different animal sources between 2008 and 2016 used to uncover the possible presence of plasmid-mediated colistin resistance genes (mcr-1 and mcr-2) by PCR. Overall, our results could not confirm the presence of any mcr-1 or mcr-2 positive E. coli among the studied isolates. It is concluded that despite the important role of food-producing animals in transferring the antibiotic resistance, they were not the main source for carriage of mcr-1 and mcr-2 in Iran until 2016. This study suggests that the other mcr variants (mcr-3 to mcr-9) might be responsible for conferring colistin resistance in animal isolates in Iran. The possible linkage between pig farming industry and high level of mcr carriage in some countries needs to be clarified in future prospective studies.

OBJECTIVES: Human T cell leukemia virus-1 (HTLV-1) infection may lead to one or both diseases including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) or adult T cell leukemia lymphoma (ATLL). The complete interactions of the virus with host cells in both diseases is yet to be determined. This study aims to construct an interaction network for distinct signaling pathways in these diseases based on finding differentially expressed genes (DEGs) between HAM/TSP and ATLL. RESULTS: We identified 57 hub genes with higher criteria scores in the primary protein-protein interaction network (PPIN). The ontology-based enrichment analysis revealed following important terms: positive regulation of transcription from RNA polymerase II promoter, positive regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle and positive regulation of transcription from RNA polymerase II promoter by histone modification. The upregulated genes TNF, PIK3R1, HGF, NFKBIA, CTNNB1, ESR1, SMAD2, PPARG and downregulated genes VEGFA, TLR2, STAT3, TLR4, TP53, CHUK, SERPINE1, CREB1 and BRCA1 were commonly observed in all the three enriched terms in HAM/TSP vs. ATLL. The constructed interaction network was then visualized inside a mirrored map of signaling pathways for ATLL and HAM/TSP, so that the functions of hub genes were specified in both diseases.

OBJECTIVES: Microbes can contaminate foodstuffs resulting in foodborne illnesses. Investigating microbial hazards in foods at the point of sale with rapid tools is required to avoid foodborne illness outbreaks. The current study aimed to identify the microbial hazards in food samples collected from retail shops at sale points using MALDI-TOF MS. RESULTS: Food samples were collected from stores and supermarkets in four Delta cities (Tanta, Kutour, Kafr-Elzayat and Benha). Analysis of 178 samples of fish, meat and dairy products revealed 20 different bacterial species. 44.76% of isolates were identified as E. coli, 17.44% were identified as Enterobacter spp., and E. cloacae was predominant. 12.2% were identified as Citrobacter spp., and C. braakii was predominant, and 8.7% were identified as Klebsiella spp., and K. pneumoniae was predominant. Moreover, eight Proteus mirabilis, six Morganella morganii, five Staphylococcus hominis, three Serratia marcescens, two Pseudomonas aeruginosa, one Salmonella typhimurium and one Enterococcus faecalis were detected. Foodstuffs not only be contaminated during production and processing but also during storage and transport. Identification of harmful human pathogens in foodstuffs is alarming and consider threatening to public health. Identification of microbiological hazards in foods using MALDI-TOF MS provides an efficient tool for identifying foodborne pathogens.

OBJECTIVE: The use of genome sequences from strains authenticated to correct species level is a prerequisite for confidently exploring the evolutionary relationship among related species. Aspergillus strains erroneously curated as Aspergillus oryzae and Aspergillus fumigatus have been noticed in the National Center for Biotechnology Information (NCBI) genome database. Aspergillus parasiticus is one of several aspergilli that produce aflatoxin, the most potent carcinogenic mycotoxin known up to now. To ensure that valid conclusions are drawn by researchers from their genomics-related studies, molecular analyses were carried out to authenticate identities of A. parasiticus strains in the NCBI genome database. RESULTS: Two of the nine supposedly A. parasiticus strains, E1365 and NRRL2999, were found to be misidentified. They turned out to be Aspergillus flavus based on genome-wide single nucleotide polymorphisms (SNPs) and genetic features associated with production of aflatoxin and cyclopiazonic acid. NRRL2999 lacked the additional partial aflatoxin gene cluster known to be present in its equivalent strain, designated as SU-1, and shared a very low total SNPs count specifically with A. flavus NRRL3357 but not with other A. flavus isolates. Therefore, the mislabeled NRRL2999 strain actually is a clonal strain of A. flavus NRRL3357, whose genome was first sequenced in 2005.

OBJECTIVE: Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. RESULTS: While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at - 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or - 20 °C). However only storage at - 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at - 20 °C to maximize sample integrity.

OBJECTIVE: The major objective of the study was to sequence the whole genome of four Bangladeshi individuals and identify variants that are known to be associated with functional changes or disease states. We also carried out an ontology analysis to identify the functions and pathways most likely to be affected by these variants. RESULTS: We identified around 900,000 common variants and close to 5 million unique ones in all four of the individuals. This included over 11,500 variants that caused nonsynonymous changes in proteins. Heart function associated pathways were heavily implicated by the ontology analysis; corroborating previous studies that claimed the Bangladeshi population as highly susceptible to heart disorders. Two variants were found that have been previously identified as pathogenic factors in familial hypercholesteremia and structural disorders of the heart. Other pathogenic variants we found were associated with pseudoxanthoma elasticum, cancer progression, polyagglutinable erythrocyte syndrome, preeclampsia, and others.

OBJECTIVE: We developed a silver-containing hydroxyapatite (Ag-HA) coating to prevent periprosthetic joint infection (PJI). Methicillin-resistant Staphylococcus aureus (MRSA) is the main PJI-causing bacteria. Previously, we had reported the combined effect of Ag-HA coating and vancomycin (VCM) on MRSA biofilm formation 24 h after MRSA inoculation. In this study, we investigated the time-dependent efficacy of Ag-HA coating and VCM on MRSA biofilm formation on Ti discs in vitro by three-dimensional confocal laser scanning microscopic analysis. RESULTS: For the Ti VCM and HA VCM groups, the total biofilm volumes per area at 96 h after MRSA inoculation were significantly larger than those at 48 h after MRSA inoculation, respectively (p < 0.001). In contrast, for the Ag-HA VCM group, the total biofilm volume per area at 96 h was significantly smaller than that at 48 h (p < 0.0001). Moreover, 96 h after MRSA inoculation, the total biofilm volume per area of the Ag-HA VCM groups was significantly smaller than those of the Ti VCM and HA VCM groups (p < 0.0001). Thus, the combination of Ag-HA and VCM might be useful for the prevention of MRSA-associated PJI.

OBJECTIVE: Diabetes mellitus is a chronic illness that requires ongoing patient self-management and support to prevent acute complications and to reduce the risk of long- term complications. The objective of the study was to assess diabetic self-care practice and its predictors among adults with diabetes mellitus on follow up at hospitals of Arsi zone, southeast Ethiopia. RESULTS: Above half (53.3%) of diabetic patients had good self-care practice. Younger age (AOR: 8.95, 95% CI 1.89,42.48), earning a high income (AOR: 2.495, 95% CI 1.0,5.85), having a family history of diabetes (AOR: 4.5, 95% CI 1.3, 15.5), long duration since the diagnosis of diabetes (AOR: 2.14,95% CI 1.127,4.05), not having diabetic complications (AOR: 3.87, 95% CI 2, 7.48), and having glucometer (AOR: 4.08, 95% CI 1.78 l, 9.33) were significantly associated factors with good diabetic self care practice. Efforts should be made to prevent complications of diabetes mellitus, to support patients who are aged and who have no glucometer at their home to promote good self-care practice. Particularly, health care providers should give special attention to newly diagnosed patients.

OBJECTIVE: To address the challenge of computational identification of cell type-specific regulatory elements on a genome-wide scale. RESULTS: We propose SeqEnhDL, a deep learning framework for classifying cell type-specific enhancers based on sequence features. DNA sequences of "strong enhancer" chromatin states in nine cell types from the ENCODE project were retrieved to build and test enhancer classifiers. For any DNA sequence, positional k-mer (k = 5, 7, 9 and 11) fold changes relative to randomly selected non-coding sequences across each nucleotide position were used as features for deep learning models. Three deep learning models were implemented, including multi-layer perceptron (MLP), Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN). All models in SeqEnhDL outperform state-of-the-art enhancer classifiers (including gkm-SVM and DanQ) in distinguishing cell type-specific enhancers from randomly selected non-coding sequences. Moreover, SeqEnhDL can directly discriminate enhancers from different cell types, which has not been achieved by other enhancer classifiers. Our analysis suggests that both enhancers and their tissue-specificity can be accurately identified based on their sequence features. SeqEnhDL is publicly available at https://github.com/wyp1125/SeqEnhDL .

OBJECTIVE: Field interventions employed to improve preventive health behaviors and outcomes generally use well-established approaches; however, recent studies have reported that health education and promotional interventions have little to no impact on health behaviors, especially in low- and middle-income countries. We aimed to develop a conceptual framework to improve intervention designs that would internalize these concerns and limitations. RESULTS: We identified three major experimental design- and implementation-related concerns associated with mental models, including the balance between the treatment and control groups, the treatment group's willingness to adopt suggested behaviors, and the type, length, frequency, intensity, and sequence of treatments. To minimize the influence of these aspects of an experimental design, we proposed a mental model-based repeated multifaceted (MRM) intervention design framework, which represents a supportive intervention design for the improvement of health education and promotional programs. The framework offers a step-by-step method that can be used for experimental and treatment design and outcome analysis, and that addresses potential implementation challenges.

OBJECTIVES: To determine the correlation between anthropometric indices and the selected hemodynamic parameters among secondary adolescents aged 12-17 years. RESULTS: Our findings showed weak positive correlation between generally body surface area, neck circumference and conicity index with the hemodynamic parameters (systolic blood pressure, diastolic blood pressure, resting pulse rate, mean arterial pressure, rate pressure product and pulse pressure). However, the ponderosity index, body mass index and waist hip ratio showed negative weak correlations with the hemodynamic parameters. There was a significant difference in pulse pressure among the BMI categories. All parameters showed significant (p < 0.05) differences across the categories of neck circumference and waist hip ratio. Generally, in multivariate regression analysis, anthropometric indices showed significant prediction of the hemodynamic parameters.

OBJECTIVE: This study evaluated the effect of an after-school group-based medium-intensity multicomponent behavioural intervention programme for children aged 8-12 years classified as overweight, obese or at risk for overweight on body mass index standard deviation score (BMI SDS). In accordance with standardized protocols body weight and height were measured in 195 participants (88 boys, 107 girls) at baseline and at the end of the programme. A total of 166 children derived from a school-based monitoring system served as control group. Multivariate regression analyses examined the effect of the intervention and the independent factors associated with better outcomes in the intervention group. RESULTS: Analysis of covariance showed a significant intervention effect on BMI SDS in favour of the intervention group (b-coefficient - 0.13 ± 0.03; p < 0.01) compared with the control group. Change in BMI SDS between baseline and follow-up in the intervention group was associated with baseline age (b-coefficient 0.03 ± 0.02; p = 0.04) but was independent from gender, ethnicity, baseline BMI SDS, time between baseline and follow-up, school year and attendance rate.

OBJECTIVE: In contrast to childhood obesity, studies involving thin children are much fewer, especially in developed countries. Furthermore, most reports do not address the impact of childhood thinness on height velocity. This study investigated the prevalence of thinness and its effect on height velocity in schoolchildren in the United Arab Emirates (UAE). Weight and height were measured in 29,410 schoolchildren (50.5% females), as part of the health assessment (academic year 2014-2015). The body mass index (BMI) was classified as normal, thinness, overweight, or obese using cutoffs established by the International Obesity Task Force (IOTF), World Health Organization, and Centers for Disease Control. RESULTS: The median age was 10.2 years (range, 3-19). Using the IOTF scale, one-quarter of the children aged 4-6 years and one-third of the children aged 7-9 years were thin (BMI ≤ 18.5 kg/m2). Thinness was less prevalent (8-10%) in adolescents. Group peak height velocity was delayed 1-3 years in thin children and was higher in children with excess body fat. In conclusion thinness was the highest (25-33%) in children aged 4-9 years of age and their peak height velocity was delayed 1-3 years when compared to the other children.

OBJECTIVE: It is widely acknowledged that recruitment to randomised controlled trials (RCTs) is challenging, particularly trials that operate across multiple sites. A research area in need of further high-quality evaluation, including RCTs, is school-based mental health interventions for refugee children and adolescents. However, engaging schools with interventions and associated evaluations can be challenging. This paper explores the application of behavioural insights, i.e. evidence-based understanding of how people behave and make decisions, to RCT recruitment at the school level via email communications. A pilot study of applying behavioural insights to mail outs attempting to recruit schools to a RCT of a trauma-focused group intervention for refugee children and adolescents experiencing symptoms of post-traumatic stress is reported. Rates of school involvement between the behavioural insights approach (n = 31) and a standard outreach approach (n = 65) are compared. RESULTS: Schools were more likely to give a positive response to the mail out designed using the behavioural insights framework than standard outreach. Accounts of recruitment strategies such as this are valuable additions to the literature on RCT methodology given the potential for recruitment issues to affect trial operations.

OBJECTIVE: Environmental surfaces may serve as potential reservoirs for nosocomial pathogens and facilitate transmissions via contact depending on its tenacity. This study provides data on survival kinetics of the most important nosocomial bacteria on a panel of commonly used surfaces. Type strains of S. aureus, K. pneumoniae, P. aeruginosa, A. baumannii, S. marcescens, E. faecium, E. coli, and E. cloacae were suspended in 0.9% NaCl solution at a McFarland of 1 and got then plated via cotton swabs either on glass, polyvinyl chloride, stainless steel, or aluminum. Surfaces were stored at regular ambient temperature and humidity to simulate routine daycare conditions. Sampling was performed by contact plates for a time period of four weeks. RESULTS: The longest survival was observed for A. baumannii and E. faecium on all materials (at least four weeks). S. aureus remained viable for at least one week. Gram negative species other than A. baumannii were usually inactivated in less than two days. Nosocomial transmission of the above mentioned bacteria may easily occur if no appropriate infection control measures are applied on a regular daily basis. This might be of particular importance when dealing with outbreaks of A. baumannii and E. faecium.

OBJECTIVE: The Middle East respiratory syndrome coronavirus (MERS-CoV) is one of the zoonotic coronaviruses [Hemida Peer J 7:e7556, 2019; Hemida et al. One Health 8:100102, 2019]. The dromedary camels remained the only known animal reservoir for this virus. Several aspects of the transmission cycle of the virus between animals, including arthropod-borne infection, is still largely unknown. The main objective of the current work was to study the possibility of MERS-CoV transmission through some arthropod vectors, particularly the hard ticks. To achieve this objective, we identified a positive MERS-CoV dromedary camel herd using the commercial available real-time PCR kits. We collected some arthropods, particularly the ticks from these positive animals as well as from the animal habitats. We tested these arthropods for the presence of MERS-CoV viral RNAs. RESULTS: Our results showing the absence of any detectable MERS-CoV-RNAs in these arthropods despite these animals were actively shedding the virus in their nasal secretions. Our results are confirming for the first the failure of detection of the MERS-CoV in ticks infesting dromedary camels. Failure of the detection of MERS-CoV in ticks infesting positive naturally infected MERS-CoV camels is strongly suggesting that ticks do not play roles in the transmission of the virus among the animals and close contact humans.

OBJECTIVE: Acute viral hepatitis (AVH) caused by hepatitis virus A and hepatitis virus E is one of the many epidemics that plague third world countries like Pakistan. The serological tests required for the diagnosis of acute viral hepatitis may be unavailable or unaffordable to the denizens of a developing country like Pakistan. In such a scenario, the clinical manifestations and the ultrasonographic findings are the only diagnostic criteria usually present and these can be used to support a clinical diagnosis. This study aims to judge the utility of ultrasound in the diagnosis of AVH. RESULTS: Among the forty-seven subjects of this study, gall bladder wall thickening (GWT) was the most common radiological finding seen in 39 (82.9%) patients. Pericholecystic edema was the second most common finding, seen in 31 (65.9%) patients. Starry sky appearance of the liver was observed in 30 (63.8) patients. Hepatomegaly and ascites were seen in 28 (59.5%) and 25 (53.2%) of the patients, respectively. The ultrasonographic findings of GWT, pericholecystic edema, and starry sky appearance of the liver were the most common ultrasonographic findings associated with AVH.

OBJECTIVE: Lymphocytes express tyrosine hydroxylase (TH), the rate-limiting enzyme for the synthesis of dopamine, norepinephrine and epinephrine. This suggests a broader role for cathecholamines in lymphocyte function, as well as the potential secretion of catecholamines by tumors of lymphoid origin. Our aim was to evaluate the expression of Th by murine lymphoma cells in an in vivo mouse model. For this, L5178Y-R lymphoma cells were implanted in nerve-intact and sympathectomized male BALB/c mice. Relative Th gene expression in tumor and brain was determined by quantitative PCR. Body composition, tumor volume, and plasma TH1/TH2/TH17 cytokines were also evaluated as markers of tumor-host condition and anti-tumor immune response in absence of adrenergic innervation. RESULTS: We found a significant (p = 0.045) 3.3-fold decrease of Th gene expression in tumor and a non-significant (p = 0.60) 6.9-fold increase in brain after sympathectomy. Sympathectomized mice also showed a significant increase in tumor mass at days 18 (p = 0.032) and 28 (p = 0.022) and increased interscapular fat (p = 0.04). TH1/TH2 and TH17 cytokines levels in plasma from sympathectomized tumor-bearing mice were not different from control mice. CONCLUSION: The L5178Y-R lymphoma does not express Th during in vivo progression.

OBJECTIVE: The objectives of this study were to investigate the antifungal susceptibility and genetic diversity of Candida albicans isolated from HIV+ patients with oropharyngeal candidiasis. A total of 50 C. albicans isolates were cultured on Sabouraud glucose agar containing chloramophenicol. The antifungal susceptibility of the isolates against fluconazole, clotrimazole, nystatin, amphotericin B, ketoconazole and flucytosine was assessed using disc diffusion method. The genetic diversity of C. albicans isolates was determined using random amplified polymorphic DNA marker. RESULTS: The inhibition zones ranged from 4 ± 1.8 to 40 ± 3.8 mm for fluconazole, 7 ± 1.0 to 37 ± 1.8 mm for ketoconazole, 14 ± 0.8 to24 ± 0.8 mm for amphotericin B, 25 ± 0.0 to 33 ± 0.0 mm for nystatin and 7 ± 4.2 to 40 ± 0.0 mm for clotrimazole. At 90% similarity, three distinct groups were observed. The smallest cluster composed of 3 isolates, whereas the largest one composed of 17 isolates. 32% (16/50), 28% (14/50) and 14% (7/50) were resistant to fluconazole, ketoconazole and clotrimazole, respectively.

OBJECTIVE: Brucellosis is a zoonosis almost chronic disease. Brucellosis bacteria can remain in the environment for a long time. Thus, climate irregularities could pave the way for the survival of the bacterium brucellosis. Brucellosis is more common in men 25 to 29 years of age, in the western provinces, and in the spring months. The aim of this study is to investigate the effect of climatic factors as well as predicting the incidence of brucellosis in Qazvin province using the Markov switching model (MSM). This study is a secondary study of data collected from 2010 to 2019 in Qazvin province. The data include brucellosis cases and climatic parameters. Two state MSM with time lags of 0, 1 and 2 was fitted to the data. The Bayesian information criterion (BIC) was used to evaluate the models. RESULTS: According to the BIC, the two-state MSM with a 1-month lag is a suitable model. The month, the average-wind-speed, the minimum-temperature have a positive effect on the number of brucellosis, the age and rainfall have a negative effect. The results show that the probability of an outbreak for the third month of 2019 is 0.30%.

OBJECTIVE: Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and functionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd members is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in differing reaction chemistries amongst i2OGdd members. An additional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. RESULTS: This work reports the implementation of [Formula: see text], a web server with dual functionality and an extension of previous work on i2OGdd enzymes [Formula: see text]. [Formula: see text], in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochemistry and function. [Formula: see text], utilizes the superior predictive propensity of HMM-profiles of laboratory validated i2OGdd members to predict probable active site geometries in user-defined protein sequences. [Formula: see text], also provides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant. [Formula: see text], is freely available ( http://204.152.217.16/Fe2OG.html ) and supersedes all previous versions, i.e., H2OGpred, DB2OG.