OBJECTIVE: The present simulation study aimed to assess positive predictive value (PPV) and negative predictive value (NPV) for our newly introduced Accounting for Expected Adjusted Effect test (AEAE test) and compare it to PPV and NPV for a traditional zero-order significance test. RESULTS: The AEAE test exhibited greater PPV compared to a traditional zero-order significance test, especially with a strong true adjusted effect, low prior probability, high degree of confounding, large sample size, high reliability in the measurement of predictor X and outcome Y, and low reliability in the measurement of confounder Z. The zero-order significance test, on the other hand, exhibited higher NPV, except for some combinations of high degree of confounding and large sample size, or low reliability in the measurement of Z and high reliability in the measurement of X/Y, in which case the zero-order significance test can be completely uninformative. Taken together, the findings demonstrate desirable statistical properties for the AEAE test compared to a traditional zero-order significance test.

OBJECTIVE: In this study, the performance of a commercially available malaria LAMP assay (Alethia® Malaria Plus LAMP) was evaluated using retrospective clinical samples obtained from travelers returning to the United States of America (USA). Recently, several laboratories in non-malaria endemic countries evaluated the use of the loop mediated isothermal amplification (LAMP) assays for the diagnosis of imported malaria cases. These tests are simpler than polymerase-chain reaction (PCR)-based assays and were shown to have high sensitivity. Much of malaria diagnoses in the USA, is undertaken at the state level using mainly microscopy and rapid diagnostic tests (RDTs). However, molecular tools offer greater sensitivity over microscopy and RDTs. A reliable, easy to perform molecular assay can provide a test of choice for the accurate detection of malaria parasites in places where expert microscopy is lacking and/or for the detection of low-parasite density infections. RESULTS: The Alethia® Malaria Plus LAMP assay was easy to use, had similar test performances as the real-time PCR reference test and results were obtained faster (within 1 h) than the reference test. The sensitivity of the assay was 100% with a kappa score of 1 when compared to the reference PET-PCR assay.

OBJECTIVE: The current experiment aimed to assess the impact of detergents such as 3% Triton X-100, 1% peracetic acid, 1% Tween-20, and 1% SDS in combination with Trypsin-EDTA on acellularization of ovine aortae after 7 days. RESULTS: Hematoxylin-Eosin staining showed an appropriate acellularization rate in ovine aortae, indicated by a lack of cell nuclei in the tunica media layer. DAPI staining confirmed the lack of nuclei in the vascular wall after being exposed to the combination of chemical and enzymatic solutions. Verhoeff-Van Gieson staining showed that elastin fibers were diminished in acellular samples compared to the control group while collagen stands were unchanged. CCK-8 survival assay showed enhanced viability in human umbilical vein endothelial cells 5 days after being cultured on decellularized samples compared to the cells cultured on a plastic surface (p < 0.05). SEM imaging showed flattening of endothelial cells on the acellular surface.

OBJECTIVE: An understanding of the trajectory and norm of development in children is needed in order to understand the concept of the spectrum in the diagnosis of autism spectrum disorder (ASD). Children's developmental growth trajectory was measured from six to 66 months in the Taiwan Birth Cohort Study dataset (N = 11,145). Additionally, over 4 years of follow-up, the negative predictive value of using the Parental Concern Checklist and Taiwan Birth Cohort Study Developmental Instrument was also investigated as the first stage of screening in a two-stage window screening method for ASD diagnosis. RESULTS: The growth trajectory showed that children's language development began to increase at 18 months, and peaked at 36 months. On the other hand, social development showed steady growth from 18 to 66 months. The increase in the trajectory of children's language development prior to age three, when compared with other developmental dimensions, may increase the difficulty of diagnosing ASD. The two-stage window screening method can be used in settings where the screening sample is large, such as in community or primary care settings, and has been found to be time- and cost-efficient. Better understanding of children's developmental trajectory can enhance detection and intervention for ASD.

OBJECTIVE: Sperm ageing has major evolutionary implications but has received comparatively little attention. Ageing in sperm and other cells is driven largely by oxidative damage from reactive oxygen species (ROS) generated by the mitochondria. Rates of organismal ageing differ across species and are theorized to be linked to somatic ROS levels. However, it is unknown whether sperm ageing rates are correlated with organismal ageing rates. Here, we investigate this question by comparing sperm ROS production in four lines of Drosophila melanogaster that have previously been shown to differ in somatic mitochondrial ROS production, including two commonly used wild-type lines and two lines with genetic modifications standardly used in ageing research. RESULTS: Somatic ROS production was previously shown to be lower in wild-type Oregon-R than in wild-type Dahomey flies; decreased by the expression of alternative oxidase (AOX), a protein that shortens the electron transport chain; and increased by a loss-of-function mutation in dj-1β, a gene involved in ROS scavenging. Contrary to predictions, we found no differences among these four lines in the rate of sperm ROS production. We discuss the implications of our results, the limitations of our study, and possible directions for future research.

OBJECTIVE: Transient receptor potential ankyrin 1 (TRPA1) is an excitatory ion channel expressed on a subset of sensory neurons. TRPA1 is activated by a host of noxious stimuli including pollutants, irritants, oxidative stress and inflammation, and is thought to play an important role in nociception and pain perception. TRPA1 is therefore a therapeutic target for diseases with nociceptive sensory signaling components. TRPA1 orthologs have been shown to have differential sensitivity to certain ligands. Cinnamaldehyde has previously been shown to activate sensory neurons via the selective gating of TRPA1. Here, we tested the sensitivity of cinnamaldehyde-evoked responses in mouse and guinea pig sensory neurons to the pore blocker ruthenium red (RuR). RESULTS: Cinnamaldehyde, the canonical TRPA1-selective agonist, caused robust calcium fluxes in trigeminal neurons dissociated from both mice and guinea pigs. RuR effectively inhibited cinnamaldehyde-evoked responses in mouse neurons at 30 nM, with complete block seen with 3 μM. In contrast, responses in guinea pig neurons were only partially inhibited by 3 μM RuR. We conclude that RuR has a decreased affinity for guinea pig TRPA1 compared to mouse TRPA1. This study provides further evidence of differences in ligand affinity for TRPA1 in animal models relevant for drug development.

OBJECTIVE: The aim of this study was to design a domestic water temperature, pH and turbidity monitoring system that could constantly log temperature, pH and turbidity of water and give alerts in case the parameters are outside the acceptable limits for potable water. RESULTS: The system was designed, assembled and performed as expected. The study indicates that the proposed and designed system outperforms the existing manual monitoring system as it can constantly track and store changes in water quality. This could be used to prepare better treatment processes as well as identify problems in the water distribution system early enough.

OBJECTIVES: The aim of the current study was to assess prevalence of Toxoplasma infection and its associated risk factors in women of childbearing-age in central Iran. RESULTS: Of 400 serum samples assessed for anti-T. gondii antibodies, 81 (20.25%) samples were positive for anti-T. gondii antibodies, including 74 positive samples (91.3%) for anti-T. gondii IgG and seven positive samples (8.7%) for IgG and IgM. Of seven IgG and IgM positive samples, five and two samples were high and low in IgG avidity, respectively. Based on PCR analysis, Toxoplasma infection was detected in one sample with anti-T. gondii IgM and low IgG avidity. The Chi-square test showed significant correlations of T. gondii seropositivity with history of undercooked meat consumption and contacts with cats (p < 0.05). In the present study, 79.75% of the participants were negative for IgG against T. gondii infection. Furthermore, recently acquired Toxoplasma infection was found using IgG avidity and PCR assays among women of childbearing-age in the study area, which would increase the risk of their fetus becoming infected. Educational program and antenatal screening of childbearing-age women for T. gondii infection may be important primary prevention strategies and help reduce the risk of congenital toxoplasmosis in this population.

OBJECTIVE: Previously we observed that maternal multiple micronutrient supplementation in pregnancy was associated with increased offspring size at birth and adiposity, as well as with maternal gestational diabetes risk, in the Cambridge Baby Growth Study. In this study we therefore investigated whether folic acid supplementation specifically is associated with similar changes, to test the hypothesis that folic acid supplementation mediates such changes. RESULTS: The majority of mothers who reported supplementing with folic acid in pregnancy (n = 776 in total, 526 of which took multiple micronutrient preparations) did so either from pre- (n = 139) or post-conception (n = 637) largely for all or just the first half of pregnancy. A minority of mothers (n = 198) reported not supplementing with folic acid. Folic acid supplementation in pregnancy was not associated with birth weight [β' = - 0.003, p = 0.9], height [β' = - 0.013, p = 0.6], head circumference [β' = 0.003, p = 0.09] or adiposity (ponderal index [β' = 0.020, p = 0.5], skinfolds thicknesses [β' = - 0.029 to + 0.008, p = 0.4-0.9]). Neither was it associated with the development of maternal gestational diabetes (risk ratio 1.2 [0.6‒2.2], p = 0.6). These results suggest that folic acid supplementation in pregnancy did not mediate the previously observed increases in offspring size at birth and adiposity, or the raised gestational diabetes risk, in response to supplementation with multiple micronutrients.

OBJECTIVE: Properties of gene products can be described or annotated with Gene Ontology (GO) terms. But for many genes we have limited information about their products, for example with respect to function. This is particularly true for long non-coding RNAs (lncRNAs), where the function in most cases is unknown. However, it has been shown that annotation as described by GO terms to some extent can be predicted by enrichment analysis on properties of co-expressed genes. RESULTS: GAPGOM integrates two relevant algorithms, lncRNA2GOA and TopoICSim, into a user-friendly R package. Here lncRNA2GOA does annotation prediction by co-expression, whereas TopoICSim estimates similarity between GO graphs, which can be used for benchmarking of prediction performance, but also for comparison of GO graphs in general. The package provides an improved implementation of the original tools, with substantial improvements in performance and documentation, unified interfaces, and additional features.

OBJECTIVE: Family-based multi-component weight management programmes are recommended for adolescents with obesity in England and Wales, however, these programmes suffer from poor uptake and high attrition rates. This study aimed to gather the views of professional stakeholders in a UK weight management programme to identify potential areas to target to improve engagement and success for such programmes. RESULTS: Semi-structured interviews were conducted with those involved in the commissioning, referral, coordination or delivery of a weight management programme (n = 11). Interviews were analysed using qualitative content analysis. Three main categories developed: professional support, tailoring and intervention content. Participants recognised the importance of support from experienced professionals, as well as family and peers. There was agreement that longer-term support was needed for adolescents with obesity; suggestions included integrating follow-up support with schools and leisure services. Emotional and psychological support must be prioritised. Having a variety of delivery modes, such as group and one to one, particularly in the home environment, were recommended. Stakeholders agreed that weight management programmes for adolescents need to be more proactive at incorporating technology. By acting on the views of those that work closely with adolescents, engagement with weight management programmes may be improved.

OBJECTIVE: Participation in physical activity and sports is known to have positive implications for physical health, and for social and emotional wellbeing of children. Following corrective spinal surgery for scoliosis, the timeline for the return to activities and sports varies from surgeon to surgeon and from location to location, and return to activities can be limited due to pain, fear, and decreased flexibility. It is critical that patients know best-practice guidelines, and it is equally critical that medical professionals know whether their patients are following those guidelines. This paper includes a summary of recommendations published in the literature, and a pilot study to address a gap in the literature on determining how long, post-surgery, adolescents with idiopathic scoliosis waited before returning to various self-care and physical activities, and what factors influenced return to activities. We used a mixed-method approach that involved two phases: a questionnaire (n = 8), and subsequent interviews of some participants (n = 3). Participants were ages 14-17 (M = 15.4) and had had posterior instrumentation and fusion for scoliosis in the past 2 years. RESULTS: Some patients were cautious about return to activities, either because of emotional or medical reasons. However, in many instances, participants returned to physical activities earlier than was recommended, primarily for emotional and social reasons.

OBJECTIVE: Psychological problems associated with isolation and mistrust are common among young adults with autism spectrum disorder (ASD). Schema therapy (ST) has recently been shown to be effective against chronic personality problems of various mental disorders, including personality disorders. This pilot clinical trial aimed to explore the feasibility and acceptability of ST in young adults with high-functioning ASD. RESULTS: Following the intervention, a significant reduction in early maladaptive schemas and improvements in quality of life and social adjustment were observed. ST may be feasible and is applicable to young adults with HF-ASD. Trial registration UMIN000014535; registered on July 11, 2014.

OBJECTIVE: Cardiac regeneration in the axolotl has been found to rely on the innate immune system, and especially macrophages have been demonstrated to play a vital role in regulating the regenerative process. In this study we wanted to induce a pro- and anti-inflammatory milieu in the axolotl during heart regeneration to test the resilience of the regenerative response. RESULTS: This was induced via repeated intrapericardial injections of lipopolysaccharide or prednisolone during a 40-day regeneration period in order to challenge the presumably fine-tuned inflammatory response that normally facilitates regeneration. We observed a local and systemic leucocyte response to pro- and anti-inflammatory stimulation, but we found cardiac regeneration to be structurally and functionally unaffected.

OBJECTIVE: Gut-microbiota plays key roles in many aspects like the health and illness of humans. It's well proved that modification of gut microbiota by probiotics is useful for improving inflammatory bowel disease (IBD) conditions. According to recent studies, different types of bacterial metabolites can affect immune cells and inflammation conditions. The present study aimed to evaluate the anti-inflammatory effects of metabolites of E. coli Nissle1917. RESULTS: The cell-free supernatant could modulate TNF-α production and affected many crucial mediators in the Toll-like receptor (TLR) signaling pathway. Also, supernatant showed significant dose-dependent properties in this regard. In this study, the TLR signaling pathway was found among probable mechanisms by which probiotics can affect inflammatory situations. These findings provide additional evidence on the use of probiotic metabolites for inhibiting and down-regulating numerous key mediator factors in the TLR signaling pathway. Aberrant or dysfunctional TLR signaling contributes to the development of acute and chronic intestinal inflammatory pathways in IBD. Therefore, finding a component that can affect this process might be considered for therapeutic targets in IBD patients.

OBJECTIVE: Human is accustomed to climatic conditions of the environment where they are born and live throughout their lifetime. The aim of this study is to examine mood swings and depression caused by sudden climate changes that have not yet given the humans a chance to adapt. RESULTS: Our results showed that depression could be affected by climate change and as a result, the behavior of climatic elements and trends has damaged mental health in the western regions of Iran. By investigating the trends and changes of climatic time series and their relationship with the rate of depression in urban areas of western Iran, it can be said that climate change is probably a mental health challenge for urban populations. Climate change is an important and worrying issue that makes the life difficult. Rapid climate changes in western Iran including rising air temperature, changes in precipitation, its regime, changes cloudiness and the amount of sunlight have a negative effects on health. The results showed that type of increasing or decreasing trend, as well as different climatic elements in various seasons did not have the same effect on the rate of depression in the studied areas.

OBJECTIVE: Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. RESULTS: The L. agilis epitranscriptome (minus rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.

OBJECTIVES: Tree legume species play an important role in forest restoration in the tropics. Understanding how different species adjust carbohydrate allocation and growth under distinct nutrient availability will enhance the success of restoring degraded areas. DATA DESCRIPTION: A 2-year tropical forest plantation of the Forest Restoration Program of the Balbina Hydropower Dam was evaluated. Three non-N-fixing (Cenostigma tocantinum, Dipteryx odorata and Senna reticulata) and three N-fixing (Clitoria fairchildiana, Inga edulis and Acacia spp.) tree legume species were either fertilized or not fertilized. Growth rates and biomass allocation were calculated, and carbon (C) fractions and nitrogen (N), phosphorus (P) and nonstructural carbohydrate (NSC) concentrations were determined. Multiple nutrient additions increased the growth rates and aboveground biomass production of fertilized plants. According to the results presented, different species and N- fixers respond differently to fertilization regimes. The authors encourage the use of the presented data in meta-analysis studies that consider the fertilization or nutrient deficiency effects on growth, carbohydrate and nutrient responses. N-fixing species with high biomass growth and foliar N are important for restoring N and C cycles in nutrient-limited soils. Fertilization treatments are fundamental during the early stages of forest plantation development.

OBJECTIVE: In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. RESULTS: The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

OBJECTIVE: Breast cancer (BC) is one of the most common diseases in women globally, with an increasing number of deaths associated with it. Recently the role of polymorphisms in the genes encoding cytokines and immune cells has been demonstrated. This study aimed to evaluate the association of IFN-Ɣ + 874 A/T polymorphism with BC clinical symptoms. RESULTS: The study included 88 women with BC and 88 healthy women who had no history of cancer and were matched for age and sex. Allele-specific oligonucleotide-polymerase chain reaction technique was used to investigate the IFN-Ɣ polymorphism. Clinical data were obtained from the patients' records. Our results showed that the frequencies of genotypes in the BC patients were not significantly different from the control subjects. However, in the patients, the AT genotype was associated with the risk of malignant BC. The age at BC diagnosis was not different in patients with AA and AT genotypes; however, it was significantly earlier in HER2 negative subjects (p = 0.002). Given the higher frequency of AT in malignant BC patients, our results confirm the association of the IFN-Ɣ polymorphism with the disease's progression to a malignant state.

OBJECTIVE: The purpose of the present study was to investigate the antimicrobial susceptibility pattern, biofilm production, and the presence of biofilm genes among the S. maltophilia clinical isolates. A total of 85 clinical isolates of S. maltophilia were collected from patients referred to several hospitals. Susceptibility to antibiotics was investigated by disc diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). By the crystal violet staining method, the capability of biofilm formation was examined. The genes associated with biofilm production were investigated by the PCR-sequencing techniques. RESULTS: All isolates were resistant to doripenem, imipenem, and meropenem. Minocycline, trimethoprim/sulfamethoxazole and levofloxacin exhibited the highest susceptibility of 100%, 97.65%, and 95.29%, respectively. The results of crystal violet staining assay showed that all isolates (100%) form biofilm. Moreover, 24 (28.23%), 32 (37.65%), and 29 (34.12%) of isolates were categorized as weak, moderate, and strong biofilm producers, respectively. Biofilm genes including rpfF, spgM and rmlA had an overall prevalence of 89.41% (76/85), 100% (85/85) and 84.71% (72/85), respectively. Rational prescribing of antibiotics and implementation of infection control protocols are necessary to prevent further infection and development of antimicrobial resistance. Combination strategies based on the appropriate antibiotics along with anti-biofilm agents can also be selected to eliminate biofilm-associated infections.

OBJECTIVE: Through collating observations from various studies and complementing these findings with one author's study, a detailed overview of the benefits and drawbacks of asynchronous email interviewing is provided. Through this overview, it is evident there is great potential for asynchronous email interviews in the broad field of health, particularly for studies drawing on expertise from participants in academia or professional settings, those across varied geographical settings (i.e. potential for global public health research), and/or in circumstances when face-to-face interactions are not possible (e.g. COVID-19). RESULTS: Benefits of asynchronous email interviewing and additional considerations for researchers are discussed around: (i) access transcending geographic location and during restricted face-to-face communications; (ii) feasibility and cost; (iii) sampling and inclusion of diverse participants; (iv) facilitating snowball sampling and increased transparency; (v) data collection with working professionals; (vi) anonymity; (vii) verification of participants; (viii) data quality and enhanced data accuracy; and (ix) overcoming language barriers. Similarly, potential drawbacks of asynchronous email interviews are also discussed with suggested remedies, which centre around: (i) time; (ii) participant verification and confidentiality; (iii) technology and sampling concerns; (iv) data quality and availability; and (v) need for enhanced clarity and precision.

OBJECTIVE: Herd immunity is achieved when in a population, immune individuals are in a sufficiently large proportion. Neutralizing antibodies specific to SARS-CoV-2 that are produced following infection or vaccination are critical for controlling the spread of COVID-19. The objective of the present work was to investigate the rate of SARS-CoV-2 natural immunization in Gabonese. RESULTS: One thousand, four hundred and ninety two people were enrolled. The overall prevalence of anti-SARS-CoV-2 antibodies was 36.2%. Moreover, 76.4% of people who developed a humoral response to SARS-CoV-2 produced both anti-SARS-CoV-2 N-protein antibodies and anti-SARS-CoV-2 S-protein antibodies, which correspond to 27.7% of the total population. In infants (0-9 month), children (1-17 years) and adults, the prevalence of anti-SARS-CoV-2 antibodies was relatively the same, between 33 and 37% (any antibody types) and between 25 and 28.6% (neutralizing antibodies). In this African context, one-third (1/3) of the screened population was exposed to SARS-CoV-2 and three-quarter (3/4) of those exposed individuals developed neutralizing antibodies against SARS-CoV-2. This data suggest that herd immunity is not yet to be achieved in Gabon.

OBJECTIVE: Deep extubation refers to endotracheal extubation performed while a patient is deeply anesthetized and without airway reflexes. After deep extubation, patients are sent to the post-anesthesia care unit (PACU) to recover, an area with notably different management and staffing than the operating room (OR). One of the most frequent and concerning complications to occur in the PACU is hypoxemia. As such, this study seeks to evaluate the incidence of desaturation, defined by SpO2 < 90% for longer than 10 s, in the PACU following deep extubation. Additionally, we hope to assess the consequence of desaturation on perioperative workflow by comparing PACU recovery times. RESULTS: Following deep extubation, 4.3% of patients (13/300) experienced desaturation in the PACU. Every episode was notably minor, with patients reverting to normal saturation levels within a minute. Of the 26 case factors assessed, 24 had no significant association desaturation in the PACU, including the amount of time spent in the PACU. History of asthma was the only statistically significant factor found to be positively associated with desaturation. We find that PACU desaturation episodes following deep extubation are rare. Our findings suggest that deep extubation is a viable and safe option for patients without significant respiratory tract pathology.

OBJECTIVE: This study aimed to identify novel genetic variants in the CR2 extracellular domain of the epidermal growth factor receptor (EGFR) in healthy individuals and patients with six different types of adenocarcinoma, in Arabian peninsula populations. It also aimed to investigate the effects of these variants on the EGFR structure and their eventual relevance to tumorigenesis. RESULTS: We detected seven new EGFR genetic variants in 168 cancer patients and 114 controls. A SNP rs374670788 was more frequent in bladder cancer but not significantly associated to. However, a missense mutation (V550M) was significantly associated to colon, ovary, lung, bladder and thyroid cancer samples (p < 0.05). Three mutations (H590R, E602K and T605T) were found in the heterozygous form only in colon cancer patients. Genomic analysis of the synonymous mutation (G632G) showed that the T/A genotype could be associated to thyroid cancer in Arab patients (p < 0.05). An additional novel SNP rs571064657 was observed in control individuals. Computational analysis of the genetic variants revealed a reduction in the stabilization of the EGFR tethered form for both V550M and the common R521K variant with low energetic state (- ∆∆G). Molecular interactions analysis suggested that these mutations might affect the receptor's function and promote tumorigenesis.

OBJECTIVES: Prediabetes is prevalent in people living with HIV (PLWH). Insufficient and irregular sleep are linked to abnormal glucose metabolism. This study aimed to investigate the differences in sleep characteristics between PLWH with and without prediabetes, determine the acceptability/feasibility and effects of a pilot six-month intensive lifestyle intervention (ILI) program on glucose metabolism in those with prediabetes, and determine how sleep modulates these effects. RESULTS: Thirty-nine PLWH (20 normoglycemia and 19 prediabetes) participated. There were no differences in sleep characteristics between individuals with normoglycemia and prediabetes. Next, thirteen individuals with prediabetes completed a six-month ILI program. The ILI program resulted in significant body weight reduction at 6 months (63.5 ± 13.9 to 61.9 ± 14.0 kg, p = 0.012), which was maintained at 12 months (p < 0.001). Waist circumferences were significantly decreased at 12 months (85.4 ± 11.7 to 82.9 ± 12.7 cm, p = 0.014). An increase in sleep variability was significantly associated with an increase in 2-h plasma glucose, independent of changes in BMI (b = 0.603), and physical activity (b = 0.774). This pilot study suggested that ILI in PLWH with prediabetes is feasible and effective in improving metabolic control, with its effects possibly modulated by sleep variability. These findings should be confirmed in a larger study to reduce diabetes risk in this population. Trail registration: ClinicalTrial.gov, NCT03545217 (date of registration: May 22, 2018).

OBJECTIVE: The aim of this study was to investigate the genetic relatedness and antimicrobial resistance among Shigella species isolated from food and stool samples. Using cross sectional study method, Shigella spp. were isolated from food and clinical samples using culture-based, biochemical and serological methods. Antimicrobial susceptibility and genetic relatedness among the isolates were evaluated using disk diffusion and RAPD-PCR methods respectively. RESULTS: The prevalence of Shigella spp. were 4.84 and 7.7% in food and stool samples respectively. All food isolates were Sh. sonnei. 91.42% of the Shigella stool isolates were Sh. sonnei. 62.5% of food isolates were resistant to tetracycline. 46.8, 50 and 65.8% of clinical isolates were resistant to imipenem, amikacin and azithromycin respectively. 50 and 85.7% of the food and clinical isolates respectively were MDR. Dendrogram generated by RAPD-PCR showed that the isolates from food and stool samples were categorized in a same group. Close genetic relatedness between MDR Shigella isolates from food and clinical samples indicate that foods can be considered as one of the main vehicles for transmission of MDR Shigella to human causing acute diseases. Survey of MDR Shigella among food and clinical samples is strongly suggested to be implemented.

OBJECTIVES: Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. DATA DESCRIPTION: We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.

OBJECTIVE: Although children from language backgrounds other than English (LBOTE) may be disadvantaged in English-reliant exams, they outperform children from an English language background (ELB) on many Australian National Assessment Program-Literacy and Numeracy (NAPLAN) assessments. Maternal alcohol and tobacco use during pregnancy and/or breastfeeding have been associated with poorer cognitive and academic performance. Using data from the Growing Up in Australia Study, this paper aimed to identify demographic, lifestyle, and prenatal and perinatal risk differences related to maternal tobacco and alcohol use between LBOTE and ELB groups, as a first step in trying to understand the academic performance differences. RESULTS: Only data from breastfed babies was included in the current analyses. Although LBOTE children were disadvantaged in several demographic areas, their NAPLAN performance was the same or superior to ELB children across all Grade 3 and 5 NAPLAN assessments. The LBOTE group were, however, breastfed for longer, and their mothers smoked fewer cigarettes and drank less alcohol on fewer occasions throughout their pregnancy. The LBOTE mothers also had lower or less risky patterns of alcohol consumption while breastfeeding. The longer breastfeeding duration of LBOTE children combined with lower maternal use of alcohol and cigarettes during pregnancy and/or breastfeeding may partially contribute to their exceptional NAPLAN performance.

OBJECTIVE: This study aimed to validate the Sick, Control, One stone, Fat, and Food (SCOFF) questionnaire in relation to the Eating Disorders Examination Questionnaire (EDE-Q) and to examine the appropriateness of a question concerning weight loss among Japanese university students. The psychometric properties of the two Japanese versions were determined among 649 Japanese college students. The original version (SCOFF-O) employed the original item 3, whereas the revised version (SCOFF-2.5) modified the item to "Have you recently lost more than 2.5 kg within three months?" Validity was tested relative to EDE-Q. RESULTS: The test-retest reliabilities of SCOFF-O and SCOFF-2.5 were 0.52 and 0.57, while the correlations of SCOFF-O and SCOFF-2.5 with EDE-Q were r = 0.53 and r = 0.56. The sensitivity and specificity of SCOFF-O were 65.2 and 89.7, and those of SCOFF-2.5 were 69.5 and 86.5, respectively. There were significant correlations between the question concerning losing 2.5 kg and the EDE-Q subscales. The Japanese version of SCOFF-2.5 is an appropriate tool for the early screening of eating disorders among Japanese university students.

OBJECTIVE: The COVID-19 pandemic and the measures implemented to stop the pandemic had a broad impact on our daily lives. Besides work and social life, health care is affected on many levels. In particular, there is concern that attendance in health care programs will drop or hospital admissions will be delayed due to COVID-19-related anxieties, especially in children. Therefore, we compared the number of weekly visits to 78 German pediatric institutions between 2019 and 2020. RESULTS: We found no significant differences during the first 10 weeks of the year. However, and importantly, from April, the weekly number of visits was more than 35% lower in 2020 than in 2019 (p = 0.005). In conclusion, the COVID-19 pandemic seems to relate to families´ utilization of outpatient well-child clinics and pediatric practice attendance in Germany.

OBJECTIVES: The study aims to generate the whole genome sequence of L. monocytogenes strain S2542 and to compare it to the genomes of strains RO15 and ScottA. In addition, we aimed to compare gene expression profiles of L. monocytogenes strains S2542, ScottA and RO15 after high-pressure processing (HPP) using ddPCR. RESULTS: The whole genome sequence of L. monocytogenes S2542 indicates that this strain belongs to serotype 4b, in contrast to the previously reported serotype 1/2a. Strain S2542 appears to be more susceptible to the treatment at 400 MPa compared to RO15 and ScottA strains. In contrast to RO15 and ScottA strains, viable cell counts of strain S2542 were below the limit of detection after HPP (400 MPa/8 min) when stored at 8 °C for 24 and 48 h. The transcriptional response of all three strains to HPP was not significantly different.

OBJECTIVE: Snails secrete different types of mucus that serve several functions, and are increasingly being exploited for medical and cosmetic applications. In this study, we explored the protein pattern and compared the biological properties of the mucus secreted from the mantle collar and foot of two snail species, Lissachatina fulica and Hemiplecta distincta. RESULT: Protein profile showed a different pattern between the two species and between the two secretory parts. The mantle-specific protein bands were further characterized and among them was an antibacterial protein, achacin. Accordingly, the mucus from the mantle exhibited the higher antibacterial activity than that from the foot in both snail species. The mucus from H. distincta, first reported here, also showed antibacterial properties, but with a lower activity compared to that for L. fulica. Snail mucus also exhibited anti-tyrosinase activity and antioxidant activity but with no significant difference between the foot and mantle mucus. These results indicate some different protein compositions and biological activities of snail slime from the mantle and foot, which might be associated with their specific functions in the animal and are useful for medical applications.

OBJECTIVES: To evaluate the number of out-of-hospital cardiac arrest (OHCA) patients eligible for extracorporeal cardiopulmonary resuscitation (ECPR) in Saskatchewan and their clinical outcomes, including survival and neurological outcomes at discharge. ECPR eligibility was assessed, using clinical criteria from the University of British Columbia (UBC, Canada), University of Michigan (UM, United States), University of California (UC, United States) and a restrictive ECPR criteria. RESULTS: We performed a retrospective cohort study of 200 OHCA patients (August 1, 2017-May 31, 2019) in Regina, Saskatchewan. Sixty-one (30%) were female, the median age was 64 years (interquartile range [IQR], 52-78), the median CPR duration was 30 min (IQR 12-47), and 20% survived to discharge. Two (1%) patients received ECPR but did not meet any ECPR criteria. Nineteen (10%), thirty (15%), twenty-two (11%), and seven (4%) patients were ECPR-eligible, using the UBC, UM, UC, and restrictive criteria. However, none of these patients had received ECPR. Only two (11%), two (7%), two (9%), and one (14%) of these patient(s) survived to discharge, respectively. Neurological outcomes were unfavourable among all ECPR-eligible patients. Future study at our centre will be necessary on how to implement ECPR program to further improve these outcomes.

OBJECTIVE: Our goal was to research and develop exploratory analysis tools for clinical notes, which now are underrepresented to limit the diversity of data insights on medically relevant applications. RESULTS: We characterize how exploratory analysis can affect representation learning on clinical narratives and present several self-developed tools to explore sepsis. Our experiments focus on patients with sepsis in the MIMIC-III Clinical Database or in our institution's research patient data repository. We found that global embeddings assist in learning local representations of clinical notes. Second, aligning at any specific time facilitates the use of learning models by pooling more available clinical notes to form a training set. Furthermore, reconstruction of the timeline enhances downstream-processing techniques by emphasizing temporal expressions and temporal relationships in clinical documentation. We demonstrate that clustering helps plot various types of clinical notes against a scale, which conveys a sense of the range or spread of the data and is useful for understanding data correlations. Appropriate exploratory analysis tools provide keen insights into preprocessing clinical notes, thereby further enhancing downstream analysis capabilities, making data driven medicine possible. Our examples can help generate better data representation of clinical documentation for models with improved performance and interpretability.

OBJECTIVES: Our study focuses on evaluating the factors associated with vasovagal syncope (VVS) when having a pain procedure at the pain clinic as well as showing variation in vital signs associated with fainting across different periods of the procedure (before, during and after).A retrospective case control study was conducted in a university hospital in Lebanon (CHU-NDS) on adult Lebanese patients with data taken from the archives covering a 4 year period (2016-2019). RESULTS: The multivariable analysis showed that a higher systolic blood pressure per-procedure was significantly associated with lower odds of having vasovagal syncope. An adequate dose of a vasopressor like ephedrine can be used to prevent a vasovagal event from happening. In our study the blood pressure component was more significant than the heart rate component which stayed in the normal range limit in the three different periods of procedure. Cases having a pain procedure for the first time represent 59.6% of the occurrence of VVS. Vasovagal syncope is a complication that can be prevented in high risk patients. Our study suggests taking preventive measures for VVS for patients with first time infiltration status especially if appearing in an anxious state.

OBJECTIVE: Skeletal muscle size is considered a predictor of prognosis in patients with respiratory diseases including Mycobacterium avium complex lung disease. However, no research focused on its impact on prognosis in patients with pulmonary tuberculosis (TB). Thus, this study aimed to assess the association between erector spinae muscle (ESM) size and in-hospital mortality among patients with pulmonary TB. RESULTS: We retrospectively included 258 consecutive patients aged over 65 years old, who were admitted to the hospital for bacteriologically confirmed pulmonary TB, and all underwent chest computed tomography (CT) scan upon admission. The cross-sectional area of the ESM (ESMcsa) was measured at the lower margin of the 12th thoracic vertebra on a single-slice CT scan image and was adjusted according to body surface area (BSA). In total, 71 (28%) patients died during hospitalization. The non-survivor group had a high incidence of respiratory failure and comorbidities and lower hemoglobin and albumin levels, performance status score, and ESMcsa/BSA. Multivariate analysis revealed that low performance status score and hemoglobin and albumin levels, but not ESMcsa/BSA and body mass index, could independently predict in-hospital mortality after adjusting for age and comorbidities. Therefore, ESM size was not associated with in-hospital mortality in patients with pulmonary TB.

OBJECTIVE: Histone acetylation is an important mechanism in the regulation of gene expression and plays a crucial role in both cellular development and cellular response to external or internal stimuli. One key aspect of this form of regulation is that acetylation marks can be added and removed from sites of regulation very quickly through the activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). The activity of both HATs and HDACs has been shown to be important for both physiological hematopoiesis as well as during development of hematological neoplasia, such as lymphomas. In the present study we analyzed the effect of knockout of the two HDACs, Hdac1 and Hdac2 in cells expressing the fractalkine receptor (Cx3cr1) on lymphocyte development. RESULTS: We report data showing a maturation defect in mice harboring a Cx3cr1 dependent knockout of Hdac1 and 2. Furthermore, we report that these mice develop a T-cell neoplasia at about 4-5 months of age, suggesting that a Cx3cr1 expressing subpopulation of immature T-cells gives rise to T-cell lymphomas in the combined absence of Hdac1 and Hdac2.

OBJECTIVE: Several essential factors have played a crucial role in the spreading mechanism of COVID-19 (Coronavirus disease 2019) in the human population. These factors include undetected cases, asymptomatic cases, and several non-pharmaceutical interventions. Because of the rapid spread of COVID-19 worldwide, understanding the significance of these factors is crucial in determining whether COVID-19 will be eradicated or persist in the population. Hence, in this study, we establish a new mathematical model to predict the spread of COVID-19 considering mentioned factors. RESULTS: Infection detection and vaccination have the potential to eradicate COVID-19 from Jakarta. From the sensitivity analysis, we find that rapid testing is crucial in reducing the basic reproduction number when COVID-19 is endemic in the population rather than contact trace. Furthermore, our results indicate that a vaccination strategy has the potential to relax social distancing rules, while maintaining the basic reproduction number at the minimum possible, and also eradicate COVID-19 from the population with a higher vaccination rate. In conclusion, our model proposed a mathematical model that can be used by Jakarta's government to relax social distancing policy by relying on future COVID-19 vaccine potential.

OBJECTIVE: The purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems. Two popular software tools were chosen as the reference: the tng and the xdrfile libraries. Current implementation of tng algorithms and library is either fast or storage efficient and xdrfile is storage efficient but slow. Our aim was to combine speed and storage efficiency through the xdrfile's code modification. RESULTS: Here we present libxtc, a ready-to-use library for reading MD trajectory files in xtc format. The effectiveness of libxtc is demonstrated for several biomolecular systems of various sizes (~ 2 × 104 to ~ 2 × 105 atoms). In sequential mode, the performance of libxtc is up to 1.8 times higher and 1.4 times lower than xdrfile and tng, respectively. In parallel mode, libxtc is about 3 and 1.3 times faster than xdrfile and tng. At the same time, MD data stored in the xtc format require about 1.3 times less disk space than those treated with the tng algorithm in the fastest reading mode, which is a noticeable saving especially when the MD trajectory is long and the number of atoms is large-this applies to most biologically relevant systems.

OBJECTIVES: Nontypeable Haemophilus influenzae (NTHi) is an important human respiratory bacterium that can cause a range of diseases including sinusitis, otitis media, conjunctivitis, pneumonia as well as acute exacerbations of chronic obstructive pulmonary disease (COPD). A number of studies have used NTHi clinical isolate RHH-3 as a laboratory strain for experimentation examining the effect of cigarette smoke and more recently, biomass smoke, on the susceptibility and response of cells lining the respiratory tract to infection. Therefore, definition of the genome content of RHH-3 is required to fully elucidate human-NTHi interactions associated with initial infection and subsequent development of respiratory disease. DATA DESCRIPTION: Here, we present the draft genome sequence of NTHi RHH-3 collected from the sputum of a patient at the Royal Hobart Hospital, Tasmania, Australia. The assembled genome size was 1,839,376 bp consisting of 61 contigs (> 500 bp), with a G+C content of 38.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession number JADPRR000000000.