OBJECTIVE: The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. RESULTS: Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.

OBJECTIVE: Assessing amniotic fluid determines an important dimension of fetal health. Significant relationships of oligohydramnios, which occurs in 1-2% of pregnancies, with abnormal pregnancy outcomes such as intrauterine growth retardation (IUGR), fetal anomalies, umbilical cord compression, fetal distress, preterm childbirth, meconium-stained amniotic fluid, perinatal mortality and cesarean section necessitate the measurement of amniotic fluid volume in many prenatal fetal health assessments. Amniotic fluid volume may significantly fluctuate between different gestational ages. Reduced uteroplacental perfusion can cause oligohydramnios by decreasing fetal renal blood flow and urine output. The appropriate management of isolated term oligohydramnios (ITO) is controversial. This study was performed aimed to assess the effect of maternal intravenous hydration on amniotic fluid index in oligohydramnios. RESULT: Forty-eight hours after completing fluid therapy, statistically significant differences were observed in the mean AFI in the intervention group (4.06 ± 0.33) and the control group (3.61 ± 0.35) (P < 0.0001) and also between the intervention group (0.532 ± 0.45) and the controls (-0.036 ± 0.18) (P < 0.0001). CONCLUSION: The results of the present study suggested that maternal intravenous hydration significantly increases AFI in women with oligohydramnios.

OBJECTIVE: Miscarriages affect 10% of women aged 25-29, and 53% of women over 45. The primary cause of miscarriage is aneuploidy that originated in eggs. The Aurora kinase family has three members that regulate chromosome segregation. Therefore, distinguishing the roles of these isoforms is important to understand aneuploidy etiology. In meiosis, Aurora kinase A (AURKA) localizes to spindle poles, where it binds TPX2. Aurora kinase C (AURKC) localizes on chromosomes, where it replaces AURKB as the primary AURK in the chromosomal passenger complex (CPC) via INCENP binding. Although AURKA compensates for CPC function in oocytes lacking AURKB/C, it is unknown whether AURKA binds INCENP in wild type mouse oocytes. ZINC08918027 (ZC) is an inhibitor that prevents the interaction between AURKB and INCENP in mitotic cells. We hypothesized that ZC would block CPC function of any AURK isoform. RESULTS: ZC treatment caused defects in meiotic progression and spindle building. By Western blotting and immunofluorescence, we observed that activated AURKA and AURKC levels in ZC-treated oocytes decreased compared to controls. These results suggest there is a population of AURKA-CPC in mouse oocytes. These data together suggest that INCENP-dependent AURKA and AURKC activities are needed for spindle bipolarity and meiotic progression.

OBJECTIVE: Laser pointers are common teaching tools used during lessons. The pointing precision may influence the teaching effectiveness. In this study, we examined the effect of four external factors, namely aiming distance, target size, light condition and colour of the laser beam on the pointing precision. RESULTS: Thirty participants (15 males and 15 females; age = 23.2 ± 4.3) were asked to aim at the target black circles with different sizes (diameters = 4 mm, 8 mm, 12 mm and 16 mm) from five various distances (2 m, 4 m, 6 m, 8 m and 10 m) at two brightness conditions (i.e., bright and dark) using two different coloured laser pointers (red and green). Three aiming parameters, namely number of hits, duration per hit and pointing precision were measured. Results showed that the aiming parameters were the highest with the aiming distance of 2 m and the use of green laser pointer towards larger target sizes regardless of the environmental brightness. Among all factors, aiming distance was the most important external factor that could influence pointing precision.

OBJECTIVE: Nipple-related complications are major factors that prevent breastfeeding for many new mothers. Hence, we tested the effects of aloe arborescens fomentation applied to the nipples as a treatment for nipple-related complications. RESULTS: This study included 60 women who breastfed for the first time on day 1 after delivery. Every 24 h, all women breastfed six times and bottle-fed two times (at night). Women were classified into an intervention group (aloe arborescens fomentation) and a control group (no treatment). Aloe fomentation was applied after breastfeeding six times per day. We observed the nipples three times per day for 5 days after delivery. The most common nipple-related complication in this study was redness. A significant decrease was observed for women in the intervention group. Trial Registration Retrospectively Registered to registry: UMIN; Registration no.: UMIN000044514; Registered on: 11th June 2021.

OBJECTIVES: The dosage of levothyroxine (LT4) during pregnancy differs among different ethnic groups worldwide. These differences are due to variations in geographical iodine distribution, autoimmunity, and variations in thyrotropin (TSH) targets for pregnancy. To the best of our knowledge, we report the levothyroxine dosage prescribed during pregnancy in hypothyroid women, for the first time from Pakistan. RESULTS: Levothyroxine dosage of 280 hypothyroid women during pregnancy were reviewed. The median LT4 dosages prescribed before conception was 85.7 mcg per day which increased by 14.3 mcg per day in the first trimester (P 0.001). A significant difference in dosage was observed between controlled and uncontrolled TSH groups in the first trimester (P 0.05). Lower LT4 dosage was prescribed for subclinical hypothyroid women as compared to overt hypothyroid cases, whereas dosages did not differ according to autoimmune status in the latter part of gestation.

OBJECTIVE: Currently, the only available staging criterion for T. b. rhodesiense requires a lumber puncture to collect and later examine cerebrospinal fluid (CSF). This study examined the potential of plasma Neuron-Specific Enolase (NSE) in discriminating between early and late-stage patients. RESULTS: When median NSE levels were compared between early and late-stage patients, results showed a significant (P < 0.02) upregulation among late-stage patients (599.8 ng/mL). No significant differences (P > 0.9) in NSE levels were observed between early-stage patients (300 ng/mL) and controls (454 ng/mL). We used Receiver Operator Characteristic (ROC) curves to explore the likelihood of using plasma NSE as a potential stage biomarker in discriminating between early and late-stage HAT patients. Our results showed that NSE demonstrated an area under the curve (AUC) of 0.702 (95% CI 0.583-0.830). A high staging accuracy for NSE was obtained by using a cutoff of > 346.5 ng/mL with a sensitivity of 68.6% (95% CI 55-79.7%) and a specificity of 93.3% (95% CI 70.2-99.7%). Although our results demonstrate that plasma NSE is upregulated in T. b. rhodesiense sleeping sickness patients, its value in discriminating between late and early-stage patients is limited. However, future studies could consider improving its specificity by combining it with other identified plasma biomarkers.

OBJECTIVE: The COVID-19 pandemic has forced many human subjects research to halt in-person activities and pivot to virtual engagement, including Focus Groups (FGs). We highlight learnings from our experience of hosting virtual FGs from our BEhavioral EConomics for Oral health iNnovation (BEECON) study focusing on oral hygiene behaviors among low-income, predominantly Hispanic families, including practical tips and potential pitfalls to avoid for researchers considering virtual engagement. RESULTS: There can be particular benefits to holding virtual sessions among minority parents of young children-to provide flexibility, comfort, and reduced logistical barriers for participation-while still facilitating friendly conversation with minimal distractions. However, extensive preparation is needed to ensure smooth execution and minimal distractions.

OBJECTIVE: Diacerein inhibits the synthesis and activity of pro-inflammatory cytokines, decreases macrophage infiltration in adipose tissue and thus increases insulin sensitivity and signalling. We conducted this study to determine the efficacy of low-dose diacerein in improving glycaemic control in type 2 diabetes mellitus (T2DM) patients with inadequate glycaemic control and to identify the metabolic determinants for such improvement. We randomised 25 T2DM patients with poor glycaemic control, despite being treated with at least three glucose-lowering agents, to receive diacerein 50 mg once-daily (n = 18) or placebo (n = 17) for 12 weeks. Changes in glycated haemoglobin (HbA1c) were evaluated at the 4th and 12th weeks. Metabolic profiling was performed using liquid chromatography electrospray ionisation quadrupole time-of-flight mass spectrometry. RESULTS: HbA1c levels were significantly reduced from baseline in the diacerein group at 12 weeks (- 0.6%, p < 0.05), whereas fasting plasma glucose (FPG) levels were not significantly decreased (- 18.9 mg/dl, p = 0.06). Partial least squares-discriminant analysis demonstrated an association between the serum abundance of threo-isocitric acid (ICA) and HbA1c response in the diacerein group. After adjusting for serum high-sensitivity C-reactive protein, ICA was still significantly related to the change in HbA1c. Retrospective trial registration Current Controlled Trials TCTR20200820004, 20 August 2020.

OBJECTIVE: Menopausal status impacts risk for many health outcomes. However, factors including hysterectomy without oophorectomy and Menopausal Hormone Therapy (MHT) can mask menopause, affecting reliability of self-reported menopausal status in surveys. We describe a step-by-step algorithm for classifying menopausal status using: directly self-reported menopausal status; MHT use; hysterectomy; oophorectomy; intervention timing; and attained age. We illustrate this approach using the Australian 45 and Up Study cohort (142,973 women aged ≥ 45 years). RESULTS: We derived a detailed seven-category menopausal status, able to be further consolidated into four categories ("pre-menopause"/"peri-menopause"/"post-menopause"/"unknown") accounting for participants' ages. 48.3% of women had potentially menopause-masking interventions. Overall, 93,107 (65.1%), 9076 (6.4%), 17,930 (12.5%) and 22,860 (16.0%) women had a directly self-reported "post-menopause", "peri-menopause", "pre-menopause" and "not sure"/missing status, respectively. 61,464 women with directly self-reported "post-menopause" status were assigned a "natural menopause" detailed derived status (menopause without MHT use/hysterectomy/oophorectomy). By accounting for participants' ages, 105,817 (74.0%) women were assigned a "post-menopause" consolidated derived status, including 15,009 of 22,860 women with "not sure"/missing directly self-reported status. Conversely, 3178 of women with directly self-reported "post-menopause" status were assigned "unknown" consolidated derived status. This algorithm is likely to improve the accuracy and reliability of studies examining outcomes impacted by menopausal status.

OBJECTIVE: The Hybrid Assistive Limb (HAL) has recently been used to treat movement disorders. Although studies have shown its effectiveness for chronic myelopathy, the immediate effects of HAL gait training on lower limb function have not been clarified. We conducted HAL gait training and examined its immediate effects on a 69-year-old man with re-deterioration of myelopathy in the chronic phase after surgery for compression myelopathy. The HAL intervention was performed every 4 weeks for 10 total sessions. Immediately before and after each session, we analyzed the patient's walking ability using the 10-m walk test. In the 4th HAL session, the gastrocnemius muscle activity was measured bilaterally using a synchronized motion capture-electromyogram system. RESULTS: The training effects became steady after the 2nd session. In sessions 2-10, the step length increased from 0.56 to 0.63 m (mean: 0.031 m) immediately after HAL training. The motion capture-electromyogram analyses showed that considerable amounts of gastrocnemius muscle activity were detected during the stance and swing phases before HAL training. During and immediately after HAL training, gastrocnemius activity during the swing phase was diminished. HAL gait training has an immediate effect for inducing a normal gait pattern with less spasticity in those with chronic myelopathy.

OBJECTIVE: A single study conducted about three decades ago on hepatitis D virus (HDV) infection among Baka pygmies in Cameroon reported a very high anti-HDV antibodies prevalence of 46%, but HDV genetic diversity has not been studied in this population. The genetic diversity of strains from endemic ancient populations may help to understand the origin and evolutionary history of viruses. This study aimed to investigate the HDV seroprevalence and the genetic diversity in three remote Cameroonian Pygmies with chronic HBV infection. RESULTS: An unusually high 69% (36/52) level of HDV infection was found among HBsAg-positive pygmies in Cameroon. HDV RNA was detected and sequenced in 38.8% (14/36). The phylogenetic analysis revealed that 9/14 strains (64.3%) were identified and classified as genotype 1 (HDV-1) and 5/14 (35.6%) as genotype 7 (HDV-7), respectively with a bootstrap value of 100%. The further analysis showed the co-circulation of highly diverse HDV genotypes HDV-1 and HDV-7 in this population. These results highlight the endemicity of HDV infection in Central Africa. The highly diverse HDV-1 and HDV-7 in pygmies suggest an African origin of HDV. However, further studies are needed with larger sample size.

OBJECTIVE: The COVID-19 pandemic has caused widespread illness and a significant proportion of the infected required hospitalisation for treatment. People in developing countries like India were vulnerable to high hospitalisation costs. Despite its crucial importance, few primary studies are available on this aspect of the pandemic. This study was aimed at finding out the out of pocket expenditure (OOPE) and incidence of catastrophic expenditure on hospitalisation of persons infected with COVID-19. A primary survey of 492 randomly selected hospitalisations of individuals tested positive for COVID-19 in high-burden districts during August to November 2020 was carried out telephonically in Chhattisgarh state of India. RESULTS: Public hospitals accounted for 69% of the hospitalisations for COVID-19 treatment. Mean OOPE per hospitalisation was Indian Rupees (INR) 4871 in public hospitals and INR 169,504 in private hospitals. Around 3% of hospitalisations in public hospitals and 59% in private hospitals resulted in catastrophic expenditure, at a threshold of 40% of non-food annual household expenditure. Enrolment under publicly or privately funded health insurance was not effective in curtailing OOPE. Multivariate analysis showed that utilisation of private hospitals was a key determinant of incurring catastrophic expenditure.

OBJECTIVE: Cholera is an intestinal infection caused by Vibrio cholerae, it is usually occurs in developing countries that lack of sanitation. In developing country including Indonesia, awareness importance of sanitation is still low. Unfortunately, research related to the detection of V. cholerae from fruit and vegetables in Indonesia is still rare. In this study, MPN method was used to determine the prevalence of V. cholerae followed by single and multiplex PCR to detect virulence genes, including toxR, ctxA, tcpA, hlyA, ace, ompU, and zot. RESULTS: We found 3 fruits and 2 vegetables positive for toxR gene. Fruit samples which were showed toxR positive found from East Jakarta while for vegetables, it was recovered from West Jakarta and Central Jakarta. Twenty-three isolates were recovered from toxR positive samples. The result of antibiotic resistance analysis showed that 4.35% of the isolates resistant to gentamicin, streptomycin (17.39%), trimethoprim (52.17%), ciprofloxacin (30.43%), ampicillin (13.04%), nalidixic acid (82.61%), and polymyxin B (91.30%). None of these isolates were resistant to kanamycin. Combination of MPN and Multiplex PCR method can be used to detect the prevalence and characterize the virulence properties of V. cholerae.

OBJECTIVE: How do birds navigate their way? It is one of the interesting question about homing pigeons, however the genetic of navigation has reminded as a puzzle. Optic lobe, olfactory bulb, hippocampus and cere were collected for RNA sampling. The generated RNA-seq represent RNA resequencing data for racing homer (homing) pigeon and other rock pigeon breeds. The obtained data set can provide new insight about hippocampus role and GSR contribution to pigeon magnetoreception. DATA DESCRIPTION: To investigate the navigation ability of rock pigeon breeds, 60 whole transcriptome sequence data sets related to homing pigeon, Shiraz tumblers, feral pigeons and Persian high flyers were obtained. RNA extraction was performed from three brain regions (optic lobe, olfactory bulb, hippocampus) and cere. Paired-end 150 bp short reads (Library size 350 bp) were sequenced by Illumina Hiseq 2000. In this way, about 342.1 Gbp and 130.3 Gb data were provided. The whole transcriptome data sets have been deposited at the NCBI SRA database (PRJNA532674). The submitted data set may play critical role to describe the mechanism of navigation ability of rock pigeon breeds.

OBJECTIVE: To design and construct a new synthetic nanobody library using a structure-based approach that seeks to maintain high protein stability and increase the number of functional variants within the combinatorial space of mutations. RESULTS: Synthetic nanobody (Nb) libraries are emerging as an attractive alternative to animal immunization for the selection of stable, high affinity Nbs. Two key features define a synthetic Nb library: framework selection and CDR design. We selected the universal VHH framework from the cAbBCII10 Nb. CDR1 and CDR2 were designed with the same fixed length as in cAbBCII10, while for CDR3 we chose a 14-long loop, which creates a convex binding site topology. Based on the analysis of the cAbBCII10 crystal structure, we carefully selected the positions to be randomized and tailored the codon usage at each position, keeping at particular places amino acids that guarantee stability, favoring properties like polarity at solvent-exposed positions and avoiding destabilizing amino acids. Gene synthesis and library construction were carried out by GenScript, using our own phagemid vector. The constructed library has an estimated size of 1.75 × 108. NGS showed that the amino acid diversity and frequency at each randomized position are the expected from the codon usage.

OBJECTIVE: We aimed to establish a novel sperm quality evaluation technology by measuring mitochondrial oxygen metabolism in human spermatozoa. RESULTS: Normozoospermic human sperm samples were used. After establishing the optimal parameters for measuring the oxygen metabolism of human sperm cells using the extracellular flux analyzer, we measured the oxygen consumption rate (OCR) of human spermatozoa exposed to different storage temperatures. Although sperm motility was significantly lower at 4 °C when compared with sperm motility at 37 °C, there were no significant differences in sperm vitality and the OCR under both conditions. The present study established a methodology for human sperm quality evaluation using extracellular flux analysis technology. The OCR evaluation could be a reliable measurement tool for assessing human sperm quality.

OBJECTIVES: Due to the increase of type 2 diabetes (T2D), the number of patients in treatment with multiple anti-diabetic agents is increased. According to the recent recommendation of treatment guidelines, sodium-glucose cotransporter 2 (SGLT2) inhibitors would be used as additional treatment to the currently administered anti-diabetic drugs for poorly controlled T2D patients. Here, we assessed the efficacy of SGLT2 inhibitors added to the current treatment with metformin, dipeptidyl peptidase-4 (DPP4) inhibitors, or both in Japanese T2D patients. RESULTS: Japanese T2D subjects with poor glucose control, who were treated with metformin (n = 10), DPP4 inhibitors (n = 11), or both (n = 28) and who were in need of additional treatment, were recruited. HbA1c levels before and 6 months after addition of SGLT2 inhibitor treatment were used to compare the effectiveness. The HbA1c levels after addition of SGLT2 inhibitors significantly decreased in all groups. The change in HbA1c levels (delta HbA1c) showed no significant difference between the three groups. The present data indicated that addition of SGLT2 inhibitors to metformin and/or DPP4 inhibitors is equally effective in the treatment of Japanese T2D patients.

OBJECTIVES: The aim of this study is to determine the metabolic impact of a nutrition education program on metabolic parameters and the presence of metabolic syndrome (MetS). RESULTS: Seventy-four patients were included (mean age, 48.7 years [Standard deviation, SD: 10.8], 55.4% men). The diagnoses of SMD were 37.8% schizophrenia and related disorders; 29.7% bipolar disorder; 25.7% depressive disorder; 4.1% personality disorders; and 2.7% obsessive compulsive disorders. Thirty-seven individuals were distributed in both the intervention group (IG) and the control group (CG). In the IG the presence of MetS was 56.3% and in the CG 46.7%, with no statistically significant difference (p = 0.309). At the end of the study, glomerular filtrate decreased in the IG, body mass index and abdominal perimeter increased in both groups, and there were no changes in metabolic parameters between the groups. Between the baseline and the end of the study, there was no increase in the number of patients diagnosed with MetS (14 at both points); and in the CG the increase was from 8 to 12 (p = 0.005). An intervention based on fruit and vegetable intake could prevent progression to MetS in individuals with SMD, decreasing the likelihood of cardiovascular disease. Trial registration The trial was retrospectively registered on International Standard Randomised Controlled Trial Number (ISRCTN) Register on 11 March 2022 (ISRCTN12024347).

OBJECTIVE: A clinical trial carried out in patients hospitalized for clinical and surgical conditions. This study evaluated the effectiveness of text messaging interventions (TM) versus telephone counseling (TC) to promote smoking cessation among hospitalized smokers in a middle-income country. Seven-day abstinence was measured during follow-up phone calls one month after discharge. The comparative cost of the two interventions considered the cost of calls, time spent on phone calls and sending SMS and cost of the professional involved in the approaches. RESULTS: Past 7-day tobacco abstinence was not statistically different between groups (30.5% in TM group and 26% in TC, p = 0.318). Costs were significantly lower in the TM group (U$9.28 × U$19.45- p < 0,001). Continuous abstinence was reported by 26% of TM participants and 24.5% of TC participants (p = 0.730). In the 3-month follow-up, 7-day abstinence was 23% in the TMI and 27% in the TC (p = 0.356) group. Continuous abstinence was reported by 20% of TM participants and 24% of TC participants (p = 0.334). TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT03237949 Registred on: 30th May 2017.

OBJECTIVE: This study was aimed to assess the enzymatic activity and pathogenicity potential of Beauveria bassiana and Metarhizium anisopliae against whiteflies in Ethiopia. RESULTS: The data showed that Beauveria bassiana AAUMB-29, AAUMFB-77, and AAUEB-59 generated the highest chitinase (EI = 3.41), lipase (EI = 4.45), and protease activities (EI = 5.44) respectively. The pathogenicity study of isolates on whitefly nymphs and adults indicated significant variation (P < 0.05) with mortality ranging from 71.67 to 98.33% and 60 to 100% against Bemisia tabaci and Trialeurodes vaporariorum nymphs respectively. The mortality of adults was between 58 and 94.27% against B. tabaci and 59.03 to 95.37% against T.vaporariorum. The result also showed that AAUMB-29, AAUMFB-77, and AAUDM-43 were the most virulent with LC50 values of 2.7 × 104, 5.3 × 104, and 5.4 × 104 conidia/ml against nymphs of B. tabaci, and with LC50 values 6.8 × 104, 8.2 × 104, and 7.2 × 104 conidia/ml against nymphs of T. vaporariorum, respectively. The B. bassiana AAUMB-29, B. bassiana AAUMFB-77, and M. anisopliae AAUDM-43 induced the highest whitefly mortality than other isolates. These isolates can be recommended for further tests under field conditions to fully realize their potential as effective biocontrol agents against whitefly pests in tomato.

OBJECTIVE: It remains unclear that the relationship between sprint and/or endurance performance and salivary immunological factors and stress hormones in athletes. The aim of this study was to investigate if salivary immunological factors and stress hormones are related to sprint and endurance performance in sprinters and long-distance runners. Fourteen male sprinters provided 100-m record and 22 male long-distance runners provided 5000-m record. Salivary IgA, MCP-1, interleukin-8, and cortisol levels in sprinters and long-distance runners were measured by ELISA assay. RESULTS: No significant differences were found in all salivary parameters between sprinters and long-distance runners. In long-distance runners, the salivary IgA and MCP-1 concentrations and secretory rate significantly correlated with their personal best 5000-m times (r = 0.534, P = 0.011; r = 0.567, P = 0.006; r = 0.452, P = 0.035, respectively). In sprinters, the salivary IgA concentration, MCP-1 concentration, and MCP-1 secretory rate did not correlate with personal best 100-m sprint times (r = - 0.260, P = 0.369; r = 0.128, P = 0.663; r = 0.122, P = 0.677, respectively). Therefore, the present study is the first to determine that immunological factors such as IgA and MCP1 may be related to endurance performance in long-distance runners.

OBJECTIVE: Musculoskeletal modeling and simulation are powerful research and education tools in engineering, neuroscience, and rehabilitation. Interactive musculoskeletal models (IMMs) can be controlled by muscle activity recorded with electromyography (EMG). IMMs are typically coded using textual programming languages that present barriers to understanding for non-experts. The goal of this project was to use a visual programming language (Simulink) to create and test an IMM that is accessible to non-specialists for research and educational purposes. RESULTS: The developed IMM allows users to practice a goal-directed task with different control modes (keyboard, mouse, and EMG) and actuator types (muscle model, force generator, and torque generator). Example data were collected using both keyboard and EMG control. One male participant in his early 40's performed a goal-directed task for four sequential trials using each control mode. For EMG control, the participant used a low-cost EMG system with consumer-grade EMG sensors and an Arduino microprocessor. The participant successfully performed the task with both control modes, but the inability to grade muscle model excitation and co-activate antagonist muscles limited performance with keyboard control. The IMM developed for this project serves as a foundation that can be further tailored to specific research and education needs.

OBJECTIVE: Discrete but ordered covariates are quite common in applied statistics, and some regularized fitting procedures have been proposed for proper handling of ordinal predictors in statistical models. Motivated by a study from neonatal medicine on Bronchopulmonary Dysplasia (BPD), we show how quadratic penalties on adjacent dummy coefficients of ordinal factors proposed in the literature can be incorporated in the framework of generalized additive models, making tools for statistical inference developed there available for ordinal predictors as well. RESULTS: The approach presented allows to exploit the scale level of ordinally scaled factors in a sound statistical framework. Furthermore, several ordinal factors can be considered jointly without the need to collapse levels even if the number of observations per level is small. By doing so, results obtained earlier on the BPD data analyzed could be confirmed.

OBJECTIVE: The redbanded stink bug (RBSB), Piezodorus guildinii (Hemiptera: Pentatomidae), is native to the Caribbean Basin and is currently considered an invasive pest in Florida, Louisiana, Mississippi, and Texas in the southern United States. Although RBSB is an economically important invasive pest in the USA, relatively few studies have been conducted to understand molecular mechanisms, population genetic structure, and the genetic basis of resistance to insecticides. The objective of this work was to obtain a high-quality genome assembly to develop genomic resources to conduct population genetic, genomic, and physiological studies of the RBSB. RESULTS: The genome of RBSB was sequenced with Pacific Biosciences technology followed by two rounds of scaffolding using Chicago libraries and HiC proximity ligation to obtain a high-quality assembly. The genome assembly contained 800 scaffolds larger than 1 kbp and the N50 was 170.84 Mbp. The largest scaffold was 222.22 Mbp and 90% of the genome was included in the 7 scaffolds larger than 118 Mbp. The number of megabase scaffolds also matched the number of chromosomes in this insect. The genome sequence will facilitate the development of resources to conduct studies on genetics, transcriptomics, and physiology of RBSB.

OBJECTIVE: In sub-Saharan Africa, 45% of the rural population uses boreholes (BHs). Despite recent gains in improved water access and coverage, parallel use of unimproved sources persists. Periodic infrastructure disrepair contributes to non-exclusive use of BHs. Our study describes functionality of BHs in 2014, 2015, and 2016 in 15 rural towns in the Eastern Region of Ghana sourced from three groundwater quality clusters (high iron, high salinity, and control). We also assess factors affecting cross-sectional and longitudinal functionality using logistic regression. RESULTS: BH functionality rates ranged between 81 and 87% and were similar across groundwater quality clusters. Of 51 BHs assessed in all three years, 34 (67%) were consistently functional and only 3 (6%) were consistently broken. There was a shift toward proactive payment for water over the course of the study in the control and high-salinity clusters. Payment mechanism, population served, presence of nearby alternative water sources, and groundwater quality cluster were not significant predictors of cross-sectional or longitudinal BH functionality. However, even in the high iron cluster, where water quality is poor and no structured payment mechanism for water exists, BHs are maintained, showing that they are important community resources.

OBJECTIVE: Mental health is a fundamental aspect in ensuring the stable and successful professional life of future physicians. Depressive symptoms can negatively affect the work-life-balance and efficiency at work of medical students. To date, there have been very few studies involving medical students that examine the association between single sleep characteristics and the outcome of the Beck Depression Inventory-II score. Therefore, the aim of the present study is to investigate this possible association. A classroom survey using socio-demographic characteristics, the Beck Depression Inventory-II, and the Pittsburgh Sleep Quality Index was conducted amongst students at a German medical school from December 2017 to September 2018. Data analysis was performed with descriptive statistics and binary logistic regression. RESULTS: Of the students surveyed, 19% showed depressive symptoms with a Beck Depression Inventory-II score over 13 and 42% of these cases were moderate or severe. The occurrence of relevant depressive symptoms was associated with lower sleep quality, higher sleep latency, and the consumption of sleeping pills. In general, female students and students from abroad had a higher risk of depressive symptoms. Addressing these relevant findings in medical school can increase awareness of mental health.

OBJECTIVES: Canine lymphoma, the most common hematological cancer in dogs, shares many molecular and clinical characteristics with human Non-Hodgkin lymphoma (NHL). The standard treatment for canine lymphoma is "CHOP" multiagent chemotherapy protocol consisting of Cyclophosphamide, Doxorubicin (Hydroxydaunorubicin), Vincristine (Oncovin™), and Prednisone. Approximately 70-85% of patients treated with CHOP achieve clinical remission. However, duration of remission varies and the majority of dogs eventually relapse. To identify possible biomarkers for patients failing to achieve remission, we performed RNA-Seq analysis on 25 cases of canine lymphoma obtained prior the start of their CHOP therapy regime and assessed gene expression associated with patient progression free survival (PFS). DATA DESCRIPTION: The data consists of (1) raw RNA-Seq reads in 75 bp fastq format from fine needle aspirate samples of enlarged lymph nodes from canine patients with naturally occurring lymphoma; (2) Fragments Per Kilobase Million (FPKM) values for each sample; (3) raw transcript counts for each sample; (4) anonymized patient details including PFS; (5) heat map of gene expression and (6) Cox proportional hazard analysis showing significantly expressed genes. These data may be useful for comparative analysis of gene expression in human NHL and analysis of gene expression associated with disease outcome in canine lymphoma.

Increasingly, policies are being introduced to reward and recognise open research practices, while the adoption of such practices into research routines is being facilitated by many grassroots initiatives. However, despite this widespread endorsement and support, as well as various efforts led by early career researchers, open research is yet to be widely adopted. For open research to become the norm, initiatives should engage academics from all career stages, particularly senior academics (namely senior lecturers, readers, professors) given their routine involvement in determining the quality of research. Senior academics, however, face unique challenges in implementing policy changes and supporting grassroots initiatives. Given that-like all researchers-senior academics are motivated by self-interest, this paper lays out three feasible steps that senior academics can take to improve the quality and productivity of their research, that also serve to engender open research. These steps include changing (a) hiring criteria, (b) how scholarly outputs are credited, and (c) how we fund and publish in line with open research principles. The guidance we provide is accompanied by material for further reading.

OBJECTIVES: The objective of this data set was to identify how interaction between temperature and the sickle-3 (sic-3) mutant alters the global messenger RNA (mRNA) content of Arabidopsis thaliana seedlings. The motivation was discovery of atypical mRNA splice variants in sic-3 that differed with seedling growth temperature. The expected outcome was identification of mRNA splice variants altered by sic-3, temperature, or the combination of temperature and genotype. DATA DESCRIPTION: The data set is RNAseq profiling of Arabidopsis (Col-0 ecotype) wild type and sic-3 seedlings under 16 °C or 28 °C. A comprehensive view of global mRNA sequences and their content was captured by deep sequencing of RNA pools made from sets of seedlings sampled every 4 h over 20 h. This data set contains sequences representing the spectrum of mRNA splice variants from individual genes, as well as from mRNA-related sequences like spliced introns. This data set enables detection of significant changes in gene-level expression and relative levels of mRNA splice variants caused by the different growth temperatures, the sic-3 mutation or both factors. This data set is useful to study production of mRNA splice variants and other mRNA-related RNAs in a range of plant species because Arabidopsis is a model plant.

OBJECTIVES: Clinicians worldwide struggle to identify the bacterial aetiology of bone and joint infections. Failure to unequivocally identify the pathogen is linked to poor clinical outcomes. We explored the added value of analysing multiple samples per patient with 16S ribosomal DNA (16S rDNA) sequencing in diagnosing postoperative bone and joint infections. All patients had received antimicrobials prior to sampling, and false-negative cultures could be suspected. Bone biopsies obtained from patients with postoperative bone and joint infections for cultures were also subjected to 16S rDNA sequencing. RESULTS: In 5/28 infectious episodes, sequencing identified the causative organism of the infection when cultures failed. In 8/28 episodes, the methods led to different results, potentially leading to different antimicrobial choices. The analysis of multiple samples per patient helped rule out potential contaminating pathogens. We conclude that 16S rDNA sequencing has diagnostic value for patients receiving antibiotic treatment. We regard the method as a complement to culturing when the cultures are negative. Multiple samples per patient should be analysed to determine the clinical significance of positive findings.

Erratum in BMC Res Notes. 2022 Aug 15;15(1):279.

OBJECTIVE: The naked mole rats (NMRs, Heterocephalus glaber) are subterranean rodents that belong to the family Bathyergidae. They gained the attention of the scientific community for their exceptionally long lifespan of up to 30 years and have become an animal model of biomedical research on neurodegenerative diseases, aging and cancer. NMRs dig and survive in a maze of underground tunnels and chambers and demarcate toilet chambers for defecation and urination. Due to their coprophagic behaviours, we believed that the toilet chamber might play a role in maintaining optimal health of the NMRs. A 16S rRNA gene amplicon sequencing was performed to characterize the bacterial microbiome of faecal samples collected from the toilet chamber of a laboratory NMR colony. RESULTS: Four faecal samples were collected at different time points from the same toilet chamber of a laboratory NMR colony for analysis. The 16S rRNA gene amplicon sequencing revealed that bacterial phyla Firmicutes and Bacteroidetes were the dominant taxa in the bacterial microbiome of NMRs. The relative abundance of the bacterial taxa shifted substantially between time points, indicating a dynamic microbiome in the toilet chamber. The data provided an insight to the faecal microbiome of NMRs in the toilet chamber.

Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products in a way that is easily findable and accessible. Consequently, scattered and incompatible metadata records create a barrier to scientific innovation, as researchers are burdened to find and link multidisciplinary datasets. One possible solution to increase data findability, accessibility, interoperability, reproducibility, and integrity within multi-institutional and interdisciplinary projects is a centralized and integrated data management platform. Overall, this type of interoperable framework supports reproducible open science and its dissemination to various stakeholders and the public in a FAIR manner by providing direct access to raw data and linking protocols, metadata and supporting workflow materials.

OBJECTIVES: Gunshot wounds are frequently studied using computed tomography (CT) to examine tissue damage. In this study, we aimed to test the potential of post-mortem CT (PMCT) in shooting distance estimation at distances 0-100 cm. We hypothesized that in addition to the wound channel, we could also potentially detect tissue damage caused by muzzle pressure on PMCT. RESULTS: A total of 59 gunshot wounds (23 contact shots, 21 close-range shots, 15 distant shots) were inflicted on eight piglet carcasses with a .22 Long Rifle handgun. PMCT scans were obtained using clinical equipment, and they were evaluated for wound characteristics by visual inspection and numeric measurements. In our data, contact shots could be clearly distinguished from close-range and distant shots by a hyperdense ring-shaped area surrounding the outermost part of the wound channel. Close-range and distant shot wounds did not have this feature and were difficult to distinguish from each other. The mean wound channel diameter ranged from 3.4 to 5.4 mm, being smallest in contact shots and largest in distant shots. These preliminary findings suggest that PMCT may aid the estimation of shooting distance. As this study only addressed low velocity gunshot wounds in carcasses, further studies are warranted.

OBJECTIVE: Erucin (ERN), an isothiocyanate, is derived from the vegetable arugula. Although ERN has antitumor and antioxidant activity, the effect of ERN on osteoclast and osteoblast differentiation is not well documented. In this study, we evaluated the effects of ERN on osteoclast and osteoblast differentiation in vitro. RESULTS: ERN significantly reduced the formation of 1α,25(OH)2D3-induced tartrate-resistant acid phosphatase (TRAP)-positive cells at non-cytotoxic concentrations. Furthermore, ERN downregulated the mRNA expression of osteoclast-associated genes, such as nuclear factor of activated T cells cytoplasmic-1, TRAP, and cathepsin K. In addition, ERN suppressed mRNA expression of dendritic cell specific transmembrane protein (DC-STAMP), which encodes cell-cell fusion. However, ERN did not affect mineralization by osteoblasts. Thus, our data suggest that ERN may attenuate osteoclastic bone resorption by inhibiting multinucleation of mononuclear pre-osteoclasts and by suppressing mRNA expression of DC-STAMP in bone marrow cells without influencing mineralization by osteoblasts.

OBJECTIVES: Tamoxifen is considered to be the most widely used adjuvant therapy for hormone receptor positive breast cancer in premenopausal women. However, it is reported that nearly 30% of patients receiving tamoxifen therapy have shown reduced or no benefits. This may be due to the high inter-individual variations in the CYP2D6 gene that is involved in tamoxifen metabolism. The CYP2D6*10 gene variant (rs1065852C>T) is reported to be commonly found in Asian and South Asian populations. The present study was undertaken to design a novel pharmacogenetic assay (Single step-Tetra Arms Polymerase Chain Reaction) for the identification of the CYP2D6*10 variant and implement the designed assay by genotyping a cohort of breast cancer patients. RESULTS: The novel assay was successfully designed, optimized and validated using Sanger sequencing. Blood samples from 70 patients were genotyped. The following bands were observed in the gel image: Control band at 454 bp; band for C allele at 195 bp; band for T allele at 300 bp. The genotype frequencies for the CYP2D6*10 (rs1065852C>T) variant were: CC-24.28% (17/70), CT-75.71% (53/70), TT-0% (0/70). The allele frequencies were: T-allele-37.86% and C-allele-62.14%.

OBJECTIVE: To describe postpartum depression and associated risk factors among postpartum patients in the United States (US) between February and July 2020. This study used a cross-sectional descriptive design to collect survey data from a convenience sample of postpartum patients who lived in the US and delivered a live infant after the US declared COVID-19 a public health emergency. RESULTS: Our sample included 670 postpartum patients who completed an online survey inclusive of the Edinburgh Postnatal Depression Scale (EPDS) and selected demographic items (e.g. NICU admission status, infant gestational age, infant feeding method). In our sample, 1 in 3 participants screened positive for postpartum depression and 1 in 5 had major depressive symptoms. Participants who fed their infants formula had 92% greater odds of screening positive for postpartum depression and were 73% more likely to screen positive for major depressive symptoms compared to those who breastfed or bottle-fed with their own human milk. Participants with infants admitted to a NICU had 74% greater odds of screening positive. Each 1 week increase in weeks postpartum increased the odds of screening positive by 4%. Participants who worried about themselves and their infants contracting COVID-19 had 71% greater odds of screening positive.

OBJECTIVE: Adaptive laboratory evolution (ALE) is an effective approach to study the evolution behavior of bacterial cultures and to select for strains with desired metabolic features. In this study, we explored the possibility of evolving Thermotoga sp. strain RQ7 for cellulose-degrading abilities. RESULTS: Wild type RQ7 strain was subject to a series of transfers over six and half years with cellulose filter paper as the main and eventually the sole carbon source. Each transfer was accompanied with the addition of 50 μg of Caldicellulosiruptor saccharolyticus DSM 8903 genomic DNA. A total of 331 transfers were completed. No cellulose degradation was observed with the RQ7 cultures. Thirty three (33) isolates from six time points were sampled and sequenced. Nineteen (19) of the 33 isolates were unique, and the rest were duplicated clones. None of the isolates acquired C. saccharolyticus DNA, but all accumulated small-scale mutations throughout their genomes. Sequence analyses revealed 35 mutations that were preserved throughout the generations and another 15 mutations emerged near the end of the study. Many of the affected genes participate in phosphate metabolism, substrate transport, stress response, sensory transduction, and gene regulation.

OBJECTIVE: In a study of potential prostate cancer therapeutics, glycerol was used to increase the density of one solution. Glycerol alone was therefore one of the controls. Tumors of human PC3 castrate-resistant prostate cancer cells were initiated in male nude mice and grown for 12 days. Mice were then sorted such that mean tumor weights were the same in each group, and osmotic minipumps delivering 0.25 µL/h of either saline or glycerol were then implanted subcutaneously. RESULTS: Contrary to our initial assumption that glycerol would be without effect, tumors grew more rapidly in the glycerol group such that tumors were twice the size of those in the saline group after 4 weeks. Given the dose delivered, analysis of the literature suggests this effect was not via the conversion of glycerol to glucose but possibly via a reduction in oxidative damage in the growing tumor. Our data demonstrate that amounts of glycerol that could reasonably be derived from the diet promote the growth of these tumors. Given the increasing use of glycerol in foods and beverages, we present these data to stimulate interest in an epidemiological study in the human population examining glycerol consumption and the aggressiveness of prostate cancer.

OBJECTIVE: Nicotine replacement therapy (NRT) helps people stop smoking. Monitoring treatment adherence is important as poor adherence to NRT limits its effectiveness. As e-cigarettes contain nicotine, their use ('vaping') is likely to affect both NRT use and smoking. We wished to measure adherence to NRT, and to investigate relationships between NRT, vaping and smoking so we developed 'NicUse', a smartphone App linked to a cloud database for collecting data relevant to NRT adherence. We report user-acceptability and investigate data validity among pregnant people by comparing heaviness of smoking reported to NicUse surveys with contemporaneous exhaled carbon monoxide readings. RESULTS: Thirty five pregnant women participating in a pilot study were asked to install and use NicUse on their smartphones. 32/35 (91%) logged into NicUse, 31 (89%) completed one or more surveys, and 22 (63%) completed these on ≥ 20 of 28 study days. Twenty-four gave end-of-study user acceptability ratings; 23 (96%) agreed or strongly agreed NicUse was 'Easy to use' and 'Instructions were clear'. There was a strong correlation between the number of daily cigarettes reported on NicUse and exhaled CO readings taken on study Day 7 (Pearson's r = 0.95, p < 0.001). NicUse appears highly acceptable, and smoking data reported to it shows validity.