bluuebunny/crossref_metadata_2025 huggingface dataset:
Diabatic Heat Effects on the Generation of Energy for Evolution of a SACZ Event: A Perspective from the Lorenz Energy Cycle
Authors: António Jaime Fernando , Aravéquia José Antonio
Published: July 2023

Here we used meteorological datasets from ERA5 to study the dynamic and thermodynamic characteristics of a SACZ event that occurred between 12 and 26 December 2013. This is an atypical SACZ episode with considerable variations in cloudiness band positioning and high rainfall amounts, causing enormous problems for society. We study this case through the Lorenz energy cycle (LEC), focusing mainly on the role of diabatic heating in energy generation and consequently in circulation aspects, analyzing the event in three stages (formation, development, and dissipation), and discussing it according to the convection localization pattern. The diabatic heat rate has a large impact on the energy generation of SACZ events at midlevels south of 24°S and below 900 hPa in the tropics. In LEC, the generation terms in the SACZ area were larger at the beginning (12–15 December) and smaller at the ending periods (23–26 December), with means of 21.23 and −7.62 W m−2, respectively. The conversion terms follow the LEC directions, except for barotropic instability [C(KE, KM) < 0] that dominates throughout the analyzed periods. The convection area expansion to the north between 16 and 22 December was reflected by the most intense heating in the tropics and weaker barotropic instability. The friction term did not favor the event decay; therefore, we concluded that the cooling through a negative covariance between Q and T contributed to the event decay. We find that these results were largely influenced by a midlatitude wave train configuration that acted to favor the persistence, expansion, and decay of the event.
Epstein-Barr virus genotype-1 and Mediterranean + strain in gastric cancer biopsies of Ghanaian patients
Authors: Ampofo-Asiedu Jeffery , Tagoe Emmanuel Ayitey , Abrahams Darkwah Owusua Afua , Petershie Bernard , Quaye Osbourne
Published: July 2023

Gastric cancer (GC) prevalence is on the increase in Ghana, and Epstein-Barr virus (EBV) is one of the factors that have been implicated in the etiology of the cancer. It is therefore important to know the contribution of EBV genotype and strains that are associated with GC. In this study, we aimed at genotyping EBV and determining predominant strains in GC biopsies in Ghanaian patients. Genomic DNA was extracted from 55 GC biopsies (cases) and 63 normal gastric tissues (controls) were amplified by polymerase chain reaction (PCR) using specific primers for EBV detection and genotyping followed by PCR fragments sequencing. Epstein-Barr virus positivity were 67.3% and 49.2% in the GC and normal biopsies, respectively. Both cases and controls had the Mediterranean + strain of EBV. The predominant genotype of the virus in the GC cases was genotype-1 (75.7%) compared to 66.7% of genotype-2 among the control group. Infection was associated with GC in the study population (OR = 2.11, P = 0.014, 95% CI: 1.19 – 3.75), and EBV genotype-1 significantly increased the risk of GC (OR = 5.88, P < 0.0001, 95% CI: 3.18–10.88). The mean EBV load in the cases (3.507 ± 0.574) was significantly higher than in the controls (2.256 ± 0.756) ( P < 0.0001). We conclude that EBV, especially Mediterranean + genotype-1, was the predominant strain in GC biopsies and GC type or progression is independent of the viral load.
Roles considered important for hospitalist and non-hospitalist generalist practice in Japan: a survey study
Authors: Miyagami Taiju , Shimizu Taro , Kosugi Shunsuke , Kanzawa Yohei , Nagasaki Kazuya , Nagano Hiroyuki , Yamada Toru , Fujibayashi Kazutoshi , Deshpande Gautam A. , Flora Kisuule  , Tazuma Susumu , Naito Toshio
Published: July 2023

Background

An increased focus on quality and patient safety has led to the evolution of hospitalists. The number of hospitalists covering ward and outpatient care is on the rise in Japan. However, it is unclear what roles hospital workers themselves consider important in their practice. Therefore, this study investigated what hospitalists and non-hospitalist generalists in Japan consider important for the practice of their specialty.

Methods

This was an observational study that included Japanese hospitalists (1) currently working in a general medicine (GM) or general internal medicine department and (2) working at a hospital. Using originally developed questionnaire items, we surveyed the items important to hospitalists and non-hospitalist generalists.

Results

There were 971 participants (733 hospitalists, 238 non-hospitalist) in the study. The response rate was 26.1%. Both hospitalists and non-hospitalists ranked evidence-based medicine as the most important for their practice. In addition, hospitalists ranked diagnostic reasoning and inpatient medical management as the second and third most important roles for their practice, while non-hospitalists ranked inpatient medical management and elderly care as second and third.

Conclusions

This is the first study investigating the roles Japanese hospitalists consider important and comparing those to that of non-hospitalist generalists. Many of the items that hospitalists considered important were those that hospitalists in Japan are working on within and outside academic societies. We found that diagnostic medicine and quality and safety are areas that are likely to see further evolution as hospitalists specifically emphasized on them. In the future, we expect to see suggestions and research for further enhancing the items that hospital workers value and emphasise upon.
Vonoprazan-based triple and dual therapy versus bismuth-based quadruple therapy for Helicobacter pylori infection in China: a three-arm, randomised clinical trial protocol
Authors: Han ShaoWei , Deng ZiJie , Cheung KaShing , Lyu Tao , Chan PuiLing , Li Ying , Ni Li , Luo XiaPeng , Li Kuan
Published: July 2023

Background

Helicobacter pylori infection and associated diseases are a growing global public health issue. H. pylori infection is the major cause of gastric cancer, over 90% of duodenal ulcers, and over 70% of gastric ulcers. The infection rate of H. pylori is approximately 50%, and approximately 50% of new cases of gastric cancer worldwide occur in China. Bismuth (BI)-based quadruple therapy is recommended as the first-line treatment for H. pylori in China. Vonoprazan (VPZ), a new potassium-competitive acid blocker that can inhibit gastric acid secretion more effectively than proton pump inhibitors (PPIs), has been combined with antibiotics to effectively eradicate H. pylori. In this study, we compared the efficacy and safety of two VPZ-based therapies with that of BI-based therapy for H. pylori treatment.

Methods

A three-armed randomised controlled trial (RCT) is being conducted in Shenzhen, with 327 participants recruited from the Gastroenterology Clinic of the University of Hong Kong-Shenzhen Hospital. Patients were diagnosed with H. pylori infection based on a positive 13C-urea breath test (UBT). Patients are kept naïve to their treatment and are randomly assigned in a 1:1:1 ratio to either VPZ-based triple, VPZ-based dual, or BI-based quadruple therapy for 14 days. All groups are subjected to follow-up evaluations of safety, adverse drug reactions, and clinical variables in the first, second, and fourth weeks after treatment. Successful eradication is confirmed by a negative 13C-UBT six weeks after treatment. If initial treatment fails, (1) those patients are turned to another regimen, or (2) a drug resistance test is conducted, after which an individualised treatment regimen shall be prescribed according to antimicrobial susceptibility testing. The resulting data will be evaluated using intention-treat and a per-protocol analysis.

Discussion

This study is the a RCT aims to evaluate the efficacy and safety of 14-day VPZ-based triple and dual therapies in comparison with BI-based quadruple therapy. The outcomes of this study may allow treatment recommendations and update drug instructions in China.

Trial registration

Chinese Clinical Trial Registry (No. ChiCTR2200056375). Registered on February 4, 2022, https://www.chictr.org.cn/showproj.aspx?proj=141314
Effectiveness of outpatient geriatric evaluation and management intervention on survival and nursing home admission: a systematic review and meta-analysis of randomized controlled trials
Authors: Yen Pei-Chia , Lo Yu-Tai , Lai Chih-Cheng , Lee Ching-Chi , Fang Ching-Ju , Chang Chia-Ming , Yang Yi-Ching
Published: July 2023

Background

The benefit of inpatient comprehensive geriatric assessment on patient survival and function has been demonstrated among frail older patients. However, the influence of outpatient geriatric evaluation and management (GEM) on clinical outcomes remains debated. This study aimed to update the research evidence detailing the effect of outpatient GEM on survival and nursing-home admission through a comparison with conventional care.

Methods

Cochrane Library, EMBASE, and MEDLINE databases were searched up to January 29th, 2022, to identify randomized controlled trials (RCTs) including older people over age 55 that compared outpatient GEM with conventional care on mortality (primary outcome) and nursing-home admission (secondary outcome) during a follow-up period of 12 to 36 months.

Results

Nineteen reports from 11 studies that recruited 7,993 participants (mean age 70–83) were included. Overall, outpatient GEM significantly reduced mortality (risk ratio (RR) = 0.87, 95% confidence interval (CI) = 0.77–0.99, I2 = 12%). For the subgroup analysis categorized by different follow-up periods, its prognostic benefit was only disclosed for 24-month mortality (RR = 0.68, 95% CI = 0.51–0.91, I2 = 0%), but not for 12- or 15 to 18-month mortality. Furthermore, outpatient GEM had significantly trivial effects on nursing-home admission during the follow-up period of 12 or 24 months (RR = 0.91, 95% CI = 0.74–1.12, I2 = 0%).

Conclusions

Outpatient GEM led by a geriatrician with a multidisciplinary team improved overall survival, specifically during the 24-month follow-up period. This trivial effect was demonstrated in rates of nursing-home admission. Future research on outpatient GEM involving a larger cohort is warranted to corroborate our findings.
Effects of intravenous administration of magnesium sulfate in propofol-based sedation for ERCP in elderly patients: a randomized, double-blind, placebo-controlled study
Authors: Chen Jie , Qian Ke , Liu Chun-hong , Li Xiao-li , Chen Yan , Wang Jin-quan
Published: July 2023

Background

Propofol-based sedations are widely used in elderly patients for endoscopic retrograde cholangiopancreatography (ERCP) procedure, but respiratory depression and cardiovascular adverse events commonly occur. Magnesium administered intravenously can alleviate pain and decrease propofol requirements during surgery. We hypothesized that intravenous magnesium was used as adjuvant to propofol might be beneficial in elderly patients undergoing ERCP procedures.

Methods

Eighty patients aged from 65 to 79 years who were scheduled for ERCP were enrolled. All patients were intravenously administered 0.1 µg/kg sufentanil as premedication. The patients were randomized to receive either intravenous magnesium sulfate 40 mg/kg (group M, n = 40) or the same volume of normal saline (group N, n = 40) over 15 min before the start of sedation. Intraoperative sedation was provided by propofol. Total propofol requirement during ERCP was the primary outcome.

Results

The total propofol consumption were reduced by 21.4% in the group M compared with the group N (151.2 ± 53.3 mg vs. 192.3 ± 72.1 mg, P = 0.001). The incidences of respiratory depression episodes and involuntary movement were less in the group M than those in the group N (0/40 vs. 6/40, P = 0.011; 4/40 vs. 11/40, P = 0.045; respectively). In the group M, the patients experienced less pain than those in the group N at 30 min after the procedure (1 [0–1] vs. 2 [1–2], P < 0.001). Correspondingly, the patients’ satisfaction was clearly higher in the group M (P = 0.005). There was a tendency towards lower intraoperative heart rate and mean arterial pressure in group M.

Conclusions

A single bolus of 40 mg/kg of intravenous magnesium can significantly reduce propofol consumption during ERCP, with higher sedation success and lower adverse events.

Trial Registration

ID UMIN000044737. Registered 02/07/2021.
Postpartum care needs assessment: women’s understanding of postpartum care, practices, barriers, and educational needs
Authors: Adams Yenupini Joyce , Miller Michelle Louise , Agbenyo John Stephen , Ehla Ethel Emefa , Clinton Grace Anne
Published: July 2023

Background

Complications in the postpartum period pose substantial risks to women and can result in significant maternal morbidity and mortality. However, there is much less attention on postpartum care compared to pregnancy and childbirth. The goal of this study was to gather information on women’s knowledge of postpartum care and complications, recovery practices after childbirth, perceived barriers to receiving care during the postpartum period, and educational needs in four health centers. The findings can inform the development of appropriate curriculum and interventions for postnatal care education in similar settings.

Methods

A descriptive qualitative study design was employed. Eight focus group discussions were conducted among 54 postpartum women who delivered in four health centers in Sagnarigu District in Tamale, Ghana. Audio recordings of focus group data were transcribed and translated, and thematic analysis was conducted.

Results

There were six main themes that emerged from the focus group discussions: 1) baby focused postpartum care; 2) postpartum practices; 3) inadequate knowledge ofpostpartum danger signs; 4) barriers to accessing postpartum care 5) experiences of poor mental health; and 6) need for postpartum education.

Conclusions

Postpartum care for women in this study was primarily perceived as care of the baby post-delivery and missing key information on physical and mental health care for the mother. This can result in poor adjustment postpartum and critically, a lack of knowledge on danger signs for common causes of morbidity and mortality in the postpartum period. Future research needs to understand how to communicate important information on postpartum mental and physical health to better protect mothers in the region.
Multidimensional assessment of infant, parent and staff outcomes during a family centered care enhancement project in a tertiary neonatal intensive care unit: study protocol of a longitudinal cohort study
Authors: Schuler Rahel , Woitschitzky Lea , Eiben Carola , Beck Judith , Jägers Alena , Windhorst Anita , Kampschulte Birgit , Petzinger Jutta , Waitz Markus , Kilsdonk Monique Oude Reimer-van , Neubauer Bernd A. , Zimmer Klaus-Peter , Ehrhardt Harald , Brosig Burkhard , Mihatsch Walter A.
Published: July 2023

Background

The therapeutic advances and progress in the care for preterm infants have enabled the regular survival of very immature infants. However, the high burden of lifelong sequelae following premature delivery constitutes an ongoing challenge. Regardless of premature delivery, parental mental health and a healthy parent–child relationship were identified as essential prerogatives for normal infant development. Family centered care (FCC) supports preterm infants and their families by respecting the particular developmental, social and emotional needs in the Neonatal Intensive Care Unit. Due to the large variations in concepts and goals of different FCC initiatives, scientific data on the benefits of FCC for the infant and family outcome are sparse and its effects on the clinical team need to be elaborated.

Methods

This prospective single centre longitudinal cohort study enrols preterm infants ≤ 32 + 0 weeks of gestation and/or birthweight ≤ 1500 g and their parents at the neonatal department of the Giessen University Hospital, Giessen, Germany. Following a baseline period, the rollout of additional FCC elements is executed following a stepwise 6-months approach that covers the NICU environment, staff training, parental education and psychosocial support for parents. Recruitment is scheduled over a 5.5. year period from October 2020 to March 2026. The primary outcome is corrected gestational age at discharge. Secondary infant outcomes include neonatal morbidities, growth, and psychomotor development up to 24 months. Parental outcome measures are directed towards parental skills and satisfaction, parent-infant-interaction and mental health. Staff issues are elaborated with particular focus on the item workplace satisfaction. Quality improvement steps are monitored using the Plan- Do- Study- Act cycle method and outcome measures cover the infant, the parents and the medical team. The parallel data collection enables to study the interrelation between these three important areas of research. Sample size calculation was based on the primary outcome.

Discussion

It is scientifically impossible to allocate improvements in outcome measures to individual enhancement steps of FCC that constitutes a continuous change in NICU culture and attitudes covering diverse areas of change. Therefore, our trial is designed to allocate childhood, parental and staff outcome measures during the stepwise changes introduced by a FCC intervention program.

Trial registration

Clinicaltrials.gov, trial registration number NCT05286983, date of registration 03/18/2022, retrospectively registered, http://clinicaltrials.gov.
Effect of Orlistat on anthropometrics and metabolic indices in children and adolescents: a systematic review and meta-analysis
Authors: Nikniaz Zeinab , Nikniaz Leila , Farhangi Mahdieh Abbasalizad , Mehralizadeh Hossein , Salekzamani Shabnam
Published: July 2023

Background

Childhood obesity is one of the main concerns of public health. Considering its long-term adverse health effect, various studies investigated the effect of drug therapy on anthropometric parameters and provided mixed results. In this systematic review and meta-analysis, we aimed to determine the effect of Orlistat on anthropometrics and biochemical parameters in children and adolescents.

Materials and methods

The databases of PubMed, Scopus, and Web of Science were searched until September 2022. Experimental and semi-experimental studies were included if they evaluated the effect of Orlistat on obesity-related parameters in children and reported the before and after anthropometric values. A revised Cochrane risk-of-bias (Rob2) was used to evaluate the methodological quality. STATA software version 16.0 was used for the meta-analysis of the random-effect model.

Results

Of 810 articles retrieved in the initial search, four experimental and two semi-experimental studies were selected for systematic review. The result of the meta-analysis of experimental studies indicated the significant effect of Orlistat on waist circumference (SMD: -0.27, 95% CI: -0.47, -0.07) and serum insulin level (SMD: -0.89, 95% CI: -1.52, 0.26). However, there were no significant effects of orlistat on body weight, body mass index, lipid profile, and serum glucose level.

Conclusion

The present meta-analysis showed the significant effect of Orlistat on the reduction of waist circumference and insulin level in overweight and obese adolescents. However, due to the paucity of studies included in the meta-analysis, more prospective studies with longer duration and more sample sizes will be needed in this age group.
Morphological evaluation of gonial and antegonial regions in bruxers on panoramic radiographic images
Authors: Unal Erzurumlu Zerrin , Sadik Elif , Gokkurt Busra Nur , Ozbey Furkan , Erzurumlu Kerem , Kasko Arici Yeliz
Published: July 2023

Background

This is the first study to report both cortical and trabecular bone evaluation of mandibles in bruxers, within the knowledge of the authors. The purpose of this study was to evaluate the effects of bruxism on both the cortical and the trabecular bone in antegonial and gonial regions of the mandible, which is the attachment of the masticatory muscles, by using panoramic radiographic images.

Methods

In this study, the data of 65 bruxer (31 female, 34 male) and 71 non-bruxer (37 female, 34 male) young adult patients (20–30 years) were evaluated. Antegonial Notch Depth (AND), Antegonial-Index (AI), Gonial-Index, Fractal Dimension (FD) and Bone Peaks (BP) were evaluated on panoramic radiographic images. The effects of the bruxism, gender and side factors were investigated according to these findings. The statistical significance level was set atP ≤ 0.05.

Results

The mean AND of bruxers (2.03 ± 0.91) was significantly higher than non-bruxers (1.57 ± 0.71; P < 0.001). The mean AND of males was significantly higher than females on both sides (P < 0.05). The mean AI of bruxers (2.95 ± 0.50) was significantly higher than non-bruxers (2.77 ± 0.43; P = 0.019). The mean FD on each side was significantly lower in bruxers than in non-bruxers (P < 0.05). The mean FD of males (1.39 ± 0.06) was significantly higher than females (1.37 ± 0.06; P = 0.049). BP were observed in 72.5% of bruxers and 27.5% of non-bruxers. The probability of existing BP, in bruxers was approximately 3.4 times higher than in non-bruxers (P = 0.003), in males was approximately 5.5 times higher than in females (P < 0.001).

Conclusion

According to the findings of this study, the morphological differences seen in cortical and trabecular bone in the antegonial and gonial regions of the mandible in bruxers can be emphasized as deeper AND, higher AI, increased of existing BPs, and lower FD, respectively. The appearance of these morphological changes on radiographs may be useful for indication and follow-up of bruxism. Gender is an effective factor on AND, existing BP and FD.
Effectiveness of a virtual program for OSCE preparation during COVID-19: a descriptive and repeated cross-sectional study among nursing students
Authors: Avraham Rinat , Cohen Tanya , Artzi-Medvedik Rada , Hurvitz Nancy , Cohen Odeya
Published: July 2023

Background

Despite the prevalence of distance learning during COVID-19, conducting clinical training for nursing students remains challenging. In compliance with social-distancing restrictions, a Zoom-based virtual OSCE preparation program for nursing students was designed, and it included clinical skills. The aims of this study were to assess nursing students’ satisfaction with a virtual program for Objective Structured Clinical Examination (OSCE) preparation, and to evaluate its learning outcomes measured by OSCE scores as compared to those of in-person preparation programs.

Methods

A descriptive and repeated cross-sectional study was designed. Students’ satisfaction with the virtual program was based on a post-course survey and personal reflections. OSCE scores of graduates of the virtual program (n = 82) tested in 2021 were compared to those of 337 graduates of in-person programs tested in 2017–2020.

Results

A post-program survey revealed that 88% of the students in 2021 were satisfied with the virtual program and felt it prepared them properly for the OSCE (26% agree and 62% strongly agree). No significant differences were found between OSCE scores following the virtual program conducted in 2021 and scores following in-person programs conducted in 2017–2020.

Conclusions

This study suggests that nursing education can benefit from integrating virtual programs which incorporate clinical practices into the curricula, without harming student competency. The study results may address the problem of maintaining clinical practices in a time of limited accessibility, and in settings of low resources. It is important to expand the investigation to long-term impact of virtual training programs on nursing students’ competencies.
Enhancing the interferon-γ release assay through omission of nil and mitogen values
Authors: Jung Yun Jung , Park Ji Eun , Park Ji Won , Lee Keu Sung , Chung Wou Young , Park Joo Hun , Sheen Seung Soo , You Seulgi , Sun Joo Sung , Park Kyung Joo , Kim Youn Jung , Park Kwang Joo
Published: July 2023

Purpose

To address the limited utility of the interferon (IFN)-γ release assay (IGRA) caused by its variability and inconsistency.

Methods

This retrospective cohort study was based on data obtained between 2011 and 2019. QuantiFERON-TB Gold-In-Tube was used to measure IFN-γ levels in nil, tuberculosis (TB) antigen, and mitogen tubes.

Results

Of 9,378 cases, 431 had active TB. The non-TB group comprised 1,513 IGRA-positive, 7,202 IGRA-negative, and 232 IGRA-indeterminate cases. Nil-tube IFN-γ levels were significantly higher in the active TB group (median = 0.18 IU/mL; interquartile range: 0.09–0.45 IU/mL) than in the IGRA-positive non-TB (0.11 IU/mL; 0.06–0.23 IU/mL) and IGRA-negative non-TB (0.09 IU/mL; 0.05–0.15 IU/mL) groups (P < 0.0001). From receiver operating characteristic analysis, TB antigen tube IFN-γ levels had higher diagnostic utility for active TB than TB antigen minus nil values. In a logistic regression analysis, active TB was the main driver of higher nil values. In the active TB group, after reclassifying the results based on a TB antigen tube IFN-γ level of 0.48 IU/mL, 14/36 cases with negative results and 15/19 cases with indeterminate results became positive, while 1/376 cases with positive results became negative. Overall, the sensitivity for detecting active TB improved from 87.2 to 93.7%.

Conclusion

The results of our comprehensive assessment can aid in IGRA interpretation. Since nil values are governed by TB infection rather than reflecting background noise, TB antigen tube IFN-γ levels should be used without subtracting nil values. Despite indeterminate results, TB antigen tube IFN-γ levels can be informative.
CXCL5 suppression recovers neovascularization and accelerates wound healing in diabetes mellitus
Authors: Chen Ching , Lin Liang-Yu , Chen Jaw-Wen , Chang Ting-Ting
Published: July 2023

Background

Higher chemokine C-X-C motif ligand 5 (CXCL5) level was observed in type 2 diabetes mellitus (DM) patients; however, its role in diabetic vasculopathy was not clarified. This study aimed to explore the impacts and mechanistic insights of CXCL5 in neovasculogenesis and wound healing in DM.

Methods

Endothelial progenitor cells (EPCs) and human aortic endothelial cells (HAECs) were used in vitro. Streptozotocin-induced diabetic mice and Leprdb/JNarl mice were used as type 1 and type 2 DM models. Moreover, CXCL5 knockout mice were used to generate diabetic mice. Hindlimb ischemia surgery, aortic ring assays, matrigel plug assay, and wound healing assay were conducted.

Results

CXCL5 concentrations were increased in plasma and EPCs culture medium from type 2 DM patients. CXCL5 neutralizing antibody upregulated vascular endothelial growth factor (VEGF)/stromal cell-derived factor-1 (SDF-1) and promoted cell function in EPCs from type 2 DM patients and high glucose-treated EPCs from non-DM subjects as well as HAECs. CXCL5 directly up-regulated interleukin (IL)-1β/IL-6/tumor necrosis factor-α and down-regulated VEGF/SDF-1 via ERK/p65 activation through chemokine C-X-C motif receptor 2 (CXCR2). CXCL5 neutralizing antibody recovered the blood flow after hindlimb ischemia, increased circulating EPC number, and enhanced VEGF and SDF-1 expression in ischemic muscle. CXCL5 suppression promoted neovascularization and wound healing in different diabetic animal models. The above observation could also be seen in streptozotocin-induced CXCL5 knockout diabetic mice.

Conclusions

CXCL5 suppression could improve neovascularization and wound healing through CXCR2 in DM. CXCL5 may be regarded as a potential therapeutic target for vascular complications of DM.
An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis
Authors: Niaré Karamoko , Greenhouse Bryan , Bailey Jeffrey A.
Published: July 2023

Background

Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples.

Methods

Control WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data.

Results

On current high-quality samples (read length = 250 bp, insert size = 405–524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection.

Conclusions

Overall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria.
Regularized linear discriminant analysis via a new difference-of-convex algorithm with extrapolation
Authors: Wang Chunyan , Wang Wenjie , Li Mengzhen
Published: July 2023

In this paper, we transform the classical linear discriminant analysis (LDA) into a smooth difference-of-convex optimization problem. Then, a new difference-of-convex algorithm with extrapolation is introduced and the convergence of the algorithm is established. Finally, for a face recognition problem, the proposed algorithm achieves better classification performance compared with several current algorithms in the literature.
Affine periodic solutions for some stochastic differential equations
Authors: Guo Ruichao , Wang Hongren
Published: July 2023

In this paper, we are study the problem of affine periodicity of solutions in distribution for some nonlinear stochastic differential equation with exponentially stable. We prove the existence and uniqueness of stochastic affine periodic solutions in distribution via the Banach fixed-point theorem.
Role of early childhood educators’ demographic characteristics and perceived work environment in implementation of a preschool health promotion intervention
Authors: Gustafsson Jasmine , Ray Carola , Lehto Elviira , Roos Eva , Lehto Reetta
Published: July 2023

Background

Research has indicated that the effectiveness of intervention programs is affected by how well these programs are implemented, but key gaps remain in our understanding of the factors that promote or inhibit implementation. This study examined how demographic characteristics and perceived work environment among early childhood educators were associated with implementation outcomes of the Increased Health and Wellbeing in Preschools (DAGIS) intervention, which was conducted as a cluster randomized trial.

Methods

Participants included 101 educators from 32 intervention preschool classrooms. Data were analyzed at the classroom level, as the DAGIS intervention was delivered in preschool classrooms consisting of several educators instead of individual implementers. Linear regression was used to estimate the associations of educators’ demographic characteristics and perceived work environment with different aspects of implementation (i.e., dose delivered; dose received – exposure; dose received – satisfaction; and perceived quality, as well as a total sum score based on these four dimensions). Municipality was controlled in the adjusted models.

Results

Findings indicated that having a higher proportion of educators with a Bachelor’s or Master’s degree in education within the classroom was associated with higher dose received – exposure and higher total degree of implementation, and the significance of the models was unaffected by adjustment for municipality. Moreover, having a higher proportion of educators younger than 35 years within the classroom was associated with higher dose received – exposure. However, the association was non-significant when adjusted for municipality. No other educator factor (i.e., work experience in years and perceived support from coworkers, group work, and innovative climate) predicted implementation outcomes.

Conclusions

Higher educational attainment and younger age among educators at the classroom level were associated with higher scores for some of the implementation outcomes. Educators’ work experience in years at the current preschool and in early childhood education, support from coworkers, group work, and innovative climate were not significantly associated with any implementation outcomes. Future research should explore ways to improve educators’ implementation of interventions aimed at promoting children’s health behaviors.
Contributions of avoidable mortality to the sex gap in life expectancy and life disparity in Iran
Authors: Bayati Mohsen , Kiadaliri Ali
Published: July 2023

Background

Public health policies and healthcare quality play a pivotal role on the health outcome level and disparities across sociodemographic groups. However, there is little evidence on their role on disparities in life expectancy (LE) and life disparity (LD) in low and middle income countries. The present study aimed to assess the contributions of avoidable mortality, as a measure of inter-sectoral public health policies and healthcare quality, into the sex gap in LE (SGLE) and LD (SGLD) in Iran.

Methods

Latest available data of death causes, according to the ICD codes, for Iran was obtained from the WHO mortality database for the period 2015–2016. An upper age limit of 75 years was applied to define avoidable causes of death. LD was measured as the average years of life lost at birth. The SGLE and SGLD (both females minus males) were decomposed by age and cause of death using a continuous-change model.

Results

Females, on average, outlived males for 3.8 years (80.0 vs. 76.2 years) with 1.9 lower life years lost (12.6 vs. 14.4 years). Avoidable causes accounted for 2.5 (67%) and 1.5 (79%) years of the SGLE and SGLD, respectively. Among avoidable causes, injury-related deaths followed by ischaemic heart disease had the greatest contributions to both SGLE and SGLD. Across age groups, the age groups 55–59 and 60–64 accounted for the greatest contributions of avoidable causes to SGLE (0.3 years each), while age groups 20–24 and 55–59 had the greatest contributions to SGLD (0.15 years each). Lower mortality rates for females than males in age groups 50–74 years accounted for about half of the SGLE, while age groups 20–29 and 50–64 years accounted for around half of SGLD.

Conclusion

More than two third of the SGLE and SGLD in Iran were attributed to the avoidable mortality, particularly preventable causes. Our results suggest the need for public health policies targeting injuries in young males as well as lifestyle risk factors including smoking in middle aged males in Iran.
Calcareous nannofossil assemblage in paintings chalk ground for provenance analysis: three original paintings compared to european source materials
Authors: Jaques Victory Armida Janine , Holcová Katarína
Published: July 2023

Chalk has been used since Antiquity for various purposes, and since Gothic for preparatory layers of painted cultural heritage objects. Several materials are called chalk in Cultural Heritage, but this work especially focuses on chalk composed of calcareous nannofossils (up to 98%). These are fossil remains of photoautotrophic algae generally smaller than 30 μm. They are mainly visible as platelets of various shapes under a cross-polarised or scanning electron microscope. The provenance of chalk can be determined using calcareous nannofossils due to their well-known paleobiogeographic localities. They are already used as proxies since the 90s in Cultural Heritage, but rarely for paintings. In this work, 6 chalk historical mining areas were chosen: Germany (Ruegen), France (Champagne, Meudon), Belgium (Mons), England (Norfolk) and Italy (Bologna). Natural and processed chalk were used as reference materials and compared to 3 original paintings. The difference between the chalks calcareous nannofossil assemblages was shown using multivariate statistical analysis based on species relative abundance. Marker nannofossil species were defined for each chalk locality. One painting material could not be originated due to the preservation of its nannofossils assemblage, but the origins of the rock chalk material from the two other paintings could be geographically located in France.
Enhanced thermoelectric performance of SnSe by controlled vacancy population
Authors: Lee Ji-Eun , Kim Kyoo , Nguyen Van Quang , Hwang Jinwoong , Denlinger Jonathan D. , Min Byung Il , Cho Sunglae , Ryu Hyejin , Hwang Choongyu , Mo Sung-Kwan
Published: July 2023

The thermoelectric performance of SnSe strongly depends on its low-energy electron band structure that provides high density of states in a narrow energy window due to the multi-valley valence band maximum (VBM). Angle-resolved photoemission spectroscopy measurements, in conjunction with first-principles calculations, reveal that the binding energy of the VBM of SnSe is tuned by the population of Sn vacancy, which is determined by the cooling rate during the sample growth. The VBM shift follows precisely the behavior of the thermoelectric power factor, while the effective mass is barely modified upon changing the population of Sn vacancies. These findings indicate that the low-energy electron band structure is closely correlated with the high thermoelectric performance of hole-doped SnSe, providing a viable route toward engineering the intrinsic defect-induced thermoelectric performance via the sample growth condition without an additional ex-situ process.

Graphical Abstract
Exploring senior engineering students’ engineering identity: the impact of practice-oriented learning experiences
Authors: Ju Tongjie , Zhu Jiabin
Published: July 2023

Background

Engineering identity reflects students' acceptance and recognition of engineering, which has a great influence on their willingness to enter and stay in the engineering field. Existing studies have shown that curricular and co-curricular practice-oriented experiences may be helpful for developing students’ engineering identity. However, the actual impact of various practice-oriented learning experiences remained to be further examined. This quantitative study aims to explore the impact of three types of practice-oriented learning experiences (capstone experiences, technological innovation and entrepreneurship competitions, and engineering-related internships) in the development of engineering talents' engineering identity. A theoretical framework of engineering identity, which consists of three dimensions, that is, Interest, Performance/Competence and Recognition, was adopted to guide the research.

Results

Through responses from 160 senior engineering students at a leading research intensive Chinese university, the study explored the relationships between engagement in practice-oriented learning experiences and engineering identity. Senior capstone design was found to be associated positively with students' development of engineering identity and recognition by others. Participating in two or more technological innovation and entrepreneurship competitions associated positively with students' development of engineering identity, performance/competence and recognition. Meanwhile, internships did not show any statistically significant effect on engineering identity. Moreover, by analyzing the potential mediating effect, we found that recognition played a complete intermediary role between senior capstone design and engineering identity. In addition, recognition and performance/competence mediated the relationship between twice or more technological innovation and entrepreneurship competitions and engineering identity.

Conclusions

These findings add to our current understanding about the role of different practice-oriented learning activities on students’ development of engineering identity. These findings point to the importance of learning activities, including technological innovation and entrepreneurship competitions and senior capstone design, on the development of engineering identity. Moreover, the results highlighted the important role of students’ engagement in multiple authentic engineering projects throughout the curriculum and their gaining recognitions through these project experiences. Based on these findings, practical suggestions are proposed to help nurture students’ engineering identity. In addition, future qualitative investigations about the underlying mechanisms are recommended to facilitate the understanding of students’ development of engineering identity.
Integrative meta-omics in Galaxy and beyond
Authors: Schiml Valerie C. , Delogu Francesco , Kumar Praveen , Kunath Benoit , Batut Bérénice , Mehta Subina , Johnson James E. , Grüning Björn , Pope Phillip B. , Jagtap Pratik D. , Griffin Timothy J. , Arntzen Magnus Ø.
Published: July 2023

Background

‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omics”, they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.

Results

In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum, Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO.

Conclusion

Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of ‘omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows.
Engineering considerations of iPSC-based personalized medicine
Authors: Park Sangbae , Gwon Yonghyun , Khan Shahidul Ahmed , Jang Kyoung-Je , Kim Jangho
Published: July 2023

Personalized medicine aims to provide tailored medical treatment that considers the clinical, genetic, and environmental characteristics of patients. iPSCs have attracted considerable attention in the field of personalized medicine; however, the inherent limitations of iPSCs prevent their widespread use in clinical applications. That is, it would be important to develop notable engineering strategies to overcome the current limitations of iPSCs. Such engineering approaches could lead to significant advances in iPSC-based personalized therapy by offering innovative solutions to existing challenges, from iPSC preparation to clinical applications. In this review, we summarize how engineering strategies have been used to advance iPSC-based personalized medicine by categorizing the development process into three distinctive steps: 1) the production of therapeutic iPSCs; 2) engineering of therapeutic iPSCs; and 3) clinical applications of engineered iPSCs. Specifically, we focus on engineering strategies and their implications for each step in the development of iPSC-based personalized medicine.
Amelioration of intestinal barrier function and reduction of blood lead level in adult women with recurrent spontaneous abortion by a novel product of dietary fiber mixture, Holofood
Authors: Tian Ye , Pan Zhiyuan , Lan Liling , Chang Yuxiao , Zhao Ting , Fu Zhihong , Wu Shuhua , Deng Tianqin , Cao Meilan , Wang Weizhou , Bi Yujing , Yang Ruifu , Yang Lee B. J. , Liu Qingzhi
Published: July 2023

Background

The elevated circulating toxins secondary to the impairment of intestinal barrier integrity commonly elicit a chronic inflammatory response and finally contribute to multiple diseases. These toxins, including bacterial by-products and heavy metals, are the potent risk factors for the development of recurrent spontaneous abortion (RSA). Preclinical evidence suggests that several dietary fibers can restore intestinal barrier function and decrease the accumulation of heavy metals. However, it is uncertain whether treatment with a newly developed blend of dietary fibers product (Holofood) benefits patients with RSA.

Methods

In this trial, we enrolled 70 adult women with RSA, who were randomly assigned into the experiment group and the control group in a 2:1 ratio. Upon the basis of conventional therapy, subjects in the experiment group (n = 48) received 8 weeks oral administration with Holofood three times daily at a dose of 10 g each time. Subjects without Holofood consumption were set as the control (n = 22). Blood samples were collected for the determinations of metabolic parameters, heavy mental lead, and the indices related to intestinal barrier integrity (d-lactate, bacterial endotoxin, and diamine oxidase activity).

Results

The reduction amplitude in blood lead from baseline to week 8 was 40.50 ± 54.28 (μg/L) in the experiment group as compared with 13.35 ± 36.81 (μg/L) in the control group (P = 0.037). The decreased level of serum d-lactate from baseline to week 8 was 5.58 ± 6.09 (mg/L) in the experiment group as compared with − 2.38 ± 8.90 (mg/L, P < 0.0001) in the control group. The change in serum DAO activity from baseline to week 8 was 3.26 ± 2.23 (U/L) in the experiment group as compared with − 1.24 ± 2.22 (U/L, P < 0.0001) in the control group. Participants who received Holofood had a greater decline in blood endotoxin from baseline to week 8 than those in the control group. Moreover, by comparing with the self-baseline, Holofood consumption significantly decreased the blood levels of lead, d-lactate, bacterial endotoxin, and DAO activity.

Conclusion

Our results suggest that Holofood affords a clinically relevant improvements in blood lead level and intestinal barrier dysfunction in patients with RSA.