bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022
Authors: Nduwimana Cassien , Nzoyikorera Néhémie , Ndihokubwayo Armstrong , Ihorimbere Théogène , Nibogora Célestin , Ndoreraho Adolphe , Hajayandi Oscar , Bizimana Jean Claude , Diawara Idrissa , Niyonizigiye Dionis , Nyandwi Joseph
Published: June 2023

Background

The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic.

We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata.

Results

In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July–October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related.

Conclusion

The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.
Triptolide attenuates irritable bowel syndrome via inhibiting ODC1
Authors: Zhu Ning , Zhu Liuyan , Zhang Xueliang , Huang Chengbin , Xiang Wenjun , Huang Bingwu
Published: June 2023

Background

Irritable bowel syndrome (IBS) is a chronic disorder of the gut-brain axis with significant morbidity. Triptolide, an active compound extracted from Tripterygium wilfordii Hook F (TwHF), has been widely used as a major medicinal herb in the treatment of inflammatory disease.

Methods

The chronic-acute combined stress (CAS) stimulation was used to establish IBS rat model. The model rats were then gavaged with triptolide. Forced swimming, marble-burying, fecal weight and abdominal withdrawal reflex (AWR) score were recorded. Pathologic changes in the ileal and colonic tissues were validated by hematoxylin and eosin staining. The inflammatory cytokines and Ornithine Decarboxylase-1 (ODC1) in the ileal and colonic tissues were performed by ELISA and WB.

Results

Triptolide didn’t have antidepressant- and antianxiety- effects in rats caused by CAS, but decreased fecal weight and AWR score. In addition, Triptolide reduced the release of IL-1, IL-6, and TNF-α and the expression of ODC1 in the ileum and colon.

Conclusion

The therapeutic efficacy of triptolide for IBS induced by CAS was revealed in this study, which may be related to the reduction of ODC1.
Risk factors of left ventricular diastolic dysfunction in maintenance hemodialysis patients
Authors: Lei Ying , Tong JinYan , Su YanYan , Wang YuQuan , Zhong BiXian , Wang Qi , Zhang YunFang
Published: June 2023

Objective

To investigate the risk factors of left ventricular diastolic dysfunction in maintenance hemodialysis (MHD) patients.

Method

We retrospectively collected data from 363 hemodialysis patients who were on dialysis for at least 3 months at January 1, 2020. According to the echocardiogram results, these patients were divided into left ventricular diastolic dysfunction (LVDD) group and non-LVDD group. The differences in basic data, cardiac structure and functiona between the two groups were analyzed. Logistic regression analysis was used to analyze the risk factors of cardiac diastolic dysfunction in MHD patients.

Results

Compared with the non-LVDD group, patients in the LVDD group were older, with an increased proportion of coronary heart disease, more prone to chest tightness, shortness of breath. Simultaneously, they had a significantly increased (p < 0.05) proportion of cardiac structural abnormalities such as left ventricular hypertrophy, left heart enlargement and systolic dysfunction. Multivariate logistic regression analysis showed that the risk of LVDD was significantly increased in elderly MHD patients older than 60 years (OR = 3.86, 95%CI 1.429–10.429), and left ventricular hypertrophy was also significantly associated with LVDD (OR = 2.227, 95% CI 1.383–3.586).

Conclusion

According to research, both age and left ventricular hypertrophy are risk factors for LVDD in MHD patients. It is recommended that early intervention for LVDD should be implemented to improve the quality of dialysis and reduce the incidence of cardiovascular events in MHD patients.
The association of periodontal disease and oral health with hypertension, NHANES 2009–2018
Authors: Li Yuting , Yuan Xiaojing , Zheng Qiutong , Mo Fengxin , Zhu Shiheng , Shen Tianran , Yang Wenhan , Chen Qingsong
Published: June 2023

Background

Hypertension is a worldwide public health problem. We sought to explore the interaction of oral health and smoking on hypertension, and periodontal disease and smoking on hypertension.

Methods

We included 21,800 participants aged ≧ 30 years from the National Health and Nutrition Examination Survey (NHANES) 2009–2018. Information of oral health and periodontal disease were self-reported. Blood pressure was taken by trained personnel and/or physicians at mobile testing center. Multiple logistic regression was used to estimate the association between oral health, periodontal disease and the prevalence of hypertension. The effects of oral health and periodontal disease on hypertension under smoking status and age were analyzed by stratified and interaction analysis.

Results

A total of 21,800 participants were investigated, including 11,017 (50.54%) in hypertensive group and 10,783 (49.46%) in non-hypertensive group. Compared with the excellent/very good of oral health, the multivariable-adjusted OR of good, fair, and poor were 1.13 (95% CI, 1.02–1.27), 1.30 (95% CI, 1.15–1.47), and 1.48 (95% CI, 1.22–1.79) (p for trend < 0.001) for hypertension, respectively. Compared without periodontal disease group, the multivariable-adjusted OR of periodontal disease for hypertension was 1.21 (95% CI ,1.09–1.35) (p for trend < 0.001). Furthermore, we found the interactions between periodontal disease and smoking, oral health and smoking, periodontal disease and age, oral health and age were p < 0.001.

Conclusions

An association between oral health and periodontal disease with the prevalence of hypertension was identified. There exists interactive effect of periodontal disease and smoking, oral health and smoking, periodontal disease and age, oral health and age on hypertension in American population over 30 years of age and older.
Magnitude of unmet need for family planning and associated factors among women in the extended postpartum period in Dabat district, Northwest Ethiopia. evidence from Dabat demographic health surveys
Authors: Gelagay Abebaw Addis , Negash Wubshet Debebe , Belachew Tadele Biresaw , Bitew Desalegn Anmut , Fentie Elsa Awoke , Worku Abebaw Gebeyehu , Bashah Debrework Tesgera , Tebeje Nigusie Birhan , Gebrie Mignote Hailu , Yeshita Hedija Yenus , Cherkose Endeshaw Adimasu , Ayana Birhanu Abera , Lakew Ayenew Molla , Asmamaw Desale Bihonegn
Published: June 2023

Background

Due to additional roles and emotional changes that occur during postpartum period, women use contraceptives differs from other times in their life. However, there is limited information about the unmet need for family planning (FP) among women in the extended postpartum period in the study area. Therefore, this study aimed to assess magnitude of unmet need for family planning and associated factors among women in the extended postpartum period in Dabat district, Northwest Ethiopia.

Methods

A secondary data analysis was performed using the Dabat Demographic and Health Survey 2021. A total sample of 634 women during the extended postpartum period was included in this study. Stata version 14 statistical software was used for data analysis. Descriptive statistics were described using frequencies, percentages, mean, and standard deviation. Multicollinearity was tested using the variance inflation factor (VIF) and we computed Hosmer and Lemeshow goodness of fit. Both bivariable and multivariable logistic regression analyses were carried out to determine the association between independent variables and outcome variable. Statistical significance was declared at a p-value ≤ 0.05 with a corresponding 95% confidence interval.

Results

The overall unmet need for FP during the extended postpartum women was 42.43% (95% CI: 38.62, 46.33), of which 33.44% was unmet need for spacing. Place of residence (AOR = 2.63, 95%CI: 1.61, 4.33), place of delivery (AOR = 2.09, 95%CI: 1.35, 3.24), and availability of radio and or TV (AOR = 1.58, 95% CI: 1.22, 2.13) were significantly associated with unmet need for family planning.

Conclusion

The magnitude of unmet need for family planning among women during the extended postpartum period in the study area was high when compared to the national average and the United Nations sphere standard of unmet need for family planning. Place of residence, place of delivery, and availability of radio and or TV were significantly associated with unmet need for family planning. Hence, the concerned bodies are recommended to promote intuitional delivery and give spatial attention to those who are residing in rural areas and to those who have had no media exposure in order to reduce the unmet need for family planning among postpartum women.
Bennett fracture combined with hamate fracture: carpometacarpal joint ‘diagonal’ fracture and dislocation: a case report
Authors: Wu Wei-Bin , Du Yun-Feng , Wang Hong-Xing , Liang Feng
Published: June 2023

Background

Multiple carpometacarpal fractures and dislocations are rare. This case report describes a novel multiple carpometacarpal injury, namely, ‘diagonal’ carpometacarpal joint fracture and dislocation.

Case presentation

A 39-year-old male general worker sustained a compression injury to his right hand in the dorsiflexion position. Radiography indicated a Bennett fracture, hamate fracture, and fracture at the base of the second metacarpal. Subsequent computed tomography and intraoperative examination confirmed an injury to the first to fourth carpometacarpal joint along a diagonal line. The normal anatomy of the patient’s hand was successfully restored via open reduction combined with Kirschner wire and steel plate fixation.

Conclusion

Our findings highlight the importance of taking the injury mechanism into account to avoid a missed diagnosis and to choose the best treatment approach. This is the first case of ‘diagonal’ carpometacarpal joint fracture and dislocation to be reported in the literature.
Physiological stress level and screening for malnutrition as preoperative predictors of postoperative complications in pancreatic surgery: a retrospective study
Authors: Kryvoruchko Igor A. , Staikov Plamen , Boyko Valeriy V. , Sartelli Massimo , Ivanova Yulia V. , Honcharov Andrij , Gramatiuk Svetlana , Sargsyan Karine
Published: June 2023

Background

Assessment of ‘physiological stress levels’ and ‘nutritional status’ before surgery is important for predicting complications and indirect interventions on the pancreas. The aim of this study was to determine neutrophil–lymphocyte ratio (NLR) and nutritional risk index (NRI) indicators before surgery to predict 90-day complications and mortality in a cohort of patients with complicated chronic pancreatitis and cancer of the head of the pancreas.

Methods

We evaluated preoperative levels of NLR and NRI among 225 subjects treated at different centres located in three countries. Short-term outcomes included length of hospital stay, postoperative complications, and mortality at 90 days and were appreciated based on NLR and NRI. The level of physiological stress was divided according by the formulas: neutrophil–lymphocyte ratio (NLR) = (neutrophil count, %)/(lymphocyte count, %). The nutritional state of the patients was divided according to the INR: NRI = (1.519 × serum albumin, g/L) + (41.7 × present weight, kg / usual weight, kg)].

Results

All patients were operated. An analysis of the operations performed in three institutions demonstrated mortality in chronic pancreatitis and pancreatic pseudocysts in 1.4%, in chronic pancreatitis and the presence of an inflammatory mass mainly in the pancreatic head in 1.2%, and in cancer of the pancreatic head in 5.9%. The mean preoperative NLR was normal in 33.8% of the patients, the mild physiologic stress level was 54.7%, and the moderate was 11.5% before surgery. 10.2% of patients had a normal nutritional status, 20% had mild, 19.6% had moderate, and 50.2% had severe malnutrition. In a univariate analysis, at the cutoff of NLR ≥ 9.5 (AUC = 0.803) and the cutoff of NRI ≤ 98.5 (AUC = 0.801), increasing the risk of complications was observed (hazard ratio, 2.01; 95% CI, 1.247–3.250, p = 0.006), but at the cutoff of NRI ≤ 83.55 (AUC = 0.81), we observed a survival difference in operated patients (hazard ratio, 2.15; 95% CI, 1.334–3.477, p = 0.0025).

Conclusions

Our study demonstrated that NLR and NRI were predictors of postoperative complications, but only NRI was a predictor of 90-day mortality in patients after surgery.
Satisfaction of health informatics professionals with Ethiopian health system: the case of three zones in Ethiopia
Authors: Gilano Girma , Sako Sewunet , Boranto Belachew , Haile Firehiwot , Hassen Hadiya
Published: June 2023

Background

The importance of the health information system faces multiple challenges such as supply, acceptance, and pressure from other professions in Ethiopia. Work-related challenges might cause low professional satisfaction and hinder service provision. There is a paucity of evidence for policy decisions to improve these challenges. Therefore, this study aims to assess Health Informatics professional satisfaction in the Ethiopian health system and associated factors to provide evidence for future improvements.

Methods

We conducted an institutions-based cross-sectional study on health informatics professionals in three zones in Southern Ethiopia in 2020. We used a simple random sampling technique to select 215 participants. The local health officials were contacted regarding the research questions, and letters of permission were collected for data collection.

Results

Out of 211(98%) Health Informatics professionals who accepted the interview, 50.8% (95%CI: 47.74%-53.86%) were satisfied. Age (AOR = 0.57; 95% CI: 0.53, 0.95), experience (AOR = 5; 95% CI: 1.50, 19.30), working time (AOR = 1.35; 95% CI: 1.10, 1.70), working as HMIS officers (AOR 2.30; 95% CI: 3.80, 13), single marital status (AOR = 9.60; 95% CI: 2.88, 32), and urban residence (AOR = 8.10; 95% CI: 2.95, 22) were some of the associated factors.

Conclusions

We found low satisfaction among health informatics professionals compared to other studies. It was suggested that the responsible bodies must keep experienced professionals and reduce pressure from other professions through panel discussions. Work departments and working hours need consideration, as they are the determinants of satisfaction. Improving educational opportunities and career structure is the potential implication area.
Ferroptosis-related signature and immune infiltration characterization in acute lung injury/acute respiratory distress syndrome
Authors: Ma Aijia , Feng Zhongxue , Li Yang , Wu Qin , Xiong Huaiyu , Dong Meiling , Cheng Jiangli , Wang Zhenling , Yang Jing , Kang Yan
Published: June 2023

Background

Acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is one of the most life-threatening diseases in the intensive care unit with high mortality and morbidity. Ferroptosis is a newly discovered immune related cell death that is associated with various lung diseases. However, the role of immune-mediated ferroptosis in ALI/ARDS has not been elucidated.

Method

We analyzed two Gene Expression Omnibus (GEO) datasets (GSE2411 and GSE109913) and extracted characteristic ferroptosis-related genes (FRGs) between the control and ALI groups through bioinformatic analysis. Then, we prospectively collected bronchoalveolar lavage fluid (BALF) from patients with ARDS and verified the expression of characteristic FRGs. Lastly, we constructed the ALI/ARDS model induced by LPS and isolated the primary neutrophils of mice. Erastin, an ferroptosis inducer, was used at the cellular level to verify the effect of neutrophils on ferroptosis in lung epithelium cells.

Result

We identified three characteristic FRGs, Cp, Slc39a14 and Slc7a11, by analyzing two gene expression profiling datasets. Immune infiltration analysis showed that the three characteristic genes were significantly positively correlated with the infiltration levels of neutrophils. We collected BALF from 59 ARDS patients to verify the expression of Cp, Slc7a11 and Slc39a14 in humans. The results showed that Cp was elevated in patients with severe ARDS (p = 0.019), Slc7a11 was significantly elevated in patients with moderate ARDS (p = 0.021) relative to patients with mild ARDS. The levels of neutrophils in the peripheral blood of ARDS patients were positively correlated with the expression levels of Slc7a11 (Pearson’s R2 = 0.086, p = 0.033). Three characteristic FRGs were significantly activated after the onset of ferroptosis (6 h) early in LPS induced ALI model, and that ferroptosis was alleviated after the organism compensated within 12 to 48 h. We extracted primary activated neutrophils from mice and co-cultured them with MLE-12 in transwell, Slc7a11, Cp and Slc39a14 in MLE-12 cells were significantly upregulated as the number of neutrophils increased. The results showed that neutrophil infiltration alleviated erastin-induced MDA accumulation, GSH depletion, and divalent iron accumulation, accompanied by upregulation of Slc7a11 and Gpx4, implying the existence of a compensatory effect of lipid oxidation in neutrophils after acute lung injury in the organism.

Conclusion

We identified three immune-mediated ferroptosis genes, namely, Cp, Slc7a11 and Slc39a14, which possibly regulated by neutrophils during the development of ALI, and their pathways may be involved in anti-oxidative stress and anti-lipid metabolism. Thus, the present study contributes to the understanding of ALI/ARDS and provide novel targets for future immunotherapeutic.
Crosstalk between diacylglycerol kinase and protein kinase A in the regulation of airway smooth muscle cell proliferation
Authors: Hernandez-Lara Miguel A. , Yadav Santosh Kumar , Conaway Stanley , Shah Sushrut D. , Penn Raymond B. , Deshpande Deepak A.
Published: June 2023

Background

Diacylglycerol kinase (DGK) regulates intracellular signaling and functions by converting diacylglycerol (DAG) into phosphatidic acid. We previously demonstrated that DGK inhibition attenuates airway smooth muscle (ASM) cell proliferation, however, the mechanisms mediating this effect are not well established. Given the capacity of protein kinase A (PKA) to effect inhibition of ASM cells growth in response to mitogens, we employed multiple molecular and pharmacological approaches to examine the putative role of PKA in the inhibition of mitogen-induced ASM cell proliferation by the small molecular DGK inhibitor I (DGK I).

Methods

We assayed cell proliferation using CyQUANT™ NF assay, protein expression and phosphorylation using immunoblotting, and prostaglandin E2 (PGE2) secretion by ELISA. ASM cells stably expressing GFP or PKI-GFP (PKA inhibitory peptide-GFP chimera) were stimulated with platelet-derived growth factor (PDGF), or PDGF + DGK I, and cell proliferation was assessed.

Results

DGK inhibition reduced ASM cell proliferation in cells expressing GFP, but not in cells expressing PKI-GFP. DGK inhibition increased cyclooxygenase II (COXII) expression and PGE2 secretion over time to promote PKA activation as demonstrated by increased phosphorylation of (PKA substrates) VASP and CREB. COXII expression and PKA activation were significantly decreased in cells pre-treated with pan-PKC (Bis I), MEK (U0126), or ERK2 (Vx11e) inhibitors suggesting a role for PKC and ERK in the COXII-PGE2-mediated activation of PKA signaling by DGK inhibition.

Conclusions

Our study provides insight into the molecular pathway (DAG-PKC/ERK-COXII-PGE2-PKA) regulated by DGK in ASM cells and identifies DGK as a potential therapeutic target for mitigating ASM cell proliferation that contributes to airway remodeling in asthma.
A novel physics-based model for fast computation of blood flow in coronary arteries
Authors: Hu Xiuhua , Liu Xingli , Wang Hongping , Xu Lei , Wu Peng , Zhang Wenbing , Niu Zhaozhuo , Zhang Longjiang , Gao Qi
Published: June 2023

Blood flow and pressure calculated using the currently available methods have shown the potential to predict the progression of pathology, guide treatment strategies and help with postoperative recovery. However, the conspicuous disadvantage of these methods might be the time-consuming nature due to the simulation of virtual interventional treatment. The purpose of this study is to propose a fast novel physics-based model, called FAST, for the prediction of blood flow and pressure. More specifically, blood flow in a vessel is discretized into a number of micro-flow elements along the centerline of the artery, so that when using the equation of viscous fluid motion, the complex blood flow in the artery is simplified into a one-dimensional (1D) steady-state flow. We demonstrate that this method can compute the fractional flow reserve (FFR) derived from coronary computed tomography angiography (CCTA). 345 patients with 402 lesions are used to evaluate the feasibility of the FAST simulation through a comparison with three-dimensional (3D) computational fluid dynamics (CFD) simulation. Invasive FFR is also introduced to validate the diagnostic performance of the FAST method as a reference standard. The performance of the FAST method is comparable with the 3D CFD method. Compared with invasive FFR, the accuracy, sensitivity and specificity of FAST is 88.6%, 83.2% and 91.3%, respectively. The AUC of FFRFAST is 0.906. This demonstrates that the FAST algorithm and 3D CFD method show high consistency in predicting steady-state blood flow and pressure. Meanwhile, the FAST method also shows the potential in detecting lesion-specific ischemia.
Abnormal HDL lipid and protein composition following pediatric cancer treatment: an associative study
Authors: Bélanger Véronique , Morel Sophia , Napartuk Mélanie , Bouchard Isabelle , Meloche Caroline , Curnier Daniel , Sultan Serge , Laverdière Caroline , Sinnett Daniel , Marcil Valérie
Published: June 2023

Background

Long-term childhood cancer survivors (CCS) are at high risk of having dyslipidemia including low high density lipoprotein cholesterol (HDL-C). However, little is known about the prevalence of low HDL-C and the impact of therapy exposure on HDL composition early after treatment is terminated.

Methods

This associative study included 50 children and adolescents who had completed their cancer treatments (< 4 years). Clinical characteristics (demographic, diagnosis, treatment, anthropometric parameters), fasting plasma lipids, apoliporoteins (Apo) A-I and composition of HDL fractions (HDL2 and HDL3) were assessed. Data were stratified according to the presence of dyslipidemia and median doses of therapeutic agents and compared using Fisher exact or Mann–Whitney tests. Univariate binary logistic regression analyses were carried out to evaluate the associations between the clinical and biochemical characteristics and having low HDL-C. Composition of HDL2 and HDL3 particles was assessed in a sub-group of 15 patients and compared to 15 age- and sex-matched healthy controls using Wilcoxon paired test.

Results

Of the 50 pediatric cancer patients included in this study (mean age: 11.30 ± 0.72 y; mean time since end of treatment: 1.47 ± 0.12 y; male: 38%), 8 had low HDL-C (16%), all of which were adolescent at diagnosis. Higher doses of doxorubicin were associated with lower HDL-C and Apo A-I levels. In hypertriglyceridemic patients and compared to normolipidemics, triglycerides (TG) content was greater in HDL2 and HDL3 fractions whereas esterified cholesterol (EC) content was lower in HDL2. Enrich TG content of HDL3 and lower EC of HDL2 was found in patients exposed to ≥ 90 mg/m2 doxorubicin. Factors positively associated with the risk of having low HDL-C were age, being overweight or obese and exposure to doxorubicin ≥ 90 mg/m2. Compared to healthy controls, a sub-group of 15 patients showed higher TG and free cholesterol (FC) content of HDL2 and HDL3 and lower EC content in HDL3.

Conclusions

Overall, we found abnormalities in HDL-C and Apo A-I levels and in HDL composition early after pediatric cancer treatment that are influenced by age, overweight or obesity status and exposure to doxorubicin.
Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic
Authors: Greer Stephanie U. , Botello Jacquelin , Hongo Donna , Levy Brynn , Shah Premal , Rabinowitz Matthew , Miller Danny E. , Im Kate , Kumar Akash
Published: June 2023

Background

Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications.

Methods

We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth.

Results

Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis.

Conclusions

We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.
Cultural considerations and beliefs surrounding preterm birth in Kenya and South Africa
Authors: Milford Cecilia , Smith Emma , Ngure Kenneth , Thuo Nicholas B. , Newmann Sara , Lazarus Nalinie , Beksinska Mags , Mugo Nelly , Rand Larry
Published: June 2023

Background

Preterm birth (PTB) is a global health epidemic, sub-Saharan Africa is severely impacted due to its limited healthcare resources. Pregnancy knowledge, cultural beliefs and practices play a role in the identification of risk and management of PTB. This study explored knowledge, understandings, cultural beliefs and attitudes to pregnancy and PTB, as well as cultural considerations for the introduction of an intravaginal device which could be used to identify PTB risk.

Methods

Qualitative research was conducted in South Africa and Kenya. In-depth interviews were conducted using semi-structured guides with women with a history of PTB (n = 10), healthcare providers (n = 16) and health systems experts (n = 10); and 26 focus group discussions with pregnant women seeking antenatal care (n = 132) and community male partners/fathers (n = 54). Interviews/discussions were transcribed, translated, and analysed thematically.

Results

Pregnancy knowledge, especially for first time pregnancies was poor, with many reporting late entry to antenatal care. Knowledge about PTB was understood in terms of gestational age, weight or small size of baby, with concerns about long term health and stigma. Various risk factors for PTB were described, including those related to traditions and beliefs of witchcraft/curses. Cultural practices, such as the use of traditional medicines and pica, and religion and its impact on health seeking behaviour were also viewed as risk factors. Although insertion of intravaginal devices was not widely acceptable in traditional communities, especially during pregnancy, it was felt that the use of one to detect risk of PTB would be accepted if proven effective in reducing PTB risk.

Conclusions

Various culturally-informed beliefs exist which explain understandings of and attitudes toward pregnancy, pregnancy risk, and PTB. An inclusive exploratory process is critical to facilitate an understanding of the beliefs and traditions which could impact the introduction and design of a product to detect the risk of PTB.
Increased prevalence of depression and anxiety among adults initiating antiretroviral therapy during the COVID-19 pandemic in Shinyanga region, Tanzania
Authors: Winters Solis , Sabasaba Amon , Fahey Carolyn A. , Packel Laura , Katabaro Emmanuel , Ndungile Yudas , Njau Prosper F. , McCoy Sandra I.
Published: June 2023

Background

Concerns about the interconnected relationship between HIV and mental health were heightened during the COVID-19 pandemic. This study assessed whether there were temporal changes in the mental health status of people living with HIV presenting for care in Shinyanga region, Tanzania. Specifically, we compared the prevalence of depression and anxiety before and during COVID-19, with the goal of describing the changing needs, if any, to person-centered HIV services.

Methods

We analyzed baseline data from two randomized controlled trials of adults initiating ART in Shinyanga region, Tanzania between April-December 2018 (pre-COVID-19 period, n = 530) and May 2021-March 2022 (COVID-19 period, n = 542), respectively. We compared three mental health indicators that were similarly measured in both surveys: loss of interest in things, hopelessness about the future, and uncontrolled worrying. We also examined depression and anxiety which were measured using the Hopkins Symptom Checklist-25 in the pre-COVID-19 period and the Patient Health Questionnaire-4 in the COVID-19 period, respectively, and classified as binary indicators per each scale’s threshold. We estimated prevalence differences (PD) in adverse mental health status before and during the COVID-19 pandemic, using stabilized inverse probability of treatment weighting to adjust for underlying differences in the two study populations.

Results

We found significant temporal increases in the prevalence of feeling ‘a lot’ and ‘extreme’ loss of interest in things [‘a lot’ PD: 38, CI 34,41; ‘extreme’ PD: 9, CI 8,12)], hopelessness about the future [‘ a lot’ PD: 46, CI 43,49; ‘extreme’ PD: 4, CI 3,6], and uncontrolled worrying [‘ a lot’ PD: 34, CI 31,37; ‘extreme’ PD: 2, CI 0,4] during the COVID-19 pandemic. We also found substantially higher prevalence of depression [PD: 38, CI 34,42] and anxiety [PD: 41, CI 37,45].

Conclusions

After applying a quasi-experimental weighting approach, the prevalence of depression and anxiety symptoms among those starting ART during COVID-19 was much higher than before the pandemic. Although depression and anxiety were measured using different, validated scales, the concurrent increases in similarly measured mental health indicators lends confidence to these findings and warrants further research to assess the possible influence of COVID-19 on mental health among adults living with HIV.

Trial Registration NCT03351556, registered November 24, 2017; NCT04201353, registered December 17, 2019.
Comparison of the clinical effects for different positions of the weight-bearing axis after high tibial osteotomy
Authors: Xu Han , Tu Huali , Zhao Tianzuo , Xu Daofei , Yu Qinglong , Liao Long , Tang Shitian , Shi Bo
Published: June 2023

Purpose

To analyze the clinical effects of different positions of the weight-bearing axis (WBA) after high tibial osteotomy (HTO).

Methods

The clinical data of 90 patients who underwent HTO in the Department of Orthopedics at our hospital from June 2018 to June 2021 were retrospectively analyzed. Patients were divided into groups A and B (n = 45 per group) according to different post-HTO WBA positions of the affected side. WBAs in both groups were at 50–60% and 62–66% of the tibial plateau, from inside to outside, respectively. American Hospital for Special Surgery Knee Score (HSS), visual analog scale (VAS) score, femorotibial angle (FTA), and medial proximal tibial angle (MPTA) were recorded and analyzed.

Results

All patients were followed up with for 12 months. HSS scores increased gradually and VAS scores decreased gradually in both groups preoperatively, and at 3 months, 6 months, and 1 year postoperatively (P < 0.05). Compared to group A, group B had better HHS scores at 6 months and 1 year postoperatively (P < 0.05). There was no significant between-group difference in VAS scores at all aforementioned timepoints (P > 0.05). Postoperative MPTA and FTA were 89.56° ± 2.18° and 177.11° ± 2.63° in group A, and 89.07° ± 1.98° and 177.07° ± 2.36° in group B, respectively, with no significant between-group difference (P > 0.05).

Conclusion

Patients with post-HTO WBA ranges of 50–60% and 62–66% achieved knee joint function improvement and pain relief. Half a year later, those with a WBA range of 62–66% had better knee joint function scores. However, a comparison of long-term effects warrants further investigation.
Managers as peer workers’ allies: A qualitative study of managers’ perceptions and actions to involve peer workers in Norwegian mental health and substance use services
Authors: Åkerblom Kristina Bakke , Mohn-Haugen Torbjørn , Agdal Rita , Ness Ottar
Published: June 2023

Background

Citizens with experience and knowledge about what it is like to use mental health and substance use services are increasingly employed within similar services as peer workers. Peer workers are portrayed as achieving societal obligations and help ensure that the outputs from service provision are more effective. Even though peer workers have worked in mental health and substance use services for a while, few studies have focused on exploring managers’ experiences and perspectives about involving peer workers. This knowledge is needed because these managers can enable and hinder equitable involvement and collaboration with peer workers.

Methods

A qualitative explorative study was chosen to explore the following research question:How do managers in Norwegian mental health and substance use services experience, relate to, and embrace peer workers as assets in these services?A researcher (Ph.D. student) and a coresearcher (peer worker) conducted four online focus groups with a strategic selection of 17 Norwegian mental health and substance use services managers who had some experience with the involvement of peer workers in their organizations.

Results

The results identified using systematic text condensation are as follows: [1]Peer workers boost the ongoing shift toward increased service user involvement.[2]Peer workers are highly valued in the service transformation process.[3]Managers involve peer workers as partners in co-creation.The results show that managers connect with peer workers and facilitate their involvement in collaborative activities across the service cycle. Peer workers’ proximity to service users and bridging capacity is highlighted as the reasons for their involvement. Thus, peer workers are involved in co-defining challenges, co-designing potential solutions, co-delivering those service solutions, and, sometimes, co-assessing service solutions to rethink and improve services. As such, peer workers are considered partners in co-creation.

Conclusion

As managers involve peer workers, they increasingly discover peer workers’ value, and because peer workers are involved, they increase their skills and capacity for collaboration. This research strengthens the knowledge base of the perceived value of peer workers’ roles, bringing in new perspectives from management about utilizing and evaluating peer worker roles.
Differences between problematic internet and smartphone use and their psychological risk factors in boys and girls: a network analysis
Authors: Rozgonjuk Dmitri , Blinka Lukas , Löchner Nana , Faltýnková Anna , Husarova Daniela , Montag Christian
Published: June 2023

Background

Problematic internet and smartphone use are significant health challenges for contemporary adolescents. However, their mutual relationship is unclear because studies investigating these phenomena are scarce. The present study aimed to investigate the psychological risks and protective factors associated with problematic internet and smartphone use.

Method

A representative sample of Slovak adolescents (N = 4070, Mage = 14.38, SDage = 0.77, 50.5% girls) from the Health Behavior in School-aged Children project was analyzed using network analysis separately for boys and girls.

Results

The results showed weak (for boys) and moderate (for girls) associations between problematic internet use and problematic smartphone use. Risk factors showed stronger associations with problematic internet use than problematic smartphone use, with the exception of fear of missing out, which was strongly associated with problematic smartphone use. The central nodes were externalizing problems for boys and internalizing problems, externalizing problems, and resilience for girls.

Conclusion

The study concluded that while problematic internet use and problematic smartphone use are somewhat related, they differ at the psychological level. In addition, the phenomena are rather different between boys and girls.
Examining the impact of a universal positive psychology program on mental health outcomes among Australian secondary students during the COVID-19 pandemic
Authors: Subotic-Kerry Mirjana , Braund Taylor A. , Gallen Dervla , Li Sophie H , Parker Belinda L. , Achilles Melinda R. , Chakouch Cassandra , Baker Simon , Werner-Seidler Aliza , O’Dea Bridianne
Published: June 2023

Background

This study aimed to examine the impact of a web-based positive psychology program delivered universally to secondary school students during school closures caused by the COVID-19 pandemic in New South Wales, Australia.

Methods

Using a quasi-experimental design conducted in 2020, 438 students aged 12–15 years (73% male) from 4 secondary schools were invited to complete the ‘Bite Back Mental Fitness Challenge’. This web-based program consisted of 7 self-directed modules that targeted 5 key domains of positive psychology. Self-reported symptoms of anxiety and depression and help-seeking intentions for mental health were assessed at baseline prior to school closures (February to March 2020) and at post-test after the return to school (July to August 2020). At post-test, students also reported on their perceived changes in mental health and help-seeking behavior for mental health during the pandemic. Completion of the program modules was recorded.

Results

A total of 445 students consented and 336 (75.5%) completed both assessments. On average, participants completed 2.31 modules (SD: 2.38, range: 0 to 7). There was no change in symptoms of anxiety and depression or help-seeking intentions between baseline and post-test, with no significant effects for gender and history of mental illness. Students who were symptomatic for anxiety and depression at baseline reported lower symptoms at post-test, but this change was not significant. Ninety-seven students (27.5%) reported that their mental health had worsened during the pandemic, and a significant increase in anxiety and depressive symptoms was found in this subsample at post-test. Only 7.7% of students reported a change in their help-seeking behavior, with increased mental health support sought from the Internet, parents, and friends.

Conclusions

The universal delivery of a web-based positive psychology program during school closures did not appear to be associated with improved mental health symptoms; however, completion of the modules was low. Different effects may emerge when selectively delivered to students with mild or greater symptoms. The findings also suggest that broader measures of mental health and wellbeing, including perceived change, are key to the mental health surveillance of students during periods of remote learning.
Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae)
Authors: Posada-López Laura , Rodrigues Bruno Leite , Velez Ivan Dario , Uribe Sandra
Published: June 2023

Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.

Graphical Abstract
The potential roles of gut microbiome in anal fistula
Authors: Cai Ping , Rong Hao , Zhu Qiaoqiao , Dai Xiaoyu , Zhao Jianpei
Published: June 2023

Anal fistula is a common proctological disease, but the thorough mechanisms of the anal fistula formation are still unclear. An increasing number of studies have revealed the crucial role of gut microbiota in intestinal diseases. We used 16S rRNA gene sequencing to analyze the intestinal microbiome in order to determine whether there are differences in the microbiome between anal fistula patients and healthy individuals. The microbiome samples were extracted by repeatedly wiping the rectal wall with intestinal swab. Before this operation, the whole intestine of all participants was irrigated and the score of the Boston bowel preparation scale reached 9. The biodiversity of gut microbiome of rectum revealed significant difference between anal fistula patients and healthy individuals. 36 discriminative taxa were identified by LEfSe analysis between two groups. At the phylum level, Synergistetes was enriched in anal fistula patients, while Proteobacteria was higher in healthy individuals. We also found that at the genus level, Blautia, Faecalibacterium, Ruminococcus, Coprococcus, Bacteroides, Clostridium, Megamonas and Anaerotruncus were highly enriched in anal fistula patients, while the microbiome of healthy individuals was enriched with Peptoniphilus and Corynebacterium. Spearman correlations showed the extensive and close association among genera and species. Finally, a diagnostic prediction model was constructed by random forest classifier, and the area under curve (AUC) reached 0.990. This study gave an important hint for analyzing gut microbiome of rectum in anal fistula patient.

Keypoints.

We use the 16S rRNA gene sequencing to test the microbiome samples extracted from the intestinal swab. This is the first study to explore the gut microbiome of rectum using this workflow. We also found the distinct gut microbiome of rectum differences between anal fistula patients and healthy individuals.
A resource scheduling method for cloud data centers based on thermal management
Authors: Mao Li , Chen Rui , Cheng Huiwen , Lin Weiwei , Liu Bo , Wang James Z.
Published: June 2023

With the rapid growth of cloud computing services, the high energy consumption of cloud data centers has become a critical concern of the cloud computing society. While virtual machine (VM) consolidation is often used to reduce energy consumption, excessive VM consolidation may lead to local hot spots and increase the risk of equipment failure. One possible solution to this problem is to utilize thermal-aware scheduling, but existing approaches have trouble realizing the balance between SLA and energy consumption. This paper proposes a novel method to manage cloud data center resources based on thermal management (TM-VMC), which optimizes total energy consumption and proactively prevents hot spots from a global perspective. Its VM consolidation process includes four phases where the VMs scheduler uses an improved ant colony algorithm (UACO) to find appropriate target hosts for VMs based on server temperature and utilization status obtained in real-time. Experimental results show that the TM-VMC approach can proactively avoid data center hot spots and significantly reduce energy consumption while maintaining low Service Level Agreement (SLA) violation rates compared to existing mainstream VM consolidation algorithms with workloads from real-world data centers.