bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and phylogenetic analysis of voltage-gated sodium channel haplotypes in the malaria vector Anopheles sinensis using a high-throughput amplicon sequencing approach
Authors: Ni Ruoyao , Liu Nian , Li Mei , Qian Weiping , Qiu Xinghui 
Published: September 2021

Abstract
Background
Anopheles sinensis is a dominant vector for malaria transmission in Asian countries. Voltage-gated sodium channel (VGSC) mutation-mediated knock-down resistance (kdr) has developed in many A. sinensis populations because of intensive and long-term use of pyrethroids. Our previous study showed that multiple mutations at position 1014 of the VGSC were heterogeneously distributed in A. sinensis populations across Sichuan, China.

Methods
To understand resistance genotypes at the haplotype level and reconstruct the phylogenetic relationship of VGSC haplotypes, a cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach was established to clarify haplotypes containing codon 1014 of the VGSC gene from a total of 446 adults collected in 12 locations of Sichuan, China.

Results
Nineteen (19) haplotypes were identified, including 11 wild 1014L, 6 resistance 1014F, and 2 resistance 1014C haplotypes. We found that resistance haplotypes of A. sinensis VGSC were widely distributed at frequencies ranging from 3.67 to 92.61%. The frequencies of the 1014C haplotype in the southeast of Sichuan (Luzhou, Guangan, and Suining) were relatively higher than those in other sampling locations. Phylogenetic analyses support that kdr-type mutation at position 1014 is not singly originated and resistance 1014C haplotypes evolve from TTT-encoding 1014F.

Conclusions
A cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach has been established in this study. The data revealed the patchy distribution of VGSC resistance haplotypes with overall high frequencies in Sichuan, China. Phylogenetic analyses support multiple origins and sequential evolution (1014L → 1014F → 1014C) for kdr-type mutations in A. sinensis.

Graphical abstract
Satellite-based modelling of potential tsetse (Glossina pallidipes) breeding and foraging sites using teneral and non-teneral fly occurrence data
Authors: Gachoki Stella , Groen Thomas , Vrieling Anton , Okal Michael , Skidmore Andrew , Masiga Daniel 
Published: September 2021

AbstractBackgroundAfrican trypanosomiasis, which is mainly transmitted by tsetse flies (Glossinaspp.), is a threat to public health and a significant hindrance to animal production. Tools that can reduce tsetse densities and interrupt disease transmission exist, but their large-scale deployment is limited by high implementation costs. This is in part limited by the absence of knowledge of breeding sites and dispersal data, and tools that can predict these in the absence of ground-truthing.MethodsIn Kenya, tsetse collections were carried out in 261 randomized points within Shimba Hills National Reserve (SHNR) and villages up to 5 km from the reserve boundary between 2017 and 2019. Considering their limited dispersal rate, we used in situ observations of newly emerged flies that had not had a blood meal (teneral) as a proxy for active breeding locations. We fitted commonly used species distribution models linking teneral and non-teneral tsetse presence with satellite-derived vegetation cover type fractions, greenness, temperature, and soil texture and moisture indices separately for the wet and dry season. Model performance was assessed with area under curve (AUC) statistics, while the maximum sum of sensitivity and specificity was used to classify suitable breeding or foraging sites.ResultsGlossina pallidipesflies were caught in 47% of the 261 traps, with teneral flies accounting for 37% of these traps. Fitted models were more accurate for the teneral flies (AUC = 0.83) as compared to the non-teneral (AUC = 0.73). The probability of teneral fly occurrence increased with woodland fractions but decreased with cropland fractions. During the wet season, the likelihood of teneral flies occurring decreased as silt content increased. Adult tsetse flies were less likely to be trapped in areas with average land surface temperatures below 24 °C. The models predicted that 63% of the potential tsetse breeding area was within the SHNR, but also indicated potential breeding pockets outside the reserve.ConclusionModelling tsetse occurrence data disaggregated by life stages with time series of satellite-derived variables enabled the spatial characterization of potential breeding and foraging sites forG. pallidipes. Our models provide insight into tsetse bionomics and aid in characterising tsetse infestations and thus prioritizing control areas.Graphical abstract
Association of retroperitoneal fibrosis with malignancy and its outcomes
Authors: Lee Sang Jin , Eun Jung Su , Kim Min Jung , Song Yeong Wook , Kang Young Mo 
Published: September 2021

Abstract
Introduction
Retroperitoneal fibrosis (RPF) is characterized by a highly fibrotic retroperitoneal mass and encompasses the idiopathic form and secondary to malignancies. Because we have limited knowledge whether RPF is associated with malignancy, we aimed to investigate the relationship between RPF and malignancy and to compare the characteristics and prognosis of cancers among patients with RPF.

Methods
Medical records of 111 patients diagnosed as having RPF were reviewed and 38 cases of cancer, confirmed by biopsy, were identified. Standardized incidence ratios (SIRs) were calculated for cancers and stratified according to cancer type and RPF-cancer diagnosis interval. Cancer characteristics and outcomes were compared between RPF-cancer diagnosis intervals.

Results
The average age at RPF diagnosis was 59.2 ± 15.0 years, and 69.4% of the patients were male. The cancer SIRs in patients with RPF relative to age- and sex-matched individuals in the general population was 2.2 (1.6–3.1). SIRs of renal pelvis cancer and multiple myeloma were significantly higher than in the general population. When stratified by RPF-cancer intervals, the SIR for cancer was 9.9 within 1 year of RPF diagnosis, while no significant increase in the SIR was found after 1 year from RPF diagnosis. Cancer stage was more advanced at the time of diagnosis in patients within a 1-year interval for RPF than those with cancer within a >5-year interval, with a correspondingly increased mortality in the former patients.

Conclusions
RPF was significantly associated with malignancy, particularly those diagnosed within 1 year of RPF diagnosis. Cancer stages at diagnosis were more advanced and the mortality rate was higher in patients within a 1-year interval between RPF and cancer diagnosis than in those with a >5-year interval between diagnoses.
Factors predicting readmission in patients with COVID-19
Authors: Nematshahi Mohammad , Soroosh Davood , Neamatshahi Mahboubeh , Attarian Fahimeh , Rahimi Faeze 
Published: September 2021

Abstract
Objective
COVID-19 has been introduced by the World Health Organization as a health emergency worldwide. Up to 9% of the patients with COVID-19 may be readmitted by 2 months after discharge. This study aimed to estimate the readmission rate and identify main risk factors for readmission in these patients. In this prospective study, 416 discharged COVID patients followed up with a minimum 1 month and the readmission rate was recorded. Evaluated characteristics included time of readmission, age and sex, main symptoms of disease, result of computed tomography scan, reverse transcription polymerase chain reaction test and treatment modalities.

Results
Regarding readmission, 51 patients of 416 discharged patients, was readmitted during the study period. The rate of readmission for 30 and 60 days after discharge was 7.6% and 8.1%, respectively. The median age of the readmitted patients was 67 years (IQR: 53–78). About 65% of readmitted patients had underlying disease. The most significant factor in readmission rate was related to the site of lung involvement (OR > 4). Age over 60 years, underlying disease especially diabetes (OR = 3.43), high creatinine level (≥ to 1.2 mg/dl) (OR = 2.15) were the most important predictors of readmission.
Socioeconomic inequalities in the prevalence and perceived dangerousness of SARS-CoV-2 infections in two early German hotspots: findings from a seroepidemiological study
Authors: Wachtler Benjamin , Müters Stephan , Michalski Niels , Koschollek Carmen , Albrecht Stefan , Haller Sebastian , Hamouda Osamah , Hövener Claudia , Hoebel Jens 
Published: September 2021

AbstractObjectiveEvidence on socioeconomic inequalities in infections with the novel coronavirus (SARS-CoV-2) is still limited as most of the available studies are ecological in nature and individual-level data is sparse. We therefore analysed individual-level data on socioeconomic differences in the prevalence and perceived dangerousness of SARS-CoV-2 infections in local populations. Data were obtained from a population-based seroepidemiological study of adult individuals in two early German SARS-CoV-2 hotspots (n = 3903). Infection was determined by IgG antibody ELISA, RT-PCR testing and self-reports on prior positive PCR tests. The perceived dangerousness of an infection and socioeconomic position (SEP) were assessed by self-reports. Logistic and linear regression were applied to examine associations of multiple SEP measures with infection status and perceptions of dangerousness.ResultsWe found no evidence of socioeconomic inequalities in SARS-CoV-2 infections by education, occupation, income and subjective social status. Participants with lower education and lower subjective social status perceived an infection as more dangerous than their better-off counterparts. In successfully contained local outbreaks of SARS-CoV-2 in Germany, infections may have been equally distributed across the socioeconomic spectrum. But residents in disadvantaged socioeconomic groups might have experienced a higher level of mental distress due to the higher perceived dangerousness of an infection.
miRkit: R framework analyzing miRNA PCR array data
Authors: Tsagiopoulou Maria , Togkousidis Anastasis , Pechlivanis Nikolaos , Maniou Maria Christina , Batsali Aristea , Matheakakis Angelos , Pontikoglou Charalampos , Psomopoulos Fotis 
Published: September 2021

Abstract
Objective
The characterization of microRNAs (miRNA) in recent years is an important advance in the field of gene regulation. To this end, several approaches for miRNA expression analysis and various bioinformatics tools have been developed over the last few years. It is a common practice to analyze miRNA PCR Array data using the commercially available software, mostly due to its convenience and ease-of-use.

Results
In this work we present miRkit, an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the proposed tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, and is freely available under a ΜΙΤ license from https://bio.tools/mirkit. Overall, miRkit offers the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.
Aerobic exercise training prevents impairment in renal parameters and in body composition of rats fed a high sucrose diet
Authors: de Souza Jaqueline A. , Pinto Angélica B. Gonçalves , de Oliveira Emerson C. , Coelho Daniel B. , Totou Nádia L. , de Lima Wanderson G. , Becker Lenice K. 
Published: September 2021

AbstractObjectiveThis study aimed to evaluate the effect of swimming training (T) on the renal system and body composition parameters in young animals treated with a high sucrose diet (SUD) during 12 weeks.ResultsThe SUD impaired the physical performance, increased the body adiposity index (BAI), Lee index (LI) and retroperitoneal adipose tissue (RAT) weight, plasma creatinine and number renal cells nuclei, decreased urinary volume and urinary creatinine excretion besides creatinine clearance. The T reversed the increased the BAI, LI, RAT weight, plasma and urinary creatinine, creatinine clearance and number renal cells nuclei in addition to promoting decrease in urinary protein excretion. This study found that eight weeks of swimming physical training protected renal function and restored normal glomerular filtration rate (GFR) values. Swimming training also contributed to prevention of the onset of a renal inflammatory process and caused a decrease in the risk of development of obesity promoted by SUD decreasing the body composition parameters (BAI, LI, and RAT weight).
App-based strength and balance self-test in older adults: an exploratory study from a user perspective
Authors: Arkkukangas Marina 
Published: September 2021

Abstract
Objectives
Falls are a common problem, especially in the older population. The number of older adults aged over 65 years is increasing globally, leading to a major challenge in providing effective fall prevention interventions to older adults requiring such interventions. This study aimed to explore the usability of an app-based strength and balance self-tests in a small sample of four older adults. This study is a side product of another project.

Results
The results from this study indicated that self-test of strength and balance by using a smartphone application is a challenge for older adults. Basic test measures, such as start and stop and counts of sit-to-stand, were difficult to self-administer. However, from a user perspective, the possibility of independently performing these measures was considered important and needed to be further developed and evaluated in future studies.
Combined effects of progesterone and SOCS3 DNA methylation on T2DM: a case–control study
Authors: Wang Lulu , Mao Zhenxing , Liu Xiaotian , Wei Dandan , Liu Pengling , Nie Luting , Fan Keliang , Kang Ning , Song Yu , Xu Qingqing , Wang Juan , Wang Mian , Liao Wei , Jing Tao , Li Wenjie , Wang Chongjian , Huo Wenqian 
Published: September 2021

Abstract
Background
This study aims to investigate the independent and combined effects of progesterone and suppressor of cytokine signaling (SOCS)-3 DNA methylation on type 2 diabetes mellitus (T2DM) among men and postmenopausal women in rural China.

Methods
A case–control study with 914 participants (329 T2DM, 585 controls) was conducted. Serum progesterone was detected with liquid chromatography-tandem mass spectrometry. DNA methylation of SOCS3 was determined by MethylTarget™. Linear regression was applied to evaluate the associations of progesterone and SOCS3 methylation with marks of glucose metabolism. Logistic regression was employed to investigate the independent and combined effects of progesterone and SOCS3 methylation with T2DM in men and postmenopausal women.

Results
After multiple adjustment, progesterone was positively associated with T2DM in both men (odds ratio (OR) (95% confidence interval (CI)): 2.77 (1.79, 4.29)) and postmenopausal women (OR (95% CI): 1.85 (1.26, 2.72)). Methylation level of Chr17:76,356,190 or Chr17:76,356,199 (SOCS3) was negatively associated with T2DM in both men (OR (95% CI): 0.58 (0.39, 0.86) or 0.27 (0.14, 0.51)) and postmenopausal women (OR (95% CI): 0.43 (0.29, 0.65) or 0.53 (0.28, 0.99)). Subjects with high progesterone and low Chr17:76,356,190 or Chr17:76,356,199 methylation were more susceptible to have a higher prevalence of T2DM (men: OR (95% CI): 5.20 (2.49, 10.85) or 5.62 (2.74, 11.54); postmenopausal women: OR (95% CI): 3.66 (1.85, 7.26) or 3.27 (1.66, 6.45)).

Conclusions
The independent and combined effects of progesterone and SOCS3 methylation on T2DM were found among men and postmenopausal women, suggesting that ensuring low levels of progesterone and high methylation of SOCS3 could reduce the prevalence of T2DM.
Trial registration The Chinese Clinical Trial registration: The Henan Rural Cohort Study, ChiCTR-OOC-15006699. Registered 06 July 2015, http://www.chictr.org.cn/showproj.aspx?proj=11375
Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism
Authors: Kupkova Kristyna , Shetty Savera J. , Haque Rashidul , Petri William A. , Auble David T. 
Published: September 2021

AbstractBackgroundStunting is a condition in which a child does not reach their full growth potential due to chronic undernutrition. It arises during the first 2 years of a child’s life and is associated with developmental deficiencies and life-long health problems. Current interventions provide some benefit, but new approaches to prevention and treatment grounded in a molecular understanding of stunting are needed. Epigenetic analyses are critical as they can provide insight into how signals from a poor environment lead to changes in cell function.ResultsHere we profiled histone H3 acetylation on lysine 27 (H3K27ac) in peripheral blood mononuclear cells (PBMCs) of 18-week-old (n = 14) and 1-year-old children (n = 22) living in an urban slum in Dhaka, Bangladesh. We show that 18-week-old children destined to become stunted have elevated levels of H3K27ac overall, functional analysis of which indicates activation of the immune system and stress response pathways as a primary response to a poor environment with high pathogen load. Conversely, overt stunting at 1-year-of age is associated with globally reduced H3K27ac that is indicative of metabolic rewiring and downregulation of the immune system and DNA repair pathways that are likely secondary responses to chronic exposure to a poor environment with limited nutrients. Among processes altered in 1-year-old children, we identified one-carbon metabolism, the significance of which is supported by integrative analysis with results from histone H3 trimethylation on lysine 4 (H3K4me3). Together, these results suggest altered one-carbon metabolism in this population of stunted children.ConclusionsThe epigenomes of stunted children undergo two global changes in H3K27ac within their first year of life, which are associated with probable initial hyperactive immune responses followed by reduced metabolic capacity. Limitation of one-carbon metabolites may play a key role in the development of stunting.Trial registrationClinicalTrials.gov NCT01375647. Registered 17 June 2011, retrospectively registered,https://clinicaltrials.gov/ct2/show/NCT01375647.
Common variable immunodeficiency (CVID) with granulomatous interstitial lung disease (GLILD) and SARS COVID-19 infection: case report and review of literature
Authors: Pattanaik Debendra , Ritter Shaunah , Fahhoum Joseph 
Published: September 2021

Abstract
Background
We present a case of CVID complicated by granulomatous interstitial lung disease (GLILD). This patient clinical course was further complicated by COVID-19 infection. This is only the 2nd known case report of COVID 19 in CVID with GLILD. The clinical course and outcome of COVID 19 infection with common variable immunodeficiency (CVID) and GLILD is not well known.

Case presentation
Our patient met the clinical features of CVID secondary to low IgG/IgA, recurrent infections, and failure to respond to pneumococcal vaccination. He was treated with monthly maintenance IVIG therapy. Our patient also was diagnosed with co-existing GLILD that despite IVIG treatment was progressing. The patient needed to be started on Rituxan and Mycophenolate mofetil to achieve control but unfortunately became infected with COVID19 delaying his treatment for GLILD. Our patient only suffered from mild COVID 19 infection and was able to make antibodies to this. We believe severe infection was avoided as his CVID was well controlled with IVIG therapy despite progression of his granulomatous interstitial lung disease.

Conclusion
In conclusion, our patient with CVID with co-existing biopsy proven granulomatous interstitial lung disease despite being very high risk for severe COVID 19 infections only had mild infection. This was believed to be due to well controlled CVID with IVIG therapy.
Anaphylaxis after jellyfish ingestion with no history of stings: a pediatric case report
Authors: Tsuge Mitsuru , Ikeda Masanori , Mitani Osamu , Yasui Masato , Tsukahara Hirokazu 
Published: September 2021

Abstract
Background
Jellyfish stings are known to induce allergic skin reactions; however, case reports of anaphylaxis after jellyfish ingestion have been increasing, especially in Asian countries. Some cases of anaphylaxis after jellyfish ingestion have been reported in patients with a previous history of frequent jellyfish stings. Herein, we report a pediatric patient with anaphylaxis after jellyfish ingestion with no history of jellyfish stings.

Case presentation
A 14-year-old girl developed two episodes of anaphylaxis, and her diet diaries revealed that edible jellyfish was common to the meals in both the anaphylaxis events. A skin prick test using five types of edible jellyfish products revealed a positive reaction to some jellyfish, and anaphylaxis was observed after the ingestion of jellyfish in an oral food challenge test. She had no history of jellyfish stings or frequent swimming in the ocean. The basophil activation test showed positive results on stimulation with extracts from various types of edible jellyfish. We observed serum immunoglobulin E (IgE) reactivity to purified jellyfish collagen and jellyfish acid-soluble extracts. Moreover, immunoblotting analysis showed IgE reactivity to two bands at approximately 40 and 70 kDa using purified jellyfish collagen, which may be a causative antigen.

Conclusions
Edible salted jellyfish can be one of the causative foods of anaphylaxis. Clinicians should be aware of the possibility of anaphylactic reactions due to jellyfish ingestion even without a history of jellyfish stings.
A renal angiomyolipoma with a challenging presentation: a case report
Authors: Bouaziz H. , Ghalleb M. , Tounsi N. , Riahi N. , Bouzaiene H. , Ziadi J. , Hassouna J. Ben , Slimane M. , Rahal K. 
Published: September 2021

Abstract
Introduction
Renal angiomyolipoma is considered a benign mesenchymal tumor composed of fat, smooth muscle, and blood vessels. It represents 1–3% of solid renal tumors. Despite this tumor’s benignity, it can be aggressive with a locoregional extension.

Case report
A 41-year-old north African caucasian woman consulted with chief complaints of right lower back pain with no hematuria and no urinal sign. Thoracic-abdominopelvic contrast-enhanced computed tomography showed a right inferior polar heterogeneous renal mass complicated with venous thrombus ascending to the right atrium level. The patient underwent radical nephrectomy under extracorporeal circulation and direct supervision of the fatty thrombus at the right atrium level. The postoperative period was uneventful. The final histologic examination was concordant with renal angiomyolipoma.

Conclusion
Renal angiomyolipoma is the most common benign kidney tumor. Despite its benignity, it can be associated with lethal complications such as hemorrhage, and it can also show signs of local extension mimicking malignant tumors. The cornerstone of the treatment remains surgery.