bluuebunny/crossref_metadata_2025 huggingface dataset:
recoup: flexible and versatile signal visualization from next generation sequencing
Authors: Moulos Panagiotis
Published: January 2021

Background

The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging.

Results

recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations.

Conclusion

While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.
Examination of hydrogen cross-feeders using a colonic microbiota model
Authors: Smith Nick W. , Shorten Paul R. , Altermann Eric , Roy Nicole C. , McNabb Warren C.
Published: January 2021

Background

Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.

Results

An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.

Conclusions

Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.
Cell-specific characterization of the placental methylome
Authors: Yuan Victor , Hui Desmond , Yin Yifan , Peñaherrera Maria S. , Beristain Alexander G. , Robinson Wendy P.
Published: January 2021

Background

DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs.

Results

The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation.

Conclusions

Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.
A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations
Authors: Zhou Shenping , Ding Rongrong , Meng Fanming , Wang Xingwang , Zhuang Zhanwei , Quan Jianping , Geng Qian , Wu Jie , Zheng Enqin , Wu Zhenfang , Yang Jianhui , Yang Jie
Published: January 2021

Background

Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.

Results

In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.

Conclusions

We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.
A review of deep learning applications for genomic selection
Authors: Montesinos-López Osval Antonio , Montesinos-López Abelardo , Pérez-Rodríguez Paulino , Barrón-López José Alberto , Martini Johannes W. R. , Fajardo-Flores Silvia Berenice , Gaytan-Lugo Laura S. , Santana-Mancilla Pedro C. , Crossa José
Published: January 2021

Background

Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed model equations. In recent years, deep learning (DL) methods have been considered in the context of genomic prediction. The DL methods are nonparametric models providing flexibility to adapt to complicated associations between data and output with the ability to adapt to very complex patterns.

Main body

We review the applications of deep learning (DL) methods in genomic selection (GS) to obtain a meta-picture of GS performance and highlight how these tools can help solve challenging plant breeding problems. We also provide general guidance for the effective use of DL methods including the fundamentals of DL and the requirements for its appropriate use. We discuss the pros and cons of this technique compared to traditional genomic prediction approaches as well as the current trends in DL applications.

Conclusions

The main requirement for using DL is the quality and sufficiently large training data. Although, based on current literature GS in plant and animal breeding we did not find clear superiority of DL in terms of prediction power compared to conventional genome based prediction models. Nevertheless, there are clear evidences that DL algorithms capture nonlinear patterns more efficiently than conventional genome based. Deep learning algorithms are able to integrate data from different sources as is usually needed in GS assisted breeding and it shows the ability for improving prediction accuracy for large plant breeding data. It is important to apply DL to large training-testing data sets.
Lifestyle modifications result in alterations in the gut microbiota in obese children
Authors: Cho Ky Young
Published: January 2021

Background

The association between the gut microbiota and pediatric obesity was analyzed in a cross-sectional study. A prospective study of obese children was conducted to assess the gut microbial alterations after a weight change. We collected fecal samples from obese children before and after a 2-month weight reduction program that consisted of individual counseling for nutritional education and physical activity, and we performed 16S rRNA gene amplicon sequencing using an Illumina MiSeq platform.

Results

Thirty-six participants, aged 7 to 18 years, were classified into the fat loss (n = 17) and the fat gain (n = 19) groups according to the change in total body fat (%) after the intervention. The baseline analysis of the gut microbiota in the preintervention stages showed dysbiotic features of both groups compared with those of normal-weight children. In the fat loss group, significantly decreased proportions of Bacteroidetes phylum, Bacteroidia class, Bacteroidales order, Bacteroidaceae family, and Bacteroides genus, along with increased proportions of Firmicutes phylum, Clostridia class, and Clostridiales order, were observed after intervention. The microbial richness was significantly reduced, without a change in beta diversity in the fat loss group. The fat gain group showed significantly deceased proportions of Firmicutes phylum, Clostridia class, Clostridiales order, Lachnospiraceae family, and Eubacterium hallii group genus, without a change in diversity after the intervention. According to the functional metabolic analysis by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, the “Nitrate Reduction VI” and “Aspartate Superpathway” pathways were predicted to increase significantly in the fat loss group. The cooccurring networks of genera were constructed and showed the different microbes that drove the changes between the pre- and postintervention stages in the fat loss and fat gain groups.

Conclusions

This study demonstrated that lifestyle modifications can impact the composition, richness, and predicted functional profiles of the gut microbiota in obese children after weight changes.

Trial registration

ClinicalTrials.govNCT03812497, registration date January 23, 2019, retrospectively registered.
Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis
Authors: Trenti Massimiliano , Lorenzi Silvia , Bianchedi Pier Luigi , Grossi Daniele , Failla Osvaldo , Grando Maria Stella , Emanuelli Francesco
Published: January 2021

Background

Understanding the complexity of the vine plant’s response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an ‘ad hoc’ association mapping panel including differentVitisspecies, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms.

The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit.

Results

In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified.

Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960,VIT_18s0001g15390) were actually induced by drought stress.

Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance.

Conclusions

Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.
Prognostic nomogram for 30-day mortality of deep vein thrombosis patients in intensive care unit
Authors: Shen Runnan , Gao Ming , Tao Yangu , Chen Qinchang , Wu Guitao , Guo Xushun , Xia Zuqi , You Guochang , Hong Zilin , Huang Kai
Published: January 2021

Background

We aimed to use the Medical Information Mart for Intensive Care III database to build a nomogram to identify 30-day mortality risk of deep vein thrombosis (DVT) patients in intensive care unit (ICU).

Methods

Stepwise logistic regression and logistic regression with least absolute shrinkage and selection operator (LASSO) were used to fit two prediction models. Bootstrap method was used to perform internal validation.

Results

We obtained baseline data of 535 DVT patients, 91 (17%) of whom died within 30 days. The discriminations of two new models were better than traditional scores. Compared with simplified acute physiology score II (SAPSII), the predictive abilities of two new models were improved (Net reclassification improvement [NRI] > 0; Integrated discrimination improvement [IDI] > 0; P < 0.05). The Brier scores of two new models in training set were 0.091 and 0.108. After internal validation, corrected area under the curves for two models were 0.850 and 0.830, while corrected Brier scores were 0.108 and 0.114. The more concise model was chosen to make the nomogram.

Conclusions

The nomogram developed by logistic regression with LASSO model can provide an accurate prognosis for DVT patients in ICU.
Time-varying discrimination accuracy of longitudinal biomarkers for the prediction of mortality compared to assessment at fixed time point in severe burns patients
Authors: Yoon Jaechul , Kym Dohern , Hur Jun , Won Jae Hee , Yim Haejun , Cho Yong Suk , Chun Wook
Published: January 2021

Background

The progression of biomarkers over time is considered an indicator of disease progression and helps in the early detection of disease, thereby reducing disease-related mortality. Their ability to predict outcomes has been evaluated using conventional cross-sectional methods. This study investigated the prognostic performance of biomarkers over time.

Methods

Patients aged > 18 years admitted to the burn intensive care unit within 24 h of a burn incident were enrolled. Information regarding longitudinal biomarkers, including white blood cells; platelet count; lactate, creatinine, and total bilirubin levels; and prothrombin time (PT), were retrieved from a clinical database. Time-dependent receiver operating characteristic curves using cumulative/dynamic and incident/dynamic (ID) approaches were used to evaluate prognostic performance.

Results

Overall, 2259 patients were included and divided into survival and non-survival groups. By determining the area under the curve using the ID approach, platelets showed the highest c-index [0.930 (0.919–0.941)] across all time points. Conversely, the c-index of PT and creatinine levels were 0.862 (0.843–0.881) and 0.828 (0.809–0.848), respectively.

Conclusions

Platelet count was the best prognostic marker, followed by PT. Total bilirubin and creatinine levels also showed good prognostic ability. Although lactate was a strong predictor, it showed relatively poor prognostic performance in burns patients.
Total cholesterol concentration predicts the effect of plasmapheresis on hypertriglyceridemic acute pancreatitis: a retrospective case–control study
Authors: Chen Zhu , Huang Xiaolong , Han Na , Guo Yanxia , Chen Jing , Ning Yaogui , Zhang Minwei
Published: January 2021

Background

What kind of patients with hypertriglyceridemic acute pancreatitis (HLAP) might benefit from plasmapheresis (PP) remains unknown. The objective of this study is to determine the predict function of total cholesterol (TC) on the Triglyceride (TG)-lowing effect in patients on either non-PP or PP therapy.

Methods

Patients were categorized into high total cholesterol (HTC)/low total cholesterol (LTC) groups based on TC level of 12.4 mmol/L. The primary outcome was TG reduction to below 500 mg/dL within 48 h. Linear mixed-effect model and logistic regression analyses were used to assess the association of TC level and TG-lowing efficacy in different therapy groups.

Results

Compared with LTC group, patients with HTC showed more severe imaging manifestations (p < 0.001) and higher APACH II scores (p = 0.036). Deaths occurred only in HTC groups. Significant interaction of time sequence with the 2 TGs-lowing therapy groups on TG level was only found in HTC group (p < 0.001). In patients with elevated TC level, primary outcome occurred in 66.67% of patients in the PP group, and 27.91% in the non-PP group. After adjustment for age, gender, CT grade and APACH II score, the odd ratio remain significant (OR 5.47, 95% confidence interval [CI] 1.84–16.25,p = 0.002). Furthermore, in patients with lower TC level, no significant difference was found in primary outcome between PP group and non-PP group (81.25% versus 62.30%, adjusted OR 2.05; 95% CI 0.45–9.40;p = 0.353).

Conclusions

TC could be a potential biomarker to predict the effects of TG-lowing therapy in patients with HLAP.
Metabolic syndrome components and acute pancreatitis: a case–control study in China
Authors: Shen Zhemin , Wang Xueqiao , Zhen Zili , Wang Yao , Sun Peilong
Published: January 2021

Background

Acute pancreatitis (AP) is a common inflammatory disorder of the pancreas. Recent evidence has shown that metabolic syndrome is positively correlated with the severity of AP. However, only a few studies have revealed the relationship between metabolic syndrome and the occurrence of AP. We therefore elucidated the association between metabolic syndrome and the occurrence of AP.

Methods

A hospital-based case–control study was conducted. A total of 705 patients admitted to our hospital from January 2016 to December 2018 were included in the study. Subjects were divided into case and control groups according to their diagnosis: (1) According to the revised Atlanta classification from 2012, patients diagnosed with AP were enrolled in the case group. (2) Patients without a history of AP or any disease related to metabolic syndrome were allocated into the control group. Controls were matched to cases individually by sex and age (control/case ratio = 1).

Results

The incidence rate of metabolic syndrome in AP patients was 30.9%, which was more frequent than that in controls (13.2%) (OR 2.837; 95% CI 1.873–4.298, p < 0.001). In the multivariate regression analysis, a history of smoking or alcohol consumption and biliary stones were significantly associated with AP (OR 2.441; 95% CI 1.865–5.172, p < 0.001; OR 1.777; 95% CI 1.060–2.977, p = 0.029; OR 28.995; 95% CI 13.253–63.435, p < 0.001). In addition, the occurrence of AP was significantly associated with total cholesterol (TC) (OR 1.992; 95% CI 1.246–3.183, p = 0.004), triglyceride (TG) (OR 2.134; 95% CI 1.403–3.245, p < 0.001), hyperglycaemia (OR 2.261; 95% CI 1.367–3.742, p = 0.001), and apolipoprotein A (Apo A) (OR 0.270; 95% CI 0.163–0.447, p < 0.001).

Conclusions

Metabolic syndrome and its components were associated with AP occurrence.
Chronic active EBV infection in refractory enteritis with longitudinal ulcers with a cobblestone appearance: an autopsied case report
Authors: Aihara Yosuke , Moriya Kei , Shimozato Naotaka , Nagamatsu Shinsaku , Kobayashi Shinya , Uejima Masakazu , Matsuo Hideki , Ishida Eiwa , Yagi Hideo , Nakatani Toshiya , Yoshiji Hitoshi , Kikuchi Eiryo
Published: January 2021

Background

Chronic active Epstein–Barr virus infection (CAEBV) is defined as Epstein–Barr virus (EBV)-positive T/NK cell-related neoplasia, and its major clinical symptom is systemic inflammation presenting as infectious mononucleocytosis, whereas enteritis and diarrhea are minor clinical symptoms. The complex mixture of tumorigenic processes of EBV-positive cells and physical symptoms of systemic inflammatory disease constitutes the varied phenotypes of CAEBV. Herein, we describe a case of CAEBV that was initially diagnosed as Crohn’s disease (CD) based on ileal ulcers and clinical symptoms of enteritis.

Case presentation

A 19-year-old woman complained of abdominal pain and fever. Blood examination showed normal blood cell counts without atypical lymphocyte but detected modest inflammation, hypoalbuminemia, slight liver dysfunction, and evidence of past EBV infection. The esophagogastroduodenoscopic findings were normal. However, colonoscopy revealed a few small ulcers in the terminal ileum. The jejunum and ileum also exhibited various forms of ulcers, exhibiting a cobblestone appearance, on capsule endoscopy. Based on these clinical findings, she was strongly suspected with CD. In the course of treatment by steroid and biologics for refractory enteritis, skin ulcers appeared about 50 months after her initial hospital visit. Immunohistology of her skin biopsy revealed proliferation of EBV-encoded small RNA (EBER)-positive atypical lymphocytes. We retrospectively assessed her previous ileal ulcer biopsy before treatment and found many EBER-positive lymphocytes. Blood EBV DNA was also positive. Therefore, she was diagnosed with extranodal NK/T-cell lymphoma with CAEBV-related enteritis rather than CD. She was treated with cyclosporine and prednisolone combination therapy for CAEBV-related systemic inflammation and chemotherapy for malignant lymphoma. Unfortunately, her disease continued to progress, leading to multiple organ failure and death at the age of 23 years.

Conclusion

Clinicians need to remember the possibility of CAEBV as a differential diagnosis of refractory enteritis. Enteritis with intestinal ulcer is a rare symptom of CAEBV, and it is impossible to acquire a definitive diagnosis by ulcer morphology only. In cases where the possibility of CAEBV remains, tissue EBVR expression should be checked by in situ hybridization and blood EBV DNA.
Is acute kidney injury age-dependent in older adults: an observational study in two centers from North China
Authors:   on behalf of China collaborative study on AKI (CCS-AKI), Xu Libin , Wu Yanhua , Chen Yuanhan , Li Ruiying , Wang Zhiqiang , Li Zhilian , Liu Guoping , Yu Lei , Shi Wei , Liang Xinling
Published: January 2021

Background

Although aging increases susceptibility to acute kidney injury (AKI), whether the AKI risk and the association between AKI and adverse outcomes are age-dependent remain unclear in older adults. The current study aimed to identify whether AKI risk was age-dependent in older adults and to investigate whether the association between AKI and mortality increased with increasing age.

Methods

Medical records from 47,012 adult hospital admissions, including 30,194 older adults aged 60 or older, in two tertiary general hospitals were studied retrospectively. AKI was identified based on changes in blood creatinine levels according to the Kidney Disease: Improving Global Outcomes criteria.

Results

Among the total population and 30,194 older adult patients, the raw incidences of AKI were 8.2 and 8.3%, respectively. The curve of the age-grouped AKI incidence was “U-shaped”, which revealed a positive relationship between the AKI incidence and age among the older adults aged 75 years or older. This trend of the age-AKI relationship was supported by further multivariable analysis. After adjusting for the Charlson Comorbidity Index score, the AKI was associated with in-hospital mortality; however, the associations did not increase with increasing age.

Conclusion

The AKI risk does not increase with age in older adults, except for those aged 75 and above. The association between AKI and in-hospital death did not increase in an age-dependent manner in older adults.

Trial registration

This study was retrospectively registered at clinicaltrials.gov (NCT03054142) on February 13, 2017.
Age-related changes in postural control in older women: transitional tasks in step initiation
Authors: Michalska Justyna , Kamieniarz Anna , Sobota Grzegorz , Stania Magdalena , Juras Grzegorz , Słomka Kajetan J.
Published: January 2021

Background

Aging, being a natural process, involves many functional and structural changes within the body. Identifying the age-related postural changes will provide insight into the role of aging on postural control during locomotion. The aim of this study was to identify age-related postural changes during a transitional task under different conditions.

Methods

Sixty healthy females divided into three age groups: A (50-60 y/o), B (60-70 y/o), and C (70-80 y/o). The transitional task was measured by two force platforms. The procedure consisted of three phases: quiet standing, transfer onto a second platform, and quiet standing on the second platform. Four different conditions were applied: unperturbed transfer, obstacle crossing, step-up, and step-down. Double-support time, transit time, and stability time before and after the step task were analyzed.

Results

The transit time was longer by 30% for subjects over 70 y/o. The double-support time was longer by 11% among adults 60-70 y/o, while in people over 70 y/o it was longer by almost 50% compared to the 50-60 y/o subjects. The stability time before the transitional task was longer by 17% among adults over 60 y/o compared to middle-age subjects. The stability times before and after the transitional task were longer for adults in the 50-60 y/o category.

Conclusion

The proposed procedure is adequate for assessing age-related changes in postural control while undergoing a transitional task. An analysis of the double-support time and stability time before and after the step task enabled the detection of early signs of balance changes in middle-age adults. Independent of age, the transitional task parameters changed with the increasing difficulty of the tasks.
Acceptance of universal varicella vaccination among Swiss pediatricians and general practitioners who treat pediatric patients
Authors: Lienert Florian , Weiss Olivia , Schmitt Kathrin , Heininger Ulrich , Guggisberg Patrik
Published: January 2021

Background

Over the last two decades, several countries have initiated universal varicella vaccination (UVV) programs in infants. In 2019, the Swiss National Immunization Technical Advisory Group (NITAG) decided to start evaluating the introduction of universal varicella vaccination. There is a theoretical concern that suboptimal vaccination coverage could lead to a shift in the varicella incidence to older age groups, thereby potentially increasing complication rates. To achieve a high vaccination coverage rate, it is important that practicing physicians comply with a potential recommendation for UVV.

We studied the perception of varicella and the current vaccination behavior among Swiss pediatricians and general practitioners (GPs) who treat children. We also assessed their intention to advise parents to vaccinate their children against varicella in the event the Swiss NITAG will recommend UVV.

Methods

Primary data was collected through a structured, 20-min online survey with Swiss pediatricians and GPs who treat children.

Results

150 physicians participated in the study: 40 GPs in the German-speaking part, 20 GPs in the French-speaking part, 67 pediatricians in the German-speaking part, and 23 pediatricians in the French-speaking part.

The majority (64%) of all participants reported that they currently recommend varicella vaccination for risk groups according to the national immunization plan. About one third of physicians (35%) – predominantly pediatricians – currently already recommend it for all infants. In these situations, a measles, mumps, rubella, varicella combination vaccine is currently used by 58% for the first dose and by 59% for the second dose.

86% of participants stated that they would advise parents to have their children vaccinated against varicella in case of a recommendation for UVV by the Swiss NITAG. 68% responded that they expect many questions from parents and 65% agreed that they have good arguments to convey the importance of varicella vaccination.

Conclusions

The survey study results show that most participating pediatricians and GPs indicated a favorable attitude towards childhood vaccination against varicella in the setting of a Swiss NITAG recommendation for UVV. This data shows the importance of NITAG recommendations in influencing vaccine education and supporting achievement of high coverage of varicella vaccination.
Etiology of diarrhea by multiplex polymerase chain reaction among young children in the United Arab Emirates: a case-control study
Authors: Alsuwaidi Ahmed R. , Al Dhaheri Klaithem , Al Hamad Sania , George Junu , Ibrahim Judy , Ghatasheh Ghassan , Issa Mohammed , Al-Hammadi Suleiman , Narchi Hassib
Published: January 2021

Background

Little is known about the etiology of childhood diarrhea in the United Arab Emirates (UAE) especially after the introduction of rotavirus vaccines. This study aimed to identify gastrointestinal pathogens in children with diarrhea (cases) and the carriage rate of these pathogens in asymptomatic children (controls).

Methods

Stool samples were collected from 203 cases and 73 controls who presented to two major hospitals in Al Ain city, UAE. Samples were analyzed with Allplex™ Gastrointestinal Full Panel Assay for common entero-pathogens. The association between diarrhea and the isolated pathogens was calculated in a multivariate logistic regression model. The adjusted attributable fractions (aAFs) were calculated for all pathogens significantly associated with cases.

Results

At least one pathogen was identified in 87 samples (42.8%) from cases and 17 (23.3%) from controls (P < 0.001). Rotavirus, norovirus GII and adenovirus were significantly more prevalent in cases. Their aAFs with 95% ci are 0.95 (0.64, 1.00) for rotavirus, 0.86 (0.38, 0.97) for norovirus GII and 0.84 (0.29, 0.96) for adenovirus. None of the 13 bacteria tested for were more commonly found in the cases than in controls. Cryptosporidium spp. were more significantly detected in cases than in controls. Co-infections occurred in 27.9% of the children. Viruses and parasites were significantly more likely to occur together only in the cases.

Conclusions

Multiplex PCR revealed high positivity rates in both cases and controls which demand a cautious interpretation. Rotavirus remains the main childhood diarrhea pathogen in UAE. Effective strategies are needed to better control rotavirus and other causative pathogens.
Enterobacter cloacae infection of the shoulder in a 52-year-old woman without apparent predisposing risk factor: a case report and literature review
Authors: Huang Jingjie , Xu Qiliang , Liu Fuyifei , Xiong Hao , Yang Junxing
Published: January 2021

Background

Enterobacter cloacae (E. cloacae) is one of the commensal flora in the human intestinal tract and a prevalent nosocomial pathogen, which rarely causes infectious osteoarthritis in immunocompetent patients without recent trauma or surgery. Here, we report the first case of septic monoarthritis of the shoulder caused by E. cloacae in an immunocompetent patient.

Case presentation

A 52-year-old female with a 6-year history of right shoulder pain was referred to our emergency department due to fever, acute severe shoulder pain, and swelling. Blood test showed elevated inflammatory markers. The patient denied any recent invasive surgical procedure and trauma. She was misdiagnosed with a frozen shoulder, and the anti-inflammatory painkiller celecoxib for symptomatic treatment was ineffective. Magnetic resonance imaging (MRI) showed a shoulder joint abscess and supraspinatus tendon tear. The joint aspirate culture showed E. cloacae. After late diagnosis, she was treated with levofloxacin and underwent surgical debridement and irrigation. Her follow-up data revealed that she did not suffer from shoulder swelling and severe pain.

Conclusion

This is a rare case of E. cloacae infected arthritis of the shoulder in an immunocompetent patient with a rotator cuff tear, indicating that even if the symptoms and age of the patients match the characteristics of frozen shoulder, the possibility of septic arthritis should be considered in the presence of fever and increasing inflammatory markers. The cases of our literature review suggest that the patients subjected to invasive procedure may develop a subsequent E. cloacae osteoarticular infection, regardless of being asymptomatic after the procedure.
User of angiotensin-converting-enzyme inhibitor and/or angiotensin II receptor blocker might be associated with vascular calcification in predialysis chronic kidney disease patients: a retrospective single-center observational study
Authors: Takaori Kaori , Iwatani Hirotsugu , Yamato Masafumi , Ito Takahito
Published: January 2021

Background

Vascular calcification is a prominent feature in chronic kidney disease (CKD) and diabetes mellitus. A recent report suggests that angiotensin II is protective to vascular calcification. Therefore, we investigated the relationship between vascular calcification and use of angiotensin-converting-enzyme inhibitor (ACEI) and/or angiotensin II receptor blocker (ARB) from a cross-sectional view.

Methods

A total of 121 predialysis CKD patients (age 71 ± 12 y; male 72; estimated glomerular filtration rate (eGFR) 20.2 (11.8 - 40.3) mL/min/1.73 m2) who underwent thoracoabdominal plain computed tomography scan were included in this study. The total vascular calcification volume (Calc) was calculated with a three-dimensional imaging software and standardized by body surface area (BSA). The relevance between log [Calc/BSA] and ACEI/ARB use was investigated by multivariate linear regression analyses with or without a time-duration factor of ACEI/ARB use.

Results

The Calc/BSA was 5.62 (2.01 - 12.7) mL/m2 in 121 patients. In multivariate analyses adjusted with age, sex, ACEI/ARB and log [eGFR], ACEI/ARB use is significantly and positively associated with log [Calc/BSA] (β = 0.2781, p = 0.0007). Even after the adjustment by age, sex, log [eGFR], phosphate, diabetes mellitus, systolic blood pressure, warfarin, hypertension, dyslipidemia, low-density lipoprotein cholesterol, diuretics and ACEI/ARB, ACEI/ARB use is significantly and positively associated with log [Calc/BSA] (β = 0.1677, p = 0.0487). When 90 patients whose time-duration of ACEI/ARB use was clear in medical records were studied, a multivariate analysis adjusted with age, sex, log [eGFR], and ACEI/ARB duration factors showed that the longer use of ACEI/ARB more than 2 years was significantly, independently and positively associated with log [Calc/BSA] (β = 0.2864, p = 0.0060).

Conclusions

ACEI/ARB user was associated with vascular calcification in predialysis patients with low eGFR. Prospective studies with larger numbers of patients or more in vitro studies are needed to confirm whether this phenomenon is due to the use of ACEI/ARB itself, the underlying disease condition or the prescription bias.
Prevalence, risk factors and impact on outcomes of 30-day unexpected rehospitalization in incident peritoneal dialysis patients
Authors: Li Jianbo , Yu Jing , Huang Naya , Ye Hongjian , Wang Dan , Peng Yuan , Guo Xiaobo , Yi Chunyan , Yang Xiao , Yu Xueqing
Published: January 2021

Background

Rehospitalization is a major problem for end stage renal disease (ESRD) populations. However, researches on 30-day unexpected rehospitalzation of incident peritoneal dialysis (PD) patients were limited. This study aimed to investigate the prevalence, risk factors and impact on outcomes of 30-day unexpected rehospitalization in incident PD patients.

Methods

This was a retrospective cohort study. Patients who accepted PD catheter implantation in our centre from Jan 1, 2006 to Dec 31, 2013 and regular follow-up were included. The demographic characteristics, laboratory parameters, and rehospitalization data were collected and analyzed. The primary outcome was all-cause mortality, and the secondary outcomes included cardiovascular disease (CVD) mortality and technical failure.

Results

Totally 1632 patients (46.9 ± 15.3 years old, 60.1% male, 25.6% with diabetes) were included. Among them, 149 (9.1%) had a 30-day unexpected rehospitalization after discharge. PD-related peritonitis (n = 48, 32.2%), catheter malfunction (n = 30, 20.1%) and severe fluid overload (n = 19, 12.8%) were the top three causes for the rehospitalization. Multivariate logistic regression analysis showed that length of index hospital stays [Odds ratio (OR) =1.02, 95% confidence interval (CI) 1.00–1.03, P = 0.036) and hyponatremia (OR = 1.85, 95% CI 1.06–3.24, P = 0.031) were independently associated with the rehospitalization. Multivariate Cox regression analysis indicated that 30-day rehospitalization was an independent risk factor for all-cause mortality [Hazard ratio (HR) =1.52, 95% CI 1.07–2.16, P = 0.019) and CVD mortality (HR = 1.73, 95% CI 1.03–2.90, P = 0.038).

Conclusions

The prevalence of 30-day unexpected rehospitalization for incident PD patients in our centre was 9.1%. The top three causes for the rehospitalization were PD-related peritonitis, catheter malfunction and severe fluid overload. Thirty-day unexpected rehospitalization increased the risk of all-cause mortality and CVD mortality for PD patients.
Immunohistochemical study for the expression of leukocyte adhesion molecules, and FGF23 and ACE2 in P. gingivalis LPS-induced diabetic nephropathy
Authors: Kajiwara Koichiro , Sawa Yoshihiko , Fujita Takahiro , Tamaoki Sachio
Published: January 2021

Objective

The present study aims to examine the expression of leukocyte adhesion molecules and renal metabolic factors in diabetic mouse kidneys with periodontal pathogen Pg-LPS-induced nephropathy.

Background

We recently reported that the glomerular endothelium expresses toll-like receptor (TLR)2 and TLR4 in diabetic environments and TLR2/4 ligand Porphyromonas (P.) gingivalis lipopolysaccharides (Pg-LPS) induce nephropathy in diabetic mice. It is thought that Pg-LPS promotes the chronic inflammation with the overexpression of leukocyte adhesion molecules and renal-specific metabolic enzymes by the recognition of Pg-LPS via TLR in the diabetic kidneys. There have been no reports of the effects of periodontopathic bacteria on the expression of leukocyte adhesion molecules and the accumulation of physiologically active substances in the kidney.

Methods

The immunohistochemical investigation was performed on diabetic mouse kidney with Pg-LPS-induced nephropathy with glomerulosclerosis in glomeruli.

Results

There were no vessels which expressed vascular cell adhesion molecule-1 (VCAM-1), E-selectin, or fibroblast growth factor (FGF) 23 in streptozotocin (STZ)-induced diabetic ICR mice (STZ-ICR), or in healthy ICR mice administered Pg-LPS (LPS-ICR). However, in diabetic ICR mouse kidneys with Pg-LPS-induced nephropathy (LPS-STZ) the expression of VCAM-1 and the accumulation of FGF23 were observed in renal tubules and glomeruli, and the expression of E-selectin was observed in renal parenchyma and glomeruli. The angiotensin-converting enzyme 2 (ACE2) was detected in the proximal tubules but not in other regions of ICR, STZ-ICR, or LPS-ICR. In LPS-STZ ACE2 was detected both in renal tubules as well as in glomeruli. The Mac-1 and podoplanin-positive cells increased in the renal parenchyma with diabetic condition and there was the distribution of a large number of Mac-1-positive cells in LPS-STZ.

Conclusions

The Pg-LPS may induce diabetic renal inflammation such as glomerulosclerosis and tubulitis with infiltration of Mac-1/podoplanin positive macrophages via glomerular overexpression of VCAM-1 and E-selectin, resulting in accumulation of both ACE2 and FGF23 which were unmetabolized with the inflammation-induced kidney damage under the diabetic condition. Periodontitis may be a critical factor in the progress of nephropathy in diabetic patients.
Paternal factors and adverse birth outcomes in Lanzhou, China
Authors: Li Jing , Qiu Jie , Lv Ling , Mao Baohong , Huang Lei , Yang Tao , Wang Cheng , Liu Qing
Published: January 2021

Background

Many maternal factors are known to be associated with adverse birth outcomes, but studies about paternal factors yielded inconsistent conclusions. The study was to assess whether paternal factors are associated with low birth weight (LBW), preterm birth (PTB), and small for gestational age (SGA).

Methods

A birth cohort study was conducted in 2010–2012 at the Gansu Provincial Maternity and Child Care Hospital, the largest maternity and childcare hospital in Lanzhou, China. Paternal age, ethnicity, educational level, height, weight, smoking, and drinking were collected. Birth outcomes and pregnancy complications were extracted from the medical records.

Results

During the study period, 10,121 participants were included; the overall prevalence of LBW, PTB, and SGA was 7.2, 9.9, and 7.8%, respectively. Paternal higher height (OR = 0.64 95%CI: 0.49, 0.83), higher weight (P for trend < 0.001), and higher BMI (P for trend < 0.001) could decrease the rate of LBW. Paternal higher education (OR = 0.55, 95%CI: 0.43, 0.71) and higher weight (P for trend < 0.001,) were associated with lower rate of PTB. Fathers who smoked more than 6 pack-years were associated with PTB (OR = 1.31, 95%CI: 1.07, 1.61). Paternal BMI > 23.9 kg/m2 (P for trend < 0.001,) and paternal education which above college (OR = 0.61, 95%CI: 0.50, 0.82) were associated with a lower rate of SGA.

Conclusion

Paternal low education is independently associated with PTB and SGA. Paternal heavy smoking is associated with PTB. Low paternal weight/BMI is independently associated with LBW, PTB, and SGA.
Appraisal of systematic reviews on interventions for postpartum depression: systematic review
Authors: Chow Ryan , Huang Eileen , Li Allen , Li Sophie , Fu Sarah Y. , Son Jin S. , Foster Warren G.
Published: January 2021

Background

Postpartum depression (PPD) is a highly prevalent mental health problem that affects parental health with implications for child health in infancy, childhood, adolescence and beyond. The primary aim of this study was to critically appraise available systematic reviews describing interventions for PPD. The secondary aim was to evaluate the methodological quality of the included systematic reviews and their conclusions.

Methods

An electronic database search of MEDLINE, Embase, and the Cochrane Library from 2000 to 2020 was conducted to identify systematic reviews that examined an intervention for PPD.A Measurement Tool to Assess Systematic Reviewswas utilized to independently score each included systematic review which was then critically appraised to better define the most effective therapeutic options for PPD.

Results

Of the 842 studies identified, 83 met the a priori criteria for inclusion. Based on the systematic reviews with the highest methodological quality, we found that use of antidepressants and telemedicine were the most effective treatments for PPD. Symptoms of PPD were also improved by traditional herbal medicine and aromatherapy. Current evidence for physical exercise and cognitive behavioural therapy in treating PPD remains equivocal. A significant, but weak relationship between AMSTAR score and journal impact factor was observed (p = 0.03, r = 0.24; 95% CI, 0.02 to 0.43) whilst no relationship was found between the number of total citations (p = 0.27, r = 0.12; 95% CI, − 0.09 to 0.34), or source of funding (p = 0.19).

Conclusion

Overall the systematic reviews on interventions for PPD are of low-moderate quality and are not improving over time. Antidepressants and telemedicine were the most effective therapeutic interventions for PPD treatment.