bluuebunny/crossref_metadata_2025 huggingface dataset:
Tamock: simulation of habitat-specific benchmark data in metagenomics
Authors: Gerner Samuel M. , Graf Alexandra B. , Rattei Thomas
Published: May 2021

Background

Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems. Conclusions from benchmark studies are therefore limited to the ecosystems they mimic. Ideally, simulations are therefore based on genomes, which resemble particular metagenomic communities realistically.

Results

We developed Tamock to facilitate the realistic simulation of metagenomic reads according to a metagenomic community, based on real sequence data. Benchmarks samples can be created from all genomes and taxonomic domains present in NCBI RefSeq. Tamock automatically determines taxonomic profiles from shotgun sequence data, selects reference genomes accordingly and uses them to simulate metagenomic reads. We present an example use case for Tamock by assessing assembly and binning method performance for selected microbiomes.

Conclusions

Tamock facilitates automated simulation of habitat-specific benchmark metagenomic data based on real sequence data and is implemented as a user-friendly command-line application, providing extensive additional information along with the simulated benchmark data. Resulting benchmarks enable an assessment of computational methods, workflows, and parameters specifically for a metagenomic habitat or ecosystem of a metagenomic study.

Availability

Source code, documentation and install instructions are freely available at GitHub (https://github.com/gerners/tamock).
Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders
Authors: Ávila Herrera Ivalú M. , Král Jiří , Pastuchová Markéta , Forman Martin , Musilová Jana , Kořínková Tereza , Šťáhlavský František , Zrzavá Magda , Nguyen Petr , Just Pavel , Haddad Charles R. , Hiřman Matyáš , Koubová Martina , Sadílek David , Huber Bernhard A.
Published: May 2021

Background

Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.

Results

Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.

Conclusions

The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome–autosome and autosome–sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.
Molecular evolutionary analysis of human primary microcephaly genes
Authors: Pervaiz Nashaiman , Kang Hongen , Bao Yiming , Abbasi Amir Ali
Published: May 2021

Background

There has been a rapid increase in the brain size relative to body size during mammalian evolutionary history. In particular, the enlarged and globular brain is the most distinctive anatomical feature of modern humans that set us apart from other extinct and extant primate species. Genetic basis of large brain size in modern humans has largely remained enigmatic. Genes associated with the pathological reduction of brain size (primary microcephaly-MCPH) have the characteristics and functions to be considered ideal candidates to unravel the genetic basis of evolutionary enlargement of human brain size. For instance, the brain size of microcephaly patients is similar to the brain size of Pan troglodyte and the very early hominids like the Sahelanthropus tchadensis and Australopithecus afarensis.

Results

The present study investigates the molecular evolutionary history of subset of autosomal recessive primary microcephaly (MCPH) genes; CEP135, ZNF335, PHC1, SASS6, CDK6, MFSD2A, CIT, and KIF14 across 48 mammalian species. Codon based substitutions site analysis indicated that ZNF335, SASS6, CIT, and KIF14 have experienced positive selection in eutherian evolutionary history. Estimation of divergent selection pressure revealed that almost all of the MCPH genes analyzed in the present study have maintained their functions throughout the history of placental mammals. Contrary to our expectations, human-specific adoptive evolution was not detected for any of the MCPH genes analyzed in the present study.

Conclusion

Based on these data it can be inferred that protein-coding sequence of MCPH genes might not be the sole determinant of increase in relative brain size during primate evolutionary history.
Sewage and sewage-contaminated environments are the most prominent sources to isolate phages against Pseudomonas aeruginosa
Authors: Aghaee Bahareh Lashtoo , Mirzaei Mohammadali Khan , Alikhani Mohammad Yousef , Mojtahedi Ali
Published: May 2021

Background

P. aeruginosa is the primary source of hospital-acquired infections. Unfortunately, antibiotic resistance is growing to precariously high levels, making the infections by this pathogen life-threatening and hard to cure. One possible alternative to antibiotics is to use phages. However, the isolation of phages suitable for phage therapy— be lytic, be efficient, and have a broad host range —against some target bacteria has proven difficult. To identify the best places to look for these phages against P. aeruginosa we screened hospital sewages, soils, and rivers in two cities.

Results

We isolated eighteen different phages, determined their host range, infection property, and plaque morphology. We found that the sewage and sewage-contaminated environments are the most reliable sources for the isolation of Pseudomonas phages. In addition, phages isolated from hospital sewage showed the highest efficiency in lysing the bacteria used for host range determination. In contrast, phages from the river had larger plaque size and lysed bacteria with higher levels of antibiotic resistance.

Conclusions

Our findings provided additional support for the importance of sewage as the source of phage isolation.
Analysis of culturable airborne fungi in outdoor environments in Tianjin, China
Authors: Nageen Yumna , Asemoloye Michael Dare , Põlme Sergei , Wang Xiao , Xu Shihan , Ramteke Pramod W. , Pecoraro Lorenzo
Published: May 2021

Background

Fungal spores dispersed in the atmosphere may become cause of different pathological conditions and allergies for human beings. A number of studies have been performed to analyze the diversity of airborne fungi in different environments worldwide, and in particular in many urban areas in China. We investigated, for the first time, the diversity, concentration and distribution of airborne fungi in Tianjin city. We sampled 8 outdoor environments, using open plate method, during a whole winter season. Isolated fungi were identified by morphological and molecular analysis. Environmental factors which could influence the airborne fungi concentration (temperature, humidity, wind speed, and air pressure) were monitored and analyzed. The effect of different urban site functions (busy areas with high traffic flow and commercial activities vs. green areas) on airborne fungal diversity was also analyzed.

Results

A total of 560 fungal strains, belonging to 110 species and 49 genera of Ascomycota (80 %), Basidiomycota (18 %), and Mucoromycota (2 %) were isolated in this study. The dominant fungal genus was Alternaria (22 %), followed by Cladosporium (18.4 %), Naganishia (14.1 %), Fusarium (5.9 %), Phoma (4.11 %), and Didymella (4.8 %). A fungal concentration ranging from 0 to 3224.13 CFU m− 3 was recorded during the whole study. Permutational multivariate analysis showed that the month was the most influential factor for airborne fungal community structure, probably because it can be regarded as a proxy of environmental variables, followed by wind speed. The two analyzed environments (busy vs. green) had no detectable effect on the air fungal community, which could be related to the relatively small size of parks in Tianjin and/or to the study season.

Conclusions

Our study shed light on the highly diverse community of airborne fungi characterizing the outdoor environments of Tianjin, and clarified the role that different environmental factors played in shaping the analyzed fungal community. The dominant presence of fungi with potential hazardous effect on human health, such as Alternaria, Cladosporium and Naganishia, deserves further attention. Our results may represent a valuable source of information for air quality monitoring, microbial pollution control, and airborne diseases prevention.
Plasma Galectin-3 is associated with progression from paroxysmal to persistent atrial fibrillation
Authors: Wang Qianhui , Xu Li , Dong Ying , Fu Yuan , Pan Yuxia , Luan Qianran , Liu Ye , Liu Zheng , Yang Xinchun , Chen Mulei , Gao Yuanfeng
Published: May 2021

Background

Galectin-3 (Gal-3) is currently recognized as a promising biomarker for myocardial fibrosis. This study aimed to explore the potential association between plasma Gal-3 concentrations and atrial fibrillation (AF) progression in paroxysmal AF (PAF) patients

Methods

A total of 213 PAF patients were included for analysis in this study. All peripheral blood samples were prospectively collected and stored at -80℃ for subsequent Gal-3 quantification. The AF progression was defined as transformation from PAF to persistent AF (PsAF).

Results

A total of 51 PAF patients progressed to PsAF during a mean follow-up period of 674.44 ± 19.48 days. Patients with AF progression had significantly higher baseline plasma Gal-3 concentrations than those stayed in PAF status (13.52 ± 0.94 vs. 7.93 ± 0.37, p < 0.001). All PAF patients were divided into two subgroups based on the median value of plasma Gal-3 concentrations. Kaplan–Meier curve analysis showed a significantly higher AF progression rate in the higher plasma Gal-3 concentration group (log-rank test p < 0.001). In the Cox regression analysis, plasma Gal-3 concentration and left atrial diameter (LAD) were showed significantly associated with AF progression, even after adjustment of other potential confounding risk factors. Discrimination for AF progression with a simple model which consists of plasma Gal-3 concentration and LAD was modest with a C-statistic 0.72 (95%CI 0.64–0.80). Plasma Gal-3 concentration significantly improved the predictability by appropriately reclassifying several patients with progression (NRI = 28.3%, p = 0.003).

Conclusion

Elevated plasma Gal-3 concentration is significantly associated with AF progression from PAF to PsAF. Plasma Gal-3 concentration could be used for PAF progression risk stratification and guiding management for PAF patients.
Association of blood culture with carbapenem use in pyogenic liver abscess: a two-center retrospective study
Authors: He Shuangjun , Yu Jie , Wang Hairong , Wang Lifeng , Chen Yi , Zhou Wei
Published: May 2021

Background

Highly empiric use of carbapenem in pyogenic liver abscess (PLA) is widespread problem. However, few studies have examined the association between blood culture and carbapenem use in patients with PLA in China. Thus, we conducted this observational study.

Methods

The data of patients diagnosed with PLA at two comprehensive tertiary care centers from 2014 to 2020 were retrospectively collected. Demographic and clinical data were analyzed, and univariate and multivariate analyses were performed to investigate the association between blood culture and carbapenem use. Subgroup analysis was conducted to explore whether the effect is different in sepsis.

Results

Blood culture was performed in 110 (46.0%) patients, of whom 44 (40.0%) patients had positive results for bacterial culture. Extended-spectrum beta-lactamase (ESBL)-positive blood culture isolates were detected in 8 (7.3%) patients. The positivity rate of blood culture in sepsis was higher than in non-sepsis (58.1% vs. 32.9%, P = 0.015). Fewer patients who had a blood culture received carbapenem treatment in comparison to patients without blood culture (19.1% vs. 31.8%, P = 0.026). Multivariate analysis showed that blood culture was independently associated with less carbapenem exposure (adjusted odds ratio [OR] = 0.33, 95% confidence interval [CI]: 0.16–0.68, P = 0.003), and this effect remained significant in the sepsis subgroup (adjusted OR = 0.17, 95% CI: 0.05–0.53, P = 0.002).

Conclusion

Blood culture had a high positivity rate and was associated with less carbapenem use in PLA, especially those who developed sepsis. More attention should be paid to performing early blood culture and less carbapenem use in PLA.
Tidal volume according to the 4-point sealing forces of a bag-valve-mask: an adult respiratory arrest simulator-based prospective, descriptive study
Authors: Uhm Dongchoon , Kim Ajung
Published: May 2021

Background

For adequate ventilation during bag-valve-mask ventilation, rescuers should ensure a proper mask seal using the one-handed or two-handed technique. Little is known about the magnitude of sealing forces of a bag-valve-mask needed for adequate ventilation. This study aimed to explore the effect of the 4-point sealing forces of a bag-valve-mask on tidal volume while using the one-handed technique, focusing on the moderating effect of C length (the distance from the thumb to the index finger in the C shape of the one-hand EC grip).

Methods

A prospective, descriptive simulation study was conducted. A convenience sample of 125 undergraduate paramedic students from two universities was recruited. A self-reported questionnaire was used to collect subjective variables. Tidal volumes, 4-point sealing forces of the mask, peak pressure, and C length of the C shape in the one-hand EC grip were measured using the mechanical lung model under a simulated adult respiratory arrest. Hierarchical regression analysis was used to determine the moderating effect of C length on tidal volume in bag-valve-mask ventilation.

Results

The average C length, peak pressure, and tidal volume were 7.54 (± 1.85) cm, 11.62 (± 5.40) cmH2O, and 321.66 (± 135.18) mL, respectively. The average range of the 4-point sealing forces was 0.03–0.69 N. The apex sealing force was the weakest among the 4-point sealing forces. Hierarchical regression analysis demonstrated that tidal volume accounted for 62.7% of the variance by C length, peak pressure, and apex sealing force during bag-valve-mask ventilation (F = 9.676, p < 0.001). C length moderated the effect of the apex sealing force and peak pressure on the tidal volume, meaning the higher the peak pressure and apex sealing force, the more the tidal volume and the longer the C length.

Conclusion

This first simulation study measuring the 4-point sealing forces during bag-valve-mask ventilation provides effective advice that can be adopted in clinical practice without side effects and underpins the importance of continuous retraining and assessment focused on individual physical characteristics, such as C length and bag-valve-mask sealing forces.
Sampling strategies to evaluate the prognostic value of a new biomarker on a time-to-event end-point
Authors: Graziano Francesca , Valsecchi Maria Grazia , Rebora Paola
Published: May 2021

Background

The availability of large epidemiological or clinical data storing biological samples allow to study the prognostic value of novel biomarkers, but efficient designs are needed to select a subsample on which to measure them, for parsimony and economical reasons. Two-phase stratified sampling is a flexible approach to perform such sub-sampling, but literature on stratification variables to be used in the sampling and power evaluation is lacking especially for survival data.

Methods

We compared the performance of different sampling designs to assess the prognostic value of a new biomarker on a time-to-event endpoint, applying a Cox model weighted by the inverse of the empirical inclusion probability.

Results

Our simulation results suggest that case-control stratified (or post stratified) by a surrogate variable of the marker can yield higher performances than simple random, probability proportional to size, and case-control sampling. In the presence of high censoring rate, results showed an advantage of nested case-control and counter-matching designs in term of design effect, although the use of a fixed ratio between cases and controls might be disadvantageous. On real data on childhood acute lymphoblastic leukemia, we found that optimal sampling using pilot data is greatly efficient.

Conclusions

Our study suggests that, in our sample, case-control stratified by surrogate and nested case-control yield estimates and power comparable to estimates obtained in the full cohort while strongly decreasing the number of patients required. We recommend to plan the sample size and using sampling designs for exploration of novel biomarker in clinical cohort data.
Intra-database validation of case-identifying algorithms using reconstituted electronic health records from healthcare claims data
Authors: Thurin Nicolas H. , Bosco-Levy Pauline , Blin Patrick , Rouyer Magali , Jové Jérémy , Lamarque Stéphanie , Lignot Séverine , Lassalle Régis , Abouelfath Abdelilah , Bignon Emmanuelle , Diez Pauline , Gross-Goupil Marine , Soulié Michel , Roumiguié Mathieu , Le Moulec Sylvestre , Debouverie Marc , Brochet Bruno , Guillemin Francis , Louapre Céline , Maillart Elisabeth , Heinzlef Olivier , Moore Nicholas , Droz-Perroteau Cécile
Published: May 2021

Background

Diagnosis performances of case-identifying algorithms developed in healthcare database are usually assessed by comparing identified cases with an external data source. When this is not feasible, intra-database validation can present an appropriate alternative.

Objectives

To illustrate through two practical examples how to perform intra-database validations of case-identifying algorithms using reconstituted Electronic Health Records (rEHRs).

Methods

Patients with 1) multiple sclerosis (MS) relapses and 2) metastatic castration-resistant prostate cancer (mCRPC) were identified in the French nationwide healthcare database (SNDS) using two case-identifying algorithms. A validation study was then conducted to estimate diagnostic performances of these algorithms through the calculation of their positive predictive value (PPV) and negative predictive value (NPV). To that end, anonymized rEHRs were generated based on the overall information captured in the SNDS over time (e.g. procedure, hospital stays, drug dispensing, medical visits) for a random selection of patients identified as cases or non-cases according to the predefined algorithms. For each disease, an independent validation committee reviewed the rEHRs of 100 cases and 100 non-cases in order to adjudicate on the status of the selected patients (true case/ true non-case), blinded with respect to the result of the corresponding algorithm.

Results

Algorithm for relapses identification in MS showed a 95% PPV and 100% NPV. Algorithm for mCRPC identification showed a 97% PPV and 99% NPV.

Conclusion

The use of rEHRs to conduct an intra-database validation appears to be a valuable tool to estimate the performances of a case-identifying algorithm and assess its validity, in the absence of alternative.
Effects of an interprofessional Quality Circle-Deprescribing Module (QC-DeMo) in Swiss nursing homes: a randomised controlled trial
Authors: Cateau Damien , Ballabeni Pierluigi , Niquille Anne
Published: May 2021

Background

Potentially inappropriate medications (PIMs) are common among nursing homes (NH) residents, as is polypharmacy. Deprescribing has emerged in the past decade as a safe and effective way to reduce the use of PIMs and improve patient outcomes. However, effective deprescribing interventions are expensive, as they require specialised staff and a great amount of time for each resident.

The Quality Circle Deprescribing Module (QC-DeMo) intervention was designed to be less resource-intensive than medication reviews, the current deprescribing gold standard. It consists of a QC session in which physicians, nurses, and pharmacists define a local deprescribing consensus for specific PIMs classes, which is then implemented in the NH. The intervention was trialled in a RCT, with the NH as unit of analysis.

Methods

After randomisation, intervention NHs enacted the QC-DeMo at the start of the follow-up year. The primary outcomes were the proportion of PIM galenic units and number of PIM defined daily dose per average resident and per day (DDD/res). PIM status was assessed by a combination of the 2015 Beers list and the Norwegian General Practice-Nursing Home criteria. Secondary outcomes were the number of DDD/res to avoid and to reevaluate; safety outcomes were mortality, hospitalisations, falls, and use of physical restraints. Outcomes were evaluated at follow-up using linear regression models, adjusting for the outcome baseline values.

Results

Fifty-eight NHs took part in the trial; no individual residents were recruited. The intervention did not reduce the primary outcomes, but a strong trend towards reduction was seen for the number of PIM DDD/res, which accounts for the doses used. PIM DDD/res to reevaluate were significantly reduced, mostly through a reduction in the use of proton-pump inhibitors. Falls and use of physical restraints were not affected, but a statistical interaction between the mission of the NH (geriatric unit or specialised dementia unit) and the intervention group was seen for mortality and hospitalisations.

Conclusions

The QC-DeMo intervention can reduce the use of some PIM classes, and could usefully complement other deprescribing interventions.

Trial registration

ClinicalTrials.gov (NCT03688542), registered on 26.09.2018, retrospectively registered.
Patterns of home- and community‐based services in older adults with dementia: an analysis of the long‐term care system in Taiwan
Authors: Wang Wen-Fu , Su Yung-Yu , Jhang Kai-Ming , Chen Chun-Min
Published: May 2021

Background

Understanding the specific characteristics of the patients with dementia is essential in developing services required to meet their needs. The purpose of this study was to investigate the patterns of use of home- and community-based services (HCBS) by patients with dementia and the factors influencing the utilisation of these services.

Methods

We analysed a dataset of patients with dementia receiving long-term care at a medical centre. All participating patients were required to complete a structured interview form every 6 months to assess their need for service utilisation. Between 2015 and 2018, a total of 822 patients fulfilled the criteria for dementia, and 737 people had assessment records, of whom 244 had used social services. Robust Poisson regression analyses were performed to estimate HCBS usage and the factors influencing service utilisation.

Results

The overall service utilisation rate was 33 %. Most patients used only one service, and assistive devices were used as the main service. Regarding the factors influencing service use, dementia concomitant with dependency increased the use of HCBS. These results suggest that patients with mild dependency might prefer to use community support services, whereas those with moderate to severe dependency being more likely to utilise in-home care services.

Conclusions

This study provides empirical evidence regarding the use of long-term care resources by patients with dementia in the community. Providing customised HCBS, rather than a non-specialised service assumed to be suitable for every patient, is essential for ensuring good patient care. In addition, attention needs to be paid to patients with care needs who do not use HCBS.
Carnobacterium inhibens isolated in blood culture of an immunocompromised, metastatic cancer patient: a case report and literature review
Authors: Lo Carson Ka-Lok , Sheth Prameet M.
Published: May 2021

Background

Carnobacterium species are lactic acid-producing Gram-positive bacteria that have been approved by the US Food and Drug Administration and Health Canada for use as a food bio-preservative. The use of live bacteria as a food additive and its potential risk of infections in immunocompromised patients are not well understood.

Case presentation

An 81-year-old male with a history of metastatic prostate cancer on androgen deprivation therapy and chronic steroids presented to our hospital with a 2-week history of productive cough, dyspnea, altered mentation, and fever. Extensive computed tomography imaging revealed multifocal pneumonia without other foci of infection. He was diagnosed with pneumonia and empirically treated with ceftriaxone and vancomycin. Blood cultures from admission later returned positive for Carnobacterium inhibens. He achieved clinical recovery with step-down to oral amoxicillin/clavulanic acid for a total 7-day course of antibiotics.

Conclusions

This is the fourth reported case of bacteremia with Carnobacterium spp. isolated from humans. This case highlights the need to better understand the pathogenicity and disease spectrum of bacteria used in the food industry for bio-preservation, especially in immunocompromised patients.
A 17 year experience of attrition from care among HIV infected children in Nnewi South-East Nigeria
Authors: Onubogu Chinyere Ukamaka , Ugochukwu Ebelechuku Francesca
Published: May 2021

Background

A large number of HIV-infected children continue to die despite reported scale-up of paediatric HIV services.

Aim

The trend in attrition among children enrolled in an anti-retroviral therapy (ART) programme was evaluated.

Methods

This was a retrospective review of children enrolled into NAUTH ART programme between 2003 and 2019.

Results

1114 children < 15 years at enrolment were studied. The male: female ratio was 1:1 while median age at enrolment was 4.3 years. About two-thirds had WHO stage 3 or 4 disease at enrolment. The rate of loss to follow-up (LTFU) and death were 41.0 and 8.4%, respectively, with overall attrition incidence of 108/1000PY. Despite the downward trend, spikes occurred among those enrolled in 2008 to 2011 and in 2017. The trend in 6-, 12-, 24- and 36-months attrition varied similarly with overall rates being 20.4, 27.7, 34.3 and 37.3%, respectively. Among those on ART, > 50% of attrition was recorded within 6 months of care. Advanced WHO stage, young age, non-initiation on ART or period of enrolment (P <  0.001), and caregiver (p = 0.026) were associated with attrition in bivariate analysis. Apart from caregiver category, these factors remained significant in multivariate analysis. Most LTFU could not be reached on phone. Among those contacted, common reasons for being lost to follow-up were financial constraints, caregiver loss, claim to divine healing, family disharmony/child custody issues and relocation of family/child.

Conclusion/recommendation

Attrition rate was high and was mostly due to LTFU. Predictors of attrition were late presentation, young age, delay in ART initiation and financial constraints. Efforts should be intensified at early diagnosis, linkage to care and implementation of “test and treat” strategy. Innovative child centered approaches should be adopted to enable the HIV-infected children remain in care despite challenges which can truncate treatment.
Analysis of enterovirus genotypes in the cerebrospinal fluid of children associated with aseptic meningitis in Liaocheng, China, from 2018 to 2019
Authors: Wang Jing , Meng Min , Xu Huan , Wang Ting , Liu Ying , Yan Han , Liu Peiman , Qin Daogang , Yang Qiaozhi
Published: May 2021

Background

Aseptic meningitis is most often caused by enteroviruses (EVs), but EVs associated with aseptic meningitis have not yet been reported in Liaocheng. The aim of this study was to determine the prevalence and genetic characteristics of EVs causing aseptic meningitis in children in Liaocheng.

Methods

We reviewed the epidemiological and clinical characteristics of 504 paediatric cases of aseptic meningitis in Liaocheng from 2018 to 2019 and analysed the phylogeny of the predominant EV types causing this disease.

Results

A total of 107 children were positive for EV in cerebrospinal fluid samples by nested PCR. Most of the positive patients were children 13 years old or younger and had symptoms such as fever, headache and vomiting (P < 0.05). The seasons with the highest prevalence of EV-positive cases were summer and autumn. The 107 EV sequences belonged to 8 serotypes, and echovirus types 18, 6 and 11 were the three dominant serotypes in Liaocheng during the 2-year study period. Phylogenetic analyses demonstrated that the E18 and E6 isolates belonged to subgenotype C2, while the E11 isolates belonged to subgenotype D5. VP1 analysis suggested that only one lineage of these three types was cocirculating in the Liaocheng region.

Conclusions

This study demonstrated the diverse EV genotypes contributing to a large outbreak of aseptic meningitis in Liaocheng. Therefore, large-scale surveillance is required to assess the epidemiology of EVs associated with aseptic meningitis and is important for the diagnosis and treatment of aseptic meningitis in Liaocheng.
The association between extreme temperature and pulmonary tuberculosis in Shandong Province, China, 2005–2016: a mixed method evaluation
Authors: Chen Dongzhen , Lu Hua , Zhang Shengyang , Yin Jia , Liu Xuena , Zhang Yixin , Dai Bingqin , Li Xiaomei , Ding Guoyong
Published: May 2021

Background

The effects of extreme temperature on infectious diseases are complex and far-reaching. There are few studies to access the relationship of pulmonary tuberculosis (PTB) with extreme temperature. The study aimed to identify whether there was association between extreme temperature and the reported morbidity of PTB in Shandong Province, China, from 2005 to 2016.

Methods

A generalized additive model (GAM) was firstly conducted to evaluate the relationship between daily reported incidence rate of PTB and extreme temperature events in the prefecture-level cities. Then, the effect estimates were pooled using meta-analysis at the provincial level. The fixed-effect model or random-effect model was selected based on the result of heterogeneity test.

Results

Among the 446,016 PTB reported cases, the majority of reported cases occurred in spring. The higher reported incidence rate areas were located in Liaocheng, Taian, Linyi and Heze. Extreme low temperature had an impact on the reported incidence of PTB in only one prefecture-level city, i.e., Binzhou (RR = 0.903, 95% CI: 0.817–0.999). While, extreme high temperature was found to have a positive effect on reported morbidity of PTB in Binzhou (RR = 0.924, 95% CI: 0.856–0.997) and Weihai (RR = 0.910, 95% CI: 0.843–0.982). Meta-analysis showed that extreme high temperature was associated with a decreased risk of PTB (RR = 0.982, 95% CI: 0.966–0.998). However, extreme low temperature was no relationship with the reported incidence of PTB.

Conclusion

Our findings are suggested that extreme high temperature has significantly decreased the risk of PTB at the provincial levels. The findings have implications for developing strategies to response to climate change.
The effects of L-carnitine on renal function and gene expression of caspase-9 and Bcl-2 in monosodium glutamate‐induced rats
Authors: Koohpeyma Farhad , Siri Morvarid , Allahyari Shaghayegh , Mahmoodi Marzieh , Saki Forough , Dastghaib Sanaz
Published: May 2021

Background

Monosodium glutamate (MSG) is frequently consumed as a flavor enhancer or food additive. Possible damages induced by MSG effects on some organs have been stated in experimental animal models. The aim of the present study was to evaluate the protective effects of L-carnitine (L-ca) on the renal tissue in MSG-Induced Rats.

Methods

In this regard, 60 male rats were randomly divided into six groups (n = 10/each): 1 (Control); 2 (sham); 3 (L-carnitine 200 mg/kg b.w); 4 (MSG 3 g/kg b.w); 5 (MSG + L-carnitine 100 mg/kg); and 6 (MSG + L-carnitine 200 mg/kg). After 6 months, the rats were sacrificed, the blood sample collected and the kidneys harvested for evaluation of biochemical analytes, genes expression, and histopathological changes.

Results

MSG significantly increased the serum level of MDA, BUN, creatinine, uric acid and renal Caspase-9, NGAL and KIM-1 expression, but it decreased the serum activity also renal expression of SOD, catalase, GPX, and Bcl-2 expression compared to the control group. Treatment with L-ca significantly reduced the serum BUN, creatinine, uric acid and MDA level and increased catalase, GPX and SOD compared to the MSG group. However, only administration of L-ca 200 significantly decreased the caspase-9, NGAL and KIM-1; also, it increased the Bcl-2 expression in the kidney compared to the MSG group.

Conclusions

Our findings indicated that L-carnitine had a major impact on the cell protection and might be an effective therapy in ameliorating the complications of the kidney induced by MSG via its antioxidant and anti-apoptotic properties.
Prednisolone treatment in acute interstitial nephritis (PRAISE) – protocol for the randomized controlled trial
Authors: Mose Frank H. , Birn Henrik , Hoffmann-Petersen Nikolai , Bech Jesper N.
Published: May 2021

Background

Acute interstitial nephritis (AIN) is an important and common cause of acute renal failure. There are no generally accepted guidelines for the treatment of AIN, due to the lack of prospective randomized trials. Since AIN is characterized by an enhanced immune response, immunosuppressive treatment could potentially improve prognosis by attenuating inflammation and subsequent fibrosis. Despite the limited evidence of effects of steroids and potential adverse effects, prednisolone is frequently used in the treatment of AIN and there is a strong need for clinical trials on the effects of immunosuppression, including steroids, in the treatment of AIN. We aimed to evaluate the effectiveness of prednisolone treatment in AIN, and hypothesized a positive effect of prednisolone treatment on renal function in AIN.

Methods

The study is a randomized, controlled, prospective, open label multicenter study, including incident adult patients with biopsy proven AIN. Patients will be randomized 1:1 to one of 2 treatment regimens:

No prednisolone treatment (control group) and

B) Oral prednisolone treatment staring with 60 mg daily tapered over 8 weeks.

One hundred ten patients (55 in each group) are planned to be included and followed for 1 year. Primary outcome is renal function estimated by eGFR 3 months after inclusion. Secondary outcomes are renal function after 12 months and need for renal replacement therapy and quality of life after 3 and 12 months. In addition, with-in prednisolone group analysis are performed to estimate the importance of treatment delay. Exploratory analyses include analysis of biomarkers in urine and plasma and the evaluation of these biomarkers in relation to renal prognosis and re-evaluation of renal biopsies to identify possible renal prognostic factors.

Discussion

Strengths and possible limitations in the design are evaluated. The study will provide important information on the effects of prednisolone treatment in AIN and as well as prognostic information relevant for future use of biomarkers and histology. Ultimately, this would lead to improved and evidence based clinical guidelines for the treatment of AIN.

Trial registration

ClinicalTrials.gov identifier NCT04376216 (Retrospectively registered on May 6, 2020).
Morvan syndrome associated with LGI1 antibody: a case report
Authors: Zhang Shui-Jing , Xue Yan-Yan , Yu Hao , Tao Qing-Qing
Published: May 2021

Background

Morvan syndrome (MoS) is a rare autoimmune syndrome associated with antibodies against two kinds of potassium channel proteins, contactin associated protein-like 2 (CASPR2) and leucine-rich glioma inactivated protein 1 (LGI1). MoS patients with only LGI1-antibody seropositivity have rarely been reported. Here, we describe a 64-year-old male MoS patient with only LGI1-antibody seropositivity.

Case presentation

A 64-year-old male patient was referred to our hospital due to limb pain, widespread myokymia, insomnia, constipation, and hyperhidrosis for 1 month. The patient was diagnosed with MoS based on the clinical symptoms and positive LGI1-antibody in serum. He was treated with intravenous immunoglobulin (IVIG), intravenous methylprednisolone followed by oral prednisone, and other drugs for symptomatic relief. Several days later, myokymia and insomnia symptoms improved. After 60 days of follow-up, all the drugs had been stopped for 2 weeks, and the patient achieved complete remission without any medical side effects.

Conclusion

We report the clinical characteristics of a Chinese MoS patient with only LGI1-antibody seropositivity, and further support the view that non-neoplasm MoS patients respond well to immunotherapy.
Preventable multiple high-risk birth behaviour and infant survival in Nigeria
Authors: Salawu Mobolaji Modinat , Afolabi Rotimi Felix , Gbadebo Babatunde Makinde , Salawu Adetokunbo Taophic , Fagbamigbe Adeniyi Francis , Adebowale Ayo Stephen
Published: May 2021

Background

Globally, infant mortality has declined considerably but has remained unacceptably high in sub-Saharan Africa, especially Nigeria where infant mortality rate is 67/1000 live births. To facilitate infant mortality reduction in Nigeria, an understanding of the synergistic effect of bio-demographic characteristics of mothers known as High Risk Birth Behaviours (HrBBs) is important. We therefore investigated the influence of HrBBs on infant survival in Nigeria.

Methods

This cross-sectional study design utilized data from the 2018 round of Nigerian Demographic Health Survey. The study participants were a representative sample of women of reproductive age (n = 21,350) who had given birth within the 5 years preceding the survey. HrBBs was measured through integration of information on maternal age at child’s birth, parity, and preceding birth interval with respect to the most recent child. The HrBBs was categorized as none, single and multiple. Data were analysed using descriptive statistics, Log-rank test and Cox proportional hazard model (α =0.05).

Results

The mean age of the women was 29.7 ± 7.2 and 4.1% had experienced infant death. Infant mortality was highest among women with multiple HrBBs (5.1%). Being a male, having small size at birth, failure to receive tetanus injection, non-use of contraceptives and living in the core-north (North West and North East) predisposed children to higher risk of dying before 12 months of age. The hazard ratio of infant mortality was significantly higher among infants of mothers in multiple HrBBs category (aHR = 1.66; CI: 1.33–2.06) compared to their counterparts with no HrBBs.

Conclusion

Multiple HrBBs increase the chances of dying among infants in Nigeria. Screening women for HrBBs for special health attention during pregnancy, birth and postnatal period will alleviate infant death in Nigeria.
Youth-centered maternity care: a binational qualitative comparison of the experiences and perspectives of Latina adolescents and healthcare providers
Authors: Decker Martha J. , Pineda Noelle , Gutmann-Gonzalez Abigail , Brindis Claire D.
Published: May 2021

Background

Although there is growing recognition of the importance of person-centered maternity care, the needs and perspectives of pregnant adolescents are rarely considered. The purpose of this study was to compare the maternity care experiences of Mexican-origin adolescents in Guanajuato, Mexico and Fresno, California from both youth and healthcare provider perspectives.

Methods

Qualitative interviews and focus groups were conducted with a total of 89 respondents, including 74 pregnant and parenting adolescents as well as 15 providers between December 2016 and July 2017. Adolescents also completed a short demographic survey prior to participation. Transcripts in English and Spanish were coded and thematically analyzed using Dedoose software. Results were compared by location and between youth and providers.

Results

Four themes emerged regarding patient-provider interactions: the need for communication and clear explanations, respectful versus judgmental providers, engaging youth in decision-making, and a focus on the age of the youth and their partners. While youth had similar perspectives and priorities in both locations, youth in Mexico reported more negative healthcare experiences than youth in California. Perspectives varied between the youth and providers, with providers in both California and Mexico identifying several structural challenges in providing quality care to adolescents. In California, challenges to supporting immigrant Latina adolescents and their families included language and translation issues as well as barriers to care due to immigration status and documentation. In both locations, providers also mentioned high patient caseloads and their own concerns about the youth’s life choices.

Conclusion

Youth-centered care requires more effective and respectful patient-provider communication, where adolescents are engaged in their healthcare decision-making and delivery options. Changes in patient-provider interactions can help improve the maternity care experiences and outcomes of Latina adolescents. Healthcare systems and providers need to reconfigure their approaches to focus on the needs and priorities of adolescents.
Increased risk of breast cancer-specific mortality among cancer survivors who developed breast cancer as a second malignancy
Authors: Wang Chengshi , Hu Kejia , Deng Lei , He Wei , Fang Fang , Tamimi Rulla M. , Lu Donghao
Published: May 2021

Background

Cancer survivors who develop breast cancer as a second malignancy (BCa-2) are common. Yet, little is known about the prognosis of BCa-2 compared to first primary breast cancer (BCa-1).

Methods

Using the Surveillance, Epidemiology, and End Results database, we conducted a population-based cohort study including 883,881 patients with BCa-1 and 36,313 patients with BCa-2 during 1990–2015. Compared with patients with BCa-1, we calculated hazard ratios (HRs) of breast cancer-specific mortality among patients with BCa-2, using multivariable Cox regression.

Results

During the follow-up (median 5.5 years), 114,964 and 3829 breast cancer-specific deaths were identified among BCa-1 and BCa-2 patients, respectively. Patients with BCa-2 had more favorable tumor characteristics and received less intensive treatment e.g., surgery and chemo−/radio-therapy, compared to patients with BCa-1. When adjusting for demographic factors, patients with BCa-2 were at similar risk of breast cancer-specific mortality (HR 1.00, 95% CI 0.97–1.03) compared to patients with BCa-1. However, when additionally controlling for tumor characteristics and treatment modes, BCa-2 patients were at an increased risk of breast cancer-specific mortality (HR 1.11, 95% CI 1.08–1.15). The risk elevation was particularly greater when the first malignancy was lung, bladder, ovarian or blood malignancy (HRs 1.16–1.85), or when the first malignancy was treated with chemotherapy and radiotherapy (HR 1.44, 95% CI 1.28–1.63).

Conclusions

Overall, patients with BCa-2 have worse breast cancer-specific survival, compared with their BCa-1 counterparts, although the risk elevation is mild. High-risk subgroups based on first malignancy’s characteristics may be considered for active clinical management.
Normal and cancer fibroblasts differentially regulate TWIST1, TOX and cytokine gene expression in cutaneous T-cell lymphoma
Authors: Mehdi Syed Jafar , Moerman-Herzog Andrea , Wong Henry K.
Published: May 2021

Background

Mycosis fungoides (MF) is a primary cutaneous T-cell lymphoma (CTCL) that transforms from mature, skin-homing T cells and progresses during the early stages in the skin. The role of the skin microenvironment in MF development is unclear, but recent findings in a variety of cancers have highlighted the role of stromal fibroblasts in promoting or inhibiting tumorigenesis. Stromal fibroblasts are an important part of the cutaneous tumor microenvironment (TME) in MF. Here we describe studies into the interaction of TME-fibroblasts and malignant T cells to gain insight into their role in CTCL.

Methods

Skin from normal (n = 3) and MF patients (n = 3) were analyzed for FAPα by immunohistochemistry. MyLa is a CTCL cell line that retains expression of biomarkers TWIST1 and TOX that are frequently detected in CTCL patients. MyLa cells were cultured in the presence or absence of normal or MF skin derived fibroblasts for 5 days, trypsinized to detached MyL

a cells, and gene expression analyzed by RT-PCR for MF biomarkers (TWIST1 and TOX), Th1 markers (IFNG, TBX21), Th2 markers (GATA3, IL16), and proliferation marker (MKI67). Purified fibroblasts were assayed for VIM and ACTA2 gene expression. Cellular senescence assay was performed to assess senescence.

Results

MF skin fibroblast showed increased expression of FAP-α with increasing stage compared to normal. Normal fibroblasts co-cultured with MyLa cells suppressed expression of TWIST1 (p < 0.0006), and TOX (p < 0.03), GATA3 (p < 0.02) and IL16 (p < 0.03), and increased expression of IFNG (p < 0.03) and TBX21 (p < 0.03) in MyLa cells. In contrast, MyLa cells cultured with MF fibroblasts retained high expression of TWIST1, TOX and GATA3. MF fibroblasts co-culture with MyLa cells increased expression of IL16 (p < 0.01) and IL4 (p < 0.02), and suppressed IFNG and TBX21 in MyLa cells. Furthermore, expression of MKI67 in MyLa cells was suppressed by normal fibroblasts compared to MF fibroblasts.

Conclusion

Skin fibroblasts represent important components of the TME in MF. In co-culture model, normal and MF fibroblasts have differential influence on T-cell phenotype in modulating expression of Th1 cytokine and CTCL biomarker genes to reveal distinct roles with implications in MF progression.