bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics
Authors: Kim Si-Hyeon , Kwon Yong-Kuk , Park Choi-Kyu , Kim Hye-Ryoung 
Published: November 2021

Abstract
Background
In July 2015, the carcasses of 11 cockatiels were submitted for disease diagnosis to the Avian Disease Division of the Animal and Plant Quarantine Agency of Korea. The cockatiels, which appeared dehydrated and underweight, had exhibited severe diarrhea and 22 % mortality over 2 weeks. Traditional diagnosis did not reveal the causes of these symptoms.

Methods
We conducted metagenomics analysis on intestines and livers from the dead cockatiels using Illumina high-throughput sequencing. To obtain more accurate and longer contigs, which are required for further genetic characterization, we compared the results of three de novo assembly tools (metaSPAdes, MEGAHIT, and IDBA-UD).

Results
Sequence reads of Campylobacter jejuni (C. jejuni) and Chlamydia psittaci (C. psittaci) were present in most of the cockatiel samples. Either of these bacteria could cause the reported symptoms in psittaciformes. metaSPAdes (ver.3.14.1) identified the 1152 bp flaA gene of C. jejuni and the 1096 bp ompA gene of C. psittaci. Genetic analysis revealed that flaA of C. jejuni was recombinant between C. jejuni and Campylobacter coli, and that ompA of C. psittaci isolated from cockatiel was closely related to strains isolated from humans.

Conclusions
C. jejuni and C. psittaci were detected in cockatiels in the Republic of Korea using metagenomic analysis. This approach is useful for understanding pathogens of pet birds. Three de novo assemblers were compared to obtain accurate contigs from large quantities of reads, and sequences of C. jejuni and C. psittaci generated by metaSPAdes were analyzed.
Osteopontin and malaria: no direct effect on parasite growth, but correlation with P. falciparum-specific B cells and BAFF in a malaria endemic area
Authors: Mortazavi Susanne E , Lugaajju Allan , Kaddumukasa Mark , Tijani Muyideen Kolapo , Kironde Fred , Persson Kristina E M 
Published: November 2021

Abstract
Background
The dysregulation of B cell activation is prevalent during naturally acquired immunity against malaria. Osteopontin (OPN), a protein produced by various cells including B cells, is a phosphorylated glycoprotein that participates in immune regulation and has been suggested to be involved in the immune response against malaria. Here we studied the longitudinal concentrations of OPN in infants and their mothers living in Uganda, and how OPN concentrations correlated with B cell subsets specific for P. falciparum and B cell activating factor (BAFF). We also investigated the direct effect of OPN on P. falciparum in vitro.

Results
The OPN concentration was higher in the infants compared to the mothers, and OPN concentration in infants decreased from birth until 9 months. OPN concentration in infants during 9 months were independent of OPN concentrations in corresponding mothers. OPN concentrations in infants were inversely correlated with total atypical memory B cells (MBCs) as well as P. falciparum-specific atypical MBCs. There was a positive correlation between OPN and BAFF concentrations in both mothers and infants. When OPN was added to P. falciparum cultured in vitro, parasitemia was unaffected regardless of OPN concentration.

Conclusions
The concentrations of OPN in infants were higher and independent of the OPN concentrations in corresponding mothers. In vitro, OPN does not have a direct effect on P. falciparum growth. Our correlation analysis results suggest that OPN could have a role in the B cell immune response and acquisition of natural immunity against malaria.
Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)
Authors: Graper Allison L. , Noyszewski Andrzej K. , Anderson Neil O. , Smith Alan G. 
Published: November 2021

Abstract
Background
Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882–2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species.

Results
We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin.

Conclusions
While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.
Data mining: traditional spring festival associated with hypercholesterolemia
Authors: Wang Danchen , Zou Yutong , Li Honglei , Yu Songlin , Xia Liangyu , Cheng Xinqi , Qiu Ling , Xu Tengda 
Published: November 2021

Abstract
Background
Serum lipid concentrations are affected by long-term high-fat diets; thus, we hypothesize that lipid levels increase after the Spring Festival in China.

Method
In total, 20,192 individuals (male: n=10,108, female: n=10,084) were enrolled in this retrospective cross-sectional study based on clinical data from the Laboratory Information System (LIS) and Hospital Information System (HIS) in Peking Union Medical College Hospital from 2014 to 2018. Total cholesterol (TC), triglycerides (TGs), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were analyzed.

Results
The serum TC [male vs. female: (4.71 ± 0.90 vs. 4.56 ± 0.85) mmol/L], TG [male vs. female: (1.71 ± 1.56 vs. 1.02 ± 0.68) mmol/L], and LDL-C [male vs. female: (3.01 ± 0.77 vs. 2.73 ± 0.74) mmol/L] levels were significantly higher in males than in females (P < 0.001); serum HDL-C [male vs. female: (1.18 ± 0.28 vs. 1.50 ± 0.34) mmol/L] was significantly lower in males (P < 0.001). In February, the TC, TG, and LDL-C levels were 8.4%, 16.3%, and 9.3% higher than the lowest levels recorded, respectively. The prevalence of dyslipidemia of the two weeks before the Spring festival was significantly lower than that of the first week after the Spring festival (43.6% (168/385) vs. 54.1% (126/233), P=0.007). Additionally, the prevalence of dyslipidemia was statistically higher in the first week after the Spring Festival than in May–January.

Conclusion
Higher TC, TG, and LDL-C in winter could be associated with high-fat diets during the Spring Festival. The Spring Festival was immediately followed by a higher lipid concentrations. Thus, we don't recommend lipid assessment or physical examination immediately after the holiday especially Spring festival.
Association between prehospital arterial hypercapnia and mortality in acute heart failure: a retrospective cohort study
Authors: Fabre Mathias , Fehlmann Christophe A. , Boczar Kevin E. , Gartner Birgit , Zimmermann-Ivol Catherine G. , Sarasin François , Suppan Laurent 
Published: November 2021

Abstract
Background
Acute Heart Failure (AHF) is a potentially lethal pathology and is often encountered in the prehospital setting. Although an association between prehospital arterial hypercapnia in AHF patients and admission in high-dependency and intensive care units has been previously described, there is little data to support an association between prehospital arterial hypercapnia and mortality in this population.

Methods
This was a retrospective study based on electronically recorded prehospital medical files. All adult patients with AHF were included. Records lacking arterial blood gas data were excluded. Other exclusion criteria included the presence of a potentially confounding diagnosis, prehospital cardiac arrest, and inter-hospital transfers. Hypercapnia was defined as a PaCO2 higher than 6.0 kPa. The primary outcome was in-hospital mortality, and secondary outcomes were 7-day mortality and emergency room length of stay (ER LOS). Univariable and multivariable logistic regression models were used.

Results
We included 225 patients in the analysis. Prehospital hypercapnia was found in 132 (58.7%) patients. In-hospital mortality was higher in patients with hypercapnia (17.4% [23/132] versus 6.5% [6/93], p = 0.016), with a crude odds-ratio of 3.06 (95%CI 1.19–7.85). After adjustment for pre-specified covariates, the adjusted OR was 3.18 (95%CI 1.22–8.26). The overall 7-day mortality was also higher in hypercapnic patients (13.6% versus 5.5%, p = 0.044), and ER LOS was shorter in this population (5.6 h versus 7.1 h, p = 0.018).

Conclusion
Prehospital hypercapnia is associated with an increase in in-hospital and 7-day mortality in patient with AHF.
Comparison of QSOFA and sirs scores for the prediction of adverse outcomes of secondary peritonitis among patients admitted on the adult surgical ward in a tertiary teaching hospital in Uganda: a prospective cohort study
Authors: Nkonge Emmanuel , Kituuka Olivia , Ocen William , Ariaka Herbert , Ogwal Alfred , Ssekitoleko Badru 
Published: November 2021

Abstract
Background
SIRS and qSOFA are two ancillary scoring tools that have been used globally, inside and outside of ICU to predict adverse outcomes of infections such as secondary peritonitis. A tertiary teaching hospital in Uganda uses SIRS outside the ICU to identify patients with secondary peritonitis, who are at risk of adverse outcomes. However, there are associated delays in decision making given SIRS partial reliance on laboratory parameters which are often not quickly available in a resource limited emergency setting. In response to the practical limitations of SIRS, the sepsis-3 task force recommends qSOFA as a better tool. However, its performance in patients with secondary peritonitis in comparison to that of SIRS has not been evaluated in a resource limited setting of a tertiary teaching hospital in a low and middle income country like Uganda.

Objective
To compare the performance of qSOFA and SIRS scores in predicting adverse outcomes of secondary peritonitis among patients on the adult surgical wards in a tertiary teaching hospital in Uganda.

Methods
This was a prospective cohort study of patients with clinically confirmed secondary peritonitis, from March 2018 to January 2019 at the Accident and Emergency unit and the adult surgical wards of a tertiary teaching hospital in Uganda. QSOFA and SIRS scores were generated for each patient, with a score of ≥2 recorded as high risk, while a score of < 2 recorded as low risk for the adverse outcome respectively. After surgery, patients were followed up until discharge or death. In-hospital mortality and prolonged hospital stay were the primary and secondary adverse outcomes, respectively. Sensitivity, specificity, PPV, NPV and accuracy at 95% confidence interval were calculated for each of the scores using STATA v.13.

Results
A total of 153 patients were enrolled. Of these, 151(M: F, 2.4:1) completed follow up and were analysed, 2 were excluded. Mortality rate was 11.9%. Fourty (26.5%) patients had a prolonged hospital stay. QSOFA predicted in-hospital mortality with AUROC of 0.52 versus 0.62, for SIRS. Similarly, qSOFA predicted prolonged hospital stay with AUROC of 0.54 versus 0.57, for SIRS.

Conclusion
SIRS is superior to qSOFA in predicting both mortality and prolonged hospital stay among patients with secondary peritonitis. However, overall, both scores showed a poor discrimination for both adverse outcomes and therefore not ideal tools.
The impact of chest pain center on treatment delay of STEMI patients: a time series study
Authors: Sun Xiaolin , Yao Bo , Shi Kexin , Xue Yajiong , Liang Huigang 
Published: November 2021

Abstract
Objective
To study the effect of the establishment of a Chest Pain Center (CPC) on the treatment delay of ST-elevation myocardial infarction (STEMI) patients and the influencing factors of treatment delay in a large hospital in China.

Methods
The study subjects are 318 STEMI patients admitted between August 2016 and July 2019 to a large general hospital in Henan, China. Data were extracted from the electronic medical records after removing personal identifiable information. The interrupted time series regression was used to analyze the treatment delay of patients before and after the CPC establishment.

Results
After the CPC establishment, the patients’ pre-hospital and in-hospital treatment delays were significantly reduced. SO-to-FMC (Symptom Onset to First Medical Contact time) decreased by 49.237 min and D-to-B (Door to Balloon time) decreased by 21.931 min immediately after the CPC establishment. In addition, SO-to-FMC delay is significantly correlated with age, occupation, nocturnal onset, and the way to hospital. D-to-B delay is significantly associated with time from initial diagnosis to informed consent of percutaneous coronary intervention (PCI), catheterization lab activation time, and time for PCI informed consent.

Conclusion
The CPC significantly reduced the treatment delay of STEMI patients undergoing PCI.
Reporting of methods to prepare, pilot and perform data extraction in systematic reviews: analysis of a sample of 152 Cochrane and non-Cochrane reviews
Authors: Büchter Roland Brian , Weise Alina , Pieper Dawid 
Published: November 2021

Abstract
Background
Previous research on data extraction methods in systematic reviews has focused on single aspects of the process. We aimed to provide a deeper insight into these methods by analysing a current sample of reviews.

Methods
We included systematic reviews of health interventions in humans published in English. We analysed 75 Cochrane reviews from May and June 2020 and a random sample of non-Cochrane reviews published in the same period and retrieved from Medline. We linked reviews with protocols and study registrations. We collected information on preparing, piloting, and performing data extraction and on use of software to assist review conduct (automation tools). Data were extracted by one author, with 20% extracted in duplicate. Data were analysed descriptively.

Results
Of the 152 included reviews, 77 reported use of a standardized extraction form (51%); 42 provided information on the type of form used (28%); 24 on piloting (16%); 58 on what data was collected (38%); 133 on the extraction method (88%); 107 on resolving disagreements (70%); 103 on methods to obtain additional data or information (68%); 52 on procedures to avoid data errors (34%); and 47 on methods to deal with multiple study reports (31%). Items were more frequently reported in Cochrane than non-Cochrane reviews. The data extraction form used was published in 10 reviews (7%). Use of software was rarely reported except for statistical analysis software and use of RevMan and GRADEpro GDT in Cochrane reviews. Covidence was the most frequent automation tool used: 18 reviews used it for study selection (12%) and 9 for data extraction (6%).

Conclusions
Reporting of data extraction methods in systematic reviews is limited, especially in non-Cochrane reviews. This includes core items of data extraction such as methods used to manage disagreements. Few reviews currently use software to assist data extraction and review conduct. Our results can serve as a baseline to assess the uptake of such tools in future analyses.
Major adverse cardiovascular event definitions used in observational analysis of administrative databases: a systematic review
Authors: Bosco Elliott , Hsueh Leon , McConeghy Kevin W. , Gravenstein Stefan , Saade Elie 
Published: November 2021

AbstractBackgroundMajor adverse cardiovascular events (MACE) are increasingly used as composite outcomes in randomized controlled trials (RCTs) and observational studies. However, it is unclear how observational studies most commonly define MACE in the literature when using administrative data.MethodsWe identified peer-reviewed articles published in MEDLINE and EMBASE between January 1, 2010 to October 9, 2020. Studies utilizing administrative data to assess the MACE composite outcome using International Classification of Diseases 9th or 10th Revision diagnosis codes were included. Reviews, abstracts, and studies not providing outcome code definitions were excluded. Data extracted included data source, timeframe, MACE components, code definitions, code positions, and outcome validation.ResultsA total of 920 articles were screened, 412 were retained for full-text review, and 58 were included. Only 8.6% (n = 5/58) matched the traditional three-point MACE RCT definition of acute myocardial infarction (AMI), stroke, or cardiovascular death. None matched four-point (+unstable angina) or five-point MACE (+unstable angina and heart failure). The most common MACE components were: AMI and stroke, 15.5% (n = 9/58); AMI, stroke, and all-cause death, 13.8% (n = 8/58); and AMI, stroke and cardiovascular death 8.6% (n = 5/58). Further, 67% (n = 39/58) did not validate outcomes or cite validation studies. Additionally, 70.7% (n = 41/58) did not report code positions of endpoints, 20.7% (n = 12/58) used the primary position, and 8.6% (n = 5/58) used any position.ConclusionsComponents of MACE endpoints and diagnostic codes used varied widely across observational studies. Variability in the MACE definitions used and information reported across observational studies prohibit the comparison, replication, and aggregation of findings. Studies should transparently report the administrative codes used and code positions, as well as utilize validated outcome definitions when possible.
The prevalence of delirium in Belgian nursing homes: a cross-sectional evaluation
Authors: Sabbe Kelly , van der Mast Roos , Dilles Tinne , Van Rompaey Bart 
Published: November 2021

Abstract
Background
Delirium is a common geriatric syndrome, but only few studies have been done in nursing home residents. Therefore, the aim of this study was to investigate (point) prevalence of and risk factors for delirium in nursing homes in Belgium.

Methods
A multisite, cross-sectional study was conducted in six nursing homes in Belgium.
Residents of six nursing homes were screened for delirium. Exclusion criteria were coma,‘end-of-life’ status and residing in a dementia ward. Delirium was assessed using the Delirium Observation Screening Scale.

Results
338 of the 448 eligible residents were included in this study. Of the 338 residents who were evaluated, 14.2 % (95 %CI:3.94–4.81) screened positive for delirium with the Delirium Observation Screening Scale. The mean age was 84.7 years and 67.5 % were female. Taking antipsychotics (p = 0.009), having dementia (p = 0.005), pneumonia (p = 0.047) or Parkinson’s disease (p = 0.03) were more present in residents with delirium. The residents were more frequently physically restrained (p = 0.001), participated less in activities (p = 0.04), had had more often a fall incident (p = 0.007), had lower levels of cognition (p < 0.001; MoCA ≥ 26, p = 0.04; MoCA ≥ 25, p = 0.008) and a higher “Activities of Daily Living” score (p = 0.001). In multivariable binary logistic regression analysis, a fall incident (2.76; 95 %CI: 1.24–6.14) and cognitive impairment (OR: 0.69; 95 %CI: 0.63–0.77) were significantly associated with delirium.

Conclusions
Delirium is an important clinical problem affecting almost 15 % of the nursing home residents at a given moment. Screening of nursing home residents for risk factors and presence of delirium is important to prevent delirium if possible and to treat underlying causes when present.
Prevention of road crashes in older adults: perspectives on facilitators, barriers and the role of the family doctor
Authors: Rivera-Izquierdo Mario , Valverde-Cano Luz María , Martínez-Ruiz Virginia , Sánchez-Pérez María Rosa , Atienza-Martín Francisco Javier , Martín-delosReyes Luis Miguel , Jiménez-Mejías Eladio 
Published: November 2021

Abstract
Background
People over 64 years have a high fatality rate when they are involved in traffic accidents. Besides, older victims of road crashes are expected to rise in the future due to population aging. The purpose of the study was to document their perception on the role of the family doctor, the main facilitating factors, and the perceived barriers to the temporary or permanent restriction of their driving.

Methods
This qualitative study used focus group methodology. A sample of 16 people over 65 years old was obtained through a series of segmentation criteria at an active participation centre for older adults in a small town in Jaén province (Spain). All were invited to participate in a discussion during which they were asked to express their opinions and subjective experiences concerning the role of their family doctor. The group conversation was taped, fully transcribed and analysed, and codes were generated with both deductive and inductive methods.

Results
After merging the codes to generate themes, we identified 9 relevant categories: perception of age-related risk, road safety, role of public authorities, driver assessment centre, role of the family doctor, role of the family, proposals for addressing traffic accidents in older adults, consequences of the driving prohibition, and public transport. All categories help to explain the subjective driving and traffic safety experiences of older road users.

Conclusions
Although family doctors do not usually ask their older patients about road driving, they are highly valued by these patients. Thus, family doctors have a great potential to act, along with the family members, for the benefit of older patients’ traffic safety, in ways that can prevent their involvement in road crashes and reduce the negative consequences of having to stop driving if necessary.