bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip
Authors: Fan Huanhuan , Wang Tianjiao , Li Yang , Liu Huitao , Dong Yimeng , Zhang Ranran , Wang Hongliang , Shang Liyuan , Xing Xiumei 
Published: September 2021

AbstractBackgroundChina is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required.ResultsIn this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources.ConclusionWe successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources.
Reverse remodeling of tricuspid valve morphology and function in chronic thromboembolic pulmonary hypertension patients following pulmonary thromboendarterectomy: a cardiac magnetic resonance imaging and invasive hemodynamic study
Authors: Frederiksen Christian Alcaraz , Waziri Farhad , Ringgaard Steffen , Mellemkjær Søren , Clemmensen Tor Skibsted , Hjortdal Vibeke Elisabeth , Nielsen Sten Lyager , Poulsen Steen Hvitfeldt 
Published: September 2021

Abstract
Background
To investigate changes in tricuspid annulus (TA) and tricuspid valve (TV) morphology among chronic thromboembolic pulmonary hypertension (CTEPH) patients before and 12 months after pulmonary thromboendarterectomy (PEA) and compare these findings to normal control subjects.

Methods
20 CTEPH patients and 20 controls were enrolled in the study. The patients were examined with echocardiography, right heart catherization and cardiac magnetic resonance imaging prior to PEA and 12 months after.

Results
Right atrium (RA) volume was significantly reduced from baseline to 12 months after PEA (30 ± 9 vs 23 ± 5 ml/m2, p < 0.005). TA annular area in systole remained unchanged (p = 0.11) and was comparable to controls. The leaflet area, tenting volume and tenting height in systole were significantly increased at baseline but decreased significantly with comparable values to controls after 12 months (p < 0.005). There was correlation between the changes of right ventricular-pulmonary artery coupling and changes of TV tenting height (r = − 0.54, p = 0.02), TV tenting volume (r = − 0.73, p < 0.001) and TV leaflet area (− 0.57, p = 0.01) from baseline to 12 months after PEA. Tricuspid regurgitation jet area/RA area was significantly (p < 0.01) reduced from baseline (30 ± 13%) to 12 months after PEA (9 ± 10%).

Conclusion
In CTEPH patients selected for PEA, TV tenting height, volume and valve area are significantly increased whereas annulus size and shape are less affected. The alterations in TV morphology are fully reversed after PEA and correlates to improvements of right ventricular-pulmonary arterial coupling.
Reproducibility and responsiveness of the Frailty Index and Frailty Phenotype in older hospitalized patients
Authors: Feenstra Marlies , Oud Frederike M.M. , Jansen Carolien J. , Smidt Nynke , van Munster Barbara C. , de Rooij Sophia E. 
Published: September 2021

Abstract
Background
There is growing interest for interventions aiming at preventing frailty progression or even to reverse frailty in older people, yet it is still unclear which frailty instrument is most appropriate for measuring change scores over time to determine the effectiveness of interventions. The aim of this prospective cohort study was to determine reproducibility and responsiveness properties of the Frailty Index (FI) and Frailty Phenotype (FP) in acutely hospitalized medical patients aged 70 years and older.

Methods
Reproducibility was assessed by Intra-Class Correlation Coefficients (ICC), standard error of measurement (SEM) and smallest detectable change (SDC); Responsiveness was assessed by the standardized response mean (SRM), and area under the receiver operating characteristic curve (AUC).

Results
At baseline, 243 patients were included with a median age of 76 years (range 70–98). The analytic samples included 192 and 187 patients in the three and twelve months follow-up analyses, respectively. ICC of the FI were 0.85 (95 % confidence interval [CI]: 0.76; 0.91) and 0.84 (95% CI: 0.77; 0.90), and 0.65 (95% CI: 0.49; 0.77) and 0.77 (95% CI: 0.65; 0.84) for the FP. SEM ranged from 5 to 13 %; SDC from 13 to 37 %. SRMs were good in patients with unchanged frailty status (< 0.50), and doubtful to good for deteriorated and improved patients (0.43–1.00). AUC’s over three months were 0.77 (95% CI: 0.69; 0.86) and 0.71 (95% CI: 0.62; 0.79) for the FI, and 0.68 (95% CI: 0.58; 0.77) and 0.65 (95% CI: 0.55; 0.74) for the FP. Over twelve months, AUCs were 0.78 (95% CI: 0.69; 0.87) and 0.82 (95% CI: 0.73; 0.90) for the FI, and 0.78 (95% CI: 0.69; 0.87) and 0.75 (95% CI: 0.67; 0.84) for the FP.

Conclusions
The Frailty Index showed better reproducibility and responsiveness properties compared to the Frailty Phenotype among acutely hospitalized older patients.
Severe bilateral pleuropneumonia caused by Legionella sainthelensi: a case report
Authors: Kamus Laure , Roquebert Bénédicte , Allyn Jérôme , Allou Nicolas , Valance Dorothée , Simon Charles , Jaffar-Bandjee Marie-Christine , Descours Ghislaine , Jarraud Sophie , Miltgen Guillaume 
Published: September 2021

Abstract
Background
Legionella spp. are ubiquitous freshwater bacteria responsible for rare but potentially severe cases of Legionnaires’ disease (LD). Legionella sainthelensi is a non-pneumophila Legionella species that was first isolated in 1980 from water near Mt. St-Helens (USA). Although rare cases of LD caused by L. sainthelensi have been reported, very little data is available on this pathogen.

Case presentation
We describe the first documented case of severe bilateral pleuropneumonia caused by L. sainthelensi. The patient was a 35-year-old woman with Sharp’s syndrome treated with long-term hydroxychloroquine and corticosteroids who was hospitalized for an infectious illness in a university hospital in Reunion Island (France). The patient’s clinical presentation was complicated at first (bilateral pneumonia, multiloculated pleural effusion, then bronchopleural fistula) but her clinical condition eventually improved with the reintroduction of macrolides (spiramycin) in intensive care unit. Etiological diagnosis was confirmed by PCR syndromic assay and culture on bronchoalveolar lavage.

Conclusions
To date, only 14 documented cases of L. sainthelensi infection have been described worldwide. This pathogen is difficult to identify because it is not or poorly detected by urinary antigen and molecular methods (like PCR syndromic assays that primarily target L. pneumophila and that have only recently been deployed in microbiology laboratories). Pneumonia caused by L. sainthelensi is likely underdiagnosed as a result. Clinicians should consider the possibility of non-pneumophila Legionella infection in patients with a compatible clinical presentation when microbiological diagnostic tools targeted L. pneumophila tested negative.
Prevention of SARS-CoV-2 (COVID-19) transmission in residential aged care using ultraviolet light (PETRA): a two-arm crossover randomised controlled trial protocol
Authors: Brass Amanda , Shoubridge Andrew P. , Crotty Maria , Morawska Lidia , Bell Scott C. , Qiao Ming , Woodman Richard J. , Whitehead Craig , Inacio Maria C. , Miller Caroline , Corlis Megan , Larby Nicolas , Elms Levi , Sims Sarah K. , Taylor Steven L. , Flynn Erin , Papanicolas Lito E. , Rogers Geraint B. 
Published: September 2021

Abstract
Background
SARS-CoV-2 poses a considerable threat to those living in residential aged care facilities (RACF). RACF COVID-19 outbreaks have been characterised by the rapid spread of infection and high rates of severe disease and associated mortality. Despite a growing body of evidence supporting airborne transmission of SARS-CoV-2, current infection control measures in RACF including hand hygiene, social distancing, and sterilisation of surfaces, focus on contact and droplet transmission. Germicidal ultraviolet (GUV) light has been used widely to prevent airborne pathogen transmission. Our aim is to investigate the efficacy of GUV technology in reducing the risk of SARS-CoV-2 infection in RACF.

Methods
A multicentre, two-arm double-crossover, randomised controlled trial will be conducted to determine the efficacy of GUV devices to reduce respiratory viral transmission in RACF, as an adjunct to existing infection control measures. The study will be conducted in partnership with three aged care providers in metropolitan and regional South Australia. RACF will be separated into paired within-site zones, then randomised to intervention order (GUV or control). The initial 6-week period will be followed by a 2-week washout before crossover to the second 6-week period. After accounting for estimated within-zone and within-facility correlations of infection, and baseline infection rates (10 per 100 person-days), a sample size of n = 8 zones (n = 40 residents/zone) will provide 89% power to detect a 50% reduction in symptomatic infection rate. The primary outcome will be the incidence rate ratio of combined symptomatic respiratory infections for intervention versus control. Secondary outcomes include incidence rates of hospitalisation for complications associated with respiratory infection; respiratory virus detection in facility air and fomite samples; rates of laboratory confirmed respiratory illnesses and genomic characteristics.

Discussion
Measures that can be deployed rapidly into RACF, that avoid the requirement for changes in resident and staff behaviour, and that are effective in reducing the risk of airborne SARS-CoV-2 transmission, would provide considerable benefit in safeguarding a highly vulnerable population. In addition, such measures might substantially reduce rates of other respiratory viruses, which contribute considerably to resident morbidity and mortality.
Trial registration Australian and New Zealand Clinical Trials Registry ACTRN12621000567820 (registered on 14th May, 2021).
Efficacy of bedaquiline in the treatment of drug-resistant tuberculosis: a systematic review and meta-analysis
Authors: Wang Ming-Gui , Wu Shou-Quan , He Jian-Qing 
Published: September 2021

AbstractBackgroundDrug-resistant tuberculosis (DR-TB) remains a major public health concern worldwide. Bedaquiline, a novel diarylquinoline, was added to the WHO-recommended all-oral regimen for patients with multidrug-resistant tuberculosis. We performed a systematic review and meta-analysis to determine the effect of bedaquiline on tuberculosis treatment outcomes.MethodsWe searched the PubMed, Web of Science and EMBASE databases for relevant studies published up to March 12, 2021. We included studies in which some participants received bedaquiline and others did not. Stata version 16.0 (Stata Corp., College Station, Texas, USA) was used to analyze the results of the meta-analysis. Risk ratios (RRs) with 95% confidence intervals (95% CIs) were calculated to evaluate the effect of bedaquiline on drug-resistant tuberculosis. Between-study heterogeneity was examined by the I-squared test. Randomized controlled trials were assessed for quality using the Jadad scale, and cohort studies were assessed using the Newcastle–Ottawa scale.ResultsEight studies, including 2 randomized controlled trials and 6 cohort studies involving a total of 21,836 subjects, were included. When compared with the control, bedaquiline treatment was associated with higher rates of culture conversion (risk ratio (RR):1.272 (1.165–1.389), P < 0.001). We found substantial evidence of a significant reduction in all-cause death (RR: 0.529 (0.454–0.616), P < 0.001)) in the bedaquiline treatment group. There was no significant reduction in treatment success (RR = 0.980 (0.948–1.013, P = 0.234)).ConclusionsThis study demonstrated that compared with patients who do not receive bedaquiline, this drug has the potential to achieve a higher culture conversion rate and a lower mortality risk among drug-resistant tuberculosis cases.
Clinical characteristics and outcomes of neonates with polymicrobial ventilator-associated pneumonia in the intensive care unit
Authors: Wang Hsiao-Chin , Tsai Ming-Horng , Chu Shih-Ming , Liao Chen-Chu , Lai Mei-Yin , Huang Hsuan-Rong , Chiang Ming-Chou , Fu Ren-Huei , Hsu Jen-Fu 
Published: September 2021

Abstract
Background
Ventilator associated pneumonia (VAP) caused by more than one microorganisms is not uncommon and may be potentially challenging, but the relevant data is scarce in ventilated neonates. We aimed to investigate the clinical characteristics and outcomes of polymicrobial VAP in the neonatal intensive care unit (NICU).

Methods
All neonates with definite diagnosis of VAP from a tertiary level neonatal intensive care unit (NICU) in Taiwan between October 2017 and September 2020 were prospectively observed and enrolled for analyses. All clinical features, therapeutic interventions and outcomes were compared between the polymicrobial VAP and monomicrobial VAP episodes. Multivariate regression analyses were used to find the independent risk factors for treatment failure.

Results
Among 236 episodes of neonatal VAP, 60 (25.4%) were caused by more than one microorganisms. Polymicrobial VAP episodes were more likely to be associated with multidrug-resistant pathogens (53.3% versus 34.7%, P = 0.014), more often occurred in later days of life and in neonates with prolonged intubation and underlying bronchopulmonary dysplasia. Otherwise most clinical characteristics of polymicrobial VAP were similar to those of monomicrobial VAP. The therapeutic responses and treatment outcomes were also comparable between these two groups, although modification of therapeutic antibiotics were significantly more common in polymicrobial VAP episodes than monomicrobial VAP episodes (63.3% versus 46.2%; P < 0.001). None of any specific pathogens was significantly associated with worse outcomes. Instead, it is the severity of illness, including presence of concurrent bacteremia, septic shock, and requirement of high-frequency oscillatory ventilator and underlying neurological sequelae that are independently associated with treatment failure.

Conclusions
Polymicrobial VAP accounted for 25.4% of all neonatal VAP in the NICU, and frequently occurred in neonates with prolonged intubation and underlying bronchopulmonary dysplasia. In our cohort, most clinical features, therapeutic responses and final outcomes of neonates with monomicrobial and polymicrobial VAP did not differ significantly.
The prevalence of denture stomatitis in cigarette and hookah smokers and opium addicts: findings from Rafsanjan Cohort Study
Authors: Sardari Farimah , Khalili Parvin , Hakimi Hamid , Mahmoudaghaei Saadat , Abedi Pouya 
Published: September 2021

AbstractBackgroundThe aim of this study was to investigate the association of denture stomatitis prevalence with cigarette, hookah and opium consumption and also dose–response relationship between the cigarette smoking duration and odds of denture stomatitis in population of Rafsanjan cohort center.MethodsThis cross-sectional study based on data of Rafsanjan Cohort Study (RCS) with 10,000 participants. After applying inclusion and exclusion criteria, 1619 participants were included in the analysis. Data were collected by oral examination and completion of pre-designed questionnaires to assess denture hygiene, smoking behavior, opium use and some other exposure variables. Multivariable logistic regression models were fitted to investigate possible association of cigarette, hookah and opium consumption and denture stomatitis.ResultsPrevalence of denture stomatitis among all 1619 denture wearers was 21.6%. Cigarette smoking was associated with a higher odds of denture stomatitis, with the adjusted odds ratio (95% CI) of 2.29 (1.53–3.41). Also, dose–response increases were observed with the highest odds ratio in the 4th quartile for denture stomatitis (p-value < 0.001). Opium consumption was associated with a decreased odds of denture stomatitis (adjusted OR; 0.81, 95% CI 0.58–1.13) which was not statistically significant. Also interaction between opium consumption and cigarette smoking was not associated with higher odds of denture stomatitis (adjusted OR: 1.65, 95% CI 0.85–3.22).ConclusionsBased on the findings of the present study, while cigarette smoking had a dose–response relationship with the increased odds of denture stomatitis; this association was not found with opium consumption.
Quality of complementary and alternative medicine information for type 2 diabetes: a cross-sectional survey and quality assessment of websites
Authors: Ng Jeremy Y. , Nayeni Manav , Gilotra Kevin 
Published: September 2021

AbstractBackgroundThe global prevalence of diabetes mellitus is projected to reach approximately 700 million by the year 2045, with roughly 90–95% of all diabetes cases being type 2 in nature. Patients with type 2 diabetes mellitus (T2DM) frequently seek information about complementary and alternative medicine (CAM) online. This study assessed the quality of publicly accessible websites providing consumer health information at the intersection of T2DM and CAM.MethodsAn online search engine (Google) was searched to identify pertinent websites containing information specific to CAM for T2DM patients, and the relevant websites were then screened with an eligibility criteria. Consumer health information found on eligible websites were then assessed for quality using the DISCERN instrument, a 16-item standardized scoring system.ResultsAcross the 480 webpages identified, 94 unique webpages remained following deduplication, and 37 eligible webpages belonged to and were collapsed into 30 unique websites that were each assessed using the DISCERN instrument. The mean overall quality score (question 16) across all 30 assessed websites was 3.55 (SD = 0.86), and the mean summed DISCERN score was 52.40 (SD = 12.11). Eighty percent of websites presented a wide range of CAM treatment options with the associated benefits/risks of each treatment, but in 56.7% of the websites, the sources used to collect information were unreliable.ConclusionThis study identified, assessed, and presents findings on the quality of online CAM information for T2DM. Although there were several high scoring websites, there was variability across most of the individual DISCERN items in the assessed websites. This study highlights the importance of awareness among healthcare providers regarding the reliability of online information about CAM treatment and management options for T2DM. Healthcare providers should be aware of patients' information seeking behaviour, guide them in navigating through the content they encounter online, and provide them with resources containing trustworthy and reliable information.
Number of musculoskeletal pain sites leads to increased long-term healthcare contacts and healthcare related costs – a Danish population-based cohort study
Authors: Mose S. , Kent P. , Smith A. , Andersen J. H. , Christiansen D. H. 
Published: September 2021

Abstract
Background
People with musculoskeletal pain seek more healthcare than the general population, however little is known about the long-term effect on healthcare use. The aim of this study was to examine the consequences of number of musculoskeletal pain sites on long-term care-seeking and healthcare-related costs and explore how health anxiety influences this relationship.

Methods
We conducted a Danish population-based longitudinal cohort study of 4883 participants combining self-reported survey data from 2008 with ten-year follow-up data from national health registers. Using a causal inference framework, we examined associations between number of pain sites (range 0–7)/level of health anxiety (high/low level) and face-to-face healthcare contacts/healthcare-related costs. Data were analyzed using negative binomial regression with generalized estimating equations. Regression models were adjusted for sex, age, duration of pain, level of education, comorbidity, personality traits, risk of depression, marital status, physical job exposure, and previous healthcare utilization.

Results
For each additional pain site general healthcare contacts (Incidence Rate Ratio (IRR): 1.04 (95% CI: 1.03–1.05)), healthcare-related costs (IRR: 1.06 (95% CI: 1.03–1.08) and musculoskeletal healthcare contacts (IRR: 1.11 (95% CI:1.09–1.14) increased. Those with high levels of health anxiety at baseline had a slightly higher number of general healthcare contacts (IRR 1.06 (1.01–1.11), independent of number of pain sites. However, level of anxiety did not influence the effect of number of pain sites on any healthcare use or cost outcomes.

Conclusions
We found evidence for a causal association between increasing number of pain sites and greater healthcare use and cost, and high levels of health anxiety did not increase the strength of this association. This suggests that number of pain sites could be a potential target for biopsychosocial interventions in order to reduce the need for future care-seeking.