bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferon-γ release assay screening in biologics: safe and reliable, but not perfect
Authors: Cafferkey John , Padayachee Yorissa , Kostich Sophia , Kumar Kartik , Jewell Paul , Patel Mikin , Chavda Aneeka , Cox Alison , Park Mirae , Russell Georgina , Coleman Meg , Martin Laura , Kon Onn Min 
Published: October 2022

BackgroundSystemic biologic agents can increase the risk of re-activation of latent tuberculosis (TB). Prior to initiation, screening for latent TB using an interferon-γ release assay (IGRA) is recommended. There is concern that false-negative IGRAs may be more likely in this context.MethodsThis retrospective analysis of IGRAs, specifically T-SPOT.TB, results and outcomes of patients already on or due to start biologics identifies the rate of TB re-activation in a low TB incidence setting. Additionally, we estimate the negative predictive value (NPV) of IGRAs in this population.ResultsPatients on biologics were more likely to have a negative IGRA result than patients not on biologics. There was no statistically significant change in conversion or reversion rates between groups. Of 9263 patients on biologics, 19 developed active TB after starting biologics at an incidence rate of 55.1 per 100 000 patient-years. This occurred despite screening in half of the 16 patients for whom we were able to review medical records. Most drugs implicated were known to be high risk, although rituximab and natalizumab were being taken by five patients and one patient, respectively. The T-SPOT.TB NPV was 99.20% and dropped only slightly to 99.17% when we simulated an approach where all borderline IGRA results were regarded as being negative.ConclusionsNegative IGRA results confer a low risk of subsequent active TB in patients on biologics in a low TB incidence setting. However, continued awareness is needed given that a number of active TB cases will have had a prior negative result.
The use of lung ultrasound in COVID-19
Authors: Blazic Ivana , Cogliati Chiara , Flor Nicola , Frija Guy , Kawooya Michael , Umbrello Michele , Ali Sam , Baranne Marie-Laure , Cho Young-Jae , Pitcher Richard , Vollmer Ivan , van Deventer Emilie , del Rosario Perez Maria 
Published: October 2022

This review article addresses the role of lung ultrasound in patients with coronavirus disease 2019 (COVID-19) for diagnosis and disease management. As a simple imaging procedure, lung ultrasound contributes to the early identification of patients with clinical conditions suggestive of COVID-19, supports decisions about hospital admission and informs therapeutic strategy. It can be performed in various clinical settings (primary care facilities, emergency departments, hospital wards, intensive care units), but also in outpatient settings using portable devices.
The article describes typical lung ultrasound findings for COVID-19 pneumonia (interstitial pattern, pleural abnormalities and consolidations), as one component of COVID-19 diagnostic workup that otherwise includes clinical and laboratory evaluation. Advantages and limitations of lung ultrasound use in COVID-19 are described, along with equipment requirements and training needs. To infer on the use of lung ultrasound in different regions, a literature search was performed using key words “COVID-19”, “lung ultrasound” and “imaging”.
Lung ultrasound is a noninvasive, rapid and reproducible procedure; can be performed at the point of care; requires simple sterilisation; and involves non-ionising radiation, allowing repeated exams on the same patient, with special benefit in children and pregnant women. However, physical proximity between the patient and the ultrasound operator is a limitation in the current pandemic context, emphasising the need to implement specific infection prevention and control measures.
Availability of qualified staff adequately trained to perform lung ultrasound remains a major barrier to lung ultrasound utilisation. Training, advocacy and awareness rising can help build up capacities of local providers to facilitate lung ultrasound use for COVID-19 management, in particular in low- and middle-income countries.
Effect of nintedanib on acute exacerbations of fibrosing interstitial lung diseases: a national database study in Japan
Authors: Urushiyama Hirokazu , Jo Taisuke , Hasegawa Wakae , Yokoyama Akira , Ando Takahiro , Sakamoto Yukiyo , Kumazawa Ryosuke , Uda Kazuaki , Michihata Nobuaki , Awano Nobuyasu , Hiroki Matsui , Fushimi Kiyohide , Yasunaga Hideo , Nagase Takahide 
Published: October 2022

BackgroundAcute exacerbation is a life-threatening event in patients with fibrosing interstitial lung diseases (ILDs). Although nintedanib reduces acute exacerbation incidence, its effectiveness during acute exacerbation is unclear.MethodsUsing data from the Diagnosis Procedure Combination database (September 2015–March 2020) in Japan, we identified patients with fibrosing ILDs who received intravenous injection of high-dose corticosteroid within 3 days post-admission and analysed their first hospitalisation. We performed overlap propensity score weighting to compare in-hospital outcomes between patients who received nintedanib within 14 days post-admission and those who did not. The primary and secondary outcomes were in-hospital mortality and length of hospitalisation in the patients discharged alive, respectively.ResultsAmong the 6235 identified patients, 353 patients received nintedanib within 14 days post-admission. In-hospital mortality occurred in 13.7% and 6.0% patients in the control (n=5882) and nintedanib-treated (n=353) patients, respectively. The mean length of hospitalisation was 39.9 and 30.4 days in the control and nintedanib-treated patients, respectively. After overlap propensity score weighting, nintedanib treatment was significantly associated with lower in-hospital mortality in the adjusted cohort (OR 0.43, 95% CI 0.27–0.70; p=0.001). The mean length of hospitalisation in nintedanib-treated patients (30.7 days) was significantly shorter than that in the control group (37.5 days; p<0.001).ConclusionsNintedanib initiation during acute exacerbation was significantly associated with a lower risk of in-hospital death and shorter length of hospitalisation in patients with fibrosing ILDs. Our results elucidate the potential role of nintedanib in the treatment of acute exacerbation in patients with fibrosing ILDs. Further prospective studies are warranted.
The demographics, clinical characteristics and quality of life of patients with chronic cough from the Isala Cough Clinic in the Netherlands
Authors: van den Berg Jan Willem K. , Baxter Carl A. , Edens Mireille A. , Patberg Kornelis W. , van der Velden Hester , Weijerse Arjan , Salomonsson Stina 
Published: October 2022

IntroductionChronic cough affects ∼10% of the population and adversely impacts quality of life. This retrospective observational cohort study aimed to identify the demographics, clinical characteristics and quality of life of the chronic cough population in a Dutch chronic cough clinic, at baseline and following treatment at 6 months. Patients were categorised based on the underlying phenotype and response to treatment.MethodsRetrospective data on 2397 patients who were diagnosed according to standard guidelines of the American College of Chest Physicians were analysed. Quality of life was capturedviathe Leicester Cough Questionnaire, the Cough Numeric Rating Scale and the Hospital Anxiety and Depression Scale.ResultsMean patient age was 59 years; 62.5% of the patients were female; and 69.1% had at least one underlying phenotype associated with chronic cough. Of the latter, 52.1% had bronchial hyperresponsiveness/airflow limitation, 33.3% had airway reflux and 20.1% had upper airway cough syndrome. 46% of patients with a phenotype, and 51% without, experienced no improvement in their quality of life or still had significant cough remaining after 6 months. Of patients with available quality-of-life data, 37.5% were categorised as having refractory chronic cough, and 9.5% were categorised as unexplained chronic cough.DiscussionThis study highlights the poor quality-of-life outcomes in patients with chronic cough, despite interventions to treat underlying conditions, and indicates a need to manage chronic cough irrespective of phenotype.
Arterial remodelling in smokers and in patients with small airway disease and COPD: implications for lung physiology and early origins of pulmonary hypertension
Authors: Bhattarai Prem , Lu Wenying , Gaikwad Archana Vijay , Dey Surajit , Chia Collin , Larby Josie , Haug Greg , Hardikar Ashutosh , Williams Andrew , Kaur Singhera Gurpreet , Hackett Tillie-Louise , Eapen Mathew Suji , Sohal Sukhwinder Singh 
Published: October 2022

IntroductionPulmonary vascular remodelling in chronic obstructive pulmonary disease (COPD) has detrimental consequences for lung physiology. The aim of our study was to provide a comprehensive size-based morphometric quantification of pulmonary arterial remodelling in smokers and in patients with small airway disease (SAD) or COPD.MethodMovat's pentachrome staining was performed on lung resections for 46 subjects: 12 never-smoker normal controls (NC), six normal lung function smokers (NLFS), nine patients with SAD, nine patients with mild-to-moderate COPD who were current smokers (COPD-CS) and 10 patients with mild-to-moderate COPD who were ex-smokers (COPD-ES). Following a size-based classification of pulmonary arteries, image analysis software was used to measure their number, total wall thickness, individual layer thickness and elastin percentage.ResultsAll pathological groups showed decreased numbers of pulmonary arteries compared with the NC group in all artery sizes. Arterial wall thickness was greater in NLFS and COPD-CS than in NC. Thickness in COPD-ES was decreased compared with COPD-CS. Intimal thickness was greater in all pathological groups in all arterial sizes than in the NC group. Medial thickness was also greater in small and medium arteries. Intimal thickness of larger arteries in COPD-CS correlated negatively to forced expiratory volume in 1 s/forced vital capacity (FVC) % and forced expiratory flow at 25–75% of FVC. Elastin deposition in small arteries was greatest in COPD-CS. Intimal elastin deposition had a more negative correlation with intimal thickness in NLFS and SAD than in COPD-CS.ConclusionSmoking, SAD and mild-to-moderate COPD are associated with pruning and a decrease in the number of pulmonary arteries, increased wall thickness and variable elastin deposition. These changes were associated with worse airway obstruction.
Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea
Authors: Somee Maryam Rezaei , Amoozegar Mohammad Ali , Dastgheib Seyed Mohammad Mehdi , Shavandi Mahmoud , Maman Leila Ghanbari , Bertilsson Stefan , Mehrshad Maliheh 
Published: October 2022

AbstractBackgroundHydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. ResultsApart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.ConclusionPhylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.
The MBS microbial rapid detection system for rapid detection of major pathogenic bacteria in feed: comparison with plate counting method
Authors: Jiang Linlin , Zhang Beibei , Liu Shuitao , Zhu Lianqin , Zhu Fenghua 
Published: October 2022

AbstractThe current methods for detecting pathogenic bacteria in feed require high technique and take a long time. The Micro Biological Survey (MBS) rapid detection system is a simple, economical and rapid microbial detection method. The purpose of this experiment was to compare the detection ofEscherichia coli(E. coli),Salmonella,Staphylococcus aureus(S. aureus),Listeria monocytogenes(LM), coliform (COLI) and total viable count (TVC) in feed by the MBS rapid microbial detection system and plate counting method (PCM). The results showed that the limit of quantitation, recovery rate and coefficient of variation of the MBS microbial rapid detection system are better than the plate counting method. When detecting the pathogenic bacteria content in artificially contaminated feed, the MBS rapid microbial detection system was positively correlated with the PCM. When the MBS microbial rapid detection system and PCM were used to detect the collected real feed samples, there was no significant difference in the detection results of the two methods in most of the feed samples. In summary, the MBS microbial rapid detection system is the most convenient and rapid detection method and is suitable for promotion and application in production lines.
Population-based pattern of medication use and prevalence of polypharmacy among patients with cardiovascular diseases: results of the Pars cohort study from Iran
Authors: Mohsenzadeh Pooran , Ardekani Ali , Poustchi Hossein , Mohammadi Zahra , Abdipour Mehrian Seyed Reza , Bazrafshan Drissi Hamed , Rahimian Zahra , Taherifard Erfan , Nabavizadeh Ali , kamalipour Alireza , Mesgarpour Bita , Malekzadeh Fatemeh , Molavi Vardanjani Hossein 
Published: October 2022

Abstract
Background
Polypharmacy in patients with cardiovascular diseases (CVDs) has been linked to several adverse outcomes. This study aimed to investigate the pattern of medication use and prevalence of polypharmacy among CVDs patients in Iran.

Method
We used the baseline data of the Pars cohort study (PCS). The participants were asked to bring their medication bags; then, the medications were classified using the Anatomical Therapeutic Chemical classification. Polypharmacy was defined as using five or more medications concurrently. Poisson regression modeling was applied. The adjusted prevalence ratios (PR) and its 95% confidence interval (CI) were estimated.

Results
Totally, 9262 participants were enrolled in the PCS, of whom 961 had CVDs. The prevalence of polypharmacy in participants with and without CVDs was 38.9% and 7.1%, respectively. The highest prevalence of polypharmacy (51.5%) was among obese patients. Abnormal waist-hip ratio (PR: 2.79; 95% CI 1.57–4.94), high socioeconomic status (PR: 1.65; 95% CI 1.07–2.54), tobacco-smoking (PR: 1.35; 95% CI 1.00–1.81), patients with more than three co-morbidities (PR: 1.41; 95% CI 1.30–1.53), high physical activity (PR: 0.66; 95% CI 0.45–0.95), use of opiate ever (PR: 0.46; 95% CI 0.26–0.82), and healthy overweight subjects (PR: 0.22; 95% CI 0.12–0.39) were associated with polypharmacy. Cardiovascular drugs (76.1%), drugs acting on blood and blood-forming organs (50.4%), and alimentary tract and metabolism drugs (33.9%) were the most frequently used drugs. Agents acting on the renin-angiotensin system were the mostly used cardiovascular system drugs among men and those above 60 years old, while beta-blocking agents were mostly prevalent among cardiovascular system drugs in women with CVDs.

Conclusion
Given the high prevalence of polypharmacy among CVDs patients, and subsequent complications, programs to educate both physicians and patients to prevent this issue is crucial.
Red blood cell distribution width predicts gastrointestinal bleeding after coronary artery bypass grafting
Authors: Liao Ying , Zhang Rongting , Shi Shanshan , Lin Xueqin , Wang Yani , Wang Yun , Chen Weihua , Zhao Yukun , Bao Kunming , Zhang Kaijun , Chen Liling , Fang Yong 
Published: October 2022

Abstract
Background
Red blood cell distribution width (RDW) is highly associated with adverse clinical outcomes in many diseases. The present study aimed to evaluate the relationship between RDW and gastrointestinal bleeding (GIB) after isolated coronary artery bypass grafting (CABG).

Methods
This was a retrospective observational study that included 4473 patients who received CABG, and all the data were extracted from the Medical Information Mart for Intensive Care III database. Data collected included patient demographics, associated comorbid illnesses, laboratory parameters, and medications. The receiver operating characteristic (ROC) curve was used to determine the best cutoff value of RDW for the diagnosis of GIB. Multivariable logistic regression analysis was used to analyze the relationship between RDW and GIB.

Results
The incidence of GIB in patients receiving CABG was 1.1%. Quartile analyses showed a significant increase in GIB incidence at the fourth RDW quartile (> 14.3%; P < 0.001). The ROC curve analysis revealed that an RDW level > 14.1% measured on admission had 59.6% sensitivity and 69.4% specificity in predicting GIB after CABG. After adjustment for confounders, high RDW was still associated with an increased risk of GIB in patients with CABG (odds ratio = 2.83, 95% confidence interval 1.46–5.51, P = 0.002).

Conclusions
Our study indicates that the elevated RDW level is associated with an increased risk of GIB after CABG, and it can be an independent predictor of GIB. The introduction of RDW to study GIB enriches the diagnosis method of GIB and ensures the rapid and accurate diagnosis of GIB.
Outcomes improvement despite continuous visits of severely injured patients during the COVID-19 outbreak: experience at a regional trauma centre in South Korea
Authors: Kang Sooyeon , Park Ji Eun , Ko Ji Wool , Kim Myoung Jun , Choi Young Un , Shim Hongjin , Bae Keum Seok , Kim Kwangmin 
Published: October 2022

Abstract
Background
Understanding the changes in characteristics of patients who visited trauma centres during the coronavirus disease 2019 (COVID-19) pandemic is important to facilitate aneffective response. This retrospective study was conducted to analyse differences in the characteristics and outcomes of patients who visited our trauma centre between pre-COVID-19 and COVID-19 eras.

Methods
Medical data of trauma patients enrolled in the Korean trauma database from 1 January 2018 to 31 August 2021 were collected. The number of trauma centre visits, patient characteristics, factors associated with in-hospital intervention, and outcomes werecompared between patients in the two time periods. Propensity score matching was performed to analyse the outcomes in patients with similar characteristics and severitybetween patients in the two time periods.

Results
The number of emergency department (ED) trauma service visits reduced in the COVID-19 era. Based on the mean age, the patients were older in the COVID-19 era. Abbreviated injury scale (AIS) 1, AIS3, AIS5, and injury severity score (ISS) were higher in the COVID-19 era. The proportion of motor vehicle collisions decreased, whereas falls increased during the COVID-19 era. Ambulance transportation, admission to the general ward, and time from injury to ED visit significantly increased. Patient outcomes, such as hospital length of stay (LOS), intensive care unit (ICU) LOS, and duration of mechanical ventilation improved, while injury severity worsened during the COVID-19 era. After adjusting for patient characteristics and severity, similar findings were observed.

Conclusion
The small reduction in the number of trauma patients and visits by patients who hadhigher ISS during the COVID-19 pandemic highlights the importance of maintaining trauma service capacity and capability during the pandemic. A nationwide or nationalmulticentre study will be more meaningful to examine the impact of the COVID-19 outbreak on the changes in trauma patterns, volume, and patient outcomes.
Anti-cholinergic drug burden in patients with dementia increases after hospital admission: a multicentre cross-sectional study
Authors: Hook Annabelle , Randall Jessica L. , Grubb Carla M. , Ellis Natalie , Wellington Jack , Hemmad Aayushi , Zerdelis Agisilaos , Winnett Andrew R. D. , Geers Benjamin D. W. , Sykes Bethany , Auty Charlotte N. , Vinchenzo Cecilia , Thorburn Christiane E. , Asogbon Daniella , Granger Emily , Boagey Heather , Raphael Juliet , Patel Kajal , Bhargava Kartik , Dolley Mary-Kate M. , Maden Matthew J. , Shah Mehdin M. , Lee Qao M. , Vaidya Ratnaraj , Sehdev Simran , Barai Sneha , Roche Sophie , Khalid Uzair , Codling David A. , Harrison Judith R. 
Published: October 2022

Abstract
Background
Anticholinergic medications are drugs that block cholinergic transmission, either as their primary therapeutic action or as a secondary effect. Patients with dementia may be particularly sensitive to the central effects of anticholinergic drugs. Anticholinergics also antagonise the effects of the main dementia treatment, cholinesterase inhibitors. Our study aimed to investigate anticholinergic prescribing for dementia patients in UK acute hospitals before and after admission.

Methods
We included 352 patients with dementia from 17 UK hospital sites in 2019. They were all inpatients on surgical, medical or Care of the Elderly wards. Information about each patient’s medications were collected using a standardised form, and the anticholinergic drug burden of each patient was calculated with an evidence-based online calculator. Wilcoxon’s rank test was used to look at the correlation between two subgroups upon admission and discharge.

Results
On admission to hospital, 37.8% of patients had an anticholinergic burden score ≥ 1 and 5.68% ≥3. On discharge, 43.2% of patients with an anticholinergic burden score ≥ 1 and 9.1% ≥3. The increase in scores was statistically significant (p = 0.001). Psychotropics were the most common group of anticholinergic medications prescribed at discharge. Of those patients taking cholinesterase inhibitors, 44.9% were also prescribed anticholinergic medications.

Conclusions
Our cross-sectional, multicentre study found that people with dementia are commonly prescribed anticholinergic medications, even if concurrently taking cholinesterase inhibitors, and are significantly more likely to be discharged from hospital with a higher anticholinergic burden than on admission.