bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide expression of the residual lung reacting to experimental Pneumonectomy
Authors: Napolioni Valerio , Bianconi Fortunato , Potenza Rossella , Carpi Francesco M. , Ludovini Vienna , Picciolini Matteo , Tofanetti Francesca R. , Bufalari Antonello , Pallotti Stefano , Poggi Camilla , Anile Marco , Daddi Niccolò , Venuta Federico , Puma Francesco , Vannucci Jacopo 
Published: December 2021

AbstractBackgroundAcute or chronic irreversible respiratory failure may occur in patients undergoing pneumonectomy. Aim of this study was to determine transcriptome expression changes after experimental pneumonectomy in swine model. Experimental left pneumonectomy was performed in five pigs under general anaesthesia. Both the resected and the remaining lung, after 60 post-operative completely uneventful days, underwent genome-wide bulk RNA-Sequencing (RNA-Seq).ResultsHistological analysis showed dilation of air spaces and rupture of interalveolar septa. In addition, mild inflammation, no fibrosis, radial stretch of the bronchus, strong enlargement of airspaces and thinning of the blood supply were observed. Bioinformatic analyses of bulk RNA-Seq data identified 553 Differentially Expressed Genes (DEGs) at adjustedP-value below 0.001, between pre- and post-pneumonectomy. The top 10 up-regulated DEGs wereEdn1, Areg, Havcr2, Gadd45g, Depp1, Cldn4, Atf3, Myc, Gadd45b, Socs3; the top 10 down-regulated DEGs wereObscn, Cdkn2b,ENSSSCG00000015738,Prrt2, Amer1, Flrt3, Efnb2, Tox3, Znf793, Znf365.Leveraging digital cytometry tools, no difference in cellular abundance was found between the two experimental groups, while the analysis of cell type-specific gene expression patterns highlighted a striking predominance of macrophage-specific genes among the DEGs. DAVID-based gene ontology analysis showed a significant enrichment of “Extrinsic apoptotic signaling pathway” (FDR q = 7.60 × 10− 3) and “Response to insulin” (FDR q = 7.60 × 10− 3) genes, along with an enrichment of genes involved as “Negative regulators of DDX58/IFIH1 signaling” (FDR q = 7.50 × 10− 4) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections.ConclusionThis translational genomics study highlighted the existence both of individual genes, mostly dysregulated in certain cellular populations (e.g., macrophages), and gene-networks involved in pulmonary reaction after left pneumonectomy. Their involvement in lung homeostasis is largely supported by previous studies, carried out both in humans and in other animal models (under homeostatic or disease-related conditions), that adopted candidate-gene approaches. Overall, the present findings represent a preliminary assessment for future, more focused, studies on compensatory lung adaptation, pulmonary regeneration and functional reload.
Clinical characteristics of patients with bronchiectasis with nontuberculous mycobacterial disease in Mainland China: a single center cross-sectional study
Authors: Yin Hongjun , Gu Xiaoying , Wang Yimin , Fan Guohui , Lu Binghuai , Liu Min , Wang Chunlei , Cao Bin , Wang Chen 
Published: December 2021

Abstract
Background
The diagnosis and treatment of patients with bronchiectasis and nontuberculous mycobacterium (NTM) pulmonary disease are challenging issues and the treatment is also prolonged and depends on the species. There is limited information on patients with bronchiectasis and NTM pulmonary disease in Mainland China.

Methods
This cross-sectional study was conducted at the China–Japan Friendship Hospital, Beijing, China. Those adult patients who met the diagnostic criteria for bronchiectasis and obtained a culture result of mycobacteria from lower respiratory tract specimens or lung tissue were included in this study. A logistic regression model was used to identify the related factors in patients with NTM pulmonary disease.

Results
A total of 202 patients with bronchiectasis from 19 cities, 155 without and 47 (23.3%) with NTM pulmonary disease, were included. In all the 47 patients with NTM pulmonary disease, Mycobacterium avium complex was the most common species (66.0%), and 72.3% of them were initiated on standard anti-NTM treatment within 3 months after the diagnosis of NTM pulmonary disease. A larger proportion of patients with NTM pulmonary disease had acute exacerbations of ≥ 3 times within 1 year and were diagnosed bronchiectasis ≥ 50 years among patients with NTM pulmonary disease. The HRCT chest images revealed higher proportions of nodular shadow (100% vs. 35.3%), tree-in-bud sign (97.9% vs. 29.0%), cavities (29.8% vs. 5.8%), and airway dilation of the right middle lobe or the left lingular lobe (63.8% vs. 23.9%) in patients with NTM pulmonary disease than in those without NTM pulmonary disease (all P values = 0.001). The multivariable logistic regression model indicated that three and more abnormal features (OR 33.8; 95% CI 11.1–102.8) and main lesions of bronchial expansion in the middle or lingual lobe (OR 6.4; 95% CI 2.4–16.6) in HRCT chest images were independently associated with NTM pulmonary disease (P values = 0.001).

Conclusion
In a single center of Mainland China, > 23% of patients with bronchiectasis had NTM pulmonary disease, and most patients were started on standard treatment within 3 months after the diagnosis of NTM pulmonary disease. These findings suggest that patients with bronchiectasis should be thoroughly examined for the presence of NTM pulmonary disease.

Trial registration

NCT03594032.
Influence of contextual socioeconomic position on hypertension risk in low- and middle-income countries: disentangling context from composition
Authors: Abba Mustapha S. , Nduka Chidozie U. , Anjorin Seun , Mohamed Shukri F. , Agogo Emmanuel , Uthman Olalekan A. 
Published: December 2021

Abstract
Background
Hypertension has emerged as the single most significant modifiable risk factor for cardiovascular disease and death worldwide. Resource-limited settings are currently experiencing the epidemiological transition from infectious diseases to chronic non-communicable diseases, primarily due to modifications in diet and lifestyle behaviour. The objective of this study was to examine the influence of individual-, community- and country-level factors associated with hypertension in low- and middle-income countries (LMICs).

Methods
Multivariable multi-level logistic regression analysis was applied using 12 Demographic and Health Survey (DHS) datasets collected between 2011 and 2018 in LMICs. We included 888,925 respondents (Level 1) nested within 33,883 neighbourhoods (Level 2) from 12 LMICs (Level 3).

Results
The prevalence of hypertension ranged from 10.3% in the Kyrgyz Republic to 52.2% in Haiti. After adjusting for the individual-, neighbourhood- and country-level factors, we found respondents living in the least deprived areas were 14% more likely to have hypertension than those from the most deprived areas (OR = 1.14, 95% CI 1.10 to 1.17). We observed a significant variation in the odds of hypertension across the countries and the neighbourhoods. Approximately 26.3 and 47.6% of the variance in the odds of hypertension could be attributed to country- and neighbourhood-level factors, respectively. We also observed that respondents moving to a different neighbourhood or country with a higher risk of hypertension had an increased chance of developing hypertension, the median increase in their odds of hypertension was 2.83-fold (95% CI 2.62 to 3.07) and 4.04- fold (95% CI 3.98 to 4.08), respectively.

Conclusions
This study revealed that individual compositional and contextual measures of socioeconomic status were independently associated with the risk of developing hypertension. Therefore, prevention strategies should be implemented at the individual level and the socioeconomic and contextual levels to reduce the burden of hypertension.
Incidence, aetiology and clinical features of eosinophilic pleural effusion: a retrospective study
Authors: Li Minfang , Zeng Yunxiang , Li Yaqing , Jia Dan , Chen Sheng , Wang Jinlin 
Published: December 2021

Abstract
Background
Eosinophilic pleural effusion (EPE) is a distinct entity among pleural effusions, but its diagnostic and prognostic significance is still controversial. This study aimed to evaluate the incidence and aetiological distribution of EPE in our institution and to assess the relationship between EPE and malignancy and other underlying diseases and the relevance of the percentage of eosinophils and other laboratory parameters.

Methods
A retrospective study was conducted by reviewing the medical records of 252 patients with PE from September 2017 to January 2021.

Results
EPE was found in 34 (13.49%) out of 252 patients. There were 20 (58.82%) males and 14 (41.18%) females in the EPE group. The mean percentage of eosinophils in EPE (21.7%, range (10.0–67.5%)) was significantly higher than the percentage of eosinophils in peripheral blood (5.65%, range (0–34.60%); p < 0.05). The most common cause of EPE was malignant disease (52.94%), followed by idiopathy (14.71%), parasites (8.82%), pneumonia (8.82%) and others (14.71%). Comparative analysis of patients with malignant versus nonmalignant EPE showed that patients with malignant EPE were significantly older, and had a lower white blood cell (WBC) count in the pleural fluid (1.8 vs 4.7 cells × 109/L, p < 0.05). However, the percentage of eosinophils in PE was not significantly different between malignant EPE and nonmalignant EPE (p = 0.66). There was no correlation between the percentage of eosinophils in PE and peripheral blood (r = 0.29; p = 0.09).

Conclusions
Malignant disease ranks as the leading cause of EPE. The presence of EPE should not be considered as a predictive factor of benign conditions. Pleural parasitic infestation (PPI) should be emphasized in areas with a high incidence of parasitic disease.
Impact of COVID-19 on patient and healthcare professional attitudes, beliefs, and behaviors toward the healthcare system and on the dynamics of the healthcare pathway
Authors: Bernacki Katarzyna , Keister Angie , Sapiro Nadia , Joo Jin Su , Mattle Lisa 
Published: December 2021

Abstract
Background
COVID-19 has dramatically changed how healthcare is delivered and experienced.

Methods
One-on-one interviews and a virtual ethnographic roundtable were conducted among 45 patients, caregivers, and healthcare professionals (HCPs) in 4 therapeutic areas from the United States and Japan: overactive bladder, vasomotor symptoms, prostate cancer, and metastatic urothelial carcinoma. The goal was to identify the impact of COVID-19 on patient/caregiver and HCP attitudes, interactions, beliefs, and behaviors toward the healthcare system and care pathway.

Results
Four foundational themes were identified: 1) COVID-19 risk is relative; 2) isolation is collateral damage; 3) telehealth is a parallel universe; and 4) COVID-19 is destabilizing the foundations of healthcare. Numerous insights, influenced by diverse cultural, social, and psychological factors, were identified within each theme.

Conclusions
The impacts of COVID-19 were noticeable at multiple points of care during the “universal” care pathway, including at initial screening, referral to specialists, diagnosis, treatment initiation/surgery, and during ongoing care. Greater appreciation of the short- and long-term impacts of COVID-19 and resulting gaps in care may act as a catalyst for positive change in future patient care.
Modular signature of long non-coding RNA association networks as a prognostic biomarker in lung cancer
Authors: Li Albert , Yu Wen-Hsuan , Hsu Chia-Lang , Huang Hsuan-Cheng , Juan Hsueh-Fen 
Published: December 2021

Abstract
Background
Increasing amount of long non-coding RNAs (lncRNAs) have been found involving in many biological processes and played salient roles in cancers. However, up until recently, functions of most lncRNAs in lung cancer have not been fully discovered, particularly in the co-regulated lncRNAs. Thus, this study aims to investigate roles of lncRNA modules and uncover a module-based biomarker in lung adenocarcinoma (LUAD).

Results
We used gene expression profiles from The Cancer Genome Atlas (TCGA) to construct the lncRNA association networks, from which the highly-associated lncRNAs are connected as modules. It was found that the expression of some modules is significantly associated with patient’s survival, including module N1 (HR = 0.62, 95% CI = 0.46–0.84, p = 0.00189); N2 (HR = 0.68, CI = 0.50–0.93, p = 0.00159); N4 (HR = 0.70, CI = 0.52–0.95, p = 0.0205) and P3 (HR = 0.68, CI = 0.50–0.92, p = 0.0123). The lncRNA signature consisting of these four prognosis-related modules, a 4-modular lncRNA signature, is associated with favourable prognosis in TCGA-LUAD (HR = 0.51, CI = 0.37–0.69, p value = 2.00e−05). Afterwards, to assess the performance of the generic modular signature as a prognostic biomarker, we computed the time-dependent area under the receiver operating characteristics (AUC) of this 4-modular lncRNA signature, which showed AUC equals 68.44% on 336th day. In terms of biological functions, these modules are correlated with several cancer hallmarks and pathways, including Myc targets, E2F targets, cell cycle, inflammation/immunity-related pathways, androgen/oestrogen response, KRAS signalling, DNA repair and epithelial-mesenchymal transition (EMT).

Conclusion
Taken together, we identified four novel LUAD prognosis-related lncRNA modules, and assessed the performance of the 4-modular lncRNA signature being a prognostic biomarker. Functionally speaking, these modules involve in oncogenic hallmarks as well as pathways. The results unveiled the co-regulated lncRNAs in LUAD and may provide a framework for further lncRNA studies in lung cancer.
Impact of perioperative use of GnRH agonist or dienogest on ovarian reserve after cystectomy for endometriomas: a randomized controlled trial
Authors: Muraoka Ayako , Osuka Satoko , Yabuki Atsushi , Bayasula  , Yoshihara Masato , Tanaka Hideaki , Sonehara Reina , Miyake Natsuki , Murakami Mayuko , Yoshita Sayako , Nakanishi Natsuki , Nakamura Tomoko , Goto Maki , Iwase Akira , Kajiyama Hiroaki 
Published: December 2021

Abstract
Background
Ovarian endometrioma is a common gynecological disease that is often treated with surgery or hormonal treatment. Ovarian cystectomy, a surgical procedure for ovarian endometrioma, can result in impaired ovarian reserve.

Methods
We conducted a randomized controlled trial to evaluate the efficacy of hormonal treatment [gonadotropin-releasing hormone agonist (GnRHa) or dienogest (DNG)] for preserving ovarian reserve after cystectomy for ovarian endometrioma. The primary endpoint was the level of serum Anti-Müllerian hormone (AMH) as a marker of ovarian reserve.

Results
Before and after laparoscopic surgery, 22 patients in the GnRHa group and 27 patients in the DNG group were administered hormonal treatment for a total of 4 months. After 1-year follow-up, >60% of the patients in the DNG group retained over 70% of their pretreatment AMH levels, whereas no patient in the GnRHa group retained their AMH levels after cystectomy (P < 0.01). Interleukin-6 (IL-6) is a key cytokine involved in inflammation. Compared with the GnRHa group, patients in the DNG group had lower IL-6 levels at the end of treatment.

Conclusions
Our data revealed that DNG is more effective than GnRHa in preserving ovarian reserve after cystectomy of ovarian endometrioma. This is achieved through the reduction of the inflammatory response during the perioperative period and other endometriosis-related inflammatory reactions.

Trial registration
The registration number of this trial is UMIN-CTR, UMIN000018569, registered 6 August 2015, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000021492, and Japan Registry of Clinical Trials, jRCTs041180140, registered 29 March 2019, https://jrct.niph.go.jp/en-latest-detail/jRCTs041180140. This randomized controlled trial was conducted in accordance with the CONSORT guidelines.
Digging deeper: exploring chiropractors online claims about non-musculoskeletal disorders
Authors: O’Neill Søren , Wahlqvist Anneline Bugge , Simonsen Natasja Kragh , Myburgh Cornelius , Jensen Rikke Krüger 
Published: December 2021

Abstract
Background
Some chiropractors suggest that chiropractic treatment is appropriate for health issues other than musculoskeletal problems. The prevalence of such claims on individual clinic websites has previously been reported as approximately one-in-four in Denmark. The underlying rationales for such claims may reflect convictions about traditional chiropractic subluxations paradigms, but are not self-evident and has not previously been studied.

Methods
An exploratory qualitative case interview study of Danish chiropractors with websites which contain claims about chiropractic efficacy in the treatment of non-musculoskeletal disorders. Websites were identified from a nation wide random sample (57%) of all chiropractic clinic websites.

Results
Of the original 139 websites, 36 were identified as mentioning non-MSK conditions. When revisited, 19 of those clinic websites still mentioned non-MSK disorders and were contacted. Eleven (11) declined our invitation to participate. Interviews were conducted with the responsible chiropractor from each of the remaining 8 clinics.
Five distinct themes were identified in the rationales for treating non-musculoskeletal disorders: ‘Positive side-effects,’ ‘Experience,’ ‘Web page,’ ‘Communication’ and ‘Conviction.’

Conclusions
A minority of Danish chiropractic websites suggest that non-musculoskeletal disorders are within the chiropractic scope of practice. Those that do, do so for varying reasons—poor communication and website maintenance were commonly cited problems. An explicitly stated adherence to traditional chiropractic subluxations concepts was uncommon. By contrast, a more tempered rationale that suggested a potential beneficial side-effect of chiropractic on non-musculoskeletal health issues were more common and was typically presented in softer-language and/or with some reservations.
Comparative analysis of long-term oncologic outcomes for minimally invasive and open Ivor Lewis esophagectomy after neoadjuvant chemoradiation: a propensity score matched observational study
Authors: Merritt Robert E. , Kneuertz Peter J. , Abdel-Rasoul Mahmoud , D’Souza Desmond M. , Perry Kyle A. 
Published: December 2021

Abstract
Background
Locally advanced esophageal carcinoma is typically treated with neoadjuvant chemoradiation and esophagectomy (trimodality therapy). We compared the long-term oncologic outcomes of minimally invasive Ivor Lewis esophagectomy (M-ILE) cohort with a propensity score weighted cohort of open Ivor Lewis esophagectomy (O-ILE) cases after trimodality therapy.

Methods
This is a retrospective review of 223 patients diagnosed with esophageal carcinoma who underwent neoadjuvant chemoradiation followed by M-ILE or O-ILE from April 2009 to February 2019. Inverse probability of treatment weighting (IPTW) adjustment was used to balance the baseline characteristics between study groups. Kaplan–Meier survival curves were calculated for overall survival and recurrence-free survival comparing the two groups. Multivariate Cox proportional hazards regression models were used to determine predictive variables for overall and recurrence-free survival.

Results
The IPTW cohort included patients with esophageal carcinoma who underwent M-ILE (n = 142) or O-ILE (n = 68). The overall rate of postoperative adverse events was not significantly different after IPTW adjustment between the O-ILE and M-ILE trimodality groups (53.4% vs. 39.2%, p = 0.089). The 3-year overall survival (OS) for the M-ILE group was 59.4% (95% CI: 49.8–67.8) compared to 55.7% (95% CI: 39.2–69.4) for the O-ILE group (p = 0.670). The 3-year recurrence-free survival for the M-ILE group was 59.9% (95% CI: 50.2–68.2) compared to 61.6% (95% CI: 41.9–76.3) for the O-ILE group (p = 0.357). A complete response to neoadjuvant chemoradiation was significantly predictive of improved OS and RFS.

Conclusion
The overall and recurrence-free survival rates for M-ILE were not significantly different from O-ILE for esophageal carcinoma after trimodality therapy. Complete response to neoadjuvant chemoradiation was predictive of improved overall and recurrence- free survival.
HSV-1 reactivation is associated with an increased risk of mortality and pneumonia in critically ill COVID-19 patients
Authors: Meyer Antoine , Buetti Niccolò , Houhou-Fidouh Nadhira , Patrier Juliette , Abdel-Nabey Moustafa , Jaquet Pierre , Presente Simona , Girard Tiphaine , Sayagh Faiza , Ruckly Stephane , Wicky Paul-Henri , de Montmollin Etienne , Bouadma Lila , Sonneville Romain , Descamps Diane , Timsit Jean-Francois 
Published: December 2021

Abstract
Background
Data in the literature about HSV reactivation in COVID-19 patients are scarce, and the association between HSV-1 reactivation and mortality remains to be determined. Our objectives were to evaluate the impact of Herpes simplex virus (HSV) reactivation in patients with severe SARS-CoV-2 infections primarily on mortality, and secondarily on hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) and intensive care unit-bloodstream infection (ICU-BSI).

Methods
We conducted an observational study using prospectively collected data and HSV-1 blood and respiratory samples from all critically ill COVID-19 patients in a large reference center who underwent HSV tests. Using multivariable Cox and cause-specific (cs) models, we investigated the association between HSV reactivation and mortality or healthcare-associated infections.

Results
Of the 153 COVID-19 patients admitted for ≥ 48 h from Feb-2020 to Feb-2021, 40/153 (26.1%) patients had confirmed HSV-1 reactivation (19/61 (31.1%) with HSV-positive respiratory samples, and 36/146 (24.7%) with HSV-positive blood samples. Day-60 mortality was higher in patients with HSV-1 reactivation (57.5%) versus without (33.6%, p = 0.001). After adjustment for mortality risk factors, HSV-1 reactivation was associated with an increased mortality risk (hazard risk [HR] 2.05; 95% CI 1.16–3.62; p = 0.01). HAP/VAP occurred in 67/153 (43.8%) and ICU-BSI in 42/153 (27.5%) patients. In patients with HSV-1 reactivation, multivariable cause-specific models showed an increased risk of HAP/VAP (csHR 2.38, 95% CI 1.06–5.39, p = 0.037), but not of ICU-BSI.

Conclusions
HSV-1 reactivation in critically ill COVID-19 patients was associated with an increased risk of day-60 mortality and HAP/VAP.