bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts
Authors: Zhang Chuanjie , Chen Tianhe , Li Zongtai , Liu Ao , Xu Yang , Gao Yi , Xu Danfeng 
Published: August 2020

Abstract
Prostate cancer stemness (PCS) cells have been reported to drive tumor progression, recurrence and drug resistance. However, there is lacking systematical assessment of stemlike indices and associations with immunological properties in prostate adenocarcinoma (PRAD). We thus collected 7 PRAD cohorts with 1465 men and calculated the stemlike indices for each sample using one-class logistic regression machine learning algorithm. We selected the mRNAsi to quantify the stemlike indices that correlated significantly with prognosis and accordingly identified 21 PCS-related CpG loci and 13 pivotal signature. The 13-gene based PCS model possessed high predictive significance for progression-free survival (PFS) that was trained and validated in 7 independent cohorts. Meanwhile, we conducted consensus clustering and classified the total cohorts into 5 PCS clusters with distinct outcomes. Samples in PCScluster5 possessed the highest stemness fractions and suffered from the worst prognosis. Additionally, we implemented the CIBERSORT algorithm to infer the differential abundance across 5 PCS clusters. The activated immune cells (CD8+ T cell and dendritic cells) infiltrated significantly less in PCScluster5 than other clusters, supporting the negative regulations between stemlike indices and anticancer immunity. High mRNAsi was also found to be associated with up-regulation of immunosuppressive checkpoints, like PDL1. Lastly, we used the Connectivity Map (CMap) resource to screen potential compounds for targeting PRAD stemness, including the top hits of cell cycle inhibitor and FOXM1 inhibitor. Taken together, our study comprehensively evaluated the PRAD stemlike indices based on large cohorts and established a 13-gene based classifier for predicting prognosis or potential strategies for stemness treatment.
AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer’s disease
Authors: Wang Zhe , Meng Lei , Liu Hong , Shen Liang , Ji Hong-Fang 
Published: August 2020

Abstract
In view of great difficulties in the pathogenesis analysis of Alzheimer’s disease (AD) presently, profiling the modifiable risk factors is crucial for early detection and intervention of AD. However, the causal associations among them have yet to be identified, and the effective integration and application of these data also remain considerable challenges due to the lack of efficient collection and analysis procedures. To address this issue, we performed comprehensive analyses by two-sample Mendelian randomization (2SMR) and established the AlzRiskMR database (https://github.com/SDBMC/RiskFactors2AD). Four 2SMR analysis methods, including inverse variance weighted (IVW), MR-Egger, weighted median, and weighted mode, were used for the complementary calculation to test the reliability of the results. The database currently comprises 1870 sets of data of Genome-Wide Association Studies (GWAS) from the MR-Base and NHGRI-EBI GWAS Catalog database. AlzRiskMR database not only estimates causal associations between modifiable risk factors and AD but also offers a useful and timely resource for early intervention of AD development incidence.
Bayesian sparse heritability analysis with high-dimensional neuroimaging phenotypes
Authors: Zhao Yize , Li Tengfei , Zhu Hongtu 
Published: August 2020

SummaryHeritability analysis plays a central role in quantitative genetics to describe genetic contribution to human complex traits and prioritize downstream analyses under large-scale phenotypes. Existing works largely focus on modeling single phenotype and currently available multivariate phenotypic methods often suffer from scaling and interpretation. In this article, motivated by understanding how genetic underpinning impacts human brain variation, we develop an integrative Bayesian heritability analysis to jointly estimate heritabilities for high-dimensional neuroimaging traits. To induce sparsity and incorporate brain anatomical configuration, we impose hierarchical selection among both regional and local measurements based on brain structural network and voxel dependence. We also use a nonparametric Dirichlet process mixture model to realize grouping among single nucleotide polymorphism-associated phenotypic variations, providing biological plausibility. Through extensive simulations, we show the proposed method outperforms existing ones in heritability estimation and heritable traits selection under various scenarios. We finally apply the method to two large-scale imaging genetics datasets: the Alzheimer’s Disease Neuroimaging Initiative and United Kingdom Biobank and show biologically meaningful results.
Electricity Use as a Real-Time Indicator of the Economic Burden of the COVID-19-Related Lockdown: Evidence from Switzerland
Authors: Janzen Benedikt , Radulescu Doina 
Published: August 2020

Abstract
We employ hourly electricity load data for Switzerland as a real-time indicator of the economic effects of the lockdown following the spread of SARS-CoV-2. Our findings reveal that following the drastic lockdown, overall electricity use decreased by 4.6%, with a reduction of even 14.3% in the Canton of Ticino where the number of confirmed cases per capita was one of the highest in Switzerland and also stricter measures such as closures of construction sites and industrial companies were implemented on top of federal regulations. Looking at working days only, we estimate a Swiss-wide decrease in electricity consumption of 7.4%. Assuming industry, services, transport, and agriculture account for 67% of electricity demand, the 4.6% decrease in electricity use implies an almost 7% output reduction in these sectors. In addition, the reduced electricity imports and the change in the generation mix of neighbouring countries, also translates into reduced CO2 emissions related to these imports. (JEL codes: C53, Q4, C3)
Treatment of Nontuberculous Mycobacterial Pulmonary Disease: An Official ATS/ERS/ESCMID/IDSA Clinical Practice Guideline
Authors: Daley Charles L , Iaccarino Jonathan M , Lange Christoph , Cambau Emmanuelle , Wallace Richard J , Andrejak Claire , Böttger Erik C , Brozek Jan , Griffith David E , Guglielmetti Lorenzo , Huitt Gwen A , Knight Shandra L , Leitman Philip , Marras Theodore K , Olivier Kenneth N , Santin Miguel , Stout Jason E , Tortoli Enrico , van Ingen Jakko , Wagner Dirk , Winthrop Kevin L 
Published: August 2020

Abstract
Nontuberculous mycobacteria (NTM) represent over 190 species and subspecies, some of which can produce disease in humans of all ages and can affect both pulmonary and extrapulmonary sites. This guideline focuses on pulmonary disease in adults (without cystic fibrosis or human immunodeficiency virus infection) caused by the most common NTM pathogens such as Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium xenopi among the slowly growing NTM and Mycobacterium abscessus among the rapidly growing NTM. A panel of experts was carefully selected by leading international respiratory medicine and infectious diseases societies (ATS, ERS, ESCMID, IDSA) and included specialists in pulmonary medicine, infectious diseases and clinical microbiology, laboratory medicine, and patient advocacy. Systematic reviews were conducted around each of 22 PICO (Population, Intervention, Comparator, Outcome) questions and the recommendations were formulated, written, and graded using the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach. Thirty-one evidence-based recommendations about treatment of NTM pulmonary disease are provided. This guideline is intended for use by healthcare professionals who care for patients with NTM pulmonary disease, including specialists in infectious diseases and pulmonary diseases.
Bacille Calmette-Guérin Vaccination in Infancy Does Not Protect Against Coronavirus Disease 2019 (COVID-19): Evidence From a Natural Experiment in Sweden
Authors: de Chaisemartin Clément , de Chaisemartin Luc 
Published: August 2020

Abstract

Background
The bacille Calmette-Guérin (BCG) tuberculosis vaccine has immunity benefits against respiratory infections. Accordingly, it has been hypothesized to have a protective effect against coronavirus disease 2019 (COVID-19). Recent research found that countries with universal BCG childhood vaccination policies tend to be less affected by the COVID-19 pandemic. However, such ecological studies are biased by numerous confounders. Instead, this paper reports on a rare nationwide natural experiment that occurred in Sweden in 1975, where discontinuation of newborns’ BCG vaccination led to a dramatic decrease in BCG coverage rate, thus allowing us to estimate BCG’s effect without the biases associated with cross-country comparisons.

Methods
Numbers of COVID-19 cases and hospitalizations were recorded for birth cohorts born just before and just after 1975, representing 1 026 304 and 1 018 544 individuals, respectively. We used regression discontinuity to assess the effect of BCG vaccination on COVID-19–related outcomes. On such a large population, this method allows for a precision that would be hard to achieve using a randomized controlled trial.

Results
The odds ratios (95% CI) for COVID-19 cases and COVID-19–related hospitalizations were 1.0005 (.8130–1.1881) and 1.2046 (.7532–1.6560), allowing us to reject fairly modest effects of universal BCG vaccination. We can reject with 95% confidence that universal BCG vaccination reduces the number of cases by 19% and the number of hospitalizations by 25%.

Conclusions
While the effect of a recent vaccination must be evaluated, we provide strong evidence that receiving the BCG vaccine at birth does not have a protective effect against COVID-19 among middle-aged individuals.
Do individual cities matter? Negotiating the particular
Authors: Beauregard Robert A 
Published: August 2020

AbstractIn this article, I reflect on how urban scholars negotiate between the general and the particular not by turning to sampling strategies or statistical techniques but by situating the city in a favourable rhetorical space. In effect, they attempt to close the gap theoretically. My substantive and specific focus is urban scholarship that addresses individual cities and that frames that city either as a laboratory in which to do urban research, a lens through which to see other cities, or as the archetype for a school of urban studies. I concentrate mainly on the work of US urban scholars.
Fidelity and Timing of Spotted Lanternfly (Hemiptera: Fulgoridae) Attack Patterns on Ornamental Trees in the Suburban Landscape
Authors: Mason Charles J , Walsh Brian , Keller Joseph , Couture John J , Calvin Dennis , Urban Julie M 
Published: August 2020

Abstract
Invasive herbivores can have dramatic impacts in new environments by altering landscape composition, displacing natives, and causing plant decline and mortality. One of the most recent invasive insects in the United States, the spotted lanternfly (Lycorma delicatula), has the potential to cause substantial economic and environmental impacts in agriculture and forestry. Spotted lanternfly exhibits a broad host range, yet reports of late-season movement from the surrounding landscapes onto select tree species in suburban environments have been reported. In this study, we aimed to evaluate the fidelity of spotted lanternfly attack on specific, individual trees within the same species during this movement period. In 2018 and 2019, we observed that individual red (Acer rubrum L. [Sapindales: Sapindaceae]) and silver maple (Acer saccharinum L. [Sapindales: Sapindaceae]) trees were preferentially attacked over other nearby trees of the same species. Foliar elemental composition was a good predictor of spotted lanternfly attack numbers, indicating that individual variation in nutrients may influence spotted lanternfly attraction to and/or retention on maple trees. Our data also confirm reports of late-season movement from surrounding landscapes throughout autumn. Collectively, our results show that spotted lanternfly exhibits some fidelity to particular trees in the landscape during this movement period. While other potential mechanisms also contribute to host plant selection by spotted lanternfly, our data show that host nutritional profiles influence spotted lanternfly infestation of suburban trees at the landscape scale. Our data establish that late-season infestations of suburban trees by spotted lanternfly occurred and that variation in host quality should be further considered in the management of this invasive insect pest.
Risk factors for non-cancer death after surgery in patients with stage I non-small-cell lung cancer
Authors: Kanzaki Ryu , Nagoya Akihiro , Kanou Takashi , Ose Naoko , Funaki Soichiro , Minami Masato , Okamoto Yuna , Tabuchi Hiroto , Hoshino Tomoko , Tajima Tetsuya , Fujii Makoto , Ohno Yuko , Shintani Yasushi 
Published: August 2020

Abstract

OBJECTIVES
With improvements in the outcome of treatment for non-small-cell lung cancer (NSCLC), other diseases may account for a high death rate after surgery in patients with stage I NSCLC. In the present study, we analysed the associations between the clinical factors and non-cancer death after surgery in these patients.

METHODS
The records of 514 patients with stage I NSCLC who underwent surgery were retrospectively reviewed; a proportional hazards model for the subdistribution of a competing risk was conducted to define the risk factors for non-cancer death.

RESULTS
The mean patient age was 67 years. A total of 367 patients (71%) underwent bilobectomy or lobectomy while 147 (29%) underwent sublobar resection. The pathological stage was IA in 386 (75%) and IB in 128 (25%) patients. Three patients (0.6%) died within 90 days after surgery, and 108 (21%) experienced postoperative complications. Until the time of writing this report, 83 patients had died during the follow-up. The cause of death was primary lung cancer in 38 (46%) patients and other diseases in 45 (54%) patients, including non-cancer causes in 29 patients, such as pneumonia, cardiac death and cerebral stroke. According to a multivariable competing risk analysis for non-cancer death age (≥70 years), sex (male), body mass index (BMI &lt;18.5), postoperative complications and % forced expiratory volume in 1 s (&lt;80) were identified as risk factors for postoperative non-cancer death.

CONCLUSIONS
Advanced age (≥70 years), male sex, low BMI (&lt;18.5), postoperative complications and low preoperative % forced expiratory volume in 1 s (&lt;80) were found to be the risk factors for postoperative non-cancer death after surgery in patients with stage I NSCLC.
Impact of Child-Pugh class A liver cirrhosis on perioperative outcomes of patients with oesophageal cancer: a propensity score-matched analysis
Authors: Cheng Chuan , Wen Yu-Wen , Tsai Chun-Yi , Chao Yin-Kai 
Published: August 2020

Abstract

OBJECTIVES
Advanced-stage (Child-Pugh classes B and C) liver cirrhosis (LC) is a contraindication for oesophagectomy. However, the question as to whether Child-Pugh class A LC may have an impact on perioperative outcomes remains unanswered. This retrospective single-centre study was designed to address this issue.

METHODS
This was a single-centre, retrospective, propensity-matched study. The perioperative outcomes of patients with Child-Pugh class A LC were compared with those of patients without LC after propensity score matching.

RESULTS
Out of a cohort consisting of 811 patients, we identified 51 cases with Child-Pugh class A LC. After the application of propensity score matching, the LC and no-LC groups consisted of 50 and 100 patients, respectively. The presence of LC did not compromise the quality of surgical resection as attested to by similar lymph node yields and R0 rates. However, patients with LC patients were more prone to developing postoperative pneumonia (22% vs 9%, P = 0.027), pleural effusion (38% vs 20%, P = 0.018) and chylothorax (10% vs 1%, P = 0.016) and had longer intensive care unit stay (mean: 6.10 vs 2.58 days, P = 0.002) compared with the no-LC group. Multivariable analysis identified thoracic duct ligation [odds ratio (OR) 12.292, P = 0.042] and a higher number of dissected nodes (OR 4.375, P = 0.037) as independent risk factors for chylothorax and pleural effusion, respectively. The detrimental effect of these variables was limited to the LC group.

CONCLUSIONS
Oesophagectomy portends a higher morbidity in patients with Child-Pugh class A LC. A meticulous management of lymphatic ducts during mediastinal dissection may improve surgical outcomes in this high-risk group.
Associations between gut microbiota, faecal short-chain fatty acids, and blood pressure across ethnic groups: the HELIUS study
Authors: Verhaar Barbara J H , Collard Didier , Prodan Andrei , Levels Johannes H M , Zwinderman Aeilko H , Bäckhed Fredrik , Vogt Liffert , Peters Mike J L , Muller Majon , Nieuwdorp Max , van den Born Bert-Jan H 
Published: August 2020

Abstract

Aims
Preliminary evidence from animal and human studies shows that gut microbiota composition and levels of microbiota-derived metabolites, including short-chain fatty acids (SCFAs), are associated with blood pressure (BP). We hypothesized that faecal microbiota composition and derived metabolites may be differently associated with BP across ethnic groups.

Methods and results
We included 4672 subjects (mean age 49.8 ± 11.7 years, 52% women) from six different ethnic groups participating in the HEalthy Life In an Urban Setting (HELIUS) study. The gut microbiota was profiled using 16S rRNA gene amplicon sequencing. Associations between microbiota composition and office BP were assessed using machine learning prediction models. In the subgroups with the largest associations, faecal SCFA levels were compared in 200 subjects with lower or higher systolic BP. Faecal microbiota composition explained 4.4% of the total systolic BP variance. Best predictors for systolic BP included Roseburia spp., Clostridium spp., Romboutsia spp., and Ruminococcaceae spp. Explained variance of the microbiota composition was highest in Dutch subjects (4.8%), but very low in South-Asian Surinamese, African Surinamese, Ghanaian, Moroccan and Turkish descent groups (explained variance &lt;0.8%). Faecal SCFA levels, including acetate (P &lt; 0.05) and propionate (P &lt; 0.01), were lower in young Dutch participants with low systolic BP.

Conclusions
Faecal microbiota composition is associated with BP, but with strongly divergent associations between ethnic groups. Intriguingly, while Dutch participants with lower BP had higher abundances of several SCFA-producing microbes, they had lower faecal SCFA levels. Intervention studies with SCFAs could provide more insight in the effects of these metabolites on BP.
Wearable cardioverter-defibrillator in patients with a transient risk of sudden cardiac death: the WEARIT-France cohort study
Authors: Garcia Rodrigue , Combes Nicolas , Defaye Pascal , Narayanan Kumar , Guedon-Moreau Laurence , Boveda Serge , Blangy Hugues , Bouet Jérôme , Briand Florent , Chevalier Philippe , Cottin Yves , Da Costa Antoine , Degand Bruno , Deharo Jean-Claude , Eschalier Romain , Extramiana Fabrice , Goralski Marc , Guy-Moyat Benoit , Guyomar Yves , Hermida Jean-Sylvain , Jourda François , Lellouche Nicolas , Mahfoud Mohanad , Manenti Vladimir , Mansourati Jacques , Martin Angéline , Pasquié Jean-Luc , Ritter Philippe , Rollin Anne , Tibi Thierry , Yalioua Arab , Gras Daniel , Sadoul Nicolas , Piot Olivier , Leclercq Christophe , Marijon Eloi 
Published: August 2020

Abstract

Aims
We aimed to provide contemporary real-world data on wearable cardioverter-defibrillator (WCD) use, not only in terms of effectiveness and safety but also compliance and acceptability.

Methods and results
Across 88 French centres, the WEARIT-France study enrolled retrospectively patients who used the WCD between May 2014 and December 2016, and prospectively all patients equipped for WCD therapy between January 2017 and March 2018. All patients received systematic education session through a standardized programme across France at the time of initiation of WCD therapy and were systematically enrolled in the LifeVest Network remote services. Overall, 1157 patients were included (mean age 60 ± 12 years, 16% women; 46% prospectively): 82.1% with ischaemic cardiomyopathy, 10.3% after implantable cardioverter-defibrillator explant, and 7.6% before heart transplantation. Median WCD usage period was 62 (37–97) days. Median daily wear time of WCD was 23.4 (22.2–23.8) h. In multivariate analysis, younger age was associated with lower compliance [adjusted odds ratio (OR) 0.97, 95% confidence interval (CI) 0.95–0.99, P &lt; 0.01]. A total of 18 participants (1.6%) received at least one appropriate shock, giving an incidence of appropriate therapy of 7.2 per 100 patient-years. Patient-response button allowed the shock to be aborted in 35.7% of well-tolerated sustained ventricular arrhythmias and in 95.4% of inappropriate ventricular arrhythmia detection, finally resulting in an inappropriate therapy in eight patients (0.7%).

Conclusion
Our real-life findings reinforce previous studies on the efficacy and safety of the WCD in the setting of transient high-risk group in selected patients. Moreover, they emphasize the fact that when prescribed appropriately, in concert with adequate patient education and dedicated follow-up using specific remote monitoring system, compliance with WCD is high and the device well-tolerated by the patient.
Volatile self-inhibitor of spore germination in pathogenic Mucorale Rhizopus arrhizus
Authors: Kaur Mahaldeep , Singh Rachna 
Published: August 2020

ABSTRACT
Rhizopus arrhizus is a common pathogenic Mucoralean mold that exists as a saprophyte, and is disseminated through sporangiospores, which germinate to form mycelia under suitable environmental or infection settings. Such morphological transitions are often mediated by self-produced effector molecules in a density-dependent fashion. This study aimed to elucidate if a quorum-dependent, cell-density-driven phenomenon exists in R. arrhizus, and identify the molecule(s) involved. The germination of R. arrhizus was observed to be reliant on the seeding density, with nearly 71% and 47% germination in Sabouraud dextrose and glucose asparagine media respectively at 1 × 105–1 × 106 spores/mL, and only 10% and 1% germination respectively with 1 × 108 spores/mL. The late-growth-stage supernatant also hindered the spore germination and liquid-culture biomass in a dose-dependent way. These effects were being mediated by a volatile inhibitor present in the headspace and supernatant of R. arrhizus cultures, identified as 2-methyl-2-butene by gas chromatography and electron ionization-quadrupole mass spectrometry. The compound was present in a density-dependent manner and considerably impaired fungal germ-tube emergence and elongation during germination. Spore swelling remained unaffected. Multiple thin protrusions comprising of F-actin and microtubules were seen emanating from the treated cells, suggestive of filopodia-like and cytoneme-like extensions. The same compound was also detected in Rhizomucor pusillus.