bluuebunny/crossref_metadata_2025_split huggingface dataset:
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs
Authors: Du Yuxuan , Sun Fengzhu 
Published: April 2022

Abstract

Motivation
Metagenomic binning aims to retrieve microbial genomes directly from ecosystems by clustering metagenomic contigs assembled from short reads into draft genomic bins. Traditional shotgun-based binning methods depend on the contigs’ composition and abundance profiles and are impaired by the paucity of enough samples to construct reliable co-abundance profiles. When applied to a single sample, shotgun-based binning methods struggle to distinguish closely related species only using composition information. As an alternative binning approach, Hi-C-based binning employs metagenomic Hi-C technique to measure the proximity contacts between metagenomic fragments. However, spurious inter-species Hi-C contacts inevitably generated by incorrect ligations of DNA fragments between species link the contigs from varying genomes, weakening the purity of final draft genomic bins. Therefore, it is imperative to develop a binning pipeline to overcome the shortcomings of both types of binning methods on a single sample.

Results
We develop HiFine, a novel binning pipeline to refine the binning results of metagenomic contigs by integrating both Hi-C-based and shotgun-based binning tools. HiFine designs a strategy of fragmentation for the original bin sets derived from the Hi-C-based and shotgun-based binning methods, which considerably increases the purity of initial bins, followed by merging fragmented bins and recruiting unbinned contigs. We demonstrate that HiFine significantly improves the existing binning results of both types of binning methods and achieves better performance in constructing species genomes on publicly available datasets. To the best of our knowledge, HiFine is the first pipeline to integrate different types of tools for the binning of metagenomic contigs.

Availability and implementation
HiFine is available at https://github.com/dyxstat/HiFine.

Supplementary information
Supplementary data are available at Bioinformatics online.
A case report of pseudoaneurysm of coronary artery within a month of percutaneous coronary intervention
Authors: Sharma Raghav , Ruia Aditya Vikram 
Published: April 2022

Abstract

Background
Coronary artery pseudoaneurysms (PSAs) are uncommon and have poorly understood natural history. Unlike true aneurysms, PSAs do not have all the three layers of the vessel in the aneurysmal wall. The PSAs are most commonly seen after an overzealous percutaneous coronary intervention (PCI) which causes damage to the vessel wall. They usually develop slowly after PCI and PSAs within a month of a PCI are not so common. The PSA may be asymptomatic or present with recurrent angina.

Case summary
Here, we report a case of symptomatic PSA to right coronary artery (RCA). The patient had a myocardial infarction for which a PCI was performed to deploy a drug-eluting stent (DES) in the RCA. The patient had in-stent restenosis (ISR) within a week of PCI for which plain old balloon angioplasty (POBA) was performed. The patient continued to have unstable angina and within a month of POBA was diagnosed as a case of PSA by intravascular ultrasound. A covered stent was deployed which effectively sealed off the PSA and resumed normal blood flow to distal vessel. Patient has been doing well on medication [aspirin 75 mg once daily, atorvastatin 80 mg once daily, and P2Y12 platelet inhibitor (Ticagrelor) 90 mg twice daily].

Discussion
The PSAs usually take 6–9 months to develop. However, PSAs have been reported within 1–2 months of PCI. This case also shows that PSAs can occur within a month of PCI. It is possible that over-aggressive and/or high-pressure dilatation and/or deep engagement during POBA performed to open up the ISR could have damaged the struts of the DES and compressed it against the vascular wall. The resultant vascular wall injury could have been the cause of early PSA formation in this case. Hence, cardiologists should be vigilant enough to suspect PSA, especially in a patient presenting with angina. The case also shows that covered stents are a viable option to treat early presentations of PSA.
Transradial versus transfemoral approach for percutaneous coronary intervention in patients with ST-elevation myocardial infarction complicated by cardiogenic shock: a systematic review and meta-analysis
Authors: Ahsan Muhammad Junaid , Ahmad Soban , Latif Azka , Lateef Noman , Ahsan Mohammad Zoraiz , Abusnina Waiel , Nathan Sandeep , Altin S Elissa , Kolte Dhaval S , Messenger John C , Tannenbaum Mark , Goldsweig Andrew M 
Published: April 2022

AbstractBackgroundIn ST-elevation myocardial infarction (STEMI), transradial access (TRA) for percutaneous coronary intervention (PCI) is associated with less bleeding and mortality than transfemoral access (TFA). However, patients in cardiogenic shock (CS) are more often treated via TFA. The aim of this meta-analysis is to compare the safety and efficacy of TRA vs. TFA in CS.MethodsSystematic review was performed querying PubMed, Google Scholar, Cochrane, and clinicaltrials.gov for studies comparing TRA to TFA in PCI for CS. Outcomes included in-hospital, 30-day and ≥1-year mortality, major and access site bleeding, TIMI3 (thrombolytics in myocardial infarction) flow, procedural success, fluoroscopy time, and contrast volume. Risk ratios (RRs) and 95% confidence intervals (CIs) were calculated using random effects models.ResultsSix prospective and eight retrospective studies (TRA, n = 8032; TFA, n = 23 031) were identified. TRA was associated with lower in-hospital (RR 0.59, 95% CI 0.52–0.66, P &lt; 0.0001), 30-day and ≥1-year mortality, as well as less in-hospital major (RR 0.41, 0.31–0.56, P &lt; 0.001) and access site bleeding (RR 0.42, 0.23–0.77, P = 0.005). There were no statistically significant differences in post-PCI coronary flow grade, procedural success, fluoroscopy time, and contrast volume between TRA vs. TFA.ConclusionsIn PCI for STEMI with CS, TRA is associated with significantly lower mortality and bleeding complications than TFA while achieving similar TIMI3 flow and procedural success rates.
Factors predicting recurrence in thymic epithelial neoplasms
Authors: Alkaaki Aroub , Abo Al-Saud Ali , Di Lena Élise , Ramirez-GarciaLuna Jose Luis , Najmeh Sara , Spicer Jonathan , Ferri Lorenzo , Mulder David , Sirois Christian , Cools-Lartigue Jonathan 
Published: April 2022

Abstract

OBJECTIVES
Thymic epithelial neoplasms (TENs) represent a heterogeneous group of rare thoracic malignancies. We analysed the clinicopathological features, survival outcomes, risk factors, and patterns of recurrence in patients undergoing resection.

METHODS
Records were reviewed for adult patients with TEN who underwent resection from 2006 to 2019. Survival rates were assessed using the Kaplan–Meier method. Univariable and multivariable analyses were performed using the log-rank test and Cox proportional hazards model.

RESULTS
A total of 100 patients were analysed (51 females, median age 58 years). Thymoma was the most common histology (n = 92), followed by thymic carcinoma (n = 5) and thymic neuroendocrine tumour (n = 3). Stage II (Masaoka) tumours were most common (n = 51), followed by stage I (n = 27). World Health Organization B2/B3 was the most prominent histological subtype (n = 34). Complete resection (R0) was achieved in 91 patients: 86/92 thymoma, 4/5 thymic carcinoma and 1/3 neuroendocrine tumour. The most common treatment modality was surgery alone in 72 patients, followed by surgery and radiation therapy in 24, and adjuvant chemoradiotherapy in 3 patients. Only one patient with thymic carcinoma received neoadjuvant chemotherapy. The 10-year overall and disease-free survival rates were 86.6% and 83.9%, respectively. Recurrence was most common in neuroendocrine tumours (3/3). Risk factors for recurrence identified on multivariable analyses were: R1/2 resection (hazard ratio 9.30; 95% confidence interval 1.82–36.1), TEN subtype (hazard ratio 8.08; 95% confidence interval 1.24–34.6), and presence of lymphovascular invasion (hazard ratio 9.56; 95% confidence interval 2.56–25.8).

CONCLUSIONS
Complete resection remains critical in patients with TEN. Incomplete resection, high-risk histology, and lymphovascular invasion highlight the need for effective adjuvant modalities. Given the rarity of these diseases, emphasis must be placed on collaborative research conducted on TEN.
International Investment Law and Discipline for the Indebted
Authors: Schneiderman David 
Published: April 2022

Abstract
The object of the article is to recover the institutional memory of the 1980s debt crisis, when the decolonized world experienced forms of tutelage at the hands of international financial institutions, so as to sketch out material and discursive continuities with investment law’s present. The paper asks whether damage awards in investment arbitration serve functions analogous to state indebtedness in the 1980s. As during the 1980–1989 debt crisis, states are expected to generate the conditions for investor confidence by, among other things, guaranteeing rights to property and to contract. State indebtedness, in both periods, places stress on government budgets and reduces the living standards of poor people, contributing to heightened inequality within and between states. The article begins with a social-theoretical discussion of how debt serves to curb the possibilities for political action. This is followed by a review of IMF borrowing practices in the 1980s and a discussion of the merits of comparison with contemporary investment law. The narrative frames arising during the 1980s debt crisis that continue to have resonance in the era of investment law are taken up in subsequent sections, focusing on the refrains of mismanagement, the missing development angle, shrunken policy space and irrelevance of ability to pay. The method is predominantly qualitative, although reference is made to relevant empirical work. In the course of the discussion, the Tethyan Copper v. Pakistan (2019) ruling is periodically revisited as a specimen of how tribunals arrive at damages assessments in investment arbitration. The upshot is that indebtedness in the contemporary world serves functions similar to that in the 1980s: principally to constrain policy capacity in a wide range of sectors. These binding constraints serve the interests of only a small set of actors, while those rendered most vulnerable by these constraints are relegated to the margins.
Single versus multiple arterial grafting in diabetic patients at 10 years: the Arterial Revascularization Trial
Authors: Taggart David P , Audisio Katia , Gerry Stephen , Robinson N Bryce , Rahouma Mohamed , Soletti Giovanni Jr , Cancelli Gianmarco , Benedetto Umberto , Lees Belinda , Gray Alastair , Stefil Maria , Flather Marcus , Gaudino Mario , Investigators A R T 
Published: April 2022

Abstract

Aims
To evaluate the impact of multiple arterial grafting (MAG) vs. single arterial grafting (SAG) in a post hoc analysis of 10-year outcomes in patients with diabetes mellitus (DM) from the Arterial Revascularization Trial (ART).

Methods and results
The primary endpoint was all-cause mortality and the secondary endpoint was a composite of major adverse cardiac events (MACE) at 10-year follow-up. Patients were stratified by diabetes status (non-DM and DM) and grafting strategy (MAG vs. SAG). A total of 3020 patients were included in the analysis; 716 (23.7%) had DM. Overall, 55.8% non-DM patients received MAG and 44.2% received SAG, while 56.6% DM patients received MAG and 43.4% received SAG. The use of MAG compared with SAG was associated with lower 10-year mortality for both non-DM [17.7 vs. 21.0%, adjusted hazard ratio (HR) 0.87, 95% confidence interval (CI) 0.72–1.06] and DM patients (21.5 vs. 29.9%, adjusted HR 0.65, 95% CI 0.48–0.89; P for interaction = 0.12). For both groups, the rate of 10-year MACE was also lower for MAG vs. SAG. Overall, deep sternal wound infections (DSWIs) were uncommon but more frequent in the MAG vs. SAG group in both non-DM (3.3 vs. 2.1%) and DM patients (7.9 vs. 4.8%). The highest rates of DSWI were in insulin-treated patients receiving MAG (9.6 vs. 6.3%, when compared with SAG).

Conclusion
In this post hoc analysis of the ART, MAG was associated with substantially lower mortality rates at 10 years after coronary artery bypass grafting in patients with DM. Patients with DM receiving MAG had a higher incidence of DSWI, especially if insulin dependent.
The collateral damage of COVID-19 to cardiovascular services: a meta-analysis
Authors: Nadarajah Ramesh , Wu Jianhua , Hurdus Ben , Asma Samira , Bhatt Deepak L , Biondi-Zoccai Giuseppe , Mehta Laxmi S , Ram C Venkata S , Ribeiro Antonio Luiz P , Van Spall Harriette G C , Deanfield John E , Lüscher Thomas F , Mamas Mamas , Gale Chris P 
Published: April 2022

Abstract

Aims
The effect of the COVID-19 pandemic on care and outcomes across non-COVID-19 cardiovascular (CV) diseases is unknown. A systematic review and meta-analysis was performed to quantify the effect and investigate for variation by CV disease, geographic region, country income classification and the time course of the pandemic.

Methods and results
From January 2019 to December 2021, Medline and Embase databases were searched for observational studies comparing a pandemic and pre-pandemic period with relation to CV disease hospitalisations, diagnostic and interventional procedures, outpatient consultations, and mortality. Observational data were synthesised by incidence rate ratios (IRR) and risk ratios (RR) for binary outcomes and weighted mean differences for continuous outcomes with 95% confidence intervals. The study was registered with PROSPERO (CRD42021265930). A total of 158 studies, covering 49 countries and 6 continents, were used for quantitative synthesis. Most studies (80%) reported information for high-income countries (HICs). Across all CV disease and geographies there were fewer hospitalisations, diagnostic and interventional procedures, and outpatient consultations during the pandemic. By meta-regression, in low-middle income countries (LMICs) compared to HICs the decline in ST-segment elevation myocardial infarction (STEMI) hospitalisations (RR 0.79, 95% confidence interval [CI] 0.66–0.94) and revascularisation (RR 0.73, 95% CI 0.62–0.87) was more severe. In LMICs, but not HICs, in-hospital mortality increased for STEMI (RR 1.22, 95% CI 1.10–1.37) and heart failure (RR 1.08, 95% CI 1.04–1.12). The magnitude of decline in hospitalisations for CV diseases did not differ between the first and second wave.

Conclusions
There was substantial global collateral CV damage during the COVID-19 pandemic with disparity in severity by country income classification.
Development and validation of a prediction model for unemployment and work disability among 55 950 Dutch workers
Authors: Ots Patricia , Oude Hengel Karen M , Burdorf Alex , Robroek Suzan J W , Nieboer Daan , Schram Jolinda L D , van Zon Sander K R , Brouwer Sandra 
Published: April 2022

Abstract

Background
This study developed prediction models for involuntary exit from paid employment through unemployment and disability benefits and examined if predictors and discriminative ability of these models differ between five common chronic diseases.

Methods
Data from workers in the Lifelines Cohort Study (n = 55 950) were enriched with monthly information on employment status from Statistics Netherlands. Potential predictors included sociodemographic factors, chronic diseases, unhealthy behaviours and working conditions. Data were analyzed using cause-specific Cox regression analyses. Models were evaluated with the C-index and the positive and negative predictive values (PPV and NPV, respectively). The developed models were externally validated using data from the Study on Transitions in Employment, Ability and Motivation.

Results
Being female, low education, depression, smoking, obesity, low development possibilities and low social support were predictors of unemployment and disability. Low meaning of work and low physical activity increased the risk for unemployment, while all chronic diseases increased the risk of disability benefits. The discriminative ability of the models of the development and validation cohort were low for unemployment (c = 0.62; c = 0.60) and disability benefits (c = 0.68; c = 0.75). After stratification for specific chronic diseases, the discriminative ability of models predicting disability benefits improved for cardiovascular disease (c = 0.81), chronic obstructive pulmonary disease (c = 0.74) and diabetes mellitus type 2 (c = 0.74). The PPV was low while the NPV was high for all models.

Conclusion
Taking workers’ particular disease into account may contribute to an improved prediction of disability benefits, yet risk factors are better examined at the population level rather than at the individual level.
Higher risk, higher protection: COVID-19 risk among immigrants in France—results from the population-based EpiCov survey
Authors: Gosselin Anne , Warszawski Josiane , Bajos Nathalie ,   for the EpiCov Study Group, Bajos Nathalie , Warszawski Josiane , Bagein Guillaume , Beck François , Counil Emilie , Jusot Florence , Lydié Nathalie , Martin Claude , Meyer Laurence , Raynaud Philippe , Rouquette Alexandra , Pailhé Ariane , Rahib Delphine , Sillard Patrick , Slama Rémy , Spire Alexis 
Published: April 2022

Abstract

Background
Immigrants and ethnic/racialized minorities have been identified as being at higher risk of coronavirus disease-19 (COVID-19) infection, but few studies report on their exposures and prevention behaviours. This study aims to examine the social distribution of COVID-19 exposure (overcrowding, working outside the home, use of public transport to go to work) and prevention behaviours (use of face masks, washing hands, respect for physical distance) in France during the first wave of the epidemic.

Methods
We used the EpiCov population-based survey from a random sample of individuals aged 15 years or more. We determined the distribution of the self-reported outcomes according to migratory status and sex, using χ2 tests. We modelled the probability of outcomes with logistic regression. Finally, we focused the analysis on the Greater Paris area and accounted for neighbourhood characteristics.

Results
A total of 111 824 participants were included in the study. Overall, immigrant groups from non-European countries were more exposed to COVID-19-related factors and more respectful of prevention measures. The probability of overcrowding and the use of public transport was higher for immigrants from sub-Saharan Africa [adjusted odds ratio (aOR) = 3.71 (3.19; 4.32), aOR = 6.36 (4.86; 8.32)] than for the majority population. Immigrant groups were less likely to have a non-systematic use of face masks and to breach physical distancing than the majority population [for immigrants from sub-Saharan Africa, aOR = 0.32 (0.28; 0.37) and aOR = 0.71 (0.61; 0.81), respectively]. Living in a neighbourhood with a higher share of immigrants was associated with higher exposure and better prevention behaviours.

Conclusions
In France, immigrants had a higher exposure to COVID-19-related factors and more systematic prevention behaviours.
Comparative Study of Protein Aggregation Propensity and Mutation Tolerance Between Naked Mole-Rat and Mouse
Authors: Besse Savandara , Poujol Raphaël , Hussin Julie G. 
Published: April 2022

Abstract
The molecular mechanisms of aging and life expectancy have been studied in model organisms with short lifespans. However, long-lived species may provide insights into successful strategies for healthy aging, potentially opening the door for novel therapeutic interventions in age-related diseases. Notably, naked mole-rats, the longest-lived rodent, present attenuated aging phenotypes compared with mice. Their resistance toward oxidative stress has been proposed as one hallmark of their healthy aging, suggesting their ability to maintain cell homeostasis, specifically their protein homeostasis. To identify the general principles behind their protein homeostasis robustness, we compared the aggregation propensity and mutation tolerance of naked mole-rat and mouse orthologous proteins. Our analysis showed no proteome-wide differential effects in aggregation propensity and mutation tolerance between these species, but several subsets of proteins with a significant difference in aggregation propensity. We found an enrichment of proteins with higher aggregation propensity in naked mole-rat, and these are functionally involved in the inflammasome complex and nucleic acid binding. On the other hand, proteins with lower aggregation propensity in naked mole-rat have a significantly higher mutation tolerance compared with the rest of the proteins. Among them, we identified proteins known to be associated with neurodegenerative and age-related diseases. These findings highlight the intriguing hypothesis about the capacity of the naked mole-rat proteome to delay aging through its proteomic intrinsic architecture.
DnaA and SspA Regulation of the iraD gene of E. coli: an alternative DNA damage response independent of LexA/RecA
Authors: Sass Thalia H , Ferrazzoli Alexander E , Lovett Susan T 
Published: April 2022

Abstract
The transcription factor RpoS (σS) of Escherichia coli controls many genes important for tolerance of a variety of stress conditions. IraD promotes the post-translation stability of RpoS by inhibition of RssB, an adaptor protein for ClpXP degradation. We have previously documented DNA damage induction of iraD expression, independent of the SOS response. Both iraD and rpoS are required for tolerance to DNA damaging treatments such as H2O2 and the replication inhibitor azidothymidine (AZT) in the log phase of growth. Using luciferase gene fusions to the 672 bp iraD upstream region, we show here that both promoters of iraD are induced by AZT. Genetic analysis suggests that both promoters are repressed by DnaA-ATP, partially dependent on a putative DnaA box at -81 bp and are regulated by RIDA (regulatory inactivation of DnaA), dependent on the DnaN processivity clamp. By electrophoretic mobility shift assays we show that purified DnaA protein binds to the iraD upstream region, so DnaA regulation of IraD is likely to be direct. DNA damage induction of iraD during log phase growth is abolished in the dnaA-T174P mutant, suggesting that DNA damage, in some way, relieves DnaA repression, possibly through the accumulation of replication clamps and enhanced RIDA. We also demonstrate that the RNA-polymerase associated factor, SspA (stringent starvation protein A), induced by the accumulation of ppGpp, also affects iraD expression, with a positive effect on constitutive expression and a negative effect on AZT-induced expression.