bluuebunny/crossref_metadata_2025_split huggingface dataset:
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
Authors: Rognes Torbjørn , Scheffer Lonneke , Greiff Victor , Sandve Geir Kjetil 
Published: July 2022

AbstractMotivationAdaptive immune receptor (AIR) repertoires (AIRRs) record past immune encounters with exquisite specificity. Therefore, identifying identical or similar AIR sequences across individuals is a key step in AIRR analysis for revealing convergent immune response patterns that may be exploited for diagnostics and therapy. Existing methods for quantifying AIRR overlap scale poorly with increasing dataset numbers and sizes. To address this limitation, we developed CompAIRR, which enables ultra-fast computation of AIRR overlap, based on either exact or approximate sequence matching.ResultsCompAIRR improves computational speed 1000-fold relative to the state of the art and uses only one-third of the memory: on the same machine, the exact pairwise AIRR overlap of 104 AIRRs with 105 sequences is found in ∼17 min, while the fastest alternative tool requires 10 days. CompAIRR has been integrated with the machine learning ecosystem immuneML to speed up commonly used AIRR-based machine learning applications.Availability and implementationCompAIRR code and documentation are available at https://github.com/uio-bmi/compairr. Docker images are available at https://hub.docker.com/r/torognes/compairr. The code to replicate the synthetic datasets, scripts for benchmarking and creating figures, and all raw data underlying the figures are available at https://github.com/uio-bmi/compairr-benchmarking.Supplementary informationSupplementary data are available at Bioinformatics online.
Doppler-derived haemodynamics performed during admission echocardiography predict in-hospital mortality in cardiac intensive care unit patients
Authors: Jentzer Jacob C , Tabi Meir , Wiley Brandon M , Lanspa Michael J , Anavekar Nandan S , Oh Jae K 
Published: July 2022

Abstract

Aims
Cardiac point-of-care ultrasound (CV-POCUS) has become a fundamental part for the assessment of patients admitted to cardiac intensive care units (CICU). We sought to refine the practice of CV-POCUS by identifying 2D and Doppler-derived measurements from bedside transthoracic echocardiograms (TTEs) performed in the CICU that are associated with mortality.

Methods and results
We retrospectively included Mayo Clinic CICU patients admitted from 2007 to 2018 and assessed the TTEs performed within 1 day of CICU admission, including Doppler and 2D measurements of left and right ventricular function. Logistic regression and classification and regression tree (CART) analysis were used to determine the association between TTE variables with in-hospital mortality. A total of 6957 patients were included with a mean age of 68.0 ± 14.9 years (37.0% females). A total of 609 (8.8%) patients died in the hospital. Inpatient deaths group had worse biventricular systolic function [left ventricular ejection fraction (LVEF) 48.2 ± 16.0% vs. 38.7 ± 18.2%, P &lt; 0.0001], higher filling pressures, and lower forward flow. The strongest TTE predictors of hospital mortality were left ventricular outflow tract velocity–time integral [LVOT VTI, adjusted OR 0.912 per 1 cm higher, 95% confidence interval (CI) 0.883–0.942, P &lt; 0.0001] followed by medial mitral E/e′ ratio (adjusted OR 1.024 per 1 unit higher, 95% CI 1.010–1.039, P = 0.0011). Classification and regression tree analysis identified LVOT VTI &lt;16 cm as the most important TTE predictor of mortality.

Conclusions
Doppler-derived haemodynamic TTE parameters have a strong association with mortality in the CICU, particularly LVOT VTI &lt;16 cm or mitral E/e′ ratio &gt;15. The incorporation of these simplified Doppler-derived haemodynamics into admission CV-POCUS facilitates early risk stratification and strengthens the clinical yield of the ultrasound exam.
Right ventricular strain related to pulmonary artery pressure predicts clinical outcome in patients with pulmonary arterial hypertension
Authors: Ünlü Serkan , Bézy Stéphanie , Cvijic Marta , Duchenne Jürgen , Delcroix Marion , Voigt Jens-Uwe 
Published: July 2022

Abstract

Aims
In pulmonary arterial hypertension (PAH), the right ventricle (RV) is exposed to an increased afterload. In response, RV mechanics are altered. Markers which would relate RV function and afterload could therefore aid to understand this complex response system and could be of prognostic value. The aim of our study was to (i) assess the RV-arterial coupling using ratio between RV strain and systolic pulmonary artery pressure (sPAP), in patients with PAH, and (ii) investigate the prognostic value of this new parameter over other echocardiographic parameters.

Methods and results
Echocardiograms of 65 pre-capillary PAH patients (45 females, age 61 ± 15 years) were retrospectively analysed. Fractional area change (FAC), sPAP, tricuspid annular plane systolic excursion, and RV free-wall (FW) longitudinal strain (LS) were measured. A primary endpoint of death or heart/lung transplantation described clinical endpoint. Patients who reached a clinical endpoint had worse functional capacity (New York Heart Association), reduced RV function, and higher sPAP. Left ventricle function was similar in both groups. Only RVFW LS/sPAP ratio was found as an independent predictor of clinical endpoint in multivariable analysis (hazard ratio 8.3, 95% confidence interval 3.2–21.6, P &lt; 0.001). The RWFW LS/sPAP (cut-off 0.19) demonstrated a good accuracy for the prediction of reaching the clinical endpoint, with a sensitivity of 92% and specificity of 82.5%.

Conclusion
RVFW LS/sPAP ratio significantly predicts all-cause mortality and heart–lung transplantation, and was superior to other well-established parameters, in patients with pre-capillary PAH. We therefore propose RVFW LS/sPAP as a new prognostic echocardiographic marker.
Clinical, Endoscopic, and Radiological Effectiveness of Ustekinumab in Bio-naïve Versus Bio-experienced Patients With Crohn’s Disease: Real-world Experience From a Large Canadian Center
Authors: Sedano Rocio , Guizzetti Leonardo , McDonald Cassandra , Beaton Melanie , Chande Nilesh , Gregor Jamie , Sey Michael , Wilson Aze , Jairath Vipul 
Published: July 2022

Abstract

Introduction
With the expanding therapeutic armamentarium for inflammatory bowel disease (IBD), real-world data may help inform drug positioning. We assessed clinical, endoscopic, imaging, and biochemical response/remission outcomes in patients with Crohn’s disease (CD) treated with ustekinumab in a large Canadian IBD center.

Methods
A retrospective cohort study of CD patients was treated with ustekinumab. Clinical, endoscopic, radiological, and biochemical response and remission outcomes were stratified by prior biologic exposure status. Hazard ratios for biologic exposure status were estimated using Cox proportional hazard models and subgroup-specific incidence rates for healing.

Results
A total of 231 patients (55.9% female, median 45.8 years) were identified as receiving ustekinumab during the study period, with 2 patients subsequently excluded (N = 229). Of these patients, 79.0% (181 of 229) were bio-experienced, with 38.7% (70 of 181) having failed 1 biologic and 61.3% (111 of 181) having failed ≥2 biologics. At 3 months of follow-up after induction, clinical remission (Harvey-Bradshaw Index ≤4) was achieved by 59.1% (62 of 105) of bio-experienced patients and 79.4% (27 of 34) of bio-naïve patients (relative risk [RR], 1.34; 95% CI, 1.06-1.70; P = .013). Endoscopic remission (absence of mucosal ulcers) was achieved in 37.9% (33 of 87) cases. Rate of endoscopic healing (either endoscopic response or remission) per 1000 person-months was 72.7 (95% CI, 42.4-125.1) and 50.2 (37.9-66.4); and the median time to endoscopic response was 8.4 months (95% CI, 6.4-9.8) and 15.4 months (95% CI, 10.3-17.9) in bio-naïve vs bio-experienced patients, respectively. Imaging response/remission and steroid-free remission rates were higher in bio-naïve patients.

Conclusion
In this large real-world cohort of CD patients with complex phenotypes and high rates of prior biologic exposure, we observed that ustekinumab was effective and safe with higher rates of improvement in bio-naïve subjects across a range of end points.
Mycobiome and Inflammatory Bowel Disease: Role in Disease Pathogenesis, Current Approaches and Novel Nutritional-based Therapies
Authors: Hsu Caitlyn , Ghannoum Mahmoud , Cominelli Fabio , Martino Luca Di 
Published: July 2022

AbstractInflammatory bowel disease (IBD), a disorder characterized by chronic inflammation of the gastrointestinal (GI) tract and a range of adverse health effects including diarrhea, abdominal pain, vomiting, and bloody stools, affects nearly 3.1 million genetically susceptible adults in the United States today. Although the etiology of IBD remains unclear, genetics, stress, diet, and gut microbiota dysbiosis— especially in immunocompromised individuals— have been identified as possible causes of disease. Although previous research has largely focused on the role of bacteria in IBD pathogenesis, recently observed alterations of fungal load and biodiversity in the GI tract of afflicted individuals suggest interkingdom interactions amongst different gut microbial communities, particularly between bacteria and fungi. These discoveries point to the potential utilization of treatment approaches such as antibiotics, antifungals, probiotics, and postbiotics that target both bacteria and fungi in managing IBD. In this review, we discuss the impact of specific fungi on disease pathogenesis, with a focus on the highly virulent genus Candida and how the presence of certain co-enzymes impacts its virulence. In addition, we evaluate current gut microbiome-based therapeutic approaches with the intention of better understanding the mechanisms behind novel therapies.
Related factors to the coping style of patients with sudden sensorineural hearing loss
Authors: Yuan Yang , Lin Lu , Wang Hong , Xie Congyan , Chen Qiuyun , Li Haixia , Tian Li 
Published: July 2022

AbstractBackgroundCoping style can affect the patient's physical and mental health management. Therefore this study aimed to identify factors related to the coping style of young and middle-aged sudden sensorineural hearing loss (SSNHL) patients to provide reference for clinical nursing practice.MethodsA cross-sectional study was conducted on young and middle-aged SSNHL patients hospitalized in the otolaryngology departments of four hospitals in Suzhou City, China. A paper-based self-administered questionnaire investigated the patient's coping style and related factors. Multiple linear stepwise regression analysed the effective related factors in patients’ coping styles.ResultsAmong 872 patients, 866 completed the survey, with an average age of 37.27 y. Factors related to the coping style of these patients included gender, chronic diseases, history of trauma, social support and type D personality (p&lt;0.05). Female patients adopt more negative coping styles than male patients. Patients with chronic diseases or a history of trauma had more positive coping styles. Higher social support scores were related to improvements in coping style. Patients with type D personality were more likely to adopt negative coping styles.ConclusionsThis study suggests that psychological assessment of patients, chronic diseases, history of trauma, social support and type D personality may benefit the understanding of these patients’ coping styles and, as a consequence, may improve their stress management.
Infrastructural Geopolitics
Authors: de Goede Marieke , Westermeier Carola 
Published: July 2022

AbstractInvisible and seemingly technical financial infrastructures have become the site of high geopolitics. Crucially, security sanctions are being leveraged through the global financial messaging network SWIFT. This article offers the term “infrastructural geopolitics” to draw attention to the ways in which hegemonic contestation and fracturing play out in and through payment infrastructures. Infrastructures are not passive sites to be used in the service of preexisting hegemonic power but can themselves route, block, challenge, or rework power in particular ways.We focus on the new trade mechanism INSTEX as a lens on the global battle over financial payment infrastructures. How and why has hegemonic contestation taken the shape of, and is in turn shaped by, struggles over payment infrastructure? As a heuristic device to analyze the hegemonic politics of financial infrastructure, we propose three terms that capture the processual nature of infrastructural politics: sedimentation, resurfacing, and fracturing. We apply these to the emergence of the payment infrastructure INSTEX. We explain how hegemonic politics become hardwired in the technical and largely invisible SWIFT infrastructure, which supported postwar financial order and sedimented its uneven power relations. The process of political resurfacing captures the ways in which infrastructural dispositions come to the surface of political discussion again, after 9/11 and through the JCPOA process. In conclusion, the introduction of INSTEX has advanced the possibility of fracturing international payment routes, with multiple alternative infrastructures emerging.
The Defeminizing Reversal: Globalization, Industrial Upgrading, and Female Labor Force Participation
Authors: Madeira Mary Anne 
Published: July 2022

Abstract
As countries integrate ever further into globalized production processes, scholars have found significant country-level variation in the extent to which women are able to increase their participation in the formal economy. In this paper, I improve on existing work by disaggregating globalization into its different processes, each of which has different expected effects on female labor force participation (FLFP). I examine how trade, foreign direct investment (FDI), and natural resource exports affect FLFP in a cross-national time-series analysis of 129 low- to middle-income economy countries over a twenty-eight-year period. A major contribution of this paper is to show an interaction effect between trade and FDI: I find that generally trade and inward FDI have a negative effect on FLFP that diminishes as they increase together, suggesting that export-oriented FDI creates more opportunities for women than domestic-oriented FDI and trade openness unaccompanied by significant foreign investment. I also find that the more positive effect of export-oriented FDI depends on the extent to which a country has experienced industrial upgrading, suggesting that gender segregation by industry also affects the extent to which global economic integration creates employment opportunities for women in developing countries.
Emergency: A Vernacular Contextual Approach
Authors: Kurylo Bohdana 
Published: July 2022

Abstract
Security scholars have traditionally viewed emergency as a state of exception that triggers a struggle for survival, justifying the breaking of rules and excesses of state power. While there have been attempts to decouple security from its survivalist logic, emergency has remained an analytical blind spot in security studies. The dominance of an elite-centric, exceptionalist paradigm in the study of emergency has foreclosed the possibility of alternative conceptions of emergency and neglected the voices of structurally disempowered agents. This paper advances a vernacular contextual research agenda that is sensitive to the empirical diversity of emergency meanings and practices while foregrounding emergency claims made by non-elite actors. Challenging the idea of emergency as a form of “anti-politics,” the paper contends that emergency should be understood as an intrinsic part of politics. It then recovers an alternative, “emancipatory” conception of emergency as an extraordinary moment of spontaneous beginnings that can activate the collective agency of marginalized actors. The final section establishes conceptual foundations for actor-centered, grounded empirical research into emergency politics and suggests avenues for future research. Contextualizing emergency and attuning to the voices and experiences of everyday actors are crucial to remove the key variable that ties security to the logic of survival and exception.
More Than Just Moral Urbanism? The Incorporation of CEDAW Principles into Local Governance Structures in the United States
Authors: Och Malliga 
Published: July 2022

AbstractThe United States is one of only six countries and the only advanced industrialized democracy that has not ratified the Convention on the Elimination of All Forms of Discrimination Against Women (CEDAW). Established in 2013, the Cities for CEDAW campaign encourages US municipalities to become a CEDAW City by incorporating the principles of the convention—elimination of sex-based discrimination and promotion of substantive equality—into municipal code. A convention ordinance/resolution requires cities to (1) conduct a gender analysis of city operations and laws; (2) establish a convention oversight body; and (3) financially underwrite any convention initiatives. As of 2021, nine US cities have adopted a convention ordinance while 33 cities have adopted convention resolutions. This article asks whether adopting a convention resolution or ordinance is little more than a sign of moral urbanism, that is, a moral language without accountability, or whether cities have committed themselves to implementing convention principles in a legally binding manner. Conducting a legal text analysis, I find that the Cities for CEDAW campaign overall has mostly led to symbolic recognition of the importance of the convention rather than creating legally binding obligations that have the potential to transform city governance.
“An Unhappy Interlude”: Trivialisation and Privatisation of Forced Marriage in Asylum-Seeker Women’s Cases in the UK
Authors: Honkala Nora 
Published: July 2022

Abstract
This article examines asylum-seeker women’s appeals involving forced marriage at the Upper Tribunal (Immigration and Asylum Chamber) in the UK over the past 20 years. Internationally forced marriage has long been understood as a human rights issue. In the UK, the government has introduced a range of policy and legislative measures to tackle forced marriage of its nationals that have been framed within human rights discourse. The aim of this article is to examine the ways in which forced marriage has been framed by the Tribunal in women’s asylum claims. Informed by feminist contributions to gender and refugee law, the article reveals two problematic and interrelated trends. First, that gendered harm in the form of forced marriage continues to be contained in the “private” sphere. And secondly, that a noteworthy trend of trivialisation through conflation of forced and arranged marriage, and the use of euphemisms emerges. As a result, these gendered representations evidence a continuing failure of refugee law to take women’s rights violations seriously.
Update and Validation of the 16S rDNA qPCR Assay for the Detection of Three ‘Candidatus Liberibacter Species’ Following Current MIQE Guidelines and Workflow
Authors: Osman Fatima , Dang Tyler , Bodaghi Sohrab , Haq Rukhama , Lavagi-Craddock Irene , Rawstern Amanda , Rodriguez Esteban , Polek MaryLou , Wulff Nelson A. , Roberts Ronel , Pietersen Gerhard , Englezou Anna , Donovan Nerida , Folimonova Svetlana Y. , Vidalakis Georgios 
Published: July 2022

An updated real-time multiplex quantitative polymerase chain reaction (qPCR) assay was designed and validated for the simultaneous detection of three ‘ Candidatus Liberibacter species’ (CLsp), ‘ Ca. Liberibacter asiaticus’ (CLas), ‘africanus’ (CLaf), and ‘americanus’ (CLam), associated with the huanglongbing disease of citrus. The multiplex assay was designed based on the qPCR assay published in 2006 by Li et al., considering all available CLsp 16S rRNA gene sequences in GenBank and the MIQE guidelines and workflow for qPCR optimization, which became available after 2006. When using the updated multiplex CLsp qPCR assay compared with singleplex qPCR, no significant increase in quantitative cycle (Cq) values was detected. The specificity and sensitivity of the updated qPCR assay was optimal, and measuring the intra- and interassay variations confirmed the reproducibility and repeatability of the assay. The assay was also successfully used with a large number of diverse samples at independent laboratories in four countries, thus demonstrating its transferability, applicability, practicability, and robustness as different qPCR reaction conditions or instruments had a minor effect on Cq values. This updated multiplex CLsp qPCR assay can be used in a variety of citrus surveys, germplasm, or nursery stock programs that require different pathogen detection tools for their successful operation. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Economic burden of drug-induced anaphylaxis: what can we do better?
Authors: Cardoso Barbara , Moscoso Teresa , Morais-Almeida Mário , Demoly Pascal , Tanno Luciana K. 
Published: July 2022

Purpose of review
This systematic review evaluates published data related to the economic burden of drug-induced anaphylaxis (DIA) to understand preventive cost saving measures that could reduce the burden of these conditions.

Recent findings
Although DIA has a relevant societal impact, there are limited and heterogenous available data related to its cost. Direct costs related to the management of acute phase of DIA was estimated by $529.6 to $3125, depending on the number of emergency room visits/hospitalizations, emergency kits and transports in ambulance. Direct costs of investigations of DIA varied from $288 to $2292.95 and the desensitization was estimated by $6796. Main variables for this were: personnel, allergy screening procedures, medical consumables and space cost. The mean indirect cost was based on a mean absenteeism of 3 days per DIA corresponding to $381.2.

Summary
More than reviewing the published data, we were able to identify variables that, if correctly managed, can reduce the economic burden of DIA, such as adjusting the timing of referral and etiological diagnosis, identification of potential risk and/or co-factors, correct written recommendations to patients. The evidence presented highlights the need of optimization of healthcare patients to patients suffering from DIA.