bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic pain in the 11th Revision of the International Classification of Diseases: users' questions answered
Authors: Korwisi Beatrice , Barke Antonia , Rief Winfried , Treede Rolf-Detlef , Kleinstäuber Maria 
Published: December 2021

Abstract
For the first time, the upcoming International Classification of Diseases and Related Health Problems, Eleventh Revision (ICD-11) will include a comprehensive classification of chronic pain, which is based on the biopsychosocial definition of chronic pain. This presents a great opportunity for pain research and clinical practice. The new classification consists of 7 main diagnostic categories of chronic pain, which are further divided into increasingly specific levels of diagnoses. Each diagnosis is characterized by clearly defined operationalized criteria. Future users will need to familiarize themselves with the new system and its application. The aim of the present publication is to provide users of the ICD-11 chronic pain classification with answers to frequently asked questions regarding the ICD-11 as a whole, the ICD-11 chronic pain classification, and its application to common pain syndromes. The questions compiled in this study reached the International Association for the Study of Pain Task Force through different routes (eg, at conferences, by letter, or during field testing). Furthermore, the authors collected questions posted to the ICD-11 browser and contacted early users of the classification to enquire about their most frequent difficulties when applying the new diagnoses. The authors of the present publication prepared answers to these frequently asked questions. This publication intends to act as a guide for the future users of the new ICD-11 chronic pain classification, hence facilitating its implementation.
Prolonged sitting time links to subclinical atherosclerosis
Authors: Lim Su Shen , Huang Chin-Chou , Hsu Pai-Feng , Lin Chung-Chi , Wang Yuan-Jen , Ding Yaw-Zon , Liou Teh-Ling , Wang Ying-Wen , Huang Shao-Sung , Lu Tse-Min , Chen Jaw-Wen , Chan Wan-Leong , Lin Shing-Jong , Leu Hsin-Bang 
Published: December 2021

Background:
This study investigates the association between daily sitting time and subclinical atherosclerosis by using coronary computed tomography angiography (CCTA).

Methods:
The study enrolled 203 subjects (age 57.6 ± 8.8 years) who underwent CCTA at annual medical checkups. Sitting time was categorized as < 5 hours/day (short), 5 to 9 hours/day (moderate) and ≥10 hours/d (long). We analyzed the coronary calcium score, plaque characteristics, and severity of coronary artery stenosis, including the segment involvement score (SIS) and segment stenosis score (SSS).

Results:
Subjects with longer sitting times tended to be male gender and have lower levels of high-density lipoprotein cholesterol (p for trend < 0.05). In addition, those with longer sitting time had higher SIS (1.2 ± 1.5 vs. 1.6 ± 2.1 vs. 2.3 ± 2.0 for short, moderate, and long sitting time, respectively) (p for trend = 0.015) and SSS (1.4 ± 2.0 vs. 1.9 ± 2.7 vs. 2.7 ± 2.6) (p for trend = 0.015), suggesting longer sitting time-correlated with the severity of coronary atherosclerosis. When considering the coronary plaque patterns, subjects with shorter sitting time (<5 hours/d) tended to have more calcified plaque and subjects with longer sitting time (≥10 hours/d) had more mixed plaque (p for trend = 0.018). After adjusting for age, gender, comorbidities, body mass index, and lipid profiles, increased sitting time was independently associated with the presence of mixed plaque, suggesting longer sitting time may be associated with higher risk of the formation of vulnerable plaque.

Conclusion:
Longer sitting time was linked to the severity of subclinical atherosclerosis and the presence of high-risk vulnerable plaque in the general population.
Symptoms of Acute Myocardial Infarction as Described in Calls to Tele-Nurses and in Questionnaires
Authors: Ängerud Karin Hellström , Ericsson Maria , Brännström Margareta , Sederholm Lawesson Sofia , Strömberg Anna , Thylén Ingela 
Published: December 2021

Background
Patient-reported symptoms of acute myocardial infarction (MI) may be affected by recall bias depending on when and where symptoms are assessed.

Aim
The aim of this study was to gain an understanding of patients' symptom description in more detail before and within 24 hours after a confirmed MI diagnosis.

Methods
A convergent parallel mixed-methods design was used to examine symptoms described in calls between the tele-nurse and the patient compared with symptoms selected by the patient from a questionnaire less than 24 hours after hospital admission. Quantitative and qualitative data were analyzed separately and then merged into a final interpretation.

Results
Thirty patients (median age, 67.5 years; 20 men) were included. Chest pain was the most commonly reported symptom in questionnaires (24/30). Likewise, in 19 of 30 calls, chest pain was the first complaint mentioned, usually described together with the symptom onset. Expressions used to describe symptom quality were pain, pressure, discomfort, ache, cramp, tension, and soreness. Associated symptoms commonly described were pain or numbness in the arms, cold sweat, dyspnea, weakness, and nausea. Bodily sensations, such as feeling unwell or weak, were also described. Fear and tiredness were described in calls significantly less often than reported in questionnaires (P = .01 and P = .02), whereas “other” symptoms were more often mentioned in calls compared with answers given in the questionnaire (P = .02). Some symptoms expressed in the calls were not listed in the questionnaire, which expands the understanding of acute MI symptoms. The results showed no major inconsistencies between datasets.

Conclusion
Patients' MI symptom descriptions in tele-calls and those reported in questionnaires after diagnosis are comparable and convergent.
Targeted Therapeutics for Transthyretin Amyloid Cardiomyopathy
Authors: Campbell Courtney M. , Baiyee Cyril Ayuk Mbeng Takem , Almaani Salem , Bumma Naresh , Sharma Nidhi , LoRusso Samantha , Redder Elyse , Bittengle Jordan , Pfund Katherine , Friemer Miriam , Tong Matthew , Kahwash Rami , Efebera Yvonne , Parikh Samir , Vallakati Ajay 
Published: December 2021

Background:
Deposition of wild-type or mutant transthyretin (TTR) amyloid fibrils in the myocardium causes TTR amyloid cardiomyopathy (ATTR-CM). Targeted therapeutics for ATTR-CM include TTR stabilizers (tafamidis and diflunisal) and oligonucleotide drugs (revusiran, patisiran, and inotersen). TTR stabilizers prevent dissociation of transthyretin tetramers. Transthyretin monomers can misfold and form amyloid fibrils. TTR stabilizers thereby limit amyloid fibrils development and deposition. Oligonucleotide drugs inhibit hepatic synthesis of transthyretin, which decreases transthyretin protein levels and thus the amyloid fibril substrate.

Areas of Uncertainty:
To study the safety and efficacy of targeted therapeutics in patients with ATTR-CM, we performed a pooled analysis. A random-effects model with the Mantel–Haenszel method was used to pool the data.

Data Sources:
A literature search was performed using PubMed, Cochrane CENTRAL, and Embase databases using the search terms “cardiac amyloidosis” AND “tafamidis” OR “patisiran” OR “inotersen” OR “revusiran” OR “diflunisal.”

Therapeutic Advances:
We identified 6 studies that compared targeted therapeutics with placebo. One study was stopped prematurely because of increased mortality in the targeted therapeutics arm. Pooled analysis included 1238 patients, of which 738 patients received targeted therapeutics and 500 patients received placebo. When compared with placebo, targeted therapeutics significantly reduced all-cause mortality [OR 0.39, 95% confidence interval (CI): 0.16–0.97, P = 0.04]. Only 2 studies reported the effect on cardiovascular-related hospitalizations. There was a trend toward an improvement in global longitudinal strain (mean difference −0.69, 95% CI: −1.44 to 0.05, P = 0.07). When compared with placebo, there was no increase in serious adverse events with targeted therapeutics (OR 1.06, 95% CI: 0.78–1.44, P = 0.72).

Conclusion:
Evidence from the pooled analysis revealed targeted therapeutics improve survival and are well-tolerated. These findings suggest a potential role for targeted therapeutics in the treatment of patients with ATTR-CM.
Sodium–Glucose Cotransporter Inhibitors Reduce Mortality and Morbidity in Patients With Heart Failure: Evidence From a Meta-Analysis of Randomized Trials
Authors: Camilli Massimiliano , Lombardi Marco , Chiabrando Juan G. , Zito Andrea , Del Buono Marco G. , Vergallo Rocco , Aspromonte Nadia , Lombardo Antonella , Montone Rocco A. , Niccoli Giampaolo , Biondi-Zoccai Giuseppe , Crea Filippo , Minotti Giorgio 
Published: December 2021

Background:
Recent trials demonstrated the clinical efficacy of sodium–glucose cotransporter-2 inhibitors (SGLT2i) in patients with heart failure (HF), regardless of the presence or absence of type 2 diabetes. These data may allow the use of this innovative drug class in clinical routine for treating these patients.

Study Question:
We aimed at further clarifying the role of SGLT2i in patients with diagnosis of HF, capitalizing on pooled sample size and heightened power for clinically relevant safety and efficacy outcomes.

Data Sources:
We conducted a systematic search of PubMed, reference lists of relevant articles, and Medline database from inception until March 1, 2021.

Study Design:
This meta-analysis was completed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched for randomized trials that evaluated the cardiovascular effects of SGLT2i in patients with HF. Three investigators independently assessed study eligibility, extracted the data, and assessed risk of bias. Hazard ratios and 95% confidence intervals (CIs) were pooled and meta-analyzed using a random-effect model. Numbers needed to treat (NNT) with the relative 95% CIs were also calculated. The primary outcome was a composite of HF hospitalization or an urgent visit for worsening HF and cardiovascular death.

Results:
Three trials were included in the study. Overall, treatment with SGLT2i was associated with a lower risk of the primary composite outcome [hazard ratios 0.73, 95% CI (0.67–0.80), NNT = 11.3]. Similarly, there was a significantly reduced risk of cardiovascular death, all-cause death, HF hospitalization and need for urgent treatment for HF, and HF hospitalization.

Conclusions:
Therefore, the available evidence supports the routine use of these drugs as standard-of-care, also given the highly favorable NNTs.
The role of fungus in the pathogenesis of chronic rhinosinusitis
Authors: Challapalli Sai D. , McKee Sean , Luong Amber U. 
Published: December 2021

Purpose of review
The etiologic role of fungi in chronic rhinosinusitis remains controversial. The purpose of this review is to further our understanding of molecular immunologic pathways activated by fungi and clinical trials of antifungals in severe subtypes of asthma and allergic fungal rhinosinusitis.

Recent findings
Various fungal components such as protease and chitin are capable of eliciting a type 2 innate and adaptive immune response. However, definitive studies on the etiologic role of fungi in chronic rhinosinusitis (CRS) is dependent on the development of a fungi-induced murine model of CRS. Short of this model, extrapolations of observations and results from clinical trials in fungi-induced asthma subtypes support a key role of fungi in the pathophysiology of allergic fungal rhinosinusitis and possibly other CRS endotypes.

Summary
Fungi plays a key role in the pathophysiology of several subtypes of chronic inflammatory respiratory diseases. However, a fungi-induced murine model of CRS is needed to explicitly investigate the molecular pathways and potential therapeutic targets.
Recent concepts in fungal involvement in skin and soft tissue infections
Authors: Peghin Maddalena , Ruiz-Camps Isabel 
Published: December 2021

As the at-risk population expands and new antifungal resistance patterns develop, it is critical to understand and recognize cutaneous manifestations of old and emerging fungal diseases.

Purpose of review
The aim of this review is to provide an overview of the most frequent and emerging deep cutaneous fungal infections following either primary inoculation or secondary spread after haematogenous seeding in disseminated infections in different geographical areas.

Recent findings
Fungal skin and soft tissue infections (SSTIs) encompass a variety of pathological conditions based on the site of the infection, route of acquisition of the pathogen, epidemiological setting and the virulence of the fungus in relation to the host. The approach to a patient suspected of having a fungal SSTI is complex and usually poses a major diagnostic challenge. The treatment approach should include attempts at immune reconstitution, targeted antifungal therapy and/or aggressive surgical debridement.

Summary
Fungal SSTIs can be an important cause of morbidity and mortality in both immunocompromised and immunocompetent patients and are being reported with increasing frequency worldwide.
Impaired Color Discrimination in Alzheimer Disease Dementia
Authors: Boedeker Sebastian , Halstenberg Eileen , Schulz Philipp , Beblo Thomas , Kreisel Stefan , Driessen Martin , Toepper Max 
Published: December 2021

Objective:
Patients with Alzheimer disease dementia (ADD) often show impaired orientation and navigation. Signage offers an opportunity to compensate for these deficits, communicate information efficiently and facilitate wayfinding. Certain properties of signs such as colors and contrasts may beneficially affect the uptake and processing of information particularly in ADD patients.

Methods:
Thirty-six healthy older adults and 30 ADD patients performed a computerized color perception task that required discriminating different color combinations. The effects of different contrast features on performance accuracy and speed in the 2 experimental groups were examined by nonparametric mixed analysis of variances.

Results:
Analyses revealed a significant effect of contrast polarity on reaction times, significant effects of group on reaction times and errors as well as a marginally significant interaction of group×color on errors. All participants benefitted from positive contrast polarity (ie, dark target on lighter background) as indicated by increased performance speed. Furthermore, ADD patients reacted slower and less accurate than healthy controls, but showed higher accuracy at black-white and red-yellow than at blue-green color combinations.

Conclusions:
Our findings suggest the implementation of signs with positive contrast polarity to ensure faster reactions. In addition, certain color combinations may enhance accuracy, particularly in patients with ADD.
Hand hygiene among nurses in pediatric blood and marrow transplantation setting: a best practice implementation project
Authors: Nedelcu Viorica , Niculiţă Oana O. , Toporaş Elena , Zazu Mariana , Mazilu Doina C. , Jiménez Marina Gallego , Grinţescu loana M. 
Published: December 2021

ABSTRACT

Objectives:
The aim of this project was to promote evidence-based best practice regarding hand hygiene among nurses in a pediatric blood and marrow transplantation (BMT) setting.

Introduction:
Healthcare-associated infections (HAI) represent important complications of healthcare with potentially major impact on patient outcomes. Most HAI are transmitted through the hands of healthcare professionals (HCP) and therefore hand hygiene is the simplest, most effective and proven method for preventing HAI. However, the overall compliance rate of HCP with hand hygiene remains at a very low level. In this case, it is necessary to implement strategies to improve the compliance with hand hygiene of the HCP with the purpose of reducing HAI rates, mortality and costs, all the more so as it is known that patients with BMT have an increased risk of HAI.

Methods:
This best practice implementation project was based on the JBI methodological approach and included three phases of activity: a baseline audit, implementation of strategies and a follow-up audit. The project was conducted in the pediatric BMT setting of a large university hospital located in Bucharest, Romania, and the sample included 10 nurses and five relatives of pediatric patients from this ward.

Results:
As a result of the implementation of strategies, improvements were observed across seven audit criteria, given that for two audit criteria out of a total of nine audit criteria compliance was maximum (100%) since the baseline phase. Moreover, the post implementation audit showed a complete compliance (100%) for six audit criteria. However, for the other three audit criteria the compliance in follow-up audit was high: 92, 85 and 80%, respectively.

Conclusion:
The strategies applied within this evidence implementation project were appropriate, so the project was a success. However, permanent actions are required to sustain changes in practice and improvements made.
Performance of genetic imputation across commercial crop species
Authors: Thorn Steve , Whalen Andrew , Kollers Sonja , Gholami Mahmood , da Silva Helena Sofia , Wimmer Valentin , Hickey John M 
Published: December 2021

AbstractWe show that accurate imputation can be carried out in three commercial plant species (maize, sugar beet and wheat) and that accurate imputation does not require a pedigree, although pedigree information can improve accuracy and speed. Our approach uses a hidden Markov model to build a haplotype library from individuals genotyped at high-density and then uses this library to impute low-density genotyped individuals to high-density. To build the library, we use founders when the pedigree is known, or a sample of progeny when the pedigree is unknown. Without a pedigree, and with 50 individuals genotyped at high-density and 100 low-density markers per chromosome, the median accuracies were 0.97 (maize), 0.96 (sugar beet), and 0.94 (wheat). We obtained similar accuracies with a pedigree. For biparental crosses with 100 markers per chromosome, median accuracies were 0.96 (maize), 0.96 (sugar beet) and 0.94 (wheat). For the imputation scenarios without a pedigree, we compared accuracies with those obtained by running Beagle 5.1. In all but one scenario, our method outperformed Beagle. We believe that plant breeders can effectively apply imputation in many crop species.
PEPPI: Whole-proteome protein-protein interaction prediction through structure and sequence similarity, functional association, and machine learning
Authors: Bell Eric W. , Schwartz Jacob H. , Freddolino Peter L. , Zhang Yang 
Published: December 2021

AbstractProteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of noninteractions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.
SARS-CoV-2 wildlife surveillance in Ontario and Québec, Canada
Authors: Greenhorn Janet E. , Kotwa Jonathon D. , Bowman Jeff , Bruce Laura , Buchanan Tore , Buck Peter A. , Dibernardo Antonia , Flockhart Logan , Gagnier Marianne , Hou Aaron , Jardine Claire M. , Lair Stephane , Lindsay L. Robbin , Masse Ariane , Muchaal Pia K. , Nituch Larissa A. , Sotto Angelo , Stevens Brian , Yip Lily , Mubareka Samira 
Published: December 2021

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic, is capable of infecting a variety of wildlife species. Wildlife living in close contact with humans are at an increased risk of SARS-CoV-2 exposure and if infected have the potential to become a reservoir for the pathogen, making control and management more difficult.ObjectiveTo conduct SARS-CoV-2 surveillance in urban wildlife from Ontario and Québec, Canada, increasing our knowledge of the epidemiology of the virus and our chances of detecting spillover from humans into wildlife.MethodsUsing a One Health approach, we leveraged activities of existing research, surveillance, and rehabilitation programs among multiple agencies to collect samples from 776 animals from 17 different wildlife species between June 2020 and May 2021. Samples from all animals were tested for the presence of SARS-CoV-2 viral RNA, and a subset of samples from 219 animals across 3 species (raccoons, Procyon lotor; striped skunks, Mephitis mephitis; and mink, Neovison vison) were also tested for the presence of neutralizing antibodies.ResultsNo evidence of SARS-CoV-2 viral RNA or neutralizing antibodies was detected in any of the tested samples.ConclusionAlthough we were unable to identify positive SARS-CoV-2 cases in wildlife, continued research and surveillance activities are critical to better understand the rapidly changing landscape of susceptible animal species. Collaboration between academic, public and animal health sectors should include experts from relevant fields to build coordinated surveillance and response capacity.
Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox
Authors: Lal Avantika , Ferrarini Mariana Galvao , Gruber Andreas J. 
Published: December 2021

AbstractViruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.