bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Quality of Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Infections
Authors: Diao Zhenli , Zhang Yuanfeng , Chen Yuqing , Han Yanxi , Chang Lu , Ma Yu , Feng Lei , Huang Tao , Zhang Rui , Li Jinming 
Published: May 2023

Abstract

Background
Laboratory-developed metagenomic next-generation sequencing (mNGS) assays are increasingly being used for the diagnosis of infectious disease. To ensure comparable results and advance the quality control for the mNGS assay, we initiated a large-scale multicenter quality assessment to scrutinize the ability of mNGS to detect pathogens in lower respiratory infections.

Methods
A reference panel containing artificial microbial communities and real clinical samples was used to assess the performance of 122 laboratories. We comprehensively evaluated the reliability, the source of false-positive and false-negative microbes, as well as the ability to interpret the results.

Results
A wide variety of weighted F1-scores was observed across 122 participants, with a range from 0.20 to 0.97. The majority of false positive microbes (68.56%, 399/582) were introduced from “wet lab.” The loss of microbial sequence during wet labs was the chief cause (76.18%, 275/361) of false-negative errors. When the human context is 2 × 105 copies/mL, most DNA and RNA viruses at titers above 104 copies/mL could be detected by &gt;80% of the participants, while &gt;90% of the laboratories could detect bacteria and fungi at titers lower than 103 copies/mL. A total of 10.66% (13/122) to 38.52% (47/122) of the participants could detect the target pathogens but failed to reach a correct etiological diagnosis.

Conclusions
This study clarified the sources of false-positive and false-negative results and evaluated the performance of interpreting the results. This study was valuable for clinical mNGS laboratories to improve method development, avoid erroneous results being reported, and implement regulatory quality controls in the clinic.
Relationship between remnant cholesterol and risk of heart failure in participants with diabetes mellitus
Authors: Wang Ruoting , Gerstein Hertzel C , Van Spall Harriette G C , Lip Gregory Y H , Olier Ivan , Ortega-Martorell Sandra , Thabane Lehana , Ye Zebing , Li Guowei 
Published: May 2023

Abstract

Background
Evidence about the association between calculated remnant cholesterol (RC) and risk of heart failure (HF) in participants with diabetes mellitus (DM) remains sparse and limited.

Methods
We included a total of 22 230 participants with DM from the UK Biobank for analyses. Participants were categorized into three groups based on their baseline RC measures: low (with a mean RC of 0.41 mmol/L), moderate (0.66 mmol/L), and high (1.04 mmol/L). Cox proportional hazards models were used to evaluate the relationship between RC groups and HF risk. We performed discordance analysis to evaluate whether RC was associated with HF risk independently of low-density lipoprotein cholesterol (LDL-C).

Results
During a mean follow-up period of 11.5 years, there were a total of 2232 HF events observed. The moderate RC group was significantly related with a 15% increased risk of HF when compared with low RC group (hazard ratio [HR] = 1.15, 95% confidence interval [CI]: 1.01—1.32), while the high RC group with a 23% higher HF risk (HR = 1.23, 95% CI: 1.05–1.43). There was significant relationship between RC as a continuous measure and the increased HF risk (P &lt; 0.01). The association between RC and risk of HF was stronger in participants with HbA1c level ≥ 53 mmol/mol when compared with HbA1c &lt; 53 mmol/mol (P for interaction = 0.02). Results from discordance analyses showed that RC was significantly related to HF risk independent of LDL-C measures.

Conclusions
Elevated RC was significantly associated with risk of HF in patients with DM. Moreover, RC was significantly related to HF risk independent of LDL-C measures. These findings may highlight the importance of RC management to HF risk in patients with DM.
An estimation of the consequences of reinforcing the 2016 and 2019 European Society of Cardiology/European Atherosclerosis Society guidelines on current lipid-lowering treatment in patients with type 2 diabetes in tertiary care—a SwissDiab study
Authors: Singeisen Hélène , Renström Frida , Laimer Markus , Lehmann Roger , Bilz Stefan , Brändle Michael 
Published: May 2023

Abstract

Aims
In 2019, the European Society of Cardiology/European Atherosclerosis Society updated the 2016 guidelines for the management of dyslipidaemias recommending more stringent low-density lipoprotein cholesterol (LDL-C) targets in diabetes mellitus type 2 (DM2). Based on a real-world patient population, this study aimed to determine the feasibility and cost of attaining guideline-recommended LDL-C targets, and assess cardiovascular benefit.

Methods and results
The Swiss Diabetes Registry is a multicentre longitudinal observational study of outpatients in tertiary diabetes care. Patients with DM2 and a visit between 1 January 2018 and 31 August 2019 that failed the 2016 LDL-C target were identified. The theoretical intensification of current lipid-lowering medication needed to reach the 2016 and 2019 LDL-C target was determined and the cost thereof extrapolated. The expected number of major adverse cardiovascular events (MACE) prevented by treatment intensification was estimated. Two hundred and ninety-four patients (74.8%) failed the 2016 LDL-C target. The percentage of patients that theoretically achieved the 2016 and 2019 target with the indicated treatment modifications were high-intensity statin, 21.4% and 13.3%; ezetimibe, 46.6% and 27.9%; proprotein convertase subtilisin/kexin type 9 inhibitor (PCSK9i), 30.6% and 53.7%; ezetimibe and PCSK9i, 1.0% and 3.1%; whereas one (0.3%) and five patients (1.7%) failed to reach target, respectively. Achieving the 2016 vs. 2019 target would reduce the estimated 4-year MACE from 24.9 to 18.6 vs. 17.4 events, at an additional annual cost of medication of 2140 Swiss francs (CHF) vs. 3681 CHF per patient, respectively.

Conclusions
For 68% of the patients, intensifying statin treatment and/or adding ezetimibe would be sufficient to reach the 2016 target, whereas 57% would require cost-intensive PCSK9i therapy to reach the 2019 target, with limited additional medium-term cardiovascular benefit.
Temporal patterns of antibiotic prescribing for sore throat, otitis media, and sinusitis: a longitudinal study of general practitioner registrars
Authors: Turner Alexandria , van Driel Mieke L , Mitchell Benjamin L , Davis Joshua S , Fielding Alison , Davey Andrew , Holliday Elizabeth , Ball Jean , Ralston Anna , Tapley Amanda , Mulquiney Katie , Baillie Emma J , Spike Neil , Clarke Lisa , Magin Parker 
Published: May 2023

Abstract

Background
Antibiotics provide minimal benefit for sore throat, otitis media, and sinusitis. Antibiotic stewardship, with reduced prescribing, is required to address antibiotic resistance. As most antibiotic prescribing occurs in general practice and prescribing habits develop early, general practitioner (GP) trainees (registrars) are important for effective antibiotic stewardship.

Objectives
To establish temporal trends in Australian registrars’ antibiotic prescribing for acute sore throat, acute otitis media, and acute sinusitis.

Design
A longitudinal analysis of data from the Registrar Clinical Encounters in Training (ReCEnT) study from 2010 to 2019.

Participants
ReCEnT is an ongoing cohort study of registrars’ in-consultation experiences and clinical behaviours. Pre-2016, 5 of 17 Australian training regions participated. From 2016, 3 of 9 regions (42% of Australian registrars) participate.

Main measures
The outcome was prescription of an antibiotic for a new acute problem/diagnosis of sore throat, otitis media, or sinusitis. The study factor was year (2010–2019).

Key results
Antibiotics were prescribed in 66% of sore throat diagnoses, 81% of otitis media, and in 72% of sinusitis. Prescribing frequencies decreased between 2010 and 2019 by 16% for sore throat (from 76% to 60%) by 11% for otitis media (from 88% to 77%) and by 18% for sinusitis (from 84% to 66%). In multivariable analyses, “Year” was associated with reduced prescribing for sore throat (OR 0.89; 95%CI 0.86–0.92; p &lt; 0.001), otitis media (OR 0.90; 95%CI 0.86–0.94; p &lt; 0.001), and sinusitis (OR 0.90; 95%CI 0.86, 0.94; p &lt; 0.001).

Conclusions
Registrars’ prescribing rates for sore throat, otitis media, and sinusitis significantly decreased during the period 2010–2019. However, educational (and other) interventions to further reduce prescribing are warranted.
Effect of Different Types of Sequence Data on Palaeognath Phylogeny
Authors: Takezaki Naoko 
Published: May 2023

AbstractPalaeognathae consists of five groups of extant species: flighted tinamous (1) and four flightless groups: kiwi (2), cassowaries and emu (3), rheas (4), and ostriches (5). Molecular studies supported the groupings of extinct moas with tinamous and elephant birds with kiwi as well as ostriches as the group that diverged first among the five groups. However, phylogenetic relationships among the five groups are still controversial. Previous studies showed extensive heterogeneity in estimated gene tree topologies from conserved nonexonic elements, introns, and ultraconserved elements. Using the noncoding loci together with protein-coding loci, this study investigated the factors that affected gene tree estimation error and the relationships among the five groups. Using closely related ostrich rather than distantly related chicken as the outgroup, concatenated and gene tree–based approaches supported rheas as the group that diverged first among groups (1)–(4). Whereas gene tree estimation error increased using loci with low sequence divergence and short length, topological bias in estimated trees occurred using loci with high sequence divergence and/or nucleotide composition bias and heterogeneity, which more occurred in trees estimated from coding loci than noncoding loci. Regarding the relationships of (1)–(4), the site patterns by parsimony criterion appeared less susceptible to the bias than tree construction assuming stationary time-homogeneous model and suggested the clustering of kiwi and cassowaries and emu the most likely with ∼40% support rather than the clustering of kiwi and rheas and that of kiwi and tinamous with 30% support each.
Pilot study of an arts- and theatre-based HIV prevention intervention for men who have sex with men and transgender women migrants in South Africa: acceptability, feasibility and preliminary efficacy
Authors: Alessi E J , Lee Y G , Chikalogwe V P , Tarusarira W , Raymond H , Lynn M , Kahn S 
Published: May 2023

Abstract
Innovative approaches addressing the elevated human immunodeficiency virus (HIV) risk among men who have sex with men (MSM) or transgender women (TGW) migrants in South Africa are urgently needed. We sought to present the acceptability, feasibility and preliminary efficacy of ‘Externalize and Mobilize!’, a multi-session arts- and theatre-based HIV prevention group intervention for MSM and TGW migrants in South Africa. Fourteen participants—MSM (n = 7; 50%), genderqueer/nonbinary persons (n = 4; 29%) and TGW (n = 3; 21%)—in Cape Town were recruited and enrolled in the intervention and administered pre- and post-intervention assessments of HIV knowledge, HIV risk-reduction self-efficacy, stigma and resilience. The intervention, delivered over 4 days, was completed by all 14 participants. Scores on HIV knowledge and HIV risk-reduction self-efficacy were statistically significantly higher at post-intervention compared with pre-intervention. Additionally, participants responded affirmatively (i.e. ‘Agree’ or ‘Strongly agree’) on all items assessing intervention acceptability. Findings demonstrate the high acceptability, feasibility and preliminary efficacy of an arts- and theatre-based intervention for increasing HIV knowledge and HIV risk-reduction self-efficacy among MSM and TGW migrants in South Africa. This study provides further support for the use of creative and innovative interventions to address entrenched HIV disparities in South Africa.
Paired passive acoustic and gillnet sampling reveal the utility of bioacoustics for monitoring fish populations in a turbid estuary
Authors: Souza Jr P M , Olsen Z , Brandl S J 
Published: May 2023

Abstract
Estuaries worldwide provide critical habitat to many ecologically and socioeconomically important fish species. However, the high turbidity and strong environmental gradients inherent to many estuaries make the monitoring of fish populations a challenging task. To assess the health and diversity of local fish populations, resource managers often employ fisheries-independent sampling methods, which result in valuable population assessments, but suffer from low-temporal resolution and high rates of mortality. Passive acoustic monitoring (PAM) provides a near-continuous, non-invasive means for monitoring soniferous fish activity over extended periods, but its utility for quantifying entire fish communities is largely untested, especially in turbid estuaries. Here, we use synchronized acoustic and gillnet sampling at 51 locations in the Mission-Aransas Estuary (TX), across two sampling seasons to test correlations between acoustic indices and gillnet catch. Positive correlations were observed between gillnet catch and sound pressure levels in both broadband (50–22050 Hz) and low-frequency (50–2500 Hz) bands. Additionally, sciaenid calling activity was positively correlated with sciaenid catch during the spring, when most spawning activity occurs. Our results indicate that PAM can be used to monitor the relative abundances of fish in Gulf of Mexico estuaries and beyond, although this is subject to species identity and seasonal dynamics.
Wheat or Chaff? A Compound Selection Model Based on Look-Up Data
Authors: Paulsen Mikkel Ekeland 
Published: May 2023

Abstract
Which compounds should be included in general-purpose dictionaries is often an open question that is answered with a case-by-case consideration of all compounds above a certain corpus frequency threshold. Another way to determine which compounds should be listed, is to examine which compounds, or rather which compound properties, are in demand by the users. This study uses look-up data from the two officially sanctioned, general-purpose dictionaries of Norwegian (Bokmålsordboka and Nynorskordboka) to derive an explicit compound selection model that performs with comparable sensitivity and specificity as the traditional procedure. These findings demonstrate that it is indeed possible to arrive at a fully operational and explicit compound selection model that meets the needs of users. With such a tool at their disposal, lexicographers would be able to separate the wheat from the chaff in the boundless field that is the compound lexicon of North Germanic Languages.
The Burden of COVID-19 in the Immunocompromised Patient: Implications for Vaccination and Needs for the Future
Authors: Antinori Andrea , Bausch-Jurken Mary 
Published: May 2023

Abstract
Approximately 3% of US adults are immunocompromised and less capable of fighting infections such as SARS-CoV-2 (the causative agent of COVID-19). Individuals may be immunocompromised for reasons related to an underlying medical condition or to immunomodulatory therapies that alter the immune response. In general, vaccination with mRNA–based vaccines is effective at reducing COVID-19–associated hospitalization and death among immunocompromised populations, particularly after 3 or more doses. However, the immunocompromised population is heterogeneous, with COVID-19 vaccine-elicited immune responses and risk for severe COVID-19 existing on a continuum. Therefore, understanding the impact of vaccination and the complexity of immune responses across heterogeneous immunocompromised individuals is essential for guiding effective vaccination regimens including additional (booster) doses. In this article, we provide an overview of the immunocompromised population and the burden of disease attributable to COVID-19, while discussing key opportunities and challenges of vaccinating immunocompromised individuals.
COVID-19 pandemic and the quality of antibiotic use in primary care: an interrupted time-series study
Authors: Domingues Mariana , Torre Carla , Guerreiro José Pedro , Barata Pedro , Correia-Neves Margarida , Rocha João , Sepodes Bruno , Teixeira Rodrigues António 
Published: May 2023

Abstract
The coronavirus disease-19 pandemic and the related public health mitigation measures have impacted the transmission of infectious diseases; however, their impact on the use of antibacterials has not yet been extensively evaluated. This study evaluated the impact of the pandemic on the consumption patterns of antibacterials for systemic use in primary care in Portugal. An interrupted time-series analysis was performed using the autoregressive integrated moving average model of the antibacterials dispensed in the community pharmacies in Portugal from 1 January 2016 to 30 June 2022. Monthly rates of absolute consumption (all antibacterials for systemic use, and specifically penicillins; cephalosporins; macrolides, lincosamides, and streptogramins; and quinolones) and the relative consumption of antibacterials (penicillins sensitive to β-lactamase, penicillin combinations including β-lactamase inhibitors, third- and fourth-generation cephalosporins, fluoroquinolones, and the ratio of broad- to narrow-spectrum antibacterials) were estimated. Antibiotic consumption was expressed in defined daily doses per 1000 inhabitants per day (DID). In Portugal, the consumption of antibacterials (J01) declined sharply immediately after the beginning of the pandemic, having a significant reduction of &gt;5 DID (P &lt; .0001). A similar, short-term impact was found for penicillins (−2.920 DID; P &lt; .0001); cephalosporins (−0.428 DID; P &lt; .0001); macrolides, lincosamides, and streptogramins (−0.681 DID; P = .0021); and quinolones (−0.320 DID; P &lt; .0001). A long-term increase was found for cephalosporins (+0.019 DID per month; P &lt; .0001). Relative consumption changes were only found for third- and fourth-generation cephalosporins (0.0734%). Our study suggests that the coronavirus disease-19 pandemic may have resulted in a decrease in antibiotic use, with no significant changes in the relative dispense. Uncertainties regarding the long-term effects of the pandemic and its impact on the rates of resistance remain.
Training for the United Nations in the Twenty-First Century; Professionalism Training on Leadership, Negotiation, and Gender for Model United Nations Simulations
Authors: O'Dell Roni Kay M , Scott Ariana B , Nealon Mark J , Franzino Brianna N 
Published: May 2023

Abstract
The world needs people who understand the crucial importance of global governance. Training students to participate in a Model United Nations (MUN) simulation provides them with the critical thinking, negotiation, and diplomacy skills that prepare them to work in international relations positions and address negotiation and diplomacy challenges. This article provides a fresh look at why MUN is important by analyzing MUN training guides used to teach students how to participate in MUN simulations. It finds that the training guides offer excellent insight into the functions and structure of the United Nations, but little in the form of learning how to negotiate or engage in diplomacy. Specifically missing are discussions of leadership, negotiation from interest, not position (also known as principled negotiation), and how to train students to be inclusive and respond to discrimination or bias during negotiations. The article includes a description of active learning and learner-centered teaching techniques and provides insight into how a specific MUN team implemented professionalism training in the 2010s. The article is written in collaboration between an MUN advisor and students who trained as MUN delegates, integrating the voices and perspectives of those who train and those who are trained.
Kappa Free Light Chain Drift Prompts the Need for a New Upper Limit of Normal Free Light Chain Ratio to Avoid an Epidemic of Kappa Light Chain Monoclonal Gammopathy of Undermined Significance
Authors: Rozenova Krasimira , Willrich Maria , Snyder Melissa , Dasari Surendra , Kourelis Taxiarchis , Rajkumar S Vincent , Kumar Shaji , Dispenzieri Angela , Murray David L 
Published: May 2023

Abstract

Background
Multiple laboratory tests are employed for detection of monoclonal proteins in patients and include serum protein electrophoresis (SPEP), immunofixation electrophoresis, free light chain (FLC) immunoassay, and mass spectrometry (Mass-Fix). Recently, reports on a drift in FLC quantitation results have been brought to light.

Methods
We studied a cohort of 16 887 patients whose sera were tested for a monoclonal protein by a FLC assay, serum protein electrophoresis, and Mass-Fix. This is a retrospective study designed to assess the impact of a drift on the performance of FLC ratio (rFLC) in groups of patients with and without detectable plasma cell disorders (PCDs).

Results
The results demonstrated that 63% of patients with monoclonal protein equal or higher than 2 g/L (by SPEP) had an abnormal rFLC (reference range 0.26–1.65). Conversely, 16% of patients with undetectable monoclonal protein by other methods (i.e., SPEP and Mass-Fix) who also had no record of treated PCD had an abnormal rFLC. In these cases, there was an imbalance in the number of kappa high rFLCs to lambda low rFLCs of 201 to 1.

Conclusions
The results of this study suggest decreased specificity of rFLC for a monoclonal kappa FLC in the 1.65 to 3.0 range.
The Role of Burn Centers in the Treatment of Necrotizing Soft-Tissue Infections: A Nationwide Dutch Study
Authors: Suijker Jaco , Wurfbain Lisca , Emmen Anouk M L H , Pijpe Anouk , Kwa Kelly A A , van der Vlies Cornelis H , Nieuwenhuis Marianne K , van Zuijlen Paul P M , Meij-de Vries Annebeth 
Published: May 2023

AbstractPatients with extensive and complex wounds due to Necrotizing Soft-Tissue Infections (NSTI) may be referred to a burn center. This study describes the characteristics, outcomes, as well as diagnostic challenges of these patients. Patients admitted to three hospitals with a burn center for the treatment of NSTI in a 5-year period were included. Eighty patients (median age 54 years, 60% male) were identified, of whom 30 (38%) were referred by other centers, usually after survival of the initial septic phase. Those referred from other centers, compared to those primarily admitted to the study hospitals, were more likely to have group A streptococcal involvement (62% vs 35%, p = .02), larger wounds (median 7% vs 2% total body surface area, p &lt; .001), and a longer length of stay (median 49 vs 22 days, p &lt; .001). Despite a high incidence of septic shock (50%), the mortality rate was low (12%) for those primarily admitted. Approximately half (53%) of the patients were initially misdiagnosed upon presentation, which was associated with delay to first surgery (16 hours vs 4 hours, p &lt; .001). Those initially misdiagnosed had more (severe) comorbidities, and less frequently reported pain or blue livid discoloration of the skin. This study underlines the burn centers’ function as referral centers for extensively affected patients with NSTI. Besides the unique wound and reconstructive expertise, the low mortality rate indicates these centers provide adequate acute care as well. A major remaining challenge remains recognition of the disease upon presentation. Future studies in which factors associated with misdiagnosis are explored are needed.