bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverting estimating equations for causal inference on quantiles
Authors: Cheng Chao , Li Fan 
Published: October 2024

Summary
The causal inference literature frequently focuses on estimating the mean of the potential outcome, whereas quantiles of the potential outcome may carry important additional information. We propose an inverse estimating equation framework to generalize a wide class of causal inference solutions from estimating the mean of the potential outcome to its quantiles. We assume that a moment function is available to identify the mean of the threshold-transformed potential outcome, based on which a convenient construction of the estimating equation of the quantiles of the potential outcome is proposed. In addition, we give a general construction of the efficient influence functions of the mean and quantiles of potential outcomes, and establish their connection. We motivate estimators for the quantile estimands with the efficient influence function, and develop their asymptotic properties when either parametric models or data-adaptive machine learners are used to estimate the nuisance functions. A broad implication of our results is that one can rework the existing result for mean causal estimands to facilitate causal inference on quantiles. Our general results are illustrated by several analytical and numerical examples.
Mycosis fungoides: differentiation from inflammation and detection of circulating tumour cells with the EuroClonality next-generation sequencing assay
Authors: Wehkamp Ulrike , Pietzka Sophie , Kotrová Michaela , Jost Marion , Oschlies Ilske , Schwarz Agatha , Baldus Claudia , Darzentas Nikos , Brüggemann Monika 
Published: October 2024

Abstract

Background
Mycosis fungoides (MF) is a rare malignancy that is characterized by the presence of circulating tumour cells (CTCs) in a subgroup of patients. Reliably distinguishing MF from inflammatory skin conditions is challenging.

Objectives
To evaluate the potential benefits of next-generation sequencing (NGS)-based T-cell receptor rearrangement repertoire analysis in detecting clonal rearrangements in MF and inflammatory skin conditions.

Methods
Skin biopsies and blood samples from 33 patients with MF and 10 patients with inflammatory skin conditions were analysed using TRB and TRG NGS. Twenty-seven patients had early-stage IA (n = 19) and IB (n = 8) MF, and six had advanced-stage disease (IIB, n = 5; IIIA, n = 1).

Results
Analysis applying standard abundance thresholds identified at least one clonal rearrangement in the skin DNA of 97% (n = 32/33) of patients with MF and in 90% (n = 9/10) of those with inflammatory skin conditions. To enhance specificity, an abundance and distribution-based approach was applied, which considered only rearrangements that significantly stood out from the physiological background as clonal (MF, n = 29/33; inflammatory skin conditions, n = 1/10), allowing for highly sensitive (88%) and specific (90%) discrimination between MF and other inflammatory skin conditions. CTCs were detected in 46% (n = 11/24) of patients with early-stage MF and in 60% (n = 3/5) of those with late-stage MF.

Conclusions
NGS-based T-cell receptor repertoire analysis is a highly sensitive and specific method for the differential diagnosis of early-stage MF vs. inflammatory skin conditions, and for the sensitive molecular detection of CTCs.
Reinforced tension-line suture after laparotomy: early results of the Rein4CeTo1 randomized clinical trial
Authors: Wenzelberg Charlotta L , Rogmark Peder , Ekberg Olle , Petersson Ulf 
Published: October 2024

Abstract

Background
The aim was to investigate whether adding a reinforced tension-line (RTL) suture to a standard 4 : 1 small-bite closure would reduce the incidence of incisional hernia after colorectal cancer surgery.

Methods
Patients aged at least 18 years, who were scheduled for elective colorectal cancer surgery through a midline incision at two Swedish hospitals (2017–2021), were randomized in a 1 : 1 ratio to either fascial closure with RTL and 4 : 1 small-bite closure with polypropylene sutures (RTL group) or 4 : 1 small-bite closure with polydioxanone suture alone (PDS group). The primary outcome was CT-detected incisional hernia 1 year after surgery. CT interpreters were blinded regarding treatment group.

Results
In all, 160 patients were randomized, 80 in each group. The study closed early to recruitment and follow-up. Some 134 patients were analysed at 1 year: 63 in the RTL group and 71 in the PDS group. Nineteen patients were found to have an incisional hernia: 4 (6%) in the RTL group and 15 (21%) in the PDS group (OR 3.95, 95% c.i. 1.24 to 12.60; P = 0.014). No unintended effects were found in either group.

Conclusion
Adding an RTL suture at fascial closure decreased the incidence of incisional hernia in patients undergoing surgery for colorectal cancer. Trial registration: NCT03390764 (https://clinicaltrials.gov).
Controlled connection: Substack and writers of color
Authors: Hewa Nelanthi , Cohen Nicole S 
Published: October 2024

Abstract
Substack, a self-described “subscription network for independent writers and creators,” launched in 2017. Substack claims to be part of a better future for news workers, yet it has been embroiled in controversy and questions, particularly in recent years. In this article, we draw on interviews we conducted with journalists and writers of color who produce newsletters to better understand the opportunities and limitations of contemporary newsletter platforms. We find that studying the experiences of journalists of color reveals a nuanced and somewhat ambivalent picture of the journalism industry and people of color’s place within it. We find that the Substack models favors the status quo, a reality that further entrenches the success of White journalists. Yet writers of color value the safety enabled by sending writing directly to a small, defined, private audience, a contrast with social media logics and their compulsory visibility.
10 tips on how to use dynamic risk assessment and alerts for AKI
Authors: Quickfall Danica , La Ashley M , Koyner Jay L 
Published: October 2024

ABSTRACT
Acute kidney injury (AKI) is a common syndrome in hospitalized patients and is associated with increased morbidity and mortality. The focus of AKI care requires a shift away from strictly supportive management of established injury to the early identification and timely prevention of worsening renal injury. Identifying patients at risk for developing or progression of severe AKI is crucial for improving patient outcomes, reducing the length of hospitalization and minimizing resource utilization. Implementation of dynamic risk scores and incorporation of novel biomarkers show promise for early detection and minimizing progression of AKI. Like any risk assessment tools, these require further external validation in a variety of clinical settings prior to widespread implementation. Additionally, alerts that may minimize exposure to a variety of nephrotoxic medications or prompt early nephrology consultation are shown to reduce the incidence and progression of AKI severity and enhance renal recovery. While dynamic risk scores and alerts are valuable, implementation requires thoughtfulness and should be used in conjunction with the overall clinical picture in certain situations, particularly when considering the initiation of fluid and diuretic administration or renal replacement therapy. Despite the contemporary challenges encountered with alert fatigue, implementing an alert-based bundle to improve AKI care is associated with improved outcomes, even when implementation is incomplete. Lastly, all alert-based interventions should be validated at an institutional level and assessed for their ability to improve institutionally relevant and clinically meaningful outcomes, reduce resource utilization and provide cost-effective interventions.
Integrated, person-centred care for patients with complex cardiovascular disease, diabetes mellitus and chronic kidney disease: a randomized trial
Authors: Evén Gudrun , Stenfors Terese , Jacobson Stefan H , Jernberg Tomas , Franzén-Dahlin Åsa , Jäghult Susanna , Kahan Thomas , Spaak Jonas 
Published: October 2024

ABSTRACT

Background
Patients with cardiovascular disease (CVD), diabetes mellitus (DM) and chronic kidney disease (CKD) often experience fragmented care, which negatively impacts outcomes and health-related quality of life (HRQoL). This study assessed whether multidisciplinary, person-centred care at an integrated clinic improves clinical outcomes and HRQoL.

Methods
This prospective, open, blinded-endpoint trial (CareHND; NCT03362983) included 131 patients with CVD, DM and CKD stages 3–4, most of whom were enrolled during or shortly after acute hospitalization. The intervention group received person-centred care from cardiologists, nephrologists, endocrinologists and specialist nurses at an integrated clinic; the control group received traditional care from separate specialists. Primary disease progression outcome was the composite of major adverse renal and cardiovascular events (MARCE) including death, heart failure (HF) readmission, myocardial infarction, percutaneous coronary intervention/coronary artery bypass graft, acute or end-stage kidney failure, or transient ischaemic attack/stroke at 2 years. Co-primary person-centred outcomes was self-reported HRQoL by RAND-36.

Results
In a pre-specified interim analysis, patients randomized to integrated care had lower estimated glomerular filtration rate and higher NT-proBNP (N-terminal pro brain natriuretic peptide) than traditional care. Follow-up ranged from 2.0 to 5.7 years. Kaplan–Meier analysis showed no difference in MARCE between groups. Cox-regression adjusting for baseline differences, indicated a trend towards reduced HF hospitalizations for integrated care (hazard ratio 0.53; confidence interval 0.28–1.01; P = .054). Integrated care improved role physical and social function scores, and self-rated health (P = .021, P = .019 and P = .011, respectively).

Conclusions
Integrated care improved several dimensions of HRQoL but did not improve MARCE compared with traditional care in this small trial. We observed a trend towards reduced HF hospitalizations. Overall, integrated care presents a promising alternative.
Comparison of strategies for vascular ACCESS closure after Transcatheter Aortic Valve Implantation: the ACCESS-TAVI randomized trial
Authors: Rheude Tobias , Ruge Hendrik , Altaner Niklas , Pellegrini Costanza , Alvarez Covarrubias Hector , Mayr Patrick , Cassese Salvatore , Kufner Sebastian , Taniguchi Yousuke , Thilo Christian , Klos Markus , Erlebach Magdalena , Schneider Simon , Jurisic Martin , Laugwitz Karl-Ludwig , Lange Rüdiger , Schunkert Heribert , Kastrati Adnan , Krane Markus , Xhepa Erion , Joner Michael 
Published: October 2024

Abstract

Background and Aims
Data from randomized trials investigating different access closure strategies after transfemoral transcatheter aortic valve implantation (TF-TAVI) remain scarce. In this study, two vascular closure device (VCD) strategies to achieve haemostasis after TF-TAVI were compared.

Methods
The ACCESS-TAVI (Comparison of Strategies for Vascular ACCESS Closure after Transcatheter Aortic Valve Implantation) is a prospective, multicentre trial in which patients undergoing TF-TAVI were randomly assigned to a strategy with a combined suture-/plug-based VCD strategy (suture/plug group) using one ProGlide™/ProStyle™ (Abbott Vascular) and one Angio-Seal® (Terumo) vs. a suture-based VCD strategy (suture-only group) using two ProGlides™/ProStyles™. The primary endpoint was a composite of major or minor access site-related vascular complications during index hospitalization according to Valve Academic Research Consortium 3 criteria. Key secondary endpoints included time to haemostasis, bleeding type ≥ 2, and all-cause mortality over 30 days.

Results
Between September 2022 and April 2024, 454 patients were randomized. The primary endpoint occurred in 27% (62/230) in the suture/plug group and 54% (121/224) in the suture-only group [relative risk .55 (95% confidence interval: .44, .68); P &lt; .001]. Time to haemostasis was significantly shorter in the suture/plug group compared with the suture-only group (108 ± 208 s vs. 206 ± 171 s; P &lt; .001). At 30 days, bleeding type ≥ 2 occurred less often in the suture/plug group compared with the suture-only group [6.2% vs. 12.1%, relative risk .66 (.43, 1.02); P = .032], with no significant difference in mortality.

Conclusions
With regard to the composite of major or minor access site-related vascular complications, a combined suture-/plug-based VCD strategy was superior to a suture-based VCD strategy for vascular access closure in patients undergoing TF-TAVI.
Genome-Wide Comparisons Reveal Extensive Divergence Within the Lichen Photobiont Genus, Trebouxia
Authors: Poquita-Du Rosa Celia , Otte Jürgen , Calchera Anjuli , Schmitt Imke 
Published: October 2024

Abstract
The green algal genus Trebouxia is the most frequently encountered photobiont of the lichen symbiosis. The single-celled symbionts have a worldwide distribution, including all continents and climate zones. The vast, largely undescribed, diversity of Trebouxia lineages is currently grouped into four phylogenetic clades (A, C, I, and S), based on a multilocus phylogeny. Genomes are still scarce, however, and it is unclear how the phylogenetic diversity, the broad ecological tolerances, and the ability to form symbioses with many different fungal host species are reflected in genome-wide differences. Here, we generated PacBio-based de novo genomes of six Trebouxia lineages belonging to the Clades A and S, isolated from lichen individuals of the genus Umbilicaria. Sequences belonging to Clade S have been reported in a previous study, but were reassembled and reanalyzed here. Genome sizes ranged between 63.08 and 73.88 Mb. Repeat content accounted for 9% to 16% of the genome sequences. Based on RNA evidence, we predicted 14,109 to 16,701 gene models per genome, of which 5,203 belonged to a core set of gene families shared by all 6 lineages. Between 121 and 454, gene families are specific to each lineage. About 53% of the genes could be functionally annotated. The presence of biosynthetic gene clusters (6 to 17 per genome) suggests that Trebouxia algae are able to synthesize alkaloids, saccharides, terpenes, NRPSs, and T3PKSs. Phylogenomic comparisons of the six strains indicate prevalent gene gain during Trebouxia evolution. Some of the gene families that exhibited significant evolutionary changes (i.e. gene expansion and contraction) are associated with metabolic processes linked to protein phosphorylation, which is known to have a role in photosynthesis regulation, particularly under changing light conditions. Overall, there is substantial genomic divergence within the algal genus Trebouxia, which may contribute to the genus’ large ecological amplitude concerning fungal host diversity and climatic niches.
Challenges in Assembling the Dated Tree of Life
Authors: Schrago Carlos G , Mello Beatriz 
Published: October 2024

Abstract
The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.
Parental-effect gene-drive elements under partial selfing, or why do Caenorhabditis genomes have hyperdivergent regions?
Authors: Rockman Matthew V 
Published: October 2024

Abstract
Self-fertile Caenorhabditis nematodes carry a surprising number of Medea elements, alleles that act in heterozygous mothers and cause death or developmental delay in offspring that do not inherit them. At some loci, both alleles in a cross operate as independent Medeas, affecting all the homozygous progeny of a selfing heterozygote. The genomic coincidence of Medea elements and ancient, deeply coalescing haplotypes, which pepper the otherwise homogeneous genomes of these animals, raises questions about how these apparent gene-drive elements persist for long periods of time. Here, I investigate how mating system affects the evolution of Medeas, and their paternal-effect counterparts, peels. Despite an intuition that antagonistic alleles should induce balancing selection by killing homozygotes, models show that, under partial selfing, antagonistic elements experience positive frequency dependence: the common allele drives the rare one extinct, even if the rare one is more penetrant. Analytical results for the threshold frequency required for one allele to invade a population show that a very weakly penetrant allele, one whose effects would escape laboratory detection, could nevertheless prevent a much more penetrant allele from invading under high rates of selfing. Ubiquitous weak antagonistic Medeas and peels could then act as localized barriers to gene flow between populations, generating genomic islands of deep coalescence. Analysis of gene expression data, however, suggests that this cannot be the whole story. A complementary explanation is that ordinary ecological balancing selection generates ancient haplotypes on which Medeas can evolve, while high homozygosity in these selfers minimizes the role of gene drive in their evolution.
Effect of integrated medicines management on quality of discharge medication information—a secondary endpoint in a randomized controlled trial
Authors: Mathiesen Liv , Nguyen Tram Bich Michelle , Dæhlen Ingrid , Mowé Morten , Lea Marianne 
Published: October 2024

Abstract

Background
High-quality discharge information is important to promote patient safety when patients are transferred from hospital to primary care. Patients with multiple long-term conditions are especially vulnerable to insufficient transfer of medication information, as they use many medications and have complex interactions with the healthcare services. The aim of this study was to investigate the effect of integrated medicines management provided to hospitalized multimorbid patients on the quality of the discharge medication information.

Methods
Multimorbid patients ≥18 years, using a minimum of four regular medications from a minimum of two therapeutic medication classes were recruited from the Internal Medicine ward, Oslo University Hospital, Norway, from August 2014 to March 2016 and randomly assigned, 1:1, to the intervention or control group. Intervention patients received integrated medicines management throughout the hospital stay. Control patients received standard care. This paper reports the results of a prespecified secondary endpoint analysis of the randomized controlled trial; the difference between the intervention and control group in the quality of discharge medication information.

Results
The analysis population comprised 384 patients. Integrated medicines management improved the discharge summary quality score of the medication information from 5.8 ± 1.5 to 8.6 ± 2.6 [mean difference 2.7, 95% confidence interval (CI) 2.3–3.2, P &lt; .001]. In total, 171 intervention patients (89%) received a patient discharge information letter, compared to 66 control patients (35%), P &lt; .001. The quality score of the medication information in the patient discharge information letter was improved from 6.0 ± 1.8 in the control group to 10.0 ± 1.3 in the intervention group (mean difference 4.0, 95% CI 3.6–4.4, P &lt; .001).

Conclusion
Integrated medicines management delivered to multimorbid patients during a hospital stay improved the quality of the medication information in discharge summaries as well as patient discharge information letters and ensured that a discharge information letter in lay language was prepared for almost all patients who were involved in the management of their medications after discharge.
Antimicrobial use in hospitalized patients: a point prevalence survey across four tertiary hospitals in Niger
Authors: Tapha Ounoussa , Degbey Cyriaque Comlan , Yacouba Abdourahamane , Mahouna Tchioundjro Espère , Nadakou N’Kpingou Théodore , Alkassoum Salifou Ibrahim , Moussa Saley Sahada , Daou Mamane , Brah Souleymane , Omar Adehossi Eric , Vikkey Hinson Antoine , Mamadou Saidou 
Published: October 2024

Abstract

Background
Antimicrobial resistance (AMR) is a global threat to public health. Misuse or overuse of antimicrobials contributes to the emergence of AMR. Data on antimicrobial prescribing represent the cornerstone for guiding antimicrobial stewardship strategies. This study aimed to assess the use, indications, classification, and quality indicators of antimicrobials prescribed to patients in four tertiary hospitals in Niger.

Methods
This cross-sectional study used the methodology for Global Point Prevalence Surveys in tertiary hospitals between January and April 2024. Hospital records of all inpatients on admission at 08:00 hours on a specific day were reviewed for antimicrobial use during the survey.

Results
The overall prevalence of antibiotic use across hospitals was 54.5% (n = 470/862), ranging between 66.2% (n = 149/234) and 44.3% (n = 183/258). Most antibiotics used were antibacterials (89.0%, n = 637). Third-generation cephalosporins (48.2%, 307/637), imidazole derivatives (14.7%, 105/716), penicillins with extended spectrum (9.6%, 69/716), and fluoroquinolones (6.1%, 44/716) were the most commonly prescribed classes of antibiotics. Most antibiotics (84.9%, n = 608) were prescribed to treat community-acquired infections, while surgical prophylaxis accounted for 6.4% (n = 47/716). Most antibiotics (96.1%; n = 688/716) were used empirically, and less than a quarter (20.7%) of antibiotics prescribed had a documented stop/review date recorded. Only, 4.2% (n = 31/716) of prescribed antibiotics had cultures and susceptibility testing requested.

Conclusion
This study shows that antibiotic prescription rates are high in tertiary hospitals, with relatively high use of third-generation cephalosporins. Most antibiotics were empirically used and not guided by culture and susceptibility testing. These results could be the subject of key interventions for hospital antibiotic stewardship strategies in Niger.
Improved dopant fraction variance estimation in statistical ALCHEMI based on correct error propagation rule
Authors: Ishizuka Akimitsu , Ohtsuka Masahiro , Muto Shunsuke 
Published: October 2024

Abstract
This report revisits the statistical atom location by channeling enhanced microanalysis method, correcting the dopant site occupancy error by applying an appropriate error propagation rule. A revised equation for calculating the uncertainty in the determined dopant fractions is proposed. The revised equation is expected to correct the uncertainty in the determined dopant fractions, which is particularly significant in cases of low dopant concentrations and variable dopant occupancies across inequivalent host atomic sites. The approach is validated using Eu-doped Ca2SnO4 as a typical model system.