bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paneth cell differentiation associated with neoadjuvant therapy in esophageal adenocarcinoma
Authors: Ramineni Madhurya , Findeis Sarah K , Ye Jiqing , Hao Yansheng 
Published: August 2024

Abstract

Objectives
Paneth cells and Paneth cell metaplasia are well-known in pathology as foundational components in the gastrointestinal system. When within malignant cells (Paneth cell differentiation [PCD]), however, the function and significance of these cells is less well understood. Here, we present findings from the first study focused on PCD in postneoadjuvant esophageal adenocarcinoma (EAC) resection specimens.

Methods
Patients with EAC treated with neoadjuvant chemoradioation and followed by esophagectomy between 2012 and 2018 in our institution were retrospectively evaluated. A tissue microarray was constructed, and special and immunohistochemical stains were performed.

Results
A total of 64 cases were collected, of which 8 had PCD, as highlighted by periodic acid–Schiff with diastase staining. Adenocarcinomas with PCD were more commonly seen in patients 60 to 70 years of age and typically had a poorly differentiated morphology, observationally fewer stromal mucinous changes, and less lymph node metastasis. β-catenin activation induced by neoadjuvant therapy was more frequent in the PCD-positive cases. Patients with PCD-positive disease had low programmed cell death 1 ligand 1 levels, no positive or equivocal ERBB2 (HER2) expression, and low CD8-positive T-cell infiltration; they were also mismatch repair proficient. Patients with PCD-positive disease showed a survival pattern inferior to that of patients with PCD-negative disease.

Conclusions
When induced by neoadjuvant therapy in EAC, PCD is associated with high β-catenin activation, less expression of targetable biomarkers, and a potentially worse clinical prognosis.
Measuring the operational performance of an artificial intelligence–based blood tube-labeling robot, NESLI
Authors: Demirci Ferhat 
Published: August 2024

Abstract

Objectives
Laboratory testing, crucial for medical diagnosis, has 3 phases: preanalytical, analytical, and postanalytical. This study set out to demonstrate whether automating tube labeling through artificial intelligence (AI) support enhances efficiency, reduces errors, and improves outpatient phlebotomy services.

Methods
The NESLI tube-labeling robot (Labenko Informatics), which uses AI models for tube selection and handling, was used for the experiments. The study evaluated the NESLI robot’s operational performance, including labelling time, technical problems, tube handling success, and critical stock alerts. The robot’s label readability was also tested on various laboratory devices. This research will contribute to the field’s understanding of the potential impact of automated tube-labeling systems on laboratory processes in the preanalytical phase.

Results
NESLI demonstrated high performance in labeling processes, achieving a success rate of 99.2% in labeling parameters and a success rate of 100% in other areas. For nonlabeling parameters, the average labeling time per tube was measured at 8.96 seconds, with a 100% success rate in tube handling and critical stock warnings. Technical issues were promptly resolved, affirming the NESLI robot’s effectiveness and reliability in automating the tube-labeling processes.

Conclusions
Robotic systems using AI, such as NESLI, have the potential to increase process efficiency and reduce errors in the preanalytical phase of laboratory testing. Integration of such systems into comprehensive information systems is crucial for optimizing phlebotomy services and ensuring timely and accurate diagnostics.
Association of anticoagulant choice with death in the primary treatment of noncancer venous thromboembolism: Medicare 2011-2018
Authors: Walker Rob F , Zakai Neil A , Maclehose Richard F , Norby Faye L , Alonso Alvaro , Lutsey Pamela L 
Published: August 2024

Abstract
Direct oral anticoagulants (DOACs; namely, rivaroxaban and apixaban) and warfarin are approved for venous thromboembolism (VTE) treatment. Few direct comparisons exist of DOACs on risk of death among patients with VTE, and for patients with concomitant conditions (eg, kidney disease, liver disease), clinical guidelines are unclear. We evaluated 6-month all-cause mortality by anticoagulant prescribed for primary treatment of VTE. Using data from a 20% sample of Medicare beneficiaries, we created a propensity score–matched analytic data set of 47 860 beneficiaries with noncancer incident VTE. We used Cox regression to estimate adjusted hazard ratios (HRs) of OACs with 6-month mortality, and tested interactions by liver and kidney disease. There were 3422 deaths over 6 months of follow-up. In adjusted models, patients prescribed rivaroxaban (HR = 0.82; 95% CI, 0.76-0.90) had lower mortality rates than those prescribed warfarin. There was no association when comparing apixaban with warfarin (HR = 0.96; 95% CI, 0.87-1.07). In head-to-head comparisons of apixaban and rivaroxaban, the HR was 1.14 (95% CI, 1.01-1.28). Findings were similar among patients with liver and kidney disease. Overall, risk of death was similar by OAC prescribed. Though it is possible residual confounding remained, there was some suggestion of lower risk with rivaroxaban than warfarin. Treatment with DOACs appears safe among patients with VTE who have concomitant kidney or liver disease.
This article is part of a Special Collection on Pharmacoepidemiology.
Healthcare workers’ experiences protecting themselves and their families during the COVID-19 pandemic in 2020–2021
Authors: Ceballos Diana M , Vasquez Diana , Ceballos Lina M , Noguchi Julia E , Levy Jonathan I , Green Jennifer Greif , Baker William E , Schechter-Perkins Elissa M , Leibler Jessica H 
Published: August 2024

Abstract
We characterized experiences and strategies used by frontline healthcare workers to prevent severe-acute-respiratory-syndrome-related coronavirus transmission at work and to household members during the coronavirus disease pandemic. Alongside an online questionnaire (n = 234), remote semi-structured interviews (n = 23: 15 clinicians, 8 non-clinicians) were conducted in 2021. Mitigation challenges and facilitators were identified from data to represent experiences as a process considering the before, during, and after work shifts. Journey mapping was utilized to visually describe how healthcare workers experienced the stages of the work environment, leaving work, commuting home, and the home environment, and strategies implemented to stay safe. Major facilitators included the uptake of coronavirus disease vaccines and testing, information regarding virus transmission, and adequate personal protective equipment. The most critical challenges identified included a lack of designated areas for end-of-day disinfection, changing rooms, showers, and lockers in the leaving work stage. Psychosocial and environmental factors must be considered in future hospital pandemic preparations.
ModDotPlot—rapid and interactive visualization of tandem repeats
Authors: Sweeten Alexander P , Schatz Michael C , Phillippy Adam M 
Published: August 2024

Abstract

Motivation
A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.

Results
In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes.

Availability and implementation
ModDotPlot is available at https://github.com/marbl/ModDotPlot.
When advanced MRI is not about naming musculoskeletal lesions
Authors: Martín-Noguerol Teodoro , Casado-Verdugo Oscar L , Vilanova Joan C , Luna Antonio 
Published: August 2024

Abstract
Nowadays, the use of advanced MRI sequences such as diffusion-weighted imaging or perfusion-weighted imaging in the field of musculoskeletal radiology remains limited compared to other anatomical regions and subspecialties. Several reasons underpin this, primarily technical challenges, and a longstanding reliance on conventional and morphological evaluations of soft tissue and bone lesions. Experienced radiologists often assert that these advanced sequences do not offer added diagnostic value, claiming that a morphological approach suffices. However, in our opinion, the role of these advanced MRI sequences extends beyond merely naming an MSK lesion. In this commentary, we elucidate how these sequences can aid radiologists in various scenarios, from determining patient prognosis and tracking treatment progress to enhancing clinical-radiological correlations or guiding less experienced radiologists in evaluating soft tissues or bone tumours.
Intratumoral vitamin D signaling and lethal prostate cancer
Authors: Vaselkiv Jane B , Shui Irene M , Grob Sydney T , Ericsson Caroline I , Giovannucci Isabel , Peng Cheng , Finn Stephen P , Mucci Lorelei A , Penney Kathryn L , Stopsack Konrad H 
Published: August 2024

Abstract
High circulating vitamin D levels and supplementation may lower prostate cancer mortality. To probe for direct effects of vitamin D signaling in the primary tumor, we assessed how activation of intratumoral vitamin D signaling in prostate cancer is associated with lethal prostate cancer during long-term follow-up. Among 404 participants with primary prostate cancer in the Health Professionals Follow-up Study and the Physicians’ Health Study, we defined a gene score of expected activated intratumoral vitamin D signaling consisting of transcriptionally upregulated (CYP27A1, CYP2R1, RXRA, RXRB, and VDR) and downregulated genes (CYP24A1 and DHCR7). We contrasted vitamin D signaling in tumors that progressed to lethal disease (metastases/prostate cancer-specific death, n = 119) over up to three decades of follow-up with indolent tumors that remained nonmetastatic for &gt;8 years post-diagnosis (n = 285). The gene score was downregulated in tumor tissue compared with tumor-adjacent histologically normal tissue of the same men. Higher vitamin D gene scores were inversely associated with lethal prostate cancer (odds ratio for highest versus lowest quartile: 0.46, 95% confidence interval: 0.21–0.99) in a dose–response fashion and after adjusting for clinical and pathologic factors. This association appeared strongest among men with high predicted plasma 25-hydroxyvitamin D3 and men with body mass index ≥25 kg/m2. Findings were replicated with broader gene sets. These data support the hypothesis that active intratumoral vitamin D signaling is associated with better prostate cancer outcomes and provide further rationale for testing how vitamin D-related interventions after diagnosis could improve prostate cancer survival through effects on the tumor.
Epidemiology, survival and risk of subsequent primary malignancies in patients with digital papillary adenocarcinoma: a retrospective study of 213 patients in the Surveillance, Epidemiology, and End Results Program
Authors: Joshi Tejas P , Kimyai-Asadi Arash 
Published: August 2024

Abstract
Digital papillary adenocarcinoma (DPAc) is a rare and aggressive cutaneous malignancy of sweat gland derivation. We conducted a retrospective study of 213 patients with DPAc using the 17 registries of the Surveillance, Epidemiology, and End Results (SEER) Program. We estimated the incidence of DPAc to be 0.11 per million persons per year, with the incidence rising over the past two decades. Our study shows DPAc to most commonly affect White men, typically in their forties to sixties. We noted a 5-year disease-specific survival of 98.3% and 5-year overall survival of 95.7%. We also showed advanced age to be associated with more aggressive disease and identified tumour size as an independent risk factor affecting disease-specific survival. Our results also suggest that patients with DPAc have an elevated risk of developing subsequent primary malignancies, with men being at increased risk of developing lung/bronchial neoplasms and women being at increased risk of developing breast cancer.
Expression of STAT3, IL27p28 and IL12p35 is deregulated and linked to autoimmune markers in chronic spontaneous urticaria
Authors: Rastgoo Sahar , Mohammadi Mojgan , Maurer Marcus , Atabaki Mahdi , Tavakkol-Afshari Jalil , Khoshkhui Maryam 
Published: August 2024

Abstract

Background
Chronic spontaneous urticaria (CSU) is a common inflammatory disorder characterized by weals, angio-oedema, or both, for more than 6 weeks. Autoimmunity is held to be one of the most frequent causes, but little is known about the expression and relevance of autoimmunity-driving genes in CSU, such as STAT3, STAT1, IL27p28 (IL30) and IL12p35 (IL12A).

Objectives
To investigate patients with CSU and the expression of STAT3, STAT1, IL27p28 and IL12p35, and possible links to clinical features.

Methods
We enrolled 26 patients with CSU and 19 healthy controls (HCs) and determined their expression levels of STAT3, STAT1, IL27p28 and IL12p35 by quantitative real-time polymerase chain reaction. Patients were assessed for total IgE and IgG-anti-thyroid peroxidase (TPO), markers of autoimmune CSU.

Results
Patients with CSU showed significantly higher expression of STAT3 but not STAT1: 17 (65%) and 10 (38%) of the 26 had elevated STAT3 expression and STAT3/STAT1 ratios, respectively, as compared with only 1 (5%) of the 19 HCs. High STAT3 expression and STAT3/STAT1 ratios were linked to low IgE and elevated IgG-anti-TPO. As compared with HCs, patients with CSU had markedly lower and correlated IL27p28 and IL12p35 mRNA expression levels. Low IL27p28 and IL12p35 expression levels were linked to higher STAT3/STAT1 ratios and low IgE.

Conclusions
STAT3 upregulation and higher STAT3/STAT1 ratios, along with IL27p28 and IL12p35 downregulation, clusters with features of autoimmune CSU. The role of STAT3 as a potential pathogenic driver of autoimmune CSU and target of treatment should be explored further.
Hospital-Acquired and Ventilator-Associated Pneumonia Early After Lung Transplantation: A Prospective Study on Incidence, Pathogen Origin, and Outcome
Authors: Walti Laura N , Ng Chun Fai , Mohiuddin Qasim , Bitterman Roni , Alsaeed Mohammed , Klement William , Martinu Tereza , Sidhu Aman , Mazzulli Tony , Donahoe Laura , Keshavjee Shaf , del Sorbo Lorenzo , Husain Shahid 
Published: August 2024

Abstract

Background
Hospital-acquired (HAP) and ventilator-associated pneumonia (VAP) are important complications early (&lt;30 days) after lung transplantation (LT). However, current incidence, associated factors, and outcomes are not well reported.

Methods
LT recipients transplanted at our institution (July 2019–January 2020 and October 2021–November 2022) were prospectively included. We assessed incidence and presentation of pneumonia and evaluated the impact of associated factors using regression models. We also evaluated molecular relatedness of respiratory pathogens collected peri-transplant and at pneumonia occurrence using pulsed-field gel electrophoresis (PFGE).

Results
In the first 30 days post-LT, 25/270 (9.3%) recipients were diagnosed with pneumonia (68% [17/25] VAP; 32% [8/25] HAP). Median time to pneumonia was 11 days (IQR, 7–13); 49% (132/270) of donor and 16% (44/270) of recipient respiratory peri-transplant cultures were positive. However, pathogens associated with pneumonia were not genetically related to either donor or recipient cultures at transplant, as determined by PFGE. Diagnosed pulmonary hypertension (HR, 4.42; 95% CI, 1.62–12.08) and immunosuppression use (HR, 2.87; 95% CI, 1.30–6.56) were pre-transplant factors associated with pneumonia. Pneumonia occurrence was associated with longer hospital stay (HR, 5.44; 95% CI, 2.22–13.37) and VAP with longer ICU stay (HR, 4.31; 95% CI, 1.73–10.75) within the first 30 days post-transplantation; 30- and 90-day mortality were similar.

Conclusions
Prospectively assessed early pneumonia incidence occurred in ∼10% of LT. Populations at increased risk for pneumonia occurrence include LT with pre-transplant pulmonary hypertension and pre-transplant immunosuppression. Pneumonia was associated with increased healthcare use, highlighting the need for further improvements by preferentially targeting higher-risk patients.
Integrase Strand Transfer Inhibitor–Related Changes in Body Mass Index and Risk of Diabetes: A Prospective Study From the RESPOND Cohort Consortium
Authors: Rupasinghe Dhanushi , Bansi-Matharu Loveleen , Law Matthew , Zangerle Robert , Rauch Andri , Tarr Philip E , Greenberg Lauren , Neesgaard Bastian , Jaschinski Nadine , De Wit Stéphane , Wit Ferdinand , d'Arminio Monforte Antonella , Fontas Eric , Castagna Antonella , Stecher Melanie , Florence Eric , Begovac Josip , Mussini Cristina , Sönnerborg Anders , Abutidze Akaki , Groh Ana , Vannappagari Vani , Cohen Cal , Young Lital , Hosein Sean , Ryom Lene , Petoumenos Kathy 
Published: August 2024

Abstract

Background
With integrase strand transfer inhibitor (INSTI) use associated with increased body mass index (BMI) and BMI increases associated with higher diabetes mellitus (DM) risk, we explored the relationships between INSTI/non-INSTI regimens, BMI changes, and DM risk.

Methods
RESPOND participants were included if they had CD4, human immunodeficiency virus (HIV) RNA, and ≥2 BMI measurements during follow-up. Those with prior DM were excluded. DM was defined as a random blood glucose ≥11.1 mmol/L, hemoglobin A1c ≥6.5%/48 mmol/mol, use of antidiabetic medication, or site-reported clinical diagnosis. Poisson regression was used to assess the association between natural log (ln) of time-updated BMI and current INSTI/non-INSTI and their interactions on DM risk.

Results
Among 20 865 people with HIV included, most were male (74%) and White (73%). Baseline median age was 45 years (interquartile range [IQR], 37–52), with a median BMI of 24 kg/m2 (IQR, 22–26). There were 785 DM diagnoses with a crude rate of 0.73 (95% confidence interval [CI], .68–.78)/100 person-years of follow-up. ln(BMI) was strongly associated with DM (adjusted incidence rate ratio [aIRR], 16.54 per log increase; 95% CI, 11.33–24.13; P &lt; .001). Current INSTI use was associated with increased DM risk (IRR, 1.58; 95% CI, 1.37–1.82; P &lt; .001) in univariate analyses and only partially attenuated when adjusted for variables including ln(BMI) (aIRR, 1.48; 95% CI, 1.29–1.71; P &lt; .001). There were no interactions between ln(BMI), INSTI, and non-INSTI use and DM (P = .130).

Conclusions
In RESPOND, compared with non-INSTIs, current use of INSTIs was associated with an increased DM risk, which partially attenuated when adjusted for BMI changes and other variables.
Changes of intracardiac flow dynamics measured by HyperDoppler in patients with aortic stenosis
Authors: Sabatino Jolanda , Leo Isabella , Strangio Antonio , La Bella Sabrina , De Sarro Rosalba , Montemurro Vincenzo , Pedrizzetti Gianni , Troilo Fabio , Maglione Marco , Torella Daniele , Di Salvo Giovanni , De Rosa Salvatore 
Published: August 2024

Abstract

Aims
Assessment of intracardiac flow dynamics has recently acquired significance due to the development of new measurement methods based on echocardiography. Recent studies have demonstrated that cardiac abnormalities are associated with changes in intracardiac vortical flows. Yet, no previous study assessed the impact of aortic stenosis (AS) on intracardiac vortices. This study aims to explore the clinical potential of additional information provided by quantifying intracardiac flow dynamics in patients with AS.

Methods and results
One hundred and twenty patients with severe AS, sixty patients with concentric ventricular remodelling (VR), and hundred controls (CTRL) were prospectively included and underwent non-invasive evaluation of intracardiac flow dynamics. In addition to standard echocardiography, fluid dynamics were assessed by means of HyperDoppler. Vortex depth (P &lt; 0.001), vortex length (P = 0.003), vortex intensity (P &lt; 0.001), and vortex area (P = 0.049) were significantly increased in AS compared with CTRL. In addition, mean energy dissipation was significantly higher in AS compared with CTRL (P &lt; 0.001) and VR (P = 0.002). At receiver operating characteristic analysis, vortex depth showed the best discrimination capacity for AS (P &lt; 0.001).

Conclusion
Changes in fluid dynamics–based HyperDoppler indices can be reliably assessed in patients with AS. Significant changes in vortex depth and intensity can selectively differentiate AS from both concentric remodelling and healthy CTRLs, suggesting that the assessment of intracardiac flow dynamics may provide complementary information to standard echocardiography to better characterize patients’ subsets.
Post-discharge pharmacotherapy in people with atrial fibrillation hospitalized for acute myocardial infarction: an Australian cohort study 2018–22
Authors: Deakin Claire T , Costa Juliana de Oliveira , Brieger David , Lin Jialing , Schaffer Andrea L , Kidd Michael , Pearson Sallie-Anne , Falster Michael O 
Published: August 2024

Abstract

Background
Dual antiplatelet therapy with P2Y12 inhibitors (P2Y12i) and aspirin following acute myocardial infarction (AMI) prevents future ischaemic events. People with atrial fibrillation (AF) also require oral anticoagulants (OAC), increasing bleeding risk. Guidelines recommend post-discharge prescribing of direct OAC with clopidogrel and discontinuation of P2Y12i after 12 months, but little is known about use in clinical practice.

Aim
To describe post-discharge use of OACs and P2Y12i in people with AF and a history of OAC use hospitalized for AMI.

Methods and results
We identified 1330 people hospitalized for AMI with a diagnosis of AF and history of OAC use in New South Wales, Australia, July 2018–June 2020. We identified three aspects of post-discharge antithrombotic medicine use with possible safety implications: (1) not being dispensed OACs; (2) dispensing OAC and P2Y12i combinations associated with increased bleeding (involving warfarin, ticagrelor, or prasugrel); and (3) P2Y12i use longer than 12 months.
After discharge, 74.3% of people were dispensed an OAC, 45.4% were dispensed a P2Y12i, and 35.8% were dispensed both. People with comorbid heart failure or cancer were less likely to receive OACs. Only 11.2% of people who dispensed both an OAC and P2Y12i received combinations associated with increased bleeding; this was more common among people with chronic kidney disease or prior warfarin or statin use. A total of 44.6% of people dispensed both medicines continued P2Y12i for over 12 months; this was more common in people who received a revascularization or lived in areas of social disadvantage.

Conclusion
We identified potential gaps in pharmacotherapy, including underuse of recommended therapies at discharge, use of combinations associated with increased bleeding, and P2Y12i use beyond 12 months. Prescribing vigilance across both hospital and community care is required.