bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiologic Manifestations in Omicron‐Type Versus Wild‐Type COVID‐19: A Systematic Echocardiographic Study
Authors: Ghantous Eihab , Shetrit Aviel , Hochstadt Aviram , Banai Ariel , Lupu Lior , Levi Erez , Szekely Yishay , Schellekes Nadav , Jacoby Tammy , Zahler David , Itach Tamar , Taieb Philippe , Gefen Sheizaf , Viskin Dana , Shidlansik Lia , Adler Amos , Levitsky Ekaterina , Havakuk Ofer , Ingbir Merav , Banai Shmuel , Topilsky Yan 
Published: January 2023

Background
Information about the cardiac manifestations of the Omicron variant of COVID‐19 is limited. We performed a systematic prospective echocardiographic evaluation of consecutive patients hospitalized with the Omicron variant of COVID‐19 infection and compared them with similarly recruited patients were propensity matched with the wild‐type variant.

Methods and Results

A total of 162 consecutive patients hospitalized with Omicron COVID‐19 underwent complete echocardiographic evaluation within 24 hours of admission and were compared with propensity‐matched patients with the wild‐type variant (148 pairs). Echocardiography included left ventricular (LV) systolic and diastolic, right ventricular (RV), strain, and hemodynamic assessment. Echocardiographic parameters during acute infection were compared with historic exams in 62 patients with the Omicron variant and 19 patients with the wild‐type variant who had a previous exam within 1 year. Of the patients, 85 (53%) had a normal echocardiogram. The most common cardiac pathology was RV dilatation and dysfunction (33%), followed by elevated LV filling pressure (E/e′ ≥14, 29%) and LV systolic dysfunction (ejection fraction <50%, 10%). Compared with the matched wild‐type cohort, patients with Omicron had smaller RV end‐systolic areas (9.3±4 versus 12.3±4 cm
2
;
P
=0.0003), improved RV function (RV fractional‐area change, 53.2%±10% versus 39.7%±13% [
P
<0.0001]; RV S′, 12.0±3 versus 10.7±3 cm/s [
P
=0.001]), and higher stroke volume index (35.6 versus 32.5 mL/m
2
;
P
=0.004), all possibly related to lower mean pulmonary pressure (34.6±12 versus 41.1±14 mm Hg;
P
=0.0001) and the pulmonary vascular resistance index (
P
=0.0003). LV systolic or diastolic parameters were mostly similar to the wild‐type variant‐matched cohort apart from larger LV size. However, in patients who had a previous echocardiographic exam, these LV abnormalities were recorded before acute Omicron infection, but not in the wild‐type cohort. Numerous echocardiographic parameters were associated with higher in‐hospital mortality (LV ejection fraction, stroke volume index, E/e′, RV S′).

Conclusions
In patients with Omicron, RV function is impaired to a lower extent compared with the wild‐type variant, possibly related to the attenuated pulmonary parenchymal and/or vascular disease. LV systolic and diastolic abnormalities are as common as in the wild‐type variant but were usually recorded before acute infection and probably reflect background cardiac morbidity. Numerous LV and RV abnormalities are associated with adverse outcome in patients with Omicron.
Association Between Duration of Transient Neurological Events and Diffusion‐Weighted Brain Lesions
Authors: Joundi Raed A. , Yu Amy Y. X. , Smith Eric E. , Zerna Charlotte , Penn Andrew M. , Balshaw Robert F. , Votova Kristine , Bibok Maximilian B. , Penn Melanie , Saly Viera , Hegedus Janka , Coutts Shelagh B. , Nikolejsin Alison , Yu Amy Y. X. , Penn Andrew M. , Trivedi Anurag , Cook Jaclyn , Morrison Jaclyn , Blackwood Kaitlin , Richards Karen , Votova Kristine , Nealis Madeline , Bibok Maximilian B. , Penn Melanie , Beattyova Pavla , Rosenberg Priya , Frost Sheilah , Grant Carolyn , Hedgedus Janka , Grant Sarah , Watson Tim , Saly Viera , Sedgwick Colin , Lesperance Mary L. , Croteau Nicole S. , Appireddy Ramana , Balshaw Robert F. , Field Thalia S. , Dubuc Veronique , Demchuk Andrew M. , Jambula Anitha , Le Anne , Menon Bijoy K. , Calvert Carly , Kenney Carol , Zerna Charlotte , Nikneshan Davar , Smith Eric E. , Klourfeld Evgenia , Wagner Gabrielle , Klein Gary , Aram Heidi , Desai Jamsheed , Ryckborst Karla , Bilston Lisa , Hill Michael D. , Almekhlafi Mohammed , Godfrey Nathan , Imoukheude Oje , Stys Peter , Barber Philip A. , Couillard Phillippe , Eswaradas Prasanna , Rhandawa Privia , Coutts Shelagh B. , Bal Simerpreet , Peters Steven , Save Supriya , Subramaniam Suresh , Musuka Tapuwa , Stewart Teri , Hong Zachary M. 
Published: January 2023

Background
The relationship between duration of transient neurological events and presence of diffusion‐weighted lesions by symptom type is unclear.

Methods and Results
This was a substudy of SpecTRA (Spectrometry for Transient Ischemic Attack Rapid Assessment), a multicenter prospective cohort of patients with minor ischemic cerebrovascular events or stroke mimics at academic emergency departments in Canada. For this study we included patients with resolved symptoms and determined the presence of diffusion‐weighted imaging (DWI) lesion on magnetic resonance imaging within 7 days. Using logistic regression, we evaluated the association between symptom duration and DWI lesion, assessing for interaction with symptom type (focal only versus nonfocal/mixed), and adjusting for age, sex, education, comorbidities, and systolic blood pressure. Of 658 patients included, a DWI lesion was present in 232 (35.1%). There was a significant interaction between symptom duration and symptom type. For those with focal‐only symptoms, there was a continuous increase in DWI probability up to 24 hours in duration (ranging from ≈40% to 80% probability). In stratified analyses, the increase in probability of DWI lesion with increased duration of focal symptoms was seen in women but not men. For those with nonfocal or mixed symptoms, predicted probability of DWI lesion was ≈35% and was greater in men, but did not increase with longer duration.

Conclusions
Increased duration of neurological deficits is associated with greater probability of DWI lesion in those with focal symptoms only. For individuals with nonfocal or mixed symptoms, about one‐third had DWI lesions, but the probability did not increase with duration. These results may be important to improve risk stratification of transient neurological events.
Evaluation of Subseasonal Drought Forecast Skill over the Coastal Western United States
Authors: Su Lu , Cao Qian , Shukla Shraddhanand , Pan Ming , Lettenmaier Dennis P. 
Published: January 2023

Abstract
Predictions of drought onset and termination at subseasonal (from 2 weeks to 1 month) lead times could provide a foundation for more effective and proactive drought management. We used reforecasts archived in NOAA’s Subseasonal Experiment (SubX) to force the Noah Multiparameterization (Noah-MP), which produced forecasts of soil moisture from which we identified drought levels D0–D4. We evaluated forecast skill of major and more modest droughts, with leads from 1 to 4 weeks, and with particular attention to drought termination and onset. We find usable drought termination and onset forecast skill at leads 1 and 2 weeks for major D0–D2 droughts and limited skill at week 3 for major D0–D1 droughts, with essentially no skill at week 4 regardless of drought severity. Furthermore, for both major and more modest droughts, we find limited skill or no skill for D3–D4 droughts. We find that skill is generally higher for drought termination than for onset for all drought events. We also find that drought prediction skill generally decreases from north to south for all drought events.
Development of the Support self-guided, web application for adults living with type 1 diabetes in Canada by a multi-disciplinary team using a people-oriented approach based on the Behaviour Change Wheel
Authors: Xie Li Feng , Roy-Fleming Amélie , Haag Sarah , Costa Deborah Da , Brazeau Anne-Sophie 
Published: January 2023

Background Diabetes self-management education and support (DSME/S) are central in type 1 diabetes (T1D) where individuals are responsible for 95% of care. In-person DSME/S programs have been proven clinically effective (e.g. optimizing glycemic management, improving diabetes-related behaviors) but are limited by a lack of accessibility and long-term follow-up. Self-guided digital tools such as web applications (web apps) can be an alternative for delivering DSME/S. Objective This article describes the development of Support, a behavioral theory-based, self-guided, web application for adults living with T1D in the province of Quebec, Canada. Methods A multi-disciplinary team developed Support. Patient partners first proposed its focus, learning topics, and expressed barriers to using digital tools for DSME/S. These barriers were analyzed based on the Behaviour Change Wheel. A group of healthcare professionals (HCPs) drafted the evidence-based learning content which was reviewed by external HCPs and by patient partners. Results Support is a bilingual (English and French) web app accessible at any time via the Internet. It has four learning paths focusing on hypoglycemia and based on the user's method of diabetes treatment. Learning modules are divided into six categories with a maximum of three learning levels. It contains features such as a discussion forum, videos, and quizzes to ensure interactivity, provide social support, and maintain the motivation and long-term engagement of users. Conclusions To the best of the authors’ knowledge, Support is the first self-guided evidence-based web app for adults living with T1D. It is currently under study to evaluate its feasibility and clinical impacts.
Outcomes of breakthrough COVID-19 infections in patients with hematologic malignancies
Authors: Chien Kelly S. , Peterson Christine B. , Young Elliana , Chihara Dai , Manasanch Elizabet E. , Ramdial Jeremy L. , Thompson Philip A. 
Published: January 2023

Abstract
Patients with hematologic malignancies have both an increased risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and higher morbidity/mortality. They have lower seroconversion rates after vaccination, potentially leading to inferior coronavirus disease 2019 (COVID-19) outcomes, despite vaccination. We consequently evaluated the clinical outcomes of COVID-19 infections in 243 vaccinated and 175 unvaccinated patients with hematologic malignancies. Hospitalization rates were lower in the vaccinated group when compared with the unvaccinated group (31.3% vs 52.6%). However, the rates of COVID-19–associated death were similar at 7.0% and 8.6% in vaccinated and unvaccinated patients, respectively. By univariate logistic regression, females, older patients, and individuals with higher modified Charlson Comorbidity Index scores were at a higher risk of death from COVID-19 infections. To account for the nonrandomized nature of COVID-19 vaccination status, a propensity score weighting approach was used. In the final propensity-weighted model, vaccination status was not significantly associated with the risk of death from COVID-19 infections but was associated with the risk of hospitalization. The predicted benefit of vaccination was an absolute decrease in the probability of death and hospitalization from COVID-19 infections by 2.3% and 22.9%, respectively. In conclusion, COVID-19 vaccination status in patients with hematologic malignancies was associated with a decreased risk of hospitalization but not associated with a decreased risk of death from COVID-19 infections in the pre-Omicron era. Protective strategies, in addition to immunization, are warranted in this vulnerable patient population.
Clinical impact of ibrutinib plus R-CHOP in untreated DLBCL coexpressing BCL2 and MYC in the phase 3 PHOENIX trial
Authors: Johnson Peter W. M. , Balasubramanian Sriram , Hodkinson Brendan , Shreeve S. Martin , Sun Steven , Srinivasan Srimathi , Steele Andrew J. , Vermeulen Jessica , Sehn Laurie H. , Wilson Wyndham H. 
Published: January 2023

Abstract
Diffuse large B-cell lymphoma (DLBCL), with high coexpression of BCL2 and MYC proteins (DE lymphoma), is considered an adverse prognostic indicator associated mostly with non-germinal center B-cell–like (non-GCB) DLBCL. BCL2/MYC overexpression is associated with B-cell receptor (BCR) pathway activation; consequently, DE DLBCL may be sensitive to BCR inhibitors. We assessed whether high BCL2/MYC coexpression by RNA sequencing could identify a patient subset responsive to ibrutinib using baseline biopsies from the PHOENIX trial, which evaluated the addition of ibrutinib to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in untreated non-GCB DLBCL. BCL2/MYC RNA expression was correlated with lower event-free survival (EFS) and overall survival (OS) using Kaplan–Meier estimates with Cox regression and log-rank testing. In total, 234 of 766 (30.5%) patients had high BCL2/MYC coexpression: 123 of 386 (31.9%) received ibrutinib plus R-CHOP and 111 of 380 (29.2%) received R-CHOP. EFS was superior with ibrutinib plus R-CHOP compared with R-CHOP alone in patients with high BCL2/MYC coexpression, but there was no significant impact on OS. However, EFS and OS showed clinically meaningful improvement with ibrutinib plus R-CHOP over R-CHOP alone in patients aged &lt;60 years with high BCL2/MYC coexpression. We observed a significant association between high BCL2/MYC coexpression and activated B-cell-like and MYD88L265P/CD79B-mutated subtypes of DLBCL. Consequently, high BCL2/MYC coexpression identified a subset of non-GCB DLBCL that may be preferentially responsive to ibrutinib and warrants further investigation. This trial was registered at www.clinicaltrials.gov as #NCT01855750.
Self and caregiver report measurement of sensory features in autism spectrum disorder: a systematic review of psychometric properties
Authors: Gunderson Jaclyn , Worthley Emma , Byiers Breanne , Symons Frank , Wolff Jason 
Published: January 2023

Abstract
Background
Unusual responses to sensory stimuli are considered a diagnostic symptom of autism spectrum disorder with mounting research efforts put towards understanding, characterizing, and treating such symptoms.

Methods
This paper examines self and caregiver report tools used to measure sensory features in ASD through a systematic review of the psychometric evidence for their use. A total of 31 empirical papers were reviewed across 20 assessment tools. Substantial differences were identified in the specific sensory features defined across assessment tools. Sensory assessment questionnaires were evaluated against quality psychometric evidence criteria to provide a use recommendation.

Results
Five assessments were identified to be “appropriate with conditions,” while no sensory assessment tools were identified to have sufficient quality psychometric evidence to provide a recommendation of “Appropriate” for measuring sensory features in ASD.

Conclusion
Evidence from this review highlights potentially significant shortcomings among the current methods used to measure sensory features in ASD and suggests the need for more efforts in developing psychometrically sound sensory assessment tools for use in ASD populations.
Nest preference and laying duration traits to select against floor eggs in laying hens
Authors: Bécot Lorry , Bédère Nicolas , Coton Jenna , Burlot Thierry , Le Roy Pascale 
Published: January 2023

Abstract
Background
Floor eggs, which are defined as eggs that hens lay off-nest, are a major issue in cage-free layer poultry systems. They create additional work for farmers because they must be collected by hand. They are also usually soiled or broken, which results in economic losses. Nonetheless, knowledge about the genetics of nesting behavior is limited. The aim of this study was to estimate genetic parameters for traits related to nest preference for laying and to time spent in the nests used for laying (laying duration).

Methods
Two pure lines of laying hens were studied: 927 Rhode Island Red and 980 White Leghorn. Electronic nests were used to record the nesting behavior of these hens in floor pens from 24 to 64 weeks of age. Nest preference was studied based on the mean distance between nests used for laying and the percentage of nests used for laying. Laying duration was studied based on mean laying duration, mean duration in the nest before laying, and mean duration in the nest after laying. Genetic parameters were estimated for each line using a restricted maximum-likelihood method applied to a pedigree-based multi-trait animal model.

Results
Estimates of genetic parameters were similar for the two lines. Estimates of heritability ranged from 0.18 to 0.37 for nest preference traits and from 0.54 to 0.70 for laying duration traits. Estimates of genetic correlations of these traits with clutch number or mean oviposition time were favorable. Positive genetic correlations were estimated between nest preference and laying rate in the nests or nest acceptance for laying (+ 0.06 to + 0.37).

Conclusions
These results show that genetics influences traits related to nest preference and laying duration. Selecting hens that have no preference for particular nests and spend little time laying in the nests could help optimize nest use, reduce their occupation rate, and thus decrease the incidence of floor eggs in cage-free systems. Genetic correlations of these traits with other traits of interest related to hen welfare and egg quality have yet to be estimated.
SUFI: an automated approach to spectral unmixing of fluorescent multiplex images captured in mouse and post-mortem human brain tissues
Authors: Sadashivaiah Vijay , Tippani Madhavi , Page Stephanie C. , Kwon Sang Ho , Bach Svitlana V. , Bharadwaj Rahul A. , Hyde Thomas M. , Kleinman Joel E. , Jaffe Andrew E. , Maynard Kristen R. 
Published: January 2023

Abstract
Background
Multispectral fluorescence imaging coupled with linear unmixing is a form of image data collection and analysis that allows for measuring multiple molecular signals in a single biological sample. Multiple fluorescent dyes, each measuring a unique molecule, are simultaneously measured and subsequently “unmixed” to provide a read-out for each molecular signal. This strategy allows for measuring highly multiplexed signals in a single data capture session, such as multiple proteins or RNAs in tissue slices or cultured cells, but can often result in mixed signals and bleed-through problems across dyes. Existing spectral unmixing algorithms are not optimized for challenging biological specimens such as post-mortem human brain tissue, and often require manual intervention to extract spectral signatures. We therefore developed an intuitive, automated, and flexible package called SUFI: spectral unmixing of fluorescent images.

Results
This package unmixes multispectral fluorescence images by automating the extraction of spectral signatures using vertex component analysis, and then performs one of three unmixing algorithms derived from remote sensing. We evaluate these remote sensing algorithms’ performances on four unique biological datasets and compare the results to unmixing results obtained using ZEN Black software (Zeiss). We lastly integrate our unmixing pipeline into the computational tool dotdotdot, which is used to quantify individual RNA transcripts at single cell resolution in intact tissues and perform differential expression analysis, and thereby provide an end-to-end solution for multispectral fluorescence image analysis and quantification.

Conclusions
In summary, we provide a robust, automated pipeline to assist biologists with improved spectral unmixing of multispectral fluorescence images.
Developing a Bayesian hierarchical model for a prospective individual patient data meta-analysis with continuous monitoring
Authors: Wu Danni , Goldfeld Keith S. , Petkova Eva 
Published: January 2023

Abstract
Background
Numerous clinical trials have been initiated to find effective treatments for COVID-19. These trials have often been initiated in regions where the pandemic has already peaked. Consequently, achieving full enrollment in a single trial might require additional COVID-19 surges in the same location over several years. This has inspired us to pool individual patient data (IPD) from ongoing, paused, prematurely-terminated, or completed randomized controlled trials (RCTs) in real-time, to find an effective treatment as quickly as possible in light of the pandemic crisis. However, pooling across trials introduces enormous uncertainties in study design (e.g., the number of RCTs and sample sizes might be unknown in advance). We sought to develop a versatile treatment efficacy assessment model that accounts for these uncertainties while allowing for continuous monitoring throughout the study using Bayesian monitoring techniques.

Methods
We provide a detailed look at the challenges and solutions for model development, describing the process that used extensive simulations to enable us to finalize the analysis plan. This includes establishing prior distribution assumptions, assessing and improving model convergence under different study composition scenarios, and assessing whether we can extend the model to accommodate multi-site RCTs and evaluate heterogeneous treatment effects. In addition, we recognized that we would need to assess our model for goodness-of-fit, so we explored an approach that used posterior predictive checking. Lastly, given the urgency of the research in the context of evolving pandemic, we were committed to frequent monitoring of the data to assess efficacy, and we set Bayesian monitoring rules calibrated for type 1 error rate and power.

Results
The primary outcome is an 11-point ordinal scale. We present the operating characteristics of the proposed cumulative proportional odds model for estimating treatment effectiveness. The model can estimate the treatment’s effect under enormous uncertainties in study design. We investigate to what degree the proportional odds assumption has to be violated to render the model inaccurate. We demonstrate the flexibility of a Bayesian monitoring approach by performing frequent interim analyses without increasing the probability of erroneous conclusions.

Conclusion
This paper describes a translatable framework using simulation to support the design of prospective IPD meta-analyses.
A clinicopathological study and survival analysis of 99 breast cancers with HER2/CEP17 ratio ≥ 2.0 and an average HER2 copy number < 4.0 per cell in China
Authors: Zhou Shuling , Lv Hong , Li Anqi , Li Ming , Zhong Siyuan , Lu Hongfen , Zhou Xiaoyan , Bai Qianming , Yang Wentao 
Published: January 2023

Abstract
Background
Breast cancer patients of American Society of Clinical Oncology and the College of American Pathologists (ASCO/CAP) Group 2 were all HER2-negative according to the 2018 guideline, not HER2-positive as defined in the 2013 guideline.

Methods
We aims to elucidate the unique clinicopathological features of ASCO/CAP Group 2 patients by comparing with classic HER2-nonamplified cancers, and reveal the efficacy of the former to anti-HER2 therapy. The clinicopathological features, treatment and prognosis information of 99 patients between 2014 and 2018 were collected. HER2 status was re-defined using the updated recommendations.

Results
Of the 99 ASCO/CAP Group 2 tumors, 25.5% (25/99) tumors were immunohistochemical (IHC) 0/1+ and 74.7% (74/99) tumors were IHC 2+. According to the updated 2018 guideline, all of them were HER2 negative. When compared to ASCO/CAP Group 5, patients of ASCO/CAP Group 2 displayed higher ratio of histological grade 3 (P = .03), high Ki67 proliferation index (P = .03) and pN3 (more than 9 lymph nodes metastasis, P = .02), and lower estrogen receptor (ER) positivity (P = .04). There was no statistical difference in the survival of patients received anti-HER2 therapy and patients not received anti-HER2 therapy.

Conclusions
Patients of ASCO/CAP Group 2 did not received apparent benefit from anti-HER2 treatment. Although according to the updated guidelines and latest reports, HER2 is negative, but when compared with classic HER2-nonamplified cancers, patients of this group seemed to be more aggressive. We suggest that this group still be regarded as an independent category, in order to accumulate more cases in the future to expand the scope of research.