bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Effects of Food Deserts and Food Swamps in an Urban Burn Patient Population
Authors: Donovan Brienne , Wiese Daniel , Henry Kevin A , Wu Jingwei , Rae Lisa , Anderson Jeffrey 
Published: April 2024

Abstract
Poverty is a known risk factor for burn injury and is associated with residency in food deserts and food swamps. Our aim was to determine the prevalence of residency in food deserts and food swamps and to investigate the relationship between food environment, comorbidities, and wound healing in patients with burns. We performed a retrospective chart review of all patients with burns aged ≥ 18 seen in the emergency department or admitted to the burn service at an American Burn Association-verified urban academic center between January 2016 and January 2022. Patient GeoIDs were used to classify residency in food deserts and food swamps, and comorbidities and demographics were recorded. A subset of patients with &lt;20% total body surface area burns who underwent single-operation split-thickness skin grafting was identified for wound healing analysis. A total of 3063 patients were included, with 206 in the heal time analysis. In total, 2490 (81.3%) lived in food swamps and 96 (3.1%) lived in food deserts. Diabetes, hypertension, and tobacco smoking were more prevalent in food swamps than in food deserts or good access areas. While there was no significant effect of the food environment on wound healing, diabetes was associated with longer healing times. Most patients with burns reside in food swamps, which are associated with a higher prevalence of hypertension, diabetes, and smoking. The food environment was not significantly associated with wound healing. Not having diabetes was associated with a shorter time for wound healing.
Virtual Visiting Professorship Program as an Opportunity for Academic and Clinical Advancement Beyond the COVID-19 Pandemic: A Survey of Participants
Authors: Elezaby Mai A , Al-Jabbari Esraa H , Mao Lu , Legha Ravinder S , Schacht David , Whitman Gary , Dodelzon Katerina , Omofoye Toma S 
Published: April 2024

Abstract

Objective
To identify structure, benefits, and shortcomings of a multi-institutional virtual visiting professorship (VVP) program from 2020 to 2022, 2 years after inception and after gradual resumption of an in-person, prepandemic academic environment.

Methods
An IRB-exempt, 70-question survey about structure, benefits, and shortcomings of the VVP program was distributed to its participants (14 breast imaging departments across the U.S.), using the snowball sampling technique.

Results
A total of 72 responses were received; 54.2% (32/59) radiologists &gt;5 years of experience, 18.6% (11/59) radiologists &lt;5 years of experience, 15.3% (9/59) residents, and 8.5% (5/59) fellows. Radiologists’ attendance increased from 8% (5/59) to 53% (31/59) over 2 years, with 69% (41/59) of respondents supporting continued participation. The most important factors for attendance were expanding breast imaging knowledge (86.4% [51/59]) and the virtual format (76.2% [45/59]). The number of presented lectures increased from 1 to 3 lectures in 43.7% (7/16) of programs in year 1 and from 4 to 9 lectures in 50% (8/16) of programs in year 2. The greatest professional benefits were collaborations on publications for organizers (56.3% [9/16]) and building academic portfolios for presenters (50% [7/14]). For trainees, attending the program increased their knowledge (64.3% [9/14]) and enthusiasm for breast imaging (50% [7/14]).

Conclusion
The VVP program facilitated scholarly collaboration among breast imaging radiologists, promoted academic portfolios for junior faculty, and increased enthusiasm for breast imaging for trainees. These accomplishments extended beyond the COVID-19 pandemic, as evidenced by the growth of the program after resumption of an in-person academic environment. Future expansion to other programs would benefit more practicing radiologists.
Diagnosis and therapeutic decisions of osteoporosis in chronic kidney disease
Authors: Jørgensen Hanne Skou , Moe Sharon , Nickolas Thomas L 
Published: April 2024

Vignette
A 63-yr-old woman with end-stage CKD secondary to glomerulonephritis, on hemodialysis therapy, presented with scoliosis, back pain, and progressive loss of physical function for which corrective surgery was planned. Optimization of bone health was requested by the surgeon as a DXA scan had revealed osteoporosis at spine, hip, and forearm. Due to previous subtotal parathyroidectomy and normal parathyroid hormone and bone-specific alkaline phosphatase levels, a low bone turnover state was suspected. An iliac bone biopsy was performed and revealed low bone turnover, a mineralization defect, and severe osteoporosis. The patient was treated with calcium and intensified vitamin D supplementation, followed by a 2-yr course of teriparatide. Monitoring of bone turnover markers indicated a bone anabolic response to therapy, and a repeat DXA showed increases in BMD at spine and hip. A repeat biopsy at end of treatment showed normal bone turnover and mineralization. This case demonstrates the complicated bone health of patients with advanced CKD. As there are no randomized trials for fracture pretention in patients with CKD, care must be individualized and is often based on expert opinion. The use of bone biopsy is safe and informative in guiding therapy.
Osteoporosis treatments for intervertebral disc degeneration and back pain: a perspective
Authors: Bhadouria Neharika , Holguin Nilsson 
Published: April 2024

Abstract
Low back pain derived from intervertebral disc (IVD) degeneration is a debilitating spinal condition that, despite its prevalence, does not have any intermediary guidelines for pharmacological treatment between palliative care and invasive surgery. The development of treatments for the IVD is complicated by the variety of resident cell types needed to maintain the regionally distinct structural properties of the IVD that permit the safe, complex motions of the spine. Osteoporosis of the spine increases the risk of vertebral bone fracture that can increase the incidence of back pain. Fortunately, there are a variety of pharmacological treatments for osteoporosis that target osteoblasts, osteoclasts and/or osteocytes to build bone and prevent vertebral fracture. Of particular note, clinical and preclinical studies suggest that commonly prescribed osteoporosis drugs like bisphosphonates, intermittent parathyroid hormone, anti-sclerostin antibody, selective estrogen receptor modulators and anti-receptor activator of nuclear factor-kappa B ligand inhibitor denosumab may also relieve back pain. Here, we cite clinical and preclinical studies and include unpublished data to support the argument that a subset of these therapeutics for osteoporosis may alleviate low back pain by also targeting the IVD.
Diet quality and cardiovascular disease risk among breast cancer survivors in the Pathways Study
Authors: Ergas Isaac J , Cheng Richard K , Roh Janise M , Kushi Lawrence H , Kresovich Jacob K , Iribarren Carlos , Nguyen-Huynh Mai , Rana Jamal S , Rillamas-Sun Eileen , Laurent Cecile A , Lee Valerie S , Quesenberry Charles P , Greenlee Heather , Kwan Marilyn L 
Published: April 2024

Abstract

Background
Women with breast cancer are at higher risk of cardiovascular disease (CVD) compared with women without breast cancer. Whether higher diet quality at breast cancer diagnosis lowers this risk remains unknown. We set out to determine if higher diet quality at breast cancer diagnosis was related to lower risk of CVD and CVD-related death.

Methods
This analysis included 3415 participants from the Pathway Study, a prospective cohort of women diagnosed with invasive breast cancer at Kaiser Permanente Northern California between 2005 and 2013 and followed through December 31, 2021. Scores from 5 diet quality indices consistent with healthy eating were obtained at the time of breast cancer diagnosis. Scores were categorized into ascending quartiles of concordance for each diet quality index, and multivariable adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated. P values were 2-sided.

Results
The Dietary Approaches to Stop Hypertension diet quality index was associated with lower risk of heart failure (HR = 0.53, 95% CI = 0.33 to 0.87; Ptrend = .03), arrhythmia (HR = 0.77, 95% CI = 0.62 to 0.94; Ptrend = .008), cardiac arrest (HR = 0.77, 95% CI = 0.61 to 0.96; Ptrend = .02), valvular heart disease (HR = 0.79, 95% CI = 0.64 to 0.98; Ptrend = .046), venous thromboembolic disease (HR = 0.75, 95% CI = 0.60 to 0.93; Ptrend = .01), and CVD-related death (HR = 0.70, 95% CI = 0.50 to 0.99; Ptrend = .04), when comparing the highest with lowest quartiles. Inverse associations were also found between the healthy plant-based dietary index and heart failure (HR = 0.60, 95% CI = 0.39 to 0.94; Ptrend = .02), as well as the alternate Mediterranean dietary index and arrhythmia (HR = 0.74, 95% CI = 0.60 to 0.93; Ptrend = .02).

Conclusion
Among newly diagnosed breast cancer patients, higher diet quality at diagnosis was associated with lower risk of CVD events and death.
Derazantinib alone and with atezolizumab in metastatic urothelial carcinoma with activating FGFR aberrations
Authors: Necchi Andrea , Ramlau Rodryg , Falcón González Alejandro , Chaudhry Arvind , Todenhöfer Tilman , Tahbaz Rana , Fontana Elisa , Giannatempo Patrizia , Deville Jean-Laurent , Pouessel Damien , Yoon Shinkyo , Powles Thomas , Bernat Mathieu , Häckl Manuel , Marszewska Michalina , McKernan Phil , Saulay Mikael , Scaleia Federica , Engelhardt Marc , Loriot Yohann , Siefker-Radtke Arlene , De Santis Maria 
Published: April 2024

Abstract

Background
This Phase 1b/2 study assessed the efficacy in terms of objective response rate (ORR) of the FGFR1/2/3 kinase inhibitor derazantinib as monotherapy or in combination with atezolizumab in patients with metastatic urothelial cancer (mUC) and FGFR1-3 genetic aberrations (FGFR1-3GA).

Methods
This multicenter, open-label study comprised 5 substudies. In Substudies 1 and 5, patients with mUC with FGFR1–3GA received derazantinib monotherapy (300 mg QD in Substudy 1, 200 mg BID in Substudy 5). In Substudy 2, patients with any solid tumor received atezolizumab 1200 mg every 3 weeks plus derazantinib 200 or 300 mg QD. In Substudy 3, patients with mUC harboring FGFR1–3GA received derazantinib 200 mg BID plus atezolizumab 1200 mg every 3 weeks. In Substudy 4, patients with FGFR inhibitor-resistant mUC harboring FGFR1–3GA received derazantinib 300 mg QD monotherapy or derazantinib 300 mg QD plus atezolizumab 1200 mg every 3 weeks.

Results
The ORR for Substudies 1 and 5 combined was 4/49 (8.2%, 95% confidence interval = 2.3% to 19.6%), which was based on 4 partial responses. The ORR in Substudy 4 was 1/7 (14.3%, 95% confidence interval = 0.4% to 57.9%; 1 partial response for derazantinib 300 mg monotherapy, zero for derazantinib 300 mg plus atezolizumab 1200 mg). In Substudy 2, derazantinib 300 mg plus atezolizumab 1200 mg was identified as a recommended dose for Phase 2. Only 2 patients entered Substudy 3.

Conclusions
Derazantinib as monotherapy or in combination with atezolizumab was well-tolerated but did not show sufficient efficacy to warrant further development in mUC.
Clinicaltrials.gov NCT04045613, EudraCT 2019-000359-15
Effect of an upper body exoskeleton for surgeons on postoperative neck, back, and shoulder complaints
Authors: Nutz Elisa , Jarvers Jan-Sven , Theopold Jan , Kleber Christian , Osterhoff Georg 
Published: April 2024

Abstract

Objectives
Surgeons are exposed to high levels of physical stress while working in the operating room. In industry, so-called exoskeletons are used to support the back and shoulder area. The aim of this study was to investigate the feasibility and effects of an upper body exoskeleton on postoperative physical complaints of surgeons.

Methods
Surgeons from a university hospital in the fields of orthopedics, trauma, and visceral surgery performed 2 operations of the same type and planned length on 2 different days. The first operation was performed without an exoskeleton, the second with an exoskeleton. The participants completed questionnaires on shoulder pain (Shoulder Pain and Disability Index [SPADI]), neck pain (Visual Analogue Scale [VAS] and Neck Disability Index [NDI]), and back pain (VAS and Oswestry Disability Index [ODI]) before and after the procedure.

Results
A total of 25 participants were included and performed 50 surgeries with a mean surgery duration of 144 minutes without and 138 minutes with the exoskeleton. Without the exoskeleton, the activity of the operation resulted in a significant increase of the VAS neck by 1.0 point (SD 1.2; P &lt; .001), NDI by 4.8 (SD 8.6; P = .010), VAS back by 0.7 (SD 1.0; P = .002), and ODI by 2.7 (SD 4.1; P = .003). With the exoskeleton the participants reported significantly fewer complaints after the surgery (VAS neck: P = .001; NDI: P = .003; VAS back: P = .036; ODI: P = .036; SPADI: P = .016).

Conclusion
An upper body exoskeleton can significantly reduce the discomfort in the neck, shoulder, and back caused to surgeons by surgery.
The Efficacy of Propensity Score Matching for Separating Selection and Measurement Effects Across Different Survey Modes
Authors: Kibuchi Eliud , Sturgis Patrick , Durrant Gabriele B , Maslovskaya Olga 
Published: April 2024

Abstract
Effective evaluation of data quality between data collected in different modes is complicated by the confounding of selection and measurement effects. This study evaluates the utility of propensity score matching (PSM) as a method that has been proposed as a means of removing selection effects across surveys conducted in different modes. Our results show large differences in estimates for the same variables between parallel face-to-face and online surveys, even after matching on standard demographic variables. Moreover, discrepancies in estimates are still present after matching between surveys conducted in the same (online) mode, where differences in measurement properties can be ruled out a priori. Our findings suggest that PSM has substantial limitations as a method for separating measurement and selection differences across modes and should be used only with caution.
Are Digital Humanities platforms facilitating sufficient diversity in research? A study of the Transkribus Scholarship Programme
Authors: Nockels Joseph , Gooding Paul , Terras Melissa 
Published: April 2024

Abstract
To what extent do Digital Humanities (DH) platforms support access to diverse user cohorts? We take, as a case study, the Automated Text Recognition (ATR) platform Transkribus and its Transkribus Scholarship Programme (TSP), which provides free processing credits to eligible users. Using a mixed methods approach we address the following questions: What are the demographics of those using the TSP scheme? What work is enabled by such a scheme? How can this inform more equitable access to DH platforms? The findings demonstrate how ATR tools are currently used and made accessible. TSP applicants are overwhelmingly students (n = 111/156, 71.15 per cent) drawn from universities and research institutes, mostly in Europe, but are globally distributed; representing institutions that do not hold shares in Transkribus, and indicating a diverse user pipeline. Further work is required to increase potential benefits of the scholarship and to ensure sustainability. Increased dialogue between the Recognition and Enrichment of Archival Document-COOP and applicants would assist in the calculation of processing costs. We show financial—or in-kind—support is necessary to increase access to paid-for platforms, ensuring a diversity of DH research. We also provide recommendations for platform providers and funding bodies regarding access and the impact this can have, including locating a sustainable balance between absorbing the costs of maintaining DH or digital scholarship tools and providing sufficient support and training to further enable diverse research.
The CluMPR galaxy cluster-finding algorithm and DESI legacy survey galaxy cluster catalogue
Authors: Yantovski-Barth M J , Newman Jeffrey A , Dey Biprateep , Andrews Brett H , Eracleous Michael , Golden-Marx Jesse , Zhou Rongpu 
Published: April 2024

ABSTRACT
Galaxy clusters enable unique opportunities to study cosmology, dark matter, galaxy evolution, and strongly lensed transients. We here present a new cluster-finding algorithm, CluMPR (Clusters from Masses and Photometric Redshifts), that exploits photometric redshifts (photo-z’s) as well as photometric stellar mass measurements. CluMPR uses a 2D binary search tree to search for overdensities of massive galaxies with similar redshifts on the sky and then probabilistically assigns cluster membership by accounting for photo-z uncertainties. We leverage the deep DESI Legacy Survey grzW1W2 imaging over one-third of the sky to create a catalogue of $\sim 300\, 000$ galaxy cluster candidates out to z = 1, including tabulations of member galaxies and estimates of each cluster’s total stellar mass. Compared to other methods, CluMPR is particularly effective at identifying clusters at the high end of the redshift range considered (z = 0.75–1), with minimal contamination from low-mass groups. These characteristics make it ideal for identifying strongly lensed high-redshift supernovae and quasars that are powerful probes of cosmology, dark matter, and stellar astrophysics. As an example application of this cluster catalogue, we present a catalogue of candidate wide-angle strongly lensed quasars in Appendix C. The nine best candidates identified from this sample include two known lensed quasar systems and a possible changing-look lensed QSO with SDSS spectroscopy. All code and catalogues produced in this work are publicly available (see Data Availability).
Spinach genomes reveal migration history and candidate genes for important crop traits
Authors: Nguyen-Hoang An , Sandell Felix L , Himmelbauer Heinz , Dohm Juliane C 
Published: April 2024

Abstract
Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.
ChimericFragments: computation, analysis and visualization of global RNA networks
Authors: Siemers Malte , Lippegaus Anne , Papenfort Kai 
Published: April 2024

AbstractRNA–RNA interactions are a key feature of post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA duplex formation on a genome-wide scale, computational methods for the analysis and interpretation of the underlying data are lagging behind. Here, we present ChimericFragments, an analysis framework for RNA-seq experiments that produce chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and provides an interactive graph-based visualization for data exploration and interpretation. ChimericFragments detects true RNA–RNA interactions with high precision and is compatible with several widely used experimental procedures such as RIL-seq, LIGR-seq or CLASH. We further demonstrate that ChimericFragments enables the systematic detection of novel RNA regulators and RNA–target pairs with crucial roles in microbial physiology and virulence. ChimericFragments is written in Julia and available at: https://github.com/maltesie/ChimericFragments.
Unique genomic alterations in the circulating tumor DNA of patients with solid tumors brain metastases
Authors: Alder Laura , Broadwater Gloria , Green Michelle , Van Swearingen Amanda E D , Lipp Eric S , Clarke Jeffrey Melson , Anders Carey K , Sammons Sarah 
Published: April 2024

Abstract

Background
Although serum circulating tumor DNA (ctDNA) is routine, data from patients with brain metastases (BrMs) is limited. We assessed genomic alterations in ctDNA from patients with solid tumor BrMs in 3 groups: Isolated BrMs with stable extracranial disease (iCNS), concurrent brain and extracranial progression (cCNS), and extracranial progression with no active BrMs (eCNS). We also compared ctDNA alterations between patients with and without BrMs.

Methods
Patients with a Guardant360 ctDNA profile with (n = 253) and without BrMs (n = 449) from the Duke Molecular Registry between January 2014 and December 2020 were identified. Actionable alterations were defined as FDA-recognized or standard-of-care biomarkers. Disease status was determined via investigator assessment within 30 days of ctDNA collection.

Results
Among the 253 patients with BrMs: 29 (12%) had iCNS, 160 (63%) cCNS, and 64 (25%) eCNS. Breast (BC; 12.0%) and non-small cell lung cancer (NSCLC; 76.4%) were the most common tumor types. ESR1 (60% vs 25%, P &lt; .001) and BRCA2 (17% vs 5%, P = .022) were more frequent in BC BrMs. In NSCLC BrMs, EGFR alterations were most frequent in the iCNS group (iCNS: 67%, cCNS: 40%, eCNS:37%, P = .08) and in patients with BrMs (36% vs 17%, P &lt; .001). Sequencing from both brain tissue and ctDNA were available for 8 patients; 7 (87.5%) had identical alterations.

Conclusions
This study illustrates the feasibility of detecting alterations from ctDNA among patients with BrMs. A higher frequency of actionable mutations was observed in ctDNA in patients with BrMs. Additional studies comparing ctDNA and alterations in BrMs tissue are needed to determine if ctDNA can be considered a surrogate to support treatment decisions.