bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wounded but unstressed: Moose tolerate injurious flies in the boreal forest
Authors: Benedict Bridgett M , Thompson Daniel P , Crouse John A , Hamer Gabriel L , Barboza Perry S 
Published: August 2024

Abstract
Moose (Alces alces) in boreal habitats feed and rest where they are exposed to Dipteran flies and the parasites they carry. We collected 31,905 flies during the summer from 12 habituated moose on the Kenai Peninsula, Alaska. Moose flies, Haematobosca alcis (Snow), Diptera: Muscidae—a species that completes its entire life cycle on or around moose—accounted for 91% of flies collected; the reminder of the flies collected included mosquitoes (Culicidae), black flies (Simuliidae), and deer flies (Tabanidae). Flies impose physiological costs for moose, e.g., vectors for parasites such as Legworm (Onchocerca spp.) which causes sores on the hind legs of moose. We found that the number of sores present on the hind legs of moose is positively correlated with body fat, which suggests a correlation between gains of energy and damage from flies. We also found that the number of sores is negatively correlated with serum albumin, which is indicative of an inflammatory response and body protein being used to repair injuries from flies and parasites. The number or type of flies present on a Moose were not correlated with the concentration of corticosteroids in saliva or feces. Flies do not elicit a stress response in moose even though the costs of repairing wounds and resisting infections of those wounds likely reduce gains of protein from summer foraging. Moose can tolerate the injuries from biting flies with regular gains from summer foraging but exposure to insect-borne parasites poses a risk to reproduction and survival.
Costs of care during chimeric antigen receptor T-cell therapy in relapsed or refractory B-cell lymphomas
Authors: Di Mengyang , Potnis Kunal C , Long Jessica B , Isufi Iris , Foss Francine , Seropian Stuart , Gross Cary P , Huntington Scott F 
Published: August 2024

Abstract
High upfront cost may be a barrier to adopting chimeric antigen receptor T-cell (CAR-T) therapy for relapsed or refractory B-cell lymphoma. Data on the real-world costs are limited. Using the Blue Cross Blue Shield Axis database, we evaluated 271 commercially insured patients who received CAR-T therapy for B-cell lymphoma (median age = 58 years; men = 68%; diffuse large B-cell lymphoma = 87%; inpatient CAR-T therapy = 85%). Our peri–CAR-T period of interest was from 41 days before to 154 days after CAR-T therapy index divided into seven 28-day intervals. Median total costs were $608 100 (interquartile range, IQR = $534 100-$732 800); 8.5% of patients had total costs exceeding $1 million. The median cost of CAR-T therapy products was $402 500, and the median out-of-pocket copayment was $510. Monthly costs were highest during the month of CAR-T therapy administration (median = $521 500), with median costs below $25 000 in all other 28-day intervals. Costs of CAR-T therapy use were substantial, largely driven by product acquisition. Future studies should examine the relationship between costs, access, and financial outcomes.
The association of perceived cannabis risks and benefits with cannabis use since cancer diagnosis
Authors: McDaniels-Davidson Corinne , Parada Jr Humberto , Kasiri Nasim , Patel Sandip P , Strong David , Doran Neal 
Published: August 2024

Abstract

Background
Many patients with cancer use cannabis to help alleviate untreated cancer symptoms and side effects.

Methods
We examined associations of perceived benefits and risks and postdiagnosis cannabis use in a weighted sample of adult cancer survivors through a 1-time survey. Fifteen perceived cannabis use benefits and 19 perceived risks were operationalized as both summary scores and report of any benefits or risks. Survey-weighted logistic regression provided covariate-adjusted odds of postdiagnosis cannabis use for each benefit-risk measure.

Results
Among the weighted population of 3785 survivors (mean [SD] age = 62.2 [13.5] years), one-third used cannabis after diagnosis. Perceiving any benefits increased the odds of postdiagnosis cannabis use more than 500%, and perceiving any risks lowered the odds by 59%. Each SD increase in endorsed benefits doubled the odds of postdiagnosis cannabis use, while each SD increase in endorsed risks reduced the odds by 36%.

Conclusion
An accurate understanding of benefits and risks is critical for informed decision making.
Cannabis and opioid perceptions, co-use, and substitution among patients across 4 NCI-Designated Cancer Centers
Authors: Ashare Rebecca L , Worster Brooke , Nugent Shannon M , Smith Danielle M , Morasco Benjamin J , Leader Amy E , Case Amy A , Meghani Salimah H 
Published: August 2024

Abstract
Prescription opioids are used for managing pain in persons with cancer, however, there are socioeconomic and racial disparities in medication access. Cannabis is increasingly used for cancer symptom management and as an opioid alternative. Limited data are available about patterns of opioid and cannabis use among patients with cancer. We used survey data from 4 National Cancer Institute–designated cancer centers in 3 states (n = 1220) to assess perceptions, use of cannabis and opioids for pain, their substitution, and racial and ethnic differences in each outcome. Compared with White patients, Black patients were less likely to use opioids for pain (odds ratio [OR] = 0.66; P = .035) and more likely to report that cannabis was more effective than opioids (OR = 2.46; P = .03). Race effects were mitigated (P &gt; .05) after controlling for socioeconomic factors. Further research is needed to understand cannabis and opioid use patterns and how overlapping social determinants of health create a disadvantage in cancer symptom management for Black patients.
Patient out-of-pocket costs for cannabis use during cancer treatment
Authors: Lapen Kaitlyn , Mishra Meza Akriti , Dee Edward Christopher , Mao Jun J , Raghunathan Nirupa Jaya , Jinna Sankeerth , Brens Jessica , Korenstein Deborah , Furberg-Barnes Helena , Salz Talya , Chino Fumiko 
Published: August 2024

Abstract

Background
We assessed patient costs associated with cannabis use during cancer treatment.

Methods
Adults treated for cancer at a large, comprehensive center completed an anonymous survey regarding their thoughts and experiences with cannabis and cancer. Bivariate and weighted multivariable logistic regression assessed clinical and sociodemographic factors associated with patient-reported out-of-pocket costs for cannabis products.

Results
Overall, 248 cannabis users provided data on cost and were analyzed. Median monthly out-of-pocket cost for cannabis was $80 (interquartile range = $25-$150). On regression analysis, male gender (odds ratio = 2.5, 95% confidence interval = 1.2 to 5.5, P = .026) and being 45 years of age or older (odds ratio = 7.5, 95% confidence interval = 1.9 to 30.0, P = .0042) were associated with spending $100 a month or more on cannabis. Of the 166 patients who stopped using cannabis early or used less than preferred, 28% attributed it to cost and 26% to lack of insurance coverage.

Conclusion
Cannabis use during cancer treatment may contribute to significant out-of-pocket costs, with men and younger patients more likely to pay higher costs.
Concurrent substance use among cancer patients with and without a history of cannabis use since cancer diagnosis at an NCI-Designated Cancer Center in Florida
Authors: Islam Jessica Y , Nguyen Oliver T , Turner Kea , Martinez Yessica C , Rodriguez Omar Garcia , Rodriguez Diane Irlanda , Rajasekhara Sahana , Chang Young D , Gonzalez Brian D , Jim Heather S L , Egan Kathleen M 
Published: August 2024

Abstract

Background
Although substance use may have adverse impacts on cancer outcomes, little is known regarding patterns of concurrent substance use with cannabis among cancer patients. Our objective was to examine predictors of concurrent substance use with cannabis among cancer patients since their cancer diagnosis and explore perceptions of cannabis among these patients.

Methods
Patients treated at a National Cancer Institute–designated comprehensive cancer center were invited to participate in an electronic survey regarding medical cannabis from August to November 2021. Survey data were linked to internal data resources including electronic health records and patient intake forms to obtain history of substance use (defined as within at least 3 months of cancer diagnosis) of cigarettes, injection drugs, high levels of alcohol, or clinically unsupervised prescription drugs (total n = 1094). Concurrent substance users were defined as those with any reported substance use and cannabis use at the time of cancer diagnosis. We used descriptive statistics (χ2 or exact tests) to compare groups and estimated adjusted odds ratios (AORs) with 95% confidence intervals (CIs) to identify predictors of substance use among users and nonusers of cannabis.

Results
Approximately 45% (n = 489) of the sample reported cannabis use since their cancer diagnosis. Of patients who reported using cannabis, 20% self-reported concurrent polysubstance use, while 8% of cannabis nonusers reported substance use (P &lt; .001). Among patients who use cannabis, those who reported 2 or more self-reported treatment-related symptoms (eg, pain, fatigue) were more likely to have self-reported concurrent substance use (AOR = 3.15, 95% CI = 1.07 to 9.27) compared with those without any symptoms. Among nonusers, those with lower educational background were more likely to have a history of concurrent substance use (AOR = 3.74, 95% CI = 1.57 to 8.92). Patients who use cannabis with concurrent substance use were more likely to report improved sleep (P = .04), increased appetite (P = .03), and treatment of additional medical conditions (P = .04) as perceived benefits of cannabis use.

Conclusions
High symptom burden may be associated with concurrent substance use with cannabis among cancer patients.
Cannabis use and patient-reported outcomes among patients at a comprehensive cancer center
Authors: Gonzalez Brian D , Li Xiaoyin , Martinez Yessica C , Jim Heather S L , Oswald Laura B , Islam Jessica Y , Turner Kea , Egan Kathleen M 
Published: August 2024

Abstract

Background
Patients with cancer report increasing rates of cannabis use, often to manage symptoms and toxicities. The efficacy and safety of cannabis, however, for some use cases remains unclear. To better understand characteristics of patients with cancer who report using cannabis, we examined data from a cannabis use survey of among patients with cancer seen at a National Cancer Institute–Designated Cancer Center.

Methods
In late 2021, patients with cancer (N = 1608) treated between July 2017 and December 2019 provided cannabis use data. Additional data were obtained from medical records data and routine patient-reported outcomes collected for clinical purposes. Univariable analyses and multivariable regression analyses were conducted to identify correlates of cannabis use at different stages in the cancer care trajectory.

Results
Rates of self-reported cannabis use by patients with cancer were 59% before cancer diagnosis and 47% after diagnosis. Longitudinal rates of cannabis use were 29% for no cannabis use, 23% before diagnosis, 12% after diagnosis, and 35% for both before and after diagnosis. Demographic factors associated with cannabis use included age, sex, race, and educational achievement. Tobacco use and binge drinking were associated with higher odds of cannabis use. Cannabis use was also associated with greater self-reported interference with physical functioning due to pain and interference with social functioning due to health problems.

Conclusions
We found high rates of cannabis use among patients with cancer, both before and after their cancer diagnosis. Future studies should further investigate psychosocial factors associated with cannabis use among patients with cancer as well as psychosocial outcomes among patients with cancer using cannabis.
Optimizing the shape of space-constrained silencers composed of multiple straight/reverse chambers using the simulated annealing method
Authors: Chiu Min-Chie , Cheng Ho-Chih , Wang Yu-Hsin 
Published: August 2024

Abstract
To address the issue of hearing health problems caused by the broadband noise emitted from space-constrained marine diesel engines on a ship, an efficient silencer equipped at the engine's venting outlet is necessary. In consideration of the space-constrained situation that often occurs in ships, a reverse silencer with multiple chambers is introduced. A mathematical model of eigenfunction is adopted to consider the acoustic effect at high frequencies. An optimization of the silencer will be performed using the acoustic model of an eigenfunction together with the simulated annealing (SA) method under space-constrained conditions to achieve the best design. To pursue an efficient silencer design, two types of reverse silencers (silencers A and B) are adopted to reduce the engine's venting noise. Acoustical models for straight chamber and reverse chamber silencers are checked before optimization. To assure the reliability of the SA scheme, a pure tone optimization at 250 Hz is exemplified. Results in silencers A and B show that the sound transmission loss is approximately maximized at the desired frequency. Thereafter, a broadband noise elimination of engine noise using silencers A and B is performed. Simulated results show that overall noise abatement can be improved when the number of inverse chambers increases. The optimization of space-constrained reverse silencers with multiple chambers using eigenfunction in cooperation with SA has been accomplished. The overall silencer system's 4-pole matrix is used to predict the silencer's acoustical performance of STL, which is achieved by multiplying individual 4-pole matrices. With the introduction of the reverse silencer, the hearing health of workers can be protected, and noise pollution can be reduced in industrial settings.
The potential of ALFA-tag and tyramide-based fluorescence signal amplification to expand the CRISPR-based DNA imaging toolkit
Authors: Potlapalli Bhanu Prakash , Fuchs Jörg , Rutten Twan , Meister Armin , Houben Andreas 
Published: August 2024

Abstract
Understanding the spatial organization of genomes within chromatin is crucial for deciphering gene regulation. A recently developed CRISPR–dCas9-based genome labeling tool, known as CRISPR–FISH, allows efficient labeling of repetitive sequences. Unlike standard fluorescence in situ hybridization (FISH), CRISPR–FISH eliminates the need for global DNA denaturation, allowing for superior preservation of chromatin structure. Here, we report on further development of the CRISPR–FISH method, which has been enhanced for increased efficiency through the engineering of a recombinant dCas9 protein containing an ALFA-tag. Using an ALFA-tagged dCas9 protein assembled with an Arabidopsis centromere-specific guide RNA, we demonstrate target-specific labeling with a fluorescence-labeled NbALFA nanobody. The dCas9 protein possessing multiple copies of the ALFA-tag, in combination with a minibody and fluorescence-labeled anti-rabbit secondary antibody, resulted in enhanced target-specific signals. The dCas9–ALFA-tag system was also instrumental in live cell imaging of telomeres in Nicotiana benthamiana. This method will further expand the CRISPR imaging toolkit, facilitating a better understanding of genome organization. Furthermore, we report the successful integration of the highly sensitive tyramide signal amplification method with CRISPR–FISH, demonstrating effective labeling of Arabidopsis centromeres.
Light Element (C, N, O) Quantification by EDXS: Application to Meteorite Water Content and Organic Composition
Authors: Le Guillou Corentin , Zanetta Pierre-Marie , Leroux Hugues , Blanchenet Anne-Marie , Marinova Maya 
Published: August 2024

Abstract
Quantifying light elements such as carbon, nitrogen, and oxygen in a transmission electron microscope (TEM) is a challenging however essential task in biology, materials, or earth and planetary sciences. We have developed an approach that allows precise quantification by energy-dispersive X-ray spectroscopy (EDXS), using sensitive windowless silicon drift detectors and homemade Python routines for hyperspectral data processing. K-factors were determined using wedge-shaped focused ion beam sections. To correct for X-ray absorption within the sample, the sample mass thickness is determined by the—revisited—two-lines method (Morris, 1980). No beam current measurement is required. Applying this method to the K and L lines of iron, we found that the tabulated mass absorption coefficient at the energy of the iron L lines was too low. This is due to X-ray self-absorption at the iron edge. Using reference material, we experimentally determined an absorption coefficient that gave the expected results. We then analyzed the complex phyllosilicate mixture of the Orgueil meteorite. We show that the N/C ratio of organics can be obtained with an accuracy better than 5 at.% and that oxygen can be quantified accurately enough to infer the hydroxyl content of phyllosilicates.
Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease
Authors: Liu Yuanhang , Vierkant Robert A , Bhagwate Aditya , Jons William A , Stallings-Mann Melody L , McCauley Bryan M , Carter Jodi M , Stephens Melissa T , Pfrender Michael E , Littlepage Laurie E , Radisky Derek C , Cunningham Julie M , Degnim Amy C , Winham Stacey J , Wang Chen 
Published: August 2024

Abstract
Transcriptome profiling using RNA sequencing (RNA-seq) of bulk formalin-fixed paraffin-embedded (FFPE) tissue blocks is a standard method in biomedical research. However, when used on tissues with diverse cell type compositions, it yields averaged gene expression profiles, complicating biomarker identification due to variations in cell proportions. To address the need for optimized strategies for defining individual cell type compositions from bulk FFPE samples, we constructed single-cell RNA-seq reference data for breast tissue and tested cell type deconvolution methods. Initial simulation experiments showed similar performances across multiple commonly used deconvolution methods. However, the introduction of FFPE artifacts significantly impacted their performances, with a root mean squared error (RMSE) ranging between 0.04 and 0.17. Scaden, a deep learning-based method, consistently outperformed the others, demonstrating robustness against FFPE artifacts. Testing these methods on our 62-sample RNA-seq benign breast disease cohort in which cell type composition was estimated using digital pathology approaches, we found that pre-filtering of the reference data enhanced the accuracy of most methods, realizing up to a 32% reduction in RMSE. To support further research efforts in this domain, we introduce SCdeconR, an R package designed for streamlined cell type deconvolution assessments and downstream analyses.
SGLT2 inhibitors and nephrolithiasis risk: a meta-analysis
Authors: Kanbay Mehmet , Brinza Crischentian , Copur Sidar , Sekreter Ozge , Burlacu Alexandru , Tuttle Katherine R , Rossing Peter , Covic Adrian 
Published: August 2024

ABSTRACT

Background
Sodium–glucose co-transporter 2 (SGLT2) inhibitors are novel anti-diabetic medications with potential beneficial effects on cardiovascular and renal outcomes, metabolic parameters and body weight. In addition to the beneficial effects on renal function, including estimated glomerular filtration rate and reduction in proteinuria, recent studies have investigated the potential role of SGLT2 inhibitor (SGLT2i) therapy on nephrolithiasis development. Nephrolithiasis, a condition affecting almost 10% of the general population at least once during a lifetime, is a common disorder with considerable risk for acute and chronic kidney injury and relatively few effective therapeutic options.

Methods
We performed a literature search through multiple databases, including PubMed, Ovid MEDLINE, Web of Science, Scopus and Cochrane Library. We followed the systematic review and meta-analysis guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. We included a total of 11 635 698 patients who experienced nephrolithiasis from six clinical trials in this meta-analysis study.

Results
In the pooled analysis, nephrolithiasis occurred in 1.27% of patients in the SGLT2i group (n = 739 197), compared with 1.56% of patients (n = 10 896 501) in the control arm (active control, placebo or no therapy). SGLT-2 inhibitor therapy has been associated with a lower risk for nephrolithiasis compared with placebo {odds ratio [OR] 0.61 [95% confidence interval (CI) 0.53–0.70], P &lt; .00001} or active therapy such as glucagon-like peptide 1 and dipeptidyl peptidase 4 inhibitors [OR 0.66 (95% CI 0.47–0.93), P = .02].

Conclusion
We demonstrated a lower risk of nephrolithiasis with SGLT2i therapy compared with placebo or active control. Potential underlying mechanisms include osmotic diuresis leading to a reduction in the concentration of lithogenic substances, anti-inflammatory and anti-fibrotic effects and an increase in urine pH. There is a clear need for future large-scale randomized clinical trials evaluating such associations for better understanding.
Outcomes of Antiviral Retreatment for Immunocompromised Hosts With Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Polymerase Chain Reaction Positivity: A Multicenter Australian Retrospective Case Series
Authors: Bond K A , Dendle C , Guy S , Slavin M A , Smibert O , Ibrahim N , Kinsella P M , Morrissey C O , Moso M A , Sasadeusz J J 
Published: August 2024

Abstract
Outcomes are presented for a multisite retrospective case series, describing a contemporary cohort of 22 immunocompromised patients with persistent coronavirus disease 2019 (COVID-19) polymerase chain reaction positivity who were retreated with antiviral therapy. For those with data available 14 and 30 days after commencement of antiviral therapy, 41% (9 of 22) and 68% (15 of 22), respectively, cleared COVID-19.
Usefulness of Xpert MTB/RIF and Xpert Ultra to Categorize Risk of Tuberculosis Transmission to Household Contacts
Authors: Mol Alexander , Sánchez-Montalvá Adrián , Espinosa-Pereiro Juan , Aznar Maria Luisa , Salvador Fernando , Bosch-Nicolau Pau , de Souza-Galvão Maria-Luiza , Jiménez María Ángeles , Rodrigo-Pendás José Ángel , Millet Joan-Pau , Saborit Nuria , Broto Claudia , Molina Israel , Tórtola Teresa 
Published: August 2024

Abstract

Background
People with pulmonary tuberculosis (PTB) are contagious, particularly to their household contacts. Their infectivity has been associated with the bacterial load in sputum samples. This study investigated if the bacterial load in sputum samples as quantified by Xpert MTB/RIF and Xpert Ultra is correlated with the extent that latent tuberculosis infection (LTBI) occurred in household contacts of people with PTB.

Methods
A retrospective study was performed including people with PTB presenting at Vall d’Hebron University Hospital, Barcelona, between 2011 and 2021. Their infection ratio, representing the proportion of household members found with LTBI in contact tracing investigation, was compared with the quantitative results of Xpert MTB/RIF and Xpert Ultra using ordinal regression analysis.

Results
A total of 107 people with PTB were included. Among their 398 household contacts, 126 (31.7%) cases of LTBI and 14 cases with active TB disease (3.5%) were reported. Higher bacterial load in Xpert MTB/RIF and Xpert Ultra baseline sputum was significantly associated with increased infection ratios, providing better estimates than conventional acid-fast bacilli (AFB) smear grading.

Conclusions
Xpert MTB/RIF and Xpert Ultra could serve as an alternative to AFB sputum-smear grading in determining contact tracing priorities.