bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Computational Efficiency in Porous Media Analysis: Integrating Machine Learning With Monte Carlo Ray Tracing
Authors: Tabassum Farhin , Hajimirza Shima 
Published: July 2024

Abstract
Monte Carlo ray tracing (MCRT) is a prevalent and reliable computation method for simulating light-matter interactions in porous media. However, modeling these interactions becomes computationally expensive due to complex structures and enormous variables. Hence, machine learning (ML) models have been utilized to overcome computational burdens. In this study, we investigate two distinct frameworks for characterizing radiative properties in porous media for pack-free and packing-based methods. We employ two different regression tools for each case, namely Gaussian process (GP) regressions for pack-free MCRT and convolutional neural network (CNN) models for pack-based MCRT to predict the radiative properties. Our study highlights the importance of selecting the appropriate regression method based on the physical model, which can lead to significant computational efficiency improvement. Our results show that both models can predict the radiative properties with high accuracy (&gt;90%). Furthermore, we demonstrate that combining MCRT with ML inference not only enhances predictive accuracy but also reduces the computational cost of simulation by more than 96% using the GP model and 99% for the CNN model.
Marine bacteria
Alteromonas
spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer
Authors: Robertson Jacob M. , Garza Erin A. , Stubbusch Astrid K. M. , Dupont Christopher L. , Hwa Terence , Held Noelle A. 
Published: July 2024

ABSTRACT

The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate,
Alteromonas
sp. ALT199 strain 4B03, and the related type-strain
A. macleodii
27126 both form large (>500 μm) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole-genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (
galEΔ
308–324). In 27126, a knock-out of
galE
(
ΔgalE
::km
r
) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective
galE
mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also form aggregates with chitin particles, but their
galE
mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their
galE
mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of
Alteromonas
, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for
galE
is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes.

IMPORTANCE

Heterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation of marine snow. We find that two members of the prevalent particle-associated genus
Alteromonas
can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for
galE
in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.
Segmentectomy for ground glass-dominant invasive lung cancer with tumour diameter of 2–3 cm: protocol for a single-arm, multicentre, phase III trial (ECTOP1012)
Authors: Chen Shiqi , Huang Qingyuan , Fu Fangqiu , Wang Zezhou , Zhang Yang , Chen Haiquan 
Published: July 2024

IntroductionPrevious studies demonstrated that wedge resection is sufficient for ground glass-dominant lung adenocarcinoma (LUAD) with tumour diameter ≤2 cm, however, the optimal surgical type for ground glass-dominant LUAD with tumour diameter of 2–3 cm remains unclear. The purpose of this trial is to investigate the safety and efficacy of segmentectomy for ground glass-dominant invasive LUAD with tumour size of 2–3 cm.Methods and analysisWe initiated a phase III trial to investigate whether segmentectomy is suitable for ground glass-dominant invasive LUAD with tumour size of 2–3 cm. This trial plans to enrol 307 patients from multiple institutions including four general hospitals and two specialty cancer hospitals over a period of 5 years. The primary endpoint is 5 year disease-free survival. Secondary endpoints are lung function, 5 year overall survival, the site of tumour recurrence and metastasis, segmentectomy completion rate, radical segmentectomy (R0 resection) completion rate and surgery-related complications.Ethics and disseminationThis trial has been approved by the Ethics Committee of Fudan University Shanghai Cancer Centre (reference 2212267-18) and by the institutional review boards of each participating centre. Written informed consent is required from all participants. The study results will be published in a peer-reviewed international journal.Trial registration numberNCT05717803.
Total brain volume is associated with severity of transverse sinus stenosis in idiopathic intracranial hypertension
Authors: Schartz Derrek , Finkelstein Alan , Akkipeddi Sajal Medha K , Kessler Alex , Williams Zoe , Vates Edward , Hauck Erik F , Fargen Kyle M , Bender Matthew T 
Published: July 2024

BackgroundIdiopathic intracranial hypertension (IIH) is a complex neurological condition characterized by symptoms of increased intracranial pressure of unclear etiology. While transverse sinus stenosis (TSS) is often present in patients with IIH, how and why it occurs remains unclear.MethodsIIH patients and a set of age-matched normal controls were identified from our single-center tertiary care institution from 2016 to 2024. Brain MRIs before treatment were computationally segmented and parcellated using FreeSurfer software. Extent of TSS on MR venograms was graded using the Farb scoring system. Relationship between normalized brain volume, normalized brain-to-CSF volume, and TSS was investigated. Multiple linear regression was conducted to investigate the association between continuous variables, accounting for the covariates body mass index, sex, and age.ResultsIn total, 84 IIH patients (mean age, 29.8 years; 87% female) and 15 normal controls (mean age, 28.1 years) were included. Overall, increasing/worsening TSS was found to be significantly associated with normalized total brain volume (p=0.018, R=0.179) and brain-to-CSF ratio volume (p=0.026, R=0.184). Additionally, there was a significant difference between controls and IIH patients with mild and severe stenosis regarding normalized total brain volume (ANCOVA, p=0.023) and brain-to-CSF ratio volume (ANCOVA, p=0.034). Likewise, IIH patients with severe TSS had a significantly higher brain-to-CSF volume compared with controls (p=0.038) and compared with IIH patients with mild TSS (p=0.038).ConclusionsThese findings suggest that total brain volume is associated with extent of TSS, which may reflect extramural venous compression due to enlarged brain and/or venous hypertension with associated cerebral congestion/swelling.
Collaborative advance care planning in palliative care: a randomised controlled trial
Authors: Seifart Carola , Koch Martin , Herzog Svenja , Leppin Nico , Nagelschmidt Katharina , Riera Knorrenschild Jorge , Timmesfeld Nina , Denz Robin , Seifart Ulf , Rief Winfried , Von Blanckenburg Pia 
Published: July 2024

ObjectiveAn effective tool for establishing concordant end-of-life (EOL) care in patients with cancer is advance care planning (ACP). However, various barriers, including psychological obstacles, hamper the access to ACP. Therefore, a new conceptual model combining a psycho-oncological approach with structured ACP was developed. The effectiveness and efficiency of this new concept of collaborative ACP (col-ACP) is evaluated in the present randomised controlled trial in patients with palliative cancer.Methods277 patients with palliative cancer and their relatives were randomised into three groups (1) collaborative ACP (col-ACP) consisting of a psycho-oncological approach addressing barriers to EOL conversations followed by a standardised ACP procedure, (2) supportive intervention (active control) and (3) standard medical care.ResultsPatients in the col-ACP group completed advance directives (p<0.01) and healthcare proxies (p<0.01) significantly more often. Additionally, they felt better planned ahead for their future treatment (p<0.01) and were significantly more confident that their relatives were aware of their treatment wishes (p=0.03). In fact, their goals of care were known and highly fulfilled. However, patients’ and caregivers’ quality of life, patients’ stress, depression and peace did not differ between the groups.ConclusionsThe new, well-received, concept of col-ACP improves readiness and access to ACP and results in more consistent EOL care. Further, even if no direct influence on quality of life could be proven, it supports patients in planning their treatment, making autonomous decisions and regaining self-efficacy in the face of life-limiting cancer. Therefore, a closer interlocking and information exchange between psycho-oncological and ACP services seems to be reasonable.Trial registration numberNCT03387436.
Oncogenic KRAS-Dependent Stromal Interleukin-33 Directs the Pancreatic Microenvironment to Promote Tumor Growth
Authors: Donahue Katelyn L. , Watkoske Hannah R. , Kadiyala Padma , Du Wenting , Brown Kristee , Scales Michael K. , Elhossiny Ahmed M. , Espinoza Carlos E. , Lasse Opsahl Emily L. , Griffith Brian D. , Wen Yukang , Sun Lei , Velez-Delgado Ashley , Renollet Nur M. , Morales Jacqueline , Nedzesky Nicholas M. , Baliira Rachael K. , Menjivar Rosa E. , Medina-Cabrera Paola I. , Rao Arvind , Allen Benjamin , Shi Jiaqi , Frankel Timothy L. , Carpenter Eileen S. , Bednar Filip , Zhang Yaqing , Pasca di Magliano Marina 
Published: July 2024

Abstract
Pancreatic cancer is characterized by an extensive fibroinflammatory microenvironment. During carcinogenesis, normal stromal cells are converted to cytokine-high cancer-associated fibroblasts (CAF). The mechanisms underlying this conversion, including the regulation and function of fibroblast-derived cytokines, are poorly understood. Thus, efforts to therapeutically target CAFs have so far failed. Herein, we show that signals from epithelial cells expressing oncogenic KRAS—a hallmark pancreatic cancer mutation—activate fibroblast autocrine signaling, which drives the expression of the cytokine IL33. Stromal IL33 expression remains high and dependent on epithelial KRAS throughout carcinogenesis; in turn, environmental stress induces interleukin-33 (IL33) secretion. Using compartment-specific IL33 knockout mice, we observed that lack of stromal IL33 leads to profound reprogramming of multiple components of the pancreatic tumor microenvironment, including CAFs, myeloid cells, and lymphocytes. Notably, loss of stromal IL33 leads to an increase in CD8+ T-cell infiltration and activation and, ultimately, reduced tumor growth.
Significance: This study provides new insights into the mechanisms underlying the programming of CAFs and shows that during this process, expression of the cytokine IL33 is induced. CAF-derived IL33 has pleiotropic effects on the tumor microenvironment, supporting its potential as a therapeutic target.
Endothelial Autophagy Promotes Atheroprotective Communication Between Endothelial and Smooth Muscle Cells via Exosome-Mediated Delivery of miR-204-5p
Authors: Tian Zhen , Ning Hua , Wang Xinyue , Wang Yu , Han Tianshu , Sun Changhao 
Published: July 2024

BACKGROUND:
Cellular communication among different types of vascular cells is indispensable for maintaining vascular homeostasis and preventing atherosclerosis. However, the biological mechanism involved in cellular communication among these cells and whether this biological mechanism can be used to treat atherosclerosis remain unknown. We hypothesized that endothelial autophagy mediates the cellular communication in vascular tissue through exosome-mediated delivery of atherosclerosis-related genes.

METHODS:

Rapamycin and adeno-associated virus carrying
Atg7
short hairpin RNA under the Tie (TEK receptor tyrosine kinase) promoter were used to activate and inhibit vascular endothelial autophagy in high-fat diet–fed
ApoE

−/−

mice, respectively. miRNA microarray, in vivo and in vitro experiments, and human vascular tissue were used to explore the effects of endothelial autophagy on endothelial function and atherosclerosis and its molecular mechanisms. Quantitative polymerase chain reaction and miRNA sequencing were performed to determine changes in miRNA expression in exosomes. Immunofluorescence and exosome coculture experiments were conducted to examine the role of endothelial autophagy in regulating the communication between endothelial cells and smooth muscle cells (SMCs) via exosomal miRNA.

RESULTS:

Endothelial autophagy was inhibited in thoracic aortas of high-fat diet–fed
ApoE

−/

−

mice. Furthermore, rapamycin alleviated high-fat diet–induced atherosclerotic burden and endothelial dysfunction, while endothelial-specific
Atg7
depletion aggravated the atherosclerotic burden. miRNA microarray, in vivo and in vitro experiments, and human vascular tissue analysis revealed that miR-204-5p was significantly increased in endothelial cells after high-fat diet exposure, which directly targeted
Bcl2
to regulate endothelial cell apoptosis. Importantly, endothelial autophagy activation decreased excess miR-204-5p by loading miR-204-5p into multivesicular bodies and secreting it through exosomes. Moreover, exosomal miR-204-5p can effectively transport to SMCs, alleviating SMC calcification by regulating target proteins such as RUNX2.

CONCLUSIONS:
Our study revealed the exosomal pathway by which endothelial autophagy protects atherosclerosis: endothelial autophagy activation transfers miR-204-5p from endothelial cells to SMCs via exosomes, both preventing endothelial apoptosis and alleviating SMC calcification.

REGISTRATION:

URL:
https://www.chictr.org.cn/
; Unique identifier: ChiCTR2200064155.
High-Sensitivity Troponin T, NT-proBNP, and Cognitive Outcomes in SPRINT
Authors: Haney Devin , Ma Yuan , Dalmacy Djhenne , Pajewski Nicholas M. , Hajjar Ihab , de Lemos James A. , Zhang Wenxin , Soliman Elsayed Z. , Ballantyne Christie M. , Nambi Vijay , Sattar Naveed , Killeen Anthony A. , Ix Joachim H. , Shlipak Michael G. , Berry Jarett D. , Ascher Simon B. 
Published: July 2024

BACKGROUND:
Hs-cTnT (cardiac troponin T measured with a highly sensitive assay) and NT-proBNP (N-terminal pro-B-type natriuretic peptide) may identify adults with hypertension who derive greater cognitive benefits from lower systolic blood pressure targets.

METHODS:
In the SPRINT (Systolic Blood Pressure Intervention Trial) MIND study, participants were categorized as having both hs-cTnT and NT-proBNP in the lower 2 tertiles (n=4226), one in the highest tertile (n=2379), and both in the highest tertile (n=1506). We assessed the effect of intensive versus standard treatment on the composite of mild cognitive impairment (MCI) or probable dementia (PD) across biomarker categories.

RESULTS:

Over a median follow-up of 5.1 years, 830 of 8111 participants (10.2%) developed MCI or PD. Participants in the highest biomarker category were at higher risk of MCI or PD compared with those in the lowest category (hazard ratio, 1.34 [95% CI, 1.00–1.56]). The effect of intensive treatment on reducing the risk of MCI or PD was greater among participants in the lowest biomarker category (hazard ratio, 0.64 [95% CI, 0.50–0.81]) than those in the intermediate (hazard ratio, 1.01 [95% CI, 0.80–1.28]) or highest categories (hazard ratio, 0.90 [95% CI, 0.72–1.13];
P
interaction
=0.02). The 5-year absolute risk differences in MCI or PD with intensive treatment were −2.9% (−4.4%, −1.3%), −0.2% (−3.0%, 2.6%), and −1.9% (−6.2%, 2.4%) in the lowest, intermediate, and highest biomarker categories, respectively.

CONCLUSIONS:
In SPRINT, the relative effect of intensive systolic blood pressure lowering on preventing cognitive impairment appears to be stronger among participants with lower compared with higher cardiac biomarker levels, though the absolute risk reductions were similar.
Trends and Factors Associated With Peripheral Vascular Interventions for the Treatment of Claudication From 2011 to 2022: A National Medicare Cohort Study
Authors: Dun Chen , Stonko David P. , Bose Sanuja , Keegan Alana C. , McDermott Katherine M. , Rumalla Kranti C. , Black James H. , Kalbaugh Corey A. , Makary Martin A. , Hicks Caitlin W. 
Published: July 2024

Background
Previous cross‐sectional studies have identified wide practice pattern variations in the use of peripheral vascular interventions (PVIs) for the treatment of claudication. However, there are limited data on longitudinal practice patterns. We aimed to describe the temporal trends and charges associated with PVI use for claudication over the past 12 years in the United States.

Methods and Results
We conducted a retrospective analysis using 100% Medicare fee‐for‐service claims data to identify all patients who underwent a PVI for claudication between January 2011 and December 2022. We evaluated the trends in utilization and Medicare‐allowed charges of PVI according to anatomic level, procedure type, and intervention settings using generalized linear models. Multinomial logistic regressions were used to evaluate factors associated with different levels and types of PVI. We identified 599 197 PVIs performed for claudication. The proportional use of tibial PVI increased 1.0% per year, and atherectomy increased by 1.6% per year over the study period. The proportion of PVIs performed in ambulatory surgical centers/office‐based laboratories grew at 4% per year from 12.4% in 2011 to 55.7% in 2022. Total Medicare‐allowed charges increased by $11 980 035 USD/year. Multinomial logistic regression identified significant associations between race and ethnicity and treatment setting with use of both atherectomy and tibial PVI.

Conclusions
The use of tibial PVI and atherectomy for the treatment of claudication has increased dramatically in in ambulatory surgical center/office‐based laboratory settings, non‐White patients, and resulting in a significant increase in health care charges. There is a critical need to improve the delivery of value‐based care for the treatment of claudication.
Neighborhood Resources and Health Outcomes Among Stroke Survivors in a Population‐Based Cohort
Authors: Delhey Leanna M. , Shi Xu , Morgenstern Lewis B. , Brown Devin L. , Smith Melinda A. , Case Erin C. , Springer Mellanie V. , Lisabeth Lynda D. 
Published: July 2024

Background
Stroke survivors believe neighborhood resources such as community centers are beneficial; however, little is known about the influence of these resources on stroke outcomes. We evaluated whether residing in neighborhoods with greater resource density is associated with favorable post‐stroke outcomes.

Methods and Results
We included Mexican American and non‐Hispanic White stroke survivors from the Brain Attack Surveillance in Corpus Christi project (2009–2019). The exposure was density of neighborhood resources (eg, community centers, restaurants, stores) within a residential census tract at stroke onset. Outcomes included time to death and recurrence, and at 3 months following stroke: disability (activities of daily living/instrumental activities of daily living), cognition (Modified Mini‐Mental State Exam), depression (Patient Health Questionnaire‐8), and quality of life (abbreviated Stroke‐Specific Quality of Life scale). We fit multivariable Cox regression and mixed linear models. We considered interactions with stroke severity, ethnicity, and sex. Among 1786 stroke survivors, median age was 64 years (interquartile range, 56–73), 55% men, and 62% Mexican American. Resource density was not associated with death, recurrence, or depression. Greater resource density (75th versus 25th percentile) was associated with more favorable cognition (Modified Mini‐Mental State Exam mean difference=0.838, 95% CI=0.092, 1.584) and among moderate–severe stroke survivors, with more favorable functioning (activities of daily living/instrumental activities of daily living=−0.156 [95% CI, −0.284 to 0.027]) and quality of life (abbreviated Stroke‐Specific Quality of Life scale=0.194 [95% CI, 0.029–0.359]).

Conclusions
We observed associations between greater resource density and cognition overall and with functioning and quality of life among moderate–severe stroke survivors. Further research is needed to confirm these findings and determine if neighborhood resources may be a tool for recovery.
Self‐Report Tool for Identification of Individuals With Coronary Atherosclerosis: The Swedish CardioPulmonary BioImage Study
Authors: Bergström Göran , Hagberg Eva , Björnson Elias , Adiels Martin , Bonander Carl , Strömberg Ulf , Andersson Jonas , Brunström Mattias , Carlhäll Carl‐Johan , Engström Gunnar , Erlinge David , Goncalves Isabel , Gummesson Anders , Hagström Emil , Hjelmgren Ola , James Stefan , Janzon Magnus , Jonasson Lena , Lind Lars , Magnusson Martin , Oskarsson Viktor , Sundström Johan , Svensson Per , Söderberg Stefan , Themudo Raquel , Östgren Carl Johan , Jernberg Tomas 
Published: July 2024

Background
Coronary atherosclerosis detected by imaging is a marker of elevated cardiovascular risk. However, imaging involves large resources and exposure to radiation. The aim was, therefore, to test whether nonimaging data, specifically data that can be self‐reported, could be used to identify individuals with moderate to severe coronary atherosclerosis.

Methods and Results

We used data from the population‐based SCAPIS (Swedish CardioPulmonary BioImage Study) in individuals with coronary computed tomography angiography (n=25 182) and coronary artery calcification score (n=28 701), aged 50 to 64 years without previous ischemic heart disease. We developed a risk prediction tool using variables that could be assessed from home (self‐report tool). For comparison, we also developed a tool using variables from laboratory tests, physical examinations, and self‐report (clinical tool) and evaluated both models using receiver operating characteristic curve analysis, external validation, and benchmarked against factors in the pooled cohort equation. The self‐report tool (n=14 variables) and the clinical tool (n=23 variables) showed high‐to‐excellent discriminative ability to identify a segment involvement score ≥4 (area under the curve 0.79 and 0.80, respectively) and significantly better than the pooled cohort equation (area under the curve 0.76,
P
<0.001). The tools showed a larger net benefit in clinical decision‐making at relevant threshold probabilities. The self‐report tool identified 65% of all individuals with a segment involvement score ≥4 in the top 30% of the highest‐risk individuals. Tools developed for coronary artery calcification score ≥100 performed similarly.

Conclusions
We have developed a self‐report tool that effectively identifies individuals with moderate to severe coronary atherosclerosis. The self‐report tool may serve as prescreening tool toward a cost‐effective computed tomography‐based screening program for high‐risk individuals.