bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of verbal autopsy in cancer registration: A mixed‐methods study from the population‐based cancer registry of Northern India
Authors: Khanna Divya , Budukh Atul , Sharma Priyanka , Shruti Tulika , Vishwakarma Rajesh , Sharma Anand N. , Bagal Sonali , Vikraman Saraswathy M. , Vaza Yagnik , Anand Akash , Chaturvedi Pankaj , Pradhan Satyajit 
Published: July 2023

AbstractObjectivesTo describe utilisation of verbal autopsy as one of the data collection approaches in cancer registration in an Indian setting. We aimed to estimate the proportion and epidemiological characteristics of malignancies identified by the Varanasi population‐based cancer registry (PBCR) using verbal autopsy between 2017 and 2019 and to develop a thematic network for implementing verbal autopsy.MethodsThis was a cross‐sectional mixed‐methods study. Quantitative methods were applied to analyse information from PBCR proforma of the verbal autopsy‐confirmed cancers; qualitative methods were applied to evaluate verbal autopsy conducted by field staff from key informants. In‐depth interviews of field staff for the challenges and potential solutions during verbal autopsy were assessed.ResultsOf 6466 registered cancers, 1103 (17.1%) were verbal autopsy‐confirmed cancers, which had no other source of information. The majority of verbal autopsy cases were from vulnerable populations who were aged >50 years (721, 65.4%), female (607, 55.1%), from rural backgrounds (853, 77.3%), illiterate or just able to read and write (636, 57.7%), and from lower and middle‐income groups (823, 74.6%). Verbal autopsy helped provide information about symptoms and site of disease, diagnostic and treatment details, and disease status. Major challenges during verbal autopsy described by field staff were incomplete cancer treatment, destruction of medical records and non‐cooperation by the community and lack of support from the local workforce as cancer is not notifiable.ConclusionVerbal autopsy helped identify cancers that would have been missed during active case finding from available resources. The majority of verbal autopsy‐confirmed patients belonged to vulnerable populations. Non‐cooperation from community and local health systems was major challenge during verbal autopsy. Developing robust cancer awareness, patient navigation, and social support programmes will strengthen verbal autopsy. Integration of standardised and reproducible methods of verbal autopsy in cancer registry and digitalization of health information, especially in limited‐resource settings with weak vital registration, will facilitate completeness in cancer registration.
RBOHF activates stomatal immunity by modulating both reactive oxygen species and apoplastic pH dynamics in Arabidopsis
Authors: Arnaud Dominique , Deeks Michael J. , Smirnoff Nicholas 
Published: July 2023

SUMMARYStomatal defences are important for plants to prevent pathogen entry and further colonisation of leaves. Apoplastic reactive oxygen species (ROS) generated by NADPH oxidases and apoplastic peroxidases play an important role in activating stomatal closure upon perception of bacteria. However, downstream events, particularly the factors influencing cytosolic hydrogen peroxide (H2O2) signatures in guard cells are poorly understood. We used the H2O2 sensor roGFP2‐Orp1 and a ROS‐specific fluorescein probe to study intracellular oxidative events during stomatal immune response using Arabidopsis mutants involved in the apoplastic ROS burst. Surprisingly, the NADPH oxidase mutant rbohF showed over‐oxidation of roGFP2‐Orp1 by a pathogen‐associated molecular pattern (PAMP) in guard cells. However, stomatal closure was not tightly correlated with high roGFP2‐Orp1 oxidation. In contrast, RBOHF was necessary for PAMP‐mediated ROS production measured by a fluorescein‐based probe in guard cells. Unlike previous reports, the rbohF mutant, but not rbohD, was impaired in PAMP‐triggered stomatal closure resulting in defects in stomatal defences against bacteria. Interestingly, RBOHF also participated in PAMP‐induced apoplastic alkalinisation. The rbohF mutants were also partly impaired in H2O2‐mediated stomatal closure at 100 μm while higher H2O2 concentration up to 1 mm did not promote stomatal closure in wild‐type plants. Our results provide novel insights on the interplay between apoplastic and cytosolic ROS dynamics and highlight the importance of RBOHF in plant immunity.
Numerical Assessment of Hydraulic Properties of Triply Periodic Minimal Surfaces Structures
Authors: Piatti Cecilia , Savoldi Laura , Fathi Nima 
Published: July 2023

Abstract
The present work is devoted to evaluating the hydraulic properties of Triply Periodic Minimal Surfaces (TPMS) structures, a generation of porous structures developed using the periodicity of trigonometric equations to generate triply periodic minimal surfaces. The thorough computational and experimental analysis coupled with verification assessment is key to using these product structures in thermal hydraulics especially to address industrial requirements. Here the hydraulic properties are computed by performing three-dimensional CFD analyses using Star-CCM+. Gyroid TPMS was hydraulically analyzed with a water flow in three-channel configurations (circular, square, and rectangular section), with the same hydraulic diameter and length, respectively 5.08cm and 10cm. Their porosity values range from 80% to 93% depending on the unit cell dimensions (chosen values were 10mm, 15mm, 20mm, 25mm, and 30mm). The CFD models for the rectangular TPMS contain the maximum epistemic uncertainty of 19% following the ASME VV 20 codes. In preparation for the forthcoming test campaign, the hydraulic characteristic of the different channels is assessed comparatively, and the friction factors are computed and compared to reach a basic understanding of the parametric effect of channel shape and cell size.
Association between Medicare eligibility at age 65 years and in-hospital treatment patterns and health outcomes for patients with trauma: regression discontinuity approach
Authors: Bhaumik Deepon , Ndumele Chima D , Scott John W , Wallace Jacob 
Published: July 2023

Abstract

Objective
To determine whether health systems in the United States modify treatment or discharge decisions for otherwise similar patients based on health insurance coverage.

Design
Regression discontinuity approach.

Setting
American College of Surgeons’ National Trauma Data Bank, 2007-17.

Participants
Adults aged between 50 and 79 years with a total of 1 586 577 trauma encounters at level I and level II trauma centers in the US.

Interventions
Eligibility for Medicare at age 65 years.

Main outcome measures
The main outcome measure was change in health insurance coverage, complications, in-hospital mortality, processes of care in the trauma bay, treatment patterns during hospital admission, and discharge locations at age 65 years.

Results
1 586 577 trauma encounters were included. At age 65, a discontinuous increase of 9.6 percentage points (95% confidence interval 9.1 to 10.1) was observed in the share of patients with health insurance coverage through Medicare at age 65 years. Entry to Medicare at age 65 was also associated with a decrease in length of hospital stay for each encounter, of 0.33 days (95% confidence interval −0.42 to −0.24 days), or nearly 5%), which coincided with an increase in discharges to nursing homes (1.56 percentage points, 95% confidence interval 0.94 to 2.16 percentage points) and transfers to other inpatient facilities (0.57 percentage points, 0.33 to 0.80 percentage points), and a large decrease in discharges to home (1.99 percentage points, −2.73 to −1.27 percentage points). Relatively small (or no) changes were observed in treatment patterns during the patients’ hospital admission, including no changes in potentially life saving treatments (eg, blood transfusions) or mortality.

Conclusions
The findings suggest that differences in treatment for otherwise similar patients with trauma with different forms of insurance coverage arose during the discharge planning process, with little evidence that health systems modified treatment decisions based on patients’ coverage.
NuHamil : A numerical code to generate nuclear two- and three-body matrix elements from chiral effective field theory
Authors: Miyagi Takayuki 
Published: July 2023

AbstractThe applicability of nuclear ab initio calculations has rapidly extended over the past decades. However, starting research projects is still challenging due to the required numerical expertise in the generation of underlying nuclear interaction matrix elements and many-body calculations. To ease the first issue, in this paper we introduce the numerical code to generate the nucleon-nucleon (NN) and three-nucleon (3N) matrix elements expressed in a spherical harmonic-oscillator basis, inputs of many-body calculations. The ground-state energies for the selected doubly closed shell nuclei are calculated with the no-core shell-model (NCSM) and in-medium similarity renormalization group (IMSRG). The code is written in modern Fortran, and OpenMP+MPI hybrid parallelization is available for the 3N matrix-element calculations.
Bayesian inference of W-boson mass
Authors: Rallapalli Aaseesh , Desai Shantanu 
Published: July 2023

AbstractWe use a Bayesian regression technique (similar to a recent analysis by Rinaldi et al.) to obtain a central estimate for the W-boson mass using four different combinations of datasets compiled by the PDG including the 2022 CDF result. We use three different priors on the unknown intrinsic scatter and also a non-parametric hierarchical Dirichlet Process Gaussian Mixture model to obtain a world average for W-boson mass. We also evaluate the statistical significance of the discrepancy with respect to the Standard model for each of the datasets. We find that for all the combination of datasets and the aformentioned prior choices, the discrepancy with respect to the Standard Model value for the W-mass is less than 3$$\sigma $$
σ
. We also checked that if we use a narrow prior on the intrinsic scatter, we get a discrepancy of about 3.8$$\sigma $$
σ
compared to the Standard model value.
Performance of the MALTA telescope
Authors: van Rijnbach Milou , Gustavino Giuliano , Allport Phil , Tortajada Ignacio Asensi , Berlea Dumitru Vlad , Bortoletto Daniela , Buttar Craig , Charbon Edoardo , Dachs Florian , Dao Valerio , Dobrijevic Dominik , de Acedo Leyre Flores Sanz , Gabrielli Andrea , Gazi Martin , Gonella Laura , Gonzalez Vicente , Guidon Stefan , LeBlanc Matt , Pernegger Heinz , Piro Francesco , Riedler Petra , Sandaker Heidi , Sharma Abhishek , Sanchez Carlos Solans , Snoeys Walter , Suligoj Tomislav , Nunez Marcos Vazquez , Weick Julian , Worm Steven , Zoubir Abdelhak M. 
Published: July 2023

AbstractMALTA is part of the Depleted Monolithic Active Pixel sensors designed in Tower 180 nm CMOS imaging technology. A custom telescope with six MALTA planes has been developed for test beam campaigns at SPS, CERN, with the ability to host several devices under test. The telescope system has a dedicated custom readout, online monitoring integrated into DAQ with realtime hit map, time distribution and event hit multiplicity. It hosts a dedicated fully configurable trigger system enabling to trigger on coincidence between telescope planes and timing reference from a scintillator. The excellent time resolution performance allows for fast track reconstruction, due to the possibility to retain a low hit multiplicity per event which reduces the combinatorics. This paper reviews the architecture of the system and its performance during the 2021 and 2022 test beam campaign at the SPS North Area.
Topology in thermodynamics of regular black strings with Kaluza–Klein reduction
Authors: Hung Tran N. , Nam Cao H. 
Published: July 2023

AbstractWe study the topological defects in the thermodynamics of regular black strings (from a four-dimensional perspective) that is symmetric under the double Wick rotation and constructed in the high-dimensional spacetime with an extra dimension compactified on a circle. We observe that the thermodynamic phases of regular black strings can be topologically classified by the positive and negative winding numbers (at the defects) which correspond to the thermodynamically stable and unstable branches. This topological classification implies a phase transition due to the decay of a thermodynamically unstable regular black string to another which is thermodynamically stable. We confirm these topological properties of the thermodynamics of regular black strings by investigating their free energy, heat capacity, and Ruppeiner scalar curvature of the state space. The Ruppeiner scalar curvature of regular black strings is found to be always negative, implying that the interactions among the microstructures of regular black strings are only attractive.
Metastasis Unleashed: Hyposialylation Empowers Chemo-Evasive Circulating Tumor Cell Clusters in Breast Cancer
Authors: Gvozdenovic Ana , Aceto Nicola 
Published: July 2023

Abstract
Therapy resistance is frequently observed in cancer patients with distant metastases and effective management of metastatic disease remains challenging. Unraveling the cellular mechanisms and molecular targets fueling metastatic spread is crucial for advancing cancer therapies. In a recent issue of Cancer Discovery, Dashzeveg and colleagues revealed that loss of terminal sialylation in glycoproteins within circulating tumor cell clusters is a dynamic process that contributes to cellular dormancy, facilitates evasion of chemotherapy, and enhances metastatic seeding. Furthermore, the study identifies the glycoprotein podocalyxin (PODXL) as a potential target for counteracting the metastasis of quiescent tumor cells associated with paclitaxel treatment in triple-negative breast cancer.
Heterochromatin-Dependent Replication Stress: A Lesson from IDH1/2 Mutants
Authors: Zou Lee 
Published: July 2023

Abstract
Oncogenic point mutants of isocitrate dehydrogenases 1 and 2 (IDH2) generate 2-hydroxyglutarate, which inhibits lysine demethylases and increases heterochromatin. Tumor cells expressing IDH mutants are sensitive to PARP inhibitors (PARPi), offering an opportunity to eliminate IDH-driven tumor cells in therapy. Expression of an oncogenic IDH1 mutant in cells leads to aberrant heterochromatin formation at DNA breaks and impairs DNA repair through homologous recombination (HR), providing a possible explanation for the PARPi sensitivity of IDH mutant cells. However, a recent study published in Molecular Cell shows that IDH mutant tumors do not display the genomic alterations associated with HR defects. Instead, IDH mutants induce heterochromatin-dependent DNA replication stress. Furthermore, PARP is activated by the replication stress induced by IDH mutants and required for suppressing the ensuing DNA damage, providing an alternative model to explain the susceptibility of IDH mutant cells to PARPis. This study presents a new example of oncogene-induced and heterochromatin-dependent replication stress, and a role of PARP in the response to the stress, extending the molecular basis for PARP-targeted therapy.
Caveolin Gene Expression Predicts Clinical Outcomes for Early-Stage HER2-Negative Breast Cancer Treated with Paclitaxel-Based Chemotherapy in the GeparSepto Trial
Authors: Williams Terence M. , Schneeweiss Andreas , Jackisch Christian , Shen Changxian , Weber Karsten E. , Fasching Peter A. , Denkert Carsten , Furlanetto Jenny , Heinmöller Ernst , Schmatloch Sabine , Karn Thomas , Szeto Christopher W. , van Mackelenbergh Marion T. , Nekljudova Valentina , Stickeler Elmar , Soon-Shiong Patrick , Schem Christian , Mairinger Thomas , Müller Volkmar , Marme Frederik , Untch Michael , Loibl Sibylle 
Published: July 2023

Abstract

Purpose:
Caveolin-1 and -2 (CAV1/2) dysregulation are implicated in driving cancer progression and may predict response to nab-paclitaxel. We explored the prognostic and predictive potential of CAV1/2 expression for patients with early-stage HER2-negative breast cancer receiving neoadjuvant paclitaxel-based chemotherapy regimens, followed by epirubicin and cyclophosphamide.

Experimental Design:
We correlated tumor CAV1/2 RNA expression with pathologic complete response (pCR), disease-free survival (DFS), and overall survival (OS) in the GeparSepto trial, which randomized patients to neoadjuvant paclitaxel- versus nab-paclitaxel–based chemotherapy.

Results:
RNA sequencing data were available for 279 patients, of which 74 (26.5%) were hormone receptor (HR)–negative, thus triple-negative breast cancer (TNBC). Patients treated with nab-paclitaxel with high CAV1/2 had higher probability of obtaining a pCR [CAV1 OR, 4.92; 95% confidence interval (CI), 1.70–14.22; P = 0.003; CAV2 OR, 5.39; 95% CI, 1.76–16.47; P = 0.003] as compared with patients with high CAV1/2 treated with solvent-based paclitaxel (CAV1 OR, 0.33; 95% CI, 0.11–0.95; P = 0.040; CAV2 OR, 0.37; 95% CI, 0.12–1.13; P = 0.082). High CAV1 expression was significantly associated with worse DFS and OS in paclitaxel-treated patients (DFS HR, 2.29; 95% CI, 1.08–4.87; P = 0.030; OS HR, 4.97; 95% CI, 1.73–14.31; P = 0.003). High CAV2 was associated with worse DFS and OS in all patients (DFS HR, 2.12; 95% CI, 1.23–3.63; P = 0.006; OS HR, 2.51; 95% CI, 1.22–5.17; P = 0.013), in paclitaxel-treated patients (DFS HR, 2.47; 95% CI, 1.12–5.43; P = 0.025; OS HR, 4.24; 95% CI, 1.48–12.09; P = 0.007) and in patients with TNBC (DFS HR, 4.68; 95% CI, 1.48–14.85; P = 0.009; OS HR, 10.43; 95% CI, 1.22–89.28; P = 0.032).

Conclusions:
Our findings indicate high CAV1/2 expression is associated with worse DFS and OS in paclitaxel-treated patients. Conversely, in nab-paclitaxel–treated patients, high CAV1/2 expression is associated with increased pCR and no significant detriment to DFS or OS compared with low CAV1/2 expression.
A Novel HOXA10-Associated 5-Gene–Based Prognostic Signature for Stratification of Short-term Survivors of Pancreatic Ductal Adenocarcinoma
Authors: Kisling Sophia G. , Atri Pranita , Shah Ashu , Cox Jesse L. , Sharma Sunandini , Smith Lynette M. , Ghersi Dario , Batra Surinder K. 
Published: July 2023

Abstract

Purpose:
Despite the significant association of molecular subtypes with poor prognosis in patients with pancreatic ductal adenocarcinoma (PDAC), few efforts have been made to identify the underlying pathway(s) responsible for this prognosis. Identifying a clinically relevant prognosis-based gene signature may be the key to improving patient outcomes.

Experimental Design:
We analyzed the transcriptomic profiles of treatment-naïve surgically resected short-term survivor (STS) and long-term survivor (LTS) tumors (GSE62452) for expression and survival, followed by validation in several datasets. These results were corroborated by IHC analysis of PDAC-resected STS and LTS tumors. The mechanism of this differential survival was investigated using CIBERSORT and pathway analyses.

Results:
We identified a short-surviving prognostic subtype of PDAC with a high degree of significance (P = 0.018). One hundred thirty genes in this novel subtype were found to be regulated by a master regulator, homeobox gene HOXA10, and a 5-gene signature derived from these genes, including BANF1, EIF4G1, MRPS10, PDIA4, and TYMS, exhibited differential expression in STSs and a strong association with poor survival. This signature was further associated with the proportion of T cells and macrophages found in STSs and LTSs, demonstrating a potential role in PDAC immunosuppression. Pathway analyses corroborated these findings, revealing that this HOXA10-driven prognostic signature is associated with immune suppression and enhanced tumorigenesis.

Conclusions:
Overall, these findings reveal the presence of a HOXA10-associated prognostic subtype that can be used to differentiate between STS and LTS patients of PDAC and inform on the molecular interactions that play a role in this poor prognosis.
Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Thummalapalli Rohit , Ricciuti Biagio , Bandlamudi Chaitanya , Muldoon Daniel , Rizvi Hira , Elkrief Arielle , Luo Jia , Alessi Joao V. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Hong Lingzhi , Zhang Jianjun , Heymach John V. , Gibbons Don L. , Plodkowski Andrew J. , Ravichandran Vignesh , Donoghue Mark T.A. , Vanderbilt Chad , Ladanyi Marc , Rudin Charles M. , Kris Mark G. , Riely Gregory J. , Chaft Jamie E. , Hellmann Matthew D. , Vokes Natalie I. , Awad Mark M. , Schoenfeld Adam J. 
Published: July 2023

Abstract

Purpose:
We sought to identify features of patients with advanced non–small cell lung cancer (NSCLC) who achieve long-term response (LTR) to immune checkpoint inhibitors (ICI), and how these might differ from features predictive of short-term response (STR).

Experimental Design:
We performed a multicenter retrospective analysis of patients with advanced NSCLC treated with ICIs between 2011 and 2022. LTR and STR were defined as response ≥ 24 months and response &lt; 12 months, respectively. Tumor programmed death ligand 1 (PD-L1) expression, tumor mutational burden (TMB), next-generation sequencing (NGS), and whole-exome sequencing (WES) data were analyzed to identify characteristics enriched in patients achieving LTR compared with STR and non-LTR.

Results:
Among 3,118 patients, 8% achieved LTR and 7% achieved STR, with 5-year overall survival (OS) of 81% and 18% among LTR and STR patients, respectively. High TMB (≥50th percentile) enriched for LTR compared with STR (P = 0.001) and non-LTR (P &lt; 0.001). Whereas PD-L1 ≥ 50% enriched for LTR compared with non-LTR (P &lt; 0.001), PD-L1 ≥ 50% did not enrich for LTR compared with STR (P = 0.181). Nonsquamous histology (P = 0.040) and increasing depth of response [median best overall response (BOR) −65% vs. −46%, P &lt; 0.001] also associated with LTR compared with STR; no individual genomic alterations were uniquely enriched among LTR patients.

Conclusions:
Among patients with advanced NSCLC treated with ICIs, distinct features including high TMB, nonsquamous histology, and depth of radiographic improvement distinguish patients poised to achieve LTR compared with initial response followed by progression, whereas high PD-L1 does not.