bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial Intelligence–Based Radiotherapy Contouring and Planning to Improve Global Access to Cancer Care
Authors: Court Laurence E. , Aggarwal Ajay , Jhingran Anuja , Naidoo Komeela , Netherton Tucker , Olanrewaju Adenike , Peterson Christine , Parkes Jeannette , Simonds Hannah , Trauernicht Christoph , Zhang Lifei , Beadle Beth M. ,   Radiation Planning Assistant Consortium, Ahmad Shareen , Anderson David , Baghwala Arjig , Chan Karen , Das Prajnan , Edwards Albert , Elbanna May , Elhalawani Hesham , Elsayed Medhat , Ewongwo Agnes , Fakie Nazia , Fuller C. David , Garden Adam , Gove Matt , Guerrero-Urbano Teresa , Kaittany Njeri , Khan Mishal , Langer Joshua , Leeig Percy , Lee Becky , Lee Anna , Lee Belinda , Leech Michelle , Li Ben , Lichter Katie , Lin Lilie , Lin Stacy , Lombe Dorothy , Mallick Indranil , Maroongroge Sean , Martin Rachael , McGinnis Gwendolyn , Mezera Megan , Mohammedsaid Mustefa , Nguyen Son , Nuanjing Jenny , Phillips Tony , Prajapati Surendra , Punt Lydia , Reed Valerie , Roniger Dominique , Shaitelman Simona , Sherriff Alicia , Shiao Jay , Skinner Heath , Susan Ashely , Sutton Jordan , Syed Hamza , Thang Sandy , Thompson Juanita , Walker Gary , Wetter Julie , White Ingrid , Xu Melody , Yousif Yousif , Zhu Simeng 
Published: March 2024

PURPOSE
Increased automation has been identified as one approach to improving global cancer care. The Radiation Planning Assistant (RPA) is a web-based tool offering automated radiotherapy (RT) contouring and planning to low-resource clinics. In this study, the RPA workflow and clinical acceptability were assessed by physicians around the world.

METHODS
The RPA output for 75 cases was reviewed by at least three physicians; 31 radiation oncologists at 16 institutions in six countries on five continents reviewed RPA contours and plans for clinical acceptability using a 5-point Likert scale.

RESULTS
For cervical cancer, RPA plans using bony landmarks were scored as usable as-is in 81% (with minor edits 93%); using soft tissue contours, plans were scored as usable as-is in 79% (with minor edits 96%). For postmastectomy breast cancer, RPA plans were scored as usable as-is in 44% (with minor edits 91%). For whole-brain treatment, RPA plans were scored as usable as-is in 67% (with minor edits 99%). For head/neck cancer, the normal tissue autocontours were acceptable as-is in 89% (with minor edits 97%). The clinical target volumes (CTVs) were acceptable as-is in 40% (with minor edits 93%). The volumetric-modulated arc therapy (VMAT) plans were acceptable as-is in 87% (with minor edits 96%). For cervical cancer, the normal tissue autocontours were acceptable as-is in 92% (with minor edits 99%). The CTVs for cervical cancer were scored as acceptable as-is in 83% (with minor edits 92%). The VMAT plans for cervical cancer were acceptable as-is in 99% (with minor edits 100%).

CONCLUSION
The RPA, a web-based tool designed to improve access to high-quality RT in low-resource settings, has high rates of clinical acceptability by practicing clinicians around the world. It has significant potential for successful implementation in low-resource clinics.
Real-World Treatment Patterns and Clinical Outcomes After Platinum-Doublet Chemotherapy and Immunotherapy in Metastatic Non–Small Cell Lung Cancer: A Multiregional Chart Review in the United States, Europe, and Japan
Authors: Leal Ticiana A. , Dasgupta Anandaroop , Latremouille-Viau Dominick , Rossi Carmine , Rai Pragya , Barlesi Fabrice , Liu Stephen V. 
Published: March 2024

PURPOSE To characterize treatment patterns and real-world clinical outcomes of patients with metastatic non–small cell lung cancer (mNSCLC) who developed progression on an anti–PD-1/anti–PD-L1, herein referred to as anti–PD-(L)1, and platinum-doublet chemotherapy. METHODS Eligible oncologists/pulmonologists in the United States, Europe (France, Germany, and United Kingdom), and Japan completed electronic case report forms for patients with mNSCLC (no evidence of EGFR/ALK/ROS1 alterations). Eligible patients had disease progression on/after an anti–PD-(L)1 and platinum-doublet chemotherapy (received concurrently or sequentially), initiated a subsequent line of therapy (LOT) between 2017 and 2021, and had an Eastern Cooperative Oncology Group (ECOG) performance status 0-2 at this subsequent LOT initiation (index date). Overall survival (OS), time to treatment discontinuation (TTD), and real-world progression-free survival (rwPFS) after index were assessed using Kaplan-Meier analysis. RESULTS Overall, 160 physicians (academic, 54.4%; community, 45.6%) provided deidentified data from 487 patient charts (United States, 141; Europe, 218; Japan, 128; at mNSCLC diagnosis: median age 66 years, 64.7% male, 81.3% nonsquamous, 86.2% de novo mNSCLC; at line of interest initiation: 86.0% ECOG 0-1, 39.6% liver metastases, 18.9% brain metastases, 79.1% smoking history). The most common treatment regimens upon progression after anti–PD-(L)1/platinum-doublet chemotherapy were nonplatinum chemotherapy (50.5%), nonplatinum chemotherapy plus vascular endothelial growth factor receptor inhibitor (12.9%), and platinum-doublet chemotherapy (6.6%). Median OS was 8.8 months (squamous, 7.8 months; nonsquamous, 9.5 months). Median TTD was 4.3 months (squamous, 4.1 months; nonsquamous, 4.3 months). Median rwPFS was 5.1 months (squamous, 4.6 months; nonsquamous, 5.4 months). CONCLUSION In this multiregional, real-world analysis of pooled patient chart data, patients with mNSCLC who had disease progression after anti–PD-(L)1/platinum-doublet chemotherapy had poor clinical outcomes with various treatment regimens, demonstrating an unmet clinical need for effective options after failure on anti–PD-(L)1 and platinum-doublet chemotherapy treatments.
Prognostic and Predictive Value of Immunoscore in Stage III Colorectal Cancer: Pooled Analysis of Cases From the SCOT and IDEA-HORG Studies
Authors: Domingo Enric , Kelly Caroline , Hay Jennifer , Sansom Owen , Maka Noori , Oien Karin , Iveson Tim , Saunders Mark , Kerr Rachel , Tomlinson Ian , Edwards Joanne , Harkin Andrea , Nowak Marta , Koelzer Viktor , Easton Alistair , Boukovinas Ioannis , Moustou Eleni , Messaritakis Ippokratis , Chondrozoumaki Maria , Karagianni Michaela , Pagès Franck , Arnoux Fanny , Lautard Christelle , Lovera Yoann , Boquet Isabelle , Catteau Aurélie , Galon Jérôme ,   TransSCOT Consortium, Souglakos Ioannis , Church David N. , Church David , Domingo Enric , Edwards Joanne , Glimelius Bengt , Gogenur Ismail , Harkin Andrea , Hay Jen , Iveson Timothy , Jaeger Emma , Kelly Caroline , Kerr Rachel , Maka Noori , Morgan Hannah , Oien Karin , Orange Clare , Palles Claire , Roxburgh Campbell , Sansom Owen , Saunders Mark , Tomlinson Ian 
Published: March 2024

PURPOSE Immunoscore (IS) is prognostic in stage III colorectal cancer (CRC) and may predict benefit of duration (6 v 3 months) of adjuvant infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX) chemotherapy. We sought to determine IS prognostic and predictive value in stage-III CRC treated with adjuvant FOLFOX or oral capecitabine and infusional oxaliplatin (CAPOX) in the SCOT and IDEA-HORG trials. METHODS Three thousand sixty-one cases had tumor samples, of which 2,643 (1,792 CAPOX) were eligible for IS testing. Predefined cutoffs (IS-Low and IS-High) were used to classify cases into two groups for analysis of disease-free survival (3-year DFS) and multivariable-adjusted hazard ratios (mvHRs) by Cox regression. RESULTS IS was determined in 2,608 (99.5%) eligible cases, with 877 (33.7%) samples classified as IS-Low. IS-Low tumors were more commonly high-risk (T4 and/or N2; 52.9% IS-Low v 42.2% IS-High; P < .001) and in younger patients ( P = .024). Patients with IS-Low tumors had significantly shorter DFS in the CAPOX, FOLFOX, and combined cohorts (mvHR, 1.52 [95% CI, 1.28 to 1.82]; mvHR, 1.58 [95% CI, 1.22 to 2.04]; and mvHR, 1.55 [95% CI, 1.34 to 1.79], respectively; P < .001 all comparisons), regardless of sex, BMI, clinical risk group, tumor location, treatment duration, or chemotherapy regimen. IS prognostic value was greater in younger (≤65 years) than older (>65 years) patients in the CAPOX cohort (mvHR, 1.92 [95% CI, 1.50 to 2.46] v 1.28 [95% CI, 1.01 to 1.63], PINTERACTION = .026), and in DNA mismatch repair proficient than deficient mismatch repair disease (mvHR, 1.68 [95% CI, 1.41 to 2.00] v 0.67 [95% CI, 0.30 to 1.49], PINTERACTION = .03), although these exploratory analyses were uncorrected for multiple testing. Adding IS to a model containing all clinical variables significantly improved prediction of DFS (likelihood ratio test, P < .001) regardless of MMR status. CONCLUSION IS is prognostic in stage III CRC treated with FOLFOX or CAPOX, including within clinically relevant tumor subgroups. Possible variation in IS prognostic value by age and MMR status, and prediction of benefit from extended adjuvant therapy merit validation.
Efficacy of Poly(ADP-ribose) Polymerase Inhibitors by Individual Genes in Homologous Recombination Repair Gene-Mutated Metastatic Castration-Resistant Prostate Cancer: A US Food and Drug Administration Pooled Analysis
Authors: Fallah Jaleh , Xu Jianjin , Weinstock Chana , Gao Xin , Heiss Brian L. , Maguire William F. , Chang Elaine , Agrawal Sundeep , Tang Shenghui , Amiri-Kordestani Laleh , Pazdur Richard , Kluetz Paul G. , Suzman Daniel L. 
Published: March 2024

PURPOSE We performed a pooled analysis of multiple trials of poly(ADP-ribose) polymerase inhibitors (PARPi) in metastatic castration-resistant prostate cancer (mCRPC) to investigate the efficacy of PARPi in each individual homologous recombination repair (HRR) mutated (m) gene. PATIENTS AND METHODS We pooled patient-level data from trials of PARPi in mCRPC that reported mutation status in individual HRR genes. Any HRR gene with available data across all the randomized trials of PARPi in first-line mCRPC was selected. The hazard ratios (HRs; 95% CI) for radiographic progression-free survival (rPFS; by blinded independent review) and overall survival (OS) of a PARPi plus an androgen receptor pathway inhibitor (ARPI) relative to placebo plus an ARPI in the pool of three randomized trials in first-line mCRPC were calculated using Kaplan-Meier estimates and a Cox proportional hazards model. RESULTS In ATMm (N = 268), rPFS HR was 1.05 (0.74 to 1.49) and OS HR was 1.18 (0.82 to 1.71). In BRCA1m (N = 64), rPFS HR was 0.51 (0.23 to 1.1) and OS HR was 0.74 (0.34 to 1.61). In BRCA2m (N = 422), rPFS HR was 0.31 (0.23 to 0.42) and OS HR was 0.66 (0.49 to 0.89). In CDK12m (N = 164), rPFS HR was 0.50 (0.32 to 0.80) and OS HR was 0.63 (0.39 to 0.99). In CHEK2m (N = 172), rPFS HR was 1.06 (0.67 to 1.66) and OS HR was 1.53 (0.95 to 2.46). In PALB2m (N = 41) rPFS HR was 0.52 (0.23 to 1.17) and OS HR was 0.78 (0.34 to 1.8). CONCLUSION In this pooled analysis, benefit from PARPi appeared greatest for patients with BRCA1m, BRCA2m, CDK12m, and PALB2m. Given limitations of this exploratory analysis, the apparent lack of benefit from PARPi in patients with CHEK2m or ATMm should be further explored in future clinical trials.
Comprehensive Analysis Identifies Variability in PI3K Pathway Alterations in Triple-Negative Breast Cancer Subtypes
Authors: Basho Reva K. , Zhao Li , White Jason B. , Huo Lei , Bassett Roland L. , Mittendorf Elizabeth A. , Thompson Alastair , Litton Jennifer K. , Ueno Naoto , Arun Banu , Lim Bora , Valero Vicente , Tripathy Debu , Zhang Jianhua , Adrada Beatriz E. , Santiago Lumarie , Ravenberg Elizabeth , Seth Sahil , Yam Clinton , Moulder Stacy L. , Damodaran Senthil 
Published: March 2024

PURPOSE The PI3K pathway is frequently altered in triple-negative breast cancer (TNBC). Limited cell line and human data suggest that TNBC tumors characterized as mesenchymal (M) and luminal androgen receptor (LAR) subtypes have increased incidence of alterations in the PI3K pathway. The impact of PI3K pathway alterations across TNBC subtypes is poorly understood. METHODS Pretreatment tumor was evaluated from operable TNBC patients enrolled on a clinical trial of neoadjuvant therapy (NAT; A Robust TNBC Evaluation fraMework to Improve Survival [ClinicalTrials.gov identifier: NCT02276443 ]). Tumors were characterized into seven TNBC subtypes per Pietenpol criteria (basal-like 1, basal-like 2, immunomodulatory, M, mesenchymal stem-like, LAR, and unstable). Using whole-exome sequencing, RNA sequencing, and immunohistochemistry for PTEN, alterations were identified in 32 genes known to activate the PI3K pathway. Alterations in each subtype were associated with pathologic response to NAT. RESULTS In evaluated patients (N = 177), there was a significant difference in the incidence of PI3K pathway alterations across TNBC subtypes ( P < .01). The highest incidence of alterations was seen in LAR (81%), BL2 (79%), and M (62%) subtypes. The odds ratio for pathologic complete response (pCR) in the presence of PIK3CA mutation, PTEN mutation, and/or PTEN loss was highest in the LAR subtype and lowest in the M subtype, but these findings did not reach statistical significance. Presence of PIK3CA mutation was associated with pCR in the LAR subtype ( P = .02). CONCLUSION PI3K pathway alteration can affect response to NAT in TNBC, and targeted agents may improve outcomes, particularly in patients with M and LAR TNBC.
Bayesian Forecasting of Mortality Rates for Small Areas Using Spatiotemporal Models
Authors: Goes Julius 
Published: March 2024

Abstract
Estimation and prediction of subnational mortality rates for small areas are essential planning tools for studying health inequalities. Standard methods do not perform well when data are noisy, a typical behavior of subnational datasets. Thus, reliable estimates are difficult to obtain. I present a Bayesian hierarchical model framework for prediction of mortality rates at a small or subnational level. By combining ideas from demography and epidemiology, the classical mortality modeling framework is extended to include an additional spatial component capturing regional heterogeneity. Information is pooled across neighboring regions and smoothed over time and age. To make predictions more robust and address the issue of model selection, a Bayesian version of stacking is considered using leave-future-out validation. I apply this method to forecast mortality rates for 96 regions in Bavaria, Germany, disaggregated by age and sex. Uncertainty surrounding the forecasts is provided in terms of prediction intervals. Using posterior predictive checks, I show that the models capture the essential features and are suitable to forecast the data at hand. On held-out data, my predictions outperform those of standard models lacking a regional component.
Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data
Authors: Furuya Shiro , Zheng Fengyi , Lu Qiongshi , Fletcher Jason M. 
Published: March 2024

Abstract
Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation (“scarring”) but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26–74%; effects on other life course outcomes also vary across selection correction methods.
Impact of Procedure Time on First Pass Effect in Mechanical Thrombectomy for Anterior Circulation Acute Ischemic Stroke
Authors: Koo Andrew B. , Reeves Benjamin C. , Renedo Daniela , Maier Ilko L. , Al Kasab Sami , Jabbour Pascal , Kim Joon-Tae , Wolfe Stacey Q. , Rai Ansaar , Starke Robert M. , Psychogios Marios-Nikos , Shaban Amir , Arthur Adam , Yoshimura Shinichi , Cuellar Hugo , Grossberg Jonathan A. , Alawieh Ali , Romano Daniele G. , Tanweer Omar , Mascitelli Justin , Fragata Isabel , Polifka Adam , Osbun Joshua , Crosa Roberto , Park Min S. , Levitt Michael R. , Brinjikji Waleed , Moss Mark , Dumont Travis , Williamson Richard , Navia Pedro , Kan Peter , Spiotta Alejandro M. , Sheth Kevin N. , de Havenon Adam , Matouk Charles C. 
Published: March 2024

BACKGROUND AND OBJECTIVES:
First pass effect (FPE) is a metric increasingly used to determine the success of mechanical thrombectomy (MT) procedures. However, few studies have investigated whether the duration of the procedure can modify the clinical benefit of FPE. We sought to determine whether FPE after MT for anterior circulation large vessel occlusion acute ischemic stroke is modified by procedural time (PT).

METHODS:
A multicenter, international data set was retrospectively analyzed for anterior circulation large vessel occlusion acute ischemic stroke treated by MT who achieved excellent reperfusion (thrombolysis in cerebral infarction 2c/3). The primary outcome was good functional outcome defined by 90-day modified Rankin scale scores of 0–2. The primary study exposure was first pass success (FPS, 1 pass vs ≥2 passes) and the secondary exposure was PT. We fit-adjusted logistic regression models and used marginal effects to assess the interaction between PT (≤30 vs >30 minutes) and FPS, adjusting for potential confounders including time from stroke presentation.

RESULTS:
A total of 1310 patients had excellent reperfusion. These patients were divided into 2 cohorts based on PT: ≤30 minutes (777 patients, 59.3%) and >30 minutes (533 patients, 40.7%). Good functional outcome was observed in 658 patients (50.2%). The interaction term between FPS and PT was significant (P = .018). Individuals with FPS in ≤30 minutes had 11.5% higher adjusted predicted probability of good outcome compared with those who required ≥2 passes (58.2% vs 46.7%, P = .001). However, there was no significant difference in the adjusted predicted probability of good outcome in individuals with PT >30 minutes. This relationship appeared identical in models with PT treated as a continuous variable.

CONCLUSION:
FPE is modified by PT, with the added clinical benefit lost in longer procedures greater than 30 minutes. A comprehensive metric for MT procedures, namely, FPE30, may better represent the ideal of fast, complete reperfusion with a single pass of a thrombectomy device.
Clearance rates of sand-burrowed and laterally pressed unburrowed Pismo clam Tivela stultorum (Mawe 1823) in a laboratory open-flow system
Authors: Zepeda Enrique , Garcia-Esquivel Zaul , González-Gómez Marco A. , Díaz Fernando , Castellanos-Martinez Sheila 
Published: March 2024

ABSTRACT
Pismo clam extraction is currently banned in Mexico to help the recovery of natural populations. Thus, the primary objective of this study was to gain insight on its basic biology and husbandry protocols. Growth and clearance rate (CR) of sand-burrowed and sediment-free, laterally pressed adult Pismo clams were quantified in the laboratory as a function of burrowing condition, flow, temperature, and microalgal concentration using open-flow chambers. After 40 days, clams remained healthy regardless of burrowing condition and showed a hyperbolic CR response pattern to increased flow, with CR directly proportional to flows lower than 1000 ml min−1. Maximal asymptotic CR values (300 to 400 ml min−1 org−1) were observed from 1000 to 2000 ml min−1. No significant CR differences were observed between burrowed and laterally pressed clams, yet microalgal concentration effects were detected, with constant maximal CRs of ∼250 ml min−1 in the range of 50 to 200 cells µl−1 and decline at higher concentrations. Maintenance protocols of laterally pressed organisms were validated in the laboratory with both weight and CR data. To our knowledge, this is the first study providing whole-body physiological data translated into effective husbandry protocols for Pismo clams. This approach represents a fresh perspective to traditional research areas, opening the possibility for continued experimentation under controlled conditions.
Students’ perception of digital media for English teaching learning
Authors: Sunjayanto Masykuri Edi , Basuki Basuki 
Published: March 2024

This research was to find out the students’ perception towards digital media for ELT in Purworejo Muhammadiyah University. This research generally answered the question: how is students’ perception towards digital media for ELT in Purworejo Muhammadiyah University. The researchers collected the data through a questionnaire. There were twenty-seven of fourth semester students at Purworejo Muhammadiyah University participated in this research. This research used case-study design. Descriptive analysis was used to analyze the data from questionnaire. The result of this research showed that the students had high perception on digital media as an English reading material. The mean score of the questionnaire was 3.55 which can be interpret in the “High” category. Besides there were some difficulties faced by students and teacher in using digital media, such as limited mobile phone facilities, limited internet packages, and poor signal problems.
Using word cross game to impprove students’ vocabulary learning at SMK Muhammadiyah 1 Yogyakarta
Authors: Nugraheni Hilda Andira , Rokhyati Umi 
Published: March 2024

This research was conducted at SMK Muhammadiyah 1 Yogyakarta. Based on the experience during the teaching practicum, it was identified that students still got problem with their vocabulary. It caused them afraid to speak English and feeling embarrassed if the word or sentence they conveyed was wrong. They also have little effort to read or look up the dictionary to know the new words. In addition, students easily got bored when learning in a conventional way. There is a problem in learning vocabulary. Based on those problems, classroom action research was conducted with two objectives: to describe the increase of students’ interest and vocabulary mastery taught using the word cross game. The subject of the research was a class consisting of 21 students. To collect the data, observation, test, and interview were done. Mixed methods were used to analyzed the data. The research was conducted in two cycles. Each cycle followed the steps of planning, acting, observing, and reflecting. The research findings revealed that the students’ interest in learning increased. They stated that learning using cross word games is fun and exciting. The other finding revealed the increase in vocabulary mastery. It was shown by the increase in score from 54.6 in post test of cycle one to 79.14 in the post test of cycle 2. Therefore, it can be concluded that the use of word cross game improved the students’ vocabulary learning.