bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in surgical mortality during COVID-19 pandemic by patients’ race, ethnicity and socioeconomic status among US older adults: a quasi-experimental event study model
Authors: Blegen Mariah B , Rook Jordan M , Jackson Nicholas J , Maggard-Gibbons Melinda , Li Ruixin , Russell Marcia M , Russell Tara A , de Virgilio Christian , Tsugawa Yusuke
Published: February 2024

Objectives

To examine changes in the 30-day surgical mortality rate after common surgical procedures during the COVID-19 pandemic and investigate whether its impact varies by urgency of surgery or patient race, ethnicity and socioeconomic status.

Design

We used a quasi-experimental event study design to examine the effect of the COVID-19 pandemic on surgical mortality rate, using patients who received the same procedure in the prepandemic years (2016–2019) as the control, adjusting for patient characteristics and hospital fixed effects (effectively comparing patients treated at the same hospital). We conducted stratified analyses by procedure urgency, patient race, ethnicity and socioeconomic status (dual-Medicaid status and median household income).

Setting

Acute care hospitals in the USA.

Participants

Medicare fee-for-service beneficiaries aged 65–99 years who underwent one of 14 common surgical procedures from 1 January 2016 to 31 December 2020.

Main outcome measures

30-day postoperative mortality rate.

Results

Our sample included 3 620 689 patients. Surgical mortality was higher during the pandemic, with peak mortality observed in April 2020 (adjusted risk difference (aRD) +0.95 percentage points (pp); 95% CI +0.76 to +1.26 pp; p<0.001) and mortality remained elevated through 2020. The effect of the pandemic on mortality was larger for non-elective (vs elective) procedures (April 2020: aRD +0.44 pp (+0.16 to +0.72 pp); p=0.002 for elective; aRD +1.65 pp (+1.00, +2.30 pp); p<0.001 for non-elective). We found no evidence that the pandemic mortality varied by patients’ race and ethnicity (p for interaction=0.29), or socioeconomic status (p for interaction=0.49).

Conclusions

30-day surgical mortality during the COVID-19 pandemic peaked in April 2020 and remained elevated until the end of the year. The influence of the pandemic on surgical mortality did not vary by patient race and ethnicity or socioeconomic status, indicating that once patients were able to access care and undergo surgery, surgical mortality was similar across groups.
Patient experiences of undergoing abortion with and without an ultrasound scan in Britain
Authors: Blaylock Rebecca , Lohr Patricia A , Hoggart Lesley , Lowe Pam
Published: February 2024

Background

Routine ultrasound scanning to determine gestational age and pregnancy location has long been part of pre-abortion assessment in Britain, despite not being legally required or recommended in national clinical guidelines. To support implementation of fully telemedical abortion care (implemented in Britain in April 2020), the Royal College of Obstetricians and Gynaecologists (RCOG) issued clinical guidance for an ‘as-indicated’ approach to pre-abortion ultrasound, removing the need for a clinic visit. We aimed to understand patient experiences of ultrasound in abortion care by conducting a qualitative study with individuals who had abortions with and without an ultrasound scan.

Methods

Between November 2021 and July 2022, we recruited patients who had a medical abortion at home without a pre-procedure ultrasound at 69 days’ gestation or less at British Pregnancy Advisory Service (BPAS), and also had at least one other abortion with an ultrasound from any provider in Britain. We conducted interviews using a semi-structured interview guide to explore our participants’ experiences and conducted reflexive thematic analysis.

Results

We recruited 24 participants and included 19 interviews in our analysis. We developed three themes from our data. These were ‘Ultrasound scans and their relationship with autonomy and decision-making’, ‘Intrusive and out of place: the ultrasound as an inappropriate technology’ and ‘Towards preference-centred, quality care’.

Conclusions

Further research and user-testing of strategies to improve the scan experience should be undertaken. Patient testimonies on the negative impact of ultrasound scans in abortion care should reassure providers that omitting them according to patient preference is a positive step towards providing patient-centred care.
Fermionic steering is not nonlocal in the background of dilaton black hole
Authors: Wu Shu-Min , Li Jin-Xuan , Jiang Xiao-Ying , Teng Xiao-Wei , Huang Xiao-Li , Lu Jianbo
Published: February 2024

We study the redistribution of the fermionic steering and the relation among fermionic Bell nonlocality, steering, and entanglement in the background of the Garfinkle–Horowitz–Strominger dilaton black hole. We analyze the meaning of the fermionic steering in terms of the Bell inequality in curved spacetime. We find that the fermionic steering, which is previously found to survive in the extreme dilaton black hole, cannot be considered to be nonlocal. We also find that the dilaton gravity can redistribute the fermionic steering, but cannot redistribute Bell nonlocality, which means that the physically inaccessible steering is also not nonlocal. Unlike the inaccessible entanglement, the inaccessible steering may increase non-monotonically with the dilaton. Furthermore, we obtain some monogamy relations between the fermionic steering and entanglement in dilaton spacetime. In addition, we show the difference between the fermionic and bosonic steering in curved spacetime.
cuFasterTucker: A Stochastic Optimization Strategy for Parallel Sparse FastTucker Decomposition on GPU Platform
Authors: Li Zixuan , Qin Yunchuan , Xiao Qi , Yang Wangdong , Li Kenli
Published: February 2024

The amount of scientific data is currently growing at an unprecedented pace, with tensors being a common form of data that display high-order, high-dimensional, and sparse features. While tensor-based analysis methods are effective, the vast increase in data size has made processing the original tensor infeasible. Tensor decomposition offers a solution by decomposing the tensor into multiple low-rank matrices or tensors that can be efficiently utilized by tensor-based analysis methods. One such algorithm is the Tucker decomposition, which decomposes an
N
-order tensor into
N
low-rank factor matrices and a low-rank core tensor. However, many Tucker decomposition techniques generate large intermediate variables and require significant computational resources, rendering them inadequate for processing high-order and high-dimensional tensors. This article introduces FasterTucker decomposition, a novel approach to tensor decomposition that builds on the FastTucker decomposition, a variant of the Tucker decomposition. We propose an efficient parallel FasterTucker decomposition algorithm, called cuFasterTucker, designed to run on a GPU platform. Our algorithm has low storage and computational requirements and provides an effective solution for high-order and high-dimensional sparse tensor decomposition. Compared to state-of-the-art algorithms, our approach achieves a speedup of approximately 7 to 23 times.
Handling Imbalance and Limited Data in Thyroid Ultrasound and Diabetic Retinopathy Datasets Using Discrete Levy Flights Grey Wolf Optimizer Based Random Forest for Robust Medical Data Classification
Authors: Aswal Shobha , Ahuja Neelu Jyothi , Mehra Ritika
Published: February 2024

In the field of disease diagnosis, medical image classification faces an inherent challenge due to various factors involving data imbalance, image quality variability, annotation variability, and limited data availability and data representativeness. Such challenges affect the algorithm's classification ability on the medical images in an adverse way, which leads to biased model outcomes and inaccurate interpretations. In this paper, a novel Discrete Levy Flight Grey Wolf Optimizer (DLFGWO) is combined with the Random Forest (RF) classifier to address the above limitations on the biomedical datasets and to achieve better classification rate. The DLFGWO-RF resolves the image quality variability in ultrasound images and limits the inaccuracies on classification using RF by handling the incomplete and noisy data. The sheer focus on the majority class may lead to unequal distribution of classes and thus leads to data imbalance. The DLFGWO balances such distribution by leveraging grey wolves and its exploration and exploitation capabilities are improved using Discrete Levy Flight (DLF). It further optimizes the classifier's performance to achieve balanced classification rate. DLFGWO-RF is designed to perform classification even on limited datasets, thereby the requirement of numerous expert annotations can thus be reduced. In diabetic retinopathy grading, the DLFGWO-RF reduces disagreements in annotation variability using subjective interpretations. However, the representativeness of the diabetic retinopathy dataset fails to capture the entire population diversity, which limits the generalization ability of the proposed DLFGWO-RF. Thus, fine-tuning of RF can robustly adapt to the subgroups in the dataset, enhancing its overall performance. The experiments are conducted on two widely used medical image datasets to test the efficacy of the model. The experimental results show that the DLFGWO-RF classifier achieves improved classification accuracy between 90-95%, which outperforms the existing techniques for various imbalanced datasets.
Hybrid Quantum-classical Search Algorithms
Authors: Rosmanis Ansis
Published: February 2024

Search is one of the most commonly used primitives in quantum algorithm design. It is known that quadratic speedups provided by Grover’s algorithm are optimal, and no faster quantum algorithms for Search exist. While it is known that at least some quantum computation is required to achieve these speedups, the existing bounds do not rule out the possibility of an equally fast hybrid quantum-classical algorithm where most of the computation is classical. In this work, we study such hybrid algorithms, and we show that classical computation, unless it by itself can solve the Search problem, cannot assist quantum computation. In addition, we generalize this result to algorithms with subconstant success probabilities.
CASTNet: A Context-Aware, Spatio-Temporal Dynamic Motion Prediction Ensemble for Autonomous Driving
Authors: Mortlock Trier , Malawade Arnav , Tsujio Kohei , Al Faruque Mohammad
Published: February 2024

Autonomous vehicles are cyber-physical systems that combine embedded computing and deep learning with physical systems to perceive the world, predict future states, and safely control the vehicle through changing environments. The ability of an autonomous vehicle to accurately predict the motion of other road users across a wide range of diverse scenarios is critical for both motion planning and safety. However, existing motion prediction methods do not explicitly model contextual information about the environment, which can cause significant variations in performance across diverse driving scenarios. To address this limitation, we propose
CASTNet
: a dynamic, context-aware approach for motion prediction that (i) identifies the current driving context using a spatio-temporal model, (ii) adapts an ensemble of motion prediction models to fit the current context, and (iii) applies novel trajectory fusion methods to combine predictions output by the ensemble. This approach enables CASTNet to improve robustness by minimizing motion prediction error across diverse driving scenarios. CASTNet is highly modular and can be used with various existing image processing backbones and motion predictors. We demonstrate how CASTNet can improve both CNN-based and graph-learning-based motion prediction approaches and conduct ablation studies on the performance, latency, and model size for various ensemble architecture choices. In addition, we propose and evaluate several attention-based spatio-temporal models for context identification and ensemble selection. We also propose a modular trajectory fusion algorithm that effectively filters, clusters, and fuses the predicted trajectories output by the ensemble. On the nuScenes dataset, our approach demonstrates more robust and consistent performance across diverse, real-world driving contexts than state-of-the-art techniques.
Examining the Effect of Combined Biochar and Lime Rates on Selected Soil Physicochemical Properties of Acid Soils in Gimbi District, Western Ethiopia
Authors: Abeba Kenea Solomon , Abera Goshu Tolera , Chimdessa Kinati
Published: February 2024

The physicochemical properties of Western Ethiopian soils were negatively threatened with continuous cultivation crop lands. Soil amendments with biochar and lime facilitate and improve soil physicochemical properties directly and indirectly and enhance crop productivity. A field experiment was conducted in Gimbi District, Western Ethiopia, to examine the effects of combined coffee husk biochar (CHB) and soil test value-based lime (STV) rate application on physicochemical properties of acid soils. The trial included eight treatments, including control, 100% STV, 10 ton of CHB, and CHB + STV rates at 10 ton + 75%, 10 ton + 50%, 7.5 ton + 75%, 7.5 ton + 50%, and 5 ton + 75% ha−1on two farm fields. The fields were laid out in RCBD with three replications. The treatments had substantial effects on P<0.05) on the soil’s physicochemical characteristics. The application of biochar and lime in Farms-1 and 2 reduced soil BD from 1.21 and 1.41 g·cm−3 to 1.15 and 1.12 to 0.90 and 0.97 g·cm−3, respectively. The soil pH level was increased from 5.10 to a range of 5.58 to 6.11 in Farm-1, and in Farm-2, from 4.64 to a range of 4.64 to 6.22 levels. The application of 10 ton of CHB + 75% of STV in Farms-1 and 2 resulted in the highest SOC of 7.44% and 7.68%, respectively. The application of 10 ton of CHB + 75% of STV in Farms-1 and 2 resulted in 4.86 mg·kg−1 and 6.96 mg·kg−1 available P, respectively. Available P was positively correlated with pH (0.62), SOC (0.63), and CEC (0.66). Exchangeable acidity was decreased from 4.64 cmol(+)kg−1 to a range from 3.19 to 0.98 cmol(+)kg−1 in Farm-1 and from 5.00 cmol(+)kg−1 to a range from 3.38 to 1.10 cmol(+)kg−1 in Farm-2. Therefore, amending the strongly acidic to very strongly acidic soil with a combined CHB (7.5 to 10 ton ha−1) and STV (50 to 75% ha−1) rates had improved the soil physicochemical properties of agricultural lands. To make a firm conclusion, research on soil analysis after crop harvest and economic benefit is required.
Sporadic Pemphigus Foliaceus in a 3-Year-Old Vietnamese Girl: A Case Report and Literature Review
Authors: Nguyen Trinh Thi Diem , Chau Trinh Ngoc To , Doan Vo Phuong Thi , Nguyen Hao Trong
Published: February 2024

Pemphigus foliaceus is an uncommon autoimmune intraepidermal blistering disease characterized by immunoglobulin (Ig) G autoantibodies that attack desmoglein-1 in the epidermis. There are two predominant forms of pemphigus foliaceus, sporadic and endemic. Sporadic pemphigus foliaceus is known to be more prevalent in middle-aged and elderly people and to be extremely rare in children. Less than 40 nonendemic pediatric pemphigus foliaceus cases have been documented in the literature. This report documents a case of sporadic pemphigus foliaceus in a 3-year-old Vietnamese girl who presented with generalized scaling and crusted erosions over the body.
Figure S3 from PD-1 Expression on Intratumoral Regulatory T Cells Is Associated with Lack of Benefit from Anti–PD-1 Therapy in Metastatic Clear-Cell Renal Cell Carcinoma Patients
Authors: Denize Thomas , Jegede Opeyemi A. , Matar Sayed , El Ahmar Nourhan , West Destiny J. , Walton Emily , Bagheri Aseman Sheshdeh , Savla Varunika , Nabil Laimon Yasmin , Gupta Saurabh , Vemula Sai Vikram , Braun David A. , Burke Kelly P. , Catalano Paul J. , Freeman Gordon J. , Motzer Robert J. , Atkins Michael B. , McDermott David F. , Sharpe Arlene H. , Choueiri Toni K. , Signoretti Sabina
Published: February 2024

Figure S3
Figure S1 from PD-1 Expression on Intratumoral Regulatory T Cells Is Associated with Lack of Benefit from Anti–PD-1 Therapy in Metastatic Clear-Cell Renal Cell Carcinoma Patients
Authors: Denize Thomas , Jegede Opeyemi A. , Matar Sayed , El Ahmar Nourhan , West Destiny J. , Walton Emily , Bagheri Aseman Sheshdeh , Savla Varunika , Nabil Laimon Yasmin , Gupta Saurabh , Vemula Sai Vikram , Braun David A. , Burke Kelly P. , Catalano Paul J. , Freeman Gordon J. , Motzer Robert J. , Atkins Michael B. , McDermott David F. , Sharpe Arlene H. , Choueiri Toni K. , Signoretti Sabina
Published: February 2024

Figure S1
Supplementary Data 2 from Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types
Authors: Kasi Pashtoon M. , Lee Jessica K. , Pasquina Lincoln W. , Decker Brennan , Vanden Borre Pierre , Pavlick Dean C. , Allen Justin M. , Parachoniak Christine , Quintanilha Julia C. F. , Graf Ryon P. , Schrock Alexa B. , Oxnard Geoffrey R. , Lovly Christine M. , Tukachinsky Hanna , Subbiah Vivek
Published: February 2024

Supplementary Tables
Supplementary Table S4 from Neoadjuvant Trebananib plus Paclitaxel-based Chemotherapy for Stage II/III Breast Cancer in the Adaptively Randomized I-SPY2 Trial—Efficacy and Biomarker Discovery
Authors: Albain Kathy S. , Yau Christina , Petricoin Emanuel F. , Wolf Denise M. , Lang Julie E. , Chien A. Jo , Haddad Tufia , Forero-Torres Andres , Wallace Anne M. , Kaplan Henry , Pusztai Lajos , Euhus David , Nanda Rita , Elias Anthony D. , Clark Amy S. , Godellas Constantine , Boughey Judy C. , Isaacs Claudine , Tripathy Debu , Lu Janice , Yung Rachel L. , Gallagher Rosa I. , Wulfkuhle Julia D. , Brown-Swigart Lamorna , Krings Gregor , Chen Yunn Yi , Potter David A. , Stringer-Reasor Erica , Blair Sarah , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Buxton Meredith , Clennell Julia L. , Sanil Ashish , Berry Scott , Asare Adam L. , Matthews Jeffrey B. , DeMichele Angela M. , Hylton Nola M. , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Symmans W. Fraser , van't Veer Laura J. , Yee Douglas , Berry Donald A. , Esserman Laura J.
Published: February 2024

Trebananib vs Control pCR–Biomarker Associations
Supplementary Table S2 from Neoadjuvant Trebananib plus Paclitaxel-based Chemotherapy for Stage II/III Breast Cancer in the Adaptively Randomized I-SPY2 Trial—Efficacy and Biomarker Discovery
Authors: Albain Kathy S. , Yau Christina , Petricoin Emanuel F. , Wolf Denise M. , Lang Julie E. , Chien A. Jo , Haddad Tufia , Forero-Torres Andres , Wallace Anne M. , Kaplan Henry , Pusztai Lajos , Euhus David , Nanda Rita , Elias Anthony D. , Clark Amy S. , Godellas Constantine , Boughey Judy C. , Isaacs Claudine , Tripathy Debu , Lu Janice , Yung Rachel L. , Gallagher Rosa I. , Wulfkuhle Julia D. , Brown-Swigart Lamorna , Krings Gregor , Chen Yunn Yi , Potter David A. , Stringer-Reasor Erica , Blair Sarah , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Buxton Meredith , Clennell Julia L. , Sanil Ashish , Berry Scott , Asare Adam L. , Matthews Jeffrey B. , DeMichele Angela M. , Hylton Nola M. , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Symmans W. Fraser , van't Veer Laura J. , Yee Douglas , Berry Donald A. , Esserman Laura J.
Published: February 2024

RPPA endpoints and genes/signatures involved in TIE2 signaling that were studied
Supplementary Table S4 from Phase I/II Study of the WEE1 Inhibitor Adavosertib (AZD1775) in Combination with Carboplatin in Children with Advanced Malignancies: Arm C of the AcSé-ESMART Trial
Authors: Gatz Susanne A. , Harttrampf Anne C. , Brard Caroline , Bautista Francisco , André Nicolas , Abbou Samuel , Rubino Jonathan , Rondof Windy , Deloger Marc , Rübsam Marc , Marshall Lynley V. , Hübschmann Daniel , Nebchi Souad , Aerts Isabelle , Thebaud Estelle , De Carli Emilie , Defachelles Anne Sophie , Paoletti Xavier , Godin Robert , Miah Kowser , Mortimer Peter G.S. , Vassal Gilles , Geoerger Birgit
Published: February 2024

Summary of WEE1 inhibitor adavosertib clinical trials
Supplementary Table 2 from Tumor-Specific Activity of Precision Medicines in the NCI-MATCH Trial
Authors: Zhou Ivvone , Plana Deborah , Palmer Adam C.
Published: February 2024

Source Data for Figure 1 and Figure 2.
Supplementary Figure S1 from TROP2 Is Associated with Primary Resistance to Immune Checkpoint Inhibition in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Bessede Alban , Peyraud Florent , Besse Benjamin , Cousin Sophie , Cabart Mathilde , Chomy François , Rey Christophe , Lara Oren , Odin Ophélie , Nafia Imane , Vanhersecke Lucile , Barlesi Fabrice , Guégan Jean-Philippe , Italiano Antoine
Published: February 2024

Supplementary Figure 1. TACSTD2 gene expression predicts response to IO independently of PD-L1 status
Supplementary Figure S7 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: February 2024

Subgroup analysis of confirmed ORR by tTMB for (A) durvalumab plus tremelimumab plus EP versus EP and (B) durvalumab plus EP versus EP. In each panel, the shaded band shows the confidence interval for the ITT population; circle sizes are proportional to the number of responses.
Supplementary Figure S5 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: February 2024

Kaplan-Meier analysis of OS in the ITT population and the tTMB BEP.
Supplementary Figure S2 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: February 2024

Kaplan-Meier analysis of OS in the ITT population and the PD-L1 BEP.
Supplementary Fig. S2 from Development of a Practical Nomogram for Personalized Anemia Management in Patients Treated with Ataxia Telangiectasia and Rad3-related Inhibitor Camonsertib
Authors: Rosen Ezra , Yap Timothy A. , Lee Elizabeth K. , Højgaard Martin , Mettu Niharika B. , Lheureux Stephanie , Carneiro Benedito A. , Plummer Ruth , Fretland Adrian J. , Ulanet Danielle , Xu Yi , McDougall Robin , Koehler Maria , Fontana Elisa
Published: February 2024

Supplementary Fig. S2. Absolute monocyte and reticulocyte counts rebound quickly following dose holds.
Supplementary Fig. S1 from Development of a Practical Nomogram for Personalized Anemia Management in Patients Treated with Ataxia Telangiectasia and Rad3-related Inhibitor Camonsertib
Authors: Rosen Ezra , Yap Timothy A. , Lee Elizabeth K. , Højgaard Martin , Mettu Niharika B. , Lheureux Stephanie , Carneiro Benedito A. , Plummer Ruth , Fretland Adrian J. , Ulanet Danielle , Xu Yi , McDougall Robin , Koehler Maria , Fontana Elisa
Published: February 2024

Supplementary Fig. S1. Summary of patient populations used in the analysis.
Supplementary Methods, Results, Figures 1 from Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma
Authors: Galbo Phillip M. , Madsen Anne Tranberg , Liu Yang , Peng Mou , Wei Yao , Ciesielski Michael J. , Fenstermaker Robert A. , Graff Sarah , Montagna Cristina , Segall Jeffrey E. , Sidoli Simone , Zang Xingxing , Zheng Deyou
Published: February 2024

a pdf file for supplemental methods and data
Supplementary Figure S4 from A Phase Ib Study of the DNA-PK Inhibitor Peposertib Combined with Neoadjuvant Chemoradiation in Patients with Locally Advanced Rectal Cancer
Authors: Romesser Paul B. , Capdevila Jaume , Garcia-Carbonero Rocio , Philip Tony , Fernandez Martos Carlos , Tuli Richard , Rodriguez-Gutierrez Almudena , Kuipers Mirjam , Becker Andreas , Coenen-Stass Anna , Sarholz Barbara , You Xiaoli , Miller Eric D.
Published: February 2024

. pDNA-PK/tDNA-PK ratios in PBMCs stimulated with bleomycin, pre- and post-dosing with peposertib.
Supplementary Table S1 from A Composite Decision Rule of CD8+ T-cell Density in Tumor Biopsies Predicts Efficacy in Early-stage, Immunotherapy Trials
Authors: Dejardin David , Kraxner Anton , Blank Annika , Rieder Natascha , Teichgräber Volker , Städler Nicolas , Beyer Ulrich , Gomes Bruno , Charo Jehad
Published: February 2024

List of studies
Supplementary Figure S3 from A Composite Decision Rule of CD8+ T-cell Density in Tumor Biopsies Predicts Efficacy in Early-stage, Immunotherapy Trials
Authors: Dejardin David , Kraxner Anton , Blank Annika , Rieder Natascha , Teichgräber Volker , Städler Nicolas , Beyer Ulrich , Gomes Bruno , Charo Jehad
Published: February 2024

Higher total CD8 T cell density is associated with better response in simlukafusp alfa studies.
Supplementary Fig. S1 from A Dysfunctional T-cell Gene Signature for Predicting Nonresponse to PD-1 Blockade in Non–small Cell Lung Cancer That Is Suitable for Routine Clinical Diagnostics
Authors: Hummelink Karlijn , Tissier Renaud , Bosch Linda J.W. , Krijgsman Oscar , van den Heuvel Michel M. , Theelen Willemijn S.M.E. , Damotte Diane , Goldwasser François , Leroy Karen , Smit Egbert F. , Meijer Gerrit A. , Thommen Daniela S. , Monkhorst Kim
Published: February 2024

PD-1T quantification by an algorithm-based immunohistochemical (IHC) imaging approach.
Supplementary Data 1 from A Composite Decision Rule of CD8+ T-cell Density in Tumor Biopsies Predicts Efficacy in Early-stage, Immunotherapy Trials
Authors: Dejardin David , Kraxner Anton , Blank Annika , Rieder Natascha , Teichgräber Volker , Städler Nicolas , Beyer Ulrich , Gomes Bruno , Charo Jehad
Published: February 2024

Association between overall response rate and CD8+ T cell density
Supplementary Figure S5 from Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma
Authors: Gleason Caroline E. , Dickson Mark A. , Klein (Dooley) Mary E. , Antonescu Cristina R. , Gularte-Mérida Rodrigo , Benitez Marimar , Delgado Juliana I. , Kataru Raghu P. , Tan Mark Wei Yi , Bradic Martina , Adamson Travis E. , Seier Kenneth , Richards Allison L. , Palafox Marta , Chan Eric , D'Angelo Sandra P. , Gounder Mrinal M. , Keohan Mary Louise , Kelly Ciara M. , Chi Ping , Movva Sujana , Landa Jonathan , Crago Aimee M. , Donoghue Mark T.A. , Qin Li-Xuan , Serra Violetta , Turkekul Mesruh , Barlas Afsar , Firester Daniel M. , Manova-Todorova Katia , Mehrara Babak J. , Kovatcheva Marta , Tan Nguan Soon , Singer Samuel , Tap William D. , Koff Andrew
Published: February 2024

Effect of shRNA hairpins on geroconversion when introduced into quiescent DDLStetONFDM2 cells
Supplementary Figure S3 from Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma
Authors: Gleason Caroline E. , Dickson Mark A. , Klein (Dooley) Mary E. , Antonescu Cristina R. , Gularte-Mérida Rodrigo , Benitez Marimar , Delgado Juliana I. , Kataru Raghu P. , Tan Mark Wei Yi , Bradic Martina , Adamson Travis E. , Seier Kenneth , Richards Allison L. , Palafox Marta , Chan Eric , D'Angelo Sandra P. , Gounder Mrinal M. , Keohan Mary Louise , Kelly Ciara M. , Chi Ping , Movva Sujana , Landa Jonathan , Crago Aimee M. , Donoghue Mark T.A. , Qin Li-Xuan , Serra Violetta , Turkekul Mesruh , Barlas Afsar , Firester Daniel M. , Manova-Todorova Katia , Mehrara Babak J. , Kovatcheva Marta , Tan Nguan Soon , Singer Samuel , Tap William D. , Koff Andrew
Published: February 2024

Durable quiescence can be established in LS8817tetONFMDM2 cells
Data from Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types
Authors: Kasi Pashtoon M. , Lee Jessica K. , Pasquina Lincoln W. , Decker Brennan , Vanden Borre Pierre , Pavlick Dean C. , Allen Justin M. , Parachoniak Christine , Quintanilha Julia C. F. , Graf Ryon P. , Schrock Alexa B. , Oxnard Geoffrey R. , Lovly Christine M. , Tukachinsky Hanna , Subbiah Vivek
Published: February 2024

AbstractPurpose:
Genomic rearrangements can generate potent oncogenic drivers or disrupt tumor suppressor genes. This study examines the landscape of fusions and rearrangements detected by liquid biopsy (LBx) of circulating tumor DNA (ctDNA) across different cancer types.
Experimental Design:
LBx from 53,842 patients with 66 solid tumor types were profiled using FoundationOneLiquid CDx, a hybrid-capture sequencing platform that queries 324 cancer-related genes. Tissue biopsies (TBx) profiled using FoundationOneCDx were used as a comparator.
Results:
Among all LBx, 7,377 (14%) had ≥1 pathogenic rearrangement detected. A total of 3,648 (6.8%) LBx had ≥1 gain-of-function (GOF) oncogene rearrangement, and 4,428 (8.2%) LBx had ≥1 loss-of-function rearrangement detected. Cancer types with higher prevalence of GOF rearrangements included those with canonical fusion drivers: prostate cancer (19%), cholangiocarcinoma (6.4%), bladder (5.5%), and non–small cell lung cancer (4.4%). Although the prevalence of driver rearrangements was lower in LBx than TBx overall, the frequency of detection was comparable in LBx with a tumor fraction (TF) ≥1%. Rearrangements in FGFR2, BRAF, RET, and ALK, were detected across cancer types, but tended to be clonal variants in some cancer types and potential acquired resistance variants in others.
Conclusions:
In contrast to some prior literature, this study reports detection of a wide variety of rearrangements in ctDNA. The prevalence of driver rearrangements in tissue and LBx was comparable when TF ≥1%. LBx presents a viable alternative when TBx is not available, and there may be less value in confirmatory testing when TF is sufficient.
Data from Neoadjuvant Trebananib plus Paclitaxel-based Chemotherapy for Stage II/III Breast Cancer in the Adaptively Randomized I-SPY2 Trial—Efficacy and Biomarker Discovery
Authors: Albain Kathy S. , Yau Christina , Petricoin Emanuel F. , Wolf Denise M. , Lang Julie E. , Chien A. Jo , Haddad Tufia , Forero-Torres Andres , Wallace Anne M. , Kaplan Henry , Pusztai Lajos , Euhus David , Nanda Rita , Elias Anthony D. , Clark Amy S. , Godellas Constantine , Boughey Judy C. , Isaacs Claudine , Tripathy Debu , Lu Janice , Yung Rachel L. , Gallagher Rosa I. , Wulfkuhle Julia D. , Brown-Swigart Lamorna , Krings Gregor , Chen Yunn Yi , Potter David A. , Stringer-Reasor Erica , Blair Sarah , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Buxton Meredith , Clennell Julia L. , Sanil Ashish , Berry Scott , Asare Adam L. , Matthews Jeffrey B. , DeMichele Angela M. , Hylton Nola M. , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Symmans W. Fraser , van't Veer Laura J. , Yee Douglas , Berry Donald A. , Esserman Laura J.
Published: February 2024

AbstractPurpose:
The neutralizing peptibody trebananib prevents angiopoietin-1 and angiopoietin-2 from binding with Tie2 receptors, inhibiting angiogenesis and proliferation. Trebananib was combined with paclitaxel±trastuzumab in the I-SPY2 breast cancer trial.
Patients and Methods:
I-SPY2, a phase II neoadjuvant trial, adaptively randomizes patients with high-risk, early-stage breast cancer to one of several experimental therapies or control based on receptor subtypes as defined by hormone receptor (HR) and HER2 status and MammaPrint risk (MP1, MP2). The primary endpoint is pathologic complete response (pCR). A therapy “graduates” if/when it achieves 85% Bayesian probability of success in a phase III trial within a given subtype. Patients received weekly paclitaxel (plus trastuzumab if HER2-positive) without (control) or with weekly intravenous trebananib, followed by doxorubicin/cyclophosphamide and surgery. Pathway-specific biomarkers were assessed for response prediction.
Results:
There were 134 participants randomized to trebananib and 133 to control. Although trebananib did not graduate in any signature [phase III probabilities: Hazard ratio (HR)-negative (78%), HR-negative/HER2-positive (74%), HR-negative/HER2-negative (77%), and MP2 (79%)], it demonstrated high probability of superior pCR rates over control (92%–99%) among these subtypes. Trebananib improved 3-year event-free survival (HR 0.67), with no significant increase in adverse events. Activation levels of the Tie2 receptor and downstream signaling partners predicted trebananib response in HER2-positive disease; high expression of a CD8 T-cell gene signature predicted response in HR-negative/HER2-negative disease.
Conclusions:
The angiopoietin (Ang)/Tie2 axis inhibitor trebananib combined with standard neoadjuvant therapy increased estimated pCR rates across HR-negative and MP2 subtypes, with probabilities of superiority >90%. Further study of Ang/Tie2 receptor axis inhibitors in validated, biomarker-predicted sensitive subtypes is warranted.
Data from Integrative Multi-omics Analysis Reveals Different Metabolic Phenotypes Based on Molecular Characteristics in Thyroid Cancer
Authors: Kim Yoo Hyung , Yoon Sang Jun , Kim Mina , Kim Hwan Hee , Song Young Shin , Jung Jin Woo , Han Dohyun , Cho Sun Wook , Kwon Sung Won , Park Young Joo
Published: February 2024

AbstractPurpose:
Thyroid cancer metabolic characteristics vary depending on the molecular subtype determined by mutational status. We aimed to investigate the molecular subtype-specific metabolic characteristics of thyroid cancers.
Experimental Design:
An integrative multi-omics analysis was conducted, incorporating transcriptomics, metabolomics, and proteomics data obtained from human tissues representing distinct molecular characteristics of thyroid cancers: BRAF-like (papillary thyroid cancer with BRAFV600E mutation; PTC-B), RAS-like (follicular thyroid cancer with RAS mutation; FTC-R), and ATC-like (anaplastic thyroid cancer with BRAFV600E or RAS mutation; ATC-B or ATC-R). To validate our findings, we employed tissue microarray of human thyroid cancer tissues and performed in vitro analyses of cancer cell phenotypes and metabolomic assays after inducing genetic knockdown.
Results:
Metabolic properties differed between differentiated thyroid cancers of PTC-B and FTC-R, but were similar in dedifferentiated thyroid cancers of ATC-B/R, regardless of their mutational status. Tricarboxylic acid (TCA) intermediates and branched-chain amino acids (BCAA) were enriched with the activation of TCA cycle only in FTC-R, whereas one-carbon metabolism and pyrimidine metabolism increased in both PTC-B and FTC-R and to a great extent in ATC-B/R. However, the protein expression levels of the BCAA transporter (SLC7A5) and a key enzyme in one-carbon metabolism (SHMT2) increased in all thyroid cancers and were particularly high in ATC-B/R. Knockdown of SLC7A5 or SHMT2 inhibited the migration and proliferation of thyroid cancer cell lines differently, depending on the mutational status.
Conclusions:
These findings define the metabolic properties of each molecular subtype of thyroid cancers and identify metabolic vulnerabilities, providing a rationale for therapies targeting its altered metabolic pathways in advanced thyroid cancer.
Data from A Phase Ib Study of the DNA-PK Inhibitor Peposertib Combined with Neoadjuvant Chemoradiation in Patients with Locally Advanced Rectal Cancer
Authors: Romesser Paul B. , Capdevila Jaume , Garcia-Carbonero Rocio , Philip Tony , Fernandez Martos Carlos , Tuli Richard , Rodriguez-Gutierrez Almudena , Kuipers Mirjam , Becker Andreas , Coenen-Stass Anna , Sarholz Barbara , You Xiaoli , Miller Eric D.
Published: February 2024

AbstractPurpose:
Peposertib—an orally administered DNA-dependent protein kinase inhibitor—has shown potent radiosensitization in preclinical models. This dose-escalation study (NCT03770689) aimed to define the maximum tolerated dose (MTD) and recommended phase II dose (RP2D) of peposertib plus capecitabine-based chemoradiotherapy (CRT) and assessed its safety and efficacy in locally advanced rectal cancer.
Patients and Methods:
Patients were treated for 5 to 5.5 weeks with 50- to 250-mg peposertib once daily, capecitabine 825 mg/m2 twice daily, and radiotherapy (RT), 5 days per week. Following clinical restaging (8 weeks after CRT completion), patients with clinical complete response (cCR) could opt for surveillance. Total mesorectal excision was recommended upon incomplete response (IR).
Results:
Nineteen patients were treated with peposertib at doses of 50 mg (n = 1), 100 mg, 150 mg, and 250 mg (n = 6 each). Dose-limiting toxicities occurred in one out of five (100 mg), one out of six (150 mg), and three out of six (250 mg) evaluable patients. Peposertib ≤150 mg once daily was tolerable in combination with CRT. After 8 weeks of treatment with peposertib and CRT, the cCR was 15.8% (n = 3). Among the three patients with cCR, two underwent surgery and had residual tumors. Among the 16 patients with IR, seven underwent surgery and had residual tumors; five of the remaining nine patients opted for consolidative chemotherapy. The combined cCR/pathologic complete response (pCR) rate was 5.3% (n = 1, 100 mg cohort).
Conclusions:
Peposertib did not improve complete response rates at tolerable dose levels. The study was closed without declaring the MTD/RP2D.
Supplementary Figure S2 from Pim Kinase Inhibitors Increase Gilteritinib Cytotoxicity in FLT3-ITD Acute Myeloid Leukemia Through GSK-3β Activation and c-Myc and Mcl-1 Proteasomal Degradation
Authors: Lee Jonelle K. , Chatterjee Aditi , Scarpa Mario , Bailey Christopher M. , Niyongere Sandrine , Singh Prerna , Mustafa Ali Moaath K. , Kapoor Shivani , Wang Yin , Silvestri Giovannino , Baer Maria R.
Published: February 2024

Concurrent Pim and FLT3 inhibitor treatment inhibits AKT, but GSK-3β activation, c-Myc and Mcl-1 downregulation and apoptosis induction are independent of AKT inhibition as well as ERK inhibition.
Silver Ion Decreases Foreign Body Reaction and Venous Neointimal Hyperplasia through the Inhibition of Interleukin-33 Expression
Authors: Zhang Cong , Wei Shunbo , Zhang Liwei , Lou Chunyang , Fang Jianbang , Liu Yuanfeng , He Hao , Li Zhuo , Li Jing’an , Bai Hualong
Published: February 2024

Introduction: Vascular prosthetic grafts are widely used in vascular surgery; however, graft infection remains a major concern. Silver-coated vascular grafts have demonstrated anti-infection properties in clinical settings; however, whether the silver irons influence foreign body reaction or neointimal hyperplasia remains unclear. Methods: Sodium alginate and hyaluronic acid (SA/HA) hydrogel patches loaded with rhodamine, with or without silver, were fabricated. Patches were implanted in the subcutaneous or abdominal cavity and inferior vena cava of rats. Samples were harvested on day 14 and examined via immunohistochemical and immunofluorescence analyses. Results: Silver hydrogel was found to decrease the foreign body reaction; after subcutaneous and abdominal cavity implantation in rats, the capsule was found to be thinner in the silver hydrogel group than in the control hydrogel group. The silver hydrogel group had fewer CD68-positive cells and proliferating cell nuclear antigen and interleukin-33 (IL-33) dual-positive cells than the control hydrogel group. Additionally, the silver hydrogel patch reduced the neointimal thickness after patch venoplasty in rats, and the number of IL-33- and IL-1β-positive cells was lower than that in the control patch. Conclusion: Silver-loaded SA/HA hydrogel patches decreased the foreign body reaction and venous neointimal hyperplasia in rats by the inhibition of IL-33 expression.
Negative Impact of Gemtuzumab Ozogamicin on CD33-Positive Early T-Cell Precursor Acute Lymphoblastic Leukemia: A Case Report
Authors: Imataki Osamu , Fujita Haruyuki , Uemura Makiko
Published: February 2024

Introduction: Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is a rare subtype of T-cell leukemia that phenotypically expresses mature T-cell markers and immature myeloid markers such as CD33. Gemtuzumab ozogamicin (GO) is a novel agent for the CD33 molecular targeting antibody conjugated to the cytotoxic agent calicheamicin. GO is anticipated to be effective against ETP-ALL. In vivo studies promise antileukemic effects in cell lines; however, clinical reports to support this research are lacking. We treated a patient who suffered from CD33-positive ETP-ALL using GO. Case Presentation: We treated an 81-year-old man who suffered from ETP-ALL. The patient’s leukemia expressed T cell and myeloid markers including cyCD3, CD5, CD7, CD33, and HLA-DR. Initially, the patient was treated using a standard chemotherapy regimen for acute lymphoblastic leukemia comprising cyclophosphamide, daunorubicin, vincristine, l-asparaginase, and prednisolone. The induction chemotherapy produced the expected complete hematological response; however, bone marrow blasts remained. Following consolidation chemotherapy, the patient maintained a full hematological response. Thereafter, we changed the consolidation regimen to nelarabine, which did not reduce bone marrow blasts effectively. After two courses of nelarabine therapy, we finally used GO at an 8 mg/m2 weekly dose after confirming that CD33 expression was still positive in the patient’s residual leukemic cells. GO was ineffective in treating the patient’s leukemia, and peripheral blasts increased 30 days following treatment. The patient died 81 days after initiating GO therapy. Conclusion: This is the first clinical case of GO having a negative impact on ETP-ALL. Because the GO resistance mechanism for ETP-ALL has not been fully elucidated, treatment modification should be considered to achieve optimal clinical efficacy.
Enhancing the performance of sustainable energy management of buildings in smart cities
Authors: Prasad Reddy Mule Pala , Karthik Mamidala Vijay , Kumar Chava Sunil , Rayudu Katuri , Rao Gurrala Madhusudhana
Published: February 2024

Energy utilization has been the most influential parameter in recent decades, especially in the smart city model. The energy management system has been a more attractive research problem due to its utility, ability, and applications. This paper has an objective that the article discusses innovative energy management methods for sustainability and highlights the potential for integrated smart energy sources. The discussion also touches on the understanding of energy management and production, various storage systems, and their potential future applications. This paper explores challenges in sustainable smart energy management, focusing on methodologies like smart energy systems, PV calculations, electric grid models, and energy management strategies in smart cities. The passive infrared receiver (PIR) sensor has been used in real-time energy management systems to integrate these methodologies into the city's infrastructure. The energy management design aims to coordinate electrical appliances such as fans and lights to minimize energy consumption. The article proposes new energy management and security techniques based on data sources to enhance city intelligence, adaptability, and sustainability by reducing human involvement in controlling electrical appliances in residential buildings. The proposed design and development system optimizes energy utilization more efficiently and effectively than conventional systems, meeting real-time energy management objectives.
Performance of low cost sensor temperature logger in double jacket reactor vacuum distillation
Authors: Wahyudi Djoko , Wignyanto Wignyanto , Hendrawan Yusuf , Hamidi Nurkholis
Published: February 2024

Heat transfer occurs due to the difference in temperature between the system and its surroundings. The effect of temperature can affect various aspects of the refining process, including efficiency, selectivity, reaction kinetics, and the quality of the final product. This study aims to analyze heat transfer in a double-jacket reactor by measuring temperature data taken using a temperature data logger system. Prototype low cost-effective temperature monitoring for double jacket reactor vacuum is this system integrates an Arduino Mega 2560, a type K thermocouple, amplifier MAX 6675 module, and an SD card data logger to measure and record reactor temperature for 30 minutes. The temperature data obtained is used to calculate the heat transfer and analyze the heat transfer characteristics of the reactor. Heat transfer analysis based on measured temperature data is able to provide insight into the characteristics of heat transfer in the observed system and can identify hot spots and heat transfer energy in the system. Thus, the temperature data logger used in the double jacket reactor in the vacuum distillation system can produce accurate data and information, and this system has broad application potential in temperature monitoring in various fields.
MAPATON 2023: implementing a tool for the analysis of forest fire zones in Arequipa
Authors: Vargas-Cuentas Natalia I. , Paico-Campos Meyluz , Cahuana Abel , Canto-Vivanco Elber E. , Valencia Tania , Ramos-Cosi Sebastian , Villena Peter , Roman-Gonzalez Avid
Published: February 2024

The "Mapaton 2023," a collaborative initiative by the Peruvian Space Agency, Paraguayan Space Agency, and AMERIGEOS, introduces an innovative approach to analyze fire-prone areas in Arequipa, a pivotal endeavor for disaster prevention. Focused on the provinces of Arequipa and Caylloma, recent studies identified over 1,500 affected hectares by forest fires, emphasizing the urgency of employing satellite images and geospatial analysis techniques. Leveraging Landsat 8 satellite imagery, the research calculated indices, including the normalized difference vegetation index (NDVI) for vegetation analysis and the differenced normalized burn ratio (dNBR) for fire severity assessment. Results revealed varying impacts, with some areas exhibiting increased vegetation and others displaying significant damage. The use of ArcGIS online facilitated the presentation of geospatial data, emphasizing the utility of remote sensing in comprehending and addressing forest fires. Drawing insights from analogous studies in Mexico and the Amazon, this research underscores the importance of remote sensing and geospatial analysis in informing preventive measures against wildfires. The findings, crucial for environmental management, are recommended for sharing with relevant authorities, and the continued use of diverse satellite imagery sources is encouraged to enhance accuracy in monitoring and mitigating forest fires.