bluuebunny/crossref_metadata_2025 huggingface dataset:
Various Approaches for Software vulnerability Assessment and Risk Identification using soft computing Techniques
Authors: Hussein Ali , Azmi Azri , Abas Hafiza
Published: July 2024

The detection of software flaws is a viable technique for enhancing the quality of technology and testing management by providing rapid detection of deficiency simulation models until the actual testing phase starts. These prediction outcomes help designers of technology effectively devote their available resources to components that are more vulnerable to deficiencies. In this research investigation, a software bug prediction model is proposed using Deep Learning (DL) approach. The Recurrent Neural Network (RNN) is used for classification of source code including numerous soft computing techniques. Numerous preprocessing and data filtration techniques have been carried out for data balancing and normalization. The Term Frequency and Inverse Document Frequency (TF-IDF) and relation features extraction techniques is used to generate Vector Space Model (VSM). The classification has been done using RNN on both training and validation dataset. The evaluation of performance of proposed work is performed using various real-time and synthetic accessible databases. It is observed from the experimental results that the proposed framework performs better when different evaluated with different datasets
The Effect of Unsteady Inlet Boundary Conditions on the Aero-Thermal Behavior of High-Pressure Turbine Vanes – A Numerical Study Using Scale-Resolving Simulations
Authors: Gründler Jonathan , Lehmann Knut , Schiffer Heinz-Peter
Published: July 2024

This paper presents the application of a novel method to prescribe unsteady boundary conditions to transient, scale-resolving computational fluid dynamics simulations of the high-pressure turbine in modern jet engines. The methodology is based on the compression of the interface data at the combustor–turbine interface, using proper orthogonal decomposition and Fourier series (PODFS). Doing so can reduce the stored data at the interface drastically. The capability of the PODFS method to produce realistic inlet boundary conditions was demonstrated in previous work. Here, the method is applied to a turbine case. The outlet data of a combustor simulation is used to create the PODFS boundary conditions for a scale-resolving simulation of a simplified first nozzle guide vane of the high-pressure turbine. This simulation is compared with simulations with steady-state boundary conditions to show the effect of unsteadiness in the inlet boundary condition on the aerodynamic and thermal behaviors of the turbine. While the aerodynamics show minor sensitivity against the way of applying the inlet boundary conditions, the thermal behavior of the vanes is strongly affected by the modeling of combustor unsteadiness.
A Hybrid Data-Driven Method Based on Data Preprocessing to Predict the Remaining Useful Life of Lithium-Ion Batteries
Authors: Huo Weiwei , Wang Aobo , Lu Bing , Jia Yunxu , Li Chen
Published: July 2024

The estimation of remaining useful life (RUL) for lithium-ion batteries is an essential part for a battery management system. A hybrid method is presented which is combining principal component analysis (PCA), improved complete ensemble empirical mode decomposition with adaptive noise (ICEEMDAN), sparrow search algorithm (SSA), Elman neural network (Elman NN), and gaussian process regression (GPR) to forecast battery RUL. First, in the data preprocessing stage, the PCA + ICEEMDAN algorithm is creatively proposed to extract features of capacity decay and fluctuation. The PCA method is used to reduce the dimensionality of the extracted indirect health indicators (HIs), and then the ICEEMDAN algorithm is introduced to decompose the fused HI sequence and actual capacity data into residuals and multiple intrinsic mode functions (IMFs). Second, in the prediction stage, feature data are corresponded one-to-one with the mixed model. The prediction models of SSA–Elman algorithm and GPR algorithm are established, with the SSA–Elman algorithm predicting the capacity decay trend and the GPR algorithm quantifying the uncertainty caused by the capacity regeneration phenomenon. The final prediction results are obtained by superimposing the two sets of prediction data, and the prediction error and RUL are calculated. The effectiveness of the proposed hybrid approach is validated by RUL prediction experiments on three kinds of batteries. The comparative experimental results indicate that the mean absolute error (MAE) and root mean square error (RMSE) of the presented prediction model for lithium-ion battery capacity are less than 0.7% and 1.0%.
Gauging and Imaging of Pipes Using a Water-Immersible Ultrasonic Instrumentation System
Authors: Pavan Kumar N. , Patankar V. H.
Published: July 2024

The purpose of this research work is to establish the functionality of the novel ultrasonic non-destructive inspection system and accurate gauging of pipes and to locate and visualize flaws in the form of B-scan cross-sectional view (front-view) of the pipe under test. This paper presents a custom-made perspex inspection head assembly integrated with a stand-alone, Li-ion battery-powered and IP67-grade water-immersible ultrasonic instrumentation and gauging system, which enables an efficient assessment of the condition and health of pipes in stringent environments. Extensive inspection was carried out on six samples of 12 in. inner diameter (ID) type carbon steel (CS) pipes with length of 500 mm and having machined wall thickness to simulate loss of wall thicknesses from 10% over a length 150 mm of pipe, using 5 MHz spherically focused transducers. Further inspection were carried out on a 12 in. CS pipe with four notches and four flat bottom holes (FBHs) machined on the outer diameter (OD) side. Identical flaws were also machined onto 12 in. CS pipe of total length 700 mm containing water inside the pipe in flowing condition with water flowrate of 100 liters per minute (LPM). The test results demonstrate the effectiveness of the developed IP67-grade water-immersible ultrasonic pipe inspection and gauging instrumentation system for assessing the condition and health of long-length carbon steel pipes operating in harsh environments.
A deep learning method for reflective boundary estimation
Authors: Arikan Toros , Weiss Amir , Vishnu Hari , Deane Grant B. , Singer Andrew C. , Wornell Gregory W.
Published: July 2024

Environment estimation is a challenging task in reverberant settings such as the underwater and indoor acoustic domains. The locations of reflective boundaries, for example, can be estimated using acoustic echoes and leveraged for subsequent, more accurate localization and mapping. Current boundary estimation methods are constrained to high signal-to-noise ratios or are customized to specific environments. Existing methods also often require a correct assignment of echoes to boundaries, which is difficult if spurious echoes are detected. To evade these limitations, a convolutional neural network (NN) method is developed for robust two-dimensional boundary estimation, given known emitter and receiver locations. A Hough transform-inspired algorithm is leveraged to transform echo times of arrival into images, which are amenable to multi-resolution regression by NNs. The same architecture is trained on transform images of different resolutions to obtain diverse NNs, deployed sequentially for increasingly refined boundary estimation. A correct echo labeling solution is not required, and the method is robust to reverberation. The proposed method is tested in simulation and for real data from a water tank, where it outperforms state-of-the-art alternatives. These results are encouraging for the future development of data-driven three-dimensional environment estimation with high practical value in underwater acoustic detection and tracking.
Standing on the Shoulders of Giants: Essential Papers in Sports and Exercise Physiology
Authors: de Koning Jos J. , Foster Carl
Published: July 2024

Purpose: The purpose of this survey was to create a list of essential historical and contemporary readings for undergraduate and graduate students in the field of exercise physiology. Methods: Fifty-two exercise physiologists/sport scientists served as referees, and each nominated ∼25 papers for inclusion in the list. In total, 396 papers were nominated by the referees. This list was then sent back to the referees, with the instructions to nominate the “100 essential papers in sports and exercise physiology.” Results: The referees cast 4722 votes. The 100 papers with the highest number of votes received 51% (2406) of the total number of votes. A total of 37 papers in the list of “100 essential papers” were published >50 years ago, and 63 papers were published since 1973. Conclusions: This list of essential studies will provide a perspective on contemporary studies, the “giant’s shoulders” to enable young scholars to “see further” or to understand where they have “come from.” This compilation is also meant to impress on students that, given the (lack of) technology available in the past, some of the early science required enormous intuitive leaps on the part of historical scientists.
Systematic analysis of the
Candida albicans
kinome reveals environmentally contingent protein kinase-mediated regulation of filamentation and biofilm formation
in vitro
and
in vivo
Authors: Kramara Juraj , Kim Min-Ju , Ollinger Tomye L. , Ristow Laura C. , Wakade Rohan S. , Zarnowski Robert , Wellington Melanie , Andes David R. , Mitchell Aaron G. , Krysan Damian J.
Published: July 2024

Protein kinases are critical regulatory proteins in both prokaryotes and eukaryotes. Accordingly, protein kinases represent a common drug target for a wide range of human diseases. Therefore, understanding protein kinase function in human pathogens such as the fungus
Candida albicans
is likely to extend our knowledge of its pathobiology and identify new potential therapies. To facilitate the study of
C. albicans
protein kinases, we constructed a library of 99 non-essential protein kinase homozygous deletion mutants marked with barcodes in the widely used SN genetic background. Here, we describe the construction of this library and the characterization of the competitive fitness of the protein kinase mutants under 11 different growth and stress conditions. We also screened the library for protein kinase mutants with altered filamentation and biofilm formation, two critical virulence traits of
C. albicans
. An extensive network of protein kinases governs these virulence traits in a manner highly dependent on the specific environmental conditions. Studies on specific protein kinases revealed that (i) the cell wall integrity MAPK pathway plays a condition-dependent role in filament initiation and elongation; (ii) the hyper-osmolar glycerol MAPK pathway is required for both filamentation and biofilm formation, particularly in the setting of
in vivo
catheter infection; and (iii) Sok1 is dispensable for filamentation in hypoxic environments at the basal level of a biofilm but is required for filamentation in normoxia. In addition to providing a new genetic resource for the community, these observations emphasize the environmentally contingent function of
C. albicans
protein kinases.

IMPORTANCE

Candida albicans
is one of the most common causes of fungal disease in humans for which new therapies are needed. Protein kinases are key regulatory proteins and are increasingly targeted by drugs for the treatment of a wide range of diseases. Understanding protein kinase function in
C. albicans
pathogenesis may facilitate the development of new antifungal drugs. Here, we describe a new library of 99 protein kinase deletion mutants to facilitate the study of protein kinases. Furthermore, we show that the function of protein kinases in two virulence-related processes, filamentation and biofilm formation, is dependent on the specific environmental conditions.
Supplemental Material: Relict soil evidence for post-Miocene aridification in the Atacama Desert of South America
Authors: Amundson Ronald , al. et
Published: July 2024

Total geochemical analyses of the soils examined.
Anesthetic management with labor epidural analgesia of the parturient with severe factor VII deficiency: a case report
Authors: Hyers Benjamin , Cabrera Camila , Walsh Christopher , Reddy Anusha , Strulowitz Talia , Hamburger Joshua , Knibbs Nakiyah , Katz Daniel , Ferrara Lauren , Beilin Yaakov
Published: July 2024

Background

Factor VII deficiency is considered a contraindication to neuraxial anesthesia due to the risk of an epidural hematoma.

Case Report

A 32 year old G1P0 parturient with severe factor VII deficiency presented for an anesthesiology consultation at 32 weeks gestation. Initial coagulation studies were significant for an elevated INR (2.0) and a low factor VII level of 6%. After interdisciplinary discussion, it was decided that neuraxial analgesia could be offered if her coagulation studies corrected after administration of recombinant activated factor VII (rFVIIa). The patient presented at 36 weeks gestation for a rFVIIa challenge. She received 22 mcg/kg rFVIIa and coagulation studies were analyzed 20 minutes later which showed complete correction of the coagulopathy. The patient presented to the hospital at 39 weeks and 3 days for delivery, received 2 mg rFVIIa and 20 minutes later, successfully received an epidural catheter. Her INR was monitored every 3 hours during her labor course and rFVIIa was given if the INR was 1.3 or greater. She required three additional doses over 22 hours. No bleeding or thrombotic events occurred, and the patient was discharged home without complications.

Conclusion

This case highlights the safe management of an epidural catheter in a parturient with severe factor VII deficiency.
Solving Sparse Linear Systems Faster than Matrix Multiplication
Authors: Peng Richard , Vempala Santosh S.
Published: July 2024

Can linear systems be solved faster than matrix multiplication? While there has been remarkable progress for the special cases of graph-structured linear systems, in the general setting, the bit complexity of solving an
n
×
n
linear system
Ax
=
b
is
Õ
(
n
ω
), where ω is the matrix multiplication exponent. Improving on this has been an open problem even for sparse linear systems with poly(
n
) condition number.

In this paper, we present an algorithm that solves linear systems with sparse coefficient matrices asymptotically faster than matrix multiplication for any ω > 2. This speedup holds for any input matrix
A
with
o
(
n
ω−1
/ log (κ(
A
))) non-zeros, where κ(
A
) is the condition number of
A
.

Our algorithm can be viewed as an efficient, randomized implementation of the block Krylov method via recursive low displacement rank factorization. It is inspired by an algorithm of Eberly et al. for inverting matrices over finite fields. In our analysis of numerical stability, we develop matrix anti-concentration techniques to bound the smallest eigenvalue and the smallest gap in the eigenvalues of semi-random matrices.
The Computational Solution of Generalized Inverse Eigenvalue Problem for Pseudo‐Jacobi Matrix
Authors: Yi Fuxia , Li Enhua
Published: July 2024

This paper is concerned with two generalized inverse eigenvalue problems for a kind of pseudo‐Jacobi matrix. From a non‐Hermite matrix, an r × r Jacobi matrix, two distinct real eigenvalues, and part of the corresponding eigenvectors, an n × n pseudo‐Jacobi matrix is constructed. Furthermore, an n × n pseudo‐Jacobi matrix can be made by two different eigenpairs and a positive definite diagonal matrix. It is shown that a unique pseudo‐Jacobi matrix can be recovered from partial eigenpairs and certain special mixed eigendata. Two algorithms are provided for the reconstruction of such a pseudo‐Jacobi matrix, and illustrative numerical examples are presented to verify the proposed algorithms.
Phacoemulsification in Nanophthalmic Eye, a Way to Manage Glaucoma: Case Report
Authors: Bamefleh Dania , Schargel Konrad , Semidey Valmore A. , Altahan Faisal A. , Schargel Edward
Published: July 2024

A rare condition called nanophthalmos causes variable degrees of vision impairment. One may present with nanophthalmos as a hereditary or sporadic condition. There have been documented cases of nanophthalmos treated with bilateral cataract extraction and intraocular lens (IOL) implantation for intractable secondary glaucoma or chronic angle‐closure glaucoma. We describe a case of closed‐angle glaucoma in a nanophthalmic eye with increased intraocular pressure (IOP) on full medical treatment, along with concurrent drug side effects. As a first surgical procedure, we recommend phacoemulsification of the clear lens + IOL. The challenge in treating nanophthalmic eyes lies in managing the possibility of developing glaucoma in an eye where anatomical conditions make surgery extremely risky. This must be balanced against the advantages of lessening exposure contact in the trabecular meshwork and optimizing the anterior chamber for potential future glaucoma surgery, which can improve the prognosis in these cases. Lastly, it is critical to have a thorough conversation with the patient about the aims, risks, and advantages. The patient’s understanding and expectations should also be crystal apparent. The primary objective should always be to enhance the circumstances for the most effective glaucoma therapy, not to perform refractive surgery.
Green Panel with Physical Variables Monitoring and Statistical Control System
Authors: Leal Lopez Luis Antonio , Gonzalez Moran Carlos Omar , Miranda Hernandez Jose Guadalupe , Lara Hernandez Gemima , Martinez Sibaja Albino , Baltazar Escalona Juan Carlos , Flores Cuautle Jose de Jesus Agustin
Published: July 2024

Global warming and energy‐saving efforts make it necessary to look for energy‐free technology to reduce buildings’ temperature. This work aims to develop a system for monitoring green panels’ physical variables (atmospheric temperature, humidity, soil humidity, amount of light, and vibration) to determine their efficiency. A model of a green panel was outfitted with detectors that recorded atmospheric variable modifications within and outside the green panel under evaluation. Open‐source code and hardware were used to record all variables and store the data. Once the monitoring system is completed, a green panel model is developed as concept proof for monitoring the physical variables; a database is created, studied, and tested using the formulated hypothesis. The variables were analyzed using current techniques of statistical description, and the results obtained support the idea underpinning the feasibility of implementing green panels in city houses and buildings. A substantial difference in temperature up to 12°C was found when using green walls and ceiling systems at the hottest times of the day. The humidity in the air is up to 88%, generating an atmosphere of comfort in buildings where these systems are installed.
Supplementary Table S2 from Association of Ideal Cardiovascular Health in Youth with Cancer Risk in Adulthood: A Cardiovascular Risk in Young Finns Study
Authors: Niemelä Jussi , Nuotio Joel , Laitinen Tomi T. , Kähönen Mika , Hutri Nina , Lehtimäki Terho , Jokinen Eero , Tossavainen Päivi , Laitinen Tomi P. , Heinonen Olli J. , Dwyer Terence , Pahkala Katja , Rovio Suvi P. , Viikari Jorma , Raitakari Olli , Juonala Markus
Published: July 2024

Supplementary Table S2: Summary Statistics of the Age at Cancer Diagnosis for the 72 Cancer Cases in YFS study Cohort with complete AHA ICH data in 1986
Supplementary Table S5 from Fraction Dose Escalation of Hypofractionated Radiotherapy with Concurrent Chemotherapy and Subsequent Consolidation Immunotherapy in Locally Advanced Non–Small Cell Lung Cancer: A Phase I Study
Authors: Zhou Rui , Liu FangJie , Zhang HongMei , Wang DaQuan , Zhang PengXin , Zheng ShiYang , Liu YiMei , Chen Li , Guo JinYu , Zou YingYi , Rong Yu-Ming , Liu Hui , Qiu Bo
Published: July 2024

Supplementary Table S5. Treatment related toxicities (n=18).
Supplementary Table S4 from Fraction Dose Escalation of Hypofractionated Radiotherapy with Concurrent Chemotherapy and Subsequent Consolidation Immunotherapy in Locally Advanced Non–Small Cell Lung Cancer: A Phase I Study
Authors: Zhou Rui , Liu FangJie , Zhang HongMei , Wang DaQuan , Zhang PengXin , Zheng ShiYang , Liu YiMei , Chen Li , Guo JinYu , Zou YingYi , Rong Yu-Ming , Liu Hui , Qiu Bo
Published: July 2024

Supplementary Table S4. Significant dosimetric parameters of PBT.
Supplementary Table S4 from Immunologic Profiling of Immune-Related Cutaneous Adverse Events with Checkpoint Inhibitors Reveals Polarized Actionable Pathways
Authors: Lacouture Mario E. , Goleva Elena , Shah Neil , Rotemberg Veronica , Kraehenbuehl Lukas , Ketosugbo Kwami F. , Merghoub Taha , Maier Tara , Bang Alexander , Gu Stephanie , Salvador Trina , Moy Andrea P. , Lyubchenko Taras , Xiao Olivia , Hall Clifton F. , Berdyshev Evgeny , Crooks James , Weight Ryan , Kern Jeffrey A. , Leung Donald Y.M.
Published: July 2024

Supplementary Table S4. Cancer types and stages of study participants by immune-related cutaneous adverse event (ircAE) phenotype.
Supplementary Table S2 from Immunologic Profiling of Immune-Related Cutaneous Adverse Events with Checkpoint Inhibitors Reveals Polarized Actionable Pathways
Authors: Lacouture Mario E. , Goleva Elena , Shah Neil , Rotemberg Veronica , Kraehenbuehl Lukas , Ketosugbo Kwami F. , Merghoub Taha , Maier Tara , Bang Alexander , Gu Stephanie , Salvador Trina , Moy Andrea P. , Lyubchenko Taras , Xiao Olivia , Hall Clifton F. , Berdyshev Evgeny , Crooks James , Weight Ryan , Kern Jeffrey A. , Leung Donald Y.M.
Published: July 2024

Supplementary Table S2. Demographics of study participants.
Supplementary Table S5 from A Cohort Study to Evaluate Genetic Predictors of Aromatase Inhibitor Musculoskeletal Symptoms: Results from ECOG-ACRIN E1Z11
Authors: Stearns Vered , Jegede Opeyemi A. , Chang Victor T.-S. , Skaar Todd C. , Berenberg Jeffrey L. , Nand Ranveer , Shafqat Atif , Jacobs Nisha L. , Luginbuhl William , Gilman Paul , Benson Al B. , Goodman Judie R. , Buchschacher Gary L. , Henry N. Lynn , Loprinzi Charles L. , Flynn Patrick J. , Mitchell Edith P. , Fisch Michael J. , Sparano Joseph A. , Wagner Lynne I.
Published: July 2024

Supplementary Table S5: Association between clinicopathological variables and treatment discontinuation due to AIMSS.
Supplementary Table S4 from A Cohort Study to Evaluate Genetic Predictors of Aromatase Inhibitor Musculoskeletal Symptoms: Results from ECOG-ACRIN E1Z11
Authors: Stearns Vered , Jegede Opeyemi A. , Chang Victor T.-S. , Skaar Todd C. , Berenberg Jeffrey L. , Nand Ranveer , Shafqat Atif , Jacobs Nisha L. , Luginbuhl William , Gilman Paul , Benson Al B. , Goodman Judie R. , Buchschacher Gary L. , Henry N. Lynn , Loprinzi Charles L. , Flynn Patrick J. , Mitchell Edith P. , Fisch Michael J. , Sparano Joseph A. , Wagner Lynne I.
Published: July 2024

Supplementary Table S4: HAQ Scores at different time points (n=970).
Supplementary Table S2 from A Cohort Study to Evaluate Genetic Predictors of Aromatase Inhibitor Musculoskeletal Symptoms: Results from ECOG-ACRIN E1Z11
Authors: Stearns Vered , Jegede Opeyemi A. , Chang Victor T.-S. , Skaar Todd C. , Berenberg Jeffrey L. , Nand Ranveer , Shafqat Atif , Jacobs Nisha L. , Luginbuhl William , Gilman Paul , Benson Al B. , Goodman Judie R. , Buchschacher Gary L. , Henry N. Lynn , Loprinzi Charles L. , Flynn Patrick J. , Mitchell Edith P. , Fisch Michael J. , Sparano Joseph A. , Wagner Lynne I.
Published: July 2024

Supplementary Table S2: All Grades Treatment Related Toxicities (CTCAE v4).
Supplementary Figure S10 from A Modular Trial of Androgen Signaling Inhibitor Combinations Testing a Risk-Adapted Strategy in Patients with Metastatic Castration–Resistant Prostate Cancer
Authors: Aparicio Ana M. , Tidwell Rebecca S.S. , Yadav Shalini S. , Chen Jiun-Sheng , Zhang Miao , Liu Jingjing , Guo Shuai , Pilié Patrick G. , Yu Yao , Song Xingzhi , Vundavilli Haswanth , Jindal Sonali , Zhu Keyi , Viscuse Paul V. , Lebenthal Justin M. , Hahn Andrew W. , Soundararajan Rama , Corn Paul G. , Zurita-Saavedra Amado , Subudhi Sumit K. , Zhang Jianhua , Wang Wenyi , Huff Chad , Troncoso Patricia , Allison James P. , Sharma Padmanee , Logothetis Christopher J.
Published: July 2024

Supplementary Figure S10. Frequencies of copy number alterations.
Supplementary Table S3 from Endometrioid Endometrial RNA Index Predicts Recurrence in Stage I Patients
Authors: Nief Corrine A. , Hammer Phoebe M. , Wang Aihui , Charu Vivek , Tanweer Amina , Litkouhi Babak , Kidd Elizabeth , Gentles Andrew J. , Howitt Brooke E.
Published: July 2024

Supplemental Table 3: Clinical and Pathologic Variables of Controls and EERI False Positives in both the Stanford-EEC controls and TCGA-UCEC non-recurrent patients
Supplementary Table S7 from A Machine Learning Algorithm Facilitates Prognosis Prediction and Treatment Selection for Barcelona Clinic Liver Cancer Stage C Hepatocellular Carcinoma
Authors: Han Ji W. , Lee Soon K. , Kwon Jung H. , Nam Soon W. , Yang Hyun , Bae Si H. , Kim Ji H. , Nam Heechul , Kim Chang W. , Lee Hae L. , Kim Hee Y. , Lee Sung W. , Lee Ahlim , Chang U I. , Song Do S. , Kim Seok-Hwan , Song Myeong J. , Sung Pil S. , Choi Jong Y. , Yoon Seung K. , Jang Jeong W.
Published: July 2024

Comparison of model performances for predicting 6-month, 12-month, and 24-month survival
Supplementary Table S2 from A Machine Learning Algorithm Facilitates Prognosis Prediction and Treatment Selection for Barcelona Clinic Liver Cancer Stage C Hepatocellular Carcinoma
Authors: Han Ji W. , Lee Soon K. , Kwon Jung H. , Nam Soon W. , Yang Hyun , Bae Si H. , Kim Ji H. , Nam Heechul , Kim Chang W. , Lee Hae L. , Kim Hee Y. , Lee Sung W. , Lee Ahlim , Chang U I. , Song Do S. , Kim Seok-Hwan , Song Myeong J. , Sung Pil S. , Choi Jong Y. , Yoon Seung K. , Jang Jeong W.
Published: July 2024

Selected factors of the XGBoost model for the prediction of 12-month survival by the feature selection algorithm.
Supplementary Figure S5 from A Machine Learning Algorithm Facilitates Prognosis Prediction and Treatment Selection for Barcelona Clinic Liver Cancer Stage C Hepatocellular Carcinoma
Authors: Han Ji W. , Lee Soon K. , Kwon Jung H. , Nam Soon W. , Yang Hyun , Bae Si H. , Kim Ji H. , Nam Heechul , Kim Chang W. , Lee Hae L. , Kim Hee Y. , Lee Sung W. , Lee Ahlim , Chang U I. , Song Do S. , Kim Seok-Hwan , Song Myeong J. , Sung Pil S. , Choi Jong Y. , Yoon Seung K. , Jang Jeong W.
Published: July 2024

Unsupervised clustering according to the 12-month mortality predicted by XGBoost and the actual observed 12-month death was performed.
Supplementary Figure S2 from Spatial Profiling of Ovarian Carcinoma and Tumor Microenvironment Evolution under Neoadjuvant Chemotherapy
Authors: Yaniz-Galende Elisa , Zeng Qinghe , Bejar-Grau Juan F. , Klein Christophe , Blanc-Durand Felix , Le Formal Audrey , Pujade-Lauraine Eric , Chardin Laure , Edmond Elodie , Marty Virginie , Ray-Coquard Isabelle , Joly Florence , Ferron Gwenael , Pautier Patricia , Berton-Rigaud Dominique , Lortholary Alain , Dohollou Nadine , Desauw Christophe , Fabbro Michel , Malaurie Emmanuelle , Bonichon-Lamaichhane Nathalie , Bello Roufai Diana , Gantzer Justine , Rouleau Etienne , Genestie Catherine , Leary Alexandra
Published: July 2024

Change in GrzB expression min paired samples post-NACT
Supplementary Table S4 from Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer
Authors: Sivars Lars , Jylhä Cecilia , Crona Guterstam Ylva , Zupancic Mark , Lindqvist Britta , Nordenskjöld Magnus , Tham Emma , Hellman Kristina
Published: July 2024

Supplementary Table S4. Normal cell-free DNA levels, using cell-free albumin DNA as a surrogate marker, in pretreatment plasma in relation to FIGO 2018 stage, HPV type, and histopathology.
Supplementary Results and Discussion S1 from Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer
Authors: Sivars Lars , Jylhä Cecilia , Crona Guterstam Ylva , Zupancic Mark , Lindqvist Britta , Nordenskjöld Magnus , Tham Emma , Hellman Kristina
Published: July 2024

Supplementary results and discussion on normal cfDNA.
Supplementary Figure S6 from Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer
Authors: Sivars Lars , Jylhä Cecilia , Crona Guterstam Ylva , Zupancic Mark , Lindqvist Britta , Nordenskjöld Magnus , Tham Emma , Hellman Kristina
Published: July 2024

Supplementary Figure S6. Number of copies of ctHPV DNA at different timepoints for all patients (n = 3) that were diagnosed with disease progression during or just at the end of treatment. Arrows indicate the approximate time of diagnosis of progression.
Supplementary Figure S5 from Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer
Authors: Sivars Lars , Jylhä Cecilia , Crona Guterstam Ylva , Zupancic Mark , Lindqvist Britta , Nordenskjöld Magnus , Tham Emma , Hellman Kristina
Published: July 2024

Supplementary Figure S5. Progression-free survival according to complete clinical response or not, at tumor evaluation, approximately 3 months after finished treatment.
Supplementary Methods S1 from Safety, Pharmacokinetics, Pharmacodynamics, and Antitumor Activity from a Phase I Study of Simlukafusp Alfa (FAP-IL2v) in Advanced/Metastatic Solid Tumors
Authors: Steeghs Neeltje , Gomez-Roca Carlos , Rohrberg Kristoffer S. , Mau-Sørensen Morten , Robbrecht Debbie , Tabernero Josep , Ahmed Samreen , Rodríguez-Ruiz Maria E. , Ardeshir Caroline , Schmid Daniela , Sleiman Nassim , Watson Carl , Piper-Lepoutre Hanna , Dejardin David , Evers Stefan , Boetsch Christophe , Charo Jehad , Teichgräber Volker , Melero Ignacio
Published: July 2024

Supplementary Methods
Supplementary Figure S1 from Safety, Pharmacokinetics, Pharmacodynamics, and Antitumor Activity from a Phase I Study of Simlukafusp Alfa (FAP-IL2v) in Advanced/Metastatic Solid Tumors
Authors: Steeghs Neeltje , Gomez-Roca Carlos , Rohrberg Kristoffer S. , Mau-Sørensen Morten , Robbrecht Debbie , Tabernero Josep , Ahmed Samreen , Rodríguez-Ruiz Maria E. , Ardeshir Caroline , Schmid Daniela , Sleiman Nassim , Watson Carl , Piper-Lepoutre Hanna , Dejardin David , Evers Stefan , Boetsch Christophe , Charo Jehad , Teichgräber Volker , Melero Ignacio
Published: July 2024

Supplementary Figure S1. Figure design. FAP-IL2v, fibroblast activation protein-α interleukin-2 variant; PD, progressive disease; QW, weekly.
Supplementary Table 1 from CD8-Targeted IL2 Unleashes Tumor-Specific Immunity in Human Cancer Tissue by Reviving the Dysfunctional T-cell Pool
Authors: Kaptein Paulien , Slingerland Nadine , Metoikidou Christina , Prinz Felix , Brokamp Simone , Machuca-Ostos Mercedes , de Roo Guido , Schumacher Ton N.M. , Yeung Yik A. , Moynihan Kelly D. , Djuretic Ivana M. , Thommen Daniela S.
Published: July 2024

Patient characteristics of resected tumor samples used for PDTF culture.
Supplementary Figure 6 from CD8-Targeted IL2 Unleashes Tumor-Specific Immunity in Human Cancer Tissue by Reviving the Dysfunctional T-cell Pool
Authors: Kaptein Paulien , Slingerland Nadine , Metoikidou Christina , Prinz Felix , Brokamp Simone , Machuca-Ostos Mercedes , de Roo Guido , Schumacher Ton N.M. , Yeung Yik A. , Moynihan Kelly D. , Djuretic Ivana M. , Thommen Daniela S.
Published: July 2024

Annotation of transcriptomic states of intratumoral CD8+ T cells.
Supplementary Figure S3 from IL2 Targeted to CD8+ T Cells Promotes Robust Effector T-cell Responses and Potent Antitumor Immunity
Authors: Moynihan Kelly D. , Kumar Manu P. , Sultan Hussein , Pappas Danielle C. , Park Terrence , Chin S. Michael , Bessette Paul , Lan Ruth Y. , Nguyen Henry C. , Mathewson Nathan D. , Ni Irene , Chen Wei , Lee Yonghee , Liao-Chan Sindy , Chen Jessie , Schumacher Ton N.M. , Schreiber Robert D. , Yeung Yik A. , Djuretic Ivana M.
Published: July 2024

Supplementary Figure S3: Biodistribution of cytokine fusion molecules in tumor-bearing mice.
Supplementary Figure S2 from IL2 Targeted to CD8+ T Cells Promotes Robust Effector T-cell Responses and Potent Antitumor Immunity
Authors: Moynihan Kelly D. , Kumar Manu P. , Sultan Hussein , Pappas Danielle C. , Park Terrence , Chin S. Michael , Bessette Paul , Lan Ruth Y. , Nguyen Henry C. , Mathewson Nathan D. , Ni Irene , Chen Wei , Lee Yonghee , Liao-Chan Sindy , Chen Jessie , Schumacher Ton N.M. , Schreiber Robert D. , Yeung Yik A. , Djuretic Ivana M.
Published: July 2024

Supplementary Figure S2: In vitro culture of human CD8+ T cells, evaluation of CD8α and CD8β expression, and cytokine release assessment.
Supplementary Figure S10 from IL2 Targeted to CD8+ T Cells Promotes Robust Effector T-cell Responses and Potent Antitumor Immunity
Authors: Moynihan Kelly D. , Kumar Manu P. , Sultan Hussein , Pappas Danielle C. , Park Terrence , Chin S. Michael , Bessette Paul , Lan Ruth Y. , Nguyen Henry C. , Mathewson Nathan D. , Ni Irene , Chen Wei , Lee Yonghee , Liao-Chan Sindy , Chen Jessie , Schumacher Ton N.M. , Schreiber Robert D. , Yeung Yik A. , Djuretic Ivana M.
Published: July 2024

Supplementary Figure S10: In vitro and in vivo activity of AB248 in cynomolgus monkey.
Table S7 from Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy
Authors: Dias Matheus Henrique , Friskes Anoek , Wang Siying , Fernandes Neto Joao M. , van Gemert Frank , Mourragui Soufiane , Papagianni Chrysa , Kuiken Hendrik J. , Mainardi Sara , Alvarez-Villanueva Daniel , Lieftink Cor , Morris Ben , Dekker Anna , van Dijk Emma , Wilms Lieke H.S. , da Silva Marcelo S. , Jansen Robin A. , Mulero-Sánchez Antonio , Malzer Elke , Vidal August , Santos Cristina , Salazar Ramón , Wailemann Rosangela A.M. , Torres Thompson E.P. , De Conti Giulia , Raaijmakers Jonne A. , Snaebjornsson Petur , Yuan Shengxian , Qin Wenxin , Kovach John S. , Armelin Hugo A. , te Riele Hein , van Oudenaarden Alexander , Jin Haojie , Beijersbergen Roderick L. , Villanueva Alberto , Medema Rene H. , Bernards Rene
Published: July 2024

Supplementary table 7: Full list of genes whose knockout was selectively toxic in the presence of LB-100 in SW-480 cells in the CRISPR-KO screen FDR smaller or equal to 0.25 and log2 fold change smaller or equal to -1 in treated/untreated comparison were criteria for hit selection.
Figure S9 from Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy
Authors: Dias Matheus Henrique , Friskes Anoek , Wang Siying , Fernandes Neto Joao M. , van Gemert Frank , Mourragui Soufiane , Papagianni Chrysa , Kuiken Hendrik J. , Mainardi Sara , Alvarez-Villanueva Daniel , Lieftink Cor , Morris Ben , Dekker Anna , van Dijk Emma , Wilms Lieke H.S. , da Silva Marcelo S. , Jansen Robin A. , Mulero-Sánchez Antonio , Malzer Elke , Vidal August , Santos Cristina , Salazar Ramón , Wailemann Rosangela A.M. , Torres Thompson E.P. , De Conti Giulia , Raaijmakers Jonne A. , Snaebjornsson Petur , Yuan Shengxian , Qin Wenxin , Kovach John S. , Armelin Hugo A. , te Riele Hein , van Oudenaarden Alexander , Jin Haojie , Beijersbergen Roderick L. , Villanueva Alberto , Medema Rene H. , Bernards Rene
Published: July 2024

Figure S9: Single-cell RNAseq identify transcriptional signatures downregulated in CRC cells after acquired resistance to the combination of LB-100 and adavosertib UMAP representations of HT-29 (A) and SW-480 (B) cells colored by the activity scores for the indicated pathways. UMAPs colored by sample of origin from both cell lines are present of the left for reference. The boxen plots show the pathway activity scores for parental (red) and resistant (blue) cells.
Figure S1 from Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy
Authors: Dias Matheus Henrique , Friskes Anoek , Wang Siying , Fernandes Neto Joao M. , van Gemert Frank , Mourragui Soufiane , Papagianni Chrysa , Kuiken Hendrik J. , Mainardi Sara , Alvarez-Villanueva Daniel , Lieftink Cor , Morris Ben , Dekker Anna , van Dijk Emma , Wilms Lieke H.S. , da Silva Marcelo S. , Jansen Robin A. , Mulero-Sánchez Antonio , Malzer Elke , Vidal August , Santos Cristina , Salazar Ramón , Wailemann Rosangela A.M. , Torres Thompson E.P. , De Conti Giulia , Raaijmakers Jonne A. , Snaebjornsson Petur , Yuan Shengxian , Qin Wenxin , Kovach John S. , Armelin Hugo A. , te Riele Hein , van Oudenaarden Alexander , Jin Haojie , Beijersbergen Roderick L. , Villanueva Alberto , Medema Rene H. , Bernards Rene
Published: July 2024

Figure S1: LB-100 engages stress-related, inflammatory response, and mitogenic signaling transcriptional programs in CRC cells (A) Dose-response assays show the effect of LB-100 in 7 CRC models. Cell viability was estimated by resazurin fluorescence after 5 days in the presence of the drug or DMSO control. The normalized values are plotted. (B) The heat map shows all “Hallmarks” and “KEGG” molecular signatures significantly enriched by LB-100 (4 µM) in both HT-29 and SW-480 cells in at least one of the addressed time points. Asterisks indicate significance level (* p-value <0.05, ** p-value <0.01, *** p-value <0.001)
Data from Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy
Authors: Dias Matheus Henrique , Friskes Anoek , Wang Siying , Fernandes Neto Joao M. , van Gemert Frank , Mourragui Soufiane , Papagianni Chrysa , Kuiken Hendrik J. , Mainardi Sara , Alvarez-Villanueva Daniel , Lieftink Cor , Morris Ben , Dekker Anna , van Dijk Emma , Wilms Lieke H.S. , da Silva Marcelo S. , Jansen Robin A. , Mulero-Sánchez Antonio , Malzer Elke , Vidal August , Santos Cristina , Salazar Ramón , Wailemann Rosangela A.M. , Torres Thompson E.P. , De Conti Giulia , Raaijmakers Jonne A. , Snaebjornsson Petur , Yuan Shengxian , Qin Wenxin , Kovach John S. , Armelin Hugo A. , te Riele Hein , van Oudenaarden Alexander , Jin Haojie , Beijersbergen Roderick L. , Villanueva Alberto , Medema Rene H. , Bernards Rene
Published: July 2024

Abstract
Cancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress response programs that counteract the inherent toxicity of such aberrant signaling. Although inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of protein phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumors in vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumors in vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor-suppressive resistance.

Significance: A therapy consisting of deliberate hyperactivation of oncogenic signaling combined with perturbation of the stress responses that result from this is very effective in animal models of colon cancer. Resistance to this therapy is associated with loss of oncogenic signaling and reduced oncogenic capacity, indicative of tumor-suppressive drug resistance.
Table 1 from Cancer-Related Fatigue and the Additive Effect of Treatment in the Context of Lymphoma: An Analysis of the Lymphoma Coalition’s 2022 Global Patient Survey
Authors: Kalloger Steve E. , Watson Amanda , Sajkowski Shawn , Warwick Lorna
Published: July 2024

Age and biological sex as reported by survey respondents distributed across the symptom/side-effect strata
The Local Government Budget Resilience: Anticipatory, Coping, and Vulnerability Indexes
Authors: Indriani Ika Kurnia , Agus Widodo  , Anik Cahyowati
Published: July 2024

The primary determinant for managing the financial distribution consequences of the COVID-19 pandemic is the resilience of the local budget. Having a substantial budget will facilitate the implementation of strategic programmes by the municipal administration during the COVID-19 epidemic, while also ensuring the maintenance of regional economic growth. The budget capability evaluation attempts to evaluate the proficiency of municipal governments in Indonesia in managing the APBD. The evaluation of budget resilience employs a descriptive quantitative methodology that encompasses three dimensions: anticipatory capacity, coping capacities, and vulnerability. The evaluation employed secondary data through the process of archive analysis. The assessment results indicated that the municipalities of Mataram, Tidore, Batam, and Sabang achieved the highest budget resilience index. The government with the highest ranking possesses the capacity to effectively manage unanticipated issues such as the COVID-19 pandemic. However, the municipalities of Bengkulu, Bontang, and Tegal showed the lowest budget capacity index. The local government with the lowest index must enhance the management system of APBD to optimise its response to the economic consequences afterwards the COVID-19 pandemic.
Dynamic network analysis of electrophysiological task data
Authors: Gohil Chetan , Kohl Oliver , Huang Rukuang , van Es Mats W.J. , Parker Jones Oiwi , Hunt Laurence T. , Quinn Andrew J. , Woolrich Mark W.
Published: July 2024

An important approach for studying the human brain is to use functional neuroimaging combined with a task. In electrophysiological data, this often involves a time-frequency analysis, in which recorded brain activity is time-frequency transformed and epoched around task events of interest, followed by trial-averaging of the power. While this simple approach can reveal fast oscillatory dynamics, the brain regions are analysed one at a time. This causes difficulties for interpretation and a debilitating number of multiple comparisons. In addition, it is now recognised that the brain responds to tasks through the coordinated activity of networks of brain areas. As such, techniques that take a whole-brain network perspective are needed. Here, we show how the oscillatory task responses from conventional time-frequency approaches can be represented more parsimoniously at the network level using two state-of-the-art methods: the HMM (Hidden Markov Model) and DyNeMo (Dynamic Network Modes). Both methods reveal frequency-resolved networks of oscillatory activity with millisecond resolution. Comparing DyNeMo, HMM, and traditional oscillatory response analysis, we show DyNeMo can identify task activations/deactivations that the other approaches fail to detect. DyNeMo offers a powerful new method for analysing task data from the perspective of dynamic brain networks.
Erratum: ROHAN MAITY, KRISHNA CHOWLU & SUDHANSU SEKHAR DASH (2024) The current status of Henckelia peduncularis (Gesneriaceae): Taxonomy, typification, distribution and IUCN Red List assessment. Phytotaxa 644 (1): 27–34.
Authors: MAITY ROHAN , CHOWLU KRISHNA , DASH SUDHANSU SEKHAR
Published: July 2024

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Ancient Grasshoppers: A revision of the genus Bullacris (Orthoptera: Pneumoridae)
Authors: GORDON MIKHAILA L. , COLVILLE JONATHAN F. , ENGELBRECHT ADRIAAN , COULDRIDGE VANESSA C. K.
Published: July 2024

The genus Bullacris in the family Pneumoridae was most recently revised by Dirsh in 1965 based on morphological comparisons between species. However, since that time, new information about the genus and the family has come to light, necessitating a revision of the genus. In addition, the species B. boschimana was originally described based on a single female specimen. Here we present and describe the male of the species for the first time. The aim of this study was to update the current species descriptions by including additional specimens and incorporating additional methods for a more comprehensive comparison. Analyses consisted of morphometric measurements from high-quality images of type specimens, existing South African museum specimens, as well as personally collected specimens. Acoustic signals are also presented and compared between species. In addition, phylogenetic analyses were conducted on the barcoding mitochondrial gene COI and two nuclear genes, namely ITS and 18S. Results show that according to morphological, acoustic and genetic data, B. discolor and B. serrata as well as B. intermedia and B. membracioides share notable similarities. Bullacris discolor and B. serrata share similar phenotypic traits, in which B. discolor can either appear uniform in colour or have a speckled variation that is very similar in appearance to B. serrata. Bullacris intermedia and B. membracioides have a 5% mitochondrial DNA pairwise distance, suggesting that they may have not be fully diverged; however, morphological analysis shows that these species are morphologically distinguishable. It is suggested that these species may have undergone spatial separation at one point; however, further investigation is required. Additional sampling across a wider geographic range is essential to clarify the relationships between B. discolor and B. serrata, as well as between B. intermedia and B. membracioides.
A new species of green pitviper of the Trimeresurus macrops complex (Reptilia: Serpentes: Viperidae) from South Central Coastal Region of Vietnam
Authors: IDIIATULLINA SABIRA S. , NGUYEN TAN VAN , BRAGIN ANDREY M. , PAWANGKHANANT PARINYA , LE DAC XUAN , VOGEL GERNOT , DAVID PATRICK , POYARKOV NIKOLAY A.
Published: July 2024

We describe a new species of green pitviper from southern and central parts of coastal Vietnam based on morphological and molecular (2406 bp from cyt b, ND4, and 16S rRNA mitochondrial DNA genes) lines of evidence. Trimeresurus cyanolabris sp. nov. is distinguished from its congeners by the combination of the following morphological characters: small size, maximum known SVL of 638 mm; dorsal scales in 21 (rarely 23)–21–15 rows, moderately keeled except the outermost rows; ventral scales 166–178; subcaudal scales 52–75, all paired; hemipenis forked, calyculate, reaching the 8th subcaudal; eye bright yellow in both sexes; dorsal surface deep green lacking cross-bands; postocular white stripe missing in both sexes; ventrolateral stripe faintly present on the first few dorsal scale rows in males, absent in females; throat, chin, and lower labials in shades of blue. The new species forms a distinct clade on the phylogenetic tree of the genus Trimeresurus and differs from the morphologically similar T. rubeus by a significant divergence in cytochrome b mitochondrial DNA gene sequences (p = 6.0%). The new species is currently known from low- to mid-elevations (ca. 90–400 m a.s.l.) in tropical forests of central-southern Vietnam. This discovery further underlines the importance of this area as a local center of herpetofaunal diversity and endemism, which is under great threat of deforestation.
A review of the Caryanda tamdaoensis species-group (Orthoptera: Acrididae), with description of a new species from Yunnan, China
Authors: SONG HONG , YIN ZHI-LONG , STOROZHENKO SERGEY YU. , MAO BEN-YONG
Published: July 2024

The species composition of the Caryanda tamdaoensis species-group (Acrididae: Caryandinae: Caryanda Stål, 1878) is discussed. A new species, Caryanda hongheensis Mao, Yin & Song, sp. nov., is described and illustrated from China. A new synonymy is proposed: Caryanda tamdaoensis Storozhenko, 1992 = Caryanda aurata Mao, Ren & Ou, 2007, syn. nov. The name of the Caryanda aurata species-group is accordingly replaced by the Caryanda tamdaoensis species-group. Caryanda azurea Gorochov & Storozhenko, 1994 is divided into two subspecies: Caryanda azurea azurea stat. nov. from Vietnam and Caryanda azurea colourfula Mao, Ren & Ou, 2011, stat. nov. from China. A key to the species and two subspecies of this species group is given. All species are illustrated.