bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of physiotherapy and home-based training in parkinsonian syndromes: protocol for a randomised controlled trial (MobilityAPP)
Authors: Raccagni Cecilia , Sidoroff Victoria , Paraschiv-Ionescu Anisoara , Roth Nils , Schönherr Gudrun , Eskofier Björn , Gassner Heiko , Kluge Felix , Teatini Francesco , Seppi Klaus , Goebel Georg , Benninger David H , Aminian Kamiar , Klucken Jochen , Wenning Gregor
Published: May 2024

Introduction

Gait and mobility impairment are pivotal signs of parkinsonism, and they are particularly severe in atypical parkinsonian disorders including multiple system atrophy (MSA) and progressive supranuclear palsy (PSP). A pilot study demonstrated a significant improvement of gait in patients with MSA of parkinsonian type (MSA-P) after physiotherapy and matching home-based exercise, as reflected by sensor-based gait parameters. In this study, we aim to investigate whether a gait-focused physiotherapy (GPT) and matching home-based exercise lead to a greater improvement of gait performance compared with a standard physiotherapy/home-based exercise programme (standard physiotherapy, SPT).

Methods and analysis

This protocol was deployed to evaluate the effects of a GPT versus an active control undergoing SPT and matching home-based exercise with regard to laboratory gait parameters, physical activity measures and clinical scales in patients with Parkinson’s disease (PD), MSA-P and PSP. The primary outcomes of the trial are sensor-based laboratory gait parameters, while the secondary outcome measures comprise real-world derived parameters, clinical rating scales and patient questionnaires. We aim to enrol 48 patients per disease group into this double-blind, randomised-controlled trial. The study starts with a 1 week wearable sensor-based monitoring of physical activity. After randomisation, patients undergo a 2 week daily inpatient physiotherapy, followed by 5 week matching unsupervised home-based training. A 1 week physical activity monitoring is repeated during the last week of intervention.

Ethics and dissemination

This study, registered as ‘Mobility in Atypical Parkinsonism: a Trial of Physiotherapy (Mobility_APP)’ at clinicaltrials.gov (NCT04608604), received ethics approval by local committees of the involved centres. The patient’s recruitment takes place at the Movement Disorders Units of Innsbruck (Austria), Erlangen (Germany), Lausanne (Switzerland), Luxembourg (Luxembourg) and Bolzano (Italy). The data resulting from this project will be submitted to peer-reviewed journals, presented at international congresses and made publicly available at the end of the trial.

Trial registration number

NCT04608604.
Status of the midwifery workforce and childbirth services and the impact of midwife staffing on birth outcomes in China: a multicentre cross-sectional study
Authors: Zhu Wenli , Zhu Chunxiang , Min Hui , Li Lingling , Wang Xiaojiao , Wu Jiangnan , Zhu Xinli , Gu Chunyi
Published: May 2024

Objective

To investigate the status of the midwifery workforce and childbirth services in China and to identify the association between midwife staffing and childbirth outcomes.

Design

A descriptive, multicentre cross-sectional survey.

Setting

Maternity hospitals from the eastern, central and western regions of China.

Participants

Stratified sampling of maternity hospitals between 1 July and 31 December 2021.

The sample hospitals received a package of questionnaires, and the head midwives from the participating hospitals were invited to fill in the questionnaires.

Results

A total of 180 hospitals were selected and investigated, staffed with 4159 midwives, 412 obstetric nurses and 1007 obstetricians at the labour and delivery units. The average efficiency index of annual midwifery services was 272 deliveries per midwife. In the sample hospitals, 44.9% of women had a caesarean delivery and 21.4% had an episiotomy. Improved midwife staffing was associated with reduced rates of instrumental vaginal delivery (adjusted β −0.032, 95% CI −0.115 to −0.012, p<0.05) and episiotomy (adjusted β −0.171, 95% CI −0.190 to −0.056, p<0.001).

Conclusion

The rates of childbirth interventions including the overall caesarean section in China and the episiotomy rate, especially in the central region, remain relatively high. Improved midwife staffing was associated with reduced rates of instrumental vaginal delivery and episiotomy, indicating that further investments in the midwifery workforce could produce better childbirth outcomes.
Practical guide to implementing patient-reported outcome measures in gender-affirming care: evaluating acceptability, appropriateness and feasibility
Authors: Kamran Rakhshan , Jackman Liam , Laws Anna , Stepney Melissa , Harrison Conrad , Jain Abhilash , Rodrigues Jeremy
Published: May 2024

Objective

Assess acceptability, appropriateness and feasibility of the Practical Guide to Implementing patient-reported outcome measures (PROMs) in Gender-Affirming Care (PG-PROM-GAC) from a sample of patients and healthcare professionals.

Design

Cross-sectional study conducted August–October 2023.

Setting

Participants were recruited from a National Health Service (NHS) gender clinic.

Participants

Patient participants seeking care and healthcare professionals working at an NHS gender clinic were eligible for participation. The PG-PROM-GAC was sent to participants via email for review.

Outcome measures

Three validated tools to measure acceptability, appropriateness and feasibility were administered: the acceptability of intervention measure (AIM), intervention appropriateness measure (IAM) and feasibility of intervention measure (FIM). The percentage of participants indicating agreement or disagreement with items on the AIM, IAM and FIM was calculated.

Results

A total of 132 transgender and gender diverse (TGD) patients (mean age, SD: 33, 14) and 13 gender-affirming healthcare professionals (mean age, SD: 43, 11) completed the AIM, IAM and FIM, representing a range of gender identities. The cumulative percentage of patients indicating agree or strongly agree on the AIM, IAM and FIM for the patient-relevant strategies in the PG-PROM-GAC was over 50% for each item. The cumulative percentage of patients indicating disagree or strongly disagree on the AIM, IAM and FIM for the PG-PROM-GAC was less than 20% for each item. The cumulative percentage of healthcare professionals indicating agree or strongly agree on the AIM, IAM and FIM for the healthcare professional-relevant strategies in the PG-PROM-GAC was over 38% for each item. The cumulative percentage of healthcare professionals indicating disagree or strongly disagree on the AIM, IAM and FIM for the PG-PROM-GAC was less than 15% for each item.

Conclusions

Gender-affirming healthcare professionals and TGD patients find the PG-PROM-GAC acceptable, appropriate and feasible. The PG-PROM-GAC is ready-to-use for clinicians, policy-makers and researchers committed to service improvement for gender-affirming care.
The Black Girls' Computing Classroom
Authors: Stewart Angela E. B.
Published: May 2024

In this forum we explore different perspectives for how to apply intersectionality as a critical framework for design across multiple contexts. ---
Yolanda A. Rankin and Jakita O. Thomas, Editors
A Survey on Privacy of Personal and Non-Personal Data in B5G/6G Networks
Authors: Sandeepa Chamara , Siniarski Bartlomiej , Kourtellis Nicolas , Wang Shen , Liyanage Madhusanka
Published: May 2024

The upcoming Beyond 5G (B5G) and 6G networks are expected to provide enhanced capabilities such as ultra-high data rates, dense connectivity, and high scalability. It opens many possibilities for a new generation of services driven by Artificial Intelligence (AI) and billions of interconnected smart devices. However, with this expected massive upgrade, the privacy of people, organisations, and states is becoming a rising concern. The recent introduction of privacy laws and regulations for personal and non-personal data signals that global awareness is emerging in the current privacy landscape. Yet, many gaps need to be identified in the case of two data types. If not detected, then they can lead to significant privacy leakages and attacks that will affect billions of people and organisations who utilise B5G/6G. This survey is a comprehensive study of personal and non-personal data privacy in B5G/6G to identify the current progress and future directions to ensure data privacy. We provide a detailed comparison of the two data types and a set of related privacy goals for B5G/6G. Next, we bring data privacy issues with possible solutions. This article also provides future directions to preserve personal and non-personal data privacy in future networks.
IMESH: A DSL for Mesh Processing
Authors: Li Yong , Kamil Shoaib , Crane Keenan , Jacobson Alec , Gingold Yotam
Published: May 2024

Mesh processing algorithms are often communicated via concise mathematical notation (e.g., summation over mesh neighborhoods). However, conversion of notation into working code remains a time-consuming and error-prone process, which requires arcane knowledge of low-level data structures and libraries—impeding rapid exploration of high-level algorithms. We address this problem by introducing a domain-specific language (DSL) for mesh processing called I

MESH, which resembles notation commonly used in visual and geometric computing and automates the process of converting notation into code. The centerpiece of our language is a flexible notation for specifying and manipulating neighborhoods of a cell complex, internally represented via standard operations on sparse boundary matrices. This layered design enables natural expression of algorithms while minimizing demands on a code generation backend. In particular, by integrating I

MESH with the linear algebra features of the I

LA DSL and adding support for automatic differentiation, we can rapidly implement a rich variety of algorithms on point clouds, surface meshes, and volume meshes.
A Systematic Literature Review on Reasons and Approaches for Accurate Effort Estimations in Agile
Authors: Pasuksmit Jirat , Thongtanunam Patanamon , Karunasekera Shanika
Published: May 2024

Background:
Accurate effort estimation is crucial for planning in Agile iterative development. Agile estimation generally relies on consensus-based methods like planning poker, which require less time and information than other formal methods (e.g., COSMIC) but are prone to inaccuracies. Understanding the common reasons for inaccurate estimations and how proposed approaches can assist practitioners is essential. However, prior systematic literature reviews (SLR) only focus on the estimation practices (e.g., References [
26
,
127
]) and the effort estimation approaches (e.g., Reference [
6
]).
Aim:
We aim at identifing themes of reasons for inaccurate estimations and classify approaches to improve effort estimation.
Method:
We conducted an SLR and identified the key themes and a taxonomy.
Results:
The reasons for inaccurate estimation are related to information quality, team, estimation practice, project management, and business influences. The effort estimation approaches were the most investigated in the literature, while only a few aim to support the effort estimation process. Yet, few automated approaches are at risk of data leakage and indirect validation scenarios.
Recommendations:
Practitioners should enhance the quality of information for effort estimation, potentially by adopting an automated approach. Future research should aim at improving the information quality, while avoiding data leakage and indirect validation scenarios.
Emotion Detection System for Malayalam Text using Deep Learning and Transformers
Authors: K Anuja , Raj P. C. Reghu , K R Remesh Babu
Published: May 2024

Recent advances in Natural Language Processing (NLP) have improved the performance of the systems that perform tasks, such as Emotion Detection (ED), Information Retrieval, Translation, etc., in resource-rich languages like English and Chinese. But similar advancements have not been made in Malayalam due to the dearth of annotated datasets. Because of its rich morphology, free word order and agglutinative character, data preparation in Malayalam is highly challenging. In this paper, we employ traditional Machine Learning (ML) techniques such as support vector machines (SVM) and multilayer perceptrons (MLP), and recent deep learning methods such as Recurrent Neural Networks (RNN) and advanced transformer-based methodologies to train an emotion detection system. This work stands out since all the previous attempts to extract emotions from Malayalam text have relied on lexicons, which are inappropriate for handling large amounts of data. By tweaking the hyperparameters, we enhanced the transformer-based model known as MuRIL to obtain an accuracy of 79%, which is then compared with the only state-of-the-art (SOTA) model. We found that the proposed techniques surpass the SOTA system available for detecting emotions in Malayalam reported so far.
The New Economics of Industrial Policy
Authors: Juhász Réka , Lane Nathan , Rodrik Dani
Published: May 2024

We discuss the considerable literature that has developed in recent years providing rigorous evidence on how industrial policies work. This literature is a significant improvement over the earlier generation of empirical work, which was largely correlational and marred by interpretational problems. On the whole, the recent crop of papers offers a more positive take on industrial policy. We review the standard rationales and critiques of industrial policy and provide a broad overview of new empirical approaches to measurement. We discuss how the recent literature, paying close attention to measurement, causal inference, and economic structure, is offering a nuanced and contextual understanding of the effects of industrial policy. We re-evaluate the East Asian experience with industrial policy in light of recent results. Finally, we conclude by reviewing how industrial policy is being reshaped by a new understanding of governance, a richer set of policy instruments beyond subsidies, and the reality of deindustrialization.
Online Fake News Opinion Spread and Belief Change: A Systematic Review
Authors: Altoe Filipe , Moreira Catarina , Pinto H. Sofia , Jorge Joaquim A.
Published: May 2024

Fake news has been linked to the rise of psychological disorders, the increased disbelief in science, and the erosion of democracy and freedom of speech. Online social networks are arguably the main vehicle of fake news spread. Educating online users with explanations is one way of preventing this spread. Understanding how online belief is formed and changed may offer a roadmap for such education. The literature includes surveys addressing online opinion formation and polarization; however, they usually address a single domain, such as politics, online marketing, health, and education, and do not make online belief change their primary focus. Unlike other studies, this work is the first to present a cross-domain systematic literature review of user studies, methodologies, and opinion model dimensions. It also includes the orthogonal polarization dimension, focusing on online belief change. We include peer-reviewed works published in 2020 and later found in four relevant scientific databases, excluding theoretical publications that did not offer validation through dataset experimentation or simulation. Bibliometric networks were constructed for better visualization, leading to the organization of the papers that passed the review criteria into a comprehensive taxonomy. Our findings show that a person’s individuality is the most significant influential force in online belief change. We show that online arguments that balance facts with emotionally evoking content are more efficient in changing their beliefs. Polarization was shown to be cross-correlated among multiple subjects, with politics being the central polarization pole. Polarized online networks start as networks with high opinion segregation, evolve into subnetworks of consensus, and achieve polarization around social network influencers. Trust in the information source was demonstrated to be the chief psychological construct that drives online users to polarization. This shows that changing the beliefs of influencers may create a positive snowball effect in changing the beliefs of polarized online social network users. These findings lay the groundwork for further research on using personalized explanations to reduce the harmful effects of online fake news on social networks.
The Reproducibility and Reliability of Insulin Sensitivity and Secretion Indices in Children and Adolescents
Authors: Hani Nellie Said , Vajravelu Mary Ellen , Meijer Jennifer L , McCaffery Harlan , Sturza Julie , Dhadphale Emily , Lee Joyce M
Published: May 2024

Context. Insulin sensitivity and secretion indices can be useful tools in understanding insulin homeostasis in children at risk for diabetes. There have been few studies examining the reproducibility of these measures in pediatrics. Objective. To determine whether fasting or oral glucose tolerance test (OGTT)-derived insulin measures would be more reproducible and whether there would be differences based on weight, sex, race, and pubertal status. Design. Observational study. Setting. Clinical research unit. Patients or Other Participants. Two hundred fifty-seven overweight/obese (BMI ≥ 85th%, n = 186) and normal weight (BMI < 85th%, n = 71) children without diabetes between ages of 8 and 17 were included in the study. Methods. OGTT tests performed in study participants at two separate visits within a 3-week period. We performed two formal oral glucose tolerance tests within a 3-week period. The reproducibility of fasting measures was compared with OGTT-derived measures by weight categories and compared by weight, sex, race, and pubertal status. Comparisons were made between the correlation coefficients of fasting vs. OGTT-derived measures and between normal weight vs. obese/overweight participants, male vs. female, White vs. Black, and pre- vs. post-midpubertal. Intraclass correlation coefficients were calculated for each comparison as well. Results. For insulin sensitivity, the OGTT-derived measure was more reproducible than the fasting measures. There were no significant differences in reproducibility in the overweight/obese population compared to the normal weight population nor by sex, race, or pubertal status. Conclusions. Nonfasting insulin sensitivity measures are more reproducible than fasting insulin sensitivity measures, regardless of weight category. Insulin secretion measures have poor reproducibility overall. Weight status, sex, race, and midpubertal stage do not impact the reproducibility of insulin sensitivity and secretion measures.
Characterisation of the Muscle Protein Synthetic Response to Resistance Exercise in Healthy Adults: A Systematic Review and Exploratory Meta-Analysis
Authors: Davies Robert W. , Lynch Arthur E. , Kumar Uttam , Jakeman Philip M.
Published: May 2024

Background and Objective. The rate of skeletal muscle protein synthesis (MPS) is the principal driving force underpinning the muscular adaptive response to resistance exercise (RE). This study aims to consolidate the literature, characterise MPS response to RE, and assess the impact of key covariates. Methods. Five electronic databases (PubMed (Medline), Web of Science, Embase, Sport Discus, and Cochrane Library) were searched for controlled trials that assessed the MPS response to RE in healthy, adult humans, postabsorptive state. Individual study and random-effects meta-analysis arewere used to inform the effects of RE and covariates on MPS. Results from 79 controlled trials with 237 participants were analysed. Results. Analysis of the pooled effects revealed robust increases in MPS following RE (weighted mean difference (WMD): 0.032% h−1, 95% CI: [0.024, 0.041] % h−1, I2 = 92%, k = 37, P<0.001). However, the magnitude of the increase in MPS was lower in older adults (>50 y: WMD: 0.015% h−1, 95% CI: [0.007, 0.022] % h−1, I2 = 76%, k = 12, P=0.002) compared to younger adults (<35 y: WMD: 0.041% h−1, 95% CI: [0.030, 0.052] % h−1, I2 = 88%, k = 25, P<0.001). Individual studies have reported that the temporal proximity of the RE, muscle group, muscle protein fraction, RE training experience, and the loading parameters of the RE (i.e., intensity, workload, and effort) appeared to affect the MPS response to RE, whereas sex or type of muscle contraction does not. Conclusion. A single bout of RE can sustain measurable increases in postabsorptive MPS soon after RE cessation and up to 48 h post-RE. However, there is substantial heterogeneity in the magnitude and time course of the MPS response between trials, which appears to be influenced by participants’ age and/or the loading parameters of the RE itself.
Computing the l,k-Clique Metric Dimension of Graphs via (Edge) Corona Products and Integer Linear Programming Model
Authors: Shahmiri Zeinab , Tavakoli Mostafa
Published: May 2024

Let G be a graph with n vertices and CG=X:X is an l-clique of G. A vertex v∈VG is said to resolve a pair of cliques X,Y in G if dGv,X≠dGv,Y where dG is the distance function of G. For a pair of cliques X,Y, the resolving neighbourhood of X and Y, denoted by RGX,Y, is the collection of all vertices which resolve the pair X,Y. A subset S of VG is called an l,k-clique metric generator for G if RGX,Y∩S≥k for each pair of distinct l-cliques X and Y of G. The l,k-clique metric dimension of G, denoted by l−cdimkG, is defined as minS:S is an l,k-clique metric generator of G. In this paper, the l,k-clique metric dimension of corona and edge corona of two graphs are computed. In addition, an integer linear programming model is presented for the l,k-clique metric basis for a given graph G and its l-cliques.
Metro Train Stopping Scheme Decision Based on Multisource Data in Express‐Local Train Mode
Authors: Li Jin , Wang Yaqiu , Zhang Shiyin , Liu Huasheng
Published: May 2024

The urban rail transit network has gradually realized grid operation with the increase in the coverage rate. Therefore, the stopping schemes in accordance with the trend of the passenger flow are more conducive to improving the attractiveness of the rail transit and improving the sharing rate of the urban public transit. Traditional data from a single source may not be sufficient to describe the overall trend of the passenger flow in a period of time, and the error is possible in the case of insufficient data. Based on the multisource data, the spatial weight function is introduced to fuse the point of interest data and real estate information data, from which one obtains the residential index and office index, and the cluster analysis is conducted to obtain the potential stop scheme. Then, the optimization model of the train operation plan is established, aiming at minimizing the passenger travel time and the generalized system cost, and is constrained by a series of driving conditions. Compared with the single data source, multisource data can better reflect passenger flow trends and land use characteristics. Compared with the traditional all‐station stopping scheme, a reasonable setting of crossing stations and running express‐local trains can better satisfy the demands of the passenger flow. Finally, the optimization of Changchun rail Transit Line 1 shows that the model can reduce the travel time of passengers and the operating cost of the rail transit company and improve the quality of service, so as to achieve a win‐win situation between passengers and the rail transit company.
Genomic Landscape Reveals Chromosomally-Mediated Antimicrobial Resistome and Virulome of a High-Risk International Clone II Acinetobacter baumannii AB073 from Thailand
Authors: Cheewapat Rattiya , Redkimned Jadsadaporn , Lekuthai Sirikran , Kitti Thawatchai , Tasanapak Kannipa , Thanwisai Aunchalee , Sitthisak Sutthirat , Sornda Thanet , Impheng Hathaichanok , Onsurathum Sudarat , Leungtongkam Udomluk , Lamlertthon Supaporn , Kucharoenphaibul Siriwat , Wongwigkarn Jintana , Singkum Pantira , Chanchaithong Pattrarat , Thummeepak Rapee
Published: May 2024

This study utilized integrative bioinformatics’ tools together with phenotypic assays to understand the whole-genome features of a carbapenem-resistant international clone II Acinetobacter baumannii AB073. Overall, we found the isolate to be resistant to seven antibiotic classes, penicillins, β-lactam/β-lactamase inhibitor combinations, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and folate pathway antagonists. These resistance phenotypes are related to various chromosomal-located antibiotic resistance determinants involved in different mechanisms such as reduced permeability, antibiotic target protection, antibiotic target alteration, antibiotic inactivation, and antibiotic efflux. IC2 A. baumannii AB073 could not transfer antibiotic resistance by conjugation experiments. Likewise, mobilome analysis found that AB073 did not carry genetic determinants involving horizontal gene transfer. Moreover, this isolate also carried multiple genes associated with the ability of iron uptake, biofilm formation, immune invasion, virulence regulations, and serum resistance. In addition, the genomic epidemiological study showed that AB073-like strains were successful pathogens widespread in various geographic locations and clinical sources. In conclusion, the comprehensive analysis demonstrated that AB073 contained multiple genomic determinants which were important characteristics to classify this isolate as a successful international clone II obtained from Thailand.
Supplementary Figure S2 from Breast Cancer Stem Cells Secrete MIF to Mediate Tumor Metabolic Reprogramming That Drives Immune Evasion
Authors: Yan Linlin , Wu Mingming , Wang Tianyu , Yuan Hui , Zhang Xiao , Zhang Huafeng , Li Tao , Pandey Vijay , Han Xinghua , Lobie Peter E. , Zhu Tao
Published: May 2024

Supplementary Figure S2 shows that BCSC CM enhances the aerobic glycolysis not oxidative phosphorylation.
Supplementary Table S3 from Severity of Complications and Duration of Type 2 Diabetes and the Risk of Cancer: A Population-Based Study
Authors: Hu Yu-Wen , Yeh Chiu-Mei , Liu Chia-Jen , Chen Tzeng-Ji , Huang Nicole , Chou Yiing-Jenq
Published: May 2024

Supplementary Table S3: Standardized incidence ratios for specific cancer types
Supplementary Table S8 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Table S8 shows Best differential lipids for differentiating early-stage OC (I and II) vs. non-OC.
Supplementary Table S4 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Table S4 shows Chromatographic gradient used for UHPLC-MS.
Supplementary Table S3 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Table S3 shows MS parameters
Supplementary Table S2 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Table S2 shows Isotopically labeled lipid internal standards (IS) used in UHPLC-MS experiments.
Supplementary Table S15 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Table S15 shows Effect size and AUC values for individual biomarkers in the 17-lipid panel.
Figure S2 from Prognostic Value of Pretreatment Plasma C-Reactive Protein in Patients with Early-Stage Breast Cancer
Authors: Andersen Høgni H. , Bojesen Stig E. , Johansen Julia S. , Ejlertsen Bent , Berg Tobias , Tuxen Malgorzata , Madsen Kasper , Danø Hella , Flyger Henrik , Jensen Maj-Britt , Nielsen Dorte L.
Published: May 2024

Distribution according to CRP
Supplementary Figure S14 from Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Kwon Sun Young , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: May 2024

Supplementary Figure S14 shows Permutation test result for the 17-lipid panel.
Figure S1 from Risk of Clinically Significant Prostate Cancer after a Nonsuspicious Prostate MRI—A Comparison with the General Population
Authors: Pylväläinen Juho , Hoffström Jaakko , Kenttämies Anu , Auvinen Anssi , Mirtti Tuomas , Rannikko Antti
Published: May 2024

Supplementary Figure S1. Formula used for calculating follow-up time for the general population. The Supplementary Figure S1 illustrates the process of used to calculate follow-up time for the men in the general population cohort at age Y. Population data (A and B) are sourced from the population data of Statistics Finland (RRID:SCR_024843) and prostate cancer (PCa) data is based on the institutional pathology data. This calculation was repeated for men of all ages (50-79 years).
Supplementary Table 3 from Association between Airport Ultrafine Particles and Lung Cancer Risk: The Multiethnic Cohort Study
Authors: Bookstein Arthur , Po Justine , Tseng Chiuchen , Larson Timothy V. , Yang Juan , Park Sung-shim L. , Wu Jun , Shariff-Marco Salma , Inamdar Pushkar P. , Ihenacho Ugonna , Setiawan Veronica W. , DeRouen Mindy C. , Le Marchand Loïc , Stram Daniel O. , Samet Jonathan , Ritz Beate , Fruin Scott , Wu Anna H. , Cheng Iona
Published: May 2024

Supplementary Table 3 shows an analysis of the association between Airport-Related UFP and Lung Cancer Risk by Smoking Status and Histology among California MEC Participants between 1993-2013.
Supplementary Table 2 from Association between Airport Ultrafine Particles and Lung Cancer Risk: The Multiethnic Cohort Study
Authors: Bookstein Arthur , Po Justine , Tseng Chiuchen , Larson Timothy V. , Yang Juan , Park Sung-shim L. , Wu Jun , Shariff-Marco Salma , Inamdar Pushkar P. , Ihenacho Ugonna , Setiawan Veronica W. , DeRouen Mindy C. , Le Marchand Loïc , Stram Daniel O. , Samet Jonathan , Ritz Beate , Fruin Scott , Wu Anna H. , Cheng Iona
Published: May 2024

Supplementary Table 2 shows an analysis of the association between Airport-Related UFP and Squamous Cell Carcinoma Risk by Smoking Status among California MEC participants between 1993-2013.
Supplementary Methods from Diffsig: Associating Risk Factors with Mutational Signatures
Authors: Park Ji-Eun , Smith Markia A. , Van Alsten Sarah C. , Walens Andrea , Wu Di , Hoadley Katherine A. , Troester Melissa A. , Love Michael I.
Published: May 2024

This document provides a more detailed explanation of the compositional nature of contributions and identifiability of associations and the priors for the hyperparameters
Supplementary Figure S2 from Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies
Authors: Ng Jin , Cai Ling , Girard Luc , Prall Owen W.J. , Rajan Neeha , Khoo Christine , Batrouney Ahida , Byrne David J. , Boyd Danielle K. , Kersbergen Ariena J. , Christie Michael , Minna John D. , Burr Marian L. , Sutherland Kate D.
Published: May 2024

Initial histopathological evaluation of SCLC xenografts.
Supplementary Table S1 from Systemic Biological Mechanisms of Neurocognitive Dysfunction in Long-Term Survivors of Childhood Hodgkin Lymphoma
Authors: Williams AnnaLynn M. , Liu Wei , Ehrhardt Matthew J. , Mirzaei Salehabadi Sedigheh , Panoskaltsis-Mortari Angela , Phillips Nicholas S. , Mulrooney Daniel A. , Flerlage Jamie E. , Yasui Yutaka , Srivastava Deokumar , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Sabin Noah D. , Krull Kevin R.
Published: May 2024

Mean neurocognitive Z-scores for any neuropsychological outcome where Hodgkin lymphoma survivors performed significantly worse than community controls after adjustment for multiple comparisons.
Supplementary Figure S1 from Systemic Biological Mechanisms of Neurocognitive Dysfunction in Long-Term Survivors of Childhood Hodgkin Lymphoma
Authors: Williams AnnaLynn M. , Liu Wei , Ehrhardt Matthew J. , Mirzaei Salehabadi Sedigheh , Panoskaltsis-Mortari Angela , Phillips Nicholas S. , Mulrooney Daniel A. , Flerlage Jamie E. , Yasui Yutaka , Srivastava Deokumar , Robison Leslie L. , Hudson Melissa M. , Ness Kirsten K. , Sabin Noah D. , Krull Kevin R.
Published: May 2024

Participation Flow Chart
Supplemental Figure 3 from Broad Next-Generation Integrated Sequencing of Myelofibrosis Identifies Disease-Specific and Age-Related Genomic Alterations
Authors: Kandarpa Malathi , Robinson Dan , Wu Yi-Mi , Qin Tingting , Pettit Kristen , Li Qing , Luker Gary , Sartor Maureen , Chinnaiyan Arul , Talpaz Moshe
Published: May 2024

Supplemental Figure 3. Circos plot and Dendrogram for Top 25 genes. A Circos plot (Panel A) depicts the relative frequency and pairwise co-occurrence of the top 25 genes mutated in patients with MF. The length of the arc corresponds to the frequency of mutations in the first gene, and the width of the ribbon corresponds to the percentage of patients who also had a mutation in the second gene. Pairwise co-occurrence of mutated genes is denoted only once, beginning with the first gene in the clockwise direction. Panels B shows the relative co-occurrence of mutated gene in a hierarchical clustering dendrogram form; the genes on the same branch are co-mutated more frequently. The shorter vertical lines greater the association.
Supplementary Video S8 from Mesothelin CAR T Cells Secreting Anti-FAP/Anti-CD3 Molecules Efficiently Target Pancreatic Adenocarcinoma and its Stroma
Authors: Wehrli Marc , Guinn Samantha , Birocchi Filippo , Kuo Adam , Sun Yi , Larson Rebecca C. , Almazan Antonio J. , Scarfò Irene , Bouffard Amanda A. , Bailey Stefanie R. , Anekal Praju Vikas , Montero Llopis Paula , Nieman Linda T. , Song Yuhui , Xu Katherine H. , Berger Trisha R. , Kann Michael C. , Leick Mark B. , Silva Harrison , Salas-Benito Diego , Kienka Tamina , Grauwet Korneel , Armstrong Todd D. , Zhang Rui , Zhu Qingfeng , Fu Juan , Schmidts Andrea , Korell Felix , Jan Max , Choi Bryan D. , Liss Andrew S. , Boland Genevieve M. , Ting David T. , Burkhart Richard A. , Jenkins Russell W. , Zheng Lei , Jaffee Elizabeth M. , Zimmerman Jacquelyn W. , Maus Marcela V.
Published: May 2024

Supplementary Video S8. Meso^CD19 CAR T cells not on target
Supplementary Video S1 from Mesothelin CAR T Cells Secreting Anti-FAP/Anti-CD3 Molecules Efficiently Target Pancreatic Adenocarcinoma and its Stroma
Authors: Wehrli Marc , Guinn Samantha , Birocchi Filippo , Kuo Adam , Sun Yi , Larson Rebecca C. , Almazan Antonio J. , Scarfò Irene , Bouffard Amanda A. , Bailey Stefanie R. , Anekal Praju Vikas , Montero Llopis Paula , Nieman Linda T. , Song Yuhui , Xu Katherine H. , Berger Trisha R. , Kann Michael C. , Leick Mark B. , Silva Harrison , Salas-Benito Diego , Kienka Tamina , Grauwet Korneel , Armstrong Todd D. , Zhang Rui , Zhu Qingfeng , Fu Juan , Schmidts Andrea , Korell Felix , Jan Max , Choi Bryan D. , Liss Andrew S. , Boland Genevieve M. , Ting David T. , Burkhart Richard A. , Jenkins Russell W. , Zheng Lei , Jaffee Elizabeth M. , Zimmerman Jacquelyn W. , Maus Marcela V.
Published: May 2024

Supplementary Video S1. Meso^FAP CAR T cells on AsPC1 + CAF
Supplementary Figure S2 from FDG PET/CT Imaging 1 Week after a Single Dose of Pembrolizumab Predicts Treatment Response in Patients with Advanced Melanoma
Authors: Anderson Thomas M. , Chang Bryan H. , Huang Alexander C. , Xu Xiaowei , Yoon Daniel , Shang Catherine G. , Mick Rosemarie , Schubert Erin , McGettigan Suzanne , Kreider Kristin , Xu Wei , Wherry E. John , Schuchter Lynn M. , Amaravadi Ravi K. , Mitchell Tara C. , Farwell Michael D.
Published: May 2024

Supplementary Figure S2. Change in SUVmax versus percentage of Ki67+ CD8 T cells.
Data from PPARα Agonism Enhances Immune Response to Radiotherapy While Dietary Oleic Acid Results in Counteraction
Authors: Ross Richard Blake , Gadwa Jacob , Yu Justin , Darragh Laurel B. , Knitz Michael W. , Nguyen Diemmy , Olimpo Nicholas A. , Abdelazeem Khalid N.M. , Nguyen Alexander , Corbo Sophia , Van Court Benjamin , Beynor Jessica , Neupert Brooke , Saviola Anthony J. , D'Alessandro Angelo , Karam Sana D.
Published: May 2024

AbstractPurpose:
Head and neck cancer (HNC) improvements are stagnant, even with advances in immunotherapy. Our previous clinical trial data show that altered fatty acid (FA) metabolism correlates with outcome. We hypothesized that pharmacologic and dietary modulation of FA catabolism will affect therapeutic efficacy.
Experimental Design:
We performed in vivo and in vitro experiments using PPARα agonism with fenofibrate (FF) or high oleic acid diets (OAD) with radiotherapy, generating metabolomic, proteomic, stable isotope tracing, extracellular flux analysis, and flow-cytometric data to investigate these alterations.
Results:
FF improved antitumor efficacy of high dose per fraction radiotherapy in HNC murine models, whereas the OAD reversed this effect. FF-treated mice on the control diet had evidence of increased FA catabolism. Stable isotope tracing showed less glycolytic utilization by ex vivo CD8+ T cells. Improved efficacy correlated with intratumoral alterations in eicosanoid metabolism and downregulated mTOR and CD36.
Conclusions:
Metabolic intervention with increased FA catabolism improves the efficacy of HNC therapy and enhances antitumoral immune response.
Supplementary Table S1 from Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
Authors: Dunbar Andrew J. , Bowman Robert L. , Park Young C. , O'Connor Kavi , Izzo Franco , Myers Robert M. , Karzai Abdul , Zaroogian Zachary , Kim Won Jun , Fernández-Maestre Inés , Waarts Michael R. , Nazir Abbas , Xiao Wenbin , Codilupi Tamara , Brodsky Max , Farina Mirko , Cai Louise , Cai Sheng F. , Wang Benjamin , An Wenbin , Yang Julie L. , Mowla Shoron , Eisman Shira E. , Hanasoge Somasundara Amritha Varshini , Glass Jacob L. , Mishra Tanmay , Houston Remie , Guzzardi Emily , Martinez Benitez Anthony R. , Viny Aaron D. , Koche Richard P. , Meyer Sara C. , Landau Dan A. , Levine Ross L.
Published: May 2024

RNA-Seq analysis - MPN vs. TAM
Supplementary Figure S4 from Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
Authors: Dunbar Andrew J. , Bowman Robert L. , Park Young C. , O'Connor Kavi , Izzo Franco , Myers Robert M. , Karzai Abdul , Zaroogian Zachary , Kim Won Jun , Fernández-Maestre Inés , Waarts Michael R. , Nazir Abbas , Xiao Wenbin , Codilupi Tamara , Brodsky Max , Farina Mirko , Cai Louise , Cai Sheng F. , Wang Benjamin , An Wenbin , Yang Julie L. , Mowla Shoron , Eisman Shira E. , Hanasoge Somasundara Amritha Varshini , Glass Jacob L. , Mishra Tanmay , Houston Remie , Guzzardi Emily , Martinez Benitez Anthony R. , Viny Aaron D. , Koche Richard P. , Meyer Sara C. , Landau Dan A. , Levine Ross L.
Published: May 2024

Assessment of tamoxifen toxicity on Jak2RL knock-in cells
Table S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Patient demographics
Figure S18 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S18. (A) UMAP embedding of single cell transcriptomes of all myeloid
cells obtained from all samples in this trial. Labeled are granular myeloid cell
types separated by tumor v.s. normal tissue, and by timepoint. (B) UMAP
embeddings showing marker gene expression for granular myeloid cell types in
(A).
Figure S15 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S15. Heatmap showing pairwise correlation of gene program activities
across all patient samples at baseline using the 90th percentile of patient-level
program activity in epithelial, myeloid, T, NK and stromal cells. Hierarchical
clustering was performed to identify clusters of co-varying proteins.
Figure S12 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

Figure S12. Mean usage of stromal cNMF programs per stromal cell subset at (A)
baseline, (B) post-chemotherapy (FU1) and (C) post-immunotherapy (FU2).
Figure S1 from Early Immune Remodeling Steers Clinical Response to First-Line Chemoimmunotherapy in Advanced Gastric Cancer
Authors: An Minae , Mehta Arnav , Min Byung Hoon , Heo You Jeong , Wright Samuel J. , Parikh Milan , Bi Lynn , Lee Hyuk , Kim Tae Jun , Lee Song-Yi , Moon Jeonghyeon , Park Ryan J. , Strickland Matthew R. , Park Woong-Yang , Kang Won Ki , Kim Kyoung-Mee , Kim Seung Tae , Klempner Samuel J. , Lee Jeeyun
Published: May 2024

(A) Swimmers plot of patient response and duration in the described
clinical trial. (B) Scatter plot showing temporal course of tumor response measured
by RECIST for all patients in the reported clinical trial. (C) Progression free survival
(PFS) and (D) overall survival (OS) for all patients in the reported clinical trial
separated by fast and slow progressors.
Supplementary Table 6 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Differentially expressed genes for MCF7: TAM latency and dormancy samples Vs POT; awakening Vs Dormancy samples
Supplementary Figure S7 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

Untreated PDX growth curves.
Supplementary Figure S3 from Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs
Authors: Pal Choudhuri Shreoshi , Girard Luc , Lim Jun Yi Stanley , Wise Jillian F. , Freitas Braeden , Yang Di , Wong Edmond , Hamilton Seth , Chien Victor D. , Kim Yoon Jung , Gilbreath Collin , Zhong Jun , Phat Sarah , Myers David T. , Christensen Camilla L. , Mazloom-Farsibaf Hanieh , Stanzione Marcello , Wong Kwok-Kin , Hung Yin P. , Farago Anna F. , Meador Catherine B. , Dyson Nicholas J. , Lawrence Michael S. , Wu Sihan , Drapkin Benjamin J.
Published: May 2024

Genomic analysis of chromosome 8 focal amplification in MGH1518-3A
Supplementary Figure S25 from Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Authors: Rosano Dalia , Sofyali Emre , Dhiman Heena , Ghirardi Chiara , Ivanoiu Diana , Heide Timon , Vingiani Andrea , Bertolotti Alessia , Pruneri Giancarlo , Canale Eleonora , Dewhurst Hannah F. , Saha Debjani , Slaven Neil , Barozzi Iros , Li Tong , Zemlyanskiy Grigory , Phillips Henry , James Chela , Győrffy Balázs , Lynn Claire , Cresswell George D. , Rehman Farah , Noberini Roberta , Bonaldi Tiziana , Sottoriva Andrea , Magnani Luca
Published: May 2024

Failed awakening characterization
Table S9 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 9 shows the top 50 combinations (all cancer types) using different % response scoring thresholds
Table S10 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 10 shows the number of hits using different % response scoring thresholds
Table S1 from Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations
Authors: Bashi Azadeh C. , Coker Elizabeth A. , Bulusu Krishna C. , Jaaks Patricia , Crafter Claire , Lightfoot Howard , Milo Marta , McCarten Katrina , Jenkins David F. , van der Meer Dieudonne , Lynch James T. , Barthorpe Syd , Andersen Courtney L. , Barry Simon T. , Beck Alexandra , Cidado Justin , Gordon Jacob A. , Hall Caitlin , Hall James , Mali Iman , Mironenko Tatiana , Mongeon Kevin , Morris James , Richardson Laura , Smith Paul D. , Tavana Omid , Tolley Charlotte , Thomas Frances , Willis Brandon S. , Yang Wanjuan , O'Connor Mark J. , McDermott Ultan , Critchlow Susan E. , Drew Lisa , Fawell Stephen E. , Mettetal Jerome T. , Garnett Mathew J.
Published: May 2024

Supplementary Table 1 lists cell lines used in this study