bluuebunny/crossref_metadata_2025 huggingface dataset:
Social factors condition consonant separation in Moroccan Arabic word-initial clusters: Amazigh-Arabic bilingualism, region, and speaking style
Authors: Zellou Georgia , Afkir Mohamed
Published: February 2025

Moroccan Arabic is a regional variety of spoken Arabic that contains linguistic features, which make it distinct from other dialects. Moroccan Arabic, for instance, contains a larger number of words with consonant clusters, a result of a historical vowel reduction process, compared to other Eastern varieties. Even within Moroccan Arabic, there is variation across speakers that is relatively understudied. The present study investigates across- and within-speaker factors that condition variation in the duration of acoustic separation between adjacent consonants in word-initial clusters in Moroccan Arabic. Three factors are examined: speaking style (clear vs fast speech), speaker region of origin (the Easternmost region of Morocco vs other regions), and speaker first language (Moroccan Arabic vs an Amazigh language). It is determined that (1) speakers produce more frequent, and longer when present, consonant separation in clear speech; (2) Amazigh-Arabic bilingual speakers produce higher rates and longer durations of consonant separations between adjacent consonants; and (3) regional dialect variation is also observed: speakers of Easternmost Moroccan Arabic produce more frequent and longer consonant separations than speakers from other Moroccan regions. Results are discussed for implications of speech production models as well as for theories of sound change.
Clostridioides difficile
infection study models and prospectives for probing the microbe-host interface
Authors: Zvonareva Tatiana , Courson David S. , Purcell Erin B.
Published: February 2025

Clostridioides difficile
infection (CDI) is an urgent public health threat with a high rate of recurrence and limited treatment options.
In vivo
models have been indispensable in understanding CDI pathophysiology and establishing treatment protocols and continue to be essential in pre-clinal testing. More importantly,
in vivo
models offer the opportunity to probe the complex systemic host response to the microbe, which is impossible to recapitulate
in vitro
. Nonetheless, constraints related to the availability of animal models, cost, ethical considerations, and regulatory control limit their accessibility for basic research. Furthermore, physiological and habitual divergences between animal models and humans often result in poor translatability to human patients. In addition to being more accessible,
in vitro
CDI models offer more control over experimental parameters and allow dynamic analysis of early infection.
In vitro
fermentation offers models for probing microbe-microbe and microbe-microbiome interactions, while continuous multi-stage platforms allow opportunities to study
C. difficile
pathophysiology and treatment in context with human-derived microbiota. However, these platforms are not suitable for probing the host-pathogen interface, leaving the challenge of modeling early CDI unanswered. As a result, alternative
in vitro
co-culture platforms are being developed. This review evaluates the strengths and weaknesses of each approach, as well as future directions for
C. difficile
research.
A new flavor of synthetic yeast communities sees the light
Authors: Rojas Vicente , Rivera Daniela , Ruiz Carlos , Larrondo Luis F.
Published: February 2025

No organism is an island: organisms of varying taxonomic complexity, including genetic variants of a single species, can coexist in particular niches, cooperating for survival while simultaneously competing for environmental resources. In recent years, synthetic biology strategies have witnessed a surge of efforts focused on creating artificial microbial communities to tackle pressing questions about the complexity of natural systems and the interactions that underpin them. These engineered ecosystems depend on the number and nature of their members, allowing complex cell communication designs to recreate and create diverse interactions of interest. Due to its experimental simplicity, the budding yeast
Saccharomyces cerevisiae
has been harnessed to establish a mixture of varied cell populations with the potential to explore synthetic ecology, metabolic bioprocessing, biosensing, and pattern formation. Indeed, engineered yeast communities enable advanced molecule detection dynamics and logic operations. Here, we present a concise overview of the state-of-the-art, highlighting examples that exploit optogenetics to manipulate, through light stimulation, key yeast phenotypes at the community level, with unprecedented spatial and temporal regulation. Hence, we envision a bright future where the application of optogenetic approaches in synthetic communities (optoecology) illuminates the intricate dynamics of complex ecosystems and drives innovations in metabolic engineering strategies.
What are the lived healthcare experiences of patients with primary sclerosing cholangitis? A community-based qualitative interview study
Authors: Arndtz Katherine , Cameron Madeline , Hirschfield Gideon , Parry Jayne , Greenfield Sheila
Published: February 2025

Objectives

Primary sclerosing cholangitis (PSC) is a rare chronic disease that presents challenges to both patients and clinicians. This study aimed to explore the experiences of patients with PSC regarding their disease and healthcare.

Design

A series of semi-structured interviews was completed with patients with PSC, including questioning their experiences of living with PSC and its related healthcare.

Setting

Participants were recruited from communities in England, Scotland and Wales, with advertisement via PSC Support (UK disease-specific charity support group).

Participants

18 patients aged between 21 and 72 years were interviewed; 10 were male (56%), and all were of Caucasian ethnicity. Inclusion criteria were as follows: adults, self-identifying as having a diagnosis of PSC, and currently under National Health Service treatment for this disease. Patients with a history of liver transplantation were excluded.

Results

Participants confirmed the ongoing physical and psychological burden of PSC and its related healthcare. Living with PSC was described as a journey; the timeline of events was important to patients, with particular challenges identified along the way. These included difficulties in obtaining a diagnosis and accessing timely and knowledgeable medical care. Overcoming the unusual combination of uncertainties that PSC presents was of particular concern to participants; these differ from those observed in more common chronic diseases with established treatment pathways. Hidden complexities within chronic illness behaviour in PSC were described, including a noteworthy fragile doctor−patient relationship and dependence on the specialist. These produce additional challenges for the optimal clinical management of such patients by generalists and specialists.

Conclusions

This study complements the existing literature on the ongoing high burden of PSC, with added value from in-depth discussions with patients themselves. Priorities for further work have been identified, including the need for improved risk stratification tools to allow individualised management and prognostication, as well as improving access to knowledgeable care while maintaining a strong doctor–patient relationship.
Transcranial direct current stimulation combined with physical exercise in rotator cuff tendinopathy: a protocol for a blinded randomised controlled trial
Authors: Silva César Augusto Medeiros , Lima Vinicius Batista , Cosme Hannely Beatriz Menezes , Fonseca Romário Nóbrega Santos , Hazime Fuad Ahmad , da Silva Rodrigo Scattone , Freitas Rodrigo Pegado de Abreu , de Souza Clecio Gabriel
Published: February 2025

Introduction

Pain is one of the primary symptoms affecting individuals with rotator cuff tendinopathy. Physical exercise serves as the main approach for managing this condition, aiming to restore movement patterns, optimise scapular kinematics and improve strength and local muscular endurance. Pain neuromodulation techniques, such as transcranial direct current stimulation (tDCS), may offer complementary non-pharmacological options for pain relief by promoting central modulation and altering cortical excitability.

Methods and analysis

This protocol outlines a randomised, blinded clinical trial. Participants will be randomly allocated to two groups: G1 (active tDCS combined with progressive exercise) and G2 (sham tDCS combined with progressive exercise). The protocol will span 4 weeks, with two sessions per week. Pain intensity, measured using the numerical pain scale, will serve as the primary outcome. Secondary outcomes will include physical function, range of motion, global perception of change and treatment adherence.

Ethics and dissemination

This protocol was approved by the Ethics Committee Health Sciences College of Trairi, Federal University of Rio Grande do Norte (number: 6.821.408). Followed the Declaration of Helsinki recommendations for research with human beings. The results will be published later in peer-reviewed journals and scientific events.

Trial registration number

The Brazilian Registry of Clinical Trials (RBR-59xmv6s); Results.
Nutritional interventions to prevent and reduce overweight and obesity during postacute stroke rehabilitation: a scoping review protocol
Authors: Nørtoft Mette , Sørensen Dorthe , Aadal Lena
Published: February 2025

Introduction

Individuals with stroke are at risk of long-term overweight and obesity due to biopsychosocial factors. Being overweight and obese is associated with an increased risk of numerous chronic conditions, including recurrent stroke. Unfortunately, recommendations for nutritional interventions vary. The objective of this scoping review is to identify and map the body of literature on professional nutritional interventions aimed at preventing or reducing overweight and obesity during postacute stroke rehabilitation.

Methods and analysis

The review follows the Joanna Briggs Institute methodology for scoping reviews. A three-step librarian-assisted search strategy will be conducted using the bibliographic databases MEDLINE (PubMed), Embase, CINAHL and Web of Science. Indexed and grey literature in English and Scandinavian languages, from January 2010 to the present, will be considered for inclusion. The scoping review will include materials such as research articles, methodological papers and clinical guidelines that report on nutritional interventions aimed at preventing or reducing overweight and obesity among individuals with stroke (aged ≥18 years) from admission to rehabilitation hospitals. We will map and identify any kind of nutritional intervention in rehabilitation hospitals, nursing homes or their own environments in high-income countries. Two independent reviewers will conduct an iterative process for screening the identified literature, paper selection and data extraction. Disagreements will be resolved through discussion or with an additional reviewer. A data extraction form will be used to guide the data extraction.

Ethics and dissemination

This review will involve the collection and analysis of secondary sources that have been published and/or are publicly available. Therefore, ethical approval is not required. The results will be published in an international peer-reviewed journal, presented at scientific conferences and disseminated through digital science communication platforms.

Trial registration number

The protocol is registered in the Open Science Framework:https://osf.io/ga63n/view_only=ee07beace7bb48d6b9c82cbf79cf2e95.
Results of a modified Delphi consensus on the optimal testing pathway for oesophago-gastric cancer care in the UK
Authors: Rodriguez-Justo Manuel , Mansoor Wasat , Bird Thomas , Eatock Martin , Starling Naureen , Taniere Philippe
Published: February 2025

Objective

To develop expert consensus on the optimal testing pathway for oesophago-gastric (OG) cancer care.

Methods and analysis

The process followed a modified Delphi methodology to develop consensus on the optimal testing pathway for OG cancer care. In November 2023, a review of available literature on the topic of OG cancer was conducted. The results of this review informed a steering group discussion on the barriers and opportunities within the OG testing pathway. Six domains of focus were agreed on and used to develop. 36 agreed statements were developed into a Likert survey, which was distributed by a third party (M3 Global Research). Completed surveys were analysed to produce an arithmetic agreement score for each statement. The results were then reviewed by the steering group to agree on any recommendations and conclusions.

Results

A total of 50 responses were received from consultant oncologists (n=25), pathologists (n=15), specialist oncology pharmacists (n=5) and specialist oncology nurses (n=5). Consensus was achieved in 35/36 statements (97%). The steering group agreed on a commentary on the results and a series of recommendations for best-practice testing in OG cancer. Given the level of agreement and that the stopping criteria were met, it was decided not to undertake further Delphi rounds.

Conclusion

The recommendations support the use of a reflex testing approach for human epidermal growth factor receptor 2, programmed death ligand 1 and microsatellite instability high/mismatch repair deficiency in patients diagnosed with OG cancer who are suitable for treatment with targeted therapy.
Global, regional and national burden of asthma attributable to NO2from 1990 to 2021: an analysis from the Global Burden of Disease Study 2021
Authors: Li Jingli , Zhang Chunyi , Qin E , Sun Jian , Liu Lingjing , Pu Guimei
Published: February 2025

Objectives

This study aims to systematically assess the global, regional, and national burden of asthma attributable to nitrogen dioxide (NO₂) pollution.

Design and setting

Analysis of population-level data from 1990 to 2021 obtained from the Global Burden of Disease Study 2021, covering 204 countries and territories.

Participants

Participants included patients with asthma attributable to NO₂ pollution.

Main outcomes and measures

Asthma-related disability-adjusted life-years (DALYs) and age-standardised DALY rates (ASDR) attributable to NO₂ pollution across 204 countries and territories. The estimated annual percentage change (EAPC) was used to assess temporal trends to identify regions with increasing or decreasing asthma burdens.

Results

In 2021, NO₂ pollution contributed to approximately 176.73 thousand DALYs globally, with an ASDR of 2.48 per 100 000 population (95% uncertainty interval (UI) −2.26 to 10.30). The global ASDR declined significantly from 1990 to 2021, with an EAPC of −1.93% (95% CI −2.14% to −1.72%). High-income North America had the highest ASDR (10.74 per 100 000; 95% UI 10.12 to 46.56), while Australasia experienced the most significant reduction in ASDR over the study period (EAPC −3.92%; 95% CI −4.46% to −3.37%). In contrast, Oceania and Southeast Asia showed increasing trends in asthma burden, with EAPCs of 2.33% (95% CI 1.57% to 3.10%) and 1.14% (95% CI 0.81% to 1.47%), respectively. The 5–9 age group carried the highest asthma burden, reflecting the vulnerability of younger children to NO₂ exposure. A positive correlation between ASDR and sociodemographic index (SDI) was observed (R=0.637, p<0.001), indicating a greater asthma burden in higher SDI regions.

Conclusion

The findings highlight significant regional and demographic disparities in asthma burden attributable to NO₂ pollution. Tailored public health strategies are needed to address the rising burden in vulnerable regions. Future research should focus on identifying effective interventions to reduce NO₂ exposure and improve asthma outcomes, especially in rapidly developing areas.
Tumor mutational burden and survival on immune checkpoint inhibition in >8000 patients across 24 cancer types
Authors: Gandara David R , Agarwal Neeraj , Gupta Shilpa , Klempner Samuel J , Andrews Miles C , Mahipal Amit , Subbiah Vivek , Eskander Ramez N , Carbone David P , Riess Jonathan W , Sammons Sarah , Snider Jeremy , Bouzit Lilia , Cho-Phan Cheryl , Price Megan , Li Gerald , Quintanilha Julia C F , Huang Richard Sheng Poe , Ross Jeffrey S , Fabrizio David , Oxnard Geoffrey R , Graf Ryon P
Published: February 2025

Background

There is uncertainty around clinical applicability of tumor mutational burden (TMB) across cancer types, in part because of inconsistency between TMB measurements from different platforms. The KEYNOTE 158 trial supported United States Food and Drug Administration (FDA) approval of the Foundation Medicine test (FoundationOneCDx) at TMB≥10 mut/Mb as a companion diagnostic (CDx) for single-agent pembrolizumab in second+line. Using a large real-world dataset with validated survival endpoint data, we evaluated clinical validity of TMB measurement by the test in over 8000 patients across 24 cancer types who received single-agent immune checkpoint inhibitor (ICI).

Methods

Patients with advanced-stage cancers from 24 cancer types treated with single-agent anti-PD(L)1 therapy in standard-of-care settings were included. Deidentified data from electronic health records from approximately 280 cancer treatment facilities were captured into a clinico-genomic database. This study used the TMB algorithm from the FDA-approved test supporting solid tumor CDx and composite mortality variable validated against the national death index: real-world overall survival (rwOS). Following a prespecified analysis plan, rwOS by TMB level was assessed using Cox PH models adjusted for Eastern Cooperative Oncology Group performance status, prior treatment, microsatellite instability, sex, age, opioid rx pretherapy, and socioeconomic assessment.

Results

8440 patients met inclusion criteria. Adjusting for aforementioned factors, increasing TMB was significantly associated with rwOS across tumor types; HRs (95% CIs) relative to TMB<5: TMB 5 to <10: 0.95 (0.89 to 1.02), TMB 10 to <20: 0.79 (0.73 to 0.85), TMB≥20: 0.52 (0.47 to 0.58). For individual cancer types with prespecified statistical power, adjusted rwOS comparing TMB≥10 vs TMB<10 significantly favored TMB≥10 in 9 of 10 cancer types. In microsatellite stable subcohorts (except colorectal cancer), TMB≥10 remained associated with enriched ICI benefit. Exploratory assessments of patients receiving ICI+chemotherapy (n=4369) observed more favorable rwOS only in TMB≥20.

Conclusions

Across >8000 patients treated with single-agent ICI, and within individual cancer types with sufficient power, elevated TMB based on the FDA-approved CDx was associated with more favorable rwOS compared with similar patients with lower TMB levels. This biomarker deserves further clinical investigation to potentially guide the use of immunotherapy in expanded clinical contexts.
Quantifying and Exploiting Adversarial Vulnerability: Gradient-Based Input Pre-Filtering for Enhanced Performance in Black-Box Attacks
Authors: Karunanayake Naveen , Silva Bhanuka , Ginige Yasod , Seneviratne Suranga , Chawla Sanjay
Published: February 2025

We investigate the vulnerability of inputs in an adversarial setting and demonstrate that certain samples are more susceptible to adversarial perturbations compared to others. Specifically, we employ a simple yet effective approach to quantify the adversarial vulnerability of inputs, which relies on the
clipped
gradients of the loss with respect to the input. Our observations indicate that inputs with a low percentage of zero gradient components tend to be more vulnerable to attacks. These findings are supported by a theoretical explanation on a linear model and empirical evidence on deep neural networks. Across all datasets we tested, we find that inputs with the lowest zero gradient percentage, on average, exhibit 34.5% more susceptibility to adversarial attacks than randomly selected inputs. Additionally, we demonstrate that the zero gradient percentage, as a metric, transfers across different model architectures. Finally, we propose a novel black-box attack pipeline that enhances the efficiency of conventional query-based black-box attacks and show that input pre-filtering based on ZGP can boost the attack success rates, particularly under low perturbation levels. On average, across all datasets we test, our approach outperforms the conventional shadow model-based and query-based black-box attack pipelines by 44.9% and 30.4%, respectively.
CPNet: Real-Time Cybersickness Prediction without Physiological Sensors for Cybersickness Mitigation
Authors: Qi Chang , Ding Ding , Chen Hao , Cao Zheyu , Zhang Wenjie
Published: February 2025

Although virtual reality (VR) has developed rapidly, offering unique user experience and broad application prospects, a significant challenge remains: its usage often induces cybersickness in users. Therefore, real-time and accurate prediction of cybersickness is essential to meet the requirements of alleviating cybersickness. Considering the limitations of using physiological signal sensors to predict cybersickness and the insufficient performance of previous methods, we introduce a novel deep learning model, CPNet, designed to effectively predict the severity of cybersickness by comprehensively considering features including head-tracking, eye-tracking, visual complexity, and experience duration. Moreover, we conducted an empirical study with 30 participants to collect a dataset aimed at validating the performance of our cybersickness prediction model. The results demonstrate that our approach achieves higher prediction accuracy than advanced models such as Informer, TimesNet, and Islam’s cybersickness prediction model.
Private Low-Rank Approximation for Covariance Matrices, Dyson Brownian Motion, and Eigenvalue-Gap Bounds for Gaussian Perturbations
Authors: Mangoubi Oren , Vishnoi Nisheeth
Published: February 2025

We consider the problem of approximating a
d
×
d
covariance matrix
M
with a rank-
k
matrix under (ε,
δ
)-differential privacy. We present and analyze a complex variant of the Gaussian mechanism and obtain upper bounds on the Frobenius norm of the difference between the matrix output by this mechanism and the best rank-
k
approximation to
M
. Our analysis provides improvements over previous bounds, particularly when the spectrum of
M
satisfies natural structural assumptions. The novel insight is to view the addition of Gaussian noise to a matrix as a continuous-time matrix Brownian motion. This viewpoint allows us to track the evolution of eigenvalues and eigenvectors of the matrix, which are governed by stochastic differential equations discovered by Dyson. These equations enable us to upper bound the Frobenius distance between the best rank-
k
approximation of
M
and that of a Gaussian perturbation of
M
as an integral that involves inverse eigenvalue gaps of the stochastically evolving matrix, as opposed to a sum of perturbation bounds obtained via Davis-Kahan-type theorems. Subsequently, again using the Dyson Brownian motion viewpoint, we show that the eigenvalues of the matrix
M
perturbed by Gaussian noise have large gaps with high probability. These results also contribute to the analysis of low-rank approximations under average-case perturbations, and to an understanding of eigenvalue gaps for random matrices, both of which may be of independent interest.
Unveiling Device Corner-Point Potential in Sensing Domain: COVID Biomarker S-Protein Detection with Novel Ge0.958Sn0.042 Material-based TFET Biosensor
Authors: Gayen Sanu , Tewari Suchismita , Chattopadhyay Avik
Published: February 2025

In this paper, a unique Ge0.958Sn0.042 TFET-based biosensor is proposed for the successful detection of the biomarker S-protein, utilizing a combination of low-k(nanogap cavity) and high-k gate insulating dielectric materials, along with an intentional corner-point at the source/channel junction. This interdisciplinary work aims to explore the potential of the corner-point, which generally produces detrimental or adverse effect in electronic or device domain, in the sensing domain in terms of responsivity, sensitivity, stability, linearity, and efficiency. For the first time, comprehensive design guidelines, optimizing channel epilayer thickness and nanogap cavity length, are provided. The paper highlights the investigation of the interplay between the electrostatics associated with the corner-point and with the low-k/high-k dielectric junction, leading to the optimization of the channel epilayer thickness and the nanogap cavity length. Additionally, the potential for reducing the minimum number of required biomolecules for successful detection is introduced for the first time in this paper. Furthermore, the steric effect on the sensitivity is also studied to incorporate some practical scenario.
Enhancing Servo Performance of a Two‐Degree‐of‐Freedom Rotary Table Using Intelligent Control Optimized by SSA–GA
Authors: Gao Xinan , Guan Xiaorong , Li Huibin , Wang Zheng , Kang Jinyu , Yang Yanlong
Published: February 2025

The two‐degree‐of‐freedom rotation stage serves as a crucial component in ground unmanned platforms, and its servo performance is pivotal to the platform’s overall functionality. To enhance the servo performance of the two‐degree‐of‐freedom rotation stage, we proposed a novel adaptive control approach: SSA–GA optimization of RBFNN integration into PID control. This method leverages the SSA–GA algorithm to optimize the parameters within the RBFNN, which is then seamlessly integrated into the PID control framework. This integration enables precise control of the two‐degree‐of‐freedom rotation stage, overcoming the limitations of traditional PID controllers. By simulating various real‐world situations such as step, noise, sinusoidal, transient excitation, impulse and modelling errors, it is demonstrated that the proposed control method achieves significant improvement in terms of control accuracy, fast response and robustness. It offers a more effective and reliable method for controlling the two‐degree‐of‐freedom rotation stage, addressing the challenges posed by various interfering factors. Meanwhile, through comprehensive comparisons with various optimization algorithms, we have proven that SSA–GA has the shortest optimization time. Consequently, the proposed method exhibits excellent application potential and broad prospects for future applications.
Table S3 from A Screen-and-Treat Strategy for Eradication of Helicobacter pylori among Patients with Family History of Gastric Cancer in a Diverse US Population
Authors: Zia Mona , Park Steven , Chen Qiaoling , Luong Tiffany Q. , Lustigova Eva , Jeon Christie Y. , Chen Wansu , Wu Bechien U.
Published: February 2025

Table S3 reports the adverse events among 15 participants who received treatment for H. pylori.
Figure S1 from A Screen-and-Treat Strategy for Eradication of Helicobacter pylori among Patients with Family History of Gastric Cancer in a Diverse US Population
Authors: Zia Mona , Park Steven , Chen Qiaoling , Luong Tiffany Q. , Lustigova Eva , Jeon Christie Y. , Chen Wansu , Wu Bechien U.
Published: February 2025

Figure S1 is a flow chart illustrating survey response and participation in screening for H. pylori. Among 280 participants who responded to the survey, 223 indicated interest in H. pylori screening, 33 patients were not interested in screening for H. pylori, and 24 patients needed more information before deciding to screen.
Supplementary Figure 1 from Effects of a Tailored Mobile Messaging Intervention for Indoor Tanning Cessation in Young Females: A Randomized Clinical Trial
Authors: Mays Darren , Alalwan Mahmood A. , Long Lauren , Atkins Michael B. , Tercyak Kenneth P.
Published: February 2025

Supplementary Figure S1 displays example message content from the tanning cessation intervention. The example shown is from the first day on which participants received messages in the intervention arm.
Supplementary Table 3 from Patterns of Subsequent Cancer Incidence Over Time in Patients with Breast Cancer
Authors: Deng Zhengyi , Visvanathan Kala
Published: February 2025

Supplementary Table 3. Risk of subsequent primary cancers among breast cancer survivors overall and by every 5 years since initial breast cancer diagnosis according to HR status of the initial breast cancer.
Supplemental Table S7 from Evaluation of Multiple Breast Cancer Polygenic Risk Score Panels in Women of Latin American Heritage
Authors: Huang Xiaosong , Lott Paul C. , Hu Donglei , Zavala Valentina A. , Jamal Zoeb N. , Vidaurre Tatiana , Casavilca-Zambrano Sandro , Navarro Vásquez Jeannie , Castañeda Carlos A. , Valencia Guillermo , Morante Zaida , Calderón Mónica , Abugattas Julio E. , Fuentes Hugo A. , Liendo-Picoaga Ruddy , Cotrina Jose M. , Neciosup Silvia P. , Rioja Viera Patricia , Salinas Luis A. , Galvez-Nino Marco , Huntsman Scott , Sanchez Sixto E. , Williams Michelle A. , Gelaye Bizu , Estrada-Florez Ana P. , Polanco-Echeverry Guadalupe , Echeverry Magdalena , Velez Alejandro , Carmona-Valencia Jenny A. , Bohorquez-Lozano Mabel E. , Torres Javier , Cruz Miguel , Ho Weang-Kee , Teo Soo Hwang , Tai Mei Chee , John Esther M. , Haiman Christopher A. , Conti David V. , Chen Fei , Torres-Mejía Gabriela , Kushi Lawrence H. , Neuhausen Susan L. , Ziv Elad , Carvajal-Carmona Luis G. , Fejerman Laura
Published: February 2025

Supplemental Table S7 shows comparisons of performance for the PRS panel pairs in different ranges of Indigenous American (IA) ancestry.
Supplemental Table S4 from Evaluation of Multiple Breast Cancer Polygenic Risk Score Panels in Women of Latin American Heritage
Authors: Huang Xiaosong , Lott Paul C. , Hu Donglei , Zavala Valentina A. , Jamal Zoeb N. , Vidaurre Tatiana , Casavilca-Zambrano Sandro , Navarro Vásquez Jeannie , Castañeda Carlos A. , Valencia Guillermo , Morante Zaida , Calderón Mónica , Abugattas Julio E. , Fuentes Hugo A. , Liendo-Picoaga Ruddy , Cotrina Jose M. , Neciosup Silvia P. , Rioja Viera Patricia , Salinas Luis A. , Galvez-Nino Marco , Huntsman Scott , Sanchez Sixto E. , Williams Michelle A. , Gelaye Bizu , Estrada-Florez Ana P. , Polanco-Echeverry Guadalupe , Echeverry Magdalena , Velez Alejandro , Carmona-Valencia Jenny A. , Bohorquez-Lozano Mabel E. , Torres Javier , Cruz Miguel , Ho Weang-Kee , Teo Soo Hwang , Tai Mei Chee , John Esther M. , Haiman Christopher A. , Conti David V. , Chen Fei , Torres-Mejía Gabriela , Kushi Lawrence H. , Neuhausen Susan L. , Ziv Elad , Carvajal-Carmona Luis G. , Fejerman Laura
Published: February 2025

Supplemental Table S4 shows a list of polymorphisms in the PRS panels with association analyses summary statistics from 7 pooled Hispanic/Latino datasets.
Supplementary Figure 2 from Patterns of Subsequent Cancer Incidence Over Time in Patients with Breast Cancer
Authors: Deng Zhengyi , Visvanathan Kala
Published: February 2025

Supplementary Figure 2. Risk of subsequent breast cancers. Risk of subsequent breast cancer by every 2 years since initial breast cancer diagnosis after removing patients who had bilateral mastectomy, unknown if surgery performed, or surgery type not specified. SIR: standardized incidence ratio; CI, confidence interval.
Supplemental Table S3 from Evaluation of Multiple Breast Cancer Polygenic Risk Score Panels in Women of Latin American Heritage
Authors: Huang Xiaosong , Lott Paul C. , Hu Donglei , Zavala Valentina A. , Jamal Zoeb N. , Vidaurre Tatiana , Casavilca-Zambrano Sandro , Navarro Vásquez Jeannie , Castañeda Carlos A. , Valencia Guillermo , Morante Zaida , Calderón Mónica , Abugattas Julio E. , Fuentes Hugo A. , Liendo-Picoaga Ruddy , Cotrina Jose M. , Neciosup Silvia P. , Rioja Viera Patricia , Salinas Luis A. , Galvez-Nino Marco , Huntsman Scott , Sanchez Sixto E. , Williams Michelle A. , Gelaye Bizu , Estrada-Florez Ana P. , Polanco-Echeverry Guadalupe , Echeverry Magdalena , Velez Alejandro , Carmona-Valencia Jenny A. , Bohorquez-Lozano Mabel E. , Torres Javier , Cruz Miguel , Ho Weang-Kee , Teo Soo Hwang , Tai Mei Chee , John Esther M. , Haiman Christopher A. , Conti David V. , Chen Fei , Torres-Mejía Gabriela , Kushi Lawrence H. , Neuhausen Susan L. , Ziv Elad , Carvajal-Carmona Luis G. , Fejerman Laura
Published: February 2025

Supplemental Table S3 shows sample sizes in the Indigenous American ancestry ranges selected for our analysis.
Supplemental Table S2 from Evaluation of Multiple Breast Cancer Polygenic Risk Score Panels in Women of Latin American Heritage
Authors: Huang Xiaosong , Lott Paul C. , Hu Donglei , Zavala Valentina A. , Jamal Zoeb N. , Vidaurre Tatiana , Casavilca-Zambrano Sandro , Navarro Vásquez Jeannie , Castañeda Carlos A. , Valencia Guillermo , Morante Zaida , Calderón Mónica , Abugattas Julio E. , Fuentes Hugo A. , Liendo-Picoaga Ruddy , Cotrina Jose M. , Neciosup Silvia P. , Rioja Viera Patricia , Salinas Luis A. , Galvez-Nino Marco , Huntsman Scott , Sanchez Sixto E. , Williams Michelle A. , Gelaye Bizu , Estrada-Florez Ana P. , Polanco-Echeverry Guadalupe , Echeverry Magdalena , Velez Alejandro , Carmona-Valencia Jenny A. , Bohorquez-Lozano Mabel E. , Torres Javier , Cruz Miguel , Ho Weang-Kee , Teo Soo Hwang , Tai Mei Chee , John Esther M. , Haiman Christopher A. , Conti David V. , Chen Fei , Torres-Mejía Gabriela , Kushi Lawrence H. , Neuhausen Susan L. , Ziv Elad , Carvajal-Carmona Luis G. , Fejerman Laura
Published: February 2025

Supplemental Table S2 shows performance of PRS panels constructed from PRS3820 European panel plus 2 H/L SNPs using different imputation r2 cutoffs.
Supplementary Figure S1 from Timeliness of Lung Cancer Care and Area-Level Determinants in Victoria: A Bayesian Spatiotemporal Analysis
Authors: Tesema Getayeneh Antehunegn , Tessema Zemenu Tadesse , Heritier Stephane , Stirling Rob G. , Earnest Arul
Published: February 2025

Inclusion and exclusion criteria
Supplementary Table S1 from Incidence of Serious Complications following Screening Colonoscopy in Adults Ages 76 to 85 Years
Authors: Chubak Jessica , Ichikawa Laura E. , Merchant Sophie A. , Dalmat Ronit R. , Ziebell Rebecca A. , Jensen Christopher D. , Lee Jeffrey K. , Corley Douglas A. , Ghai Nirupa R. , Green Beverly B. , Skinner Celette Sugg , Schottinger Joanne E. , Breslau Erica S. , Levin Theodore R.
Published: February 2025

Supplementary Table S1: Study design elements for narrow and broad risk models of harms associated with screening colonoscopy in adults 76-85 years old in three integrated healthcare delivery systems, 2010-2019
Supplementary Figure S1 from Incidence of Serious Complications following Screening Colonoscopy in Adults Ages 76 to 85 Years
Authors: Chubak Jessica , Ichikawa Laura E. , Merchant Sophie A. , Dalmat Ronit R. , Ziebell Rebecca A. , Jensen Christopher D. , Lee Jeffrey K. , Corley Douglas A. , Ghai Nirupa R. , Green Beverly B. , Skinner Celette Sugg , Schottinger Joanne E. , Breslau Erica S. , Levin Theodore R.
Published: February 2025

Supplementary Figure S1: Schematic of time frames used for outcome assessment in risk models.
Supplementary Table 7 from Significant Disparities in Hepatocellular Carcinoma Outcomes by Race/Ethnicity and Sociodemographic Factors
Authors: Patel Shyam , Khalili Mandana , Singal Amit G. , Pinheiro Paulo S. , Jones Patricia D. , Kim Rebecca G. , Kode Vishwajit , Thiemann Anna , Zhang Wei , Cheung Ramsey , Wong Robert J.
Published: February 2025

Supplementary Table 7 shows results from the adjusted multivariable competing risks analyses evaluating for predictors of HCC-specific mortality, stratified by race/ethnicity.
Supplementary Table 5 from Significant Disparities in Hepatocellular Carcinoma Outcomes by Race/Ethnicity and Sociodemographic Factors
Authors: Patel Shyam , Khalili Mandana , Singal Amit G. , Pinheiro Paulo S. , Jones Patricia D. , Kim Rebecca G. , Kode Vishwajit , Thiemann Anna , Zhang Wei , Cheung Ramsey , Wong Robert J.
Published: February 2025

Supplementary Table 5 shows results from the adjusted multivariable Cox proportional hazards model evaluating for predictors of overall mortality, stratified by race/ethnicity
Supplementary Table 3 from Significant Disparities in Hepatocellular Carcinoma Outcomes by Race/Ethnicity and Sociodemographic Factors
Authors: Patel Shyam , Khalili Mandana , Singal Amit G. , Pinheiro Paulo S. , Jones Patricia D. , Kim Rebecca G. , Kode Vishwajit , Thiemann Anna , Zhang Wei , Cheung Ramsey , Wong Robert J.
Published: February 2025

Supplementary Table 3 shows results from the adjusted multivariable logistic regression analyses evaluating for predictors of receiving HCC surgical treatment, stratified by race/ethnicity.
Supplementary Table 1 from Significant Disparities in Hepatocellular Carcinoma Outcomes by Race/Ethnicity and Sociodemographic Factors
Authors: Patel Shyam , Khalili Mandana , Singal Amit G. , Pinheiro Paulo S. , Jones Patricia D. , Kim Rebecca G. , Kode Vishwajit , Thiemann Anna , Zhang Wei , Cheung Ramsey , Wong Robert J.
Published: February 2025

Supplementary Table 1 shows the results of adjusted multivariable logistic regression analyses evaluating for predictors of tumor stage at diagnosis among patients with HCC, stratified by race/ethnicity.
Supplementary Table S8 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Association between weighted lifestyle score and colorectal cancer risk
Supplementary Table S2 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Healthy lifestyle factor definitions
Supplementary Table S12 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Risk of colorectal cancer incidence across lifestyle categories within genetic risk levels based on quartiles or tertiles of polygenic risk score
Supplementary Table S1 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Summary of 205 colorectal cancer GWAS-reported SNPs involved in polygenic risk score
Supplementary Figure S5 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Lifetime risk of colorectal cancer in the PLCO cohort across genetic risk levels and lifestyle levels. (A) Lifetime risk of colorectal cancer incidence for different PRS categories in the PLCO cohort, using age as the time scale. (B) Lifetime risk of colorectal cancer incidence for different lifestyle levels in the PLCO cohort, using age as a time scale. Abbreviations: CI, confidence interval; PLCO, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial; PRS, polygenic risk score.
Figure S7 from CYP2D6 Phenotype and Breast Cancer Outcomes: A Bias Analysis and Meta-Analysis
Authors: MacLehose Richard F. , Ahern Thomas P. , Collin Lindsay J. , Li Aixin , Lash Timothy L.
Published: February 2025

Supplementary Figure S7: Forest plot of IM vs NM, studies from primarily Asian populations only.
Supplementary Figure S4 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Effect of genetic risk and lifestyle factors on the risk of colorectal cancer in the PLCO cohort. (A) Participants were divided into five equal groups (quintiles) according to polygenic risk score, and the HRs for each group were compared with those in quintile 1 of the polygenic risk score; error bars show the 95% CIs. (B) Participants were divided into seven groups according to the number of healthy lifestyle factors, and the HRs for each group were compared with those who adopted no healthy lifestyle factor; error bars show the 95% CIs. Abbreviations: CI, confidence interval; HR, hazards ratio; PLCO, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.
Supplementary Figure S3 from Polygenic Risk Score, Healthy Lifestyle Score, and Colorectal Cancer Risk: A Prospective Cohort Study
Authors: Shen Yuefan , Chen Weiwei , Fu Chengqu , Liu Xinyi , Miao Junyan , Li Jiacong , Li Ni , Hang Dong
Published: February 2025

Effect of genetic and lifestyle factors on the risk of incident colorectal cancer stratified by race. The cumulative incidence of colorectal cancer in low (quintile 1), intermediate (quintiles 2–4), and high (quintile 5) genetic risk groups in white (A) and non-white (B), P for heterogeneity = 0.512. The cumulative incidence of colorectal cancer in participants who had a favorable lifestyle (adopted at least four healthy lifestyle factors), an intermediate lifestyle (adopted two or three healthy lifestyle factors), and an unfavorable lifestyle (adopted none or one healthy lifestyle factor) in the white population (C) and in the non-white population (D), P for heterogeneity = 0.068. Abbreviations: CI, confidence interval; HR, hazards ratio.
Figure S2 from CYP2D6 Phenotype and Breast Cancer Outcomes: A Bias Analysis and Meta-Analysis
Authors: MacLehose Richard F. , Ahern Thomas P. , Collin Lindsay J. , Li Aixin , Lash Timothy L.
Published: February 2025

Supplementary Figure S2: Inverse normal rank percentile of bias adjusted effects.
Figure S1 from CYP2D6 Phenotype and Breast Cancer Outcomes: A Bias Analysis and Meta-Analysis
Authors: MacLehose Richard F. , Ahern Thomas P. , Collin Lindsay J. , Li Aixin , Lash Timothy L.
Published: February 2025

Supplementary Figure S1: Forest plot of poor vs normal metabolizers.
Data from A Screen-and-Treat Strategy for Eradication of Helicobacter pylori among Patients with Family History of Gastric Cancer in a Diverse US Population
Authors: Zia Mona , Park Steven , Chen Qiaoling , Luong Tiffany Q. , Lustigova Eva , Jeon Christie Y. , Chen Wansu , Wu Bechien U.
Published: February 2025

AbstractBackground:
Screening and eradication of Helicobacter pylori reduce the risk of gastric cancer in patients with a family history. We assessed patient perspectives on H. pylori screening and treatment within a diverse regional US population.
Methods:
Between July 2022 and August 2022, we conducted a cross-sectional study among patients with ≥1 first-degree relative(s) with gastric cancer. Eligible patients were between 18 and 75 years of age without history of H. pylori infection or gastric cancer. A survey assessed interest in testing and willingness to complete treatment for H. pylori. Interested patients were offered H. pylori testing and treatment. We examined interest and effectiveness of treatment by race and ethnicity.
Results:
We identified 15,255 eligible patients, and 1,500 patients were randomly selected for the survey; 280 (19%) patients, including two relatives not initially invited but asked to participate, responded following outreach. Respondents were 65% male and averaged 57 years (SD = 13) with 36% Hispanic, 36% non-Hispanic White, 15% Asian/Pacific Islander, and 9% non-Hispanic Black. Overall, 223 (80%) were interested in H. pylori screening; of these, 89% would take antibiotics as prescribed. Willingness to screen was consistent across racial and ethnic groups. Among 223 respondents interested in screening, 128 (57%) completed testing with 15 screen-detected cases; all 15 completed treatment, and 11 had confirmed eradication.
Conclusions:
Patients with family history of gastric cancer had a high level of interest in H. pylori screening and successful eradication when detected.
Impact:
A screen-and-treat strategy for H. pylori may be considered for patients with family history of gastric cancer.
Data from Adverse Birth and Obstetric Outcomes in the Offspring of Male Adolescent and Young Adult Cancer Survivors: A Nationwide Population-Based Study
Authors: Kao Wei-Heng , Chuang Yi-Fang , Huang Yi-Wei , Chen Po-Jui , Liu Yu-Cheng , Wang Chun-Chieh , Hsu Jun-Te , Shueng Pei-Wei , Kuo Chang-Fu
Published: February 2025

AbstractBackground:
The growing population of male adolescent and young adult (AYA, ages 15–40 years) cancer survivors has heightened interest in their reproductive health. However, studies have reported conflicting findings on the potential risks of cancer and its treatments on birth and obstetric outcomes.
Methods:
We used encrypted identification numbers for both fathers and mothers to link three nationwide Taiwan datasets from 2004 to 2019, identifying 3,785 births with a paternal history of AYA cancer. For comparison, we included 37,850 matched fathers without a cancer history, matched by paternal age and infant birth year. We used multivariable logistic regression analysis to identify independent associations between adverse birth outcomes (e.g., preterm labor, low birthweight, and congenital malformations) and obstetric outcomes (e.g., fetal growth restriction, threatened labor, and threatened abortion) and being born to male AYA cancer survivors.
Results:
The offspring of male AYA cancer survivors did not exhibit a significantly increased risk of adverse birth (OR = 1.0; 95% confidence interval, 0.9−1.1) or obstetric (OR = 1.1; 95% confidence interval, 1.0−1.1) outcomes compared with offspring born to cancer-free matched fathers. Furthermore, the risk of preterm labor, low birthweight, congenital malformations, fetal growth restriction, and threatened labor or miscarriage was comparable between groups.
Conclusions:
Paternal cancer history during adolescence or young adulthood does not seem to increase the risk of adverse birth or obstetric outcomes in offspring.
Impact:
This study reassures the reproductive health of this population, providing valuable insights for oncology and reproductive medicine, potentially influencing patient counseling and guidelines.
Data from Timeliness of Lung Cancer Care and Area-Level Determinants in Victoria: A Bayesian Spatiotemporal Analysis
Authors: Tesema Getayeneh Antehunegn , Tessema Zemenu Tadesse , Heritier Stephane , Stirling Rob G. , Earnest Arul
Published: February 2025

AbstractBackground:
The reports have stated that the timeliness of lung cancer care varies significantly across different regions. According to the Victorian Lung Cancer Registry report, the timeliness of lung cancer care in Victoria has changed over time. Therefore, we aimed to quantify the extent of these spatial inequalities over time and to identify area-level determinants contributing to these changes.
Methods:
The study analyzed lung cancer cases reported to the Victorian Lung Cancer Registry between 2011 and 2022. Bayesian spatiotemporal conditional autoregressive models were fitted, incorporating spatial random effects, temporal random effects, and spatiotemporal interactions. The best performing model was selected using the deviance information criterion. For the final best fit model, the adjusted RRs and their 95% credible intervals were reported.
Results:
More than half (51.24%) of patients with lung cancer experienced treatment delays, whereas approximately one third (30.98%) encountered diagnostic delays. Moderate spatiotemporal variations were observed in both delayed diagnosis and treatment. In the final best fit model for treatment delay, an increase in the percentage of smokers was significantly associated with a higher risk of treatment delay (RR = 2.13; 95% credible interval, 1.13–4.20).
Conclusions:
Identifying high-risk areas provides useful information for policymakers, helping in the reduction of delays in lung cancer diagnosis and treatment.
Impact:
This study has revealed spatiotemporal inequalities in diagnostic and treatment delays, providing valuable insights for identifying areas that should be prioritized to ensure timely care for lung cancer.