bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-molecule tracking reveals dynamic regulation of ribosomal scanning
Authors: Hong Hea Jin , Zhang Antonia L. , Conn Adam B. , Blaha Gregor , O’Leary Seán E.
Published: October 2024

How eukaryotic ribosomes traverse messenger RNA (mRNA) leader sequences to search for protein-synthesis start sites remains one of the most mysterious aspects of translation and its regulation. While the search process is conventionally described by a linear “scanning” model, its exquisitely dynamic nature has restricted detailed mechanistic study. Here, we observed single
Saccharomyces cerevisiae
ribosomal scanning complexes in real time, finding that they scan diverse mRNA leaders at a rate of 10 to 20 nt s
−1
. We show that specific binding of a protein to its mRNA leader sequence substantially arrests scanning. Conversely, impairing scanning-complex guanosine 5′-triphosphate hydrolysis results in native start-site bypass. Our results illustrate an mRNA-centric, kinetically controlled regulatory model where the ribosomal pre-initiation complex amplifies a nuanced energetic landscape to regulate scanning and start-site selection fidelity.
SRSF6 modulates histone-chaperone HIRA splicing to orchestrate AR and E2F activity in prostate cancer
Authors: Montero-Hidalgo Antonio J. , Jiménez-Vacas Juan M. , Gómez-Gómez Enrique , Porcel-Pastrana Francisco , Sáez-Martínez Prudencio , Pérez-Gómez Jesús M. , Fuentes-Fayos Antonio C. , Blázquez-Encinas Ricardo , Sánchez-Sánchez Rafael , González-Serrano Teresa , Castro Elena , López-Soto Pablo J. , Carrasco-Valiente Julia , Sarmento-Cabral André , Martinez-Fuentes Antonio J. , Eyras Eduardo , Castaño Justo P. , Sharp Adam , Olmos David , Gahete Manuel D. , Luque Raúl M.
Published: October 2024

Despite novel therapeutic strategies, advanced-stage prostate cancer (PCa) remains highly lethal, pointing out the urgent need for effective therapeutic strategies. While dysregulation of the splicing process is considered a cancer hallmark, the role of certain splicing factors remains unknown in PCa. This study focuses on characterizing the levels and role of SRSF6 in this disease. Comprehensive analyses of SRSF6 alterations (copy number/mRNA/protein) were conducted across eight well-characterized PCa cohorts and the Hi-MYC transgenic model. SRSF6 was up-regulated in PCa samples, correlating with adverse clinical parameters. Functional assays, both in vitro (cell proliferation, migration, colony, and tumorsphere formation) and in vivo (xenograft tumors), demonstrated the impact of SRSF6 modulation on critical cancer hallmarks. Mechanistically, SRSF6 regulates the splicing pattern of the histone-chaperone
HIRA
, consequently affecting the activity of H3.3 in PCa and breast cancer cell models and disrupting pivotal oncogenic pathways (AR and E2F) in PCa cells. These findings underscore SRSF6 as a promising therapeutic target for PCa/advanced-stage PCa.
Activation of NOD1 on tumor-associated macrophages augments CD8+T cell–mediated antitumor immunity in hepatocellular carcinoma
Authors: Zhang Feng , Jiang Qiuyu , Cai Jialiang , Meng Fansheng , Tang Wenqing , Liu Zhiyong , Lin Xiahui , Liu Wenfeng , Zhou Yi , Shen Xizhong , Xue Ruyi , Dong Ling , Zhang Si
Published: October 2024

The efficacy of immunotherapy targeting the PD-1/PD-L1 pathway in hepatocellular carcinoma (HCC) is limited. NOD-like receptors (NLRs) comprise a highly evolutionarily conserved family of cytosolic bacterial sensors, yet their impact on antitumor immunity against HCC remains unclear. In this study, we uncovered that NOD1, a well-studied member of NLR family, exhibits predominant expression in tumor-associated macrophages (TAMs) and correlates positively with improved prognosis and responses to anti–PD-1 treatments in patients with HCC. Activation of NOD1 in vivo augments antitumor immunity and enhances the effectiveness of anti–PD-1 therapy. Mechanistically, NOD1 activation resulted in diminished expression of perilipin 5, thereby hindering fatty acid oxidation and inducing free fatty acid accumulation in TAMs. This metabolic alteration promoted membrane localization of the costimulatory molecule OX40L in a lipid modification–dependent manner, thereby activating CD8+T cells. These findings unveil a previously unrecognized role for NOD1 in fortifying antitumor T cell immunity in HCC, potentially advancing cancer immunotherapy.
Quantifying the topology of magnetic skyrmions in three dimensions
Authors: Raftrey David , Finizio Simone , Chopdekar Rajesh V. , Dhuey Scott , Bayaraa Temuujin , Ashby Paul , Raabe Jörg , Santos Tiffany , Griffin Sinéad , Fischer Peter
Published: October 2024

Magnetic skyrmions have so far been treated as two-dimensional spin structures characterized by a topological winding number. However, in real systems with the finite thickness of the device material being larger than the magnetic exchange length, the skyrmion spin texture extends into the third dimension and cannot be assumed as homogeneous. Using soft x-ray laminography, we reconstruct with about 20-nanometer spatial (voxel) size the full three-dimensional spin texture of a skyrmion in an 800-nanometer-diameter and 95-nanometer-thin disk patterned into a 30× [iridium/cobalt/platinum] multilayered film. A quantitative analysis finds that the evolution of the radial profile of the topological skyrmion number is nonuniform across the thickness of the disk. Estimates of the micromagnetic energy densities suggest that the changes in topological profile are related to nonuniform competing energetic interactions. Our results provide a foundation for nanoscale metrology for spintronics devices using topology as a design parameter.
Structural insights into phosphatidylethanolamine
N
-methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis
Authors: Salsabila Salma D. , Kim Jungwook
Published: October 2024

Phosphatidylethanolamine
N
-methyltransferase (PmtA) catalyzes the biosynthesis of phosphatidylcholine (PC) from phosphatidylethanolamine (PE). Although PC is one of the major phospholipids constituting bilayer membranes in eukaryotes, certain bacterial species encode PmtA, a membrane-associated methyltransferase, to produce PC, which is correlated with cellular stress responses, adaptability to environmental changes, and symbiosis or virulence with eukaryotic hosts. Depending on the organism, multiple PmtAs may be required for producing monomethyl- and dimethyl-PE derivatives along with PC, whereas in organisms such as
Rubellimicrobium thermophilum
, a single enzyme is sufficient to direct all three methylation steps. In this study, we present the x-ray crystal structures of PmtA from
R. thermophilum
in complex with dimethyl-PE and
S
-adenosyl-
l
-homocysteine, as well as in its lipid-free form. Moreover, we demonstrate that the enzyme associates with the cellular membrane via electrostatic interactions facilitated by a group of critical basic residues and can successively methylate PE and its methylated derivatives, culminating in the production of PC.
Complete genome sequence of the avian paramyxovirus serotype 9 strain duck/Miyazaki/128/2021
Authors: Mekata Hirohisa , Yamamoto Mari , Matsui Yuto , Niazi Ahmad Massoud , Yamada Kentaro , Okabayashi Tamaki , Cha Se-Yeoun , Jang Hyung-Kwan
Published: October 2024

Here, we report the complete genome sequence of the avian paramyxovirus serotype 9 strain duck/Miyazaki/128/2021, which was determined using the Illumina MiSeq platform. The position of the hemagglutinin-neuraminidase stop codon differed from that of the only other available completely sequenced prototype strain, duck/New York/22/1977.
Impact of community-based multidomain preventive health program on healthcare utilisation among elderly persons in Singapore: a propensity score matched and difference-in-differences study
Authors: Phng Francis , Yap Adrian Ujin , Teo Wesley , Chong Jesslyn Hwei Sing , Wu Christine Xia , Tan Eugene Eng Kee , Chin Chi Hsien , Chee Thong Gan , Lee Hee Hoon , Phan Phillip , Chua Ai Ping
Published: October 2024

Objectives

Ageing populations present substantial challenges for healthcare systems. Community-based health worker (CHW) interventions for promoting healthy ageing and preventing/managing non-communicable diseases have gained considerable attention in recent years. This study aimed to assess the impacts of a multidomain preventive health initiative delivered by CHWs, specifically the ‘My Health Map (MHM)’ programme, on participants’ health service utilisation using a propensity score matching methodology.

Design, setting and participants

The multidomain MHM programme, which was implemented in Bukit Batok township, encompassed screenings, vaccinations, chronic disease management, counselling and socio-environmental interventions. Individuals, aged ≥40 years old, who received care at Ng Teng Fong General Hospital and were enrolled in the MHM programme constituted the intervention group. Outcomes of the intervention group were compared with a 1:1 propensity-matched comparison group at enrolment and 1-year follow-up. The outcome measures were emergency department (ED) utilisation and hospital admissions. Statistical evaluations were performed using χ2/non-parametric tests and difference-in-difference (DiD) estimation with a bias-adjusted generalised estimating equation (α=0.05).

Results

A comparable comparison group was formed with no significant differences in baseline characteristics between groups. Data from a total of 299 MHM participants (mean age 70.7 (SD 9.6); 62.5% women) and 299 matched comparisons (mean age 72.1 (SD 16.6); 61.5% women) were appraised. DiD analysis indicated a significant reduction in ED attendance (−16.7%, p<0.001) and hospital admission (−18.4%, p<0.001) among intervention participants than the comparison participants.

Conclusions

The multidomain MHM programme proved effective in reducing ED attendances and hospital admissions in older adults. CHWs have the potential to serve as change agents in healthcare and should be systematically integrated into preventive health programmes.
Cancer cell-specific PD-L1 expression is a predictor of poor outcome in patients with locally advanced oral cavity squamous cell carcinoma
Authors: Wang Minyu , Qin Lei , Thia Kevin , Nguyen Thu , MacDonald Sean , Belobrov Simone , Kranz Sevastjan , Goode David , Trapani Joseph A , Wiesenfeld David , Neeson Paul Joseph
Published: October 2024

Background

Locally advanced oral cavity squamous cell carcinoma (OCSCC) presents a significant clinical challenge despite being partially responsive to standard treatment modalities. This study investigates the prognostic implications of programmed death-ligand 1 (PD-L1) expression in these tumors, focusing on its association with treatment outcomes and the immune microenvironment.

Methods

We assessed tumor-infiltrating lymphocytes (TILs) in 132 patients with OCSCC to evaluate their impact on survival. Multiplex immunohistochemistry staining for CD3, CD68, CD11c, PD-L1, and P40 was used to explore correlations with clinical outcomes in patients with early-stage (n=22) and locally advanced (n=36) OCSCC. These initial findings were validated through differential gene expression analysis, gene set enrichment, and immune cell deconvolution in a The Cancer Genome Atlas cohort of 163 locally advanced OCSCC tumors. Additionally, single-cell RNA sequencing (scRNA-seq) on a smaller cohort (n=10) further characterized the PD-L1hior PD-L1locancer cells in these tumors.

Results

Elevated PD-L1 expression was associated with poor outcomes in patients with locally advanced OCSCC undergoing standard adjuvant therapy, irrespective of “hot” or “cold” classification based on TILs assessment. PD-L1hitumors exhibited an active immune response phenotype, enriched with M1 macrophages, CD8+T cells and T regulatory cells in the tumor microenvironment. Notably, the negative impact of PD-L1 expression on outcomes was primarily attributed to its expression by cancer cells, rather than immune cells. Furthermore, scRNA-seq revealed that immune interactions were not essential for PD-L1 upregulation in cancer cells, instead, complex regulatory networks were involved. Additionally, PD-L1lolocally advanced tumors exhibited more complex pathway enrichment and diverse T-cell populations compared with those in the early-stage.

Conclusion

Our findings underscore the prognostic significance of PD-L1 expression in locally advanced OCSCC, and unveil the complex interplay between PD-L1 expression, immune responses, and molecular pathways in the tumor microenvironment. This study provides insights that may inform future therapeutic strategies, including the possibility of tailored immunotherapeutic approaches for patients with PD-L1hilocally advanced OCSCC.
Gene therapy for intracranial aneurysms: systemic review
Authors: McAvoy Malia , Ratner Buddy , Ferreira Manuel J , Levitt Michael R
Published: October 2024

Treatment of intracranial aneurysms is currently limited to invasive surgical and endovascular modalities, and some aneurysms are not treatable with these methods. Identification and targeting of specific molecular pathways involved in the pathogenesis of aneurysms may improve outcomes. Low frequency somatic variants found in cancer related genes have been linked to intracranial aneurysm development. In particular, mutations in thePDGFRBgene lead to constitutively activated ERK and nuclear factor κB signaling pathways, which can be targeted with tyrosine kinase inhibitors. In this review, we describe how low frequency somatic variants in oncogenic and other genes affect the pathogenesis of aneurysm development, with a focus on gene therapy applications, such as endovascular in situ delivery of chemotherapeutics.
What do family caregivers of patients with life-threatening diseases need from healthcare professionals? A qualitative study
Authors: Hoffstädt Hinke Elisabeth , Tam Marcella Cecilia , Stoppelenburg Arianne , Stoevelaar Rik , van Bodegom-Vos Leti , van der Steen Jenny Theodora , van der Linden Yvette Milene , Hartog Iris Dewi
Published: October 2024

Objectives

To explore the common ground of what family caregivers need in their various roles (caregiver, care recipient and patient’s partner, child or friend) from healthcare professionals across healthcare settings and disease trajectories.

Design

Interviews were conducted with family caregivers of patients with life-threatening diseases who were treated at home, in hospitals, nursing homes or hospices between 2017 and 2022. Reflexive thematic analysis was performed.

Setting/participants

63 family caregivers of 65 patients were interviewed. Of the patients, 36 (55%) had COVID-19 and 29 (45%) had other life-threatening diseases (eg, advanced cancer, dementia). The majority of family caregivers were women (83%) and children of the patient (56%).

Results

Three themes were developed regarding family caregivers’ core needs across their different roles: (1) ‘feeling seen and valued’, (2) ‘experiencing trust in the provided care’ and (3) ‘experiencing guidance and security’. Actions of healthcare professionals that meet those needs relate to their contact and relationship with family caregivers, information provision, practical and emotional support, the care for the patient and facilitating the connection between family caregivers and patients.

Discussion

Healthcare professionals should be trained in meeting family caregivers’ core needs, in which their (collaborative) relationship with them plays an important role. Efforts to meet the core needs should be incorporated into healthcare organisations’ workflows, and future research should investigate related barriers and facilitators.
Extracellular vesicles bearing serum amyloid A1 exacerbate neuroinflammation after intracerebral haemorrhage
Authors: Zhu Huimin , Wang Ningning , Chang Yingying , Zhang Ying , Jiang Shihe , Ren Xiaoping , Yuan Meng , Chang Haoxiao , Jin Wei-Na
Published: October 2024

Introduction

Intracerebral haemorrhage (ICH) elicits a robust inflammatory response, which significantly contributes to secondary brain damage. Extracellular vesicles (EVs) play a pivotal role in intercellular communication by transporting immune-regulatory proteins. However, the precise contribution of these EV-carried proteins to neuroinflammation following ICH remains elusive. Here, we identified proteins dysregulated in EVs and further studied the EVs-enriched Serum amyloid A 1 (SAA1) to understand its role in neuroinflammation and ICH injury.

Methods

We used mass spectrometry to analyse the EV protein cargo isolated from plasma samples of 30 ICH patients and 30 healthy controls. To validate the function of the dysregulated protein SAA1, an ICH mouse model was conducted to assess the effects of SAA1 neutralisation on brain oedema, neurological function and infiltration of peripheral leucocytes.

Results

49 upregulated proteins and 12 downregulated proteins were observed in EVs from ICH patients compared with controls. Notably, SAA1 demonstrated a significant increase in EVs associated with ICH. We observed that exogenous SAA1 stimulation led to an augmentation in the population of microglia and astrocytes, exacerbating neuroinflammation. Neutralising SAA1 with an anti-SAA1 monoclonal antibody (mAb) diminished the prevalence of proinflammatory microglia and the infiltration of peripheral leucocytes, which ameliorates brain oedema and neurological function in ICH mice.

Conclusion

Our findings provide compelling evidence implicating EVs and their cargo proteins in ICH pathogenesis. SAA1 emerges as a potential therapeutic target for mitigating neuroinjury and neuroinflammation following ICH.
(Co)homology of racks and multiple group racks for compact oriented surfaces in the 3-sphere
Authors: Matsuzaki Shosaku , Murao Tomo
Published: October 2024

We introduce (co)homology theory for multiple group racks and construct cocycle invariants of compact oriented surfaces in the 3-sphere using their 2-cocycles, where a multiple group rack is a rack consisting of a disjoint union of groups. We provide a method to find new rack cocycles and multiple group rack cocycles from existing rack cocycles and quandle cocycles. Evaluating cocycle invariants, we determine several symmetry types, caused by chirality and invertibility, of compact oriented surfaces in the 3-sphere.
Enhancing Operational Risk Management in Distribution Networks: A Comprehensive Framework
Authors: Yang Yingchun , Zhao Xu , Han Tianxi , Xu Min , Li Chen
Published: October 2024

The ongoing expansion of power grid infrastructure has led to more complex line configurations and increased operational intricacies. Presently, there’s a noticeable gap in targeted, categorized analysis of operational factors influencing the risks and compliance issues in distribution network operations. The challenge in prioritizing and assessing these risks is compounded by the lack of measurable indicators, posing safety risks at operational sites. This study presents a comprehensive analysis of risk factor dimensions in distribution network operations and introduces measurable indicators for these risks. We propose a three-level risk assessment framework for distribution network operations, categorizing risks associated with personnel, the operational environment, equipment and management shortcomings. The Analytic Hierarchy Process (AHP) is utilized to determine the weights of 34 specific risk indicators within this framework. Furthermore, we explore the implementation of this risk assessment model, considering the real-world conditions of distribution network management centers, operational sites and inspection equipment. The practicality of the proposed framework and methods is validated through a case study of a power supply bureau’s distribution network operations. This research aims to enhance the safety risk management strategies in power grid companies, offering insights for improving on-site operational risk control in these enterprises.
Linking HEXACO Personality Traits to Affective Commitment and Knowledge Sharing Behaviour in Higher Education Institutions
Authors: Karim Dewan Niamul , Chowdhury Suman Paul , Majid Abdul Halim Abdul , Rubel Mohammad Rabiul Basher , Rimi Nadia Newaz , Amin Muhammad Ruhul
Published: October 2024

Abstract.This study aimed to assess the connection between HEXACO personality traits (i.e. honesty–humility, emotionality, extraversion, agreeableness, conscientiousness, and openness to experience) and knowledge sharing behaviour (KSB) of university academic staff. Moreover, based on the theory of planned behaviour (TPB), this study aimed to examine the underlying process through which HEXACO personality traits contribute to academics’ KSB by examining mediating role of affective commitment. With a structured questionnaire survey, the data was conveniently collected from 234 full-time university faculty members employed in 20 private universities located in Bangladesh. Structural equation modelling partial least square (SEM-PLS) was utilised to analyse the research model. The results revealed that, with the exception of emotionality, all HEXACO personality traits (i.e. honesty– humility, extraversion, agreeableness, conscientiousness, and openness to experience) have positive direct effects on academics’ KSB. The study further showed that the effects of honesty–humility, extraversion, agreeableness and conscientiousness on KSB were significantly mediated by affective commitment. Thus, universities should focus on academics’ personality profiles to improve knowledge sharing practices within the institutions. In particular, personality test should be introduced in the selection process of university teachers to identify the candidates with desirable personality traits. The findings offer a new understanding of how HEXACO personality traits result in academics’ KSB directly as well as via affective commitment.
Novel Fractional-Order ESO-Based Distributed Control for Multi-Agent Systems to Pass a Curve Virtual Tube with Matched and Mismatched Disturbances
Authors: Long Shike , Sun Shanlin , Wang Yongjun , Tang Zeyu , Wang Zhi
Published: October 2024

To guide multi-agent systems (MASs) through a cluttered environment, this paper proposes a distributed control method based on a novel fractional-order extended state observer (NFO-ESO). First, unlike the traditional multi-agent double-integral model, the agent model constructed in this paper contains external wind disturbances (mismatched disturbances) and internal unmodeled dynamics (matched disturbances), and these disturbances are treated as matched disturbance equivalent. Then, the designed disturbance observer is added to the robust distributed controller to coordinate the disturbance, which is used to accomplish the curve virtual tube crossing task in the perturbed case. The disturbance observer is NFO-ESO, which is implemented in this paper by constructing a neural network based on fractional-order discrete theory. It improves the weakness of the traditional ESO that only observes low-frequency slow time-varying disturbances and can be more suitable for nonlinear fast time-varying disturbance estimation. Finally, to demonstrate the advantages of the proposed controller, we show an example of MASs with wind disturbance and unmodeled dynamic through numerical simulation experiment. The instance shows the effectiveness of the proposed distributed control method under external disturbances.
Lipid Droplets Big and Small: Basic Mechanisms That Make Them All
Authors: Klemm Robin W. , Carvalho Pedro
Published: October 2024

Lipid droplets (LDs) are dynamic storage organelles with central roles in lipid and energy metabolism. They consist of a core of neutral lipids, such as triacylglycerol, which is surrounded by a monolayer of phospholipids and specialized surface proteins. The surface composition determines many of the LD properties, such as size, subcellular distribution, and interaction with partner organelles. Considering the diverse energetic and metabolic demands of various cell types, it is not surprising that LDs are highly heterogeneous within and between cell types. Despite their diversity, all LDs share a common biogenesis mechanism. However, adipocytes have evolved specific adaptations of these basic mechanisms, enabling the regulation of lipid and energy metabolism at both the cellular and organismal levels. Here, we discuss recent advances in the understanding of both the general mechanisms of LD biogenesis and the adipocyte-specific adaptations controlling these fascinating organelles.
HIF1α Counteracts TGFβ1-Driven TSP1 Expression in Endothelial Cells to Stimulate Angiogenesis in the Hypoxic Tumor Microenvironment
Authors: Luo Yu-Wei , Fang Yang , Zeng Hui-Xian , Ji Yu-Chen , Wu Meng-Zhi , Li Hui , Chen Jie-Ying , Zheng Li-Min , Fang Jian-Hong , Zhuang Shi-Mei
Published: October 2024

Emerging evidence suggests that TGFβ1 can inhibit angiogenesis, contradicting the coexistence of active angiogenesis and high abundance of TGFβ1 in the tumor microenvironment. Here, we investigated how tumors overcome the antiangiogenic effect of TGFβ1. TGFβ1 treatment suppressed physiologic angiogenesis in chick chorioallantoic membrane and zebrafish models but did not affect angiogenesis in mouse hepatoma xenografts. The suppressive effect of TGFβ1 on angiogenesis was recovered in mouse xenografts by a hypoxia-inducible factor 1α (HIF1α) inhibitor. In contrast, a HIF1α stabilizer abrogated angiogenesis in zebrafish, indicating that hypoxia may attenuate the antiangiogenic role of TGFβ1. Under normoxic conditions, TGFβ1 inhibited angiogenesis by upregulating antiangiogenic factor thrombospondin 1 (TSP1) in endothelial cells (EC) via TGFβ type I receptor (TGFβR1)–SMAD2/3 signaling. In a hypoxic microenvironment, HIF1α induced miR145 expression; miR145 abolished the inhibitory effect of TGFβ1 on angiogenesis by binding and repressing SMAD2/3 expression and subsequently reducing TSP1 levels in ECs. Primary ECs isolated from human hepatocellular carcinoma displayed increased miR145 and decreased SMAD3 and TSP1 compared with ECs from adjacent nontumor livers. The reduced SMAD3 or TSP1 in ECs was associated with increased angiogenesis in hepatocellular carcinoma tissues. Collectively, this study identified that TGFβ1–TGFβR1–SMAD2/3–TSP1 signaling in ECs inhibits angiogenesis. This inhibition can be circumvented by a hypoxia–HIF1α–miR145 axis, elucidating a mechanism by which hypoxia promotes angiogenesis.

Significance: Suppression of angiogenesis by TGFβ1 is mediated by TSP1 upregulation in endothelial cells and abrogated by HIF1α–miR145 activity in the hypoxic tumor microenvironment, providing potential targets to remodel the tumor vasculature.
Supplementary Table S3 from Radiodensities of Skeletal Muscle and Visceral Adipose Tissues Are Prognostic Factors in Clear-Cell Renal Cell Carcinoma
Authors: Bradshaw Patrick T. , Olsson Linnea T. , Sanchez Alejandro , Knezevic Andrea , Akin Oguz , Scott Jessica M. , Hakimi A. Ari , Russo Paul , Caan Bette J. , Mourtzakis Marina , Furberg Helena
Published: October 2024

Joint effects for relationship between body composition features and tumor characteristics for disease free survival.
Supplementary Table 1 from Blood Leukocyte DNA Methylation Markers of Periodontal Disease and Risk of Lung Cancer in a Case–Control Study Nested in the CLUE II Cohort
Authors: Mulvaney Rachel , Pan Yongyi , Zhao Naisi , Teles Flavia , Lu Jiayun , Platz Elizabeth A. , Kelsey Karl T. , Michaud Dominique S.
Published: October 2024

Table S1 shows the associations between CpGs selected and periodontal disease in the ARIC cohort, among participants of European Ancestry
Supplementary Table S3 from Neighborhood Disadvantage and Prostate Tumor Aggressiveness among African American and European American Men
Authors: Boyle Joseph , Yau Jessica , Slade Jimmie L. , Butts Derrick A. , Wimbush Jessica , Park Jong Y. , Hussain Arif , Onukwugha Eberechukwu , Knott Cheryl L. , Wheeler David C. , Barry Kathryn Hughes
Published: October 2024

Supplementary Table S3: Summary of models of neighborhood disadvantage and the likelihood of aggressive prostate cancer by neighborhood metric, additionally adjusting for primary payer at diagnosis.
Supplementary Figure S3 from Neighborhood Disadvantage and Prostate Tumor Aggressiveness among African American and European American Men
Authors: Boyle Joseph , Yau Jessica , Slade Jimmie L. , Butts Derrick A. , Wimbush Jessica , Park Jong Y. , Hussain Arif , Onukwugha Eberechukwu , Knott Cheryl L. , Wheeler David C. , Barry Kathryn Hughes
Published: October 2024

Supplementary Figure S3: Values of the Racial Isolation (RI) index for participants with residential addresses in Maryland.
Supplemental Table 1. from Breast, Colorectal, and Prostate Cancer Incidence among Filipino Americans by Generational Status in the Multiethnic Cohort Study
Authors: Abe Janine V. , Legaspi Justin , Guillermo Cherie , Bogumil David , Setiawan Veronica Wendy , Le Marchand Loïc , Hernandez Brenda Y. , Wilkens Lynne R. , Maskarinec Gertraud
Published: October 2024

Supplemental Table 1 shows cancer risk by generational status among Filipino participants, excluding part Native Hawaiian, in the Multiethnic Cohort, 1993-2017.
Supplementary Table 4 from Association between Long-term Energy Balance–Related Factors and Survival in Colorectal Cancer Overall and by Metabolic Warburg-Subtypes
Authors: Offermans Kelly , Jenniskens Josien C.A. , Simons Colinda C.J.M. , Samarska Iryna , Fazzi Gregorio E. , Smits Kim M. , Schouten Leo J. , Weijenberg Matty P. , Grabsch Heike I. , van den Brandt Piet A.
Published: October 2024

Supplementary Table 4 – Multivariable-adjusted hazard ratios (HRs) for associations between long-term energy balance-related factors and survival of colorectal cancer (CRC) patients within the Netherlands Cohort Study (NLCS, 1986-2006). Patients diagnosed within 5 years after baseline were excluded from analyses.
Table S7 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S7 compares effect sizes, distributions, and attributable proportions of breast cancer risk factors reported in prospective studies among post-menopausal Asian and European women.
Table S4 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S4 presents the relevant estimates with 95% confidence intervals of the association between breast cancer risk factors and breast cancer risk, categorised by breast cancer subtype in Asian populations.
Table S3 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S3 tabulates individual study characteristics extracted from each respective study, including region, country, study design, type of population, number of cases, total sample size, birth cohort, and study quality.
Table S1 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Table S1 lists the keywords used for the systematic search in PubMed and ProQuest to identify studies evaluating breast cancer risk among women in Asian countries.
Figure S1 from Systematic Review and Meta-Analysis of Lifestyle and Reproductive Factors Associated with Risk of Breast Cancer in Asian Women
Authors: Ang Boon Hong , Teo Soo-Hwang , Ho Weang-Kee
Published: October 2024

Supplementary Figure S1 presents a PRISMA flowchart outlining the stepwise study selection process from identifying relevant studies in electronic databases and via other methods to screening and including them in qualitative and quantitative analyses.
Supplementary Table S3 Metastatic Disease Trastuzumab Receipt Sensitivity Analysis from Sociodemographic Disparities in HER2+ Breast Cancer Trastuzumab Receipt: An English Population-Based Study
Authors: Norris Ruth P. , Dew Rosie , Greystoke Alastair , Cresti Nicola , Cain Henry , Todd Adam , Sharp Linda
Published: October 2024

Supplementary Table S3 Metastatic Disease Trastuzumab Receipt Sensitivity Analysis_Clean
Supplementary Table S2 Early-stage Disease Trastuzumab Receipt Sensitivity Analysis from Sociodemographic Disparities in HER2+ Breast Cancer Trastuzumab Receipt: An English Population-Based Study
Authors: Norris Ruth P. , Dew Rosie , Greystoke Alastair , Cresti Nicola , Cain Henry , Todd Adam , Sharp Linda
Published: October 2024

Supplementary Table S2 Early-stage Disease Trastuzumab Receipt Sensitivity Analysis_Clean
Supplementary Table S2 from Blood Magnesium Level and Risk of Hepatocellular Carcinoma in a Prospective Liver Cirrhosis Cohort
Authors: Zhang Xinyuan , Zhao Longgang , Dai Qi , Hou Tao , Danford Christopher J. , Lai Michelle , Zhang Xuehong
Published: October 2024

Interaction between blood magnesium and potential confounders for risk of hepatocellular carcinoma.
Supplementary Table S1 from Blood Magnesium Level and Risk of Hepatocellular Carcinoma in a Prospective Liver Cirrhosis Cohort
Authors: Zhang Xinyuan , Zhao Longgang , Dai Qi , Hou Tao , Danford Christopher J. , Lai Michelle , Zhang Xuehong
Published: October 2024

Baseline characteristics of the Harvard Mass General Brigham Biobank Liver Cirrhosis Cohort by blood magnesium lab test record availability in the Electronic Medical Record.
Supplementary Table S3 from Prospective Analysis of Circulating Biomarkers and Ovarian Cancer Risk in the UK Biobank
Authors: Sasamoto Naoko , Hathaway Cassandra A. , Townsend Mary K. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2024

Free testosterone, free estradiol, rheumatoid factor and ovarian cancer risk in the UK Biobank by histologic subtype.
Supplementary Table S1 from Prospective Analysis of Circulating Biomarkers and Ovarian Cancer Risk in the UK Biobank
Authors: Sasamoto Naoko , Hathaway Cassandra A. , Townsend Mary K. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2024

Free testosterone, free estradiol, rheumatoid factor and ovarian cancer risk in the UK Biobank
Data from Patient Characteristics Associated with Intended Nonguideline Chemotherapy in Women with Stage I to IIIA Breast Cancer
Authors: Bhimani Jenna , O’Connell Kelli , Persaud Sonia , Blinder Victoria , Burganowski-Doud Rachael P. , Ergas Isaac J. , Gallagher Grace B. , Griggs Jennifer J. , Heon Narre , Kolevska Tatjana , Kotsurovskyy Yuriy , Kroenke Candyce H. , Laurent Cecile. A. , Liu Raymond , Nakata Kanichi G. , Rivera Donna R. , Roh Janise M. , Tabatabai Sara , Valice Emily , Bandera Elisa V. , Aiello Bowles Erin J. , Kushi Lawrence H. , Kantor Elizabeth D.
Published: October 2024

AbstractBackground:
Guidelines informing chemotherapy regimen selection are based on clinical trials with participants who do not necessarily represent general populations with breast cancer. Understanding who receives nonguideline regimens is important for understanding real-world chemotherapy administration and how it relates to patient outcomes.
Methods:
Using data from the Optimal Breast Cancer Chemotherapy Dosing (OBCD) study, based at Kaiser Permanente Northern California (2006–2019) and Kaiser Permanente Washington (2004–2015), we use logistic regression to examine the associations between patient characteristics and receipt of nonguideline chemotherapy regimens among 11,293 women with primary stage I to IIIA breast cancer receiving chemotherapy.
Results:
The use of nonguideline regimens was strongly associated with several factors, including older age [≥80 vs. 18–39 years: OR, 5.25; 95% confidence interval (CI), 3.06–9.00; P-trend = 0.002] and HER2 status (HER2+ vs. HER2−: OR, 3.44; 95% CI, 3.06–3.87) and was less likely in women with larger tumor size (>5 cm vs. 0.1 to ≤0.5 cm: OR, 0.56; 95% CI, 0.36–0.87; P-trend = 0.01) and diagnosed in later years (2012–2019 vs. 2005–2011: OR, 0.80; 95% CI, 0.71–0.90). Factors associated varied by type of nonguideline regimens. For example, women with comorbidity and older age were more likely to receive nonguideline drug combinations in particular, whereas women with larger tumor size were less likely to receive nonguideline administration schedules.
Conclusions:
Nonguideline chemotherapy regimens are more likely in certain patient populations.
Impact:
These associations highlight that vulnerable patient populations may be less likely to receive guideline care, and thus, real-world studies are essential for understanding how the use of nonguideline regimens impacts patient outcomes in these groups.
Data from Neighborhood Disadvantage and Prostate Tumor Aggressiveness among African American and European American Men
Authors: Boyle Joseph , Yau Jessica , Slade Jimmie L. , Butts Derrick A. , Wimbush Jessica , Park Jong Y. , Hussain Arif , Onukwugha Eberechukwu , Knott Cheryl L. , Wheeler David C. , Barry Kathryn Hughes
Published: October 2024

AbstractBackground:
Studies have identified associations between neighborhood disadvantage (ND), which is more likely to affect African American (AA) individuals, and aggressive prostate cancer. Thus, ND may contribute to prostate cancer disparities. However, it is unknown what ND components drive aggressive disease and whether associations vary by race.
Methods:
We evaluated associations between aggressive prostate cancer and four ND metrics—Area Deprivation Index (ADI), validated Bayesian Neighborhood Deprivation Index (NDI), racial isolation (RI) index, and historical redlining, and whether these factors interacted with race, among men with prostate cancer treated at the University of Maryland Greenebaum Comprehensive Cancer Center (2004–2021).
Results:
We included 1,458 men (698 European American and 760 AA). AA men were more likely to experience ND. In adjusted models, the ADI, RI, and redlining were significantly associated with aggressive versus nonaggressive prostate cancer overall [ADI, OR for one SD increase = 1.14, 95% confidence interval (CI), 1.00–1.30; RI, OR = 1.27, CI, 1.07–1.51; redlining, OR = 1.77; CI, 1.23–2.56] and among AA men. The NDI was associated with aggressive prostate cancer among AA men (OR = 1.32, 95% credible interval: 1.13–1.57); percent in poverty received the largest importance weight. The ADI (P heterogeneity = 0.002) and NDI (exceedance probability heterogeneity = 98.1%) significantly interacted with race, such that associations were significantly stronger for AA men.
Conclusions:
We identified novel significant positive associations for racial segregation and historical redlining with aggressive prostate cancer and significant interactions between ND indices and race.
Impact:
Findings inform specific ND components that are associated with aggressive prostate cancer and suggest the ND effect is stronger for AA men, which has implications for interventions to reduce disparities.
Data from Association between Long-term Energy Balance–Related Factors and Survival in Colorectal Cancer Overall and by Metabolic Warburg-Subtypes
Authors: Offermans Kelly , Jenniskens Josien C.A. , Simons Colinda C.J.M. , Samarska Iryna , Fazzi Gregorio E. , Smits Kim M. , Schouten Leo J. , Weijenberg Matty P. , Grabsch Heike I. , van den Brandt Piet A.
Published: October 2024

AbstractBackground:
Long-term energy balance–related factors (i.e., lifestyle and physiologic factors that influence the equilibrium between energy intake and energy expenditure over an extended period) such as body mass index (BMI) are linked to colorectal cancer risk, but their impact on colorectal cancer survival is unclear. We explored associations between these long-term energy balance–related factors and survival and examined potential differences across metabolic Warburg-subtypes.
Methods:
Associations between long-term energy balance–related factors and survival in the total series of patients with colorectal cancer (n = 2,347) obtained from the prospective Netherlands Cohort Study, as well as according to Warburg-subtype (Warburg-low: n = 652, Warburg-moderate: n = 802, Warburg-high: n = 797), were investigated using Cox regression analysis.
Results:
Among the long-term energy balance–related factors studied, only increasing prediagnostic BMI was associated with a borderline significant poorer overall survival in patients with colorectal cancer [HR5kg/m2, 1.07; 95% confidence interval (CI), 0.99–1.15]. Stratified analyses showed that prediagnostic weight gain (HR5kg, 1.04; 95% CI, 0.99–1.09) and potentially increased height (HR5cm, 1.04; 95% CI, 0.98–1.11) were associated with poor overall survival only in patients with Warburg-high colorectal cancer. Increasing prediagnostic BMI was associated with poor survival only in patients with Warburg-moderate colorectal cancer (colorectal cancer–specific: HR5kg/m2, 1.12; 95% CI, 0.96–1.32; overall: HR5kg/m2, 1.20; 95% CI, 1.05–1.36). No consistent patterns were observed across energy restriction proxies.
Conclusions:
Maintaining a healthy prediagnostic BMI may be beneficial for colorectal cancer survival. Moreover, associations between prediagnostic BMI, weight change, early-life energy restriction, height, and colorectal cancer survival differed according to Warburg-subtypes.
Impact:
Understanding the biologic pathways involved in associations between energy balance–related factors and colorectal cancer survival could help refine prevention strategies in the future.
Supplementary Figure 7 from Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy
Authors: Seremak Juliette R. , Gupta Kunj Bihari , Bonigala Sunilkanth , Liu Elise , Marshall Brendan , Zhi Wenbo , Bokhtia Riham M. , Panda Siva S. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: October 2024

Supplementary Figure 7 with legends
Supplementary Figure 6 from Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy
Authors: Seremak Juliette R. , Gupta Kunj Bihari , Bonigala Sunilkanth , Liu Elise , Marshall Brendan , Zhi Wenbo , Bokhtia Riham M. , Panda Siva S. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: October 2024

Supplementary Figure 6 with legends.
Supplementary Figure 4 from Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy
Authors: Seremak Juliette R. , Gupta Kunj Bihari , Bonigala Sunilkanth , Liu Elise , Marshall Brendan , Zhi Wenbo , Bokhtia Riham M. , Panda Siva S. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: October 2024

Supplementary Figure 4 with legends
Supplementary Figure 5 from Targeting Chemoresistance in Advanced Bladder Cancers with a Novel Adjuvant Strategy
Authors: Seremak Juliette R. , Gupta Kunj Bihari , Bonigala Sunilkanth , Liu Elise , Marshall Brendan , Zhi Wenbo , Bokhtia Riham M. , Panda Siva S. , Lokeshwar Vinata B. , Lokeshwar Bal L.
Published: October 2024

Supplementary Figure 5 with legends.
Supplementary Table S2 from Lactate Induces Tumor Progression via LAR Motif-Dependent Yin-Yang 1 Degradation
Authors: Du Shujuan , Chen Xiaoting , Han Xiao , Wang Yuyan , Yu Dan , Li Ying , Zhu Caixia , Tong Yin , Gao Shujun , Wang Junwen , Wei Fang , Cai Qiliang
Published: October 2024

Supplementary Table S2. Hit-region sequences
Supplementary Figure S6 from Lactate Induces Tumor Progression via LAR Motif-Dependent Yin-Yang 1 Degradation
Authors: Du Shujuan , Chen Xiaoting , Han Xiao , Wang Yuyan , Yu Dan , Li Ying , Zhu Caixia , Tong Yin , Gao Shujun , Wang Junwen , Wei Fang , Cai Qiliang
Published: October 2024

S6. Brief schematic of lactate-induced YY1 degradation via chaperone-mediated autophagy for tumor growth and malignancy.
Supplementary Table 5 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Table 5 shows the accurate sequences of PDCD4 3’UTR used for the luciferase assays.
Supplementary Table 3 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Table 3 shows respective PCR primers used for ChIP assay.
Supplementary Table 1 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Table 1 shows Patients’ characteristics.
Supplementary Table 7 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Summary of statistics and data used to generate NAD+ pathway gene expression correlation plots.
Supplementary Figure S2 from RNA-Binding Protein Lin28B Promotes Chronic Myeloid Leukemia Blast Crisis by Transcriptionally Upregulating miR-181d
Authors: Zhou Minran , Yin Xiaolin , Zhang Lu , Cui Zelong , Jiang Xinwen , Ji Qingli , Ma Sai , Chen Chunyan
Published: October 2024

Supplementary Figure S2 shows shLin28B-1/shLin28B-2 significantly knockdown Lin28B expression in K562 and HL60 cells.
Supplementary Table 3 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Statistics for CpG island comparisons between mean methylation of probes in FH-deficient cell lines.
Supplementary Figure 9 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

BLISS synergy scores for FH-deficient renal cell lines.
Supplementary Figure 5 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Relationships between NAPRT, NAMPT, PARP, and QPRT expression in cancer cell lines.
Supplementary Figure 2 from NAPRT Silencing in FH-Deficient Renal Cell Carcinoma Confers Therapeutic Vulnerabilities via NAD+ Depletion
Authors: Noronha Katelyn J. , Lucas Karlie N. , Paradkar Sateja , Edmonds Joseph , Friedman Sam , Murray Matthew A. , Liu Samantha , Sajed Dipti P. , Sachs Chana , Spurrier Josh , Raponi Mitch , Liang Jiayu , Zeng Hao , Sundaram Ranjini K. , Shuch Brian , Vasquez Juan C. , Bindra Ranjit S.
Published: October 2024

Hypermethylation of patient derived cell line models and patient samples impacts various cancer related pathways and NAPRT expression.
Supplementary Table 2 from The Complex Regulation of Cytokinesis upon Abscission Checkpoint Activation
Authors: Gibieža Paulius , Petrikaitė Vilma
Published: October 2024

Different activation pathways of abscission checkpoint