bluuebunny/crossref_metadata_2025 huggingface dataset:
Coastal Wetlands in the Anthropocene
Authors: Day John , Anthony Edward , Costanza Robert , Edmonds Douglas , Gunn Joel , Hopkinson Charles , Mann Michael E. , Morris James , Osland Michael , Quirk Tracy , Rovai Andre , Rybczyk John , Spencer Thomas , Stephens Jessica , Syvitski Jaia , Twilley Robert , Visser Jenneke , White John R.
Published: September 2024

We review the functioning and sustainability of coastal marshes and mangroves. Urbanized humans have a 7,000-year-old enduring relationship to coastal wetlands. Wetlands include marshes, salt flats, and saline and freshwater forests. Coastal wetlands occur in all climate zones but are most abundant in deltas. Mangroves are tropical, whereas marshes occur from tropical to boreal areas. Quantification of coastal wetland areas has advanced in recent years but is still insufficiently accurate. Climate change and sea-level rise are predicted to lead to significant wetland losses and other impacts on coastal wetlands and the humans associated with them. Landward migration and coastal retreat are not expected to significantly reduce coastal wetland losses. Nitrogen watershed inputs are unlikely to alter coastal marsh stability because watershed loadings are mostly significantly lower than those in fertilization studies that show decreased belowground biomass and increased decomposition of soil organic matter. Blue carbon is not expected to significantly reduce climate impacts. The high values of ecosystem goods and services of wetlands are expected to be reduced by area losses. Humans have had strong impacts on coastal wetlands in the Holocene, and these impacts are expected to increase in the Anthropocene.
Population Genomic Scans for Natural Selection and Demography
Authors: Cheng Xiaoheng , Steinrücken Matthias
Published: September 2024

Uncovering the fundamental processes that shape genomic variation in natural populations is a primary objective of population genetics. These processes include demographic effects such as past changes in effective population size or gene flow between structured populations. Furthermore, genomic variation is affected by selection on nonneutral genetic variants, for example, through the adaptation of beneficial alleles or balancing selection that maintains genetic variation. In this article, we discuss the characterization of these processes using population genetic models, and we review methods developed on the basis of these models to unravel the underlying processes from modern population genomic data sets. We briefly discuss the conditions in which these approaches can be used to infer demography or identify specific nonneutral genetic variants and cases in which caution is warranted. Moreover, we summarize the challenges of jointly inferring demography and selective processes that affect neutral variation genome-wide.
The Nature and Nurture of Extracellular Vesicle–Mediated Signaling
Authors: Buck Amy H. , Nolte-'t Hoen Esther N.M.
Published: September 2024

In the last decade, it has become clear that extracellular vesicles (EVs) are a ubiquitous component of living systems. These small membrane-enclosed particles can confer diverse functions to the cells that release, capture, or coexist with them in an environment. We use examples across living systems to produce a conceptual framework that classifies three modes by which EVs exert functions: (a) EV release that serves a function for producing cells, (b) EV modification of the extracellular environment, and (c) EV interactions with, and alteration of, receiving cells. We provide an overview of the inherent properties of EVs (i.e., their nature) as well as factors in the environment and receiving cell (i.e., nurture) that determine whether transmission of EV cargo leads to functional cellular responses. This review broadens the context for ruminating on EV functions and highlights the emergent properties of EVs that define their role in biology and will shape their applications in medicine.
Coral Disease: Direct and Indirect Agents, Mechanisms of Disease, and Innovations for Increasing Resistance and Resilience
Authors: Vega Thurber Rebecca L. , Silva Denise , Speare Lauren , Croquer Aldo , Veglia Alex J. , Alvarez-Filip Lorenzo , Zaneveld Jesse R. , Muller Erinn M. , Correa Adrienne M.S.
Published: September 2024

As climate change drives health declines of tropical reef species, diseases are further eroding ecosystem function and habitat resilience. Coral disease impacts many areas around the world, removing some foundation species to recorded low levels and thwarting worldwide efforts to restore reefs. What we know about coral disease processes remains insufficient to overcome many current challenges in reef conservation, yet cumulative research and management practices are revealing new disease agents (including bacteria, viruses, and eukaryotes), genetic host disease resistance factors, and innovative methods to prevent and mitigate epizootic events (probiotics, antibiotics, and disease resistance breeding programs). The recent outbreak of stony coral tissue loss disease across the Caribbean has reenergized and mobilized the research community to think bigger and do more. This review therefore focuses largely on novel emerging insights into the causes and mechanisms of coral disease and their applications to coral restoration and conservation.
Somatic Mosaicism in Brain Disorders
Authors: Corrigan Rachel R. , Mashburn-Warren Lauren M. , Yoon Hyojung , Bedrosian Tracy A.
Published: September 2024

Research efforts over the past decade have defined the genetic landscape of somatic variation in the brain. Neurons accumulate somatic mutations from development through aging with potentially profound functional consequences. Recent studies have revealed the contribution of somatic mosaicism to various brain disorders including focal epilepsy, neuropsychiatric disease, and neurodegeneration. One notable finding is that the effect of somatic mosaicism on clinical outcomes can vary depending on contextual factors, such as the developmental origin of a variant or the number and type of cells affected. In this review, we highlight current knowledge regarding the role of somatic mosaicism in brain disorders and how biological context can mediate phenotypes. First, we identify the origins of brain somatic variation throughout the lifespan of an individual. Second, we explore recent discoveries that suggest somatic mosaicism contributes to various brain disorders. Finally, we discuss neuropathological associations of brain mosaicism in different biological contexts and potential clinical utility.
Pollution of Soil by Pharmaceuticals: Implications for Metazoan and Environmental Health
Authors: Zhang Chubin , Barron Leon P. , Stürzenbaum Stephen R.
Published: September 2024

The use of pharmaceuticals has grown substantially and their consequential release via wastewaters poses a potential threat to aquatic and terrestrial environments. While transportation prediction models for aquatic environments are well established, they cannot be universally extrapolated to terrestrial systems. Pharmaceuticals and their metabolites are, for example, readily detected in the excreta of terrestrial organisms (including humans). Furthermore, the trophic transfer of pharmaceuticals to and from food webs is often overlooked, which in turn highlights a public health concern and emphasizes the pressing need to elucidate how today's potpourri of pharmaceuticals affect the terrestrial system, their biophysical behaviors, and their interactions with soil metazoans. This review explores the existing knowledge base of pharmaceutical exposure sources, mobility, persistence, (bio)availability, (bio)accumulation, (bio)magnification, and trophic transfer of pharmaceuticals through the soil and terrestrial food chains.
Performance Investigations on All-Solid-State Polymer-Ceramic Sodium-Ion Batteries through a Spatially Resolved Electrochemical Model
Authors: Gerbig F. , Chauhan A. , Gietl S. , Nirschl H.
Published: September 2024

Rechargeable batteries are crucial in modern energy storage, with lithium-ion batteries dominating the market. However, the scarcity and environmental concerns associated with lithium have spurred interest in alternative battery chemistries, particularly sodium-ion batteries (SIBs), which utilize abundant sodium resources. Despite extensive experimental research on all-solid-state SIBs (ASSSIBs), theoretical investigations have primarily focused on molecular-level analyses, overlooking the impact of cell composition on overall performance. This paper aims to address this gap by developing a physical model for simulating ASSSIBs at the particle scale. Our methodology involves integrating experimental data with simulation results to identify key factors influencing battery performance. The study reveals slow sodium ion transport as a significant bottleneck, attributed to factors such as low porosity of the half-cell and limited electrolyte ionic conductivity. Simulation outcomes emphasize the importance of advancing fast-ion-conducting solid electrolytes to enhance ASSSIB performance. Moreover, the results suggest that electrodes with high electrolyte active filler content and reduced thickness are necessary for achieving optimal battery capacity utilization. Overall, this research underscores the intricate relationship between electrode microstructure and battery performance, offering valuable insights for the design and optimization of sustainable sodium-ion battery systems suitable for stationary and mobile applications.
Comparative Analysis of 50 MeV Li3+ and 100 MeV O7+ Ion Beam Induced Electrical Modifications in Silicon Photodetectors
Authors: Mariswamy Vinay Kumar , Sannathammegowda Krishnaveni , Kumar Santosh , Kumar Ashish
Published: September 2024

This article investigates the impact of 100 MeV O7+ and 50 MeV Li3+ ions on Silicon Photodetectors, focusing on their electrical characteristics with similar Sn/Se ratios. Elevated ion fluences led to a significant rise in the ideality factor “n”, indicating the presence of Generation-Recombination (G-R) current due to introduced defects, especially those with deep energy levels in the forbidden gap acting as G-R centers. While Ideality factor (n) values decreased for oxygen ions at maximum fluence, they increased for lithium ions, reflecting consistent patterns in series resistance (Rs) and reverse leakage current (IR), attributed to ion-induced defects. Oxygen ions showed a monotonic variation in Rs, whereas lithium ions exhibited a slight reduction at maximum fluence, possibly due to defect annihilation. Despite differing Se values, 50 MeV Li3+ ions demonstrated improved device characteristics, suggesting potential defect annihilation. The ratio of Sn to Se indicated comparable damage contributions from nuclear and electronic energy. Additionally, TRIM computations revealed non-uniform damage distributions, with ions penetrating deep into the substrate, away from the n+/p junction.
Structural and Magnetic Properties of Nano Manganite La0.6Sr0.4MnO3 Obtained by Mechanochemical Synthesis Influenced by Preparation Conditions
Authors: Ibrahim Peter N. G. , Hannora Ahmed E. , Hanna Farid F.
Published: September 2024

Single phase La0.6Sr0.4MnO3 nanoparticles with perovskite structure (

R

3

̅

C

symmetry) were successfully prepared by ball milling (mechanochemical synthesis) for 1 and 10 h followed by annealing treatment at temperature 900 or 1100 °C. It was found that, the lattice parameters increase with the increase of milling time or annealing temperature. The increase of the annealing temperature results in the increase of crystallite size and the particle size. The obtained samples were found to be ferromagnetic at room temperature. The sample obtained by one hour of milling and 900 °C annealing showed high value of saturation magnetization (about 56 emu g−1) and small value of coercivity (about 31 Oe) at room temperature, while the other samples show reduced value of magnetization and higher value of coercivity. The obtained magnetic results are discussed in light of the core/shell model of nanoparticles. The effect of the presence of oxygen vacancies on the lattice parameters and magnetic properties of the obtained samples is also discussed.
Explicit and implicit locomotor learning in individuals with chronic hemiparetic stroke
Authors: Wood Jonathan M. , Thompson Elizabeth , Wright Henry , Festa Liam , Morton Susanne M. , Reisman Darcy S. , Kim Hyosub E.
Published: September 2024

Motor learning involves both implicit and explicit processes, the underlying neural substrates of which could be damaged after stroke. Although both learning processes are typically used in concert in daily life and rehabilitation, no gait studies have determined how these processes function together after stroke. Using a locomotor task that elicits dissociable contributions from both processes and computational modeling, we found evidence that chronic stroke causes deficits in both explicit and implicit locomotor learning.
Achilles tendon morpho-mechanical parameters are related to triceps surae motor unit firing properties
Authors: Contreras-Hernandez Ignacio , Arvanitidis Michail , Falla Deborah , Negro Francesco , Martinez-Valdes Eduardo
Published: September 2024

By employing HD-sEMG, conventional B-mode ultrasonography, and shear-wave elastography, we showed that the resting stiffness of the Achilles tendon is related to mean discharge rate of triceps surae motor units during low-force isometric plantarflexion contractions, providing relevant information about the complex interaction between rate coding and the muscle-tendon unit.
Pruritus Is the Painter on the Skin: The Prevalence and Pattern of Scratch Lesions in 124 Pruritus Patients
Authors: Mueller Simon M. , Zhu Jie , Chee Alvyn , Itin Peter
Published: September 2024

Background: The urge to scratch is, by definition, an integral part of the perception of itch. Consequently, scratch lesions can reflect the patient’s perception of itch, and underlying disease. However, only little is known about scratch patterns among different itchy conditions. Methods: In this cross‐sectional study, we analyzed and compared the prevalence, type, site, and distribution of scratch lesions in patients across 11 diagnostic groups of itchy conditions. Statistical analysis was performed using chi‐squared test or Mann–Whitney U tests when appropriate. Results: A total of 124 patients with acute or chronic pruritus were enrolled, 82 (66.1%) of whom presented scratch lesions. Among these, erosions/excoriations were the most prevalent (56.1%), followed by erythematous striated lesions (36.6%) and crusts (35.4%). Scratch lesions were present in descending prevalence on the arms (78.2%), trunk (75.6%), legs (74.4%), and head (19.2%). Distinct scratch lesions were identified in some diagnoses, enabling us to develop a diagnostic algorithm. Conclusions: In the present study, we characterized scratch patterns in various itchy skin conditions and developed a diagnostic algorithm accordingly. However, larger studies are necessary to support our findings.
A Pelvic Abscess and a Pelvic Stone Secondary to a Ureteral Calculus
Authors: An Bo-Ran , Ma Ze-Peng , Gao Chao
Published: September 2024

The patient presented with abdominal pain for the first time 10 years ago and was diagnosed with a left ureteral calculus, left hydronephrosis, and hydroureter. The patient’s abdominal pain disappeared after palliative treatment, but he refused any treatment measures for his calculus and hydrops. He was readmitted due to chronic pelvic pain 8 years ago and was diagnosed with a pelvic abscess and left renal atrophy after imaging examination. We performed pus aspiration treatment under the guidance of transrectal B‐mode ultrasound and used antibiotic fluid for purulent cavity rinse, followed by intravenous injection of antibiotics. The abscess shrank in follow‐up magnetic resonance imaging (MRI), and the pain symptom disappeared in his pelvic. We followed up with the patient for 6 months, and he had no symptoms related to his pelvic abscess that was diagnosed before. Recent abdominal computed tomography (CT) images revealed that his left kidney atrophy still exists, and a pelvic stone was found at the site of the original abscess. This case once again proves that a ureteral calculus should be treated in time; otherwise, it can lead to serious complications such as a pelvic abscess and renal atrophy. A pelvic stone can be caused by a ureteral calculus migration. Minimally invasive treatments have minimal damage to the body and are widely applicable, and the patient was cured by one of them, abscess aspiration, which implies that they can also be used for patients who cannot tolerate surgical procedures.
Physicochemical and Antibacterial Properties of Myristica fragrans and Syzygium aromaticum Methanolic Extract Soap Formulations
Authors: Arhin Reuben Essel , Gordon Andrew , Nuhu Yussif , Boakye Elizabeth Esinam , Owusu Isaac , Oppong-Mensah Jessica , Alhassan Saeed
Published: September 2024

The rapid emergence of antimicrobial resistance and the preference of consumers for natural products are driving the exploration of herbal skin care products, including soaps. This study aimed to determine the physicochemical and antibacterial properties of herbal soaps formulated from single and combined methanolic extracts of Myristica fragrans and Syzygium aromaticum. The methanolic extracts of Myristica fragrans (Mf), Syzygium aromaticum (Sa), and a combination (MfSa) were used in the formulation of soaps. Antibacterial activities, minimum inhibitory concentrations, minimum bactericidal concentrations, moisture content (MC), total fatty matter (TFM), iodine value (IV), pH, free caustic alkali (FCA), total alkali content (TAC), and foaming capacity (FC) of the formulae were determined. The MC of the formulations ranged from 22.0% to 39.13%, TFM from 35.3% to 52.2%, IV from 0.57 gI2/100 g to 10.40 gI2/100 g, pH from 10.35 to 10.54, TAC from 5.81 to 6.06, FCA from 0.0406% to 0.03391%, and FC from 20 cm to 15 cm for the extract formulations. The antibacterial activity of Sa (12.0 ± 3.5 mm) against Staphylococcus aureus ATCC 29213 was the greatest, and it had the lowest MIC (2.5 × 10−2 mg/mL), lowest MBC (6.25 × 10−3 mg/mL), and highest activity indices. The MC, TFM, and FC of MfSa were significantly greater than the corresponding values for the non‐extract formula. In conclusion, the Sa extract formula was the most potent in terms of antibacterial activity against S. aureus.
A New Method to Optimize Deep CNN Model for Classification of Regular Cucumber Based on Global Average Pooling
Authors: Haseli Golzar Sajad , Bagherpour Hossein , Amiri Parian Jafar
Published: September 2024

Traditional methods of separating defective cucumbers are inherently labor‐intensive and time‐consuming. However, with the emergence of intelligent farming practices, deep learning (DL) algorithms, particularly in the fields of image processing and machine vision, have demonstrated significant potential to address this challenge. The main objective of this research study is to develop a DL‐based algorithm capable of classifying cucumbers into three distinct categorical groups based on their visual characteristics: defective, curved, and sound (straight green). For this purpose, in addition to inspect the more accurate InceptionResNetV2 as a transfer learning method, the modified convolutional neural network (CNN) (MCNN) incorporating global average pooling (GAP) was proposed to streamline the architecture and minimize trainable parameters. The results demonstrate that the accuracy of CNN with the GAP layer outperforms the fully connected (FC) layer (FCL). The accuracies for the proposed CNN with GAP, proposed CNN with FCL, and InceptionResNetV2 were 94.14%, 92.92%, and 91.21%, respectively, highlighting the efficiency of the CNN with GAP in cucumber classification and its potential to replace conventional grading methods. The overall results indicated that the implementation of dropout did not yield any improvements for the developed models. Rather, the best performance of the CNNs was achieved when utilizing 64 neurons in the hidden layer.
Assessment of Water Quality Parameters in Lake Hayq, Northeastern Ethiopia
Authors: Tecklie Assefa , Nigussie Yohannes , Bilale Adem
Published: September 2024

Lake Hayq is one of the highland lakes of Ethiopia that furnishes very important ecosystem services, fishing, tourism, transportation, drinking water, livestock watering, and irrigation. However, the lake ecosystem is being degraded by pollution, siltation, and excessive growth of macrophytes, buffer zone degradation, overfishing, and climate variability. Therefore, this study was conducted to assess the physicochemical, heavy metals, and biological water quality parameters of Lake Hayq. Physiochemical (pH, water temperature, conductivity, TDS, total alkalinity, dissolved oxygen, Ca2+, Mg2+, Na+, K+, NH4+, NH3, NO2−, NO3−, CO3−, HCO3−, SO42−, PO43−, SiO2, and total phosphorus), heavy metals (Pb, Fe, Zn, Cr, Cu2+, Mn2+, and Ni), and biological (BOD5 and total coliforms) water quality parameters were analyzed both in situ and ex situ. The physicochemical parameters were measured using portable water quality measuring multimeters, the heavy metal analysis was done using the Atomic Absorption Spectrometer, the BOD5 was measured using a BOD5 meter, and the total coliform analysis was done using the spread plate technique. The collected data were analyzed using multivariate, two‐way ANOVA to see the mean difference among sampling sites and seasons through the application of SPSS 16. Most of the water quality parameters of Lake Hayq have met the WHO standards for recreation, aquatic life, and drinking water quality. However, some parameters, such as Pb, BOD5, and total coliforms, were above WHO water quality permissible limits. Therefore, ecohydrological (nature‐based) waste treatment methods such as macrophyte restoration in buffer zones and ecofriendly farming activities should be practiced to minimize the contamination of the lake.
A Conceptual Map of Knowledge Transfer in Occupational Therapy Clinical Practice in Central South Africa
Authors: Swanepoel Azette , Janse van Vuuren Corlia , Nayar Shoba
Published: September 2024

Introduction: Empirical evidence has confirmed that all types of knowledge (propositional, procedural, personal, and client) contribute to evidence‐based practice (EBP) and should be transferred in clinical practice to inform quality service delivery. However, it is unclear how the integration of the types of knowledge that are transferred in clinical practice manifests. Given this gap in understanding, the current research sought to build a conceptual map of knowledge transfer in clinical practice in central South Africa.

Method: A qualitative approach was followed, and data to build the conceptual map was obtained from a scoping review that explored the landscape of knowledge transfer in occupational therapy clinical practice, nine semistructured interviews with occupational therapists working in central South Africa, and a Q Method survey.

Results: The conceptual map–building process delivered a multidimensional, multidirectional conceptual map consisting of four concepts (theory and research, practice experience, patient–therapist relationship, and patient’s voice in clinical practice) and four types of knowledge (propositional, procedural, personal, and client). The results show the integration of the types of knowledge and confirm that knowledge transfer in clinical practice is a complex and ongoing process.

Conclusion: The conceptual map, a first of its kind in South Africa, presents empirical evidence of knowledge that is created and transferred in clinical practice in central South Africa. The conceptual map might provide a framework for collaboration amongst all stakeholders, such as patients, occupational therapists, and academics, to produce practice guidelines and occupational outcome measures to support evidence‐based clinical practice.
Capacidad de investigación de las universidades chilenas: Efectos producto de la Crisis Sanitaria
Authors: Barrera Vera Cristopher Gabriel , Moreno Rojas Diego Sebastián
Published: September 2024

Este artículo analiza los efectos de la pandemia respecto de la capacidad y el desempeño investigativo de las universidades chilenas. Se construyó una base de datos para el periodo 2018 - 2021 a partir de la información entregada en las páginas web de universidades, la Agencia Nacional de Investigación y Desarrollo (ANID), la Superintendencia de Educación Superior (SES), el Ministerio de Educación de Chile (MINEDUC) y otras. Los datos recolectados se centran en la cantidad de publicaciones anuales por universidad, número de académicos, su grado de formación, el total de activos que declara cada universidad en sus ESF, las áreas de conocimiento e información similar. Se observó que hubo un aumento en la cantidad de publicaciones anuales en las universidades, se notó una disminución en la cantidad total de académicos en comparación a años anteriores. En términos generales, la capacidad investigativa de las universidades no se vio afectada negativamente por este suceso.
Supplementary Tables 1-5 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary tables of the revised manuscript.
Supplementary Tables from RUVBL1/2 Blockade Targets YTHDF1 Activity to Suppress m6A-Dependent Oncogenic Translation and Colorectal Tumorigenesis
Authors: Chen Danyu , Ji Fenfen , Zhou Qiming , Cheung Henley , Pan Yasi , Lau Harry C.-H. , Liang Cong , Yang Zhenjie , Huang Pingmei , Wei Qinyao , Cheung Alvin H.-K. , Kang Wei , Chen Huarong , Yu Jun , Wong Chi Chun
Published: September 2024

Supplementary Tables
Supplementary Figure 1 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary Figure 1 and related legend of the revised manuscript.
Data from Obesity Induces Temporally Regulated Alterations in the Extracellular Matrix That Drive Breast Tumor Invasion and Metastasis
Authors: Conner Sydney J. , Borges Hannah B. , Guarin Justinne R. , Gerton Thomas J. , Yui Anna , Salhany Kenneth J. , Mensah Diamond N. , Hamilton Grace A. , Le Giang H. , Lew Katherine C. , Zhang Crystal , Oudin Madeleine J.
Published: September 2024

Abstract
Obesity is associated with increased incidence and metastasis of triple-negative breast cancer, an aggressive breast cancer subtype. The extracellular matrix (ECM) is a major component of the tumor microenvironment that drives metastasis. To characterize the temporal effects of age and high-fat diet (HFD)–driven weight gain on the ECM, we injected allograft tumor cells at 4-week intervals into mammary fat pads of mice fed a control or HFD, assessing tumor growth and metastasis and evaluating the ECM composition of the mammary fat pads, lungs, and livers. Tumor growth was increased in obese mice after 12 weeks on HFD. Liver metastasis increased in obese mice only at 4 weeks, and elevated body weight correlated with increased metastasis to the lungs but not the liver. Whole decellularized ECM coupled with proteomics indicated that early stages of obesity were sufficient to induce changes in the ECM composition. Obesity led to an increased abundance of the proinvasive ECM proteins collagen IV and collagen VI in the mammary glands and enhanced the invasive capacity of cancer cells. Cells of stromal vascular fraction and adipose stem and progenitor cells were primarily responsible for secreting collagen IV and collagen VI, not adipocytes. Longer exposure to HFD increased the invasive potential of ECM isolated from the lungs and liver, with significant changes in ECM composition found in the liver with short-term HFD exposure. Together, these data suggest that changes in the breast, lungs, and liver ECM underlie some of the effects of obesity on triple-negative breast cancer incidence and metastasis.

Significance: Organ-specific extracellular matrix changes in the primary tumor and metastatic microenvironment are mechanisms by which obesity contributes to breast cancer progression.
Figure S9 from HPN328, a Trispecific T Cell–Activating Protein Construct Targeting DLL3-Expressing Solid Tumors
Authors: Molloy Mary E. , Aaron Wade H. , Barath Manasi , Bush Mabel C. , Callihan Evan C. , Carlin Kevin , Cremin Michael , Evans Thomas , Guerrero Maria G. , Hemmati Golzar , Hundal Avneel S. , Lao Llewelyn , Laurie Payton , Lemon Bryan D. , Lin S.J. , O’Rear Jessica , Patnaik Purbasa , Sotelo Rocha Sony , Santiago Linda , Strobel Kathryn L. , Valenzuela Laura B. , Wu Chi-Heng , Yu Stephen , Yu Timothy Z. , Anand Banmeet S. , Law Che-Leung , Sun Liping L. , Wesche Holger , Austin Richard J.
Published: September 2024

HPN328 directs T activation in the presence of DLL3 expressing SHP-77 cells.
Figure S5 from HPN328, a Trispecific T Cell–Activating Protein Construct Targeting DLL3-Expressing Solid Tumors
Authors: Molloy Mary E. , Aaron Wade H. , Barath Manasi , Bush Mabel C. , Callihan Evan C. , Carlin Kevin , Cremin Michael , Evans Thomas , Guerrero Maria G. , Hemmati Golzar , Hundal Avneel S. , Lao Llewelyn , Laurie Payton , Lemon Bryan D. , Lin S.J. , O’Rear Jessica , Patnaik Purbasa , Sotelo Rocha Sony , Santiago Linda , Strobel Kathryn L. , Valenzuela Laura B. , Wu Chi-Heng , Yu Stephen , Yu Timothy Z. , Anand Banmeet S. , Law Che-Leung , Sun Liping L. , Wesche Holger , Austin Richard J.
Published: September 2024

HPN328 binding cross-reactivity to cynomolgus monkey and mouse targets.
Supplementary Figure 1 from Prognostic Significance of SASP-Related Gene Signature of Radiation Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Lee Min Kyeong , Woo Seon Rang , Noh Joo Kyung , Min Soonki , Kong Moonkyoo , Lee Young Chan , Ko Seong-Gyu , Eun Young-Gyu
Published: September 2024

Supplementary Figure 1. The accuracy of the model predictions was validated using LOOCV. the training set was used to assess the accuracy of predictions on the validation set.
Figure S1 from Pretargeted Radioimmunotherapy with the Novel Anti-oxMIF/HSG Bispecific Antibody ON105 Results in Significant Tumor Regression in Murine Models of Cancer
Authors: Puchol Tarazona Alejandro A. , Schinagl Alexander , Mirkina Irina , Rossmueller Gregor , Kerschbaumer Randolf J. , Bachmann Friedmund , Thiele Michael
Published: September 2024

Figure S1
Supplementary Table S2 from Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , To Francis , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gibaja Veronica , Arnoult Nausica , Cocozaki Alexis , Chuong Edward B. , Bitler Benjamin G.
Published: September 2024

Supplementary Table S2 shows the guide RNA sequences for the CRISPRi of MDA5 and RIG-I.
Supplementary Figure 5 from Enhancing Neutrophil Cytotoxicity of a Panel of Clinical EGFR Antibodies by Fc Engineering to IgA3.0
Authors: Chan Chilam , Jansen J.H. Marco , Hendriks Ilona S.T. , van der Peet Ida C. , Verdonschot Meggy E.L. , Passchier Elsemieke M. , Tsioumpekou Maria , Nederend Maaike , Klomp Sharon A. , Valerius Thomas , Peipp Matthias , Leusen Jeanette H.W. , Olofsen Patricia A.
Published: September 2024

Supplementary Figure 5: Tumor outgrowth in A431-luc2 tumor-bearing mice treated with IgA3.0 Matuzumab.
Supplementary Figure S4 from Crizotinib Enhances PARP Inhibitor Efficacy in Ovarian Cancer Cells and Xenograft Models by Inducing Autophagy
Authors: Santiago-O’Farrill Janice M. , Blessing Bollu Alicia , Yang Hailing , Orellana Vivian , Pina Marc , Zhang Xudong , Liu Jinsong , Bast Robert C. , Lu Zhen
Published: September 2024

Supplementary Figure S4 shows induction of autophagy after treatment with the combination of Olaparib and crizotinib
Supplementary Table 2 from Hepatitis B Virus X Protein Represses Expression of Tumor Suppressor PTPN18 in Hepatocellular Carcinoma
Authors: Zhou Zhenyu , Yu Wei , Li Huoming , Shi Juanyi , Meng Shiyu , Yan Yongcong , Chen Ruibin , Liu Haohan , Wang Jie , Sun Jian , Xiao Zhiyu , Zhang Jianlong
Published: September 2024

Univariate and multivariate Cox regression analysis (OS).
Supplementary Table S2 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

Supplementary table 2
Figure S8 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Activation of TMEM16A like current in GASCs.
Figure S3 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

The addition of Yoda 1 on patient-derived GSCs had a similar effect to that described for U87 cells, but the ratio between the amplitude of the Ca2+ and Cl- flares, and the kinetics of Ca2+coupled Cl− responses varied in different patients.
Figure 6 from Clinically Relevant Humanized Mouse Models of Metastatic Prostate Cancer Facilitate Therapeutic Evaluation
Authors: Kostlan Raymond J. , Phoenix John T. , Budreika Audris , Ferrari Marina G. , Khurana Neetika , Choi Jae E. , Juckette Kristin , Mahapatra Somnath , McCollum Brooke L. , Moskal Russell , Mannan Rahul , Qiao Yuanyuan , Vander Griend Donald J. , Chinnaiyan Arul M. , Kregel Steven
Published: September 2024

Immune-dampened profile of T cells in huNOG-EXL tumors. A, Gating strategy for determining the activation state of T cells and regulatory-like T cells. B, Representative data showing the activation state of the CD3+ cells harvested from tumors under different treatment categories through the presence of the surface markers: CD25, CD44, CD69, and PD-1 and regulatory-like cells (CD3+CD25+PD-1+). C, Quantitation showing the expression of CD25 (D), CD44 (E), CD69 (F), PD-1 (G) regulatory-like T cells.
Supplementary Table S4 from CHD2 Regulates Neuron–Glioma Interactions in Pediatric Glioma
Authors: Zhang Xu , Duan Shoufu , Apostolou Panagiota E. , Wu Xiaoping , Watanabe Jun , Gallitto Matthew , Barron Tara , Taylor Kathryn R. , Woo Pamelyn J. , Hua Xu , Zhou Hui , Wei Hong-Jian , McQuillan Nicholas , Kang Kyung-Don , Friedman Gregory K. , Canoll Peter D. , Chang Kenneth , Wu Cheng-Chia , Hashizume Rintaro , Vakoc Christopher R. , Monje Michelle , McKhann Guy M. , Gogos Joseph A. , Zhang Zhiguo
Published: September 2024

Primers and sgRNAs.
Supplementary Figure S3 from CHD2 Regulates Neuron–Glioma Interactions in Pediatric Glioma
Authors: Zhang Xu , Duan Shoufu , Apostolou Panagiota E. , Wu Xiaoping , Watanabe Jun , Gallitto Matthew , Barron Tara , Taylor Kathryn R. , Woo Pamelyn J. , Hua Xu , Zhou Hui , Wei Hong-Jian , McQuillan Nicholas , Kang Kyung-Don , Friedman Gregory K. , Canoll Peter D. , Chang Kenneth , Wu Cheng-Chia , Hashizume Rintaro , Vakoc Christopher R. , Monje Michelle , McKhann Guy M. , Gogos Joseph A. , Zhang Zhiguo
Published: September 2024

CHD2 binds to the gene regulatory elements of axon-guidance and synaptic genes.
Supplemental Figure S2 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S2 shows the percentage of KRAS G12C target engagement determined by different methods.
Figure S1 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Figure S1. Preclinical characterization of PF-07799933 and comparison to other RAF inhibitors.
Supplementary Table 2 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Glycoproteomics
Supplementary Figure S4 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

In Silico Saturation Mutagenesis of 10 CH genes
Supplementary Figure S15 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Association of CH mutations and the development of solid malignancies in UKB
Data from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Abstract
First-generation KRAS G12C inhibitors, such as sotorasib and adagrasib, are limited by the depth and duration of clinical responses. One potential explanation for their modest clinical activity is the dynamic “cycling” of KRAS between its guanosine diphosphate (GDP)– and guanosine triphosphate (GTP)–bound states, raising controversy about whether targeting the GDP-bound form can fully block this oncogenic driver. We herein report that D3S-001, a next-generation GDP-bound G12C inhibitor with faster target engagement (TE) kinetics, depletes cellular active KRAS G12C at nanomolar concentrations. In the presence of growth factors, such as epithelial growth factor and hepatocyte growth factor, the ability of sotorasib and adagrasib to inhibit KRAS was compromised whereas the TE kinetics of D3S-001 was nearly unaffected, a unique feature differentiating D3S-001 from other GDP-bound G12C inhibitors. Furthermore, the high covalent potency and cellular TE efficiency of D3S-001 contributed to robust antitumor activity preclinically and translated into promising clinical efficacy in an ongoing phase 1 trial (NCT05410145).

Significance: The kinetic study presented in this work unveils, for the first time, that a GDP-bound conformation-selective KRAS G12C inhibitor can potentially deplete cellular active KRAS in the presence of growth factors and offers new insights into the critical features that drive preclinical and clinical efficacy for this class of drugs.
Data from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Abstract
RAF inhibitors have transformed treatment for patients with BRAFV600-mutant cancers, but clinical benefit is limited by adaptive induction of ERK signaling, genetic alterations that induce BRAFV600 dimerization, and poor brain penetration. Next-generation pan-RAF dimer inhibitors are limited by a narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant, selective, pan-mutant BRAF inhibitor. PF-07799933 inhibited signaling in vitro, disrupted endogenous mutant-BRAF:wild-type-CRAF dimers, and spared wild-type ERK signaling. PF-07799933 ± binimetinib inhibited growth of mouse xenograft tumors driven by mutant BRAF that functions as dimers and by BRAFV600E with acquired resistance to current RAF inhibitors. We treated patients with treatment-refractory BRAF-mutant solid tumors in a first-in-human clinical trial (NCT05355701) that utilized a novel, flexible, pharmacokinetics-informed dose escalation design that allowed rapid achievement of PF-07799933 efficacious concentrations. PF-07799933 ± binimetinib was well-tolerated and resulted in multiple confirmed responses, systemically and in the brain, in patients with BRAF-mutant cancer who were refractory to approved RAF inhibitors.

Significance: PF-07799933 treatment was associated with antitumor activity against BRAFV600- and non-V600-mutant cancers preclinically and in treatment-refractory patients, and PF-07799933 could be safely combined with a MEK inhibitor. The novel, rapid pharmacokinetics (PK)-informed dose escalation design provides a new paradigm for accelerating the testing of next-generation targeted therapies early in clinical development.
Tuning Responses to Polatuzumab Vedotin in B-cell Lymphoma
Authors: Leveille Etienne , Kothari Shalin , Cosgun Kadriye N. , Mlynarczyk Coraline , Müschen Markus
Published: September 2024

Polatuzumab vedotin, an antibody–drug conjugate targeting CD79B, is the first new drug approved for first-line therapy of diffuse large B-cell lymphoma in more than two decades, although factors determining treatment responses to polatuzumab vedotin remain unknown. Two new studies identified central mechanisms of lower sensitivity, namely reduced accessibility of the CD79B epitope through N-linked glycosylation of CD79B and lower CD79B surface expression levels due to the activity of the KLHL6 E3 ligase.

See related article by Corcoran et al., p. 1653 (6)

See related article by Meriranta et al. (7).
Figure 1 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Construction and clinical characterization of the RT and CTRL cohorts. A, Flowchart representing identification and filtering of patients included or excluded in each cohort. Barplots of distribution of (B) T, (C) N, and (D) M stage tumors for both the CTRL and RT cohorts. Bar height represents the proportion of cohort with the absolute number inset in the respective box. Fisher exact test was performed to calculate significance between CTRL and RT sample distribution. E, Kaplan–Meier (KM) curves representing OS for patients with CTRL (gold), RT–short latency (dark blue), and RT–long latency (light blue) tumors. F, KM curves representing OS for RT patients grouped by smoking status at the time of the bladder cancer diagnosis. For KM curves, dashed lines indicate median survival. Significance was calculated using the Cox proportional hazard model with CTRL and never smokers as the reference, respectively. G, Forest plot visualizing a multivariate Cox proportional model for OS incorporating smoking and latency. Reference groups are indicated within the figure. H, Swimmer plot showing time from RT to end of follow-up. Solid black lines represent the age of patients at the time of prostate RT. The x-axis origin denotes the time of RT, with the teal bar length proportional to the latency and the pink bar indicating length of follow-up to death or last follow-up. Vital status is noted by either a circle (alive at last follow-up) or a triangle (deceased). UTUC; upper tract urothelial carcinoma.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2024

Fold-changes and adjusted p-values for all microbes associated with hypoxic or normoxic tumors in the ORIEN and TCGA datasets (associated with Figure 2A). Results of survival analyses of interactions between microbes and hypoxia in COADREAD patients receiving radiation therapy.
Supplementary Data from The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik C. , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2024

Log2 fold changes of annotated Cutibacterium genes between hypoxic and normoxic tumors in nude and BALB/c mice.