bluuebunny/crossref_metadata_2025 huggingface dataset:
Leveraging medical Twitter to build a visual–language foundation model for pathology AI
Authors: Huang Zhi , Bianchi Federico , Yuksekgonul Mert , Montine Thomas , Zou James
Published: April 2023

The lack of annotated publicly available medical images is a major barrier for innovations. At the same time, many de-identified images and much knowledge are shared by clinicians on public forums such as medical Twitter. Here we harness these crowd platforms to curate OpenPath, a large dataset of 208,414 pathology images paired with natural language descriptions. This is the largest public dataset for pathology images annotated with natural text. We demonstrate the value of this resource by developing PLIP, a multimodal AI with both image and text understanding, which is trained on OpenPath. PLIP achieves state-of-the-art zero-shot and transfer learning performances for classifying new pathology images across diverse tasks. Moreover, PLIP enables users to retrieve similar cases by either image or natural language search, greatly facilitating knowledge sharing. Our approach demonstrates that publicly shared medical information is a tremendous resource that can be harnessed to advance biomedical AI.
Ensemble of BLUP, Machine Learning, and Deep Learning Models Predict Maize Yield Better Than Each Model Alone
Authors: Kick Daniel R. , Washburn Jacob D.
Published: April 2023

Predicting phenotypes accurately from genomic, environment, and management factors is key to accelerating the development of novel cultivars with desirable traits. Inclusion of management and environmental factors enablesin silicostudies to predict the effect of specific management interventions or future climates. Despite the value such models would confer, much work remains to improve the accuracy of phenotypic predictions. Rather than advocate for a single specific modeling strategy, here we demonstrate within large multi-environment and multi-genotype maize trials that combining predictions from disparate models using simple ensemble approaches most often results in better accuracy than using any one of the models on their own. We investigated various ensemble combinations of different model types, model numbers, and model weighting schemes to determine the accuracy of each.

We find that ensembling generally improves performance even when combining only two models. The number and type of models included alter accuracy with improvements diminishing as the number of models included increases. Using a genetic algorithm to optimize ensemble composition reveals that, when weighted by the inverse of each model’s expected error, using combinations of best linear unbiased predictors, linear fixed effects models, deep learning models, and select machine learning models perform best on our datasets.
Dietary environmental factors shape the immune defence againstCryptosporidiuminfection
Authors: Maradana Muralidhara Rao , Marzook N. Bishara , Diaz Oscar E. , Mkandawire Tapoka , Diny Nicola Laura , Li Ying , Liebert Anke , Shah Kathleen , Tolaini Mauro , Kváč Martin , Stockinger Brigitta , Sateriale Adam
Published: April 2023

Cryptosporidiumis a leading cause of diarrheal-related deaths in children, especially in resource-poor settings. It also targets the immunocompromised, chronically infecting people living with HIV and primary immunodeficiencies. There is no vaccine or effective treatment. While it is known from human cases and animal models that CD4+T-cells play a role in curbingCryptosporidium, the role of CD8+cells remains to be defined. Using aCryptosporidium tyzzerimouse model, we show that gut-resident CD8+intraepithelial lymphocytes (IELs) confer resistance to parasite growth. CD8+IELs express, and are dependent on, the ligand-dependent transcription factor aryl hydrocarbon receptor (AHR). AHR deficiency reduced CD8+IELs, decreased their cytotoxicity, and worsened infection. Transfer of CD8+IELs rescued severely immunodeficient mice from death followingCryptosporidiumchallenge. Finally, dietary supplementation of the AHR pro-ligand indole-3-carbinol to new-born mice promoted resistance to infection. Therefore, common dietary metabolites augment the host immune response to cryptosporidiosis, protecting against disease.
Analysis of Arabidopsisvenosa4-0supports the role of VENOSA4 in dNTP homeostasis
Authors: Sarmiento-Mañús Raquel , González-Bayón Rebeca , Fontcuberta-Cervera Sara , Hannah Matthew A. , Álvarez-Martínez Francisco Javier , Barrajón-Catalán Enrique , Micol Vicente , Quesada Víctor , Ponce María Rosa , Micol José Luis
Published: April 2023

An imbalance in the deoxyribonucleoside triphosphate (dNTP) pool caused by an increase or decrease in the levels of any of the four dNTPs leads to increased DNA mutations, overloading DNA repair mechanisms. The human protein SAMHD1 (Sterile alpha motif and histidine-aspartate domain containing protein 1) functions as a dNTPase to maintain the balance of the dNTP pool, as well as in DNA repair. In eukaryotes, the limiting step inde novodNTP synthesis is catalyzed by RIBONUCLEOTIDE REDUCTASE (RNR), which consists of two R1 and two R2 subunits. In Arabidopsis, RNR1 is encoded byCRINKLED LEAVES 8(CLS8) and RNR2 by three paralogous genes, includingTSO2(TSO MEANING ’UGLY’ IN CHINESE 2). In plants, thede novobiosynthesis of purines occurs within the chloroplast, and DOV1 (DIFFERENTIAL DEVELOPMENT OF VASCULAR ASSOCIATED CELLS 1) catalyzes the first step of this pathway. Here, to explore the role ofVENOSA4(VEN4), the most likely Arabidopsis ortholog of humanSAMHD1, we studied theven4-0mutant. The mutant leaf phenotype caused by theven4-0point mutation was stronger than those of T-DNA insertionalven4mutations. Structural predictions suggested that the E249L amino acid substitution in the mutated VEN4-0 protein rigidifies its 3D structure compared to wild-type VEN4. The morphological phenotypes of theven4,cls8, anddov1single mutants were similar, and those of theven4 tso2andven4 dov1double mutants were synergistic. Theven4-0mutant had reduced levels of four amino acids related to dNTP biosynthesis, including glutamine and glycine, which are precursors in thede novopurine biosynthesis pathway. Finally, despite its annotation in some databases, At5g40290, a paralog ofVEN4, is likely a pseudogene. These observations support the previously proposed role of VEN4 in dNTP metabolism. Our results reveal a high degree of cross-kingdom functional conservation between VEN4 and SAMHD1 in dNTP homeostasis.
Determining epitope specificity of T-cell receptors with transformers
Authors: Khan Abdul Rehman , Reinders Marcel JT , Khatri Indu
Published: April 2023

Motivation

T-cell receptors (TCR) on T cells recognize and bind to epitopes presented by the major histocompatibility complex (MHC) in case of an infection or cancer. However, the high diversity of TCRs, as well as their unique and complex binding mechanisms underlying epitope recognition, make it difficult to predict the binding between TCR and epitope. Here, we present the utility of transformers, a deep learning strategy that incorporates an attention mechanism that learns the informative features, and show that these models pretrained on a large set of protein sequences outperform current strategies.

Method

We compared three pre-trained auto-encoder transformer models (ProtBERT, ProtAlbert, ProtElectra) and one pre-trained auto-regressive transformer model (ProtXLNet) to predict the binding specificity of TCRs to 25 epitopes from the VDJdb database (human and murine). Two additional modifications were performed to incorporate gene usage of the TCRs in the four transformer models.

Results

Of all 12 transformer implementations (4 models with 3 different modifications), a modified version of the ProtXLNet model could predict TCR-epitope pairs with the highest accuracy (weighted F1 score 0.55 simultaneously considering all 25 epitopes). The modification included additional features representing the gene names for the TCRs. We also showed that the basic implementation of transformers outperformed the previously available methods, i.e. TCRGP, TCRDist and DeepTCR, developed for the same biological problem, especially for the hard-to-classify labels.

Conclusion

We show that the proficiency of transformers in attention learning can indeed be made operational in a complex biological setting like TCR binding prediction. Further ingenuity in utilizing the full potential of transformers, either through attention head visualization or introducing additional features, can further extend T-cell research avenues.

Availability

Data and code are available onhttps://github.com/InduKhatri/tcrformer
The positioning mechanics of microtubule asters inDrosophilaembryo explants
Authors: de-Carvalho Jorge , Tlili Sham , Saunders Timothy E. , Telley Ivo A.
Published: April 2023

Microtubule asters are essential in localizing the action of microtubules in processes including mitosis and organelle positioning. In large cells, such as the one-cell sea urchin embryo, aster dynamics are dominated by hydrodynamic pulling forces. However, in systems with more densely positioned nuclei such as the earlyDrosophilaembryo, which packs around 6000 nuclei within the syncytium in a crystalline-like order, it is unclear what processes dominate aster dynamics. Here, we take advantage of a cell cycle regulationDrosophilamutant to generate embryos with multiple asters, independent from nuclei. We use anex vivoassay to further simplify this biological system to explore the forces generated by and between asters. Through live imaging, drug and optical perturbations, and theoretical modelling, we demonstrate that these asters likely generate an effective pushing force over short distances.

Significance Statement

Using cytosolic explants fromDrosophilasyncytial embryos combined with quantitative microscopy and perturbations, de-Carvalhoet al., reveal the mechanical forces separatingDrosophilamicrotubule asters. Aster separation drives precise nuclear positioning in multinucleated embryo cells, a vital process for tissue formation and gene expression during subsequent embryo development.
Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy
Authors: Mistretta Maxime , Cimino Mena , Campagne Pascal , Volant Stevenn , Kornobis Etienne , Hebert Olivier , Rochais Christophe , Dallemagne Patrick , Lecoutey Cédric , Tisnerat Camille , Lepailleur Alban , Ayotte Yann , LaPlante Steven R. , Gangneux Nicolas , Záhorszká Monika , Korduláková Jana , Vichier-Guerre Sophie , Bonhomme Frédéric , Pokorny Laura , Albert Marvin , Tinevez Jean-Yves , Manina Giulia
Published: April 2023

Drug-recalcitrant infections are a leading global-health concern. Bacterial cells benefit from phenotypic variation, which can suggest effective anti-microbial strategies. However, probing phenotypic variation entails spatiotemporal analysis of individual cells that is technically challenging, and hard to integrate into drug discovery. To address this, we developed a flow-controlled multi-condition microfluidic platform suitable for imaging two-dimensional growth of bacterial cells, compressed inside separate microchambers by a soft hydro-pneumatic membrane. With this platform, we implemented a dynamic single-cell screening for compounds that induce a phenotypic change while decreasing cell-to-cell variation, aiming to undermine the bacterial population, making it more vulnerable to other drugs. We first applied this strategy to mycobacteria, as tuberculosis poses a major public-health threat. Our top hit impairsMycobacterium tuberculosisvia a peculiar mode of action and enhances other anti-tubercular drugs. This work proves that pheno-tuning compounds represent a successful approach to tackle pathogens that are increasingly difficult to treat.
The diversity of splicing modifiers acting on A-1bulged 5’-splice sites reveals rules to guide rational design
Authors: Florian Malard , Wolter Antje , Marquevielle Julien , Morvan Estelle , Allain Frédéric HT. , Sebastien Campagne
Published: April 2023

Non-physiological alternative splicing patterns are associated with numerous human diseases. Among the strategies developed to treat these diseases, small molecule splicing modifiers are emerging as a new class of RNA therapeutics. TheSMN2splicing modifier SMN-C5 was used as a prototype to understand their mode of action and discover the concept of 5’-splice site bulge repair. However, different small molecules harbouring a similar activity were also identified. In this study, we combined NMR spectroscopy and computational approaches to determine the binding modes of otherSMN2andHTTsplicing modifiers at the interface between U1 snRNP and an A-1bulged 5’-splice site. Our results show that the other splicing modifiers interact with the intermolecular RNA helix epitope containing an unpaired adenine within a G-2A-1G+1U+2motif, which is essential for their biological activity. We also determined structural models of risdiplam, SMN-CX, and branaplam bound to RNA, and solved the solution structure of the most divergentSMN2splicing modifier, SMN-CY, in complex with the RNA helix. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1bulged 5’-splice sites, but also identify common pharmacophores required for modulating 5’-splice site selection with small molecules.
A rapid and robust leaf ablation method to visualize bundle sheath cell chloroplasts in C3species
Authors: Billakurthi Kumari , Hibberd Julian M
Published: April 2023

Background

It has been proposed that engineering the C4photosynthetic pathway into C3crops could significantly increase yield. This goal requires an increase in the chloroplast compartment of bundle sheath cells in C3species. To facilitate large-scale testing of candidate regulators of chloroplast development in the rice bundle sheath, a simple and robust method to phenotype this tissue in C3species is required.

Results

We established a leaf ablation method to accelerate phenotyping of rice bundle sheath cells. The approach allowed bundle sheath cell dimensions, chloroplast area and chloroplast number per cell to be measured. Using this method, bundle sheath cell dimensions of maize were also measured and compared with rice. Our data show that bundle sheath width but not length significantly differed between C3rice and C4maize. Comparison of paradermal versus transverse bundle sheath cell width indicated that bundle sheath cells were intact after leaf ablation. Moreover, comparisons of planar chloroplast areas and chloroplast numbers per bundle sheath cell between wild-type and transgenic rice lines expressing the maizeGOLDEN-2(ZmG2) showed that the leaf ablation method allowed differences in chloroplast parameters to be detected.

Conclusions

Leaf ablation is a simple approach to accessing bundle sheath cell files in C3species. We show that this method is suitable for obtaining parameters associated with bundle sheath cell size, chloroplast area and chloroplast number per cell.
TCR2vec: a deep representation learning framework of T-cell receptor sequence and function
Authors: Jiang Yuepeng , Huo Miaozhe , Zhang Pingping , Zou Yiping , Li Shuai Cheng
Published: April 2023

The T-cell receptor (TCR) repertoires are critical components of the adaptive immune system, and machine learning methods were proposed to analyze the TCR repertoire data. However, most methods work solely on the hypervariable CDR3 regions of TCRs, overlooking the information encoded in other domains. Representing full TCRs as informative vectors can be indispensable for developing reliable and effective machine learning models. We introduce TCR2vec, a deep representation learning framework with 12 layers of transformer blocks, to pave the way for downstream modelings of full TCRs. Together with masked language modeling (MLM), we propose a novel pretraining task named similarity preservation modeling (SPM) to capture the sequence similarities of TCRs. Through a multi-task pretraining procedure on MLM and SPM, TCR2vec learns a contextual understanding of TCRs within a similarity-preserved vector space. We first verify the effectiveness of TCR2vec in predicting TCR’s binding specificity and TCR clustering through comparison with three other embedding approaches. TCR2vec can be finetuned on small task-specific labeled data for enhanced performance, which outperforms state-of-the-art models by 2-25% in predicting TCR’s binding specificity. Next, we compare the performance of two versions of TCR2vec pretrained on full TCRs (TCR2vec) or CDR3s (CDR3vec) and demonstrate that TCR2vec consistently outperforms CDR3vec by 12-14%. Further analysis of attention maps reveals that residues outside CDR3 also make notable contributions to the recognition of antigens. TCR2vec is available athttps://github.com/jiangdada1221/TCR2vec.
PanKmer:k-mer based and reference-free pangenome analysis
Authors: Aylward Anthony J. , Petrus Semar , Mamerto Allen , Hartwick Nolan T. , Michael Todd P.
Published: April 2023

Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thou-sands of individual genomes. PanKmer decomposes a set of input genomes into a table of observedk-mers and their presence-absence values in each genome. These are stored in an efficientk-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of thek-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example,k-mers can be “anchored” in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.

Availability and implementation

PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) athttps://pypi.org/project/pankmer/as well as Gitlab athttps://gitlab.com/salk-tm/pankmer. Full documentation is available athttps://salk-tm.gitlab.io/pankmer/.

Supplementary information

Supplementary data are available online
Increase in primary cilia number and length upon VDAC1 depletion contributes to attenuated proliferation of cancer cells
Authors: Dutta Arpita , Halder Priyadarshini , Gayen Anakshi , Mukherjee Avik , Mukherjee Chandrama , Majumder Shubhra
Published: April 2023

Primary cilia (PCs) that are present in most human cells and perform sensory function or signal transduction are lost in many solid tumors. Previously, we identified VDAC1, best known to regulate mitochondrial bioenergetics, to negatively regulate ciliogenesis. Here, we show that downregulation of VDAC1 in pancreatic cancer-derived Panc1 and glioblastoma-derived U-87 cells significantly increased ciliation. Those PCs were remarkably longer than the control cells. Such increased ciliation inhibited cell cycle, which contributed to reduced proliferation of these cells. VDAC1-depletion also led to longer PCs in quiescent RPE1 cells. Therefore, serum-induced PC disassembly was slower in VDAC1-depleted RPE1 cells. Overall, this study reiterates the importance of VDAC1 in modulating tumorigenesis, due to its novel role in regulating PC length and disassembly.
Anti-nucleolin aptamer, iSN04, inhibits the inflammatory responses in myoblasts by modulating the β-catenin/NF-κB signaling pathway
Authors: Yamamoto Machi , Miyoshi Mana , Morioka Kamino , Mitani Takakazu , Takaya Tomohide
Published: April 2023

A myogenetic oligodeoxynucleotide, iSN04, is the 18-base single-stranded DNA that acts as an anti-nucleolin aptamer. iSN04 has been reported to restore myogenic differentiation by suppressing inflammatory responses in myoblasts isolated from patients with diabetes or healthy myoblasts exposed to cancer-releasing factors. Thus, iSN04 is expected to be a nucleic acid drug for the muscle wasting associated with chronic diseases. The present study investigated the anti-inflammatory mechanism of iSN04 in the murine myoblast cell line C2C12. Tumor necrosis factor-α (TNF-α) or Toll-like receptor (TLR) ligands (Pam3CSK4and FSL-1) induced nuclear translocation and transcriptional activity of nuclear factor-κB (NF-κB), resulting in upregulated expression of TNF-α and interleukin-6. Pre-treatment with iSN04 significantly suppressed these inflammatory responses by inhibiting the nuclear accumulation of β-catenin induced by TNF-α or TLR ligands. These results demonstrate that antagonizing nucleolin with iSN04 downregulates the inflammatory effect mediated by the β-catenin/NF-κB signaling pathway in myoblasts. In addition, the anti-inflammatory effects of iSN04 were also observed in smooth muscle cells and pre-adipocytes, suggesting that iSN04 may be useful in preventing inflammation induced by metabolic disorders.
Adapting the endoplasmic reticulum proteostasis rescues epilepsy-associated NMDA receptor variants
Authors: Zhang Pei-Pei , Benske Taylor M. , Paton James C. , Paton Adrienne W. , Mu Ting-Wei , Wang Ya-Juan
Published: April 2023

TheGRINgenes encoding N-methyl-D-aspartate receptor (NMDAR) subunits are remarkably intolerant to variation. Many pathogenic NMDAR variants result in their protein misfolding, inefficient assembly, reduced surface expression, and impaired functionality at the plasma membrane, causing neurological disorders including epilepsy and intellectual disability. Here, we concentrate on the proteostasis maintenance of NMDARs containing epilepsy-associated variations in the GluN2A (or NR2A) subunit, including M705V and A727T. We showed that these two variants are targeted to the proteasome for degradation and have reduced functional surface expression. We demonstrated that the application of BIX, a known small molecule activator of an HSP70 family chaperone BiP (Binding immunoglobulinProtein) in the endoplasmic reticulum (ER), significantly increases total and surface protein levels, and thus the function of the M705V and A727T variants in HEK293T cells. Mechanistic studies revealed that BIX promotes folding, inhibits degradation, and enhances anterograde trafficking of the M705V variant by modest activation of the IRE1 pathway of the unfolded protein response. Our results showed that adapting the ER proteostasis network restores the folding, trafficking, and function of pathogenic NMDAR variants, representing a potential treatment for neurological disorders resulting from NMDAR dysfunction.
Cascading failure in guarantee networks from the perspective of equilibrium
Authors: Ren Chao , Liu Xiaoxing , Zhu Ziyan
Published: April 2023

Purpose

The purpose of this paper is to test the invulnerability of the guarantee network at the equilibrium point.

Design/methodology/approach

This paper introduces a tractable guarantee network model that captures the invulnerability of the network in terms of cascade-based attack. Furthermore, the equilibrium points are introduced for banks to determine loan origination.

Findings

The proposed approach not only develops equilibrium analysis as an extended perspective in the guarantee network, but also applies cascading failure method to construct the guarantee network. The equilibrium points are examined by simulating experiment. The invulnerability of the guarantee network is quantified by the survival of firms in the simulating progress.

Research limitations/implications

There is less study in equilibrium analysis of the guarantee network. Additionally, cascading failure model is expressed in the presented approach. Moreover, agent-based model can be extended in generating the guarantee network in the future study.

Originality/value

The approach of this paper presents a framework to analyze the equilibrium of the guarantee network. For this, the systemic risk of the whole guarantee network and each node's contribution are measured to predict the probability of default on cascading failure. Focusing on cascade failure process based on equilibrium point, the invulnerability of the guarantee network can be quantified.
Development of an activated carbon‐geopolymer composite for treatment of Pb(II) polluted water and soil
Authors: He Panyang , Xin Kaineng , Zhang Xiaomin , Guo Zhonglin , Zheng Wei
Published: April 2023

An activated carbon‐geopolymer composite (ACGC) was prepared by using fly ash as raw materials via a simple geopolymerization process for treating the Pb(II) contaminant in wastewater and soil. The phase composition, microtopography, pore structure, and surface groups of the composites were studied by X‐ray diffractometer, field emission scanning electron microscopy, X‐ray photoelectron spectroscopy, N2 adsorption‐desorption isotherm, and Fourier transform infrared spectroscope. It was discovered that there was a synergistic effect between geopolymer matrix and activated carbon (AC), that is, addition of AC particles could increase the pores in geopolymer while strong alkalis condition provided by geopolymer enhanced the contents of oxygenic groups of AC. When the composite was used as the adsorbent, the sample containing 20 wt% AC (40ACGC) showed the maximum adsorption capacity (319.72 mg/g), and its adsorption isotherm fitted the Langmuir model well, suggesting the monolayer adsorption of Pb2+ on the 40ACGC. The kinetics of Pb2+ adsorption on the 40ACGC belonged to the pseudo‐second‐order model, indicating that Pb2+ adsorption on the composite followed chemical adsorption. In addition, the 40ACGC sample showed excellent stabilization performance for Pb2+ in soil. This work offered a new thinking to the application of geopolymers into remediation of heavy metal‐polluted soil.
Use of different ratios of by‐product from mung bean dry‐dehulling in pasta making: nutritional quality, textural and cooking attributes, overall acceptability and in‐vitro antioxidant release from the pasta
Authors: Le Thi Thuc Man , Nguyen Phuong Thao , Tran Thi Thu Tra , Ton Nu Minh Nguyet , Le Van Viet Man
Published: April 2023

The production of dehulled mung bean seeds generates a by‐product which includes husk particles and finely broken endosperm. In this study, the mung bean by‐product flour (MBBF) was used as an antioxidant dietary fibre ingredient for pasta formulation. Increase in MBBF ratio in the pasta recipe from 0% to 25% enhanced total dietary fibre and total phenolic of the product by 4.2 and 4.5 times, respectively; in addition, the cooking loss of pasta increased while its optimal cooking time and swelling index were reduced. The pasta samples supplemented with MFFB had increased hardness but decreased cohesiveness, tensile strength, and elongation rate. The pasta samples incorporated with 10–20% MFFB were accepted by consumers and could be considered as a high‐fibre food product since their total dietary fibre content was varied from 7.5 to 13.5 g/100 g. The pasta cooking decreased its chlorophyll content but improved the phenolic level. At 20% MFFB level, the 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activity and ferric‐reducing antioxidant power of the product released at the in‐vitro intestinal step were 2.2 and 6.8 times, respectively, higher than those of the undigested cooked pasta. MBBF is a potential antioxidant dietary fibre ingredient to produce healthy pasta and the use of this by‐product would contribute to sustainable development of circular economy in the near future.
Mechanisms of microstructural deformation governing Vickers hardness in phase‐separated calcium aluminosilicate glasses
Authors: Clark Nicholas L. , Chuang Shih‐Yi , Mauro John C.
Published: April 2023

The impact of microstructure on hardness in phase‐separated calcium aluminosilicate glasses is investigated. Changes in hardness are governed by microstructure deformations that occur during indentation. Phase separation leads to decreased hardness due to the incongruent yielding of the droplet and matrix phases. Moreover, the deformation of microstructures possessing dilute, spherical droplets did not have a significant impact on hardness. Microstructures characterized by concentrated, acicular droplets were found to deform through a process of droplet coalescence. This process absorbs additional energy during yielding and results in glasses that deform through droplet coalescence possessing improved hardness.
Supplementary Table 3 from Identification and Characterization of Ovarian Cancer-Initiating Cells from Primary Human Tumors
Authors: Zhang Shu , Balch Curt , Chan Michael W. , Lai Hung-Cheng , Matei Daniela , Schilder Jeanne M. , Yan Pearlly S. , Huang Tim H-M. , Nephew Kenneth P.
Published: April 2023

Supplementary Table 3 from Identification and Characterization of Ovarian Cancer-Initiating Cells from Primary Human Tumors
Supplementary Table A, Figures 1-7 from A Novel Lung Cancer Signature Mediates Metastatic Bone Colonization by a Dual Mechanism
Authors: Vicent Silvestre , Luis-Ravelo Diego , Antón Iker , García-Tuñón Ignacio , Borrás-Cuesta Francisco , Dotor Javier , De Las Rivas Javier , Lecanda Fernando
Published: April 2023

Supplementary Table A, Figures 1-7 from A Novel Lung Cancer Signature Mediates Metastatic Bone Colonization by a Dual Mechanism
Supplementary Figure Legends 1-6 from The Kringle 1 Domain of Hepatocyte Growth Factor Has Antiangiogenic and Antitumor Cell Effects on Hepatocellular Carcinoma
Authors: Shen Zan , Yang Zhen Fan , Gao Yi , Li Ji Cheng , Chen Hai Xiao , Liu Ching Chiu , Poon Ronnie T.P. , Fan Sheung Tat , Luk John M. , Sze Kong Hung , Li Tsai Ping , Gan Ren Bao , He Ming Liang , Kung Hsiang Fu , Lin Marie C.M.
Published: April 2023

Supplementary Figure Legends 1-6 from The Kringle 1 Domain of Hepatocyte Growth Factor Has Antiangiogenic and Antitumor Cell Effects on Hepatocellular Carcinoma
Supplement 3 from Regulation of Id1 Expression by Src: Implications for Targeting of the Bone Morphogenetic Protein Pathway in Cancer
Authors: Gautschi Oliver , Tepper Clifford G. , Purnell Phillip R. , Izumiya Yoshihiro , Evans Christopher P. , Green Tim P. , Desprez Pierre Y. , Lara Primo N. , Gandara David R. , Mack Philip C. , Kung Hsing-Jien
Published: April 2023

Supplement 3 from Regulation of Id1 Expression by Src: Implications for Targeting of the Bone Morphogenetic Protein Pathway in Cancer
Supplementary Table from Histamine Suppresses Fibulin-5 and Insulin-like Growth Factor-II Receptor Expression in Melanoma
Authors: Pos Zoltan , Wiener Zoltan , Pocza Peter , Racz Melinda , Toth Sara , Darvas Zsuzsanna , Molnar Viktor , Hegyesi Hargita , Falus Andras
Published: April 2023

Supplementary Table from Histamine Suppresses Fibulin-5 and Insulin-like Growth Factor-II Receptor Expression in Melanoma
Supplementary Figure 7 from A Human Breast Cell Model of Preinvasive to Invasive Transition
Authors: Rizki Aylin , Weaver Valerie M. , Lee Sun-Young , Rozenberg Gabriela I. , Chin Koei , Myers Connie A. , Bascom Jamie L. , Mott Joni D. , Semeiks Jeremy R. , Grate Leslie R. , Mian I. Saira , Borowsky Alexander D. , Jensen Roy A. , Idowu Michael O. , Chen Fanqing , Chen David J. , Petersen Ole W. , Gray Joe W. , Bissell Mina J.
Published: April 2023

Supplementary Figure 7 from A Human Breast Cell Model of Preinvasive to Invasive Transition
Supplementary Table 1 from The Pervasive Presence of Fluctuating Oxygenation in Tumors
Authors: Cárdenas-Navia Laura I. , Mace Daniel , Richardson Rachel A. , Wilson David F. , Shan Siqing , Dewhirst Mark W.
Published: April 2023

Supplementary Table 1 from The Pervasive Presence of Fluctuating Oxygenation in Tumors
Supplementary Figure 1 from A Human Breast Cell Model of Preinvasive to Invasive Transition
Authors: Rizki Aylin , Weaver Valerie M. , Lee Sun-Young , Rozenberg Gabriela I. , Chin Koei , Myers Connie A. , Bascom Jamie L. , Mott Joni D. , Semeiks Jeremy R. , Grate Leslie R. , Mian I. Saira , Borowsky Alexander D. , Jensen Roy A. , Idowu Michael O. , Chen Fanqing , Chen David J. , Petersen Ole W. , Gray Joe W. , Bissell Mina J.
Published: April 2023

Supplementary Figure 1 from A Human Breast Cell Model of Preinvasive to Invasive Transition
Supplementary Figure 1 from Roles for MicroRNAs, miR-93 and miR-130b, and Tumor Protein 53–Induced Nuclear Protein 1 Tumor Suppressor in Cell Growth Dysregulation by Human T-Cell Lymphotrophic Virus 1
Authors: Yeung Man Lung , Yasunaga Jun-ichirou , Bennasser Yamina , Dusetti Nelson , Harris David , Ahmad Nafees , Matsuoka Masao , Jeang Kuan-Teh
Published: April 2023

Supplementary Figure 1 from Roles for MicroRNAs, miR-93 and miR-130b, and Tumor Protein 53–Induced Nuclear Protein 1 Tumor Suppressor in Cell Growth Dysregulation by Human T-Cell Lymphotrophic Virus 1
Supplementary Table 2 from Glycogen Synthase Kinase-3 Inhibition Induces Glioma Cell Death through c-MYC, Nuclear Factor-κB, and Glucose Regulation
Authors: Kotliarova Svetlana , Pastorino Sandra , Kovell Lara C. , Kotliarov Yuri , Song Hua , Zhang Wei , Bailey Rolanda , Maric Dragan , Zenklusen Jean Claude , Lee Jeongwu , Fine Howard A.
Published: April 2023

Supplementary Table 2 from Glycogen Synthase Kinase-3 Inhibition Induces Glioma Cell Death through c-MYC, Nuclear Factor-κB, and Glucose Regulation
Supplementary Table 1 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma
Authors: Monnier Yan , Farmer Pierre , Bieler Gregory , Imaizumi Natsuko , Sengstag Thierry , Alghisi Gian Carlo , Stehle Jean-Christophe , Ciarloni Laura , Andrejevic-Blant Snezana , Moeckli Raphael , Mirimanoff René-Olivier , Goodman Simon L. , Delorenzi Mauro , Rüegg Curzio
Published: April 2023

Supplementary Table 1 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma
Supplementary Figures 1-4 from Role of Acetylation and Extracellular Location of Heat Shock Protein 90α in Tumor Cell Invasion
Authors: Yang Yonghua , Rao Rehka , Shen Jie , Tang Yun , Fiskus Warren , Nechtman John , Atadja Peter , Bhalla Kapil
Published: April 2023

Supplementary Figures 1-4 from Role of Acetylation and Extracellular Location of Heat Shock Protein 90α in Tumor Cell Invasion
Supplementary Figure 6 from Identification of Alternative Splicing Markers for Breast Cancer
Authors: Venables Julian P. , Klinck Roscoe , Bramard Anne , Inkel Lyna , Dufresne-Martin Geneviève , Koh ChuShin , Gervais-Bird Julien , Lapointe Elvy , Froehlich Ulrike , Durand Mathieu , Gendron Daniel , Brosseau Jean-Philippe , Thibault Philippe , Lucier Jean-Francois , Tremblay Karine , Prinos Panagiotis , Wellinger Raymund J. , Chabot Benoit , Rancourt Claudine , Elela Sherif Abou
Published: April 2023

Supplementary Figure 6 from Identification of Alternative Splicing Markers for Breast Cancer
Supplementary Figures 1-4 from PI3K Pathway Activation Mediates Resistance to MEK Inhibitors in KRAS Mutant Cancers
Authors: Wee Susan , Jagani Zainab , Xiang Kay Xiaoqin , Loo Alice , Dorsch Marion , Yao Yung-Mae , Sellers William R. , Lengauer Christoph , Stegmeier Frank
Published: April 2023

Supplementary Figures 1-4 from PI3K Pathway Activation Mediates Resistance to MEK Inhibitors in KRAS Mutant Cancers
Supplementary Figure 2 from K-ras and Wnt Signaling Synergize to Accelerate Prostate Tumorigenesis in the Mouse
Authors: Pearson Helen B. , Phesse Toby J. , Clarke Alan R.
Published: April 2023

Supplementary Figure 2 from K-ras and Wnt Signaling Synergize to Accelerate Prostate Tumorigenesis in the Mouse
Supplementary Figures 1-3 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway
Authors: Crabtree Judy S. , Jelinsky Scott A. , Harris Heather A. , Choe Sung E. , Cotreau Monette M. , Kimberland Michelle L. , Wilson Ewa , Saraf Kathryn A. , Liu Wei , McCampbell Adrienne S. , Dave Bhuvanesh , Broaddus Russell R. , Brown Eugene L. , Kao Wenling , Skotnicki Jerauld S. , Abou-Gharbia Magid , Winneker Richard C. , Walker Cheryl L.
Published: April 2023

Supplementary Figures 1-3 from Comparison of Human and Rat Uterine Leiomyomata: Identification of a Dysregulated Mammalian Target of Rapamycin Pathway
Supplementary Figure 7 from Vascular Endothelial Growth Factor-C Protects Prostate Cancer Cells from Oxidative Stress by the Activation of Mammalian Target of Rapamycin Complex-2 and AKT-1
Authors: Muders Michael H. , Zhang Heyu , Wang Enfeng , Tindall Donald J. , Datta Kaustubh
Published: April 2023

Supplementary Figure 7 from Vascular Endothelial Growth Factor-C Protects Prostate Cancer Cells from Oxidative Stress by the Activation of Mammalian Target of Rapamycin Complex-2 and AKT-1
Supplementary Video 1 from The Role of Transforming Growth Factor-β–Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative Approach
Authors: Basanta David , Strand Douglas W. , Lukner Ralf B. , Franco Omar E. , Cliffel David E. , Ayala Gustavo E. , Hayward Simon W. , Anderson Alexander R.A.
Published: April 2023

Supplementary Video 1 from The Role of Transforming Growth Factor-β–Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative Approach
Free Article from The Role of Transforming Growth Factor-β–Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative Approach
Authors: Basanta David , Strand Douglas W. , Lukner Ralf B. , Franco Omar E. , Cliffel David E. , Ayala Gustavo E. , Hayward Simon W. , Anderson Alexander R.A.
Published: April 2023

Free Article from The Role of Transforming Growth Factor-β–Mediated Tumor-Stroma Interactions in Prostate Cancer Progression: An Integrative Approach
Supplementary Figure 1 from Computational Identification of a p38SAPK-Regulated Transcription Factor Network Required for Tumor Cell Quiescence
Authors: Adam Alejandro P. , George Ajish , Schewe Denis , Bragado Paloma , Iglesias Bibiana V. , Ranganathan Aparna C. , Kourtidis Antonis , Conklin Douglas S. , Aguirre-Ghiso Julio A.
Published: April 2023

Supplementary Figure 1 from Computational Identification of a p38SAPK-Regulated Transcription Factor Network Required for Tumor Cell Quiescence
Supplementary Table 3 from Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines
Authors: Marella Narasimharao V. , Malyavantham Kishore S. , Wang Jianmin , Matsui Sei-ichi , Liang Ping , Berezney Ronald
Published: April 2023

Supplementary Table 3 from Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines
Supplementary Figure 1 from Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines
Authors: Marella Narasimharao V. , Malyavantham Kishore S. , Wang Jianmin , Matsui Sei-ichi , Liang Ping , Berezney Ronald
Published: April 2023

Supplementary Figure 1 from Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines
Supplementary Figure 4 from Reversal of P-glycoprotein–Mediated Multidrug Resistance by the Murine Double Minute 2 Antagonist Nutlin-3
Authors: Michaelis Martin , Rothweiler Florian , Klassert Denise , von Deimling Andreas , Weber Kristoffer , Fehse Boris , Kammerer Bernd , Doerr Hans Wilhelm , Cinatl Jindrich
Published: April 2023

Supplementary Figure 4 from Reversal of P-glycoprotein–Mediated Multidrug Resistance by the Murine Double Minute 2 Antagonist Nutlin-3
Supplementary Figure 2 from Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry
Authors: Hirayama Akiyoshi , Kami Kenjiro , Sugimoto Masahiro , Sugawara Maki , Toki Naoko , Onozuka Hiroko , Kinoshita Taira , Saito Norio , Ochiai Atsushi , Tomita Masaru , Esumi Hiroyasu , Soga Tomoyoshi
Published: April 2023

Supplementary Figure 2 from Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry
Supplementary Table 2 from Cathepsin D and Eukaryotic Translation Elongation Factor 1 as Promising Markers of Cellular Senescence
Authors: Byun Hae-Ok , Han Na-Kyung , Lee Hae-June , Kim Ki-Bum , Ko Young-Gyu , Yoon Gyesoon , Lee Yun-Sil , Hong Seok-Il , Lee Jae-Seon
Published: April 2023

Supplementary Table 2 from Cathepsin D and Eukaryotic Translation Elongation Factor 1 as Promising Markers of Cellular Senescence
Supplementary Figure 5 from ERG Is a Megakaryocytic Oncogene
Authors: Salek-Ardakani Samira , Smooha Gil , de Boer Jasper , Sebire Neil J. , Morrow Michelle , Rainis Liat , Lee Sandy , Williams Owen , Izraeli Shai , Brady Hugh J.M.
Published: April 2023

Supplementary Figure 5 from ERG Is a Megakaryocytic Oncogene
Supplementary Figure Legends 1-12, Table Legends 1-4, Results from Cancer Vaccine Enhanced, Non–Tumor-Reactive CD8+ T Cells Exhibit a Distinct Molecular Program Associated with “Division Arrest Anergy”
Authors: Beyer Marc , Karbach Julia , Mallmann Michael R. , Zander Thomas , Eggle Daniela , Classen Sabine , Debey-Pascher Svenja , Famulok Michael , Jäger Elke , Schultze Joachim L.
Published: April 2023

Supplementary Figure Legends 1-12, Table Legends 1-4, Results from Cancer Vaccine Enhanced, Non–Tumor-Reactive CD8+ T Cells Exhibit a Distinct Molecular Program Associated with “Division Arrest Anergy”
Supplementary Figure 5 from White Adipose Tissue Cells Are Recruited by Experimental Tumors and Promote Cancer Progression in Mouse Models
Authors: Zhang Yan , Daquinag Alexes , Traktuev Dmitry O. , Amaya-Manzanares Felipe , Simmons Paul J. , March Keith L. , Pasqualini Renata , Arap Wadih , Kolonin Mikhail G.
Published: April 2023

Supplementary Figure 5 from White Adipose Tissue Cells Are Recruited by Experimental Tumors and Promote Cancer Progression in Mouse Models
Supplementary Table 1 from Host Genetic Variants in the Interleukin-6 Promoter Predict Poor Outcome in Patients with Estrogen Receptor-Positive, Node-Positive Breast Cancer
Authors: DeMichele Angela , Gray Robert , Horn Michelle , Chen Jinbo , Aplenc Richard , Vaughan William P. , Tallman Martin S.
Published: April 2023

Supplementary Table 1 from Host Genetic Variants in the Interleukin-6 Promoter Predict Poor Outcome in Patients with Estrogen Receptor-Positive, Node-Positive Breast Cancer
Supplementary Figure 2 from Novel Lipogenic Enzyme ELOVL7 Is Involved in Prostate Cancer Growth through Saturated Long-Chain Fatty Acid Metabolism
Authors: Tamura Kenji , Makino Asami , Hullin-Matsuda Françoise , Kobayashi Toshihide , Furihata Mutsuo , Chung Suyoun , Ashida Shingo , Miki Tsuneharu , Fujioka Tomoaki , Shuin Taro , Nakamura Yusuke , Nakagawa Hidewaki
Published: April 2023

Supplementary Figure 2 from Novel Lipogenic Enzyme ELOVL7 Is Involved in Prostate Cancer Growth through Saturated Long-Chain Fatty Acid Metabolism
Supplementary Figure 4 from Blockade of PAR1 Signaling with Cell-Penetrating Pepducins Inhibits Akt Survival Pathways in Breast Cancer Cells and Suppresses Tumor Survival and Metastasis
Authors: Yang Eric , Boire Adrienne , Agarwal Anika , Nguyen Nga , O'Callaghan Katie , Tu Powen , Kuliopulos Athan , Covic Lidija
Published: April 2023

Supplementary Figure 4 from Blockade of PAR1 Signaling with Cell-Penetrating Pepducins Inhibits Akt Survival Pathways in Breast Cancer Cells and Suppresses Tumor Survival and Metastasis
Supplementary Figure 3 from Blockade of PAR1 Signaling with Cell-Penetrating Pepducins Inhibits Akt Survival Pathways in Breast Cancer Cells and Suppresses Tumor Survival and Metastasis
Authors: Yang Eric , Boire Adrienne , Agarwal Anika , Nguyen Nga , O'Callaghan Katie , Tu Powen , Kuliopulos Athan , Covic Lidija
Published: April 2023

Supplementary Figure 3 from Blockade of PAR1 Signaling with Cell-Penetrating Pepducins Inhibits Akt Survival Pathways in Breast Cancer Cells and Suppresses Tumor Survival and Metastasis
Supplementary Figure 1 from Increased Susceptibility to Skin Carcinogenesis in TREX2 Knockout Mice
Authors: Parra David , Manils Joan , Castellana Bàrbara , Viña-Vilaseca Arnau , Morán-Salvador Eva , Vázquez-Villoldo Nuria , Tarancón Gemma , Borràs Miquel , Sancho Sara , Benito Carmen , Ortega Sagrario , Soler Concepció
Published: April 2023

Supplementary Figure 1 from Increased Susceptibility to Skin Carcinogenesis in TREX2 Knockout Mice
Supplementary Methods and Materials, Figure Legends 1-4 from Combined Transductional Untargeting/Retargeting and Transcriptional Restriction Enhances Adenovirus Gene Targeting and Therapy for Hepatic Colorectal Cancer Tumors
Authors: Li Hua-Jung , Everts Maaike , Yamamoto Masato , Curiel David T. , Herschman Harvey R.
Published: April 2023

Supplementary Methods and Materials, Figure Legends 1-4 from Combined Transductional Untargeting/Retargeting and Transcriptional Restriction Enhances Adenovirus Gene Targeting and Therapy for Hepatic Colorectal Cancer Tumors
Supplementary Tables 1-2, Appendix materials, Figures 1-2 from In vitro and In vivo Activity of Novel Small-Molecule Inhibitors Targeting the Pleckstrin Homology Domain of Protein Kinase B/AKT
Authors: Moses Sylvestor A. , Ali M. Ahad , Zuohe Song , Du-Cuny Lei , Zhou Li Li , Lemos Robert , Ihle Nathan , Skillman A. Geoffrey , Zhang Shuxing , Mash Eugene A. , Powis Garth , Meuillet Emmanuelle J.
Published: April 2023

Supplementary Tables 1-2, Appendix materials, Figures 1-2 from In vitro and In vivo Activity of Novel Small-Molecule Inhibitors Targeting the Pleckstrin Homology Domain of Protein Kinase B/AKT
Supplementary Figure 1 from Peptidyl-Prolyl Isomerase Pin1 Markedly Enhances the Oncogenic Activity of the Rel Proteins in the Nuclear Factor-κB Family
Authors: Fan Gaofeng , Fan Yongjun , Gupta Nupur , Matsuura Isao , Liu Fang , Zhou Xiao Zhen , Lu Kun Ping , Gélinas Céline
Published: April 2023

Supplementary Figure 1 from Peptidyl-Prolyl Isomerase Pin1 Markedly Enhances the Oncogenic Activity of the Rel Proteins in the Nuclear Factor-κB Family
Supplementary Table 2 from Functional Phosphodiesterase 11A Mutations May Modify the Risk of Familial and Bilateral Testicular Germ Cell Tumors
Authors: Horvath Anelia , Korde Larissa , Greene Mark H. , Libe Rossella , Osorio Paulo , Faucz Fabio Rueda , Raffin-Sanson Marie Laure , Tsang Kit Man , Drori-Herishanu Limor , Patronas Yianna , Remmers Elaine F. , Nikita Maria Eleni , Moran Jason , Greene Joseph , Nesterova Maria , Merino Maria , Bertherat Jerome , Stratakis Constantine A.
Published: April 2023

Supplementary Table 2 from Functional Phosphodiesterase 11A Mutations May Modify the Risk of Familial and Bilateral Testicular Germ Cell Tumors
Supplementary Figure 2 from Differentiation-Related Gene-1 Decreases Bim Stability by Proteasome-Mediated Degradation
Authors: Ambrosini Grazia , Seelman Sharon L. , Schwartz Gary K.
Published: April 2023

Supplementary Figure 2 from Differentiation-Related Gene-1 Decreases Bim Stability by Proteasome-Mediated Degradation
Supplementary Figure 1 from Differentiation-Related Gene-1 Decreases Bim Stability by Proteasome-Mediated Degradation
Authors: Ambrosini Grazia , Seelman Sharon L. , Schwartz Gary K.
Published: April 2023

Supplementary Figure 1 from Differentiation-Related Gene-1 Decreases Bim Stability by Proteasome-Mediated Degradation
Supplementary Figure Legends 1-2 from In situ Stimulation of CD40 and Toll-like Receptor 3 Transforms Ovarian Cancer–Infiltrating Dendritic Cells from Immunosuppressive to Immunostimulatory Cells
Authors: Scarlett Uciane K. , Cubillos-Ruiz Juan R. , Nesbeth Yolanda C. , Martinez Diana G. , Engle Xavier , Gewirtz Andrew T. , Ahonen Cory L. , Conejo-Garcia Jose R.
Published: April 2023

Supplementary Figure Legends 1-2 from In situ Stimulation of CD40 and Toll-like Receptor 3 Transforms Ovarian Cancer–Infiltrating Dendritic Cells from Immunosuppressive to Immunostimulatory Cells