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Changed Regulation Enables Pragmatic Solution for Cancer Patients




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SophosAI team presents three papers on AI applied to cybersecurity at CAMLIS

On October 24 and 25, SophosAI presents ideas on how to use models large and small—and defend against malignant ones.




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Sophos Firewall hardening best practices

Make the most of your Sophos Firewall.




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Pacific Rim timeline: Information for defenders from a braid of interlocking attack campaigns

Sophos X-Ops unveils five-year investigation tracking China-based groups targeting perimeter devices




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Digital Detritus: The engine of Pacific Rim and a call to the industry for action

Decades of obsolete and unpatched hardware and software endanger us all






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VEEAM exploit seen used again with a new ransomware: “Frag”

Last month, Sophos X-Ops reported several MDR cases where threat actors exploited a vulnerability in Veeam backup servers. We continue to track the activities of this threat cluster, which recently included deployment of a new ransomware. The vulnerability, CVE-2024-40711, was used as part of a threat activity cluster we named STAC 5881. Attacks leveraged compromised […]




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Re: Voluntary assisted death: how to ensure access and safety




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Overdose crisis: more common sense and less ideology




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Addressing Climate Catastrophe Concerns in Asthma Medication Delivery: Rethinking Inhaler Use for Environmental and Clinical Efficacy




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Greenwashing assisted dying




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Re: Decompression alone or with fusion for degenerative lumbar spondylolisthesis (Nordsten-DS): five year follow-up of a randomised, multicentre, non-inferiority trial




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A Comprehensive Gender-related Secretome of Plasmodium berghei Sexual Stages

Felicia Grasso
Dec 1, 2020; 19:1986-1996
Research




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Novel Proteomic Profiling of Epididymal Extracellular Vesicles in the Domestic Cat Reveals Proteins Related to Sequential Sperm Maturation with Differences Observed between Normospermic and Teratospermic Individuals

Tricia Rowlison
Dec 1, 2020; 19:2090-2103
Research




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Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MS

Simone Kurz
Dec 29, 2020; 0:RA120.002266v1-mcp.RA120.002266
Research




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High-throughput and site-specific N-glycosylation analysis of human alpha-1-acid glycoprotein offers a great potential for new biomarker discovery

Toma Keser
Dec 29, 2020; 0:RA120.002433v1-mcp.RA120.002433
Research




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Identification of novel serological autoantibodies in Takayasu arteritis patients using HuProt arrays

Xiao-Ting Wen
Dec 17, 2020; 0:RA120.002119v1-mcp.RA120.002119
Research




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Interspecies differences in proteome turnover kinetics are correlated with lifespans and energetic demands

Kyle Swovick
Dec 28, 2020; 0:RA120.002301v1-mcp.RA120.002301
Research




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A Mouse Brain-based Multi-omics Integrative Approach Reveals Potential Blood Biomarkers for Ischemic Stroke

Alba Simats
Dec 1, 2020; 19:1921-1935
Research




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OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS

Eugen Netz
Dec 1, 2020; 19:2157-2167
Technological Innovation and Resources




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Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 as Candidate Therapeutic Target

Alison M. Kurimchak
Dec 1, 2020; 19:2068-2089
Research




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A Novel Mechanism for NF-{kappa}B-activation via I{kappa}B-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation

Yi Liu
Dec 1, 2020; 19:1968-1985
Research




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The role of Data-Independent Acquisition for Glycoproteomics

Zilu Ye
Dec 28, 2020; 0:R120.002204v1-mcp.R120.002204
Review




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Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries

Peter Lasch
Dec 1, 2020; 19:2125-2138
Technological Innovation and Resources




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Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor

Sylwia Struk
Dec 28, 2020; 0:RA119.001766v1-mcp.RA119.001766
Research




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CMMB (Carboxylate Modified Magnetic Bead) -based isopropanol gradient peptide fractionation (CIF) enables rapid and robust off-line peptide mixture fractionation in bottom-up proteomics

Weixian Deng
Dec 22, 2020; 0:RA120.002411v1-mcp.RA120.002411
Research




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Systematic identification of P. falciparum sporozoite membrane protein interactions reveals an essential role for the p24 complex in host infection

Julia Knöckel
Dec 22, 2020; 0:RA120.002432v1-mcp.RA120.002432
Research




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Thyroglobulin interactome profiling defines altered proteostasis topology associated with thyroid dyshormonogenesis

Madison T Wright
Nov 18, 2020; 0:RA120.002168v1-mcp.RA120.002168
Research




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Proteome analysis reveals a significant host-specific response in Rhizobium leguminosarum bv viciae endosymbiotic cells

David Durán
Nov 19, 2020; 0:RA120.002276v1-mcp.RA120.002276
Research




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A proteomics-based assessment of inflammation signatures in endotoxemia

Sean A Burnap
Dec 7, 2020; 0:RA120.002305v1-mcp.RA120.002305
Research




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A potential role for the Gsdf-eEF1{alpha} complex in inhibiting germ cell proliferation: A protein-interaction analysis in medaka (Oryzias latipes) from a proteomics perspective

Xinting Zhang
Dec 8, 2020; 0:RA120.002306v1-mcp.RA120.002306
Research




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Proteogenomic characterization of the pathogenic fungus Aspergillus flavus reveals novel genes involved in aflatoxin production

Mingkun Yang
Nov 24, 2020; 0:RA120.002144v1-mcp.RA120.002144
Research




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Quantitative proteomics reveal neuron projection development genes ARF4, KIF5B and RAB8A associated with Hirschsprung disease

Qin Zhang
Nov 17, 2020; 0:RA120.002325v1-mcp.RA120.002325
Research




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Proteomic analyses identify differentially expressed proteins and pathways between low-risk and high-risk subtypes of early-stage lung adenocarcinoma and their prognostic impacts

Juntuo Zhou
Nov 30, 2020; 0:RA120.002384v1-mcp.RA120.002384
Research




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A proteomic approach to understand the clinical significance of acute myeloid leukemia-derived extracellular vesicles reflecting essential characteristics of leukemia

Ka-Won Kang
Nov 30, 2020; 0:RA120.002169v1-mcp.RA120.002169
Research




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Prediction and validation of mouse meiosis-essential genes based on spermatogenesis proteome dynamics

Kailun Fang
Nov 30, 2020; 0:RA120.002081v1-mcp.RA120.002081
Research




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Imaging Mass Spectrometry and Lectin Analysis of N-linked Glycans in Carbohydrate Antigen Defined Pancreatic Cancer Tissues

Colin T. McDowell
Nov 24, 2020; 0:RA120.002256v1-mcp.RA120.002256
Research




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Peptidomics-driven strategy reveals peptides and predicted proteases associated with oral cancer prognosis

Leandro Xavier Neves
Nov 11, 2020; 0:RA120.002227v1-mcp.RA120.002227
Research




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Proteomic identification of Coxiella burnetii effector proteins targeted to the host cell mitochondria during infection

Laura F Fielden
Nov 11, 2020; 0:RA120.002370v1-mcp.RA120.002370
Research




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Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches

Congcong Lu
Nov 17, 2020; 0:R120.002257v1-mcp.R120.002257
Review




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PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

Daniel J. Geiszler
Dec 1, 2020; 0:TIR120.002216v1-mcp.TIR120.002216
Technological Innovation and Resources




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ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

Johannes Griss
Dec 1, 2020; 19:2115-2124
Technological Innovation and Resources




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Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy

Tirsa L. E. van Westering
Dec 1, 2020; 19:2047-2067
Research




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Plasma proteomic data can contain personally identifiable, sensitive information and incidental findings

Philipp Emanuel Geyer
Dec 17, 2020; 0:RA120.002359v1-mcp.RA120.002359
Research




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Pluripotency of embryonic stem cells lacking clathrin-mediated endocytosis cannot be rescued by restoring cellular stiffness [Molecular Biophysics]

Mouse embryonic stem cells (mESCs) display unique mechanical properties, including low cellular stiffness in contrast to differentiated cells, which are stiffer. We have previously shown that mESCs lacking the clathrin heavy chain (Cltc), an essential component for clathrin-mediated endocytosis (CME), display a loss of pluripotency and an enhanced expression of differentiation markers. However, it is not known whether physical properties such as cellular stiffness also change upon loss of Cltc, similar to what is seen in differentiated cells, and if so, how these altered properties specifically impact pluripotency. Using atomic force microscopy (AFM), we demonstrate that mESCs lacking Cltc display higher Young's modulus, indicative of greater cellular stiffness, compared with WT mESCs. The increase in stiffness was accompanied by the presence of actin stress fibers and accumulation of the inactive, phosphorylated, actin-binding protein cofilin. Treatment of Cltc knockdown mESCs with actin polymerization inhibitors resulted in a decrease in the Young's modulus to values similar to those obtained with WT mESCs. However, a rescue in the expression profile of pluripotency factors was not obtained. Additionally, whereas WT mouse embryonic fibroblasts could be reprogrammed to a state of pluripotency, this was inhibited in the absence of Cltc. This indicates that the presence of active CME is essential for the pluripotency of embryonic stem cells. Additionally, whereas physical properties may serve as a simple readout of the cellular state, they may not always faithfully recapitulate the underlying molecular fate.




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Secretory galectin-3 induced by glucocorticoid stress triggers stemness exhaustion of hepatic progenitor cells [Signal Transduction]

Adult progenitor cell populations typically exist in a quiescent state within a controlled niche environment. However, various stresses or forms of damage can disrupt this state, which often leads to dysfunction and aging. We built a glucocorticoid (GC)-induced liver damage model of mice, found that GC stress induced liver damage, leading to consequences for progenitor cells expansion. However, the mechanisms by which niche factors cause progenitor cells proliferation are largely unknown. We demonstrate that, within the liver progenitor cells niche, Galectin-3 (Gal-3) is responsible for driving a subset of progenitor cells to break quiescence. We show that GC stress causes aging of the niche, which induces the up-regulation of Gal-3. The increased Gal-3 population increasingly interacts with the progenitor cell marker CD133, which triggers focal adhesion kinase (FAK)/AMP-activated kinase (AMPK) signaling. This results in the loss of quiescence and leads to the eventual stemness exhaustion of progenitor cells. Conversely, blocking Gal-3 with the inhibitor TD139 prevents the loss of stemness and improves liver function. These experiments identify a stress-dependent change in progenitor cell niche that directly influence liver progenitor cell quiescence and function.




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VBP1 modulates Wnt/{beta}-catenin signaling by mediating the stability of the transcription factors TCF/LEFs [Signal Transduction]

The Wnt/β-catenin pathway is one of the major pathways that regulates embryonic development, adult homeostasis, and stem cell self-renewal. In this pathway, transcription factors T-cell factor and lymphoid enhancer factor (TCF/LEF) serve as a key switch to repress or activate Wnt target gene transcription by recruiting repressor molecules or interacting with the β-catenin effector, respectively. It has become evident that the protein stability of the TCF/LEF family members may play a critical role in controlling the activity of the Wnt/β-catenin signaling pathway. However, factors that regulate the stability of TCF/LEFs remain largely unknown. Here, we report that pVHL binding protein 1 (VBP1) regulates the Wnt/β-catenin signaling pathway by controlling the stability of TCF/LEFs. Surprisingly, we found that either overexpression or knockdown of VBP1 decreased Wnt/β-catenin signaling activity in both cultured cells and zebrafish embryos. Mechanistically, VBP1 directly binds to all four TCF/LEF family members and von Hippel-Lindau tumor-suppressor protein (pVHL). Either overexpression or knockdown of VBP1 increases the association between TCF/LEFs and pVHL and then decreases the protein levels of TCF/LEFs via proteasomal degradation. Together, our results provide mechanistic insights into the roles of VBP1 in controlling TCF/LEFs protein stability and regulating Wnt/β-catenin signaling pathway activity.




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Functions of Gle1 are governed by two distinct modes of self-association [Gene Regulation]

Gle1 is a conserved, essential regulator of DEAD-box RNA helicases, with critical roles defined in mRNA export, translation initiation, translation termination, and stress granule formation. Mechanisms that specify which, where, and when DDXs are targeted by Gle1 are critical to understand. In addition to roles for stress-induced phosphorylation and inositol hexakisphosphate binding in specifying Gle1 function, Gle1 oligomerizes via its N-terminal domain in a phosphorylation-dependent manner. However, a thorough analysis of the role for Gle1 self-association is lacking. Here, we find that Gle1 self-association is driven by two distinct regions: a coiled-coil domain and a novel 10-amino acid aggregation-prone region, both of which are necessary for proper Gle1 oligomerization. By exogenous expression in HeLa cells, we tested the function of a series of mutations that impact the oligomerization domains of the Gle1A and Gle1B isoforms. Gle1 oligomerization is necessary for many, but not all aspects of Gle1A and Gle1B function, and the requirements for each interaction domain differ. Whereas the coiled-coil domain and aggregation-prone region additively contribute to competent mRNA export and stress granule formation, both self-association domains are independently required for regulation of translation under cellular stress. In contrast, Gle1 self-association is dispensable for phosphorylation and nonstressed translation initiation. Collectively, we reveal self-association functions as an additional mode of Gle1 regulation to ensure proper mRNA export and translation. This work also provides further insight into the mechanisms underlying human gle1 disease mutants found in prenatally lethal forms of arthrogryposis.




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Angiostatic cues from the matrix: Endothelial cell autophagy meets hyaluronan biology [Glycobiology and Extracellular Matrices]

The extracellular matrix encompasses a reservoir of bioactive macromolecules that modulates a cornucopia of biological functions. A prominent body of work posits matrix constituents as master regulators of autophagy and angiogenesis and provides molecular insight into how these two processes are coordinated. Here, we review current understanding of the molecular mechanisms underlying hyaluronan and HAS2 regulation and the role of soluble proteoglycan in affecting autophagy and angiogenesis. Specifically, we assess the role of proteoglycan-evoked autophagy in regulating angiogenesis via the HAS2-hyaluronan axis and ATG9A, a novel HAS2 binding partner. We discuss extracellular hyaluronan biology and the post-transcriptional and post-translational modifications that regulate its main synthesizer, HAS2. We highlight the emerging group of proteoglycans that utilize outside-in signaling to modulate autophagy and angiogenesis in cancer microenvironments and thoroughly review the most up-to-date understanding of endorepellin signaling in vascular endothelia, providing insight into the temporal complexities involved.