gebhart/patrepeval huggingface dataset:
Activation of ATP-ubiquitin-dependent proteolysis in skeletal muscle in vivo and murine myoblasts in vitro by a proteolysis-inducing factor (PIF) (2001)

Loss of skeletal muscle is a major factor in the poor survival of patients with cancer cachexia. This study examines the mechanism of catabolism of skeletal muscle by a tumour product, proteolysis-inducing factor (PIF). Intravenous administration of PIF to normal mice produced a rapid decrease in body weight (1.55 +/- 0.12 g in 24 h) that was accompanied by increased mRNA levels for ubiquitin, the Mr 14 000 ubiquitin carrier-protein, E2, and the C9 proteasome subunit in gastrocnemius muscle. There was also increased protein levels of the 20S proteasome core and 19S regulatory subunit, detectable by immunoblotting, suggesting activation of the ATP-ubiquitin-dependent proteolytic pathway. An increased protein catabolism was also seen in C(2)C(12)myoblasts within 24 h of PIF addition with a bell-shaped dose-response curve and a maximal effect at 2-4 nM. The enhanced protein degradation was attenuated by anti-PIF antibody and by the proteasome inhibitors MG115 and lactacystin. Glycerol gradient analysis of proteasomes from PIF-treated cells showed an elevation in chymotrypsin-like activity, while Western analysis showed a dose-related increase in expression of MSSI, an ATPase that is a regulatory subunit of the proteasome, with a dose-response curve similar to that for protein degradation. These results confirm that PIF acts directly to stimulate the proteasome pathway in muscle cells and may play a pivotal role in protein catabolism in cancer cachexia.
Editorial: Interdisciplinary surgical strategies for complex tumor defects in modern oncology (2023)

EDITORIAL article Front. Oncol., 10 February 2023Sec. Surgical Oncology Volume 13 - 2023 | https://doi.org/10.3389/fonc.2023.1146719
Corrigendum: Exploring Peritumoral Neural Tracts by Using Neurite Orientation Dispersion and Density Imaging (2021)

[This corrects the article DOI: 10.3389/fnins.2021.702353.].
Transcriptional changes in LMH cells induced by Eimeria tenella rhoptry kinase family protein 17 (2022)

Though a number of <i>Eimeria tenella</i> rhoptry kinase family proteins have been identified, little is known about their molecular functions. In the present study, the gene fragment encoding the matured peptide of <i>E. tenella</i> rhoptry kinase family protein 17 (EtROP17) was used to construct a recombinant vector, followed by transfection into leghorn male hepatoma (LMH) cells. Then, the transcriptional changes in the transfected cells were determined by RNA-seq. The expression of EtROP17 in LMH cells was validated by both Western blot and indirect immunofluorescence analysis. Our analysis showed that EtROP17 altered the expression of 309 genes (114 downregulated genes and 195 upregulated genes) in LMH cells. The quantitative real-time polymerase chain reaction (qRT-PCR) results of the selected differentially expressed genes (DEGs) were consistent with the RNA-seq data. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were significantly enriched in nine pathways, such as toll-like receptor signaling pathway, ECM-receptor interaction, intestinal immune network for IgA production and focal adhesion. These findings reveal several potential roles of EtROP17, which contribute to understanding the molecular mechanisms underlying the host-parasite interplay.
Controlling Pattern Formation in Nanoparticle Assemblies via Directed Solvent Dewetting (2007)

We have achieved highly localized control of pattern formation in two-dimensional nanoparticle assemblies by direct modification of solvent dewetting dynamics. A striking dependence of nanoparticle organization on the size of atomic force microscope-generated surface heterogeneities is observed and reproduced in numerical simulations. Nanoscale features induce a rupture of the solvent-nanoparticle film, causing the local flow of solvent to carry nanoparticles into confinement. Microscale heterogeneities instead slow the evaporation of the solvent, producing a remarkably abrupt interface between different nanoparticle patterns.
Some factors influencing the proliferation and differentiation of myelin‐forming cells (1978)

Fundamental questions arising from study of the multiple sclerosis lesion are: (1) why the myelin-forming oligodendrocyte is adversely affected; and (2) what factors might induce the proliferation and differentiation of replacement oligodendrocytes. This paper discusses factors that influence the number and differentiative capacity of myelin-forming cells both in the central nervous system (CNS) and the peripheral nervous system (PNS). New experiments utilizing cultures of fetal rat sensory and autonomic ganglia are also herein reported. It has been found that in cultures free of fibroblasts, normal Schwann cell proliferation and ensheathment of axons require contact with a collagen substrate and may be facilitated by a medium containing chick embryo extract. This demonstration of a connective tissue requirement for normal Schwann cell function raises the question of whether additional factors are necessary for normal oligodendrocyte activity.
On occluding contour artifacts in stereo vision (2002)

We study occluding contour artifacts in area-based stereo matching: they are false responses of the matching operator to the occlusion boundary and cause the objects extend beyond their true boundaries in disparity maps. Most of the matching methods suffer from these artifacts; the effect is so strong that it cannot be ignored. We show what gives rise to the artifacts and design a matching criterion that accommodates the presence of occlusions as opposed to methods that identify and remove the artifacts. This approach leads to the problem of measurement contamination studied in statistics. We show that such a problem is hard given finite computational resources, unless more independent measurements directly related to occluding contours is available. What can be achieved is a substantial reduction of he artifacts, especially for large matching templates. Reduced artifacts allow for easier hierarchical matching and for easy fusion of reconstructions from different viewpoints into a coherent whole.
One-Dimensional Transient Model for Frost Heave in Polymer Electrolyte Fuel Cells (2006)

To better understand, control, and mitigate degradation during freezing of a polymer electrolyte fuel cells (PEFCs), a one-dimensional (1D) transient model has been formulated, based on theories of porous media flow and soil frost heave. The model is essentially a modified hybrid of Harlan's hydraulic model and Miller's rigid ice model with additional improvements for suitable application to PEFCs. It is found that the three types of characteristic curves for unfrozen water flow and frost heave modeling can be well unified. Methods to derive the unfrozen water vs temperature characteristic curves for PEFC components are also given. Through the formulated model, it is predicted that ice lens will occur most likely around the catalyst layer, either between catalyst layer and diffusion media, or between catalyst layer and Nafion membrane. Lens formation under the lands is unlikely due to high overburden pressure. Ice lens growth may explain breakthrough observed in carbon paper after freeze-thaw tests. Another phenomenon, the delamination between Nafion and catalyst layer, can possibly be explained by the formation of an ice lens from water expelled from the electrolyte during freezing. The Nafion thickness and initial water content have direct impact on the damage in this mode.
Endophilin B1/Bif-1 Stimulates BAX Activation Independently from Its Capacity to Produce Large Scale Membrane Morphological Rearrangements (2008)

Endophilin B1/BAX-interacting factor 1 (Bif-1) is a protein that cooperates with dynamin-like protein 1 (DLP1/Drp1) to maintain normal mitochondrial outer membrane (MOM) dynamics in healthy cells and also contributes to BAX-driven MOM permeabilization (MOMP), the irreversible commitment point to cell death for the majority of apoptotic stimuli. However, despite its importance, exactly how Bif-1 fulfils its proapoptotic role is unknown. Here, we demonstrate that the stimulatory effect of Bif-1 on BAX-driven MOMP and on BAX conformational activation observed in intact cells during apoptosis can be recapitulated in a simplified system consisting of purified proteins and MOM-like liposomes. In this reconstituted model system the N-BAR domain of Bif-1 reproduced the stimulatory effect of Bif-1 on functional BAX activation. This process was dependent on physical interaction between Bif-1 N-BAR and BAX as well as on the presence of the mitochondrion-specific lipid cardiolipin. Despite that Bif-1 N-BAR produced large scale morphological rearrangements in MOM-like liposomes, this phenomenon could be separated from functional BAX activation. Furthermore, DLP1 also caused global morphological changes in MOM-like liposomes, but DLP1 did not stimulate BAX-permeabilizing function in the absence or presence of Bif-1. Taken together, our findings not only provide direct evidence for a functional interplay between Bif-1, BAX, and cardiolipin during MOMP but also add significantly to the growing body of evidence indicating that components of the mitochondrial morphogenesis machinery possess proapoptotic functions that are independent from their recognized roles in normal mitochondrial dynamics.
Bone-conduction propagation in the human body: implications for high-frequency therapy. (2007)

We assessed ultrasonic transmission in a dry skull; in a dry skull with water, simulating the living condition; in a cadaver head; and in six human subjects, one of whom exhibited no measurable hearing. By using these preparations, we concluded that fluid conduction is essential in the propagation of sound across the head, whereas the bone pathway is far less effective in that regard. Thus, there is little ear isolation beyond 10 dB even up to 80 kHz, extending the masking dilemma in cases of unilateral hearing loss.
Diabetic Kidney Disease: Act Now or Pay Later (2010)

The 21st century has the most diabetogenic environment in human history with the number of people with diabetes worldwide increasing to 380 million by 2025. The fastest rate of increase will be in developing countries. Diabetes is now the major cause of end-stage kidney disease globally; 20%-40% of people on dialysis are diabetic. In Australia, the number of people with type 2 diabetes starting dialysis increased fivefold between 1993 and 2007. We must act now at local, national and international levels to prevent type 2 diabetes; screen for early diabetic kidney disease; increase public awareness of kidney disease; treat with medications proven to reduce kidney disease progression; and promote research into and trialling of new therapies. The problem is global yet requires local action. World Kidney Day on 11 March 2010 is a time to intensify action on diabetic kidney disease and to continue to do so until this huge but largely preventable health burden is controlled.
On the Design of Quantization Functions for Uplink Massive MIMO with Low-Resolution ADCs (2021)

Quantization is the characterization of analogue-to-digital converters (ADC) in massive MIMO systems. The design of quantization function or quantization thresholds is found to relate to quantization step, which is the factor that adapts with the changing of transmit power and noise variance. With the objective of utilizing low-resolution ADC is reducing the cost of massive MIMO, we propose an idea as if it is necessary to have adaptive-threshold quantization function. It is found that when maximum-likelihood (ML) is employed as the detection method, having quantization thresholds fixed for low-resolution ADCs will not cause significant performance loss. Moreover, such fixed-threshold quantization function does not require any information of signal power which can reduce the hardware cost of ADCs. Simulations have been carried out in this paper to make comparisons between fixed-threshold and adaptive-threshold quantization regarding various factors.
The Rep78 gene product of adeno-associated virus (AAV) self-associates to form a hexameric complex in the presence of AAV ori sequences (1997)

The Rep78 and Rep68 proteins of adeno-associated virus (AAV) are replication initiator proteins that bind the viral replicative-form origin of replication, nick the origin in a site- and strand-specific fashion, and mediate vectorial unwinding of the DNA duplex via an ATP-dependent helicase activity, thus initiating a strand displacement mechanism of viral DNA replication. Genetic and biochemical studies have identified Rep mutants that demonstrate a trans-dominant negative phenotype in vitro and in vivo, suggesting the possibility that multimerization of Rep is essential for certain replicative functions. In this study, we have investigated the ability of the largest of the Rep proteins, Rep78, to self-associate in vitro and in vivo. Self-association of Rep78 in vivo was demonstrated through the use of a mammalian two-hybrid system. Rep-Rep protein interaction was confirmed in vitro through coimmunoprecipitation experiments with a bacterially expressed maltose-binding protein-Rep78 fusion protein in combination with [35S]methionine-labeled Rep78 synthesized in a coupled in vitro transcription-translation system. Mapping studies with N- and C-terminal truncation mutant forms of Rep indicate that amino acid sequences required for maximal self-association occur between residues 164 and 484. Site-directed mutagenesis identified two essential motifs within this 321-amino-acid region: (i) a putative alpha-helix bearing a 3,4-hydrophobic heptad repeat reminiscent of those found in coiled-coil domains and (ii) a previously recognized nucleoside triphosphate-binding motif. Deletion of either of these regions from the full-length polypeptide resulted in severe impairment of Rep-Rep interaction. In addition, gel filtration chromatography and protein cross-linking experiments indicated that Rep78 forms a hexameric complex in the presence of AAV ori sequences.
ChemInform Abstract: Sp3‐sp3 Coupling Reactions in the Synthesis of Natural Products and Biologically Active Molecules (2014)

Abstract Review: 42 refs.
Zur Struktur rhodiumhaltiger Corrinoide (1980)

Abstract Durch Umsetzung von Hydrogenobyrinsäure‐a,c‐diamid (1) mit [Rh(CO) 2 Cl] 2 in Eisessig/Ethanol (1:1; Vol.: Vol.) erhält man als Hauptprodukt Rhodibyrinsäure‐a,c‐diamid 2 . Die Identität von 2 wird durch Röntgenstrukturanalyse bestätigt. Veresterung von 2 mit Methanol/Schwefelsäure führt neben Rhodibyrinsäure‐pentamethylester‐a,c‐diamid 3a zu den entsprechenden 8‐ und 13‐Epimeren. Deren Konfiguration wird durch CD, 1 H‐ und 13 C‐NMR‐Spektroskopie gesichert.
Table S8 from SHP2 Inhibition Sensitizes Diverse Oncogene-Addicted Solid Tumors to Re-treatment with Targeted Therapy (2023)

&lt;p&gt;Supplementary Table 8: Comparison of clinical safety data for SHP2 inhibitors&lt;/p&gt;
A Genomic Analysis of Chicken Cytokines and Chemokines (2005)

As most mechanisms of adaptive immunity evolved during the divergence of vertebrates, the immune systems of extant vertebrates represent different successful variations on the themes initiated in their earliest common ancestors. The genes involved in elaborating these mechanisms have been subject to exceptional selective pressures in an arms race with highly adaptable pathogens, resulting in highly divergent sequences of orthologous genes and the gain and loss of members of gene families as different species find different solutions to the challenge of infection. Consequently, it has been difficult to transfer to the chicken detailed knowledge of the molecular mechanisms of the mammalian immune system and, thus, to enhance the already significant contribution of chickens toward understanding the evolution of immunity. The availability of the chicken genome sequence provides the opportunity to resolve outstanding questions concerning which molecular components of the immune system are shared between mammals and birds and which represent their unique evolutionary solutions. We have integrated genome data with existing knowledge to make a new comparative census of members of cytokine and chemokine gene families, distinguishing the core set of molecules likely to be common to all higher vertebrates from those particular to these 300 million-year-old lineages. Some differences can be explained by the different architectures of the mammalian and avian immune systems. Chickens lack lymph nodes and also the genes for the lymphotoxins and lymphotoxin receptors. The lack of functional eosinophils correlates with the absence of the eotaxin genes and our previously reported observation that interleukin- 5 (IL-5) is a pseudogene. To summarize, in the chicken genome, we can identify the genes for 23 ILs, 8 type I interferons (IFNs), IFN-gamma, 1 colony-stimulating factor (GM-CSF), 2 of the 3 known transforming growth factors (TGFs), 24 chemokines (1 XCL, 14 CCL, 8 CXCL, and 1 CX3CL), and 10 tumor necrosis factor superfamily (TNFSF) members. Receptor genes present in the genome suggest the likely presence of 2 other ILs, 1 other CSF, and 2 other TNFSF members.
Enhancing Scatterplots with Multi‐Dimensional Focal Blur (2016)

Abstract Scatterplots directly depict two dimensions of multi‐dimensional data points, discarding all other information. To visualize all data, these plots are extended to scatterplot matrices, which distribute the information of each data point over many plots. Problems arising from the resulting visual complexity are nowadays alleviated by concepts like filtering and focus and context. We present a method based on depth of field that contains both aspects and injects information from all dimensions into each scatterplot. Our approach is a natural generalization of the commonly known focus effects from optics. It is based on a multidimensional focus selection body. Points outside of this body are defocused depending on their distance. Our method allows for a continuous transition from data points in focus, over regions of blurry points providing contextual information, to visually filtered data. Our algorithm supports different focus selection bodies, blur kernels, and point shapes. We present an optimized GPU‐based implementation for interactive exploration and show the usefulness of our approach on several data sets.
Gifted students in rural environments: Implications for school programs (1987)

This article considers factors in rural environments that influence the achievement of the brightest students in such areas. It examines the educational needs of those rural students who are identified as gifted and explores some characteristics of rural families and communities that may contribute to the underachievement of gifted students in those communities. Implications for curriculum, instruction, and achievement are discussed.
Topological Transformations of Synthetic DNA Knots (1995)

Two synthetic DNA molecules that can be knotted have been employed as substrates for E. coli DNA topoisomerases I and III. Both molecules contain 104 nucleotides, including sequences that can form two single-turn helical domains, connected by single-stranded oligo(dT) linkers in an X-Y-X'-Y' pairing motif. One of the knots can be ligated to form cyclic molecules with the topologies of a circle, a trefoil knot with negative nodes, or a figure-8 knot. Cyclic molecules constructed from the other molecule can form a circle, a figure-8 knot, and trefoil knots with either positive or negative nodes. The topologically negative nodes in these knots are derived from right-handed B-DNA, and the positive nodes are derived from left-handed Z-DNA. The topoisomerases can catalyze the interconversion of the different topological forms of these molecules, as a function of solution conditions and the extent to which they favor B-DNA or Z-DNA. The enzymes appear to catalyze a single strand-passage event at a time. The topoisomerases can catalyze strand passage events involving both positive and negative nodes as substrates. Gel retention experiments show that both knots can bind up to four molecules of E. coli DNA topoisomerase I. The thermal denaturation of the domains of a trefoil knot closely related to these knots suggests that the two helical domains are uncoupled, so the single-stranded linkers in the knots are not taut. Chemical ligation experiments yield a distribution of products similar to those of enzymatic ligation, showing that the ATP cofactor in DNA knot ligation does not appear to skew the products markedly. Knots that are stressed by being placed in unfavorable solution conditions have been shown to be a highly sensitive system for detecting topoisomerase activity.
Trifluoroacylation. Syntheses of w-Trifluororesacetophenone and w-Trifluorophloroacetophenone. (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTrifluoroacylation. Syntheses of w-Trifluororesacetophenone and w-Trifluorophloroacetophenone.Arthur MendelCite this: J. Chem. Eng. Data 1966, 11, 4, 585–586Publication Date (Print):October 1, 1966Publication History Published online1 May 2002Published inissue 1 October 1966https://pubs.acs.org/doi/10.1021/je60031a039https://doi.org/10.1021/je60031a039research-articleACS PublicationsRequest reuse permissionsArticle Views57Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Joint depth and alpha matte optimization via fusion of stereo and time-of-flight sensor (2009)

We present a new approach to iteratively estimate both high-quality depth map and alpha matte from a single image or a video sequence. Scene depth, which is invariant to illumination changes, color similarity and motion ambiguity, provides a natural and robust cue for foreground/ background segmentation - a prerequisite for matting. The image mattes, on the other hand, encode rich information near boundaries where either passive or active sensing method performs poorly. We develop a method to combine the complementary nature of scene depth and alpha matte to mutually enhance their qualities. We formulate depth inference as a global optimization problem where information from passive stereo, active range sensor and matte is merged. The depth map is used in turn to enhance the matting. In addition, we extend this approach to video matting by incorporating temporal coherence, which reduces flickering in the composite video. We show that these techniques lead to improved accuracy and robustness for both static and dynamic scenes.