gebhart/patrepeval huggingface dataset:
PARK2 promotes mitochondrial pathway of apoptosis and antimicrotubule drugs chemosensitivity <i>via</i> degradation of phospho-BCL-2 (2020)

<b>Rationale:</b> Neoadjuvant chemotherapy has become the standard treatment of locally advanced breast cancer. Antimicrotubule drugs and DNA-damaging drugs are the most popular medicines used for neoadjuvant chemotherapy. However, we are unable to predict which chemotherapeutic drug will benefit to an individual patient. PARK2 as a tumor suppressor in breast cancer has been reported. While the role of PARK2 in chemotherapy response remains unknown. In this study, we explore the impact of PARK2 on chemosensitivity in breast cancer. <b>Methods:</b> PARK2 expression in breast cancer patients with different neoadjuvant chemotherapeutic regimens was studied using immunohistochemistry. Data was correlated to disease-free survival (DFS), overall survival and pathologic complete response (pCR). The functional roles of PARK2 were demonstrated by a series of <i>in vitro</i> and <i>in vivo</i> experiments. Including mass spectrometry, Co-immunoprecipitation, isolation of subcellular fractionation, fluorescence microscopy, <i>in vivo</i> ubiquitination assay and luciferase analyses. <b>Results:</b> Highly expressed PARK2 predicted better response to antimicrotubule drugs-containing regimen associated with higher rate of pathologic complete response (pCR). In contrast, PARK2 expression did not predict response to the DNA-damaging drugs regimen. Following antimicrotubule drugs treatment, levels of PARK2 was upregulated due to the repression of STAT3-mediated transcriptional inhibition of PARK2. Moreover, overexpression of PARK2 specifically rendered cells more sensitive to antimicrotubule drugs, but not to DNA-damaging drugs. Depletion of PARK2 enhanced resistance to antimicrotubule drugs. Mechanistically, PARK2 markedly activated the mitochondrial pathway of apoptosis after exposure to antimicrotubule drugs. This occurred through downregulating the antiapoptotic protein, phospho-BCL-2. BCL-2 phosphorylation can be specifically induced by antimicrotubule drugs, whereas DNA-damaging drugs do not. Notably, PARK2 interacted with phospho-BCL-2 (Ser70) and promoted ubiquitination of BCL-2 in an E3 ligase-dependent manner. Hence, PARK2 significantly enhanced the chemosensitivity of antimicrotubule drugs both <i>in vitro and in vivo</i>, while loss-of-function PARK2 mutants did not. <b>Conclusions:</b> Our findings explained why PARK2 selectively confers chemosensitivity to antimicrotubule drugs, but not to DNA-damaging drugs. In addition, we identified PARK2 as a novel mediator of antimicrotubule drugs sensitivity, which can predict response of breast cancer patients to antimicrotubule drugs-containing regime.
mUBC9, a Novel Adenovirus E1A-interacting Protein That Complements a Yeast Cell Cycle Defect (1996)

Adenovirus E1A encodes two nuclear phosphoproteins that can transform primary rodent fibroblasts in culture. Transformation by E1A is mediated at least in part through binding to several cellular proteins, including the three members of the retinoblastoma family of growth inhibitory proteins. We report here the cloning of a novel murine cDNA whose encoded protein interacts with both adenovirus type 5 and type 12 E1A proteins. The novel E1A-interacting protein shares significant sequence homology with ubiquitin-conjugating enzymes, a family of related proteins that is involved in the proteasome-mediated proteolysis of short-lived proteins. Highest homology was seen with a Saccharomyces cerevisiae protein named UBC9. Importantly, the murine E1A-interacting protein complements a cell cycle defect of a S. cerevisiae mutant which harbors a temperature-sensitive mutation in UBC9. We therefore named this novel E1A-interacting protein mUBC9. We mapped the region of E1A that is required for mUBC9 binding and found that the transformation-relevant conserved region 2 of E1A is required for interaction.
BaCe<sub>1</sub><sub>-</sub><i><sub>x</sub></i>Pd<i><sub>x</sub></i>O<sub>3</sub><sub>-</sub><sub>δ</sub> (0 ≤ <i>x</i> ≤ 0.1):  Redox Controlled Ingress and Egress of Palladium in a Perovskite (2007)

We demonstrate using a combination of X-ray and neutron diffraction and X-ray photoelectron spectroscopy that Pd2+ ions can be substituted for Ce in perovskite BaCeO3 and that, under oxidizing conditions, BaCe1-xPdxO3-δ (0 ≤ x ≤ 0.1) compositions can be prepared. Neutron diffraction has helped verify that δ ≈ x, implying that Ce4+ ions are substituted by Pd2+ and that a vacancy is concurrently created on the oxygen sublattice. The structure of the host compound and models for Pd substitution have also been studied using density functional theory, which has provided a detailed local description of the structure. The Pd2+-containing perovskite phases extrude elemental face-centered cubic palladium when heated in a reducing atmosphere. This elemental palladium is re-absorbed as ions into the perovskite lattice upon heating in flowing oxygen. Evidence for such cyclable ingress and egress of palladium under redox conditions is presented. A curious morphological change that results from the redox cycling of BaCe1-xPdxO3-δ is the formation of perovskite nanowires, which we believe to arise from regrowth of the perovskite around particles of elemental palladium.
Sensitivity and Specificity Table and ROC Curve from Circulating Tumor Cells and Early Relapse in Node-positive Melanoma (2023)

&lt;p&gt;Sensitivity and Specificity CTC Detection Table and ROC Curve&lt;/p&gt;
ASSESSMENT OF BONE MASS AT DIFFERING SKELETAL SITES BY MULTIPLE DIAGNOSTIC PARAMETERS. (1983)

Chesnut, Charles H.; Hanson, James A.; Kilcoyne, Raymond F.; Murano, Robert; Lewellen, Thomas K.; Nelp, Wil B.; Mack, Lawrence; Graham, Michael M. Author Information
Towards myocardial contraction force image reconstruction for heart disease assessment and intervention planning (2015)

It is clinically vital to devise a technique to evaluate regional functionality of the myocardium in order to determine the extent and intensity of local damage to the cardiac tissue caused by ischemic injuries. Such a technique can potentially enable cardiologists to discriminate between reversible and irreversible ischemic injuries and to devise appropriate revascularization therapy in case of reversible lesions. The technique is founded on the premise that sufficient contraction force generated by the cardiac tissue can be regarded as a direct and reliable criterion for regional analysis of tissue healthy functionality. To this end, a number of imaging techniques have been developed and, to our knowledge, none of them assess regional cardiac functionality based on a straightforward mechanical measure such as local cardiac contraction forces. . As such, a novel imaging technique is being developed on the basis of quantification and visualisation of local myocardial contraction forces. In this technique, cardiac contraction force distribution is attained through solving an inverse problem within an optimization framework which uses iterative forward mechanical modelling of the myocardium. Hence, a forward mechanical model of the myocardium which is computationally efficient, robust, and adaptable to diverse pathophysiological conditions is necessary for this development. As such, this paper is geared towards developing a novel mechanical model of the healthy and pathological myocardium which considers all aspects of the myocardial mechanics including hyperelasticity, anisotropy, and active contraction force. In this investigation, two major parts, including background tissue and reinforcement bars (fibers) have been considered for modelling the myocardium. The model was implemented using finite element (FE) approach and demonstrated very good performance in simulating normal and infarcted left ventricle (LV) contractile function.
Synthesis of biologically active compounds using photochemical pericyclic reactions. (1986)

Novel Synthetic approaches to β-lactams and Corey lactone analogues via four-membered ring intermediates formed by photochemical pericyclic reaction, followed by subsequent retro-aldol-type C-C bond fission are described. The same approach to carbocyclic C-nucleosides which involves thermal 4 + 2 addition reaction in the first step is also reported. These examples demonstrate that pericyclic reactions, if combined with C-C bond fission of the carbocyclic rings thus formed, provide productive synthetic methods of biologically active substances which allow strict regio-and stereochemical control of the required functionality of the target molecules.
Enhanced thermal energy harvesting performance of a cobalt redox couple in ionic liquid–solvent mixtures (2015)

Thermoelectrochemical cells are increasingly promising devices for harvesting waste heat, offering an alternative to the traditional semiconductor-based design. Advancement of these devices relies on new redox couple/electrolyte systems and an understanding of the interplay between the different factors that dictate device performance. The Seebeck coefficient (Se) of the redox couple in the electrolyte gives the potential difference achievable for a given temperature gradient across the device. Prior work has shown that a cobalt bipyridyl redox couple in ionic liquids (ILs) displays high Seebeck coefficients, but the thermoelectrochemical cell performance was limited by mass transport. Here we present the Se and thermoelectrochemical power generation performance of the cobalt couple in novel mixed IL/molecular solvent electrolyte systems. The highest power density of 880 mW m(-2), at a ΔT of 70 °C, was achieved with a 3 : 1 (v/v) MPN-[C2mim][B(CN)4] electrolyte combination. The significant power enhancement compared to the single solvent or IL systems results from a combination of superior ionic conductivity and higher diffusion coefficients, shown by electrochemical analysis of the different electrolytes. This is the highest power output achieved to-date for a thermoelectrochemical cell utilising a high boiling point redox electrolyte.
Multifocal tDCS modulates resting-state functional connectivity in older adults depending on induced electric field and baseline connectivity (2020)

Abstract Background Advancing age affects the brain’s resting-state functional networks. Combining non-invasive brain stimulation (NIBS) with neuroimaging is a promising approach to modulate activity across resting-state functional systems and explore their true contribution to cognitive function in aging. However, substantial individual variability in the response to NIBS has been reported and, hence, identifying the individual predictors of NIBS-induced modulatory effects is crucial if we are to harness their potential. Methods Thirty-one cognitively healthy older adults (71.68 ± 2.5 years; 19 females) underwent two different multifocal real tDCS conditions (C1 and C2) and a sham condition in a crossover design during a resting-state functional magnetic resonance imaging (rs-fMRI) acquisition. The real tDCS conditions were designed to induce two distinct electric field distribution patterns either targeting generalized cortical overactivity or a dissociation between the frontal areas and the posteromedial cortex. Stimulation was delivered through an MRI-compatible device using 8 small circular electrodes. Each individuals’ anatomical T1-weighted MRI was used to generate a finite element model to define the individual electric field generated by each tDCS condition. Results The two tDCS conditions modulated resting-state connectivity differently. C1 increased the coactivation of numerous functional couplings as compared to sham, however, a smaller amount of connections increased in C1 as compared to C2, while no differences between C2 and sham were appreciated. At the group level, C1-induced modulations primarily included temporo-occipital areas and distinct cerebellar regions. This functional pattern was anatomically consistent with the estimated distribution of the induced electric field in the C1 condition. Finally, at the individual level, the extent of tDCS-induced rs-fMRI modulation in C1 was predicted by baseline resting-state connectivity and simulation-based electric field magnitude. Discussion Our results highlighted that multifocal tDCS procedures can effectively change neural dynamics in the elderly consistently with the spatial distribution of the estimated electric fields on the brain. Furthermore, we showed that specific brain factors that have been revealed to explain part of the individual variability to NIBS in young samples are also relevant in older adults. In accordance, designing multifocal tDCS configurations based on specific fMRI patterns appears to be a valuable approach to precisely adjust those complex neural dynamics sustaining cognition that are affected as a function of age. Furthermore, these innovative NIBS-based interventions should be individually-tailored based on subject-specific structural and functional data to ultimately boost their potential in aged populations.
HREELS, XPS, and Electrochemical Study of Benzenethiol Adsorption on Au(111) (1998)

Benzenethiol adsorption from the liquid phase on Au(111) has been studied using high-resolution electron energy loss spectroscopy (HREELS), X-ray photoelectron spectroscopy (XPS), and electrochemistry. The absence of a S−H stretching vibration and the presence of benzene-like bands indicate that the sulfhydryl hydrogen is lost during adsorption, consistent with the formation of a thiolate intermediate. On the basis of the intensity of the out-of-plane C−H deformation, an adsorption geometry with a strong inclination of the plane of the phenyl ring toward an upright orientation on the Au(111) surface is favored. XPS provides further evidence that the primary adsorbate species is bonded to Au through the sulfur atom. The monolayer film thickness, absolute sulfur surface coverage and molecular packing density confirm a bonding arrangement in which the phenyl ring is aligned largely perpendicular to the substrate surface. Attenuation of a voltammetric peak, associated with reversible removal of the Au(111)−(√3×22) reconstruction, and inhibition of chloride anion adsorption, suggest that benzenethiol chemisorption gradually deconstructs the Au(111) surface to the (1×1) bulk truncated phase and self-assembles through a mechanism involving growth of two-dimensional islands. Specifically adsorbing anions leads to formation of a (1×1) surface structure, causing reorganization of the organic adlayer, reducing the ability of the Au(111) surface to undergo reversible reconstruction. The influence of benzenethiol on the underpotential deposition (UPD) of Cu on Au(111) is investigated. At sub-monolayer thiol coverages, a series of broad adsorption features are observed. In contrast, desorption peaks are readily identified from sub-monolayer to high thiol coverages. It appears that saturation coverage of benzenethiol passivates the surface toward Cu adsorption and desorption processes. A benzenethiol coverage-dependent study of Cu UPD supported by XPS uptake data suggests a multistep adsorption mechanism comprising an initial rapid adsorption step with benzenethiol adopting a flat-lying bonding geometry, followed by a slow orientational phase transition to form islands of densely packed upright adsorbate.
Effects of Exercise Training on Insulin Sensitivity and Lipid Adaptations With and Without Weight loss (2016)

PURPOSE: Achieving at least modest weight loss (MWL) (≥3.0% from baseline) with exercise training is associated with improvements in cardiometabolic risk factors, however the independent contributions of exercise versus weight loss is unclear. The present study evaluated whether the achievement of at least MWL with aerobic training results in greater improvements in insulin sensitivity and lipid metabolism compared to those who do not achieve MWL. METHODS: In the Studies of Targeted Risk Reduction Interventions through Defined Exercise (STRRIDE) overweight and obese adults with dyslipidemia completed 8 months of aerobic training at low amount, moderate intensity (LAMI), low amount, high intensity (LAHI), and high amount, high intensity (HAHI). We analyzed data from participants (N=163) who were adherent to training (>70%). Participant data were categorized based on whether or not MWL was achieved. Insulin sensitivity (intravenous glucose tolerance test), lipid concentrations and lipoprotein particle size were assessed at baseline and follow-up. RESULTS: Response rates for MWL were 18.9%, 16.7% and 32.1% in the LAMI, LAHI and HAHI groups, respectively (22.7% overall). A greater increase in insulin sensitivity was observed in participants that achieved MWL compared to those that did not in the LAMI (MWL: 1.3, no MWL: 3.4, p=0.002) and the HAHI (MWL: 0.7, No MWL: 1.8, p=0.04), but not the LAHI group (MWL: 0.6, No MWL: 1.4, p=0.37). When exercise groups were collapsed together, similar effects were observed for changes in insulin sensitivity (MWL: 2.2, No MWL: 0.9), triglycerides (MWL: -44.2 mg/dL, No MWL: -20.1 mg/dL), low density lipoprotein (LDL) particle size (MWL: 0.30 nm, No MWL: 0.07 nm), and high density lipoprotein (HDL) particle size (MWL: 0.12 nm, No MWL: 0.02 nm) (p<0.05). No significant effects were observed for changes in LDL, HDL, or total cholesterol concentrations (p>0.05). CONCLUSION: The results of the present study suggest that modest weight loss with aerobic exercise training enhances the changes in insulin sensitivity and elements of lipid metabolism compared to no weight loss. Although exercise has independent effects in improving health, clinicians should encourage weight loss with exercise training to maximize cardiometabolic health benefits in overweight and obese adults.
A Novel Mechanism of Latency in Matrix Metalloproteinases (2015)

The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.
Trichostatin A preferentially reverses the upregulation of gene‐expression levels induced by gain of chromosome 7 in colorectal cancer cell lines (2017)

Epithelial cancers are defined by a tumor-specific distribution of chromosomal aneuploidies that are maintained when cells metastasize and are conserved in cell lines derived from primary tumors. Correlations between genomic copy number and gene expression have been observed for different tumors including, colorectal (CRC), breast, and pancreatic cancer. These ploidy-driven transcriptional deregulations are characterized by low-level expression changes of most genes on the affected chromosomes. The emergence of these aberrations at an early stage of tumorigenesis and the strong selection for the maintenance of these aneuploidies suggest that aneuploidy-dependent transcriptional deregulations might contribute to cellular transformation and maintenance of the malignant phenotype. The histone deacetylase inhibitor (HDACi) Trichostatin A (TSA) has anticancer effects and is well known to lead to large-scale gene-expression changes. Here we assessed if TSA could disrupt the aneuploidy-driven gene expression in the aneuploid colon cancer cell line SW480 and the artificially generated aneuploid cell line DLD-1 + 7. We found that TSA increases transcriptional activity throughout the genome, yet inhibits aneuploidy-induced gene-expression changes on chromosome 7. Among the TSA affected genes on chromosome 7, we identified potential CRC oncogenes. These experiments represent the first attempt to explain how histone acetylation affects aneuploidy-driven gene-expression changes.
Correcting one error in channels with feedback (2023)

We address the problem of correcting a single error in an arbitrary discrete memoryless channel with error-free instantaneous feedback. For the case of a one-time feedback, we propose a method for constructing optimal transmission strategies. The obtained result allows us to prove that for a binary channel, two feedbacks are sufficient to transmit the same number of messages as in the case of complete feedback. We also apply the developed techniques to a binary asymmetric channel to construct transmission strategies for small lengths.
The use of echocardiography to determine left ventricular size. A simultaneous echocardiographic and angiocardiographic study. (2022)

Foi feito o estudo simultâneo das dimensões do ventrículo esquerdo por cineangiocardiografia e ecocardiografia em 15 doentes sem cardiopatia isquémica, durante o exame hemodinâmico de rotina. O feixe de ultrassons interceptou o eixo menor ventricular segundo ângulos variáveis (de -11° a +18°) na diástole e na sístole, e o eixo longitudinal de 28% a 64% do seu comprimento na diástole e de 15 % a 64 % na sístole. As dimensões ventriculares foram maiores quando medidas a partir dos angiogramas no mesmo plano do feixe de ultrassons, embora exista uma boa correlação entre as dimensões ecocardiográficas e angiocardiográficas. Também a fracção de ejecção determinada a partir dos volumes ventriculares obtidos angiograficamente, se correlaciona bem com a fracção de encurtamento obtida ecocardiograficamente. São discutidos os erros práticos envolvidos nas medições ecocardiográficas e conclui-se que a extrapolação dessas dimensões, para a determinação de volumes ventriculares, deve ser executada cautelosamente.