gebhart/patrepeval huggingface dataset:
Reactions of 2-Propanol with Cu+ in the Gas Phase:  A Density Functional Theory Study (2002)

The gas phase reactions between Cu+ and 2-propanol have been investigated using density functional theory at the B3LYP/6-311+G(d) and B3LYP/6-311++G(d,p) levels of theories. Seven reaction pathways have been studied. Of all reaction paths, the mechanism involving an electrophile-induced one step syn elimination of H2O has the lowest energy barrier. Dehydration also occurs via the intermediate corresponding to C−O insertion of Cu+. On the H2 elimination channel, reaction begins with C−H insertion of Cu+, followed by hydrogen migrations to form H2−Cu+−acetone or the H2−Cu+−2-propenol intermediates. Our results show that the reaction with copper cation insertion into the H−OCH(CH3)2 bond is unlikely, for its activation energy is 24.5 kcal/mol higher than those of the reactants (Cu+ and 2-propanol). The mechanism involving C−C insertion of Cu+ is also energetically unfavorable. The predicted potential energy surface of reaction and relative energies of the fragmentation products are consistent with available gas phase experiments.
Is IL-1β Further Evidence for the Role of Propionibacterium acnes in Degenerative Disc Disease? Lessons From the Study of the Inflammatory Skin Condition Acne Vulgaris (2018)

The pathogenesis of degenerative disc disease is a complex and multifactorial process in which genetics, mechanical trauma, altered loading and nutrition present significant etiological factors. Infection of the intervertebral disc with the anaerobic bacterium <i>Propionibacterium acnes</i> is now also emerging as a potentially new etiological factor. This human commensal bacterium is well known for its long association with the inflammatory skin condition acne vulgaris. A key component of inflammatory responses to <i>P. acnes</i> in acne appears to be interleukin (IL)-1β. Similarly, in degenerative disc disease (DDD) there is compelling evidence for the fundamental roles of IL-1β in its pathology. We therefore propose that <i>P. acnes</i> involvement in DDD is biologically very plausible, and that IL-1β is the key inflammatory mechanism driving the host response to <i>P. acnes</i> infection. Since there is a solid theoretical basis for this phenomenon, we further propose that the relationship between <i>P. acnes</i> infection and DDD is causal.
The Precipitation of Alpha Phase in Metastable Beta Phase Titanium Alloys. (1975)

This paper describes the results of a microstructural study of the crystallography, morphology and kinetics of formation of alpha-phase during decomposition of the metastable beta-phase in a Ti-Mo-Al ternary alloy and a Ti-Mo binary alloy.
The Use of Implantable Direct Current Stimulation in Multilevel Spinal Fusion Without Instrumentation (1996)

Multilevel fusion in this series with long-term follow-up evaluation of direct current stimulated patients without instrumentation showed clinical and radiographic success higher than in recent studies without instrumentation and comparable with recent studies using instrumentation.
Acidosis induces reprogramming of cellular metabolism to mitigate oxidative stress (2013)

Acidosis alters the cellular metabolism of several major metabolites, which induces a significant degree of metabolic inflexibility. Cells exposed to acidosis largely rely upon mitochondrial metabolism for energy generation to the extent that metabolic intermediates are redirected away from several other critical metabolic processes, including ribose and glutathione synthesis. These alterations lead to both a decrease in cellular proliferation and increased sensitivity to ROS. Collectively, these data reveal a role for p53 in cellular metabolic reprogramming under acidosis, in order to permit increased bioenergetic capacity and ROS neutralization. Understanding the metabolic adaptations that cancer cells make under acidosis may present opportunities to generate anti-tumor therapeutic agents that are more tumor-specific.
Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo (2010)

An open chromatin architecture devoid of compact chromatin is thought to be associated with pluripotency in embryonic stem cells. Establishing this distinct epigenetic state may also be required for somatic cell reprogramming. However, there has been little direct examination of global structural domains of chromatin during the founding and loss of pluripotency that occurs in preimplantation mouse development. Here, we used electron spectroscopic imaging to examine large-scale chromatin structural changes during the transition from one-cell to early postimplantation stage embryos. In one-cell embryos chromatin was extensively dispersed with no noticeable accumulation at the nuclear envelope. Major changes were observed from one-cell to two-cell stage embryos, where chromatin became confined to discrete blocks of compaction and with an increased concentration at the nuclear envelope. In eight-cell embryos and pluripotent epiblast cells, chromatin was primarily distributed as an extended meshwork of uncompacted fibres and was indistinguishable from chromatin organization in embryonic stem cells. In contrast, lineage-committed trophectoderm and primitive endoderm cells, and the stem cell lines derived from these tissues, displayed higher levels of chromatin compaction, suggesting an association between developmental potential and chromatin organisation. We examined this association in vivo and found that deletion of Oct4, a factor required for pluripotency, caused the formation of large blocks of compact chromatin in putative epiblast cells. Together, these studies show that an open chromatin architecture is established in the embryonic lineages during development and is sufficient to distinguish pluripotent cells from tissue-restricted progenitor cells.
P1‐231: Correlation of amyloid deposition with local and distal glucose metabolism in cognitively normal elderly, MCI and Alzheimer's disease (2008)

Amyloid deposition is hypothesized to be involved in the events leading to Alzheimer's disease (AD), but the mechanism is unclear. Inverse correlations between amyloid deposition and glucose metabolism in parietal regions of AD patients have been shown, suggesting local amyloid toxicity. However, the complexity of brain connectivity suggests that amyloid effects could be far removed as well. Determine associations of amyloid deposition with metabolism in amyloid-positive normal control subjects, MCI and AD patients. PiB PET and FDG PET scans were performed on 60 normal control subjects (by standard neuropsychological battery). Sixteen controls (26%; 56–80yrs) with amyloid deposition were included. Of 24 MCI patients, 14 (58%) were amyloid-positive (65–82yrs) and were included, along with 18 AD patients (100% amyloid positive; 56–94yrs). Regional PiB retention (DVR: cerebellum reference, DVR=VT/VND) and glucose metabolism (SUVR: cerebellum reference) measures were determined and atrophy-corrected using an MR-based method. PiB retention and metabolism were compared across cortical regions using Pearson's correlations. Similar to previous reports, glucose metabolism in parietal and precuneus cortices of AD patients was negatively correlated with PiB retention locally, and with PiB retention in frontal and lateral temporal cortices. Positive correlations between PiB retention and metabolism were uncommon in AD (mainly anterior cingulate). In controls, a few negative correlations were found in frontal cortex, while numerous positive correlations were found between metabolism in anterior cingulate and precuneus and PiB retention in several brain areas. In MCI, this effect was more pronounced. There were no significant negative correlations observed in MCI subjects. However, glucose metabolism in anterior cingulate showed positive correlations with PiB retention in most brain areas. Metabolism in precuneus and parietal cortex also was positively correlated with PiB retention in most posterior regions. The association of amyloid deposition and glucose metabolism appears to vary with increasing cognitive severity. In controls with amyloid deposition, we observed positive correlations of glucose metabolism in anterior cingulate and precuneus with global amyloid deposition. In MCI, this phenomenon became exaggerated and predominant. In AD, these positive correlations were rare, and negative correlations become predominant, particularly in precuneus and parietal cortex.
Kidney cancer mortality in The Netherlands, 1950-94: prediction of a decreasing trend. (1999)

The decreasing risk for generations born after 1930 will probably result in a decreasing trend in kidney cancer mortality in the near future. It is suggested that at least part of this changing trend in men (but not in women) is caused by the changing smoking behaviour of the Dutch population.
WINNER model for subway tunnel at 5.8 GHz (2012)

5 pages
Distributed faulty node detection in DTNs in presence of Byzantine attack (2017)

This paper considers a delay tolerant network consisting of nodes equipped with sensors, some of them producing outliers. A distributed faulty node detection (DFD) algorithm, whose aim is to help each node in estimating the status of its sensors, has been proposed recently by the authors. The aim of this paper is to analyze the robustness of the DFD algorithm to the presence of misbehaving nodes performing Byzantine attacks. Two types of attacks are considered and analyzed, each trying to mislead the other nodes in the estimation of the status of their sensors. This provides insights on the way the parameters of the DFD algorithm should be adapted to minimize the impact of misbehaving nodes. Theoretical results are illustrated with simulations considering nodes with random displacements, as well as traces of node inter-contact times from real databases.
Intellectual disability-associated disruption of O-GlcNAc cycling impairs habituation learning in Drosophila (2022)

O-GlcNAcylation is a reversible co-/post-translational modification involved in a multitude of cellular processes. The addition and removal of the O-GlcNAc modification is controlled by two conserved enzymes, O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA). Mutations in OGT have recently been discovered to cause a novel Congenital Disorder of Glycosylation (OGT-CDG) that is characterized by intellectual disability. The mechanisms by which OGT-CDG mutations affect cognition remain unclear. We manipulated O-GlcNAc transferase and O-GlcNAc hydrolase activity in Drosophila and demonstrate an important role of O-GlcNAcylation in habituation learning and synaptic development at the larval neuromuscular junction. Introduction of patient-specific missense mutations into Drosophila O-GlcNAc transferase using CRISPR/Cas9 gene editing leads to deficits in locomotor function and habituation learning. The habituation deficit can be corrected by blocking O-GlcNAc hydrolysis, indicating that OGT-CDG mutations affect cognition-relevant habituation via reduced protein O-GlcNAcylation. This study establishes a critical role for O-GlcNAc cycling and disrupted O-GlcNAc transferase activity in cognitive dysfunction, and suggests that blocking O-GlcNAc hydrolysis is a potential strategy to treat OGT-CDG.
Dynamic behavior of the PV Grid-connected inverter based on L and LCL filter with active damping control (2015)

PV Grid-connected inverters must fulfill the standards specifications of current harmonics injected to the grid. In order to satisfy these grid requirements, passive filters are connected between the inverter and the grid. This paper compares the response characteristic of the traditional inductive (L) filter with the inductive-capacitive-inductive (LCL) filter. It is shown that the increasing the inductance L leads to a good ripple current suppression around the inverter switch frequency. The LCL filter provides better harmonic attenuation and reduces the filter size. The main drawback is the LCL filter impedance, which is characterized by a typical resonance peak, which has to be damped to avoid instability. Passive or active techniques can be used to damp the LCL resonance. To address this issue, this paper presents a comparison of passive and active damping strategies. Experimental results are given to support the theoretical analysis and to illustrate the performance of grid connected PV inverter system.
A Rapid Access to (±)-Sedamine and Some Original N-Benzyl Unsaturated Analogues (2010)

International audience
Smac mimetic and glucocorticoids synergize to induce apoptosis in childhood ALL by promoting ripoptosome assembly (2014)

Apoptosis resistance contributes to poor outcome in pediatric acute lymphoblastic leukemia (ALL). Here, we identify a novel synergistic combination of Smac mimetic BV6 and glucocorticoids (GCs) (ie, dexamethasone, prednisolone) to trigger apoptosis in ALL cells. BV6 and GCs similarly cooperate to induce apoptosis in patient-derived leukemia samples, underlining the clinical relevance. Importantly, BV6/dexamethasone cotreatment is significantly more effective than monotherapy to delay leukemia growth in a patient-derived xenograft model of pediatric ALL without causing additional side effects. In contrast, BV6 does not increase cytotoxicity of dexamethasone against nonmalignant peripheral blood lymphocytes, mesenchymal stromal cells, and CD34-positive hematopoietic cells. We identify a novel mechanism by showing that BV6 and dexamethasone cooperate to deplete cIAP1, cIAP2, and XIAP, thereby promoting assembly of the ripoptosome, a RIP1/FADD/caspase-8-containing complex. This complex is critical and is required for BV6/dexamethasone-induced cell death, because RIP1 knockdown reduces caspase activation, reactive oxygen species production, and cell death. Ripoptosome formation occurs independently of autocrine/paracrine loops of death receptor ligands, because blocking antibodies for TNFα, tumor necrosis factor-related apoptosis-inducing ligand, or CD95 ligand or knockdown of death receptors fail to rescue BV6/dexamethasone-induced cell death. This is the first report showing that BV6 sensitizes for GC-triggered cell death by promoting ripoptosome formation with important implications for apoptosis-targeted therapies of ALL.
Minimax emission computed tomography using high-resolution anatomical side information and B-spline models (1999)

In this paper a minimax methodology is presented for combining information from two imaging modalities having different intrinsic spatial resolutions. The focus application is emission computed tomography (ECT), a low-resolution modality for reconstruction of radionuclide tracer density, when supplemented by high-resolution anatomical boundary information extracted from a magnetic resonance image (MRI) of the same imaging volume. The MRI boundary within the two-dimensional (2-D) slice of interest is parameterized by a closed planar curve. The Cramer-Rao (CR) lower bound is used to analyze estimation errors for different boundary shapes. Under a spatially inhomogeneous Gibbs field model for the tracer density a representation for the minimax MRI-enhanced tracer density estimator is obtained. It is shown that the estimator is asymptotically equivalent to a penalized maximum likelihood (PML) estimator with resolution-selective Gibbs penalty. Quantitative comparisons are presented using the iterative space alternating generalized expectation maximization (SAGE-FM) algorithm to implement the PML estimator with and without minimax weight averaging.
Beta-VLDL-induced cholesterol ester deposition in macrophages may be regulated by neutral cholesterol esterase activity. (1992)

We examined the role of enzyme activities involved in cholesterol ester metabolism in the accumulation of cholesterol ester in macrophages. When [3H]cholesterol linoleate-beta-very low density lipoproteins (beta-VLDLs) were incubated with rat resident peritoneal macrophages (RPMs), thioglycolate-elicited macrophages (TEMs), or alveolar macrophages (AMs), cholesterol ester accumulation was the greatest in TEMs and the least in AMs. The uptake of [3H]cholesterol linoleate-beta-VLDL into AMs was four times that into RPMs, and the uptake into TEMs was twice that into RPMs. The [3H]cholesterol released from [3H]cholesterol linoleate-beta-VLDL-loaded AMs was five times higher than from TEMs and RPMs, whereas those from RPMs and TEMs were almost the same. In studies using cell homogenates, the acid cholesterol esterase activity in AMs was 1.7 times that in TEMs and six times that in RPMs. The acyl-coenzyme A:cholesterol acyltransferase (ACAT) activities in AMs and TEMs were similar but were higher than that in RPMs. The neutral cholesterol esterase activity was seven times higher in AMs than in RPMs and TEMs. In the study using intact cells, the hydrolysis of loaded [3H]cholesterol linoleate-beta-VLDL in the presence of the ACAT inhibitor CL277,082 and the cholesterol [14C]oleate synthesis from [14C]oleate were enhanced in AMs about twofold compared with RPMs and TEMs. The reduction of de novo synthesized cholesterol [14C]oleate in the presence of CL277,082 was enhanced in AMs four times compared with TEMs or RPMs.(ABSTRACT TRUNCATED AT 250 WORDS)
Computer-Aided Patient-Specific Coronary Artery Graft Design Improvements Using CFD Coupled Shape Optimizer (2010)

This study aims to (i) demonstrate the efficacy of a new surgical planning framework for complex cardiovascular reconstructions, (ii) develop a computational fluid dynamics (CFD) coupled multi-dimensional shape optimization method to aid patient-specific coronary artery by-pass graft (CABG) design and, (iii) compare the hemodynamic efficiency of the sequential CABG, i.e., raising a daughter parallel branch from the parent CABG in patient-specific 3D settings. Hemodynamic efficiency of patient-specific complete revascularization scenarios for right coronary artery (RCA), left anterior descending artery (LAD), and left circumflex artery (LCX) bypasses were investigated in comparison to the stenosis condition. Multivariate 2D constraint optimization was applied on the left internal mammary artery (LIMA) graft, which was parameterized based on actual surgical settings extracted from 2D CT slices. The objective function was set to minimize the local variation of wall shear stress (WSS) and other hemodynamic indices (energy dissipation, flow deviation angle, average WSS, and vorticity) that correlate with performance of the graft and risk of re-stenosis at the anastomosis zone. Once the optimized 2D graft shape was obtained, it was translated to 3D using an in-house "sketch-based" interactive anatomical editing tool. The final graft design was evaluated using an experimentally validated second-order non-Newtonian CFD solver incorporating resistance based outlet boundary conditions. 3D patient-specific simulations for the healthy coronary anatomy produced realistic coronary flows. All revascularization techniques restored coronary perfusions to the healthy baseline. Multi-scale evaluation of the optimized LIMA graft enabled significant wall shear stress gradient (WSSG) relief (~34%). In comparison to original LIMA graft, sequential graft also lowered the WSSG by 15% proximal to LAD and diagonal bifurcation. The proposed sketch-based surgical planning paradigm evaluated the selected coronary bypass surgery procedures based on acute hemodynamic readjustments of aorta-CA flow. This methodology may provide a rational to aid surgical decision making in time-critical, patient-specific CA bypass operations before in vivo execution.
On‐line sample concentration techniques in capillary electrophoresis: Velocity gradient techniques and sample concentration techniques for biomolecules (2004)

Methods with a high sensitivity and high separation efficiency are goals in analytical separation techniques. On-line sample concentration techniques in capillary electrophoresis (CE) separations have rapidly grown in popularity over the past few years because they achieve this goal. This review describes the methodology and theory associated with a number of different techniques, including electrokinetic and chromatographic methods. For small molecules, several on-line concentration methods based on velocity gradient techniques are described, in which the electrophoretic velocities of the analyte molecules are manipulated by field amplification, sweeping, and isotachophoretic migration, resulting in the on-line concentration of the analyte zones. In addition, the on-line concentration methods for macromolecules are described, since the techniques used for macromolecules (DNAs and proteins), are different from those for small molecules, with respect to either mechanism or methodology. Recent studies relating to this topic are also discussed, including electrophoretic and chromatographic techniques on capillary or microchip.
Cell cycle controls: potential targets for chemical carcinogens? (1993)

The progression of the cell cycle is controlled by the action of both positive and negative growth regulators. The key players in this activity include a family of cyclins and cyclin-dependent kinases, which are themselves regulated by other kinases and phosphatases. Maintenance of balanced cell cycle controls may be directly linked to genomic stability. Loss of the check-points involved in cell cycle control may result in unrepaired DNA damage during DNA synthesis or mitosis leading to genetic mutations and contributing to carcinogenesis.
Automated feature learning using deep convolutional auto-encoder neural network for clustering electroencephalograms into sleep stages (2019)

Deep neural networks have emerged as popular machine learning tools due to their ability to automatically learn feature representations from raw input data. An auto-encoder neural network is a special network that can be trained in an unsupervised manner for automated feature learning. Unsupervised analysis of EEG signals is highly desirable since supervised analysis requires manual labeling of EEG signals which can be labor intensive and time consuming given the large amount of EEG data collected. We present a deep convolutional auto-encoder neural network to automatically learn feature representations from raw EEG signals in an unsupervised manner. We use the features extracted from the auto-encoder neural network for clustering EEG signals into sleep stages. For clustering, we test two algorithms: K-means - which is a single-membership model, and the latent Dirichlet allocation (LDA) topic model - which is a mixed membership model. Results are presented demonstrating an improvement in clustering performance using auto-encoder features compared to standard manually extracted features.