gebhart/patrepeval huggingface dataset:
The Novel Calpain Inhibitor SJA6017 Improves Functional Outcome after Delayed Administration in a Mouse Model of Diffuse Brain Injury (2001)

A principal mechanism of calcium-mediated neuronal injury is the activation of neutral proteases known as calpains. Proteolytic substrates for calpain include receptor and cytoskeletal proteins, signal transduction enzymes and transcription factors. Recently, calpain inhibitors have been shown to provide benefit in rat models of focal head injury and focal cerebral ischemia. The present study sought to investigate, in experiment 1, the time course of calpain-mediated cytoskeletal injury in a mouse model of diffuse head injury by measuring the 150- and 145-kDa alpha-spectrin breakdown products (SBDP). Secondly, in experiment 2, we examined the effect of early (20 min postinjury) administration of the novel calpain inhibitor SJA6017 on functional outcome measured 24 h following injury and its effect on posttraumatic alpha-spectrin degradation. Lastly, in experiment 3, we examined the effect of delayed (4 or 6 h postinjury) administration of SJA6017 on 24-h postinjury functional outcome. In experiment 1, isoflurane-anesthetized male CF-1 mice (18-22 g) were subjected to a 750 g-cm weight drop-induced injury and were sacrificed for SBDP analysis at postinjury times of 30 min, and 1, 2, 6, 24 and 48 h (plus sham). In experiments 2 and 3, mice were injured as described, and delivered a single tail vein injection of either SJA6017 (0.3, 1, or 3 mg/kg) or vehicle (administered immediately, 4 or 6 h postinjury [3 mg/kg]). Functional outcome was evaluated in both studies, and, in experiment 2, 24-h postinjury assessment of SBDPs was determined. Following injury, the level of SBDP 145 was significantly different from sham at 24 and 48 h in cortical and at 24 h in the hippocampal tissues and at 48 h in the striatum. Immediate postinjury administration of SJA6017 resulted in a dose-related improvement in 24-h functional outcome (p < 0.05 at 3 mg/kg). Significance was maintained after a 4-h delay of the 3 mg/kg, but was lost after a 6-h delay. Despite improvement in functional outcome at 24 h, SJA6017 did not reduce spectrin breakdown in cortical or hippocampal tissues. These results support a role for calpain-mediated neuronal injury and the potential for a practical therapeutic window for calpain inhibition following traumatic brain injury. However, measurements of regional spectrin degradation may not be the most sensitive marker for determining the effects of calpain inhibition.
Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate (2008)

Kinesin-5 inhibitors (K5I) are promising antimitotic cancer drug candidates. They cause prolonged mitotic arrest and death of cancer cells, but their full range of phenotypic effects in different cell types has been unclear. Using time-lapse microscopy of cancer and normal cell lines, we find that a novel K5I causes several different cancer and noncancer cell types to undergo prolonged arrest in monopolar mitosis. Subsequent events, however, differed greatly between cell types. Normal diploid cells mostly slipped from mitosis and arrested in tetraploid G(1), with little cell death. Several cancer cell lines died either during mitotic arrest or following slippage. Contrary to prevailing views, mitotic slippage was not required for death, and the duration of mitotic arrest correlated poorly with the probability of death in most cell lines. We also assayed drug reversibility and long-term responses after transient drug exposure in MCF7 breast cancer cells. Although many cells divided after drug washout during mitosis, this treatment resulted in lower survival compared with washout after spontaneous slippage likely due to chromosome segregation errors in the cells that divided. Our analysis shows that K5Is cause cancer-selective cell killing, provides important kinetic information for understanding clinical responses, and elucidates mechanisms of drug sensitivity versus resistance at the level of phenotype.
Instantaneous frequency, spectral centroid, and even wavelets (1991)

The Fourier spectral centroid formula for instantaneous frequency is extended to all times and to all analytic signals and is in a convenient computable form. Examples using two different synthetic even seismic wavelets show that the peaks and troughs of their instantaneous frequency may occur at the envelope maxima or minima, with possible singularities at the envelope minima. For a purely even or odd wavelet, either a turning point or a point of inflection occurs at the wavelet center of the instantaneous frequency and envelope.
Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics (2023)

The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a <i>quasi</i>-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.
Analytical Study of leakage characteristics change during multilevel interconnect process using porogen-type porous SiOC (k=2.4)/Cu system (2008)

The change in leakage I-V characteristics by multilevel processing of Cu interconnects with porogen-type p-SiOC (k=2.4) was investigated. Although the change can be eliminated by UV-cure condition, it was found that another process conditions can affect the leakage characteristics; the combination of NH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> plasma treatment after Cu-CMP and the additional UV-cure in multilevel process. It was also found that the influence of NH <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> plasma damage on interface between p-SiOC and cap-CVD was decreased using low-pressure ion-reaction oriented trench etching (LP-RIE).
Stable and Nondisruptive In Vitro / In Vivo Labeling of Mesenchymal Stem Cells by Internalizing Quantum Dots (2009)

Progress in stem cell research has prioritized the refinement of cell-labeling techniques for in vitro and in vivo basic and therapeutic studies. Although quantum dots, because of their optical properties, are emerging as favorable nanoparticles for bioimaging, substantial refinements or modifications that would improve their biocompatibility are still required. We report here that internalizing quantum dots (i-QDs) generated by their conjugation with an internalizing antibody against a heat shock protein-70 family stress chaperone, mortalin, offered an efficient, genetically noninvasive, nontoxic, and functionally inert way to label mesenchymal stem cells (MSCs). The i-QD-labeled MSCs underwent normal adipocyte, osteocyte, and chondrocyte differentiation in vitro and in vivo, suggesting the potential application of i-QDs in in vivo diagnostics, regenerative and therapeutic medicine.
O-Acetyl-GD2 as a Therapeutic Target for Breast Cancer Stem Cells (2022)

OAcGD2 is a novel marker for CSC in various subtypes of breast cancer. Anti-OAcGD2 mAb8B6 directly eradicated OAcGD2<sup>+</sup> cells and reduced tumor growth in PDX model. Our data demonstrate the potential of mAb8B6 as a promising immunotherapeutic agent to target BCSCs.
Recognizing the Continuous Nature of Expression Heterogeneity and Clinical Outcomes in Clear Cell Renal Cell Carcinoma (2016)

Abstract PURPOSE Evaluation of 12 ccRCC publicly-available ccRCC gene expression datasets showed that previously proposed discrete molecular subtypes are unstable. To reflect the continuous nature of gene expression observed, we developed a quantitative score (Continuous Linear Enhanced Assessment of Renal cell carcinoma, or CLEAR) using expression analysis founded on pathologic parameters. MATERIALS AND METHODS 265 ccRCC gene expression profiles were used to develop the CLEAR score, representing a genetic correlate of the continuum of morphological tumor grade. A signature derivation method based on correlation of CLEAR score with gene expression ranking was used to derive an 18-transcript signature. External validation was conducted in multiple public expression datasets. Results As a measure of intertumoral gene expression heterogeneity, the CLEAR score demonstrated both superior prognostic estimates (94% vs 83% adequacy index in TCGA dataset) and inverse correlation with anti-angiogenic tyrosine-kinase inhibition (65% vs 55% adequacy index) in comparison to previously proposed discrete subtyping classifications. Inverse correlation with high-dose interleukin-2 outcomes was also observed for the CLEAR score (p=0.05). Multiple somatic mutations (VHL, PBRM1, SETD2, KDM5C, TP53, BAP1, PTEN, MTOR) were associated with the CLEAR score. Application of the CLEAR score to independent expression profiling of intratumoral ccRCC regions demonstrated its ability to reflect intratumoral expression heterogeneity and further analysis showed average intertumoral heterogeneity exceeded intratumoral heterogeneity. Conclusions The CLEAR score, a gene expression signature developed on histopathology, outperformed discrete subtype-classification in prognostic estimates and correlated better with treatment outcomes. Recognizing cancer as a continuum has important implications for laboratory and clinical research.
Video Collections in Panoramic Contexts Supplemental Material (2013)

This document contains additional information on video alignment, the display applications exploration, and on the user study conducted to evaluate our system. We give de-tails on homography validation, estimating missing homogra-
Externally determined and intrinsic contributions to the polarization switching currents in SrBi2Ta2O9 thin films (1998)

Abstract It has been shown that ferroelectric materials are suitable for non volatile memories. To replace other technologies these materials have to fulfill several requirements, one is a sufficient switching velocity of the material. At present, memory access times amount to 10 to 50 ns. Hence, ferroelectric materials should exhibit access times similar to these values. As a result, the polarization switching must be completed within a few nanoseconds. This work presents fast pulse switching measurements with speeds equal to the speed in a real memory device. For all samples studied, a significant increase in the coercive voltage has been observed at rise times of the excitation signal of about one nanosecond. A qualitative model is suggested to explain the behavior of the material at highest speed compared to the hysteresis curve data recorded by low frequencies. It is distinguished between externally determined and intrinsic part of the polarization switching current.
Process Development and Pilot-Scale Synthesis of New Cyclization Conditions of Substituted Phenylacetamides to Tetrahydroisoquinoline-2-ones Using Eaton’s Reagent (2009)

Tetrahydroisoquinoline is a ubiquitous structural framework presented in numerous pharmacologically relevant molecules. Although accessible by the Pictet−Spengler cyclization, conditions commonly used for such cyclizations are often difficult to implement on scale. Herein, we report the development of a scaleable approach utilizing Eaton’s reagent for the cyclization of substituted phenylacetamide analogues to tetrahydroisoquinoline-2-one. The development, optimization, and safety hazard evaluations, which outline the benefits and ease of workup of this new process, are discussed.
Systemic mastocytosis with associated clonal haematological non-mast cell lineage diseases: a histopathological challenge (2004)

SM-AHNMD can be diagnosed histologically in bone marrow trephines only after immunostaining with antibodies against tryptase, KIT, and CD25. Eighteen of 20 AHNMDs were of myeloid origin. C-KIT point mutations were present in 16 of 20 cases. The prognostic relevance of detecting SM associated with another haematological neoplasm remains unclear, but mast cell resistance to most cytoreductive agents is of major importance for treatment planning.
Norpiperidine Imidazoazepines as a New Class of Potent, Selective, and Nonsedative H1 Antihistamines (2004)

Clinical doses of available H(1) antihistamines are limited mainly by sedative side effects. However, higher doses are often required to obtain optimal therapeutic activity, especially in dermatology. We report the synthesis of three norpiperidine imidazoazepines representative of a new class of selective and nonsedating H(1) antihistamines. The compounds were at least as potent as cetirizine and loratadine as measured by H(1) receptor binding affinity, by protection against compound 48/80- and histamine-induced lethality in rats and guinea pigs, respectively, and by skin reaction tests in rats, guinea pigs, and dogs. The compounds, in particular 3a, were less prone than the reference compounds to penetrate the brain and to occupy central H(1) receptors, suggesting absence of sedative side effects. In vitro and in vivo cardiovascular safety tests showed that 3a had no intrinsic potential to prolong ventricular repolarization or induce cardiac arrhythmias. Compound 3a has been selected for further clinical development, mainly for application in dermatology.
Characterization of de novo microdeletions involving 17q11.2q12 identified through chromosomal comparative genomic hybridization (2007)

High-resolution array-comparative genome hybridization (CGH) is a powerful tool for detection of submicroscopic chromosome deletions and duplications. We describe two patients with mild mental retardation (MR) and de novo microdeletions of 17q11.2q12. Although the deletions did not involve the neurofibromatosis type 1 (NF1) gene, they overlap with long-range deletions of the NF1 region which have been encountered in a small group of NF1 patients with more severe MR. Given the overlap of the deletions in our two patients with the large-sized NF1 microdeletions but not with the more frequent and smaller NF1 deletions, we hypothesize that more than one gene in the 17q11.2q12 region may be involved in MR. We discuss candidate genes for MR within this interval that was precisely defined through array-CGH analysis.
ChemInform Abstract: Synthesis of (1S,2R,5R)‐2‐Ethyl‐1,5‐dimethyl‐6,8‐dioxabicyclo(3.2.1) octane, the Aggregation Pheromone of Male Beech Bark Beetles, Taphrorychus bicolor (Col., Scol.). (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 6 from A Smac Mimetic Rescue Screen Reveals Roles for Inhibitor of Apoptosis Proteins in Tumor Necrosis Factor-α Signaling (2023)

Supplementary Figure 6 from A Smac Mimetic Rescue Screen Reveals Roles for Inhibitor of Apoptosis Proteins in Tumor Necrosis Factor-α Signaling
Nuclear magnetic resonance imaging of the cardiovascular system: normal and pathologic findings. (1983)

Whole body nuclear magnetic resonance (NMR) imaging of the cardiovascular system was carried out in early clinical trials in 244 volunteers and patients using a 3.5 KGauss (0.35 T) unit. The spin echo technique with multiple imaging parameters was used. Blood vessels were clearly discriminated from solid organs and lesions because little or no intraluminal signal is seen with laminar blood flow at normal velocities, whereas a more intense image is generated by solid organs. Characteristic flow signals were observed in normal patients and were accentuated by varying the imaging parameters. Cardiac chambers were well delineated in some patients on nongated images. In one case, internal topography of the ventricles was exquisitely displayed on a gated image. Intraluminal pathology, such as dissection of the aorta, aneurysms of the aorta and left ventricle, and aortic atheroma, was clearly demonstrated. Patency of coronary arterial bypass grafts was shown. Abnormal flow patterns due to slow or turbulent flow were accentuated on images using the second spin echo. This preliminary experience indicates the considerable potential of NMR imaging in the evaluation of cardiovascular diseases.
Measurement of the underlying event activity using charged-particle jets in proton-proton collisions at s = 2.76 $$ \sqrt{s}=2.76 $$ TeV (2015)

A measurement of the underlying event (UE) activity in proton-proton collisions is performed using events with charged-particle jets produced in the central pseudorapidity region (| jet | < 2) and with transverse momentum 1 p jet T < 100 GeV. The analysis uses a data sample collected at a centre-of-mass energy of 2.76 TeV with the CMS experiment at the LHC. The UE activity is measured as a function of p jet T in terms of the average multiplicity and scalar sum of transverse momenta (p T ) of charged particles, with || < 2 and p T > 0.5 GeV, in the azimuthal region transverse to the highest p T jet direction. By further dividing the transverse region into two regions of smaller and larger activity, various components of the UE activity are separated. The measurements are compared to previous results at 0.9 and 7 TeV, and to predictions of several Monte Carlo event generators, providing constraints on the modelling of the UE dynamics.
Reservoir Saturation Mapping from Electromagnetic Geophysical Surveys using Advanced Uncertainty Quantification Methods (2017)

Abstract Electromagnetic methods are a promising technology that allows measuring spatial distribution of resistivity in the inter-well region; its deployment has the objective to map and monitor fluid distribution deep into the reservoirs, kilometers away from the surveyed wells. There are many challenges in the interpretation of resistivity distribution in terms of fluid saturation. The management of the uncertainties in the knowledge of reservoir properties in the inter-well regions is very critical to the petrophysical interpretation of the resistivity surveys. Most reservoir characterization and saturation tools provide data at specific locations in the reservoir, with a limited radius of investigation around wellbores, typically cores, production and well logs data. This study introduces a novel approach in interpreting electromagnetic surveys and producing robust saturation maps that can guide reservoir management policies, with the ultimate objective of increasing hydrocarbon recovery. The developed workflow will apply dynamic simulation and advanced uncertainty quantification methods. The uncertain parameter considered is the permeability which is assumed to be spatial uncertainty. Two methods were applied to efficiently quantify uncertainty in the permeability its effect on the salinity distribution. The first method is the probabilistic collocation method (PCM). The PCM is based on the use of polynomial chaos expansion, which is used to develop a polynomial proxy model. The coefficients of this model are determined by performing reservoir simulation using an optimized set of collocation points, which approximate the sample space. The number of these samples that are required are significantly fewer than those required for a typical Monte Carlo or Latin Hypercube Simulation. The second method is the Multi-Level Monte Carlo (MLMC) method, which is based on the use of a combination of multi-level sequentially coarsened (upscaled) grids which shift most of the computational cost to the coarsened grids while minimizing the computational cost of running the simulator on the finer grid level. The results obtained showed that it is possible to investigate a wide range of uncertainty in a computationally efficient manner providing more robust saturation maps compared to current practices.
Fabrication and Characterization of an MR Cantilever with a Spin-Valve Sensor for a Scanning Magnetoresistance Microscope (2005)

We developed a new micro-fabricated cantilever with a spin-valve sensor (MR cantilever) for a scanning magentoresistance microscope (SMRM). Since thespin-valve sensor has a self-biasing mechanism, it allowsthe SMRM to respond to an observed magnetic field linearly without any external bias magnetic field, and itmakes the SMRM more sensitive to magnetic fields. Wehave succeeded in introducing the self-biasing mechanism into the SMRM system by fabricating the spin-valve sensor on a cantilever.
System evaluation of optimal downlink beamforming with congestion control in wireless communication (2006)

We investigate the use of congestion control and joint optimal downlink beamforming, power control, and access point allocation, in a multi-cell wireless communication system. The access points of the system employ smart antennas and single antennas are used at the terminals. The possibility to send messages to multiple terminals at the same frequency in the same time slot is exploited. We show how previously proposed algorithms for optimal downlink beamforming easily can be extended to determine also the optimal access point for each mobile terminal. In order to assign resources, optimal beamforming requires a feasible set of mobiles, i.e. that all admitted users can be offered the required signal-to-interference-and-noise ratio. Therefore, an algorithm for deciding which mobile terminals to admit or reject from a congested system is proposed and evaluated. Using the proposed congestion algorithm, joint optimal downlink beamforming is evaluated and the throughput increase as compared to decentralized beamforming algorithms and other congestion control strategies is assessed from a system point of view. The results show that the proposed strategy can almost double the throughput compared to decentralized beamforming algorithms and give a fivefold increase in throughput compared to conventional beamforming without any interference suppression.