gebhart/patrepeval huggingface dataset:
Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase (2017)

Human farnesyl pyrophosphate synthase (hFPPS) catalyzes the production of the 15-carbon isoprenoid farnesyl pyrophosphate. The enzyme is a key regulator of the mevalonate pathway and a well-established drug target. Notably, it was elucidated as the molecular target of nitrogen-containing bisphosphonates, a class of drugs that have been widely successful against bone resorption disorders. More recently, research has focused on the anticancer effects of these inhibitors. In order to achieve increased non-skeletal tissue exposure, we created phenylaminopyridine bisphosphonates (PNP-BPs) that have bulky hydrophobic side chains through a structure-based approach. Some of these compounds have proven to be more potent than the current clinical drugs in a number of antiproliferation assays using multiple myeloma cell lines. In the present work, we characterized the binding of our most potent PNP-BPs to the target enzyme, hFPPS. Co-crystal structures demonstrate that the molecular interactions designed to elicit tighter binding are indeed established. We carried out thermodynamic studies as well; the newly introduced protein-ligand interactions are clearly reflected in the enthalpy of binding measured, which is more favorable for the new PNP-BPs than for the lead compound. These studies also indicate that the affinity of the PNP-BPs to hFPPS is comparable to that of the current drug risedronate. Risedronate forms additional polar interactions via its hydroxyl functional group and thus exhibits more favorable binding enthalpy; however, the entropy of binding is more favorable for the PNP-BPs, owing to the greater desolvation effects resulting from their large hydrophobic side chains. These results therefore confirm the overall validity of our drug design strategy. With a distinctly different molecular scaffold, the PNP-BPs described in this report represent an interesting new group of future drug candidates. Further investigation should follow to characterize the tissue distribution profile and assess the potential clinical benefits of these compounds.
ENVIRONMENTAL MONITORING OF GASES USING NEAR-INFRARED DIODE LASERS (1996)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text DAVID BOMSE, "ENVIRONMENTAL MONITORING OF GASES USING NEAR-INFRARED DIODE LASERS," Optics & Photonics News 7(9), 31- (1996) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Planar optical implementation of fractional correlation (1997)

The fractional Fourier transform (FRT) has recently been developed as a generalized form of the conventional Fourier transform[1]. Since the FRT can represent both the spatial-domain and frequency-domain information, the fractional correlator(FC) on the basis of the FRT operation is known as one of powerful approaches to obtain space-variant pattern recognition[2]. The space-variant property of FRT can make correlation peaks which are much brighter and narrower than the exact Fourier transform-based correlation peaks. This space-variance of the fractional correlation, however, requires high accuracy in alignment and robust stability in maintenance.
Noncanonical transnitrosylation network contributes to synapse loss in Alzheimer’s disease (2020)

Here we describe mechanistically distinct enzymes (a kinase, a guanosine triphosphatase, and a ubiquitin protein hydrolase) that function in disparate biochemical pathways and can also act in concert to mediate a series of redox reactions. Each enzyme manifests a second, noncanonical function-transnitrosylation-that triggers a pathological biochemical cascade in mouse models and in humans with Alzheimer's disease (AD). The resulting series of transnitrosylation reactions contributes to synapse loss, the major pathological correlate to cognitive decline in AD. We conclude that enzymes with distinct primary reaction mechanisms can form a completely separate network for aberrant transnitrosylation. This network operates in the postreproductive period, so natural selection against such abnormal activity may be decreased.
Impact of methane adsorption on tight rock permeability measurements using pulse-decay (2019)

The permeability of the rock is usually measured by the injection of gas using Darcy's flow model (pulse-decay). For oil formations, helium and nitrogen are the most common gases used to measure the permeability of the rock. However, recent approaches are based on the use of methane as it minimizes the properties difference between the testing fluid and reservoir fluid. This work focused on the latter approach to compute the correction of gas adsorption. The most widely used model is Cui et al. model that is based on Langmuir adsorption isotherm. In this work, we introduced a modified model that is based on Freundlich isotherm. This model also includes the correction for gas adsorption such as Freundlich isotherms proved to be more appropriate for the adsorption on intact reservoir rock. The model is based on gas and rock properties and reduced pressure and temperature were used to accommodate the gas compressibility. The modified model can also capture effective porosity of adsorption (ϕa) that can correct the pulse-decay storage capacity parameters a and b. The permeability estimation of ultra-tight samples using the modified approach is enhanced owing to the correction in the storage volume and rock porosity. Including the proper adsorption isotherm enhanced the porosity estimation because Langmuir isotherm yielded 11% porosity and Freundlich isotherm yielded 12% porosity. Similar results were obtained in the permeability estimation, Langmuir isotherm resulted in a 1.5% error compared to zero error in the Freundlich isotherm estimation.
RNA Extraction, Separation, and Analysis (2009)

This chapter contains sections titled: The Need to Be Able to Extract, Manipulate, and Analyze RNA Using Chemical Tools to Solve the Problem of Analysis of Biological Processes The Principle of Chromatography and Solid-Phase Extraction RNA Chromatography Enzymatic Treatment of RNA and Analysis Content and Organization of This Book References
Effect of a chimeric anti‐ganglioside GM2 antibody on ganglioside GM2‐expressing human solid tumors In vivo (1999)

Ganglioside GM2 is expressed on the surface of neuroblastoma and glioblastoma cells, and may also be detected on lung cancer cells. We reported previously that anti-ganglioside GM2 antibody exhibited strong in vitro anti-tumor activity against adriamycin-resistant cancer cells, which overexpressed ganglioside GM2. In the present study, we examined the in vivo anti-tumor effect of the chimeric anti-ganglioside GM2 antibody, KM966, against human lung and breast carcinoma cells, SBC-3 and MCF-7, and respective adriamycin-resistant clones, SBC-3/ADM and AdrR MCF-7 in BALB/c nu/nu mice. Ratios of tumor volume (T/C) between KM966-treated group and control group were 0.01 for SBC-3, 0.00 for SBC-3/ADM, 0.85 for MCF-7 and 0.34 for AdrR MCF-7 cells, respectively. Nude mice, which were pretreated with anti-asialo GM1 antibody to remove natural killer cells, were transplanted with 4 × 107 of SBC-3 and SBC-3/ADM subcutaneously. Seven days later, when tumors had grown to a diameter of over 8 mm, mice began to receive intravenous treatment of 120 μg/mouse KM966 daily. Fourteen daily treatments induced regression to less than 4-mm diameter in 4/5 SBC-3 tumors and 5/5 of SBC-3/ADM tumors. All SBC-3/ADM tumors disappeared completely, suggesting that KM966 exerts a strong in vivo anti-tumor effect on ganglioside GM2-expressing cancer cells. In KM966-treated mice, the surface of the tumor cells stained positive with anti-human IgG. In addition, numerous leukocytes had infiltrated into the tumor mass. Antibody-dependent cell-mediated cytotoxicity (ADCC) of KM966 against tumor cells was examined in vitro by 51Cr-release assay and revealed that KM966 induces ADCC activity against ganglioside GM2-expressing tumors. Our results suggest that immunotherapy using KM966 may be useful for the treatment of ganglioside GM2-expressing solid tumors. Int. J. Cancer 82:759–764, 1999. © 1999 Wiley-Liss, Inc.
Supplementary Data from Evaluation and Clinical Analyses of Downstream Targets of the Akt Inhibitor GDC-0068 (2023)

&lt;p&gt;PDF file 117K, Supplementary Materials and Methods -Supplementary Figure Legends -Supplementary Table Legends&lt;/p&gt;
Copper Catalyzed ATRP of Methyl Methacrylate Using Aliphatic α‐Bromo Ketone Initiator (2006)

Abstract The atom transfer radical polymerization (ATRP) of MMA was examined using 3‐bromo‐3‐methyl‐butanone‐2 (MBB) as an initiator in the presence of CuBr as catalyst and 2,6‐ bis [1‐(2,6‐diisopropylphenylimino)ethyl]pyridine (BPIEP) as a tridentate N‐donor ligand. The effect of various other N‐donor ligands including a bisoxazoline ligand, namely, 2,6‐ bis (4,4‐dimethyl‐2‐oxazolin‐2‐yl) pyridine (d m PYBOX) was studied in ATRP and reverse ATRP of MMA. The ATRP of MMA in toluene at 90 °C using MBB as initiator was relatively slow in the case of bidentate and faster in the case of tridentate N‐donor ligands. The apparent rate constant, k app , with MBB as initiator and BPIEP as ligand in toluene (50%, v/v) at 90 °C was found to be 7.15 × 10 −5 s −1 . In addition, reverse ATRP of MMA in diphenylether at 70 °C using BPIEP/CuBr 2 as catalyst system was very effective in reducing the reaction time from several hours to 24 h for polymerization of MMA.
Mesoscale Transport in Magnetite Electrodes for Lithium-Ion Batteries (2015)

The mass transport processes occurring within magnetite electrodes during discharge and voltage recovery are investigated using a combined experimental and modeling approach. Voltage recovery data are analyzed through a comparison of the mass transport time-constants associated with different length-scales within the electrode. The long voltage recovery times can be hypothesized to result from the relaxation of concentration profiles on the mesoscale, which consists of the agglomerate and crystallite length-scales. The hypothesis was tested through the development of a multi-scale mathematical model, which showed good agreement with experimental data.
Quantum computing with spin cluster qubits (2002)

We study the low energy states of finite spin chains with isotropic (Heisenberg) and anisotropic (XY and Ising-like) exchange interaction with uniform and non-uniform coupling constants. We show that for an odd number of sites a spin cluster qubit can be defined in terms of the ground state doublet. This qubit is remarkably insensitive to the placement and coupling anisotropy of spins within the cluster. One- and two-qubit quantum gates can be generated by magnetic fields and inter-cluster exchange, and leakage during quantum gate operation is small. Spin cluster qubits inherit the long decoherence times and short gate operation times of single spins. Control of single spins is hence not necessary for the realization of universal quantum gates.
Protoporphyrin IX delayed fluorescence imaging: a modality for wide range surgical guidance (2023)

Hypoxia imaging for surgical guidance has never been possible, yet it is well known that most tumors have microregional chronic and/or cycling hypoxia present as well as chaotic blood flow. The ability to image oxygen partial pressure (pO<sub>2</sub>) is therefore a unique control of tissue metabolism and can be used in a range of disease applications to understand the complex biochemistry of oxygen supply and consumption. Delayed fluorescence (DF) from the endogenous molecule protoporphyrin IX (PpIX) has been shown to be a truly unique reporter of the local oxygen partial pressure in tissue. PpIX is endogenously synthesized by mitochondria in most tissues and the particular property of DF emission is directly related to low microenvironmental oxygen concentration. Here it is shown that protoporphyrin IX (PpIX) has a unique emission in hypoxic tumor tissue regions, that is measured as a delayed fluorescence (DF) signal in the red to near-infrared spectrum. A time-gated imaging system was used for PpIX DF for wide field direct mapping of pO<sub>2</sub> changes. Acquiring both prompt and delayed fluorescence in a rapid sequential cycle allowed for imaging oxygenation in a way that was insensitive to the PpIX concentration. By choosing adequate parameters, the video rate acquisition of pO<sub>2</sub> images could be achieved, providing real-time tissue metabolic information. In this report, we show the first demonstration of imaging hypoxia signals from PpIX in a pancreatic cancer model, exhibiting &gt;5X contrast relative to surrounding normal oxygenated tissues. Additionally, tissue palpation amplifies the signal and provides intuitive temporal contrast based upon neoangiogenic blood flow differences. PpIX DF provides a new mechanism for tumor contrast that could easily be translated to human use as an intrinsic contrast mechanism for oncologic surgical guidance.
Towards a Generic Neural Network Architecture for Approximating Tone Mapping Algorithms (2021)

Tone curves are a key feature in any image processing pipeline, and are used to change the pixel values of an input image to find an output image that looks better. Perhaps the most widely deployed tone curve algorithm is Contrast Limited Histogram Equalisation (CLHE). CLHE is an iterative algorithm that tone maps an input image so that the histogram of the output is (approximately) maximally uniform subject to the constraint that the tone curve has bounded slope (neither too large or too small).In this paper, we build upon a neural network framework [1] that was recently developed to deliver CLHE in fewer iterations (each layer in the neural network is analogous to a single iteration of CLHE, but the network has fewer layers than the number of iterations needed by CLHE). The key contribution of this paper is to show that the same network architecture can be used to implement a more complex (and more powerful) tone mapping algorithm. Experiments validate our method.
Direct, indirect and total effect of HIV coinfection on the risk of non‐liver‐related cancer in hepatitis C virus‐infected patients treated by direct‐acting antivirals: a mediation analysis (2021)

In HCV participants treated with DAAs, the direct effect of HIV coinfection, reflecting chronic inflammation and immunosuppression, was associated with a 3.7-fold higher risk of non-liver-related cancer. By contrast, the indirect effect of HIV coinfection, reflecting higher tobacco and alcohol consumption and metabolic dysregulation, was not significantly associated with the risk of non-liver-related cancers.
IN VITRO COMPARISON OF SHOCK WAVE LITHOTRIPSY MACHINES (2000)

Shock wave lithotriptors vary in fragmentation ability. The HM3, Modulith SLX and Lithostar C machines yield smaller fragments than other machines.
Identifizierung von Pyrrolopyrazinen als polypotente Liganden mit Antimalariawirkung (2014)

Starke Aktivität gegen Plasmodium-falciparum-Parasiten und Plasmodium-berghei-Leberschizonten wurde bei Pyrrolopyrazinen gefunden (siehe allgemeine Struktur). Gründliche bioinformatische Analysen und Targetpanel-Tests sprechen für eine IspD- und Multikinase-Hemmung als wahrscheinlichen Wirkmechanismus. Die vorliegende Analyse zeigt einen einzigartigen Zugang zur Entschlüsselung polypharmakologischer Effekte neuer bioaktiver chemischer Substanzen auf.
Worst-case analysis of electronic circuits based on an analytic forward solver approach (2019)

Purpose The purpose of this paper is to evaluate the worst-case behavior of a given electronic circuit by varying the values of the components in a meaningful way in order not to exceed pre-defined currents or voltages limits during a transient operation. Design/methodology/approach An analytic formulation is used to identify the time-dependent solution of voltages or currents using proper state equations in closed form. Circuits with linear elements can be described by a system of differential equations, while circuits composing nonlinear elements are described by piecewise-linear models. A sequential quadratic program (SQP) is used to find the worst-case scenario. Findings It is found that the worst-case scenario can be obtained with as few solutions to the forward problem as possible by applying an SQP method. Originality/value The SQP method in combination with the analytic forward solver approach shows that the worst-case limit converges in a few steps even if the worst-case limit is not on the boundary of the parameters.
The Somatic Genomic Landscape of Glioblastoma (2020)

We describe the landscape of somatic genomic alterations based on multi-dimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.
The Bus Crusher and The Armageddon Device Part I (2004)

&lt;div class="htmlview paragraph"&gt;Most testing is done in a clean or static environment. The electrical power is connected to a constant voltage power supply. This is not very representative of the automotive environment. Electrically the automobile is very noisy, has dynamic behavior, and can be difficult to model and emulate.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Microprocessors can make mistakes at a rate of 1 million mistakes per second. If we can't test the software 100%, we need methods that will give us some level of confidence that the product is of high quality and will satisfy the customer. The test methods detailed in this paper can help gauge the robustness of the software.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;These extraordinary tests are not part of standard test methods. Standard test methods use traceability of the functional requirements to develop the test. Each function is tested once per test cycle. Most of these tests are “Happy Path”. [&lt;span class="xref"&gt;3&lt;/span&gt;] Occasionally, failure modes and the effects are included in the test plan.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Most of the tests defined in this document are either based on lessons learned or are trying to find ways to expose non-robust software designs. These tests may also exacerbate software and hardware signal race conditions.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The background of the author is in the realm of body module controller behavior; therefore examples detailed in this document are related to body module controllers. There is no reason the methods can't be applied to other ECUs (Electronic Control Unit) on the vehicle.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper discusses the evolution and development of a method and process to stress automotive embedded software. The intended process will look for abnormal or undesired operation in the ECU.&lt;/div&gt;
Reversible Electrochemical Phase Change in Monolayer to Bulk-like MoTe2 by Ionic Liquid Gating (2020)

Transition-metal dichalcogenides (TMDs) exist in various crystal structures with semiconducting, semi-metallic, and metallic properties. The dynamic control of these phases is of immediate interest for next-generation electronics such as phase change memories. Of the binary Mo and W-based TMDs, MoTe<sub>2</sub> is attractive for electronic applications because it has the lowest energy difference (40 meV) between the semiconducting (2H) and semi-metallic (1T') phases, allowing for MoTe<sub>2</sub> phase change by electrostatic doping. Here, we report phase change between the 2H and 1T' polymorphs of MoTe<sub>2</sub> in thicknesses ranging from the monolayer to bulk-like case (73 nm) using an ionic liquid electrolyte at room temperature and in air. We find consistent evidence of a partially reversible 2H-1T' transition using <i>in situ</i> Raman spectroscopy where the phase change occurs in the topmost layers of the MoTe<sub>2</sub> flake. We find a thickness-dependent transition voltage where higher voltages are necessary to drive the phase change for thicker flakes. We also show evidence of electrochemical activity during the gating process by observation of Te metal formation. This finding suggests the formation of Te vacancies which have been reported to lower the energy difference between the 2H and 1T' phases, potentially aiding the phase change process. Our discovery that the phase change can be achieved on the surface layer of bulk-like materials reveals that this electrochemical mechanism does not require isolation of a single layer and the effect may be more broadly applicable than previously thought.
Introduction: The Future of Carbon Materials – The Industrial Perspective (2021)

Carbon and graphite materials had gained tremendous industrial importance at the beginning of the twentieth century. The Hall–Héroult process for the production of aluminum and the EAF process for the recycling of steel scrap consume more than 20 million t of carbon materials today with a market value of about 24 billion €. Fine-grained graphite is indispensable for the production of solar cells and manifolds other applications. The growing need for efficient use of energy opens an enormous potential for CFRP in lightweight constructions for automotives, industrial applications, and construction. Natural graphite, synthetic graphite, and carbon materials are key components in Li-ion and redox flow batteries and EDLCs, i.e. energy storage. Nanoforms of carbon are used in polymers and spectacular applications in microelectronics seem realistic. The close networking between academia and industry is the precondition for the future success of carbon materials. The scientific carbon community did provide great contributions in the last decades to the understanding of various novel form of carbon. The carbon industry however recognizes the disappearance in competence for the traditional carbon materials. Needless to say, the profit created in these still growing traditional material markets provides the financial backbone for the development of new carbon materials.
ChemInform Abstract: A New Method for Preparation of 3,6‐Dihydro‐2H‐1,3‐oxazines and Explorations of Their Use in Stereoselective Synthesis of 1,3‐Amino Alcohol Derivatives. (1996)

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.