gebhart/patrepeval huggingface dataset:
Abstract 3609: Homology structure-based design, synthesis and biological evaluation of a series of novel Axl and Mer kinase inhibitors (2011)

Abstract Axl and Mer kinases belong to the TAM family that was first identified as a transforming gene in chronic myeloid leukemia. Its intracellular region has the typical receptor tyrosine kinase (RTK) structure and its extracellular domain is similar to cadherin-type adhesion molecules in that it is composed of fibronectin type II and immunoglobulin (Ig) motifs. Axl binds various growth factors, with vitamin K-dependent protein growth-arrest-specific gene 6 (GAS6) being the best studied. Axl is involved in mesenchymal and neuronal development as well as in cell survival, adhesion and blood vessel function. High levels of Axl are found in various tumors, including malignant glioma and metastatic colon, ovarian and breast cancers, and it plays a role in cancer invasion. Recent development of Axl inhibitors suggested that inhibition of Axl activity may be impact both tumor angiogenesis and tumor growth. We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, inhibitors of Axl and Mer kinases. Our initial lead compound was identified via cross-docking experiments utilizing the homology model of Axl kinase and screening of a diverse in-house chemical library. We subsequently carried out structure-activity relationship studies and optimized the lead structure which has 2 to 6.1 μM inhibition activity to 2-fold improvement in the Axl and Mer kinase activities to 730 nM. As a starting point for further optimization, it was considered that the modest of these series could be improved by introducing a spacer at the aryl piperazine moiety and focused on maximizing the in vitro potency, addressing the SAR and molecular properties. We further explored Leu620, hydrophobic, Gly543, Phe547 and DFG motif sites through scaffold hoping lead to the identification of an electron-withdrawing functional groups lead to the compound HCI-2084 and HCI-2091 which exhibited potent Axl kinase inhibition activity of 7 and 12 nM in Axl kinase assay and 30-50 nM is panel of cancer cell lines. These novel series of compounds were synthesized in two-step procedure via a standard cross-coupling reaction or with various substituted aryl amine derivatives under amination conditions. In a subsequent step we employed Buchwald-Hartwig amination reaction to prepare target molecules. Due to the ready synthesis accessibility, we extensively investigated the SAR improving the RO5, solubility and permeability parameters. The details of these results will be presented. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3609. doi:10.1158/1538-7445.AM2011-3609
ChemInform Abstract: New Modified Nucleoside 5′‐Triphosphates: Synthesis, Properties Towards DNA Polymerases, Stability in Blood Serum and Antiviral Activity. (1999)

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.
Distribution of Amphotericin B-Arabinogalactan Conjugate in Mouse Tissue and Its Therapeutic Efficacy against Murine Aspergillosis (2004)

The pharmacokinetic characteristics and tissue distribution of a novel water-soluble, nontoxic amphotericin B-arabinogalactan (AMB-AG) conjugate exhibited distinct differences from those of micellar and liposomal amphotericin B formulations. These differences included extended persistence of drug in the body and its accumulation in the lungs; thus, the AMB-AG conjugate was highly effective in treating systemic murine aspergillosis.
(Invited) Current Status of High-k and Metal Gates in CMOS (2013)

Continued scaling of microelectronic devices has driven the change from SiO2 to alternative, Hf-based, high-k gate dielectric materials in recent years. This materials change has enabled device performance scaling without the gate leakage current becoming unacceptably high. The change from doped poly-Si to metal(s) as the gate electrode material also occurred simultaneously with the introduction of high-k materials, as the resulting high-k / metal gate (HKMG) device can effectively overcome depletion effects in poly-Si gate devices. Processing of the metal gate stack is a challenging task in terms of meeting requirements in effective work function for both nMOS and pMOS, as well as enabling low resistivity gate/contact metal fill. The introduction of 3D device structures such as FinFETs serves as an inflection point for novel materials and the transition from PVD to ALD processes.
Map kinase MGV1: a potential shared control point of butenolide and deoxynivalenol biosynthesis In Fusarium graminearum (2011)

The mitogen-activated protein kinase (MAPK) MGV1 has been knocked out in Fusarium graminearum to produce the mutant FgMGV1. The mutant displays complementary phenotypes concerning deoxynivalenol (DON) and butenolide (BT) biosynthesis in vitro. In the rich medium 15-ADON accumulates are at low levels as detected by HPLC, whereas the accumulation of BT is substantial in FgMGV1. This is supported by the high expression of butenolide cluster genes in the mutant compared to the wild-type strain. Under nutrient-limiting conditions, where DON biosynthesis is normally favoured, the expression of genes of the trichothecene cluster does not differ between the two strains. However, the accumulation of 15-ADON is vastly different in FgMGV1. There is a reduction of 15-ADON accumulation with a concomitant accumulation of a novel compound. Although gene clusters comprising the synthesis of DON and BT have been identified, their regulation at the molecular level has not been fully elucidated. Since the expression levels of two regulatory genes from the trichothecene gene cluster and three regulatory genes from the butenolide gene cluster remained unchanged between WT and FgMGV1, we suggest that differential accumulation of both BT and DON biosynthesis is at least partially under post-transcriptional and/or post-translational control.
MAP1A Light Chain-2 Interacts with GTP-RhoB to Control Epidermal Growth Factor (EGF)-dependent EGF Receptor Signaling (2007)

Rho GTPases have been implicated in the control of several cellular functions, including regulation of the actin cytoskeleton, cell proliferation, and oncogenesis. Unlike RhoA and RhoC, RhoB localizes in part to endosomes and controls endocytic trafficking. Using a yeast two-hybrid screen and a glutathione S-transferase pulldown assay, we identified LC2, the light chain of the microtubule-associated protein MAP1A, as a novel binding partner for RhoB. GTP binding and the 18-amino acid C-terminal hypervariable domain of RhoB are critical for its binding to MAP1A/LC2. Coimmunoprecipitation and immunofluorescence experiments showed that this interaction occurs in U87 cells. Down-regulation of MAP1A/LC2 expression decreased epidermal growth factor (EGF) receptor expression and modified the signaling response to EGF treatment. We concluded that MAP1A/LC2 is critical for RhoB function in EGF-induced EGF receptor regulation. Because MAP1A/LC2 is thought to function as an adaptor between microtubules and other molecules, we postulate that the RhoB and MAP1A/LC2 interactions facilitate endocytic vesicle trafficking and regulate the trafficking of signaling molecules.
ChemInform Abstract: REACTIONS OF ALKOXYPYRYLIUM SALTS WITH DIMETHYLSULFONIUM METHYLIDE AND NITROMETHANE ANION (1983)

Abstract Bei der Umsetzung der Pyry1ium‐Salze (I), (VI), (XII) bzw. (XIV) mit Dimethylsulfoniummethylid (II) bzw. dem Nitromethan‐Anion (IX) entstehen die im Formelschema zusammengestellten Derivate.
Efficient excitation of cavity resonances of subwavelength metallic gratings (2005)

One-dimensional rectangular metallic gratings enable enhanced transmission of light for specific resonance frequencies. Two kinds of modes participating in enhanced transmission have already been demonstrated: waveguide modes and surface plasmon polaritons. Since the original article by Hessel and Oliner [Appl. Opt. 4, 1275 (1965)] pointing out the existence of waveguide modes, little progress was made in their understanding. We present here a careful analysis, and show that the coupling between the light and such resonances can be tremendously improved using an evanescent wave. This leads to enhanced localization of light in cavities, yielding, in particular, a very selective light transmission through these gratings.
Dermal nerve fibre and mast cell density, and proximity of mast cells to nerve fibres in the skin of patients with complex regional pain syndrome (2018)

An interaction between cutaneous nerves and mast cells may contribute to pain in complex regional pain syndrome (CRPS). To explore this, we investigated the density of dermal nerve fibres, and the density and proximity of mast cells to nerve fibres, in skin biopsies obtained from the affected and unaffected limbs of 57 patients with CRPS and 28 site-matched healthy controls. The percentage of the dermis stained by the pan-neuronal marker protein gene-product 9.5 was lower in the affected limb of patients than in controls (0.12 ± 0.01% vs 0.22 ± 0.04%, P < 0.05), indicating a reduction in dermal nerve fibre density. This parameter did not correlate with CRPS duration. However, it was lower in the affected than unaffected limb of patients with warm CRPS. Dermal mast cell numbers were similar in patients and controls, but the percentage of mast cells less than 5 µm from nerve fibres was significantly lower in the affected and unaffected limbs of patients than in controls (16.8 ± 1.7%, 16.5 ± 1.7%, and 31.4 ± 2.3% respectively, P < 0.05). We confirm previous findings of a mild neuropathy in CRPS. Our findings suggest that this either develops very early after injury or precedes CRPS onset. Loss of dermal nerve fibres in CRPS might result in loss of chemotactic signals, thus halting mast cell migration toward surviving nerve fibres. Failure of normal nerve fibre-mast cell interactions could contribute to the pathophysiology of CRPS.
Dual System Encryption via Doubly Selective Security: Framework, Fully-secure Functional Encryption for Regular Languages, and More. (2014)

Dual system encryption techniques introduced by Waters in Crypto’09 are powerful approaches for constructing fully secure functional encryption (FE) for many predicates. However, there are still some FE for certain predicates to which dual system encryption techniques seem inapplicable, and hence their fully-secure realization remains an important problem. A notable example is FE for regular languages, introduced by Waters in Crypto’12. We propose a generic framework that abstracts the concept of dual system encryption techniques. We introduce a new primitive called pair encoding scheme for predicates and show that it implies fully secure functional encryption (for the same predicates) via a generic construction. Using the framework, we obtain the first fully secure schemes for functional encryption primitives of which only selectively secure schemes were known so far. Our three main instantiations include FE for regular languages, unbounded attribute-based encryption (ABE) for large universes, and ABE with constant-size ciphertexts. Our main ingredient for overcoming the barrier of inapplicability for the dual system techniques to certain predicates is a computational security notion of the pair encoding scheme which we call doubly selective security. This is in contrast with most of the previous dual system based schemes, where information-theoretic security are implicitly utilized. The doubly selective security notion resembles that of selective security and its complementary notion, co-selective security, and hence its name. Our framework can be regarded as a method for boosting doubly selectively security (of encoding) to full security (of functional encryption). Besides generality of our framework, we remark that improved security is also obtained, as our security proof enjoys tighter reduction than previous schemes, notably the reduction cost does not depend on the number of all queries, but only that of pre-challenged queries.
Longitudinal 23Na MRI in mild traumatic brain injury (2023)

In this longitudinal sodium MRI study, mild traumatic brain injury (mTBI) patients and controls were scanned at 3T. Linear regression analysis was used to calculate total sodium concentrations (TSC) in global grey and white matter (GM, WM). Patient GM TSC increased back to control levels at 3-month and 1-year follow-ups. Decreased GM and WM TSC measured at one month were associated with worse cognitive performance, but not worse symptomalogy, at the follow-up visits.
Attosecond streaking metrology with isolated nanotargets (2017)

The development of attosecond metrology has enabled time-resolved studies on atoms, molecules, and (nanostructured) solids. Despite a wealth of theoretical work, attosecond experiments on isolated nanotargets, such as nanoparticles, clusters, and droplets have been lacking. Only recently, attosecond streaking metrology could be extended to isolated silica nanospheres, enabling real-time measurements of the inelastic scattering time in dielectric materials. Here, we revisit these experiments and describe the single-shot analysis of velocitymap images, which permits to evaluate the recorded number of electrons. Modeling of the recorded electron histograms allows deriving the irradiated nanoparticle statistics. Theoretically, we analyze the influence of the nanoparticle size on the field-induced delay, which is one of the terms contributing to the measured streaking delay. The obtained new insight into attosecond streaking experiments on nanoparticles is expected to guide wider implementation of the approach on other types of nanoparticles, clusters, and droplets.
Preliminary evaluation of robotic needle distal tip repositioning (2011)

Advances in medical imaging now provide detailed images of solid tumors inside the body and miniaturized energy delivery systems enable tumor destruction through local heating powered by a thin electrode. We have developed a robot for accurately repositioning the distal tip of a medical instrument such an ablation probe to adjacent points within tissue. The position accuracy in ballistics gelatin was evaluated in a 2D experimental setup with a digital SLR camera that was fixed to a rig that also contained the gelatin. The robot was mounted to the rig in such a way that the stylet was deployed in a plane parallel the camera's lens. A grid paper attached to the back of the box containing the gelatin provided a stationary reference point for each of the pictures taken and also served as a coordinate system for making measurements. The measurement repeatability error was found by taking a stylet tip position measurement five times for two different pictures and found to be 0.26 mm. For a stylet with a radius of curvature of 31.5 mm and a diameter of 0.838 mm, the targeting accuracy was found to be 2.5 ± 1.4 mm at points that were approximately 38 mm lateral from the cannula axis.
Unlocking the Structural Mystery of Vaterite CaCO3 (2023)

Calcium carbonate (CaCO3), the most abundant biogenic mineral on earth, plays a crucial role in various fields. Of the four polymorphs, calcite, aragonite, vaterite, and amorphous CaCO3, vaterite is the most enigmatic one due to an ongoing debate regarding its structure that has persisted for nearly a century. In this work, based on systematic transmission electron microscopy characterizations, elaborate crystallographic analysis and machine learning aided molecular dynamics simulations with ab initio accuracy, we reveal that vaterite can be regarded as a polytypic structure. The basic phase is a monoclinic lattice possessing pseudohexagonal symmetry. Direct imaging and atomic-scale simulations provide evidence that a single grain of vaterite can have three orientation variants. Additionally, we find that vaterite undergoes a second-order phase transition. These atomic scale insights provide a comprehensive understanding of the structure of vaterite and offer new perspectives on the biomineralization process of calcium carbonate.
Organic Sulfur Products and Peroxy Radical Isomerization in the OH Oxidation of Dimethyl Sulfide (2021)

The atmospheric oxidation of dimethyl sulfide (DMS) represents a large natural source of sulfate particles and thus is a major contributor to the global radiative effect of aerosols; however, its underlying chemical mechanism remains poorly constrained. In particular, DMS oxidation generates a variety of intermediate organic sulfur species, whose fate and kinetics govern the ultimate amount and distribution of sulfate aerosol. There is thus a need to understand the production and chemistry of such intermediates, including the recently discovered hydroperoxymethyl thioformate, formed from the isomerization of the methylthiomethylperoxy radical (CH3SCH2OO). Here, chamber experiments were performed to measure product formation from the OH-initiated oxidation of DMS. Three real-time mass spectrometers were used to measure the formation and evolution of a broad suite of gas- and aerosol-phase sulfur-containing compounds, including nearly all the closed-shell organic sulfur species included in current mechanisms; some additional species not predicted by such mechanisms are detected as well. The rapid decay of many of the more oxidized organic sulfur species suggests that aerosol uptake and loss to surfaces can be important processes under the conditions of this study. In addition, the isomerization rate constant of the CH3SCH2OO radical was experimentally determined to be 0.09 s–1 (0.03–0.3 s–1, 1σg), in broad agreement with results from other studies.
SiC-Based MOSFETs for Harsh Environment Emissions Sensors (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Point-of-care test for early-stage Lyme disease using a multiplexed paper-based assay and machine learning (2020)

We report a multiplexed paper-based assay powered by mobile imaging and machine learning for point-of-care diagnosis of Lyme Disease. Blind testing of 96 serum samples showed a sensitivity and specificity of 85.7% and 96.3%, respectively.
CCDC 1841122: Experimental Crystal Structure Determination (2018)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Collective network for computer structures (2023)

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network and class structures. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to needs of a processing algorithm.
ANÁLISE DA FREQUÊNCIA DA MUTAÇÃO C282Y NA POPULAÇÃO PARANAENSE (2004)

A hemocromatose (HH) é uma doença hereditária do metabolismo do ferro que resulta na absorção excessiva de ferro e seu acúmulo progressivo no fígado, pâncreas, coração e outros órgãos. É uma doença autossômica recessiva que se expressa mais freqüentemente e com sintomas mais severos nos homens que nas mulheres, numa relação estimada de 10:1. A mutação C282Y é descrita como a troca das bases nitrogenadas C por A no nucleotídeo 845 resultando na substituição do aminoácido cisteína por tirosina na posição 282. Apresenta-se como a mutação mais comum para hemocromatose, porém, com diferentes freqüências genotípicas entre as populações. Os estudos de prevalência da HH no Brasil são ainda muito escassos, porém, em 4% a 7% da população geral é possível encontrar um alelo mutante. A análise da freqüência da mutação C282Y na população paranaense é necessária visto que se trata da mais freqüente mutação para a HH em caucasóides. A finalidade deste estudo é determinar a freqüência da mutação C282Y do gene da HH na população paranaense, comparando os resultados obtidos nesta pesquisa com dados já descritos. Para tanto, as amostras foram submetidas a PCR seguido de eletroforese para confirmação da amplificação. Em seguida, foram feitas as análises através da técnica de RFLP (para caracterização dos controles) ou SSCP (para a análise das amostras). A análise da freqüência da mutação C282Y indicou num total de 289 amostras, a ocorrência de 279 indivíduos homozigotos normais (96,5%), 1 indivíduo homozigoto mutado para a mutação C282Y (0,3%) e 9 indivíduos heterozigotos (3,2%).
ChemInform Abstract: Preparation of 2‐, 4‐, 5‐, and 6‐Aminonicotinic Acid tert‐Butyl Esters. (2012)

Abstract An improved three‐step procedure is developed to prepare the title esters, e.g. (V), performing the esterification before hydrazine formation, and without the need for purification of the intermediates.
Retinal Prostheses for the Blind (2006)

While the development of various retinal prostheses have shown promise in limited clinical trials, there are distinct advantages and disadvantages for each type of prosthesis. This review will focus primarily on the Epiretinal Intraocular Retinal Prosthesis, studied by our group, but will also briefly review other modalities: the subretinal prosthesis, cortical prosthesis, and optic nerve prosthesis.
Modeling Multi-Frequency Characteristics for Classroom and Hall Scenarios at 2-4, 9-11 and 27-29 GHz Bands (2021)

This paper investigates the wideband channel characteristics obtained in a classroom and a hall indoor scenarios at 2-4, 9-11 and 27-29GHz. A virtual uniform circular array (UCA) based channel sounding system was utilized to capture wideband spatial channel characteristics. The propagation parameters of multipath components (MPCs) were estimated by using a high resolution parameter estimation (HRPE) algorithm. The estimated MPCs are further grouped into clusters via a novel clustering identification algorithm based on the KPowerMeans algorithm. The comparison of the composite and cluster-level characteristics at multiple frequency bands in both scenarios is investigated. Moreover, the impact of the indoor room environment, i.e. dimension and furniture, on the propagation channel is also analyzed. The statistics of channel parameters at multiple frequency bands extracted constitute a stochastic clustered spatial channel model.
Supplementary Figure 1 from Selectin Ligand Sialyl-Lewis x Antigen Drives Metastasis of Hormone-Dependent Breast Cancers (2023)

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