gebhart/patrepeval huggingface dataset:
A DFT Study of the Conversion of CO2in Dimethylcarbonate Catalyzed by Sn(IV) Alkoxides (2014)

Density functional theory (DFT) calculations of intermediates and transition states of the reaction between CO2 and methanol over different R2Sn(OCH3)2 catalysts (R = alkyl, phenyl and halogens) were carried out. The interaction of the CO2 molecule with the tin catalyst was controlled by the entropic term, being disfavored at room temperature and atmospheric pressure. On the other hand, the insertion of the CO2 molecule into the Sn–OCH3 bond is thermodynamic favorable for all the catalysts studied. The computed free-energy of activation varied with the nature of the substituent R. Phenyl groups exhibit the smallest barrier, whereas halogen atoms the highest. Alkyl groups present intermediate barriers. The results are in agreement with recent experimental results that indicated a higher turnover number (TON) for dimethylcarbonate (DMC) formation when Ph2SnO was used as catalyst. The whole mechanistic scheme was then computed for phenyl and methyl as substituents, considering a dimer tin species.
Event sequence detector (1973)

An event sequence detector is described with input units, each associated with a row of bistable elements arranged in an array of rows and columns. The detector also includes a shift register which is responsive to clock pulses from any of the units to sequentially provide signals on its output lines each of which is connected to the bistable elements in a corresponding column. When the event-indicating signal is received by an input unit it provides a clock pulse to the shift register to provide the signal on one of its output lines. The input unit also enables all its bistable elements so that the particular element in the column supplied with the signal from the register is driven to an event-indicating state.
The current role of mass spectrometry in forensics and future prospects (2020)

Mass spectrometry (MS) techniques are highly prevalent in crime laboratories, particularly those coupled to chromatographic separations like gas chromatography (GC) and liquid chromatography (LC). These methods are considered "gold standard" analytical techniques for forensic analysis and have been extensively validated for producing prosecutorial evidentiary data. However, factors such as growing evidence backlogs and problematic evidence types (e.g., novel psychoactive substance (NPS) classes) have exposed limitations of these stalwart techniques. This critical review serves to delineate the current role of MS methods across the broad sub-disciplines of forensic science, providing insight on how governmental steering committees guide their implementation. Novel, developing techniques that seek to broaden applicability and enhance performance will also be highlighted, from unique modifications to traditional hyphenated MS methods to the newer "ambient" MS techniques that show promise for forensic analysis, but need further validation before incorporation into routine forensic workflows. This review also expounds on how recent improvements to MS instrumental design, scan modes, and data processing could cause a paradigm shift in how the future forensic practitioner collects and processes target evidence.
Chromatin Remodeling and Modification during HIV-1 Tat-activated Transcription (2003)

Human immunodeficiency virus type 1 (HIV-1) is the etiologic agent of AIDS. Following entry into the host cell, the viral RNA is reverse transcribed into DNA and subsequently integrated into the host genome as a chromatin template. Chromatin structure may be responsible for silencing retroviral gene expression. Transcriptional activation occurs after ATP-dependent chromatin remodeling complexes alter chromatin structure and positioning of nucleosomes. Histone acetyltransferases (HATs), histone deacetylases (HDACs), kinases, and methyltransferases (HMTs), covalently modify nucleosomes by adding or removing chemical moieties in the N-terminal tails of histones. Recent advances have indicated that HIV-1 encoded proteins interact with chromatin remodeling complexes and histone modifying enzymes, implying that chromatin remodeling plays an important role in the HIV-1 life cycle. Nucleosomes are positioned on the HIV-1 LTR and are barriers to transcription. Following cellular activation, these nucleosomes are modified and repositioned allowing for activation of viral gene expression. Tat recruits various HATs to the HIV-1 promoter region and can also be acetylated by some of these enzymes. Unmodified Tat is involved in binding to the CBP/p300 and cdk9/cyclin T complexes and facilitates transcription initiation. Acetylated Tat dissociates from the TAR RNA structure and recruits bromodomain-containing chromatin modifying complexes such as p/CAF and SWI/SNF to facilitate transcription elongation. This review summarizes our current knowledge and understanding of chromatin remodeling complexes and their regulation of HIV-1 replication, and highlights the important contributions HIV-1 research has made to further our understanding of the transcription process.
J-104 Geenius HIV 1/2 Supplemental Assay: A Rapid, Reliable and Simple System for the Confirmation and Differentiation of Antibodies to HIV (2018)

INTRODUCTION: In 2017 Bio-Rad Laboratories completed launching the FDA-approved Geenius HIV-1/HIV-2 Supplemental assay to replace Multispot HIV-1/HIV-2 in the current CDC HIV Diagnostic Algorithm. The Geenius cassette contains antibody-binding protein A, which is conjugated to colloidal gold dye particles; HIV-1 (p31, gp160, p24, gp41) and HIV-2 (gp36, gp140) antigens are bound to the membrane solid phase. Serum, plasma, or whole blood may be tested. Geenius uses an automated cassette reader and proprietary software to interpret HIV-1 and HIV-2 results. We report more recent performance data for this system, as well as an investigational protocol for testing dried blood spot (DBS) specimens. METHODS: (1) WHO evaluated the Geenius HIV-1/HIV-2 Supplemental testing system with a panel of 1117 specimens. (2) DBS specimens were tested on Geenius using an investigational procedure (40 μ L of DBS eluate and one drop of assay buffer). Samples included established infections (131 HIV-1, 31 HIV-2, one dual), 60 seroconversion specimens, and 106 DBS collected by CDC during HIV surveillance. RESULTS: (1) Geenius sensitivity in the WHO evaluation was 100% and specificity was 97.4%. Seroconversion samples were detected +0.875 days vs. the benchmark. All the mixed titer and reference specimens were correctly classified. (2) Geenius DBS correctly detected HIV-1 and HIV-2 DBS with minor exceptions. DBS seroconversions showed slightly reduced sensitivity vs. plasma. CONCLUSIONS: (1) The Geenius HIV-1/2 Confirmatory Assay was accepted for the WHO list of prequalified diagnostics (March 17, 2017). (2) Results of an investigational Geenius DBS procedure appear promising for settings without capacity for venipuncture.
Crossed orbit interferometry: theory and experimental results from SIR-B (1988)

Abstract In a conventional imaging radar interferometer, two receiving antennas separated slightly in the cross-track direction view the same scene and altimetry information is deduced from the phase differences between the corresponding pixels in each image. It is possible to perform the same measurements with only one antenna by making two images of the scene on two separate passes; for SIR-B this involved imaging on two separate orbits. If the two orbits are parallel and separated in the cross-track direction, altitude information is derived exactly as in the two-antenna interferometer and the baseline is determined by the orbit separation. For the available SIR-B data, however, the orbits were skewed, which substantially increases the difficulty of finding altitudes. Since the orbits were not exactly parallel, the antenna on one orbit was pointed slightly forward or backward compared to the other; this was compensated for in the azimuth processing. Furthermore, the skew gave the images a cross-track displacement that increased linearly with azimuth distance, which was removed by resampling and stretching one of the images. Because of the skewing, the baseline increased with distance from the crossing point and theory indicates that altitude variation appears as a change in the along-track position of a given pixel. This is borne out in the experimental data which is then used to construct a coarse altitude map. Additionally, the phase difference of each overlaid pixel is related to the altitude in a complicated way. An algorithm was developed to invert this relationship, the results of which were then used to construct a more refined altitude map.
RSVP Extensions for Policy Control (2000)

This memo presents a set of extensions for supporting generic policy based admission control in RSVP. It should be perceived as an extension to the RSVP functional specifications [RSVP] These extensions include the standard format of POLICY_DATA objects, and a description of RSVP's handling of policy events.
Effect of phenobarbital and other model inducers on cytochrome P450 isoenzymes in primary culture of dog hepatocytes (1993)

1. The effects of phenobarbital (PB), beta-naphthoflavone (beta-NF), omeprazole (Omep) and rifampicin (Rif) on drug-metabolizing activities in dog hepatocytes, cultured with William's medium E, were examined. 2. The drug metabolizing activities of the hepatocytes decreased during culture; 7-ethoxycoumarin O-deethylase (ECOD) activity was nearly 70% of initial value at 72 h, but 7-methoxycoumarin O-demethylase (MCOD), 7-propoxycoumarin O-depropylase (PCOD), progesterone 6 beta-hydroxylase (6 beta-OH-P), progesterone 16 alpha-hydroxylase (16 alpha-OH-P), progesterone 21-hydroxylase (21-OH-P), 7-ethoxyresorufin O-deethylase (EROD) activities and total cytochrome P450 content were approx. 50%. 3. When the hepatocytes were cultured with PB, the enzyme activities increased time- and dose-dependently. MCOD, ECOD and PCOD activities increased 5-8 fold with 2 mM PB in 96 h. Similar results were obtained for 6 beta-OH-P, 16 alpha-OH-P and 21-OH-P activities, and total cytochrome P450. The effect of PB was abolished when 2.5 microM cycloheximide or 0.1 microM actinomycin D was included in the culture. 4. Treatment of hepatocytes with 40 microM beta-NF for 72 h resulted in 25-fold elevation of EROD activity. beta-NF enhanced PCOD activity approx. six-fold, while ECOD increased only slightly, and 7-MCOD negligibly. 5. Omep (100 microM) increased EROD activity nearly 10-fold, and 25 microM Rif increased 6 beta-OH-P activity approx. 8-fold, but ECOD only slightly. 6. Western blot analysis of microsomes from cultured dog hepatocytes with anti-rat CYP 2B1 antibodies indicated that PB increased an immunochemically-reactive protein. The protein showed the same mobility as the major dog P450 isozyme (cytochrome P450 PBD-2 or CYP 2B11) purified from liver microsomes of PB-treated male beagle dog. In a similar manner, induction of cytochrome P450 PBD-1 (CYP 3A12) by PB was confirmed.
Volume-Sensitive Transport Systems and Volume Homeostasis in Vertebrate Red Blood Cells (1997)

Animal cells regulate their volume in the short term by controlling solute movements into and out of the cell. A quite of dissipative transport systems are involved which allow either regulatory volume increase (RVI) or decrease (RVD) responses depending upon the direction of the electrochemical gradients of the solutes. Many of these transporters have been identified at the molecular level and structure-function studies have identified transmembrane transport domains and cytoplasmic regulatory domains. In vertebrate red blood cells, protein phosphorylation appears to be central to the coordinated regulation of transporter activity. Inhibitors of protein phosphatases (PPs) cause inhibition of the K+/Cl- cotransporter (a transporter mediating RVD), whilst some inhibitors of protein kinases (PKs) cause activation. A sequence of potential phosphorylation sites appears to constitute a cascade of reactions leading to transporter regulation. PP and PK inhibitors have opposite effects on transporters mediating RVI responses, which is consistent with the coordinated but reciprocal regulation of transporters activated during both RVI and RVD using some common phosphorylation reactions. The transporters are sensitive to other stimuli including, in red blood cells, changes in PO2 and pH. These responses are also sensitive to PK/PP inhibitors and may involve elements of the volume-sensitive transduction pathway.
The / fold family of proteins database and the cholinesterase gene server ESTHER (1997)

ESTHER (for esterases, alpha/betahydrolase enzyme and relatives) is a database of sequences phylogenetically related to cholinesterases. These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) sharing a similar structure of a central beta-sheet surrounded by alpha-helices. Among these proteins a wide range of functions can be found (hydrolases, adhesion molecules, hormone precursors). The purpose of ESTHER is to help comparison of structures and functions of members of the family. Since the last release, new features have been added to the server. A BLAST comparison tool allows sequence homology searches within the database sequences. New sections are available: kinetics and inhibitors of cholinesterases, fasciculin-acetylcholinesterase interaction and a gene structure review. The mutation analysis compilation has been improved with three-dimensional images. A mailing list has been created.
Checking OCL Constraints in Distributed Systems Using J2EE/EJB (2001)

We present a pragmatic approach using formal methods to increase the quality of distributed component based systems: Based on UML class diagrams annotated with OCL constraints, code for runtime checking of components in J2EE/EJB is automatically generated. Thus, a UML–model for a component can be used in a black–box test for the component. Further we introduce different design patterns for EJBs, which are motivated by different levels of abstraction, and show that these patterns work smoothly together with our OCL constraint checking. A prototypic implementation of the code generator, supporting our design patterns with OCL support, has been integrated into a commercial software development tool.
Tumor-Associated Macrophages Mediate Immunosuppression in the Renal Cancer Microenvironment by Activating the 15-Lipoxygenase-2 Pathway (2011)

Renal cell carcinoma (RCC), the most common human kidney cancer, is frequently infiltrated with tumor-associated macrophages (TAM) that can promote malignant progression. Here, we show that TAMs isolated from human RCC produce substantial amounts of the proinflammatory chemokine CCL2 and immunosuppressive cytokine IL-10, in addition to enhanced eicosanoid production via an activated 15-lipoxygenase-2 (15-LOX2) pathway. TAMs isolated from RCC tumors had a high 15-LOX2 expression and secreted substantial amounts of 15(S)-hydroxyeicosatetraenoic acid, its major bioactive lipid product. Inhibition of lipoxygenase activity significantly reduced production of CCL2 and IL-10 by RCC TAMs. In addition, TAMs isolated from RCC were capable of inducing in T lymphocytes, the pivotal T regulatory cell transcription factor forkhead box P3 (FOXP3), and the inhibitory cytotoxic T-lymphocyte antigen 4 (CTLA-4) coreceptor. However, this TAM-mediated induction of FOXP3 and CTLA-4 in T cells was independent of lipoxygenase and could not be reversed by inhibiting lipoxygenase activity. Collectively, our results show that TAMs, often present in RCCs, display enhanced 15-LOX2 activity that contributes to RCC-related inflammation, immunosuppression, and malignant progression. Furthermore, we show that TAMs mediate the development of immune tolerance through both 15-LOX2-dependent and 15-LOX2-independent pathways. We propose that manipulating LOX-dependent arachidonic acid metabolism in the tumor microenvironment could offer new strategies to block cancer-related inflammation and immune escape in patients with RCC.
Deuteron NMR Study of Molecular Mobility in a Polymer Model Membrane (1985)

Abstract The molecular mobility of a polymer model membrane is studied by 2 H NMR. The lipid analogue consists of a quaternary ammonium ion, to which a methacryloylic moiety is attached via a spacer to the hydrophilic head group. A methylene group of the spacer, the methyl‐head group and methylene groups in the 1‐, 2‐, and 7‐position of the lipid chains are selectively deuterated. Temperature dependent 2 H NMR spectra are reported for both, the monomer and the polymer membrane below and above the main phase transition. The data are quantitatively analyzed in terms of a simple motional model, in which the complex molecular dynamics is approximated by a six‐site jump model describing rotations about the long axis of the molecule and conformational changes. The increasing mobility with increasing temperature is only in part due to an increase of the jump rate between different sites. It also reflects the increase in the number of conformations accessible. As a quantitative measure of the mobility at a given site, a mean jump frequency is extracted from the data. For the monomer Ω˜ and its temperature dependence in the liquid crystalline phase is almost independent of the site being studied. In the polymer, however, major differences are observed, Ω˜ for the head group and the 7‐position of the lipid chain differing by two orders of magnitude. The mobility of the spacer is even lower. This 2 H NMR study thus shows that although the polymerization largely hinders the head group mobility, the chain flexibility most important for membrane applications is retained.
Distribution of taste and general sensory nerve endings in fungiform papillae of the hamster (1985)

Sensory endings of chorda tympani and lingual (trigeminal) nerve fibers were identified by selective denervation and localized within specific regions of fungiform pipillae in the hamster. The chorda tympani was resected from the middle ear and the peripheral fibers were allowed to degenerate for 1, 3, or 8 days prior to perfusion-fixation and electron-microscopic examination of the anterior tongue. Taste buds were virtually devoid of intact nerves by 3 days following chorda tympani denervation. Remnants of the fibers were restricted to taste buds. Lingual fibers, on the other hand, persist in normal numbers after chorda tympani resection and populate perigemmal areas of connective tissue and extragemmal areas located apically in the squamous, nontaste epithelium surrounding the taste bud. This study provides evidence of a segregation of chorda tympani fibers in the taste bud and lingual nerve fibers in the apical fungiform papilla. The lingual nerve-epithelial arrangement and superficial location, near the least cornified area of the tongue, may be well suited for relatively sensitive somatosensation, possibly mechanoreception. Thus, the apical fungiform papilla appears to be a site where both taste and tactile oral stimuli interact with receptors.
Agonistic anti‐human Fas monoclonal antibody induces fibroblast‐like synoviocyte apoptosis in haemophilic arthropathy: potential therapeutic implications (2013)

Haemophilic arthropathy (HA) is characterized by chronic proliferative synovitis leading to cartilage destruction and shares some pathological features with rheumatoid arthritis (RA). Apoptosis has been implicated in RA pathogenesis, and an agonistic anti-Fas monoclonal antibody (mAb) was found to induce RA fibroblast-like synoviocyte (FLS) apoptosis and suppress synovial hyperplasia in animal models of RA. The aim of this study was to evaluate the effect of anti-Fas mAb on HA-FLS. FLS were isolated from knee synovial biopsies from six HA patients, six RA patients and six healthy subjects. The expression of Fas in synovial biopsies was investigated by immunohistochemistry. FLS were stimulated with anti-Fas mAb at different concentrations, alone or in combination with tumour necrosis factor-α (TNF-α) and basic fibroblast growth factor (bFGF). Fas expression in FLS was assessed by Western blot. Cell viability was studied with the WST-1 assay. Active caspase-3 levels were measured using ELISA and Western blot. A strong Fas-immunoreactivity was observed in different cells of HA synovium, including FLS, inflammatory cells and endothelial cells. Fas antigen was constitutively overexpressed in cultured HA-FLS. Anti-Fas mAb had a significant cytotoxicity on HA-FLS in a dose-dependent manner, either alone or in combination with TNF-α and bFGF. These cytotoxic effects were due to the ability of anti-Fas to induce HA-FLS apoptosis, as shown by the increased active caspase-3 levels. Anti-Fas mAb exhibited a more pronounced pro-apoptotic effect on HA-FLS than RA-FLS. Fas antigen is highly expressed on HA-FLS and its stimulation by anti-Fas mAb may be an effective strategy to induce HA-FLS apoptosis.
An image method to compute the static magnetic field due to currents injected into a homogeneous, conducting, and magnetically polarizable half‐space (1988)

An image method for computing the static magnetic field due to an arbitrary current injected into a conducting and polarizable half‐space is derived. The advantage of this approach is that the magnetic field is given in terms of a Biot‐Savart integral over only the impressed current sources and their finitely many images. Integration over the conducting currents, which are distributed in the entire conductive half‐space, is avoided. The magnetic field is evaluated in closed form when the conductors that feed current to the electrodes are laid out in a rectilinear path.
Surface-Enhanced Raman Spectroscopy at a Silver Electrode as a Real-Time Detector in Flowing Streams (1992)

An analytical application for Surface-Enhanced Raman Spectroscopy at a silver electrode is described. Real-time SER spectra of adenine and cytosine have been recorded in a 10-µL spectroelectrochemical flow cell under flowing conditions. Charge-coupled-device detection allowed high-quality spectra spanning a ∼1200 cm −1 region to be recorded with integration times of 4 seconds. A low-power He Ne laser was used as a source. SERS at the silver electrode offers rapid time response to adsorption/desorption by appropriate potential modulation. The technique is extremely reproducible and insensitive to temperature and flow rate. The effects of incident photon energy and applied potential on the intensity of the Raman signal are discussed.
Supplementary Figure 4C-E from YB-1 Bridges Neural Stem Cells and Brain Tumor–Initiating Cells via Its Roles in Differentiation and Cell Growth (2023)

Supplementary Figure 4C-E from YB-1 Bridges Neural Stem Cells and Brain Tumor–Initiating Cells via Its Roles in Differentiation and Cell Growth
ChemInform Abstract: Conformationally Mobile Wide Rim Carbamoylmethylphosphine Oxide (CMPO)‐Calixarenes. (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.
ChemInform Abstract: Morita—Baylis—Hillman and Rauhut—Currier Reactions of Conjugated Nitroalkenes (2013)

Abstract Review: 81 refs.