gebhart/patrepeval huggingface dataset:
ChemInform Abstract: SYNTHESIS AND ANTICONVULSANT ACTIVITY OF N‐(BENZOYLALKYL)IMIDAZOLES AND N‐(Ω‐PHENYL‐Ω‐HYDROXYALKYL)IMIDAZOLES (1981)

Abstract Die Halogenketone (I) reagieren mit Imidazol zu einem Gemisch der Verbindungen (III) und (IV), von denen letztere zu den Alkoholen (V) reduziert werden.
ChemInform Abstract: REACTION OF CARBON MONOXIDE WITH (η5‐PENTAMETHYLCYCLOPENTADIENYL)TETRAMETHYLTANTALUM. INTRAMOLECULAR REDUCTIVE COUPLING OF CARBON MONOXIDE VIA AN “η2‐ACETONE” INTERMEDIATE (1979)

Abstract Der Ta‐Komplex (I) reagiert mit CO zu einem "η 2 ‐Aceton"‐Komplex, der aufgrund seines IR‐Spektrums als Tantalaheterocyclus angesehen wird.
Bilateral granulomatous panuveitis in two patients with T-cell type of chronic active Epstein-Barr virus infection (2019)

Granulomatous panuveitis can develop in eyes with CAEBV as a primary symptom. Ophthalmologists should rule out CAEBV when EBV-DNA is positive in the intraocular fluids of steroid-resistant panuveitis.
Atypical Multiple Site Behavior of Hafnocene Catalysts in Ethylene/1-Hexene Copolymerization Using Trioctylaluminum and Borate (2018)

Solution copolymerizations of ethylene and 1-hexene were performed using the dichloride (HfCl2) and dimethyl (HfMe2) analogues of the bis(n-propylcyclopentadienyl)hafnium precatalyst. Tetrakis(pentafluorophenyl) borate dimethylanilinium salt ([B(C6F5)4]−[Me2NHPh]+) (B) or methylaluminoxane (MAO) was employed as activator, and tri-n-octylaluminum (TOA) was used as scavenger. Crystallization analysis fractionation (CRYSTAF) or crystallization elution fractionation (CEF) was used to measure the chemical composition distributions (CCD). Above a minimum 1-hexene threshold concentration, the CCD profiles of all copolymers were bimodal, and the areas under the peaks depended on the B/HfCl2 and B/Al ratios. Decreasing the TOA concentration reduced the weight fraction of the higher crystallinity copolymer. Copolymerizations using MAO also produced copolymers with bimodal CCDs. Copolymerizations using HfMe2/B without TOA produced copolymers with unimodal CCD. These results suggest that TOA reacts with either the catalyst or the activator, generating a new active site with a lower propensity for incorporating comonomer than the original catalyst system.
Priming of adult pain responses by neonatal pain experience: maintenance by central neuroimmune activity (2011)

Adult brain connectivity is shaped by the balance of sensory inputs in early life. In the case of pain pathways, it is less clear whether nociceptive inputs in infancy can have a lasting influence upon central pain processing and adult pain sensitivity. Here, we show that adult pain responses in the rat are 'primed' by tissue injury in the neonatal period. Rats that experience hind-paw incision injury at 3 days of age, display an increased magnitude and duration of hyperalgesia following incision in adulthood when compared with those with no early life pain experience. This priming of spinal reflex sensitivity was measured by both reductions in behavioural withdrawal thresholds and increased flexor muscle electromyographic responses to graded suprathreshold hind-paw stimuli in the 4 weeks following adult incision. Prior neonatal injury also 'primed' the spinal microglial response to adult injury, resulting in an increased intensity, spatial distribution and duration of ionized calcium-binding adaptor molecule-1-positive microglial reactivity in the dorsal horn. Intrathecal minocycline at the time of adult injury selectively prevented both the hyperalgesia and early microglial reactivity associated with prior neonatal injury. The enhanced neuroimmune response seen in neonatally primed animals could also be demonstrated in the absence of peripheral tissue injury by direct electrical stimulation of tibial nerve fibres, confirming that centrally mediated mechanisms contribute to these long-term effects. These data suggest that early life injury may predispose individuals to enhanced sensitivity to painful events.
Antimicrobial photodynamic inactivation is potentiated by the addition of selenocyanate: Possible involvement of selenocyanogen? (2018)

We previously showed that antimicrobial photodynamic inactivation (aPDI) of Gram-positive and Gram-negative bacteria mediated by the phenothiazinium dye, methylene blue (MB), was potentiated by the addition of potassium thiocyanate (10 mM). The mechanism was suggested to involve a singlet oxygen-mediated reaction with SCN to form sulfite and cyanide and then to produce sulfur trioxide radical anion. We now report that potassium selenocyanate (concentrations up to 100 mM) can also potentiate (up to 6 logs of killing) aPDI mediated by a number of different photosensitizers (PS): MB, rose bengal and 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin dihydrochloride (as low as 200 nM). When a mixture of selenocyanate with these PS in solution was illuminated and then bacteria were added after the light, there was up to 6 logs of killing (Gram-negative > Gram-positive) but the antibacterial species decayed rapidly (by 20 minutes). Our hypothesis to explain this antibacterial activity is the formation of selenocyanogen (SeCN)<sub>2</sub> by reaction with singlet oxygen (<sup>1</sup> O<sub>2</sub> ) as shown by quenching of <sup>1</sup> O<sub>2</sub> by SeCN and increased photoconsumption of oxygen. The fact that lead tetraacetate reacted with SeCN (literature preparation of (SeCN)<sub>2</sub> ) also produced a short-lived antibacterial species supports this hypothesis.
A Psychoacoustic "NofM"-Type Speech Coding Strategy for Cochlear Implants (2005)

We describe a new signal processing technique for cochlear implants using a psychoacoustic-masking model. The technique is based on the principle of a so-called "NofM" strategy. These strategies stimulate fewer channels ( ) per cycle than active electrodes (NofM; ). In "NofM" strategies such as ACE or SPEAK, only the channels with higher amplitudes are stimulated. The new strategy is based on the ACE strategy but uses a psychoacoustic-masking model in order to determine the essential components of any given audio signal. This new strategy was tested on device users in an acute study, with either 4 or 8 channels stimulated per cycle. For the first condition (4 channels), the mean improvement over the ACE strategy was . For the second condition (8 channels), no significant difference was found between the two strategies.
Binding determinants of the sialic acid-specific lectin from the slug Limax flavus. (1993)

The specific structural features of 24 N-acetylneuraminic acid derivatives required for the high affinity interaction of sialoglycoconjugates with the sialic acid-specific lectin from the slug Limax flavus were studied by hapten inhibition of precipitation. These results provide insight regarding the structure of the binding pocket for N-acetylneuraminic acid that exists in L. flavus agglutinin (LFA). The alpha-anomer of sialic acid is a very important factor in binding to the slug lectin. The carboxylic acid group makes only a moderate contribution to binding, since modifications of the carboxylic group decrease binding approximately 5-fold. Modification or removal of the hydroxyl group on carbon 4 does not affect binding. However, when the C4 epimer was tested, there was a dramatic decrease in binding, suggesting that whereas the equatorial hydroxyl at C4 does not contribute to binding, the introduction of an axial hydroxyl group at C4 sterically hinders the binding interaction. The substituent on the 5-amino group occupies an important role in binding of Neu5Ac to LFA as well. When the acetyl is modified by the addition of a hydroxyl group to yield the N-glycolyl derivative, we observed a 20-fold decrease, while the removal of the methyl to form the N-formyl derivative resulted in a 50-fold decrease. The 5-amino derivative was the poorest inhibitor of all compounds examined, indicating a critical role for the N-acetyl group in high affinity binding to LFA. The glyceryl tail also appears to be critical for binding inasmuch as acetylation of the C9 hydroxyl group or periodate cleavage of carbons 8 and 9 resulted in a 20- to 50-fold decrease in binding. The equilibrium constant (K(a)) for binding of Neu5Ac to LFA is 3.8 x 10(4) M-1, with a single binding site (n = 0.85) per monomer.
Three-dimensional model for acoustic field created by a piezoelectric plate in a resonator (2017)

A three-dimensional model is developed to describe an acoustic field excited by a piezoelectric plate of finite size in a fluid filled resonator. First, the eigenfunctions (modes) of a bare plate are derived using the general piezoelectric equations considering the elastic and electric properties of the plate. Then, the piezoelectric plate is placed into a fluid media such that only one plate side is in the fluid and an acoustic field generated by the plate in the fluid is estimated. Finally, a reflector is placed to be parallel to the piezoelectric plate and acoustic field in a resonator is evaluated. The solution for a piezoelectric plate of finite size is obtained using Singular Value Decomposition (SVD) method. Equations for acoustic and electric variables are presented. Numerical results are presented to show the three-dimensional modal displacement and electrical characteristics of the plate at various frequencies and aspect ratio. Finally, the analytical results are compared with finite element results using COMSOL Multiphysics commercial software.
Experimental Analysis of Guess-and-Determine Attacks on Clock-Controlled Stream Ciphers (2005)

Guess-and-Determine (GD) attacks have recently been proposed for the effective analysis of word-oriented stream ciphers. This paper discusses GD attacks on clock-controlled stream ciphers, which use irregular clocking for a non-linear function. The main focus is the analysis of irregular clocking for GD attacks. We propose GD attacks on a typical clock-controlled stream cipher AA5, and calculate the process complexity of our proposed GD attacks. In the attacks, we assume that the clocking of linear feedback shift registers (LFSRs) is truly random. An important consideration affecting the practicality of these attacks is the question of whether these assumptions are realistic. Because in practice, the clocking is determined by the internal states. We implement miniature ciphers to evaluate the proposed attacks, and show that they are applicable. We also apply the GD attacks to other clock controlled stream ciphers and compare them. Finally, we discuss some properties of GD attacks on clock-controlled stream ciphers and the effectiveness of the clock controllers. Our research results contain information that are useful in the design of clock-controlled stream ciphers.
Probing reflectivity profiles with a random sensing matrix (Conference Presentation) (2019)

In contrast to conventional imaging systems that map an object point by point, measurements with random sensing functions in combination with computational reconstruction may afford novel imaging architectures. Here we demonstrate imaging of axial reflectivity profiles using random temporal-spatial encoding created by modal interference in a multimode fiber (MMF). Light from a broadband source (∆λ = 60nm) centered at 1310nm is split into a sample and a reference arm. In the sample arm, light in a single spatial mode is reflected by the axial reflectivity profile of the sample and coupled back into the same spatial mode. The reference light propagates through a MMF and interferes with the sample light in an off-axis geometry on a camera for holographic recording. Since the MMF supports various guided modes with distinct propagation constants, the short-coherence sample light only interferes with the spatial modes of the reference light that have matching path length. During an initial calibration procedure, interference patterns of a mirror reflection in the sample arm are recorded for varying axial mirror positions. Once this random sensing matrix (RSM) is established, the axial reflectivity profile of an object in the sample arm can be reconstructed from a single interference pattern by the multiplication with the inverse of RSM. By using a 2m long 0.22 NA MMF and tailoring the coupling regime within the MMF, we achieved axial ranging more than a centimeter. Flexible integration of polarization sensing or multi-focus imaging in a single snapshot could be envisioned in this random imaging architecture.
Synthetic Studies on Echinulin and Related Natural Products. V. : Isolation, Structure and Synthesis of Echinulin-Neoechinulin Type Alkaloids isolated from Aspergillus amstelodami (1977)

Six natural products, named E-6, E-7, E-8, E-9, E-10, and E-11, were isolated from ether and methylene chloride extracts of freeze-dried mycelium of Aspergillus amstelodami IFO-6667. E-9 and E-11 were found to be identical with neoechinulin (2) and echinulin (1), respectively, from spectroscopic and melting point data. Alkaline hydrolysis of E-7, E-8, and E-10 gave indole-3-carbaldehydes (4a, 4b and 4c), respectively. Analysis of the spectroscopic data revealed the presence of a methylenediketopiperazine moiety in E-7, E-8, and E-10. Based on these informations, the structures 3a, 3b, and 3c were assigned to E-7, E-8, and E-10, respectively. These three alkaloids were synthesized by condensation of indole-3-carbaldehydes (4a, 4b, and 4c) with methylenediketopiperazine (5). The stereochemistry of E-7, E-8, and E-10 were determined as shown in the structures. A possible rationalization to explain the isopentenylation in the echinulin-neoechinulin alkaloid biosyntheses was presented.
Effect of etersalate on human platelet responsiveness. A study in healthy volunteers. (1987)

Ex vivo antiplatelet properties of 2-(p-acetamido-phenoxy)ethyl-o-acetoxybenzoate (etersalate, Daital) and its effects on serum thromboxane A2 (TXA2) levels and prostaglandin I2 (PGI2) generation were studied in human volunteers at two levels of oral dosing. Etersalate inhibited at the lower dosage platelet function and decreased TXA2 levels, but PGI2 generation from rat aortic rings was stimulated when incubated with plasma from etersalate-treated donors. Blood coagulation parameters remained within normal values. It is suggested that etersalate administration could act on platelet arachidonate metabolism at a different level than that of the cyclooxygenase pathway.
NIPP1-mediated Interaction of Protein Phosphatase-1 with CDC5L, a Regulator of Pre-mRNA Splicing and Mitotic Entry (2000)

NIPP1 is a regulatory subunit of a species of protein phosphatase-1 (PP1) that co-localizes with splicing factors in nuclear speckles. We report that the N-terminal third of NIPP1 largely consists of a Forkhead-associated (FHA) protein interaction domain, a known phosphopeptide interaction module. A yeast two-hybrid screening revealed an interaction between this domain and a human homolog (CDC5L) of the fission yeast protein cdc5, which is required for G(2)/M progression and pre-mRNA splicing. CDC5L and NIPP1 co-localized in nuclear speckles in COS-1 cells. Furthermore, an interaction between CDC5L, NIPP1, and PP1 in rat liver nuclear extracts could be demonstrated by co-immunoprecipitation and/or co-purification experiments. The binding of the FHA domain of NIPP1 to CDC5L was dependent on the phosphorylation of CDC5L, e.g. by cyclin E-Cdk2. When expressed in COS-1 or HeLa cells, the FHA domain of NIPP1 did not affect the number of cells in the G(2)/M transition. However, the FHA domain blocked beta-globin pre-mRNA splicing in nuclear extracts. A mutation in the FHA domain that abolished its interaction with CDC5L also canceled its anti-splicing effects. We suggest that NIPP1 either targets CDC5L or an associated protein for dephosphorylation by PP1 or serves as an anchor for both PP1 and CDC5L.
Data from Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4<sup>+</sup> T-cell Responses in Glioblastoma (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The low mutational load of some cancers is considered one reason for the difficulty to develop effective tumor vaccines. To overcome this problem, we developed a strategy to design neopeptides through single amino acid mutations to enhance their immunogenicity.&lt;/p&gt;Experimental Design:&lt;p&gt;Exome and RNA sequencing as well as &lt;i&gt;in silico&lt;/i&gt; HLA-binding predictions to autologous HLA molecules were used to identify candidate neopeptides. Subsequently, &lt;i&gt;in silico&lt;/i&gt; HLA-anchor placements were used to deduce putative T-cell receptor (TCR) contacts of peptides. Single amino acids of TCR contacting residues were then mutated by amino acid replacements. Overall, 175 peptides were synthesized and sets of 25 each containing both peptides designed to bind to HLA class I and II molecules applied in the vaccination. Upon development of a tumor recurrence, the tumor-infiltrating lymphocytes (TIL) were characterized in detail both at the bulk and clonal level.&lt;/p&gt;Results:&lt;p&gt;The immune response of peripheral blood T cells to vaccine peptides, including natural peptides and designed neopeptides, gradually increased with repetitive vaccination, but remained low. In contrast, at the time of tumor recurrence, CD8&lt;sup&gt;+&lt;/sup&gt; TILs and CD4&lt;sup&gt;+&lt;/sup&gt; TILs responded to 45% and 100%, respectively, of the vaccine peptides. Furthermore, TIL-derived CD4&lt;sup&gt;+&lt;/sup&gt; T-cell clones showed strong responses and tumor cell lysis not only against the designed neopeptide but also against the unmutated natural peptides of the tumor.&lt;/p&gt;Conclusions:&lt;p&gt;Turning tumor self-peptides into foreign antigens by introduction of designed mutations is a promising strategy to induce strong intratumoral CD4&lt;sup&gt;+&lt;/sup&gt; T-cell responses in a cold tumor like glioblastoma.&lt;/p&gt;&lt;/div&gt;
Molecular network analysis of signaling pathways in metastatic breast cancer in patients treated with erlotinib (2006)

10064 Erlotinib, an epidermal growth factor receptor tyrosine kinase inhibitor, is under active clinical investigation. It may have profound effects on the cellular molecular network by affecting downstream signaling and inhibiting tumor cell proliferation. Knowledge about the specificity of drug effects on the signaling pathways might enable therapy tailored specifically for each patient’s defect. We examined the activation of cellular signaling pathways involved in cell survival and proliferation in response to erlotinib treatment using a biopsy study set that comprised patient-matched breast cancer metastases from 8 women obtained prior to treatment with erlotinib and after 1 month of therapy. We procured pure cancer cell lysates from very small amounts of frozen tissue by Laser Capture Microdissection (about 60,000 cells). Matching lysates were printed on nitrocellulose and incubated with antibodies against the endpoints of interest. Using the Reverse Phase Protein Microarray technology we were able to generate a portrait of 18 phosphorylated kinase substrate endpoints as well as total expression levels of ERK, EGFR, Her2/neu, and IGF1R that revealed an upregulation of pro-survival pathway signaling in the post-erlotinib treatment set. Especially the measurement of the pro-survival, apoptosis-inhibiting signal transduction pAkt (S473) protein alone showed a statistically significant stronger staining in post-erlotinib treatment samples (p=0.019) in each of the individual patient-matched specimens as well as the entire post-treatment group, showing concordance with the clinical data of the trial, i.e. progressive disease observed for all participating patients. The results indicate the feasibility of this approach to monitor signaling events and molecular pathways in clinical specimens taken during targeted therapy trials. No significant financial relationships to disclose.
Collaborative personalization of image enhancement (2011)

While most existing enhancement tools for photographs have universal auto-enhancement functionality, recent research shows that users can have personalized preferences. In this paper, we explore whether such personalized preferences in image enhancement tend to cluster and whether users can be grouped according to such preferences. To this end, we analyze a comprehensive data set of image enhancements collected from 336 users via Amazon Mechanical Turk. We find that such clusters do exist and can be used to derive methods to learn statistical preference models from a group of users. We also present a probabilistic framework that exploits the ideas behind collaborative filtering to automatically enhance novel images for new users. Experiments show that inferring clusters in image enhancement preferences results in better prediction of image enhancement preferences and outperforms generic auto-correction tools.
Condensate Recovery from Tight Gas-Condensate Reservoirs using a new Method Based on a Gas-Based Chemical (2021)

Abstract Recovery from gas condensate reservoirs, when the pressure is below dew point pressure (Pdew), is adversely affected by the accumulation of condensate in the near wellbore region. The mitigation of the near-well bore condensate banking is the main purpose of any enhanced recovery method implemented in gas condensate reservoirs. In this work, a new method was tested to improve condensate recovery by using a chemical that was delivered using hydrocarbon gas as a carrier into a very low permeability and very low porosity reservoir rock. Chemicals are typically injected using liquid carrier solvents. The use of hydrocarbon gas as the carrier provides a remedy to mitigate condensate banking in very low permeability cores by minimizing complications associated with low injectivity and back flow clean-up process requirements of an injected liquid. The chemical potential was evaluated by recording production data from unsteady-state coreflood experiments. The injection of the chemical with equilibrated gas resulted in condensate saturation to decrease from 19.6% to 6.5%. This decrease was not instantaneous and took some time to occur indicating that the chemical needs time to interact with the resident fluid and rock. The benefit of the method, at the field scale, was also estimated by performing single-well numerical simulations that use relative permeability (kr) data which history matched the measured coreflood production data. The results of these preliminary simulations also showed improved recovery of gas and condensate compared to pure depletion, without chemical, by around 40% for the cases considered.
Use of Nonclinical and Expanded Access Clinical Study data to Guide Development Programs Targeting Mitochondrial Diseases of Lipid Peroxidation (2021)

Background: Many diseases of neurodegeneration associated with mitochondrial Lipid Peroxidation have poorly
 predictive animal models and present unique challenges for clinical trial design. RT001 is a dideuterated isotopomer
 of linoleic acid that inhibits Lipid Peroxidation. To correlate non clinical models with clinical response, we reviewed
 the effects of RT001 in disease models and clinical indications associated with Lipid Peroxidation.
Methods: We identified 10 specific target diseases known to be associated with Lipid Peroxidation. We evaluated the
 effects of RT001 in cellular models, animal models, and expanded access clinical study of these Lipid Peroxidation
 associated diseases.
Results: Significant beneficial effects were seen in 7 disorders. Clinical efficacy was seen in 6, no benefits were seen
 in 3, and data was inconclusive in 1. Inconsistencies between nonclinical and clinical experiences were seen; in vitro and animal models often demonstrate a lack of consistency with clinical response.
Conclusion: The response to RT001 in nonclinical models often demonstrated little concordance with the clinical
 effects in patients with the corresponding disease. The best predictor of RT001’s beneficial effects in patients remains
 clinical exposure. Thus, because RT001 has efficacy in some diseases and not others, there is no substitute for
 performing definitive clinical trials disease by disease in order to determine clinical benefit.