gebhart/patrepeval huggingface dataset:
Identification of amino acids involved in histamine potentiation of GABAA receptors (2015)

Histamine is a neurotransmitter involved in a number of physiological and neuronal functions. In mammals, such as humans, and rodents, the histaminergic neurons found in the tuberomamillary nucleus project widely throughout the central nervous system. Histamine acts as positive modulator of GABAA receptors (GABAARs) and, in high concentrations (10 mM), as negative modulator of the strychnine-sensitive glycine receptor. However, the exact molecular mechanisms by which histamine acts on GABAARs are unknown. In our study, we aimed to identify amino acids potentially involved in the modulatory effect of histamine on GABAARs. We expressed GABAARs with 12 different point mutations in Xenopus laevis oocytes and characterized the effect of histamine on GABA-induced currents using the two-electrode voltage clamp technique. Our data demonstrate that the amino acid residues β2(N265) and β2(M286), which are important for modulation by propofol, are not involved in the action of histamine. However, we found that histamine modulation is dependent on the amino acid residues α1(R120), β2(Y157), β2(D163), β3(V175), and β3(Q185). We showed that the amino acid residues β2(Y157) and β3(Q185) mediate the positive modulatory effect of histamine on GABA-induced currents, whereas α1(R120) and β2(D163) form a potential histamine interaction site in GABAARs.
Segregation and linkage analysis of serum angiotensin I-converting enzyme levels: evidence for two quantitative-trait loci. (1995)

Human serum angiotensin I-converting enzyme (ACE) levels vary substantially between individuals and are highly heritable. Segregation analysis in European families has shown that more than half of the total variability in ACE levels is influenced by quantitative-trait loci (QTL). One of these QTLs is located within or close to the ACE locus itself. Combined segregation/linkage analysis in a series of African Caribbean families from Jamaica shows that the ACE insertion-deletion polymorphism is in moderate linkage disequilibrium with an ACE-linked QTL. Linkage analysis with a highly informative polymorphism at the neighboring growth-hormone gene (GH) shows surprisingly little support for linkage (LOD score [Z] = 0.12). An extended analysis with a two-QTL model, where an ACE-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL and GH polymorphism (Z = 5.0). We conclude that two QTLs jointly influence serum ACE levels in this population. One QTL is located within or close to the ACE locus and explains 27% of the total variability; the second QTL is unlinked to the ACE locus and explains 52% of the variability. The identification of the molecular mechanisms underlying both QTLs is necessary in order to interpret the role of ACE in cardiovascular disease.
Application of scatterometry for CD and profile metrology in 193-nm lithography process development (2003)

ArF resist lines are tested using scatterometry to study the CD correlation with CDSEM, profile variation caused by baking temperature and pattern environment, as well as the evaluation of optical proximity effect (OPE). Results show reasonable profiles variation predicted by scatterometry spectra from different baking temperatures. Other good matches are the predicted resist line profiles from dark-field and clear-field pattern environment and various line-pitch ratios. They are found to be very similar with the images from the cross-section SEM. On the other hand, the CD linearity and OPE are also found with good matches between scatterometry CD and SEM CD. However, the maximum pitch size tested for OPE is 0.6 &mu;m. More sparse patterns aer believed to have lower sensitivity caused by the weak characteristics spectrum detected. The spectrum sensitivity is another important topic in this paper. The CD and pitch information is contained across the entire spectrum while small profile variations, like t-top and footing, are predicted in the shorter wavelength region. To predict accurate resist profile for small CD, the usage of the shorter wavelength spectrum is inevitable.
MICROBIAL OXIDATION OF FINASTERIDE WITH MACROPHOMINA PHASEOLINA(KUCC 730) (2017)

Objectives: New microbial oxidative derivatives of Finasteride [17β-(N-tert-butylcarbamoyl)-4-aza-5α-androst-1-en-3-one] (1) has been investigated with Macrophomina phaseolina (ATCC730).Methods: Fermented media of Macrophomina phaseolina (ATCC730) was prepared to cultivate the fungal cultures . Substrate 1 was incubated in liquid media for 16 days. After sixteen days, filtration and extraction of the fermented media was carried out with 9 L DCM in three portions. Resulting organic extract was dried using anhydrous (Na2SO4), and evaporated to afford a brown gum (950 mg). This on chromatographic purification with MeOH in CH2Cl2 afforded the metabolites 2-4 . Results: Three oxidised metabolites of finasteride (1) which were identified as 15-oxo-finasteride (2), 11a-hydroxyfinasteride (3), and 15β-hydroxyfinasteride (4). Metabolite 2 was found to be new. The structure of the oxidised metabolites were elucidated by 1-D (1H, 13C) and 2-D NMR (COSY, HMBC, HMQC, NOESY) techniques and MS analyses.Conclusion: As a result of these study, oxidation at C-7, C-11 and C-15 positions were found. Metabolite 2 was identified as a new metabolite.
The failure of Daudi cells to express the cellular prion protein is caused by a lack of glycosyl‐phosphatidylinositol anchor formation (2001)

The cellular prion protein (PrPc) is a glycosyl-phosphatidylinositol (GPI)-linked cell surface protein, which is expressed at high density on nervous tissues and at lower levels on most other solid-organ tissues. It is also expressed on peripheral blood mononuclear cells (PBMC) of all lineages. In lymphocytes, its level of expression is dependent upon the state of cell activation, and polyclonal anti-PrP antisera partially block lectin-induced T-cell activation, suggesting a functional role of the protein in this process. Using the monoclonal antibody (mAb) 3F4 we examined PrPc surface immunoreactivity on leukaemic cell lines of T- and B-cell origin, and unexpectedly observed a complete lack of PrPc cell-surface expression in Daudi cells, while all other cell lines displayed discernible reactivity. We demonstrated the intracellular presence of PrP-specific mRNA and PrP protein. The lack of surface PrPc is unrelated to the well-known defect of beta2-microglobulin (beta2m) expression in Daudi cells as other beta2m-deficient cells, such as the melanoma cell line F0-1 and spleen cells from beta2m gene-deleted mice, were not deficient in cell-surface PrPc. Daudi cells failed to bind antibodies directed against all GPI-linked cell surface proteins. In somatic hybridization experiments using murine spleen cells as partners, we observed de novo expression of human PrPc, CD55 and CD59, thus demonstrating in Daudi cells the availability of these gene products for GPI linkage and cell-surface expression.
A Compact, Low Power, Quantum Cascade Laser-based Sensor for CO (2012)

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 D. Sonnenfroh, K. Parameswaran, D. Biss, and J. Bradshaw, "A Compact, Low Power, Quantum Cascade Laser-based Sensor for CO," in Lasers, Sources, and Related Photonic Devices, OSA Technical Digest (CD) (Optica Publishing Group, 2012), paper LT6B.6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
S100A4 Is a Biomarker of Tumorigenesis, EMT, Invasion, and Colonization of Host Organs in Experimental Malignant Mesothelioma (2020)

Recent findings suggest that S100A4, a protein involved in communication between stromal cells and cancer cells, could be more involved than previously expected in cancer invasiveness. To investigate its cumulative value in the multistep process of the pathogenesis of malignant mesothelioma (MM), SWATH-MS (sequential window acquisition of all theoretical fragmentation spectra), an advanced and robust technique of quantitative proteomics, was used to analyze a collection of 26 preneoplastic and neoplastic rat mesothelial cell lines and models of MM with increasing invasiveness. Secondly, proteomic and histological analyses were conducted on formalin-fixed paraffin-embedded sections of liver metastases vs. primary tumor, and spleen from tumor-bearing rats vs. controls in the most invasive MM model. We found that S100A4, along with 12 other biomarkers, differentiated neoplastic from preneoplastic mesothelial cell lines, and invasive vs. non-invasive tumor cells in vitro, and MM tumors in vivo. Additionally, S100A4 was the only protein differentiating preneoplastic mesothelial cell lines with sarcomatoid vs. epithelioid morphology in relation to EMT (epithelial-to-mesenchymal transition). Finally, S100A4 was the most significantly increased biomarker in liver metastases vs. primary tumor, and in the spleen colonized by MM cells. Overall, we showed that S100A4 was the only protein that showed increased abundance in all situations, highlighting its crucial role in all stages of MM pathogenesis.
Supplemental Figure 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Figure S3&lt;/p&gt;
21.2: Materials and Inks for Full Color PLED‐Displays (2002)

Abstract Progress in new materials for full color displays are presented. New polymers based on the “Spiro‐Principle” show encouraging properties in electroluminescence performance and lifetime. The spiro‐polymers can be tailor made to fit the RGB color requirements of a full color display. They are readily soluble, show excellent thermal stability and their synthesis is scalable to an industrially viable scale.
The Photo Never Lies (2004)

THERE IS NO INNOCENT EYE. THE PHOTOS OF A STARVING SOMALIAN CHILD AND THE REPORT OF A MASSACRE IN ALGERIA COME FROM AND BRING WITH THEM POINTS OF VIEW
Codes correcting phased burst erasures (1998)

We introduce a family of binary array codes of size t/spl times/n, correcting multiple phased burst erasures of size t. The codes achieve maximal correcting capability, i.e., being considered as codes over GF(2/sup t/) they are MDS. The length of the codes is n=/spl Sigma//sub l=1//sup L/(/sub l//sup t/) where L is a constant or is slowly growing in t. The complexity of encoding and decoding is proportional to rnmL where r is the number of correctable erasures, and m is the smallest number such that 2/sup t/=1 modulo m. This compares favorably with the complexity of decoding codes obtained from the shortened Reed-Solomon codes having the same parameters.
The Three-Dimensional Morphology of Growing Dendrites (2015)

The processes controlling the morphology of dendrites have been of great interest to a wide range of communities, since they are examples of an out-of-equilibrium pattern forming system, there is a clear connection with battery failure processes, and their morphology sets the properties of many metallic alloys. We determine the three-dimensional morphology of free growing metallic dendrites using a novel X-ray tomographic technique that improves the temporal resolution by more than an order of magnitude compared to conventional techniques. These measurements show that the growth morphology of metallic dendrites is surprisingly different from that seen in model systems, the morphology is not self-similar with distance back from the tip, and that this morphology can have an unexpectedly strong influence on solute segregation in castings. These experiments also provide benchmark data that can be used to validate simulations of free dendritic growth.
Molecular Design for Coloring/Decoloring Properties in Rewritable Paper Using Leuco Dyes: Effects of Long-chain Alkyl Group (2005)

Printing systems with an information-display function are attracting increasing interest as greater volumes of information become available in digital format. We recently developed a practical rewritable printing system for displaying documents in which the coloring-decoloring reaction cycles are thermally controlled using leuco dyes. This system is composed of leuco dye molecules and acidic developer molecules with long-chain alkyl groups and associative groups; it exhibits colored/decolored states that can be reversed by varying the heat conditions. Since the reversibility property mainly depends on the molecular structure of the developer, we prepared simple developers with different alkyl lengths to investigate the structural effects. We found that controlling the physical properties of the long-chain alkyl group of the developer is the key to achieving both thermal stability of the colored state and rapid erasability.
Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies (2022)

The Janus kinase 2 (JAK2) pseudokinase domain (JH2) is an ATP-binding domain that regulates the activity of the catalytic tyrosine kinase domain (JH1). Dysregulation of JAK2 JH1 signaling caused by the V617F mutation in JH2 is implicated in various myeloproliferative neoplasms. To explore if JAK2 activity can be modulated by a small molecule binding to the ATP site in JH2, we have developed several ligand series aimed at selectively targeting the JAK2 JH2 domain. We report here the evolution of a false virtual screen hit into a new JAK2 JH2 series. Optimization guided by computational modeling has yielded analogues with nanomolar affinity for the JAK2 JH2 domain and >100-fold selectivity for the JH2 domain over the JH1 domain. A crystal structure for one of the potent compounds bound to JAK2 JH2 clarifies the origins of the strong binding and selectivity. The compounds expand the platform for seeking molecules to regulate JAK2 signaling, including V617F JAK2 hyperactivation.
Detecting Rational Points on Hypersurfaces over Finite Fields (2008)

We study the complexity of deciding whether a given homogeneous multivariate polynomial has a non- trivial root over a finite field. Given a homogeneous algebraic circuit C that computes an n- variate polynomial p(x) of degree d over a finite field F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> , we wish to determine if there exists a nonzero xisinF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> with C(x)=0. For constant n there are known algorithms for doing this efficiently. However for linear n, the problem becomes NP hard. In this paper, using interesting algebraic techniques, we show that if d is prime and n>d/2, the problem can be solved over sufficiently large finite fields in randomized polynomial time. We complement this result by showing that relaxing any of these constraints makes the problem intractable again.
Low-Frequency Vibrations Enhance Thrombolytic Therapy and Improve Stroke Outcomes (2020)

Background and Purpose- We aim to determine the potential impact on stroke thrombolysis of drip-and-ship helicopter flights and specifically of their low-frequency vibrations (LFVs). Methods- Mice with a middle cerebral artery autologous thromboembolic occlusion were randomized to receive rtPA (recombinant tissue-type plasminogen activator; or saline) 90 minutes later in 3 different settings: (1) a motion platform simulator that reproduced the LFV signature of the helicopter, (2) a standardized actual helicopter flight, and (3) a ground control. Results- Mice assigned to the LFV simulation while receiving tPA had smaller infarctions (31.6 versus 54.9 mm<sup>3</sup>; <i>P</i>=0.007) and increased favorable neurological outcomes (86% versus 28%; <i>P</i>=0.0001) when compared with ground controls. Surprisingly, mice receiving tPA in the helicopter did not exhibit smaller infarctions (47.8 versus 54.9 mm<sup>3</sup>; <i>P</i>=0.58) nor improved neurological outcomes (37% versus 28%; <i>P</i>=0.71). This could be due to a causative effect of the 20- to 30-Hz band, which was inadvertently attenuated during actual flights. Mice using saline showed no differences between the LFV simulator and controls with respect to infarct size (80.9 versus 95.3; <i>P</i>=0.81) or neurological outcomes (25% versus 11%; <i>P</i>=0.24), ruling out an effect of LFV alone. There were no differences in blood-brain barrier permeability between LFV simulator or helicopter, compared with controls (2.45-3.02 versus 4.82 mm<sup>3</sup>; <i>P</i>=0.14). Conclusions- Vibration in the low-frequency range (0.5-120 Hz) is synergistic with rtPA, significantly improving the effectiveness of thrombolysis without impairing blood-brain barrier permeability. Our findings reveal LFV as a novel, safe, and simple-to-deliver intervention that could improve the outcomes of patients. Visual Overview- An online visual overview is available for this article.
Identification, at the genomic level, of an HLA-DR restriction element for cloned antigen-specific T4 cells. (1985)

Two T4 cell clones (TLC) specific for antigenic epitopes on Chlamydia trachomatis were studied. Using a panel of allogeneic antigen-presenting cells (APC), both TLC were found to be restricted by HLA class II elements closely associated with, but not identical to the DRw5S specificity, as determined by highly selected alloantisera, a monoclonal antibody (mAb), 109d6, and confirmed on the DNA level by determination of restriction fragment length polymorphisms (RFLP) with a DR beta probe. Furthermore, HLA-DR-specific mAb, including 109d6, but not other HLA class II- or class I-specific antibodies inhibited the two TLC, strongly suggesting that the restriction element is expressed by a DR molecule. Using digestion with Hind III restriction enzyme and a DR beta probe, we found a complete concordance between the appearance of a 9.3 kilobase band and the ability of allogeneic APC to restimulate the T cell clones. Thus, the restriction element for these T cell clones appear to be expressed by DR molecules, but can, at present, only be detected at the genomic level.
Combined Experimental and Computational Approach for Rational Design of Bio-Nano Interfaces (2015)

Various approaches have been developed in the last 5 years regarding targeted enzyme orientation on the electrode surface but no explanation of enzyme orientation on electron transfer properties have been provided. The same can be said about the utilization of mediators for enhancement of the interfacial electron transfer. Facing this fundamental challenge we started using computational approaches along with experimental efforts to gain knowledge of the underlying processes. In our computational and experimental benchmark studies soluble PQQ-dependent glucose dehydrogenase (PQQ-sGDH) have been explored since this enzyme is known as capable of direct electron transfer (DET). Various techniques for PQQ-sGDH immobilization and/or enhanced electron transfer have been developed over the years and a key question regarding the “proper” orientation of PQQ-sGDH has been raised. Should the substrate-binding pocket and thus PQQ be placed facing the electrode surface or it should be fully exposed to the electrolyte? To resolve this question and to enhance the electron transfer at the enzyme-electrode interface, quinones were explored in solution and immobilized on carbon support material. In both cases the current densities generated form the glucose oxidation through PQQ-sGDH were increased from 1.5 to 5 times depending on the properties of the explored quinones. In addition to the electrochemical characterization of the designed enzymatic anodes, molecular computational calculations, such as Density Functional Theory (DFT) and Molecular Docking Simulations, were used to gain insight into interactions between the quinones and PQQ-sGDH from one hand and the quinones and the support material, from another (Fig. 1). The role of the two types of benzoquinones, 1,2- and 1,4-benzoquinone, and ubiquinone in the operation and mechanism of the electron transfer in PQQ-sGDH anodes has been addressed 1 . It was established that the higher electrochemical performance of PQQ-sGDH anodes in the presence of free 1,2- and 1,4-benzoquinones is due to the smaller distance between these molecules and the enzyme cofactor (PQQ). It was proposed that when 1,4-benzoquinone is adsorbed, it plays the role of a mediator as a result of its high electron transfer rate ability and smaller PQQ-quinone distance. At the same time when 1,2-benzoquinone is adsorbed on the electrode surface, the enzyme will transfer the electrons directly to the support and the modifier will mostly play the role of an orienting agent. Similar conclusion can be made for the PQQ-sGDH anode modified with physically adsorbed ubiquinone for which purely orientation role was proposed. 1.Babanova, S., Matanovic, I. &amp; Atanassov, P. Quinone-modified surfaces for enhanced enzyme-electrode interactions in PQQ-dependent glucose dehydrogenase anodes. Chem. Electro. Chem. 1 , 2017–2028 (2014). Figure 1
A Memetic Algorithm configured via a problem solving environment for the Hamiltonian Cycle problems (2007)

Algorithm Development Environment for Permutation-based problems (ADEP) is a software environment for configuring meta-heuristics for solving combinatorial optimization problems. This paper describes the key features of ADEP and how the environment was used to generate a Memetic Algorithm (MA) solution for Hamiltonian Cycle Problems (HCP). The effectiveness of the MA algorithm is demonstrated through computer simulations and its performance is compared with backtracking and other heuristic techniques such as Simulated Annealing, Tabu Search, and Ant Colony Optimization.