gebhart/patrepeval huggingface dataset:
Xanthine dehydrogenase and 2-furoyl-coenzyme A dehydrogenase from Pseudomonas putida Fu1: two molybdenum-containing dehydrogenases of novel structural composition (1990)

The constitutive xanthine dehydrogenase and the inducible 2-furoyl-coenzyme A (CoA) dehydrogenase could be labeled with [185W]tungstate. This labeling was used as a reporter to purify both labile proteins. The radioactivity cochromatographed predominantly with the residual enzymatic activity of both enzymes during the first purification steps. Both radioactive proteins were separated and purified to homogeneity. Antibodies raised against the larger protein also exhibited cross-reactivity toward the second smaller protein and removed xanthine dehydrogenase and 2-furoyl-CoA dehydrogenase activity up to 80 and 60% from the supernatant of cell extracts, respectively. With use of cell extract, Western immunoblots showed only two bands which correlated exactly with the activity stains for both enzymes after native polyacrylamide gel electrophoresis. Molybdate was absolutely required for incorporation of 185W, formation of cross-reacting material, and enzymatic activity. The latter parameters showed a perfect correlation. This evidence proves that the radioactive proteins were actually xanthine dehydrogenase and 2-furoyl-CoA dehydrogenase. The apparent molecular weight of the native xanthine dehydrogenase was about 300,000, and that of 2-furoyl-CoA dehydrogenase was 150,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of both enzymes revealed two protein bands corresponding to molecular weights of 55,000 and 25,000. The xanthine dehydrogenase contained at least 1.6 mol of molybdenum, 0.9 ml of cytochrome b, 5.8 mol of iron, and 2.4 mol of labile sulfur per mol of enzyme. The composition of the 2-furoyl-CoA dehydrogenase seemed to be similar, although the stoichiometry was not determined. The oxidation of furfuryl alcohol to furfural and further to 2-furoic acid by Pseudomonas putida Fu1 was catalyzed by two different dehydrogenases.
Metabolic Derangement in Polycystic Kidney Disease Mouse Models Is Ameliorated by Mitochondrial-Targeted Antioxidants (2021)

ABSTRACT Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressively enlarging cysts. Here we elucidate the interplay between oxidative stress, mitochondrial dysfunction, and metabolic derangement using two mouse models of PKD1 mutation, PKD1 RC/null and PKD1 RC/RC . Mouse kidneys with PKD1 mutation have decreased mitochondrial complexes activity. Targeted proteomics analysis shows a significant decrease in proteins involved in the TCA cycle, fatty acid oxidation (FAO), respiratory complexes, and endogenous antioxidants. Overexpressing mitochondrial-targeted catalase (mCAT) using adeno-associated virus reduces mitochondrial ROS, oxidative damage, ameliorates the progression of PKD and partially restores expression of proteins involved in FAO and the TCA cycle. In human ADPKD cells, inducing mitochondrial ROS increased ERK1/2 phosphorylation and decreased AMPK phosphorylation, whereas the converse was observed with increased scavenging of ROS in the mitochondria. Treatment with the mitochondrial protective peptide, SS31, recapitulates the beneficial effects of mCAT, supporting its potential application as a novel therapeutic for ADPKD.
A quantum-trace determinantal formula for matrix commutators, and\n applications (2010)

In this paper, we establish a determinantal formula for 2 x 2 matrix\ncommutators [X,Y] = XY - YX over a commutative ring, using (among other\ninvariants) the quantum traces of X and Y. Special forms of this determinantal\nformula include a "trace version", and a "supertrace version". Some\napplications of these formulas are given to the study of value sets of binary\nquadratic forms, the factorization of 2 x 2 integral matrices, and the solution\nof certain simultaneous diophantine equations over commutative rings.\n
Poly(thieno[3,4-b]thiophene):  A p- and n-Dopable Polythiophene Exhibiting High Optical Transparency in the Semiconducting State (2002)

Herein we report the synthesis and electrochemical characterization of poly(thieno[3,4-b]thiophene), a new low band gap conducting polymer with a high redox switching stability that exhibits high optical transparency in the semiconductive state. The monomer, thieno[3,4-b]thiophene (T34bT), has a low oxidation potential for polymerization, 1.02 V vs Ag/Ag+ (1.25 V vs SCE), a potential between that for the oxidation of 3,4-ethylenedioxythiopene and pyrrole. Poly(T34bT) has a band gap of ca. 0.85 eV (1459 nm) as determined by the onset for the π-to-π* transition from the UV−vis−NIR spectrum and 0.8 V from the difference in the onsets for both the p- and n-doping processes from cyclic voltammetry. Stability studies as determined from chronocoulometry and chronoabsorptometry indicate that the polymer retains 95% electroactivity and 96% change in optical density after 100 double potential steps. Poly(T34bT) is sky-blue in the reduced form and optically transparent (no observable color) in the oxidized state with a coloration efficiency of 160 cm2/C at 800 nm.
Effect of grain boundaries on local mechanical response in β type titanium alloy (2020)

Gum Metal is a β type titanium alloy that has both low Young’s modulus and high strength, and exhibits various other properties different from ordinary metallic materials. These specific functions have been considered to be related to its deformation mechanism. Therefore, the deformation mechanism in Gum Metal has been analyzed so far but has not been clarified yet. So we have investigated the local mechanical response near grain boundaries of Gum Metal for the purpose of examining the contribution of dislocation motion in the plastic deformation mechanism. Here we used Gum Metal and Ti20%Mo alloy for comparison. Mechanical characteristics in the nanometer range have been directly evaluated by nanoindentation and the effect of grain boundaries on the deformation behavior has been studied.
ChemInform Abstract: Synthesis of 4‐Substituted‐9,10‐Dialkoxy‐1,6,7,11b‐tetrahydro‐2H‐pyrimido[6,1‐a]‐ isoquinolin‐2‐ones. (1984)

Abstract Aus der Tetrahydrochinolin‐essigsäure (I) werden mit den Iminoestern (II) die Amide (III) erhalten.
Portfolio Optimization through Data Conditioning and Aggregation (2011)

In this paper, we present a novel portfolio optimization method that aims to generalize the delta changes of future returns, based on historical delta changes of returns learned in a past window of time. Our method addresses two issues in portfolio optimization. First, we observe that daily returns of stock prices are very noisy and often non-stationary and dependent. In addition, they do not follow certain well-defined distribution functions, such as the Gaussian distribution. To address this issue, we first aggregate the return values over a multi-day period into an average return in order to reduce the noise of daily returns. We further propose a pre-selection scheme based on stationarity, normality and independence tests in order to select a subset of stocks that have promising statistical properties. Second, we have found that optimizing the average risk in a past window does not typically generalize to future returns with minimal risks. To this end, we develop a portfolio optimization method that uses the delta changes of aggregated returns in a past window to optimize the delta changes of future expected returns. Our experimental studies show that data conditioning and aggregation in our proposed method is an effective means of improving the generalizability while simultaneously minimizing the risk of the portfolio.
High-Rate Analysis of Vector Quantization for Noisy Channels (2006)

In this paper, the sensitivity of the high-rate performance of conventional source coding to symmetric channel errors (i.e., a channel where all index errors are equally likely) with arbitrary distortion measures is analyzed. It is shown that, in general, the overall distortion due to source quantization and channel errors cannot be expressed as the sum of the distortion due to the finite bit representation of the source and the distortion due to channel errors. An exception to this is when the distortion is measured as the mean-squared error. The binary symmetric channel with random index assignment is a special case of the analysis, and as the number of code-points gets large, the performance approaches a nonzero constant. Finally, the framework is applied to the wideband speech spectrum quantization problem, where it correctly predicts the channel error rate permissible for operation at a particular distortion level
A bulk-driven CMOS OTA with 68 dB DC gain (2005)

An ultra-low voltage rail-to-rail operational transconductance amplifier, (OTA) based on a standard digital 0.18 /spl mu/m CMOS process, is described in this paper. Techniques for designing a 0.8 V fully differential OTA are discussed, including bias and reference current generator circuits. To achieve rail-to-rail operation, complementary input differential pairs are used, where the bulk-driven technique is applied to reduce the threshold limitation of the MOSFET transistors. The OTA gain is increased by using auxiliary gain boosting amplifiers. This additional circuitry enables the OTA to operate at 0.8 V, achieving an open loop gain of 68 dB while consuming 94 /spl mu/W. The DC gain of the amplifier is the highest gain achieved to date in bulk-driven amplifiers.
Drug Nanoparticles: Formulating Poorly Water-Soluble Compounds (2008)

More than 40% of compounds identified through combinatorial screening programs are poorly soluble in water. These molecules are difficult to formulate using conventional approaches and are associated with innumerable formulation-related performance issues. Formulating these compounds as pure drug nanoparticles is one of the newer drug-delivery strategies applied to this class of molecules. Nanoparticle dispersions are stable and have a mean diameter of less than 1 micron. The formulations consist of water, drug, and one or more generally regarded as safe excipients. These liquid dispersions exhibit an acceptable shelf-life and can be postprocessed into various types of solid dosage forms. Drug nanoparticles have been shown to improve bioavailability and enhance drug exposure for oral and parenteral dosage forms. Suitable formulations for the most commonly used routes of administration can be identified with milligram quantities of drug substance, providing the discovery scientist with an alternate avenue for screening and identifying superior analogs. For the toxicologist, the approach provides a means for dose escalation using a formulation that is commercially viable. In the past few years, formulating poorly water-soluble compounds using a nanoparticulate approach has evolved from a conception to a realization whose versatility and applicability are just beginning to be realized.
Map of Japan (2014)

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Interferon Lambda-1 (IFN-L1/IL-29) Induces ELR- CXC chemokine mRNA in human peripheral blood mononuclear cells, in an IFN-g independent manner (2007)

Interferon lambda-1 (IFN-λ1), the prototype Type-Ill interferon, has antiviral functions similar to those of the Type-1 interferons, IFN-α and IFN-β. However, IFN-λ1 is capable of signaling through almost all STAT molecules and so it is possible that it may have novel immunoregulatory functions in addition to antiviral ones. IFN-λ, the only member of the Type-II interferon family, induces the upregulation of a number of chemokines, including “Monokine induced by IFN-gamma” (MIG/CXCL9), “IFN-gamma inducible protein-10” (IP-10/CXCL10) and “IFN-gamma inducuble T-cell alpha chemotractant” (I-TAC/CXCL11). We investigated the ability of IFN-λ1 to replicate this immunoregulatory action of IFN-λ on human peripheral blood mononuclear cells (PBMC). Human PBMC were stimulated with IFN-λ 1 in vitro over a time period of fifteen minutes to 72 hours. mRNA and supernatants were harvested. The relative quantities of mRNA for MIG, IP-10 and I-TAC were determined by real-time RT-PCR. In order to determine whether actions of IFN-λ1 were mediated by IFNg, mRNA and secreted protein were quantitated by Q-RTPCR and ELISA respectively. IFN-λ1 elevated mRNA levels for these three chemokines. This activity did not depend on intermediate induction of IFN-λ and is therefore likely to be independent of IFN-λ. Further, our results suggest that donors responded to IFN-λ1 stimulation either “early” or “late”. Overall the action of IFN-λ1 was similar to that previously reported for IFN-λ and may invite more detailed investigation of the role of IFN-λ1 at the innate/adaptive interface.
Microwave Scattering by Nonspherical Particles (1965)

A method for obtaining detailed dependence of extinction cross sections on the orientation of nonspherical particles is described. The results of experimental scattering studies of several different particles are presented.
Indexing Medical WWW Documents by Morphemes (2001)

Assisting users to search medical information on the WWW is here considered from two perspectives--the linguistic complexity of medical terms, nominal compounds in particular, and cross-lingual relationships between monolingual medical terminologies. In order to solve the first problem, we present an approach to automatic indexing in which medically plausible morphological units are used. Semantic value is added to these index terms by a compact domain-specific thesaurus. We further discuss tools for morphological segmentation and morphosemantic normalization of HTML documents, as well as an adaptation of a standard WWW search engine for morpheme-based retrieval. The second problem, cross-lingual medical document retrieval, is dealt with by defining cross-lingual equivalence relations on the emerging morpheme sets.
A content integrity service for digital repositories (2008)

We present a “content integrity service” for long-lived digital documents, especially for objects stored in digital repositories. The goal of the service is to demonstrate that information in the repository is authentic and has not been unintentionally or maliciously altered, even after its bit representation in the repository has undergone one or more transformations. We describe our design for an efficient, secure service that achieves this, and our implementation of a prototype of such a service that we developed for DSpace. Our solution relies on one-way hashing and digital time-stamping procedures. Our service applies not only to transformations to archival content such as format changes, but also to the introduction of new cryptographic primitives, such as the new one-way hash function family that will be chosen by NIST in the competition that was recently announced [9]. In the face of recent attacks on hash functions, this feature is absolutely necessary to the design of an integrity-preserving system that is meant to endure for decades.
ChemInform Abstract: Selective Sequential Cross‐Coupling Reactions on Imidazole Towards Neurodazine and Analogues. (2013)

Abstract A synthesis of 2,4,5‐triarylated imidazoles is developed and applied to the preparation of neurodazine (XIb), a molecule affecting neuronal cell differentiation.
Wave-number domain representation of tire vibration (2000)

In the work to be described here, wave-number decomposition techniques have been used to study tire vibration. In the experimental component of this work, a tire was driven radially at a point on its treadband. Measurements of the resulting radial treadband vibration were made at approximately 200 points around the treadband circumference by using a laser Doppler velocimeter. From an inspection of the resulting space-frequency data, it was possible to identify the frequency ranges in which the tire responded either modally or nonmodally. Further, by performing a circumferential wave-number decomposition of the space-frequency data, the propagation characteristics of the wave types that contributed to the response of a tire could be determined. It was observed that a small number of circumferentially propagating waves combine to control the response of a tire in both low- and high-frequency ranges. The cut-on and propagation characteristics of these waves are closely related to propagating waveguide modes of flexural wave-bearing systems. Together, these results are consistent with a curved waveguide model of a tire. It is therefore suggested that a membrane-like waveguide model combined with a propagating wave representation of the tire vibration may offer an efficient way of representing tire vibration.
Energy Distribution Among Reaction Products: H + SCl_2 → HCl + SCl (1971)

The method of arrested relaxation has been applied to the study of infrared chemiluminescence arising from HCl(upsilon'>0) formed in the reaction H + SCl(2) ? HCI + SCl. The main findings are (a) that the mean fraction of the available energy entering vibration in the new bond is similar to that for the reaction H + Cl(2) ? HCl + Cl, the value being f (upsilon') approximately 0.43 (assuming the energy available for distribution among the products to be E'(tot) = 48 kcal mole(-1)); (b) that the breadth of the distribution over the populated vibrational levels, upsilon' = 1-5, substantially exceeds that for H + Cl(2) ? HCl + Cl, indicating altered reaction dynamics; (c) that the rotational distribution in the newly formed HCl is double-peaked, suggesting two distinct types of reaction dynamics (neither closely resembling that for H + Cl(2)), one of which gives rise to HCl with modest rotational excitation and one to HCl with a high degree of rotational excitation; (d) the mean fraction of E'(tot) entering product rotation (averaged over all reactive encounters) is f (R') asymptotically equal to 0.19; (e) the group of reactive encounters that result in less rotationally excited HCl are distinguished from the group that result in highly rotationally excited HCl, by differing correlation with upsilon'; this is further evidence that two distinct types of dynamics are involved in the reaction H + SCl(2) ? HCl + SCl.
Silicon nitride integrated optics (2020)

Silicon nitride has emerged as a highly versatile integrated optics material. Its ultra-low losses and mature processing methods provide advantages for passive, active and non-linear optical devices and microsystems operating in the visible, near-infrared (NIR) and mid-infrared (MIR) wavelength ranges. This chapter reviews progress in silicon nitride waveguide technology, devices and photonic integrated circuits (PICs) and recent efforts to build novel materials and devices onto silicon nitride platforms.
Stability of the carrier state in bacteriophage M13-infected cells (1977)

Bacteriophage M13-infected carrier cells were shown to be unstable to prolonged growth under all conditions. Carrier Hfr cells were transferred in dilute culture (10(3) to 10(4)/ml), where reinfection was impossible and the physiology of the cell was minimally altered. After an initial period of about 10 generations, during which all cells in the culture remained infected, there was exponential decay in the proportion of infected cells in the culture. Uninfected cells that appeared were M13 sensitive. Hfr and F' males were also transferred serially at high cell densities (10(7) to 10(9)/ml), where high levels of phage should permit reinfection. The proportion of phage-producing cells in the cultures remained constant for 7 to 15 generations and then dropped exponentially on further growth. Non-phage-producing cells appearing in the culture were refractory to infection by M13; in some cases cells scored as non-phage producers for 20 generations were observed to produce phage on further growth in liquid culture. F'trp+ males infected with M13 lost trp+ function almost immediately; this was not regained in these experiments. Infected cells grown in dilute culture or on plates remained infected longer, produced more PFU per cell for a longer period, and retained trp+ function in F'trp+ males for over 90 generations. Non-phage-producing cells that appeared were sometimes phage resistant, sometimes phage sensitive. The existence of a phage-related material accumulating at high cell densities and affecting expression of free episomes, episomal expression in Hfr males, and phage synthesis itself is suggested.
Verification of the control system performance using viability theory (2017)

The development of efficient methods for the control system performance verification has drawn a lot of attention recently. In this paper, the use of viability theory for this purpose is investigated in case of non-linear systems. In particular, verification algorithms based on the use of the computation of invariance and viability kernels and capture basin are proposed. A Lagrangian method has been used in order to approximate these sets for nonlinear systems. Because of simplicity and efficient computations, zonotopes are adopted for set representation. An application example based on a well known control benchmark is provided in order to show the effectiveness of the proposed method.
Phage Community Dynamics in Hot Springs (2004)

In extreme thermal environments such as hot springs, phages are the only known microbial predators. Here we present the first study of prokaryotic and phage community dynamics in these environments. Phages were abundant in hot springs, reaching concentrations of a million viruses per milliliter. Hot spring phage particles were resistant to shifts to lower temperatures, possibly facilitating DNA transfer out of these extreme environments. The phages were actively produced, with a population turnover time of 1 to 2 days. Phage-mediated microbial mortality was significant, making phage lysis an important component of hot spring microbial food webs. Together, these results show that phages exert an important influence on microbial community structure and energy flow in extreme thermal environments.
Autoantibodies and CD (2014)

Celiac disease (CD) is triggered by the consumption of gluten-containing cereals to which patients mount a T-lymphocyte and antibody response in both immunoglobulin A and immunoglobulin G classes coupled with autoantibody production against self-proteins, predominantly type-2 (tissue) transglutaminase (TG2). TG2 autoantibodies are biologically active and bind to their target protein in the patients' tissues, including the gut and extraintestinal tissues. This peculiar systemic anti-TG2 reaction is dependent on the presence of dietary gluten and stops after its elimination. As both anti-TG2 and anti-gliadin antibodies are activity markers, their detection is valuable for the disease recognition and therapy monitoring. High concentrations of serum anti-TG2 antibody positivity supported by highly specific positivity for endomysial antibodies became the critical component of celiac disease diagnosis, although serum antibodies as indirect markers have limitations and are not able to replace histology analysis in all cases. Studies focusing on tissue-bound antibodies may further improve our understanding of their role.
Conformational Preference in Heteroatomic Analogues of Ethane, H3X−YH3 (X = B, Al; Y = N, P):  Implications of Charge Transfer (2006)

Quantum chemical conformational analysis for electron donor-acceptor (EDA) systems, H3B-NH3, H3B-PH3, H3Al-NH3 and H3Al-PH3, has been performed. For H3B-NH3 and H3B-PH3, the rotational barrier is found to be invariant with an increase in the central bond (X-Y) length. For H3Al-NH3 and H3Al-PH3, however, the rotational barrier increases with an increase in the central bond length. Decomposition of the total energy into various components and their contributions to the frontier orbitals (HOMO, HOMO-1, HOMO-2 and HOMO-3) have been analyzed in detail to explain the origin of such anomalous changes in the rotational barrier. Charge transfer and favorable "back bonding" are found to be the crucial factors governing the variations in the rotational barrier for such systems.