gebhart/patrepeval huggingface dataset:
Transfer of oxygen from an artificial protease to peptide carbon during proteolysis. (1991)

Site-specific cleavage of proteins with metal chelates is an approach for designing artificial proteolytic reagents that are directed by proximity to a peptide bond rather than by an amino acid residue type. In the presence of ascorbate and H2O2, an iron chelate attached to Cys-212 of the enzyme human carbonic anhydrase I quickly cleaved the protein between residues Leu-189 and Asp-190 to produce two discrete fragments. The transfer of an 18O atom from [18O]H2O2 (or [18O]O2) to the carboxyl group of Leu-189 was demonstrated by mass spectrometry. Quantitative experiments revealed that one molecule of H2O2 and one molecule of ascorbate afforded the hydrolysis of one peptide bond (1:1:1 stoichiometry) and that the reaction required ascorbate and H2O2. The process is catalytic, since related experiments on the protein bovine serum albumin revealed two cleavage events for each polypeptide chain cleaved. Hydroxyl radical scavengers had no significant effect. These results may be explained by generation of a highly nucleophilic oxygen species, such as peroxide coordinated to the iron chelate, that attacks a carbonyl carbon nearby.
Fundamental Limits of Caching (2014)

Caching is a technique to reduce peak traffic rates by prefetching popular content into memories at the end users. Conventionally, these memories are used to deliver requested content in part from a locally cached copy rather than through the network. The gain offered by this approach, which we term local caching gain, depends on the local cache size (i.e., the memory available at each individual user). In this paper, we introduce and exploit a second, global, caching gain not utilized by conventional caching schemes. This gain depends on the aggregate global cache size (i.e., the cumulative memory available at all users), even though there is no cooperation among the users. To evaluate and isolate these two gains, we introduce an information-theoretic formulation of the caching problem focusing on its basic structure. For this setting, we propose a novel coded caching scheme that exploits both local and global caching gains, leading to a multiplicative improvement in the peak rate compared with previously known schemes. In particular, the improvement can be on the order of the number of users in the network. In addition, we argue that the performance of the proposed scheme is within a constant factor of the information-theoretic optimum for all values of the problem parameters.
Solution dynamics of p21ras proteins bound with fluorescent nucleotides: A time-resolved fluorescence study (1993)

The solution dynamics of normal and transforming p21ras proteins in both the GTP- and GDP-bound forms were examined with time-resolved fluorescence spectroscopy. The fluorescent 2'(3')-O-(N-methylanthraniloyl) derivatives (mant derivatives) of GTP, dGTP, and GDP and the aminocoumarin and fluorescein derivatives of GTP and GDP were synthesized and used as reporter groups. The fluorescence lifetimes at 5 degrees C of the mant nucleotide derivatives increased from approximately 4 ns in solution to approximately 9 ns when bound to p21ras. At 30 degrees C, there was a 7.8% difference in lifetime between normal p21ras.mantGTP and p21ras.mantGDP, but no difference between similar complexes of the [Asp-12]p21ras protein. These data are consistent with steady-state fluorescence intensity differences among p21ras.mantGTP, p21ras.mantGDP, and the free nucleotides. Rotational correlation times for the mantGTP- and mantGDP-bound p21 proteins, N-ras, K-ras, and H-ras, were similar at 26 ns (5 degrees C), which is significantly longer than the 15-ns rotational correlation time predicted for a globular 21,000-Da protein. The p21-bound fluorescein and aminocoumarin nucleotide derivatives reported correlation times of 19 and 29 ns, respectively. Global analysis of the three fluorophore.p21 complexes with linked protein rotational correlation functions were best fit with a common rotational correlation time of 28 ns. Gel permeation chromatography of the GDP and mantGDP complexes of normal p21N-ras also showed greater apparent molecular weights than were expected in both cases, demonstrating that the high rotational correlation times obtained from time-resolved fluorescence measurements were not a result of the introduction of the fluorophore.(ABSTRACT TRUNCATED AT 250 WORDS)
In vitro killing of microfilariae of <i>Brugia pahangi</i> and <i>Brugia malayi</i> by eosinophil granule proteins. (1990)

Eosinophil infiltration and degranulation around the tissue-invasive stages of several species of helminths have been observed. Release of eosinophil granule contents upon the worms is supported by localization of two of the major granule proteins, major basic protein (MBP) and eosinophil peroxidase (EPO), on and around species of trematodes, nematodes, and cestodes. In the case of filarial worms, MBP is deposited on degenerating microfilariae (mf) of Onchocerca volvulus. Here, we performed in vitro assays of the toxicity of four purified eosinophil granule proteins, namely, MBP, EPO, eosinophil cationic protein (ECP), and eosinophil-derived neurotoxin (EDN), for the mf of Brugia pahangi and Brugia malayi. MBP, ECP, and EDN killed these worms in a dose-related manner although relatively high concentrations of EDN were necessary. EPO, in the presence of a H2O2-generating system and a halide, was the most potent toxin on a molar basis; here, the most potent halide was I- followed by Br- and Cl-. Surprisingly, EPO in the absence of H2O2 killed mf at concentrations comparable to those required for MBP and ECP. The toxicity of EPO + H2O2 + halide was inhibited by heparin, catalase, or 1% BSA, whereas the toxicity of EPO alone was inhibited only by heparin. Heparin also inhibited killing by both MBP and ECP. Despite the homology of ECP with certain RNases, placental RNasin, an RNase inhibitor, was unable to inhibit ECP-mediated toxicity. These results indicate that all of the eosinophil granule proteins are toxic to mf and they support the hypothesis that eosinophil degranulation causes death of mf in vivo.
Carcinogen-Specific Gene Expression Profiles in Short-term Treated Eker and Wild-type Rats Indicative of Pathways Involved in Renal Tumorigenesis (2007)

Eker rats heterozygous for a dominant germline mutation in the tuberous sclerosis 2 (Tsc2) tumor suppressor gene were used as a model to study renal carcinogenesis. Eker and corresponding wild-type rats were exposed to genotoxic aristolochic acid (AA) or non-genotoxic ochratoxin A (OTA) to elucidate early carcinogen-specific gene expression changes and to test whether Eker rats are more sensitive to carcinogen-induced changes in gene expression. Male Eker and wild-type rats were gavaged daily with AA (10 mg/kg body weight) or OTA (210 microg/kg body weight). After 1, 3, 7, and 14 days of exposure, renal histopathology, tubular cell proliferation, and Affymetrix gene expression profiles from renal cortex/outer medulla were analyzed. AA-treated Eker and wild-type rats were qualitatively comparable in all variables assessed, suggesting a Tsc2-independent mechanism of action. OTA treatment resulted in slightly increased cortical pathology and significantly elevated cell proliferation in both strains, although Eker rats were more sensitive. Deregulated genes involved in the phosphatidylinositol 3-kinase-AKT-Tsc2-mammalian target of rapamycin signaling, among other important genes prominent in tumorigenesis, in conjunction with the enhanced cell proliferation and presence of preneoplastic lesions suggested involvement of Tsc2 in OTA-mediated toxicity and carcinogenicity, especially as deregulation of genes involved in this pathway was more prominent in the Tsc2 mutant Eker rat.
Resonance in a spherical-circular microstrip structure with an airgap (1993)

The resonance problem of the spherical-circular microstrip structure with an airgap between the substrate layer and the ground conducting sphere is studied by using a rigorous Green's function formulation in the spectral domain and Galerkin's moment method calculation. Complex resonant frequencies are obtained in this study, which provide the resonant frequencies and half-power bandwidth of the structure. From the numerical results, it is found that with the increasing of the airgap thickness, the half-power bandwidth of the structure is considerably increased. This improves the low-bandwidth characteristics of microstrip structures. Details of the numerical results are presented and discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Hardware-Based Countermeasure to Reduce Side-Channel Leakage: Design, Implementation, and Evaluation (2015)

Side-channel attacks are one of the major concerns for security-enabled applications as they make use of information leaked by the physical implementation of the underlying cryptographic algorithm. Hence, reducing the side-channel leakage of the circuits realizing the cryptographic primitives is amongst the main goals of circuit designers. In this paper, we present a novel circuit concept, which decouples the main power supply from an internal power supply that is used to drive a single logic gate. The decoupling is done with the help of buffering capacitances integrated into semiconductor. We also introduce-compared to the previously known schemes-an improved decoupling circuit which reduces the crosstalk from the internal to the external power supply. The result of practical side-channel evaluation on a prototype chip fabricated in a 150nm CMOS technology shows a high potential of our proposed technique to reduce the side-channel leakages.
The Chirp Up-Converter and Amplifier (CUCA) for the ERS-1 Radar Altimeter (1986)

The paper describes the microwave signal processor under development for the transmitting chain of the radar altimeter to be placed on board the ERS-1 remote sensing satellite. The unit is fed by 450 MHz and 7.35 GHz signals coming from the radar chirp generator and frequency generator; it provides 13.8 GHz outputs to the HPA and to the receiver LO port. Functions performed are: up-conversion from 450 MHz to 6.9 GHz: filtering and amplification at 6.9 GHz: bandwidth expansion by frequency doubling to 13.8 GHz and filtering: pulse modulation and amplification at 13.8 GHz. Design solutions and attained performance are described.
MicroRNA and stem cell regulation. (2009)

Stem cells and microRNAs (miRNAs) represent two fast-developing frontiers of biological research. Stem cells function in embryonic development and tissue maintenance and are characterized by two fundamental properties: self-renewal and multipotency. Within many types of cancers, a small population of cells possesses stem cell-like characteristics. These cancer stem cells (CSCs) have been hypothesized to represent the disease-propagating and drug-resisting cell population. An increased understanding of the biology of stem cells and CSCs offers potential in the development of regenerative medicine and treatments for oncological disease. miRNAs are emerging as important regulators of post-transcriptional gene regulation, and have been demonstrated to be an integral component in stem cell regulation. This article reviews recent advances in the understanding of the roles of miRNAs in regulating various stem cell types, including embryonic stem cells, adult stem cells and CSCs.
Proteomic analysis of pericardial effusion: Characteristics of tuberculosis‐related proteins (2008)

The aim of this study has been designed to identify the tuberculosis (TB)-related proteins in pericardial effusion by proteomic approaches. TB is one of the major infectious diseases causing pericardial effusion. This study details protein profiles in pericardial effusion from three TB patients and three heart failure patients. Pericardial effusions were analyzed using 2-DE combined with the nano-HPLC-ESI-MS/MS. Eleven protein spots with differential expression in pericardial effusion were identified between the two groups of TB and heart failure patients (the control group). Seven protein spots were upregulated and four were downregulated. The composition of the pericardial effusion proteome may reflect the pathophysiological conditions affecting the progression of tuberculous pericarditis. The proteins in the tuberculous pericardial effusion with differential expression may serve as new and direct indicators of drug treatment. A possible conclusion is indicated that fibrinogen may play an important role for fibrin assembly in tuberculous pericardial effusion.
Vers une thérapie génique pour la cardiomyopathie associée à l’ataxie de Friedreich (2014)

Les ataxies crbelleuses sont caractrises par des troubles de la coordination des mouvements volontaires, de l'quilibre et de la mobilit, lis une atteinte du cervelet et/ou des voies spinocrbelleuses. L'ataxie de Friedreich (AF), la plus frquente des ataxies hrditaires avec une incidence de 1 : 30 000, est une maladie neurodgnrative progressive incurable [1]. Les signes cliniques sont domins par l'ataxie, due la perte de coordination motrice (syndrome crbelleux) et aux troubles de l'quilibre (perte de la sensibilit profonde), qui volue jusqu' la perte de la capacit ambulatoire en moyenne aprs une dizaine d'annes [1]. Ces signes neurologiques sont frquemment associs une cardiomyopathie hypertrophique (80 % des cas), cause de mortalit prcoce pour 60 % des patients [2]. L'ataxie de Friedreich est due un dficit en frataxine (FXN), une protine mitochondriale ubiquitaire essentielle la vie La mutation principale est une rptition du triplet GAA dans le premier intron du gne FXN. Elle induit une rpression transcriptionnelle par la formation d'htrochromatine, qui rsulte en une diminution drastique du niveau de FXN, entre 5 et 30 % du niveau normal dans tous les tissus La FXN joue un rle essentiel dans la rgulation de la synthse des centres fer-soufre (Fe-S), cofacteurs essentiels de nombreuses voies cellulaires, notamment la respiration mitochondriale et la rgulation du mtabolisme du fer. L'tude du dficit en FXN dans diffrents modles (levure, cellulaires et murins) a permis
The antigen of hepatitis delta virus: examination of in vitro RNA-binding specificity (1991)

The only known protein of hepatitis delta virus (HDV), the delta antigen, is found both within virus particles and within the nucleus of the infected cell, where it has one or more roles essential for RNA genome replication. Others have demonstrated that the antigen has the ability, in vitro, to specifically bind HDV RNA species. We report a further examination of this phenomenon, using partially purified recombinant protein, expressed as a fusion with the staphylococcal protein A. From Northwestern (RNA-immunoblot) analyses with both complete and various subdomains of HDV genomic and antigenomic RNAs, we found that a necessary feature for specific binding was that the RNA be able to fold to some extent into the so-called rodlike structure; this structure is a predicted intramolecular partial base-pairing of the circular RNA, with about 70% of all bases involved, so as to produce an unbranched rodlike structure. Six different subregions of the HDV rodlike structure, three on the genomic RNA and three on its complement, the antigenomic RNA, were tested and found to be sufficient for antigen binding. However, features in addition to the rodlike structure may also be necessary for specific binding, because we found that a similar structure present in the RNA of the potato spindle tuber viroid did not allow binding.
Stacked I<sup>2</sup>L Circuit (1976)

A "stacked circuit" with T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> L configuration is discussed which cuts effective power dissipation to one-third that of conventional T2L circuits.
Nickel Ferrocyanide as High-Performance Next Generation Electrocatalyst for Urea Oxidation (2020)

Abstract Urea oxidation, a key process in energy and environmental science, faces challenges because of the insufficient understanding of its mechanism and the lack of efficient catalysts. Here we demonstrate that nickel ferrocyanide (Ni 2 Fe(CN) 6 ) molecular catalyst supported on Ni form can drive urea oxidation reaction (UOR) with the record electrochemical activity and stability among all supported catalysts reported so far. A combination of kinetics data, in-situ spectroscopic measurements and energy computations suggests a new UOR pathway that delivers such outstanding performance. Different from most studied Ni-based catalysts with NiOOH derivative as a real catalytically active site for UOR, Ni 2 Fe(CN) 6 appears to be a next-generation catalyst able to directly facilitate a two-step reaction pathway involving a critical reaction of intermediate ammonia’s production (on Ni site) and oxidation (on Fe site). Due to the alternative rate-determining step with a more favorable thermal energetics, Ni 2 Fe(CN) 6 broke the limiting activity of the reported so far UOR catalysts. As a result, the UOR process on Ni 2 Fe(CN) 6 can replace conventional water oxidation process in various energy-saving systems for hydrogen and hydrogen peroxide production.
Involvement of Postsynaptic EP<sub>4</sub> and Presynaptic EP<sub>3</sub> Receptors in Actions of Prostaglandin E<sub>2</sub> in Rat Supraoptic Neurones (2002)

We have reported that supraoptic nucleus (SON) neurones are excited by prostaglandin E2 (PGE2) presumably via dual postsynaptic PG receptors, FP receptors and unidentified EP receptors, and that presynaptic EP receptors may also be involved in the excitation. In the present study, to clarify the receptor mechanism of the PGE2-mediated actions on SON neurones, we studied the pre- and postsynaptic effects of four newly developed EP agonists that are selective for each of the four EP receptors, EP1-4, on rat SON neurones using extracellular recording and whole-cell patch-clamp techniques. The EP4 agonist ONO-AE1-329 mimicked the excitatory effects of PGE2, whereas the EP1 agonist ONO-DI-004, the EP2 agonist ONO-AE1-257 and the EP3 agonist ONO-AE-248 had little or no effect. The effects of ONO-AE1-329 were unaffected by the EP1/FP/TP antagonist, ONO-NT-012, which potently suppressed the excitation caused by the FP agonist fluprostenol and PGE2. ONO-AE1-329 caused marked excitation when responses to fluprostenol were desensitized by repeated applications of fluprostenol. Patch-clamp analysis in SON neurones showed that ONO-AE1-329 induced inward currents at a holding potential of -70 mV and the reversal potential of the currents was -35.1 +/- 2.3 mV. On the other hand, the frequency of spontaneous inhibitory postsynaptic currents recorded from SON slice preparations was suppressed by ONO-AE-248, but unaffected by the other three EP agonists. These results suggest that SON neurones possess postsynaptic EP4 receptors and that gamma-aminobutyric acid neurones innervating SON neurones possess presynaptic EP3 receptors in their terminals. Activation of the two EP receptors may be involved in the excitatory regulation of SON neurones by PGE2.
Electron response in windowless Si(Li), SDD and PIN diode photodetectors (2011)

The photon response of small volume, low capacitance semiconductor X-ray detectors is widely reported and is characterized by the ability to resolve closely spaced X-ray lines. But the response to electrons is less well known. We present spectra from commercially available high-resolution X-ray detectors irradiated with mono-energetic internal conversion electrons with energies from 45 keV to 300 keV. Many radioisotopes emit conversion electrons in this range, and electron spectroscopy offers an additional tool for detection and identification. One application reported in this work is the detection of trace amounts of radioactive Xenon gas, where the simultaneous measurement of high-resolution X-rays and conversion electrons in Silicon X-ray detectors offers an improvement in the Xenon detection limit compared to scintillator-based systems. Future plans for improvements by the use of multiple detector arrays and coincidence gating are briefly discussed.
Surgical implantation of adipose tissue reverses diabetes in lipoatrophic mice (2000)

In lipoatrophic diabetes, a lack of fat is associated with insulin resistance and hyperglycemia. This is in striking contrast to the usual association of diabetes with obesity. To understand the underlying mechanisms, we transplanted adipose tissue into A-ZIP/F-1 mice, which have a severe form of lipoatrophic diabetes. Transplantation of wild-type fat reversed the hyperglycemia, dramatically lowered insulin levels, and improved muscle insulin sensitivity, demonstrating that the diabetes in A-ZIP/F-1 mice is caused by the lack of adipose tissue. All aspects of the A-ZIP/F-1 phenotype including hyperphagia, hepatic steatosis, and somatomegaly were either partially or completely reversed. However, the improvement in triglyceride and FFA levels was modest. Donor fat taken from parametrial and subcutaneous sites was equally effective in reversing the phenotype. The beneficial effects of transplantation were dose dependent and required near-physiological amounts of transplanted fat. Transplantation of genetically modified fat into A-ZIP/F-1 mice is a new and powerful technique for studying adipose physiology and the metabolic and endocrine communication between adipose tissue and the rest of the body.
Accidental Selection and Intentional Restoration of Sporulation-Deficient<i>Bacillus anthracis</i>Mutants (2010)

We demonstrate the frequent accidental enrichment of spontaneous sporulation-deficient mutants of Bacillus anthracis on solid medium and identify contributing factors. Mutations in spo0A, encoding the master regulator of sporulation initiation, were found in 38 of 53 mutants. Transductions using bacteriophage CP51 propagated on sporogenic bacteria allowed for the restoration of sporulation phenotypes.
Advanced controls improve performance of two-shell, dual-pressure column (1990)

This paper describes the study and implementation of advanced controls on a two-shell depropanizer, with the shells operating at significantly different pressures. The authors also discuss the feasibility of computer control.
A stereo vision based method for autonomous spray of pesticides to plant leaves (2009)

In this paper, a 3D leaf position measurement method based on stereo vision is proposed for guidance of an autonomous spray robot. A binocular stereo vision system is constructed by a single camera, which can move up and down on the vertical arm of the robot. With this vision system, a disparity map that contains the depth information of the plant leaves are calculated from the acquired image pairs firstly. Disparity map is a mid-step of 3D reconstruction and describes the relative changing depth and contour of the object surface. After processing the disparity map, leaves are segmented and their depth regarding local camera coordinates could be measured. However, camera coordinates does not provide complete 3D information for autonomous spray. The measured results from the local camera coordinates were further converted to the robot coordinates that are uniform for the robot control. The experimental data carried out with simple-shaped leaves were evaluated with the results from the proposed method.
High energy nanosecond laser pulses delivered single-mode through hollow-core PBG fibers (2004)

We report on the development of hollow-core photonic bandgap fibers for the delivery of high energy pulses for precision micromachining applications. Short pulses of (65ns pulse width) and energies of the order of 0.37mJ have been delivered in a single spatial mode through hollow-core photonic bandgap fibers at 1064nm using a high repetition rate (15kHz) Nd:YAG laser. The ultimate laser-induced damage threshold and practical limitations of current hollow-core fibers for the delivery of short optical pulses are discussed.