gebhart/patrepeval huggingface dataset:
The Use of Glycidol to Introduce Aldehyde Functions Into Proteins – Application to the Fluorescent Labelling of Bovine Serum Albumin and Avidin (2007)

Abstract The reactions between 2,3‐epoxypropan‐1‐ol (glycidol) and either the nonglycosylated protein bovine serum albumin (BSA) or the glycoprotein avidin (AV) allowed the successful introduction of diol groups through the addition of some of the proteins' nucleophilic residues to the epoxide ring. The extent of glycolation could be readily tuned by varying the reaction time, the pH of reaction and the concentration of glycidol. Treatment of the stable protein‐diol intermediates with sodium periodate resulted in the generation of reactive aldehyde functionalities through the oxidation of the glycol moieties. At this step, the amount of generated aldehydes could also be modulated by changing the time and/or pH of oxidation. As an application, both formylated proteins were successfully labelled with the hydrazide‐containing fluorescent dye Lucifer Yellow CH (LyCH), affording highly fluorescent conjugates. Mild oxidation of the avidin‐diol left untouched glycol moieties that contributed to greatly enhance water solubility in the avidin‐LyCH bioconjugates. In certain cases the avidin‐LyCH conjugates retained a good affinity for biotin, as shown in a competitive binding assay. Glycidol thus appears to be an attractive low‐cost reagent for protein chemical activation aimed at further coupling of amine‐containing species.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Differential Modes of Nuclear Localization Signal (NLS) Recognition by Three Distinct Classes of NLS Receptors (1997)

The targeting of karyophilic proteins to nuclear pores is mediated via the formation of a nuclear pore-targeting complex, through the interaction of nuclear localization signal (NLS) with its NLS receptor. Recently, a novel human protein, Qip1, was identified from a yeast two-hybrid system with DNA helicase Q1. This study demonstrates that Qip1 is a novel third class of NLS receptor that efficiently recognizes the NLS of the helicase Q1. Moreover, the data obtained in this study show that the specific interaction between Qip1 and the NLS of the helicase Q1 requires its upstream sequence of the minimal essential NLS. By using purified recombinant proteins alone in the digitonin-permeabilized cell-free transport system, it was demonstrated that the two known human NLS receptors, Rch1 and NPI-1, are able to transport all the tested NLS substrates into the nucleus, while Qip1 most efficiently transports the helicase Q1-NLS substrates, which contain its upstream sequence in so far as we have examined the system. Furthermore, in HeLa cell crude cytosol, it was found that endogenous Rch1 binds to all the tested NLS substrates, while the binding of endogenous NPI-1 is restricted to only some NLSs, despite the fact that NPI-1 itself shows binding activity to a variety of NLSs. These results indicate that at least three structurally and functionally distinct NLS receptors exist in the human single cell population, and suggest that the nuclear import of karyophilic proteins may be controlled in a complex manner at the NLS recognition step by the existence of a variety of NLS receptors with various specificities to each NLS.
Engineering of Efficient Panchromatic Sensitizers for Nanocrystalline TiO<sub>2</sub>-Based Solar Cells (2001)

A new series of panchromatic ruthenium(II) sensitizers derived from carboxylated terpyridyl complexes of tris-thiocyanato Ru(II) have been developed. Black dye containing different degrees of protonation [(C(2)H(5))(3)NH][Ru(H(3)tcterpy)(NCS)(3)] 1, [(C(4)H(9))(4)N](2)[Ru(H(2)tcterpy)(NCS)(3)] 2, [(C(4)H(9))(4)N](3)[Ru(Htcterpy)(NCS)(3)] 3, and [(C(4)H(9))(4)N](4)[Ru(tcterpy)(NCS)(3)] 4 (tcterpy = 4,4',4' '-tricarboxy-2,2':6',2' '-terpyridine) have been synthesized and fully characterized by UV-vis, emission, IR, Raman, NMR, cyclic voltammetry, and X-ray diffraction studies. The crystal structure of complex 2 confirms the presence of a Ru(II)N6 central core derived from the terpyridine ligand and three N-bonded thiocyanates. Intermolecular H-bonding between carboxylates on neighboring terpyridines gives rise to 2-D H-bonded arrays. The absorption and emission maxima of the black dye show a bathochromic shift with decreasing pH and exhibit pH-dependent excited-state lifetimes. The red-shift of the emission maxima is due to better pi-acceptor properties of the acid form that lowers the energy of the CT excited state. The low-energy metal-to-ligand charge-transfer absorption band showed marked solvatochromism due to the presence of thiocyanate ligands. The Ru(II)/(III) oxidation potential of the black dye and the ligand-based reduction potential shifted cathodically with decreasing number of protons and showed more reversible character. The adsorption of complex 3 from methoxyacetonitrile solution onto transparent TiO(2) films was interpreted by a Langmuir isotherm yielding an adsorption equilibrium constant, K(ads), of (1.0 +/- 0.3) x 10(5) M(-1). The amount of dye adsorbed at monolayer saturation was (n(alpha) = 6.9 +/- 0.3) x 10(-)(8) mol/mg of TiO(2), which is around 30% less than that of the cis-di(thiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylate)ruthenium(II) complex. The black dye, when anchored to nanocrystalline TiO(2) films achieves very efficient sensitization over the whole visible range extending into the near-IR region up to 920 nm, yielding over 80% incident photon-to-current efficiencies (IPCE). Solar cells containing the black dye were subjected to analysis by a photovoltaic calibration laboratory (NREL, U.S.A.) to determine their solar-to-electric conversion efficiency under standard AM 1.5 sunlight. A short circuit photocurrent density obtained was 20.5 mA/cm(2), and the open circuit voltage was 0.72 V corresponding to an overall conversion efficiency of 10.4%.
A simple one‐step real‐time RT‐PCR for diagnosis of dengue virus infection (2008)

Dengue is the most important arbovirus disease in tropical and sub-tropical countries, and can be caused by infection with any of the four-dengue virus (DENV) serotypes. Infection with DENV can lead to a broad clinical spectrum, ranging from sub-clinical infection or an influenza-like disease known as dengue fever (DF) to a severe, sometimes fatal, disease characterized by hemorrhage and plasma leakage that can lead to shock, known as dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). The diagnosis of dengue is routinely accomplished by serologic assays, such as IgM and IgG ELISAs, as well as HI tests, analyzing serum samples obtained from patients with at least 7 days of symptoms onset. These tests cannot be used for diagnosis during the early symptomatic phase. In addition, antibodies against dengue are broad reactive with other flaviviruses. Therefore, a specific diagnostic method for acute DENV infection is of great interest. In that sense, the real-time RT-PCR has become an important tool that can be used for early and specific detection of dengue virus genome in human serum samples. This study describes a simple, specific, and sensitive real-time RT-PCR for early diagnosis of dengue virus infection.
Evidence for Molecular Mimicry between Human T Cell Epitopes in Rotavirus and Pancreatic Islet Autoantigens (2010)

In type 1 diabetes, insulin-producing beta cells in the islets of the pancreas are destroyed by autoreactive T cells. Rotavirus (RV) has been implicated in the pathogenesis of type 1 diabetes. Peptides in VP7, a major immunogenic protein of RV, have high sequence similarity to T cell epitope peptides in the islet autoantigens tyrosine phosphatase-like insulinoma Ag 2 (IA2) and glutamic acid decarboxylase 65 (GAD65). We aimed to educe evidence for the hypothesis that molecular mimicry with RV promotes autoimmunity to islet autoantigens. Peptides in RV and their sequence-similar counterparts in IA2 and GAD65 were assayed for binding to HLA molecules associated with type 1 diabetes and for the ability to elicit T cell proliferative responses in HLA-typed individuals. T cells expanded or cloned to epitopes in IA2 or RV were then tested for cross-reactivity with these epitopes. Peptides in RV-VP7, similar to T cell epitopes in IA2 and GAD65, bound strongly to HLA-DRB1*04 molecules that confer susceptibility to type 1 diabetes and were also T cell epitopes in humans at risk for type 1 diabetes. The proliferative responses of T cells to the similar peptides in RV and islet autoantigens were significantly correlated. T cells expanded to the IA2 epitope could be restimulated to express IFN-gamma by the similar peptide in RV-VP7, and T cell clones generated to this RV-VP7 peptide cross-reacted with the IA2 epitope. Our findings are consistent with the hypothesis that molecular mimicry with RV could promote autoimmunity to islet Ags.
Critique: The potential role of speech production models in automatic speech recognition (1996)

This paper presents a critique (by a ‘‘speech technologist’’) of ‘‘The potential role of speech production models in automatic speech recognition’’ by R. C. Rose, J. Schroeter, and M. M. Sondhi which was presented at the 1994 ASA Special Session on ‘‘Speech Recognition and Perception from an Articulatory Point of View.’’ While in general agreement with the points raised in the Rose paper, this article focuses on issues such as (a) whether articulatory information should be ‘‘recovered’’ as part of a recognition process as opposed to that process being ‘‘constrained’’ by articulatory information, (b) how optimum recognition performance is achieved by compromising the ‘‘quality’’ of the underlying generative model, and (c) if recent developments in speech pattern modeling will lead to more powerful generative models of speech. Finally, it is noted that the special session highlighted the fact that a convergence is long overdue between the speech science and speech technology communities toward common (mathematically and computationally based) theories of ‘‘speech pattern processing.’’
Subnanometer Porous Thin Films by the Co-assembly of Nanotube Subunits and Block Copolymers (2011)

Porous thin films containing subnanometer channels oriented normal to the surface exhibit unique transport and separation properties and can serve as selective membranes for separation and protective coatings. While molecularly defined nanoporous inorganic and organic materials abound, generating flexible nanoporous thin films with highly aligned channels over large areas has been elusive. Here, we developed a new approach where the growth of cyclic peptide nanotubes can be directed in a structural framework set by the self-assembly of block copolymers. By conjugating polymers to cyclic peptides, the subunit of an organic nanotube can be selectively solubilized in one copolymer microdomain. The conjugated polymers also mediate the interactions between nanotube and local medium and guide the growth of nanotubes in a confined geometry. This led to subnanometer porous membranes containing high-density arrays of through channels. This new strategy takes full advantage of nanoscopic assembly of BCPs and the reversibility of organic nanotube growth and circumvents impediments associated with aligning and organizing high aspect ratio nano-objects normal to the surface. Furthermore, the hierarchical coassembly strategy described demonstrates the feasibility of synchronizing multiple self-assembly processes to achieve hierarchically structured soft materials with molecular level control.
Formation of isolated and clustered Au nanoparticles in the presence of polyelectrolyte molecules using a flow-through Si chip reactor (2005)

The formation of colloidal gold at room temperature was studied in a micro-reaction system. Ascorbic acid and Fe(II) were used as reducing agents. Besides citric acid, sodium metasilicate and poly(vinyl alcohol) were added as effectors for the formation of nanoparticles. The experimental set-up was based on a 2 + 1 + 1 static micro-mixer in order to test the successive addition of reaction components in a micro-continuous flow process. The residence times for a single mixing step in the chip device were chosen in the range between about 1 second and 1 minute. As a result, single particles of different sizes, simple particle aggregates, core–shell particles as well as complex aggregates and hexagonal nanocrystallites were obtained under different reaction conditions. The reaction mixtures were characterized by UV-Vis spectroscopy as well as by differential centrifugal sedimentation (DCS) and scanning electron microscopy (SEM) reflecting the variety of colloidal gold formed in the microreactor.
Benzoxaboroles: A New Class of Potential Drugs for Human African Trypanosomiasis (2011)

Human African trypanosomiasis, caused by the kinetoplastid parasite Trypanosoma brucei, affects thousands of people across sub-Saharan Africa, and is fatal if left untreated. Treatment options for this disease, particularly stage 2 disease, which occurs after parasites have infected brain tissue, are limited due to inadequate efficacy, toxicity and the complexity of treatment regimens. We have discovered and optimized a series of benzoxaborole-6-carboxamides to provide trypanocidal compounds that are orally active in murine models of human African trypanosomiasis. A key feature of this series is the presence of a boron atom in the heterocyclic core structure, which is essential to the observed trypanocidal activity. We also report the in vivo pharmacokinetic properties of lead compounds from the series and selection of SCYX-7158 as a preclinical candidate.
Clinical correlation between atlantoxial osteoarthritis and atlantoxial instability (2012)

Objective To investigate the relationship between atlantoxial instability and atlantoxial osteoarthritis.Methods Various imaging datas of 82 patients with atlantoxial osteoarthritis were reviewed retrospectively.And the existence of the atlantoaxial instability in patients with atlantoxial osteoarthritis was observed.Eighty-two patients without atlantoxial osteoarthritis were enrolled as control.Restults Among the patients with atlantoxial osteoarthritis,atlantoaxial instability was found in 15 cases(18.29％).In control group,atlantoxial instability was found in 3 cases(3.65％).The difference was significant between the two groups.Conclusions The patients with atlantoxial osteoarthritis has the tendency of atlantoxial instability,atlantoxial osteoarthritis may play an important role in the progress of atlantoxial instability.

Key words: 
Atlantoxial instability; Osteoarthritis; Anatomy
Sparse Gauss-Hermite Quadrature Filter with Application to Spacecraft Attitude Estimation (2011)

A novel sparse Gauss―Hermite quadrature filter is proposed using a sparse-grid method for multidimensional numerical integration in the Bayesian estimation framework. The conventional Gauss―Hermite quadrature filter is computationally expensive for multidimensional problems, because the number of Gauss―Hermite quadrature points increases exponentially with the dimension. The number of sparse-grid points of the computationally efficient sparse Gauss―Hermite quadrature filter, however, increases only polynomially with the dimension. In addition, it is proven in this paper that the unscented Kalman filter using the suggested optimal parameter is a subset of the sparse Gauss―Hermite quadrature filter. The sparse Gauss-Hermite quadrature filter is therefore more flexible to use than the unscented Kalman filter in terms of the number of points and accuracy level, and it is more efficient than the conventional Gauss―Hermite quadrature filter. The application to the spacecraft attitude estimation problem demonstrates better performance of the sparse Gauss―Hermite quadrature filter in comparison with the extended Kalman filter, the cubature Kalman filter, and the unscented Kalman filter.
Information processing in medical imaging : 14th International Conference, Ile de Berder, France, June 1995 (1995)

Part 1. Long papers on: Image formation. Bayesian tomographic reconstruction. Tomographic reconstruction and image quality. Image matching. Model based image segmentation. Shape description. Segmentation. Image understanding. Image registration. Functional imaging. Applications. Part 2. Short papers on: Image formation, tomographic reconstruction and image quality. Shape description. Image segmentation. Image registration. Applications.
A Formal Model of Crash Recovery in a Distributed System (1983)

A formal model for atomic commit protocols for a distributed database system is introduced. The model is used to prove existence results about resilient protocols for site failures that do not partition the network and then for partitioned networks. For site failures, a pessimistic recovery technique, called independent recovery, is introduced and the class of failures for which resilient protocols exist is identified. For partitioned networks, two cases are studied: the pessimistic case in which messages are lost, and the optimistic case in which no messages are lost. In all cases, fundamental limitations on the resiliency of protocols are derived.
Direct fabrication of carbon nanotube circuits by selective area chemical vapour deposition on pre-patterned structures (2000)

We report on a method for self-assembly of integrated carbon nanotube circuits using selective area chemical vapour deposition on pre-patterned catalyst electrodes. The circuits consist of a multi-wall carbon nanotube bridging a pair of electrodes, forming a metal/carbon nanotube/metal structure. Electron-beam lithography was used to define electrode sets separated by a desired distance on a 500 nm thick SiO2 film on Si substrates. Following metal evaporation and lift-off, chemical vapour deposition was used for selective growth of carbon nanotubes on the catalyst electrodes. The carbon nanotubes eventually form a bridge between nearby electrodes consisting of one, or in some cases more than one, multi-wall nanotube. The resistance of the carbon nanotube circuits at room temperature is typically less than 100 kΩ. For a few high-resistance samples (>>100 kΩ) transport properties were studied in a temperature range from room temperature to 2 K. At room temperature the I-V is linear. The resistance increases with decreasing temperature, and the I-V gradually becomes nonlinear. At low temperatures a gap appears around V = 0 suggesting semiconducting behaviour.
Digital error correction technique for binary decision successive approximation ADCs (2009)

A digital error correction technique with negligible hardware overhead is proposed for binary successive approximation ADCs. A redundant decision phase is inserted between the normal SAR operations, and the coarse decision error caused by incomplete DAC settling is corrected by a digital code addition. The relaxed DAC settling requirement for coarse decision increases the conversion speed.
Effects of dietary methionine, cystine, and glycine on endogenous hypercholesterolemia in hepatoma-bearing rats. (1986)

The effects on hypercholesterolemia of dietary additions of cystine (Cys), methionine (Met), glycine (Gly), and a combination of Met and Gly to a 20% casein diet were studied in male Donryu rats subcutaneously implanted with an ascites hepatoma line of AH109A cells. The hepatoma-bearing rats fed the 20% casein diet lapsed into both endogenous hypertriglyceridemia and hypercholesterolemia when compared to hepatoma-free (normal) rats fed the same diet. The hypercholesterolemia was due to an elevation (3.2 fold) in the very low-density lipoprotein plus low-density lipoprotein (VLDL + LDL)-cholesterol (Ch) level. The high-density lipoprotein (HDL)-Ch level was slightly but significantly decreased. These lipoprotein changes in hepatoma-bearing rats resulted in a marked (4.5 fold) increase in the atherogenic index (AI, (VLDL + LDL)-Ch/HDL-Ch) in comparison with that of tumor-free rats. The dietary additions of 1.2% Met, 1.2% Cys, and a combination of 1.2% Met and 2.5% Gly significantly suppressed the hepatoma-induced increase in (VLDL + LDL)-Ch with no influence on the hepatoma-induced decrease in HDL-Ch, leading to a noticeable fall in AI. These results indicate that hepatoma-bearing rats are useful as an endogenously hyperlipidemic model and that some dietary amino acids are capable of improving hepatoma-induced hypercholesterolemia and abnormal serum lipoprotein profiles.
Measurement of trace atmospheric species by chemical ionization mass spectrometry: Speciation of reactive nitrogen and future directions (2007)

Chemical ionization mass spectrometry (CIMS) has proven to be a powerful method for sensitive, fast time response (t approximately 1 sec) measurements of various atmospheric compounds with limits of detection (LOD) of the order of tens of pptv and lower. The rapid time response of CIMS is particularly well suited for airborne measurements and its application has largely grown out of airborne measurements in the stratosphere and upper troposphere. This work reviews some of the advances in CIMS technology that have occurred in the past decade. In particular, CIMS methods for selective measurement of reactive nitrogen species (e.g., HNO3, HO2NO2, PAN, and NH3) in the lower atmosphere (altitudes approximately 0-8 km) are described. In addition, recent developments in CIMS technology for the selective measurement of gas-phase hydroperoxides and aerosol chemical composition are briefly described.
Mechanism of Cell Death Initiation in the Rat Uterine Epithelia During the Proestrus-Estrus Transition. (2008)

The rodent uterus is a classical target tissue for sexual steroid hormones. During the estrous cycle, the uterus presents morphological changes including marked proliferation of both luminal and glandular epithelia, followed by its regression in response to cyclic changes in serum steroid hormone levels. The aim of the present study was to assess the apoptotic mechanism involved in cellular death of the uterine epithelial cells from 13:00 h of proestrus day to 13:00 h of estrus day, when apoptosis initiates in this tissue. The apoptotic index was evaluated by TUNEL assay, caspases-8, -9 and -3 activation was detected by western blot and active caspase-3 expression was detected by immunohistochemistry. Our results show that apoptosis was first detected in the glandular epithelium, beginning at 00:00 h on the day of estrus, and it increased during the next hours, presenting its highest levels at 13:00 h on the day of estrus. In the luminal epithelium, apoptotic cells were first detected at 06:00 h on the day of estrus, and the apoptotic index increased during the next hours presenting its highest levels at 13:00 h on the day of estrus. We also demonstrate the activation of caspase-8, -9 and -3. Caspase-8 was activated since 17:00 h of proestrus day presenting its maximal level at 06:00 h of estrus day. Active caspase-9 was detected beginning at 13:00 h on the day of proestrus and increased gradually presenting its maximal level at 06:00 h on the day of estrus. Active caspase-3 presented a significant increase since 00:00 h on the day of estrus presenting its maximal level at 06:00 h on the day of estrus. Active caspase-3 was detected both in the luminal and glandular epithelium. The active caspase-3 immunostaining was first detected in the glandular epithelium from 00:00 h on the day of estrus, and the highest level was observed, in both epithelia, at 13:00 h on the day of estrus. These results are in agreement with the data obtained by TUNEL. In conclusion, our results show a differential timing of cell death between glandular and luminal epithelium. Interestingly, both apoptotic pathways, the receptor-mediated pathway and the mitochondria dependent pathway, are involved in the initiation of apoptosis mediated by caspase-3. This research was supported by CONACYT P47829-Q and 46759-Q.