gebhart/patrepeval huggingface dataset:
An engineered disulfide bridge mimics the effect of calcium to protect neutral protease against local unfolding (2005)

The extreme thermal stabilization achieved by the introduction of a disulfide bond (G8C/N60C) into the cysteine-free wild-type-like mutant (pWT) of the neutral protease from Bacillus stearothermophilus[Mansfeld J, Vriend G, Dijkstra BW, Veltman OR, Van den Burg B, Venema G, Ulbrich-Hofmann R & Eijsink VG (1997) J Biol Chem272, 11152-11156] was attributed to the fixation of the loop region 56-69. In this study, the role of calcium ions in the guanidine hydrochloride (GdnHCl)-induced unfolding and autoproteolysis kinetics of pWT and G8C/N60C was analyzed by fluorescence spectroscopy, far-UV CD spectroscopy and SDS/PAGE. First-order rate constants (kobs) were evaluated by chevron plots (ln kobs vs. GdnHCl concentration). The kobs of unfolding showed a difference of nearly six orders of magnitude (DeltaDeltaG# = 33.5 kJ.mol(-1) at 25 degrees C) between calcium saturation (at 100 mM CaCl2) and complete removal of calcium ions (in the presence of 100 mM EDTA). Analysis of the protease variant W55F indicated that calcium binding-site III, situated in the critical region 56-69, determines the stability at calcium ion concentrations between 5 and 50 mM. In the chevron plots the disulfide bridge in G8C/N60C shows a similar effect compared with pWT as the addition of calcium ions, suggesting that the introduced disulfide bridge fixes the region (near calcium binding-site III) that is responsible for unfolding and subsequent autoproteolysis. Owing to the presence of the disulfide bridge, the DeltaDeltaG# is 13.2 kJ.mol(-1) at 25 degrees C and 5 mM CaCl2. Non-linear chevron plots reveal an intermediate in unfolding probably caused by local unfolding of the loop 56-69. The occurrence of this intermediate is prevented by calcium concentrations of > 5 mM, or the introduction of the disulfide bridge G8C/N60C.
Regulation of the expression of multiple class II genes in murine B cells by B cell stimulatory factor-1 (BSF-1). (1986)

We have studied the mechanisms governing the induction of class II major histocompatibility complex (MHC) antigens on murine B lymphocytes by B cell stimulatory factor-1 (BSF-1). BSF-1 induced a dramatic (10- to 15-fold) and selective increase in class II MHC antigen expression, as judged by flow cytometry. Analysis of radiolabeled membrane proteins on BSF-1-induced B cells also showed that the expression of class II MHC antigens was increased 10- to 15-fold. Biosynthetic labeling studies established that a selective increase in the translation of class II MHC molecules could be detected at 5 to 6 hr post-addition of BSF-1 to culture. After 16 hr of culture, when cell surface expression was induced 12- to 15-fold, biosynthesis rates of class II MHC antigens was induced fivefold to sixfold. The biosynthesis of the I region-associated invariant chain (Ii) was also enhanced. Actinomycin D abrogated the increased biosynthetic labeling of class II products, suggesting transcriptional regulation of expression. At 6 hr after addition of BSF-1, there was a twofold increase in the steady-stage level of class II mRNA, which was slightly increased at 16 hr. The BSF-1-induced increase in surface Ia antigen is dependent on new transcription and translation. However, posttranslational events that lead to a decrease in membrane antigen turnover rate or to an increase in protein stability probably also play a significant role in the hyperexpression of class II antigens on BSF-1-treated B lymphocytes.
Microchip technology in mass spectrometry-based bioanalysis: Advances in the analysis of peptides, proteins, and pharmaceuticals (2015)

Analytical microsystems are attractive in modern bioanalysis where sample amounts often are low and fast analyses are required. Microsystems also provide the prospect of integrating several functional elements on a single platform. The aim of this work was to develop analytical microsystems for fast analysis of bio- and drug molecules. For this, microchips with separation- and injection channels and monolithically integrated electrospray ionization (ESI) emitter were fabricated of epoxy photoresist SU-8 by photolithography and adhesive bonding. &#13;\n&#13;\nFor peptide mass fingerprinting and protein sequencing characteristic tryptic peptides were fast and easily separated and detected by microchip capillary electrophoresis (MCE)-ESI/mass spectrometry (MS). Additionally, protein identification based on tandem MS fragmentation data of a single tryptic peptide was achieved. Finally, this rapid (total analysis time below ten minutes) microchip method permitted analysis of human muscle cell lysates. &#13;\n&#13;\nFor online coupling of microchip capillary isoelectric focusing (cIEF) to ESI/MS a bilateral sheath flow interface or a two-dimensional separation unit was integrated on-chip. Rapid focusing of peptides by their isoelectric points (pI) was achieved without pretreatment of the SU-8 surface. After focusing the peptides were electrokinetically mobilized toward ESI/MS. The two-dimensional chip design enabled unique separation selectivity for peptides based on both pI values and intrinsic electrophoretic mobilities by multiplex-cIEF-transient-isotachophoresis. &#13;\n&#13;\nRapid metabolic profiling was demonstrated from urine after intake of tramadol or paracetamol. Both phase I- and II metabolites were separated and detected by MCE-ESI/MS within 35 s. In addition, Michaelis-Menten kinetics was successfully determined for the CYP450-mediated oxidation of bufuralol to 1-hydroxybufuralol. &#13;\n&#13;\nSample preconcentration (pretreatment) was integrated on-chip by solid-phase extraction (SPE) and liquid-phase microextraction (LPME). For SPE, a monolith zone was firmly anchored at the injection cross of the MCE-ESI/MS microchip by laser induced photopolymerization. The monolith was selective toward hydrophobic and hydrophilic sample molecules and enrichment factors as high as 23-fold was achieved with a loading time as short as 25 s. In addition, LPME was easily downscaled to low volume applications and offered selectivity in the analysis of phase I metabolites compared to SPE. &#13;\n&#13;\nIn contrast to previous research in the same field this work offers bioanalysis with several on-chip integrated steps (preconcentration, injection, separation, and analysis) without considerably increasing the short analysis times characteristic of microchip assays.
Fast restoration of ATM networks (1994)

Asynchronous transfer mode (ATM) is now well recognized as the fundamental switching and multiplexing technique for future broadband ISDN. As these networks will be increasingly relied upon for providing a multitude of integrated voice, data, and video services, network reliability is a key concern. There are several intrinsic features of ATM networks that could potentially be exploited to provide improved restoration techniques, beyond those established for synchronous transfer mode (STM) networks, such as digital cross-connect restoration or self-healing rings. These features include ATM cell level error detection, inherent rate adaptation and nonhierarchical multiplexing. The authors explore the use of these features in developing fast restoration strategies for ATM networks. In particular, they address: (1) ATM error detection capabilities for enhanced failure detection, (2) network rerouting strategies, (3) spare capacity allocation, and (4) network control architecture and related implementation aspects. Their findings suggest that fast network span failure detection and bandwidth-efficient rerouting capabilities can be combined to develop restoration strategies for ATM networks with significantly greater performance-cost ratios when compared to existing STM network restoration strategies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rat Parathyroid Hormone-Like Peptide: Comparison with the Human Homologue and Expression in Malignant and Normal Tissue (1989)

A rat Leydig cell tumor cDNA library was screened with a 32P-labeled genomic restriction fragment encoding human PTH-like peptide (hPLP), and three cDNA clones were isolated. The largest cDNA insert contained 1146 nucleotides. The cloned cDNA encodes a 177-amino acid protein consisting of a predicted 36-amino acid leader sequence and a 141-amino acid mature peptide in which 9 of 13 amino-terminal residues are identical to rat PTH (rPTH). Comparison of rPLP with hPLP reveals marked conservation of both the nucleotide and amino acid sequences through the prepro, amino-terminal, and midregion portions of the molecules. There is also striking conservation of the 3' noncoding regions of rPLP and hPLP mRNAs, both of which contain AU-rich repeated sequences that may affect mRNA stability. A single species of mRNA of approximately 1.4-kilobases was identified in the rat Leydig cell tumor and in normal rat stomach. Southern blot analysis is consistent with the presence of a single copy of the rPLP gene per haploid genome, and there is no major rearrangement or amplification of the rPLP gene in DNA isolated from the tumor per se. The results demonstrate the presence of a single gene transcript in a rat model of malignancy associated with hypercalcemia which encodes a peptide homologous to hPLP, document the marked interspecies sequence conservation that exists in major functional domains of the mRNAs and peptides, and show the expression of mRNA encoding rPLP in normal stomach as well as in neoplastic rat tissue.
Investigation of Freeze/Thaw-Related Quality Attributes of a Liquid Biopharmaceutical Formulation: The Role of Saccharide Excipients (2012)

Saccharides, including sucrose, trehalose, mannitol, and sorbitol, are commonly employed as stabilizers, cryoprotectants and/or tonicity adjusters in protein formulations. During thawing of formulated bulk drug substance, a white, crystalline precipitate was observed. In addition, upon thawing, vial breakage was observed for filled drug product that had been previously frozen at -40 °C. To investigate the causes of both phenomena, multiple physical characterization techniques were utilized to characterize the formulations. The powder X-ray diffraction pattern of precipitate collected from thawed bulk was consistent with that of a mannitol control. Upon linking the detrimental behavior to the freeze/thaw properties of the tonicity adjustor, mannitol, alternative saccharide excipients, including sorbitol, sucrose, and trehalose, were evaluated at isotonic concentrations over a temperature range of -80 to 25 °C using physico-chemical techniques and visual observation. Neither precipitation nor vial breakage was observed for the alternate saccharides. Recommendations for saccharide selection are given based on storage conditions and scale considerations for liquid biopharmaceutical formulations.
A Novel Therapeutic Approach to Treating Obesity through Modulation of TGFβ Signaling (2012)

Obesity results from disproportionately high energy intake relative to energy expenditure. Many therapeutic strategies have focused on the intake side of the equation, including pharmaceutical targeting of appetite and digestion. An alternative approach is to increase energy expenditure through physical activity or adaptive thermogenesis. A pharmacological way to increase muscle mass and hence exercise capacity is through inhibition of the activin receptor type IIB (ActRIIB). Muscle mass and strength is regulated, at least in part, by growth factors that signal via ActRIIB. Administration of a soluble ActRIIB protein comprised of a form of the extracellular domain of ActRIIB fused to a human Fc (ActRIIB-Fc) results in a substantial muscle mass increase in normal mice. However, ActRIIB is also present on and mediates the action of growth factors in adipose tissue, although the function of this system is poorly understood. In the current study, we report the effect of ActRIIB-Fc to suppress diet-induced obesity and linked metabolic dysfunctions in mice fed a high-fat diet. ActRIIB-Fc induced a brown fat-like thermogenic gene program in epididymal white fat, as shown by robustly increased expression of the thermogenic genes uncoupling protein 1 and peroxisomal proliferator-activated receptor-γ coactivator 1α. Finally, we identified multiple ligands capable of reducing thermogenesis that represent likely target ligands for the ActRIIB-Fc effects on the white fat depots. These data demonstrate that novel therapeutic ActRIIB-Fc improves obesity and obesity-linked metabolic disease by both increasing skeletal muscle mass and by inducing a gene program of thermogenesis in the white adipose tissues.
Text Independent Writer Identification for Oriya Script (2012)

Automatic identification of an individual based on his/her handwriting characteristics is an important forensic tool. In a computational forensic scenario, presence of huge amount of text/information in a questioned document cannot be ensured. Lack of data threatens system reliability in such cases. We here propose a writer identification system for Oriya script which is capable of performing reasonably well even with small amount of text. Experiments with curvature feature are reported here, using Support Vector Machine (SVM) as classifier. We got promising results of 94.00% writer identification accuracy at first top choice and 99% when considering first three top choices.
Coded Orbital Angular Momentum Based Free‐Space Optical Transmission (2016)

In this article, we explore orbital‐angular‐momentum‐based (OAM) free‐space optical (FSO) transmission systems using low‐density parity‐check (LDPC) coded quadrature phase‐shift keying (QPSK) modulation format. The theory of OAM modes is discussed first, followed by the schemes to generate, multiplex/demultiplex, and detect OAM modes. Then, the FSO transmission systems with and without atmospheric turbulence are studied. The spatial‐ and time‐varying atmospheric turbulence is simulated via fast‐changing phase patterns, which are recorded by modified von Karman spectrum statistics. The atmospheric turbulence effects are discussed in terms of the intensity profile of OAM beam and power distribution among adjacent mode channels. In addition, we review the performance of LDPC coding based FSO transmission systems with a single OAM mode and with OAM multiplexing.
An Efficient Gene-Trap Method Using Poly A Trap Vectors and Characterization of Gene-Trap Events1 (1993)

New trap vectors (U1 and U2) have been developed to trap genes in murine embryonic stem (ES) cells. The polyA addition signal of the neomycin phosphotransferase II (neo) gene was removed from these vectors so that they needed to trap an endogenous polyA signal for expression of the neo gene. The frequency of gene-trap events of these vectors was about five times higher than with the vector containing the polyA signal, and only one copy of the trap vector was integrated in most cases. Four out of five 5'-flanking regions of the integrated vector in ES cell lines were found to be novel endogenous promoters, suggesting that this method is efficient for trapping genes in ES cells. In two cases analyzed, large deletions or rearrangements spanning more than 10 kb were found in the 3'-flanking region of the trap vector introduced by electroporation. This result suggests that phenotypes observed in homozygotes with a mutated allele could be due to the disruption of a gene adjacent to the trapped gene, but not of the trapped gene.
Amino Acid Composition of an Organic Brown Rice Protein Concentrate and Isolate Compared to Soy and Whey Concentrates and Isolates (2014)

A protein concentrate (Oryzatein-80™) and a protein isolate (Oryzatein-90™) from organic whole-grain brown rice were analyzed for their amino acid composition. Two samples from different batches of Oryzatein-90™ and one sample of Oryzatein-80™ were provided by Axiom Foods (Los Angeles, CA, USA). Preparation and analysis was carried out by Covance Laboratories (Madison, WI, USA). After hydrolysis in 6-N hydrochloric acid for 24 h at approximately 110 °C and further chemical stabilization, samples were analyzed by HPLC after pre-injection derivitization. Total amino acid content of both the isolate and the concentrate was approximately 78% by weight with 36% essential amino acids and 18% branched-chain amino acids. These results are similar to the profiles of raw and cooked brown rice except in the case of glutamic acid which was 3% lower in the isolate and concentrate. The amino acid content and profile of the Oryzatein-90™ isolate was similar to published values for soy protein isolate but the total, essential, and branched-chain amino acid content of whey protein isolate was 20%, 39% and 33% greater, respectively, than that of Oryzatein-90™. These results provide a valuable addition to the nutrient database of protein isolates and concentrates from cereal grains.
β-Adrenergic receptor blockade arrests myocyte damage and preserves cardiac function in the transgenic Gsα mouse (1999)

Transgenic (TG) mice with cardiac G(salpha) overexpression exhibit enhanced inotropic and chronotropic responses to sympathetic stimulation, but develop cardiomyopathy with age. We tested the hypothesis that cardiomyopathy in TG mice with G(salpha) overexpression could be averted with chronic beta-adrenergic receptor (beta-AR) blockade. TG mice and age-matched wild-type littermates were treated with the beta-AR blocker propranolol for 6-7 months, starting at a time when the cardiomyopathy was developing but was not yet severe enough to induce significant cardiac depression (9.5 months of age), and ending at a time when cardiac depression and cardiomyopathy would have been clearly manifest (16 months of age). Propranolol treatment, which can induce cardiac depression in the normal heart, actually prevented cardiac dilation and the depressed left ventricular function characteristic of older TG mice, and abolished premature mortality. Propranolol also prevented the increase in myocyte cross-sectional area and myocardial fibrosis. Myocyte apoptosis, already apparent in 9-month-old TG mice, was actually eliminated by chronic propranolol. This study indicates that chronic sympathetic stimulation over an extended period is deleterious and results in cardiomyopathy. Conversely, beta-AR blockade is salutary in this situation and can prevent the development of cardiomyopathy.
A 10-Gb/s CMOS clock and data recovery circuit (2002)

A 10-Gb/s phase-locked clock and data recovery circuit incorporates a 5-GHz interpolating voltage-controlled oscillator and a half-rate phase detector. The phase detector provides a linear characteristic while retiming and demultiplexing the data with no systematic phase offset. Fabricated in a 0.18-/spl mu/m CMOS technology, the circuit exhibits an rms jitter of 6.6 ps in the recovered clock with random data input of length 2/sup 23/-1. The power dissipation is 99 mW from a 2.6-V supply.
Neurobehavioral radiation mitigation to standard brain cancer therapy regimens by Mn(III) n‐butoxyethylpyridylporphyrin‐based redox modifier (2016)

Combinations of radiotherapy (RT) and chemotherapy have shown efficacy toward brain tumors. However, therapy-induced oxidative stress can damage normal brain tissue, resulting in both progressive neurocognitive loss and diminished quality of life. We have recently shown that MnTnBuOE-2-PyP(5+) (Mn(III)meso-tetrakis(N-n-butoxyethylpyridinium -2-yl)porphyrin) rescued RT-induced white matter damage in cranially-irradiated mice. Radiotherapy is not used in isolation for treatment of brain tumors; temozolomide is the standard-of-care for adult glioblastoma, whereas cisplatin is often used for treatment of pediatric brain tumors. Therefore, we evaluated the brain radiation mitigation ability of MnTnBuOE-2-PyP(5+) after either temozolomide or cisplatin was used singly or in combination with 10 Gy RT. MnTnBuOE-2-PyP(5+) accumulated in brains at low nanomolar levels. Histological and neurobehavioral testing showed a drastic decrease (1) of axon density in the corpus callosum and (2) rotorod and running wheel performance in the RT only treatment group, respectively. MnTnBuOE-2-PyP(5+) completely rescued this phenotype in irradiated animals. In the temozolomide groups, temozolomide/ RT treatment resulted in further decreased rotorod responses over RT alone. Again, MnTnBuOE-2-PyP(5+) treatment rescued the negative effects of both temozolomide ± RT on rotorod performance. While the cisplatin-treated groups did not give similar results as the temozolomide groups, inclusion of MnTnBuOE-2-PyP(5+) did not negatively affect rotorod performance. Additionally, MnTnBuOE-2-PyP(5+) sensitized glioblastomas to either RT ± temozolomide in flank tumor models. Mice treated with both MnTnBuOE-2-PyP(5+) and radio-/chemo-therapy herein demonstrated brain radiation mitigation. MnTnBuOE-2-PyP(5+) may well serve as a normal tissue radio-/chemo-mitigator adjuvant therapy to standard brain cancer treatment regimens. Environ. Mol. Mutagen. 57:372-381, 2016. © 2016 Wiley Periodicals, Inc.
13C nuclear magnetic resonance studies of Pseudomonas putida fatty acid metabolic routes involved in poly(3-hydroxyalkanoate) synthesis (1994)

The formation of poly(3-hydroxyalkanoates) (PHAs) in Pseudomonas putida KT2442 from various carbon sources was studied by 13C nuclear magnetic resonance spectroscopy, gas chromatography, and gas chromatography-mass spectroscopy. By using [1-13C]decanoate, the relation between beta-oxidation and PHA formation was confirmed. The labeling pattern in PHAs synthesized from [1-13C]acetate corresponded to the formation of PHAs via de novo fatty acid biosynthesis. Studies with specific inhibitors of the fatty acid metabolic pathways demonstrated that beta-oxidation and de novo fatty acid biosynthesis function independently in PHA formation. Analysis of PHAs derived from [1-13C]hexanoate showed that both fatty acid metabolic routes can function simultaneously in the synthesis of PHA. Furthermore, evidence is presented that during growth on medium-chain-length fatty acids, PHA precursors can be generated by elongation of these fatty acids with an acetyl coenzyme A molecule, presumably by a reverse action of 3-ketothiolase.
Facial performance sensing head-mounted display (2015)

There are currently no solutions for enabling direct face-to-face interaction between virtual reality (VR) users wearing head-mounted displays (HMDs). The main challenge is that the headset obstructs a significant portion of a user's face, preventing effective facial capture with traditional techniques. To advance virtual reality as a next-generation communication platform, we develop a novel HMD that enables 3D facial performance-driven animation in real-time. Our wearable system uses ultra-thin flexible electronic materials that are mounted on the foam liner of the headset to measure surface strain signals corresponding to upper face expressions. These strain signals are combined with a head-mounted RGB-D camera to enhance the tracking in the mouth region and to account for inaccurate HMD placement. To map the input signals to a 3D face model, we perform a single-instance offline training session for each person. For reusable and accurate online operation, we propose a short calibration step to readjust the Gaussian mixture distribution of the mapping before each use. The resulting animations are visually on par with cutting-edge depth sensor-driven facial performance capture systems and hence, are suitable for social interactions in virtual worlds.
Symmetrical refractive error elevates stereo thresholds (1992)

We measured the effects of symmetrical spectacle blur on stereo thresholds using anaglyphlc dynamic random element stereograms (ADRES) across a two octave range of hypercyclopean spatial frequencies in three subjects. Symmetrical blur elevated subjects' stereo thresholds. The absolute and relative amount of threshold elevation increased with hypercyclopean spatial frequency.