gebhart/patrepeval huggingface dataset:
Increased Myogenic Potential and Fusion of Matrilysin-Expressing Myoblasts Transplanted in Mice (1999)

The success of myoblast transplantation in clinical trials has been limited in part by the low dispersion of grafted cells outside the injection site. Our research group previously reported that the culture of myoblasts with concanavalin A, a stimulator of metalloproteinase production, increased their migration. Several lines of evidence also suggested that muscle cell fusion involves metalloproteinase-sensitive mechanisms. To determine whether the increased expression of metalloproteinases had an influence on myoblast fusion and dispersion through the muscle following transplantation, we generated a myoblast cell line expressing human matrilysin (MMP-7). The MMP-7-expressing myoblasts were obtained by the stable transfection of a matrilysin expression vector in a TnILacZ immortomouse myoblast clone. Matrilysin-expressing myoblasts showed a highly increased in vitro fusion index, forming seven times (p < 0.001) more myotubes than the control cell line and three times (p < 0.001) more myotubes than the Immortomyoblast parental clone. Single-site transplantation of matrilysin-expressing myoblasts generated more fibers (p < 0.001), over a greater surface (p < 0.001) than the control cell line. The cotransplantation of matrilysin-expressing myoblasts and of normal human myoblasts in SCID mice increased the number of human dystrophin-positive fibers and myotubes by sixfold. Although no significant increased migration of myoblasts outside the injection sites was observed, our results show that the metalloproteinase activity can improve the myogenic potential of myoblasts in vitro and the fusion of myoblasts with host fibers in vivo. MMP-7 expression may be useful in increasing myoblast transplantation success.
Mode-Locked Topological Insulator Laser Utilizing Synthetic Dimensions (2020)

The unique properties of topological physics allow for the design of an array of synchronized, mutually locked semiconductor laser resonators, which could be used as a source of high-power mode-locked laser pulses.
Expression of recombinant murine pregnancy‐associated plasma protein‐A (PAPP‐A) and a novel variant (PAPP‐Ai) with differential proteolytic activity (2002)

Murine pregnancy-associated plasma protein-A (PAPP-A) cDNA encoding a 1545 amino-acid protein has been cloned. We have also identified and cloned cDNA that encodes a novel variant of PAPP-A, PAPP-Ai, carrying a 29-residue highly basic insert. The point of insertion corresponds to a junction between two exons in the human PAPP-A gene. The human intron flanked by these exons does not encode a homologous corresponding insert, which is unique to the mouse. The overall sequence identity between murine and human PAPP-A is 91%, and murine PAPP-A contains sequence motifs previously described in the sequence of human PAPP-A. Through expression in mammalian cells, we show that murine PAPP-A and PAPP-Ai are active metalloproteinases, both capable of cleaving insulin-like growth factor binding protein (IGFBP)-4 and -5. Cleavage of IGFBP-4 is dramatically enhanced by the addition of IGF, whereas cleavage of IGFBP-5 is slightly inhibited by IGF, as previously established with human PAPP-A. Surprisingly, however, quantitative analyses demonstrate that the murine PAPP-Ai cleaves IGFBP-4 very slowly compared to PAPP-A, even though its ability to cleave IGFBP-5 is unaffected by the presence of the insert. By RT-PCR analysis, we find that both variants are expressed in several tissues. The level of mRNA in the murine placenta does not exceed the levels of other tissues analyzed. Furthermore, the IGFBP-4-proteolytic activity of murine pregnancy serum is not elevated. This is in striking contrast to the increase seen in human pregnancy serum, and the expression of PAPP-A in the human placenta, which exceeds other tissues at least 250-fold. Interestingly, the position of the insert of PAPP-Ai, within the proteolytic domain, lies in close proximity to the cysteine residue, which in human PAPP-A forms a disulfide bond with the proform of eosinophil major basic protein (proMBP). ProMBP functions as a proteinase inhibitor in the PAPP-A-proMBP complex, but whether any mechanistic parallel on regulation of proteolytic activity can be drawn between the insert of PAPP-Ai and the linkage to proMBP is not known. Importantly, these data support the development of the mouse as a model organism for the study of PAPP-A, which must take into account the differences between the mouse and the human.
Determination of Carbon Content in Steels Using Laser-Induced Breakdown Spectroscopy Assisted with Laser-Induced Radical Fluorescence (2017)

Carbon is a key element for steel properties but hard to be determined by laser-induced breakdown spectroscopy (LIBS). Utilizing the combination of carbon in analytes and nitrogen in ambient gas to generate carbon-nitrogen (CN) radicals, LIBS assisted with laser-induced radical fluorescence (LIBS-LIRF) was proposed to resonantly excite radicals instead of atoms in plasmas. The CN radicals in the B<sup>2</sup>Σ-A<sup>2</sup>Π band were stimulated by a 421.60 nm laser wavelength and emitted 388.34 nm fluorescence. The results show that the spectral intensity of the CN radicals was enhanced by 2 orders of magnitude using LIBS-LIRF. Then carbon content in steels was accurately and sensitively determined without spectral interference. The limits of detection (LoDs) were 0.039 and 0.013 wt % in air and nitrogen gas, respectively. The limits of quantification (LoQs) were 0.130 and 0.043 wt % in air and nitrogen gas, respectively. This work demonstrated the feasibility of LIBS to realize reliable carbon determination in steel industry.
Therapeutic Efficacy of an Fc-Enhanced TCR-like Antibody to the Intracellular WT1 Oncoprotein (2014)

The data provide proof of concept that an Fc-enhanced mAb can improve efficacy against a low-density, tumor-specific, peptide/MHC target, and support further development of this mAb against an important intracellular oncogenic protein.
New low inductance gas switches for linear transformer drivers (2010)

We have developed two new gas switches that are designed to be used with linear transformer drivers. The switches, which can be DC charged to 200 kV and triggered with less than a 2-ns $1\mathrm{\text{\ensuremath{-}}}\ensuremath{\sigma}$ jitter, have overall inductances ranging from 69 to 85 nH. When transferring 400 J of energy per shot, the switches have lifetimes in excess of 5000 shots. The two switches are insulated with 130--270 PSIA of air and are submerged in transformer oil during operation. These switches should allow development of linear transformer drivers that are more compact and have higher peak power.
Cleavage specificity of type IV collagenase (gelatinase) from human skin (1989)

Type IV collagenase (gelatinase) has a marked substrate specificity for denatured collagen (gelatin). Cleavage site specificity of type IV collagenase from human skin was determined using small collagenous peptides with varied sequences around Gly-Leu or Gly-Ile. Type IV collagenase showed essentially the same order of preference for the peptide substrates as did interstitial collagenase. Both required a peptide with a minimum of six amino acid residues to demonstrate significant gelatinolytic activity and were able to cleave uncharged molecules more rapidly than charged molecules. the repeating Gly-X-Y-Gly sequence of collagen is not an absolute requirement for either enzyme since both digested AcPro-Leu-Gly-Ile-Leu-Ala-Ala-OC2H5 at 70% of the rate of the best substrate peptide, AcPro-Leu-Gly-Leu-Leu-Gly-OC2H5. Km and kcat (Vmax) values were determined for several of the peptides and for the native substrate. Turnover numbers with type IV collagenase were similar to those with interstitial collagenase (Weingarten, H., Martin, R., and Feder, J. (1985) Biochemistry 24, 6730-6734). However, the Km for all peptides investigated was approximately 10-fold lower for type IV collagenase than for interstitial collagenase. Because type IV collagenase does not cleave helical interstitial collagens, the data support the conclusion that secondary structure determines whether the peptide bond can be hydrolyzed at any potential cleavage site.
Purine Nucleoside Phosphorylase Inhibition Attenuates the Progression of Anemia and Organ Damage in Sickle Cell Mice (2022)

Purine nucleoside phosphorylase (PNP) converts guanosine to guanine, inosine to hypoxanthine, and 2'-deoxyguanosine to guanine, and leads to the downstream formation of the pro-oxidant and vasculotoxic hypoxanthine and xanthine. Red blood cells are rich in PNP, yet PNP's role in the pathogenesis of sickle cell disease (SCD) is not known. Our group showed that patients with SCD have increased PNP release and activity, leading to accelerated guanosine/inosine metabolism and increased production of vasculotoxic hypoxanthine/xanthine (Bilan VP et al. 2018). Thus, we proposed that PNP may have a major pathogenic role in red blood cell sickling, hemolytic angioproliferation, cell aggregation and end organ damage, and that PNP inhibition may be beneficial in the treatment of SCD. The highly potent PNP inhibitor 8-aminoguanine is the product of the conversion of the endogenous guanosine metabolite and pro-drug 8-aminoguanosine (8-AG). We investigated the safety and efficacy of short-term (8 weeks) and chronic (20 weeks) treatment of Townes sickle mice (SS) and their non-sickling controls (AA) with 8-AG (60mg/kg/day administered ad libitum in the drinking water). We collected blood and urine samples at multiple intervals using metabolic cages. To determine 8-AG body disposition and PNP inhibition, urine samples were analyzed for purines by liquid chromatography - tandem mass spectrometry (LC-MS/MS). Both AA and SS mice tolerated 8-AG well with no evidence of toxicity. In both AA (n= 15) and SS (n=40) mice there was very efficient conversion of 8-AG that resulted in a 40-50-fold increase in urinary 8-aminoguanine concentrations (p<0.001). In 8-AG treated SS mice we observed reduced hypoxanthine levels, with an increased inosine/hypoxanthine ratio. Additionally, guanosine was increased, guanine was reduced, and an increased guanosine/guanine ratio was observed (p<0.05), suggesting potent PNP inhibition. In SS mice, the 8-week treatment with 8-AG significantly reduced hemoglobinuria (p<0.05) and albuminuria (p<0.05), attenuated left ventricular (LV, p<0.01) and right ventricular (RV, p<0.05) hypertrophy, limited hepatomegaly (p<0.001), and improved RV contractility (p<0.05), with a trend towards reduced lung weights and splenomegaly. In SS mice, 20-week treatment with 8-AG significantly slowed the progression of anemia as evidenced by attenuated age-related drops in hemoglobin and hematocrit levels, and it attenuated hemoglobinuria and albuminuria while significantly reducing splenomegaly (p=<0.05) and hepatomegaly (p<0.05, Figure). Semi-quantitative histopathological analysis suggested reduced iron deposition (Prussian blue stain, Figure), and reduced ischemic (H&E stain) and fibrotic (trichrome stain, Figure) injury in the spleen and liver from SS mice treated with 8-AG. Our data suggest that the PNP inhibitor 8-AG may have a pharmacological benefit in SCD and may warrant further investigation as a multi-pronged treatment approach for SCD. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal
The use of multichip module technology for power electronics miniaturization and packaging (2002)

This paper describes the design and fabrication of a highly integrated, intelligent, integral horsepower, three-phase induction motor drive based on multichip module (MCM) technology. This solid-state controller-known as a multichip power module (MCPM)-uses known good die to obtain minimal footprint, volume, and mass, while maximizing efficiency, reliability, and manufacturability.
Nonbinary LDPC Coding for Multicarrier Underwater Acoustic Communication (2008)

Recently, multicarrier modulation in the form of orthogonal frequency division multiplexing (OFDM) has been shown feasible for underwater acoustic communications via effective algorithms to handle the channel time-variability. In this paper, we propose to use nonbinary low density parity check (LDPC) codes to address two other main issues in OFDM: (i) plain (or uncoded) OFDM has poor performance in fading channels, and (ii) OFDM transmission has high peak to average power ratio (PAPR). We develop new methods to construct nonbinary regular and irregular LDPC codes that achieve excellent performance, match well with the underlying modulation, and can be encoded in linear time and in a parallel fashion. Based on the fact that the generator matrix of LDPC codes has high density, we further show how to reduce the PAPR considerably with minimal overhead. Experimental results confirm the excellent performance of the proposed nonbinary LDPC codes in multicarrier underwater acoustic communications.
Muller C-element Self-corrected Triple Modular Redundant Logic with Multithreading and Low Power Modes (2017)

This work describes voting feedback circuits for triple modular redundant (TMR) self-correcting flip-flops that reduce the flip-flop circuit area by 20% and the energy consumption by 10% over the conventional use of a majority gate. A fully pipelined 256-bit key and 128-bit data advanced encryption standard (AES) engine implemented at the 90 nm technology node using the proposed design and has a maximum performance of 400 MHz and 297 mW in TMR and multi-thread modes. It operates in a low-power, non-redundant mode at 102 mW power dissipation. Testability modes are are also described.
Synthesis, Biological Properties, and Molecular Modeling Investigation of the First Potent, Selective, and Water-Soluble Human A<sub>3</sub> Adenosine Receptor Antagonist (2002)

A new, highly potent, selective, and water-soluble antagonist of the hA(3) adenosine receptor was synthesized and tested in binding and functional assays. Compound 4 (5-[[(4-pyridyl)amino]carbonyl]amino-8-methyl-2-(2-furyl)-pyrazolo[4,3-e]1,2,4-triazolo[1,5-c]pyrimidine hydrochloride) displayed high water solubility (15 mM) and the highest affinity (K(i) = 0.01 nM) and selectivity for the hA(3) versus A(1), A(2A), and A(2B) receptors (>10000-fold) ever reported. A Schild analysis of the antagonism by 4 of agonist-induced inhibition of cAMP production in CHO cells expressing the hA(3) receptor indicated a K(B) value of 0.20 nM.
Intergallery Living Polymerization Using Silicate-Anchored Photoiniferter. A Versatile Preparatory Method for Exfoliated Silicate Nanocomposites (2006)

Living free radical polymerization of a variety of monomers using dithiocarbarmate photoiniferter modified silicate gave dispersed polymer/silicate nanocomposites, even for nanocomposites with very high silicate contents (7−63 wt %). Thus, nanocomposites containing polystyrene, poly(methyl methacrylate), poly(tert-butyl methacrylate), and poly(methyl methacrylate-b-styrene) of controlled molecular weight, architecture, and polydispersity were prepared. Dispersion and random orientation of the silicate layers in the polymer matrix were confirmed by both wide-angle X-ray diffraction and transmission (TEM) and scanning transmission electron microscopy (STEM). One principal finding is that exfoliated nanocomposites with very high silicate contents (above 20 wt %) could be used as nanoadditives or masterbatches to prepare all kinds of nanocomposites by simple blending without always having to begin from scratch. The exfoliation remained stable to subsequent thermal processing. The storage modulus of PMMA/silicate nanocomposite at only 3.2 wt % silicate loading was 30−40% higher than that of neat PMMA at all temperatures in the glassy region below the Tg of PMMA. The method is versatile, simple, and applicable to many monomers and requires no additional catalyst.
Scanning quantum dot microscopy: A quantitative method to measure local electrostatic potential near surfaces (2016)

Abstract In this paper we review a recently introduced microscopy technique, scanning quantum dot microscopy (SQDM), which delivers quantitative maps of local electrostatic potential near surfaces in three dimensions. The key to achieving SQDM imaging is the functionalization of a scanning probe microscope tip with a π-conjugated molecule that acts as a gateable QD. Mapping of electrostatic potential with SQDM is performed by gating the QD by the bias voltage applied to the scanning probe microscope junction and registering changes of the QD charge state with frequency-modulated atomic force microscopy.
Simultaneous time slack budgeting and retiming for dual-Vdd FPGA power reduction (2006)

Field programmable dual-Vdd interconnects are effective to reduce FPGA power.Assuming uniform length interconnects,existing work has developed time slack budgeting to minimize power based on estimating the lower bound of power reduction using dual-Vdd for given time slack.In this paper,we show that such lower bound estimation cannot be extended to mixed length interconnects that are used in modern FPGAs.We develop a technique to estimate power reduction using dual-Vdd for mixed length interconnects, and apply linear programming (LP)to solve slack budgeting to minimize power for mixed length interconnects.Experiments show 53%power reduction on average compared to single-Vdd interconnects.Furthermore,this paper presents a simultaneous retiming and slack budgeting algorithm to reduce power in dual-Vdd FPGAs considering placement and.ip-.op binding constraints.The algorithm is based on mixed integer and linear programming (MILP)and achieves up to 20%power reduction compared to retiming followed by slack budgeting.We propose a runtime e fficient flow to apply simultaneous retiming and slack budgeting only when it is necessary.To the best of our knowledge,this paper is the first in-depth study of simultaneous retiming and slack budgeting for dual-Vdd programmable FPGA power reduction while considering layout constraints.
Multi-seam carving via seamlets (2011)

Seam carving is a powerful retargeting algorithm for mapping images to arbitrary sizes with arbitrary aspect ratios. Meanwhile, the seamlet transform has been introduced as an efficient image representation for seam-carving-based retargeting over heterogeneous multimedia devices with a broad range of display sizes. The original seamlet transform was developed using Haar filters, and hence it enabled traditional single-seam carving by removing a single seam at a time in a recursive manner until the desired image size was reached. In this paper, we develop a more efficient approach for seam carving by enabling multi-seam carving, where at each step of the retargeting algorithm, multiple seams are carved simultaneously. We achieve multi-seam carving by (a) extending the seamlet transform to allow for larger filters, and (b) employing local circular convolution in the vicinity of the selected seams. We show that by extending the seamlet transform we can employ popular filterbanks such as Daubechies' wavelets to achieve efficient multi-seam carving with visual quality that is comparable to single-seam carving using the Haar transform. Furthermore, with multi-seam carving, the number of iterations needed to achieve a given target size can be reduced significantly.
Magnetic-field-induced recovery strain in polycrystalline Ni–Mn–Ga foam (2010)

Recently, we have shown that a polycrystalline Ni–Mn–Ga magnetic shape-memory alloy, when containing two populations of pore sizes, shows very high magnetic-field-induced strain of up to 8.7%. Here, this double-porosity sample is imaged by x-ray microtomography, showing a homogenous distribution of both pore populations. The orientation of six large grains—four with 10M and two with 14M structure—is identified with neutron diffraction. In situ magnetomechanical experiments with a rotating magnetic field demonstrate that strain incompatibilities between misoriented grains are effectively screened by the pores which also stop the propagation of microcracks. During uniaxial compression performed with an orthogonal magnetic bias field, a strain as high as 1% is recovered on unloading by twinning, which is much larger than the elastic value of &lt;0.1% measured without field. At the same time, repeated loading and unloading results in a reduction in the yield stress, which is a training effect similar to that in single crystals.
A monolithic three-axis silicon capacitive accelerometer with micro-g resolution (2004)

A monolithic three-axis silicon capacitive accelerometer utilizing a combined surface and bulk micromachining technology is demonstrated with micro-g resolution. The accelerometer consists of three individual single-axis accelerometers. All three devices have full-wafer thick silicon proof-mass, large area polysilicon sense/drive electrodes, and small sensing gap (<1.5 /spl mu/m) formed by a sacrificial oxide layer. The fabricated accelerometer system is 7/spl times/9 mm/sup 2/ in size, has >5pF/g measured sensitivity and sub-/spl mu/g//spl radic/Hz mechanical noise floor for all three axes. The total measured noise floor of the accelerometer hybrid assembled with CMOS interface circuit is 1.60 /spl mu/g//spl radic/Hz, 1.08 /spl mu/g//spl radic/Hz for in-plane and out-of-plane devices, respectively.
Discovering Known and Unanticipated Protein Modifications Using MS/MS Database Searching (2005)

We present an MS/MS database search algorithm with the following novel features: (1) a novel protein database structure containing extensive preindexing and (2) zone modification searching, which enables the rapid discovery of protein modifications of known (i.e., user-specified) and unanticipated delta masses. All of these features are implemented in Interrogator, the search engine that runs behind the Pro ID, Pro ICAT, and Pro QUANT software products. Speed benchmarks demonstrate that our modification-tolerant database search algorithm is 100-fold faster than traditional database search algorithms when used for comprehensive searches for a broad variety of modification species. The ability to rapidly search for a large variety of known as well as unanticipated modifications allows a significantly greater percentage of MS/MS scans to be identified. We demonstrate this with an example in which, out of a total of 473 identified MS/MS scans, 315 of these scans correspond to unmodified peptides, while 158 scans correspond to a wide variety of modified peptides. In addition, we provide specific examples where the ability to search for unanticipated modifications allows the scientist to discover: unexpected modifications that have biological significance; amino acid mutations; salt-adducted peptides in a sample that has nominally been desalted; peptides arising from nontryptic cleavage in a sample that has nominally been digested using trypsin; other unintended consequences of sample handling procedures.
Dictionary learning for signal-to-noise ratio enhancement (2015)

Summary We investigate dictionary learning (DL) method for enhancing the signal-to-noise ratio (SNR) of a seismic data. The method is applied in windows, where each of these windows is subdivided into overlapping small two dimensional (2D) patches. Each patch is approximated using a linear combination of elementary signals (or atoms) from a set called dictionary. Denoising is performed by assuming the signal in each patch can be represented as a linear combination of a few of the atoms in the dictionary. This dictionary can be constructed either assuming a mathematical model for the signal (e.g. wavelets and curvelets) or can be learned to perform best on a training set. Unlike predefined general purpose dictionaries, learned dictionaries avoid any assumption about the morphology of the seismic data. Hence, denoising by DL ought to provide state-ofthe-art results. In this paper, we demonstrate the performance of the K-means singular value decomposition (K-SVD) based DL denoising both on synthetic and field datasets. The significantly high signal preservation and SNR enhancement ability of DL denoising is illustrated with a comparison with that of conventional FX deconvolution.