gebhart/patrepeval huggingface dataset:
Bovine Proenteropeptidase Is Activated by Trypsin, and the Specificity of Enteropeptidase Depends on the Heavy Chain (1997)

Enteropeptidase, also known as enterokinase, initiates the activation of pancreatic hydrolases by cleaving and activating trypsinogen. Enteropeptidase is synthesized as a single-chain protein, whereas purified enteropeptidase contains a approximately 47-kDa serine protease domain (light chain) and a disulfide-linked approximately 120-kDa heavy chain. The heavy chain contains an amino-terminal membrane-spanning segment and several repeated structural motifs of unknown function. To study the role of heavy chain motifs in substrate recognition, secreted variants of recombinant bovine proenteropeptidase were constructed by replacing the transmembrane domain with a signal peptide. Secreted variants containing both the heavy chain (minus the transmembrane domain) and the catalytic light chain (pro-HL-BEK (where BEK is bovine enteropeptidase)) or only the catalytic domain (pro-L-BEK) were expressed in baby hamster kidney cells and purified. Single-chain pro-HL-BEK and pro-L-BEK were zymogens with extremely low catalytic activity, and both were activated readily by trypsin cleavage. Trypsinogen was activated efficiently by purified enteropeptidase from bovine intestine (Km = 5.6 microM and kcat = 4.0 s-1) and by HL-BEK (Km = 5.6 microM and kcat = 2.2 s-1), but not by L-BEK (Km = 133 microM and kcat = 0.1 s-1); HL-BEK cleaved trypsinogen at pH 5.6 with 520-fold greater catalytic efficiency than did L-BEK. Qualitatively similar results were obtained at pH 8.4. In contrast to this striking difference in trypsinogen recognition, the small synthetic substrate Gly-Asp-Asp-Asp-Asp-Lys-beta-naphthylamide was cleaved with similar kinetic parameters by both HL-BEK (Km = 0.27 mM and kcat = 0.07 s-1) and L-BEK (Km = 0.60 mM and kcat = 0.06 s-1). The presence of the heavy chain also influenced the rate of reaction with protease inhibitors. Bovine pancreatic trypsin inhibitor preferred HL-BEK (initial Ki = 99 nM and final Ki* = 1.8 nM) over L-BEK (Ki = 698 nM and Ki* = 6.2 nM). Soybean trypsin inhibitor exhibited a reciprocal pattern, inhibiting L-BEK (Ki* = 1.6 nM), but not HL-BEK. These kinetic data indicate that the enteropeptidase heavy chain has little influence on the recognition of small peptides, but strongly influences macromolecular substrate recognition and inhibitor specificity.
Specific telomerase RNA residues distant from the template are essential for telomerase function (1998)

The reverse transcriptase telomerase is a ribonucleoprotein complex that adds telomeric repeats to chromosome ends, using a sequence within its endogenous RNA component as a template. Although templating domains of telomerase RNA have been studied in detail, little is known about the roles of the remaining residues, particularly in yeast. We examined the functions of nontemplate telomerase residues in the telomerase RNA of budding yeast Kluyveromyces lactis. Although approximately half of the RNA residues were dispensable for function, four specific regions were essential for telomerase action in vivo. We analyzed the effects of mutating these regions on in vivo function, in vitro telomerase activity, and telomerase RNP assembly. Deletion of two regions resulted in synthesis of stable RNAs that appeared unable to assemble into a stable RNP. Mutating a region near the 5' end of the RNA allowed RNP assembly but abolished enzymatic activity. Mutations in another specific small region of the RNA led to an inactive telomerase RNP with an altered RNA conformation.
An error control scheme based on adaptation of polling schedule for real-time communication on IEEE 802.11 wireless LANs (2003)

The paper proposes an error control scheme that dynamically adjusts the polling schedule so that more corrupted messages can be manipulated within their deadlines for real-time communication on IEEE 802.11 wireless LAN. Monitoring the current traffic in the CFP (collision free period) interval as well as inspecting whether a node is executing an error control procedure, the AP (access point) terminates CFP, if possible, to extend the duration of the next CP (collision period). With the enlarged time, the AP gives more polls to the node in need to increase the number of timely recovered messages. Simulation result performed via SMPL shows that this adaptation scheme can reduce the message discard due to transmission error by 5.5%, compared with the existing error controls method for real-time communication on WLAN.
The inversion problem and applications of the generalized radon transform (1984)

Abstract We prove that under certain conditions the inversion problem for the generalized Radon transform reduces to solving a Fredholm integral equation and we obtain the asymptotic expansion of the symbol of the integral operator in this equation. We consider applications of the generalized Radon transform to partial differential equations with variable coefficients and provide a solution to the inversion problem for the attenuated and exponential Radon transforms.
Induction of Long-Term Remission in Advanced Hepatocellular Carcinoma With Percutaneous Isolated Liver Chemoperfusion (1998)

The results suggest that percutaneous isolated liver chemoperfusion with HVI-CHP is an effective palliative treatment in the majority of patients and yields long-term complete remission in some patients with multiple advanced HCC.
Drying properties of metathesized soybean oil (1997)

Abstract Soybean oil was metathesized with the standard homogenous metathesis catalyst, which consisted of tungsten hexachloride (WCl 6 ) and tetramethyl tin (Me 4 Sn) in chlorobenzene as solvent. The reactions were terminated at different time intervals. Soybean oil was mixed with metathesized soybean oil in the presence of cobalt‐drier to evaluate drying properties. Five weight percentage (% w) of metathesized oil was found to be all that was needed to decrease the drying time of soybean oil from 312 to 182 min. Drying times for heat‐polymerized soybean oil with Gardner‐Holdt viscosity of Z 1 –Z 2 and Z 3 –Z 4 were 71 and 75 min, respectively. In both cases, 5% weight metathesized soybean oil in the blend gave the best results for reducing drying time to 67 and 69 min, respectively.
Multi-View Clustering and Feature Learning via Structured Sparsity (2013)

Combining information from various data sources has become an important research topic in machine learning with many scientific applications. Most previous studies employ kernels or graphs to integrate different types of features, which routinely assume one weight for one type of features. However, for many problems, the importance of features in one source to an individual cluster of data can be varied, which makes the previous approaches ineffective. In this paper, we propose a novel multi-view learning model to integrate all features and learn the weight for every feature with respect to each cluster individually via new joint structured sparsity-inducing norms. The proposed multi-view learning framework allows us not only to perform clustering tasks, but also to deal with classification tasks by an extension when the labeling knowledge is available. A new efficient algorithm is derived to solve the formulated objective with rigorous theoretical proof on its convergence. We applied our new data fusion method to five broadly used multi-view data sets for both clustering and classification. In all experimental results, our method clearly outperforms other related state-of-the-art methods. 1.
Properties of IgA myeloma proteins isolated rom sera of patients with the hyperviscosity syndrome. (1977)

Sera, purified myeloma proteins, and urinary proteins obtained from eight patients with igA multiple myeloma were studied by physical-chemical and immunochemical methods. In six patients whose serum viscosity was increased, the sedimentation constants of the principal component of myeloma proteins ranged from 9.1 to 10.2 S. In two patients with nearly normal serum viscosity, the sedimentation constants of these proteins were 6.2 and 7.2 S. IGA-albumin complexes were detected in most of the sera, but invarying amounts; no complexes of ig with amylase, secretory component, or alpha(1)-antitrypsin were observed. Studies on isolated myeloma proteins revealed that all igA proteisn from sera with increased viscosity represented true polymers, linked by disulfide bonds, rather than noncovalently associated aggregates; J chain was detecable by both alkaline-urea disc electrophoresis and immunoelectrophoresis with a monospecific anti-J chain serum. Increased serum viscosity was not related to the igA subclass, L chain type, or the carbohydrate compositions of individual igA myeloma proteins. The urine of five patients contained free light chains corresponding in type to the light chain of the particular igA myeloma protein. However, free J chain was not detected. The immunoelectrophoretic analysis for the presence of J chain in sera of myeloma patients may be used for early and simple detection of polymeric forms of myeloma proteins.
Diffusion of implanted beryllium in <i>n</i>- and <i>p</i>-type GaAs (1989)

The diffusion of ion-implanted Be in GaAs is studied by comparing the diffusion of implanted Be in undoped GaAs and in GaAs uniformly doped with Zn or Si. The Si-doped sample exhibits much less Be diffusion compared to the undoped case, while the Zn-doped sample shows much more Be diffusion. The diffusion in the doped substrate cases can be simulated with a constant Be diffusivity, as opposed to a concentration-dependent diffusivity in the undoped case. The results are consistent with the substitutional-interstitial diffusion mechanism, which predicts a diffusivity that is dependent on the net hole concentration.
Proteoglycan‐induced arthritis and recombinant human proteoglycan aggrecan G1 domain–induced arthritis in BALB/c mice resembling two subtypes of rheumatoid arthritis (2011)

GIA is a novel model of seropositive RA that exhibits all of the characteristics of PGIA. Although the clinical phenotypes are similar, GIA and PGIA are characterized by different autoantibody profiles, and the 2 models may represent 2 subtypes of seropositive RA, in which more than 1 type of autoantibody can be used to monitor disease severity and response to treatment.
MicroRNA-1 and -499 Regulate Differentiation and Proliferation in Human-Derived Cardiomyocyte Progenitor Cells (2010)

Objective— To improve regeneration of the injured myocardium, it is necessary to enhance the intrinsic capacity of the heart to regenerate itself and/or replace the damaged tissue by cell transplantation. Cardiomyocyte progenitor cells (CMPCs) are a promising cell population, easily expanded and efficiently differentiated into beating cardiomyocytes. Recently, several studies have demonstrated that microRNAs (miRNAs) are important for stem cell maintenance and differentiation via translational repression. We hypothesize that miRNAs are also involved in proliferation/differentiation of the human CMPCs in vitro. Methods and Results— Human fetal CMPCs were isolated, cultured, and efficiently differentiated into beating cardiomyocytes. miRNA expression profiling demonstrated that muscle-specific miR-1 and miR-499 were highly upregulated in differentiated cells. Transient transfection of miR-1 and -499 in CMPC reduced proliferation rate by 25% and 15%, respectively, and enhanced differentiation into cardiomyocytes in human CMPCs and embryonic stem cells, likely via the repression of histone deacetylase 4 or Sox6. Histone deacetylase 4 and Sox6 protein levels were reduced, and small interference RNA (siRNA)-mediated knockdown of Sox6 strongly induced myogenic differentiation. Conclusion— miRNAs regulate the proliferation of human CMPC and their differentiation into cardiomyocytes. By modulating miR-1 and -499 expression levels, human CMPC function can be altered and differentiation directed, thereby enhancing cardiomyogenic differentiation.
Co/Si(111) interface: Formation of an initial CoSi2 phase at room temperature (1987)

Ultrathin films (≲50 monolayers) of Co have been deposited on atomically clean 7×7 Si(111) surfaces at room temperature and characterized by in situ surface techniques such as Auger electron spectroscopy and low-energy electron diffraction. Formation of a boundary CoSi2-like phase is surprisingly found at a very low coverage range (≲4 monolayers) as evidenced by low-temperature transport measurements (resistivity and Hall effect) and also by cross-sectional high-resolution transmission electron microscopy.
High-throughput chromatin accessibility profiling at single-cell resolution (2018)

We have developed a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 hour on-chip processing time) and cost (~98¢ per cell) compared to prior microfluidic implementations. We applied this method to measure regulatory variation in Peripheral Blood Mononuclear Cells (PBMCs) and show robust, de-novo clustering of single cells by hematopoietic cell type.
ChemInform Abstract: Plasma‐Enhanced Etching of Tungsten and Tungsten Silicide in Chlorine‐Containing Discharges. (1987)

Abstract W and WSix films have been etched in Cl2 and Cl2/BCl3 plasmas using two different reactor designs (radial and flow systems, 0.1‐1.0 torr Cl2, 30‐170 °C).
Coherent Subnanosecond Switching of Perpendicular Magnetization by the Fieldlike Spin-Orbit Torque without an External Magnetic Field (2015)

The recently discovered spin-orbit torque could be used to flip bits in spintronic devices. The authors investigate its less-studied component, the fieldlike torque, and find that with the help of this piece, there is no need for an external magnetic field to achieve the deterministic reversal of magnetization. In principle this solves one of the critical issues in spintronics, and is promising for applications in terms of speed and energy efficiency.
A novel wide-angle low-loss dielectric slab waveguide Y-branch (1994)

A new Y-branch structure for dielectric waveguides is proposed and analysed using simple geometrical optics and beam propagation methods. It is shown both qualitatively and quantitatively that the proposed structure has larger branching angles but lower radiation loss than those associated with either conventional Y-branches or structures with antenna coupled and phase front accelerators. The optimal design parameters calculated by numerical simulations are in very good agreement with those found from the geometrical optics. The simulations also reveal that the performance is fairly insensitive to fabrication errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experimental and theoretical investigations on nonlinear resonances of composite buckled microbridges (1999)

Theoretical and experimental investigations have been conducted to study the nonlinear vibrations of a clamped–clamped beam with the effect of the initial deflection taken into consideration. A preliminary study analyzed the linear vibrations of a composite microcantilever beam. A very good agreement is found between theoretical and experimental values of the first three resonant frequencies of composite cantilever beams by taking into account the effect of the gold layer on the shift of the resonant frequencies. With this preliminary result, an exact solution is given to the linear problem associated with the nonlinear vibrations of initially buckled clamped–clamped structures using a direct analytical model. Several experimental multimode dynamic responses of composite buckled beams are also given to illustrate the validity and accuracy of this analytical model. Then, the influence of the interaction between resonant modes and the microstructure imperfections (nonideal boundary conditions, composite morphology, etc.) on the shift between the theoretical and experimental values of the resonant frequencies is considered.
A simple model for the etching of photoresist with plasma-generated reactants (1992)

The neutral heterogeneous chemistry between reactive species formed in a glow discharge plasma and a polymer surface is investigated. Oxygen and fluorine atom concentrations in an O2/CF4 plasma afterglow are measured by gas phase electron resonance spectroscopy. These atom concentrations are correlated to etch rate data via a simple heterogeneous model which divides the etching process into three steps: initiation, etching, and passivation. The model predicts etch rate data well using measured atom concentrations. When the substrate temperature is changed, the etching step is affected most, presumably limited by product desorption. Dilution of the discharge with argon enhances the etch rate in two ways. First, the homogeneous chemistry is altered, most notably affecting the fluorine atom concentration. The homogeneous effects are taken into account through measured atom concentrations. Second, the argon metastables play a role in the heterogeneous chemistry, enhancing the etching step. From an estimation of this enhancement based on the shift in etch rate maximum, the magnitude of etching in an argon diluted discharge can be predicted.
Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development (2008)

CTCF is a multifunctional nuclear factor involved in epigenetic regulation. Despite recent advances that include the systematic discovery of CTCF-binding sites throughout the mammalian genome, the in vivo roles of CTCF in adult tissues and during embryonic development are largely unknown. Using transgenic RNAi, we depleted maternal stores of CTCF from growing mouse oocytes, and identified hundreds of misregulated genes. Moreover, our analysis suggests that CTCF predominantly activates or derepresses transcription in oocytes. CTCF depletion causes meiotic defects in the egg, and mitotic defects in the embryo that are accompanied by defects in zygotic gene expression, and culminate in apoptosis. Maternal pronuclear transfer and CTCF mRNA microinjection experiments indicate that CTCF is a mammalian maternal effect gene, and that persistent transcriptional defects rather than persistent chromosomal defects perturb early embryonic development. This is the first study detailing a global and essential role for CTCF in mouse oocytes and preimplantation embryos.
QOS based performance of selective repeat transport user in hybrid ATM/TDMA networks (2002)

The selective repeat (SR) transport user end-to-end throughput and delay characteristics are analyzed in a hybrid asynchronous transfer mode/time division multiple access (ATM/TDMA) network. The SR transport user is assumed with an underlying cell-level global congestion control in the ATM multiplexer node. The analysis is based on the interaction of packet level control with the queue management at the ATM cell level. The end-to-end transport users are assumed over an M-node virtual circuit (VC) to derive the throughput and delay using Norton equivalent queueing model. The transport service characteristic of the model is obtained from the end-to-end protocol efficiency. The ATM layer is assumed with a leaky bucket (LB), virtual leaky bucket (VLB), modified LB (mLB), or modified VLB (mVLB) congestion control. A global congestion control scheme prioritizes transit traffic over local traffic and ensures the quality of service (QOS) to several classes of traffic. Based on global congestion status, the transport users modulate their end-to-end flow control parameters, i.e., packet size for video and voice users and window size for data users. The probability of cell-loss at the ATM layer is reflected at the transport layer to derive the effective throughput and delay characteristics. The mVLB scheme consistently provided better end-to-end throughput and delay performance for SR transport user.
Digital Calibration for Monotonic Pipelined A/D Converters (2004)

The original digital calibration approach for 1 b/stage and 1.5 b/stage pipeline analog-digital converters produces missing or nonmonotonic digital codes with the device and circuit impairments typical of modern deep submicrometer CMOS technologies. Two digital calibration algorithms are introduced to improve pipeline performance when using low-voltage low-gain nonlinear operational amplifiers and high random dc offset voltage comparators. The first technique computes calibration coefficients for each stage at actual transition points of the residue characteristic to assure converter monotonicity in the presence of random comparator offset voltages. The second augments a conventional pipelined architecture with an input-dependent level-shifting stage and additional digital calibration circuitry to achieve high differential and integral linearity with low-gain nonlinear operational amplifiers.
Novel amphiphilic graft copolymers bearing hydrophilic poly(acrylic acid) backbones and hydrophobic poly(butyl methacrylate) side chains (2006)

Abstract A novel amphiphilic graft copolymer consisting of hydrophilic poly(acrylic acid) backbones and hydrophobic poly(butyl methacrylate) side chains was synthesized by successive atom transfer radical polymerization followed by hydrolysis of poly‐(methoxymethyl acrylate) backbone. A grafting‐from strategy was employed for the synthesis of graft copolymers with narrow molecular weight distributions (polydispersity index < 1.40). Hydrophobic side chains were connected to the backbone through stable CC bonds instead of ester connections. Poly(methoxymethyl acrylate) backbone was easily hydrolyzed to poly(acrylic acid) backbone with HCl without affecting the hydrophobic side chains. The amphiphilic graft copolymer could form stable micelles in water. The critical micelle concentration in water was determined by a fluorescence probe technique. The morphology of the micelles was preliminarily explored with transmission electron microscopy and was found to be spheres. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6857–6868, 2006
Transganglionic regulation of the primary sensory neuron. (1987)

Central terminals of the primary sensory neurons depend on the integrity of the retrograde transport mechanism within the peripheral axon. Whenever retrograde transport is impaired (either by injury or by blockade induced by perineural application of microtubule inhibitors) central terminals undergo transganglionic degenerative atrophy (TDA), characterized by depletion of substance P, somatostatin, FRAP (fluoride resistant acid phosphatase), TMPase (thiamine monophosphatase) and lectin-binding fucose-terminated glyco-conjugates. The TDA is essentially a failure of the central terminals to bind the above genuine marker substances. TDA-inflicted central terminals undergo a slowly proceeding ultrastructural deterioration, accompanied by derangement of the dorsal root potential, reflecting decreased functional activity of synaptic transmission between first and second-order cells. One of the important trophic substances carried by retrograde axoplasmic transport to dorsal root ganglion cells is nerve growth factor (NGF); blockade of NGF transport results in TDA; conversely, locally applied NGF delays or prevents TDA.
A 90-dB DC gain high-speed nested gain-boosted folded-cascode opamp (2015)

A novel folded-cascode operational amplifier (opamp) employing the nested gain-boosted technique is presented. The gain-booster in the signal path consists of two-level recursive folded-cascode amplifier to achieve high gain and high speed. The opamp is designed and simulated in 0.13μm CMOS technology, bode-plot results that an open-loop gain over 90dB and a unity-gain frequency up to 4.75G for loads of 1.6pF have been obtained. Settling measurements shows that the opamp has a settling time less than 2.5ns. So the proposed opamp can be employed in high speed and high resolution Analog-to-Digital converters (ADCs) such as pipelined ADC.