gebhart/patrepeval huggingface dataset:
Isolation and characterization of a dibasic selective metalloendopeptidase from rat testes that cleaves at the amino terminus of arginine residues. (1994)

A metalloendopeptidase that selectively cleaves doublets of basic amino acids on the amino-terminal side of arginine residues was purified to homogeneity from rat testes and analyzed further. Two catalytically active forms with apparent relative molecular masses of 110,000 and 140,000 Da, respectively, were present in the purified preparation of the enzyme. Antibodies raised against the purified testis endopeptidase revealed by immunoblot both the 110- and 140-kDa forms in both rat testis and brain cortex extracts. The isolated enzyme was inhibited by metal chelators and divalent cations. Its activity, lost after preincubation with EDTA, was restored by low concentrations of Zn2+ and Mn2+, thus demonstrating the metallopeptidase nature of the enzyme. This endopeptidase also exhibited a high sensitivity to amastatin (100% inhibition at 20 microM), an aminopeptidase inhibitor. A substrate specificity study using physiologically important or synthetic peptides containing a processing dibasic site indicated that cleavage occurred selectively at the amino-terminal side of an arginine residue, independent of the nature of the basic doublet. The enzyme produced such a cleavage at the Arg-Lys doublet of somatostatin 28 (Km = 43 microM), at the Arg-Arg doublet of dynorphin A (Km = 6.45 microM) and atrial natriuretic factor (Km = 6.25 microM), and at the Lys-Arg doublet of preproneurotensin-(154-170) (Km = 17.3 microM). Moreover, cleavage efficiency was found to be higher for the larger substrates. The distinctive properties of this endopeptidase imply that this protein is a member of a novel class of proteolytic enzymes that may be involved in the endoproteolytic maturation of hormonal precursors.
The Broadly Neutralizing Anti-Human Immunodeficiency Virus Type 1 4E10 Monoclonal Antibody Is Better Adapted to Membrane-Bound Epitope Recognition and Blocking than 2F5 (2008)

The broadly neutralizing 2F5 and 4E10 monoclonal antibodies (MAbs) recognize epitopes within the membrane-proximal external region (MPER) that connects the human immunodeficiency virus type 1 (HIV-1) envelope gp41 ectodomain with the transmembrane anchor. By adopting different conformations that stably insert into the virion external membrane interface, such as helical structures, a conserved aromatic-rich sequence within the MPER is thought to participate in HIV-1-cell fusion. Recent experimental evidence suggests that the neutralizing activity of 2F5 and 4E10 might correlate with the MAbs' capacity to recognize epitopes inserted into the viral membrane, thereby impairing MPER fusogenic activity. To gain new insights into the molecular mechanism underlying viral neutralization by these antibodies, we have compared the capacities of 2F5 and 4E10 to block the membrane-disorganizing activity of MPER peptides inserted into the surface bilayer of solution-diffusing unilamellar vesicles. Both MAbs inhibited leakage of vesicular aqueous contents (membrane permeabilization) and intervesicular lipid mixing (membrane fusion) promoted by MPER-derived peptides. Thus, our data support the idea that antibody binding to a membrane-inserted epitope may interfere with the function of the MPER during gp41-induced fusion. Antibody insertion into a cholesterol-containing, uncharged virion-like membrane is mediated by specific epitope recognition, and moreover, partitioning-coupled folding into a helix reduces the efficiency of 2F5 MAb binding to its epitope in the membrane. We conclude that the capacity to interfere with the membrane activity of conserved MPER sequences is best correlated with the broad neutralization of the 4E10 MAb.
A graphene oxide–peptide fluorescence sensor tailor-made for simple and sensitive detection of matrix metalloproteinase 2 (2011)

A graphene oxide–peptide based fluorescence sensor has been developed for matrix metalloproteinase 2 (MMP2), and its applicability has been demonstrated by monitoring the concentration of MMP2 secreted by HeLa cells, revealing that HeLa cells with a density of 5.48 × 105cells per mL can produce 22 nM in cell culture media in 24 h.
Divergent hTAFII31-binding Motifs Hidden in Activation Domains (2000)

Activation domains are functional modules that enable DNA-binding proteins to stimulate transcription. Characterization of these essential modules in transcription factors has been hampered by their low sequence homology. Here we delineate the peptide sequences that are required for transactivation and interaction with hTAF(II)31, a classical target of the acidic class of activation domains. Our analyses indicate that hTAF(II)31 recognizes a diverse set of sequences for transactivation. This information enabled the identification of hTAF(II)31-binding sequences that are critical for the activity of the activation domains of five human transcription factors: NFAT1, ALL1, NF-IL6, ESX, and HSF-1. The interaction surfaces are localized in short peptide segments of activation domains. The brevity and heterogeneity of the motifs may explain the low sequence homology among acidic activation domains.
Desensitized Half-Band Filters (2009)

A common component in digital circuitry for communication systems is the half-band filter. Digital half-band filters are often used in cooperation with upsamplers and downsamplers in multirate systems when a sampling-rate change is required. While techniques for designing these filters are well known, an entirely new method for the design and implementation of lowpass FIR half-band filters is presented in this paper, one in which the filter's frequency response can be provided with a significant insensitivity to the filter's tap-coefficient values. Such insensitivity can be exploited in the filter-design process to yield half-band filters with reduced hardware requirements, which can lead to circuits having lower power consumption, higher operating speeds, and smaller IC area.
Tesmin transcription is regulated differently during male and female meiosis (2003)

Tesmin is a protein with homology to the metal-binding motif of the metallothionein protein family. Tesmin has been described as a testis-specific transcript, which starts to accumulate in 8-day-old mouse spermatocytes. Herein, a differential display comparing meiotic gene expression in embryonic ovaries and mature testes also revealed the presence of the Tesmin transcript in fetal ovaries as well as in fetal and adult heart. Time-course experiments showed that Tesmin was expressed in a characteristic development-related manner in fetal ovaries. Only a weak expression was observed at E12(1/2), the strongest signal was reached at E14(1/2), whereas the signal declined between E14(1/2) and E16(1/2). This transitional expression coincides with the early stages of the female meiotic prophase I. In the male, however, Tesmin was expressed in all stages of meiotic prophase I except preleptonema and leptonema. In situ hybridization further showed that the mRNA level increased during prophase I in the male, with the strongest expression seen at the transition from mid- to late pachytema (Stage VII-VIII). Furthermore, initiation of Tesmin transcription paralleled that of the synaptonemal complex protein 1 transcript (Scp1) in the fetal ovary and prepubertal testis. We, therefore, propose that Tesmin is likely to have a function in both the male and female meiotic prophase I. Moreover, the distinct difference in both the timing and the level of mRNA accumulation in the two gender's meiotic prophase I suggests that Tesmin transcription may be controlled by two different mechanisms during male and female meiosis. Mol. Reprod. Dev. 67: 116-126, 2004.
Universal Dynamics and Controlled Switching of Dissipative Kerr Solitons in Optical Microresonators (2016)

We discover a novel mechanism allowing for successive reduction of the number of dissipative Kerr solitons in optical microresonators. It is demonstrated that multiple and single soliton state can be deterministically accessed.
Neuroprotective Properties of Nitric Oxide (1999)

The discoveries of physiological roles of nitric oxide (.NO) as the mediator of endothelium-derived relaxing factor (EDRF) action and the activator of guanylyl cyclase to increase cyclic guanosine monophosphate (cGMP), which lead to vasorelaxation in the cardiovascular system, have been awarded with the 1998 Nobel Prize of Medicine. The present review discusses putative beneficial effects of .NO in the central nervous system (CNS). In addition to its prominent roles of the regulation of cerebral blood flow and the modulation of cell to cell communication in the brain, recent in vitro and in vivo results indicated that .NO is a potent antioxidative agent. .NO terminates oxidant stress in the brain by (i) suppressing iron-induced generation of hydroxyl radicals (.OH) via the Fenton reaction, (ii) interrupting the chain reaction of lipid peroxidation, (iii) augmenting the antioxidative potency of reduced glutathione (GSH) and (iv) inhibiting cysteine proteases. It is apparent that .NO--a relative long half-life nitrogen-centered weak radical--scavenges those short-lived, highly reactive free radicals such as superoxide anion (O2.-), .OH, peroxyl lipid radicals (LOO.) and thiyl radicals (i.e., GS.), yielding reactive nitrogen species including nitrites, nitrates, S-nitrosoglutathione (GSNO) and peroxynitrite (ONOO-). GSNO is 100-fold more potent than GSH; it completely inhibits the weak peroxidative effect of ONOO-. Moreover, CO2 and .NO neutralize prooxidative effects of ONOO-. CO2 prevents protein oxidation but not 3-nitrotyrosine formation caused by ONOO-. Finally, neuroprotective effects of GSNO and .NO have been demonstrated in brain preparations in vivo. These novel neuroprotective properties of .NO and GSNO may have their physiological significance, since oxidative stress depletes GSH while increasing GS. and .NO formation in astroglial and endothelial cells, resulting in the generation of a more potent antioxidant GSNO and providing additional neuro-protection at microM concentrations. This putative GSNO pathway (GSH-->GS.-->GSNO-->.NO + GSSG-->GSH) may be an important part of endogenous antioxidative defense system, which could protect neurons and other brain cells against oxidative stress caused by oxidants, iron complexes, proteases and cytokines. In conclusion, .NO is a potent antioxidant against oxidative damage caused by reactive oxygen species, which are generated by Fenton reaction or other mechanisms in the brain via redox cycling of iron complexes.
B-Type Natriuretic Peptide in Heart Failure (2005)

Chronic heart failure affects nearly 5 million people living in the United States, and the majority of economic burden is the result of hospitalizations for acute decompensated congestive heart failure. Patient history and symptom assessment, physical examination, and chest radiography remain the cornerstones of diagnosis and prognostic assessment. Evaluation of endogenous B-type natriuretic peptide (BNP) has emerged as a useful addition to standard methods for diagnosis and risk stratification of suspected congestive heart failure, and final diagnosis requires integration of BNP assays with traditional methods. BNP levels >500 pg/mL are more likely to be comfirmative of a primary diagnosis of heart failure and are also important predictors for long-term adverse prognosis; >100 pg/mL but <500 pg/mL suggests a reasonable likelihood for the diagnosis of heart failure but does require thoughtful exclusion of other potential confounders such as pulmonary disease resulting in right heart failure; and <100 indicates that heart failure is very unlikely. Positive physiological effects of BNP, including improvements in hemodynamics, suppression of neurohormonal activity, preservation of renal function, diuresis and natriuresis, and balanced arterial and venous dilatation have suggested that this peptide also may have therapeutic use in congestive heart failure. In clinical trials, treatment of patients with acute decompensated congestive heart failure with nesiritide, a recombinant form of human BNP, was shown to significantly reduce pulmonary capillary wedge pressure versus placebo plus standard care, as well as provide a significant improvement in dyspnea versus placebo. Diagnostic, prognostic, and therapeutic applications of BNP can be integrated easily with standard methods to provide physicians with a useful evaluation and treatment algorithm that may result in faster identification of patients likely to benefit from early therapy, including nesiritide, thereby leading to the potential for more favorable patient outcomes.
Analyzing and Controlling Information Inference of Fine-Grained Access Control Policies in Relational Databases (2013)

As a more flexible and effective access control mechanism in databases, fine-grained access control (FGAC) has drawn considerable attention from industrial and research community. While providing more effective protection for databases, FGAC also incurs new loopholes for attacks. When FGAC policies are defined inconsistently, performing UPDATE/DELETE operations might cause information inference, called UD inference, probably leading to the disclosure of sensitive data to unauthorized users. In order to protect database security, UD inference must be controlled. However, it is challenging to control such inference, due to the flexibility of FGAC policies. In this paper, we aim to provide an effective approach to control UD inference under the circumstance of FGAC policies. We first propose a formal framework for FGAC policies, and in-depth analyze UD inference based on this framework. Then, we propose a security condition to guarantee that there is no UD inference under the circumstances of FGAC policies, while these FGAC policies satisfy the proposed security condition. Finally, we present an effective approach to control UD inference by dynamically modifying FGAC policies.
Multifunctional conjugation of proteins on/into bio-nanoparticles prepared by amphiphilic poly(γ-glutamic acid) (2006)

The present study focuses on nanoparticles composed of amphiphilic poly(gamma-glutamic acid) (gamma-PGA) as potential protein carriers. Amphiphilic graft co-polymers composed of y-PGA as the hydrophilic backbone and L-phenylalanine ethylester (L-PAE) as the hydrophobic segment were synthesized by grafting L-PAE to y-PGA using water-soluble carbodiimide (WSC). Due to their amphiphilic properties, the gamma-PGA-graft-L-PAE co-polymer formed monodispersed nanoparticles in water. The particle size of the nanoparticles composed of gamma-PGA-graft-L-PAE (gamma-PGA nanoparticles) was about 200 nm and showed a highly negative zeta potential. To evaluate their potential applications as multifunctional protein carrier, we prepared protein-entrapped gamma-PGA nanoparticles by encapsulation, covalent immobilization or physical adsorption methods. For this purpose, 11 different proteins with various molecular weights and isoelectric points (pI values) were used as model proteins. The encapsulation of the protein into the nanoparticles was observed for all tested proteins. The amount of protein covalently immobilized or adsorbed onto the nanoparticles showed different tends based on the molecular weight and pI of each protein. Positively charged proteins could be adsorbed onto the negatively charged nanoparticles by electrostatic interaction. Moreover, it was found that enzyme-encapsulated nanoparticles showed higher enzymatic activity than surface-immobilized nanoparticles. These results indicated that the enzymatic activity of the enzyme-entrapped nanoparticles was significantly affected by the conjugation method, and that encapsulation was the optimal method for the conjugation of proteins and nanoparticles. It is expected that the y-PGA nanoparticle will have great potential as multifunctional carriers in pharmaceutical and biomedical applications, such as drug and vaccine delivery systems.
Inhibition of leukocyte L-selectin function with a monoclonal antibody attenuates reperfusion injury to the rabbit ear (1994)

Abstract The leukocyte adhesion molecule L-selectin mediates neutrophil adhesive interactions with endothelial cells and is in part responsible for neutrophil rolling. We examined the role of L-selectin in ischemia- reperfusion injury of rabbit ears using a monoclonal antibody (MoAb) directed to a functional epitope of L-selectin. Arterial blood flow to the rabbit ear was occluded for six hours with ambient temperature at 23 degrees C to 24 degrees C. Rabbits were treated at reperfusion with saline (n = 8), the L-selectin function-blocking LAM1–3 MoAb (2 mg/kg), or the nonfunction-blocking LAM1–14 MoAb (2 mg/kg). Tissue injury was determined by measuring edema and necrosis. Edema in the LAM1–3 MoAb- treated group (peak = 25 +/- 4 mL) was significantly less (P &lt; .05) than in saline-treated (peak = 40 +/- 8 mL) and LAM1–14 MoAb-treated (peak = 41 +/- 6 mL) groups. Tissue necrosis at 7 days was not observed in the LAM1–3 MoAb-treated group, whereas significant necrosis (P &lt; .05) was seen in the saline- (8% +/- 3% necrosis) and LAM1–14 MoAb- treated (7% +/- 3% necrosis) group. We conclude that blocking L- selectin ameliorates necrosis and edema after ischemia and reperfusion in the rabbit ear, presumably by blocking neutrophil rolling.
A Computer Program for Statistically-Based Decision Analysis (1990)

The majority of patients with coronary artery disease do not fall into the well defined populations from randomized clinical trials. Observational databases contain a rich source of information that could be used by practicing physicians to evaluate treatment alternatives for their patients. We describe a computer system, the CABG Kibitzer, which uses an integrated approach to evaluate the treatment alternatives for CAD patients. We combine a statistical multivariate model for calculating survival advantages with DA techniques for assessing patient preferences and sensitivity analysis, to create one tool that physicians find easy to use in daily clinical practice. The development of tools of this kind is a necessary step in making the data of outcome studies accessible to practicing physicians.
The systematic synthesis of complexes containing µ3-CS ligands as two-electron donors. The preparation and structure of [{Co(η-C5H5)}2{Fe(PPh3)(CO)2}(µ3-S)(µ3-CS)] (1992)

The η2-(CS)-CS2 ligand in [Fe{PPh3}2(CO)2(η2-CS2)] is cleaved by [Co(η-C5H5)[PPh3}2] at room temperature with formation of [{Co(η-C5H5)}2{Fe(PPh3)(CO)2](µ3-S)] in which the CS ligand acts as a µ3 two-electron donor to the Co2Fe triangle.
A 130 nm generation high density Etox/sup TM/ flash memory technology (2002)

A 130 nm-generation flash memory technology has been developed, optimized for small cell size, high performance low voltage operation and multi-level-cell and embedded logic capability. Memory cell scaling utilizes the architecture features from the 180 nm technology along with channel erase, advanced 130 nm lithography, dielectric scaling, junction scaling, dual trench and dual spacer technology. 32 Mbit flash memories with a 0.16 um/sup 2/ cell size have been built on this technology showing good yield, performance and reliability.
Imprint lithography for integrated circuit fabrication (2003)

The escalating cost for next generation lithography (NGL) tools is driven in part by the need for complex sources and optics. The cost for a single NGL tool could exceed $50M in the next few years, a prohibitive number for many companies. As a result, several researchers are looking at low cost alternative methods for printing sub-100 nm features. In the mid-1990’s, several research groups started investigating different methods for imprinting small features. Many of these methods, although very effective at printing small features across an entire wafer, are limited in their ability to do precise overlay. In 1999, Colburn et al. [Proc. SPIE 379 (1999)] discovered that imprinting could be done at low pressures and at room temperatures by using low viscosity UV curable monomers. The technology is typically referred to as step and flash imprint lithography. The use of a quartz template enabled the photocuring process to occur and also opened up the potential for optical alignment of the wafer and template. This article traces the development of nanoimprint lithography and addresses the issues that must be solved if this type of technology is to be applied to high-density silicon integrated circuitry.
Appearance-preserving simplification (1998)

25th International Conference on Computer Graphics and Interactive Techniques, July 19-24, 1998, Orlando, Florida, USA
Opioid Therapy as a Component of Chronic Pain Management (2008)

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System Modeling and Design Refinement in ForSyDe (2003)

Advances in microelectronics allow the integration of more andmore functionality on a single chip. Emerging system-on-a-chiparchitectures include a large amount of heterogeneous componentsand are of increasing complexity. Applications using thesearchitectures require many low-level details in order to yield anefficient implementation. On the other hand constanttime-to-market pressure on electronic systems demands a shortdesign process that allows to model a system at a highabstraction level, not taking low-level implementation detailsinto account. Clearly there is a significant abstraction gapbetween an ideal model for specification and another one forimplementation. This abstraction gap has to be addressed bymethodologies for electronic system design. This thesis presents the ForSyDe (Formal System Design)methodology, which has been developed with the objective to movesystem design to a higher level of abstraction and to bridge theabstraction gap by transformational design refinement. ForSyDe isbased on carefully selected formal foundations. The initialspecification model uses a synchronous model of computation,which separates communication from computation and has anabstract notion of time. ForSyDe uses the concept of processconstructors to implement the synchronous model, to allow fordesign transformation and the mapping of a refined model onto thetarget architecture. The specification model is refined into adetailed implementation model by the stepwise application ofwell-defined design transformation rules. These rules are eithersemantic preserving or they inflict a design decision modifyingthe semantics. These design decisions are used to introduce thelow-level implementation details that are needed for an efficientimplementation. The implementation model is mapped onto thecomponents of the target architecture. At present ForSyDe modelscan be mapped onto VHDL or C/C++ in order to allow commercialtools to generate custom hardware or sequential software. Thethesis uses a digital equalizer to illustrate the concepts andpotential of ForSyDe. Electronic System Design, Hardware/Software Co-Design,Electrical Engineering
Congenital hypomyelinating neuropathy. (1985)

Two patients with congenital hypomyelinating neuropathy are reported with details of sural nerve pathology. The resemblance of this condition to the hypomyelinating neuropathy of Trembler mice is discussed and the pertinent medical literature reviewed.