gebhart/patrepeval huggingface dataset:
Distinct Specificities of Mycobacterium tuberculosis and Mammalian Proteasomes for N-Acetyl Tripeptide Substrates (2008)

The proteasome of Mycobacterium tuberculosis (Mtb) is a validated and drug-treatable target for therapeutics. To lay ground-work for developing peptide-based inhibitors with a useful degree of selectivity for the Mtb proteasome over those of the host, we used a library of 5,920 N-acetyl tripeptide-aminomethylcoumarins to contrast the substrate preferences of the recombinant Mtb proteasome wild type and open gate mutant, the Rhodococcus erythropolis proteasome, and the bovine proteasome with activator PA28. The Mtb proteasome was distinctive in strictly preferring P1 = tryptophan, particularly in combination with P3 = glycine, proline, lysine or arginine. Screening results were validated with Michalis-Menten kinetic analyses of 21 oligopeptide aminomethyl-coumarin substrates. Bortezomib, a proteasome inhibitor in clinical use, and 17 analogs varying only at P1 were used to examine the differential impact of inhibitors on human and Mtb proteasomes. The results with the inhibitor panel confirmed those with the substrate panel in demonstrating differential preferences of Mtb and mammalian proteasomes at the P1 amino acid. Changing P1 in bortezomib from Leu to m-CF(3)-Phe led to a 220-fold increase in IC(50) against the human proteasome, whereas changing a P1 Ala to m-F-Phe decreased the IC(50) 400-fold against the Mtb proteasome. The change of a P1 Ala to m-Cl-Phe led to an 8000-fold shift in inhibitory potency in favor of the Mtb proteasome, resulting in 8-fold selectivity. Combinations of preferred amino acids at different sites may thus improve the species selectivity of peptide-based inhibitors that target the Mtb proteasome.
Flavor Studies of Nootkatone in Grapefruit Juice (1967)

SUMMARY —Nootkatone, a sesquiterpene ketone previously reported as a primary flavoring constituent in grapefruit oil, has been tested for flavoring effect in grapefruit juice reconstituted from foam‐mat‐dried crystals. Unexpected difficulties were encountered in achieving uniform dispersion of the nootkatone. After a satisfactory method was developed, flavor thresholds and preferences were established by comparing samples of juice containing nootkatone with controls. Nootkatone was detectable at 1 ppm in water and at 6 ppm in 10.5’Brix reconstituted grapefruit juice. Threshold levels were the same in samples with and without “locked‐in” oil. Flavor effects were evaluated on four samples: 1) nootkatone isolated from grapefruit oil; 2) a sample of nootkatone synthesized from valencene, and purified repeatedly by GLC; 3) a routinely purified sample of synthetic nootkatone purified by GLC; and 4) a sample of crystalline nootkatone. All had the same threshold. To some judges the nootkatone was very bitter at a level above 7 ppm. For most iudges however, at slightly above threshold level (about 6—7 ppm) the flavor and aroma of grapefruit iuice were enhanced by the presence of nootkatone.
On LTE Security: Closing the Gap Between Standards and Implementation (2015)

Modern cellular networks including LTE (Long Term Evolution) and the evolving LTE- Advanced provide high-speed and high-capacity data services for mobile users. As we become more reliant on wireless connectivity, the security of voice and data transmissions on the network becomes increasingly important. While the LTE network standards provide strict security guidelines, these requirements may not be completely followed when LTE networks are deployed in practice. This project provides a method for improving the security of LTE networks by 1) characterizing a gap between security requirements defined in the standards and practical implementations, 2) designing a language to express the encoding formats of one of LTEâ€™s network-layer protocols, 3) developing a compiler to translate a protocol description in our language into an implementation, and 4) providing recommendations on lessons learned during development of the language and compiler to support development of future protocols that employ formal representations. In this way, our work demonstrates how a formal language can be utilized to represent a cellular network protocol and serves as an example for further research on how adding formalism to network standards can help ensure that the security goals defined in the standards can be upheld in an implementation.
A Polylogarithmic Approximation of the Minimum Bisection (2002)

A bisection of a graph with n vertices is a partition of its vertices into two sets, each of size n/2. The bisection cost is the number of edges connecting the two sets. It is known that finding a bisection of minimum cost is NP-hard. We present an algorithm that finds a bisection whose cost is within ratio of O(log2n ) from the minimum. For graphs excluding any fixed graph as a minor (e.g., planar graphs) we obtain an improved approximation ratio of O(log n). The previously known approximation ratio for bisection was roughly $\sqrt{n}$.
Cost-Effectiveness of Detecting and Treating Diabetic Retinopathy (1996)

Our analysis indicates that prevention programs aimed at improving eye care for diabetic persons not only result in substantial federal budgetary savings but are highly cost-effective health investments for society. Ophthalmologic screening for diabetic persons is more cost-effective than many routinely provided health interventions. Because diabetic eye disease is the leading cause of new cases of blindness among working-age Americans, these results support the widespread use of screening and treatment for diabetic eye disease.
MAX Phases and Ultra-High Temperature Ceramics for Extreme Environments (2013)

Ceramics are a versatile material, more so than is widely known. They are thermal resistant, poor electrical conductors, insulators against nuclear radiation, and not easily damaged, making ceramics a key component in many industrial processes.MAX Phases and Ultra-High Temperature Ceramics for Extreme Environments investigates a new class of ultra-durable ceramic materials, which exhibit characteristics of both ceramics and metals. Readers will explore recent advances in the manufacturing of ceramic materials that improve their durability and other physical properties, enhancing their overall usability and cost-effectiveness. This book will be of primary use to researchers, academics, and practitioners in chemical, mechanical, and electrical engineering. This book is part of the Research Essentials collection.
A recent approach to the study of dolichyl monophosphate topology in the rough endoplasmic reticulum. (1994)

Amphomycin though withdrawn as an antibiotic against the gram-positive bacterial infection, can certainly serve as an excellent tool for determination of the topology of Dol-P in the endoplasmic reticulum membranes which has been otherwise impossible.
Mechanical, biochemical, and extracellular matrix effects on vascular smooth muscle cell phenotype (2005)

The vascular smooth muscle cell (VSMC) is surrounded by a complex extracellular matrix that provides and modulates a variety of biochemical and mechanical cues that guide cell function. Conventional two-dimensional monolayer culture systems recreate only a portion of the cellular environment, and therefore there is increasing interest in developing more physiologically relevant three-dimensional culture systems. This review brings together recent studies on how mechanical, biochemical, and extracellular matrix stimulation can be applied to study VSMC function and how the combination of these factors leads to changes in phenotype. Particular emphasis is placed on in vitro experimental studies in which multiple stimuli are combined, especially in three-dimensional culture systems and in vascular tissue engineering applications. These studies have provided new insight into how VSMC phenotype is controlled, and they have underscored the interdependence of biochemical and mechanical signaling. Future improvements in creating more complex in vitro culture environments will lead to a better understanding of VSMC biology, new treatments for vascular disease, as well as improved blood vessel substitutes.
Dietary support with Boswellia resin in canine inflammatory joint and spinal disease (2004)

An open multi-centre veterinary clinical trial, comparing conditions before and after treatment with a herbal dietary supplement consisting of a natural resin extract of Boswellia serrata, was conducted by 10 practicing veterinarians in Switzerland. This traditional plant-based supplement is known for its anti-rheumatic and anti-inflammatory properties. 29 dogs with manifestations of chronic joint and spinal disease were enrolled. Osteoarthritis and degenerative conditions were confirmed radiologically in 25 of 29 cases. The resin extract (BSB108, product of Bogar AG) was administered with the regular food at a dose of 400 mg/10 kg body weight once daily for 6 weeks. Already after two weeks of treatment, an overall efficacy of the dietary supplement was evident in 71% of 24 eligible dogs. A statistically significant reduction of severity and resolution of typical clinical signs in individual animals, such as intermittent lameness, local pain and stiff gait, were reported after 6 weeks. Effects of external factors that aggravate lameness, such as "lameness when moving" and "lameness after a long rest" diminished gradually. In 5 dogs, reversible brief episodes of diarrhea and flatulence occurred, but only once was a relationship to the study preparation suspected. Because quality and stability of the resin extract were ensured, these data suggest that a standardized preparation can be recommended as a herbal dietary supplement providing symptomatic support in canine osteoarthritic disease.
Biochemical Characterization of the FEZ-1 Metallo-β-Lactamase of <i>Legionella gormanii</i> ATCC 33297 <sup>T</sup> Produced in <i>Escherichia coli</i> (2001)

The bla(FEZ-1) gene coding for the metallo-beta-lactamase of Legionella (Fluoribacter) gormanii ATCC 33297T was overexpressed via a T7 expression system in Escherichia coli BL21(DE3)(pLysS). The product was purified to homogeneity in two steps with a yield of 53%. The FEZ-1 metallo-beta-lactamase exhibited a broad-spectrum activity profile, with a preference for cephalosporins such as cephalothin, cefuroxime, and cefotaxime. Monobactams were not hydrolyzed. The beta-lactamase was inhibited by metal chelators. FEZ-1 is a monomeric enzyme with a molecular mass of 29,440 Da which possesses two zinc-binding sites. Its zinc content did not vary in the pH range of 5 to 9, but the presence of zinc ions modified the catalytic efficiency of the enzyme. A model of the FEZ-1 three-dimensional structure was built.
Cloud detection and clearing for the Earth Observing System Terra satellite Measurements of Pollution in the Troposphere (MOPITT) experiment (2001)

The Measurements of Pollution in the Troposphere (MOPITT) instrument, which was launched aboard the Earth Observing System (EOS) Terra spacecraft on 18 December 1999, is designed to measure tropospheric CO and CH(4) by use of a nadir-viewing geometry. The measurements are taken at 4.7 mum in the thermal emission and absorption for the CO mixing ratio profile retrieval and at 2.3 and 2.2 mum in the reflected solar region for the total CO column amount and CH(4) column amount retrieval, respectively. To achieve the required measurement accuracy, it is critical to identify and remove cloud contamination in the radiometric signals. We describe an algorithm to detect cloudy pixels, to reconstruct clear column radiance for pixels with partial cloud covers, and to estimate equivalent cloud top height for overcast conditions to allow CO profile retrievals above clouds. The MOPITT channel radiances, as well as the first-guess calculations, are simulated with a fast forward model with input atmospheric profiles from ancillary data sets. The precision of the retrieved CO profiles and total column amounts in cloudy atmospheres is within the expected ?10% range. Validations of the cloud-detecting thresholds with the moderate-resolution imaging spectroradiometer airborne simulator data and MOPITT airborne test radiometer measurements were performed. The validation results showed that the MOPITT cloud detection thresholds work well for scenes covered with more than 5-10% cloud cover if the uncertainties in the model input profiles are less than 2 K for temperature, 10% for water vapor, and 5% for CO and CH(4).
High-power low-threshold graded-index separate confinement heterostructure AlGaAs single quantum well lasers on Si substrates (1989)

A high-power low-threshold graded-index separate confinement heterostructure AlGaAs single quantum well laser on Si substrates has been demonstrated for the first time by a hybrid growth of migration-enhanced molecular beam epitaxy followed by metalorganic vapor phase epitaxy. The quantum well laser showed an output power of more than 400 mW per facet under pulsed conditions. A room-temperature threshold current of 300 mA was obtained with a differential quantum efficiency of 40% without facet coating. The threshold current density was 550 A/cm2 for a cavity length of 500 μm. These results show the highest peak power reported to date for low-threshold lasers on Si substrates. The full width at half maximum of the far-field pattern parallel to the junction was 6°. Threshold current densities as low as 250 A/cm2 were obtained for lasers on GaAs substrates.
A Reconfigurable Filter Using Defected Ground Structure for Wideband Common-Mode Suppression (2019)

A wideband common-mode (CM) suppression reconfigurable filter is proposed for high-speed all-pass differential circuits. The filter adopts three varactor-loaded compact defected ground structures (DGSs) to achieve continuous reconfigurability in its operation frequency with a large CM suppression dynamic range in the bandwidth. The varactors play an important role in widening the accessible instantaneous bandwidth and miniaturizing the structure. The three DGS cells with a total area of 15 mm × 10 mm are implemented symmetrically under the differential lines, to obtain reconfigurable CM bandstop characteristics which can be continuously adjusted from 1.8 to 8.1 GHz. A coupled LC resonator equivalent model is developed to represent and analyze the proposed filter, which explains its operation principle and assists in accelerating the reconfiguration design method. A good agreement between full-wave simulations and measured results is demonstrated, which validates the proposed design.
Studies on Optically Active Amino Acids. I. Preparation of 3-(3, 4-Methylenedioxyphenyl)-D-, and -L-alanine (1962)

The preparation of 3-(3, 4-methylenedioxyphenyl)-D-, and -L-alanine (D-and L-(V)) was carried out by the chemical or biological resolution of N-acety1-3-(3, 4-methylenedioxyphenyl)-DL-alanine (DL-(IV)). The N-acetyl-DL-amino acid prepared from 3, 4-methylenedioxybenzyl chloride (H) and diethyl acetamidomalonate (I), via the diester (III), was resolved into two forms, D-and L-(IV), by means of fractional recrystallization of their cinchonine salts from ethanol, followed by the liberation of cinchonine base. Asymmetric hydrolysis of DL-(W) was also smoothly effected by Takadiastase to give the L-amino acid (L-(V)) and N-acetyl-D-amino acid (D-(W)). The latter as well as the one derived from the chemical resolution was converted by boiling it with 10% hydrochloric acid into the D-amino acid (D-(V)) in good yield.
The transcriptional PPARβ/δ network in human macrophages defines a unique agonist-induced activation state (2015)

Peroxisome proliferator-activated receptor β/δ (PPARβ/δ) is a lipid ligand-inducible transcription factor with established metabolic functions, whereas its anti-inflammatory function is poorly understood. To address this issue, we determined the global PPARβ/δ-regulated signaling network in human monocyte-derived macrophages. Besides cell type-independent, canonical target genes with metabolic and immune regulatory functions we identified a large number of inflammation-associated NFκB and STAT1 target genes that are repressed by agonists. Accordingly, PPARβ/δ agonists inhibited the expression of multiple pro-inflammatory mediators and induced an anti-inflammatory, IL-4-like morphological phenotype. Surprisingly, bioinformatic analyses also identified immune stimulatory effects. Consistent with this prediction, PPARβ/δ agonists enhanced macrophage survival under hypoxic stress and stimulated CD8(+) T cell activation, concomitantly with the repression of immune suppressive target genes and their encoded products CD274 (PD-1 ligand), CD32B (inhibitory Fcγ receptor IIB) and indoleamine 2,3-dioxygenase 1 (IDO-1), as well as a diminished release of the immune suppressive IDO-1 metabolite kynurenine. Comparison with published data revealed a significant overlap of the PPARβ/δ transcriptome with coexpression modules characteristic of both anti-inflammatory and pro-inflammatory cytokines. Our findings indicate that PPARβ/δ agonists induce a unique macrophage activation state with strong anti-inflammatory but also specific immune stimulatory components, pointing to a context-dependent function of PPARβ/δ in immune regulation.
Aseismic Base Isolation (1982)

Developpement dans ce domaine depuis mai 1981. Recherche a la fois theorique et experimentale dans un nombre accru de centre de recherche. Plusieurs bâtiments nouveaux utilisent diverses formes d'isolation. Description de ces developpements recents: appuis en caoutchouc; appuis en bouchon de plomb, systemes de pieux a manchon, systemes glissants, systemes a palier de roulement, systemes melanges. Developpement d'un code. Rehabilitation des bâtiments en utilisant une isolation parasismique. Suggestion de recherches futures
Preparation of Pyrimidines and Pyridines from Alkyl Ketones and Nitriles in Presence of Phosphoryl Chloride (1985)

H nmr ( ~0 ~1 ~) : 8[ppm] -7.9-7.25 (m, IOH.arom) ; 6.96 (6, IH.NH) ; 3.66 (d.2H.CH2, J -8 HZ); 2.0 ( 0 , 3H.C H ~) ; 1.88 (a.3H.C H ~) c.
Compilation techniques for low energy: an overview (2002)

Recent years have witnessed a rapid growth in research activity targeted at reducing energy consumption in microprocessor based systems. However, this research has by and large not recognised the potential energy savings achievable through optimization of software running on the microprocessor. This paper presents an overview of techniques used in our work and in other recent research in this area. Several possible techniques for energy reduction through code compilation are presented. Examples with energy reduction of up to 40% on an Intel 486DX2 based system, obtained by rewriting code, demonstrate the potential of these ideas. Several additional avenues for reducing CPU and memory system energy through code compilation are identified. The effect of traditional compilation techniques on energy reduction is discussed and some of these techniques that can be beneficial in this regard are reviewed.
Using Online Traffic Statistical Matching for Optimizing Packet Filtering Performance (2007)

Packet classification plays a critical role in many of the current networking technologies, and efficient yet lightweight packet classification techniques are highly crucial for their successful deployment. Most of the current packet classification techniques exploit the characteristics of classification policies, without considering the traffic behavior in optimizing their search data structures. In this paper, we present novel techniques that utilize traffic characteristics coupled with careful analysis of the policy to obtain adaptive methods that can accommodate varying traffic statistics while maintaining a high throughput. The first technique uses segmentation of the traffic space to achieve disjoint subsets of traffic properties and build bounded depth Huffman trees using the statistics collected for these segments. The second technique simplifies the structure maintenance by keeping the segments ordered in a most-recently-used (MRU) list instead of a tree. The techniques are evaluated and their performance are compared. Moreover, attacks targeting the firewall performance are discussed and corresponding protection schemes are presented.
Lewis Acid-Assisted Isotopic <sup>18</sup>F-<sup>19</sup>F Exchange in BODIPY Dyes: Facile Generation of Positron Emission Tomography/Fluorescence Dual Modality Agents for Tumor Imaging (2013)

Positron emission tomography (PET) is a powerful technique for imaging biological pathways in vivo, particularly those that are key targets in disease processes. In contrast, fluorescence imaging has demonstrated to be a superior method for image-guided surgery, such as tumor removal. Although the integration of PET and optical imaging could provide an attractive strategy for patient management, there is a significant shortage of established platforms/methods for PET/optical probe construction. In this study, various reaction conditions were explored to develop a simple and fast method allowing for the introduction of [(18)F]-fluoride into BODIPY dyes. Through a systematic optimization of the reaction conditions, we found that BODIPY dyes, including commercial amine-reactive BODIPY succinimidyl esters, may be converted into their radioactive analogues in the matter of minutes via a (18)F-(19)F isotopic exchange reaction promoted by a Lewis acid such as SnCl4. An integrin-targeting RGD peptide was also conjugated with [(18)F]BODIPY® R6G , derived from the commercially available BODIPY® R6G fluorescent tag, to provide a [(18)F]-RGD conjugate in 82% yield. In vivo evaluation of this imaging probe showed a discernible tumor uptake in the U87MG xenograft model. The dual modality imaging properties of the probe was confirmed by ex vivo fluorescence and microPET imaging experiments. In summary, in the matter of minutes, BODIPY dyes were converted into their "hot" radioactive analogues via a (18)F-(19)F isotopic exchange reaction promoted by a Lewis acid. This approach, which can be applied to commercial BODIPY dyes, provides easy access to positron emission tomography/fluorescence dual modality imaging agents.
Design and Testing for a Nontagged F1‐V Fusion Protein as Vaccine Antigen against Bubonic and Pneumonic Plague (2005)

A two-component recombinant fusion protein antigen was re-engineered and tested as a medical counter measure against the possible biological threat of aerosolized Yersinia pestis. The active component of the proposed subunit vaccine combines the F1 capsular protein and V virulence antigen of Y. pestis and improves upon the design of an earlier histidine-tagged fusion protein. In the current study, different production strains were screened for suitable expression and a purification process was optimized to isolate an F1-V fusion protein absent extraneous coding sequences. Soluble F1-V protein was isolated to 99% purity by sequential liquid chromatography including capture and refolding of urea-denatured protein via anion exchange, followed by hydrophobic interaction, concentration, and then transfer into buffered saline for direct use after frozen storage. Protein identity and primary structure were verified by mass spectrometry and Edman sequencing, confirming a purified product of 477 amino acids and removal of the N-terminal methionine. Purity, quality, and higher-order structure were compared between lots using RP-HPLC, intrinsic fluorescence, CD spectroscopy, and multi-angle light scattering spectroscopy, all of which indicated a consistent and properly folded product. As formulated with aluminum hydroxide adjuvant and administered in a single subcutaneous dose, this new F1-V protein also protected mice from wild-type and non-encapsulated Y. pestis challenge strains, modeling prophylaxis against pneumonic and bubonic plague. These findings confirm that the fusion protein architecture provides superior protection over the former licensed product, establish a foundation from which to create a robust production process, and set forth assays for the development of F1-V as the active pharmaceutical ingredient of the next plague vaccine.