gebhart/patrepeval huggingface dataset:
Impact of HIV Type 1 Drug Resistance Mutations and Phenotypic Resistance Profile on Virologic Response to Salvage Therapy (2001)

This study examines the association between presence of drug resistance mutations and phenotypic resistance at baseline to virologic response to salvage therapy in a community setting. The study population consisted of 58 antiretroviral drug-experienced patients with HIV-1 infection who had recently switched therapy because of virologic failure. Drug resistance mutations in the reverse transcriptase- and protease-coding regions and phenotypic susceptibility to 13 antiretroviral drugs were assessed at baseline. Plasma HIV-1 RNA levels were assessed at baseline and at subsequent clinic visits. Results showed that three variables were significant in predicting virologic response: HIV-1 levels at baseline, number of protease mutations, and phenotypic sensitivity score for the regimen at baseline. For four drugs there was a significant association between the presence of specific drug resistance mutations and >10-fold phenotypic resistance to that drug. With phenotypic resistance defined as >4-fold resistance, the association between specific drug resistance mutations and phenotypic resistance was significant for seven drugs. Overall, these data show that phenotypic susceptibility and absence of drug resistance mutations, particularly protease mutations, are significant predictors of virologic response. For several drugs, specific combinations of drug resistance mutations are associated with decreased phenotypic susceptibility and might provide useful clinical guidelines in selecting therapeutic options.
New crystalline polymers: poly(2,5-dialkyl-1,4-phenylene oxide)s (2000)

New heat-reversibly crystalline poly-(alkylated phenylene oxide)s are described. the oxidative polymerization of 2,5-dimethylphenol catalyzed by (1,4,7-triisopropyl-1,4,7-triazacyclononane) copper dichloride produced poly(2,5-dimethyl-1,4-phenylene oxide), which showed heat-reversible crystallinity with a high melting point at ca. 300°C, although the isomeric polymer, poly(2,6-dimethyl-1,4-phenylene oxide), never recrystallizes once melted. The polymerization of 2,5-diethylphenol and 2,5-dipropylphenol gave the polymers consisting of 1,4-phenylene oxide units; the latter polymer possessed heat-reversible crystallinity, however, the former one did not.
Time Synchronizing Using IEEE 1588 + Synchronous Ethernet in a “Time-Setting” Mode of Operation (2010)

Abstract : The IEEE 1588 precision time protocol (PTP) time-setting mode of operation can be used to dramatically improve the quality of time-based systems that rely on a physical layer syntonization source in addition to PTP. Based on the standardized PTP protocol and common network frequency distribution techniques, the PTP time-setting mode of operation is capable of distributing time over packet-based facilities with little or no impact by network packet delay variation (PDV). In essence, the timing performance at a slave clock is directly related to the traceability, accuracy, and stability of physical layer packet-based systems (e.g., Synchronous Ethernet) or existing syntonization-based networks (e.g., SONET/SDH, DS1, or E1).
The Use of Enzymes to Regioselectively Deacylate Sucrose Esters (1992)

The deacylation activity of a range of hydrolytic enzymes on octa-O-acetyl sucrose has been investigated. From a total of 96 enzymes tested, 55 were active; 16 produced only heptaacetates, 12 produced hexaacetates and 27 could deacylate at 3 or more positions. Hydrolysis could only be achieved at 5 positions; the 3 primary positions plus the 4 and 4′ positions. The remaining 3 positions (2, 3 and 3′) were not hydrolysed. Only one enzyme tested was sufficiently active at all 5 positions to yield 2,3,3′-tri-O-acetyl sucrose. Acyl migration occurred on the glucose ring of partially deacylated products, but this could be minimised by conducting reactions between pH 4 and 5. A range of specifically protected sucrose esters was obtained by using a combination of enzymes in sequence. No activity towards pentanoyl and butyryl esters of sucrose was detected. This finding was exploited by using butyryl groups as protecting groups in the enzymic deacylation of sucrose acetyl esters. These strategies can be used to synthesise specifically substituted sugars.
Murine tenascin-W: a novel mammalian tenascin expressed in kidney and at sites of bone and smooth muscle development (2004)

We cloned and characterized a novel member of the tenascin family of extracellular matrix proteins--the murine orthologue of zebrafish tenascin-W. Full-length recombinant tenascin-W was expressed and purified from mammalian cell cultures. Rotary shadowing followed by electron microscopy showed that tenascin-W forms hexabrachions. We studied its expression during development and in the adult by immunohistochemistry, in situ hybridization and immunoblotting. Tenascin-W is expressed during palate formation, osteogenesis and smooth muscle development. In the adult, tenascin-W is found in the kidney, cardiac semilunar valves, corneal limbus and periosteum. Tenascin-W and tenascin-C expression overlap in many of these areas. Bone-morphogenic-protein-2 treated C2C12 cells secrete tenascin-W and are able to adhere to and to extend actin-rich processes on a tenascin-W substratum. In vitro, cells bind to tenascin-W in an RGD-dependent manner. This adhesion is increased by transfection of alpha8 integrin, which localizes with tenascin-W in the periosteum and kidney.
Hybrid vitronectin-mimicking polycaprolactone scaffolds for human retinal progenitor cell differentiation and transplantation (2014)

Many advances have been made in an attempt to treat retinal degenerative diseases, such as age-related macular degeneration and retinitis pigmentosa. The irreversible loss of photoreceptors is common to both, and currently no restorative clinical treatment exists. It has been shown that retinal progenitor and photoreceptor precursor cell transplantation can rescue the retinal structure and function. Importantly, retinal progenitor cells can be collected from the developing neural retina with further expansion and additional modification in vitro, and the delivery into the degenerative host can be performed as a single-cell suspension injection or as a complex graft transplantation. Previously, we have described several polymer scaffolds for culture and transplantation of retinal progenitor cells of both mouse and human origin. This tissue engineering strategy increases donor cell survival and integration. We have also shown that biodegradable poly(ɛ-caprolactone) induces mature photoreceptor differentiation from human retinal progenitor cells. However, poor adhesive properties limit its use, and therefore it requires additional surface modification. The aim of this work was to study vitronectin-mimicking oligopeptides (Synthemax II-SC) poly(ɛ-caprolactone) films and their effects on human retinal progenitor cell adhesion, proliferation, and differentiation. Here, we show that the incorporation of vitronectin-mimicking oligopeptide into poly(ɛ-caprolactone) leads to dose-dependent increases in cell adhesion; the optimum dose identified as 30 µg/ml. Inhibition of human retinal progenitor cells proliferation was seen on poly(ɛ-caprolactone) and was maintained with the hybrid scaffold. This has been shown to be beneficial for driving cell differentiation. Additionally, we observed equal expression of Nrl, rhodopsin, recoverin, and rod outer membrane 1 after differentiation on the hybrid scaffold as compared to the standard fibronectin coating of poly(ɛ-caprolactone). After transplantation into rd1 retina degenerative mice, human retinal progenitor cells were able to migrate to the outer nuclear layer and survive for three weeks. We conclude that Synthemax II-SC can be incorporated into poly(ɛ-caprolactone) to create a hybrid chemically defined scaffold for clinical application.
Shape-Regulated Particle Filtering for Tracking Non-Rigid Objects (2006)

This paper presents an active contour based algorithm for tracking non-rigid objects in heavily cluttered scenes. We decompose the non-rigid contour tracking problem into three subproblems: 2D motion estimation, deformation detection, and shape regulation. First, we employ a particle filter to estimate the affine transform parameters between successive frames. Second, by using a dynamic object model, we generate a probabilistic map of deformation to reshape its contour. Finally, we project the updated model onto a trained shape subspace to constrain deformations to be within possible object appearances. Our experiments show that the proposed algorithm significantly improves the performance of the tracker.
Interactions of TMPyP4 and TMPyP2 with Quadruplex DNA. Structural Basis for the Differential Effects on Telomerase Inhibition (1999)

The cationic porphyrins TMPyP4 and TMPyP2 possess similar structures but have strikingly different potencies for telomerase inhibition. To rationalize this difference, the interactions of TMPyP4 and TMPyP2 with an antiparallel quadruplex DNA were investigated. A single-stranded DNA oligonucleotide (G4A) containing four human telomere repeats of GGGTTA has been designed to form an intramolecular quadruplex DNA and was confirmed to form such a structure under 100 mM KCl by a DNA ligase assay, DMS footprinting, and CD spectrum analysis. By carrying out UV spectroscopic studies of the thermal melting profiles of G4A−porphyrin complexes, we provide evidence that TMPyP4 and TMPyP2 both stabilize quadruplex DNA to about the same extent. A photocleavage assay was used to determine the precise location for TMPyP4 and TMPyP2 in their interactions with quadruplex DNA. The results show that TMPyP4 binds to the intramolecular quadruplex DNA by stacking externally to the guanine tetrad at the GT step, while TMPyP2 binds predominantly to the same G4 DNA structure via external binding to the TTA loop. We propose that the inability of TMPyP2 to bind to the G4A by stacking externally to the guanine tetrad accounts for the differential effects on telomerase inhibition by TMPyP4 and TMPyP2.
Motor bearing damage detection using stator current monitoring (2002)

This paper addresses the application of motor current spectral analysis for the detection of rolling-element bearing damage in induction machines. Vibration monitoring of mechanical bearing frequencies is currently used to detect the presence of a fault condition. Since these mechanical vibrations are associated with variations in the physical air gap of the machine, the air gap flux density is modulated and stator currents are generated at predictable frequencies related to the electrical supply and vibrational frequencies. This paper takes the initial step of investigating the efficacy of current monitoring for bearing fault detection by correlating the relationship between vibration and current frequencies caused by incipient bearing failures. The bearing failure modes are reviewed and the characteristic bearing frequencies associated with the physical construction of the bearings are defined. The effects on the stator current spectrum are described and the related frequencies determined. This is an important result in the formulation of a fault detection scheme that monitors the stator currents. Experimental results which show the vibration and current spectra of an induction machine with different bearing faults are used to verify the relationship between the vibrational and current frequencies. The test results clearly illustrate that the stator current signature can be used to identify the presence of a bearing fault.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Terahertz four-wire waveguides for broadband signal processing and multiplexing (2022)

In this work, we introduce a versatile metal-wire waveguide geometry, namely a four-wire waveguide, which is capable of sustaining two independent and orthogonally polarized fundamental modes, thus acting as a broadband polarization-division multiplexer. By integrating multiscale-structured grooves into the wires of such a waveguide, we demonstrate the independent manipulation of polarization-division terahertz signals.
Efficient Minimization of New Quadric Metric for Simplifying Meshes with Appearance Attributes (Addendum to IEEE Visualization 1999 paper) (2000)

In an earlier paper we introduced a new quadric metric for simplifying triangle meshes using the edge collapse operation. The quadric measures both the geometric accuracy of the simplified mesh surface and the fidelity of appearance fields defined on the surface (such as normals or colors). The minimization of this quadric metric involves solving a linear system of size (3+m)(3+m) ,w herem is the number of distinct appearance attributes. The system has only O(m) nonzero entries, so it can be solved in O(m 2 ) time using traditional sparse solvers such as the method of conjugate gradients. In this short addendum, we show that the special structure of the sparsity permits the system to be solved in O(m) time.
Synthesis and Structure–Activity Relationship of Dual-Stage Antimalarial Pyrazolo[3,4-<i>b</i>]pyridines (2020)

Malaria remains one of the most deadly infectious diseases, causing hundreds of thousands of deaths each year, primarily in young children and pregnant mothers. Here, we report the discovery and derivatization of a series of pyrazolo[3,4-<i>b</i>]pyridines targeting <i>Plasmodium falciparum</i>, the deadliest species of the malaria parasite. Hit compounds in this series display sub-micromolar <i>in vitro</i> activity against the intraerythrocytic stage of the parasite as well as little to no toxicity against the human fibroblast BJ and liver HepG2 cell lines. In addition, our hit compounds show good activity against the liver stage of the parasite but little activity against the gametocyte stage. Parasitological profiles, including rate of killing, docking, and molecular dynamics studies, suggest that our compounds may target the Q<sub>o</sub> binding site of cytochrome <i>bc</i><sub>1</sub>.
An evaluation of model-based stator resistance estimation for induction motor stator winding temperature monitoring (2002)

In this paper, the feasibility of using an estimate of the stator resistance (R/sub s/) as an indicator of stator winding temperature (T/sub s/) is evaluated. The advantages of resistance-based temperature monitoring over conventional thermal model-based methods are presented. Since obtaining an accurate estimate of R/sub s/ is critical for this approach, an investigation of existing R/sub s/ estimation schemes, and an analysis showing the sensitivity of model-based R/sub s/ estimation due to the uncertainties in motor parameters and variables, are given. It is shown that R/sub s/ estimation is difficult during high-speed operation, because estimated R/sub s/ becomes sensitive to errors in motor electrical parameters and variables, as the input excitation frequency (speed) increases. A new R/sub s/ estimation scheme for the purpose of monitoring the temperature in steady state is proposed. Experimental results on a line-connected induction machine verify the validity of the proposed method and the analysis.
Strain variability among Kaposi sarcoma-associated herpesvirus (human herpesvirus 8) genomes: evidence that a large cohort of United States AIDS patients may have been infected by a single common isolate (1997)

Previous analysis of the majority of Kaposi's sarcoma (KS) tumors, in both AIDS and non-AIDS populations, has revealed the consistent presence of two small subsegments (open reading frame 25/26 [ORF25/26] and ORF75) of a novel human gamma class herpesvirus genome referred to as KSHV or HHV-8. We have carried out DNA sequence comparisons with DNAs encompassing a total of 2,500 bp each over three separate PCR-amplified fragments from KS lesions and body cavity-based lymphoma (BCBL) samples from 12 distinct patients, including four African and two classical or endemic non-AIDS KS samples. The results revealed differences at 37 of 2,500 nucleotide positions (i.e., 1.5% overall variation). However, the 12 HHV-8 genomes examined fell into three distinct but very narrow subgroupings (A, B, and C strains). All A strain isolates differed from B strain isolates at 16 positions, but of the eight U.S. samples tested, six were A strains, and these differed at no more than two positions among them. Similarly, three of the four African samples were B strains, which differed from each other at only one position. The two C strain genomes also displayed only one nucleotide variation, but they differed from all A strains at 26 positions and from all B strains at 20 positions. One C strain genome was present in all six independent lesions from an AIDS KS patient with disseminated disease, and the other represented a mosaic A/C recombinant genome from the HBL6 cell line derived from a BCBL tumor. Evaluation of previous data suggests that B and C strains may predominate in Africa and that A strains predominate in classical Mediterranean samples. Although both B and C strains are represented in U.S. AIDS patients, the majority (70 to 80%) of samples from the mid-East Coast region at least appear to be virtually identical, supporting the concept that they may all derive from the spread during the AIDS epidemic of a single recently transmitted infectious agent.
Confocal-rainbow volume holographic imaging system (2011)

The performance of broadband volume holographic imaging system in terms of depth selectivity is investigated. The mechanism for depth resolution degradation is explained. In order to overcome this resolution degradation, a novel imaging device, the confocal-rainbow volume holographic imaging system, is proposed. Modeling and experimental validation of the performance of this novel imaging system indicates that depth resolution <16 μm is achievable. The lateral resolution of this device is <2.5 μm along a field of view of 300 μm×100 μm.
The specificity of Sushi peptides for endotoxin and anionic phospholipids: potential application of POPG as an adjuvant for anti-LPS strategies (2006)

Sushi peptides [S1 (Sushi 1 peptide) and S3] are derived from the LPS (lipopolysaccharide; also known as endotoxin)-binding domains of an LPS-sensitive serine protease, Factor C, from the horseshoe crab (Carcinoscorpius rotundicauda). S1 and S3 interact at high affinity with LPS. The intermolecular disulphide bonding in the S3 dimer is indispensable for its LPS binding, disruption and consequent neutralization. Simultaneously, the specific interaction between the Sushi peptides and bacterial membrane phospholipids further explains the selective propensity of these peptides for the gram-negative bacteria. Our findings yield insights into a complex molecular paradigm in which the juxtaposition of LPS molecules and the anionic phospholipid POPG (1-palmitoyl-2-oleoyl phosphatidylglycerol) on the bacterial outer membrane confers such interfacial properties which create the optimal environment for the interaction between the peptides and bacterial membrane lipids.
Conjugate Addition/Cyclization Sequence Enables Selective and Simultaneous Fluorescence Detection of Cysteine and Homocysteine (2011)

Similar but different: A benzothiazole derivative can be used to detect cysteine (Cys) and homocysteine (Hcy) simultaneously in neutral media. The method involves thioether formation followed by cyclization to release 2-(2′-hydroxy-3′-methoxyphenyl)benzothiazole (HMBT) and a lactam. The differences in ring-formation kinetics allow spectral or kinetic modes to be used to identify Cys and Hcy. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Background-Free Direction-Sensitive Neutron (2009)

The detection and measurements of properties of neutrons are of great importance in many fields of research, including neutron scattering and radiography, measurements of solar and cosmic ray neutron flux, measurements of neutron interaction cross sections, monitoring of neutrons at nuclear facilities, oil exploration, and searches for fissile weapons of mass destruction. Many neutron detectors are plagued by large backgrounds from x-rays and gamma rays, and most current neutron detectors lack single-event energy sensitivity or any information on neutron directionality. Even the best detectors are limited by cosmic ray neutron backgrounds. All applications would benefit from improved neutron detection sensitivity and improved measurements of neutron properties. Here we show data from a new type of detector that can be used to determine neutron flux, energy distribution, and direction of neutron motion. The detector is free of backgrounds from x-rays, gamma rays, beta particles, and relativistic singly charged particles. It is relatively insensitive to cosmic ray neutrons because of their distinctive angular and energy distributions. It is sensitive to thermal neutrons, fission spectrum neutrons, and high energy neutrons, with detection features distinctive for each energy range. It is capable of determining the location of a source of fission neutrons based on characteristics of elastic scattering of neutrons by helium nuclei. A portable detector could identify one gram of reactor grade plutonium, one meter away, with less than one minute of observation time.