gebhart/patrepeval huggingface dataset:
The Inference of Phased Haplotypes for the Immunoglobulin H Chain V Region Gene Loci by Analysis of VDJ Gene Rearrangements (2011)

The existence of many highly similar genes in the lymphocyte receptor gene loci makes them difficult to investigate, and the determination of phased "haplotypes" has been particularly problematic. However, V(D)J gene rearrangements provide an opportunity to infer the association of Ig genes along the chromosomes. The chromosomal distribution of H chain genes in an Ig genotype can be inferred through analysis of VDJ rearrangements in individuals who are heterozygous at points within the IGH locus. We analyzed VDJ rearrangements from 44 individuals for whom sufficient unique rearrangements were available to allow comprehensive genotyping. Nine individuals were identified who were heterozygous at the IGHJ6 locus and for whom sufficient suitable VDJ rearrangements were available to allow comprehensive haplotyping. Each of the 18 resulting IGHV│IGHD│IGHJ haplotypes was unique. Apparent deletion polymorphisms were seen that involved as many as four contiguous, functional IGHV genes. Two deletion polymorphisms involving multiple contiguous IGHD genes were also inferred. Three previously unidentified gene duplications were detected, where two sequences recognized as allelic variants of a single gene were both inferred to be on a single chromosome. Phased genomic data brings clarity to the study of the contribution of each gene to the available repertoire of rearranged VDJ genes. Analysis of rearrangement frequencies suggests that particular genes may have substantially different yet predictable propensities for rearrangement within different haplotypes. Together with data highlighting the extent of haplotypic variation within the population, this suggests that there may be substantial variability in the available Ab repertoires of different individuals.
Perfluoroalkylene‐linked aromatic polymers (1970)

Abstract Polymers of the type ( m ‐C 6 H 4 ·(CF 2 ) m · m ‐C 6 H 4 ‐X))n have been synthesised and their properties are reported. They include polyesters and polycarbonates, polysiloxanes, polyimides and poly‐(1,3‐phenylenehexafluoro‐trimethylene. Preparation of the precursors was facilitated by the discovery of a direct fluoroalkylation process involving fluoroalkylcopper intermediates. In various instances, the effects of introducing m ‐phenylene‐perfluoroalkylene units on the properties of these polymers, particularly their glass transition temperatures, are compared with the corresponding effects from m ‐phenylene ether units.
BEAR-FP: A ROBUST FRAMEWORK FOR FLOORPLANNING (1992)

This paper presents a hierarchical floorplanning approach for macrocell layouts which is based on the bottom-up clustering, shape function computation, and top-down floorplan optimization with integrated global routing and pin assignment. This approach provides means for specifying and techniques for satisfying a wide range of constraints (physical, topological, timing) and is, therefore, able to generate floorplans for a number of different layout styles. A systematic and efficient optimization procedure during the selection of suitable floorplan patterns that integrates floorplanning, global routing and pin assignment, a new pin assignment technique based on linear assignment and driven by the global routing solution and floorplan topology, and an effective timing-driven floorplanning scheme are among the other novel features of the floorplanner. These techniques have been incorporated in BEAR-FP, a macrocell layout system developed at the University of California, Berkeley. Results on various placement and floorplanning benchmarks are quite good.
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease (2008)

Our study demonstrates that highly differentially expressed genes are more likely to harbor disease-associated DNA variants. FitSNPs can serve as an effective tool to systematically prioritize candidate SNPs from GWASs.
Dynamic Rotary Torque Measurement Using Surface Acoustic Waves (2001)

This paper identifies a new, potentially low cost, non-contact, frequency domain strain torque sensor utilising SAW (Surface Acoustic Wave) Technology for surface strain measurement. The sensor has a short axial length making it flexible in terms of integration into a variety of applications, encompassing both static and dynamic measurement. The paper presents a technical description of the resulting transducer, regarding its operation and construction.
From data to speech: a general approach (2001)

We present a data-to-speech system called D2S, which can be used for the creation of data-to-speech systems in different languages and domains. The most important characteristic of a data-to-speech system is that it combines language and speech generation: language generation is used to produce a natural language text expressing the system's input data, and speech generation is used to make this text audible. In D2S, this combination is exploited by using linguistic information available in the language generation module for the computation of prosody. This allows us to achieve a better prosodic output quality than can be achieved in a plain text-to-speech system. For language generation in D2S, the use of syntactically enriched templates is guided by knowledge of the discourse context, while for speech generation pre-recorded phrases are combined in a prosodically sophisticated manner. This combination of techniques makes it possible to create linguistically sound but efficient systems with a high quality language and speech output.
Phase evolution, microstructure and transport property of (Bi, Pb)-2223/Ag tapes prepared using powders of varying particle size distribution (2001)

(Bi, Pb)-2223/Ag sheathed tapes were prepared using precursor powders with different particle size distributions which were obtained by grinding the calcined powder for different durations. DTA results revealed that the reaction temperature of the precursor powder depends on the particle size and is at a minimum for the finest powder. Phase evolution studies, transport current measurement at 77 K with and without the application of an external field, microstuctural examination etc, were carried out in order to evaluate the relative performance of the tapes. The results showed that the particle size has significant effects on the reaction kinetics, ultimate phase fraction, microstructure and transport critical current density. For the tapes fabricated using coarser powder, the reaction kinetics were found to be slower and the microstructure contained smaller grains with many misalignments and voids. On the other hand use of extremely fine precursors yielded tapes with a large fraction of secondary phases due to the degradation of the crystallinity of the precursor and a consequent change in the reaction sequence. The tape prepared using a precursor with an average particle size of 3-4 µm showed the best results with respect to JC, high-TC phase fraction, microstructure and JC-B characteristics.
Global UPT architecture with international mobility management (2003)

Universal personal telecommunications (UPT) is an emerging service to allow the user to make a communication anywhere in the world with personalized addressing and service features. FPLMTS (future public land mobile telecommunication systems) is an emerging system to allow terminal mobility also on a worldwide scale. As both UPT and FPLMTS are targeted to be provided on a global scale and they are complementary to each other, serviceability of UPT is amplified if it is combined with the FPLMTS capability. The authors after analyzing the functions required for UPT and FPLMTS, identify possible scenarios of UPT service provision over FPLMTS. Their characteristics are then compared and evaluated from various viewpoints. Finally, the conditions for selection and steps of evolution among these scenarios are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Theory of Phase Separation in Polymer Nanocomposites (2006)

The microscopic polymer reference interaction site model theory of polymer nanocomposites composed of flexible chains and spherical nanoparticles has been employed to study second virial coefficients and spinodal demixing over a wide range of interfacial chemistry, chain length, and particle size conditions. For hard fillers, two distinct phase separation behaviors, separated by a miscibility window, are generically predicted. One demixing curve occurs at relatively low monomer−particle attraction strength and corresponds to a very abrupt transition from an entropic depletion attraction-induced phase separated state to an enthalpically stabilized miscible fluid. The homogeneous mixture arises via a steric stabilization mechanism associated with the formation of thin, thermodynamically stable bound polymer layers around fillers. The second demixing transition occurs at relatively high monomer−particle adsorption energy and is inferred to involve the formation of an equilibrium physical network phase with local bridging of particles by polymers. This spinodal is sensitive to both particle−monomer diameter ratio and the spatial range of the interfacial attraction. The miscibility window narrows, and can ultimately disappear, with increasing polymer chain length, direct van der Waals attractions between fillers, and/or particle−monomer size asymmetry ratio. The implications of our results for the design of well-dispersed thermodynamically stable polymer nanocomposites, and the formation of nonequilibrium gels, are discussed.
Biomarkers and Multiple Drug Resistance in Breast Cancer (2006)

Breast cancer, the most common form of cancer among women in North America and almost all of Europe, is a significant health problem in terms of both morbidity and mortality. It is estimated that each year this disease is diagnosed in over one million people worldwide and is the cause of more than 400,000 deaths. Although chemotherapy forms part of a successful treatment regime in many cases, as few as 50% patients may benefit from this, as a result of intrinsic or acquired multiple drug resistance (MDR). Through the use of in vitro cell culture models, a number of mechanisms of MDR have been identified; many, if not all, of which may contribute to breast cancer resistance in the clinical setting. This phenomenon is complicated by the likely multi-factorial nature of clinical resistance combined with the fact that, although apparently studied extensively in breast cancer, reported analyses have been performed using a range of analytical techniques; many on small sub-groups of patients, with different clinicopathological characteristics and receiving a range of therapeutic approaches. Larger defined studies, using standardised genomic and proteomics profiling approaches followed by functional genomics studies, are necessary in order to definitively establish the degree of complexity contributing to drug resistance and to identify novel therapeutic approaches - possibly involving chemotherapy, drug resistance modulators, and novel targeted therapies - to combat this disease.
Guaranteed-Availability Network Function Virtualization with Network Protection and VNF Replication (2017)

Network function virtualization (NFV) provides an efficient and flexible way to deploy network services in the form of service function chains (SFCs) by adopting generalized equipment. However, software-based virtualized network functions (VNFs) bring new challenge for network operators in providing service availability guarantees. Traditionally, network-level protection mechanisms are considered separately from function-level VNF backup mechanisms. However, a SFC's availability cannot be guaranteed if only network- level protection mechanisms or only function-level VNF backup mechanisms are considered. In this paper, we propose a coordinated protection mechanism that adopts both backup path protection in the network and VNF replicas at nodes to guarantee a SFC's availability. The proposed mechanism determines the number of replicas required for each VNF in the SFC, and allocates the replicas to physical nodes on the working and backup paths while maintaining ordered dependency among VNFs. Simulation results show that the proposed algorithms contribute to reducing the SFC blocking and the cost of computing resources.
Satellite Dynamics Simulator Development Using Lie Group Variational Integrator (2011)

Simulation technology is becoming increasingly crucial in the design and optimization of satellites due to the difficulties in testing and verifying system parameters on the ground. Computationally tractable and accurate methods are required in order to test satellite parameters in the complex and dynamic space environment. Although various satellite teams have developed simulation tools, many suffer from inaccurate numerical integrators, resulting in their simulations being of low fidelity for long duration simulations. This paper presents a MATLAB/Simulink-based simulator which includes high fidelity integration and modeling for accurate and relatively quick results. The simulator includes an energy-preserving variational integrator for both translational and rotational dynamics. A Lie Group Variational Integrator is used for the rotational dynamics, which enforces an orthogonality constraint for improved accuracy. This approach requires less computational time relative to other integration methods such as Runge-Kutta method for the same level of integration accuracy. The simulator includes perturbations to the orbital motion and attitude, including Earth oblateness, aerodynamic drag, solar pressure, gravity gradient, and residual dipole. The simulator also includes an advanced hysteresis model for improved modeling of magnetic attitude control systems. Simulation results are provided for a representative small satellite mission in low earth orbit with a passive magnetic stabilization control system. We compare the novel integration and hysteresis techniques to conventional simulators for long duration simulations for a realistic mission scenario.
Effect of Calponin on Actin-Activated Myosin ATPase Activity1 (1990)

Calponin inhibited the actin-activated myosin MgATPase activity in a dose-dependent manner without affecting the phosphorylation level of myosin light chain. This inhibition was Ca2(+)-independent. The decrease in enzymatic activity of myosin was correlated with binding of calponin to actin-tropomyosin filaments. Caldesmon showed a further inhibition of the calponin-induced inhibition of MgATPase activity of the thiophosphorylated myosin. Calponin-induced inhibition of the myosin MgATPase activity was reversed by the addition of calmodulin only in the presence of Ca2+. These results suggest that calponin acts as an inhibitory component of smooth muscle thin filaments.
The efficacy of an imidacloprid/moxidectin combination against naturally acquired <i>Sarcoptes scabiei</i> infestations on dogs (2006)

The study was undertaken to evaluate and compare the efficacy of an imidacloprid (10% w/v)/moxidectin (2.5% w/v) combination (Advocate Bayer HealthCare, Animal Health) with that of selamectin for the treatment of Sarcoptes scabiei on dogs. Thirty naturally infested dogs, of which one was later withdrawn because of distemper, were allocated to two equal groups and individually housed. The dogs in each group were treated twice, four weeks apart, with either the combination product (0.1 mL/kg body weight) or with selamectin (0.05 mL/kg body weight) administered topically. Skin scrapings were made every 14 days over a period of 50 to 64 days after the first treatment to quantify mite numbers. Clinical signs and the extent of sarcoptic lesions were assessed on each dog when skin scrapings were made. Efficacy was based on the presence or absence of mites, supported by clinical signs associated with canine sarcoptic mange. From Day 22 and onwards no Sarcoptes mites were found in the skin scrapings of any of the treated dogs. Treatment with the imidacloprid/moxidectin formulation or with selamectin was highly effective against Sarcoptes scabiei and resulted in an almost complete resolution of clinical signs within 50 to 64 days after the initial treatment.
DNA as a Molecular Ruler: Interrogation of a Tandem SH2 Domain with Self‐Assembled, Bivalent DNA–Peptide Complexes (2011)

Two peptides on display: The self-assembly of DNA complexes enables the bivalent presentation of phosphopeptides. Flexibility and distance in the ligand arrangement can be adjusted through the choice of appropriate DNA templates. Spatial screening of the tandem SH2 domain of Syk kinase with these probes (see picture) indicated the accessible arrangements of the two homologous binding pockets and the flexibility of the connecting protein linker. 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.
[Screening of short peptides binding to cell surface interleukin-2 receptor alpha chain]. (2006)

The peptide sequences containing Tyr, Phe conservative residues identified in this study can bind to cell surface IL-2Ralpha.
Use of enzyme-labeled antibodies to detect Salmonella in foods (1977)

An indirect enzyme-labeled antibody technique (ELAT), in which Salmonella typhimurium was used as a model, was developed as a method to detect Salmonella in food samples. A cellulose-acetate membrane filter, the matrix for detection, was placed on a membrane-filter base and overlaid with a multiwelled lucite template. Mixed broth enrichment cultures were dispensed in the template wells, and cells were spotted onto the membrane via suction. After fixation, the membranes were immersed in rabbit anti-S. typhimurium flagella antibody, washed, immersed in goat anti-rabbit antibody conjugated to peroxidase, and washed. Exposure of membranes to the substrates 3,3'-diaminobenzidine or benzidine resulted in development of brown or blue macroscopic reaction products, respectively, on spots containing S. typhimurium. ELAT results agreed with those of enrichment serology and cultural procedures on three food products containing known levels of S. typhimurium. Because of the magnification effect of the enzyme-substrate reaction, fewer cells were needed for detection than with enrichment serology, thereby reducing the total analysis time. The ability to test 14 or more samples simultaneously on a 47-mm membrane filter would facilitate screening large number of samples. Pending the development of a pure H antisera pool for the common Salmonella serotypes free from O antibodies, the ELAT demonstrated potential as a Salmonella detection methodology.
Regulation of fatty acid degradation in Escherichia coli: dominance studies with strains merodiploid in gene fadR (1980)

Strains stably merodiploid in the 25-min region of the chromosome of Escherichia coli were constructed and used in dominance tests between various wild-type and mutant alleles of the fadR gene. Whereas the monoploid fadR+ and fadR strains were inducible and constitutive, respectively, for the enzymes involved in fatty acid degradation (fad), merodiploids with at least one fadR+ allele were inducible. This observation was true whether the fadR+ allele resided on the main chromosome or on the episome. These results show that fadR+ is trans dominant to fadR, and they are consistent with the proposal that the fadR gene product is a repressor protein. Complementation tests were also performed by constructing 24 merodiploids harboring fadR alleles on both the main chromosome and the episome. All of these fadR/fadR diploids were able to utilize the noninducing substrate decanoate as sole carbon source, suggesting that only one polypeptide is encoded by the fadR gene.
Testing for Drugs of Abuse in Hair - Experimental Observations and Indications for Future Research. (1997)

The testing of hair for drugs of abuse is gaining popularity primarily due to the possibility that hair concentrations of drugs will reflect drug exposure for a longer period of time than either plasma or urine. Data produced by experimental research, rather than those resulting from anecdotal observations, uncontrolled research, or irrelevant experimental models, will be more likely to prove whether this is true and to determine whether drug concentrations in hair can be accurately interpreted in relation to drug dosage. Experimental observations have established that: (a) parent drug concentrations in hair are generally greater than their metabolites; (b) chemical structure of the drug is important in determining its incorporation into hair; (c) pigmentation of hair plays an important role in determining drug incorporation. Data resulting from models (including animal models, in vitro models, transplantation of human hair onto athymic mice, and human subjects) designed for studying hypotheses concerning the mechanism of drug incorporation into hair are also reviewed.
ChemInform Abstract: Glycosylation on the Merrifield Resin Using Anomeric Sulfoxides. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Robust object tracking based on tracking-learning-detection (2012)

Current state-of-the-art methods for object tracking perform adaptive tracking-by-detection, meaning that a detector predicts the position of an object and adapts its parameters to the object's appearance at the same time.While suitable for cases when the object does not disappear from the scene, these methods tend to fail on occlusions.In this work, we build on a novel approach called Tracking-Learning-Detection (TLD) that overcomes this problem.In methods based on TLD, a detector is trained with examples found on the trajectory of a tracker that itself does not depend on the object detector.By decoupling object tracking and object detection we achieve high robustness and outperform existing adaptive tracking-by-detection methods.We show that by using simple features for object detection and by employing a cascaded approach a considerable reduction of computing time is achieved.We evaluate our approach both on existing standard single-camera datasets as well as on newly recorded sequences in multi-camera scenarios.i
Comparison of <i>Neisseria gonorrhoeae</i> Multiantigen Sequence Typing and <i>porB</i> Sequence Analysis for Identification of Clusters of <i>N. gonorrhoeae</i> Isolates (2008)

porB DNA sequence analysis and Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) methods were compared for their abilities to discriminate strains and to identify epidemiologically congruent pairs of N. gonorrhoeae. Both methods provided high-level discrimination of strains. NG-MAST further differentiated large porB-based clusters. However, considerations of cost suggest that porB DNA sequence analysis is a useful tool for preliminary molecular analysis of the epidemiology of N. gonorrhoeae.