gebhart/patrepeval huggingface dataset:
Humanized V(D)J-rearranging and TdT-expressing mouse vaccine models with physiological HIV-1 broadly neutralizing antibody precursors (2022)

Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through nontemplated nucleotide additions ("N-regions") by terminal deoxynucleotidyl transferase (TdT). HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs. Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC V<sub>H</sub>1-2 and commonly use human LCs Vκ3-20 or Vκ1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3. Prior VRC01-class models had nonphysiological precursor levels and/or limited precursor diversity. Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of V<sub>H</sub>1-2, as well as Vκ1-33 and/or Vκ3-20 in association with diverse CDR3s. Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted the generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vκ-to-Jκ joins. Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center B cell responses. Vκ3-20-based responses were enhanced by N-region addition, which generates Vκ3-20-to-Jκ junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens. These new VRC01-class mouse models establish a prototype for the generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.
A novel gastric release PEG‐enclatherated polymethacrylate‐based memblet system (2012)

Abstract A novel polymethacrylate‐based membranous system referred to as a “memblet” was developed for potential application in controlled gastric drug delivery. A polymethacrylate‐based latex, Eudragit® E100, was enclatherated with a 60% w/v and a 30% w/v solution of polyethylene glycol 4000 to form hydrogel formulations A and B, respectively. The hydrogels were subsequently compressed into memblets that were characterized for thermal, rheological, morphological, mechano‐chemical properties, and in vitro gastric drug release analysis. Molecular mechanics (MM) simulations were performed to corroborate the experimental findings. Critical yield values of 15.39 and 5.239 Pa were obtained for hydrogel A and B, respectively. The viscoelastic region was found to be &lt;10.67 and 2.542 Pa for hydrogels A and B, respectively. The storage modulus was greater than the loss modulus for hydrogel A while the inverse was true for hydrogel B. Thermal, mechanical, and surface morphology evaluation revealed that the converse was true for the dried membrane structure with hydrogel B having superior characterization profiles than hydrogel A. Notably, the lower PEG concentration (30% w/v) displayed better characterization profiles than a higher concentration (60% w/v). Through MM simulations, desirable agreement between the theoretical and experimental results was achieved over the given concentration range of PEG. Based on the gastric drug release analysis, memblets formulated with hydrogel B displayed superior control of drug release. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Cystic fibrosis-type mutational analysis in the ATP-binding cassette transporter signature of human P-glycoprotein MDR1. (1994)

Members of the ATP-binding cassette transporter superfamily such as the P-glycoproteins (MDR) and the cystic fibrosis transmembrane conductance regulator (CFTR) share conserved sequence motifs in their nucleotide binding fold that are the major targets for CFTR mutations in patients with cystic fibrosis. Cystic fibrosis-type mutations were introduced at analogous positions into the human MDR1 gene. Heterologous expression of wild-type or mutated MDR1 revealed similar mRNA transcript levels in Chinese hamster ovary K1 recipients, but the subsequent processing was defective for all mutations that give rise to severe cystic fibrosis in the case of CFTR. Functional multidrug transporter MDR1, however, was obtained when amino acid substitutions were introduced into a less conserved position of the ATP-binding cassette transporter signature (codon 536 in MDR1). The profile of cross-resistance and chemosensitization was modulated in these codon 536 variants, which suggests that this region is involved in the drug transport function of P-glycoprotein.
Scaling up genome annotation using MAKER and work queue (2014)

Next generation sequencing technologies have enabled sequencing many genomes. Because of the overall increasing demand and the inherent parallelism available in many required analyses, these bioinformatics applications should ideally run on clusters, clouds and/or grids. We present a modified annotation framework that achieves a speed-up of 45x using 50 workers using a Caenorhabditis japonica test case. We also evaluate these modifications within the Amazon EC2 cloud framework. The underlying genome annotation (MAKER) is parallelised as an MPI application. Our framework enables it to now run without MPI while utilising a wide variety of distributed computing resources. This parallel framework also allows easy explicit data transfer, which helps overcome a major limitation of bioinformatics tools that often rely on shared file systems. Combined, our proposed framework can be used, even during early stages of development, to easily run sequence analysis tools on clusters, grids and clouds.
High rate fabrication of compression molded components (2023)

A method for fabricating a thermoplastic composite component comprises inductively heating a thermoplastic pre-form with a first induction coil by inducing current to flow in susceptor wires disposed throughout the pre-form, inductively heating smart susceptors in a molding tool to a leveling temperature with a second induction coil by applying a high-strength magnetic field having a magnetic flux that passes through surfaces of the smart susceptors, shaping the magnetic flux that passes through surfaces of the smart susceptors to flow substantially parallel to a molding surface of the smart susceptors, placing the heated pre-form between the heated smart susceptors; and applying molding pressure to the pre-form to form the composite component.
Cavity-enhanced second-harmonic generation via nonlinear-overlap optimization (2016)

We describe an approach based on topology optimization that enables automatic discovery of wavelengthscale photonic structures for achieving high-efficiency second-harmonic generation (SHG).A key distinction from previous formulation and designs that seek to maximize Purcell factors at individual frequencies is that our method not only aims to achieve frequency matching (across an entire octave) and large radiative lifetimes, but also optimizes the equally important nonlinear-coupling figure of merit β, involving a complicated spatial overlap-integral between modes.We apply this method to the particular problem of optimizing micropost and grating-slab cavities (one-dimensional multilayered structures) and demonstrate that a variety of material platforms can support modes with the requisite frequencies, large lifetimes Q > 10 4 , small modal volumes ∼ (λ/n) 3 , and extremely large β 10 -2 , leading to orders of magnitude enhancements in SHG efficiency compared to state of the art photonic designs.Such giant β alleviate the need for ultranarrow linewidths and thus pave the way for wavelength-scale SHG devices with faster operating timescales and higher tolerance to fabrication imperfections.
Transcription of hexose transporters of Saccharomyces cerevisiae is affected by change in oxygen provision (2008)

When oxygen becomes limiting in a glucose-limited chemostat cultivation, the glucose uptake rate per cell increases. However, the expression of none of the hexose transporter encoding genes was increased in anaerobic conditions. It thus seems that the decrease in the moderately low affinity uptake and consequently the relative increase of high affinity uptake may itself allow the higher specific glucose consumption rate to occur in anaerobic compared to aerobic conditions.
An open software architecture for virtual reality interaction (2001)

This article describes OpenTracker, an open software architecture that provides a framework for the different tasks involved in tracking input devices and processing multi-modal input data in virtual environments and augmented reality application. The OpenTracker framework eases the development and maintenance of hardware setups in a more flexible manner than what is typically offered by virtual reality development packages. This goal is achieved by using an object-oriented design based on XML, taking full advantage of this new technology by allowing to use standard XML tools for development, configuration and documentation. The OpenTracker engine is based on a data flow concept for multi-modal events. A multi-threaded execution model takes care of tunable performance. Transparent network access allows easy development of decoupled simulation models. Finally, the application developer's interface features both a time-based and an event based model, that can be used simultaneously, to serve a large range of applications. OpenTracker is a first attempt towards a "'write once, input anywhere"' approach to virtual reality application development. To support these claims, integration into an existing augmented reality system is demonstrated. We also show how a prototype tracking equipment for mobile augmented reality can be assembled from consumer input devices with the aid of OpenTracker. Once development is sufficiently mature, it is planned to make Open-Tracker available to the public under an open source software license.
Pushing multiple patterning in sub-10nm (2015)

Due to elongated delay of extreme ultraviolet lithography (EUVL), the semiconductor industry has been pushing the 193nm immersion lithopgrahy using multiple patterning to print critical features in 22nm/14nm technology nodes and beyond. Multiple patterning lithography (MPL) poses many new challenges to both mask design and IC physical design. The mask layout decomposition problem has been extensively studied, first on double patterning, then on triple or even quadruple patterning. Meanwhile, many studies have shown that it is very important to consider MPL implications at early physical design stages so that the overall design and manufacturing closure can be reached. In this paper, we provide a comprehensive overview on the state-of-the-art research results for MPL, from synergistic mask synthesis to physical design. We will also discuss the open problems as to pushing multiple patterning in sub-10nm.
Laser Driven Dielectric Accelerator in the Non-relativistic Energy Region (2016)

Laser-driven dielectric accelerator (LDA) is suitable for delivering a submicron-size ultra-short electron beam, which is useful for studying basic processes of the radiation effect in a biological cell. Both the oblique incidence and the normal incidence configurations of LDA were studied. The oblique incidence configuration of LDA relaxes the synchronization condition as v_{e}=¥pm c L_{G}/¥left(¥λ+ L_{G} n ¥sin ¥theta ¥right) and is somewhat suitable for accelerating the non-relativistic electrons. The required energy to accelerate electrons in the oblique incidence configuration is smaller than that in the normal incidence configuration by a factor of ¥cos ¥theta, where ¥theta is the incidence angle of the laser beam. Two gratings each were made of different material structure of silica ({¥rm SiO₂}) were fabricated by the electron beam lithography. When a crystal silica was adopted, many large humps of several hundred nm size were observed in grooves of the grating. On the other hand, a glass silica had smoother grooves.
Novel Architecture for LTE World-Phones (2013)

The 4th Generation of mobile communications (4G) came with new challenges on the antenna bandwidth and on the front-end architecture of mobile phones. This letter proposes a novel architecture overcoming these challenges. It includes narrowband tunable antennas, co-designed with a tunable front rnd (FE). Simulations and measurements demonstrate the concept for low and high bands of the LTE frequency spectrum.
Nucleotide variation at the hypervariable esterase 6 isozyme locus of Drosophila simulans. (1995)

Esterase 6 (Est-6/EST6) is polymorphic in both Drosophila melanogaster and D. simulans for two common allozyme forms, as well as for several other less common variants. Parallel latitudinal clines in the frequencies of the common EST6-F and EST6-S allozymes in these species have previously been interpreted in terms of a shared amino acid polymorphism that distinguishes the two variants and is subject to selection. Here we compare the sequences of four D. simulans Est-6 isolates and show that overall estimates of nucleotide heterozygosity in both coding and 5' flanking regions are more than threefold higher than those obtained previously for this gene in D. melanogaster. Nevertheless, the ratio of replacement to exon silent-site polymorphism in D. simulans is less than the ratio of replacement to silent divergence between D. simulans and D. melanogaster, which could be the result of increased efficiency of selection against replacement polymorphisms in D. simulans or to divergent selection between the two species. We also find that the amino acid polymorphisms separating EST6-F and EST6-S in D. simulans are not the same as those that separate these allozymes in D. melanogaster, implying that the shared clines do not reflect shared molecular targets for selection. All comparisons within and between the two species reveal a remarkable paucity of variation in a stretch of nearly 400 bp immediately 5' of the gene, indicative of strong selective constraint to retain essential aspects of Est-6 promoter function.
[Response to influenza vaccine in uremic patients: relation to erythrocyte magnesium and the value of a second injection]. (1987)

Humoral response to influenza vaccination being variable in uremic patients and being negatively correlated to red blood cell magnesium (RBC Mg) in non-uremic subjects, RBC Mg as well as plasma concentration of Mg were measured simultaneously with the antibodies titers after 1 and 2 injections of influenza vaccine in 21 non-uremic subjects and 47 patients on chronic hemodialysis. The RBC Mg and plasma Mg (MgP) were significantly higher in the dialysed patients (74 +/- 12 mg/l; 25 +/- 8 mg/l) than in the non-uremic subjects (54 +/- 5 mg/l; 19.4 +/- 1.5 mg/l). Furthermore, in the uremics RBC Mg was correlated to PMg whereas such a correlation was absent in the non-uremic patients. The humoral response of the uremic patients is depressed and becomes comparable to that of the non-uremic subjects after 1 injection only after 2 injections. In the uremic patients, the depressed humoral response is associated with higher RBC Mg (greater than 70 mg/l). The humoral response to influenza vaccine is depressed in uremic patients who have either the HBs antigen or no response to the hepatitis B vaccine but no link has been found between this immune status against the hepatitis B and RBC Mg. In conclusion, the humoral response of the uremic patients to influenza vaccine is depressed so that a second injection is necessary to give them sufficient protection.
Grid Synchronization in Three‐Phase Power Converters (2010)

This chapter contains sections titled: Introduction The Three-Phase Voltage Vector under Grid Faults The Synchronous Reference Frame PLL under Unbalanced and Distorted Grid Conditions The Decoupled Double Synchronous Reference Frame PLL (DDSRF-PLL) The Double Second-Order Generalized Integrator FLL (DSOGI-FLL) Summary References
Can Negligible Cooperation Increase Network Reliability? (Extended Version). (2016)

In network cooperation strategies, nodes work together with the aim of increasing transmission rates or reliability. For example, cooperation can be employed to obtain a code with small maximal-error from a code with small average-error that does not make use of cooperation. In networks where rates achievable under a maximal-error constraint differ from those achievable under an average-error constraint, such a benefit can be potentially viewed as both increasing reliability and increasing rate. Let us define the cooperation rate as the number of bits per channel use shared with each node as part of the cooperation strategy. We here demonstrate that even a negligible cooperation rate can sometimes yield a non-negligible benefit. Precisely, we employ Dueck's example of a multiple access channel whose maximal and average-error sum-capacities differ, to show that there exists a network whose maximal-error sum-capacity is not continuous with respect to its edge capacities.
Enhancement of the toxic vapor identification capability of portable sensors using pattern recognition techniques (1985)

A portable instrument is being developed that can detect, identify, and warn US Coast Guard emergency response personnel of the presence of hazardous concentration of toxic gases and vapors. The toxic compounds are detected by an array of inexpensive, semiselective electrochemical sensors, and the complex output is analyzed using pattern recognition methods. The phototype device incorporates an array of four different electrochemical sensors, each of which can be operated in four different modes. The device thus obtains 16 channels of data for each chemical species present in the air sample. Pattern recognition analysis of these data can be used to determine the uniqueness of the information obtained for each of the 16 channels. A set of patterns for 22 gases and vapors detected with a chemical sensor array was examined. Results indicate that approximately half of the channels provide unique information and the data from 8 to 10 channels are sufficient to identify individual compounds.
Catadioptric lens design: the breakthrough to hyper-NA optics (2006)

To enable optical lithography for sub 55 nm features, ArF immersion lithography requires numerical apertures to be significantly larger than 1 - thus leading to new challenges for optical design. Refractive lens designs are not capable to capture these extreme etendues. Catadioptric lens designs can overcome these fundamental issues by keeping the diameters of the optical materials acceptable. We have studied various catadioptric design approaches. The main criteria used to evaluate the potential of the different solutions include mechanical complexity, reticle compatibility, optical sensitivities, polarization capabilities, image field shape, as well as enabling extendibility to even higher NAs. Our assessment leads us to a new design type called catadioptric in-line design which shows superior performance for high NA systems with NA > 1.1.
Measurement of Glutamate Carboxypeptidase II (NAALADase) Enzyme Activity by the Hydrolysis of [3H]‐N‐Acetylaspartylglutamate (NAAG) (2001)

The peptide N-Acetylaspartylglutamate (NAAG) is hydrolyzed by N-Acetylated-alpha-linked-acidic dipeptidase (NAALADase, glutamate carboxypeptidase II) into N-Acetylated aspartate (NAA) and glutamate. Hydrolysis can be measured as described in this unit by employing radiolabeled NAAG (NAA-[(3)H]glu) as the substrate. The occurrence of NAALADase activity in a wide range of tissues has implications for a variety of physiological purposes. The assay described here is useful for the analysis of NAALADase activity and its inhibition in brain synaptosomal preparations, tissue homogenates and tissue culture cell pellets.
Joint power and spectrum optimization in wireless localization networks (2015)

Network localization is a key feature in many wireless services and applications. In typical rang-based localization techniques, “agents” try to perform position estimation through ranging with respect to “anchors” with known positions. Based on the definition of squared positional error bound (SPEB), the localization accuracy can be determined by the transmit power, carrier frequency and signal bandwidth, etc. This paper analyzes the joint power and spectrum allocation (JPSA) optimization problems in resource restricted wireless localization systems. We first formulate both interference-free and interference-limited JPSA problems. Since both problems are non-convex, we then develop two approximation algorithms based on single condensation and Taylor linearization. Both algorithms are able to find solutions close the global optimum. Numeric results validate our analysis, and show that, we are able to find optimal resource deployment in wireless localization networks based on the proposed frameworks.
Solid Phase DNA Extraction with a Flexible Bead-Packed Microfluidic Device to Detect Methicillin-Resistant Staphylococcus aureus in Nasal Swabs (2012)

We have developed a bead-packed microfluidic device with a built-in flexible wall to automate extraction of nucleic acids from methicillin-resistant Staphylococcus aureus (MRSA) in nasal swabs. The flexible polydimethylsiloxane (PDMS) membrane was designed to manipulate the surface-to-volume ratio (SVR) of bead-packed chambers in the range of 0.05 to 0.15 (μm(-1)) for a typical solid phase extraction protocol composed of binding, washing, and eluting. In particular, the pneumatically assisted close packing of beads led to an invariant SVR (0.15 μm(-1)) even with different bead amounts (10-16 mg), which allowed for consistent operation of the device and improved capture efficiency for bacteria cells. Furthermore, vigorous mixing by asynchronous membrane vibration enabled ca. 90% DNA recovery with ca. 10 μL of liquid solution from the captured cells on the bead surfaces. The full processes to detect MRSA in nasal swabs, i.e., nasal swab collection, prefiltration, on-chip DNA extraction, and real-time polymerase chain reaction (PCR) amplification, were successfully constructed and carried out to validate the capability to detect MRSA in nasal swab samples. This flexible microdevice provided an excellent analytical PCR detection sensitivity of ca. 61 CFU/swab with 95% confidence interval, which turned out to be higher than or similar to that of the commercial DNA-based MRSA detection techniques. This excellent performance would be attributed to the capability of the flexible bead-packed microdevice to enrich the analyte from a large initial sample (e.g., 1 mL) into a microscale volume of eluate (e.g., 10 μL). The proposed microdevice will find many applications as a solid phase extraction method toward various sample-to-answer systems.