gebhart/patrepeval huggingface dataset:
Butyrophilin 2A1 is essential for phosphoantigen reactivity by gamma delta T cells (2020)

Gamma delta (γδ) T cells are essential to protective immunity. In humans, most γδ T cells express Vγ9Vδ2+ T cell receptors (TCRs) that respond to phosphoantigens (pAgs) produced by cellular pathogens and overexpressed by cancers. However, the molecular targets recognized by these γδTCRs are unknown. Here, we identify butyrophilin 2A1 (BTN2A1) as a key ligand that binds to the Vγ9+ TCR γ chain. BTN2A1 associates with another butyrophilin, BTN3A1, and these act together to initiate responses to pAg. Furthermore, binding of a second ligand, possibly BTN3A1, to a separate TCR domain incorporating Vδ2 is also required. This distinctive mode of Ag-dependent T cell activation advances our understanding of diseases involving pAg recognition and creates opportunities for the development of γδ T cell-based immunotherapies.
A 1.75 GHz piezoelectrically-transduced SiC lateral overmoded bulk acoustic-wave resonator (2011)

This paper presents the development and study of a novel lateral overmoded bulk acoustic-wave resonator (LOBAR) using piezoelectric AlN on SiC technology. The SiC LOBAR is a new class of resonant devices in which multiple longitudinal vibrations are excited in a high quality factor (Q) acoustic cavity (SiC) by means of a miniaturized AlN transducer that occupies a small fraction of the device volume (210 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> of AlN versus 42,021 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> of SiC). The first LOBAR prototype reported herein exhibits a Q of 4250 for a series resonance at 1.75 GHz - one of the highest Q demonstrated for micro-resonators using piezoelectric transduction at GHz frequencies. The use of two materials capable of operations at high temperature and in harsh environments simultaneously offers high Q (SiC) and high transduction efficiency (AlN) and enables, for the first time, the development of RF MEMS components for a new realm of applications.
Electrokinetic Instabilities and Sample Stacking (2005)

Electrokinetic instabilities occur in electrokinetic microchannel flows with heterogeneous electrolytes. These instabilities can be leveraged in providing rapid mixing, but are often unwanted in microfluidic applications which use heterogeneous electrolytes to achieve high resolution and new functionality. One important application of heterogeneous electrolytes is field-amplified sample stacking methods which use conductivity gradients to achieve sample preconcentration prior to electrophoretic separation. In this work, we analyze the flow physics of electrokinetic flows with conductivity gradients using theoretical analyses, numerical computations, and experimental observations. Various models including twodimensional and depth-averaged formulations have been developed, and modeling results compare well with experimental observations. Based on this understanding, we have developed novel sample stacking methods with sample preconcentrations exceeding 1,000 fold. The work also provides guidelines for the design and optimization of on-chip chemical and bio-analytical assays.
Analysis of the Rigid Motion of a Conical Developable Mechanism (2021)

Abstract We demonstrate analytically that it is possible to construct a developable mechanism on a cone that has rigid motion. We solve for the paths of rigid motion and analyze the properties of this motion. In particular, we provide an analytical method for predicting the behavior of the mechanism with respect to the conical surface. Moreover, we observe that the conical developable mechanisms specified in this article have motion paths that necessarily contain bifurcation points, which lead to an unbounded array of motion paths in the parameterization plane.
Simulation of rare events in quantum error correction (2013)

We consider the problem of calculating the logical error probability for a stabilizer quantum code subject to random Pauli errors. To access the regime of large code distances where logical errors are extremely unlikely we adopt the splitting method widely used in Monte Carlo simulations of rare events and Bennett's acceptance ratio method for estimating the free energy difference between two canonical ensembles. To illustrate the power of these methods in the context of error correction, we calculate the logical error probability ${P}_{L}$ for the two-dimensional surface code on a square lattice with a pair of holes for all code distances $d\ensuremath{\le}20$ and all error rates $p$ below the fault-tolerance threshold. Our numerical results confirm the expected exponential decay ${P}_{L}\ensuremath{\sim}\mathrm{exp}[\ensuremath{-}\ensuremath{\alpha}(p)d]$ and provide a simple fitting formula for the decay rate $\ensuremath{\alpha}(p)$. Both noiseless and noisy syndrome readout circuits are considered.
Integrins and Other Cell Adhesion Molecules in Endometrium and Endometriosis (1997)

Endometriosis is a disease that affects about 5% of women of reproductive age, but is found much more frequently in those with pelvic pain and/or infertility. In affected individuals, shed endometrium is thought to attach and spread within the pelvis through specific cell adhesion receptors. To understand why some women develop endometriosis while others do not, researchers have begun to examine these receptors and their extracellular matrix ligands. Cell adhesion molecules fall into 4 major groups including cadherins, selectins, members of the immunoglobulin superfamily, and integrins. Based on our current understanding, each may potentially play a role in the development or progression of this disease. In addition, the use of integrins as markers of the normal endometrial phenotype may be useful for the diagnosis of endometriosis and may identify women with defects in endometrial function leading to infertility or recurrent pregnancy loss. As more information becomes available, it may be possible to develop better treatments for endometriosis based on these concepts and to identify those women at risk for development of this common yet serious disorder.
Use of CrKα radiation to enhance the signal from anomalous scatterers including sulfur (2000)

The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr K α radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu K α and Cr K α data were similar but better than that for Au L α. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr K α data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au L α data. The ability to enhance the S-derived anomalous signal using Cr K α radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr K α data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method.
Affinity electrophoresis in multisectional polyacrylamide slab gels is a useful and convenient technique for measuring binding constants of aryl sulfonamides to bovine carbonic anhydrase B (1993)

This paper describes convenient preparations of heterogeneous multisectional polyacrylamide slab gels and the protocols that use these gels to measure protein-ligand binding constants [using bovine carbonic anhydrase B (CAB) as a model system]. Unlike procedures for affinity electrophoresis using tube gels, all binding information concerning protein-ligand interactions was encoded in a single multisectional gel: the procedure involving for measuring binding constants required no postelectrophoresis manipulation of gels. Use of these types of gels improves the accuracy of affinity gel electrophoresis (AGE) by providing reliable internal protein standards. Binding constants measured by AGE agree with those determined in homogeneous solution by spectrophotometric measurements. This technique has been used to investigate the influence of the length of the spacer separating the ligand and the polyacrylamide backbone on the binding constants. Dissociation constants obtained using the affinity gels approach the values measured in free solution, when the spacer is sufficiently long (> or = 18 A); affinity ligands having short spacers give high apparent dissociation constants.
Anthropometric measures and absolute cardiovascular risk estimates in the Australian Diabetes, Obesity and Lifestyle (AusDiab) Study (2007)

Measurement of waist-to-hip ratio is more useful than BMI or waist circumference in the identification of individuals estimated to be at increased risk for future primary cardiovascular events.
Electrical and magnetic measurements for LiyMg(Yb2)X4, X=S or Se (1987)

The lithiated spinels LiyMg(Yb2)X4, X=S or Se and y approximately=0.8, have been compared with the parent spinels via the following physical measurements: electron paramagnetic resonance. AC and DC electrical conductivity, high-pressure electrical conductivity and magnetic susceptibility. The lithiated compounds are shown to be of mixed valence with a partially occupied Yb3+/2+:4f13/14 redox couple located well below the bottom of the Yb 5d conduction band. In contrast to intermediate-valence compounds, these mixed-valence compounds behave magnetically as their non lithiated analogues Mg(Yb2)X4, but with a dilution of the magnetic Yb3+:4f13 ion due to transfer of one electron per lithium ion to the host to create diamagnetic Yb2+:4f14 ions. The small-polaron motional enthalpy is Delta Hm<or=0.23 eV in LiyMg(Yb2)S4 and Delta Hm<or=0.14 eV in LiyMg(Yb2)Se.
A Parallel Two-Pass MDL Context Tree Algorithm for Universal Source\n Coding (2014)

We present a novel lossless universal source coding algorithm that uses\nparallel computational units to increase the throughput. The length-$N$ input\nsequence is partitioned into $B$ blocks. Processing each block independently of\nthe other blocks can accelerate the computation by a factor of $B$, but\ndegrades the compression quality. Instead, our approach is to first estimate\nthe minimum description length (MDL) source underlying the entire input, and\nthen encode each of the $B$ blocks in parallel based on the MDL source. With\nthis two-pass approach, the compression loss incurred by using more parallel\nunits is insignificant. Our algorithm is work-efficient, i.e., its\ncomputational complexity is $O(N/B)$. Its redundancy is approximately\n$B\\log(N/B)$ bits above Rissanen's lower bound on universal coding performance,\nwith respect to any tree source whose maximal depth is at most $\\log(N/B)$.\n
Advanced laser system for 3D optoacoustic tomography of the breast (2016)

We describe the ongoing development and performance of a high-pulse-energy wavelength-cycling laser system for three-dimensional optoacoustic tomography of the breast. Joule-level energies are desired for achieving the required penetration depths while maintaining safe fluence levels. Wavelength cycling provides a pulse sequence which repeatedly alternates between two wavelengths (approximately 756 and 797 nm) that provide differential imaging. This improves co-registration of captured differential images and quantification of blood oxygen saturation. New design features have been developed for and incorporated into a clinical prototype laser system, to improve efficacy and ease of use in the clinic. We describe the benefits of these features for operation with a clinical pilot optoacoustic / ultrasound dual-modality three-dimensional imaging system.
Development of Second- and Third-Generation Bovine Immunodeficiency Virus-Based Gene Transfer Systems (2002)

Lentivirus-based gene transfer systems have demonstrated their utility in mediating gene transfer to dividing and nondividing cells both in vitro and in vivo. An early-generation gene transfer system developed from bovine immunodeficiency virus (BIV) has been described (Berkowitz et al., J. Virol. 2001;75:3371-3382). In this paper, we describe the development of second-generation (three-plasmid) and third-generation (four-plasmid) BIV-based systems. All accessory genes (vif, vpw, vpy, and tmx) and the regulatory gene tat were deleted or largely truncated from the packaging construct. Furthermore, we split the packaging function into two constructs by expressing Rev in a separate plasmid. Together with our minimal BIV transfer vector construct and a vesicular stomatitis virus G glycoprotein-expressing plasmid, the BIV vectors were generated. The vectors produced by the three- and four-plasmid systems had titers greater than 1 x 10(6) transducing units per milliliter and were fully functional as indicated by their ability to efficiently transduce both dividing and nondividing cells. These results suggest that the accessory genes vif, vpw, vpy, and tmx are dispensable for functional BIV vector development. The modifications made to the packaging constructs improve the safety profile of the vector system. Finally, BIV vectors provide an alternative to human immunodeficiency virus-based gene transfer systems.
Fabrication of ideally ordered TiO2 through-hole membranes by two-layer anodization (2020)

Ideally ordered TiO<sub>2</sub> through-hole membranes were obtained by a combination of Ti substrate pre-patterning and two-layer anodization. The Ti substrate was pre-patterned by Ar ion milling using ideally ordered porous alumina as an etching mask. Each concave pit formed by dry etching acted as an initiation site for hole development during anodization, and ideally ordered anodic porous TiO<sub>2</sub> was produced by anodization using an electrolyte containing fluoride ions. Two-layered anodic porous TiO<sub>2</sub> samples with different solubilities were formed by heat treatment for the crystallization of the first anodized oxide layer and a subsequent second anodization. The selective dissolution of the lower part of the two-layered porous TiO<sub>2</sub> produced an ideally ordered TiO<sub>2</sub> through-hole membrane. Using the present process, the repeated preparation of ideally ordered TiO<sub>2</sub> membranes can be conducted because the ideally ordered concave array, which corresponds to the hole arrangement at the bottom of the detached TiO<sub>2</sub> membrane, is maintained even after detaching the membrane. The obtained samples can be applied to various functional devices, such as photonic crystals and filtration membranes with photocatalytic properties.
[P1–523]: THE ADHERENCE/RETENTION PLAN OF THE ALZHEIMER's PREVENTION INITIATIVE (API) COLOMBIA TRIAL (2017)

The Alzheimer's Prevention Initiative (API) Colombia Trial is a collaborative project involving the Neurosciences Group of Antioquia (GNA), Genentech/Roche, and the Banner Alzheimer's Institute studying whether crenezumab can delay or prevent the clinical onset of Alzheimer's disease in asymptomatic individuals who carry the PSEN1 E280A mutation. In an effort to optimize participant compliance and adherence, and maintain interest in the trial for its duration, the GNA developed an “Adherence/Retention Plan.” This Plan identifies potential barriers related to characteristic of participants and study partners, protocol design, sponsors, investigators, contextual and environment factors, and characteristics of this population in general. GNA designed and implemented a number of strategies including: a carefully designed schedule of visits and assessments, appointment reminders, reimbursement for transportation and missed work, meals during study procedures, birthday cards, quarterly newsletters, annual in-person feedback meetings, provision of a health plan to participants and a social plan to family members. In the context of health care in Colombia, we determined that a study-related health plan was needed to ensure timely evaluation, treatment and follow up of adverse events, conduct additional testing if needed, offer contraception, and provide gynecological and other specialist evaluations for participants in instances where their standard medical care could not address health concerns in a timely way or at all. The social plan consists of programs/workshops to assist affected individuals and their families, provide coping strategies, support their participation in relevant research, and improve the quality of their lives. The social plan does not benefit trial participants directly and all services are provided whether or not family members participate in GNA research. All strategies are approved by a local Ethics Committee, reevaluated using an annual survey and adjusted according to the needs of participants, investigators and to the experience gained during the study. By the end of third year, the trial, retention of participants is 96.6% and 80.3% of participants report feeling “very satisfied” with their experience. The Adherence/Retention Plan plays a crucial role in maintaining adherence and compliance needed to achieve the ambitious goals of the Colombian API Autosomal Dominant Alzheimer's Disease Trial.
ChemInform Abstract: Probes for Narcotic Receptor Mediated Phenomena. Part 19. Synthesis of (+)‐4‐((αR)‐α‐((2S,5R)‐4‐Allyl‐2,5‐dimethyl‐1‐piperazinyl)‐ 3‐methoxybenzyl)‐N,N‐diethylbenzamide (SNC 80): A Highly Selective, Nonpeptide δ Opioid Receptor Agonist. (1994)

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.
Encoder Complexity Control in SVT-AV1 by Speed-Adaptive Preset Switching (2023)

Current developments in video encoding technology lead to continuously improving compression performance but at the expense of increasingly higher computational demands. Regarding the online video traffic increases during the last years and the concomitant need for video encoding, encoder complexity control mechanisms are required to restrict the processing time to a sufficient extent in order to find a reasonable trade-off between performance and complexity. We present a complexity control mechanism in SVT-AV1 by using speed-adaptive preset switching to comply with the remaining time budget. This method enables encoding with a user-defined time constraint within the complete preset range with an average precision of 8.9 \% without introducing any additional latencies.
Particle Swarm with Domain Partition and Control Assignment for Time-Optimal Maneuvers (2017)

A novel approach has been proposed for planning time-optimal maneuvers imposing a bang–bang external control. The optimizer was based on the particle swarm optimization and only required setting the maximum number of switches allowed for each axis. Two different test cases were analyzed and solved to validate the optimizer. In the first example, characterized by four state-space variables and no path constraints, the convergence toward the optimal solution has been demonstrated with different values of the maximum number of switches. For the second example, described by six state-space variables and nonlinear path constraints, the optimal solution was reached in more than 70% of the cases over 100 simulations, path constraints were completely satisfied, and errors on the final conditions were lower than 10-8 in normalized units. The computational effort was rather small because about 2000 iterations were required to reach convergence. Moreover, the second example has shown that the solution obtained with the described method could be better than the solutions obtained with pseudospectral optimization algorithms.
Interleukin-4 induces association of the c-fes proto-oncogene product with phosphatidylinositol-3 kinase (1996)

We have previously demonstrated that interleukin-4 (IL-4) induces tyrosine phosphorylation of a protein closely related or identical to the c-fes proto-oncogene product (FES) and association of this protein with the IL-4 receptor alpha chain (IL-4R alpha). IL-4 is known to induce association of phosphatidylinositol-3 (PI3) kinase with the IL-4R alpha. Since FES contains the consensus motifs for PI3 kinase binding, we tested the possibility that FES may associate with PI3 kinase upon IL-4 stimulation. We demonstrate herein that IL-4 stimulation induced rapid association of FES or a related protein with PI3 kinase in mouse T-cell lines. We also show an association of human FES (hFES) with the src homology 2 (SH2) domain of PI3 kinase in a COS7 cell expression system. The in vitro PI3 kinase assay using COS7 cells suggested that hFES partly contributes to the association between the hIL-4R alpha and PI3 kinase. We have further identified the important region in the cytoplasmic domain of the hIL-4R alpha for association of tyrosine-phosphorylated hFES with the hIL-4R alpha and SH2 domain of PI3 kinase using a COS7 cell expression system. These results suggest that FES or a related protein/PI3 kinase pathway may play a role in the pleiotropic effects of IL-4.
Factors associated with lifetime risk of open‐angle glaucoma blindness (2013)

Higher IOP and worse visual field status at baseline were important risk factors, as was older age at death.
Synthesis of Hematite Nanodiscs from Natural Laterites and Investigating Their Adsorption Capability of Removing Ni2+ and Cd2+ Ions from Aqueous Solutions (2020)

In this work, disc-like hematite (Fe2O3) nanoparticles were prepared using a readily available inexpensive earth material, ferruginous laterite, via a low-cost synthesis route. Prepared hematite nanoparticles were characterized using X-Ray diffraction (XRD), inductively coupled plasma mass spectroscopy (ICP-MS), particle size analyzer (PSA), Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), and nitrogen adsorption-desorption analyzer. The performance of hematite nanoparticles was evaluated as a heavy metal ion adsorbent. Batch adsorption experiments were conducted to study the adsorption behaviour of Ni2+ and Cd2+ ions as a function of the amount of adsorbent, contact time, and pH. Adsorption data fitted to the linearized Langmuir and Freundlich kinetic models were compared and discussed. The correlation coefficient (R2) was used to determine the best fit kinetic model. Our data fitted the Langmuir kinetic model well and the highest adsorption efficiencies were found to be 62.5 mg/g for Ni2+ and 200 mg/g for Cd2+, respectively. Due to high surface area, pore volume with active sites, and sorption capabilities, hematite nanoparticles can be used as efficient and economical nano-adsorbents for the removal of Ni2+ and Cd2+ ions from industrial wastewater.