gebhart/patrepeval huggingface dataset:
Selection and Characterization of Single Domain Antibodies Specific for Bacillus anthracis Spore Proteins (2013)

To obtain thermostable immunoreagents specific for the spore form of Bacillus anthracis two llamas were immunized with a combination of six different recombinant proteins. These proteins BclA, gerQ, SODA1, SOD15, BxpB and the protein p5303 have all been shown as components of the B. anthracis spore and could potentially serve as targets for the detection of spores in multiplexed biosensors. Peripheral blood lymphocytes were used to construct a phage display library from which single domain antibodies (sdAbs) targeting each of the proteins were isolated. Unique sdAbs exhibiting nanomolar or better affinities for the recombinant proteins were obtained and most of the isolated sdAbs retained their ability to bind antigen after cycles of heating as determined by enzyme linked immunosorbent assay (ELISA). SdAbs targeting the BclA and gerQ proteins were able to successfully detect bacterial spores, whether broken or intact, using a direct ELISA; the sdAbs were specific, showing binding only to B. anthracis spores and not to other Bacillus species. Additionally, SODA1 and p5303 binding sdAbs detected spores in sandwich assays serving as both captures and tracers. Used in combination, sdAbs targeting B. anthracis proteins could be integrated into emerging biosensors to improve specificity in multiplex assays.
Dispersive chiral frequency selective surfaces simulated via FEBI and FDTD (2007)

This paper will discuss the simulation of dispersive chiral frequency selective surfaces (FSS) through the use of a periodic finite-difference time-domain (FDTD) and a periodic finite-element boundary-integral (FEBI) method. The periodic numerical methods will be used to model a dispersive chiral polarizer with a FSS embedded within. This device will be designed to convert a linearly polarized wave of arbitrary polarization into a circularly polarized wave over a finite bandwidth. The two numerical methods will be compared and contrasted in reference to the design of the chiral polarizer.
Topology optimization and 3D printing of multimaterial magnetic actuators and displays (2019)

Upcoming actuation systems will be required to perform multiple tightly coupled functions analogous to their natural counterparts; e.g., the ability to control displacements and high-resolution appearance simultaneously is necessary for mimicking the camouflage seen in cuttlefish. Creating integrated actuation systems is challenging owing to the combined complexity of generating high-dimensional designs and developing multifunctional materials and their associated fabrication processes. Here, we present a complete toolkit consisting of multiobjective topology optimization (for design synthesis) and multimaterial drop-on-demand three-dimensional printing for fabricating complex actuators (>10<sup>6</sup> design dimensions). The actuators consist of soft and rigid polymers and a magnetic nanoparticle/polymer composite that responds to a magnetic field. The topology optimizer assigns materials for individual voxels (volume elements) while simultaneously optimizing for physical deflection and high-resolution appearance. Unifying a topology optimization-based design strategy with a multimaterial fabrication process enables the creation of complex actuators and provides a promising route toward automated, goal-driven fabrication.
On path planning methods for automotive collision avoidance (2013)

There is a strong trend for increasingly sophisticated Advanced Driver Assistance Systems (ADAS) such as Autonomous Emergency Braking (AEB) systems, Lane Keeping Aid (LKA) systems, and indeed autonomous driving. This trend generates a need for online maneuver generation, for which numerous approaches can be found in the large body of work related to path planning and obstacle avoidance. In order to ease the challenge of choosing a method, this paper reports quantitative and qualitative insights about three different path planning methods: a state lattice planner, predictive constraint-based planning, and spline-based search tree. Each method is described, implemented and compared on two specific traffic situations. The paper will not provide a final answer about which method is best. This depends on several factors such as computational constraints and the formulation of maneuver optimality that is appropriate for a given assistance or safety function. Instead, the conclusions will highlight qualitative merits and drawbacks for each method, in order to provide guidance for choosing a method for a specific application.
Color responses of the human lateral geniculate nucleus: selective amplification of S‐cone signals between the lateral geniculate nucleno and primary visual cortex measured with high‐field fMRI (2008)

The lateral geniculate nucleus (LGN) is the primary thalamic nucleus that relays visual information from the retina to the primary visual cortex (V1) and has been extensively studied in non-human primates. A key feature of the LGN is the segregation of retinal inputs into different cellular layers characterized by their differential responses to red-green (RG) color (L/M opponent), blue-yellow (BY) color (S-cone opponent) and achromatic (Ach) contrast. In this study we use high-field functional magnetic resonance imaging (4 tesla, 3.6 x 3.6 x 3 mm(3)) to record simultaneously the responses of the human LGN and V1 to chromatic and Ach contrast to investigate the LGN responses to color, and how these are modified as information transfers between LGN and cortex. We find that the LGN has a robust response to RG color contrast, equal to or greater than the Ach response, but a significantly poorer sensitivity to BY contrast. In V1 at low temporal rates (2 Hz), however, the sensitivity of the BY color pathway is selectively enhanced, rising in relation to the RG and Ach responses. We find that this effect generalizes across different stimulus contrasts and spatial stimuli (1-d and 2-d patterns), but is selective for temporal frequency, as it is not found for stimuli at 8 Hz. While the mechanism of this cortical enhancement of BY color vision and its dynamic component is unknown, its role may be to compensate for a weak BY signal originating from the sparse distribution of neurons in the retina and LGN.
Cryokinetic studies of the intermediates in the mechanism of carboxypeptidase A (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCryokinetic studies of the intermediates in the mechanism of carboxypeptidase AAlphonse Galdes, David S. Auld, and Bert L. ValleeCite this: Biochemistry 1983, 22, 8, 1888–1893Publication Date (Print):April 12, 1983Publication History Published online1 May 2002Published inissue 12 April 1983https://pubs.acs.org/doi/10.1021/bi00277a023https://doi.org/10.1021/bi00277a023research-articleACS PublicationsRequest reuse permissionsArticle Views72Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Expression of Concern: Accurate modeling of substrate coupling for substrates without grounded backplates (2003)

An accurate and numerically stable formulation is presented for the substrate resistive coupling using boundary element methods, for floating substrates (without grounded backplates).
IL-6 produced by immune complex-activated follicular dendritic cells promotes germinal center reactions, IgG responses and somatic hypermutation (2009)

Reports that follicular dendritic cells (FDCs) produce IL-6 prompted the hypotheses that immune complexes (ICs) induce FDCs to produce IL-6 and that FDC-IL-6 promotes germinal center (GC) reactions, somatic hypermutation (SHM) and IgG production. FDCs were activated in vitro by addition of ICs and FDC-IL-6 production was determined. Wild-type (WT) and IL-6 knockout (KO) mice, as well as chimeras with WT and IL-6 KO cells, were immunized with (4-hydroxy-3-nitrophenyl)-acetyl (NP)-chicken gamma globulin (CGG) and used to study anti-(4-hydroxy-3-iodo-5-nitrophenyl) acetyl (NIP) responses, GC formation and SHM in the VH186.2 gene segment in Ig-gamma. FDC-IL-6 increased when FDCs encountered ICs. At low immunogen dose, 1 microg NP-CGG per mouse, the IgG anti-NIP response in IL-6 KO mice was low and immunohistochemistry revealed a reduction in both the number and size of GCs. The physiological relevance of FDC-IL-6 was apparent in the chimeric mice where total splenocytes from WT mice were unable to provide the IL-6 needed for normal IgG and GC responses in IL-6 KO animals with IL-6-defective FDCs. Moreover, the rate of mutation decreased from 18 to 8.9 mutations per 1000 bases (P < 0.001) in WT versus IL-6 KO mice. Addition of anti-IL-6 to GC reactions in vitro reduced antibody levels and SHM from 3.5 to 0.65 mutations per 1000 bases (P < 0.02). Thus, the absence of FDC-IL-6 correlated with a reduction in SHM that coincided with the reduction in GCs and specific anti-NIP. This is the first study to document that ICs induce FDC-IL-6 and that FDC-derived IL-6 is physiologically relevant in generating optimal GC reactions, SHM and IgG levels.
Independent Country Program Review Jamaica 2016-2022 (2022)

This Independent Country Program Review (ICPR) analyzes the Inter-American Development Bank (IDB) Group's country strategy (CS) and country program with Jamaica during the 2016-2022 period. ICPRs assess the relevance of a CS, provide aggregate information on the alignment and execution of the corresponding country program and, data permitting, its contribution to strategic objectives (SOs) set in the CS. ICPRs are primarily addressed to the IDB Group's Boards of Executive Directors. They seek to provide the Boards with relevant information, otherwise not readily available to them, to inform their consideration of the upcoming CSs.
Terahertz imaging technique for monitoring the flow of buffer solutions at different pH values through a microfluidic chip (2021)

Abstract Polydimethylsiloxane (PDMS)-based mold prepared using a 3D-printed structure is a cost-effective material and tool to fabricate robust microfluidic chips (MCs) without requiring expensive clean room facilities. A capillary-based MC made of PDMS can be attached onto a glass substrate to visualize the chemical reactions in different types of pH buffer solutions (BSs) flowing through microflow channels (MFCs) using terahertz (THz) image sensing technology. In this study, we designed a microfluidic structure with two inlet wells and an outlet well, equipped with a Si:sapphire substrate to visualize the chemical interaction between BSs injected at different pH values (4 and 10) through an MFC. THz imaging maps were captured during the flow of the BSs using a THz chemical microscope, and the fluid dynamics was studied. We determined and plotted the variation in the THz amplitude data with respect to the BS concentration and analyzed the characteristics of the data.
Methods to Maintain Genetic Purity of Seed Stocks (2006)

Production and distribution of high-quality seeds is fundamental to modern agricultural systems. The majority of annual crops are established each season from seeds, and seed quality can have a major impact on potential crop yield. Seeds carry the genetic traits incorporated by years of breeding and selection to create varieties that are adapted to specific production environments and will produce high yields and product quality. The genetic purity of seeds (i.e., the percentage of contamination by seeds or genetic material of other varieties or species), their physiological quality (or vigor), and the presence of weed seeds, seedborne diseases, or other materials (dirt or plant residues) contribute to overall seed quality.
Mesenchymal traits at the convergence of tumor-intrinsic and -extrinsic mechanisms of resistance to immune checkpoint blockers (2017)

Targeting of immune checkpoint blockers (ICBs), such as cytotoxic T-lymphocyte antigen-4 and programmed-death 1/programmed-death ligand 1, has dramatically changed the landscape of cancer treatment. Seeing patients who were refractory to conventional therapy recover after immunotherapy, with high rates of objective durable responses and increased overall survival, has raised great enthusiasm in cancer care and research. However, to date, only a restricted portion of patients benefit from these therapies, due to natural and acquired resistance relying on the ever-evolving cross-talk between tumor and stromal cells. Here, we review the convergence of tumor-intrinsic and -extrinsic cues, both affecting tumor plasticity and tumor stroma leading to an immunosuppressive tumor microenvironment, which may account for the heterogeneous responses and resistance to ICB therapies. A deeper knowledge of the mechanisms and fingerprints involved in natural and acquired resistance is likely to bring clinical benefit to the majority of patients, offering important clues for overcoming drug resistance and boosting the effectiveness of treatment. We discuss the need to define tumor subtypes based on the tumor, immune and stromal gene signature and propose that the better we understand tumor mesenchymal traits, the more we will be able to identify predictive biomarkers of response to ICB treatments.
Deterministic approach to pure 2/sup nd/ order polarization mode dispersion compensation (2002)

We have designed a deterministic 2/sup nd/ order PMD compensator. This design is based on the assumption that the first order PMD has been compensated and we know the residual 2/sup nd/ order PMD. In addition, we have solved analytically the required rotation matrices of the polarization rotators and the required differential group delay (DGD) of a variable delay line in a 3-segments compensator.
ChemInform Abstract: Synthesis of 6‐Aza‐bicyclo[3,2,1]octan‐3‐ones via Vinylogous Imide Photochemistry: An Approach to the Synthesis of the Hetisine Alkaloids. (2001)

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.
Constructing elliptic curves with a given number of points over a finite field (2001)

In using elliptic curves for cryptography, one often needs to construct elliptic curves with a given or known number of points over a given finite field. In the context of primality proving, Atkin and Morain suggested the use of the theory of complex multiplication to construct such curves. One of the steps in this method is the calculation of the Hilbert class polynomial HD (X) modulo some integer p for a certain fundamental discriminant D. The usual way of doing this is to compute HD (X) over the integers and then reduce modulo p. But this involves computing the roots with very high accuracy and subsequent rounding of the coefficients to the closest integer. (Such accuracy issues also arise for higher genus cases.) We present a modified version of the Chinese remainder theorem (CRT) to compute HD (X) modulo p directly from the knowledge of HD (X) modulo enough small primes. Our algorithm is inspired by Couveigne&amp;apos;s method for computing square roots in the number field sieve, which is useful in other scenarios as well. It runs in heuristic expected time less than the CRT method in [CNST]. Moreover, our method requires very few digits of precision to succeed, and avoids calculating the exponentially large coefficients of the Hilbert class polynomial over the integers.
Modeling and Analysis of a Micro-Reactor Using the DireWolf Code Suite (2022)

Micro-reactors, specifically those cooled with heat pipes, are tightly coupled systems which require multi-physics tools to accurately model both steady-state and transient behavior. Idaho National Laboratory’s DireWolf code suite is tailor-built to model heat-pipe reactors. DireWolf’s ability to model the coupled steady-state behavior of a heat-pipe micro-reactor are demonstrated herein. The DireWolf modeling methodology is described, and a micro-reactor design is introduced. A full-core model is developed, and the steady-state coupled neutronics-thermal analysis is performed. Results of the analyses, including flux, power, and temperature distributions are presented and discussed. This is a Westinghouse Electric Company (WEC) led publication.
Low temperature recovery of acetone–butanol–ethanol (ABE) fermentation products via microwave induced membrane distillation on carbon nanotube immobilized membranes (2020)

Microwave induced ABE separation <italic>via</italic> breakdown of H-bonded ABE–water clusters and preferential adsorption of ABE on a CNT surface.
Nanofibers Produced from Agro-Industrial Plant Waste Using Entirely Enzymatic Pretreatments (2018)

Cellulose fibers can be freed from the cell-wall skeleton via high-shear homogenization, to produce cellulose nanofibers (CNF) that can be used, for example, as the reinforcing phase in composite materials. Nanofiber production from agro-industrial byproducts normally involves harsh chemical-pretreatments and high temperatures to remove noncellulosic polysaccharides (20-70% of dry weight). However, this is expensive for large-scale processing and environmentally damaging. An enzyme-only pretreatment to obtain CNF from agro-industrial byproducts (potato and sugar beet) was developed with targeted commercial enzyme mixtures. It is hypothesized that cellulose can be isolated from the biomass, using enzymes only, due to the low lignin content, facilitating greater liberation of CNF via high-shear homogenization. Comprehensive Microarray Polymer Profiling (CoMPP) measured remaining extractable polysaccharides, showing that the enzyme-pretreatment was more successful at removing noncellulosic polysaccharides than alkaline- or acid-hydrolysis alone. While effective alone, the effect of the enzyme-pretreatment was bolstered via combination with a mild high-pH pretreatment. Dynamic rheology was used to estimate the proportion of CNF in resultant suspensions. Enzyme-pretreated suspensions showed 4-fold and 10-fold increases in the storage modulus for potato and sugar beet, respectively, compared to untreated samples. A greener yet facile method for producing CNF from vegetable waste is presented here.
Efficient proximal gradient algorithm for inference of differential gene networks (2019)

With its superior performance over existing algorithms, ProGAdNet provides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene interactions changed under different conditions.
Data from Functional Silencing of <i>HSD17B2</i> in Prostate Cancer Promotes Disease Progression (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Steroidogenic enzymes are essential for prostate cancer development. Enzymes inactivating potent androgens were not investigated thoroughly, which leads to limited interference strategies for prostate cancer therapy. Here we characterized the clinical relevance, significance, and regulation mechanism of enzyme &lt;i&gt;HSD17B2&lt;/i&gt; in prostate cancer development.&lt;/p&gt;Experimental Design:&lt;p&gt;&lt;i&gt;HSD17B2&lt;/i&gt; expression was detected with patient specimens and prostate cancer cell lines. Function of &lt;i&gt;HSD17B2&lt;/i&gt; in steroidogenesis, androgen receptor (AR) signaling, and tumor growth was investigated with prostate cancer cell lines and a xenograft model. DNA methylation and mRNA alternative splicing were investigated to unveil the mechanisms of &lt;i&gt;HSD17B2&lt;/i&gt; regulation.&lt;/p&gt;Results:&lt;p&gt;&lt;i&gt;HSD17B2&lt;/i&gt; expression was reduced as prostate cancer progressed. 17βHSD2 decreased potent androgen production by converting testosterone (T) or dihydrotestosterone (DHT) to each of their upstream precursors. &lt;i&gt;HSD17B2&lt;/i&gt; overexpression suppressed androgen-induced cell proliferation and xenograft growth. Multiple mechanisms were involved in &lt;i&gt;HSD17B2&lt;/i&gt; functional silencing including DNA methylation and mRNA alternative splicing. DNA methylation decreased the &lt;i&gt;HSD17B2&lt;/i&gt; mRNA level. Two new catalytic-deficient isoforms, generated by alternative splicing, bound to wild-type 17βHSD2 and promoted its degradation. Splicing factors SRSF1 and SRSF5 participated in the generation of new isoforms.&lt;/p&gt;Conclusions:&lt;p&gt;Our findings provide evidence of the clinical relevance, significance, and regulation of &lt;i&gt;HSD17B2&lt;/i&gt; in prostate cancer progression, which might provide new strategies for clinical management by targeting the functional silencing mechanisms of &lt;i&gt;HSD17B2&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;See related commentary by Mostaghel, p. 1139&lt;/p&gt;&lt;/div&gt;
<title>Behavior of adaptive digital erosions</title> (1996)

Design of statistically optimal erosion-based filters is problematic due to the complexity of the search process. Specialized search techniques and constraints on optimality are used to mitigate the full search. Adaptation of structuring elements has also ben employed. The present paper looks at the behavior of an adaptive filter relative to the actual optimal filter for a single erosion in two models, signal-union-noise and dilation. It does so in the context of state transitions, where filter states are stacks that determine the structuring element upon thresholding.
Genomic characteristics of trastuzumab-resistant Her2-positive metastatic breast cancer (2017)

Mutational burden in heavily treated trastuzumab-resistant Her2-positive metastatic breast cancer is highly variable and not directly correlated with outcome. Activation of the MAPK/ERK pathway through mutations in EGFR, BRAF or KIT may mediate resistance to trastuzumab.
Figure S1 from Selective Inhibition of the Second Bromodomain of BET Family Proteins Results in Robust Antitumor Activity in Preclinical Models of Acute Myeloid Leukemia (2023)

&lt;p&gt;Figure S1.ABBV-744 exhibits potent anti-proliferative activity against AML cells through cell cycle arrest and induction of apoptosis.&lt;/p&gt;
Etude expérimentale de l'émulsification continue à forts débits à travers des micro-canaux (2021)

National audience
SAFETY OF KETOROLAC FOR ANALGESIA IN CHILDREN AFTER CARDIAC SURGERY. (2006)

Inoue, Miho; Ito, Shinya; Caldarone, Christopher A; Cox, Peter N; Frndova, Helena; Guerguerian, Anne-Marie; Tadido, Anna Author Information