gebhart/patrepeval huggingface dataset:
MagniFinger (2019)

We propose MagniFinger, a fingertip-worn microscopy device that augments the limited abilities of human visual and tactile sensory systems in micrometer-scale environments. MagniFinger makes use of the finger's dexterous motor skills to achieve precise and intuitive control while allowing the user to observe the desired position simply by placing a fingertip. To implement the fingertip-sized device and its tactile display, we have built a system comprising a ball lens, an image sensor, and a thin piezoelectric actuator. Vibration-based tactile feedback is displayed based on the luminance of a magnified image, providing the user with the feeling of touching the magnified world.
Asteraceae Artemisia campestris and Artemisia herba-alba Essential Oils Trigger Apoptosis and Cell Cycle Arrest in Leishmania infantum Promastigotes (2016)

We report the chemical composition and anti-<i>Leishmania</i> and antioxidant activity of <i>Artemisia campestris</i> L. and <i>Artemisia herba</i>-<i>alba</i> Asso. essential oils (EOs). Our results showed that these extracts exhibit different antioxidant activities according to the used assay. The radical scavenging effects determined by DPPH assay were of IC<sub>50</sub> = 3.3 mg/mL and IC<sub>50</sub> = 9.1 mg/mL for <i>Artemisia campestris</i> and <i>Artemisia herba</i>-<i>alba</i> essential oils, respectively. However, antioxidant effects of both essential oils, determined by ferric-reducing antioxidant power (FRAP) assay, were in the same range (2.3 and 2.97 mg eq EDTA/g EO, resp.), while the <i>Artemisia herba</i>-<i>alba</i> essential oil showed highest chelating activity of Fe<sup>2+</sup> ions (27.48 mM Fe<sup>2+</sup>). Interestingly, we showed that both EOs possess dose-dependent activity against <i>Leishmania infantum</i> promastigotes with IC<sub>50</sub> values of 68 <i>μ</i>g/mL and 44 <i>μ</i>g/mL for <i>A. herba</i>-<i>alba</i> and <i>A. campestris</i>, respectively. We reported, for the first time, that antileishmanial activity of both EOs was mediated by cell apoptosis induction and cell cycle arrest at the sub-G0/G1 phase. All our results showed that EOs from <i>A. herba</i>-<i>alba</i> and <i>A. campestris</i> plants are promising candidates as anti-<i>Leishmania</i> medicinal products.
Program Synthesis of FEA Constitutive Behavior Modules Through Data Driven Design Optimization (2002)

Design optimization in the context of finite element modeling (FEM) and analysis (FEA) has been traditionally used to help designers determine optimal structural geometry and/or material property parameters according to objective functions of interest and necessary constraints. In the present paper it is attempted to generalize the design optimization methodology into a program synthesis technique for determining the code necessary to encapsulate the constitutive behavior of the material system required for generalized FEA applications. The core concept behind the methodology followed by our group in the past, has been the experimental identification of a dissipated energy density (DED) function for polymer matrix composites (PMCs) through a non-linear optimization scheme for determining the free coefficients of the sum of the basis functions that are used to construct the DED function and is based on the energy balance of the specimen under testing. The utilized testing generated massive amounts of experimental data that would be produced by exposing PMC specimens to multidimensional loading paths with the help of custom made multi-axial computer-controlled testing machines. The variety of custom environments utilized to implement the analytical and numerical details has often created difficulties in transferring our technology to end users in the design and material communities. The present implementation was greatly enabled by recent advances in finite element techniques and “of the shelf” design optimization integration technologies along with the parallel hardware and software evolution. The program synthesis lies on a process that automatically generates the code of a user material subroutine through minimization of the error between measured and simulated specimen behavior. The generated code can be subsequently used with any geometry and loading specification definable within the limits of the non-linear element library in commercial codes such as ANSYS and ABAQUS.
Using multiple sequence correlation analysis to characterize functionally important protein regions (2003)

Protein co-evolution under structural and functional constraints necessitates the preservation of important interactions. Identifying functionally important regions poses many obstacles in protein engineering efforts. In this paper, we present a bioinformatics-inspired approach (residue correlation analysis, RCA) for predicting functionally important domains from protein family sequence data. RCA is comprised of two major steps: (i) identifying pairs of residue positions that mutate in a coordinated manner, and (ii) using these results to identify protein regions that interact with an uncommonly high number of other residues. We hypothesize that strongly correlated pairs result not only from contacting pairs, but also from residues that participate in conformational changes involved during catalysis or important interactions necessary for retaining functionality. The results show that highly mobile loops that assist in ligand association/dissociation tend to exhibit high correlation. RCA results exhibit good agreement with the findings of experimental and molecular dynamics studies for the three protein families that are analyzed: (i) DHFR (dihydrofolate reductase), (ii) cyclophilin, and (iii) formyl-transferase. Specifically, the specificity (percentage of correct predictions) in all three cases is substantially higher than those obtained by entropic measures or contacting residue pairs. In addition, we use our approach in a predictive fashion to identify important regions of a transmembrane amino acid transporter protein for which there is limited structural and functional information available.
Abstract W P238: Selective Deletion of Pi3-kinase Gamma in the Brain Inhibits Tissue Plasminogen Activator-induced Brain Hemorrhage (2015)

Background: PI3-kinase gamma (PI3Kγ), a key modulator in inflammation, is involved in many inflammatory diseases. We recently reported that PI3Kγ deficiency protects the brain from ischemic injury in PI3Kγ-/- mice by reducing blood-brain barrier damage and tissue infarction through inhibition of NF-kB-dependent inflammation, mainly involved in reduced MMP-9 activity in ischemic brain endothelium, microglia activation, and neutrophil infiltration into the ischemic brain. Meanwhile, we reported that ischemic brain endothelium, activated microglia, and infiltrating neutrophils represent the major cellular sources of PI3Kγ expressed in the brain within 24 h after cerebral ischemia. Brain hemorrhage is a serious complication of recombinant tissue plasminogen activator (tPA) therapy for ischemic stroke. In this study, we further investigated potential involvement of PI3Kγ, in particular the expression of PI3Kγ in the brain, in tPA-induced brain hemorrhage after ischemic stroke. Methods and Results: Focal ischemic stroke was induced by transient middle cerebral artery occlusion and reperfusion. PI3Kγ deficiency in PI3Kγ-/- mice not only reduced tissue infarction but also almost completely blocked brain hemorrhage induced by delayed tPA treatment at 6 hours after stroke. Bone marrow chimeras reveal that chimeric mice lacking PI3Kγ in the brain (WT BM →KO) blocked the delayed tPA-induced brain hemorrhage effectively as found in PI3Kγ-/- mice while chimeric mice lacking PI3Kγ expressed in leukocytes (KO BM →WT) had minimal effect on the tPA-induced brain hemorrhage. These effects could be attributed to a profound inhibition of MMP-9 activity in ischemic brain endothelium found in both PI3Kγ-/- mice and (WT BM →KO) chimeric mice but not in (KO BM →WT) chimeric mice, as determined by double IHC staining of MMP-9 in brain endothelial cells and by zymographic analysis of MMP-9 activity using microvessels isolated from the brain. Conclusion: Our findings suggest that PI3Kγ in the brain may play a predominant role in delayed tPA-induced brain hemorrhage after ischemic stroke. Our future study will define the role of PI3Kγ derived from brain endothelial cells versus microglia by generation of tissue/cell-specific knockout mice using the Cre-loxP system.
Lessons Learned in Developing a Commercial FIV Vaccine: The Immunity Required for an Effective HIV-1 Vaccine (2018)

The feline immunodeficiency virus (FIV) vaccine called Fel-O-Vax<sup>®</sup> FIV is the first commercial FIV vaccine released worldwide for the use in domestic cats against global FIV subtypes (A⁻E). This vaccine consists of inactivated dual-subtype (A plus D) FIV-infected cells, whereas its prototype vaccine consists of inactivated dual-subtype whole viruses. Both vaccines in experimental trials conferred moderate-to-substantial protection against heterologous strains from homologous and heterologous subtypes. Importantly, a recent case-control field study of Fel-O-Vax-vaccinated cats with outdoor access and ≥3 years of annual vaccine boost, resulted in a vaccine efficacy of 56% in Australia where subtype-A viruses prevail. Remarkably, this protection rate is far better than the protection rate of 31.2% observed in the best HIV-1 vaccine (RV144) trial. Current review describes the findings from the commercial and prototype vaccine trials and compares their immune correlates of protection. The studies described in this review demonstrate the overarching importance of ant-FIV T-cell immunity more than anti-FIV antibody immunity in affording protection. Thus, future efforts in developing the next generation FIV vaccine and the first effective HIV-1 vaccine should consider incorporating highly conserved protective T-cell epitopes together with the conserved protective B-cell epitopes, but without inducing adverse factors that eliminate efficacy.
Data from Targeting Multiple Myeloma with AMG 424, a Novel Anti-CD38/CD3 Bispecific T-cell–recruiting Antibody Optimized for Cytotoxicity and Cytokine Release (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Despite advances in the treatment of multiple myeloma, new therapies are needed to induce more profound clinical responses. T-cell–redirected lysis triggered by bispecific antibodies recruiting T cells to cancer cells is a clinically validated mechanism of action against hematologic malignancies and CD38 is a tumor-associated antigen with near-universal expression in multiple myeloma. Thus, an anti-CD38/CD3 bispecific T-cell–recruiting antibody has the potential to be an effective new therapeutic for multiple myeloma.&lt;/p&gt;Experimental Design:&lt;p&gt;Anti-CD38/CD3 XmAb T-cell–recruiting antibodies with different affinities for CD38 and CD3 were assessed &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; for their redirected T-cell lysis activity against cancer cell lines, their lower levels of cytokine release, and their potency in the presence of high levels of soluble CD38. Select candidates were further tested in cynomolgus monkeys for B-cell depletion and cytokine release properties.&lt;/p&gt;Results:&lt;p&gt;AMG 424 was selected on the basis of its ability to kill cancer cells expressing high and low levels of CD38 &lt;i&gt;in vitro&lt;/i&gt; and trigger T-cell proliferation, but with attenuated cytokine release. &lt;i&gt;In vivo&lt;/i&gt;, AMG 424 induces tumor growth inhibition in bone marrow–invasive mouse cancer models and the depletion of peripheral B cells in cynomolgus monkeys, without triggering excessive cytokine release. The activity of AMG 424 against normal immune cells expressing CD38 is also presented.&lt;/p&gt;Conclusions:&lt;p&gt;These findings support the clinical development of AMG 424, an affinity-optimized T-cell–recruiting antibody with the potential to elicit significant clinical activity in patients with multiple myeloma.&lt;/p&gt;&lt;/div&gt;
An auto-focus sharpness function for stereo image pairs (2011)

Auto-focusing is a key feature of modern camera systems that ensures a focused image is captured without the need for any user intervention. Passive auto-focusing is achieved based on a measure of sharpness or a sharpness function that is extracted from a series of images at different focal positions. With the rapid growth of stereo camera systems for 3D applications, this paper introduces a sharpness function when a series of stereo image pairs are captured at different focal positions. This function is defined based on the joint information between the left and right images. A comparison is carried out between the introduced sharpness function and the conventional sharpness functions when considering the left and right images separately in terms of sharpness accuracy and computation time.
An eight‐channel sodium/proton coil for brain MRI at 3 T (2017)

The purpose of this work is to illustrate a new coil decoupling strategy and its application to a transmit/receive sodium/proton phased array for magnetic resonance imaging (MRI) of the human brain. We implemented an array of eight triangular coils that encircled the head. The ensemble of coils was arranged to form a modified degenerate mode birdcage whose eight shared rungs were offset from the z-axis at interleaved angles of ±30°. This key geometric modification resulted in triangular elements whose vertices were shared between next-nearest neighbors, which provided a convenient location for counter-wound decoupling inductors, whilst nearest-neighbor decoupling was addressed with shared capacitors along the rungs. This decoupling strategy alleviated the strong interaction that is characteristic of array coils at low frequency (32.6 MHz in this case) and allowed the coil to operate efficiently in transceive mode. The sodium array provided a 1.6-fold signal-to-noise ratio advantage over a dual-nuclei birdcage coil in the center of the head and up to 2.3-fold gain in the periphery. The array enabled sodium MRI of the brain with 5-mm isotropic resolution in approximately 13 min, thus helping to overcome low sodium MR sensitivity and improving quantification in neurological studies. An eight-channel proton array was integrated into the sodium array to enable anatomical imaging.
Clearance of hepatitis C in chimpanzees is associated with intrahepatic T-cell perforin expression during the late acute phase (2009)

The liver is the primary site of hepatitis C virus (HCV) replication. Therefore, we undertook detailed intrahepatic studies of T-cell dynamics, apoptosis, and gene expression during the acute phase of infection using liver biopsies from chimpanzees that developed persistent infection or spontaneously cleared the virus. We examined more than 40 liver biopsies histologically and quantitatively for T-cell infiltration, hepatocyte apoptosis and perforin expression. These data were correlated with outcome and viral kinetics. We observed intrahepatic T-cell infiltration in both groups of animals with CD8(+) T cells representing the major population. The appearance of T cells was always associated with apoptosis and mild alanine aminotransferase (ALT) elevations. Apoptosis (5-20% of hepatocytes) always occurred prior to serum ALT peak. Quantification of intrahepatic ALT mRNA revealed no upregulation of gene expression confirming that serum ALT increases were due to release of this enzyme from cells. During the late acute phase, cleared animals showed an increased frequency of hepatocyte apoptosis relative to persistently infected animals (P < 0.05). This correlated with a higher intrahepatic CD8(+) T-cell frequency in the cleared group (P < 0.01) with a greater proportion of lymphocytes expressing perforin compared with the persistent group (P < 0.001). All infected animals mounted intrahepatic immune responses during the acute phase, but these were not maintained in frequency or efficacy in persistent infections. There is a reduction in the numbers of intrahepatic T cells during the late acute phase in infections that become persistent with significantly fewer of these cells functional in clearing the virus by killing infected hepatocytes.
A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators (2021)

Abstract Background: Sphaerophoria rueppellii , a European species of hoverfly, is a highly effective beneficial predator of crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii . Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione- S -transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs). Methods and findings: In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily levels between S. rueppellii and some crop pests. Conclusion and significance: This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.
A Methodology for Prototyping Flexible Embedded Systems (2007)

A methodology is presented for prototyping flexible, custom embedded systems using low-cost reconfigurable hardware, open-source FPGA-ware, and open-source software. This is done through a case study of the complete design of a custom embedded system. The system is intended as a low-cost, flexible, and reconfigurable platform with multimedia and networking capabilities, for prototyping interactive entertainment applications. The system features an FPGA system-on-chip design supported by a custom board with a versatile set of interfaces including Ethernet, color television, stereo audio and others. The project contains work in three main areas: board design, HDL chip design, and software.
Hydrocarbon-Bridged Methyldimethoxysilanes as new Co-condensation Agents for the Sol−Gel Process of the Rhodium(I) Complex ClRh(CO)(P∼O)2Containing the Ligand PhP(CH2CH2OCH3)(CH2)3Si(OCH3)31|Pv3 (1997)

New hydrocarbon bridged co-condensation agents of the type MeSi(OMe)2(CH2)z(MeO)2SiMe [1(D0−Cz−D0), z = length of the flexible bridging group (z = 6, 8, 14)] were synthesized and polycondensed to give the polysiloxanes 1(Di−Cz−Di). These monomers were employed in variable amounts y in the sol−gel processing of the monomeric ether−phosphine ligand PhP(CH2CH2OMe)(CH2)3Si(OMe)3 [2(T0)] and its P-coordinated trimethoxysilyl-(T)-functionalized rhodium(I) complex ClRh(CO)(P∼O)2 [3(T0)2] to yield the polysiloxane-bound ether−phosphine ligands 2(Tn)(Di−Cz−Di) and the rhodium complexes 3(Tn)2(Di−Cz−Di)y [O∼P: η1-P-coordinated ether−phosphine ligand; y = number of co-condensed D−Cz−D molecules; D = D-type silicon atom (two oxygen neighbors), T = T-type silicon atom (three oxygen neighbors); i, n = number of Si−O−Si bonds; i = 0−2; n = 0−3]. The relative amounts of T and D silyl species and the degree of condensation were determined by 29Si CP/MAS NMR spectroscopic investigations. The polysiloxanes 1(Di−Cz−Di) which are regarded as “organofunctionalized Q analogues” display a higher degree of condensation than their Q counterpart [Q = Q-type silicon atom (four oxygen neighbors)]. The highest degrees of condensation of the D groups were obtained for the D−C14−D polymer and the F−T/D−C14−D copolymers [F = (Ph)P(CH2CH2OMe)(CH2)3− (2), [ClRh(CO)]1/2(Ph)P(CH2CH2OMe)(CH2)3− (3)]. 31P and 13C CP/MAS NMR spectroscopic studies give evidence that the ligand and the geometry of the complex is preserved during the entire sol−gel process. In addition an EXAFS spectroscopic analysis of the complex 3(Tn)2 gave a more detailed description of its structure. 31P CP/MAS NMR relaxation time studies (T1P, TPH, T1ρH), 2D WISE NMR experiments, and the line widths of the 31P CP/MAS NMR spectra were applied for dynamic investigations. The noncomplexed ether−phosphine ligand in the F−T/D−Cz−D copolymers is more mobile than that in the F−T/Q copolymer 2(Tn)(Qk)2 [k = number of Si−O−Si bonds; k = 0−4]. The P-coordination of only two ether−phosphines in the complex leads to an additional cross-linking in the matrixes. Thereby the ligands become more rigid due to strong phosphorus−rhodium bonds.
Natural killer-sensitive targets stimulate production of TNF-alpha but not TNF-beta (lymphotoxin) by highly purified human peripheral blood large granular lymphocytes. (1986)

Highly purified populations of large granular lymphocytes (LGL) have been shown to mediate natural killer (NK) cell activity. The mechanism of target cell killing by NK cells is as yet undefined; however, it has been postulated that such killing may involve soluble cytotoxic factors produced and secreted by NK cells. The data presented show that NK-sensitive, but not NK-resistant, tumor cell lines induce highly purified populations of human LGL to produce factors with cytotoxic and/or cytostatic activities. We have identified one of these factors as tumor necrosis factor-alpha (TNF-alpha), and have shown that production of this factor is enhanced by recombinant human interferon-gamma (rHuIFN-gamma). We have also examined the role of TNF-alpha in the cytotoxic function of NK cells. The data show that although highly purified LGL populations produce low levels of TNF-alpha, the cytotoxic/cytostatic activity of this lymphokine on tumor target cells does not correlate with the cytotoxic activity of highly purified populations of LGL on tumor target cells. Furthermore, NK cell-mediated cytotoxicity is not reliably inhibited by antibodies directed against various epitopes of recombinant human TNF-alpha and/or recombinant TNF-beta (lymphotoxin) or rHuIFN-gamma. These data show that although TNF-alpha is produced by highly purified NK-containing LGL cell populations, this factor does not appear to be responsible for NK cell cytotoxicity against classical NK target cells such as Molt-4 or K562. We suggest that NK function can be attributed to a combination of factors rather than to a single factor alone, and that at least two major phenomena are involved in LGL function: the rapid cytotoxic events which lead to the cell lysis measured in classical in vitro NK assays such as against K562; and the release of factors such as TNF-alpha with cytotoxic/cytostatic activities which would inhibit the growth of invading tumor cells in vivo.