gebhart/patrepeval huggingface dataset:
High resolution material ablation and deposition with femtosecond lasers and applications to photomask repair (2004)

Abstract We describe experiments using 100 femtosecond pulses of 266 nm light to ablate Cr defects from photomasks with resolution below 100 nm. In addition to the ablative removal of Cr, experiments were carried out to deposit Cr metal onto fused silica substrates using 100 fs, 400 nm light at atmospheric pressure. Multiphoton dissociation of Cr(CO)6 adsorbed on fused silica substrates initiates Cr deposition. The mechanisms for deposition on both transparent (fused silica) and absorbing (Cr metal) substrates are discussed. Finally we describe initial experiments to ablate Cr metal at wavelengths below 200 nm using light generated by frequency mixing of ultrashort, 30 fs pulses in an Ar filled capillary.
Identification of Aberrantly Methylated Genes in Association with Adult T-Cell Leukemia (2004)

In this study, we identified 53 aberrantly hypermethylated DNA sequences in adult T-cell leukemia (ATL) cells using methylated CpG island amplification/representational difference analysis method. We also observed a proportionate increase in the methylation density of these regions with disease progression. Seven genes, which were expressed in normal T cells, but suppressed in ATL cells, were identified near the hypermethylated regions. Among these silenced genes, Kruppel-like factor 4 (KLF4) gene is a cell cycle regulator and early growth response 3 (EGR3) gene is a critical transcriptional factor for induction of Fas ligand (FasL) expression. Treatment with 5-aza-2'-deoxycytidine resulted in the recovery of their transcription, indicating that their silencing might be associated with DNA hypermethylation. To study their functions in ATL cells, we transfected recombinant adenovirus vectors expressing KLF4 and EGR3 genes. Expression of KLF4 induced apoptosis of ATL cells whereas enforced expression of EGR3 induced the expression of FasL gene, resulting in apoptosis. Thus, suppressed expression of EGR3 enabled ATL cells to escape from activation-induced cell death mediated by FasL. Our results showed that the methylated CpG island amplification/representational difference analysis method allowed the isolation of hypermethylated DNA regions specific to leukemic cells and thus shed light on the roles of DNA methylation in leukemogenesis.
Effect of external reflectors on radiation profile of grating coupled surface emitting lasers (1993)

Grating coupled surface emitting distributed feedback lasers are analysed by our recently developed model. The model takes into account spontaneous emission, the longitudinal variation of carrier concentration and that of photon density, calculated by a self-consistent technique. The emission spectrum and near and far field radiation patterns are determined as a function of the injection current and external optical feedback. It is found that a single lobed far field radiation pattern is favoured by asymmetric coating of the facets. In addition, the phase margin to achieve a single lobed radiation profile can be increased by increasing the amplitude of the reflection.
Validation and Development of a Predictive Paradigm for Hemotoxicology Using a Multifunctional Bioluminescence Colony-Forming Proliferation Assay (2005)

The lympho-hematopoietic colony-forming assay has been redesigned into a rapid, nonsubjective and standardized proliferation assay that can measure the effects of compounds on multiple stem and progenitor cell populations from different species simultaneously using a sensitive, high-throughput bioluminescence readout. Eleven reference compounds from the Registry of Cytotoxicity (RC) and eight other compounds, including anticancer drugs, were studied over an 8- to 9-log dose range for their effects on seven cell populations from both human and mouse bone marrow simultaneously. The cell populations studied included a primitive (HPP-SP) and mature (CFC-GEMM) stem cell, three hematopoietic (BFU-E, GM-CFC, Mk-CFC) and two lymphopoietic (T-CFC, B-CFC) populations. The results reveal a five-point prediction paradigm for lympho-hematotoxicity. Depending on how and which populations are affected, the resulting effects in the periphery can be predicted. Validation against the RC Prediction Model produces a high degree of correlation between the in vitro IC(50) values and known in vivo LD(50) values, thereby allowing preclinical dosing to be predicted. If primary human hematopoietic target tissue is used, inhibitory concentration (IC(50)/IC(75)/IC(90)) values of anticancer and other drugs can be converted into predicted clinical doses which, when compared to published chemotherapeutic dosing regimen, are very similar. When performed during early drug screening, the prediction value of the assay should help reduce time and cost, but above all, provide increase efficacy and safety for the patient.
Pan‐Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity (2007)

The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger-scale studies will be necessary to determine whether particular substrains of viruses confer an elevated risk of asthma exacerbation.
Autoregressive acoustical modelling of free field cough sound (2002)

In this paper the performance and assumptions of linear prediction acoustical modelling are assessed on the free field cough sound. Four distinct free field cough classes originating from animal and human species in different health conditions are considered. Firstly based on the prediction signal-to-noise ratio the model order for each cough class was chosen to 14. Secondly for each cough class the vocal tract formants are estimated from the linear prediction parameters. Finally the occurrence of subglottal resonances in the cough-sound is investigated.
Heparin and Basic Fibroblast Growth Factor Are Associated with Preservation of Latissimus Cardiomyoplasties in Goats: A Retrospective Study (1996)

bFGF's protection against degeneration may have involved angiogenesis and myogenesis, whereas that of heparin appears to have involved only myogenesis. While the mechanism(s) of the effects of heparin and bFGF remain to be defined, we conclude that they may be a useful adjunct for cardiomyoplasty.
Long-Term Behavioral Recovery in Parkinsonian Rats by an HSV Vector Expressing Tyrosine Hydroxylase (1994)

One therapeutic approach to treating Parkinson's disease is to convert endogenous striatal cells into levo-3,4-dihydroxyphenylalanine (L-dopa)-producing cells. A defective herpes simplex virus type 1 vector expressing human tyrosine hydroxylase was delivered into the partially denervated striatum of 6-hydroxydopamine-lesioned rats, used as a model of Parkinson's disease. Efficient behavioral and biochemical recovery was maintained for 1 year after gene transfer. Biochemical recovery included increases in both striatal tyrosine hydroxylase enzyme activity and in extracellular dopamine concentrations. Persistence of human tyrosine hydroxylase was revealed by expression of RNA and immunoreactivity.
Biogenesis of Lysosome-related Organelles Complex-1 Subunit 1 (BLOS1) Interacts with Sorting Nexin 2 and the Endosomal Sorting Complex Required for Transport-I (ESCRT-I) Component TSG101 to Mediate the Sorting of Epidermal Growth Factor Receptor into Endosomal Compartments (2014)

Biogenesis of lysosome-related organelles complex-1 (BLOC-1) is a component of the molecular machinery required for the biogenesis of specialized organelles and lysosomal targeting of cargoes via the endosomal to lysosomal trafficking pathway. BLOS1, one subunit of BLOC-1, is implicated in lysosomal trafficking of membrane proteins. We found that the degradation and trafficking of epidermal growth factor receptor (EGFR) were delayed in BLOS1 knockdown cells, which were rescued through BLOS1 overexpression. A key feature to the delayed EGFR degradation is the accumulation of endolysosomes in BLOS1 knockdown cells or BLOS1 knock-out mouse embryonic fibroblasts. BLOS1 interacted with SNX2 (a retromer subunit) and TSG101 (an endosomal sorting complex required for transport subunit-I) to mediate EGFR lysosomal trafficking. These results suggest that coordination of the endolysosomal trafficking proteins is important for proper targeting of EGFR to lysosomes.
Magnetic Clusters on Single-Walled Carbon Nanotubes: The Kondo Effect in a One-Dimensional Host (2000)

Single-walled carbon nanotubes are ideal systems for investigating fundamental properties and applications of one-dimensional electronic systems. The interaction of magnetic impurities with electrons confined in one dimension has been studied by spatially resolving the local electronic density of states of small cobalt clusters on metallic single-walled nanotubes with a low-temperature scanning tunneling microscope. Spectroscopic measurements performed on and near these clusters exhibit a narrow peak near the Fermi level that has been identified as a Kondo resonance. Using the scanning tunneling microscope to fabricate ultrasmall magnetic nanostructures consisting of small cobalt clusters on short nanotube pieces, spectroscopic studies of this quantum box structure exhibited features characteristic of the bulk Kondo resonance, but also new features due to finite size.
Human PEP‐1‐ribosomal protein S3 protects against UV‐induced skin cell death (2006)

The consequences of ultraviolet (UV) exposure are implicated in skin aging and cell death. The ribosomal protein S3 (rpS3) is one of the major proteins by which cells counteract the deleterious effects of UV and it plays a role in the repair of damaged DNA. In the present study, we investigated the protective effects of PEP-1-rpS3 fusion protein after UV-induced cell injury. A human rpS3 gene was fused with PEP-1 peptide in a bacterial expression vector to produce a genetic in-frame PEP-1-rpS3 fusion protein. The expressed and purified fusion proteins were efficiently transduced into skin cells in a time- and dose-dependent manner. Once inside the cells, transduced PEP-1-rpS3 fusion protein was stable for 48h. We showed that transduced PEP-1-rpS3 fusion protein increased cell viability and dramatically reduced DNA lesions in the UV exposed skin cells. Immunohistochemical analysis revealed that PEP-1-rpS3 fusion protein efficiently penetrated the epidermis as well as the dermis of the subcutaneous layer when sprayed on animal skin. These results suggest that PEP-1-rpS3 fusion protein can be used in protein therapy for various disorders related to UV, including skin aging and cancer.
Fusion of human immunodeficiency virus type 1 (HIV-1) with human cells as measured by membrane fluorescence dequenching (DQ) method; roles of HIV-1-cell fusion in AIDS pathogenesis. (1990)

HIV-1, the primary etiologic agent of AIDS, is a non-transforming human retrovirus which shares many physical and functional characteristics with viruses from the lentivirus family. One of these characteristics is that HIV-1 infection has profound cytopathic effects on host cells. Studies by the membrane fluorescence dequenching (DQ) method using HIV-1 virions labeled with octadecylrhodamine B-chloride (R-18) have shown that HIV-1 enters host cells by a process of fusion between viral envelope and target cell plasma membrane. The parameters of HIV-1-cell fusion are similar to those established for paramyxoviruses and other enveloped fusogenic viruses. HIV-1-cell fusion requires the presence of surface CD4 receptors on human T cell and monocytes, but not on human glial and neuronal cells. It is proposed that cell surface effects of HIV-1 due to the interaction between HIV-1 fusion glycoproteins and membrane receptors are major contributors to the cytopathic and pathogenic function of this virus.
CD40L-CD40 interactions regulate endothelial cell surface tissue factor and thrombomodulin expression (1998)

During immune responses, activated endothelial cells down-regulate thrombomodulin and up-regulate tissue factor expression leading to the development of a procoagulant surface. CD4+ T cells are known to promote endothelial cell procoagulant activity, however, the molecular interactions that mediate this effect are not completely known. CD40L is an activation-induced CD4+ T cell surface molecule that functionally interacts with CD40 expressed on endothelial cells. In this study we ask if CD40L-CD40 interactions modulate endothelial cell surface tissue factor or thrombomodulin expression in vitro. Human umbilical vein endothelial cells (HUVEC) were cocultured with control cells or CD40L+ Jurkat T cells in the presence or absence of anti-CD40L mAb. By two-color FACS analysis we demonstrated that CD40 ligation induces HUVEC tissue factor expression and thrombomodulin down-regulation. Utilizing neutralizing antibodies, we show that CD40L-mediated tissue factor and thrombomodulin modulation, as well as E-selectin and VCAM-1 upregulation, is independent of tumor necrosis factor alpha, interleukin-1alpha, or interleukin-1beta production. Together these data suggest that CD40L-CD40 interactions may directly regulate endothelial cell procoagulant activity during inflammatory responses.
Scanning characteristics of infinite arrays of printed antenna subarrays (1992)

The analysis and scanning characteristics of several different types of infinite arrays composed of subarrayed printed dipole and microstrip patch elements are presented. The analysis is based on full-wave moment method theory, and includes mutual coupling between elements in the subarray as well as between subarrays. The effect of subarraying on scan blindness is demonstrated for arrays using two-element subarrays of printed dipoles and microstrip patches. Results are also given for the amount of power radiated in grating lobes. The effect of a subarray composed of one driven element and one parasitic element, and the use of a four-element synchronous subarray of microstrip patches to generate circular polarization are also considered. Data are given for impedance mismatch, power radiated into grating lobes, and the axial ratio; both square and rectangular patches area considered. Results are also shown for an infinite array of seven-element hexagonal subarrays of printed dipoles, and it is found that the large spacing between subarrays leads to a limited scan range.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Computer vision for interactive computer graphics (1998)

Vision can be a powerful interface device for computers because of its potential for sensing body position, head orientation, direction of gaze, pointing commands, and gestures. Such unencumbered interaction can make computers easier to use. We describe vision algorithms for interactive graphics and present vision-controlled graphics applications using these algorithms. Some applications employ an artificial retina chip for image detection or preprocessing.
Inferring human gaze from appearance via adaptive linear regression (2011)

The problem of estimating human gaze from eye appearance is regarded as mapping high-dimensional features to low-dimensional target space. Conventional methods require densely obtained training samples on the eye appearance manifold, which results in a tedious calibration stage. In this paper, we introduce an adaptive linear regression (ALR) method for accurate mapping via sparsely collected training samples. The key idea is to adaptively find the subset of training samples where the test sample is most linearly representable. We solve the problem via l <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> -optimization and thoroughly study the key issues to seek for the best solution for regression. The proposed gaze estimation approach based on ALR is naturally sparse and low-dimensional, giving the ability to infer human gaze from variant resolution eye images using much fewer training samples than existing methods. Especially, the optimization procedure in ALR is extended to solve the subpixel alignment problem simultaneously for low resolution test eye images. Performance of the proposed method is evaluated by extensive experiments against various factors such as number of training samples, feature dimensionality and eye image resolution to verify its effectiveness.
Wnt/β-catenin signaling mediates oval cell response in rodents (2007)

The Wnt/beta-catenin pathway plays a key role in the normal activation and proliferation of adult hepatic stem cells.
Antigenic and Biochemical Characterization of the C-type Particle of the Stable Porcine Kidney Cell Line PK-15 (1973)

The C-type particles observed by electron microscopy in PK-15 cells were demonstrated to have biochemical and biophysical properties associated with the oncornavirus group: density of 1:16 in a sucrose gradient, 70S RNA, and the RNA-dependent DNA polymerase. The group-specific interspecies antigen, gs-3, was not present. Evidence of a latent infection with a porcine parvovirus was also obtained.
A Kinetic Threshold between Negative and Positive Selection Based on the Longevity of the T Cell Receptor–Ligand Complex (1999)

We have developed a unique in vivo system to determine the relationship between endogenous altered peptide ligands and the development of major histocompatibility complex class II- restricted T cells. Our studies use the 3.L2 T cell receptor (TCR) transgenic mouse, in which T cells are specific for Hb(64-76)/I-Ek and positively selected on I-Ek plus self-peptides. To this endogenous peptide repertoire, we have individually added one of six well-characterized 3.L2 ligands. This transgenic approach expands rather than constrains the repertoire of self-peptides. We find that a broad range of ligands produce negative selection of thymocytes in vivo. When compared with the in vitro TCR-ligand binding kinetics, we find that these negatively selecting ligands all have a half-life of 2 s or greater. Additionally, one of two ligands examined with no detectable binding to the 3.L2 TCR and no activity on mature 3.L2 T cells (Q72) enhances the positive selection of transgenic thymocytes in vivo. Together, these data establish a kinetic threshold between negative and positive selection based on the longevity of TCR-ligand complexes.
USE OF PLURONIC MICELLES TO OVERCOME MULTIDRUG-RESISTANCE (1994)

Pluronic P-85 (poly(55)(oxypropylene)dipoly(s)(oxyethylene)) was used to form daunorubicin containing micelles. This new carrier was tested in vitro on sensitive and resistant ovarian cancer cell lines. Drug incorporation was measured by cytofluorometry and the cytotoxicity was measured by the tetrazolium formazan XTT assay. ID50 of 0.16 and 25 mu g/ml were obtained for conjugated and free daunorubicin respectively. The results obtained suggest that this approach may be used in combination with a chemotherapeutic agent to overcome multidrug resistance.
Anti-Human CD73 Monoclonal Antibody Inhibits Metastasis Formation in Human Breast Cancer by Inducing Clustering and Internalization of CD73 Expressed on the Surface of Cancer Cells (2013)

Recent studies have shown that Abs that target the cell-surface enzyme CD73 (ecto-5'-nucleotidase) reduce growth of primary tumors and metastasis in syngenic mice by inhibiting the catalytic activity of CD73, and thus increasing the activity of cytotoxic T lymphocytes. In this article, we report another anticancer mechanism of anti-CD73 Abs and show that an anti-CD73 mAb (AD2) inhibits metastasis formation by a mechanism independent of CD73 catalytic activity and inhibition of primary tumor growth. This mechanism involves clustering and internalization of CD73, but does not require cross-linking of CD73, because both whole IgG anti-CD73 AD2 mAb and Fab' fragments thereof exhibited this effect. Ex vivo treatment of different breast cancer cell lines with anti-CD73 AD2 mAb before i.v. injection into mice inhibited extravasation/colonization of circulating tumor cells and significantly reduced metastasis development. This effect was also observed when the cancer cell-surface expression of CD73 was significantly reduced by small interfering RNA knockdown. The antimetastatic activity is epitope specific, as another Ab that efficiently binds CD73-expressing live cancer cells did not lead to CD73 internalization and metastasis inhibition. Furthermore, anti-CD73 AD2 mAb inhibited development of metastasis in a spontaneous animal model of human metastatic breast cancer. Our study shows that some anti-CD73 mAbs cause cell-surface clustering of CD73 followed by internalization, thus inhibiting the ability of circulating tumor cells to extravasate and colonize, leading to inhibition of metastasis. Ab-based CD73 cancer therapy should include a combination of Abs that target the catalytic activity of CD73, as well as those with the characteristics described in this article.
Walk the talk: connecting language, knowledge, and action in route instructions (2006)

Following verbal route instructions requires knowledge of language, space, action and perception. We present MARCO, an agent that follows free-form, natural language route instructions by representing and executing a sequence of compound action specifications that model which actions to take under which conditions. MARCO infers implicit actions from knowledge of both linguistic conditional phrases and from spatial action and local configurations. Thus, MARCO performs explicit actions, implicit actions necessary to achieve the stated conditions, and exploratory actions to learn about the world. We gathered a corpus of 786 route instructions from six people in three large-scale virtual indoor environments. Thirtysix other people followed these instructions and rated them for quality. These human participants finished at the intended destination on 69 % of the trials. MARCO followed the same instructions in the same environments, with a success rate of 61%. We measured the efficacy of action inference with MARCO variants lacking action inference: executing only explicit actions, MARCO succeeded on just 28 % of the trials. For this task, inferring implicit actions is essential to follow poor instructions, but is also crucial for many highly-rated route instructions.
Optimal Design of Composite Granular Protectors (2009)

We employ an evolutionary algorithm to investigate the optimal design of composite protectors using one-dimensional granular chains composed of beads of various sizes, masses, and stiffnesses. We define a fitness function using the maximum force transmitted from the protector to a “wall” that represents the body to be protected and accordingly optimize the topology (arrangement), size, and material of the chain. We obtain optimally randomized granular protectors characterized by high-energy equipartition and the transformation of incident waves into interacting solitary pulses. We consistently observe that the pulses traveling to the wall combine to form an extended (long-wavelength), small-amplitude pulse.