gebhart/patrepeval huggingface dataset:
Cadherin switching in human prostate cancer progression. (2000)

The progression of carcinomas is associated with the loss of epithelial morphology and a concomitant acquisition of a more mesenchymal phenotype, which in turn is thought to contribute to the invasive and/or metastatic behavior of the malignant process. Changes in the expression of cadherins, "cadherin switching," plays a critical role during embryogenesis, particularly in morphogenetic processes. Loss of E-cadherin is reported to be associated with a poor prognosis; however, thus far, evidence (R. Umbas, et al., Cancer Res. 54: 3929-3933, 1994) for up-regulation of other cadherins has only been reported in vitro, ie., we have found evidence (M. J. G. Bussemakers et al., Int. J. Cancer, 85: 446-450, 2000) for cadherin switching in prostate cancer cell lines (up-regulation of N-cadherin and cadherin-11, two mesenchymal cadherins, in cell lines that lack a functional E-cadherin-catenin adhesion complex). Here, we report on the immunohistochemical analysis of the expression of N-cadherin and cadherin-11 in human prostate cancer specimens. N-cadherin was not expressed in normal prostate tissue; however, in prostatic cancer, N-cadherin was found to be expressed in the poorly differentiated areas, which showed mainly aberrant or negative E-cadherin staining. Cadherin-11 is expressed in the stroma of all prostatic tumors, in the area where stromal and epithelial cells are found. In addition, cadherin-11 is also expressed in a dotted pattern or at the membrane of the epithelial cells of high-grade cancers. In a number of metastatic lesions, N-cadherin and cadherin-11 are expressed homogeneously. These data raise the possibility that cadherin switching plays an important role in prostate cancer metastasis.
Regulation of insulin-like growth factor I receptor expression by the pure antiestrogen ICI 182780. (1996)

Insulin-like growth factor I (IGF-I) is a mitogen for human breast cancer cells both in vivo and in vitro. We demonstrate here that the antiestrogen ICI 182780 (ICI) at 10(-8) m decreases IGF-I receptor (IGF-IR) mRNA levels by 70% after treatment for 48 h. Measurements of mRNA stability indicate that the half-life of IGF-IR mRNA is approximately 3 h. Estradiol treatment increases the half-life of the IGF-IR mRNA to approximately 6 h and the level of IGF-IR gene transcription by 1.8-fold, whereas ICI treatment not only decreases the IGF-IR transcription rate by 50% but also decreases the IGF-IR mRNA half-life to less than 3 h. Affinity labeling studies with [125I]-IGF-I show 35% increased labeled IGF-I to MCF-7 cell membrane following estradiol treatment and 40% decreased labeling following ICI treatment. We also demonstrate that ICI attenuates IGF-I-stimulated growth. Our data suggest that attenuation of IGF-I responsivity by ICI may be due in part to reducing the IGF-IR expression.
Large Kernel Matters — Improve Semantic Segmentation by Global Convolutional Network (2017)

One of recent trends [31, 32, 14] in network architecture design is stacking small filters (e.g., 1×1 or 3×3) in the entire network because the stacked small filters is more efficient than a large kernel, given the same computational complexity. However, in the field of semantic segmentation, where we need to perform dense per-pixel prediction, we find that the large kernel (and effective receptive field) plays an important role when we have to perform the classification and localization tasks simultaneously. Following our design principle, we propose a Global Convolutional Network to address both the classification and localization issues for the semantic segmentation. We also suggest a residual-based boundary refinement to further refine the object boundaries. Our approach achieves state-of-art performance on two public benchmarks and significantly outperforms previous results, 82.2% (vs 80.2%) on PASCAL VOC 2012 dataset and 76.9% (vs 71.8%) on Cityscapes dataset.
Run-to-Run Control in Semiconductor Manufacturing (2010)

Introduction What is Run-top-Run Control? Target Audience Purpose of this Book Outline Background Current State-of-the-Art in Semiconductor Manufacturing Process Control History of the Development of Run-to-Run Control Current State o-of-the-Art in Run-to-Run Control Development and Deployment Simple Example: Run-to-Run Control and Comparison to Statistical Process Control Identifying Target Applications for Run-to-Run Control Class of Applications that can Utilize Run-t0-Run Control General Run-to-Run Control Development and Deployment Process Issues in Deploying Run-to-Run Control Developing a Run-to-Run Solution: Run-to-Run Algorithms Introduction Linear Approximation Algorithms Higher Order Approximation Algorithms Neural Network Algorithms Other Approaches Developing a Run-to-Run Solution: Practical Extensions to Algorithms Developing and Deploying Run-to-Run Solutions: Integrating Control Introduction The Generic Cell Controller Other Approaches Integrating into Factory-Wide Manufacturing System Run-to-Run Solution Development, Deployment, and Customization Methodology Introduction Process Identification Choosing a Run-to-Run Control Solution Customizing the Run-to-Run Control Solution to the Process Issues Run-to-Run Control System Deployment Case Studies Chemical-Mechanical Planarization Vapor Phase Epitaxy Advanced Topics Feasibility Analysis of Run-to-Run Control Solutions Stability Analysis of Run-to-Run Control Solutions Combining Process Run-to-Run Control with Inter-Process Control Conclusions Summary of Run-to-Run Development and Deployment Process Deploying Run-to-Run Control in a Timely and Cost Effective Manner Overcoming Barriers to Deployment Future Research and Development Issues References
Protein binding to the abscisic acid-responsive element is independent of VIVIPAROUS1 in vivo. (1997)

The plant hormone abscisic acid and the transcriptional activator VIVIPAROUS1 have a synergistic effect on transcription during embryo development. An abscisic acid-responsive element (ABRE) mediates induction by abscisic acid and VIVIPAROUS1, but the mechanism involved has not been determined. In this study, we explore the interaction between abscisic acid and VIVIPAROUS1 and its effect on the ABRE from the maize rab28 gene. In transient transformation experiments, abscisic acid stimulated transcription via several elements, whereas activation by VIVIPAROUS1 was mediated exclusively through the ABRE. In vivo footprinting showed only minor differences in binding to the ABRE between wild-type and VIVIPAROUS1-deficient embryos, suggesting that VIVIPAROUS1 stimulates transcription through the ABRE without major changes in protein-DNA interactions. A factor that bound to the ABRE in electrophoretic mobility shift assays was present at the same developmental stages as rab28 mRNA and had binding characteristics similar to those observed by in vivo footprinting. This suggests that the factor binds to the ABRE in the rab28 promoter in vivo. We discuss the constraints that our results put on the possible mechanism for action of VIVIPAROUS1 in vivo.
Induction of Immune Responses in Patients with B-Cell Lymphoma against the Surface-Immunoglobulin Idiotype Expressed by Their Tumors (1992)

These results demonstrate that autologous immunoglobulin idiotype can be formulated into an immunogenic, tumor-specific antigen in humans with B-cell lymphoma, and they provide the background for large-scale trials of active specific immunotherapy of this disease.
ChemInform Abstract: Hyaluronan Derivatives: Chemistry and Clinical Applications (1998)

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.
Salmeterol, a long‐acting β2‐adrenoceptor agonist mediating cyclic AMP accumulation in a neuronal cell line (1993)

1. The accumulation of cyclic AMP stimulated by salmeterol, a long-acting beta 2-adrenoceptor agonist and by isoprenaline, a non-selective beta-adrenoceptor agonist have been compared in the B50 neuroblastoma cell line. 2. Salmeterol produced a concentration-dependent increase in the accumulation of total [3H]-cyclic AMP in B50 cells yielding an EC50 value of 37 nM which was lower than that obtained with isoprenaline (294 nM). The maximum response to salmeterol was only 46% of that obtained with isoprenaline. 3. The beta 2-adrenoceptor antagonist, ICI 118551, inhibited the responses to both salmeterol (apparent KD 2.2 nM) and isoprenaline (apparent KD 1.6 nM). However, the beta 1-adrenoceptor antagonist, atenolol, produced no significant effect at concentrations up to 100 microM. 4. Salmeterol (1 microM) changed the concentration-response curve of isoprenaline in the manner of a partial agonist interacting with a full agonist. The KD of salmeterol obtained from the interaction was 55.6 nM. 5. Whereas salmeterol has a slow onset of action in airway smooth muscle compared to other beta 2-adrenoceptor agonists, in B50 monolayers both salmeterol and isoprenaline produced a rapid increase in cyclic AMP accumulation (t1/2 1.1 min and 0.4 min respectively). 6. Despite the existence of cyclic AMP efflux mechanisms that exist in this cell line it was possible to investigate the duration of agonist action by measuring intracellular levels of the second messenger. Replacement of drug-containing medium with fresh buffer led to a rapid reduction in intracellular levels of cyclic AMP in isoprenaline-stimulated cells whereas cyclic AMP accumulation was sustained for much longer periods in salmeterol-stimulated cells. However, the persistent action of salmeterol could be reversed by the addition of a beta2-selective antagonist.7. These results confirm that salmeterol has a high affinity, but low efficacy (relative to isoprenaline) for beta2-adrenoceptors coupled to cyclic AMP accumulation and that the drug persists at its site of action for long periods in the B50 neuronal cell line.
Photocleavable Molecule for Laser Desorption Ionization Mass Spectrometry (2007)

A new photocleavable molecule for laser desorption ionization mass spectrometry (LDI-MS) was designed and synthesized. The molecule exhibited high sensitivity for negative mode MS detection with good chemical stability. The molecule was successfully applied to molecular tag for (LDI-MS). Kinetic measurement of the amidation reaction and monitoring of aminolysis of acetylated sugars were demonstrated with the molecular tag.
Detection of methicillin resistance in coagulase-negative staphylococci and in staphylococci directly from simulated blood cultures using the EVIGENE MRSA Detection Kit (2003)

The EVIGENE MRSA Detection Kit was evaluated on coagulase-negative staphylococci (CoNS) from agar plates and on staphylococci directly from positive spiked blood cultures. For the CoNS study, a total of 242 isolates were tested, and of these 237 gave valid test results. For the 237 valid tests, all gave correct mecA classification. For the blood culture procedure, a collection of 51 mecA-positive Staphylococcus aureus, 21 mecA-negative S. aureus, 31 mecA-positive CoNS and 28 mecA-negative CoNS were used for the simulated blood cultures. For the S. aureus strains, all gave valid test results and correct mecA classification. One of the MRSA isolates gave a very faint nuc signal, and another four isolates gave results close to the cut-off of the kit; however, these were still clearly positive when read by the naked eye. For the CoNS isolates, 51 of the 59 strains gave valid results. All of these 51 strains gave correct mecA status. Thus the EVIGENE MRSA Detection Kit can provide fast and accurate determination of methicillin resistance in CoNS. This preliminary study of the blood culture procedure indicates that it is possible to achieve determination of methicillin resistance in staphylococci 8 h after positivity of the blood culture, making same-day detection of methicillin resistance possible.
Midterm Follow-up Results of Combined Phacoemulsification, Lens Implantation, and Mitomycin-C Trabeculectomy Procedure (1997)

The combined procedure technique that we describe appears to be effective at restoring visual acuity and significantly reducing IOP. Nevertheless, many visual fields showed continued, diffuse glaucomatous progression in the year or two following surgery and the development of late endophthalmitis in two eyes is a concern.
Oncogenic KRAS modulates mitochondrial metabolism in human colon cancer cells by inducing HIF-1α and HIF-2α target genes (2010)

Our findings suggest novel strategies for treating tumors with oncogenic KRAS mutations.
Resistance of the Human Immunodeficiency Virus to the Inhibitory Action of Negatively Charged Albumins on Virus Binding to CD4 (1999)

Negatively charged albumins (NCAs) have been identified as potent inhibitors of HIV-1 replication in vitro. Time of addition studies suggest that succinylated and aconitylated human serum albumin (Suc-HSA and Aco-HSA) act at an early stage of the virus life cycle, and surface plasmon resonance (BIAcore) experiments have confirmed a direct interaction of NCAs with HIV-1 gp120. Resistance to Suc-HSA and Aco-HSA was analyzed by characterizing HIV-1 variants that were selected in cell culture after serial passage of the NL4-3 strain in the presence of the compounds. After 24 passages (126 days) we isolated variants that were resistant to Suc-HSA (>27-fold) and Aco-HSA (37-fold), as compared with the wild-type NL4-3 virus. The binding of the NCA-resistant HIV strains to CD4+ MT-4 cells could no longer be inhibited by either Suc- or Aco-HSA. The emergence of mutations in the envelope gp120 of the resistant virus paralleled the emergence of the resistant phenotype. The Suc-HSA-resistant strain was 100-fold cross-resistant to the G quartet-containing oligonucleotide AR177 (Zintevir, an HIV-binding inhibitor), and partially cross-resistant to dextran sulfate, but remained sensitive to the bicyclam AMD3100 and the chemokine SDF-1alpha, which block HIV replication by interaction with the chemokine receptor CXCR4. Furthermore, neither Suc-HSA nor Aco-HSA inhibited the binding of monoclonal antibodies 12G5 and 2D7 (directed to CXCR4 and CCR5, respectively) in SUPT-1 cells or THP-1 cells. These results confirm that NCAs bind primarily to gp120 and do not interact directly with the HIV chemokine receptor but block the binding of the virus particles (through gp120) with CD4+ cells.
Blocking IDO activity to enhance anti-tumor immunity (2011)

Tumors express potentially immunogenic antigens, yet the immune response to these antigens is typically profoundly suppressed. Patients with established tumors behave as if they were functionally tolerant to any antigens associated with the tumor. This tolerance reflects a process of active immune suppression elicited by the tumor, and represents a critical barrier to successful anti-tumor immunotherapy. Indoleamine 2,3-dioxygenase (IDO) is a natural immunoregulatory mechanism contributes to immune suppression and tolerance in a variety of settings. In tumor-bearing hosts, animal models suggest that tumor-induced IDO helps create a tolerogenic milieu within the tumor and the associated tumor-draining lymph nodes. IDO directly suppresses the proliferation and differentiation of effector T cells, and markedly enhances the suppressor activity of regulatory T cells (Tregs). Together, these effects contribute to the inability of the immune system to respond effectively to tumor antigens. Treatment of tumor-bearing animals with IDO-inhibitor drugs enhances anti-tumor immune responses, and IDO-inhibitors are synergistic with a variety of chemotherapeutic drugs, anti-tumor vaccines and other immunotherapy. Strategies to pharmacologically inhibit IDO may thus enhance immune-mediated responses following conventional chemotherapy, and may be synergistic with other forms of immunotherapy.
New heterocyclic betaines (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew heterocyclic betainesKevin T. Potts and William R. KuehnlingCite this: J. Org. Chem. 1984, 49, 19, 3672–3673Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/jo00193a052https://doi.org/10.1021/jo00193a052research-articleACS PublicationsRequest reuse permissionsArticle Views158Altmetric-Citations28LEARN 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
LY146032 in a Hamster Model of <i>Staphylococcus aureus</i> Pneumonia – Effect on in vivo Clearance and Mortality and in vitro Opsonophagocytic Killing (1988)

The effect of the new peptolide LY146032 (LY) was studied in a hamster model of methicillin-resistant Staphylococcus aureus (MRSA) pneumonia. In vivo, after infection with one of two well-encapsulated strains of MRSA, A83 and A116 (type 8 and type 5), LY was protective only in A116 pneumonia. An in vitro assay of the effect of subinhibitory concentrations of LY on opsonophagocytic killing by pulmonary phagocytes demonstrated marked enhancement of killing of A116 (92.6 and 63.8% kill with 1/10 MIC and 1/50 MIC LY; no kill in the absence of LY). This effect was dependent on the presence of fresh serum. LY in subinhibitory concentrations produces a surface effect that may allow complement binding and activation and subsequent phagocytosis and killing to take place. The opsonizing effect of subinhibitory concentrations of LY was not demonstrable for the A83 strain. Differences in capsular types may be determinants of response to therapy of MRSA infections.
Coherent Coupled Qubits for Quantum Annealing (2017)

Although quantum annealing has received considerable interest as a potential computing paradigm, it has not met the key criterion of improved scaling over classical methods. Qubit coherence is currently a major limitation. Starting from a detailed theoretical understanding of the system, the authors demonstrate tunably coupled flux qubits with a circuit geometry similar to those used in existing annealers, but with coherence times that are roughly two orders of magnitude longer. Their design concepts are not limited to superconducting qubits, and could be generalized to other types being considered for quantum annealing.
A polarization-independent grating resonator (1997)

A polarization-independent optical resonator based on a novel phase-shifted grating structure is proposed and analyzed. Its application as a polarization-independent optical wavelength filter with ultranarrow bandwidth and fine tunability is described.
Synchronization of Concurrently-Implemented Fluidic Operations in Pin-Constrained Digital Microfluidic Biochips (2010)

The implementation of bioassays in pin-constrained biochips may involve pin-actuation conflicts if the concurrently implemented fluidic operations are not carefully synchronized. We propose a two-phase optimization method to identify and synchronize the fluidic operations that can be executed in parallel. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after the synchronization. The effectiveness of the proposed two-phase optimization method is demonstrated for a representative 3-plex assay performed on a fabricated pin-constrained biochip.
<title>Comprehensive focus-overlay-CD correlation to identify photolithographic performance</title> (1996)

In this study we evaluate the focus budget of an i-line stepper, examining the sources of focus erosion for a 0.40 micrometers process. The analysis first examines the best focus of the system as predicted by the several common tools currently used in the industry. Using the overlay focus- monitor, we then determine the value of lens aberrations such as astigmatism and field curvature. The results of lens heating examined for the lens using these common techniques. A model describing the focus aberrations is then developed and applied to the data. This model uses data derived from the focus monitor to determine lens errors such as coma, astigmatism and field curvature. Using this model, data gathered over various numerical aperture and partial coherence values are evaluated to determine the variation of lens aberrations over their range and the depth of focus. Finally, data consisting of critical dimension information gathered using an commercial, automated SEM is used to validate the predictions of the focus model.
Identification of a Single Nucleotide Polymorphism in the <i>MxA</i> Gene Promoter (G/T at nt –88) Correlated with the Response of Hepatitis C Patients to Interferon (2000)

The interferon (IFN)-inducible MxA protein is known to play an important role in the host defense against certain viruses. We aimed to see if any genetic polymorphism in the promoter region of the MxA gene is associated with the IFN responsiveness of hepatitis C virus (HCV)-infected patients. Initially we sequenced the promoter region of the MxA gene in 12 subjects and found a polymorphic site. We then constructed a specific PCR-RFLP system for this site and subjected 63 samples from chronic hepatitis C patients who were nonresponders (NR) to IFN therapy to it, 52 with sustained response (SR), and 42 healthy controls. Subjects were all Japanese, and unrelated. A single nucleotide polymorphism (SNP) was identified in the MxA promoter region: G/T alleles at nt position -88. Interestingly, this SNP was involved in a genetic element highly homologous to the IFN-stimulated response element consensus sequence, and the G-to-T change there makes this homology a little greater. The rate of G.G homozygosity was 31% in the SR patients, significantly lower than in the NR patients (62%, p = 0.0009), while that of healthy controls was between the two groups (48%). Differences in HCV genotypes did not influence this result. Based on these findings, we propose that the SNP of the MxA promoter at nt -88 identified in this study affects the expression of MxA protein, and may thus be associated with the response of HCV patients to IFN.