gebhart/patrepeval huggingface dataset:
Selection of peptides that functionally replace a zinc finger in the Sp1 transcription factor by using a yeast combinatorial library (1997)

We have developed a strategy for the identification of peptides able to functionally replace a zinc finger domain in a transcription factor. This strategy could have important ramifications for basic research on gene regulation and for the development of therapeutic agents. In this study in yeast, we expressed chimeric proteins that included a random peptide combinatorial library in association with two zinc finger domains and a transactivating domain. The library was screened for chimeric proteins capable of activating transcription from a target sequence in the upstream regulatory regions of selectable or reporter genes. In a screen of approximately 1.5 x 10(7) transformants we identified 30 chimeric proteins that exhibited transcriptional activation, some of which were able to discriminate between wild-type and mutant DNA targets. Chimeric library proteins expressed as glutathione S-transferase fusions bound to double-stranded oligonucleotides containing the target sequence, suggesting that the chimeras bind directly to DNA. Surprisingly, none of the peptides identified resembled a zinc finger or other well-known transcription factor DNA binding domain.
The dielectric properties of biological tissues: I. Literature survey (1996)

The dielectric properties of tissues have been extracted from the literature of the past five decades and presented in a graphical format. The purpose is to assess the current state of knowledge, expose the gaps there are and provide a basis for the evaluation and analysis of corresponding data from an on-going measurement programme.
Wnt Signaling in Melanoma (2014)

Given the scarcity of effective therapeutic options for malignant melanoma, research efforts have focused on understanding mechanisms of melanoma initiation and progression in order to develop novel treatment strategies. Numerous studies now implicate changes in the activity of both β-catenin-dependent Wnt signaling pathways and β-catenin-independent Wnt signaling pathways in melanoma development and progression. This chapter attempts to answer the following critical questions regarding the Wnt signaling pathways in melanoma: (i) Can measures of Wnt signaling activity provide any prognostic information in a clinical setting? (ii) How do Wnt signaling pathways functionally contribute to melanoma tumorigenesis, progression, and/or metastasis? (iii) What endogenous and exogenous factors determine the relative activity of Wnt signaling pathways in melanoma? and (iv) Can we leverage our emerging understanding of Wnt signaling towards the development of new clinical strategies for therapeutically intractable melanomas?
An enterprise intelligence system integrating WWW and intranet resource (1999)

Internet and intranet technologies make an unprecedented quantity and variety of information available at the desktop. However, key elements of competitive information may not be found in a timely manner because of unknown location among many diverse sources, information overload, variant research techniques, variant schemata, variant formats and protocols. It is difficult for users to integrate information across sources; the abundant information may thus not contribute to understanding for decision making. The Enterprise Intelligence System Network (EisNet) was funded in 1996 to assess intranet/intranet and InfoWeb technology as a business model for TRW System and Information Technology Group (S&ITG) program development and business opportunity management. EisNet is a prototype competitive intelligence system developed by researchers at TRW's Digital Media Systems Laboratory. EisNet uses TRW's InfoWeb/sup TM/ multimedia archive platform to integrate information harvested from Web servers, Web search services, and corporate intranet servers. InfoWeb/sup TM/ generates metadata through the natural language analysis of text, providing indexes based on concepts and structured data to complement full-text retrieval. InfoWeb/sup TM/ also generates automatically, providing a navigation method that supplements complex searching (i.e. mixing topical, relational, free-text, and geospatial queries in a single expression). The goal of EisNet is to make diverse information resources both internal and external to the enterprise accessible to users consistently and seamlessly.
Ex Vivo Staining of Metastatic Lymph Nodes by Class I Major Histocompatibility Complex Tetramers Reveals High Numbers of Antigen-experienced Tumor-specific Cytolytic T Lymphocytes (1998)

Characterization of cytolytic T lymphocyte (CTL) responses to tumor antigens has been impeded by a lack of direct assays of CTL activity. We have synthesized reagents ("tetramers") that specifically stain CTLs recognizing melanoma antigens. Tetramer staining of tumor-infiltrated lymph nodes ex vivo revealed high frequencies of tumor-specific CTLs which were antigen-experienced by surface phenotype. In vitro culture of lymph node cells with cytokines resulted in very large expansions of tumor-specific CTLs that were dependent on the presence of tumor cells in the lymph nodes. Tetramer-guided sorting by flow cytometer allowed isolation of melanoma-specific CTLs and confirmation of their specificity and their ability to lyse autologous tumor cells. Our results demonstrate the value of these novel reagents for monitoring tumor-specific CTL responses and for generating CTLs for adoptive immunotherapy. These data also indicate that strong CTL responses to melanoma often occur in vivo, and that the reactive CTLs have substantial proliferative and tumoricidal potential.
One by one: Single molecule tools for genomics (2003)

Much of the effort in any genomics programme arises from the need to generate and purify large numbers of identical molecules, since most analytical tools rely on the analysis of bulk DNA. Biological steps such as bacterial cloning--commonly used to prepare bulk samples of defined DNA fragments--are capricious and introduce their own restrictions and distortions. The analysis of single molecules, either directly or by in vitro enzymatic amplification, makes possible the examination of native genomic DNA without the complications and restrictions of biological propagation. Techniques already exist for the in vitro propagation of genomic fragments and for genome mapping, and offer the advantages of speed, flexibility and predictable behaviour. Single molecule sequencing, for which many approaches are being developed, is more challenging, but offers even greater rewards in terms of throughput and read length.
Methylated DNA Immunoprecipitation and High-Throughput Sequencing (MeDIP-seq) Using Low Amounts of Genomic DNA (2014)

DNA modifications, such as methylation and hydroxymethylation, are pivotal players in modulating gene expression, genomic imprinting, X-chromosome inactivation, and silencing repetitive sequences during embryonic development. Aberrant DNA modifications lead to embryonic and postnatal abnormalities and serious human diseases, such as cancer. Comprehensive genome-wide DNA methylation and hydroxymethylation studies provide a way to thoroughly understand normal development and to identify potential epigenetic mutations in human diseases. Here we established a working protocol for methylated DNA immunoprecipitation combined with next-generation sequencing [methylated DNA immunoprecipitation (MeDIP)-seq] for low starting amounts of genomic DNA. By using spike-in control DNA sets with standard cytosine, 5-methylcytosine (5mC), and 5-hydroxymethylcytosine (5hmC), we demonstrate the preferential binding of antibodies to 5mC and 5hmC, respectively. MeDIP-PCRs successfully targeted highly methylated genomic loci with starting genomic DNA as low as 1 ng. The enrichment efficiency declined for constant spiked-in controls but increased for endogenous methylated regions. A MeDIP-seq library was constructed starting with 1 ng of DNA, with the majority of fragments between 250 bp and 600 bp. The MeDIP-seq reads showed higher quality than the Input control. However, after being preprocessed by Cutadapt, MeDIP (97.53%) and Input (94.98%) reads showed comparable alignment rates. SeqMonk visualization tools indicated MeDIP-seq reads were less uniformly distributed across the genome than Input reads. Several commonly known unmethylated and methylated genomic loci showed consistent methylation patterns in the MeDIP-seq data. Thus, we provide proof-of-principle that MeDIP-seq technology is feasible to profile genome-wide DNA methylation in minute DNA samples, such as oocytes, early embryos, and human biopsies.
Androgen Receptor Splice Variant 7 and Efficacy of Taxane Chemotherapy in Patients With Metastatic Castration-Resistant Prostate Cancer (2015)

Detection of AR-V7 in CTCs from men with metastatic CRPC is not associated with primary resistance to taxane chemotherapy. In AR-V7-positive men, taxanes appear to be more efficacious than enzalutamide or abiraterone therapy, whereas in AR-V7-negative men, taxanes and enzalutamide or abiraterone may have comparable efficacy. Circulating tumor cell-based AR-V7 detection may serve as a treatment selection biomarker in CRPC.
Algorithms for Cytoplasm Segmentation of Fluorescence Labelled Cells (2002)

Automatic cell segmentation has various applications in cytometry, and while the nucleus is often very distinct and easy to identify, the cytoplasm provides a lot more challenge. A new combination of image analysis algorithms for segmentation of cells imaged by fluorescence microscopy is presented. The algorithm consists of an image pre-processing step, a general segmentation and merging step followed by a segmentation quality measurement. The quality measurement consists of a statistical analysis of a number of shape descriptive features. Objects that have features that differ to that of correctly segmented single cells can be further processed by a splitting step. By statistical analysis we therefore get a feedback system for separation of clustered cells. After the segmentation is completed, the quality of the final segmentation is evaluated. By training the algorithm on a representative set of training images, the algorithm is made fully automatic for subsequent images created under similar conditions. Automatic cytoplasm segmentation was tested on CHO-cells stained with calcein. The fully automatic method showed between 89% and 97% correct segmentation as compared to manual segmentation.
Faster laziness using dynamic pointer tagging (2007)

In the light of evidence that Haskell programs compiled by GHC exhibit large numbers of mispredicted branches on modern processors, we re-examine the "tagless" aspect of the STG-machine that GHC uses as its evaluation model.
Expression of the C–Kit Proto–Oncogene in Rat Hepatic Allografts During Acute Rejection (1999)

The role of the c-kit proto-oncogene in organ allograft rejection is not known. We investigated the level of c-kit expression following allogeneic transplantation of ACI rat liver grafts into LEW recipients. We studied c-kit mRNA and protein expression in groups of transplant recipients receiving hepatic isografts, hepatic allografts, or hepatic allografts after donor-specific blood transfusion (DST). Pretransplantation DST significantly prolonged survival of hepatic allografts. Infiltrates expressing c-kit were observed in allografts to untreated rats but not in groups receiving isografts or allografts following DST. Northern analysis also demonstrated abundant c-kit mRNA transcripts in the untreated allograft group in contrast to the isograft and the DST-treated groups. In addition, significantly more transcripts for interleukin-12 (IL-12), which is synergistic with c-kit, were present in untreated than in DST-treated allograft groups. In contrast, transforming growth factor beta (TGF-beta), which inhibits c-kit synthesis, was expressed abundantly in hepatic allografts to DST-treated rats but not in allografts to untreated animals. Transcripts for IL-10, which inhibits IL-12 production, were significantly more plentiful in hepatic allografts following DST than in those without DST. The results suggest that c-kit proto-oncogene expression in infiltrating cells is associated with rat hepatic allograft rejection.
Intelligent human computer interaction based on non redundant EMG signal (2020)

Human computer interaction plays an increasingly important role in our life. People need more intelligent, concise and efficient human-computer interaction. It is of great significance to optimize the process of human-computer interaction by using appropriate calculation methods. In order to eliminate the interference data of thumb recognition based on sEMG signal in the process of human-computer interaction, simplify the data processing, and improve the working efficiency of general equipment of sEMG signal. In the process of gesture recognition using sEMG signals generated by thumb, a method of redundant electrode determination based on variance theory is proposed. The redundancy of five groups of action signals is divided into 16 levels and visualized. By comparing the results of thumb motion recognition when different redundant channels are removed, the optimal channel combination in the process of thumb motion recognition is obtained. Finally, two kinds of classifiers suitable for sEMG signal field are selected, and the classification results are compared, and the best method of thumb motion pattern recognition is obtained.
Peripheral lymph node stromal cells can promote growth and tumorigenicity of breast carcinoma cells through the release of IGF‐I and EGF (2002)

The regional lymph nodes draining primary breast carcinomas are generally the first site to be invaded by disseminating tumor cells. The extent of lymph node involvement remains the most reliable indicator for staging and prognosis of breast cancer. We have investigated host-tumor interactions between breast carcinoma cells and the lymph node stroma, which may control the outcome of lymph node infiltration. In a previous study, we identified integrin-mediated cell adhesion as a correlate of the metastatic potential of human and rat carcinoma cells. Our present objective was to determine whether lymphatic stromal cells can affect cancer cell growth through the elaboration of growth-modulating factors. Two lymphatic stromal cell lines, ST-A4 and ST-B12, were established from normal rat lymph node stromal cell cultures. SFM conditioned by these cells increased the proliferation of human (Hs578T and MCF-7) and rat (TMT-081) breast carcinoma cells by up to 7-fold and augmented their ability to form colonies in semisolid agar by up to 41-fold. This effect was specific as normal, diploid human breast epithelial cells (Hs578Bst), a nontumorigenic, immortalized human breast epithelial cell line (MCF-10A) and a nonmetastatic rat mammary carcinoma cell line (MT-W9B) had either no or reduced responses. RT-PCR analysis revealed that both lymph node stromal cell lines expressed mRNA transcripts for multiple growth factors, including IGF-I, EGF, HGF and PDGF-alpha, and produced detectable levels of IGF-I, EGF and PDGF-alpha, as assessed by Western blotting. Antibody-mediated depletion assays identified IGF-I and EGF as the major mitogenic factors in the CM. The identification of these cells raises the possibility that the lymph node microenvironment may contribute actively to the process of cancer cell dissemination.
Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data (2013)

Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms ( Z max ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers ( Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f ′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct structural analysis.
Spacing and Timing (2004)

The aim of this special issue is to explore organizing processes in ways which do not assume an a priori existence of space and time. Rather than providing a summary of the papers collected here, this introduction illustrates how Spacing and Timing relate to issues of knowing, organizing, mediation, engagement, alterity and absence/presence. We examine how various actions and practices may be seen as seeking to achieve order but also concomitantly create further openings and orderings. Finally, while this introduction attempts to highlight a range of issues relating to this process, the development of alternative vocabularies, approaches, and insights are required to develop this work further.
Prostaglandin D 2 as a Mediator of Allergic Asthma (2000)

Allergic asthma is caused by the aberrant expansion in the lung of T helper cells that produce type 2 (TH2) cytokines and is characterized by infiltration of eosinophils and bronchial hyperreactivity. This disease is often triggered by mast cells activated by immunoglobulin E (IgE)-mediated allergic challenge. Activated mast cells release various chemical mediators, including prostaglandin D2 (PGD2), whose role in allergic asthma has now been investigated by the generation of mice deficient in the PGD receptor (DP). Sensitization and aerosol challenge of the homozygous mutant (DP-/-) mice with ovalbumin (OVA) induced increases in the serum concentration of IgE similar to those in wild-type mice subjected to this model of asthma. However, the concentrations of TH2 cytokines and the extent of lymphocyte accumulation in the lung of OVA-challenged DP-/- mice were greatly reduced compared with those in wild-type animals. Moreover, DP-/- mice showed only marginal infiltration of eosinophils and failed to develop airway hyperreactivity. Thus, PGD2 functions as a mast cell-derived mediator to trigger asthmatic responses.
Homeostatic regulation of hepatocyte nuclear transcription factor 1 expression in cultured hepatoma cells. (1994)

Serum colloid osmotic pressure is believed to control the hepatic output of plasma proteins, including albumin. The present study was aimed at identifying the molecular basis for feedback control of albumin gene expression in highly differentiated hepatoma cells. The steady-state level of albumin mRNA and the activity of a 282-bp albumin promoter-chloramphenicol acetyltransferase reporter gene in cells incubated in the presence of increasing amounts of serum albumin or dextran were significantly and selectively decreased. When nuclear extracts from cells exposed to 5% (wt/vol) serum albumin were tested in a gel-retardation assay with six oligonucleotide probes containing DNA elements of the albumin promoter, only the element B-retarded band, which contains the nucleotide recognition sequence for hepatocyte nuclear transcription factor 1 alpha (HNF-1 alpha), was consistently decreased as compared to nuclear extract from cells not exposed to serum albumin. Moreover, the activity of a reporter gene with a basal TATA-promoter driven by multiple HNF-1 alpha recognition elements was selectively inhibited in cells incubated in the presence of 5% serum albumin. A reduction of HNF-1 alpha mRNA appears to be responsible for this response to a change in the level of macromolecules in the incubation medium. These results indicate that activity of a dominant liver transcription factor, HNF-1 alpha, controlling the transcription of several liver-specific genes, is modulated by a fluctuation in the level of oncotically active macromolecules.
Investigation of a highly efficient LINC amplifier topology (2002)

The LINC transmitter is an architecture that provides linear amplification using nonlinear but power efficient amplifiers. The realization of the high power efficiency potential is the most critical issue of LINC. We have investigated a promising LINC amplifier topology that, using ideal bilateral PA devices, theoretically achieves linear amplification with 100% efficiency at all output levels. Circuit simulations based on integrated circuit (IC) techniques show good linearity and power efficiency results up to a few hundred MHz but gradually degrading performance as we approach the GHz range. With the advance of IC technology, this LINC amplifier topology offers a good possibility for obtaining highly efficient linear RF power amplifiers.
Guiding and confining light in void nanostructure (2004)

We present a novel waveguide geometry for enhancing and confining light in a nanometer-wide low-index material. Light enhancement and confinement is caused by large discontinuity of the electric field at high-index-contrast interfaces. We show that by use of such a structure the field can be confined in a 50-nm-wide low-index region with a normalized intensity of 20 microm(-2). This intensity is approximately 20 times higher than what can be achieved in SiO2 with conventional rectangular waveguides.
Electrochemical Synthesis of Urea at Gas‐Diffusion Electrodes: III. Simultaneous Reduction of Carbon Dioxide and Nitrite Ions with Various Metal Catalysts (1998)

Simultaneous reduction of carbon dioxide and nitrite ions was examined at the gas‐diffusion electrodes with various catalysts (Cr, Mo, Mn, Ru, Co, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au, Zn, Cd, In, Tl, Sn, and Pb). The formation of urea, CO, formic acid, and ammonia at the gas‐diffusion electrodes with the catalysts of groups 11–14 was found on the simultaneous reduction. The maximum current efficiency (c.e.) of urea formation at Cd catalysts is approximately 55% at −1.0 V. The formation of urea at the gas‐diffusion electrodes with the catalysts of groups 6–10, except Pd, was not found for the simultaneous reduction of and nitrite. Relationship of the ability of urea formation to the ability of CO and formation was investigated at various catalysts. The c.e. of urea increases with increasing the c.e of CO and on the reduction of alone and nitrite ions alone, respectively. Hence, the ability of urea formation at the catalysts depends on the ability of CO and formation. The catalysts with the high ability of CO and formation could form large amounts of CO‐like and ammonia‐like precursors. Urea would be formed from both the ammonia‐like precursor formed from nitrite ions, and the CO‐like precursor formed from at the groups 11–14 catalysts.