gebhart/patrepeval huggingface dataset:
Patch‐based Texture Interpolation (2010)

Abstract In this paper, we present a novel exemplar‐based technique for the interpolation between two textures that combines patch‐based and statistical approaches. Motivated by the notion of texture as a largely local phenomenon, we warp and blend small image neighborhoods prior to patch‐based texture synthesis. In addition, interpolating and enforcing characteristic image statistics faithfully handles high frequency detail. We are able to create both intermediate textures as well as continuous transitions. In contrast to previous techniques computing a global morphing transformation on the entire input exemplar images, our localized and patch‐based approach allows us to successfully interpolate between textures with considerable differences in feature topology for which no smooth global warping field exists.
Studies on the vasoocclusive crisis of sickle cell disease. III. In vitro and in vivo effect of the pyrimido-pyrimidine derivative, RA-233: studies on its mechanism of action. (1987)

Red cell deformability was found to be impaired in SS- and SC-genotype and to a lesser extent SA-genotype red blood cells as compared with those of AA-genotype. RA-233 in vitro improved deformability according to a bell-shaped dose-response curve. RA-233 also prevented experimental vasoocclusive crisis in Macaca arctoides. Deoxygenation of SS-genotype red cells resulted in sickle shape transformation, ATP depletion, potassium efflux, and attachment of hemoglobin molecules to the membrane. These changes were prevented by RA-233. Suspending SS-genotype red blood cells in potassium rich tris-buffer also prevented potassium efflux during deoxygenation and also decreased cellular deformability. RA-233 had no effect on osmotic fragility of SS-genotype red blood cells.
Real-time monitoring of organic vapor-phase deposition of molecular thin films using high-pressure reflection high-energy electron diffraction (2007)

The crystalline thin film growth of the organic material, copper phthalocyanine (CuPc), by organic vapor-phase deposition (OVPD) is studied using high-pressure reflection high-energy electron diffraction (HP-RHEED). In situ growth of this material was monitored, in real time, on both highly oriented pyrolytic graphite and native SiO2 on Si(100) substrates. The growth of the first several monolayers on both substrates was found to be independent of the growth conditions; however, the crystalline texture of thicker films was controlled through changes in the substrate temperature and deposition rate. Higher substrate temperatures lead to an increase in crystalline ordering for growth on both substrates. This work shows that HP-RHEED is a powerful tool for real-time monitoring of growth morphology in the low-vacuum OVPD environment, ultimately leading to in situ control of thin film crystalline order.
The PROSITE dictionary of sites and patterns in proteins, its current status (1993)

PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences. In some cases the sequence of an unknown protein is too distantly related to any protein of known structure to detect its resemblance by overall sequence alignment, but relationships can be revealed by the occurrence in its sequence of a particular cluster of residue types which is variously known as a pattern, motif, signature, or fingerprint. These motifs arise because specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity are conserved in both structure and sequence. These structural requirements impose very tight constraints on the evolution of these small but important portion(s) of a protein sequence. The use of protein sequence patterns to determine the function of proteins is becoming very rapidly one of the essential tools of sequence analysis. This reality has been recognized by many authors [1,2]. While there have been a number of reviews of published patterns [3,4,5], no attempt had been made until very recently Based on these observations, we decided in 1988, to actively pursue the development of a database of patterns which would be used to search against sequences of unknown function. This database, called PROSITE, contains some patterns which have been published in the literature, but the majority have been developed in the last four years by the author.
Small Interference RNA-mediated Gene Silencing of Human Biliverdin Reductase, but Not That of Heme Oxygenase-1, Attenuates Arsenite-mediated Induction of the Oxygenase and Increases Apoptosis in 293A Kidney Cells (2005)

BVR reduces biliverdin, the HO-1 and HO-2 product, to bilirubin. Human biliverdin (BVR) is a serine/threonine kinase activated by free radicals. It is a leucine zipper (bZip) DNA-binding protein and a regulatory factor for 8/7-bp AP-1-regulated genes, including HO-1 and ATF-2/CREB. Presently, small interference (si) RNA constructs were used to investigate the role of human BVR in sodium arsenite (As)-mediated induction of HO-1 and in cytoprotection against apoptosis. Activation of BVR involved increased serine/threonine phosphorylation but not its protein or transcript levels. The peak activity at 1 h (4-5-fold) after treatment of 293A cells with 5 mum As preceded induction of HO-1 expression by 3 h. The following suggests BVR involvement in regulating oxidative stress response of HO-1: siBVR attenuated As-mediated increase in HO-1 expression; siBVR, but not siHO-1, inhibited As-dependent increased c-jun promoter activity; treatment of cells with As increased AP-1 binding of nuclear proteins; BVR was identified in the DNA-protein complex; and AP-1 binding of the in vitro translated BVR was phosphorylation-dependent and was attenuated by biliverdin. Most unexpectedly, cells transfected with siBVR, but not siHO-1, displayed a 4-fold increase in apoptotic cells when treated with 10 mum As as detected by flow cytometry. The presence of BVR small interference RNA augmented the effect of As on levels of cytochrome c, TRAIL, and DR-5 mRNA and cleavage of poly(ADP-ribose) polymerase. The findings describe the function of BVR in HO-1 oxidative response and, demonstrate, for the first time, not only that BVR advances the role of HO-1 in cytoprotection but also affords cytoprotection independent of heme degradation.
Prism coupled terahertz waveguide sensor (2005)

A simple THz waveguide element has been used as a sensitive sensor for adsorbates on surfaces. The evanescent wave from total internal reflection off a silicon prism was used to couple pulsed THz radiation frequency selectively into the waveguide. The coupled frequencies were determined via time domain spectroscopy and react sensitively to any changes of thickness or phase shift upon reflection. In particular, the sensitivity to phase shifts makes this waveguide sensor attractive for the detection of very thin adsorbates. Typical sensitivity and reliability limits for the detection of adsorbates are discussed.
Night myopia: implications for the young driver. (1992)

A total of 380 randomly selected patients aged 16 to 80 years who did not have eye disease underwent testing for night myopia between August and October 1989 with a laser speckle generator under both photopic and scotopic conditions. For the first 308 subjects the speckles were continuously run, and for the next 72 subjects a timer was used to minimize the accommodative stimulus. An increase in myopia of 0.75 dioptres or more from the photopic to the scotopic state, equivalent to a visual acuity of 20/45 or less, was considered indicative of night myopia. Overall, 17% of the subjects were found to have night myopia. Of the 26 subjects aged 16 to 25 years in the timer group 38% had night myopia of 0.75 D or more, 23% had night myopia of 1.00 D or more, and 4% had night myopia of 2.50 D, which is equivalent to an acuity of 20/265. The results indicate that driving in the dark could create visual difficulties for certain younger patients that a night myopic correction would eliminate.
Molecular imaging and contrast agent database (MICAD): Progress and current status (2010)

1043 Learning Objectives 1. Description of the National Institutes of Health MICAD program. 2. Detail the new search filters, imaging agent viewing categories and download of all entries as a CSV file from the MICAD home page. 3. Describe the MICAD Guest Author program. 4. Discuss the Supplemental Information Section available in each chapter of MICAD. 5. Mention the MICAD eAnnouncement. The MICAD program is a key component of the NIH Roadmap that promotes and facilitates research and development in molecular imaging by providing freely accessible, current, online information regarding molecular imaging and contrast agents. The MICAD website will have approximately 850 imaging agents by June, 2010. Changes implemented in MICAD are: (1) New, redesigned homepage and search filters that perform MICAD searches based on the method of detection, source of signal, agent or target category, available research studies, and text words. All entries in MICAD are now categorized and arranged according to the imaging modality used. A summary of all MICAD entries can be downloaded as a CSV file from the homepage. 2) A MICAD Guest Author Program was implemented so that members of the imaging community can write and submit chapters for publication on the MICAD website. Contributing authors are duly acknowledged and the chapters are citable as references in other publications. 3) A largely unrestricted Supplemental Information Section was added to each MICAD chapter to promote the sharing of cutting-edge, unpublished or as yet unavailable information regarding an agent (images, research data etc.) in each chapter. 4) Each month an email announcement (eAnnouncement) that describes the new agents added to the database is sent to members of the imaging community registered with MICAD (visit www.micad.nih.gov to register). Research Support This research is supported by the Intramural Research Program of the NIH
Transfection of a DNA/protein complex into nuclei of mammalian cells using polyoma capsids and electroporation (1987)

We used empty capsids of polyoma virus to transfer DNA fragments and DNA/protein complexes into human cells. We encapsulated labeled and unlabeled single stranded DNA fragments by viral capsids. A complex of DNA with a DNA binding protein, recA, will also be taken up by the capsids, whereas the free protein is not incorporated. We further compared this gentle biological method of DNA transfection with a well-established physical method, electroporation. Electroporation also allows the transfer of DNA as well as protein into cells, although there is no proof that a DNA/protein complex can survive the procedure functionally. Whereas the viability of capsid transfected cells is unaffected (100%), electroporation reduces the viability to 90-95%. On the other hand, the amount of DNA found in the nucleus of electroporated cells is higher than for cells treated with loaded viral capsids.
Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction (2005)

Biological systems are known to be highly transparent to 700- to 1,100-nm near-infrared (NIR) light. It is shown here that the strong optical absorbance of single-walled carbon nanotubes (SWNTs) in this special spectral window, an intrinsic property of SWNTs, can be used for optical stimulation of nanotubes inside living cells to afford multifunctional nanotube biological transporters. For oligonucleotides transported inside living cells by nanotubes, the oligos can translocate into cell nucleus upon endosomal rupture triggered by NIR laser pulses. Continuous NIR radiation can cause cell death because of excessive local heating of SWNT in vitro. Selective cancer cell destruction can be achieved by functionalization of SWNT with a folate moiety, selective internalization of SWNTs inside cells labeled with folate receptor tumor markers, and NIR-triggered cell death, without harming receptor-free normal cells. Thus, the transporting capabilities of carbon nanotubes combined with suitable functionalization chemistry and their intrinsic optical properties can lead to new classes of novel nanomaterials for drug delivery and cancer therapy.
Basal-Like Breast Cancer: A Critical Review (2008)

Recent gene expression profiling of breast cancer has identified specific subtypes with clinical, biologic, and therapeutic implications. The basal-like group of tumors is characterized by an expression signature similar to that of the basal/myoepithelial cells of the breast and is reported to have transcriptomic characteristics similar to those of tumors arising in BRCA1 germline mutation carriers. They are associated with aggressive behavior and poor prognosis, and typically do not express hormone receptors or HER-2 ("triple-negative" phenotype). Therefore, patients with basal-like cancers are unlikely to benefit from currently available targeted systemic therapy. Although basal-like tumors are characterized by distinctive morphologic, genetic, immunophenotypic, and clinical features, neither an accepted consensus on routine clinical identification and definition of this aggressive subtype of breast cancer nor a way of systematically classifying this complex group of tumors has been described. Different definitions are, therefore, likely to produce variable and contradictory results that may hamper consistent identification and development of treatment strategies for these tumors. In this review, we discuss definition, heterogeneity, morphologic spectrum, relation to BRCA1, and clinical significance of this important class of breast cancer.
An optimal image operator design technique for coded excitation ultrasound imaging system (1994)

We have recently proposed a new coded excitation ultrasound imaging system. The system is based on a discretized linear model of the received data from the region of interest (ROI). Thus the system can be characterized by a linear equation with operator G consisting of on-grid impulse responses. The image reconstruction is obtained by solving the equation with a pseudo-inverse image operator (PIO). Since the reconstruction quality of the system is determined by the PIO, an effective design method is necessary to find an optimal PIO (i.e., a PIO has small noise sensitivity and the degradation of its performance caused by off-grid scatterers is well below a pre-specified tolerable level). In this report, an optimal PIO design method is presented with the help of singular value decomposition (SVD) technique. Given specifications imposed on the PIO, the proposed design method provides effective procedures for searching a set of suitable system parameters (such as grid size, codes, transmit channels, etc.). Then, the desirable PIO is evaluated by a method based on the SVD rank reduction technique. Simulation results are given to show the efficiency of the proposed PIO design method
Identification of a conserved oxidation-sensitive cysteine residue in the NFI family of DNA-binding proteins. (1994)

The nuclear factor I (NFI) family of site-specific DNA-binding proteins plays a role in both transcription and adenovirus DNA replication. The DNA binding domain of NFI family members contains 4 cysteine residues (Cys-2, Cys-3, Cys-4, and Cys-5) that are conserved in all NFI proteins. Mutation of the Cys-2, Cys-4, and Cys-5 residues in the human NFI-C protein to several other amino acids abolished DNA binding, while 8 of 10 mutations of the Cys-3 residue had little or no effect on binding. Wild-type NFI-C was inactivated by N-ethylmaleimide in vitro, while the active Cys-3 mutant proteins were resistant to N-ethylmaleimide. Treatment of wild-type NFI in vitro with the oxidizing agent diamide also inactivated DNA binding, and subsequent reduction with dithiothreitol restored binding activity. The active Cys-3 mutant NFI proteins were resistant to diamide-inactivation, indicating that the Cys-3 residue is required for modulation of DNA-binding by oxidation state. These studies indicate that oxidative-inactivation can play an important role in the modifying NFI-DNA-protein interactions. The presence of this nonessential Cys-3 residue in all known NFI proteins raises the possibility that it may function in a manner similar to redox-sensitive cysteine residues found in other site-specific DNA-binding proteins.
No evidence for a clear link between active intestinal inflammation and autism based on analyses of faecal calprotectin and rectal nitric oxide (2007)

By the use of two independent markers of inflammatory reactions in the gut, i.e. rectal NO and faecal calprotectin we were not able to disclose evidence of a link between the autistic disorder and active intestinal inflammation.
94GHz power-combining power amplifier with +13dBm saturated output power in 65nm CMOS (2011)

A power combining power amplifier utilizing cascode topology and transformer-based matching elements is presented in this paper. The amplifier achieves +13 dBm saturated output power at 94 GHz with a standard 1.2 V supply and occupies an active area of only 0.069 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Amplifier is implemented in an industrial 65nm CMOS process taking into account reliability issues at high output power level. The amplifier is also ESD-protected at the input and at the output.
Semantic integration (2004)

Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontologies. This paper provides a brief survey of the approaches to semantic integration developed by researchers in the ontology community. We focus on the approaches that differentiate the ontology research from other related areas. The goal of the paper is to provide a reader who may not be very familiar with ontology research with introduction to major themes in this research and with pointers to different research projects. We discuss techniques for finding correspondences between ontologies, declarative ways of representing these correspondences, and use of these correspondences in various semantic-integration tasks
An α-Formylglycine Building Block for Fmoc-Based Solid-Phase Peptide Synthesis (2005)

[reaction: see text] Nearly all known sulfatases share a common active site modification that is required for their activity: conversion of cysteine to alpha-formylglycine. We report the synthesis of an alpha-formylglycine building block suitable for Fmoc-based solid-phase peptide synthesis. The building block was incorporated into a synthetic peptide derived from the active site of a Mycobacterium tuberculosis sulfatase.
Src Kinases Mediate STAT Growth Pathways in Squamous Cell Carcinoma of the Head and Neck (2003)

Signal transducer and activator of transcription (STAT) proteins are constitutively activated in many malignancies, including squamous cell carcinoma of the head and neck (SCCHN). Previously, we reported that phosphorylation of the epidermal growth factor receptor (EGFR) is linked to activation of STATs 3 and 5 in SCCHN cells. The present study was undertaken to determine the role of Src family kinases in STAT activation and SCCHN growth. The Src family kinases c-Src, c-Yes, Fyn, and Lyn were expressed and activated by transforming growth factor-alpha stimulation in all four SCCHN cell lines examined but not in corresponding normal epithelial cells. In nine SCCHN cell lines tested, Src phosphotyrosine expression levels were highly correlated with activation levels of STATs 3 and 5. Co-immunoprecipitation analysis demonstrated interaction between c-Src and STATs 3 or 5 and EGFR in SCCHN cells, but no heterodimerization was detected between STAT3 and STAT5. SCCHN cells treated with either of two Src-specific inhibitors or transfected with a dominant-negative c-Src construct demonstrated decreased activation of STATs 3 and 5 and reduced growth rates in vitro. These results demonstrate a role for Src kinases in mediating activation of STATs 3 and 5 in concert with the EGFR in SCCHN cells. Strategies to target Src activation may contribute to the treatment of cancers that demonstrate increased levels of EGFR and STATs, including SCCHN.
Biomarker-Driven Early Clinical Trials in Oncology (2009)

Early clinical trials represent a crucial bridge between preclinical drug discovery and the especially resource-intense randomized phase III trial-the definitive regulatory hurdle for drug approval. High attrition rates and rising costs, when coupled with the extraordinary opportunities opened up by cancer genomics and the promise of personalized medicine call for new approaches in the conduct and design of phase I/II trials. The key challenge lies in increasing the odds for successful and efficient transition of a compound through the drug development pipeline. The incorporation of scientifically and analytically validated biomarkers into rationally designed hypothesis-testing clinical trials offers a promising way forward to achieving this objective. In this article, we provide an overview of biomarkers in early clinical trials, including examples where they have been particularly successful, and the caveats and pitfalls associated with indiscriminate application. We describe the use of pharmacodynamic end points to demonstrate the proof of modulation of target, pathway, and biologic effect, as well as predictive biomarkers for patient selection and trial enrichment. Establishing the pharmacologic audit trail provides a means to assess and manage risk in a drug development program and thus increases the rationality of the decision-making process. Accurate preclinical models are important for pharmacokinetic-pharmacodynamic-efficacy modeling and biomarker validation. The degree of scientific and analytical validation should ensure that biomarkers are fit-for purpose, according to the stage of development and the impact on the trial; specifically they are either exploratory or used to make decisions within the trial. To be maximally useful at an early stage, these must be in place before the commencement of phase I trials. Validation and qualification of biomarkers then continues through clinical development. We highlight the impact of modern technology platforms, such as genomics, proteomics, circulating tumor cells, and minimally invasive functional and molecular imaging, with respect to their potential role in improving the success rate and speed of drug development and in interrogating the consequences of therapeutic intervention and providing a unique insight into human disease biology. With these technologies already having an impact in the clinic today, we predict that further future advances will come from the application of network analysis to clinical trials, leading to individualized systems-based medicine for cancer.