gebhart/patrepeval huggingface dataset:
Crystal and molecular structure of paclitaxel (taxol). (1995)

Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus several water and dioxane solvent molecules. Taxane ring conformation is very similar in both paclitaxel molecules and is similar to the taxane ring conformation found in the crystal structure of the paclitaxel analogue docetaxel (formerly called taxotere). The two paclitaxel molecules have carbon-13 side-chain conformations that differ from each other and from that of the corresponding side chain in the docetaxel crystal structure. The carbon-13 side-chain conformation of one paclitaxel molecule is similar to what was proposed from NMR studies done in polar solvents, while that of the other paclitaxel molecule is different and hitherto unobserved. The paclitaxel molecules interact with each other and with solvent atoms through an extensive network of hydrogen bonds. Analysis of the hydrogen-bonding network together with structure-activity studies may suggest which atoms of paclitaxel are important for binding to microtubule receptors.
Evaluation of the performance of crystalline lens refilled with polymer gel with an improved ex vivo accommodation simulator (2005)

The ex vivo accommodation simulator stretches crystalline lenses radially under controlled conditions, while monitoring the changes in zonular tension and lens diameter. A dual coaxial laser beam system was added for measuring changes in optical power as the lens is stretched. The EVAS instrument was fully characterized and calibrated. The results from 3 porcine eyes will be presented. Several crystalline lenses, similar in shape and size to porcine lenses, were cast molded in silicone gels of different stiffness. These lenses were evaluated using the EVAS instrument and custom made lens holding fixtures. With their well defined shape and material properties, results from these measurements will be useful for cross-validation of finite element models.
<title>Digital watermarks as a security feature for identity documents</title> (2000)

The personal computer and digital photography boom of the last decade has fueled growth of a variety of high quality imaging peripherals. Personal computer scanners and color printers are now widely available as prices have fallen rapidly and quality continues to improve. The cost of a high-quality color scanner has stabilized under 150 dollars US. High-quality ink-jet printers are available for under 200 dollars US. Powerful, easy to use image processing software is typically with both printers and scanners at no additional charge. This combination of powerful technology at a low price point has increased the counterfeiting and forgery threat for valuable identity documents. As traditional, optically based techniques have become less effective against digital reproduction, new methods must be developed to mitigate the threat. Digital watermarks can be used to create self-authenticating identify documents to directly address these new threats. Digital watermarks are: imperceptible, so they do not impact the visual quality of the document; robust through the print and scan operation; and require not physical real estate on the document. This aper examines how digital watermarks can be used in identity documents. It explores the key system requirements and technical challenges in enhancing physical document authentication systems with digital watermarks.
Lymphatic vessels and lymphangiogenesis in female cancer: Mechanisms, clinical impact and possible implications for anti-lymphangiogenic therapies (Review) (2002)

Lymphatic vessels play a crucial role in a variety of human cancers, since invasion of lymphatic vessels by tumor cells and subsequent development of lymph node metastases significantly influences prognosis of cancer patients and therefore represent an integral part of tumor staging. Recent evidence on the important influence of lymphangiogenetic growth factors on intralymphatic cancer growth and metastasis raises hopes that lymphatic vessels and factors inducing their growth could serve as an additional target for tumor therapy. Nevertheless, in contrast to blood vessel angiogenesis, the mechanisms of new lymphatic vessel formation in human cancers, i.e. lymphangiogenesis, are still relatively unclear. In addition, only little data exist so far on the quantification and impact of this lymphangiogenesis, evident by lymphatic microvessel density (LMVD), on the prognosis of cancer patients. With expectation of possible anti-lymphangiogenic therapies, this review focuses on the mechanisms of lymphangiogenesis in general, and especially on the role of lymphatic vessels in gynecological and breast cancer, which are the so far most detailed investigated malignancies with regard to lymphangiogenesis.
Digital television system design study (1976)

The use of digital techniques for transmission of pictorial data is discussed for multi-frame images (television). Video signals are processed in a manner which includes quantization and coding such that they are separable from the noise introduced into the channel. The performance of digital television systems is determined by the nature of the processing techniques (i.e., whether the video signal itself or, instead, something related to the video signal is quantized and coded) and to the quantization and coding schemes employed.
Twentieth century brouhaha (2002)

When I listen for voices of our twentieth century nation I hear a brouhaha - a loud, confused commotion or hubbub. Listen to some of my voices from twentieth century Australia: a chorus of tour guides singsong through museum, historic house, theme park and mall. Youth 'duff duff' pumps from passing car or club. Family chatter and clatter of pans spill from every kitchen. The slam of a door in another adolescent rage and another parental sigh of, 'What else to do?'. A chattering nation sips cappuccinos at new cafes, beer at old pubs, wine at swanky functions or water on lunchtime jogs.
Formation of Protein-Bound 3,4-Dihydroxyphenylalanine and 5-S-Cysteinyl-3,4-dihydroxyphenylalanine as New Cross-Linkers in Gluten (1997)

The formation of protein-bound 5-S-cysteinyl-3,4-dihydroxyphenylalanine (5-S-cysteinyldopa) and 3,4-dihydroxyphenylalanine (dopa) as new cross-linkers in gluten was investigated. Gas-phase acid hydrolysis of gluten was carried out in the presence of 5% phenol. For identification of dopa and 5-S-cysteinyldopa, alumina extraction of catechols in the hydrolysates was performed. The presence of dopa and 5-S-cysteinyldopa in the hydrolysates of gluten was determined using HPLC equipped with an electrochemical detector. When mushroom tyrosinase, which has an oxidant-like effect on the physical properties of dough, was added to dough, the amount of protein-bound 5-S-cysteinyldopa increased. It is concluded that the oxidizing effect of tyrosinase is due to the formation of protein-bound 5-S-cysteinyldopa and dopa as cross-linkers of gluten. Keywords: 5-S-cysteinyl-3,4-dihydroxyphenylalanine (5-S-cysteinyldopa); 3,4-dihydroxyphenylalanine (dopa); gluten; tyrosinase
Evaluating architectures for multithreaded object request brokers (1998)

x x x x x x x x x x x x x x x x Multithreading allows operations to execute simultaneously without impeding the progress of other operations. Likewise, multithreading can minimize latency and ensure predictability in real-time systems This article describes and evaluates common CORBA multithreading architectures used by ORB implementations, including CORBAplus, HP ORB Plus, miniCOOL, MT-Orbix, TAO, and VisiBroker.
Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage (1987)

The emergence of a simple translation device consisting of an assembler strand (primordial mRNA) and RNA hairpins (primordial tRNA) is presumed to be an important step leading to the origin of life. The assumption of a non-enzymatic interaction of primordial tRNA and mRNA is experimentally approached. DNA hairpins containing five or more adenosine residues in the loop are able to bind to complementary oligonucleotides covalently bound to cellulose. The exact number of base pairs formed between the hairpins and the assembler strand is determined by two methods applied to DNA hairpin/assembler complexes. The melting temperature of a complex is measured and the cleavage pattern by nuclease from mung bean is determined. The loop of the smallest hairpin able to bind consists of five adenosine residues and only three base pairs are formed. This supports the idea of a primordial recognition similar to the contemporary codon-anticodon interaction.
SRQL: Sorted Relational Query Language (2002)

A relation is an unordered collection of records. Often, however there is an underlying order (e.g., a sequence of stock prices), and users want to pose queries that reflect this order (e.g., find a weekly moving average). SQL provides no support for posing such queries. We show how a rich class of queries reflecting sort order can be naturally expressed and efficiently executed with simple extensions to SQL.
Controlled Synthesis and Photoluminescence Properties of ZnS Nanowires and Nanoribbons (2005)

Rapid synthesis of wurtzite ZnS nanowires and nanoribbons has been achieved by a simple thermal evaporation of ZnS powder onto Si substrate in the presence of Au catalyst. A vapor-liquid-solid process is proposed for the formation of the ZnS nanostructures. The flow rate of the inert carrier Ar gas along with the temperature play an important role in defining the morphology of the ZnS nanostructures. The morphological change of the ZnS nanostructures and their growth sequence were studied through scanning electron microscopy. Room-temperature photoluminescence measurements showed intense blue emission at approximately 398 nm from both the nanowires and the nanoribbons.
Toward an Understanding of the Chemical Etiology for DNA Minor‐Groove Recognition by Polyamides (2002)

Abstract Crescent‐shaped polyamides composed of aromatic amino acids, i.e. , 1‐methyl‐1 H ‐imidazole Im , 1‐methyl‐1 H ‐pyrrole Py , and 3‐hydroxy‐1 H ‐pyrrole Hp , bind in the minor groove of DNA as 2 : 1 and 1 : 1 ligand/DNA complexes. DNA‐Sequence specificity can be attributed to shape‐selective recognition and the unique corners or pairs of corners presented by each heterocycle(s) to the edges of the base pairs on the floor of the minor groove. Here we examine the relationship between heterocycle structure and DNA‐sequence specificity for a family of five‐membered aromatic amino acids. By means of quantitative DNase‐I footprinting, the recognition behavior of polyamides containing eight different aromatic amino acids, i.e. , 1‐methyl‐1 H ‐pyrazole Pz , 1 H ‐pyrrole Nh , 5‐methylthiazole Nt , 4‐methylthiazole Th , 3‐methylthiophene Tn , thiophene Tp , 3‐hydroxythiophene Ht , and furan Fr , were compared with the polyamides containing the parent‐ring amino acids Py, Im , and Hp for their ability to discriminate between the four WatsonCrick base pairs in the DNA minor groove. Analysis of the data and molecular modeling showed that the geometry inherent to each heterocycle plays a significant role in the ability of polyamides to differentiate between DNA sequences. Binding appears sensitive to changes in curvature complementarity between the polyamide and DNA. The Tn / Py pair affords a modest 3‐fold discrimination of T⋅A vs. A⋅T and suggests that an S‐atom in the thiophene ring prefers to lie opposite T not A.
A phase 1b study of the anticancer stem cell agent demcizumab (DEM), pemetrexed (PEM), and carboplatin (CARBO) in pts with first-line nonsquamous NSCLC. (2014)

2544 Background: Delta-like ligand 4 (DLL4) activates the Notch pathway and is important for cancer stem cell (CSC) survival. DEM is a humanized IgG2 anti-DLL4 antibody that has been shown to inhibit tumor growth, decrease CSC frequency & cause dysfunctional sprouting of new vessels resulting in an antiangiogenic effect in human tumor xenograft models. Methods: Pts received DEM (2.5, 5 or 7.5 mg/kg), PEM 500 mg/m2 & CARBO (AUC = 6) every 3 weeks followed by maintenance DEM or PEM (7.5 mg/kg cohort) every 3 weeks until progression. The objectives were to determine the MTD, safety, efficacy, immunogenicity, pharmacokinetics & biomarkers of Notch signaling. Results: Thirty-two pts were enrolled; 6 received 2.5 mg/kg, 20 received 5 mg/kg & 6 received 7.5 mg/kg of DEM. Related AEs in > 20% of pts were: nausea (53%), fatigue (47%), hypertension (41%), vomiting (34%), edema (28%), neutropenia (25%), & increased B-type natriuretic peptide (BNP) (22%). Increased BNP values are an early indicator of the cardiac effects of DEM & mildly elevated values are being used to initiate cardioprotective therapy with an ACE inhibitor or carvedilol. Two pts receiving 5 mg/kg developed reversible pulmonary hypertension & heart failure on days 167 and 183, respectively. As a result, DEM treatment was limited to 63 days in subsequent cohorts. One of 28 (4%) evaluable pts had a RECIST CR, 12 (43%) had a PR and 11 had SD. The Kaplan Meier estimated median progression free survivals for the 2.5, 5 and 7.5 mg/kg pts were 4.8, 5.3 and 4.4 months, respectively. Five pts who discontinued the study for a reason other than progression (3 continued to receive CARBO & PEM off-study) were progression-free through Day 223+, 243+, 457+, 497+, 680+ and a sixth pt (who continued to receive CARBO & PEM off-study) progressed at Day 850. Conclusions: DEM, CARBO & PEM was generally well tolerated with nausea, fatigue & hypertension being the most common drug related toxicities. The duration of DEM therapy is being limited to 63 days due to cardiopulmonary toxicity which was observed following more prolonged administration. Encouraging early clinical activity has been observed. Enrollment is ongoing and updated results will be presented. Clinical trial information: NCT01189968.
Spatial/spectral endmember extraction by multidimensional morphological operations (2002)

Spectral mixture analysis provides an efficient mechanism for the interpretation and classification of remotely sensed multidimensional imagery. It aims to identify a set of reference signatures (also known as endmembers) that can be used to model the reflectance spectrum at each pixel of the original image. Thus, the modeling is carried out as a linear combination of a finite number of ground components. Although spectral mixture models have proved to be appropriate for the purpose of large hyperspectral dataset subpixel analysis, few methods are available in the literature for the extraction of appropriate endmembers in spectral unmixing. Most approaches have been designed from a spectroscopic viewpoint and, thus, tend to neglect the existing spatial correlation between pixels. This paper presents a new automated method that performs unsupervised pixel purity determination and endmember extraction from multidimensional datasets; this is achieved by using both spatial and spectral information in a combined manner. The method is based on mathematical morphology, a classic image processing technique that can be applied to the spectral domain while being able to keep its spatial characteristics. The proposed methodology is evaluated through a specifically designed framework that uses both simulated and real hyperspectral data.
Clinical experience with rhenium-186-labeled monoclonal antibodies for radioimmunotherapy: results of phase I trials. (1992)

Rhenium is a radionuclide with physical and chemical properties suitable for radioimmunotherapy. Two Phase I trials were carried out using 186Re-labeled murine monoclonal antibodies. Patients with refractory metastatic epithelial carcinoma received single doses of either 186Re-labeled intact NR-LU-10, a pancarcinoma antibody, 25-120 mCi/m2 (n = 15) or 186Re-labeled F(ab')2 fragment of NR-CO-02, an anti-CEA variant antibody, 25-200 mCi/m2 (n = 31). Prior to radioimmunotherapy, tumor localization of antibody was confirmed by 99mTc-labeled NR-LU-10 Fab or 99mTc-labeled NR-CO-02 F(ab')2 imaging. Dose-limiting myelosuppression was observed at 120 mCi/m2 following 186Re-NR-LU-10 intact antibody and at 150 mCi/m2 following NR-CO-02 F(ab')2 fragment in heavily pretreated patients. In patients with minimal prior therapy, a maximum tolerated dose for NR-CO-02 F(ab')2 was not reached by 200 mCi/m2. Non-marrow toxicity was minimal. Human anti-mouse antibody developed in all patients receiving intact NR-LU-10, and in 86% patients receiving F(ab')2 NR-CO-02. One patient treated with 186Re NR-CO-02 achieved a partial response. We conclude that 186Re-labeled antibody can be safely administered with significant toxicity limited to marrow.
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs (2004)

The factors regulating the expression of microRNAs (miRNAs), a ubiquitous family of approximately 22-nt noncoding regulatory RNAs, remain undefined. However, it is known that miRNAs are first transcribed as a largely unstructured precursor, termed a primary miRNA (pri-miRNA), which is sequentially processed in the nucleus, to give the approximately 65-nt pre-miRNA hairpin intermediate, and then in the cytoplasm, to give the mature miRNA. Here we have sought to identify the RNA polymerase responsible for miRNA transcription and to define the structure of a full-length human miRNA. We show that the pri-miRNA precursors for nine human miRNAs are both capped and polyadenylated and report the sequence of the full-length, approximately 3433-nt pri-miR-21 RNA. This pri-miR-21 gene sequence is flanked 5' by a promoter element able to transcribe heterologous mRNAs and 3' by a consensus polyadenylation sequence. Nuclear processing of pri-miRNAs was found to be efficient, thus largely preventing the nuclear export of full-length pri-miRNAs. Nevertheless, an intact miRNA stem-loop precursor located in the 3' UTR of a protein coding gene only moderately inhibited expression of the linked open reading frame, probably because the 3' truncated mRNA could still be exported and expressed. Together, these data show that human pri-miRNAs are not only structurally similar to mRNAs but can, in fact, function both as pri-miRNAs and mRNAs.
Lignins as macromonomers for polyurethane synthesis: A comparative study on hydroxyl group determination (2008)

Abstract The hydroxyl group contents of four technical lignins [Indulin AT (Meadwestvaco), Alcell (Repap), Curan 27‐11P (Borregaard LignoTech), and Sarkanda (Granit SA)] were investigated in view of their valorization as polyols in polyurethane synthesis. The different hydroxyl group contents were determined by the following methods: titration and 1 H‐NMR, 13 C‐NMR, and 31 P‐NMR spectroscopy. The titration method chosen was on the basis of a standard method commonly used to characterize commercial polyols for polyurethanes synthesis. The values of the total and phenolic hydroxyl contents determined by the different techniques were found to be in good agreement. For the total hydroxyl contents, coefficients of variation of 5.6% (Alcell), 3.2% (Indulin AT), 2.3% (Sarkanda), and 6.2% (Curan 27‐11P) were established. For the phenolic hydroxyl contents, a good correlation was observed between data obtained from 31 P‐NMR and 13 C‐NMR for all lignin samples, except for the Sarkanda lignin, for which a relatively high coefficient of variation (12.6%) was found. For softwood lignins (Indulin AT and Curan 27‐11P), the phenolic hydroxyl content determined by 1 H‐NMR was always lower than that deduced from 31 P‐NMR and 13 C‐NMR spectroscopy. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
The cysteine-rich region of respiratory syncytial virus attachment protein inhibits innate immunity elicited by the virus and endotoxin (2005)

The attachment protein (glycoprotein) of respiratory syncytial virus (RSV) has long been associated with disease potentiation and respiratory symptoms. The glycoprotein has a conserved cysteine-rich region (GCRR) whose function is unknown and which is not necessary for efficient viral replication. In this report, we show that the GCRR is a powerful inhibitor of the innate immune response against RSV, and that early secretion of glycoprotein is critical to modulate inflammation after RSV infection. Importantly, the GCRR is also a potent inhibitor of cytokine production mediated by several TLR agonists, indicating that this peptide sequence displays broad antiinflammatory properties. These findings have important implications for RSV pathogenesis and describe an inhibitor of TLR-mediated inflammatory responses that could have clinical applications.
The α 1 (VIII) collagen gene is homologous to the α 1 (X) collagen gene and contains a large exon encoding the entire triple helical and carboxyl-terminal non-triple helical domains of the α 1 (VIII) polypeptide (1991)

We recently cloned and sequenced alpha 1 (VIII) collagen cDNAs and demonstrated that type VIII collagen is a short-chain collagen that contains both triple helical and carboxyl-terminal non-triple helical domains similar to those of type X collagen (Yamaguchi, N., Benya, P., van der Rest, M., and Ninomiya, Y. (1989) J. Biol. Chem. 264, 16022-16029). We report here on the structural organization of the gene encoding the rabbit alpha 1 (VIII) collagen chain. The alpha 1 (VIII) gene contains four exons, whose sizes are 69, 120, 331, and 2278 base pairs. The first and second exons encode only 5'-untranslated sequences, whereas the third exon codes for a very short (3 nucleotides) stretch of 5'-untranslated sequence, the signal peptide, and almost the entire amino-terminal non-triple helical (NC2) domain (109 1/3 codons). Interestingly, the last exon encodes the rest of the translated region, including 7 2/3 codons of the NC2 domains, the complete triple helical domain (COL1, 454 amino acid residues), the entire carboxyl-terminal non-triple helical domain (NC1, 173 amino acid residues), and the 3'-untranslated region. This exon-intron structure is in stark contrast to the multi-exon structure of the fibrillar collagen (types I, II, III, V, and XI) genes, but it is remarkably similar to that of the type X collagen gene (LuValle, P., Ninomiya, Y., Rosenblum, N. D., and Olsen, B. R. (1988) J. Biol. Chem. 263, 18278-18385). The data suggest that the alpha 1 (VIII) and the alpha 1 (X) genes belong to the same subclass within the collagen family and that they arose from a common evolutionary precursor.
Thiocarbonylthio end group removal from RAFT‐synthesized polymers by a radical‐induced process (2009)

Abstract The removal of thiocarbonylthio end groups by radical‐addition‐fragmentation‐ coupling from polymers synthesized by RAFT polymerization has been studied. We found that a method, which involves heating the polymer with a large excess (20 molar equivalents) of azobis(isobutyronitrile) (AIBN), while successful with methacrylic polymers, is less effective with styrenic or acrylic polymers and provides only partial end group removal. This is attributed to the propagating radicals generated from the latter polymers being poor radical leaving groups relative to the cyanoisopropyl radical. Similar use of lauroyl peroxide (LPO) completely removes the thiocarbonylthio groups from styrenic or acrylic polymers but, even with LPO in large excess, produces a polymer with a bimodal molecular weight distribution. The formation of a peak of double molecular weight is indicative of the occurrence of self‐termination and ineffective radical trapping. We now report that by use of a combination of LPO (2 molar equivalents) and AIBN (20 molar equivalents) we are able to completely remove thiocarbonylthio end groups of styrenic or acrylic polymers and minimize the occurrence of self termination. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6704–6714, 2009