gebhart/patrepeval huggingface dataset:
Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene (1992)

An open reading frame partially overlaps pvuIIR, and genetic evidence implies that this open reading frame, named pvuIIC, specifies a positive regulator of pvuIIR (T. Tao, J. C. Bourne, and R. M. Blumenthal, J. Bacteriol. 173:1367-1375, 1991). Inducible constructs of pvuIIC produced a protein of the expected size. The site of C.PvuII action appears to lie within pvuIIC itself; thus, pvuIIC may be a self-contained regulatory cassette.
The Lysyl Oxidase LOX Is Absent in Basal and Squamous Cell Carcinomas and Its Knockdown Induces an Invading Phenotype in a Skin Equivalent Model (2006)

Lysyl oxidase initiates the enzymatic stage of collagen and elastin cross-linking. Among five isoforms comprising the lysyl oxidase family, LOX is the better studied. LOX is associated to an antitumor activity in ras-transformed fibroblasts, and its expression is down-regulated in many carcinomas. The aim of this work was to shed light on LOX functions within the epidermis by studying its expression in human basal and squamous cell carcinomas and analyzing the effect of its enzymatic activity inhibition and protein absence on human keratinocytes behavior in a skin equivalent. In both carcinomas, LOX expression by epidermal tumor cells was lacking, while it was up-regulated around invading tumor cells in association with the stromal reaction. Lysyl oxidase activity inhibition using beta-aminoproprionitrile in a skin equivalent model prepared with both primary human keratinocytes and HaCaT cell line affected keratin 10 and filaggrin expression and disorganized the collagen network and the basement membrane. In spite of all these changes, no invasion phenotype was observed. Modelization of the invasive phenotype was only noticed in the skin equivalent developed with LOX antisense HaCaT cell line, where the protein LOX is specifically absent. Our results clearly indicate that lysyl oxidase enzymatic activity is essential not only for the integrity maintenance of the dermis but also for the homeostasis of the epidermis. Moreover, LOX protein plays a role in the skin carcinomas and invasion but not through its enzymatic activity.
Tunable, Temperature‐Responsive Polynorbornenes with Side Chains Based on an Elastin Peptide Sequence (2009)

Live on: Random copolymers made by living ring-opening metathesis polymerization of norbornene monomers containing either the elastin peptide sequence -(VPGVG)- or pentaethylene glycol (see scheme; Mes=mesityl, pyr=pyridine) exhibit a lower critical solution temperature (LCST). The LCST can be easily modified by varying the ratio of the co-monomers in the polymer feed. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A NEUROCOMPUTATIONAL PERSPECTIVE - THE NATURE OF MIND AND THE STRUCTURE OF SCIENCE - CHURCHLAND,PM (1992)

906-908
A Defect-Tolerant Computer Architecture: Opportunities for Nanotechnology (1998)

Teramac is a massively parallel experimental computer built at Hewlett-Packard Laboratories to investigate a wide range of different computational architectures. This machine contains about 220,000 hardware defects, any one of which could prove fatal to a conventional computer, and yet it operated 100 times faster than a high-end single-processor workstation for some of its configurations. The defect-tolerant architecture of Teramac, which incorporates a high communication bandwith that enables it to easily route around defects, has significant implications for any future nanometer-scale computational paradigm. It may be feasible to chemically synthesize individual electronic components with less than a 100 percent yield, assemble them into systems with appreciable uncertainty in their connectivity, and still create a powerful and reliable data communications network. Future nanoscale computers may consist of extremely large-configuration memories that are programmed for specific tasks by a tutor that locates and tags the defects in the system.
Restrictions of the Mini-Mental State Examination in acute stroke (2005)

While the Mini-Mental State Examination (MMSE) was originally developed to screen for dementia and delirium, many neurologists use this measure as a screening instrument for 'cognitive impairment' in hospitalized stroke patients. However, the validity of the MMSE as such has never been evaluated in acute stroke. We administered the MMSE in addition to a neuropsychological examination covering six cognitive domains to 34 stroke patients (mean interval between stroke and examination, 6.5+/-2.9 days) and 34 healthy controls. The area under the receiver operating characteristic curve (AUC) was calculated in addition to the sensitivity and specificity for various cut-off points on the MMSE. Seventy percent of the patients were impaired in at least one cognitive domain. The accuracy of the MMSE in detecting cognitive impairment was no better than chance (AUC = 0.67; p = 0.13). No optimum MMSE cut-off value could be identified. The MMSE is particularly insensitive to impairments in abstract reasoning, executive functioning, and visual perception/construction.
Arabinose-derived bicyclic amino acids: synthesis, conformational analysis and construction of an αvβ3-selective RGD peptide (2002)

The synthesis, NMR structure determination, and molecular modelling of the conformationally restricted diastereomeric sugar azido acids 1 and 2 are presented. The bicyclic structures of these compounds are obtained through a iodocyclization reaction on the C-allyl glycoside of the D-arabinofuranose. Cyclic tetrapeptide 11 containing the amino acid derived from 1 linked to the RGD sequence has been synthesized; this compound was found to be a selective antagonist of αvβ3 integrins expressed on GM 7373 cells.
Genetic Transformation of Yeast (2001)

Genetic transformation was first described by Griffith in 1928 and has since been demonstrated in a variety of organisms, including many species of fungi. This review focuses on the history and technology of the transformation of Saccharomyces cerevisiae. The application of protocols developed for S. cerevisiae to other important yeast species is discussed. The protocols for transformation by spheroplasting, LiAc/ssDNA/PEG, and electroporation are compared, and possible mechanisms for transformation are discussed.
Two beta‐alanyl‐CoA:ammonia lyases in Clostridium propionicum (2005)

The fermentation of beta-alanine by Clostridium propionicum proceeds via activation to the CoA-thiol ester, followed by deamination to acryloyl-CoA, which is also an intermediate in the fermentation of l-alanine. By shifting the organism from the carbon and energy source alpha-alanine to beta-alanine, the enzyme beta-alanyl-CoA:ammonia lyase is induced 300-fold (approximately 30% of the soluble protein). The low basal lyase activity is encoded by the acl1 gene, whereas the almost identical acl2 gene (six amino acid substitutions) is responsible for the high activity after growth on beta-alanine. The deduced beta-alanyl-CoA:ammonia lyase proteins are related to putative beta-aminobutyryl-CoA ammonia lyases involved in lysine fermentation and found in the genomes of several anaerobic bacteria. beta-Alanyl-CoA:ammonia lyase 2 was purified to homogeneity and characterized as a heteropentamer composed of 16 kDa subunits. The apparent K(m) value for acryloyl-CoA was measured as 23 +/- 4 microm, independent of the concentration of the second substrate ammonia; k(cat)/K(m) was calculated as 10(7) m(-1) x s(-1). The apparent K(m) for ammonia was much higher, 70 +/- 5 mm at 150 microm acryloyl-CoA with a much lower k(cat)/K(m) of 4 x 10(3) m(-1) x s(-1). In the reverse reaction, a K(m) of 210 +/- 30 microM was obtained for beta-alanyl-CoA. The elimination of ammonia was inhibited by 70% at 100 mm ammonium chloride. The content of beta-alanyl-CoA:ammonia lyase in beta-alanine grown cells is about 100 times higher than that required to sustain the growth rate of the organism. It is therefore suggested that the enzyme is needed to bind acryloyl-CoA, in order to keep the toxic free form at a very low level. A formula was derived for the calculation of isomerization equilibra between L-alanine/beta-alanine or D-lactate/3-hydroxypropionate.
Predicting the semantic orientation of adjectives (1997)

We identify and validate from a large corpus constraints from conjunctions on the positive or negative semantic orientation of the conjoined adjectives. A log-linear regression model uses these constraints to predict whether conjoined adjectives are of same or different orientations, achieving 82% accuracy in this task when each conjunction is considered independently. Combining the constraints across many adjectives, a clustering algorithm separates the adjectives into groups of different orientations, and finally, adjectives are labeled positive or negative. Evaluations on real data and simulation experiments indicate high levels of performance: classification precision is more than 90% for adjectives that occur in a modest number of conjunctions in the corpus.
Classifier fusion for outdoor obstacle detection (2004)

This work describes an approach for using several levels of data fusion in the domain of autonomous off-road navigation. We are focusing on outdoor obstacle detection, and we present techniques that leverage on data fusion and machine learning for increasing the reliability of obstacle detection systems. We are combining color and infrared (IR) imagery with range information from a laser range finder. We show that in addition to fusing data at the pixel level, performing high level classifier fusion is beneficial in our domain. Our general approach is to use machine learning techniques for automatically deriving effective models of the classes of interest (obstacle and non-obstacle for example). We train classifiers on different subsets of the features we extract from our sensor suite and show how different classifier fusion schemes can be applied for obtaining a multiple classifier system that is more robust than any of the classifiers presented as input. We present experimental results we obtained on data collected with both the experimental unmanned vehicle (XUV) and a CMU developed robotic tractor.
Synthesis of Biocompatible PEG-Based Star Polymers with Cationic and Degradable Core for siRNA Delivery (2011)

Star polymers with poly(ethylene glycol) (PEG) arms and a degradable cationic core were synthesized by the atom transfer radical copolymerization (ATRP) of poly(ethylene glycol) methyl ether methacrylate macromonomer (PEGMA), 2-(dimethylamino)ethyl methacrylate (DMAEMA), and a disulfide dimethacrylate (cross-linker, SS) via an "arm-first" approach. The star polymers had a diameter ~15 nm and were degraded under redox conditions by glutathione treatment into individual polymeric chains due to cleavage of the disulfide cross-linker, as confirmed by dynamic light scattering. The star polymers were cultured with mouse calvarial preosteoblast-like cells, embryonic day 1, subclone 4 (MC3T3-E1.4) to determine biocompatibility. Data suggest star polymers were biocompatible, with ≥ 80% cell viability after 48 h of incubation even at high concentration (800 μg/mL). Zeta potential values varied with N/P ratio confirming complexation with siRNA. Successful cellular uptake of the star polymers in MC3T3-E1.4 cells was observed by confocal microscopy and flow cytometry after 24 h of incubation.
Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes (2011)

All in all, we show that BMP signaling has a remarkable effect on gene transcription in breast cancer cells and that the functions affected follow a logical temporal pattern. Our results also uncover components of the common cellular transcriptional response to BMP4 and BMP7. Most importantly, this study provides a list of potential novel BMP target genes relevant in breast cancer.
Deciphering the mystery of thalidomide teratogenicity (2011)

Thalidomide was originally developed in 1954 as a sedative that was commonly used to ameliorate morning sickness. However, thalidomide exposure during the first trimester of pregnancy caused multiple birth defects (e.g. phocomelia and amelia), affecting ≈ 10,000 children worldwide in the late 1950s and early 1960s. Thalidomide is now recognized as a clinically effective, albeit strictly restricted, drug for the treatment of leprosy and multiple myeloma. Investigators have studied thalidomide teratogenicity for half a century, proposing over 30 hypotheses to account for its actions. Among these, the anti-angiogenesis and oxidative stress models have gained widespread support. Nonetheless, the precise molecular mechanisms and direct targets of thalidomide have not heretofore been elucidated. We developed ferrite-glycidyl methacrylate beads that enable magnetic separation and efficient purification of ligand-binding molecules; the beads were recently employed to identify cereblon as a primary target of thalidomide. Cereblon forms an E3 ubiquitin ligase complex with DDB1, Cul4A, and Roc1, which is important for the expression of fibroblast growth factor 8, an essential regulator of limb development. Expression of a drug binding-deficient mutant of cereblon suppressed thalidomide-induced effects in zebrafish and chicks. This suggests that thalidomide downregulates fibroblast growth factor 8 expression and induces limb malformation by binding to wild-type cereblon, inhibiting the function of the associated E3 ubiquitin ligase. The present review summarizes the teratogenicity of thalidomide, including existing models for its mode of action, and discusses the identification of cereblon as a key molecule for deciphering the longstanding mystery of thalidomide teratogenicity.
Proton‐ionizable crown compounds. 4. New macrocyclic polyether ligands containing a triazole subcyclic unit (1986)

Abstract A series of macrocyclic polyether (crown) ligands containing the proton‐ionizable s‐triazole subcyclic unit were prepared by reacting the 1‐THP blocked 3,5‐bis(chloromethyl)‐1 H ‐1,2,4‐triazole with various oligoethylene glycols. The starting bis(chloromethyl)triazole is a vessicant and must be used with caution. Triazolo‐18‐crown‐6 ( 5 ) formed stable complexes with barium, strontium, copper and benzylammonium cations but not with potassium or lithium. The crystal structure of 5 showed the triazole proton to be on nitrogen 3 which is outside the macroring cavity.
Seven-membered heterocycles. 9. Synthesis and properties of some 5-alkyl and 5-aryl derivatives of 1-benzothiepin (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSeven-membered heterocycles. 9. Synthesis and properties of some 5-alkyl and 5-aryl derivatives of 1-benzothiepinVincent J. Traynelis, John A. Schield, William A. Lindley, and Denis W. H. MacDowellCite this: J. Org. Chem. 1978, 43, 17, 3379–3384Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/jo00411a025https://doi.org/10.1021/jo00411a025research-articleACS PublicationsRequest reuse permissionsArticle Views160Altmetric-Citations21LEARN 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
Human interdigitating dendritic cells directly stimulate CD40‐activated naive B cells (1997)

Human interdigitating dendritic cells (IDC) were isolated from tonsils based on their CD40+ lineage-negative expression in situ. Isolated IDC displayed a phenotypic profile similar to that of IDC in tonsils and spleen in situ, characterized by high-level expression of major histocompatibility complex class II, the co-stimulatory molecules B7.1 (CD80) and B7.2 (CD86), expression of the late DC maturation marker CD83, and no expression of CD1a, CD13, or CD33. IDC also showed weak nonspecific esterase staining and had the ability to induce an allogeneic mixed lymphocyte reaction. In this study, we further show that in the presence of surrogate activated T cells in the form of CD40 ligation and IL-2, IDC enhance the proliferation of naive B cells and induce their differentiation into plasma cells producing IgM. Evidence for the anatomical co-localization of naive B cells and IDC in the T cell area together with the data obtained in vitro implies a role for IDC in the initiation of the extrafollicular reaction.
Solar optical materials for innovative window design (1983)

New and innovative optical materials and coatings can greatly improve the efficiency of window energy systems. These potential materials and coatings increase energy efficiency by reducing radiative losses in the infrared, or reducing visible reflection losses or controlling overheating due to solar gain. Current progress in heat mirror coatings for glass a polymeric substrates is presented. Highly doped semiconducting oxides and metal/dielectric interference coatings are reviewed. Physical and optical properties are outlined for antireflection films and transparent aerogel insulation media. The potential for optical switching films as window elements includes discussions of electrochromic, photochromic and other physical switching processes.
Dynamic Hydrogels: Translating a Protein Conformational Change into Macroscopic Motion (2007)

Natural inspiration: A bioinspired functional material in the form of a hydrogel created by cross-linking an engineered version of calmodulin, a protein which undergoes a conformational change in response to ligand binding (see schematic representation), with a four-armed poly(ethylene glycol) molecule terminated with acrylate groups decreased in volume by 20 % when treated with the ligand trifluoperazine. Multiple cycles of gel swelling and shrinkage were possible.
Adult stem cells (2006)

Adult tissues contain a continuum of precursor cells, ranging from very primitive stem cells to tissue‐committed progenitor cells. The very primitive stem cells have essentially an unlimited proliferation potential and will form all cell types of the body. The tissue‐committed progenitor cells have a limited proliferation potential, and are very limited in their differentiation potential. They are the immediate precursors of adult differentiated tissues. All these precursor cells are located throughout the body during the postnatal lifespan of an individual. Precursor cells can be isolated from solid tissues using mechanical disruption and/or enzymatic digestion. The cells can be cultured, cloned, cryopreserved, and characterized utilizing unique cell surface markers and differentiation potentials. We have isolated, cloned, and characterized three categories of adult‐derived stem cells: totipotent stem cells, pluripotent stem cells, and germ layer lineage‐committed stem cells. Here we report the use of a genomically‐labeled adult‐derived very primitive stem cell clone in the following models: the regeneration of cardiac tissues following myocardial infarction, the formation of dopaminergic neurons in a rat model of Parkinson’s disease, and the generation of three‐dimensional islet‐like structures that secrete species‐specific insulin after a glucose challenge. Because they are easily isolated from adults, adult‐derived stem cells are suitable for use in autologous replacement therapies and regenerative medicine. Grant sponsor: Rubye Ryle Smith Charitable Trust and MedCen Community Health Foundation.
Trivalent Gd-DOTA reagents for modification of proteins (2015)

The development of novel protein-targeted MRI contrast agents crucially depends on the ability to derivatise suitable targeting moieties with a high payload of relaxation enhancer (<i>e.g.</i>, gadolinium(iii) complexes such as Gd-DOTA), without losing affinity for the target proteins. Here, we report robust synthetic procedures for the preparation of trivalent Gd-DOTA reagents with various chemical handles for site-specific modification of biomolecules. The reagents were shown to successfully label proteins through isothiocyanate ligation or through site-specific thiol-maleimide ligation and strain-promoted azide-alkyne cycloaddition.
Development of combined HDD and recordable-DVD video recorder (2003)

A hybrid type video disk recorder, in which HDD and recordable-DVD drives are combined, was developed. The developed key technologies are such as (1) user interface suitable for simultaneous recording and playback, (2) file system suitable for automatic updating recording, and (3) wide bandwidth data buffer. The developed hybrid type video disk recorder has achieved well-balanced user-convenient features as a consumer appliance.
Synthesis, Characterization, and Photovoltaic Properties of a Low Band Gap Polymer Based on Silole-Containing Polythiophenes and 2,1,3-Benzothiadiazole (2008)

A new low band gap silole-containing conjugated polymer, PSBTBT, was designed and synthesized. Photovoltaic properties of PSBTBT were initially investigated, and an average power conversion efficiency (PCE) of 4.7% with a best PCE of 5.1% was recorded under illumination (AM 1.5G, 100 mW/cm(2)). The response range of the device covers the whole visible range from 380 to 800 nm. These results indicate that PSBTBT is a promising polymer material for applications in polymer solar cells.
A Novel Class of Phosphonate Nucleosides. 9-[(1-Phosphonomethoxycyclopropyl)methyl]guanine as a Potent and Selective Anti-HBV Agent (2004)

9-[1-(Phosphonomethoxycyclopropyl)methyl]guanine (PMCG, 1), representative of a novel class of phosphonate nucleosides, blocks HBV replication with excellent potency (EC(50) = 0.5 microM) in a primary culture of HepG2 2.2.15 cells. It exhibits no significant cytotoxicity in several human cell lines up to 1.0 mM. It does not inhibit replication of human immunodeficiency virus (HIV-1) or herpes simplex virus (HSV-1) at 30 microM. Many purine base analogues of 1 also exhibit inhibitory activity against HBV, but at 30 microM, pyrimidine analogues do not. 1 is 4 times more potent than 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA), which was used as a positive control (EC(50) = 2.0 microM). The characteristic cyclopropyl moiety at the 2'-position of 1 was prepared by titanium-mediated Kulinkovich cyclopropanation. 1 was modified to give the orally available drug candidate, PMCDG Dipivoxil (2). Compound 2 exhibited excellent efficacy when administered at 5 mg per kg per day in a study with woodchucks infected with woodchuck hepatitis B virus (WHBV). Drug candidate 2 has successfully completed phase I clinical trials and is currently undergoing phase II clinical studies for evaluation of efficacy.