gebhart/patrepeval huggingface dataset:
Blocking and isolation of a calcium channel from neurons in mammals and cephalopods utilizing a toxin fraction (FTX) from funnel-web spider poison. (1989)

A Ca2+-channel blocker derived from funnel-web spider toxin (FTX) has made it possible to define and study the ionic channels responsible for the Ca2+ conductance in mammalian Purkinje cell neurons and the preterminal in squid giant synapse. In cerebellar slices, FTX blocked Ca2+-dependent spikes in Purkinje cells, reduced the spike afterpotential hyperpolarization, and increased the Na+-dependent plateau potential. In the squid giant synapse, FTX blocked synaptic transmission without affecting the presynaptic action potential. Presynaptic voltage-clamp results show blockage of the inward Ca2+ current and of transmitter release. FTX was used to isolate channels from cerebellum and squid optic lobe. The isolated product was incorporated into black lipid membranes and was analyzed by using patch-clamp techniques. The channel from cerebellum exhibited a 10- to 12-pS conductance in 80 mM Ba2+ and 5-8 pS in 100 mM Ca2+ with voltage-dependent open probabilities and kinetics. High Ba2+ concentrations at the cytoplasmic side of the channel increased the average open time from 1 to 3 msec to more than 1 sec. A similar channel was also isolated from squid optic lobe. However, its conductance was higher in Ba2+, and the maximum opening probability was about half of that derived from cerebellar tissue and also was sensitive to high cytoplasmic Ba2+. Both channels were blocked by FTX, Cd2+, and Co2+ but were not blocked by omega-conotoxin or dihydropyridines. These results suggest that one of the main Ca2+ conductances in mammalian neurons and in the squid preterminal represents the activation of a previously undefined class of Ca2+ channel. We propose that it be termed the "P" channel, as it was first described in Purkinje cells.
Automatic wrappers for large scale web extraction (2011)

We present a generic framework to make wrapper induction algorithms tolerant to noise in the training data. This enables us to learn wrappers in a completely unsupervised manner from automatically and cheaply obtained noisy training data, e.g., using dictionaries and regular expressions. By removing the site-level supervision that wrapper-based techniques require, we are able to perform information extraction at web-scale, with accuracy unattained with existing unsupervised extraction techniques. Our system is used in production at Yahoo! and powers live applications.
Identification of Components of Osage Orange Fruit (Maclura pomifera) and Their Repellency to German Cockroaches (2002)

Abstract The fruit of the Osage orange tree (Maclura pomifera (Raf.) Schnied.) was extracted by several methods: solid phase microextraction (SPME) volatile trapping of the headspace, solvent extraction with hexane, soxhlet extraction with hexane or methylene chloride and steam distillation. The isolates from each technique were subjected to GC/MS to compare extract components. Ripe and unripe fruits were compared using SPME. Several compounds of terpenoid structure, mostly sesquiterpenoids, were determined as present in the isolates. Among these were elemol/hedycaryol, α-copaene, α-cubebene, δ-cadinene, β-elemene, β-caryophyllene, α-ylangene/valencene, (Z,E)-farnesol and the green volatile hexyl hexanoate. The behavioral response of German cockroaches [Blattella germanica (L.)] to the oil and extracts was examined in a choice arena, and the extracts were found to be repellent. Individual compounds, including the isoflavones osajin and pomiferin, were purchased or isolated and tested directly, and several were found to be repellent to the cockroaches. Key Word Index: Madura pomifera MoraceaeOsage orangeessential oil compositionextract compositionheadspace analysiselemol/hedycaryolα-cubebeneγ-cadineneβ-elemene(Z,E)-farnesolhexyl hexanoateosajinpomiferin Blattella germanica cockroach repellency
3D graphics processor chip set (1995)

Increasingly, 3D graphics is becoming the rule rather than the exception in applications such as games, CAD/CAM, and video production. Some LSIs provide rendering capabilities, but require an additional CPU to perform essential geometry transformations. Fujitsu's chip set solves that problem using two processors to render 300,000 polygons per second (for flat-shaded triangles with texture)-performance comparable to that of advanced game machines.
Efficient parallel global garbage collection on massively parallel computers (1994)

On distributed-memory high-performance massively parallel computers (MPPs) where processors are interconnected by an asynchronous network, efficient garbage collection (GC) becomes difficult, due to inter-node references and references within pending, unprocessed messages. Our parallel global GC algorithm (1) takes advantage of reference locality, (2) efficiently traverses references over nodes, (3) admits a minimum pause time for the ongoing computations, and (4) has been shown to scale up to 1024-node MPPs. The algorithm employs a global weight counting scheme to substantially reduce message traffic. Two methods for confirming the arrival of pending messages are used: one counts the number of messages and the other uses network 'bulldozing'. Performance evaluations in actual implementations on a multicomputer with from 32 to 1024 nodes, the Fujitsu AP1000, reveals various favorable properties of the algorithm. >
Somatic mutation of fibroblast growth factor receptor‐3 (FGFR3) defines a distinct morphological subtype of high‐grade urothelial carcinoma (2011)

FGFR3 mutations are common in low-grade urothelial carcinoma and represent a potential therapeutic target in this disease. Their incidence and functional role in high-grade urothelial carcinoma (HGUC), which displays an increased propensity for recurrence and muscularis propria invasion, is less well defined. We developed a mass spectrometry-based genotyping assay to define the incidence of FGFR3 mutations in a large clinically annotated set of urothelial carcinomas. FGFR3 mutations were found in 17% of HGUC versus 84% of low-grade lesions. Retrospective pathological review of the class of FGFR3 mutant HGUC revealed unique histological features, characterized by a bulky, exophytic component with branching papillary architecture as well as irregular nuclei with a koilocytoid appearance. The predictive value of this histological appearance was confirmed using a prospective set of 49 additional HGUCs. Prospective histological review was able to correctly predict for the presence of an FGFR3 mutation in 13/24 HGUC specimens that exhibited the distinct morphology (54%). All 25 specimens lacking the defined histological features were FGFR3 wild-type for a negative predictive value of 100%. Macrodissection of individual tumours confirmed the presence of the FGFR3 mutant allele in non-invasive and invasive, low and high-grade regions of individual tumours and in the lymph node metastases of patients whose tumours possessed the characteristic morphological signature, suggesting that FGFR3 mutations are not restricted to the more clinically indolent regions of HGUCs. These data suggest that histological screening of HGUCs followed by confirmatory genotyping can be used to enrich for the population of HGUCs most likely to harbour activating mutations in the FGFR-3 receptor tyrosine kinase. Histological review could thus aid in the development of targeted inhibitors of FGFR-3 by facilitating the identification of the subset of patients most likely to harbour activating mutations in the FGFR3 gene.
Substituted imidazo[2,1-b]thiazoles from 2-aminothiazoles and α-bromo ketones: efficient preparation and proof of structure (1989)

The salts formed from α-aminothiazoles and α-bromo ketones (RCOCH2Br) have been basified, and the products converted into amides. Examination of the amides established that they are 2-acylimino-2,3-dihydrothiazoles rather than 2-acylaminothiazoles. Thus the α-bromo ketones attack the endo-N of the 2-aminothiazoles, and the imidazo[2,1-b]thiazoles obtained by cyclising the salts have the substituent (R) of the bromo ketone at position 6. Efficient procedures have been developed for preparing a range of imidazo[2,1-b]thiazoles.Related reactions of 2-aminothiazoles, with an α-bromo aldehyde and with ethyl bromoacetate, have been studied.
Patterns of disease progression in type 2 and 3 SMA: Implications for clinical trials (2015)

The aim of the study was to establish 12-month changes in the Hammersmith Functional motor scale in a large cohort of SMA patients, to identify patterns of disease progression and the effect of different variables. 268 patients were included in this multicentric study. Their age ranged between 2.5 and 55.5 years at baseline, 68 were ambulant and 200 non-ambulant. The baseline scores ranged between 0 and 66 (mean 23.91, SD 20.09). The 12-month change was between -14 and +9 (mean -0.56, SD 2.72). Of the 268 patients, 206 (76.86%) had changes between -2 and +2 points. Ambulant and non-ambulant subjects had a different relationship between baseline values and age (p for age X ambulation interaction = 0.007). There was no association with age in ambulant subjects, while there was a significant heterogeneity at different age for non-ambulant patients (p < 0.001). The 12-month change (adjusted for baseline) was not associated with age in ambulant patients (p = 0.34), but it was significantly different among various age groups in non-ambulant patients. Our results suggest that there are different profiles of progression in ambulant and non-ambulant patients, and that age may play an important role in the progression of non-ambulant patients.
Fiber Bragg Gratings Written Through a Fiber Coating (1997)

Mass production of fiber gratings has been limited by the time-consuming steps of stripping and recoating of the grating section [1].
Targeting Stat3 with G-Quartet Oligodeoxynucleotides in Human Cancer Cells (2003)

Stat3 is an oncogene that is activated in many human cancer cells. Genetic approaches that disrupt Stat3 activity result in inhibition of cancer cell growth and enhanced cell apoptosis supporting the development of novel drugs targeting Stat3 for cancer therapy. G-quartet oligodeoxynucleotides (ODNs) were demonstrated to be potent inhibitors of Stat3 DNA binding activity in vitro with the G-quartet ODN, T40214, having an IC(50) of 7 microM. Computer-simulated docking studies indicated that G-quartet ODNs mainly interacted with the SH2 domain of Stat3 and were capable of inserting between the SH2 domains of Stat3 dimers bound to DNA. We demonstrated that the G-rich ODN T40214, which forms a G-quartet structure at intracellular but not extracellular K+ ion concentrations, is delivered efficiently into the cytoplasm and nucleus of cancer cells where it inhibited IL-6-stimulated Stat3 activation and suppressed Stat3-mediated upregulation of bcl-x and mcl-1 gene expression. Thus, G-quartet represents a new class of drug for targeting of Stat3 within cancer cells.
Circular dichroism of nucleoside derivatives. IX. Vicinal effects on the circular dichroism of pyrimidine nucleosides (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCircular dichroism of nucleoside derivatives. IX. Vicinal effects on the circular dichroism of pyrimidine nucleosidesDaniel W. Miles, Warren H. Inskeep, Morris J. Robins, Michael W. Winkley, Roland K. Robins, and Henry EyringCite this: J. Am. Chem. Soc. 1970, 92, 13, 3872–3881Publication Date (Print):July 1, 1970Publication History Published online1 May 2002Published inissue 1 July 1970https://pubs.acs.org/doi/10.1021/ja00716a007https://doi.org/10.1021/ja00716a007research-articleACS PublicationsRequest reuse permissionsArticle Views171Altmetric-Citations67LEARN 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
RcsB-BglJ-mediated activation of Cascade operon does not induce the maturation of CRISPR RNAs inE. coliK12 (2013)

Prokaryotic immunity against foreign nucleic acids mediated by clustered, regularly interspaced, short palindromic repeats (CRISPR) depends on the expression of the CRISPR-associated (Cas) proteins and the formation of small CRISPR RNAs (crRNAs). The crRNA-loaded Cas ribonucleoprotein complexes convey the specific recognition and inactivation of target nucleic acids. In E. coli K12, the maturation of crRNAs and the interference with target DNA is performed by the Cascade complex. The transcription of the Cascade operon is tightly repressed through H-NS-dependent inhibition of the Pcas promoter. Elevated levels of the LysR-type regulator LeuO induce the Pcas promoter and concomitantly activate the CRISPR-mediated immunity against phages. Here, we show that the Pcas promoter can also be induced by constitutive expression of the regulator BglJ. This activation is LeuO-dependent as heterodimers of BglJ and RcsB activate leuO transcription. Each transcription factor, LeuO or BglJ, induced the transcription of the Cascade genes to comparable amounts. However, the maturation of the crRNAs was activated in LeuO but not in BglJ-expressing cells. Studies on CRISPR promoter activities, transcript stabilities, crRNA processing and Cascade protein levels were performed to answer the question why crRNA maturation is defective in BglJ-expressing cells. Our results demonstrate that the activation of Cascade gene transcription is necessary but not sufficient to turn on the CRISPR-mediated immunity and suggest a more complex regulation of the type I-E CRISPR-Cas system in E. coli.
Direct Measurement of Hydrodynamic Cross Correlations between Two Particles in an External Potential (1999)

We report a direct measurement of the hydrodynamic interaction between two colloidal particles. Two micron-sized latex beads were held at varying distances in optical tweezers while their Brownian displacements were measured. In spite of the fact that fluid systems at low Reynolds number are generally considered to have no ``memory,'' the cross-correlation function of the bead positions shows a pronounced, time-delayed anticorrelation. We show that the anticorrelations can be understood in terms of the standard Oseen tensor hydrodynamic coupling.
BRCA1 regulates human mammary stem/progenitor cell fate (2008)

Although it is well established that women with germ-line mutations in the BRCA1 gene have a greatly increased lifetime incidence of breast and ovarian cancer, the molecular mechanisms responsible for this tissue-specific carcinogenesis remain undefined. The majority of these breast cancers are of the basal-like phenotype characterized by lack of expression of ER, PR, and ERBB2. Because this phenotype has been proposed to resemble that of normal breast stem cells, we examined the role of BRCA1 in human mammary stem cell fate. Using both in vitro systems and a humanized NOD/SCID mouse model, we demonstrate that BRCA1 expression is required for the differentiation of ER-negative stem/progenitor cells to ER-positive luminal cells. Knockdown of BRCA1 in primary breast epithelial cells leads to an increase in cells displaying the stem/progenitor cell marker ALDH1 and a decrease in cells expressing luminal epithelial markers and estrogen receptor. In breast tissues from women with germ-line BRCA1 mutations, but not normal controls, we detect entire lobules that, although histologically normal, are positive for ALDH1 expression but are negative for the expression of ER. Loss of heterozygosity for BRCA1 was documented in these ALDH1-positive lobules but not in adjacent ALDH1-negative lobules. Taken together, these studies demonstrate that BRCA1 plays a critical role in the differentiation of ER-negative stem/progenitor cells to ER-positive luminal cells. Because BRCA1 also plays a role in DNA repair, our work suggests that loss of BRCA1 may result in the accumulation of genetically unstable breast stem cells, providing prime targets for further carcinogenic events.
Evidence Regarding the UV Sunscreen Role of a Mycosporine-Like Compound in the Cyanobacterium Gloeocapsa sp (1993)

The UV sunscreen role commonly ascribed to mycosporine-like amino acids (MAAs) was investigated with an isolate of the terrestrial cyanobacterium Gloeocapsa sp. strain C-90-Cal-G.(2), which accumulates intracellularly an MAA with absorbance maximum at 326 nm but produces no extracellular sunscreen compound (i.e., scytonemin). The intracellular concentrations of MAA achieved were directly related to the intensity of the UV radiation (maximum at 320 nm) received by the cells. However, the presence of high concentrations of MAA was not necessary for the physiological acclimation of the cultures to UV radiation. The measured sunscreen factor due to MAA in single cells was 0.3 (the MAA prevented 3 out of 10 photons from hitting potential cytoplasmic targets). High contents of MAA in the cells correlated with increased resistance to UV radiation. However, when resistance was gauged under conditions of desiccation, with inoperative physiological photoprotective and repair mechanisms, cells with high MAA specific contents were only 20 to 25% more resistant. Although UV radiation centered around both 320 and 365 nm resulted in chlorophyll a photobleaching and photoinhibition of photosynthesis, the difference in sensitivity correlated with MAA accumulation occurred only at 320 nm (absorbed by MAA) and not at 365 nm (not absorbed by MAA). This difference represents the maximal protection ascribable to the presence of MAA for single cells, i.e., if one does not consider the enhancing effects of colony formation on protection by sunscreens.
Bovine enterovirus as an oncolytic virus: Foetal calf serum facilitates its infection of human cells (2002)

Many viruses have been investigated for their oncolytic properties and potential use as therapeutic agents for cancer treatment. Most of these replication-competent viruses are human pathogens. We investigated the oncolytic properties of an animal virus which is non pathogenic for both its natural host and humans. Bovine enterovirus has previously been shown to exhibit a very wide tissue tropism for cell types in vitro. We compare the ability of bovine enterovirus to replicate in and to cause cytopathic effect in freshly isolated human monocytes and monocyte derived macrophages with the monocyte-like U937 tumour cell line. We also include the adherent ZR-75-1 human breast cancer cell line. We have also carried out infections of bovine enterovirus in the presence and in the absence of serum of bovine origin. Our study shows that the virus will replicate in and produce cytopathic effect in the U937 and ZR-75-1 cell types to the same extent as the cells (BHK-21) in which the virus is routinely propagated. We believe bovine enterovirus to be a worthwhile candidate for further study as an anti-tumour agent.
Identification of Transcripts Initiated from an Internal Promoter in the c-erbAα Locus That Encode Inhibitors of Retinoic Acid Receptor-α and Triiodothyronine Receptor Activities (1997)

The thyroid hormone receptor-coding locus, c-erbA alpha, generates several mRNAs originating from a single primary transcript that undergoes alternative splicing. We have identified for the first time two new transcripts, called TRdelta alpha1 and TRdelta alpha2 [mRNA for isoform alpha1 and alpha2 of the T3 receptor (TR), respectively], whose transcription is initiated from an internal promoter located within intron 7 of the c-erbA alpha gene. These two new transcripts exhibit tissue-specific patterns of expression in the mouse. These two patterns are in sharp contrast with the expression patterns of the full-length transcripts generated from the c-erbA alpha locus. TR alpha1 and TRdelta alpha2 mRNAs encode N-terminally truncated isoforms of T3R alpha1 and T3R alpha2, respectively. The protein product of TRdelta alpha1 antagonizes the transcriptional activation elicited by T3 and retinoic acid. This protein inhibits the ligand-induced activating functions of T3R alpha1 and 9-cis-retinoic acid receptor-alpha but does not affect the retinoic acid-dependent activating function of retinoic acid receptor-alpha. We predict that these truncated proteins may work as down-regulators of transcriptional activity of nuclear hormone receptors in vivo.
The physiology and biochemistry of the proteolytic system in lactic acid bacteria (1993)

The inability of lactic acid bacteria to synthesize many of the amino acids required for protein synthesis necessitates the active functioning of a proteolytic system in those environments where protein constitutes the main nitrogen source. Biochemical and genetic analysis of the pathway by which exogenous proteins supply essential amino acids for growth has been one of the most actively investigated aspects of the metabolism of lactic acid bacteria especially in those species which are of importance in the dairy industry, such as the lactococci. Much information has now been accumulated on individual components of the proteolytic pathway in lactococci, namely, the cell envelope proteinase(s), a range of peptidases and the amino acid and peptide transport systems of the cell membrane. Possible models of the proteolytic system in lactococci can be proposed but there are still many unresolved questions concerning the operation of the pathway in vivo. This review will examine current knowledge and outstanding problems regarding the proteolytic system in lactococci and also the extent to which the lactococcal system provides a model for understanding proteolysis in other groups of lactic acid bacteria.
Global impact of Vibrio cholerae interactions with chitin (2008)

The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria-substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae-chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease.