gebhart/patrepeval huggingface dataset:
A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity (2007)

Here, we report a catalytic beacon sensor for uranyl (UO2(2+)) based on an in vitro-selected UO2(2+)-specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3' quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5' and 3' ends, respectively. The presence of UO2(2+) causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of approximately 230 microM. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.
Achieving confocal-point performance in confocal-line microscopy (1994)

Microscopical imaging methods, based on the confocal-line approach, offer practical advantages over confocal-point techniques, and some unique peculiarities. However, the extended illumination geometry, and the consequent spatial filtering limitations at the detection level, cause a semi-confocal performance affecting the spatial resolution. The present paper describes modifications to the confocal-line method, resulting from the introduction of an aligned-confocal-points illumination and detection approach. Firstly, with the aid of an appropriate shaping technique, the spatial distribution of the illumination beam is modified, in order to concentrate the light in a sequence of spaced spots. Secondly, a spatially matched electronic gating process is applied to the response of a linear image sensor, obtaining the equivalent of individual point detectors being positionally conjugated to the illumination spots. The coverage of the full specimen is afforded with the association of electro-mechanical scanning devices. The technique maintains the advantages present in confocal-line instrumentation, while achieving true confocal performance, typical of other point and multi-point confocal systems. The measurements reported, regarding confocal transmission imaging of thick specimens, demonstrate some of the peculiarities and the improved capabilities of the method, compared to the results obtained in conventional and confocal-line microscopies.
Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning. (1994)

Restriction landmark genomic scanning (RLGS) is a novel method which enables us to simultaneously visualize a large number of loci as two-dimensional gel spots. By this method, the status of DNA methylation can efficiently be determined by monitoring the appearance or disappearance of spots by using a methylation-sensitive restriction enzyme. In the present study, using RLGS with NotI, we examined, in comparison with a brain RLGS profile, the status of DNA methylation of more than 900 loci among three types of mouse cell lines: the embryonal carcinoma cell line P19, the stable mesenchymal cell line 10T1/2, and our established neuroepithelial (EM) cell lines. We found that the relative numbers of RLGS spots which appeared were less than 3.3% of those surveyed in all cell lines examined. However, 5 to 14% of spots disappeared, the numbers increasing with an increase in the length of the culture period, and many spots were commonly lost in 10T1/2 and in three EM cell lines. Thus, for these cell lines, many more spots disappeared than appeared. However, the numbers of spots disappearing and appearing were well balanced, and the ratio in P19 cells was almost equal to that in liver cells in vivo. These RLGS experimental observations suggested that permanent cell lines such as 10T1/2 are hypermethylated and that our newly established EM cell lines are also becoming heavily methylated at common loci. On the other hand, methylation and demethylation seem to be balanced in P19 cells in a manner similar to that in in vivo liver tissue.
Impact of Injury Location and Severity on Posttraumatic Epilepsy in the Rat: Role of Frontal Neocortex (2010)

Human posttraumatic epilepsy (PTE) is highly heterogeneous, ranging from mild remitting to progressive disabling forms. PTE results in simple partial, complex partial, and secondarily generalized seizures with a wide spectrum of durations and semiologies. PTE variability is thought to depend on the heterogeneity of head injury and patient's age, gender, and genetic background. To better understand the role of these factors, we investigated the seizures resulting from calibrated fluid percussion injury (FPI) to adolescent male Sprague-Dawley rats with video electrocorticography. We show that PTE incidence and the frequency and severity of chronic seizures depend on the location and severity of FPI. The frontal neocortex was more prone to epileptogenesis than the parietal and occipital, generating earlier, longer, and more frequent partial seizures. A prominent limbic focus developed in most animals, regardless of parameters of injury. Remarkably, even with carefully controlled injury parameters, including type, severity, and location, the duration of posttraumatic apnea and the age and gender of outbred rats, there was great subject-to-subject variability in frequency, duration, and rate of progression of seizures, indicating that other factors, likely the subjects' genetic background and physiological states, have critical roles in determining the characteristics of PTE.
Continued Cigarette Smoking by Patients Receiving Concurrent Chemoradiotherapy for Limited-Stage Small-Cell Lung Cancer Is Associated With Decreased Survival (2003)

LSCLC patients who continue to smoke during CHT/RT have poorer survival rates than those who do not. Smoking did not have an impact on the rate of treatment interruptions attributed to toxicity.
An advanced multiple channel cochlear implant (1989)

An advanced multiple channel cochlear implant hearing prosthesis is described. Stimulation is presented through an array of 20 electrodes located in the scala tympani. Any two electrodes can be configured as a bipolar pair to conduct a symmetrical, biphasic, constant-current pulsatile stimulus. Up to three stimuli can be presented in rapid succession or effectively simultaneously. For simultaneous stimulation, a novel time-division current multiplexing technique has been developed to obviate electrode interactions that may compromise safety. The stimuli are independently controllable in current amplitude, duration, and onset time. Groups of three stimuli can be generated at a rate of typically 500 Hz. Stimulus control data and power are conveyed to the implant through a single transcutaneous inductive link. The device also incorporates a telemetry system that enables electrode voltage waveforms to be monitored externally in real time. The electronics of the implant are contained almost entirely on a custom designed integrated circuit. Preliminary results obtained with the first patient to receive the advanced implant are included.
Instrumentos, iniciativas y normas relacionadas con la responsabilidad social corporativa (RSC) en el ámbito de los recursos humanos (RRHH) (2011)

Se efectua en este trabajo un analisis del concepto de Responsabilidad Social 
Corporativa (RSC) en relacion a la gestion de Recursos Humanos (RR HH). Para 
ello, en primer lugar se ponen de manifiesto algunos aspectos relacionados con este 
contexto, tales como la deslocalizacion y la consiguiente explotacion de la mano de 
obra. A continuacion, se definen seis posibles iniciativas o instrumentos de posible 
desarrollo, mencionando algunas de sus ventajas e inconvenientes, con especial 
referencia al grado de implantacion entre las empresas espanolas. Para finalizar se 
estudia la implantacion de la herramienta mas avanzada y potente en este ambito: 
la norma SA8000.
Food density estimation using fuzzy logic inference (2010)

This paper presents a novel application of fuzzy logic inference to food density estimation to support research in nutrition science. French fries are taken as an example of this new application. A fuzzy Inference System (FIS) is constructed to estimate the bulk density of French fries under different cooking conditions. Our experimental results show that our density estimation method is accurate with a mean error of 2.2%.
Antigens expressed on NIH 3T3 cells following transformation with DNA from human pancreatic tumor. (1986)

This report documents that the pancreatic adenocarcinoma cell line, HPAF, contains oncogene activity detected by transformation of NIH 3T3 cells through transfection with HPAF DNA. The HPAF transfected NIH 3T3 cells do not contain oncogenes homologous with c-H-ras, c-K-ras, c-N-ras, v-fms, c-myb, c-sis, v-fgr, c-mos, c-myc, c-fos, v-fes, v-src, v-erb A, v-erb B, c-N-myc, v-raf, or v-abl, other than the endogenous mouse genes. The transfectants do express proteins detected by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis which were not found in nontransfected NIH 3T3 cells. Monoclonal antibodies raised against the transfectants recognize proteins not found in untransfected NIH 3T3 cells that are antigenically identical to proteins found in the HPAF cells. These antigens are also detected on six other human pancreatic adenocarcinoma cell lines but show a much more restricted distribution on lymphoblastoid, melanoma, prostatic carcinoma, and normal skin fibroblast cell lines.
Recommending from content (2000)

We are conducting an ongoing experiment into the effects of various forms of recommendations on consumer behavior at a web site. In this paper, we report on measures of the usefulness and effectiveness of recommendations based on content. During a three month period, we provided recommendations on over 2000 products at an e-commerce web site. To evaluate the effectiveness of recommendations on customer behavior, we collected three sets of metrics. First, we measured the rate at which recommendations were actually viewed by visitors. Second, we analyzed the paths visitors took through the recommendations. Finally, we measured the impact of recommended items on number of items purchased and on revenue.
Crystal structure of the receptor-binding domain of human B7-2: Insights into organization and signaling (2003)

B7-1 and B7-2 are homologous costimulatory ligands expressed on the surfaces of antigen-presenting cells. Their interactions with CD28/CTLA-4 receptors expressed on T cell surfaces are crucial for the proper regulation of T cell activity. B7-1 and B7-2 display distinct roles in immune regulation, although they are usually considered to have redundant functions. Here, we report the crystal structure of the receptor-binding (Ig V-type) domain of human B7-2 at 2.7-A resolution. Structures of unliganded and liganded B7-1 and B7-2 suggest a physical-chemical basis for the observed functional similarities and differences between these two costimulatory ligands. Of particular note, whereas the majority of the residues mediating B7-1 dimerization are hydrophobic, the B7-2 dimer observed in the B7-2/CTLA-4 complex displays a very hydrophilic dimer interface. These differences provide a mechanism for preventing the formation of B7-1/B7-2 heterodimers. The divergence at the putative dimer interface is also consistent with the lower tendency of B7-2 to dimerize, as shown by the monomeric state of unliganded B7-2 both in solution and crystalline form, and may result in detailed differences in signaling mechanisms associated with B7-1 and B7-2.
Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism (2010)

Like many microalgae, Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient deprived. To begin studying the mechanisms underlying this process, nitrogen (N) deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and noninduced conditions was applied as a first approach to studying molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment. Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of eight biologically independent libraries, four for each condition, N replete and N deprived, allowing a statistically sound comparison of expression levels under the two tested conditions. As expected, N deprivation activated a subset of control genes involved in gametogenesis while down-regulating protein biosynthesis. Genes for components of photosynthesis were also down-regulated, with the exception of the PSBS gene. N deprivation led to a marked redirection of metabolism: the primary carbon source, acetate, was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogenesis but funneled directly into fatty acid biosynthesis. Additional fatty acids may be produced by membrane remodeling, a process that is suggested by the changes observed in transcript abundance of putative lipase genes. Inferences on metabolism based on transcriptional analysis are indirect, but biochemical experiments supported some of these deductions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae.
Steric Tuning of Reactivity and Enantioselectivity in Addition of Thiophenol to Enoates Catalyzed by an External Chiral Ligand (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSteric Tuning of Reactivity and Enantioselectivity in Addition of Thiophenol to Enoates Catalyzed by an External Chiral LigandKatsumi Nishimura, Masashi Ono, Yasuo Nagaoka, and Kiyoshi TomiokaView Author Information Graduate School of Pharmaceutical Sciences Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-01, Japan Cite this: J. Am. Chem. Soc. 1997, 119, 52, 12974–12975Publication Date (Web):December 31, 1997Publication History Received26 August 1997Published online31 December 1997Published inissue 1 December 1997https://doi.org/10.1021/ja9729950Copyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1227Altmetric-Citations114LEARN 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 InReddit Read OnlinePDF (59 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Hydrocarbons,Ligands,Lithium,Reactivity,Stereoselectivity Get e-Alerts
Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences (1998)

Genomic science and structural biology meet in the relationship between the sequence and the structure of nucleic acids. The structure that supports each function is preserved in the process of evolution as specific sequences. Particularly, the same sequence which appears in a different place such as a palindromic or repetitive sequence has biophysical meaning: recognition site of dimers, forming stem-loops, and contributions to global structure of nucleic acids. Also, the genetic network, transduction pathway, and tissue specificity largely depend on these. Although the relationship between them can be found experimentally, there is increasing demand for automated analysis. Especially, it is desirable to extract the same character sequences of arbitrary length (especially, very long ones) which co-occur at an arbitrary separation. We propose an algorithm to identify the maximum match sequence at each position with a calculation cost of O(N log N) and memory space of O(N). Applying it to some sequences, we found unexpectedly large palindromes and repeats in DNA.
Expression of the Bacillus anthracis protective antigen gene by baculovirus and vaccinia virus recombinants (1990)

The gene encoding Bacillus anthracis protective antigen (PA) was modified by site-directed mutagenesis, subcloned into baculovirus and vaccinia virus plasmid transfer vectors (pAcYM1 and pSC-11, respectively), and inserted via homologous recombinations into baculovirus Autographa californica nuclear polyhedrosis virus or vaccinia virus (strains WR and Connaught). Expression of PA was detected in both systems by immunofluorescence assays with antisera from rabbits immunized with B. anthracis PA. Western blot (immunoblot) analysis showed that the expressed product of both systems was slightly larger (86 kilodaltons) than B. anthracis-produced PA (83.5 kilodaltons). Analysis of trypsin digests of virus-expressed and authentic PA suggested that the size difference was due to the presence of a signal sequence remaining with the virus-expressed protein. Immunization of mice with either recombinant baculovirus-infected Spodoptera frugiperda cells or with vaccinia virus recombinants elicited a high-titer, anti-PA antibody response.
A direct pathway for the conversion of propionate into pyruvate in Moraxella lwoffi (1968)

1. The identity of the organism previously known as Vibrio O1 (N.C.I.B. 8250) with a species of Moraxella is established. 2. The ability of cells to oxidize propionate is present only in cells with an endogenous respiration and this ability is increased 80-fold when the organism is grown with propionate. 3. Isocitrate lyase activity in extracts from propionate-grown cells is the same as that in extracts from lactate-grown cells, about tenfold greater than that in extracts from succinate-grown cells and slightly greater than half the activity in extracts from acetate-grown cells. 4. With arsenite as an inhibitor conditions were found in which the organism would catalyse the quantitative oxidation of propionate to pyruvate. When propionate was completely utilized pyruvate was metabolized further to 2-oxoglutarate. 5. The oxidation of propionate by cells was incomplete both in a ;closed system' with alkali to trap respiratory carbon dioxide and in an ;open system' with an atmosphere of oxygen+carbon dioxide (95:5). Acetate accumulated. Under these conditions [2-(14)C]- and [3-(14)C]-propionate gave rise to [(14)C]acetate. The rate of conversion of [2-(14)C]propionate into (14)CO(2), although much less than the rate of conversion of [1-(14)C]propionate into (14)CO(2), was slightly greater than the rate of conversion of [3-(14)C]propionate into (14)CO(2). 6. The oxidation of propionate by cells was complete in an ;open system' with an atmosphere of either oxygen or air. Under these conditions very little [1-(14)C]propionate was converted into (14)C-labelled cell material. The conversion of [2-(14)C]- and [3-(14)C]-propionate into (14)C-labelled cell material occurred at an appreciable rate, the rate for the incorporation of [3-(14)C]propionate being slightly more rapid. In the absence of a utilizable nitrogen source part of the [(14)C]propionate was incorporated into some reserve material, which was oxidized when added substrate had been completely utilized. 7. [(14)C]-Pyruvate produced from [(14)C]propionate was chemically degraded. The C((1)) of propionate was found only in C((1)) of pyruvate. At least 86% of C((2)) of pyruvate was derived from C((2)) of propionate and at least 92% of C((3)) of pyruvate from C((3)) of propionate. 8. These results are incompatible with the operation of any of the previously described pathways for propionate metabolism except the direct one, perhaps via an activated acrylate.
High-intensity strength training in nonagenarians. Effects on skeletal muscle. (1990)

Muscle dysfunction and associated mobility impairment, common among the frail elderly, increase the risk of falls, fractures, and functional dependency. We sought to characterize the muscle weakness of the very old and its reversibility through strength training. Ten frail, institutionalized volunteers aged 90 +/- 1 years undertook 8 weeks of high-intensity resistance training. Initially, quadriceps strength was correlated negatively with walking time (r = -.745). Fat-free mass (r = .732) and regional muscle mass (r = .752) were correlated positively with muscle strength. Strength gains averaged 174% +/- 31% (mean +/- SEM) in the 9 subjects who completed training. Midthigh muscle area increased 9.0% +/- 4.5%. Mean tandem gait speed improved 48% after training. We conclude that high-resistance weight training leads to significant gains in muscle strength, size, and functional mobility among frail residents of nursing homes up to 96 years of age.
Discoidin Domain Receptor 1 Is Activated Independently of β1 Integrin (2000)

Various types of collagen have been identified as potential ligands for the two mammalian discoidin domain receptor (DDR) tyrosine kinases, DDR1 and DDR2. It is presently unclear whether collagen-induced DDR receptor activation, which occurs with very slow kinetics, involves additional proteins with kinase activity or membrane-anchored proteins serving as coreceptors. In particular, the role of the collagen-binding integrins alpha(1)beta(1) or alpha(2)beta(1) in the DDR activation process is undefined. Here, we provide three lines of evidence suggesting that DDR1 signaling is distinct from integrin activation. First we demonstrate that the enzymatic activity of DDR1 is essential for receptor tyrosine phosphorylation. Collagen-induced DDR receptor autophosphorylation can be blocked either by a dominant negative mutant or by a preparation of recombinant extracellular domain. Second, we show DDR1 signals independent of the epidermal growth factor (EGF) receptor. In cells that endogenously express both DDR1 and the EGF receptor, stimulation with EGF does not induce DDR activation. Third, we detected full DDR1 activation after collagen stimulation in cells that have been treated with blocking antibodies for alpha(2)beta(1) integrin or in cells with a targeted deletion of the beta(1) integrin gene. Finally, we show that overexpression of dominant negative DDR1 in the myoblast cell line C2C12 blocks cellular differentiation and the formation of myofibers.