gebhart/patrepeval huggingface dataset:
Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells (2009)

Oligonucleotide-templated reactions are attracting attention as a method for RNA detection in living cells. Previously, a reduction-triggered fluorescence probe has been reported that is based on azide reduction to switch fluorescence on. In this article, we report a more advanced probe, a reduction-triggered fluorescent amplification probe that is capable of amplifying a target signal. Azidomethyl fluorescein was newly synthesized and introduced into a probe. Azido-masked fluorescein on the probe showed a strong turn-on fluorescence signal upon oligonucleotide-templated Staudinger reduction. The catalytic reaction of the probe offered a turnover number of 50 as fluorescence readout within 4 h. Finally, probes were introduced into human leukemia HL-60 cells by use of streptolysin O pore-forming peptide. We successfully detected and quantitated the 28S rRNA and beta-Actin mRNA signal above the background by flow cytometry. In addition, the same RNA targets were imaged by fluorescence microscopy. The data suggest that a reduction-triggered amplification probe may be a powerful tool in analyzing the localization, transcription, or processing of RNA species in living eukaryotic cells.
Heterogeneous distributed database management: The HD-DBMS (1987)

The proliferation of different DBMS and advances in computer networking and communications have led to increasing heterogeneous distributed DBMS network scenarios. Major heterogeneity problems and challenges include: different database models, syntactically and semantically different DBMS, different types of controls (recovery, etc.), etc. We address herein the long-range goal for a heterogeneous distributed DBMS (HD-DBMS) to be able to support a network in which any user in any node can be given an integrated and tailored view or schema, while in reality the data may reside in one single database or in physically separated databases, managed individually by the same type of DBMS (by the only one the user understands) or by different DBMS. We cite the major approaches to data sharing and accessing: from the primitive commercial file and database unload/load and PC download, to common interfaces on top of existing DBMS, to the R&D and prototype efforts toward the long-range desires. Commercial availability of the more encompassing thrusts may become a reality with the mounting problems, opportunity costs, and demand for data sharing in the heterogeneous world. Major research and development projects in this arena are leading toward some partial attainment of the long-range objective. The UCLA HD-DBMS project is highlighted herein, with a presentation of its status, progress, and plans. It is a longer range project, with the unique feature of allowing any user in the network to use a preferred database model and DML to access or update any data in the heterogeneous network. HD-DBM5 is to provide a multilingual interface to heterogeneous distributed databases.
The GABA<sub>A</sub>Receptor α<sub>1</sub>Subtype in the Ventral Pallidum Regulates Alcohol-Seeking Behaviors (2002)

We investigated the potential role of the alpha1-containing GABA(A) receptor in regulating the reinforcing properties of alcohol. To accomplish this, we developed 3-propoxy-beta-carboline hydrochloride (3-PBC), a mixed agonist-antagonist benzodiazepine site ligand with binding selectivity at the alpha1 receptor. We then tested the capacity of 3-PBC to block alcohol-maintained responding in the ventral pallidum (VP), a novel alcohol reward substrate, which primarily expresses the alpha1-receptor isoform. Our results demonstrated that bilateral microinfusion of 3-PBC (0.5-40 microg) in the anterior and medial VP produced marked reductions in alcohol-maintained responding in a genetically selected rodent model of alcohol drinking. The VP infusions showed both neuroanatomical and reinforcer specificity because no effects were seen in sites dorsal to the VP (e.g., nucleus accumbens, caudate putamen). The saccharin-maintained responding was reduced only with the highest dose (40 microg). Parenteral injections of 3-PBC (1-20 mg/kg) also showed a similar selectivity on alcohol-maintained responding. Complementary in vitro studies revealed that 3-PBC exhibited a low partial agonist efficacy profile at recombinant diazepam-sensitive receptors (e.g., alpha1beta3gamma2, alpha2beta3gamma, and alpha3beta3gamma2). The selective suppression of 3-PBC on alcohol-maintained responding after central and parenteral administrations, together with its low-efficacy agonist profile, suggest that the reduction in alcohol-maintained behaviors was not attributable to a general suppression on consummatory behaviors. These results demonstrate that the alpha1-containing GABA(A) receptors in both the anterior and medial VP are important in regulating the reinforcing properties of alcohol. These receptors represent novel targets in the design and development of pharmacotherapies for alcohol-dependent subjects.
Foley Catheter Balloon Puncture and the Risk of Free Fragment Formation (1990)

The incidence of free fragment formation following balloon puncture or spontaneous bursting was examined in 294 Foley catheters immersed for 48 h in urine. The catheters were divided into 3 groups: 100 were inflated to the manufacturer's recommended volume, 100 to twice the volume and 94 to 3 times the recommended volume. The catheter balloons were punctured by pricking with a hypodermic needle. The overall incidence of free fragment formation was 27.3%. For both types of catheter examined, increasing balloon volume was not associated with an increased risk of free fragment formation following puncture. However, increasing volume was associated with increased free fragment formation when the balloon burst spontaneously. In view of the high risk of free fragment formation, cystoscopy should be performed in all cases of spontaneous catheter balloon rupture or after percutaneous balloon puncture.
ION EXCHANGE CHROMATOGRAPHY OF THE FREE AMINO ACIDS IN THE PLASMA OF THE NEWBORN INFANT (1965)

1. A micromethod for the determination of amino acids by ion exchange chromatography was applied to the quantitative determination of the free amino acids in 0.1 ml of plasma of the newborn infant. The precision of the method was in general within the range ± 5%. An interpretive analysis of a typical chromatogram is given. 2. Plasma was best stored at -68°C pending analysis; errors likely to arise on storage at -20°C and higher temperatures are pointed out. Some errors likely to arise in the preparation and storage of plasma protein free filtrates are also indicated. 3. Comparison of the free amino acids in the femoral vein plasma of 25 newborn infants was made with the literature values of the free amino acids in the plasma of adults. The differences noted were not great, but were apparently characteristic. On comparing heel puncture plasma, some amino acids were higher than in femoral vein plasma, but it was concluded that heel puncture plasma would be satisfactory for routine clinical purposes. Some possible sources of error which might explain the elevated amino acids in the heel puncture plasma were noted. 4. On comparison of newborn with 3-day-old infants, some changes in amino acid levels were noted. The changes were not great, but seemed to be characteristic and consistent. 5. A number of small peaks which have not been noted previously in plasma have been indicated on the chromatogram. They were not identified, but were mentioned to draw attention to the possibilities of hitherto unrecognized ninhydrin-positive components of plasma.
Chemically Assisted Laser Ablation ICP Mass Spectrometry (2002)

A new laser ablation technique combined with a chemical evaporation reaction has been developed for elemental ratio analysis of solid samples using an inductively coupled plasma mass spectrometer (ICPMS). Using a chemically assisted laser ablation (CIA) technique developed in this study, analytical repeatability of the elemental ratio measurement was successively improved. To evaluate the reliability of the CLA-ICPMS technique, Pb/U isotopic ratios were determined for zircon samples that have previously been analyzed by other techniques. Conventional laser ablation for Pb/U shows a serious elemental fractionation during ablation mainly due to the large difference in elemental volatility between Pb and U. In the case of Pb/U ratio measurement, a Freon R-134a gas (1,1,1,2-tetrafluoroethane) was introduced into the laser cell as a fluorination reactant. The Freon gas introduced into the laser cell reacts with the ablated sample U, and refractory U compounds are converted to a volatile U fluoride compound (UF6) under the high-temperature condition at the ablation site. This avoids the redeposition of U around the ablation pits. Although not all the U is reacted with Freon, formation of volatile UF compounds improves the transmission efficiency of U. Typical precision of the 206Pb/238U ratio measurement is 3-5% (2sigma) for NIST SRM 610 and Nancy 91500 zircon standard, and the U-Pb age data obtained here show good agreement within analytical uncertainties with the previously reported values. Since the observed Pb/U ratio for solid samples is relatively insensitive to laser power and ablation time, optimization of ablation conditions or acquisition parameters no longer needs to be performed on a sample-to-sample basis.
Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments (2016)

Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemical treatment causes strand scission, which depletes the number of sequenceable DNA fragments in a library and thus necessitates PCR amplification. The AT-rich nature of the library generated from bisulfite treatment adversely affects this amplification, resulting in the introduction of major biases that can confound methylation analysis. Here, we report a method that enables more accurate methylation analysis, by rebuilding bisulfite-damaged components of a DNA library. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We apply the ReBuilT method for the first whole methylome analysis of the highly AT-rich genome of Plasmodium berghei. Side-by-side comparison to a commercial protocol involving amplification demonstrates a substantial improvement in uniformity of coverage and reduction of sequence context bias. Our method will be widely applicable for quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.
Wnt pathway and breast cancer (2007)

Breast cancer is one of the most debilitating human carcinomas with second highest mortality rate after lung cancer in women. Recent advancement in genetic and biochemical analyses has deciphered the molecular pathways involved in breast cancer development. Wnt signal has long been established to play a critical role in normal development as well as in tumorigenesis. In this review, we summarize the role of Wnt signal in the development of mammary carcinoma, the molecular mechanism via which Wnt signal exerts its malignant potential and various nodal points in the Wnt cascade that can be targeted for drug development and cancer treatment.
Efficacy of chemical and botanical over‐the‐counter pediculicides available in Brazil, and off‐label treatments, against head lice <i>ex vivo</i> (2010)

Most Brazilian OTC products did not show a satisfactory efficacy against head lice. Resistance may be present. Ivermectin and coconut oil are promising compounds for topical treatment. Laboratory-based tests should be used to assess resistance patterns and to identify formulations of the active ingredient that increase the efficacy. Standardized testing should be performed before a product is licensed for head lice treatment.
Adaptation and Self-Repair in Parallel Computing Structures (1984)

This paper reports a study of the dynamics of highly concurrent computing structures capable of learning and storing several input patterns. The existence of attractors in their dynamical behavior leads to a novel self-repairing mechanism. Quantitative experiments on adaptive processor arrays demonstrate the existence of attractive fixed points in their adaptation and recognition properties, as well as the immunity of these collective computation machines to random errors.
<i>In vitro</i> maturation, fertilization and development of follicular oocytes from buffalo ( <i>Bubalus bubalis</i> ) (1992)

Cumulus-oocyte complexes, 5596, were cultured for 24 h in either TCM-199 or Ham's F-10 with or without gonadotrophins and supplemented with either 20% buffalo oestrous serum (BES) or fetal calf serum (FCS). The maturation rates of oocytes cultured in TCM-199 or Ham's F-10 medium supplemented with 20% BES were 47.4 +/- 17.8 and 44.8 +/- 25.6, respectively. Addition of luteinizing hormone (LH) (5 micrograms ml-1) significantly improved the maturation rate in the Ham's F-10 medium supplemented with 20% BES (76.8 +/- 18.3), but follicle-stimulating hormone (FSH) (0.5 micrograms ml-1) and oestradiol (1 microgram ml-1) failed to synergize with LH (71.7 +/- 19.5). In the TCM-199 system, LH failed to enhance the maturation rate but the addition of FSH and oestradiol significantly enhanced the proportion of mature oocytes (42.7 +/- 1.4 and 81.7 +/- 14.5, respectively; P less than 0.05). Frozen-thawed spermatozoa prepared in Bracket and Oliphant (BO) medium and treated with 5 mmol caffeine 1(-1) + 10 micrograms heparin showed a higher fertilization rate (29.8%) than those treated in Hepes-Talp and treated with 10 micrograms heparin ml-1 (19.6%). Fertilization rate was significantly improved when fresh ejaculated spermatozoa treated with 5 mmol caffeine 1-1 and 10 micrograms heparin in BO medium (50%) was used. Rate of cleavage and development were also higher when in vitro fertilization was carried out with fresh ejaculated spermatozoa treated with caffeine and heparin (34.1 and 36.8%, respectively) than with frozen-thawed spermatozoa (27.0 and 22.0%, respectively). Development rate was enhanced when fertilized ova were cultured in ligated rabbit oviduct (28.0%) than when co-cultured on oviductal cell monolayers (8.2%). The results indicate that oocytes cultured in medium supplemented with BES and gonadotrophins reveal high rates of maturation and development to the blastocyst stage after fertilization with fresh ejaculated spermatozoa.
Dlx and Other Homeobox Genes in the Morphological Development of the Dentition (1995)

The dentition is a segmental system whose evolution and morphology bears analogy to the evolution of segmentation in the vertebral column and limb. Combinatorial expression of members of the large "Hox" class of homeobox regulatory genes has been shown to play an important role in positional specification in these skeletal systems. This raises the possibility that homeobox genes are also used for positional specification in the dentition, and several homeobox genes are known to be expressed in developing teeth. To identify additional dentally expressed homeobox genes, cDNA from from murine tooth germs at 9.5, 14.5, and 17.5 days gestational age was amplified by PCR using sets of degenerate primers to the homeodomains of 18 different classes of homeobox genes. Amplification products were cloned and sequenced and compared to known gene sequences. To date this approach has confirmed the presence of Msx1, Msx2, Dlx1, and Dlx2, and identified several other homeobox genes not previously known to be expressed in teeth: Dbx, MHox, and Mox2A, plus an a additional Dlx gene, Dlx7. The Msx and Dlx genes are the best current candidates for a combinatorial mechanism that controls the differentiation of structures within and between teeth, and perhaps also the evolution of those structures.
Demonstration of npn InAs bipolar transistors with inverted base doping (1996)

We demonstrate np/sup +/n InAs bipolar transistors that operate under room temperature and cryogenic conditions. InAs transistors on an InP substrate were characterized as a function of temperature and exhibited good room temperature and low temperature common-emitter characteristics. Although the base doping density exceeded the emitter doping density by a factor of 20, current gains of 30 were achieved at room temperature. Junction leakage currents and contact resistance were identified as problems to address.
Reference Functions for Synthesis and Analysis of Multiview and Integral Images (2013)

We propose one- and two-dimensional reference functions for processing of integral/multiview imaging. The functions provide the synthesis/analysis of the integral image by distance, as an alternative to the composition/decomposition by view images (directions). The synthesized image was observed experimentally. In analysis confirmed by simulation in a qualitative sense, the distance was obtained by convolution of the integral image with the reference functions.
Profiling Individual Human Embryonic Stem Cells by Quantitative RT-PCR (2014)

Heterogeneity of stem cell population hampers detailed understanding of stem cell biology, such as their differentiation propensity toward different lineages. A single cell transcriptome assay can be a new approach for dissecting individual variation. We have developed the single cell qRT-PCR method, and confirmed that this method works well in several gene expression profiles. In single cell level, each human embryonic stem cell, sorted by OCT4::EGFP positive cells, has high expression in OCT4, but a different level of NANOG expression. Our single cell gene expression assay should be useful to interrogate population heterogeneities.
BCL2 Inhibitors as Anticancer Drugs: A Plethora of Misleading BH3 Mimetics (2016)

Antiapoptotic BCL2 proteins play a major role in tumor cell survival. Hence, BCL2 inhibitors have been developed as direct inducers of apoptosis. ABT-199 (venetoclax) received breakthrough therapy designation from the FDA due to its apparent efficacy in CLL and AML. However, resistance to ABT-199 is mediated by other BCL2 proteins including BCLXL and MCL1. Considerable effort has been expended seeking novel "BH3 mimetics" that inhibit all of these BCL2 proteins. While many BH3 mimetics inhibit BCL2 proteins in vitro, they fail to directly inhibit them in intact cells. Many BH3 mimetics induce the unfolded protein response culminating in induction of the proapoptotic protein NOXA, which in turn inhibits MCL1. We propose simple experiments to validate BH3 mimetics in cells. A true BCL2 inhibitor will rapidly induce apoptosis in chronic lymphocytic leukemia cells ex vivo A BCLXL inhibitor will rapidly induce apoptosis in platelets. Finally, a BH3 mimetic targeting MCL1 will inhibit its degradation thereby inducing rapid MCL1 accumulation. Compounds that fail these tests should no longer be called BH3 mimetics. We now have a toolbox of selective inhibitors for most of the BCL2 proteins, and we hope these new tools will lead to effective treatment options for many cancers. Mol Cancer Ther; 15(9); 2011-7. ©2016 AACR.
Antigenic Specificity of the<i>Mycobacterium leprae</i>Homologue of ESAT-6 (2002)

The sequence of the Mycobacterium leprae homologue of ESAT-6 shows only 36% amino acid correspondence to that from Mycobacterium tuberculosis. Anti-M. leprae ESAT-6 polyclonal and monoclonal antibodies and T-cell hybridomas reacted only with the homologous protein and allowed identification of the B- and T-cell epitopes. The protein is expressed in M. leprae and appears in the cell wall fraction. Thus, M. leprae ESAT-6 shows promise as a specific diagnostic agent for leprosy.
Rewriting History: The Biasing Effects of Attitudes on Memory (1982)

The present study examines whether people's memories for events are distorted to become more consistent with their attitudes and beliefs. It was hypothesized that this distortion might occur as a result of reconstructive memory processes at the time of retrieval. That is, when people are asked to remember an event, they may employ their attitudes and beliefs about a topic to reconstruct their memories of the relevant incident. In the process of reconstructing the incident, they may introduce new information and distort old information. Subjects, after responding to a questionnaire about their attitudes toward nuclear power, read a story describing a fire at a nuclear power plant. They were then given a recognition test over the material, either immediately or at 1- or 2-week delays. At the immediate test, there was no relationship between subjects' attitudes and their recognition performance. At both delays, however, subjects were more likely to recognize belief-consistent information; this was true both for actual material from the passage and for distortions and introductions to it. This suggests that reconstructive processes resulted in subjects' memories becoming the more belief-consistent as veridical memory decayed.
Absorption and scattering of light by nonspherical particles (1986)

Using the example of the polarization of scattered light, it is shown that the scattering matrices for identical, randomly ordered particles and for spherical particles are unequal. The spherical assumptions of Mie theory are therefore inconsistent with the random shapes and sizes of atmospheric particulates. The implications for corrections made to extinction measurements of forward scattering light are discussed. Several analytical methods are examined as potential bases for developing more accurate models, including Rayleigh theory, Fraunhoffer Diffraction theory, anomalous diffraction theory, Rayleigh-Gans theory, the separation of variables technique, the Purcell-Pennypacker method, the T-matrix method, and finite difference calculations.
Fiber wavelet filters [and planar waveguide couplers for full-wavelength demultiplexers] (2002)

The passive optical networks proposed by Marhic and Siegman to evaluate the discrete Fourier transform (DFT) of a linear array or a pixellated image (parallel input) are redesigned for the discrete wavelet transform or the wavelet packet (WP) decomposition. Using only asymmetric optical couplers, with a suitable power coupling ratio, it is shown that it is possible to optically implement Mallat's pyramidal decomposition scheme with a compactly supported wavelet basis function. The case of a serial input has a larger number of potential applications to optical communications systems or optical computing, and simple passive optical networks are presented that evaluate the DFT or the wavelet transform of a stream of optical digits, by using only Mach-Zehnder interferometers with output asymmetric couplers. In particular, an all-optical implementation of the WP-division demultiplexer for a waveform coded transmission system is given. The proposed networks are full-wavelength demultiplexers, as they split the spectrum of the incoming signal into a set of closed frequency channels; the filters have identical bandwidth and span the whole input spectrum. Using the WP-decomposition method, different subband filtering schemes can be designed, fabricating trees of quadrature mirror filters with the fiber or the integrated optics technology.
An advanced submicron CMOS technology with 2&amp;#181;m pitch at all levels (1987)

A CMOS technology with 2.0 µm pitch at isolation, poly, and metal interconnects is demonstrated using optical lithography. The "front-end" process defining the active regions uses a sealed interface process for bird's beak reduction and deep trenches in well-to-well isolation for latch-up suppression. The "back-end" process, where the metal interconnects are defined, replaces contacts and vias with posts. Metal posts (studs or pillars) were used to connect the first interconnect layer to poly and active regions and also to connect first and second interconnect layers. The resulting ring speed is 100 ps at 5.0 V for 0.8 µm (NMOS) and 0.9 µm (PMOS) channel lengths.