gebhart/patrepeval huggingface dataset:
Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae (1999)

Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.
The Numeric Rating Scale for Clinical Pain Measurement: A Ratio Measure? (2003)

The Numeric Rating Scale (NRS-11) has been widely used clinically for the assessment of pain. Its use for clinical research is controversial. Reports differ as to whether or not the NRS-11 should be treated as a ratio pain measurement tool. This study compared the NRS-11 to a ratio measure for pain assessment: the visual analog scale (VAS). Simultaneous pain measurements using these 2 scales were compared in clinical situations commonly encountered in a tertiary community hospital. Whereas linear relationships were noted in laboring patients and in postoperative patients with thoracic or abdominal incisions during cough, no such correlations were noted for the same postoperative patients at rest or for postoperative orthopedic patients. The NRS-11 should not be considered to be interchangeable with the VAS. Its use for clinical research should be limited to situations where it has specifically demonstrated linear properties.
siRNA carrying an (E)-vinylphosphonate moiety at the 5΄ end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2 (2016)

Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5΄- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5΄- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5΄-(E)-vinylphosphonate (5΄-E-VP) guide RNA at 2.5-Å resolution. The structure demonstrates how the 5΄ binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5΄-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5΄-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA.
A biomarker that identifies senescent human cells in culture and in aging skin in vivo. (1995)

Normal somatic cells invariably enter a state of irreversibly arrested growth and altered function after a finite number of divisions. This process, termed replicative senescence, is thought to be a tumor-suppressive mechanism and an underlying cause of aging. There is ample evidence that escape from senescence, or immortality, is important for malignant transformation. By contrast, the role of replicative senescence in organismic aging is controversial. Studies on cells cultured from donors of different ages, genetic backgrounds, or species suggest that senescence occurs in vivo and that organismic lifespan and cell replicative lifespan are under common genetic control. However, senescent cells cannot be distinguished from quiescent or terminally differentiated cells in tissues. Thus, evidence that senescent cells exist and accumulate with age in vivo is lacking. We show that several human cells express a beta-galactosidase, histochemically detectable at pH 6, upon senescence in culture. This marker was expressed by senescent, but not presenescent, fibroblasts and keratinocytes but was absent from quiescent fibroblasts and terminally differentiated keratinocytes. It was also absent from immortal cells but was induced by genetic manipulations that reversed immortality. In skin samples from human donors of different age, there was an age-dependent increase in this marker in dermal fibroblasts and epidermal keratinocytes. This marker provides in situ evidence that senescent cells may exist and accumulate with age in vivo.
Novel Capacitorless 1T-DRAM Cell for 22-nm Node Compatible With Bulk and SOI Substrates (2011)

A new concept of multibody single-transistor dynamic-random-access-memory cell fully compatible with both standard bulk and silicon-on-insulator substrates is presented. Its novelty comes from the juxtaposition of two silicon films with opposed doping polarities (i.e., a p-n junction), which define a body partitioning for hole storage and current sense. The charge accumulated in the top body controls the current flowing through the bottom body. The scalability is ensured due to the suppression of the supercoupling effect, thus allowing the coexistence of electrons and holes in very thin transistors. Numerical simulations of electrostatics and dynamic operation show how the transient response of this device can be used for dynamic-memory applications, achieving attractive performance in terms of state discrimination and retention time in very scaled devices.
Signature for Long-Term Vaccine-Mediated Control of a Simian and Human Immunodeficiency Virus 89.6P Challenge: Stable Low-Breadth and Low-Frequency T-Cell Response Capable of Coproducing Gamma Interferon and Interleukin-2 (2005)

In 2001, we reported 20 weeks of control of challenge with the virulent 89.6P chimera of simian and human immunodeficiency viruses (SHIV-89.6P) by a Gag-Pol-Env vaccine consisting of DNA priming and modified vaccinia virus Ankara boosting. Here we report that 22 out of 23 of these animals successfully controlled their viremia until their time of euthanasia at 200 weeks postchallenge. At euthanasia, all animals had low to undetectable viral loads and normal CD4 counts. During the long period of viral control, gamma interferon (IFN-gamma)-producing antiviral T cells were present at unexpectedly low breadths and frequencies. Most animals recognized two CD8 and one CD4 epitope and had frequencies of IFN-gamma-responding T cells from 0.01 to 0.3% of total CD8 or CD4 T cells. T-cell responses were remarkably stable over time and, unlike responses in most immunodeficiency virus infections, maintained good functional characteristics, as evidenced by coproduction of IFN-gamma and interleukin-2. Overall, high titers of binding and neutralizing antibody persisted throughout the postchallenge period. Encouragingly, long-term control was effective in macaques of diverse histocompatibility types.
Magnetoencephalography using a compact multichannel atomic magnetometer with pump-probe configuration (2018)

Optically pumped atomic magnetometers operating in the spin exchange relaxation free (SERF) regime play increasingly important roles in magnetoencephalography measurements. In this application, a multichannel arrangement is necessary. A method to construct the multichannel system is to arrange multiple individual sensor modules, where each sensor module is designed in the one-beam configuration with the necessary magnetic modulation. However, such an arrangement restricts the spatial resolution, affects the uniformity of the sensor characteristics, and increases the system complexity. To address these issues, we developed a compact multichannel pump-probe configuration magnetometer based on a single vapor cell. Each channel of the multichannel system shares the same vapor cell. As a result, the influence of different cells is eliminated. Further, a two-beam configuration with an independent pump and probe beam is introduced. Compared with the one-beam configuration, the two-beam magnetometer achieves a higher sensitivity and does not require extra magnetic modulation. And then the magnetic field crosstalk between adjacent channels can be avoided. A sensitivity of 10 fT/Hz1/2 at 2 Hz is achieved for all channels. Using the compact multichannel magnetometer, an auditory evoked response is clearly observed. If more channels are required, the arrangement based on the single vapor cell configuration can be easily expanded by applying the photodiode with more than four quadrants.
[Sildenafil citrate for erectile dysfunction in male kidney transplant recipients]. (2004)

Sildenafil is an effective and safe agent for the treatment of ED in kidney transplant recipients.
Osteoblast responses to BMP-2-treated titanium in vitro. (1997)

In this study, the phenotypic expression of osteoblast progenitor cells, 2T9, on characterized titanium surfaces was examined in the presence of a bone morphogenetic protein-2 (BMP-2). X-ray photoelectron spectroscopy spectra indicated the presence of titanium dioxide on titanium surfaces, along with surface contaminants such as carbon and nitrogen. In the in vitro study, the activity of BMP-2-treated osteoblast cells on titanium surfaces was marked by significantly higher alkaline phosphatase-specific activity and 1,25 (OH2) vitamin D3-stimulated osteocalcin production when compared to the untreated cells on titanium surfaces.
Phase behavior and structures of mixtures of anionic and cationic surfactants (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhase behavior and structures of mixtures of anionic and cationic surfactantsEric W. Kaler, Kathleen L. Herrington, A. Kamalakara Murthy, and Joseph A. N. ZasadzinskiCite this: J. Phys. Chem. 1992, 96, 16, 6698–6707Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://pubs.acs.org/doi/10.1021/j100195a033https://doi.org/10.1021/j100195a033research-articleACS PublicationsRequest reuse permissionsArticle Views3457Altmetric-Citations529LEARN 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 options Get e-Alerts
Endogenous Neuroprotection Factors and Traumatic Brain Injury: Mechanisms of Action and Implications for Therapy (1994)

Throughout evolution the brain has acquired elegant strategies to protect itself against a variety of environmental insults. Prominent among these are signals released from injured cells that are capable of initiating a cascade of events in neurons and glia designed to prevent further damage. Recent research has identified a remarkably large number of neuroprotection factors (NPFs), whose expression is increased in response to brain injury. Examples include the neurotrophins (NGF, NT-3, NT-5, and BDNF), bFGF, IGFs, TGFs, TNFs and secreted forms of the beta-amyloid precursor protein. Animal and cell culture studies have shown that NPFs can attenuate neuronal injury initiated by insults believed to be relevant to the pathophysiology of traumatic brain injury (TBI) including excitotoxins, ischemia, and free radicals. Studies of the mechanism of action of these NPFs indicate that they enhance cellular systems involved in maintenance of Ca2+ homeostasis and free radical metabolism. Recent work has identified several low-molecular-weight lipophilic compounds that appear to mimic the action of NPFs by activating signal transduction cascades involving tyrosine phosphorylation. Such compounds, alone or in combination with antioxidants and calcium-stabilizing agents, have proved beneficial in animal studies of ischemic brain injury and provide opportunities for development of preventative/therapeutic approaches for TBI.
Characterization of the bonding strength and interface current of p-Si/n-InP wafers bonded by surface activated bonding method at room temperature (2002)

Bonding between p-Si and n-InP was performed through the surface activated bonding method at room temperature. Tensile results show that the samples were visibly separated from the bonded interface, indicating a weak bonding strength. The cause of the weak bonding strength was intensively investigated. Consistent results between x-ray photoelectron spectroscopy and atomic force microscope investigations show that a weak phase of indium is terminated on the InP due to the depletion of phosphorus in the sputtered surface. Existence of indium layers on the debonded Si surface indicate that the samples were separated from the interface of In/InP, but not across the bonded interface of Si and indium. Typical pn junction current–voltage behavior indicates no high resistance interface layer that can withstand the flow of current through the interface. Remarkably, sputtering time as well as energy dependence on the interface current is found to be due to the accumulation of sputtering induced defects.
Carbon nanotube technologies for future ULSIs (2004)

In this paper, we discuss CNT technologies for future ULSIs, in particular, CNT via interconnects and CNT-FET technologies, including single electron transistors.
Path planning for permutation-invariant multirobot formations (2006)

In many multirobot applications, the specific assignment of goal configurations to robots is less important than the overall behavior of the robot formation. In such cases, it is convenient to define a permutation-invariant multirobot formation as a set of robot configurations, without assigning specific configurations to specific robots. For the case of robots that translate in the plane, we can represent such a formation by the coefficients of a complex polynomial whose roots represent the robot configurations. Since these coefficients are invariant with respect to permutation of the roots of the polynomial, they provide an effective representation for permutation-invariant formations. In this paper, we extend this idea to build a full representation of a permutation-invariant formation space. We describe the properties of the representation, and show how it can be used to construct collision-free paths for permutation-invariant formations
Robot grasp detection using multimodal deep convolutional neural networks (2016)

Autonomous manipulation has enabled a wide range of exciting robot tasks. However, perceiving outside environment is still a challenging problem in the field of intelligent robotic research due to the lack of object models, unstructured environments, and time-consuming computation. In this article, we present a novel robot grasp detection system that maps a pair of RGB-D images of novel objects to best grasping pose of a robotic gripper. First, we segment the graspable objects from the unstructured scene using the geometrical features of both the object and the robotic gripper. Then, a deep convolutional neural network is applied on these graspable objects, which aims to find the best graspable area for each object. In order to improve the efficiency in the detection system, we introduce a structured penalty term to optimize the connections between multimodality, which significantly mitigates complexity of the network and outperforms fully connected multimodal processing. We also present a two-stage closed-loop grasping candidate estimator to accelerate the searching efficiency of grasping-candidate generation. Moreover, the combination of a two-stage estimator with the grasping detection network naturally improves detection accuracy. Experiments have been conducted to validate the proposed methods. The results show that our method outperforms the state of the art and runs at real-time speed.
Diversity and stability of restriction enzyme profiles of plasmid DNA from methicillin-resistant Staphylococcus aureus (1990)

Nosocomial infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a significant epidemiological problem. Detecting the sources of epidemic strains and preventing their access to patients, however, depend upon the availability of techniques to reliably distinguish among MRSA strains. We evaluated restriction enzyme analysis of plasmid DNA for use as an epidemiological marker of MRSA strains. The diversity of plasmid types was assessed by examining 120 clinical and environmental MRSA isolates from five southern California hospitals and from the American Type Culture Collection. Thirty-seven distinctive EcoRI digestion patterns were observed. We characterized each strain by the number of plasmids it contained and the sizes of the fragments that were generated by EcoRI. Very few of the isolates (4.2%) lacked plasmids, and some (6.7%) contained DNA that was not digested by EcoRI. Several isolates (12.5%) contained two or more plasmids. We were able to assess the stability of MRSA plasmid types by tracking epidemic strains over a 2-year period. We also examined successive isolates from 10 individual patients during their hospitalization. In all but one case, the patient's plasmid profiles remained unchanged. We conclude that the diversity and stability of MRSA plasmid types make them excellent epidemiological markers. In support of this conclusion, we found that our data provided significant epidemiological insights. Two epidemic strains, accounting for more than half of the infections, were identified in the five hospitals. The remaining cases were sporadic, caused by MRSA strains that appeared very infrequently and that may have originated from sources outside the hospitals.
Should the Asymmetry of Enzymatic Active Centers Always Correlate with the Asymmetry of their Substrates? (1996)

Abstract Analysis of the substrate specificity of DNA polymerases and in part some other enzymes of nucleic acid metabolism towards unnatural L-stereomeric nucleosides and nucleotides was made. As a result, the hypothesis is proposed that when the chiral part of the substrate molecule does not interact specifically with the enzyme, substitution of natural D enantiomers by L compounds is possible.
Defining the "S" in SERMs (2002)

Tamoxifen, which opposes estrogen action in some tissues while mimicking its action in others, has reduced breast cancer mortality significantly during the past decade. In their Perspective,
 Katzenellenbogen and Katzenellenbogen
 discuss new findings (Shang and Brown) that unravel the molecular basis of tamoxifen9s differential activity in breast and uterine tissue.
Detection of Minimal Residual Disease in B Lymphoblastic Leukemia by High-Throughput Sequencing of IGH (2014)

Our results provide strong support for HTS of IGH to enhance clinical prognostication in B-ALL.
The effect of contract type and size on competitiveness in bidding (1997)

Multiple regression is used to construct a prediction equation relating bidder competitiveness (the dependent variable) to the independent variables of bidder, contract type and contract size. The regression model shows that differences in contractor competitiveness are greater for different contract sizes than for different contract types. The most competitive contractors appear to be those with a preferred contract size range. Such a model can be used as part of a more systematic approach in prequalifying contractors. It may also be used by contractors as a basis for assessing bidding performance.
Agrobacterium-mediated transformation of safflower and the efficient recovery of transgenic plants via grafting (2011)

This protocol demonstrates significant improvements in both the efficiency and ease of use over existing safflower transformation protocols. This is the first complete method of genetic transformation of safflower that generates stably-transformed plants and progeny, allowing this crop to benefit from modern molecular applications.
DEVELOPMENT OF A NEW ELECTRONIC BLOCKING SYSTEM (1989)

Since 1986 an electronic blocking system has been installed on 18 low traffic lines in Japan. However, a much cheaper system with simple structure is required which is applicable to less busy traffic lines with a total length of 1700 km. This paper presents a new electronic blocking system. Blocking operation and train detection are done by using an optical-wireless transmission. Safety is ensured by fail-safe microcomputer, and error detection/diagnosis mechanism. The cost will be reduced by 50 percent compared with that of existing system.
Direct visualization of dispersed 11q13 chromosomal translocations in mantle cell lymphoma by multicolor DNA fiber fluorescence in situ hybridization (1996)

Several hematologic malignancies are associated with specific chromosomal translocations. Because of the dispersed distribution, chromosomal breakpoints may be difficult to detect using molecular techniques. We present a new application of a recently developed method, DNA fiber fluorescence in situ hybridization (fiber FISH), which allows direct visualization and mapping of chromosomal breakpoints. We tested this method for detection of the t(11;14)(q13;q32) translocation in mantle cell lymphoma. In DNA fiber FISH, a series of fluorochrome-labeled DNA probes covering several hundreds of kilobasepairs is hybridized to linear DNA molecules (or fibers) prepared from frozen tissue or intact cells. By using alternate fluorescent colors, a potential breakpoint region is stained in a color barcode pattern. Breaks in this region will split the barcode in two complementary parts, from which the breakpoint position can be derived. We used a 250-kb barcode covering the BCL-1 locus to detect 11q13 breakpoints in 20 well-characterized mantle cell lymphomas. A t(11;14) was shown by cohybridization of these probes with probes for the Ig heavy chain locus at 14q32. In 18 of 20 mantle cell lymphomas, a breakpoint within the 11q13/BCL-1 barcode was shown by the presence of multiple, complementary translocation products. Fusion of 11q13 and 14q32 sequences on single fibers indicating t(11;14)(q13;q32) was found in all 18 breakpoint-positive mantle cell lymphomas. In one additional case, fusion of an intact 11q13 barcode with 14q32 sequences indicated a breakpoint 100 kb centromeric of the major translocation cluster of BCL-1. Within the 120-kb region of BCL-1, breakpoints were widely scattered. This explains why, so far, a BCL-1 breakpoint had been detected by Southern blot analysis in only 10 of 19 cases. DNA fiber FISH analysis showed a t(11;14) in 95% of mantle cell lymphoma. The results indicate that DNA fiber FISH is a rapid, simple, and equally powerful method for detection of clustered and dispersed translocation breakpoints.