gebhart/patrepeval huggingface dataset:
Efficient packet marking for large-scale IP traceback (2002)

We present a new approach to IP traceback based on the probabilistic packet marking paradigm. Our approach, which we call randomize-and-link, uses large checksum cords to "link" message fragments in a way that is highly scalable, for the checksums serve both as associative addresses and data integrity verifiers. The main advantage of these checksum cords is that they spread the addresses of possible router messages across a spectrum that is too large for the attacker to easily create messages that collide with legitimate messages. Our methods therefore scale to attack trees containing hundreds of routers and do not require that a victim know the topology of the attack tree a priori. In addition, by utilizing authenticated dictionaries in a novel way, our methods do not require routers sign any setup messages individually.
Renal and Anti-Aldosterone Actions of Vasopressin-2 Receptor Antagonism and B-Type Natriuretic Peptide in Experimental Heart Failure (2010)

Coadministration of TLV and BNP in experimental HF resulted in a beneficial profile of renal, neurohumoral, and hemodynamic actions, specifically potent diuresis with natriuresis, neutral effect on mean arterial pressure, and lack of aldosterone activation.
Virus-Induced Immunoinflammatory Lesions in the Absence of Viral Antigen Recognition (1998)

Herpetic stromal keratitis (HSK) is a CD4+ T cell-controlled immunopathologic lesion in the eye that results from infection with herpes simplex virus (HSV). Target Ags involved in HSK remain undefined. In this study, we determined if HSK could be induced in animals genetically incapable of generating HSV Ag-specific CD4+ T cells. Mice bearing transgenic TCR specific to OVA peptide 323-339 (DO11.10) were crossed to SCID mice whose offspring (Tg-SCID) possessed CD4+ T cells, >98% of which expressed the OVA peptide-specific TCR. HSV infection of Tg-SCID mice was lethal, and mice failed to generate detectable T cell responses even after repeated immunization with a mutant avirulent virus (AN-1). Immunization with AN-1 virus followed by ocular challenge with HSV resulted in ocular inflammation before encephalitis, in contrast to the protection conferred in the control BALB/c and DO11.10 mice. These results indicate that clinical HSK may not require viral Ag recognition by CD4+ T cells and that T cells of irrelevant specificity can be recruited, activated, and driven into effector function in the HSV-infected cornea. This is suggested to represent a bystander activation effect resulting from the presence of proinflammatory mediators resulting from HSV replication.
Multispectral Object Segmentation and Retrieval in Surveillance Video (2006)

This paper describes a system for object segmentation and feature extraction for surveillance video. Segmentation is performed by a dynamic vision system that fuses information from thermal infrared video with standard CCTV video in order to detect and track objects. Separate background modelling in each modality and dynamic mutual information based thresholding are used to provide initial foreground candidates for tracking. The belief in the validity of these candidates is ascertained using knowledge of foreground pixels and temporal linking of candidates. The transferable belief model is used to combine these sources of information and segment objects. Extracted objects are subsequently tracked using adaptive thermo-visual appearance models. In order to facilitate search and classification of objects in large archives, retrieval features from both modalities are extracted for tracked objects. Overall system performance is demonstrated in a simple retrieval scenario.
Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase (1988)

We have determined the fidelity of in vitro DNA synthesis catalyzed at high temperature by the DNA polymerase from the thermophilic bacterium Thermus aquaticus. Using a DNA substrate that contains a 3'-OH terminal mismatch, we demonstrate that the purified polymerase lacks detectable exonucleolytic proofreading activity. The fidelity of the Taq polymerase was measured by two assays which score errors produced during in vitro DNA synthesis of the lacZ alpha complementation gene in M13mp2 DNA. In both assays, the Taq polymerase produces single-base substitution errors at a rate of 1 for each 9000 nucleotides polymerized. Frameshift errors are also produced, at a frequency of 1/41,000. These results are discussed in relation to the effects of high temperature on fidelity and the use of the Taq DNA polymerase as a reagent for the in vitro amplification of DNA by the polymerase chain reaction.
Infusion of platelet-derived growth factor or basic fibroblast growth factor induces selective glomerular mesangial cell proliferation and matrix accumulation in rats. (1993)

Mesangial cell (MC) proliferation and extracellular matrix expansion are involved in the pathogenesis of glomerulosclerosis and renal failure. In vitro, PDGF and basic fibroblast growth factor (bFGF) regulate MC proliferation and/or matrix production. To elucidate the role of PDGF and bFGF in vivo, equimolar concentrations of recombinant PDGF-BB or bFGF or vehicle were infused intravenously into rats over a 7-d period. Rats were either nonmanipulated ("normals") or had received a subnephritogenic dose of anti-MC antibody ("anti-Thy 1.1 rats") before the infusion period. Glomerular cell proliferation (anti-proliferating cell nuclear antigen immunostaining) on days 2, 4, and 7 was unchanged in vehicle-infused normals or anti-Thy 1.1 rats. PDGF infusion increased glomerular cell proliferation 32-fold in anti-Thy 1.1 rats and an 11-fold in normals on day 2. bFGF increased glomerular cell proliferation fourfold in anti-Thy 1.1 rats but was ineffective in normals. Induction of cell proliferation in all kidneys was limited to the glomerulus. The majority of proliferating cells were identified as MC by double immunolabeling. No significant proteinuria, glomerular leukocyte, or platelet influx developed in any group. Glomerular matrix expansion with increased deposition of type IV collagen, laminin, and fibronectin, as well as upregulated laminin and collagen IV mRNA expression was confined to PDGF-infused anti-Thy 1.1 rats. These results show that PDGF and, to a lesser degree, bFGF are selective MC mitogens in vivo and that previous subclinical injury can enhance this MC response. The data thereby support a role of these cytokines in the pathogenesis of glomerulosclerosis.
A video retrieval and sequencing system (1995)

Video is an effective medium for capturing the events in the real world around us, and a vast amount of video materials exists, covering a wide range of applications. However, widespread use of video in computer applications is often impeded by the lack of effective tools to manage video information systematically. This article discusses the design and implementation of a frame-based video retrieval and sequencing system (VRSS). The system is designed to support the entire process of video information management: segmenting, indexing, retrieving, and sequencing of video data. A semiautomatic tool is developed to divide video sequences into meaningful shots. Each video shot is logged using text descriptions, audio dialogue, and cinematic attributes. A two-layered, concept-based model is used as the basis for accurately retrieving relevant video shots based on users' free-text queries. A cinematic, rule-based, virtual editing tool is also developed to sequence the video shots retrieved for presentation within a specified time constraint. The system has been tested on a video documentary on the NUS (National University of Singapore) engineering faculty. The results of video retrieval experiments are encouraging.
When the bed takes the similarity of the grave. (1977)

Photoexcitation of p-nitroaniline (PNA) and its N-alkyl derivs. results in the formation of triplet states with dipole moments considerably larger than that of the ground state, as monitored by time-resolved microwave cond. (TRMC). The triplet state lifetime, tT, is only 54 ns for PNA in benzene but increases to 1400 ns on N,N-di-Me substitution and to 275 ns in the more polar solvent p-dioxane. This sensitivity of tT is attributed to the close proximity of all of the lowest lying singlet and triplet np* and pp* states of PNA, which results in substantial S1 .tautm. T1 mixing. The dipole moment of the \\"pure\\" 3pp* state is estd. to be 11 D. Methylene-bridged arrays of PNA moieties with two- and three-fold Dn symmetry, 2-PNA and 3-PNA, are also found to have highly dipolar triplet states, indicating that symmetry breaking and exciton localization occur in T1. Flip-flop interchange between the resonant dipolar structures is estd. to take place on a time scale of tens of picoseconds. Collective interactions between the PNA moieties in the multichromophoric arrays results in a marked blue shift in the first absorption max. from 384 nm for 1-PNA to 375 nm for 2-PNA and to 354 nm for 3-PNA
Mapping the human genome (1989)

The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.
Kerr-Nonlinearity Optical Parametric Oscillation in an Ultrahigh-QToroid Microcavity (2004)

Kerr-nonlinearity induced optical parametric oscillation in a microcavity is reported for the first time. Geometrical control of toroid microcavities enables a transition from stimulated Raman to optical parametric-oscillation regimes. Optical parametric oscillation is observed at record low threshold levels (174 micro-Watts of launched power) more than 2 orders of magnitude lower than for optical-fiber-based optical parametric oscillation. In addition to their microscopic size (typically tens of microns), these oscillators are wafer based, exhibit high conversion efficiency (36%), and are operating in a highly ideal "two photon" emission regime, with near-unity (0.97+/-0.03) idler-to-signal ratio.
Experiments in Thermal Spallation of Various Rocks (1996)

The greatest limitation of the spallation process is its inability to spall (or to consistently spall) many rocks encountered in petroleum drilling and mining operations. The New Mexico Institute of Mining and Technology has conducted a series of experiments to investigate the possibility of expanding the use of the spallation process to the penetration of rocks generally considered not to be spallable. The methods used during this work were 1) spalling at temperatures below that produced by the stoichiometric burning of fuel oil and air, and 2) spalling by alternately heating and quenching the rock surfaces. No success was experienced in spalling at the lower temperatures, but initial tests showed the alternate heating and chilling system to be successful, particularly in penetrating travertine limestone. However, continued testing indicated that, unless the rocks are extremely uniform in composition, spalling will result in highly irregular holes or holes that cannot be directionally controlled.
Early development of serotonin‐containing neurons and pathways as seen in wholemount preparations of the fetal rat brain (1988)

The early development of serotonin-containing neurons was studied in wholemounts of the fetal rat brain (E12-E18). The wholemounts were treated immunocytochemically according to an immunoperoxidase technique to reveal a panorama of developing serotoninergic neurons. Serotoninergic neurons were localized to two discrete groups or clusters within the brainstem. Serotonin-containing neurons were identified first at E12 forming a rostral cluster of cells just caudal to the mesencephalic flexure. The more caudal cluster of cells first appeared at E14 in the medulla. During the period from E12 to E18, the immunoreactive cells increased in number and acquired a more complex dendritic tree while migrating to their permanent position. At E16, cells of the rostral group exhibited remarkably uniform mediolateral orientation. The rostral group of immunoreactive neurons gave rise to almost all ascending fibers, whereas the caudal group gave rise to the majority of descending fibers. Growing serotoninergic fibers were tipped by prominent growth cones, which were strongly immunoreactive. The fibers demonstrated prominent orientational selectivity with an almost total separation into ascending and descending bundles. Some of the ascending immunoreactive fibers displayed acute changes in their direction of growth, suggesting that the orientation of serotininergic fibers is mediated by directional cues that are specific to particular populations of serotoninergic fibers. Serotoninergic axons within the medial forebrain bundle were demonstrated particularly well and their ascent and rate of growth toward the forebrain could be easily followed. Immunoreactive fibers entered the telencephalon at E17 two portals, one along the lateral border of the hypothalamus and one rostrally, adjacent to the olfactory tubercle. In wholemounts at E18, fibers arising from this latter location could be followed as two distinct bands within the pallium; a basal band located ventrolaterally, adjacent to the lateral olfactory tract, and a dorsal band located at the medial edge of the telencephalon. Both fascicles were directed toward the occipital pole and contained unbranched fibers. At E18, serotoninergic axons arising from these two loosely organized fascicles covered most of the frontal telencephalon. The results of the present study indicate that wholemounts of embryonic brain can provide novel spaciotemporal data on the development of neuro-transmitter systems and may in the future prove to be useful experimental preparations in developmental neurobiology.
Receptor-mediated in vitro gene transformation by a soluble DNA carrier system. (1987)

We present, here, evidence that foreign DNA can be specifically delivered to cells by a soluble carrier system that takes advantage of receptor-mediated endocytosis. Our experiments were based on the following concepts: hepatocytes possess a unique receptor that binds and internalizes galactose-terminal (asialo-)glycoproteins; DNA can bind to polycations in a strong but noncovalent manner forming soluble complexes; and the gene for chloramphenicol acetyltransferase, a bacterial enzyme that acetylates chloramphenicol, is not present in mammalian cells. We coupled asialoorosomucoid (ASOR) to poly-L-lysine to form an asialoorosomucoid-poly-L-lysine conjugate. The plasmid, pSV2 CAT, was complexed to the conjugate in a molar ratio of 1:2. To test this complex, a model system was used consisting of hepatoma cell lines, Hep G2, asialoglycoprotein receptor (+), and SK-Hep 1, receptor (-). Each cell line was incubated with filtered ASOR X poly-L-lysine X DNA complex, or controls consisting of DNA plus ASOR, DNA plus poly-L-lysine, or DNA alone. Cells were assayed for the presence of chloramphenicol acetyltransferase activity as a measure of gene transformation. SK-Hep 1, receptor (-) cells, produced no detectable acetylated chloramphenicol derivatives under any condition. However, Hep G2, receptor (+) cells, incubated with the ASOR X poly-L-lysine X DNA complex were transformed as indicated by the presence of chloramphenicol acetyltransferase activity (0.028 chloramphenicol acetyltransferase units/10(6) cells). Mixtures of individual components of the complex failed to transform these cells. Competition by a 10-fold excess of ASOR prevented gene transformation by the ASOR X poly-L-lysine X DNA complex.
The Olfactory Bulb: Coding and Processing of Odor Molecule Information (1999)

Olfactory sensory neurons detect a large variety of odor molecules and send information through their axons to the olfactory bulb, the first site for the processing of olfactory information in the brain. The axonal connection is precisely organized so that signals from 1000 different types of odorant receptors are sorted out in 1800 glomeruli in the mouse olfactory bulb. Individual glomerular modules presumably represent a single type of receptor and are thus tuned to specific molecular features of odorants. Local neuronal circuits in the bulb mediate lateral inhibition among glomerular modules to sharpen the tuning specificity of output neurons. They also mediate synchronized oscillatory discharges among specific combinations of output neurons and may contribute to the integration of signals from distinct odorant receptors in the olfactory cortex.
Nerve cuff electrode with shape memory alloy armature: design and fabrication. (2002)

In this paper, a new nerve cuff electrode with shape memory alloy armature is presented. The proposed electrode is dedicated either to peripheral nerve stimulation or recording and its manufacturing does not require any expensive or complex technique. Shape Memory Alloy (SMA) armature ensures the complete and firm closing of the electrode, so that the complexity of the installation procedure is considerably reduced. A preliminary analysis of the electrode mechanical behavior prior, during and after installation has been done through numerical simulations and in vitro testing. It was proved theoretically and experimentally that the SMA electrode closes completely with an appropriate few second delay after its installation. No external fixation such as sutures is needed to secure permanent electrode-nerve contact. Furthermore, theoretical analysis has shown that the design of SMA electrode can be adapted for safe close-fitting installation, thanks to the device partial opening in case of nerve swelling.
Zipper Protein, a B-G Protein with the Ability to Regulate Actin/Myosin 1 Interactions in the Intestinal Brush Border (1996)

We recently identified a 28-kDa protein in the intestinal brush border that resembled tropomyosin in terms of size, homology, and alpha helical content. This protein contained 27 heptad repeats, nearly all of which began with leucine, leading to its name zipper protein. Subsequent analysis, however, indicated that both a 49-kDa and a 28-kDa immunoreactive protein existed in intestinal brush-border extracts. Using 5'-rapid amplification of cDNA ends analysis, we extended the N-terminal sequence of zipper protein to the apparent translation start site. This additional sequence contained a putative transmembrane domain and two potential tryptic cleavage sites C-terminal to the transmembrane domain which would release a 28-kDa cytoplasmic protein if utilized. The additional sequence was highly homologous to members of the B-G protein family, a family with no known function. Immunoelectron microscopy showed that zipper protein was confined to the membrane of the microvillus where it was in close association with brush-border myosin 1 (BBM1). Recombinant zipper protein (28-kDa cytoplasmic portion) blocked the binding of actin to BBM1 and inhibited actin-stimulated BBM1 ATPase activity. In contrast, zipper protein had no effect on endogenous or K/EDTA-stimulated BBM1 ATPase activity. Furthermore, zipper protein displaced tropomyosin from binding to actin, suggesting that these homologous proteins bind to the same sites on the actin molecule. We conclude that zipper protein is a transmembrane protein of the B-G family localized to the intestinal epithelial cell microvillus. The extended cytoplasmic tail either in the intact molecule or after tryptic cleavage may participate in regulating the binding and, thus, activation of BBM1 by actin in a manner similar to tropomyosin.
Stereospecificity of nucleases towards phosphorothioate-substituted RNA: stereochemistry of transcription by T7 RNA polymerase (1987)

Transcription by T7 RNA polymerase has been studied using a chiral ATP analogue. The Sp diastereoisomer of adenosine 5'-O-(1-thiotriphosphate) (ATP alpha S) was incorporated into RNA with an apparent KM of approximately 15 microM, similar to that for ATP; the Rp diastereoisomer was neither a substrate nor a competitive inhibitor. The configuration of the phosphodiester link in the RNA produced was analyzed with stereospecific nucleases. The rate of nuclease digestion was compared with the rate of digestion of phosphorothioate-substituted RNA of known stereochemistry synthesized by E. coli RNA polymerase. Surprisingly, the nucleases exhibited reduced discrimination compared with their activity on dinucleotides. The results show that phosphorothioate-substituted RNA transcribed by T7 RNA polymerase has the same configuration as that transcribed by E. coli RNA polymerase, ie. Rp. Thus, the reaction proceeds with inversion of configuration at phosphorus.
Exploring and Engineering the Cell Surface Interface (2005)

Cells are inherently sensitive to local mesoscale, microscale, and nanoscale patterns of chemistry and topography. We review current approaches to control cell behavior through the nanoscale engineering of materials surfaces. Far-reaching implications are emerging for applications including medical implants, cell supports, and materials that can be used as instructive three-dimensional environments for tissue regeneration.
Platemate (2011)

We introduce PlateMate, a system that allows users to take photos of their meals and receive estimates of food intake and composition. Accurate awareness of this information can help people monitor their progress towards dieting goals, but current methods for food logging via self-reporting, expert observation, or algorithmic analysis are time-consuming, expensive, or inaccurate. PlateMate crowdsources nutritional analysis from photographs using Amazon Mechanical Turk, automatically coordinating untrained workers to estimate a meal's calories, fat, carbohydrates, and protein. We present the Management framework for crowdsourcing complex tasks, which supports PlateMate's nutrition analysis workflow. Results of our evaluations show that PlateMate is nearly as accurate as a trained dietitian and easier to use for most users than traditional self-reporting.