gebhart/patrepeval huggingface dataset:
Loss of RAB1B promotes triple-negative breast cancer metastasis by activating TGF-β/SMAD signaling (2015)

Triple-negative breast cancer (TNBC) is a highly aggressive tumor subtype associated with a poor prognosis. The mechanism involved in TNBC progression remains largely unknown. To date, there are no effective therapeutic targets for this tumor subtype. In this study, by performing quantitative proteomic analyses in highly metastatic and parental breast cancer cell line, we found that RAB1B, a member of the RAS oncogene family, was significantly down-regulated in highly metastatic breast cancer cells. Moreover, down-regulation of RAB1B was also found to promote the proliferation and migration of TNBC cells in vitro and in vivo. Mechanistically, loss of RAB1B resulted in elevated expression of TGF-β receptor 1 (TβR1) through decreased degradation of ubiquitin, increased levels of phosphorylated SMAD3 and TGF-β-induced epithelial-mesenchymal transition (EMT). Furthermore, low RAB1B expression correlated with poor prognosis in breast cancer patients. Taken together, our findings reveal that RAB1B acts as a metastasis suppressor in TNBC by regulating the TGF-β/SMAD signaling pathway and RAB1B may serve as a novel biomarker of prognosis and the response to anti-tumor therapeutics for patients with TNBC.
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria (2003)

The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205) of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.
A family of human receptors structurally related to <i>Drosophila</i>  Toll (1998)

The discovery of sequence homology between the cytoplasmic domains of Drosophila Toll and human interleukin 1 receptors has sown the conviction that both molecules trigger related signaling pathways tied to the nuclear translocation of Rel-type transcription factors. This conserved signaling scheme governs an evolutionarily ancient immune response in both insects and vertebrates. We report the molecular cloning of a class of putative human receptors with a protein architecture that is similar to Drosophila Toll in both intra- and extracellular segments. Five human Toll-like receptors--named TLRs 1-5--are probably the direct homologs of the fly molecule and, as such, could constitute an important and unrecognized component of innate immunity in humans. Intriguingly, the evolutionary retention of TLRs in vertebrates may indicate another role--akin to Toll in the dorsoventralization of the Drosophila embryo--as regulators of early morphogenetic patterning. Multiple tissue mRNA blots indicate markedly different patterns of expression for the human TLRs. By using fluorescence in situ hybridization and sequence-tagged site database analyses, we also show that the cognate Tlr genes reside on chromosomes 4 (TLRs 1, 2, and 3), 9 (TLR4), and 1 (TLR5). Structure prediction of the aligned Toll-homology domains from varied insect and human TLRs, vertebrate interleukin 1 receptors and MyD88 factors, and plant disease-resistance proteins recognizes a parallel beta/alpha fold with an acidic active site; a similar structure notably recurs in a class of response regulators broadly involved in transducing sensory information in bacteria.
Does tumor necrosis factor α inhibition promote or prevent heart failure in patients with rheumatoid arthritis? (2008)

The findings of this study indicate that TNFalpha inhibitor treatment that effectively reduces the inflammatory activity of RA is more likely to be beneficial than harmful with regard to the risk of heart failure, especially if there is no concomitant therapy with glucocorticoids or cyclooxygenase 2 inhibitors. Furthermore, the data suggest that TNFalpha inhibition does not increase the risk of worsening of prevalent heart failure.
Optical scanning system for light-absorption measurement of deep biological tissue (2011)

A noncontact near-infrared scanning system for multi-distance absorption measurement of deep biological tissue was developed. An 808-nm laser, whose focal point on the surface of biological tissue is controlled by a galvano scanner, is used as a light source. A phosphor is placed at a detection focal point on the tissue surface. The light that propagates through tissue and exits from the tissue surface beneath the phosphor excites the phosphor. The fluorescence emitted from the phosphor is detected by an avalanche photodiode. The system is used to measure 20 points on tissue surface at which source-detector (S-D) distances are 7-45 mm (with 2-mm intervals). Neither the light source nor the detector contacts the tissue surface. The system was validated by using it to measure the absorption change of an absorber (which is embedded in a deep layer of a tissue-simulating phantom) while the surface-layer thickness of the phantom was changed from 1 to 12 mm. It was demonstrated that both the relative absorption change of the absorber and the absolute thickness of the surface layer can be estimated from the measured optical-density change (ΔOD) and the dependence of ΔOD on S-D distance, respectively.
Bounds on the throughput performance of ARQ selective-repeat protocol in Markov channels (2002)

In this paper, we consider the ARQ selective repeat protocol with time-out mechanism, in the presence of Markovian errors on both the forward and the feedback communication channels. Renewal theory is used in order to find performance bounds for the protocol. This technique makes it possible to overcome the computational complexity of an exact analytical approach. Simulation results, that confirm the analysis and document the accuracy of the bounds are also presented. An application to mobile radio is also discussed.
The 'intrinsic adjuvanticity' and immunogenicity of trinitrophenylated lipopolysaccharide. (1975)

One thymus-independent immunogen, trinitrophenylated lipopolysaccharide (TNP-LPS) has been studied in vivo and in vitro in C3H/He and C3H/HeJ strains of mice. C3H/HeJ mice have been shown to be low responders, and C3H/He mice high responders to this immunogen. This 'low responder' status of C3H/HeJ mice has been demonstrated to be consequent to an intrinsic defect present at least at the level of B cells. It was demonstrated that high responder cells or 'in vivo milieu' could not restore this deficit to C3H/HeJ cells. It is proposed that the adjuvanticity, mitogenicity and polyclonal activating capacity of LPS are all fundamental to its property of acting as a thymus-independent carrier for the TNP determinant. This observation is discussed from the point of view that the T-cell independence for an antigen cannot derive solely from its multivalency but must depend upon the intrinsic adjuvanticity of that molecule.
WPI Precision Personnel Locator System: Antenna Geometry Estimation using a Robust Multilateralization Technique (2009)

This paper describes further efforts towards antenna geometry estimation in the WPI Precision Personnel Locator
system, which is under development as a portable, zero-fixedinfrastructure, and spectrally compliant RF-based system for location and tracking of personnel situated in indoor environments. The system consists of transmitters worn by individuals to be tracked, and receiver hardware which collectively estimates position mounted upon response vehicles. Pursuit of any location solution requires the availability of an estimate of the receivers’ antenna positions of sufficient accuracy so as not to contribute superfluous error to personnel location estimates. By utilizing each receiving antenna temporarily as a transmitter, sufficient information is collected to derive
a solution for the antenna positions, however, while these
antennas are outdoors, they experience the same multipath
effects as the indoor-to-outdoor radio channel and require
application of a robust multilateralization technique not considered in the previous paper. This paper presents methods for antenna geometry estimation based on such a technique and will present results, from a number of experimental tests, illustrating antenna location error as well as total system error when driven by such antenna geometry solutions.
Synthetic Control Methods for Comparative Case Studies: Estimating the Effect of California’s Tobacco Control Program (2010)

Building on an idea in Abadie and Gardeazabal (2003), this article investigates the application of synthetic control methods to comparative case studies. We discuss the advantages of these methods and apply them to study the effects of Proposition 99, a large-scale tobacco control program that California implemented in 1988. We demonstrate that, following Proposition 99, tobacco consumption fell markedly in California relative to a comparable synthetic control region. We estimate that by the year 2000 annual per-capita cigarette sales in California were about 26 packs lower than what they would have been in the absence of Proposition 99. Using new inferential methods proposed in this article, we demonstrate the significance of our estimates. Given that many policy interventions and events of interest in social sciences take place at an aggregate level (countries, regions, cities, etc.) and affect a small number of aggregate units, the potential applicability of synthetic control methods to comparative case studies is very large, especially in situations where traditional regression methods are not appropriate.
Evaluation of electromyographic monitoring during insertion of thoracic pedicle screws (2001)

We prospectively studied the use of intercostal EMG monitoring as an indicator of the accuracy of the placement of pedicle screws in the thoracic spine. We investigated 95 thoracic pedicles in 17 patients. Before insertion of the screw, the surgeon recorded his assessment of the integrity of the pedicle track. We then stimulated the track using a K-wire pedicle probe connected to a constant current stimulator. A compound muscle action potential (CMAP) was recorded from the appropriate intercostal or abdominal muscles. Postoperative CT was performed to establish the position of the screw. The stimulus intensity required to evoke a muscle response was correlated with the position of the screw on the CT scan. There were eight unrecognised breaches of the pedicle. Using 7.0 mA as a threshold, the sensitivity of EMG was 0.50 in detecting a breached pedicle and the specificity was 0.83. Thoracic pedicle screws were accurately placed in more than 90% of patients. EMG monitoring did not significantly improve the reliability of placement of the screw.
Design of SAW Filter with Minimum Phase Response (1978)

Synthes s of SAW filters is generally achieved in terms of transversal linear phase response. However, this procedure only leads to approximative constant time delay because of recursive effects like triple transit echos and because of distorsions from this simple model in SAW transducers. On the other hand, it is possible to synthetize minimum phase transversal filters with a slight improvement in terms of weighting coefficient number of required coefficients. In addition , the actualgroup delay is then shorter which is of interest in some applications. Moreover, in the minimum phase design, the largest coefficients are located at the same end of the transducer which is favourable for a better accuracy of the transversal filter model. sis will be described and experimental results corresponding to both implementations will be reported on a 70 MHz - center frequency, 5 X and 10 % bandwidth Li Ta 03 filter. sensitivity or
SELF‐INJURIOUS BEHAVIOR: SHAPING “HEAD‐BANGING” IN MONKEYS<sup>1</sup> (1970)

Head-banging, a common phenomenon among the mentally retarded, was shaped, brought under stimulus control, extinguished, and re-established in two monkeys through reinforcement and discrimination procedures of operant conditioning. The behavior was stable and led to lacerations, a condition that qualifies head-banging as self-injurious. The principles of the analysis of behavior used here may well be of value in the etiology and treatment of some human head-banging.
First results in autonomous landing and obstacle avoidance by a full-scale helicopter (2012)

Currently deployed unmanned rotorcraft rely on carefully preplanned missions and operate from prepared sites and thus avoid the need to perceive and react to the environment. Here we consider the problems of finding suitable but previously unmapped landing sites given general coordinates of the goal and planning collision free trajectories in real time to land at the “optimal” site. This requires accurate mapping, fast landing zone evaluation algorithms, and motion planning. We report here on the sensing, perception and motion planning integrated onto a full-scale helicopter that flies completely autonomously. We show results from 8 experiments for landing site selection and 5 runs at obstacles. These experiments have demonstrated the first autonomous full-scale helicopter that successfully selects its own landing sites and avoids obstacles.
Crystallization of polyethylene at elevated pressures (1971)

Abstract The crystallization from the melt of three sharp polyethylene fractions has been studied at 5 kbar. It has been shown that the thickness of so‐called extended‐chain lamellae is a function of time, temperature, and molecular weight. There is by no means just the fully extended molecular configuration present. Crystallization is qualitatively similar to that of chain‐folded crystals at 1 bar, giving an optimum lamellar thickness which increases with time and decreasing supercooling. Fractional crystallization is widespread and is a major cause of disparate lamellar thickness. Isothermal thickening of lamellae during crystallization has been established directly. Morphological detail suggests further that layers can increase their thickness tenfold over their initial size.
Elevated C-Reactive Protein Levels and Impaired Endothelial Vasoreactivity in Patients With Coronary Artery Disease (2000)

Thus, elevated CRP serum levels indicative of a systemic inflammatory response are associated with a blunted systemic endothelial vasodilator function. The identification of elevated CRP levels as a transient independent risk factor for endothelial dysfunction might provide an important clue to link a systemic marker of inflammation to atherosclerotic disease progression.
The electrical conductivity and breakdown phenomena in polyester polymer-quinoline salt of tetracyanoquinodimethane composites (2003)

The author studied the influence of the length of the conducting particle of the filler on the electrical conductivity of the composites obtained by embedding into polyester polymer needlelike conducting crystals of quinoline salt of tetracyanoquinodimethane. The results clearly demonstrated the importance of shape factors for the formation of a conducting network and percolative charge transport in composite systems. The results are in agreement with the previous data, which have shown that very low values of threshold contents of conducting fillers are observed for large particle-length-to-diameter ratios. Other results confirmed the assumption that the decrease of electrical conductivity of samples after the critical field is exceeded is caused by breaks of the conduction network at the weak points, and that the electrical conduction of low-conduction samples is probably dominated by injection of charge carriers, fluctuation-induced tunneling, and prebreakdown effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Instrument for rock bolt inspection by means of ultrasound (2015)

In this paper we present a new digital ultrasonic instrument for nondestructive inspection of rock bolts using guided waves. The Rock Bolt Tester (RBT) instrument applies long-range ultrasound to investigate bolt's status, especially its grouting condition. RBT features an application tailored ultrasound probe that transmits high-energy, low frequency (below 100kHz) guided waves. It is also capable of receiving weak echoes reflected from the discontinuities at the bolt surface as well its end-echo, which have propagated back and forth in the range of up to 4 meters. The RBT is a portable instrument that consists of a specially designed analog electronics for generation and reception of guided waves and an embedded digital computer that performs for signal processing, operator communication and data storage. In the paper we will focus on advanced processing techniques applied to enhance tiny echo signals received by the probe.
Structure of the lipophosphoglycan from Leishmania major. (1990)

The major cell surface glycoconjugate of the parasitic protozoan Leishmania major is a heterogeneous lipophosphoglycan. It has a tripartite structure, consisting of a phosphoglycan (Mr 5,000-40,000), a variably phosphorylated hexasaccharide glycan core, and a lysoalkylphosphatidylinositol (lysoalkyl-PI) lipid anchor. The structures of the phosphoglycan and the hexasaccharide core were determined by monosaccharide analysis, methylation analysis, fast atom bombardment-mass spectrometry, one- and two-dimensional 500-MHz (correlated spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA] 1H NMR spectroscopy, and exoglycosidase digestions. The phosphoglycan consists of eight types of phosphorylated oligosaccharide repeats which have the general structure, [formula: see text] where R = H, Galp(beta 1-3), Galp(beta 1-3)Galp(beta 1-3), Arap(alpha 1-2)Galp(beta 1-3), Glcp(beta 1-3)Galp(beta 1-3), Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3), Arap(alpha 1-2)Galp(beta 1-3)Galp(beta 1-3), or Arap(alpha 1-2)Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3)Galp(beta 1-3), and where all the monosaccharides, including arabinose, are in the D-configuration. The average number of repeat units/molecule (n) is 27. Data are presented which suggest that the nonreducing terminus of the phosphoglycan is capped exclusively with the neutral disaccharide Manp(alpha 1-2)Manp alpha 1-. The structure of the glycan core was determined to be, [formula: see text] where approximately 60% of the mannose residues distal to the glucosamine are phosphorylated and where the inositol is part of the lysoalkyl-PI lipid moiety containing predominantly 24:0 and 26:0 alkyl chains. The unusual galactofuranose residue is in the beta-configuration, correcting a previous report where this residue was identified as alpha Galf. Although most of the phosphorylated repeat units are attached to the terminal galactose 6-phosphate of the core to form a linear lipophosphoglycan (LPG) molecule, some of the mannose 6-phosphate residues may also be substituted to form a Y-shaped molecule. The L. major LPG is more complex than the previously characterized LPG from Leishmania donovani, although both LPGs have the same repeating backbone structure and glycolipid anchor. Finally we show that the LPG anchor is structurally related to the major glycolipid species of L. major, indicating that some of these glycolipids may have a function as precursors to LPG.
GeoLife2.0: A Location-Based Social Networking Service (2009)

GeoLife2.0 is a GPS-data-driven social networking service where people can share life experiences and connect to each other with their location histories. By mining peoplepsilas location history, GeoLife can measure the similarity between users and perform personalized friend recommendation for an individual. Later, we can predict the individualpsilas interest level in the locations visited by their friends while have not been found by them. The locations with relatively high interesting level can be recommended. Therefore, GeoLife2.0 can expand a userpsilas social network, provide them with a trustworthy resource matching their interests and help them sponsor geo-related activities like cycling with minimal effort.
The sea within us: disorders of body water homeostasis. (2007)

The use of a sensitive radioimmunoassay to measure plasma vasopressin led to the clarification of the role of vasopressin in most clinical hyponatremic states, an advance that had been impossible with the less sensitive bioassay for antidiuretic hormone. The cloning of the V2 vasopressin receptor on the basolateral membrane of the principal cells of the collecting duct demonstrated that the majority of congenital nephrogenic diabetes insipidus (NDI) was caused by mutations in this V2 receptor gene. The Nobel Prize discovery of the first membrane water channel by Agre and colleagues allowed for the molecular understanding of many disorders of water homeostasis, several of which are discussed in this review. Mutations of the vasopressin-regulated water channel on the principal cells of the collecting duct, namely aquaporin (AQP)2, account for a minority of cases of congenital NDI. Downregulation of AQP2 expression has subsequently proved important in an array of clinically significant causes of acquired NDI. Most important clinically, has been the discovery of several orally active, non-peptide V2 receptor antagonists, which have significant implications in the treatment of hyponatremic states. This review discusses the major advances that have increased our understanding of the mechanisms of renal water regulation in health and disease. The relationship between osmotic and non-osmotic regulation of antidiuretic hormone (arginine vasopressin) release is discussed.
A Signal-to-Interference Ratio Based Downlink Scheduling Scheme for WCDMA Mobile Communication System (2005)

In this paper, we propose a QoS-aware power-strength classified packet scheduling (PCPS) scheme that can classify the transmission power-strength of a VBR connection into several classes and determine the admitted service rate of each class at connection setup time. During the transmission time of each connection, PCPS scheme can dynamically adjust the downlink service rate of each connection in accordance with the admitted service rate of the current transmission power-strength class while retaining all connection's frame error rate requirements. With this power-strength classified scheduling, PCPS scheme can decrease the average packet delay and increase the bandwidth utilization. Furthermore, a two-stage scheduling architecture is also employed to reduce the scheduling complexity resulted from simultaneous adjustment of both service rate and transmission power-strength in WCDMA. Performance results show that the delay bound and the packet loss ratio of a VBR connection can be guaranteed.