gebhart/patrepeval huggingface dataset:
A Blackboard Architecture for Query Optimization in Object Bases (1993)

Adopting the blackboard architecture from the area of Artificial Intelligence, a novel kind of optimizer enabling two desirable ideas will be proposed. Firstly, using such a well-structured approach backpropagation of the optimized queries allows an evolutionary improvement of (crucial) parts of the optimizer. Secondly, the A 3 search strategy can be applied to harmonize two contrary properties: Alternatives are generated whenever necessary, and straight-forward optimizing is performed whenever possible, however. The generic framework for realizing a blackboard optimizer is proposed first. Then, in order to demonstrate the viability of the new approach, a simple example optimizer is presented. It can be viewed as an incarnation of the generic framework. 1 Introduction Query optimizers---no matter whether relational or object-oriented---are among the most complex software systems that have been built. Therefore, it is not surprising that the design of query optimizers is still a &quot;hot...
A novel method achieving ultra-high geometrical resolution in scanning tunnelling microscopy (2008)

We report a new contrast mechanism in which scanning tunnelling micrographs of a certain class of molecules resemble chemists' structure formulae. The method is based on adding molecular hydrogen below its condensation temperature to the tunnelling junction of a low-temperature scanning tunnelling microscope. In the presence of hydrogen, the scanning tunnelling microscope contrast can be switched between the conventional mapping of the electronic local density of states and the new geometric imaging by selecting the appropriate bias voltage. Scanning tunnelling spectroscopy suggests that the coupling of the electron tunnelling current to an internal degree of freedom in the tunnelling junction is responsible for the geometric contrast. The new scanning tunnelling hydrogen microscopy (STHM) allows the chemical identification of certain molecular species by their structure.
Thermal stability of Pd/Ge-based ohmic contacts to n-type GaAs (1998)

The microstructural changes that occur during high temperature annealing (450–600 °C) of Pt/Ti/Ge/Pd ohmic contacts to n-type GaAs have been studied using transmission electron microscopy (TEM). The metal layers were deposited sequentially by electron beam evaporation onto GaAs doped with Si to a level of ≈5×1018 cm−3. The deposition sequence and metal layer thicknesses were: Pt (50 nm), Ti (30 nm), Ge (90 nm) and Pd (45 nm). The contact microstructure remained uniform up to 550 °C and consisted of a continuous polycrystalline layer of GePd at the semiconductor surface, along with pockets of epitaxially grown Ge. Annealing at 550 °C resulted in the nucleation of a Ge-deficient phase, Ge8Pd21, at the GePd/GaAs interface, which protruded into the GaAs and deteriorated the uniformity of the contact. At higher annealing temperatures, the contact degraded rapidly due to inward diffusion of Ti and Pt and outward diffusion of As, leading to the formation of several binary and ternary phases.
Complete clot ingestion with cyclical ADAPT increases first-pass recanalization and reduces distal embolization (2019)

Complete clot ingestion results in fewer distal emboli and the highest rates of first-pass complete recanalization. The rate of complete ingestion during aspiration thrombectomy is a function of both the inner diameter of the aspiration catheter and use of cyclical aspiration.
Determinants of 24-hour energy expenditure in man. Methods and results using a respiratory chamber. (1986)

Daily human energy requirements calculated from separate components of energy expenditure are inaccurate and usually in poor agreement with measured energy intakes. Measurement of energy expenditure over periods of 24 h or longer is needed to determine more accurately rates of daily energy expenditure in humans. We provide a detailed description of a human respiratory chamber and methods used to determine rates of energy expenditure over 24-h periods in 177 subjects. The results show that: fat-free mass (FFM) as estimated by densitometry is the best available determinant of 24-h energy expenditures (24EE) and explains 81% of the variance observed between individuals (24EE [kcal/d] = 597 + 26.5 FFM); 24EE in an individual is very reproducible (coefficient of variation = 2.4%); and even when adjusted for differences in FFM, there is still considerable interperson variability of the daily energy expenditure. A large portion of the variability of 24EE among individuals, independent of differences in body size, was due to variability in the degree of spontaneous physical activity, i.e., "fidgeting," which accounted for 100-800 kcal/d in these subjects.
Epitaxially Regrown GaAs-Based Photonic Crystal Surface-Emitting Laser (2012)

A GaAs-based epitaxially regrown photonic crystal surface-emitting laser is proposed and demonstrated at room temperature. The photonic crystal band-structure is mapped through the angular dependence of subthreshold electroluminescence, allowing the photonic crystal coupling coefficients to be determined.
Lack of correlation between basal expression levels and susceptibility to transcriptional shutdown among single-gene murine leukemia virus vector proviruses (1994)

Integrated retroviruses or retroviral vectors may be transcriptionally inactive although their promoter-enhancer regions are able to direct transcription in the host cell. We have used single-gene retroviral vectors with a long terminal repeat-directed neo marker gene to determine if the level of transcription relates to the susceptibility of a provirus to inactivation. We used two isogenic vectors, carrying long terminal repeats with a strong and a weak transcriptional enhancer derived from SL3-3 and Akv murine leukemia viruses, respectively. Nonselected cell clones of the murine lymphoid cell line L691 with single integrated vector proviruses exhibiting a 20-fold range of initial expression levels were studied. The basal expression level of a given cell clone with a single provirus did not show any pattern of correlation with the long-term stability of expression, as monitored for periods up to 150 days. Our results thus indicate that the inactivation mechanism operates independently of the initial transcriptional activity of the provirus.
6 Did the RNA World Exploit an Expanded Genetic Alphabet (1999)

SINGLE BIOPOLYMER LIFE FORMS BASED ON RNA In terms of its macromolecular chemistry, life on Earth can be classified as a “two-biopolymer” system. Nucleic acid is the encoding biopolymer, storing information within an organism and passing it to its descendants. Nucleic acids also direct the biosynthesis of the second biopolymer, proteins. Proteins generate most of the selectable traits in contemporary organisms, from structure to motion to catalysis. The two-biopolymer strategy evidently works rather well. It has lasted on Earth for several billion years, adapting in this time to a remarkable range of environments, surviving formidable geobiological (and perhaps cosmic) events that threatened its extinction, and generating intelligence capable of exploring beyond Earth. The terrestrial version of two-biopolymer life contains a well recognized paradox, however, one relating to its origins. It is difficult enough to envision a nonbiological mechanism that would allow either proteins or nucleic acids to emerge spontaneously from nonliving precursors. But it seems astronomically improbable that both biopolymers arose simultaneously and spontaneously, and even more improbable (if that can be imagined) that both biopolymers so arose with an encoder-encoded relationship. Accordingly, a variety of “single-biopolymer” models have been proposed as forms of life that antedated the two-biopolymer system. These (presumably) could have emerged more easily than a two-biopolymer system. Such models postulate that a single biopolymer can perform the catalytic and information repository roles and undergo the Darwinian evolution that defines life (Joyce 1994). For example, Rich (1962), Woese (1967), Orgel (1968), and Crick (1968) proposed that the...
Shear Orientation of Lyotropic Hexagonal Phases (1998)

The shear orientation of the hexagonal liquid crystal phase of nonionic surfactant/water mixtures was investigated by means of different techniques, namely, microscopy, small-angle light and neutron scattering, (SALS, SANS), birefringence, and nuclear magnetic resonance (NMR). On a microscopic length scale probed by NMR, SANS, and birefringence, the shear flow results in an alignment of rodlike micelles along the flow direction. The 10 plane was parallel to the shear plane. On a mesoscopic length scale, studied by microscopy and SALS, a stripe texture was observed. This is due to an undulation of the director which is on average aligned in flow direction. The corresponding SALS pattern shows a better orientation correlation perpendicular to the flow direction.
Refuse acidogenesis and methanogenesis: effects of fermentation gases (H<sub>2</sub>, CO<sub>2</sub>, CH<sub>4</sub>) (1990)

The effects of selected fermentation gases (H2, CO2, CH4) on refuse acidogenesis and methanogenesis were examined with laboratory batch cultures. Although extremely limited initial stimulation of total methanogenesis resulted from H2 supplementation, both acetogenesis and acetate methanogenesis were inhibited. A culture headspace atmosphere of 100% CO2 effected 98% inhibition of methanogenesis and partial suppression of acetogenesis. A gas mixture of CO2‐CH4 (40: 60) also exerted inhibitory effects on methanogenesis but not acetogenesis. Conversely, 100% CH4 did not significantly reduce methanogenesis or acetogenesis. Individual supplementation with N2 or CO2 in conjunction with increased culture headspace pressure (1.6 bar) approximately doubled the CH4 volumes but volatile fatty acid pattern changes were not apparent. The possible implications of high partial pressures of gas on refuse methanogenesis are discussed.
Stereo Vision for Unrestricted Human-Computer Interaction (2008)

Since the advent of the electronic computer there have been constant developments in human-computer interaction. Researchers strive towards creating an input method that is natural, compelling and most of all effective. The ideal computer interface would interpret natural human interactions in much the same way another human would. As humans we are used to giving instructions with our voice, body language and gestures: i.e. pointing at objects of interest, looking at things we interact with and using our hands to move objects. The ideal visual input device, the "holy grail" of human computer interfaces would be capable of accepting visual cues and gestures much as another human being would. Although this theoretical ideal is not feasible with current technologies it serves to guide research in the field. Stereo vision has been researched for the purpose of studying human motion for many years (Aggarwal & Cai 1997; Much effort has gone into achieving full body motion capture with multiple cameras, in order to overcome the need for artificial markers. This allows for unrestricted movement for the user, improves flexibility and overcomes occlusion problems with marker based approaches. However the processor time required to locate and track arbitrary objects in 3D has until recently been prohibitive for use in interactive scenarios. Faster processors, memory, bus/interface speeds are helping overcome a significant constraint in using stereo vision for human-computer interaction (HCI), that of: producing real-time refresh rates and low latency response. Now that interactive 3D human motion capture is becoming a reality, it's necessary to take stock of what can be achieved with this approach. This chapter will not cover the theory behind stereo vision. Nor will we be considering technologies such as motion capture, as these are not intended for everyday computer usage. We are interested in applications that allow unencumbered interactions and operate without requiring the user to attach special devices to their body. We will be looking the current state of the art and where the next could be taken.
Merlin, a multi‐suppressor from cell membrane to the nucleus (2012)

Recent evidence suggests that the neurofibromatosis type 2 (NF2) gene encoded protein merlin suppresses mitogenic signalling not only at the cell membrane but also in the nucleus. At the membrane, merlin inhibits signalling by integrins and tyrosine receptor kinases (RTKs) and the activation of downstream pathways, including the Ras/Raf/MEK/ERK, FAK/Src, PI3K/AKT, Rac/PAK/JNK, mTORC1, and Wnt/β-catenin pathways. In the nucleus, merlin suppresses the E3 ubiquitin ligase CRL4(DCAF1) to inhibit proliferation. Gene expression analysis suggested that CRL4(DCAF1) could also regulate the expression of integrins and RTKs. In this review, we explore the links between merlin function at the membrane and in the nucleus, and discuss the potential of targeting the master regulator CRL4 (DCAF1) to treat NF2 and other merlin-deficient tumours.
Siderophore-mediated signaling regulates virulence factor production in <i>Pseudomonas</i> <i>aeruginosa</i> (2002)

Numerous bacteria secrete low molecular weight compounds termed siderophores that have a high affinity for iron ions. Siderophores have a well-documented role as iron-scavenging chemicals, chelating iron ions in the environment whereupon the ferrisiderophores reenter the bacterial cells by means of specific cell-surface receptors. The iron is then released for incorporation into bacterial proteins. Here we show that in addition to its role as an iron-scavenger, the siderophore pyoverdine that is secreted by Pseudomonas aeruginosa regulates the production of at least three virulence factors (exotoxin A, an endoprotease, and pyoverdine itself), which are major contributors to the ability of this bacterium to cause disease. Regulation occurs through a transmembrane signaling system that includes an outer membrane receptor for ferripyoverdine, a signal-transducing protein that is predicted to extend from the periplasm into the cytoplasm, and a sigma factor. Expression of genes that form part of the regulon is triggered by pyoverdine so that this siderophore acts as a signaling molecule to control the production of secreted products. Recognition that a siderophore acts as a signaling molecule has important implications for the understanding of interactions between bacterial cells.
Real-Time People Counting Using Multiple Lines (2008)

A novel real-time people counting system is presented in this paper. Using a single overhead mounted camera, the system counts the number of people going in and out of an observed area. Counting is performed by analyzing an image zone composed by a set of virtual counting lines. The system runs on a commercial PC, does not need a special background and is easily adjustable to different camera height requirements. We have tested the performance of the system, achieving a correct people counting rate of 95%.
Analysis of the red optical emission in cubic GaN grown by molecular-beam epitaxy (1999)

The red optical emission band in cubic GaN is examined for the first time by cathodoluminescence as well as steady-state and time-resolved photoluminescence. We establish a close analogy between the red emission band in cubic GaN and the yellow emission in wurtzite GaN, and assign it to a donor-acceptor process involving a shallow donor and a deep acceptor with similar ionization energies in both phases. We show a range of properties of the red emission which clearly indicate its donor-acceptor pair origin, namely the blueshift with excitation intensity, the power-law evolution at increasing excitation, and the blueshift with temperature. The line shape of the red band indicates that the deep acceptor is strongly coupled to the lattice. The photoluminescence decay curves show a fast decay at higher energies within the emission band, while at lower energies the decay is much slower, typical of donor-acceptor pair transitions. An analytical expression for the time-dependent emission intensity for donor-acceptor pair transitions in which one of the centers is strongly coupled to the lattice is derived, extending the theory of Thomas et al. [Phys. Rev. B 140, A202 (1995)]. The observed decay curves are found to be well described by the theory using the donor Bohr radius of 1.7 nm, while temperature quenching of the emission gives an activation energy of 15\ifmmode\pm\else\textpm\fi{}5 meV. Evidence of Coulomb attraction between a shallow donor and a deep acceptor is presented.
21 Solution Structures of DNA-binding Domains of Eukaryotic Transcription Factors (1992)

OVERVIEW The modular architecture of transcription factors frequently allows isolation of small domains suitable for structural determination by nuclear magnetic resonance (NMR) methods. NMR has played a major role in structural characterization of zinc-containing DNA-binding domains. Three-dimensional structures have been determined for classic TFIIIA-like zinc fingers (C 2 H 2 zinc fingers), for nuclear receptor DNA-binding domains (C 2 C 2 zinc fingers), and for the zinc-binding motif of a retroviral single-stranded nucleic-acid-binding protein (C 2 HC zinc finger). In the C 2 H 2 and C 2 C 2 zinc finger domains, the zinc plays an important role in stabilization of a helix for sequence-specific interaction with the major groove of DNA. In contrast, the basic region of the leucine-zipper-type DNA-binding motif is predominantly unfolded in the free protein and forms a stable helix only upon formation of a specific complex with DNA. INTRODUCTION In recent years, multidimensional NMR spectroscopy has developed into a powerful technique for determining the three-dimensional structures of proteins in solution. Although intact transcription factors are too large for direct NMR studies, their modular architecture frequently allows isolation of small domains suitable for structure determination by NMR methods (for a brief discussion of the principles and methodology of NMR spectroscopy, see Wuthrich and Gehring, this volume). Much of our knowledge of the three-dimensional structures of eukaryotic transcription factors came originally from NMR spectroscopy. These structures and their functional implications are reviewed in this chapter, with particular emphasis on zinc-containing DNA-binding domains and the dimerization and DNA-binding domains of leucine zipper transcription factors. NMR structures of the Antennapedia homeodomain, which...
3‐methyladenine DNA glycosylases: structure, function, and biological importance (1999)

The genome continuously suffers damage due to its reactivity with chemical and physical agents. Finding such damage in genomes (that can be several million to several billion nucleotide base pairs in size) is a seemingly daunting task. 3-Methyladenine DNA glycosylases can initiate the base excision repair (BER) of an extraordinarily wide range of substrate bases. The advantage of such broad substrate recognition is that these enzymes provide resistance to a wide variety of DNA damaging agents; however, under certain circumstances, the eclectic nature of these enzymes can confer some biological disadvantages. Solving the X-ray crystal structures of two 3-methyladenine DNA glycosylases, and creating cells and animals altered for this activity, contributes to our understanding of their enzyme mechanism and how such enzymes influence the biological response of organisms to several different types of DNA damage. BioEssays 21:668–676, 1999. © 1999 John Wiley & Sons, Inc.
Apoptosis and Autophagy in Breast Cancer Cells following Exemestane Treatment (2012)

Aromatase inhibitors (AIs), which block the conversion of androgens to estrogens, are used for hormone-dependent breast cancer treatment. Exemestane, a steroidal that belongs to the third-generation of AIs, is a mechanism-based inhibitor that binds covalently and irreversibly, inactivating and destabilizing aromatase. Since the biological effects of exemestane in breast cancer cells are not totally understood, its effects on cell viability, cell proliferation and mechanisms of cell death were studied in an ER-positive aromatase-overexpressing breast cancer cell line (MCF-7aro). The effects of 3-methyladenine (3-MA), an inhibitor of autophagy and of ZVAD-FMK, an apoptotic inhibitor, in exemestane treated cells were also investigated. Our results indicate that exemestane induces a strong inhibition in MCF-7aro cell proliferation in a dose- and time-dependent manner, promoting a significant cell cycle arrest in G(0)/G1 or in G(2)/M phases after 3 and 6 days of treatment, respectively. This was accompanied by a decrease in cell viability due to activation of cell death by apoptosis, via mitochondrial pathway and the occurrence of autophagy. Inhibition of autophagy by the autophagic inhibitor, 3-MA, resulted in a reduction of cell viability and activation of caspases. All together the results obtained suggest that exemestane induced mitochondrial-mediated apoptosis and autophagy, which act as a pro-survival process regulating breast cancer cell apoptosis.
Rearrangements of the BCL-6 gene in acquired immunodeficiency syndrome- associated non-Hodgkin's lymphoma: association with diffuse large-cell subtype (1994)

Acquired immunodeficiency syndrome (AIDS)-associated non-Hodgkin's lymphomas (AIDS-NHL), a major source of morbidity and mortality among AIDS patients, are derived from B cells and can be classified into two main histologic categories, small noncleaved cell lymphoma (SNCCL) and diffuse large-cell lymphoma (DLCL). DLCL includes two histologic subsets, ie, large noncleaved cell lymphoma (LNCCL) and large cell-immunoblastic plasmacytoid lymphoma (LC-IBPL). Several studies have shown that AIDS-SNCCL is associated with the clonal accumulation of multiple genetic lesions, including Epstein-Barr virus (EBV) infection, activation of the c-MYC and RAS oncogenes, as well as inactivation of the p53 tumor suppressor gene at variable frequencies. On the contrary, the molecular pathogenesis of AIDS-DLCL is largely obscure, because no genetic lesion other than EBV infection has been specifically identified in this group. In this study, we have tested a panel of 40 AIDS-NHL for structural alterations of BCL-6, a putative proto-oncogene that is frequently altered in DLCL in the immunocompetent host. Our results show that rearrangements of BCL-6 are present in 20% of AIDS-DLCL (5 of 24), including 2 of 8 LNCCL and 3 of 16 LC-IBPL, but in no case of AIDS-SNCCL. BCL-6 rearrangements were detected both in the presence and in the absence of EBV infection of the tumor clone, but in no case were associated with activation of c-MYC or mutations of p53. These data identify a novel genetic lesion in AIDS-DLCL and corroborate the notion that lymphomagenesis in AIDS follows two distinct molecular pathways that are associated with the development of histologically distinct types of AIDS-NHL.