gebhart/patrepeval huggingface dataset:
A purine-rich DNA sequence motif present in SV40 and lymphotropic papovavirus binds a lymphoid-specific factor and contributes to enhancer activity in lymphoid cells. (1987)

The enhancer of simian virus 40 (SV40) is active in a wide variety of tissues and hosts and thus has been called a general enhancer. Previous work has established that this region contains a number of subsegments, each with a different cell type specificity. By analyzing enhancer deletion mutants of SV40 with a restricted cell type specificity, we have identified a purine-rich DNA motif (Pu box) that is essential for activity of the mutant enhancer in lymphoid cells and also obtained evidence for an independent element that confers activity in kidney CV-1 cells. The Pu box element is positively regulated since binding of a cognate factor(s) was only observed in lymphoid cell extracts. The Pu box is also present in the 63-bp enhancer repeat of lymphotropic papovavirus (LPV), and competition experiments show that the SV40 and LPV sequences bind the same factor(s). Thus, the Pu box is likely to be a major determinant of the lymphotropic host range of LPV. In SV40, however, the Pu box is one of several enhancer elements with different cell specificities. We suggest that such an arrangement reflects a diversification strategy of SV40 to maximize its chance of adaptation to various types of host cells.
PCR-Tree: A Compression-Based Index Structure for Similarity Searching in High-Dimensional Image Databases (2007)

The vector approximation file (VA-file) approach is an efficient high-dimensional indexing method using compression technique to overcome the difficulty of 'curse of dimensionality'. The VA-file method combined with tree-based index structure can improve the querying efficiency, but it still succumbs to the 'curse of dimensionality'. In this paper, a new high-dimensional indexing structure called PCR-tree for non-uniform distributed data sets was presented, which employs R-tree to manage the approximate vectors in the reduced-dimensionality space. The approximate vectors can be built in the KL transform domain, and low dimensional MBRs (minimum bounding rectangles) can be used to manage the approximations on the first few principal components. When performing k-nearest neighbor search, a lower-bound filtering algorithm is used to reject the improper nodes of PCR-tree, which can reduce the computational complexity and I/O cost without any dismissals. The experiment results on large image databases show that the new approach provides a faster search speed than other tree-structured vector approximation approaches.
Enhancement of Carrier Mobility in Semiconductor Nanostructures by Dielectric Engineering (2007)

We propose a technique for achieving large improvements in carrier mobilities in 2- and 1-dimensional semiconductor nanostructures by modifying their dielectric environments. We show that by coating the nanostructures with high-kappa dielectrics, scattering from Coulombic impurities can be strongly damped. Though screening is also weakened, the damping of Coulombic scattering is much larger, and the resulting improvement in mobilities of carriers can be as much as an order of magnitude for thin 2D semiconductor membranes, and more for semiconductor nanowires.
Parameterization of tight-binding models from density functional theory calculations (2011)

We present a rigorous bottom-up approach for the derivation of the electronic structure part of tight-binding (TB) models from density functional theory (DFT) calculations. The approach is based on a simultaneous optimization and projection of atomic-like orbitals on self-consistent DFT wave functions and is universally applicable to elements and compounds in arbitrary structural arrangements. The quality and transferability of the derived TB bond and overlap integrals are demonstrated for the examples of a covalent semiconductor (carbon), a transition metal (titanium), and a binary compound with mixed metallic-covalent bonding (TiC). The method can serve as a transparent and physically justified coarse-graining scheme for the construction of nonorthogonal and orthogonal TB total-energy models as well as the closely related bond-order potentials.
Influence of Engine Operating Conditions on Diesel Particulate Matter Emissions in Relation to Transient and Steady-State Conditions (2007)

Airborne particulate matter is an important pollutant affecting air quality. Currently, diesel PM regulations are based on emitted particle mass; however, the particle size distributions are also important factors in air quality. While the distributions of particulate emissions under steady-state conditions are well-known and have been generalized, varying distributions undertransient conditions are not well-understood. This study investigates the size distributions of PM, focusing on the nuclei- and accumulation-modes, emitted from diesel engines under transient operations. Some engine conditions during transient testing produced particle size distributions that were notably different from those produced under steady-state conditions. During transient operation, the size distributions were either mono- or bimodal with peaks that were able to switch quickly between the nuclei- and accumulation-modes. These distributions have not been observed during steady-state testing but are significant because environmental and health effects and emission control solutions are highly dependent on particle size.
Facile Synthesis of α-Substituted Acrylate Esters (2002)

Treatment of 5-monosubstituted Meldrum's acids with dimethylmethyleneimmonium iodide (Eschenmoser's iodide salt) in methanol gives alpha-substituted acrylate methyl esters in good yields. Easy access to 5-monosubstituted Meldrum's acids allowed us to synthesize a wide variety of alpha-substituted acrylate methyl esters. The reaction conditions are mild and tolerate many functional groups commonly used in organic synthesis; thus, this new method has potential as an alternative to conventional preparative methods for alpha-substituted acrylate esters.
Using Multiple Alignments to Improve Gene Prediction (2006)

The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the aligned genome sequences, context dependent substitution rates, and insertions and deletions. An implementation of N-SCAN was created and used to generate predictions for the entire human genome and the genome of the fruit fly Drosophila melanogaster. Analyses of the predictions reveal that N-SCAN's accuracy in both human and fly exceeds that of all previously published whole-genome de novo gene predictors.
Suppression of Glucose Absorption by Various Health Teas in Rats (2004)

The inhibitory effects on the intestinal digestion and absorption of sugar of health teas that claim beneficial dietary and diabetes-controlling effects were compared in rats using portal cannulae. The measured durations were the times during which the elevation of portal glucose levels resulting from continuous intragastric infusion of sucrose or maltose was suppressed by concentrated teas. The teas investigated included salacia oblonga, mulberry, guava, gymunema, taheebo, yacon, and banaba. The duration of the inhibitory effect on the sucrose load of salacia oblonga, mulberry, and guava were 110 min, 20 min, and 10 min, respectively. In contrast, gymunema, taheebo, yacon, and banaba had no significant effect on the continuous infusion of sucrose. These results suggest that there is considerable difference in the efficacy of commercial health teas in influencing glucose absorption.
Effects of excess vitamin A and canthaxanthin on salivary gland tumors (1988)

The effects of feeding semipurified diets supplemented with excess retinyl palmitate (20,000 and 100,000 IU/kg), beta-carotene (250 mg/kg), and canthaxanthin (250 mg/kg) on 7,12-dimethylbenz[a]anthracene (DMBA)-induced salivary gland tumors were studied in rats. None of the dietary supplements had a significant effect on tumor incidence. Tumor weights, however, tended to be lower in rats fed the dietary supplements compared with the controls. The incidence of tumor-bearing rats with large tumors was significantly lower in rats fed canthaxanthin than in the control rats. At termination of the experiment, the levels of vitamin A were higher in plasma, liver, normal salivary glands, and the tumor of rats fed diets supplemented with the higher level of retinyl palmitate. Feeding the canthaxanthin-supplemented diet had the opposite effect on tissue and plasma vitamin A levels. beta-Carotene supplementation was associated with higher vitamin A concentrations in the liver but not in plasma, salivary glands, or the tumor. The levels of beta-carotene were increased in tissues and plasma of rats fed the beta-carotene-supplemented diet. The results suggest that in this experimental model, the diet-induced modification of tissue or plasma vitamin A levels did not have an effect on tumor incidence.
Economic reasoning and artificial intelligence (2015)

The field of artificial intelligence (AI) strives to build rational agents capable of perceiving the world around them and taking actions to advance specified goals. Put another way, AI researchers aim to construct a synthetic homo economicus, the mythical perfectly rational agent of neoclassical economics. We review progress toward creating this new species of machine, machina economicus, and discuss some challenges in designing AIs that can reason effectively in economic contexts. Supposing that AI succeeds in this quest, or at least comes close enough that it is useful to think about AIs in rationalistic terms, we ask how to design the rules of interaction in multi-agent systems that come to represent an economy of AIs. Theories of normative design from economics may prove more relevant for artificial agents than human agents, with AIs that better respect idealized assumptions of rationality than people, interacting through novel rules and incentive systems quite distinct from those tailored for people.
Fault detection and classification through multivariate statistical techniques (2005)

A technique for on-line process fault detection and diagnosis based on statistical analysis of process data is presented in this paper. A principal component model is developed from the normal operating data and the process operation is monitored form the plots of squared prediction errors and scores. Through multivariate statistical data analysis, the features of various faults can be discovered and used in fault diagnosis. In the technique presented here, principal component analysis is performed for the data corresponding to each fault to extract the fault direction in the measurement space. Fault diagnosis is performed by comparing the direction of the current online measurements with those of various faults. The fault whose direction is very aligned with the current data direction is a plausible fault and is taken as the diagnosis result. Fault diagnosibility is investigated. The technique is very easy to implement and can be used to complement current fault diagnosis techniques. Applications of the proposed technique to the on-line fault diagnosis of a continuous stirred tank reactor (CSTR) system demonstrate that the technique is very effective.
A possible role for the cholinergic anti-inflammatory pathway in increased mortality observed in critically ill patients receiving nicotine replacement therapy (2007)

Kox, Matthijs MSc; Hoedemaekers, Astrid W. MD, PhD; Pickkers, Peter MD, PhD; van der Hoeven, Johannes G. MD, PhD; Pompe, Jan C. MD Author Information
<i>p</i> H-Sensitive Liposomes: Possible Clinical Implications (1980)

When pH-sensitive molecules are incorporated into liposomes, drugs can be specifically released from these vesicles by a change of pH in the ambient serum. Liposomes containing the pH-sensitive lipid palmitoyl homocysteine (PHC) were constructed so that the greatest pH differential (6.0 to 7.4) of drug release was obtained near physiological temperature. Such liposomes could be useful clinically if they enable drugs to be targeted to areas of the body in which pH is less than physiological, such as primary tumors and metastases or sites of inflammation and infection.
Apoptosis of androgen-independent mammary and prostate cell lines induced by topoisomerase inhibitors: common pathway of gene regulation. (1997)

New treatments for hormone-independent tumor are urgently needed since androgen-dependent cancer cells eventually progress to -independent cells after hormonal manipulation. In the present study, etoposide and camptothecin were used to induce proliferation-dependent death of these cells. Each of the agents, at the doses used, induces the apoptosis of AT-3, CS 2, and TSU-pr1 cells based upon the temporal sequence of DNA fragmentation, morphologic changes and loss of cell viability. Northern blot analysis was used to identify a series of genes whose expression is enhanced during the apoptotic pathway. During the apoptotic process induced by the agents, expression of cyclin-dependent kinase inhibitor p27 increased. Flow cytometric analysis showed that the treatment resulted in a block in G2/M of the cell cycle. These results demonstrate that these cells retain the ability to undergo apoptosis by etoposide and camptothecin, and cyclin-dependent kinase inhibitor plays some role during apoptotic pathway.
Long term prognosis of chronic inflammatory demyelinating polyneuropathy: a five year follow up of 38 cases (2005)

The long term prognosis of CIDP patients was generally favourable, but 39% of patients still required immune treatments and 13% had severe disabilities. Mode of onset, distribution of symptoms, and electrophysiological characteristics may be prognostic factors for predicting a favourable outcome.
Interaction of rat ascites hepatoma cells with cultured mesothelial cell layers: a model for tumor invasion. (1986)

Interactions of rat ascites hepatoma cells with primary cultured layers of rat mesentery-derived cells were studied. The mesentery-derived cells were isolated from rat mesentery and cultured in Eagle's minimum essential medium with a 2-fold concentration of amino acids and vitamins supplemented with 10% calf serum. The primary cultured cells, consisting mainly of mesothelial cells in polygonal shape, forms a "paving stone" sheet. Upon seeding the tumor cells on the mesentery-derived cell layers, three different types of tumor cell growth were observed. Type 1 was the formation of piled-up tumor cell nests on mesothelial cell layers. Type 2 was the formation of flattened tumor cell islands underneath mesothelial cell layers. This island formation was clearly observed under a phase contrast microscope 2 days after the tumor cell seeding. Protrusion of cellular processes of the tumor cells beneath mesothelial cells was occasionally seen. Type 3 was the growth of tumor cells in suspension. These types of tumor cell growth closely resemble those in the peritoneal cavity observed after i.p. implantation of the tumor cells. When the tumor cells recovered from the blood of tumor-bearing rats were seeded, flattened tumor cell islands were formed 15 times more frequently than when the tumor cells isolated from host peritoneal cavity were seeded. Shortly after the appearance of small flattened tumor cell islands, a distinct morphological change of mesothelial cells from polygonal to spindle shape was seen preferentially at the marginal area of the cell layers (a partial retraction of cell edges). The retraction of mesothelial cells was induced not only by seeding the tumor cells but by adding the tumor ascites fluid or the medium conditioned by the tumor cell culture. The morphological change was reversed by changing the culture medium to remove the effectors. These results indicate that the system described in this study can provide a useful model to study tumor cell invasion.
Inflammatory cytokines induce the transformation of human dermal microvascular endothelial cells into myofibroblasts: a potential role in skin fibrogenesis (2006)

Long-term exposure to TNF-alpha or IL-1beta induced the permanent transformation of HDMEC into myofibroblasts in cell culture. A similar transformation following chronic inflammatory stimulation in vivo may explain one source of myofibroblasts in skin fibrogenesis.
Efficient Communications in Training Large Scale Neural Networks (2017)

We consider the problem of how to reduce the cost of communication that is required for the parallel training of a neural network. The state-of-the-art method, Bulk Synchronous Parallel Stochastic Gradient Descent (BSP-SGD), requires many collective communication operations, like broadcasts of parameters or reductions for partial gradient aggregations, which for large messages quickly dominates overall execution time and limits parallel scalability. To address this problem, we develop a new technique for collective operations, referred to as Linear Pipelining (LP). It is tuned to the message sizes that arise in BSP-SGD, and works effectively on multi-GPU systems. Theoretically, the cost of LP is invariant to P, where P is the number of GPUs, while the cost of the more conventional Minimum Spanning Tree (MST) scales like O(log P). LP also demonstrates up to 2x higher bandwidth than Bidirectional Exchange (BE) techniques that are widely adopted by current MPI implementations. We apply these collectives to BSP-SGD, showing that the proposed implementations reduce communication bottlenecks in practice while preserving the attractive convergence properties of BSP-SGD.
Rules for ring closure (1976)

Three rules which have been found useful, on an empirical basis, to predict the relative facility of ring forming reactions are presented; the physical bases of such rules are described.
Scheduling for very large virtual environments and networked games using visibility and priorities (2002)

The problem of network bandwidth limitations is encountered in almost any distributed virtual environment or networked game. In a typical client-server setup, where the virtual world is managed by a server and replicated by connected clients which visualize the scene, the server must repeatedly transmit update messages to the clients. By employing visibility information, the number of messages transmitted over the network can be reduced by sending each client only update messages for objects which are visible from the viewpoint of the client. This paper presents a technique that allows the server to manage the transmission of update messages for each client with a constant overhead reducing overall computational cost to a linear effort. We show how the server can employ visibility information to schedule all objects using the Priority Round-Robin algorithm. This algorithm is further enhanced with activity monitoring that provides a graceful degradation of the system's performance, even if the behavior of objects is unpredictable. This makes the algorithm suited to schedule update messages regarding server-controlled objects us well as user-controlled avatars.
The Epidemiology of Revision Total Knee Arthroplasty in the United States (2009)

Understanding the cause of failure and type of revision TKA procedure performed are essential in guiding research, implant design, and clinical decision making in TKA. The purpose of this study was to assess the most common mechanisms of failure and types of revision TKA procedures performed in the United States using newly implemented ICD-9-CM diagnosis and procedure codes related to revision TKA.
Adherence of Erythrocytes to <i>Mycoplasma pneumoniae</i> (1979)

The human pathogen Mycoplasma pneumoniae adheres to a variety of cells, including erythrocytes. A hemadsorption technique was developed to quantitate adherence by photometric measurement of lysates of erythrocytes that attached to sheets of M. pneumoniae grown in cups of Linbro plates. Attachment of sheep erythrocytes (SE) increased with higher ionic strength, was unaffected by minor pH variations (6 to 9), and was blocked by anti- M. pneumoniae antiserum, but was not inhibited by a variety of sugars, amino acids, and bovine serum albumin. The reaction was time and temperature dependent. The temperature curve showed peaks at 14 and 28°C with untreated SE but only one peak at about 38°C with glutaraldehyde-treated SE. The temperature dependence indicated involvement of either metabolic or membrane activities in the binding process. Trypsin treatment of the M. pneumoniae sheet abolished adherence of SE but was only partially effective with human erythrocytes and noneffective with rabbit erythrocytes. The binding capacity of the mycoplasma cells for SE was restored by incubation in growth medium for 3 to 4 h; this restoration was inhibited by 10 μg of chloramphenicol per ml. Neuraminidase treatment of SE removed their attachment capacity but had no effect on attachment of rabbit erythrocytes and only a slight effect on attachment of human erythrocytes. Pretreatment of M. pneumoniae with neuraminic acid partially blocked the adherence of SE, whereas rabbit erythrocyte attachment was not affected. Attached SE could be detached by trypsin, but not by neuraminidase. For human and rabbit erythrocytes, the results suggest binding mechanisms other than the interaction between neuraminidase-sensitive receptors and protein-containing binding sites shown for SE.
Descriptions of Nests and Eggs New to Science (1915)

Microeca brunneicauda
Abnormal calcium homeostasis and protein folding stress at the ER (2011)

Prion-related disorders (PrDs) are caused by the accumulation of a misfolded and protease-resistant form of the cellular prion, leading to neuronal dysfunction and massive neuronal loss. In humans, PrDs have distinct etiologies including sporadic, infectious and familial forms, which present common clinical features; however, the possible existence of common neuropathogenic events are not known. Several studies suggest that alterations in protein folding and quality control mechanisms at the endoplasmic reticulum (ER) are a common factor involved in PrDs. However, the mechanism underlying ER dysfunction in PrDs remains unknown. We have recently reported that alterations in ER calcium homeostasis are common pathological events observed in both infectious and familial PrD models. Perturbation in calcium homeostasis directly correlated with the occurrence of ER stress and higher susceptibility to protein folding stress. We envision a model where alterations in ER function are central and common events underlying prion pathogenesis, leading to general alterations on protein homeostasis networks.
Hydrogen Permeability Requirements and Testing for Reusable Launch Vehicle Tanks (2002)

*Under the Space Launch Initiative (SLI) program, NASA, Boeing, and Northrop Grumman are conducting design trade studies and technology development for composite cryogenic tanks for launch vehicles. A fundamental issue for composite tanks is hydrogen permeability, particularly since the recent failure of the X-33 hydrogen tank was permeability-related. SLI program progress in the development of hydrogen permeability allowables and in the generation of permeation test data are presented.