gebhart/patrepeval huggingface dataset:
Preferential Groundwater Flow Pathways and Hydroperiod Alterations Indicated by Georectified Lineaments and Sinkholes at Proposed Karst Nuclear Power Plant and Mine Sites (2012)

Sustainable development of any type that utilizes water or involves excavations in karst aquifer systems, such as the regional Floridan aquifer system (FAS), requires knowledge of preferential groundwater flow pathways that can extend adverse impacts beyond the development site and alter natural hydroperiods. Such pathways include fractures and other types of karst conduits that are associated with modern and relict sinkholes. Developments, including power plants and mines, that have not accounted for these features have caused induced recharge, altered hydroperiods and saltwater intrusion in the FAS, resulting in destruction of wetlands and adverse impacts to other surface waters, wildlife habitat and threatened and endangered species. This study analyzed indicators of preferential groundwater flow by considering surface expressions of underlying geological conditions (lineaments and modern sinkholes) in the FAS, which coincide with the United States southeastern coastal plain. Lineament mapping by Vernon (1951) and the Florida Department of Transportation (FDOT, 1973), incorporating analog mapping techniques and hardcopy prints of satellite imagery, preceded extensive urbanization, groundwater extractions, and mining in the region. All of these alterations limit the ability to identify fractures using lineaments by reducing groundwater discharges and vegetation indicative of those discharges. In this study, established methods for georectification, including control-point identification and spatial matching of scanned maps and remotely sensed images, were applied to these previously mapped lineaments. These results were applied to the environmentally sensitive karst study area of Citrus and Levy Counties, Florida in the southern extent of the FAS. Geospatial analyses of lineament distribution and modern sinkhole locations from the state database showed a dense network of lineaments with associated sinkholes throughout the study area and seven surrounding counties, including the proposed sites for a nuclear power plant and two mines in Levy County. Proposed excavations and water use for construction and operation of the power plant and mines would result in irreversible adverse environmental impacts on extensive depressional wetlands beyond the surface-footprint impact of these developments via these preferential flow pathways that were not evaluated during the review process.
Gene Content and Function of the Ancestral Chromosome Fusion Site in Human Chromosome 2q13–2q14.1 and Paralogous Regions (2002)

Various portions of the region surrounding the site where two ancestral chromosomes fused to form human chromosome 2 are duplicated elsewhere in the human genome, primarily in subtelomeric and pericentromeric locations. At least 24 potentially functional genes and 16 pseudogenes reside in the 614-kb of sequence surrounding the fusion site and paralogous segments on other chromosomes. By comparing the sequences of genomic copies and transcripts, we show that at least 18 of the genes in these paralogous regions are transcriptionally active. Among these genes are new members of the cobalamin synthetase W domain (CBWD) and forkhead domain FOXD4 gene families. Copies of RPL23A and SNRPA1 on chromosome 2 are retrotransposed-processed pseudogenes that were included in segmental duplications; we find 53 RPL23A pseudogenes in the human genome and map the functional copy of SNRPA1 to 15qter. The draft sequence of the human genome also provides new information on the location and intron-exon structure of functional copies of other 2q-fusion genes (PGM5, retina-specific F379, helicase CHLR1, and acrosin). This study illustrates that the duplication and rearrangement of subtelomeric and pericentromeric regions have functional relevance to human biology; these processes can change gene dosage and/or generate genes with new functions.
An efficient sequential quadratic programming formulation of optimal wire spacing for cross-talk noise avoidance routing (1999)

In thii paper we propose a new, and effective, approach to cross-talk noise avoidance routing. In our new approach we attack the cross-talk noise problem immediately following topological routing, which is the point in the routing process that gives the best trade off between the ability to detect cross-talk noise problems and the ability to correct the problems. We formulate the heart of this new approach as a convex, nonlinear, mathematical programming problem which determines an optimal set of wire spacings under cross-talk noise constraints. This new mathematical programming formulation is based on a detailed knowledge of the underlying cross-talk noise mechanisms and accounts for coupling capacitance, interconnect resistance, and aggressor net signal rise time on nets with arbitrarily complex tree topologies. Finally, by slightly restricting this programming problem we formulate it as a linearly constrained, convex, nonlinesr, mathematical program which can be quickly and efficiently solved using sequential quadratic programming.
Fisher discriminant analysis with kernels (2003)

A non-linear classification technique based on Fisher's discriminant is proposed. The main ingredient is the kernel trick which allows the efficient computation of Fisher discriminant in feature space. The linear classification in feature space corresponds to a (powerful) non-linear decision function in input space. Large scale simulations demonstrate the competitiveness of our approach.
Fragments of Ribosomal Protein S1 and Its Mutant Form m1‐S1 (1981)

Escherichia coli ribosomal protein S1 and its mutant, shorter, form m1-S1 were cleaved at internal methionyl residues to yield, respectively, six and five fragments of Mr ranging from 1000 to 24000. Methods are described to isolate the fragments in pure form. Four of the fragments (designated F2a, F2b, F3 and F4) contain between 86 and 215 amino acids and are therefore as large as other ribosomal proteins. Fragment F2a, derived from the N-terminal region, has previously been shown to contain the major ribosome binding domain of S1 [S. Giorginis and A. R. Subramanian (1980) J. Mol. Biol. 141, 393--408]. Here we show that the RNA binding domain of S1 is essentially contained in F3 derived from the middle region of S1 and carrying the nonreactive--SH group. The reactive--SH group of S1, whose activity is modified by ligand binding, was localized in F2b, a fragment with little RNA binding capacity. The characteristic RNA binding domain and a weak ribosome binding domain of S1 have previously been localized in the large trypsin-resistent core S1-F1 [T. Suryanarayana and A. R. Subramanian (1979) J. Mol. Biol. 127, 41--54]. Together these data indicate that two of the key functional domain of S1 are located in two regions of the molecule separated by an open, exposed segment. The present study also revealed that the nonreactive--SH group of S1 becomes reactive in m1-S1 by the loss of the remote C-terminal region in the latter.
Internet Group Management Protocol, Version 2 (1997)

This memo documents IGMPv2, used by IP hosts to report their multicast group memberships to routers. It updates STD 5, RFC 1112.
Antigen Localization and Migration in Immunity and Tolerance (1998)

Survival in a hostile environment requires the ability to mount a protective immune response while avoiding a reaction of the immune system against the self. We propose that the migration and localization of antigen are the governing factors in immunologic responsiveness or unresponsiveness against infections, tumors, and self and against xenografts and allografts. This conclusion is based largely on studies of experimental viral infection13 and of the small numbers of donor leukocytes found in the blood and tissues of human and animal recipients of organ allografts (microchimerism).46 Under both circumstances, an immune response can be construed as a . . .
The Computational Detection of Functional Nucleotide Sequence Motifs in the Coding Regions of Organisms (2008)

A new algorithm has been constructed for finding under- and overrepresented oligonucleotide motifs in the protein coding regions of genomes that have been normalized for G/C content, codon usage, and amino acid order. This Robins-Krasnitz algorithm has been employed to compare the oligonucleotide frequencies between many different prokaryotic genomes. Evidence is presented demonstrating that at least some of these sequence motifs are functionally important and selected for or against during the evolution of these prokaryotes. The applications of this method include the optimization of protein expression for synthetic genes in foreign organisms, identification of novel oligonucleotide signals used by the organism and the examination of evolutionary relationships not dependent upon different gene sequence trees.
A simple typed intermediate language for object-oriented languages (2005)

Traditional class and object encodings are difficult to use in practical type-preserving compilers because of the complexity of the encodings. We propose a simple typed intermediate language for compiling object-oriented languages and prove its soundness. The key ideas are to preserve lightweight notions of classes and objects instead of compiling them away and to separate name-based subclassing from structure-based subtyping. The language can express standard implementation techniques for both dynamic dispatch and runtime type tests. It has decidable type checking even with subtyping between quantified types with different bounds. Because of its simplicity, the language is a more suitable starting point for a practical type-preserving compiler than traditional encoding techniques.
Setting Up a Bioluminescence Resonance Energy Transfer High throughput Screening Assay to Search for Protein/Protein Interaction Inhibitors in Mammalian Cells (2012)

Each step of the cell life and its response or adaptation to its environment are mediated by a network of protein/protein interactions termed "interactome." Our knowledge of this network keeps growing due to the development of sensitive techniques devoted to study these interactions. The bioluminescence resonance energy transfer (BRET) technique was primarily developed to allow the dynamic monitoring of protein/protein interactions (PPI) in living cells, and has widely been used to study receptor activation by intra- or extra-molecular conformational changes within receptors and activated complexes in mammal cells. Some interactions are described as crucial in human pathological processes, and a new class of drugs targeting them has recently emerged. The BRET method is well suited to identify inhibitors of PPI and here is described why and how to set up and optimize a high throughput screening assay based on BRET to search for such inhibitory compounds. The different parameters to take into account when developing such BRET assays in mammal cells are reviewed to give general guidelines: considerations on the targeted interaction, choice of BRET version, inducibility of the interaction, kinetic of the monitored interaction, and of the BRET reading, influence of substrate concentration, number of cells and medium composition used on the Z' factor, and expected interferences from colored or fluorescent compounds.
A rat model against chemotherapy plus radiation-induced oral mucositis (2012)

Oral mucositis was established successfully in rats by the combination of chemotherapeutic agent and IR radiation. This may be a useful model for screening drugs in the treatment of oral mucositis.
Some Effects of Crosslinking Upon the Foaming Behavior of Heat Plastified Polystyrene (1965)

Crosslinking of polystyrene containing blowing agents has a large effect upon foam ing behavior at elevated temperatures. The foam volume and resistance to thermal col lapse are both greatly increased by lightly crosslinking the polymer. If the crosslink density is too high, however, expansion is re stricted and foam stability decreases. The foaming behavior of a series of styrene-di vinyl benzene copolymers impregnated with carbon dioxide has been studied in detail at temperatures from 100 to 200°C. An at tempt has been made to correlate the in ternal pressures at maximum expansion with the theoretical elastic retractive forces of the copol ymer networks. A mechanism for ther mocollapse of polystyrene foams is proposed.
An osmolyte effect on the heat capacity change for protein folding (1995)

We have carried out a differential scanning calorimetry study into the pH effect on the thermal denaturation of ribonuclease A at several concentrations of the osmolyte sarcosine. In order to properly analyze these data, we have elaborated the thermodynamic theory of the linkage between temperature, cosolvent, and pH effects. The denaturation heat capacity increases with sarcosine concentration. The effects of temperature and sarcosine concentration on the denaturation enthalpy and entropy values are well described by convergence equations, with convergence temperatures of around 100 degrees C for the enthalpy and around 112 degrees C for the entropy; we suggest that these effects might be related to a solvent-induced alteration of the apolar-group-hydration contribution to the folding thermodynamics. From our data, we estimate that about 70 extra molecules of water are thermodynamically bound upon ribonuclease denaturation in diluted aqueous solutions of sarcosine; this number is 6-9 times smaller than that predicted on the basis of the following two premises: (a) the osmolyte is strongly excluded from the surface of both the native and the denatured protein and (b) the denatured state is a fully solvated chain. We suggest that at least one of these two premises does not hold. We briefly comment on the potential use of cosolvent effects on thermal denaturation to evaluate the degree of hydration of denatured proteins (thus providing an independent measure of the consequence of their possible residual structure) and, also, on the possibility of finding substances that are more efficient protein stabilizers than known osmolytes are.
Administration of Dexmedetomidine inhibited NLRP3 inflammasome and microglial cell activities in hippocampus of traumatic brain injury rats (2018)

The abnormally high nucleotide-binding oligomerization domain (NOD)-like receptor family pyrin domain containing 3 (NLRP3) inflammasome activity is a typical characteristic of traumatic brain injury (TBI). Dexmedetomidine (Dex) is a highly selective α-2 adrenergic receptor agonist that inhibits the activation of NLRP3. Thus, it was hypothesized that Dex could attenuate TBI by inhibiting NLRP3 inflammasome activity in hippocampus. Rats were subjected to controlled cortical impact method to induce TBI, and treated with Dex. The effect of Dex treatment on the cognitive function, NLRP3 activity, and microglial activation in rat brain tissues was assessed. The administration of Dex improved performance of TBI rats in Morris water maze (MWM) test, which was associated with the increased neurone viability and suppressed microglia activity. Moreover, the administration of Dex inhibited the neuroinflammation in brain tissue as well as the expressions of NLRP3 and caspase-1. Additionally, Dex and NLRP3 inhibitor, BAY-11-7082 had a synergistic effect in inhibiting NLRP3/caspase-1 axis activity and improving TBI. The findings outlined in the current study indicated that the improvement effect of Dex on TBI was related to its effect on NLRP3 activity.
Micro-accelerometer based hardware interfaces for wearable computer mixed reality applications (2003)

Human interaction with wearable computers is an important research issue, especially when combined with mixed reality (MR) applications. Natural and non-obtrusive means of interaction calls for new devices, which should be simple to use. This paper considers the design of new interaction hardware, such as a wearable computer pen, a tilt pad, a wand, and a gesture pad designed using accelerometers for such scenarios. The very difficult problem of noise in small hardware accelerometers (in the form of random bias drifts), which seriously impedes it's application in position measurement is also examined in detail. Kalman filtering has resulted in improved results, which are presented herewith. The application of accelerometers to design interfaces for use in mixed reality environments is also explained.
Nonviral Vectors for In Vivo Gene Delivery: Physicochemical and Pharmacokinetic Considerations (1997)

The use of nonviral vectors is an attractive in vivo gene delivery strategy that is simpler than, and lacks some risks inherent in, viral systems. Liposomes and receptor-mediated polycation systems are promising carriers for delivery and expression of plasmid DNA encoding genes into the target cells. Many barriers need to be overcome for successful in vivo DNA delivery using these carrier systems. Such factors as extent of DNA condensation, particle size of the DNA complex, route of administration, stability against nucleases, target sites, in vivo disposition, binding to cell surface receptor and internalization, and intracellular trafficking affect in vivo gene delivery and expression. This review will provide a critical discussion of the merits and limitations of liposomal and polycationic carrier systems for gene transfer from the viewpoints of their physicochemical and pharmacokinetic properties.
Maintenance therapy with recombinant interferon alpha-2B (alpha IFN) in prognostically unfavourable aggressive non-Hodgkin's lymphomas (NHL) (1996)

Fifteen patients from a series of 37 consecutive patients with aggressive NHL who achieved a complete remission (CR) with first line chemotherapy were defined at high or high-intermediate risk of relapse according to International Prognostic Risk Index and were treated with alpha IFN as maintenance therapy for two years. After a median follow-up of 62 months only 3/15 patients (20%) relapsed and 2/15 (13.3%) died in the alpha IFN treated group, favourably comparing with the expected relapse and death rate in that setting; on the other hand 40.9% of 'low risk' patients from the same series, who did not receive alpha IFN, had relapsed. alpha IFN maintenance therapy appears to result in prolonged response duration and survival in patients with aggressive and prognostically unfavourable NHL.
GPS-based tracking systems for taxi cab fleet operations (1993)

Different technologies and systems have been proposed for the safety of taxicab drivers. Of these, a global positioning system (GPS)-based tracking systems has attracted the attention of taxi commissions. The reasons include the compact size of GPS receivers, the low cost of GPS receivers, 24 hour GPS operation in all weather conditions anywhere on the earth. Very similar GPS-based tracking systems can be used for fleet/dispatch operations. Both systems are described.
Effects of Pt Particle Size on Hydrogen Storage on Pt-Doped Metal−Organic Framework IRMOF-8 (2011)

A series of Pt-doped IRMOF-8 samples with different Pt catalyst sizes have been prepared via organometallic chemical-vapor deposition (CVD). The Pt catalyst size effects on the spillover storage on IRMOF-8 (or any MOF) were studied for the first time. Our studies showed that the Pt catalyst size is a crucial factor determining whether a significant enhancement in storage can be achieved in the hydrogen spillover system at ambient temperature. Compared to undoped IRMOF-8, the spillover storage capacities on Pt-doped IRMOF-8 samples were enhanced by factors ranging from 1.1 to 1.9 because of different Pt catalyst sizes. The doped Pt size was controlled by varying the CVD conditions to yield mean sizes of 2.2, 3.9, and 9.1 nm, and the results showed that smaller sizes were needed for spillover. Temperature-programmed desorption of dosed H2/D2 further shed light on the mechanism of spillover and reverse spillover, confirming undercoordinated sites on the particle-enhanced spillover.
Generation of a drug resistance profile by quantitation of mdr-1/P-glycoprotein in the cell lines of the National Cancer Institute Anticancer Drug Screen. (1995)

Identifying new chemotherapeutic agents and characterizing mechanisms of resistance may improve cancer treatment. The Anticancer Drug Screen of the National Cancer Institute uses 60 cell lines to identify new agents. Expression of mdr-1/P-glycoprotein was measured by quantitative PCR. Expression was detected in 39 cell lines; the highest levels were in renal and colon carcinomas. Expression was also detected in all melanomas and central nervous system tumors, but in only one ovarian carcinoma and one leukemia cell line. Using a modified version of the COMPARE program, a high correlation was found between expression of mdr-1 and cellular resistance to a large number of compounds. Evidence that these compounds are P-glycoprotein substrates includes: (a) enhancement of cytotoxicity by verapamil; (b) demonstration of cross-resistance in a multidrug-resistant cell line, (c) ability to antagonize P-glycoprotein, increasing vinblastine accumulation by decreasing efflux; and (d) inhibition of photoaffinity labeling by azidopine. Identification of many heretofore unrecognized compounds as substrates indicates that P-glycoprotein has a broader substrate specificity than previously recognized. This study confirms the validity of this novel approach and provides the basis for similar studies examining a diverse group of gene products, including other resistance mechanisms, putative drug targets, and genes involved in the cell cycle and apoptosis.
StarNet: Targeted Computation for Object Detection in Point Clouds (2019)

Detecting objects from LiDAR point clouds is an important component of self-driving car technology as LiDAR provides high resolution spatial information. Previous work on point-cloud 3D object detection has re-purposed convolutional approaches from traditional camera imagery. In this work, we present an object detection system called StarNet designed specifically to take advantage of the sparse and 3D nature of point cloud data. StarNet is entirely point-based, uses no global information, has data dependent anchors, and uses sampling instead of learned region proposals. We demonstrate how this design leads to competitive or superior performance on the large Waymo Open Dataset and the KITTI detection dataset, as compared to convolutional baselines. In particular, we show how our detector can outperform a competitive baseline on Pedestrian detection on the Waymo Open Dataset by more than 7 absolute mAP while being more computationally efficient. We show how our redesign---namely using only local information and using sampling instead of learned proposals---leads to a significantly more flexible and adaptable system: we demonstrate how we can vary the computational cost of a single trained StarNet without retraining, and how we can target proposals towards areas of interest with priors and heuristics. Finally, we show how our design allows for incorporating temporal context by using detections from previous frames to target computation of the detector, which leads to further improvements in performance without additional computational cost.