gebhart/patrepeval huggingface dataset:
Cryo-EM structures reveal distinct mechanisms of inhibition of the human multidrug transporter ABCB1 (2020)

ABCB1 detoxifies cells by exporting diverse xenobiotic compounds, thereby limiting drug disposition and contributing to multidrug resistance in cancer cells. Multiple small-molecule inhibitors and inhibitory antibodies have been developed for therapeutic applications, but the structural basis of their activity is insufficiently understood. We determined cryo-EM structures of nanodisc-reconstituted, human ABCB1 in complex with the Fab fragment of the inhibitory, monoclonal antibody MRK16 and bound to a substrate (the antitumor drug vincristine) or to the potent inhibitors elacridar, tariquidar, or zosuquidar. We found that inhibitors bound in pairs, with one molecule lodged in the central drug-binding pocket and a second extending into a phenylalanine-rich cavity that we termed the "access tunnel." This finding explains how inhibitors can act as substrates at low concentration, but interfere with the early steps of the peristaltic extrusion mechanism at higher concentration. Our structural data will also help the development of more potent and selective ABCB1 inhibitors.
Wide-band Fabry-Perot-like filters in optical fibre (2002)

An important component in optical systems which has to date been difficult to produce in a format compatible with optical fibre systems is the Fabry-Perot (FP) resonator. Although narrow-band devices have been reported with very high finesse, for applications in short pulse lasers and high speed communication system a response over several nanometres or more is required. The primary problem preventing the fabrication of wide-band filters using unchirped Bragg gratings written in photosensitive optical fibre is that the limited /spl Delta/n which may be achieved without loss limits the bandwidth of the device. In this paper we demonstrate a method to produce Fabry-Perot-like structures in which the bandwidth is limited primarily by the range of chirp that can be produced in the grating.
Multiwavelength ellipsometry for real-time process control of the plasma etching of patterned samples (1997)

We present a quantitative model to understand the ellipsometry traces recorded while etching patterned wafers in a high-density plasma reactor. This model allows one to determine the real-time thickness of a film as it etches, and data are presented showing the real-time thickness of TiN and polysilicon layers while etching. The model is generic to the film type and can be applied to any arbitrary stack of materials. Knowing the thickness in real time allows greater process control, as it enables one to stop or change the process at a specified remaining film thickness. The model is essentially geometric and does not include the effect of diffraction. It has been applied successfully to many samples, each with different integrated circuit layouts. The results are in good agreement with scanning electron microscopy measurements.
Splice-junction recognition on gene sequences (DNA) by BRAIN learning algorithm (2002)

Splice junctions are points on a DNA sequence at which superfluous DNA is removed during the process of protein creation in higher organisms. The problem afforded in this paper is to recognize, given a sequence of DNA, the boundaries between exons (the parts of the DNA sequence retained after splicing) and introns (the parts of the DNA sequence that are spliced out). This is achieved by means of a new learning algorithm (BRAIN), described in the paper, inferring Boolean formulae from examples, and by considering the splicing rules as disjunctive normal form formulae. The formula terms are computed in an iterative way, by identifying from the training set a relevance coefficient for each attribute. The classification accuracy is then refined by a neural network hybrid approach.
Relational versus non-relational database systems for data warehousing (2010)

Relational database systems have been the dominating technology to manage and analyze large data warehouses. Moreover, the ER model, the standard in database design has a close relationship with the relational model. Recently, there has been a surge of alternative technologies for large scale analytic processing, most of which are not based on the relational model. Out of these proposals, distributed file systems together with MapReduce have become strong competitors to relational database systems to analyze large data sets, exploiting parallel processing. Moreover, there is progress on using MapReduce to evaluate relational queries. With that motivation in mind, this panel will compare pros and cons of each technology for data warehousing and will identify research issues, considering practical aspects like ease of use, programming flexibility and cost; as well as technical aspects like data modeling, storage, hardware, scalability, query processing, fault tolerance and data mining.
Monitoring of radioiodine from containment accidents (1977)

An air sampling system was developed that merged the useful properties of solid adsorbers, vacuum cleaner air movers, and Civil Defense GM survey meters. The system can be used to monitor the environmental levels of /sup 131/I produced by release from containment accidents in nuclear power reactors.
Improvement of FISH mapping resolution on combed DNA molecules by iterative constrained deconvolution: a quantitative study (2001)

Image restoration approaches, such as digital deconvolution, are becoming widely used for improving the quality of microscopic images. However, no quantification of the gain in resolution of fluorescence images is available. We show that, after iterative constrained deconvolution, fluorescent cosmid signals appear to be 25% smaller, and 1.2-kb fragment signals on combed molecules faithfully display the expected length.
Drilling and demolition of rocks by pulsed power (2003)

There are various methods of rock drilling and demolition. Recently, a method utilizing pulsed power technology has appeared. This method is based on the difference of the dynamic breakdown field strength of liquid and solid dielectrics. The applicability of this method was examined. The features of the rock destruction have been studied. The mechanism explaining the breakdown of the dielectrics with high intrinsic inhomogeneity like natural rocks and concrete is proposed and proved experimentally. An inductive energy storage-opening switch system for the destruction of solid materials is designed allowing higher destruction efficiency. The experimental results using advanced diagnostics such as an image converter camera and X-ray computer tomography of samples are presented. High pulse energy experiments (up to 60 kT in pulse) have been conducted.
One-way and near-absolute polarization insensitive near-perfect absorption by using an all-dielectric metasurface (2020)

In this Letter, we numerically propose the one-way perfect absorption of near-infrared radiation in a tunable spectral range with high transmission in the neighboring spectral ranges. This functionality is obtained by using a two-dimensional, guided-mode resonance-based grating-waveguide metasurface that acts as a frequency-selective reflector, a spacer dielectric, and an absorbing oxide layer. Within the bandwidth of the excited guided-mode resonance excited at 1.82 µm (with a full-width at half-maximum of 19 nm), we confirmed perfect absorption when light was incident from one of the two opposite directions, whereas in the other direction, perfect reflection was observed. The forward-to-backward absorption ratio reached as high as 60, while the thickness of the entire structure was on the order of the operating wavelength. In addition to the spectral tunability of the excited resonances and their bandwidths, our proposed device supports transparency windows with 65% transmission in the adjacent frequency bands. Our 2D grating is also verified to enable near-absolute insensitivity to the polarization state of incident light. Geometrical parameter modification also gives our design great tunability, as we also designed a device with a 300 nm absorption/reflection linewidth.
Homologous Recombination in Rat Germline Stem Cells1 (2011)

Spermatogonial stem cells (SSCs) are the only stem cells in the body with germline potential, which makes them an attractive target for germline modification. We previously showed the feasibility of homologous recombination in mouse SSCs and produced knockout (KO) mice by exploiting germline stem (GS) cells, i.e., cultured spermatogonia with SSC activity. In this study, we report the successful homologous recombination in rat GS cells, which can be readily established by their ability to form germ cell colonies on culture plates whose surfaces are hydrophilic and neutrally charged and thus limit somatic cell binding. We established a drug selection protocol for GS cells under hypoxic conditions. The frequency of the homologous recombination of the Ocln gene was 4.2% (2 out of 48 clones). However, these GS cell lines failed to produce offspring following xenogeneic transplantation into mouse testes and microinsemination, suggesting that long-term culture and drug selection have a negative effect on GS cells. Nevertheless, our results demonstrate the feasibility of gene targeting in rat GS cells and pave the way toward the generation of KO rats.
Correction to: Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume–rhizobia symbiosis (2021)

A correction to this paper has been published: https://doi.org/10.1007/s10265-021-01295-3
Brillouin scattering in thin film optical waveguides. I. Theory of the phonon modes (1982)

The phonon modes of a thick plate and a thick plate coated with a thin film are discussed in the light of recent experiments on Brillouin scattering in thin film optical waveguides. Using the reflection coefficients for bulk waves, we have obtained the field structures, the mode normalization for excitation by thermal fluctuations, and the density of states for these modes. Both bulk and surface (Rayleigh, Sezawa, and Love) phonons are discussed.
Supplementary Figure 4 from Context-Dependent Role of Angiopoietin-1 Inhibition in the Suppression of Angiogenesis and Tumor Growth: Implications for AMG 386, an Angiopoietin-1/2–Neutralizing Peptibody (2023)

Supplementary Figure 4 from Context-Dependent Role of Angiopoietin-1 Inhibition in the Suppression of Angiogenesis and Tumor Growth: Implications for AMG 386, an Angiopoietin-1/2–Neutralizing Peptibody
A small number of residues in the class II molecule I-Auconfer the ability to bind the myelin basic protein peptide Ac1-11 (1999)

The N-terminal peptide Ac1-11 of myelin basic protein induces experimental autoimmune encephalomyelitis in H-2(u) and (H-2(u) x H-2(s)) mice but does not in H-2(s) mice. Ac1-11 binds weakly to the class II major histocompatibility complex (MHC) molecule I-Au but not at all to I-As. We have studied the interaction of Ac1-11 and I-Au as a model system for therapeutic intervention in the autoimmune response seen in experimental autoimmune encephalomyelitis. Two polymorphic residues that differ between I-Au and I-As, Y26beta and T28beta, and one conserved residue, E74beta, confer specific binding of Ac1-11 to I-Au. A fourth residue, R70beta in I-Au, affects both peptide binding and T cell recognition. These results are consistent with a model that places arginine at position five of Ac1-11 in pockets 4 and 7 of the MHC groove, which is formed in part by residues 26, 28, 70, and 74 of Abetau and places lysine at position four of Ac1-11, previously shown to be a major MHC contact, in hydrophobic pocket 6. The data indicate that the primary region of I-Au that confers specific binding of Ac1-11 lies in the center of the peptide binding groove rather than in the region that contacts the N terminus of the peptide, as has been shown for HLA DR and the homologous I-E molecules.
Driver crash risk factors and prevalence evaluation using naturalistic driving data (2016)

The accurate evaluation of crash causal factors can provide fundamental information for effective transportation policy, vehicle design, and driver education. Naturalistic driving (ND) data collected with multiple onboard video cameras and sensors provide a unique opportunity to evaluate risk factors during the seconds leading up to a crash. This paper uses a National Academy of Sciences-sponsored ND dataset comprising 905 injurious and property damage crash events, the magnitude of which allows the first direct analysis (to our knowledge) of causal factors using crashes only. The results show that crash causation has shifted dramatically in recent years, with driver-related factors (i.e., error, impairment, fatigue, and distraction) present in almost 90% of crashes. The results also definitively show that distraction is detrimental to driver safety, with handheld electronic devices having high use rates and risk.
Abstract P151: Salt Sensitivity in Male and Female C57BL/6J Mice: Role of Renal Angiotensin and Dopamine Receptors and Sodium Transporters (2017)

To test if there is a sex difference in the salt sensitivity of C57Bl/6J mice, we studied blood pressure (BP), renal dopamine receptors, and sodium transporters in response to high salt diet (4% NaCl, 1 wk) and candesartan. Similar to males, the night-time systolic BP (SBP, telemetry, n=4) in females started to increase on day 1, peaked on day 2 (130±1 vs 117±1, mm Hg) and remained at high levels (126±1); the daytime SBP started to increase on day 2 that became significant on day 6 (124±1 vs 111±1). The high salt-diet induced-increase in SBP was prevented by candesartan (1 mg/kg, 1 wk, subcutaneously via osmotic mini-pump) (82±3 vs. 117±2 in males; 86±2 vs. 121±1 in females, under anesthesia, n=5/group). There were no sex differences in the SBP response to diet and candesartan, food and water intakes, urinary excretions of water and electrolytes, and serum concentrations of creatinine and electrolytes on high and normal salt diet. In females fed a high salt diet, candesartan increased renal D 1 R (151±12, immunoblotting, % of control, n=5/group) and D 5 R (156±5) but not D 2 R, D 3 R , or D 4 R protein expression, increased renal mRNA expression of D 1 R(160±17) but not D 5 R (real-time PCR), and decreased the renal protein expressions of sodium-hydrogen exchanger isoform 3 (36±6), sodium-potassium-2 chloride cotransporter (8±2), sodium-chloride cotransporter (30±3), and α (55±4), β (60±8) and γ (9±1) epithelial sodium channel, but not type 2 sodium phosphate cotransporter and α1Na + K + ATPase. Those changes were also seen in males except that renal D 1 R protein expression was not increased. Under normal salt intake, AT 1A R KO females (C57Bl/6J background) had increased renal protein expressions of D 1 R (152±8), D 5 R (131±6), and D 4 R (114±4), but not D 2 R and D 3 R; renal protein expressions of sodium-hydrogen exchanger isoform 3 (47±8), sodium-potassium-2 chloride cotransporter (52±11), and α (42±9) and γ (46±7) epithelial sodium channel were decreased. We conclude that the increase in BP caused by high salt diet and the effect of AT 1 R blockade on BP, renal dopamine receptors and sodium transporters are similar in male and female C57Bl/6J mice . The consequences of the sex-related differential regulation of D 1 R and D 5 R, in pathophysiology, other than BP, remain to be determined.
Optical modeling of agricultural fields and rough-textured rock and mineral surfaces (1973)

Review was made of past models for describing the reflectance and/or emittance properties of agricultural/forestry and geological targets in an effort to select the best theoretical models. An extension of the six parameter Allen-Gayle-Richardson model was chosen as the agricultural plant canopy model. The model is used to predict the bidirectional reflectance of a field crop from known laboratory spectra of crop components and approximate plant geometry. The selected geological model is based on Mie theory and radiative transfer equations, and will assess the effect of textural variations of the spectral emittance of natural rock surfaces.
Digital optical phase conjugation of fluorescence in turbid tissue (2012)

We demonstrate a method for phase conjugating fluorescence. Our method, called reference free digital optical phase conjugation, can conjugate extremely weak, incoherent optical signals. It was used to phase conjugate fluorescent light originating from a bead covered with 0.5 mm of light-scattering tissue. The phase conjugated beam refocuses onto the bead and causes a local increase of over two orders of magnitude in the light intensity. Potential applications are in imaging, optical trapping, and targeted photochemical activation inside turbid tissue.
Palladium-catalysed sequential carboxylation–alkoxycarbonylation of acetylenic amines (1997)

Carbon dioxide and carbon monoxide react in sequence in an intramolecular carboxy–carbonylation reaction of N-alkyl-substituted dialkylpropynylamines, under the catalytic action of palladium iodide–potassium iodide in methanol in the presence of oxygen.
Inflammation in Mice Ectopically Expressing Human Pyogenic Arthritis, Pyoderma Gangrenosum, and Acne (PAPA) Syndrome-associated PSTPIP1 A230T Mutant Proteins (2013)

Pyogenic Arthritis, Pyoderma Gangrenosum and Acne Syndrome (PAPA syndrome) is an autoinflammatory disease caused by aberrant production of the proinflammatory cytokine interleukin-1. Mutations in the gene encoding proline serine threonine phosphatase interacting protein-1 (PSTPIP1) have been linked to PAPA syndrome. PSTPIP1 is an adaptor protein that interacts with PYRIN, the protein encoded by the Mediterranean Fever (MEFV) gene whose mutations cause Familial Mediterranean Fever (FMF). However, the pathophysiological function of PSTPIP1 remains to be elucidated. We have generated mouse strains that either are PSTPIP1 deficient or ectopically express mutant PSTPIP1. Rusults from analyzing these mice suggested that PSTPIP1 is not an essential regulator of the Nlrp3, Aim2 or Nlrc4 inflammasomes. Although common features of human PAPA syndrome such as pyogenic arthritis and skin inflammation were not recapitulated in the mouse model, ectopic expression of the mutant but not the wild type PSTPIP1 in mice lead to partial embryonic lethality, growth retardation and elevated level of circulating proinflammatory cytokines.
Energy deficit of pulsed-laser field-ionized and field-emitted ions from non-metallic nano-tips (2014)

The energy deficit of pulsed-laser field-evaporated ions and field-ionized atoms of an inert gas from the surface of a non-metallic nano-metric tip is reported as a function of the laser intensity, ion current, and temperature. A new model is proposed to explain these results, taking into account the resistive properties of non-metallic nano-tips. A good agreement between the theoretical predictions and the experimental results is obtained for all parameters investigated experimentally. This model is also used to discuss the evaporation behavior of oxides analyzed in laser-assisted atom probe tomography. New insight into the contribution of the electrostatic field and the laser illumination on the evaporation process of non-metallic materials is given.
Letters (2008)

Department of Orthopedic Surgery, University of California, San Diego, CA (Kim) Orthopedic Biomechanics Research Center, Department of Orthopedics, Rady Childrens Hospital, San Diego, CA, Department of Orthopedic Surgery, University of California, San Diego, CA (Mahar) Department of Orthopedic Surgery, University of California, San Diego, CA (Garfin)
Effect of arginine and canavanine on arginine messenger RNA synthesis (1971)

The level of messenger RNA for the arg ECBH gene cluster in Escherichiacoli was determined by hybridization of 3H-pulse-labeled RNA with DNA from 80darg. L-Arginine repressed the level of hybridizable message 7 to 24 fold lower than that observed in arginine-deprived cells. Added L-canavanine had little effect on the level of hybridizable message during arginine-deprivation. Our data suggest that the arginine regulon is repressed at both the level of transcription and translation.
Effects of patterning on perpendicular exchange bias probed by extraordinary Hall effect (2004)

In this work, the evolution of the exchange bias in epitaxial CoO/Pt/Co/Pt/Al2O3 structures with perpendicular anisotropy is studied by using extraordinary Hall effect. It is shown that for nonpatterned films, a perpendicular exchange bias is present with a blocking temperature around 150 K. However, when the structures are patterned into 1-μm-wide and 15-μm-long wires, the exchange bias disappears at any temperature.
Apartment Building Energy Management System in Group Optimization with Electricity Interchange Using In-Vehicle Batteries (2015)

In Vehicle-to-Home (V2H) systems, charge/discharge scheduling of in-vehicle battery installed in Electric Vehicles (EVs) or Plug-in Hybrid Vehicles (PHVs) is very important in order to operate the battery as an storage and a source of electricity for the car owner&#39;s home. This significance of the battery is similarly applied to apartment buildings not only to homes. In this paper, the authors proposed an Energy Management System (EMS) for apartment buildings based on model-predictive control (MPC) using group optimization with electricity interchange from in-vehicle batteries, and the authors investigate and verify the usefulness of the proposed system for apartment buildings where households have various patterns in profiles of electricity consumption and vehicle use.
Massive Spatial Data Processing Model Based on Cloud Computing Model (2010)

Cloud computing model can take advantage of the network resources, creating a powerful computing capacity to meet the real-time processing a large amount of spatial data. So this paper showed a cloud computing model based on a large amount of spatial data processing model. It used not only controller to implement the distribution of spatial data processing tasks but cloud computing power to achieve the corresponding supervised classification and unsupervised classification as well as the surface features information extraction, the extraction of NDVI (Normal Differential Vegetation Index), and made it possible to monitor the application and rapid flooding and the realization of real-time monitoring for dust storms. Forest fires can be used in monitoring, timely understanding of the spread of fire, as well as control of key areas. At the same time, in the aspect of environmental protection, the system can be applied to the ozone layer and the monitoring of glacier flow and determine the direction of study. While the ocean remote sensing can provide real-time data processing of marine red tide monitoring data, and propose feasible solutions.
Rights Management for Role-Based Access Control (2008)

Healthcare requires a new approach with respect to the secure management of information. For this purpose we extend the Role Based Access Control model with exceptions, context awareness, and delegation. By combining this extended model with common notions from the field of Enterprise/Digital Rights Management we obtain a framework for controlling shared information in a distributed environment.