gebhart/patrepeval huggingface dataset:
A transgenic strategy for analyzing the regulatory regions of the human prostate-specific antigen gene: potential applications for the treatment of prostate cancer (Review). (1998)

Prostate-specific antigen (PSA) has been used clinically as a marker for the diagnosis and staging of prostate cancer due to its specific expression in prostate epithelial cells. In addition to its medical importance, its complex hormonal and tissue-specific regulation makes it an attractive model to study gene regulation. Two approaches have been applied to the identification of regulatory regions which confer this specific expression pattern. In vitro analysis of the regulatory regions of the human PSA gene using promoter reporter constructs and tumor cell lines has revealed a number of the DNA sequences involved in the hormone-dependent expression of PSA. We have pursued an alternative in vivo approach using transgenic animal technology, which is the focus of this review. Using this second approach, a transgenic mouse was generated using a 14 kilobase (kb) region of the human PSA gene encompassing the coding region and intervening sequences as well as 6 kb of upstream sequence and 2 kb of downstream sequence. This genomic DNA clone confers a PSA expression pattern in mice which appears to be very similar if not identical to that of humans, allowing us to investigate tissue-specificity and developmental regulation of PSA expression. In addition, these mice, for which PSA is a self-antigen, provide a model to test the feasibility and efficacy of PSA-directed immunotherapy for prostate cancer. The further identification of the PSA regulatory regions important for tissue-specificity may ultimately allow the design of new therapeutics for the treatment of prostate cancer.
Add-drop photonic crystals filters (2002)

The transmission spectra of photonic crystal add-drop filters created in the microwave region are measured. The photonic crystal is a two dimensional square lattice of dielectric rods. The add-drop filters consist of two waveguides formed by removing rods along a line and a cavity lying between the two waveguides. The cavity is formed by removing rods or by replacing them with smaller diameter rods. Depending on the cavity geometry, certain wavelengths can be dropped from one waveguide and added to the other waveguide via resonant coupling through the cavity. A systematic study of the add-drop characteristics is performed as the cavity region is modified. Theoretical results, obtained from finite difference time domain calculations, are in good agreement with measurements.
Gel permeation chromatography as a multifunctional processor for nanocrystal purification and on-column ligand exchange chemistry (2016)

This article illustrates the use of gel permeation chromatography (GPC, organic-phase size exclusion chromatography) to separate nanocrystals from weakly-bound small molecules, including solvent, on the basis of size. A variety of colloidal inorganic nanocrystals of different size, shape, composition, and surface termination are shown to yield purified samples with greatly reduced impurity concentrations. Additionally, the method is shown to be useful in achieving a change of solvent without requiring precipitation of the nanocrystals. By taking advantage of the different rates at which small molecules and nanoparticles travel through the column, we show that it is furthermore possible to use the GPC column as a multi-functional flow reactor that can accomplish in sequence the steps of initial purification, ligand exchange with controlled reactant concentration and interaction time, and subsequent cleanup without requiring a change of phase. This example of process intensification <i>via</i> GPC is shown to yield nearly complete displacement of the initial surface ligand population upon reaction with small molecule and macromolecular reactants to form ligand-exchanged nanocrystal products.
Induction of Triploidy in Channel Catfish (1981)

Triploidy was induced in channel catfish (Ictalurus punctatus) by cold-shocking fertilized eggs at 5 C for 1.0 hour starting 5 minutes after fertilization. Chromosome counts from lymphocytes and kidney tissues showed 100% triploidy in the cold-shocked group and 100% diploidy in the controls. Hatching success of eggs cold-shocked 1.0 hour was 79% compared to 89% in the controls. Cold shocks longer than 1.0 hour caused 100% mortality.
Massively parallel, large-area maskless lithography (2004)

We have developed a high-throughput scanning maskless lithography technology for patterning high-resolution features on large-area substrates. This technology, which features a spatial light modulator array and a seamless-stitching scanning technique, was used to perform imaging exposures at micron-level resolution, patterning seamlessly over exposure areas significantly larger than the field size of the projection lens. This technology is attractive for a variety of applications that currently rely on mask-based lithographic processes.
Multilevel Data Storage Memory Using Deterministic Polarization Control (2011)

Multilevel non-volatile memory for high-density date storage is achieved by using the deterministic control of ferroelectric polarization. In a real ferroelectric thin-film system, eight stable and reproducible polarization states are realized (i.e., 3-bit data storage) by adjusting the displacement current. This approach can be used to triple or quadruple the memory density, even at existing feature scales.
No-reference video quality assessment for SD and HD H.264/AVC sequences based on continuous estimates of packet loss visibility (2011)

In this paper, a novel method for predicting the visibility of packet losses in SD and HD H.264/AVC video sequences and modeling their impact on perceived quality is proposed. Based on the findings of a new subjective experiment it is initially shown that the classification of packet loss visibility in a binary fashion is not sufficient to model the perceptual degradations caused by the transmission errors. The proposed no-reference algorithm extracts a set of features from the video bit-stream to account for the spatial and temporal characteristics of the video content and the induced distortion due to the network impairments. Subsequently, the visibility of packet losses is predicted in a continuous fashion using Support Vector Regression. Finally, a no-reference bit-stream based video quality assessment model that explicitly employs the predicted packet loss visibility estimates is presented. The evaluation of the proposed model demonstrates that the use of continuous estimates for the visibility of packet losses improves the performance of the video quality assessment model.
Prion protein expression in different species: Analysis with a panel of new mAbs (1998)

By immunizing prion knockout mice (Prnp-/-) with recombinant murine prion protein (PrPc), we obtained a panel of mAbs specific for murine PrPc. These mAbs can be applied to immunoblotting, cell surface immunofluorescent staining, and immunohistochemistry at light and electron microscopy. These mAbs recognize both the normal (PrPc) and protease-resistant (PrPres) isoforms of PrP. Some mAbs are species restricted, while others react with PrP from a broad range of mammals including mice, humans, monkeys, cows, sheep, squirrels, and hamsters. Moreover, some of the mAbs selectively recognize different PrP glycoforms as well as the metabolic fragments of PrPc. These newly generated PrPc antibodies will help to explore the biology of PrPc and to establish the diagnosis of prion diseases in both humans and animals.
Efficacy and safety of dapagliflozin according to aetiology in heart failure with reduced ejection fraction: insights from the <scp>DAPA‐HF</scp> trial (2021)

Dapagliflozin reduced the risk of worsening HF and death, and improved symptoms, similarly in patients with ischaemic and non-ischaemic aetiology. In addition, dapagliflozin was safe and well-tolerated, irrespective of aetiology.
Simple and flexible technique for spectrally designing all-fibre filter and apodizing fibre gratings (1997)

A new technique for spectrally designing all-fibre filter and apodizing fibre gratings is presented. Longitudinally uniform average index change is induced by a small angle dithering of the writing UV beam incident on a phase mask.
Theory and Experiments on Electrorheological Fluids (1999)

By carrying out first principles calculations, particles fabrication and experiments, we demonstrate the enhancement of the electrorheological effect through the use of microstructured composite particles, consisting of a spherical dielectric core coated with a thin layer of metal and an additional outer layer of insulating material with high dielectric constant. It is argued that through the choice of the core material and the outer layer material, the outer layer thickness, and the particle size, there can be a path of continuous improvement on the electrorheological fluid properties that makes possible the eventual fulfillment of the diverse application requirements.
Intercooler arrangement for a supercharged internal combustion engine (1986)

This patent describes a cooling system for a supercharged internal combustion engine having a combustion chamber, a compressor, and an induction circuit leading from the compressor to the combustion chamber and through which supercharging air passes. The cooling system described has a number of interacting components. The first component described is a first coolant jacket formed around that structure of the engine subject to high heat flux. Closely associated with the coolant jacket is a radiator within which coolant vapor is condensed to its liquid form, as well as a first vapor transfer conduit leading from the first coolant jacket to the radiator. A modality is described for returning liquid coolant from the radiator to the first coolant jacket in a manner designed to maintain the engine structure subject to high heat flux immersed in liquid coolant and also to define a vapor collection space within the first coolant jacket. In addition, a description of a second coolant jacket associated with the induction conduit for cooling the air which passes through the conduit, as well as a second vapor transfer conduit leading from the second coolant jacket to the radiator, is provided. The final member described is a first pumpmore » which pumps liquid coolant from the radiator to the second coolant jacket in response to a sensor which senses a parameter which varies with the supercharging of the engine.« less
Multicompartment microfibers: fabrication and selective dissolution of composite droplet-in-fiber structures (2014)

We present a microfluidic method to continuously produce multicompartment microfibers, where embedded single or double emulsion droplets are regularly spaced along the length of the fiber. Both hydrophobic and hydrophilic compounds can be encapsulated in different microcompartments of the fiber for storage, selective dissolution, and delivery applications, as well as to provide multifunctionality.
Effect of Dapagliflozin in DAPA-HF According to Background Glucose-Lowering Therapy (2020)

In DAPA-HF, dapagliflozin improved outcomes irrespective of use or no use of GLT or by GLT type used in patients with type 2 diabetes and HFrEF.
Electrical measurement of alignment for 3D stacked chips (2005)

This paper presents an electronic system based on integrated CMOS capacitive sensors that enables to determine the alignment between two chips assembled in a three-dimensional (3D) stacking configuration. Two different interface circuits are described for the on-chip measurement of alignment along vertical Z-axis and lateral X/Y-axis. A test chip has been fabricated in 0.13/spl mu/m, 6 metal standard CMOS process to test the multi-axis alignment system based on 3D sensors. A capacitive charge variation of 1 fF over 15fF corresponding to a resolution accuracy of 0.5/spl mu/m over a range of 50/spl mu/m has been measured. Sensors are 120/spl mu/m /spl times/ 30/spl mu/m and power consumption is 200/spl mu/W.
Drum priming : A non-osmotic method of priming seeds (1996)

A new seed priming method is described in which seeds were hydrated to a predetermined water content over a 1 day period, by placing them inside a horizontal rotating drum into which water vapour was released. The drum was mounted on an electronic balance, linked to a computer which monitored the seed water content, and controlled the production of water vapour so that at no time were the seeds visibly wet. Hydrated seeds were kept in a rotating drum for a further 14 days before being either sown immediately (non-dried seed) or dried to facilitate storage. Drum-primed seeds of ten leek cultivars germinated faster and more uniformly than seeds primed for the same period by placing them on paper saturated with a solution of polyethylene glycol (PEG) MW 20,000 with an osmotic potential of -1.5 MPa. A similar difference was observed when seeds primed by both methods were germinated at all combinations of 4 temperatures (5, 10, 15, and 20 deg C) and 5 osmotic potentials (0, -0.1, -0.2, -0.3, -0.4 MPa). Drum priming enables large quantities of seed to be primed without the use of large quantities of PEG solutions
CDK7 Inhibition Is Effective in all the Subtypes of Breast Cancer: Determinants of Response and Synergy with EGFR Inhibition (2020)

CDK7, a transcriptional cyclin-dependent kinase, is emerging as a novel cancer target. Triple-negative breast cancers (TNBC) but not estrogen receptor-positive (ER+) breast cancers have been reported to be uniquely sensitive to the CDK7 inhibitor THZ1 due to the inhibition of a cluster of TNBC-specific genes. However, bioinformatic analysis indicates that CDK7 RNA expression is associated with negative prognosis in all the major subtypes of breast cancer. To further elucidate the effects of CDK7 inhibition in breast cancer, we profiled a panel of cell lines representing different breast cancer subtypes. THZ1 inhibited cell growth in all subtypes (TNBC, HER2+, ER+, and HER2+/ER+) with no apparent subtype selectivity. THZ1 inhibited CDK7 activity and induced G1 arrest and apoptosis in all the tested cell lines, but THZ1 sensitivity did not correlate with CDK7 inhibition or CDK7 expression levels. THZ1 sensitivity across the cell line panel did not correlate with TNBC-specific gene expression but it was found to correlate with the differential inhibition of three genes: CDKN1B, MYC and transcriptional coregulator CITED2. Response to THZ1 also correlated with basal CITED2 protein expression, a potential marker of CDK7 inhibitor sensitivity. Furthermore, all of the THZ1-inhibited genes examined were inducible by EGF but THZ1 prevented this induction. THZ1 had synergistic or additive effects when combined with the EGFR inhibitor erlotinib, with no outward selectivity for a particular subtype of breast cancer. These results suggest a potential broad utility for CDK7 inhibitors in breast cancer therapy and the potential for combining CDK7 and EGFR inhibitors.
Certified concurrent abstraction layers (2018)

Concurrent abstraction layers are ubiquitous in modern computer systems because of the pervasiveness of multithreaded programming and multicore hardware. Abstraction layers are used to hide the implementation details (e.g., fine-grained synchronization) and reduce the complex dependencies among components at different levels of abstraction. Despite their obvious importance, concurrent abstraction layers have not been treated formally. This severely limits the applicability of layer-based techniques and makes it difficult to scale verification across multiple concurrent layers. In this paper, we present CCAL---a fully mechanized programming toolkit developed under the CertiKOS project---for specifying, composing, compiling, and linking certified concurrent abstraction layers. CCAL consists of three technical novelties: a new game-theoretical, strategy-based compositional semantic model for concurrency (and its associated program verifiers), a set of formal linking theorems for composing multithreaded and multicore concurrent layers, and a new CompCertX compiler that supports certified thread-safe compilation and linking. The CCAL toolkit is implemented in Coq and supports layered concurrent programming in both C and assembly. It has been successfully applied to build a fully certified concurrent OS kernel with fine-grained locking.
Preclinical evaluation of the fluorinated 2-nitroimidazole N-(2-hydroxy-3,3,3-trifluoropropyl)-2-(2-nitro-1-imidazolyl) acetamide (SR-4554) as a probe for the measurement of tumor hypoxia. (1997)

A novel probe, N-(2-hydroxy-3,3,3,-trifluoropropyl)-2-(2-nitro-1-imidazolyl) acetamide (SR-4554), has been used to detect tumor hypoxia noninvasively by 19F magnetic resonance spectroscopy (19F MRS). The compound was designed to undergo a hypoxia-dependent, one-electron reduction to metabolites that are selectively retained in tumors and has attractive pharmacokinetic, toxicological, and detection sensitivity properties. As a prelude to clinical studies, we report here for the first time on the ability to detect a MR signal following SR-4554 administration in various transplantable tumors and describe validation studies, consisting of a correlation between signal retention and radiobiological hypoxic fraction, and the effects of modulating the degree of hypoxia by hydralazine and carbogen breathing. SR-4554 was absorbed and then eliminated from EMT6 tumors with a half-life of 51 min following an injection of 180 mg/kg i.p. of SR-4554. Using a quantitative 19F MRS technique, the 19F retention index (19FRI; 19F signal level at 6 h/45 min) was determined for four commonly used murine tumors (EMT6, SCCVII, KHT, and RIF-1). The retention of high tumor concentrations of fluorinated probe at 6 h, despite the much lower (20-fold) concentration of parent SR-4554 detected by high-performance liquid chromatography, was consistent with the involvement of one or more nitroreduced metabolites and suggested that 19F MRS might give a quantitative measure of tumor hypoxia. In these murine tumors, 19FRI correlated with the reported radiobiological hypoxic fraction of the tumors (r = 0.988; P = 0.01). In addition, changes in tumor microenvironment were detected by 19F MRS. An increase in hypoxia induced by hydralazine treatment of RIF-1 tumor-bearing mice was associated with a 2.4-fold increase in 19FRI compared to untreated controls. In contrast, carbogen breathing by C3H mammary tumor-bearing mice produced a 6-fold decrease in the 19FRI compared to air-breathing mice. The data presented support the preclinical and clinical development of SR-4554 as a noninvasive probe for tumor hypoxia.
Capacity Maximizing Constellations (2010)

Some non-traditional signal constellations have been proposed for transmission of data over the Additive White Gaussian Noise (AWGN) channel using such channel-capacity-approaching codes as low-density parity-check (LDPC) or turbo codes. Computational simulations have shown performance gains of more than 1 dB over traditional constellations. These gains could be translated to bandwidth- efficient communications, variously, over longer distances, using less power, or using smaller antennas. The proposed constellations have been used in a bit-interleaved coded modulation system employing state-ofthe-art LDPC codes. In computational simulations, these constellations were shown to afford performance gains over traditional constellations as predicted by the gap between the parallel decoding capacity of the constellations and the Gaussian capacity
Identification of Regions of the Chromosome of <i>Neisseria meningitidis</i> and <i>Neisseria gonorrhoeae</i> Which Are Specific to the Pathogenic <i>Neisseria</i> Species (1999)

Neisseria meningitidis and Neisseria gonorrhoeae give rise to dramatically different diseases. Their interactions with the host, however, do share common characteristics: they are both human pathogens which do not survive in the environment and which colonize and invade mucosa at their port of entry. It is therefore likely that they have common properties that might not be found in nonpathogenic bacteria belonging to the same genetically related group, such as Neisseria lactamica. Their common properties may be determined by chromosomal regions found only in the pathogenic Neisseria species. To address this issue, we used a previously described technique (C. R. Tinsley and X. Nassif, Proc. Natl. Acad. Sci. USA 93:11109-11114, 1996) to identify sequences of DNA specific for pathogenic neisseriae and not found in N. lactamica. Sequences present in N. lactamica were physically subtracted from the N. meningitidis Z2491 sequence and also from the N. gonorrhoeae FA1090 sequence. The clones obtained from each subtraction were tested by Southern blotting for their reactivity with the three species, and only those which reacted with both N. meningitidis and N. gonorrhoeae (i.e., not specific to either one of the pathogens) were further investigated. In a first step, these clones were mapped onto the chromosomes of both N. meningitidis and N. gonorrhoeae. The majority of the clones were arranged in clusters extending up to 10 kb, suggesting the presence of chromosomal regions common to N. meningitidis and N. gonorrhoeae which distinguish these pathogens from the commensal N. lactamica. The sequences surrounding these clones were determined from the N. meningitidis genome-sequencing project. Several clones corresponded to previously described factors required for colonization and survival at the port of entry, such as immunoglobulin A protease and PilC. Others were homologous to virulence-associated proteins in other bacteria, demonstrating that the subtractive clones are capable of pinpointing chromosomal regions shared by N. meningitidis and N. gonorrhoeae which are involved in common aspects of the host interaction of both pathogens.
An efficient QoS-aware routing algorithm for LEO polar constellations (2013)

In this work, a Quality of Service (QoS)-aware routing (QAR) algorithm is developed for Low-Earth Orbit (LEO) polar constellations. LEO polar orbits are the only type of satellite constellations where inter-plane inter-satellite links (ISLs) are implemented in real world. The QAR algorithm exploits features of the topology of the LEO satellite constellation, which makes it more efficient than general shortest path routing algorithms such as Dijkstra’s or extended Bellman-Ford algorithms. Traffic density, priority, and error QoS requirements on communication delays can be easily incorporated into the QAR algorithm through satellite distances. The QAR algorithm also supports efficient load balancing in the satellite network by utilizing the multiple paths from the source satellite to the destination satellite, and effectively lowers the rate of network congestion. The QAR algorithm supports a novel robust routing scheme in LEO polar constellation, which is able to significantly reduce the impact of inter-satellite link (ISL) congestions on QoS in terms of communication delay and jitter.