gebhart/patrepeval huggingface dataset:
Transcription factors NF-IL6 and CREB recognize a common essential site in the human prointerleukin 1 beta gene. (1994)

A site located between -2782 and -2729 of the human prointerleukin-1 beta (IL1B) gene functions as a strong lipopolysaccharide (LPS)-responsive enhancer independent of the previously identified enhancer located between -2896 and -2846 (F. Shirakawa, K. Saito, C.A. Bonagura, D.L. Galson, M. J. Fenton, A. C. Webb, and P. E. Auron, Mol. Cell. Biol. 13:1332-1344, 1993). Although these two enhancers appear to function cooperatively in the native sequence context, they function independently as LPS-responsive elements upon removal of an interposed silencer sequence. The new enhancer is not induced by dibutyryl cyclic AMP (dbcAMP) alone but is superinduced by costimulation with LPS-dbcAMP. This pattern of induction depends upon the nature of the sequence, a composite NF-IL6-cAMP response element (CRE) binding site. This pseudosymmetrical sequence is shown to contrast with a classical symmetric CRE which responds to dbcAMP but not LPS. DNA binding studies using in vivo nuclear extract, recombinant proteins, and specific antibodies show that LPS induces the formation of two different complexes at the enhancer: (i) an NF-IL6-CREB heterodimer and (ii) a heterodimer consisting of NF-IL6 and a non-CREB, CRE-binding protein. Cotransfection studies using NF-IL6 and CREB expression vectors show that NF-IL6 transactivates the enhancer in the presence of LPS, whereas CREB acts either positively or negatively, depending upon its cAMP-regulated phosphorylation state. Our data demonstrate that the newly identified enhancer is a specialized LPS-responsive sequence which can be modulated by cAMP as a result of the involvement of NF-IL6-CRE-binding protein heterodimers.
<title>Ultrasonic beamforming architectures</title> (1998)

Basic digital beamforming architectures will be reviewed. Architectures will be analyzed for spectral characterization and hardware considerations which consist of A/D converter requirements, data storage strategies, and computational complexity. The goals of parallel processing will be illustrated along with the basic forms of parallel computation.Granularity issues which measure the ratio of the amount of computation done in a parallel task to the amount of inter-processor communication will be illustrated. Software systems will be described that allow the beamforming architectures to be modeled and tested for data throughput requirements as well as computational loading with respect to application specific concurrent architectures. One specific structure, MPI, will be described and used to illustrate how parallel processing architectures may be synthesized and tested.
A Cabled Acoustic Telemetry System for Detecting and Tracking Juvenile Salmon: Part 1. Engineering Design and Instrumentation (2011)

In 2001 the U.S. Army Corps of Engineers, Portland District (OR, USA), started developing the Juvenile Salmon Acoustic Telemetry System, a nonproprietary sensing technology, to meet the needs for monitoring the survival of juvenile salmonids through eight large hydroelectric facilities within the Federal Columbia River Power System (FCRPS). Initial development focused on coded acoustic microtransmitters and autonomous receivers that could be deployed in open reaches of the river for detection of the juvenile salmonids implanted with microtransmitters as they passed the autonomous receiver arrays. In 2006, the Pacific Northwest National Laboratory began the development of an acoustic receiver system for deployment at hydropower facilities (cabled receiver) for detecting fish tagged with microtransmitters as well as tracking them in two or three dimensions for determining route of passage and behavior as the fish passed at the facility. The additional information on route of passage, combined with survival estimates, is used by the dam operators and managers to make structural and operational changes at the hydropower facilities to improve survival of fish as they pass the facilities through the FCRPS.
Cavernous Malformations: A Review and Current Controversies (2006)

Cavernous malformations, also known as cavernous angiomas, are a specific type of cerebrovascular anomaly. Cavernous malformations have characteristic pathologic, radiographic, and genetic characteristics. Conservative management, radiation therapy, and surgical resection have been employed in the management of these lesions. In this review, we will discuss various aspects of cavernous malformations. We will present the pathology of the lesion and the differences between normal microvascular architecture and that found in cavernous malformations. We will present the epidemiology, clinical presentation, and natural history of intracranial and spinal cavernous malformations. Radiologic characteristics and the genetic and molecular causes of these lesions will be reviewed. Current treatment strategies will be discussed and controversies will be addressed.
What you see if what you get (2004)

A self-calibration method is presented for self-calibrating camera lens distortion by using only the image correspondences of two views. Two images of a single object are related by the epipolar geometry, which can be described by a 3 /spl times/ 3 singular matrix called fundamental matrix. It captures all geometric information contained in two images. An optimization method is applied to minimize the epipolar distances of the two images by adjusting the camera lens radial distortion coefficient. The merit of the method is that it does not rely on any ground truth data. Simulation and experimental results are given to demonstrate the applicability of the method.
Experiment of Differentiation of Rat Bone Marrow Mesenchymal Stem Cells into Adipocyte (2007)

Objective To explore the cultivation of rat bone marrow mesenchymal stem cells(MSCs) and the potency of differentiating into adipocytes in vitro.Methods MSCs were obtained from rat bone marrow.cultured and passaged.MSCs were induced to differentiate into adipocytes in induction medium containing desamethasone and insulin.Then differentiated cells were identificated by Sudan IV stain.Results In vitro BMSCs differentiated into adipocytes and lipid droplets were scarlet red by Sudan Ⅳ staining on the 12th day after being induced,approximately 60% rat MSCs were induced to adipogenic cells.Conclusion MSCs can culture and differentiate into adipocytes in vitro.
Molecular imaging with nanoparticles: giant roles for dwarf actors (2008)

Molecular imaging, first developed to localise antigens in light microscopy, now encompasses all imaging modalities including those used in clinical care: optical imaging, nuclear medical imaging, ultrasound imaging, CT, MRI, and photoacoustic imaging. Molecular imaging always requires accumulation of contrast agent in the target site, often achieved most efficiently by steering nanoparticles containing contrast agent into the target. This entails accessing target molecules hidden behind tissue barriers, necessitating the use of targeting groups. For imaging modalities with low sensitivity, nanoparticles bearing multiple contrast groups provide signal amplification. The same nanoparticles can in principle deliver both contrast medium and drug, allowing monitoring of biodistribution and therapeutic activity simultaneously (theranostics). Nanoparticles with multiple bioadhesive sites for target recognition and binding will be larger than 20 nm diameter. They share functionalities with many subcellular organelles (ribosomes, proteasomes, ion channels, and transport vesicles) and are of similar sizes. The materials used to synthesise nanoparticles include natural proteins and polymers, artificial polymers, dendrimers, fullerenes and other carbon-based structures, lipid-water micelles, viral capsids, metals, metal oxides, and ceramics. Signal generators incorporated into nanoparticles include iron oxide, gadolinium, fluorine, iodine, bismuth, radionuclides, quantum dots, and metal nanoclusters. Diagnostic imaging applications, now appearing, include sentinal node localisation and stem cell tracking.
Reduced basal release of serotonin from the ventrobasal thalamus of the rat in a model of neuropathic pain (2002)

Drugs that inhibit reuptake of monoamines are frequently used to treat pain syndromes, e.g. neuropathy or fibromyalgia, where mechanical allodynia is present. Several lines of evidence suggest the involvement of supraspinal sites of action of these drugs. However, a direct study of supraspinal serotonin (5-HT) or norepinephrine (NE) release in an animal model in which allodynia is expressed, e.g. neuropathy, has not been done. The ventrobasal (VB) thalamus and the hypothalamus are major supraspinal projection regions for spinal neurons that transmit nociceptive information and are innervated by monoaminergic fibers. This study determined if peripheral neuropathy would induce changes in extracellular monoamines in VB thalamus and hypothalamus. Male Sprague-Dawley rats had spinal nerve roots L5 and L6 tightly ligated (neuropathic rats; NP) or sham (SHAM) surgery; contralateral and ipsilateral VB thalamus and contralateral hypothalamus were dialyzed with modified artificial cerebral spinal fluid (aCSF), with and without fluoxetine. NP rats had significantly decreased 5-HT content in dialysates of the contralateral VB thalamus compared with SHAM rats with (82% decrease) or without (63% decrease) fluoxetine in the perfusion medium over the 180 min of the study. There were no differences in the ipsilateral VB thalamus. In contrast, release of 5-HT was unchanged in the hypothalamic dialysates of SHAM vs. NP rats. NE release was not different in dialysates of either the VB thalamus or hypothalamus of SHAM vs. NP rats. Synthesis of 5-HT, as assessed by accumulation of 5-hydroxytrytophan after treatment with an L-amino acid decarboxylase inhibitor, was not different between NP and SHAM rats in VB thalamic and hypothalamic brain tissue. This study is the first to demonstrate changes in monoamine release supraspinally in NP rats. The differential effect between VB thalamus and hypothalamus suggests that a terminal field change may be involved. Putative mechanisms for mediating this change include alterations of GABA-ergic systems and/or plasticity related to alterations in N-methyl-D-aspartate receptor activation and nitric oxide release related to afferent hyperactivity induced by neuropathic pain.
Cosmic-ray neutron transport at a forest field site: the sensitivity to various environmental conditions with focus on biomass and canopy interception (2017)

Abstract. Cosmic-ray neutron intensity is inversely correlated to all hydrogen present in the upper decimeters of the subsurface and the first few hectometers of the atmosphere above the ground surface. This correlation forms the base of the cosmic-ray neutron soil moisture estimation method. The method is, however, complicated by the fact that several hydrogen pools other than soil moisture affect the neutron intensity. In order to improve the cosmic-ray neutron soil moisture estimation method and explore the potential for additional applications, knowledge about the environmental effect on cosmic-ray neutron intensity is essential (e.g., the effect of vegetation, litter layer and soil type). In this study the environmental effect is examined by performing a sensitivity analysis using neutron transport modeling. We use a neutron transport model with various representations of the forest and different parameters describing the subsurface to match measured height profiles and time series of thermal and epithermal neutron intensities at a field site in Denmark. Overall, modeled thermal and epithermal neutron intensities are in satisfactory agreement with measurements; however, the choice of forest canopy conceptualization is found to be significant. Modeling results show that the effect of canopy interception, soil chemistry and dry bulk density of litter and mineral soil on neutron intensity is small. On the other hand, the neutron intensity decreases significantly with added litter-layer thickness, especially for epithermal neutron energies. Forest biomass also has a significant influence on the neutron intensity height profiles at the examined field site, altering both the shape of the profiles and the ground-level thermal-to-epithermal neutron ratio. This ratio increases with increasing amounts of biomass, and was confirmed by measurements from three sites representing agricultural, heathland and forest land cover. A much smaller effect of canopy interception on the ground-level thermal-to-epithermal neutron ratio was modeled. Overall, the results suggest a potential to use ground-level thermal-to-epithermal neutron ratios to discriminate the effect of different hydrogen contributions on the neutron signal.
Complete primary structures of the E beta chain and gene of the mouse major histocompatibility complex. (1983)

Using the cross-hybridization with plasmid pDC beta-1, containing the cDNA coding for the DC beta chain of the human major histocompatibility complex class II molecules, we have cloned and subjected to sequence analysis both the cDNA and genomic gene for the E beta chain of the BALB/c (d haplotype) mouse. The nucleotide sequences of the cDNA and genomic DNA clones permitted us to deduce the entire primary structure of the E beta chain and the complete exon-intron structure of the E beta gene. Unlike alpha chain genes that contain five exons, the E beta gene consists of six exons corresponding to the six functional domains--the leader, beta 1 and beta 2 domains, transmembrane peptide, intracytoplasmic peptide, and 3' untranslated region. In addition, two short blocks of sequences common to alpha and beta chain genes were identified in the 5' flanking regions. We propose that these sequences are involved in the coordinate expression of alpha and beta chains.
DATm: Diderot's Automated Testing Model (2017)

Diderot is a parallel domain-specific language forthe analysis and visualization of multidimensional scientific images, such as those produced by CT and MRI scanners. Diderot is designed to support algorithms that are based on differential tensor calculus and produces a higher-order mathematical model which allows direct manipulation of tensor fields. One of the main challenges of the Diderot implementation is bridging this semantic gap by effectively translating high-level mathematical notation of tensor calculus into efficient low-level code in the target language. A key question for a high-level language, such as Diderot, is how do we know that the implementation is correct. We have previously presented and defended a core set of rewriting rules, but the full translation from source to executable requires much more work. In this paper, we present DATm, Diderot's automated testing model to check the correctness of the core operations in the programming language. DATm can automatically create test programs, and predict what the outcome should be. We measure the accuracy of the computations written in the Diderot language, based on how accurately the output of the program represents the mathematical equivalent of the computations. This paper describes a model for testing a high-level language based on correctness. It introduces the pipeline for DATm, a tool that can automatically create and test tens of thousands of Diderot test programs and that has found numerous bugs. We make a case for the necessity of extensive testing by describing bugs that are deep in the compiler, and only could be found with a unique application of operations. Lastly, we demonstrate that the model can be used to create other types of tests by visual verification.
The Design and Implementation of an Integrity Subsystem for the Relational DBMS RAP (1985)

Although a sequential work-up for deep vein thrombosis has reached agreement worldwide, the mysterious nature of DVT following fractures brings challenges to early diagnosis and intervention. The objective of the present study was to develop and validate a nomogram for predicting preoperative DVT risk in patients with thoracolumbar fractures using readily available clinical data. Of the 1350 patients, 930 were randomly assigned to the training cohort. A prediction model was established and visualized as a nomogram based on eight predictors related to preoperative DVT. The performance of the model was tested by the receiver operating characteristic curve, Hosmer-Lemeshow test, calibration curve, and decision curve analysis. We further verified the model in the validation cohort. The AUCs of the prediction model were 0.876 and 0.853 in training and validation cohorts, respectively. The Hosmer-Lemeshow test demonstrated good fitness in the training set (X<sup>2</sup> = 5.913, P = 0.749) and the validation set (X<sup>2</sup> = 9.460, P = 0.396). Calibration and decision curve analyses performed well in training and validation sets. In short, we developed a prediction model for preoperative DVT risk in patients with thoracolumbar fractures and verified its accuracy and clinical utility.
The role of IL-17 in joint destruction (2002)

Interleukin-17 (IL-17) is a recently cloned cytokine secreted by activated memory CD4(+) T cells and modulates the early stage of immune responses. IL-17 stimulates epithelial, endothelial and fibroblastic stromal cells to secrete several cytokines such as IL-6, IL-8 and granulocyte colony-stimulating factor, as well as prostoglandin E2. IL-17 also stimulates the production and expression of proinflammatory cytokines, IL-1beta and tumor necrosis factor-alpha by human macrophages. IL-17 may be involved in osteoclastic bone resorption in rheumatoid arthritis patients. Recently, several groups have reported that IL-17 plays important roles in both the immune response and joint destruction in patients with rheumatoid arthritis. The control of IL-17 expression in these patients could provide directions for the development of new treatment strategies for joint destruction. (c) 2002 Prous Science. All rights reserved.
40% efficient thin-film surface-textured light-emitting diodes by optimization of natural lithography (2000)

In conventional light-emitting diodes (LEDs), the external efficiency is limited by total internal reflection at the semiconductor-air interface. The problem can be overcome by the concept of the nonresonant cavity LED, which is an LED with a textured top surface and a rear reflector. The surface is textured using natural lithography. A monolayer of randomly positioned polystyrene spheres acts as a mask for dry etching. We present details about the optimization of the parameters of the texturing process for GaAs/AlGaAs LEDs. The studied parameters are the size of the spheres, the distribution of the spheres on the surface and the etching depth. Using optimized texturing conditions, we have realized un-encapsulated top-emitting oxide-confined GaAs/AlGaAs nonresonant cavity LEDs with an external quantum efficiency of 40%.
Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly (2008)

The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de-convolution and positioning of sequence scaffolds (see BES_scaffolds section of SoyGD). This approach will assist genome annotation for paleopolyploid and true polyploid genomes such as soybean and many important cereal and fruit crops.
All-optical wavelength-routing switch with monolithically integrated filter-free tunable wavelength converters and an AWG (2010)

We present a compact 4x8 wavelength-routing switch that monolithically integrates fast tunable wavelength converters (TWCs) and an arrayed-waveguide grating (AWG) for optical packet switching. The TWC consists of a double-ring-resonator-coupled tunable laser which allows rapid and stable switching, and an optical gate based on a parallel amplifier structure which prevents an input optical signal from being routed through the AWG (filter-free operation). A deep-ridge waveguide technology, employed for the AWG and ring resonators, facilitates the fabrication of the switch and makes the device compact. The filter-free TWCs achieve low crosstalk of the input optical signal of less than -22 dB. The wavelength routing operation of a non-return-to-zero (NRZ) signal at 10 Gbit/s is achieved with a switching time of less than 5 ns.
Global prevalence of anxiety disorders: a systematic review and meta-regression (2012)

Anxiety disorders are common and the substantive and methodological factors identified here explain much of the variability in prevalence estimates. Specific attention should be paid to cultural differences in responses to survey instruments for anxiety disorders.
Sarcoglycanopathies: molecular pathogenesis and therapeutic prospects (2009)

Sarcoglycanopathies are a group of autosomal recessive muscle-wasting disorders caused by genetic defects in one of four cell membrane glycoproteins, alpha-, beta-, gamma- or delta-sarcoglycan. These four sarcoglycans form a subcomplex that is closely linked to the major dystrophin-associated protein complex, which is essential for membrane integrity during muscle contraction and provides a scaffold for important signalling molecules. Proper assembly, trafficking and targeting of the sarcoglycan complex is of vital importance, and mutations that severely perturb tetramer formation and localisation result in sarcoglycanopathy. Gene defects in one sarcoglycan cause the absence or reduced concentration of the other subunits. Most genetic defects generate mutated proteins that are degraded through the cell's quality control system; however, in many cases, conformational modifications do not affect the function of the protein, yet it is recognised as misfolded and prematurely degraded. Recent evidence shows that misfolded sarcoglycans could be rescued to the cell membrane by assisting their maturation along the ER secretory pathway. This review summarises the etiopathogenesis of sarcoglycanopathies and highlights the quality control machinery as a potential pharmacological target for therapy of these genetic disorders.
[Spine disc MR image analysis using improved independent component analysis based active appearance model and Markov random field]. (2010)

As there are not many research reports on segmentation and quantitative analysis of soft tissues in lumbar medical images, this paper presents an algorithm for segmenting and quantitatively analyzing discs in lumbar Magnetic Resonance Imaging (MRI). Vertebrae are first segmented using improved Independent component analysis based active appearance model (ICA-AAM), and lumbar curve is obtained with Minimum Description Length (MDL); based on these results, fast and unsupervised Markov Random Field (MRF) disc segmentation combining disc imaging features and intensity profile is further achieved; finally, disc herniation is quantitatively evaluated. The experiment proves that the proposed algorithm is fast and effective, thus providing doctors with aid in diagnosing and curing lumbar disc herniation.