gebhart/patrepeval huggingface dataset:
Analysis of NF-kappa B in hepatocellular carcinoma (HCC) reveals frequent activation of p50 and bcl-3 (2005)

9621 Background: The pathogenesis of HCC remains poorly characterized. The transcription regulator NF-κB is implicated in the pathogenesis of HCC. Nuclear expression implies NF-κB activation. We examined the activation state of NF-κB subunits using IHC in resected HCC. Methods: 64 resected HCCs were identified in our tumor registry. 30 were suitable for creation of tissue microarrays (TMA). Tumor and adjacent non-cancerous liver were identified, and cores from disparate areas were inserted in triplicate into the TMA. TMAs were stained using Ab against NF-κB subunits p65 (along with a phospho-specific p65 Ab), p50, p52, and Bcl-3. Nuclear NF-κB staining was characterized from 0 to 3+ and % of + nuclei noted. Tumors with ≥1+ intensity in >10% of cell nuclei were positive. Results: Concordance for staining for cores from each patient was high. 78% (15/19) of tumors compared with 27% (4/15) of adjacent liver samples were p50 +. Bcl-3 was + in 83% of tumors (19/23) vs. 48% (10/21) of adjacent liver. Staining was almost uniformly more + in tumors than adjacent liver for p50 and bcl-3. The majority of + tumors were + in all evaluable cores. 22% of tumors (6/23) were + for p65, but only 8% were + using the phospho-p65 Ab. All p65 + tumors were also p50 +. All but one of these was also Bcl-3 +. Few were p52 subunit + (3/23). There was no statistical correlation between any marker and survival, however no patient negative for p50 OR Bcl-3 lived < 2 years. Conclusions: p50 homodimers and Bcl-3 are frequently active in HCC, suggesting a role in pathogenesis. Prior work has focused mainly on the p65 subunit, which we found to be active relatively infrequently. This sample is too small to make a correlation between p50 homodimer activation and prognosis, but it is interesting that no patient who was negative for p50 or bcl-3 lived < two years, suggesting positivity for either could influence prognosis negatively. This correlation will be explored in a larger group of samples. Bcl-3 has been noted to bind p50 homodimers in nasopharyngeal cancer. We have also seen frequent activation of Bcl-3/p50 in breast cancer. The role of Bcl-3 and p50 in hepatocarcinogenesis should be explored further based on these results. Research supported by NIH P50-CA106991 and K12-RR17667. No significant financial relationships to disclose.
Theoretical study of a three-dimensional all-sp2structure (1998)

We present a study of a highly symmetric crystal made of exclusively ${\mathrm{sp}}^{2}$ bonded atoms. Calculations of the structural and electronic properties are performed within the pseudopotential-density-functional approach for two different compositions made of (i) pure carbon and (ii) carbon and nitrogen compound. In both solids, one of the carbon-carbon bond lengths is found to be 1.35 \AA{}, which is considerably smaller than any carbon-carbon bond length found in other carbon solids. The bulk moduli are calculated to be 241 and 286 GPa for the pure carbon and the carbon-nitride compounds, respectively. We demonstrate that the relatively low bulk moduli, considering the short bond lengths found in the structure, is due to the disruption of the carbon \ensuremath{\pi} bonding states. This is probably unavoidable when trying to form a three-dimensional structure out of a planar configuration like the ${\mathrm{sp}}^{2}$ bonds. The calculated density of states and band structures show that the pure carbon form is metallic whereas the carbon nitride is semiconducting. When carbon atoms are added to the interstitial regions, the carbon solid becomes insulating and the bulk modulus increases to 282 GPa.
Development of simultaneous measurement system for strain and acoustic emission using a fiber bragg grating sensor and a fiber ring laser (2011)

A simultaneous measurement system for strain and acoustic emission signals (AE signals) was developed for one fiber Bragg grating sensor (FBG sensor) using a fiber ring laser. The system consists of an erbium-doped fiber amplifier (EDFA), an optical circulator, optical couplers, photo detectors and an FBG sensor. A CFRP beam bending test was carried out to confirm the possibility of simultaneous measurement of both strain and AE signals from a single FBG sensor. In the test, signals from a conventional electric resistive strain gage and piezo-electric AE sensors were compared to those from the FBG sensor. Those were equivalent each other, and the simultaneous measurement of strain and AE signals using the newly developed system was verified.
Generation and propagation of radially polarized beams in optical fibers (2009)

Beams with polarization singularities have attracted immense recent attention in a wide array of scientific and technological disciplines. We demonstrate a class of optical fibers in which these beams can be generated and propagated over long lengths with unprecedented stability, even in the presence of strong bend perturbations. This opens the door to exploiting nonlinear fiber optics to manipulate such beams. This fiber also possesses the intriguingly counterintuitive property of being polarization maintaining despite being strictly cylindrically symmetric, a prospect hitherto considered infeasible with optical fibers.
The European contribution to the SPICA mission (2008)

The Japanese led Space Infrared telescope for Cosmology and Astrophysics (SPICA) will observe the universe over the 5 to 210 micron band with unprecedented sensitivity owing to its cold (~5 K) 3.5m telescope. The scientific case for a European involvement in the SPICA mission has been accepted by the ESA advisory structure and a European contribution to SPICA is undergoing an assessment study as a Mission of Opportunity within the ESA Cosmic Vision 1015-2015 science mission programme. In this paper we describe the elements that are being studied for provision by Europe for the SPICA mission. These entail ESA directly providing the cryogenic telescope and ground segment support and a consortium of European insitutes providing a Far Infrared focal plane instrument. In this paper we describe the status of the ESA study and the design status of the FIR focal plane instrument.
Machine Learning for the Geosciences: Challenges and Opportunities (2019)

Geosciences is a field of great societal relevance that requires solutions to several urgent problems facing our humanity and the planet. As geosciences enters the era of big data, machine learning (ML)-that has been widely successful in commercial domains-offers immense potential to contribute to problems in geosciences. However, geoscience applications introduce novel challenges for ML due to combinations of geoscience properties encountered in every problem, requiring novel research in machine learning. This article introduces researchers in the machine learning (ML) community to these challenges offered by geoscience problems and the opportunities that exist for advancing both machine learning and geosciences. We first highlight typical sources of geoscience data and describe their common properties. We then describe some of the common categories of geoscience problems where machine learning can play a role, discussing the challenges faced by existing ML methods and opportunities for novel ML research. We conclude by discussing some of the cross-cutting research themes in machine learning that are applicable across several geoscience problems, and the importance of a deep collaboration between machine learning and geosciences for synergistic advancements in both disciplines.
Plenary talks: From whiskers to fingertips &#x2014; A biomimetic approach to active touch sensing (2013)

How do animals understand the physical world they live in? One answer, due to Gibson, is that their sensory systems are tuned to pick up relevant affordances for behavior, but how is it that the brain and the sensory apparatus become suitably adapted to perform this feat? To cast light on this question we have been investigating active touch sensing in mammals, including humans, and developing biomimetic robots that can help us understand these biological systems whilst also developing useful haptic technologies. An important focus has been on the vibrissal (whisker) system of rodents, and its emergence through evolution and development, which we have investigated through a combination of (i) ethological studies of behaving animals, (ii) computational neuroscience models of the neural circuits involved in vibrissal processing, and (iii) biomimetic robots embodying many of the characteristics of whiskered animals in their design and control. This work has resulted in a series of whiskered robots, the most recent of which, Shrewbot, is able to construct tactile maps of its environment and recognize and track moving objects. We are also studying humanoid touch, focusing on the development of Bayesian strategies for active tactile sensing with robot hands. Here our results have provided the first demonstration of hyperacuity in robot touch whilst also indicating that tactile perception is improved in unstructured environments by appropriate active control. The active sensing framework can also be applied to the development of haptic interfaces for human users that can augment our existing sensory capability. For instance, we are developing a head-mounted “remote touch” system that links distance sensors (ultrasound arrays) with vibrotactile displays. Here an interesting question is how the signals that are delivered through the displays should be modulated to take into account the intentional head and body movements of the user and in order to provide a meaningful and intuitive experience. The talk will present converging lines of evidence, from these different research strands, for the importance of active control in haptics. Our results will also be used to illustrate how experimental, computational, and robotic approaches can operate together to advance our understanding of sensorimotor cognition in behaving systems.
Complications of axillary lymph node dissection for carcinoma of the breast (1998)

Mild symptoms, especially pain and numbness, are common 2-5 years after axillary lymph node dissection. The frequency of inflammation or infection in patients treated with radiation to the breast or chest wall after an axillary lymph node dissection may be greater than previously appreciated. Severe complications or symptoms that have a major impact on daily activities are uncommon. These findings should help health care providers and their patients with breast carcinoma weigh the pros and cons of axillary lymph node dissection.
Abstract 4731: Resequencing of the MYC-335 enhancer in the colorectal cancer associated 8q24 region (2010)

Abstract Genome-wide association studies have identified multiple different regions at 8q24 associated with risk of colorectal, prostate, breast and bladder cancers. It has been suggested that the cancer predisposition could be mediated through altered MYC expression. One of the regions, marked by SNP rs6983267, has been consistently shown to confer susceptibility to colorectal and prostate cancers. In our previous work, we aimed to understand the biological basis of the colorectal cancer (CRC) predisposition associated with the G allele of rs6983267. By utilizing a computer program, Enhancer Element Locator, we showed that rs6983267 affects a TCF4 binding site in an evolutionary conserved enhancer element (MYC-335). Enhancer activity of this element was confirmed in vitro and in vivo. The G allele of rs6983267 was shown to enhance the activity of the MYC-335, and in the presence of active Wnt signaling potentially lead to increased expression of a target gene, possibly MYC. To examine the contribution of other variants in the MYC-335 to CRC predisposition, we determined the genetic variation within MYC-335 in different ethnic groups by resequencing the 1271-bp genomic fragment in Caucasian, African and African American samples. This effort identified eight variants which showed population-specific allele frequencies. One variant, a 2-bp deletion, affected a putative transcription factor binding site and was present only in individuals with African origin. The deletion affected GA nucleotides at the fifth and sixth position of the putative binding sequence for transcriptional repressor GFI1 (CAGAGATTGC). The identified GFI1 binding sequence is evolutionary highly conserved and the deletion is predicted to cause a 5.5-fold lower binding affinity. Both the SNP rs6983267 and the GA deletion affect transcription factor binding sites and are differentially distributed in different ethnic populations, which suggests that both alleles are functional and under selective pressure from environmental exposure. We hypothesized that the deletion could contribute to CRC predisposition by abolishing the binding of the repressor, which in turn would lead to enhanced transcriptional activity. Here, we show preliminary results that GFI1 has preferential binding affinity for the wild type allele in the heterozygous cell line HeLa. Also, we investigated the role of the deletion in CRC predisposition in African American individuals. The 2-bp deletion identified here might be a novel population-specific colorectal cancer risk variant. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4731.
Feature-Driven Direct Non-Rigid Image Registration (2007)

The registration problem for images of a deforming surface has been well studied. Parametric warps, for instance Free-Form Deformations and Radial Basis Functions such as Thin-Plate Spline, are often estimated using additive Gauss-Newton-like algorithms. The recently proposed compositional framework has been shown to be more efficient, but can not be directly applied to such non-groupwise warps. We bring two contributions. First, we propose a Feature-Driven approach making possible the use of compositional algorithms for most parametric warps such as those mentioned above. This is demonstrated by an Inverse Compositional algorithm for Thin-Plate Spline warps. Second, we propose a piecewise linear learning approach to the local registration problem. Experimental results show that the basin of convergence is enlarged, computational cost reduced and alignment accuracy improved compared to previous methods. 1
Combined encryption and image compression using adaptive quadtree decomposition and coupled chaotic systems (2005)

The proposed technique combines quadtree-based compression and chaotic-encryption, and can be used for secure image transmission over the internet. The method of quadtree decomposition, an image representation technique, essentially decomposes a given image into its four major quadrants, which are further decomposed progressively. The technique provides for a powerful variable resolution or variable block size image coding with potential for flexible and more efficient bit allocation than other fixed block size schemes. In the proposed technique, the quadtree decomposition is not regular but is varied adaptively according to a parameter of irregularity resulting in unequal block quadrant sizes. We have used the coupled chaotic system process for this purpose. We have compared the compression performance of our new scheme with regular decomposition and the two compare well. Thus, if the parameter of irregularity is incorporated into the key along with the tree structure of the image, then our algorithm transforms into a fast image encryption tool, providing medium to high level security for multimedia and internet applications.
Two causes of instability of cellular neural networks (2003)

Since a cellular neural network (CNN) is a nonlinear analog circuit, its solution may have a complex dynamical behavior, from complete stability to chaos. It is shown that this behavior may depend strongly on the boundary conditions set at the borders of the finite-sized CNN, the network being stable with some boundary conditions and unstable with others. Two kinds of completely unstable CNNs are distinguished: those that are unstable because of the boundary conditions and those that are unstable because of the template that defines them regardless of the boundary conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transcutaneous electrical nerve stimulation (TENS) as compared to placebo TENS for the relief of acute oro-facial pain (1983)

The present paper describes the effect of high frequency, low frequency and placebo TENS on acute oro-facial pain in 62 patients, attending to an emergency clinic for dental surgery; they had all suffered pain for 1-4 days. The patients were randomly assigned to one of three groups receiving either high frequency (100 Hz), low frequency (2 Hz) or placebo TENS. In the two groups receiving TENS (42 patients) 16 patients reported a reduction in pain intensity exceeding 50%; out of these 16 patients, 4 patients reported complete relief of pain. In the placebo group (20 patients) 2 patients reported a pain reduction of more than 50%; out of these 2 patients, none reported a complete pain relief. Mechanical vibratory stimulation augmented the pain reduction obtained by TENS in 5 out of 10 patients.
Evaluation of Acrylate-Based Block Copolymers Prepared by Atom Transfer Radical Polymerization as Matrices for Paclitaxel Delivery from Coronary Stents (2005)

Acrylate-based block copolymers, synthesized by atom transfer radical polymerization (ATRP) processes, were evaluated as drug delivery matrices for the controlled release of paclitaxel from coronary stents. The polymers were multiblock copolymers consisting of poly(butyl acrylate) or poly(lauryl acrylate) soft blocks and hard blocks composed of poly(methyl methacrylate), poly(isobornyl acrylate), or poly(styrene) homo- or copolymers. Depending on the ratio of hard to soft blocks in the copolymers, coating formulations were produced that possessed variable elastomeric properties, resulting in stent coatings that maintained their integrity when assessed by scanning electron microscopy (SEM) imaging of overexpanded stents. In vitro paclitaxel release kinetics from coronary stents coated with these copolymers typically showed an early burst followed by sustained release behavior, which permitted the elution of the majority of the paclitaxel over a 10-day time period. It was determined that neither the nature of the polyacrylate (n-butyl or lauryl) nor that of the hard block appeared to affect the release kinetics of paclitaxel at a loading of 25% drug by weight, whereas some effects were observed at lower drug loading levels. Differential scanning calorimetry (DSC) analysis indicated that the paclitaxel was at least partially miscible with the poly(n-butyl acrylate) phase of those block copolymers. The copolymers were also evaluated for sterilization stability by exposing both the copolymer alone and copolymer/paclitaxel coated stents to e-beam radiation at doses of 1-3 times the nominal dose used for medical device sterilization (25 kGy). It was found that the copolymers containing blocks bearing quaternary carbons within the polymer backbone were less stable to the radiation and showed a decrease in molecular weight as determined by gel-permeation chromatography. Conversely, those without quaternary carbons showed no significant change in molecular weight when exposed to 3 times the standard radiation dose. There was no significant change in drug release profile from any of the acrylate-based copolymers after exposure to 75 kGy of e-beam radiation, and this was attributed to the inherent radiation stability of the poly(n-butyl acrylate) center block.
Clinical epidemiology of carbapenem-intermediate or -resistant Enterobacteriaceae (2011)

A patient's cumulative antibiotic exposure history is likely to be more important than any one specific exposure when determining the likelihood of developing a CIRE infection.
PEG-based Surface Modification on Upconversion Nanophosphors for Bio-imaging under IR Excitation (2006)

One of the most serious problems in fluorescence bio-imaging is the limitation of observation time due to color-fading of the fluorescence probes and damages on the bio system, both of which are caused by the excitation ultraviolet irradiation. This problem can be solved by using an upconversion emission of rare-earth doped inorganic nanophosphors under infrared excitation. For the application of nanophosphors as bio-imaging probes, surface modification by biocompatible polymers is needed to obtain biological functionality in organic tissues. In this paper, authors demonstrate the formation of poly(acrylic acid) (PAAc) and &alfa;-acetal-poly (ethylene glycol)-block-[poly (2-(N,N-dimethylamino) ethyl methacrylate)] multilayers on the Er-doped Y2O3 nanoparticles as an upconversion nanophosphor. The existence of the layers was confirmed by using zeta electrometry and infrared vibrational spectroscopy measurements.
Facilitating functional analysis of theSaccharomyces cerevisiae genome using anEGFP-based promoter library and flow cytometry (1999)

A promoter library was generated to facilitate identification of differentially regulated promoters in Saccharomyces cerevisiae. The library was constructed in a vector containing two reporter genes (EGFP and lacZ) divergently arranged about a unique cloning site. Approximately 2x10(5) clones were obtained and a flow cytometer was used to screen the library for copper-induced EGFP expression. A DNA fragment conferring copper-inducible expression of EGFP was rapidly identified. This DNA fragment, which contained several motifs associated with copper and oxidative stress homeostasis, lies upstream of two 'orphan' genes of unknown function. Further studies comparing expression from episomal vs. integrative vectors showed that construction of a similar library using an integrative vector would further enhance rapid identification of genes that are differentially regulated in S. cerevisiae. The ability to identify regulated promoters rapidly should facilitate the functional analysis of the yeast genome by identifying genes induced by specific physiological conditions.
Suppression of endogenous avidin-binding activity in tissues and its relevance to biotin-avidin detection systems. (1981)

As biotin-avidin systems continue to be developed for applications involving single cells, cell suspensions, and especially tissue sections, the need arises for a method of blocking endogenous avidin-binding activity. One such method is described and its proposed mechanism is discussed. Utilizing this method, endogenous avidin-binding activity was detected and suppressed in selected human and murine tissues, thus facilitating the interpretation of specific immunohistochemical staining utilizing hybridoma monoclonal antibodies in a biotin-avidin-horseradish peroxidase detection system.
Novel three-component coupling reaction of carbodiimide, methyl hydrogen maleate, and an alcohol or amine: synthesis of N-carbamoylaspartic acid derivatives (1994)

A novel three-component coupling reaction of methyl hydrogen maleate 1, a carbodiimide 2, and an alcohol or amine gave derivatives of N-carbamoylaspartic acid (3) in moderate to excellent yields. In the coupling, an intramolecular Michael addition of the acylisourea 6 subsequently occurs to give a new intermediate, 2-iminooxazolidin-5-one 7. The addition of alcohol or amine to the second intermediate 7 completes the three-component coupling.