gebhart/patrepeval huggingface dataset:
Multiparametric study (SAMBA 200) of estrogen receptor immunocytochemical assay in 400 human breast carcinomas: analysis of estrogen receptor distribution heterogeneity in tissues and correlations with dextran coated charcoal assays and morphological data. (1988)

Estrogen receptor (ER) immunocytochemical assay (ER-ICA) was assessed in 400 human breast carcinomas. In all cases, patient's age, tumor size, histological type and Scarff-Bloom-Richardson grade, and presence or absence of axillary lymph node metastases and of vessel invasion in tumor borders were recorded. In 310 cases estrogen and progesterone receptors were concomitantly evaluated (dextran coated charcoal method). In 60 of these cases the ER immunoenzymatic assay (ER-IEA) was also assessed. Monoclonal H222sp gamma and peroxidase antiperoxidase procedures (Abbott kit) were applied in frozen sections, tumor imprints, and fine-needle aspirates. A computerized system of image analysis referred to as SAMBA (TITN), permitted a multiparametric quantitative analysis of ER-positive surfaces. With this system, in each tumor, the cellularity, percentage of ER surface versus the total cell surface and versus the epithelial (keratin-positive) surface, integrated optical density, mean optical density, index of the concentration of labeled objects, and integrated optical density histograms, were obtained and correlated to histological and biochemical data. It was shown that (a) ER antigenic sites were heterogeneously distributed in ER-positive tumors, with a specific nuclear localization in epithelial cells; (b) SAMBA 200 multiparametric analysis of the ER sites distribution in tissue was appropriate, accurate, reproducible, and therefore more reliable than the semiquantitative analysis; (c) standardization and complete automation of this method of immunoprecipitates evaluation on tissue section permits daily and routine analysis of a large number of preparations; (d) there was a correlation between ER binding sites evaluation (dextran coated charcoal) and ER antigenic sites immunodetection (ER-ICA and ER-IEA); (e) there was a correlation between the SAMBA evaluation of ER-ICA and other histological prognostic factors such as small tumor size, low Scarff-Bloom-Richardson grade; (f) the preliminary SAMBA analysis of ER-ICA in tissue sections, imprints, and fine needle aspirates suggest that fine needle aspirates may not reflect accurately the tumor cell heterogeneity.
Anticonvulsants (Antineuropathics) for Neuropathic Pain Syndromes (2000)

Our knowledge about the pathogenesis of neuropathic pain has grown significantly during last two decades. Basic research with animal models of neuropathic pain and human clinical trials with neuropathic pain have accumulated solid evidence that a number of pathophysiologic and biochemical changes take place in the nervous system at a peripheral or central level as a result of the insult or disease. Many similarities between the pathophysiologic phenomena observed in some epilepsy models and neuropathic pain models justify the rationale for the use of anticonvulsant drugs in the symptomatic management of neuropathic pain disorders. Carbamazepine (CBZ) was the first representative from this class of drugs to be studied in clinical trials. It has been used for the treatment of neuropathic pain syndromes, in particular, trigeminal neuralgia (TN), for the longest time of any of the drugs in this class. Results from clinical trials support the use of CBZ in the treatment of TN, painful diabetic neuropathy, and postherpetic neuralgia. The use of CBZ was not studied for complex regional pain syndrome, phantom limb pain, and other neuropathic conditions, however. Phenytoin was the first anticonvulsant to be used as an antinociceptive agent, but based on clinical trials, there is no evidence for its efficacy in relieving neuropathic pain. Newer anticonvulsants have marked a new era in the treatment of neuropathic pain, with clinical trials of higher quality standards. Gabapentin (GBP) has most clearly demonstrated an analgesic effect for the treatment of neuropathic pain, specifically for the treatment of painful diabetic neuropathy and postherpetic neuralgia. Gabapentin has a favorable side effects profile, and based on the results of these studies, it should be considered a first-line treatment for neuropathic pain. Gabapentin mechanisms of action are still not thoroughly defined, but GBP is effective in relieving indexes of allodynia and hyperalgesia in animal models. It still remains to be seen whether GBP is as effective in other painful disorders. One small clinical trial with lamotrigine demonstrated improved pain control in TN. Evidence in support of the efficacy of anticonvulsant drugs in the treatment of neuropathic pain continues to evolve, and benefits have been clearly demonstrated in the case of GBP and CBZ. More advances in our understanding of the mechanisms underlying neuropathic pain syndromes should further our opportunities to establish the role of anticonvulsants in the treatment of neuropathic pain.
Performance studies of the hodoscope prototype for the NA62 experiment (2016)

A hodoscope prototype to detect charged particles in the NA62 experiment at CERN SPS has been installed within the experimental setup in 2014 and exposed to the beam during the data taking period. Efficiency and time resolution for hodoscope tiles are measured. The average signal amplitude (proportional to the light yield) is estimated from the efficiency curves. The results of the tests have lead to several improvements in the final design of the hodoscope.
Endometriosis (2010)

A healthy 25-year-old woman presents with worsening dysmenorrhea, new-onset left lower quadrant pain, and dyspareunia. She has regular menstrual cycles, and her last menstrual period was 3 weeks before presentation. How should this patient be evaluated and treated?
Aliasing-Free Wideband Beamforming Using Sparse Signal Representation (2011)

Sparse signal representation (SSR) is considered to be an appealing alternative to classical beamforming for direction-of-arrival (DOA) estimation. For wideband signals, the SSR-based approach constructs steering matrices, referred to as dictionaries in this paper, corresponding to different frequency components of the target signal. However, the SSR-based approach is subject to ambiguity resulting from not only spatial aliasing, just like in classical beamforming, but also from the over-completeness of the dictionary, which is typical to SSR. We show that the ambiguity caused by the over-completeness of the dictionary can be alleviated by using multiple measurement vectors. In addition, by considering the uniform linear array (ULA) structure, we argue that if the target signal contains at least two frequencies, whose absolute difference phrased in wavelengths is larger than twice the array spacing, the spatial aliasing corresponding to these frequencies will be completely distinct. These properties enable us to adapt the existing ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> algorithms to extract the target DOAs without ambiguity.
Multi‐element and multi‐site isotopic analysis of nicotine from tobacco leaves (1997)

ABSTRACT The carbon, nitrogen and hydrogen stable‐isotope contents of nicotine extracted from tobacco leaves were determined by Isotope Ratio Mass Spectrometry (overall 2 H, 13 C and 15 N contents) and by the SNIF‐NMR method (site‐specific deuterium content). In addition, nicotine was chemically degraded into nicotinic acid so that the intramolecular distribution of carbon and nitrogen isotopes could be studied. A prerequisite for reliable measurements is the use of experimental procedures free of isotopic fractionation. Therefore, it was ensured that isotopic integrity was maintained throughout extraction, purification and chemical degradation steps. The multi‐element and multi‐site information provided is tentatively interpreted in terms of biochemical isotopic effects on intramolecular distribution patterns and of the influence of environmental factors on nicotine isotopic parameters.
Efficient XML Structural Similarity Detection using Sub-tree Commonalities (2007)

Abstract. Developing efficient techniques for comparing XML-based documents becomes essential in the database and information retrieval communities. Various algorithms for comparing hierarchically structured data, e.g. XML documents, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being modeled as ordered labeled trees. Nevertheless, a thorough investigation of current approaches led us to identify several unaddressed structural similarities, i.e. sub-tree related similarities, while comparing XML documents. In this paper, we provide an improved comparison method to deal with such resemblances. Our approach is based on the concept of tree edit distance, introducing the notion of commonality between sub-trees. Experiments demonstrate that our approach yields better similarity results with respect to alternative methods, while maintaining quatratic time complexity. 1.
Induction, isolation, and characterization of aspergillus niger mutant strains producing elevated levels of beta-galactosidase (1981)

An Aspergillus niger mutant strain, VTT-D-80144, with an improvement of three- to fourfold in the production of extracellular beta-galactosidase was isolated after mutagenesis. The production of beta-galactosidase by this mutant was unaffected by fermentor size, and the enzyme was also suitable for immobilization.
Fast-Switching Printed Organic Electrochemical Transistors Including Electronic Vias Through Plastic and Paper Substrates (2013)

A novel vertical architecture for all-printed organic electrochemical transistors, based on poly(3, 4-ethylenedioxythiophene):poly(styrene sulfonate), realized on flexible substrates, is reported. The transistors are manufactured along both faces of plastic or paper substrates and via connections are realized using laser ablation or simple punch through using a pin. Successful modulation of the electric current that flows between the two sides of the substrate is achieved using electrolyte-gating and electrochemical modulation of the electronic charge transport of the bulk of the transistor channel. In addition to this, the transistors are exhibiting fast switching and high ON/OFF current ratios.
Vast-scale Outdoor Navigation Using Adaptive Relative Bundle Adjustment (2010)

In this paper we describe a relative approach to simultaneous localization and mapping, based on the insight that a continuous relative representation can make the problem tractable at large scales. First, it is well known that bundle adjustment is the optimal non-linear least-squares formulation for this problem, in that its maximum-likelihood form matches the definition of the Cramer—Rao lower bound. Unfortunately, computing the maximum-likelihood solution is often prohibitively expensive: this is especially true during loop closures, which often necessitate adjusting all parameters in a loop. In this paper we note that it is precisely the choice of a single privileged coordinate frame that makes bundle adjustment costly, and that this expense can be avoided by adopting a completely relative approach. We derive a new relative bundle adjustment which, instead of optimizing in a single Euclidean space, works in a metric space defined by a manifold. Using an adaptive optimization strategy, we show experimentally that it is possible to solve for the full maximum-likelihood solution incrementally in constant time, even at loop closure. Our approach is, by definition, everywhere locally Euclidean, and we show that the local Euclidean estimate matches that of traditional bundle adjustment. Our system operates online in realtime using stereo data, with fast appearance-based loop closure detection. We show results on over 850,000 images that indicate the accuracy and scalability of the approach, and process over 330 GB of image data into a relative map covering 142 km of Southern England. To demonstrate a baseline sufficiency for navigation, we show that it is possible to find shortest paths in the relative maps we build, in terms of both time and distance. Query images from the web of popular landmarks around London, such as the London Eye or Trafalgar Square, are matched to the relative map to provide route planning goals.
Nanoparticles Heat through Light Localization (2014)

Aqueous solutions containing light-absorbing nanoparticles have recently been shown to produce steam at high efficiencies upon solar illumination, even when the temperature of the bulk fluid volume remains far below its boiling point. Here we show that this phenomenon is due to a collective effect mediated by multiple light scattering from the dispersed nanoparticles. Randomly positioned nanoparticles that both scatter and absorb light are able to concentrate light energy into mesoscale volumes near the illuminated surface of the liquid. The resulting light absorption creates intense localized heating and efficient vaporization of the surrounding liquid. Light trapping-induced localized heating provides the mechanism for low-temperature light-induced steam generation and is consistent with classical heat transfer.
Modeling and Predicting Human Infectious Diseases (2015)

The spreading of infectious diseases has dramatically shaped our history and society. The quest to understand and prevent their spreading dates more than two centuries. Over the years, advances in Medicine, Biology, Mathematics, Physics, Network Science, Computer Science, and Technology in general contributed to the development of modern epidemiology. In this chapter, we present a summary of different mathematical and computational approaches aimed at describing, modeling, and forecasting the diffusion of viruses. We start from the basic concepts and models in an unstructured population and gradually increase the realism by adding the effects of realistic contact structures within a population as well as the effects of human mobility coupling different subpopulations. Building on these concepts we present two realistic data-driven epidemiological models able to forecast the spreading of infectious diseases at different geographical granularities. We conclude by introducing some recent developments in diseases modeling rooted in the big-data revolution.
Development of a 100 GHz Grooved Circular Empty Cavity for Complex Permittivity Measurements in W Band (2011)

A 100GHz grooved circular empty cavity is proposed for the low loss dielectric substrate measurements by the cut-off circular waveguide method in W band. The influence of the excitation holes for the coaxial cable with a small loop are revealed by an FEM based 3D electromagnetic simulator. And also, the diameter of the excitation hole is determined based on the calculated results and the manufacturing accuracy. Then, two kinds of four 100GHz grooved circular empty cavities are fabricated. Comparative experiments of the cavities with the different excitation holes validate the simulated results. Moreover, the complex permittivity of a PTFE plate is measured using the fabricated four cavities by the cut-off circular waveguide method around 84GHz. The measured results agree within measurement error about 0.5% for εr and 5% for tanδ. Also, these results accord with results measured by the Whispering-Gallery mode resonator method in 85-110GHz band. It verifies that the proposed 100GHz cavity for the cut-off waveguide method is useful for the complex permittivity measurement of low loss dielectric substrates in W band.
Assembly, Target‐Signaling and Intracellular Transport of Tyrosinase Gene Family Proteins in the Initial Stage of Melanosome Biogenesis (2000)

Assembly, target-signaling and transport of tyrosinase gene family proteins at the initial stage of melanosome biogenesis are reviewed based on our own discoveries. Melanosome biogenesis involves four stages of maturation with distinct morphological and biochemical characteristics that reflect distinct processes of the biosynthesis of structural and enzymatic proteins, subsequent structural organization and melanin deposition occurring in these particular cellular compartments. The melanosomes share many common biological properties with the lysosomes. The stage I melanosomes appear to be linked to the late endosomes. Most of melanosomal proteins are glycoproteins that should be folded or assembled correctly in the ER through interaction with calnexin, a chaperone associated with melanogenesis. These melanosomal glycoproteins are then accumulated in the trans Golgi network (TGN) and transported to the melanosomal compartment. During the formation of transport vesicles, coat proteins assemble on the cytoplasmic face of TGN to select their cargos by interacting directly or indirectly with melanosomal glycoproteins to be transported. Adapter protein-3 (AP-3) is important for intracellular transport of tyrosinase gene family proteins from TGN to melanosomes. Tyrosinase gene family proteins possess a di-leucine motif in their cytoplasmic tail, to which AP-3 appears to bind. Thus, the initial cascade of melanosome biogenesis is regulated by several factors including: 1) glycosylation of tyrosinase gene family proteins and their correct folding and assembly within ER and Golgi, and 2) supply of specific signals necessary for intracellular transport of these glycoproteins by vesicles from Golgi to melanosomes.
Direct adsorption of chemically modified biomolecules onto gold: a rapid method for biological functionalization of MEMS (2006)

The present work reports a simple, rapid and versatile strategy for glycoprotein immobilization, based on the targeted functionalization of carbohydrate residues with disulphide "anchors" derivatives able to spontaneously chemisorb onto gold, with no need of surface pre-functionalization. Different glycoproteins as enzymes and antibodies were chemically modified using this "one step" bio-immobilization protocol and directly adsorbed onto gold coated interfaces. Surface plasmon resonance (SPR) and Electrochemistry techniques revealed that direct adsorption of a modified glyco-enzyme (horseradish peroxidase) onto gold led to the formation of a densely packed SAM, where each single biomolecule is several thousand times more active than a non modified one. In the case of antibodies, the specific location of the carbohydrate moieties in the constant region resulted in the formation of active and site-oriented SAMs. This bio- immobilization method was applied to the bio- functionalization of a degenerate mode MEMS sensor (MEMSens). Preliminary results obtained for the detection of protein S-100ββ (brain injury marker), indicate a promising low detection limit.
Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis (2007)

Quercetin has been shown to act as an anticarcinogen in experimental colorectal cancer (CRC). The aim of the present study was to characterize transcriptome and proteome changes occurring in the distal colon mucosa of rats supplemented with 10 g quercetin/kg diet for 11 wk. Transcriptome data analyzed with Gene Set Enrichment Analysis showed that quercetin significantly downregulated the potentially oncogenic mitogen-activated protein kinase (Mapk) pathway. In addition, quercetin enhanced expression of tumor suppressor genes, including Pten, Tp53, and Msh2, and of cell cycle inhibitors, including Mutyh. Furthermore, dietary quercetin enhanced genes involved in phase I and II metabolism, including Fmo5, Ephx1, Ephx2, and Gpx2. Quercetin increased PPARalpha target genes, and concomitantly enhanced expression of genes involved in mitochondrial fatty acid (FA) degradation. Proteomics performed in the same samples revealed 33 affected proteins, of which four glycolysis enzymes and three heat shock proteins were decreased. A proteome-transcriptome comparison showed a low correlation, but both pointed out toward altered energy metabolism. In conclusion, transcriptomics combined with proteomics showed that dietary quercetin evoked changes contrary to those found in colorectal carcinogenesis. These tumor-protective mechanisms were associated with a shift in energy production pathways, pointing at decreased cytoplasmic glycolysis and toward increased mitochondrial FA degradation.
Chemical Composition and Carcinogenicity of Smokeless Tobacco (1997)

In the United States, smokeless tobacco (ST) is marketed as chewing tobacco and as oral snuff. During the past 15 years, consumption of chewing tobacco has declined by 30.6%, whereas snuff use has significantly increased, namely, by 51.8%. This increase is primarily due to the growing popularity of oral snuff use among teenage and young adolescent males. Chewing of tobacco is associated with an increased risk for oral cancer. Snuff dipping is causally and specifically associated with cancer of the cheek, gum, and pharynx. In laboratory animals, snuff induces cancer of the mouth. Several carcinogens have been identified in ST, the tobacco-specific N-nitrosamine (TSNA), N'-nitrosonornicotine (NNN), and 4(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) being the most important. NNN and NNK are formed from nicotine during curing, aging, and especially during fermentation of tobacco. Oral swabbing of a low concentration of a mixture of NNN plus NNK in water induces oral tumors in rats. The concentration of the strongly carcinogenic TSNA is higher in snuff than in other ST products. According to our analytical studies, the three leading snuff brands in the US (92% of the market) contain far higher concentrations of nicotine, unprotonated nicotine, and TSNA than the less popular brands. Thus, the leading US snuff brands are the strongest inducers of nicotine dependence and also have the highest carcinogenic potential.
Moral Economies: Interrogating the Interactions of NGOs, Journalists and Freelancers (2016)

Using Sayer’s ideas about the moral economy, this article generates a new theoretical model for interrogating complex relations between journalists and their sources, especially nongovernmental organizations. It tests this framework using a case study about the production of a TV report about a Congolese rebel commander wanted for war crimes. This news story involved exchanges between Human Rights Watch, the United Kingdom’s Channel 4 News, and several freelancers and was indirectly shaped by Amnesty International and Invisible Children Inc., the creators of Kony2012. In analyzing these exchanges and their mixed effects, this article refines notions of trust, news cloning, and information subsidies.
Automatic induction of finite state transducers for simple phonological rules (1995)

This paper presents a method for learning phonological rules from sample pairs of underlying and surface forms, without negative evidence. The learned rules are represented as finite state transducers that accept underlying forms as input and generate surface forms as output. The algorithm for learning them is an extension of the OSTIA algorithm for learning general subsequential finite state transducers. Although OSTIA is capable of learning arbitrary s.f.s.t's in the limit, large dictionaries of actual English pronunciations did not give enough samples to correctly induce phonological rules. We then augmented OSTIA with two kinds of knowledge specific to natural language phonology, biases from "universal grammar". One bias is that underlying phones are often realized as phonetically similar or identical surface phones. The other biases phonological rules to apply across natural phonological classes. The additions helped in learning more compact, accurate, and general transducers than the unmodified OSTIA algorithm. An implementation of the algorithm successfully learns a number of English postlexical rules.