gebhart/patrepeval huggingface dataset:
Multidimensional indexing for recognizing visual shapes (1994)

This paper introduces an analytical framework for studying some properties of model acquisition and recognition techniques based on indexing. The goal is to demonstrate that several problems previously associated with the approach can be attributed to the low dimensionality of invariants used. These include limited index selectivity. Excessive accumulation of votes in the look-up table buckets, and excessive sensitivity to quantization parameters. Theoretical results demonstrate that using high-dimensional, highly descriptive global invariants produces better results in terms of accuracy, false positive suppression, and computation time. A practical example of high-dimensional global invariants is introduced and used to implement a 2-D shape acquisition/recognition system. The acquisition/recognition system is based on a two-step table look-up mechanism. First, local curve descriptors are obtained by correlating image contour information at short range. Then, seven-dimensional global invariants are computed by correlating triplets of local curve descriptors at longer range. This experimental system is meant to illustrate the behavior of a high-dimensional indexing scheme. Indeed, its performance shows good agreement with the analytical model with respect to database size, fault tolerance, and recognition speed. Model acquisition time is linear to cubic in the number of object features. Object recognition time is constant to linear in the number of models in the database and linear to cubic in the number of features in the image. The system has been tested extensively. With more than 250 arbitrary shapes in the database. Unsupervised shape and subpart acquisition is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interrelations of the proliferation and differentiation processes during cardiact myogenesis and regeneration. (1977)

This chapter discusses the interrelations of the proliferation and differentiation processes during cardiac myogenesis and regeneration. Myogenesis has attracted the ever-increasing interest of investigators for more than 100 years. Interrelationships between cytodifferentiation and the proliferation of myogenic cells have been found to be highly complicated and apparently not identical in diverse types of myogeneses. Some investigators believe that myocardial cells possess an intrinsic capacity to dedifferentiate and multiply at the borders of necroses which, however, is not manifested overtly because of the lack of permissive conditions and appropriate stimuli or, possibly, because of nonmuscle cell overgrowth. The chapter describes the complicated proliferative behavior of cardiac-muscle cells both in normal myogenesis and regeneration and its dependence on the differentiative properties of these cells.
A query mediation approach to interoperability of heterogeneous databases (2002)

The need to transform queries between heterogeneous databases arises in many circumstances, including query transformation between a global and a local query. This paper describes a query mediation approach to the interoperability of heterogeneous databases. We develop a query mediation architecture that facilitates automated query transformation, which is applicable in many circumstances, such as query transformation in a federated database environment. Different application languages are transformed into intermediate representations that can be processed by the query mediator. The main characteristic of our system is that the query transformation agent, which acts as a mediator, is used to support automated query transformation which protects users from the troublesome task of semantic and representational discrepancies. Two query languages, ODMG-OQL and SQL, have been used to investigate the query mediation architecture.
Seeded oscillatory growth of Si over SiO2 by cw laser irradiation (1982)

Extensive seeded epitaxial growth of crystalline Si over SiO2 was achieved by an oscillatory regrowth method applied to rectangular Si pads recessed into a thick SiO2 film. Narrow (≃5 μm) via holes linked the pads with the bulk (100) Si substrate. Oriented single crystals propagated as far as 500 μm from the seeding area, following the long term advance of a scanned focused laser beam.
The Diagnostic Accuracy of Reverse Transcription-PCR Quantification of Cytokeratin mRNA in the Detection of Sentinel Lymph Node Invasion in Oral and Oropharyngeal Squamous Cell Carcinoma: A Comparison with Immunohistochemistry (2006)

Quantitative RT-PCR for SLN staging in cN(0) patients with oral and oropharyngeal squamous cell carcinoma seems to be a promising approach.
Effect of Functional Magnetic Particles on Radiofrequency Capacitive Heating: An in vivo Study (2002)

Specific heating of magnetic particles in radiofrequency (RF) capacitive hyperthermia and its hyperthermic effect were investigated in an in vivo study. Magnetite cationic liposomes (MCLs) were injected into a rat tumor on the femur and 8 MHz-RF capacitive heating was applied to the rat under "mild heating" conditions. Although the input power of RF capacitive heating was low under the same power conditions, the MCLs-injected tumor was heated over 43 degrees C, whereas it was only heated to 41 degrees C in the case of the rats not injected with MCLs. A necrotic area in the tumor was observed in the heated rats. From the results of histological observation of the removed tissue, the necrotic area in the MCLs-injected tumor was wider than that in MCLs-free tumor. Complete tumor suppression was observed in 71% (5 / 7) of MCLs-injected rats, and the hyperthermic effect was greatly improved by the MCLs.
Binding Properties of Monoclonal Antibodies against Human Fragment D-Dimer of Cross-Linked Fibrin to Human Plasma Clots in an In Vivo Model in Rabbits (1989)

Summary Two (MA-15C5 and MA-8D3) out of approximately 500 monoclonal antibodies, obtained by fusion of P3X63-Ag8-6.5.3 myeloma cells with spleen cells of mice immunized with purified fragment D-dimer from human fibrin, demonstrated a more than 1,000-fold higher affinity for fragment D-dimer than for native fibrinogen. MA-15C5 was directed against a neoantigenic determinant only expressed in fragment D-dimer. MA-8D3 reacted equally well with fragment D-dimer of crosslinked fibrin and with fragment D of non-crosslinked fibrin but not with fragment D of fibrinogen. Both monoclonal antibodies did not crossreact with rabbit fibrin and its degradation products. The binding of 125I-labeled Fab fragments to human plasma clots, introduced and aged for 1 hr in the jugular vein of heparinized rabbits was studied. Following injection of an equimolar mixture of Fab fragments derived from MA-15C5 and MA-8D3, the clot to blood ratios of radioactivity increased from 3.2 ± 1.2(mean ± SD) at 4 hr to 7.2 ± 1.4 at 17 hr. The binding of Fab fragments of MA-15C5 and MA-8D3 was independent of the age (1 to 72hrs) of the clot and of heparin anticoagulation and was only slightly decreased (by 20%) in the presence of circulating human fibrinogen (90 mg/kg body weight) and of human crosslinked fibrin degradation products at a plasma concentration of 10 pg/ml. The binding of Fab fragments of MA-15C5 and MA-8D3 to occlusive human plasma clots in the femoral artery of rabbits was comparable to that of the non-occlusive human plasma clots in the jugular vein. The Fab fragments of MA-15C5 and MA-8D3, labeled with 123I to a specific activity of 10 μCi/pg were injected intravenously (3 μg/kg) in 72 rabbits with a nonocclusive 0.2 ml human plasma clot in the jugular vein and in 7 control rabbits that underwent the surgical procedure without clot formation. Total body scans performed at hourly intervals revealed a higher relative increase in gamma counts over the thrombus region in the group with thrombus as compared to controls: at 6 hr 54 ± 18 vs 16 ± 13% (mean ± SEM, p &lt;0.1) and at12 hrs 35 ± 11 vs –7 ± 12 (p &lt;0.05). The vein segment to blood ratios of 123I at 24 hrs were 6.6 ± 2.4 in the group with clot and 1.5 to 0.7 in the control group (p &lt;0.01). We conclude that these Fab fragments may have a sufficiently high fibrin-affinity to allow in vivo thrombus localization by external scanning.
Functionalized Protein-like Structures from Conformationally Defined Synthetic Combinatorial Libraries (1996)

An approach is described for the de novo design of protein-like structures in which synthetic combinatorial libraries (SCLs) were incorporated into an amphipathic alpha-helical scaffold (an 18-mer sequence made up of leucine and lysine residues) to generate conformationally defined SCLs. In particular, the SCLs in which the "combinatorialized" positions were on the hydrophilic face showed an alpha-helical conformation in mild buffer. These SCLs were used to generate context-independent but position-dependent scales of alpha-helical propensity for the L-amino acids. These scales were then used to design highly alpha-helical peptides that self-associated in mild buffer. The same approach was also found to permit the identification of conformation-dependent decarboxylation catalysts.
Nanostructured GaN: Microstructure and optical properties (1996)

In the present study, the microstructure and optical properties of a nanostructured composite that consists of nanocrystalline GaN imbedded in a poly)methyl methacrylate) thin film matrix (GaN/PMMA) are reported. X-ray powder diffraction and high-resolution transmission electron microscopy were performed to analyze the microstructure, while the optical properties were measured by optical absorption and photoluminescence. Microstructural analyses showed that GaN nanocrystallites imbedded in the PMMA matrix have a size of about 5.5 nm, and crystallize in the zinc-blende lattice (the lattice constant ${a}_{0}\ensuremath{\sim}0.45$ nm) with a considerable fraction of structural defects such as nitrogen vacancies and stacking faults. Optical-absorption measurements indicate that the band-gap energy of the GaN/PMMA composite is approximately 3.51 eV.
Hormonal requirements of baby hamster kidney cells in culture (1980)

Baby hamster kidney cells (BHK) were able to proliferate in the complete absence of serum in synthetic medium supplemented with insulin, transferrin, fibroblast growth factor and epidermal growth factor on cell culture dishes coated with fibronectin. Although the addition of individual supplements had little or no effect on cell growth, the combination of the supplements resulted in a significant synergistic effect. The defined medium was also capable of supporting the clonal growth of BHK cells in the absence of serum. Studies on the effect of hormonal supplementation in the presence of low concentrations of fetal calf serum suggest that the function of serum is to supply hormones and growth factors for cell growth.
Nucleoside Reverse Transcriptase Inhibitor Resistance (2001)

Summary: Nucleoside reverse transcriptase inhibitors (NRTls) comprise the first class of drug with proven antiretroviral efficacy against HIV-1, and the first in which drug resistance was reported. Ongoing research in the area of NRT] resistance and crossresistance contributes much to what we know about the failure of antiretroviral therapy. The genetic mutation patterns responsible for resistance to the available NRTIs have been well documented. This information is being used to plan rational drug therapy. Furthermore, it serves as the standard against which to evaluate response patterns to multiple-drug regimens, ultimately enabling more accurate prediction of outcome with combination therapies. Other features of NRTI resistance, such as the theoretic reversal of zidovudine resistance associated with the M184V mutation or the powerful influence of the Q151M multiple-drug resistance mutation, have revealed the unpredictable nature of HIV resistance and how much we still need to learn. Although NRTIs are the cornerstone of antiretroviral therapy at present and are used to control disease progression for extended periods, it is clear that eventually resistance occurs with all antiretroviral regimens. Future research into NRTI-resistance mutations, mutational interactions, treatment sequencing, and viral fitness and fidelity will continue to refine our understanding of drug resistance and improve our ability to delay or eliminate resistance and advance HIV control.
Chain model of a magnetorheological suspension in a rotating field (2003)

We develop an athermal chain model for magnetorheological suspensions in rotating magnetic fields. This model is based on a balance of hydrodynamic and magnetostatic forces and focuses on the mechanical stability of chains. Using a linear approximation of the chain shape, we compute the orientation and size of a critical chain in a rotating magnetic field as a function of the Mason number Mn, which is the ratio of dipolar to hydrodynamic forces between two particles in contact. The critical chain length is found to scale with the inverse square root of Mn, and its orientation relative to the instantaneous field is independent of Mn. The actual nonlinear shape of a chain in a rotating field is then computed self-consistently. Finally, the effect of local fields on the dipolar interaction force is considered, leading to predictions for the chain shape and orientation that depend rather strongly on the magnetic permeability of the particles. A principal finding is the possibility of brittle or ductile chain fracture, depending on the permeability of the particles. Single-chain simulations confirm this prediction, as do experimental measurements.
Noise Robust Generative Adversarial Networks (2019)

Generative adversarial networks (GANs) are neural networks that learn data distributions through adversarial training. In intensive studies, recent GANs have shown promising results for reproducing training images. However, in spite of noise, they reproduce images with fidelity. As an alternative, we propose a novel family of GANs called noise robust GANs (NR-GANs), which can learn a clean image generator even when training images are noisy. In particular, NR-GANs can solve this problem without having complete noise information (e.g., the noise distribution type, noise amount, or signal-noise relationship). To achieve this, we introduce a noise generator and train it along with a clean image generator. However, without any constraints, there is no incentive to generate an image and noise separately. Therefore, we propose distribution and transformation constraints that encourage the noise generator to capture only the noise-specific components. In particular, considering such constraints under different assumptions, we devise two variants of NR-GANs for signal-independent noise and three variants of NR-GANs for signal-dependent noise. On three benchmark datasets, we demonstrate the effectiveness of NR-GANs in noise robust image generation. Furthermore, we show the applicability of NR-GANs in image denoising. Our code is available at https://github.com/takuhirok/NR-GAN/.
EEG Analysis in Structural Focal Epilepsy Using the Methods of Nonlinear Dynamics (Lyapunov Exponents, Lempel–Ziv Complexity, and Multiscale Entropy) (2020)

This paper analyzes a case with the patient having focal structural epilepsy by processing electroencephalogram (EEG) fragments containing the "sharp wave" pattern of brain activity. EEG signals were recorded using 21 channels. Based on the fact that EEG signals are time series, an approach has been developed for their analysis using nonlinear dynamics tools: calculating the Lyapunov exponent's spectrum, multiscale entropy, and Lempel-Ziv complexity. The calculation of the first Lyapunov exponent is carried out by three methods: Wolf, Rosenstein, and Sano-Sawada, to obtain reliable results. The seven Lyapunov exponent spectra are calculated by the Sano-Sawada method. For the observed patient, studies showed that with medical treatment, his condition did not improve, and as a result, it was recommended to switch from conservative treatment to surgical. The obtained results of the patient's EEG study using the indicated nonlinear dynamics methods are in good agreement with the medical report and MRI data. The approach developed for the analysis of EEG signals by nonlinear dynamics methods can be applied for early detection of structural changes.
Microbial composition analysis ofClostridium difficileinfections in an ulcerative colitis patient treated with multiple fecal microbiota transplantations (2014)

Fecal microbiota transplantation (FMT) is a promising therapy for Clostridium difficile infection (CDI). However, questions remain regarding efficacy and safety in inflammatory bowel disease (IBD) patients, as well as longitudinal stability of donor stool composition. This report describes an IBD patient with two CDIs 18 months apart, each successfully treated with FMT with no IBD flares or complications. Microbiome composition analysis of patient samples during each infection revealed low-diversity microbiota patterns similar to those previously described in non-IBD patients with CDI and active IBD alone. Samples taken after each transplant demonstrated quick remodeling towards the donor's sample composition coinciding with symptom resolution. Of note, samples taken from the same donor 18 months apart reflected marked differences in microbiota abundances, suggesting that the use of single donors in FMT programs offers little benefit in ensuring predictability of donor stool composition over time. This report describes similar microbial composition patterns during CDI in IBD patients to those described previously in non-IBD patients, and supports FMT as safe and effective treatment for recurring CDI in this patient population.
Peroxisome proliferator-activated receptors as targets to treat non-alcoholic fatty liver disease (2015)

Lately, the world has faced tremendous progress in the understanding of non-alcoholic fatty liver disease (NAFLD) pathogenesis due to rising obesity rates. Peroxisome proliferator-activated receptors (PPARs) are transcription factors that modulate the expression of genes involved in lipid metabolism, energy homeostasis and inflammation, being altered in diet-induced obesity. Experimental evidences show that PPAR-alpha is the master regulator of hepatic beta-oxidation (mitochondrial and peroxisomal) and microsomal omega-oxidation, being markedly decreased by high-fat (HF) intake. PPAR-beta/delta is crucial to the regulation of forkhead box-containing protein O subfamily-1 expression and, hence, the modulation of enzymes that trigger hepatic gluconeogenesis. In addition, PPAR-beta/delta can activate hepatic stellate cells aiming to the hepatic recovery from chronic insult. On the contrary, PPAR-gamma upregulation by HF diets maximizes NAFLD through the induction of lipogenic factors, which are implicated in the fatty acid synthesis. Excessive dietary sugars also upregulate PPAR-gamma, triggering de novo lipogenesis and the consequent lipid droplets deposition within hepatocytes. Targeting PPARs to treat NAFLD seems a fruitful approach as PPAR-alpha agonist elicits expressive decrease in hepatic steatosis by increasing mitochondrial beta-oxidation, besides reduced lipogenesis. PPAR-beta/delta ameliorates hepatic insulin resistance by decreasing hepatic gluconeogenesis at postprandial stage. Total PPAR-gamma activation can exert noxious effects by stimulating hepatic lipogenesis. However, partial PPAR-gamma activation leads to benefits, mainly mediated by increased adiponectin expression and decreased insulin resistance. Further studies are necessary aiming at translational approaches useful to treat NAFLD in humans worldwide by targeting PPARs.
Reinforcement of Colonic Anastomoses With a Laser and Dye–Enhanced Fibrinogen (1990)

The incidence of anastomotic leakage in colonic surgery is approximately 10%. We evaluated a technique of laser-fibrinogen reinforcement to strengthen experimental colonic anastomoses. The technique consisted of the topical application of indocyanine green dye-enhanced fibrinogen to the serosal surface of two-layer inverting anastomoses, followed by exposure with an 808-nm diode laser. In the 28 rabbits used for this study, mean bursting pressure at time 0 was 108 +/- 13 mm Hg in the group receiving anastomoses with sutures alone and 173 +/- 20 mm Hg in the group for which the sutured anastomosis was reinforced with laser-fibrinogen. The difference in bursting pressures between the two groups was statistically significant at time 0. However, at 1, 3, 5, and 7 days, the anastomosis became stronger in both groups and the difference in strength was reduced; the sutured group had more exceptionally weak (less than 110 mm Hg) bonds than the group treated by laser. Thus, laser-fibrinogen reinforcement significantly enhances the early strength of sutured colonic anastomoses. This technique may reduce the incidence of leakage during the first postoperative week and the associated complications in a clinical setting.
Improvements to the Burrows-Wheeler Compression Algorithm: After BWT Stages (2003)

... This article describes improved algorithms for the run length encoding, inversion frequencies and weighted frequency count stages that follow the Burrows-Wheeler Transform. Results for compression rates are presented for different variations of the algorithm together with compression and decompression times. Finally, an implementation with a compression rate of 2.238 bps on the Calgary Corpus is introduced, which is the best result published in this field to date.
Murine histidine‐rich glycoprotein: Cloning, characterization and cellular origin (2000)

Histidine-rich glycoprotein (HRG) is a plasma protein of vertebrates that has been implicated in the regulation of several important biological functions, including the immune response and blood clotting. In the present study, we have isolated and determined the sequence of the cDNAs for both mouse and rat HRG. The deduced amino acid sequences of mouse and rat HRG are 525 and 510 amino acids, respectively, and they show the same three-domain structure that has been predicted for human HRG, with which they share high amino acid identity. Northern blot analysis indicates that the mouse HRG mRNA is 1.7 kb and is localized specifically to the liver. It has been suggested, somewhat controversially, that some immune cells, such as monocytes and megakaryocytes, also synthesize HRG. Reverse transcriptase-polymerase chain reaction analysis has failed to show any HRG mRNA in immune tissues of the mouse, including the spleen, thymus, lymph node, bone marrow and peripheral blood leucocytes. These data suggest that HRG expression by immune cells is due to the acquisition of plasma HRG derived from the liver. Finally, genomic Southern blot analysis of the mouse HRG gene suggests that it is a single copy gene.
A Self-Configuring Schema Matching System (2012)

Mapping complex metadata structures is crucial in a number of domains such as data integration, ontology alignment or model management. To speed up the generation of such mappings, automatic matching systems were developed to compute mapping suggestions that can be corrected by a user. However, constructing and tuning match strategies still requires a high manual effort by matching experts as well as correct mappings to evaluate generated mappings. We therefore propose a self-configuring schema matching system that is able to automatically adapt to the given mapping problem at hand. Our approach is based on analyzing the input schemas as well as intermediate matching results. A variety of matching rules use the analysis results to automatically construct and adapt an underlying matching process for a given match task. We comprehensively evaluate our approach on different mapping problems from the schema, ontology and model management domains. The evaluation shows that our system is able to robustly return good quality mappings across different mapping problems and domains.