gebhart/patrepeval huggingface dataset:
Molecular interactions of the aryl hydrocarbon receptor and its biological and toxicological relevance for reproduction (2005)

The dioxin/aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor responsive to both natural and man-made environmental compounds. AhR and its nuclear partner ARNT are expressed in the female reproductive tract in a variety of species and several indications suggest that the AhR might play a pivotal role in the physiology of reproduction. Furthermore, it appears to be the mediator of most, if not all, the adverse effects on reproduction of a group of highly potent environmental pollutants collectively called aryl hydrocarbons (AHs), including the highly toxic compound 2,3,7,8-tetrachlor-odibenzo-p-dioxin (TCDD). Although a large body of recent literature has implicated AhR in multiple signal transduction pathways, the mechanisms of action resulting in a wide spectrum of effects on female reproduction are largely unknown. Here we summarize the major types of molecular cross-talks that have been identified for the AhR and linked cell signaling pathways and that are relevant for the understanding of the role of this transcription factor in female reproduction.
Alzheimer's disease (1991)

Alzheimer's disease is a costly illness affecting large numbers of older Americans, and its prevalence is increasing. The major symptom of the condition is progressive forgetfulness. The course is variable, depending on which areas of the brain are affected earliest and most severely. In diagnosing Alzheimer's disease, it is important to rule out other types of dementia that may be treatable, as well as systemic and affective disorders and other brain diseases. The Mini-Mental State Examination and the category fluency test are often diagnostically useful. There is no evidence that any of the therapeutic agents studied so far are of much value, but pharmacologic agents can be useful in treating the depression, psychoses, and anxiety that may accompany cognitive decline. Patients cared for at home need a structured, orderly environment that has been modified for their safety.
Myosin isoenzyme changes in several models of rat cardiac hypertrophy. (1981)

We studied the effect of chronic mechanical overloading on the isoenzyme composition of rat cardiac myosin in several experimental models: aortic stenosis (AS), aortic incompetence (AI), aortocaval fistula (ACF), overload of the non-infarcted area after left coronary ligation (INF), and overload of the spontaneously hypertensive rats (SHR). Samples of the left and right ventricles were isolated from these hearts, and myosins were analyzed by electrophoresis in non-dissociating conditions. The myosin isoenzymes were called V1, V2, and V3 in order of decreasing mobility, according to the nomenclature of Hoh et al. Controls of the Wistar and Wistar Kyoto (WKY) strains were almost exclusively V1, A slow age-dependent shift toward V3 was observed in the left ventricles of adult Wistar rats, which at 30 weeks of age (body weight 600 g) contained approximately 15% of this form. In all models of cardiac hypertrophy, an isoenzymic redistribution was observed with a significant increase in V3. The level of V3 was statistically correlated with the degree of hypertrophy in the AS, (n = 11, r - 0.6, P less than 0.05), the AI (n = 14, 4 = 0.88, P less than 0.001), and the AS + AI(n = 14, 4 = 0.69, P less than 0.01) but not in the ACF (n = 16, r = 0.46). The isoenzymic changes could account for the decreases in both myosin ATPase activity and cardiac contractility described previously in our laboratory and by others. They also demonstrate that changes in myosin isoenzymes represent a general response of the rat heart, to chronic mechanical overloading.
High Thoracic Epidural Anesthesia Does Not Alter Airway Resistance and Attenuates the Response to an Inhalational Provocation Test in Patients with Bronchial Hyperreactivity (1994)

We conclude that in patients with bronchial hyperreactivity 1. blockade of pulmonary sympathetic innervation seems to be of no relevance for airway resistance and 2. both epidural and intravenous bupivacaine substantially attenuate the response to an inhalational provocation with acetylcholine.
On application of multiple-input multiple-output antennas to CDMA cellular systems (2002)

Our focus in this paper is on applying multiple-input multiple-output (MIMO) antenna systems to the time division multiplexed (TDM) shared channel on the WCDMA forward link. We describe cellular system-level simulations with and without MIMO. These simulations include multipath channel models and they account for other-cell interference. We compute the SINR at the output of a linear MMSE receiver and map these values to throughput using simulated turbo code results. Simulation results are presented with various numbers of antennas at the transmitter and receiver. We show that with two transmit and two receive antennas, system capacity can be doubled relative to one transmit and one receive antenna. Two transmit and four receive antennas can provide three times the capacity of a one transmit and one receive antenna system. Also, results are presented that compare three sector systems to six sector systems.
Blind separation of dependent source signals for MEG sensory stimulation experiments (2013)

Sensorisch evozierte Magnetenenzephalographie-Daten (MEG-Daten) sind stark durch das Hintergrundrauschen im Gehirn und durch technische Rauschquellen gestört. Um die Signalqualität zu verbessern sind moderne Verfahren der Signalverarbeitung notwendig, insbesondere für eine Single-Trial-Analyse. Für die Verbesserung der MEG-Signalqualität werden oft lineare Zerlegungsmethoden eingesetzt, wobei die Methoden der Independent Component Analysis (ICA) eine weite Verbreitung gefunden haben. Lineare Zerlegungsmethoden versuchen anhand gemischter Daten eine Entmischungsmatrix zu gewinnen, um durch eine lineare Entmischung die Quellsignale wiederherzustellen. ICA wird für MEG-Daten auch benutzt, um die Anzahl der Rauschquellen zu reduzieren - im optimalen Fall, um ein gewünschtes MEG-Quellsignal unverrauscht zu rekonstruieren. Für den Fall der sensorisch evozierten MEG-Daten treten die gewünschten MEG-Quellsignale erst nach erfolgter sensorischer Reizung auf. Eine ICA-Zerlegung evozierter MEG-Daten zeigt oft eine Komponente mit entsprechendem zeitlichen Verhalten; man ist versucht diese Komponente als das originale evozierte MEG-Quellsignal zu interpretieren. ICA nimmt jedoch die statistische Unabhängigkeit der Quellsignale an. Werden durch eine sensorische Stimulation mehrere Quellsignale im Gehirn evoziert, so kann die Unabhängigkeitsannahme verletzt sein. In dieser Arbeit wird in dem Zusammenhang abhängiger evozierter MEG-Quellsignale ICA untersucht und eine neue Zerlegungsmethoden vorgestellt. Es wird eine virtuelle Simulationsumgebung mit steuerbaren Quellsignalabhängigkeiten vorgestellt und zur Untersuchung der verschiedenen Zerlegungsverfahren eingesetzt. Es wird gezeigt, dass ICA in Sonderfällen stark abhängige Signale trennen kann. Anhand dieser Erkenntnis wird der Nutzen von ICA zur Signaltrennung und zur Unterraumanalyse von evozierten MEG-Daten diskutiert. Ein reales MEG-Experiment zeigt das Verhalten der Methoden auch für den Fall von echten evozierten MEG-Daten. Als neue Methode wird Time Domain Shifted Factor Analysis (TDSFA) vorgestellt. TDSFA basiert auf einer Taylorreihenentwicklung des Modells der Shifted Factor Analysis (SFA), welches eindeutig identifizierbar ist ohne die Unabhängigkeit der Quellsignale annehmen zu müssen. Die Verbindung zu den etablierten trilinearen Methoden wird untersucht, und es wird gezeigt, dass die etablierten trilinearen Methoden Schwierigkeiten mit zeitlicher Signalverschiebung haben. TDSFA bezieht Zeitverschiebung in das Modell ein und ist für die lineare Zerlegung von evozierten MEG-Daten besser geeignet. Für echte und simulierte evozierte MEG-Daten zeigen die Ergebnisse, dass ICA und andere moderne Methoden falsche Ergebnisse liefern können. Die neue Zerlegungsmehtode TDSFA liefert bessere Ergebnisse und weist hohes Potential im Kontext evozierter MEG-Daten auf.
Robust Physical-World Attacks on Deep Learning Visual Classification (2018)

Recent studies show that the state-of-the-art deep neural networks (DNNs) are vulnerable to adversarial examples, resulting from small-magnitude perturbations added to the input. Given that that emerging physical systems are using DNNs in safety-critical situations, adversarial examples could mislead these systems and cause dangerous situations. Therefore, understanding adversarial examples in the physical world is an important step towards developing resilient learning algorithms. We propose a general attack algorithm, Robust Physical Perturbations (RP2), to generate robust visual adversarial perturbations under different physical conditions. Using the real-world case of road sign classification, we show that adversarial examples generated using RP2 achieve high targeted misclassification rates against standard-architecture road sign classifiers in the physical world under various environmental conditions, including viewpoints. Due to the current lack of a standardized testing method, we propose a two-stage evaluation methodology for robust physical adversarial examples consisting of lab and field tests. Using this methodology, we evaluate the efficacy of physical adversarial manipulations on real objects. With a perturbation in the form of only black and white stickers, we attack a real stop sign, causing targeted misclassification in 100% of the images obtained in lab settings, and in 84.8% of the captured video frames obtained on a moving vehicle (field test) for the target classifier.
Particle trace visualization of intracardiac flow using time-resolved 3D phase contrast MRI (1999)

The flow patterns in the human heart are complex and difficult to visualize using conventional two-dimensional (2D) modalities, whether they depict a single velocity component (Doppler echocardiography) or all three components in a few slices (2D phase contrast MRI). To avoid these shortcomings, a temporally resolved 3D phase contrast technique was used to derive data describing the intracardiac velocity fields in normal volunteers. The MRI data were corrected for phase shifts caused by eddy currents and concomitant gradient fields, with improvement in the accuracy of subsequent flow visualizations. Pathlines describing the blood pathways through the heart were generated from the temporally resolved velocity data, starting from user-specified locations and time frames. Flow trajectories were displayed as 3D particle traces, with simultaneous demonstration of morphologic 2D slices. This type of visualization is intuitive and interactive and may extend our understanding of dynamic and previously unrecognized patterns of intracardiac flow.
Studies on 4(1H)-quinazolinones. IV. Convenient syntheses of 12-methyl-6H-isoquino(2,1-a)quinazolin-6-one and 6-methyl-13H-quinazolino(3,4-a)quinazolin-13-one. (1984)

Two novel ring systems, 12-methyl-6H-isoquino [2, 1-a] quinazolin-6-one (2) and 6-methyl-13H-quinazolino [3, 4-a] quinazolin-13-one (3a), were synthesized. Reaction of 3-methylisocoumarin (4) with 2-cyanoaniline gave 2-(2-cyanophenyl)-3-methylisocarbostyril (5), which was converted to 2-(2-carbamoylphenyl)-3-methylisocarbostyril (6) by treatment with alkaline hydrogen peroxide. The cyclization of 6 with boron trifluoride etherate afforded 2. Compound 3a was prepared by the reaction of 2-methyl-4H-3, 1-benzoxazin-4-one (8a) with 2-cyanoaniline in one step. Some derivatives (3b-g) were also prepared by this method. The reaction mechanism is discussed.
Multicriteria decision analysis to assess options for managing contaminated sediments: Application to Southern Busan Harbor, South Korea (2009)

Many years of untreated effluent discharge from residential areas, a shipyard, a marina, and a large fish market resulted in substantial contamination of bottom sediment in Southern Busan Harbor, South Korea. Contaminants in these sediments include heavy metals and organic compounds. Newly introduced regulations for ocean disposal of dredged material in South Korea pose significant challenges, because the previous practice of offshore disposal of contaminated dredged material was no longer possible after August 2008. The South Korean government has mandated that such sediments be assessed in a way that identifies the most appropriate dredged material management alternative, addressing environmental, social, and cost objectives. An approach using multicriteria decision analysis (MCDA) in combination with comparative risk assessment was used as a systematic and transparent framework for prioritizing several dredged sediment management alternatives. We illustrate how MCDA can recognize the multiple goals of contaminated sediment management. Values used in weighting decision criteria were derived from surveys of stakeholders who were sediment management professionals, business owners, or government decision makers. The results of the analysis showed that land reclamation was the preferred alternative among cement-lock, sediment washing, 3 contained aquatic disposal alternatives (one in combination with a hopper dredge), geotextile tubes, solidification, and land reclamation after solidification treatment. Land reclamation was the preferred alternative, which performed well across all MCDA objectives, because of the availability of a near-shore confined disposal facility within a reasonable distance from the dredging area.
Genomic fingerprinting of Yersinia enterocolitica species by degenerate oligonucleotide‐primed polymerase chain reaction (1994)

A novel version of the polymerase chain reaction (PCR) termed degenerate oligonucleotide-primed PCR (DOP-PCR) was used to fingerprint the bacterial genome of Yersinia enterocolitica species. Eight well-characterized reference strains of Y. enterocolitica (ribotype, serotype, biotype and zymotype) were examined. Optimal experimental conditions for reproducibility, sensitivity and specificity were obtained using a single DOP-primer. All the strains gave distinct DOP-PCR profiles composed of 12 to 19 fragments with sizes from 200 to 1.500 bp. Thus, the DOP-PCR, which has so far been used to fingerprint human, mouse, fruitfly and plant DNA, is also well-suited to bacterial DNA.
Pulmonary surfactant‐associated polypeptide C in a mixed organic solvent transforms from a monomeric α‐helical state into insoluble β‐sheet aggregates (1998)

In the 35-residue pulmonary surfactant-associated lipopolypeptide C (SP-C), the stability of the valyl-rich alpha-helix comprising residues 9-34 has been monitored by circular dichroism, nuclear magnetic resonance, and Fourier transform infrared spectroscopy in both a mixed organic solvent and in phospholipid micelles. The alpha-helical form of SP-C observed in freshly prepared solutions in a mixed solvent of CHCl3/CH3OH/0.1 M HCl 32:64:5 (v/v/v) at 10 degrees C undergoes within a few days an irreversible transformation to an insoluble aggregate that contains beta-sheet secondary structure. Hydrogen exchange experiments revealed that this conformational transition proceeds through a transition state with an Eyring free activation enthalpy of about 100 kJ mol(-1), in which the polypeptide segment 9-27 largely retains a helical conformation. In dodecylphosphocholine micelles, the helical form of SP-C was maintained after seven weeks at 50 degrees C. The alpha-helical form of SP-C thus seems to be the thermodynamically most stable state in this micellar environment, whereas its presence in freshly prepared samples in the aforementioned mixed solvent is due to a high kinetic barrier for unfolding. These observations support a previously proposed pathway for in vivo synthesis of SP-C through proteolytic processing from a 21-kDa precursor protein.
Measurement of thermal and ultrasonic properties of some biological tissues (2009)

The measurement of thermal and ultrasonic properties of biological tissues is essential for the assessment of the temperature rise induced in vivo by diagnostic ultrasound. In this paper, we present measurements of thermal conductivity, thermal diffusivity, speed of sound and ultrasonic attenuation of fresh ex vivo porcine tissue, namely 'muscle' (from abdomen and leg), 'skin with subcutaneous fat' (from abdomen and leg), 'abdominal fat' and 'bone'. The measurements of the thermal properties of biological tissue samples are based on a transient method. Thermal property measurements show that subcutaneous fat has the lowest thermal conductivity (0.23 W m(-1) K(-1)), while muscle gives the highest values (0.46 W m(-1) K(-1)). Thermal diffusivity of muscle tissue recorded the highest value among the studied tissues (0.16 mm(2) s(-1)) while that of skin with subcutaneous fat gave the lowest value (0.11 mm(2) s(-1)). A scanning acoustic macroscope was used to measure attenuation coefficient and speed of sound for the tissue samples. The results for the speed of sound are broadly similar to those reported in the literature. The power law dependence of the attenuation coefficient of the form eta = a f (b) as a function of frequency was found to be more appropriate than the linear fit in this study.
Guessing morphology from terms and corpora (1997)

This study proposes an algorithm for automatically acquiring morphological Iinks between words. This algorithm relies on the concurrent use of a corpus and a list of multi-word terms, and does not require any prior linguistic knowledge. The four steps of the algorithm are (1) single-word truncation, (2) conflation of multi-word terms, (3) classification and filtering, and (4) clustering of contiation clasea. At each step a precise evaluation is performed in order to chose the optimal parameters. The final results indicate a clustering of 45% of the classes with a prectilon of 87Y0. The derivational knowledge acquired through this method can be used for conceiving a domain-oriented stemmer for scientific and technical corpora.
Coordinating Multiple Robots with Kinodynamic Constraints Along Specified Paths (2005)

This paper focuses on the collision-free coordination of multiple robots with kinodynamic constraints along specified paths. We present an approach to generate continuous velocity profiles for multiple robots; these velocity profiles satisfy the dynamics constraints, avoid collisions, and minimize the completion time. The approach, which combines techniques from optimal control and mathematical programming, consists of identifying collision segments along each robot’s path, and then optimizing the robots’ velocities along the collision and collision-free segments. First, for each path segment for each robot, the minimum and maximum possible traversal times that satisfy the dynamics constraints are computed by solving the corresponding two-point boundary value problems. The collision avoidance constraints for pairs of robots can then be combined to formulate a mixed integer nonlinear programming (MINLP) problem. Since this nonconvex MINLP model is difficult to solve, we describe two related mixed integer linear programming (MILP) formulations, which provide schedules that give lower and upper bounds on the optimum; the upper bound schedule is designed to provide continuous velocity trajectories that are feasible. The approach is illustrated with coordination of multiple robots, modeled as double integrators subject to velocity and acceleration constraints. An application to coordination of nonholonomic car-like robots is described, along with implementation results for 12 robots.
Proteomic analysis of melanoma‐derived exosomes by two‐dimensional polyacrylamide gel electrophoresis and mass spectrometry (2004)

Exosomes are 40-100 nm vesicles released by numerous cell types and are thought to have a variety of roles depending on their origin. Exosomes derived from antigen presenting cells have been shown to be capable of initiating immune responses in vivo and eradicating established tumours in murine models. Tumour-derived exosomes can be utilised as a source of tumour antigen for cross-priming to T-cells and are thus of interest for use in anti-tumour immunotherapy. Further exploration into the protein composition of exosomes may increase our understanding of their potential roles in vivo and this study has examined the proteome of exosomes purified from cell supernatants of the melanoma cell lines MeWo and SK-MEL-28. The vesicular nature and size (30-100 nm) of the purified exosomes was confirmed by electron microscopy and sucrose density gradient centrifugation. Western blotting demonstrated the absence of calnexin and cytochrome c, verifying the purity of the exosome preparations, as well as enrichment of MHC class I and the tumour-associated antigens Mart-1 and Mel-CAM. The two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) protein profiles of exosomes from the two cell lines were highly comparable and strikingly different from the profiles of the total cell lysates. Mass spectrometric sequencing identified proteins present in 49 protein spots in the exosome lysates. Several of these have been identified previously in exosomes but some are novel, including p120 catenin, radixin, and immunoglobulin superfamily member 8 (PGRL). Proteins present in whole-cell lysates that were significantly reduced or excluded from exosomes were also identified and included several mitochondrial and lysosomal proteins, again confirming the proposed endosomal origin of exosomes. This study presents a starting point for future more in-depth protein studies of tumour-derived exosomes which will aid the understanding of their biogenesis and targeting for use in anti-tumour immunotherapy protocols.
Role of the Classical Pathway of Complement Activation in Experimentally Induced Polymicrobial Peritonitis (2001)

The complement system and the natural antibody repertoire provide a critical first-line defense against infection. The binding of natural antibodies to microbial surfaces opsonizes invading microorganisms and activates complement via the classical pathway. Both defense systems cooperate within the innate immune response. We studied the role of the complement system in the host defense against experimental polymicrobial peritonitis using mice lacking either C1q or factor B and C2. The C1q-deficient mice lacked the classical pathway of complement activation. The factor B- and C2-deficient mice were known to lack the classical and alternative pathways, and we demonstrate here that these mice also lacked the lectin pathway of complement activation. Using inoculum doses adjusted to cause 42% mortality in the wild-type strain, none of the mice deficient in the three activation routes of complement (factor B and C2 deficient) survived (mortality of 100%). Mortality in mice deficient only in the classical pathway of complement activation (C1q deficient) was 83%. Application of further dilutions of the polymicrobial inoculum showed a dose-dependent decrease of mortality in wild-type controls, whereas no changes in mortality were observed in the two gene-targeted strains. These results demonstrate that the classical activation pathway is required for an effective antimicrobial immune defense in polymicrobial peritonitis and that, in the infection model used, the remaining antibody-independent complement activation routes (alternative and lectin pathways) provide a supporting line of defense to gain residual protection in classical pathway deficiency.