gebhart/patrepeval huggingface dataset:
Bayesian non-parametrics and the probabilistic approach to modelling (2013)

Modelling is fundamental to many fields of science and engineering. A model can be thought of as a representation of possible data one could predict from a system. The probabilistic approach to modelling uses probability theory to express all aspects of uncertainty in the model. The probabilistic approach is synonymous with Bayesian modelling, which simply uses the rules of probability theory in order to make predictions, compare alternative models, and learn model parameters and structure from data. This simple and elegant framework is most powerful when coupled with flexible probabilistic models. Flexibility is achieved through the use of Bayesian non-parametrics. This article provides an overview of probabilistic modelling and an accessible survey of some of the main tools in Bayesian non-parametrics. The survey covers the use of Bayesian non-parametrics for modelling unknown functions, density estimation, clustering, time-series modelling, and representing sparsity, hierarchies, and covariance structure. More specifically, it gives brief non-technical overviews of Gaussian processes, Dirichlet processes, infinite hidden Markov models, Indian buffet processes, Kingman's coalescent, Dirichlet diffusion trees and Wishart processes.
Crystal Organic Light‐Emitting Diodes with Perfectly Oriented Non‐Doped Pt‐Based Emitting Layer (2016)

Organic light-emitting diodes with external quantum efficiency of 38.8% are realized using a Pt-based thin-film emitting layer with photoluminescence quantum yield of 96% and transition dipole ratio of 93%. The emitting dipole orientation of the thin films fabricated using Pt complexes is investigated and the structural relationship between X-ray structural analysis and the structures in thin films are discussed based on quantum chemical calculations.
R-ketamine: a rapid-onset and sustained antidepressant without psychotomimetic side effects (2015)

Although the efficacy of racemate ketamine, a rapid onset and sustained antidepressant, for patients with treatment-resistant depression was a serendipitous finding, clinical use of ketamine is limited, due to psychotomimetic side effects and abuse liability. Behavioral and side-effect evaluation tests were applied to compare the two stereoisomers of ketamine. To elucidate their potential therapeutic mechanisms, we examined the effects of these stereoisomers on brain-derived neurotrophic factor (BDNF)-TrkB signaling, and synaptogenesis in selected brain regions. In the social defeat stress and learned helplessness models of depression, R-ketamine showed a greater potency and longer-lasting antidepressant effect than S-ketamine (esketamine). Furthermore, R-ketamine induced a more potent beneficial effect on decreased dendritic spine density, BDNF-TrkB signaling and synaptogenesis in the prefrontal cortex (PFC), CA3 and dentate gyrus (DG) of the hippocampus from depressed mice compared with S-ketamine. However, neither stereoisomer affected these alterations in the nucleus accumbens of depressed mice. In behavioral tests for side effects, S-ketamine, but not R-ketamine, precipitated behavioral abnormalities, such as hyperlocomotion, prepulse inhibition deficits and rewarding effects. In addition, a single dose of S-ketamine, but not R-ketamine, caused a loss of parvalbumin (PV)-positive cells in the prelimbic region of the medial PFC and DG. These findings suggest that, unlike S-ketamine, R-ketamine can elicit a sustained antidepressant effect, mediated by increased BDNF-TrkB signaling and synaptogenesis in the PFC, DG and CA3. R-ketamine appears to be a potent, long-lasting and safe antidepressant, relative to S-ketamine, as R-ketamine appears to be free of psychotomimetic side effects and abuse liability.
Post-segregational Killing and Phage Inhibition Are Not Mediated by Cell Death Through Toxin/Antitoxin Systems (2018)

The toxin/antitoxin (TA) field, born of controversy, is plagued by several prevailing misperceptions. For example, some TA systems stabilize plasmids and other genomic regions; however, the evidence of post-segregational killing by toxins of TA systems is weak. In addition, there are few credible reports of cell death via TA systems like MazF/MazE and via phage exclusion systems. Although many aspects of the biological roles of TA systems remain enigmatic, there are now some clear, confirmed TA functions: (i) phage inhibition, (ii) plasmid maintenance, (iii) stress response (including regulation of loci distinct from the TA pair itself), (iv) biofilm formation, and (v) persistence. Therefore, this opinion piece aims to challenge the oft-repeated claims of cell killing related to TA systems with the goal of emphasizing their primary biological role: constraining metabolism in a reversible manner. Hence, their roles in their five confirmed functions all stem from their ability to rapidly and reversibly reduce metabolic activity.
Theory of Bragg fiber* (1978)

The possibility of using Bragg reflection in a cylindrical fiber to obtain lossless confined propagation in a core with a lower refractive index than that of the cladding medium is proposed and analyzed.
Aggressive peripheral T-cell lymphomas containing Epstein-Barr viral DNA: a clinicopathologic and molecular analysis (1991)

Abstract The Epstein-Barr virus (EBV) has been shown to be associated with posttransplant lymphoma, Hodgkin's disease, and T-cell lymphoma, in addition to African Burkitt's lymphoma. In a retrospective study of 56 consecutive cases of T-cell lymphoma, EBV DNA was found by Southern blot and in situ DNA hybridization in 10 (20%) of 50 peripheral T-cell lymphomas, but in none of six cases of T-lymphoblastic lymphoma. Peripheral T-cell lymphomas containing EBV DNA could be subclassified into three categories according to histology and immunophenotypic studies: (1) T-cell lymphoma of the helper phenotype, five cases. Two cases had histologic features resembling angioimmunoblastic lymphadenopathy (AILD). (2) T-cell lymphoma of the cytotoxic/suppressor phenotype, four cases. AILD-like features could also be recognized in two cases. Reed-Sternberg-like giant cells were identified in three cases designated Hodgkin-like T-cell lymphoma. (3) Angiocentric T-cell lymphoma or lymphomatoid granulomatosis in one case, initially affecting the skin and nose; no T-cell subset could be defined. Six of the eight EBV DNA-positive patients tested for serum EBV antibodies had elevated titers of IgG antiviral capsid antigen (greater than 640) and/or early antigen (greater than 10). From combined studies of Southern blot hybridization by using EBV termini fragment probe and in situ DNA hybridization, the EBV genomes appeared to be clonotypically proliferated in the neoplastic T cells. The patients in all three groups usually had prolonged fever preceding the diagnosis, hepatosplenomegaly, an aggressive clinical course, and poor response to chemotherapy; nine died with a median survival of only 8 months. We propose that these EBV-associated aggressive T-cell lymphomas, like human T-cell leukemia/lymphoma virus-positive T-cell lymphoma, have characteristic clinicopathologic features and should be treated as a separate disease entity.
VEGF enhances angiogenesis and promotes blood-brain barrier leakage in the ischemic brain (2000)

VEGF is a secreted mitogen associated with angiogenesis and is also a potent vascular permeability factor. The biological role of VEGF in the ischemic brain remains unknown. This study was undertaken to investigate whether VEGF enhances cerebral microvascular perfusion and increases blood-brain barrier (BBB) leakage in the ischemic brain. Using magnetic resonance imaging (MRI), three-dimensional laser-scanning confocal microscope, and functional neurological tests, we measured the effects of administrating recombinant human VEGF(165) (rhVEGF(165)) on angiogenesis, functional neurological outcome, and BBB leakage in a rat model of focal cerebral embolic ischemia. Late (48 hours) administration of rhVEGF(165) to the ischemic rats enhanced angiogenesis in the ischemic penumbra and significantly improved neurological recovery. However, early postischemic (1 hour) administration of rhVEGF(165) to ischemic rats significantly increased BBB leakage, hemorrhagic transformation, and ischemic lesions. Administration of rhVEGF(165) to ischemic rats did not change BBB leakage and cerebral plasma perfusion in the contralateral hemisphere. Our results indicate that VEGF can markedly enhance angiogenesis in the ischemic brain and reduce neurological deficits during stroke recovery and that inhibition of VEGF at the acute stage of stroke may reduce the BBB permeability and the risk of hemorrhagic transformation after focal cerebral ischemia.
Chemotypes of Mycobacterium malmoense based on glycolipid profiles (1991)

Thin-layer chromatographic analysis of 72 Finnish clinical mycobacterial isolates presumptively identified as Mycobacterium malmoense revealed four major glycolipid profiles with two minor variations. An additional glycolipid profile was found in three British M. malmoense-like strains. No clear distinction between the strains could be made by means of gas chromatography of cellular fatty acids. The two M. malmoense-specific constituents, 2-methyleicosanoate and 2,4,6-trimethyltetracosanoate, were detected in all strains. The frequency of chemotypes other than that of the type strain was 8% among the Finnish isolates. This variation should be recognized when confirmative identification of mycobacteria is based on thin-layer chromatography of glycolipid extracts.
In Vivo Interaction of Human MCM Heterohexameric Complexes with Chromatin (1997)

The MCM protein family, which consists of at least six members, has been implicated in the regulatory machinery causing DNA to replicate once in the S phase. Mammalian MCM proteins are present in the nucleus in two different forms, one extractable by nonionic detergents and the other resistant to such extraction. The latter is assumed to be tightly associated with nuclear structures and released at the time of initiation of replication. However, details of the mode of binding remain unclear. In the present study, we found that, in nonionic detergent-permeabilized nuclei, the association of human MCM (hMCM) proteins with them could be stabilized by the addition of ATP. The hMCMs bound to the nuclei in the presence of ATP were released by digestion with nucleases, suggesting that they are chromatin-associated. The nuclease-directed solubilization of the chromatin-bound hMCMs thus provided a means to analyze them as well as soluble hMCMs by co-immunoprecipitation. The results indicate that the six hMCM members exist as heterocomplexes, whether bound or unbound. We therefore propose that hMCM proteins may function in DNA replication as heterohexamers associated with chromatin and that ATP is possibly involved in the association. Nuclease digestion-immunoprecipitation techniques of the type described here should facilitate further elucidation of the mode of interaction between hMCMs and chromatin.
Bonding of silicon wafers for silicon-on-insulator (1988)

Several aspects of a new silicon-on-insulator technique utilizing bonding of oxidized silicon wafers were investigated. The bonding was achieved by heating in an inert atmosphere a pair of wafers with hydrophilic surfaces contacted face-to-face. A quantitative method for the evaluation of the surface energy of the bond based on crack propagation theory was developed. The bond strength was found to increase with the bonding temperature from about 60–85 erg/cm2 at room temperature to ≂2200 erg/cm2 at 1400 °C. The strength was essentially independent of the bond time. Bonds created during 10-s annealing at 800 °C were mechanically strong enough to withstand the mechanical and/or chemical thinning of the top wafer to the desired thickness and subsequent device processing. A model was proposed to explain three distinct phases of bonding in the temperature domain. Electrical properties of the bond were tested using metal-oxide-semiconductor (MOS) capacitors. The results were consistent with a negative charge density at the bond interface of approximately 1011 cm−2. A double-etch-back procedure was used to thin the device wafer to the desired thickness with ±20 nm thickness uniformity across a 4-in. wafer. The density of threading dislocations in the remaining silicon layer was 102 –103 cm−2, and the residual dopant concentration less than 5×1015 cm−3, both remnants of the etchstop layer. Complimentary metal-oxide-semiconductor (CMOS) devices made in the 20–100 nm silicon thick layers had subthreshold slopes of 68 mV/decade (both n- and p-channel MOS transistors). The effective carrier lifetime was 15–20 μs in 80- and 300-nm-thick Si films and the interface state density at the Si film-buried oxide interface was ≤5×1010 cm−2.
Quantitation of articular cartilage using magnetic resonance imaging and three‐dimensional reconstruction (1995)

A quadrature knee coil was used in conjunction with a magnetic resonance imaging scanner for quantitation of test phantom volumes, ex vivo bovine cartilage thickness, and in vivo human articular cartilage volumes. Optimal magnetic resonance parameters were obtained by testing a series of spin-echo and gradient-echo pulse sequences to determine the sequence that provided the highest resolution of articular cartilage and best defined the cartilage interfaces with synovial fluid and subchondral bone. Extensive testing revealed that two sequences were required to define articular cartilage accurately: a spoiled gradient-echo sequence and a steady state free-precession sequence. Three-dimensional reconstruction and statistical analyses of test phantoms and of bovine and human cartilage images were performed. Differences between actual phantom volumes and three-dimensional measurements demonstrated that, as magnetic resonance slice thickness was increased, the measurement variability also increased (coefficient of variation ranging from 1.7 +/- 1.3% for 1.0 mm slice thickness to 22.7 +/- 1.9% for 3.0 mm slice thickness). When the phantom volume was greater than 1,800 mm3, the intraobserver, interobserver and interscan accuracies were greater than 97, 98, and 96%, respectively. This high degree of reproducibility pertained for the data on in vivo human cartilage data also. For experienced observers, the intraobserver and interobserver reproducibility were greater than 98 and 97%, respectively. The interscan reproducibility was greater than 98%. These data demonstrate that improved magnetic resonance pulse sequencing, in conjunction with three-dimensional reconstruction and measurement techniques, can accurately and reproducibly measure the volume of articular cartilage. Clinical application of this approach offers the potential for early diagnosis of osteoarthritis and for serial, noninvasive assessment of changes in articular cartilage volume in response to therapeutic modalities.
Cutaneous nociception and neurogenic inflammation evoked by PACAP38 and VIP (2010)

Pituitary adenylate cyclase-activating peptide-38 (PACAP38) and vasoactive intestinal peptide (VIP) belong to the same secretin-glucagon superfamily and are present in nerve fibers in dura and skin. Using a model of acute cutaneous pain we explored differences in pain perception and vasomotor responses between PACAP38 and VIP in 16 healthy volunteers in a double-blind, placebo-controlled, crossover study. All participants received intradermal injections of 200 pmol PACAP38, 200 pmol VIP and placebo into the volar forearm. Measurements included pain intensity on a visual analog scale (VAS), blood flow by laser Doppler flowmetry, visual flare and wheal. Pain intensities after PACAP38 and VIP were mild and limited to a short time of about 100 s after injection. The area under the VAS-time curve was larger following PACAP38 (P = 0.004) and VIP (P = 0.01) compared to placebo. We found no statistical difference in pain perception between PACAP38 and VIP. Skin blood flow increase, flare and wheal were larger after both PACAP38 (P = 0.011) and VIP (P = 0.001) compared to placebo. VIP induced a considerably larger increase in skin blood flow, flare and wheal than PACAP38 (P = 0.002). In conclusion, we found that peripheral nociceptive cutaneous responses elicited by PACAP38 and VIP are similar in healthy volunteers. This suggests that acute pain and vasomotor responses following intradermal injections of PACAP38 and VIP are primarily mediated by VPAC receptors.
Interleukin-8 as a Macrophage-Derived Mediator of Angiogenesis (1992)

Angiogenic factors produced by monocytes-macrophages are involved in the pathogenesis of chronic inflammatory disorders characterized by persistent angiogenesis. The possibility was tested that interleukin-8 (IL-8), which is a cytokine that is chemotactic for lymphocytes and neutrophils, is also angiogenic. Human recombinant IL-8 was potently angiogenic when implanted in the rat cornea and induced proliferation and chemotaxis of human umbilical vein endothelial cells. Angiogenic activity present in the conditioned media of inflamed human rheumatoid synovial tissue macrophages or lipopolysaccharide-stimulated blood monocytes was equally blocked by antibodies to either IL-8 or tumor necrosis factor-alpha. An IL-8 antisense oligonucleotide specifically blocked the production of monocyte-induced angiogenic activity. These data suggest a function for macrophage-derived IL-8 in angiogenesis-dependent disorders such as rheumatoid arthritis, tumor growth, and wound repair.
Chronic obstructive pulmonary disease in the older patient (2008)

Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity, mortality, and health care problems in older patients. Recently, our country became an ageing society and the prevalence of COPD in older patients will be increasing continuously. The diagnosis of COPD is confirmed by spirometry. An obstructive defect is defined as a reduced post expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) ratio. Using the fixed FEV1/FVC ratio may create a risk for under diagnosis in young patients and overdiagnosis in older patients. The FEV1/FVC ratio decreases with age and clear consensus definition of diagnostic criteria for COPD in older patients is needed. Older patients who have COPD benefit from all effective therapies available to treat COPD. Older patients have more comorbidities that influence quality of life, prognosis and medical management. Attention for comorbidities improves the lives of older patients who have COPD.
Specification-based anomaly detection (2002)

Unlike signature or misuse based intrusion detection techniques, anomaly detection is capable of detecting novel attacks. However, the use of anomaly detection in practice is hampered by a high rate of false alarms. Specification-based techniques have been shown to produce a low rate of false alarms, but are not as effective as anomaly detection in detecting novel attacks, especially when it comes to network probing and denial-of-service attacks. This paper presents a new approach that combines specification-based and anomaly-based intrusion detection, mitigating the weaknesses of the two approaches while magnifying their strengths. Our approach begins with state-machine specifications of network protocols, and augments these state machines with information about statistics that need to be maintained to detect anomalies. We present a specification language in which all of this information can be captured in a succinct manner. We demonstrate the effectiveness of the approach on the 1999 Lincoln Labs intrusion detection evaluation data, where we are able to detect all of the probing and denial-of-service attacks with a low rate of false alarms (less than 10 per day). Whereas feature selection was a crucial step that required a great deal of expertise and insight in the case of previous anomaly detection approaches, we show that the use of protocol specifications in our approach simplifies this problem. Moreover, the machine learning component of our approach is robust enough to operate without human supervision, and fast enough that no sampling techniques need to be employed. As further evidence of effectiveness, we present results of applying our approach to detect stealthy email viruses in an intranet environment.
ECOSystem (2002)

Energy consumption has recently been widely recognized as a major challenge of computer systems design. This paper explores how to support energy as a first-class operating system resource. Energy, because of its global system nature, presents challenges beyond those of conventional resource management. To meet these challenges we propose the Currentcy Model that unifies energy accounting over diverse hardware components and enables fair allocation of available energy among applications. Our particular goal is to extend battery lifetime by limiting the average discharge rate and to share this limited resource among competing task according to user preferences. To demonstrate how our framework supports explicit control over the battery resource we implemented ECOSystem, a modified Linux, that incorporates our currentcy model. Experimental results show that ECOSystem accurately accounts for the energy consumed by asynchronous device operation, can achieve a target battery lifetime, and proportionally shares the limited energy resource among competing tasks.
Dysfunction of Lacrimal and Salivary Glands in Sjögren′s Syndrome: Nonimmunologic Injury in Preinflammatory Phase and Mouse Model (2011)

Sjögren's syndrome (SjS) is a chronic autoimmune disorder characterized by dry eyes and dry mouth due to dacryoadenitis and sialoadenitis with SS-A/Ro and/or SS-B/La autoantibodies in genetically predisposed individuals. Destruction of lacrimal and salivary glands by autoimmune reactions may lead to clinical manifestation. However, the mechanisms behind the decreased volume of secretions in tears and saliva are complex and are not fully understood. Exocrine gland dysfunction may precede autoimmunity (acquired immunity) or represent a process independent from inflammation in the pathogenesis of SjS. The preceded functional and morphologic changes of those tissues by nonimmunologic injury before the development of inflammation at the sites of target organs have been implicated. This paper focuses on the several factors and components relating to glandular dysfunction and morphologic changes by nonimmunologic injury during the preinflammatory phase in mouse model, including the factors which link between innate immunity and adaptive immunity.
Interactions between surfaces bearing end-adsorbed chains in a good solvent (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteractions between surfaces bearing end-adsorbed chains in a good solventHillary J. Taunton, Chris Toprakcioglu, Lewis J. Fetters, and Jacob KleinCite this: Macromolecules 1990, 23, 2, 571–580Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/ma00204a033https://doi.org/10.1021/ma00204a033research-articleACS PublicationsRequest reuse permissionsArticle Views883Altmetric-Citations308LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts