gebhart/patrepeval huggingface dataset:
Metal Binding to Pseudomonas aeruginosa Azurin: a Kinetic Investigation (2000)

The interaction between azurin from Pseudomonas aeruginosa and Ag(I), Cu(II), Hg(II), was investigated as a function of protein state, i.e. apo-, reduced and oxidised azurin. Two different metal binding sites, characterized by two different spectroscopic absorbancies, were detected: one is accessible to Ag(I) and Cu(II) but not to Hg(II); the other one binds Ag(I) and Hg(II) but not copper. When added in stoichiometric amount, Ag(I) shows high affinity for the redox center of apo-azurin, to which it probably binds by the -SH group of Cys112; it can displace Cu(I) from reducedazurin, while it does not bind to the redox center of oxidizedazurin. Kinetic experiments show that Ag(I) binding to the reduced form is four times faster than binding to the apo-form. This result suggests that metal binding requires a conformational rearrangement of the active site of the azurin. Interaction of Ag(I) or Hg(II) ions to the second metal binding site, induces typical changes of UV spectrum and quenching of fluorescence emission.
A Clustering Algorithm Based on Grid Partition of Space-Filling Curve (2009)

In spatial data mining, clustering is one of useful techniques for discovering interesting data in the underlying data objects. The k-means algorithm is probably the most widely applied clustering method. But a major drawback of k-means algorithm is that it is difficult to determine the parameter k to represent natural cluster, and it is only suitable for concave spherical clusters. Therefore, the paper presents an efficient clustering algorithm for large spatial databases. It combines the hierarchical approach with the grid partition. The hierarchical approach is applied to find the genuine clusters by repeatedly combining together these blocks. Hilbert curve is a continuous path which passes through every point in a space once to form a one-one correspondence between the coordinates of the points and the one-dimensional sequence numbers of the points on the curve. The goal of using Hilbert curve is to preserve the distance of that points which are close in space and represent similar data should be stored close together in the linear order. This kind of mapping also can minimize the disk access effort and provide high speed for clustering. The simulation shows that the clustering algorithm can have shorter execution time than k-means algorithms for the large databases. Moreover, the algorithm can deal with clusters with arbitrary shapes in which the k-means algorithm can not discover.
Performance evaluation of 70 hepatitis B virus (HBV) surface antigen (HBsAg) assays from around the world by a geographically diverse panel with an array of HBV genotypes and HBsAg subtypes (2009)

Diagnostic efficacy of the evaluated HBsAg test kits differed substantially. Laboratories should therefore be aware of the analytical sensitivity for HBsAg and check for the relevant HBV variants circulating in the relevant population.
New MRI-safe implant electrode design (2016)

Medical implants often prevent patients having Magnetic Resonance Imaging (MRI) scans because the leads behave as antennas with respect to the RF excitation and cause hazardous heating in neural tissue. This manuscript describes an approach that virtually eliminates the risk of RF heating by means of easily-incorporated, mutually-coupled filars. The resulting leads need be neither physically larger nor significantly more costly than existing designs. Combined with thin insulation and surface roughening techniques, this manuscript represents the first complete release of recently-patented technologies. Both simulations and measurements at 128MHz are presented to confirm performance in 3-Tesla MRI machines.
182. The mechanism of heterocyclic ring expansions. Part II. The reaction of methylindoles with halogenocarbenes (1964)

C. W. Rees and C. E. Smithen, J. Chem. Soc., 1964, 938 DOI: 10.1039/JR9640000938
Protective Effects of Gastrodin on Hypoxia-Induced Toxicity in Primary Cultures of Rat Cortical Neurons (2007)

The phenolic glucoside gastrodin is the main component extracted from the rhizome of Gastrodia elata (Orchidaceae), a Chinese herbal medicine, which has long been used for treating dizziness, epilepsy, stroke and dementia. The present study aims to investigate the effect of gastrodin on hypoxia-induced neurotoxicity in cultured rat cortical neurons. Neuron survival and extracellular glutamate level were measured after an insult by hypoxia. Glutamate concentrations were determined by an HPLC-ECD system. The results demonstrated that neurons were significantly damaged by hypoxia for 24 h. When pretreated with gastrodin (100, 200 microg/mL) in hypoxia, neuron survival was significantly increased compared with no gastrodin treatment. Moreover, the enhancement of extracellular glutamate level stimulated by hypoxia was inhibited by pretreatment with gastrodin (100 microg/mL). Further studies demonstrated that gastrodin prevented glutamate- and NMDA-induced neurotoxicity. In addition, gastrodin also inhibited the extracellular glutamate level induced by NMDA insult. These findings suggest that gastrodin has a neuroprotective action against hypoxia in the cultured cortical neuron, and the mechanism may involve a decreasing of the extracellular glutamate level.
Heterogeneity of autoantibodies in 100 patients with autoimmune myositis: insights into clinical features and outcomes (2007)

The objective of this study was to determine the prevalence, mutual associations, clinical manifestations, and diagnoses associated with serum autoantibodies, as detected using recently available immunoassays, in patients with autoimmune myositis (AIM). Sera and clinical data were collected from 100 patients with AIM followed longitudinally. Sera were screened cross-sectionally for 21 autoantibodies by multiplex addressable laser bead immunoassay, line blot immunoassay, immunoprecipitation of in vitro translated recombinant protein, protein A assisted immunoprecipitation, and enzyme-linked immunosorbent assay. Diagnoses were determined using the Bohan and Peter classification as well as recently proposed classifications. Relationships between autoantibodies and clinical manifestations were analyzed by multiple logistic regression. One or more autoantibodies encompassing 19 specificities were present in 80% of the patients. The most common autoantibodies were anti-Ro52 (30% of patients), anti-Ku (23%), anti-synthetases (22%), anti-U1RNP (15%), and anti-fibrillarin (14%). In the presence of autoantibodies to Ku, synthetases, U1RNP, fibrillarin, PM-Scl, or scleroderma autoantigens, at least one more autoantibody was detected in the majority of sera and at least two more autoantibodies in over one-third of sera. The largest number of concurrent autoantibodies was six autoantibodies. Overall, 44 distinct combinations of autoantibodies were counted. Most autoantibodies were unrestricted to any AIM diagnostic category. Distinct clinical syndromes and therapeutic responses were associated with anti-Jo-1, anti-fibrillarin, anti-U1RNP, anti-Ro, anti-Ro52, and autoantibodies to scleroderma autoantigens. We conclude that a significant proportion of AIM patients are characterized by complex associations of autoantibodies. Certain myositis autoantibodies are markers for distinct overlap syndromes and predict therapeutic outcomes. The ultimate clinical features, disease course, and response to therapy in a given AIM patient may be linked to the particular set of associated autoantibodies. These results provide a rationale for patient profiling and its application to therapeutics, because it cannot be assumed that the B-cell response is the same even in the majority of patients in a given diagnostic category.
Effects of chronic HIV-1 Tat exposure in the CNS: heightened vulnerability of males versus females to changes in cell numbers, synaptic integrity, and behavior (2013)

HIV-associated damage to the central nervous system results in cognitive and motor deficits. Anti-retroviral therapies reduce the severity of symptoms, yet the proportion of patients affected has remained the same or increased. Although approximately half of HIV-infected patients worldwide are women, the question of whether biological sex influences outcomes of HIV infection has received little attention. We explored this question for both behavioral and cellular/morphologic endpoints, using a transgenic mouse that inducibly expresses HIV-1 Tat in the brain. After 3 months of HIV-1 Tat exposure, both sexes showed similar reduced open field ambulation. Male Tat(+) mice also showed reduced forelimb grip strength and enhanced anxiety in a light-dark box assay. Tat(+) males did not improve over 12 weeks of repeated rotarod testing, indicating a motor memory deficit. Male mice also had more cellular deficits in the striatum. Neither sex showed a change in volume or total neuron numbers. Both had equally reduced oligodendroglial populations and equivalent microglial increases. However, astrogliosis and microglial nitrosative stress were higher in males. Dendrites on medium spiny neurons in male Tat(+) mice had fewer spines, and levels of excitatory and inhibitory pre- and post-synaptic proteins were disrupted. Our results predict sex as a determinant of HIV effects in brain. Increased behavioral deficits in males correlated with glial activation and synaptic damage, both of which are implicated in cognitive/motor impairments in patients. Tat produced by residually infected cells despite antiretroviral therapy may be an important determinant of the synaptodendritic instability and behavioral deficits accompanying chronic infection.
High Resolution Order Tracking at Extreme Slew Rates, Using Kalman Tracking Filters (1993)

<div class="htmlview paragraph">The analysis of the periodic components in noise and vibration signals measured on rotating equipment, like car power trains, must more and more be done under rapid changes of an axle, or reference RPM. Normal tracking filters (analog, or digital implementations) have limited resolution in such situations; wavelet methods, even when applied after resampling the data to be proportional to an axle RPM, must compromise between time and frequency resolution. The authors propose the application of nonstationary Kalman filters for the tracking of periodic components in such noise and vibration signals. These filters are designed to track accurately signals with a known structure among noise and signal components of different, ‘unknown’, structure. The tracking characteristics of these filters, i.e., the predicted signal amplitude vs. time values versus exact signal amplitude vs. time values, can be tailored to accurate tracking of harmonics buried in other signal components and noise, even at high rates of change of the reference RPM. A key to the successful construction is the precise knowledge of the structure of the signal to be tracked. For signals that vary with an axle RPM, an accurate estimate of the instantaneous RPM is essential, and procedures to this end will also be presented.</div>
Consistency and coupling in human model likelihoods (2003)

This paper presents two novel likelihood terms for silhouettes and contours in model-based contexts. Despite the power of such formulations, building likelihoods that truly reflect the good configurations of the problem is by no means easy due to, most commonly, the violation of consistency principle resulting in the introduction of spurious, unrelated peaks/minima that make target localization difficult. We introduce an entirely continuous formulation which enforces consistency by means of an attraction/explanation pair for silhouettes. For contours, we address the search window vs. noise level dilemma by means of a combined robust estimation and feature coupling solution which builds a likelihood model not only in terms of individual contour responses but also "Gestalt" type higher-order couplings between matched configurations. We subsequently show how the proposed method provides significant consolidation and improved attraction zone around the true cost minima and elimination of some of the spurious ones.
Waveguide grating routers with greaterchannel uniformity (1997)

Previous waveguide grating routers have much more loss at edge wavelengths or channels. Here, the authors propose a novel design that spreads the loss more uniformly among the channels. It is even possible to have more losses in the centre then in some of the edge ports.
NON-DISCRETIONARY ACCESS CONTROL FOR DECENTRALIZED COMPUTING SYSTEMS (1977)

This thesis examines the issues relating to non-discretionary access controls for decentralized computing systems. Decentralization changes the basic character of a computing system from a set of processes referencing a data base to a set of processes sending and receiving messages. Because messages must be acknowledged, operations that were read-only in a centralized system become read-write operations. As a result, the lattice model of non-discretionary access control, which mediates operations based on read versus read-write considerations, does not allow direct transfer of algorithms from centralized systems to decentralized systems. This thesis develops new mechanisms that comply with the lattice model and provide the necessary functions for effective decentralized computation. Secure
Efficient Hypervisor Based Malware Detection (2014)

Recent years have seen an uptick in master boot record (MBR) based rootkits that load before the Windows operating system and subvert the operating system’s own procedures. As such, MBR rootkits are difficult to counter with operating system-based antivirus software that runs at the same privilege-level as the rookits. Hypervisors operate at a higher privilege level than the guests they manage, creating a high-ground position in the host. This high-ground position can be exploited to perform security checks on the virtual machine guests where the checking software is isolated from guest-based viruses. The efficient introspection system described in this thesis targets existing virtualized systems to improve security with real-time, concurrent memory introspection capabilities. Efficient introspection decouples memory introspection from virtual machine guest execution, establishes coherent and consistent memory views between the host and running guest, while maintaining normal guest operation. Existing introspection systems have provided one or two of these properties but not all three at once. This thesis presents a new concurrent-computing approach – high-performance memory snapshotting – to accelerating hypervisor based introspection of virtual machine guest memory that combines all three elements to improve performance and security. Memory snapshots create a coherent and consistent memory view of the guest that can be shared with the independently running introspection application. Three memory snapshotting mechanisms are presented and evaluated for their impact on normal guest operation. Existing introspection systems and security protection techniques that were previously dismissed as too slow are now be enabled by efficient introspection. This thesis explains why existing introspection systems are inadequate, describes how existing system performance can be improved, evaluates an efficient introspection prototype on both applications and microbenchmarks, and discusses two potential security applications that are enabled by efficient introspection. These applications point to efficient introspection’s utility for supporting useful security applications.
Detecting oral cancer: a new technique and case reports. (2006)

The VELscope is an important aid in patient assessment, and when added to a well-thought out clinical assessment process that takes into consideration the age of the patient and risk factors that include tobacco, alcohol, and immunologic status, it increases the clinician's ability to detect oral changes that may represent premalignant or malignant cellular transformation. False positive findings are possible in the presence of highly inflamed lesions, and it is possible that use of the scope alone may result in failure to detect regions of dysplasia, but it has been our experience that use of the VELscope improves clinical decision making about the nature of oral lesions and aids in decisions to biopsy regions of concern. Where tissue changes are generalized or cover significant areas of the mouth, use of the scope has allowed us to identify the best region for biopsy. As with all clinical diagnostic activities, no single system or process is enough, and all clinicians are advised to use good clinical practice to assess patients and to recall and biopsy lesions that do not resolve within a predetermined time frame. Lesions that are VELscope-positive and absorb light need to be followed with particular caution, and if they do not resolve within a 2-week period, then further assessment and biopsy are generally advised. It is much better to occasionally sample tissue that turns out to be benign than to fail to diagnose dysplastic or malignant lesions. In our fight to protect patients from cancer, the VELscope improves our odds for early detection, hopefully resulting in fewer deaths from oral cancer.
Olive oil phenolics: effects on DNA oxidation and redox enzyme mRNA in prostate cells (2002)

Hydroxytyrosol, tyrosol and caffeic acid effects on hydrogen peroxide-induced DNA damage, hydroperoxide generation and redox enzyme gene expression were studied in oxidative-stress-sensitive human prostate cells (PC3). Hydroxytyrosol led to lower levels of hydroperoxides, DNA damage, and mRNA levels of classic glutathione peroxidase (GPx) for all the studied concentrations. Only hydroxytyrosol was effective at low concentrations (10 microm). Tyrosol reduced DNA oxidation only at high (>50 microm) concentrations and increased hydroperoxides, GPx and phospholipid hydroperoxide GPx mRNA levels. Caffeic acid elicited effects between those of the other two phenolics. Results indicate that hydroxytyrosol is the only significant antioxidant phenolic in olive oil and may be the major component accounting for its beneficial properties. Tyrosol appeared to exhibit pro-oxidant effects (only at high concentrations) and caffeic acid was neutral. Both number and position of hydroxyl groups appear to play a role in the cellular effects of hydroxytyrosol.
Serving Database Information Using a Flexible Server in a Three Tier Architecture (2003)

The D0 experiment at Fermilab relies on a central Oracle database for storing all detector calibration information. Access to this data is needed by hundreds of physics applications distributed worldwide. In order to meet the demands of these applications from scarce resources, we have created a distributed system that isolates the user applications from the database facilities. This system, known as the Database Application Network (DAN) operates as the middle tier in a three tier architecture. A DAN server employs a hierarchical caching scheme and database connection management facility that limits access to the database resource. The modular design allows for caching strategies and database access components to be determined by runtime configuration. To solve scalability problems, a proxy database component allows for DAN servers to be arranged in a hierarchy. Also included is an event based monitoring system that is currently being used to collect statistics for performance analysis and problem diagnosis. DAN servers are currently implemented as a Python multithreaded program using CORBA for network communications and interface specification. The requirement details, design, and implementation of DAN are discussed along with operational experience and future plans.
Biochemistry of Mitochondrial Nitric-oxide Synthase (2002)

We reported that the generation of nitric oxide by mitochondria is catalyzed by a constitutive, mitochondrial nitric-oxide synthase (mtNOS). Given that this production may establish the basis for a novel regulatory pathway of energy metabolism, oxygen consumption, and oxygen free radical production, it becomes imperative to identify unequivocally and characterize this enzyme to provide a basis for its regulation. The mitochondrial localization of mtNOS was supported by following the hepatic distribution of mtNOS, immunoblotting submitochondrial fractions, and immunohistochemistry of liver tissues. mtNOS was identified as brain NOS alpha by various methods (mass spectrometry of proteolytic fragments, amino acid analysis, molecular weight, pI, and analysis of PCR fragments), excluding the occurrence of a novel isoform or other splice variants. Distribution of mtNOS transcript indicated its occurrence in liver, brain, heart, muscle, kidney, lung, testis, and spleen. In contrast to brain NOS, mtNOS has two post-translational modifications: acylation with myristic acid and phosphorylation at the C terminus. The former modification is a reversible and post-translational process, which may serve for subcellular targeting or membrane anchoring. The latter modification could be linked to enzymatic regulation. These results are discussed in terms of the role that nitric oxide may have in cellular bioenergetics.
Experimental Investigation of the Temperature Dependence of InAs–AlSb–GaSb Resonant Interband Tunnel Diodes (2004)

The temperature dependence of the current-voltage (I-V) characteristics of InAs-AlSb-GaSb resonant interband tunnel diodes (RITDs) has been investigated from 223 to 423 K. Several device structures were examined, with tunnel barrier thicknesses from 0.6 to 2.0 nm. For all barrier thicknesses, the peak current density (J/sub p/) decreases slightly as the temperature is increased, while the valley current density (J/sub v/) increases with temperature. We found that the temperature rate of change for the peak current density with temperature (/spl part/J/sub p///spl part/T) is nearly independent of barrier thickness, while J/sub v/ increases more rapidly for devices with thicker barriers. In addition, the peak voltage (V/sub p/) was found to be independent of temperature, regardless of barrier thickness. However, the valley voltage (V/sub v/) was observed to decrease with increasing temperature, with more rapid changes observed for RITDs with thicker barriers. Comparison of the temperature performance of RITDs with different barrier thicknesses shows that devices with thinner barriers have I-V characteristics that are less sensitive to temperature, as well as having larger peak and valley current density and voltage for the temperature range from 223 to 423 K. To our knowledge, this is the first report of the temperature dependence of the device characteristics of Sb-based RITDs as a function of barrier width.
Isomerisations akin to the Dimroth rearrangement. Part II. The equilibria of 4-mercapto-1,2,3,5,7-penta-azaindenes with 4-amino-1-thia-2,3,5,7-tetra-azaindenes (1967)

When 1-benzyl-4-mercapto-1,2,3,5,7-penta-azaindene or 4-benzylamino-1-thia-2,3,5,7-tetra-azaindene is boiled in an alcohol or maintained in the molten state, the equilibrium mixture consists largely of the thia-isomer. Analogues in which the benzyl group is replaced by a phenyl or p-substituted phenyl group behave similarly. For each pair of isomers, the first-order rate constant for equilibration in butanol–methoxyethanol, and the equilibrium constant are recorded. The plot, log forward component of the rate constant versus Hammett's sigma value for the p-substituent, is rectilinear. Equilibrium constants also vary with the substituents and with temperature: the thiaisomer is more strongly favoured by electron withdrawal and by higher temperatures. In dimethyl sulphoxide solution equilibrium lies about midway; in aqueous sodium hydroxide, the penta-azaindene (anion) is favoured. Each compound was prepared by a direct route as well as by isomerisation.
A Discriminatively Trained Fully Connected Conditional Random Field Model for Blood Vessel Segmentation in Fundus Images (2016)

Results suggest that this method is suitable for the task of segmenting elongated structures, a feature that can be exploited to contribute with other medical and biological applications.