gebhart/patrepeval huggingface dataset:
Geometric modeling of the human normal cerebral arterial system (2005)

We propose an anatomy-based approach for an efficient construction of a three-dimensional human normal cerebral arterial model from segmented and skeletonized angiographic data. The centerline-based model is used for an accurate angiographic data representation. A vascular tree is represented by tubular segments and bifurcations whose construction takes into account vascular anatomy. A bifurcation is defined quantitatively and the algorithm calculating it is given. The centerline is smoothed by means of a sliding average filter. As the vessel radius is sensitive to quality of data as well as accuracy of segmentation and skeletonization, radius outlier removal and radius regression algorithms are formulated and applied. In this way, the approach compensates for some inaccuracies introduced during segmentation and skeletonization. To create the frame of vasculature, we use two different topologies: tubular and B-subdivision based. We also propose a technique to prevent vessel twisting. The analysis of the vascular model is done on a variety of data containing 258 vascular segments and 131 bifurcations. Our approach gives acceptable results from anatomical, topological and geometrical standpoints as well as provides fast visualization and manipulation of the model. The approach is applicable for building a reference cerebrovascular atlas, developing applications for simulation and planning of interventional radiology procedures and vascular surgery, and in education.
Usefulness of enzyme-linked immunosorbent assay using recombinant desmogleins 1 and 3 for serodiagnosis of pemphigus (1999)

Pemphigus is an autoimmune blistering disease with two major subtypes, pemphigus vulgaris (PV) and pemphigus foliaceus (PF). Patients with pemphigus have circulating antidesmoglein (Dsg)1 and/or anti-Dsg3 IgG autoantibodies. We have previously developed enzyme-linked immunosorbent assays (ELISAs) using recombinant Dsg1 and Dsg3 expressed by baculovirus as a diagnostic tool for pemphigus. The purpose of this study was to evaluate the practical application of these ELISAs for clinical use with a large number of serum samples. We used 81 PV sera, 48 PF sera, 114 bullous pemphigoid (BP) sera, 124 collagen disease sera, nine sera of other non-pemphigus bullous diseases and 179 normal control sera. A cut-off value was determined by receiver-operating-characteristic plots. Forty-seven of 48 PF sera (97.9%) were positive in the Dsg1 ELISA and 79 of 81 PV sera (97.5%) were positive in the Dsg3 ELISA, while only two (1. 1%) and four (2.2%) of 179 normal sera were positive in Dsg1 and Dsg3 ELISAs, respectively. However, some disease control sera of BP and collagen diseases exceeded the cut-off value. Introduction of a grey zone helped to decrease the number of these false-positive sera. Furthermore, in three patients studied, the respective Dsg1 and Dsg3 ELISA scores showed parallel fluctuation with the disease activity along the time course. We conclude that Dsg1 and Dsg3 ELISAs provide a simple, sensitive and highly specific assay for the diagnosis of patients with PV and PF and that these ELISAs may be a valuable tool to monitor the disease activity. We also propose diagnostic criteria for pemphigus based on ELISA reactivity: if a serum is positive against Dsg3 it indicates a diagnosis of PV, regardless of reactivity against Dsg1; if a serum is negative for Dsg3 and positive for Dsg1, it indicates a diagnosis of PF.
The Smart Party: A Personalized Location-Aware Multimedia Experience (2008)

The Smart Party is a new ubiquitous computing application for the home environment. This application gathers musical preferences for guests located in different rooms of a user's house. Based on their preferences and available media, the application chooses a music play list for each room, adjusting to changing membership as guests move through the party. We describe the application, its architecture, and our implementation, including key performance characteristics.
In-Cylinder Measurement of Combustion Characteristics Using Ionization Sensors (1986)

<div class="htmlview paragraph">This paper documents the results of an engine dynamometer study into the use of in-cylinder ionization probes on a 1.6L EFI engine. The objective of the investigation was to determine if there is sufficient correlation between ionization probe information and other combustion parameters to allow use of the ionization probe as a sensing element as part of a direct feedback control system to control engine air-fuel ratio and/or spark timing. Specific emphasis was placed on determining performance at lean air-fuel ratios with the goal of controlling the engine near the lean limit of operation. Use of the spark plug as an ionization sensor was also investigated.</div>
Mutations in hamster single-strand break repair gene XRCC1 causing defective DNA repair (1998)

The molecular basis for the DNA repair dysfunction observed in mutant Chinese hamster ovary cell lines of X-ray repair cross complementing group 1 (XRCC1) is unknown and the exact role of the XRCC1 protein remains unclear. To help clarify the role of the XRCC1 gene we analyzed four mutant cell lines of this complementation group and a revertant cell line for XRCC1 protein content and for sequence alterations in the XRCC1 coding region. Immunoblot analysis of cellular extracts indicated that each of four mutant lines was lacking XRCC1 protein, whereas the repair-proficient revertant line derived from one of these mutants contained a normal level of XRCC1. Although each of these cell lines expressed XRCC1 mRNA, we found in all cases a distinct point mutation resulting in crucial alterations in the encoded XRCC1 protein sequence of 633 amino acids. Two of the mutations cause non-conservative amino acid changes, Glu102-->Lys and Cys390-->Tyr, at positions that are invariant among hamster, mouse and human XRCC1 sequences and are located in putative functional domains. A third debilitating mutation disrupts RNA splicing, generating multiple transcripts of different length that contain deletions spanning a region of >100 amino acids in the midsection of the XRCC1 coding sequence. A fourth mutation results in a termination codon that shortens the open reading frame to 220 amino acids, however, in the revertant cell line a further mutation in the same codon, Stop221-->Leu, permits translation of a full-length functional variant protein. These mutational data indicate the importance of the putative functional regions in XRCC1, such as the BRCA1 C-terminal (BRCT) domain found in common with BRCA1 and other DNA repair and cell cycle checkpoint proteins, and also regions necessary for interaction with DNA polymerase beta and DNA ligase III.
ICCI: In-Cache Coherence Information (2014)

In this paper we introduce ICCI, a new cache organization that leverages shared cache resources and flat coherence protocols to provide inexpensive hardware cache coherence for large core counts (e.g., 512), achieving execution times close to a non-scalable sparse directory while noticeably reducing the energy consumption of the memory system. Very simple changes in the system with respect to traditional bit-vector directories are enough to implement ICCI. Moreover, ICCI does not introduce any storage overhead with respect to a broadcast-based protocol, yet it provides large storage space for coherence information. ICCI makes smarter use of cache resources by dynamically allowing last-level cache entries to store blocks or sharing codes. This way, just the minimum number of directory entries required at runtime are allocated. Besides, ICCI suffers a negligible amount of directory-induced invalidations. Results for a 512-core CMP show that ICCI reduces the energy consumption of the memory system by up to 48 percent compared to a tag-embedded directory, up to 15 percent compared to a sparse directory, and up to 8 percent compared to the state-of-the-art Scalable Coherence Directory which ICCI also outperforms in execution time. In addition, ICCI can be used in combination with elaborated sharing codes to apply it to extremely large core counts. We also show analytically that ICCI’s dynamic allocation of entries makes it a suitable candidate to store coherence information efficiently for very large core counts (e.g., over 200K cores), based on the observation that data sharing makes fewer directory entries necessary per core as core count increases.
A generalized biometric identification system model (2002)

Commonly-held knowledge and oft-repeated descriptions of biometric identification systems are more complicated than necessary because of the lack of a generally accepted system model. A good example is the supposed difference between "identification" and "verification". We present a system model applicable to all biometric systems showing the relationship between "verification" and "identification" and "enrollment" and "operation", illustrating where commonalities exist between seemingly disparate systems, and suggesting where interface standards might be useful. Further, we develop a general mathematical formulation to show "verification" to be the degenerate case of M-to-N matching, with N=1. Similarly, "PIN-less verification" is recognized as the degenerate case with small N with M=1, and "identification" can be seen as the more general case with small M and large N.
Virtual view face image synthesis using 3D spring-based face model from a single image (2002)

It is known that 2D views of a person can be synthesised if the face 3D model of that person is available. This paper proposes a new method, called 3D spring-based face model (SBFM), to determine the precise face model of a person with different poses and facial expressions from a single image. The SBFM combines the concepts of generic 3D face model in computer graphics and deformable template in computer vision. Face image databases from MIT AI laboratory and Yale University are used to test our proposed method and the results are encouraging.
Statistical applications of wavelets on time series (1996)

This thesis deals with the applications of wavelet theory to time series data. We first focus on stationary times series. For dependent observations forming a stationary time series, we study the autocovariance or autocorrelation structure of wavelet coefficients at each level of the discrete wavelet decomposition of the data. We show how the variance and autocovariance of wavelet coefficients differ across each level of the wavelet decompositon structure for correlated time series. Thus the thresholds for the wavelet shrinkage method proposed by Donoho and Johnstone should be level dependent. We show how the autocovariance of wavelet coefficients on a given level can be exactly derived from those on the previous level. The sum of the autocovariances of scaling coefficients and wavelet coefficients for a given level and a given lag is twice the autocovariance of scaling coefficients at the previous level at twice the lag. We provide a pair of two-level formulae, an algorithm, and a list of coefficients to perform the calculation. We show that the theory we develop in time domain has a nice counterpart in the frequency domain. In one application, we apply the wavelet filters to estimate the power spectrum of a time series from a sinusoidal model. In another application, we use the cumulative sum of squares (CUSUM) of the first level wavelet coefficients to detect multiple change of variances of a time series. Next, we study nonparametric regression with heteroscedastic time series. We use a two step method to estimate the nonconstant variances. In the first step, a weighted local average in quadratic form is used and the estimated variances are local but noisy. In the second step, wavelet nonparametric regression is used to smooth the estimated variance obtained in the first step. We assume that the observations obtained in the first step are $\phi$-mixing and stationary.
Endogenous Retinoids in Mammalian Growth Plate Cartilage (2010)

The growth plate contains resting and proliferating chondrocytes in its upper zones (UGP) and maturing and hypertrophic chondrocytes in its lower zones (LGP), but the mechanisms by which it operates to sustain skeletal growth are not fully clear. Retinoid signaling was previously found to be nearly absent in UGP, but to be much stronger in LGP coincident with hypertrophy, extracellular matrix turnover and endochondral bone formation. To determine whether such distinct signaling levels and phenotypic events reflect different endogenous retinoid levels, the upper two-thirds and lower one-third of rabbit rib growth plates were microsurgically isolated and processed for ultrasensitive retinoid LC-tandem MS quantification. Indeed, the UGP samples contained only about a 0.6 nm concentration of all-trans-retinoic acid (atRA) that is the most active natural retinoid in tissues, whereas LGP samples contained nearly 3-fold higher atRA levels (about 1.8 nM). Perichondrium was quite rich in atRA (about 4.9 nM). Interestingly, the levels of retinol, the major but inactive atRA precursor, were similar in all tissues (1.1-1.6 μM), suggesting that the distinct atRA levels in UGP and LGP reflect different retinoid anabolic capacity. Indeed, RALDH2 and CRABP1 transcript levels were much higher in LGP than UGP samples. To determine the minimum effective atRA concentration, chondrogenic cells transfected with a retinoic acid response element (RARE)-luc reporter plasmid were treated with different concentrations of exogenous atRA (0-100 nM). About 3 nm atRA was needed to elicit appreciable RARE-luc reporter activity and to decrease proteoglycan synthesis and activity of an aggrecan enhancer reporter plasmid. In sum, the data indicate that (i) the endogenous levels of atRA are significantly higher in hypertrophic than upper zones of growth plate; (ii) such difference likely reflects distinct retinoid anabolic capacity; and (iii) importantly, atRA levels in hypertrophic portion are within effective ranges to elicit retinoid signaling and action, but those in upper zones are not.
Input selection for fast feature engineering (2016)

The application of machine learning to large datasets has become a vital component of many important and sophisticated software systems built today. Such trained systems are often based on supervised learning tasks that require features, signals extracted from the data that distill complicated raw data objects into a small number of salient values. A trained system's success depends substantially on the quality of its features. Unfortunately, feature engineering—the process of writing code that takes raw data objects as input and outputs feature vectors suitable for a machine learning algorithm—is a tedious, time-consuming experience. Because “big data” inputs are so diverse, feature engineering is often a trial-and-error process requiring many small, iterative code changes. Because the inputs are so large, each code change can involve a time-consuming data processing task (over each page in a Web crawl, for example). We introduce Zombie, a data-centric system that accelerates feature engineering through intelligent input selection, optimizing the “inner loop” of the feature engineering process. Our system yields feature evaluation speedups of up to 8× in some cases and reduces engineer wait times from 8 to 5 hours in others.
Distributed and retinotopically asymmetric processing of coherent motion in mouse visual cortex (2020)

Perception of visual motion is important for a range of ethological behaviors in mammals. In primates, specific visual cortical regions are specialized for processing of coherent visual motion. However, whether mouse visual cortex has a similar organization remains unclear, despite powerful genetic tools available for measuring population neural activity. Here, we use widefield and 2-photon calcium imaging of transgenic mice to measure mesoscale and cellular responses to coherent motion. Imaging of primary visual cortex (V1) and higher visual areas (HVAs) during presentation of natural movies and random dot kinematograms (RDKs) reveals varied responsiveness to coherent motion, with stronger responses in dorsal stream areas compared to ventral stream areas. Moreover, there is considerable anisotropy within visual areas, such that neurons representing the lower visual field are more responsive to coherent motion. These results indicate that processing of visual motion in mouse cortex is distributed heterogeneously both across and within visual areas.
Antiviral Activities and Putative Identification of Compounds in Microbial Extracts from the Hawaiian Coastal Waters (2012)

Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1), vesicular stomatitis virus (VSV), vaccinia virus and poliovirus type one (poliovirus-1) using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H),17α(H),(20R)-beta-acetoxyergost-8(14)-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies.
Adenosine triphosphate-dependent transport of doxorubicin, daunomycin, and vinblastine in human tissues by a mechanism distinct from the P-glycoprotein. (1994)

Previous studies have demonstrated that a human glutathione conjugate transporter, designated as dinitrophenyl-S-glutathione ATPase (DNP-SG ATPase), catalyzed ATP hydrolysis in the presence of several amphiphilic compounds other than glutathione conjugates (Singhal, S. S., R. Sharma, S. Gupta, H. Ahmad, P. Zimniak, A. Radominska, R. Lester, and Y. C. Awasthi. 1991. FEBS [Fed. Eur. Biochem. Soc.] Lett. 281:255-257). We now demonstrate that DNP-SG ATPase purified from human lung and erythrocyte membranes catalyzed the hydrolysis of ATP in the presence of doxorubicin and its metabolites. Doxorubicin-stimulated ATP hydrolysis by DNP-SG ATPase was saturable with respect to doxorubicin (Km 1.2 and 2.8 microM for the lung and erythrocyte enzymes, respectively). Antibodies against DNP-SG ATPase immunoprecipitated the ATP hydrolyzing activity stimulated by doxorubicin, its metabolites, and glutathione conjugates. Inside our vesicles prepared from erythrocyte membranes took up doxorubicin, daunomycin, and vinblastine in an ATP-dependent manner. The uptake was linear with respect to time and vesicle protein, was dependent on ATP and magnesium, was inhibited by heavy metal salts or by heating the vesicles, and was sensitive to both osmolarity and orientation of the vesicles. The transport had an activation energy of 13 kcal/mol, was saturable with respect to both doxorubicin and ATP (Km values of 1.8 microM and 1.9 mM, respectively), and was competitively inhibited by glutathione conjugates as well as by a number of amphiphiles such as daunomycin or vinblastine. Transport was diminished upon coating the vesicles with antibodies against DNP-SG ATPase. Incorporation of increasing amounts of purified DNP-SG ATPase into the vesicles resulted in a linear increase in transport of doxorubicin. These studies demonstrated for the first time that a membrane protein that catalyzed the transport of anionic amphiphilic molecules such as glutathione conjugates could also mediate the transport of weakly cationic antitumor antibiotic, doxorubicin. Notably, the Km of transport was in the range of doxorubicin concentration achievable in human serum after intravenous dosing of doxorubicin.
POCS-based error concealment for packet video using multiframe overlap information (1998)

This paper proposes a new error concealment algorithm for packet video, effectively eliminating error propagation effects. Most standard video codecs use motion compensation to remove temporal redundancy. With such motion-compensated interframe processing, any packet loss may generate serious error propagation over more than ten consecutive frames. This kind of error propagation leads to perceptually annoying artifacts. Thus, proper error concealment algorithms need to be used to reduce this effect. The proposed algorithm adopts a one-pixel block overlap structure. With the redundancy information from the damaged frame and the following frames, the proposed POCS-based method can have consistently high performance in error concealment. According to the experimental results, the proposed algorithm can successfully eliminate visible error propagation. In addition, the proposed algorithm is very robust. Experimental results show that it can have good error concealment results, even when the damaged frame loses all the DCT coefficients.
Photosynthesis-deficient Mutants of <i>Chlamydomonas reinhardii</i> with Associated Light-sensitive Phenotypes (1981)

A series of non-photoautotrophic mutants of Chlamydomonas reinhardii was isolated by replica-plating mutagenized cells which had been grown in the dark. Many of these acetate-requiring mutants are photosensitive, showing poor growth on acetate medium in the light, but normal growth in the dark. Biochemical characterization showed that the photosensitive mutants all had specific lesions in photosynthesis or photosynthetic pigment accumulation. The acetate-requiring mutants which were not photosensitive were all able to fix CO(2). Among the light-sensitive mutants are 15 which show uniparental inheritance. These include six with specific lesions in photosystem II and one with an altered large subunit of ribulose-1,5-bisphosphate carboxylase. Since these two classes of uniparental mutants have been rare or not previously reported, it seems likely that photosensitivity is an important factor which limited their detection in previous mutant isolation experiments.
Enhanced Electroluminescence Efficiency in a Spiro‐Acridine Derivative through Thermally Activated Delayed Fluorescence (2012)

Fluoreszierend: Ein auf einem Spiroacridin-Derivat basierendes Molekül (siehe Bild) wurde synthetisiert, und seine Photo-und Elektrolumineszenz wurden untersucht. Durch Kombination der Donor- und Akzeptoreinheiten wurde eine kleine Energielücke zwischen den niedrigsten Singulett- und Triplettzuständen erhalten. Das Design führte zu einer organischen Leuchtdiode, die bezüglich der Effizienz der Exciton-Erzeugung mit phosphoreszierenden Bauteilen konkurriert.
PERFORMANCE EVALUATION AND ECONOMIC ANALYSIS OF COMBINATIONS OF DURABILITY ENHANCING ADMIXTURES (MINERAL AND CHEMICAL) IN STRUCTURAL CONCRETE FOR THE NORTHEAST U.S.A. (2003)

The performance of single, double, and triple combinations of corrosion preventing admixtures was investigated. An extensive literature review, a survey of New England States mix design procedures, and 108 weeks of accelerated corrosion study results are presented. The experimental study included slab specimens subjected to severe salt water ponding conditions to evaluate the corrosion inhibiting performance of each mix design. Both non-cracked and precracked specimens were evaluated for fourteen mix designs (42 specimens). Admixtures studied were: calcium nitrite, silica fume, fly ash, ground blast furnace slag, and DSS (referred to as disodium tetrapropenyl succinate). Corrosion was monitored through half-cell and macrocell potential readings, visual observation, and autopsies of specimens at the end of testing. Based on these results, mix designs including a triple combination of calcium nitrite, silica fume, and fly ash, or a double combination of calcium nitrite and slag, are currently recommended. DSS alone or in combination with calcium nitrite provided the best performance of all mixes studied, but requires further study prior to widespread acceptance.