gebhart/patrepeval huggingface dataset:
Rank-order polynomial subband decomposition for medical image compression (2000)

In this paper, the problem of progressive lossless image coding is addressed. A nonlinear decomposition for progressive lossless compression is presented. The decomposition into subbands is called rank-order polynomial decomposition (ROPD) according to the polynomial prediction models used. The decomposition method presented here is a further development and generalization of the morphological subband decomposition (MSD) introduced earlier by the same research group. It is shown that ROPD provides similar or slightly better results than the compared coding schemes such as the codec based on set partitioning in hierarchical trees (SPIHT) and the codec based on wavelet/trellis-coded quantization (WTCQ). Our proposed method highly outperforms the standard JPEG. The proposed lossless compression scheme has the functionality of having a completely embedded bit stream, which allows for data browsing. It is shown that the ROPD has a better lossless rate than the MSD but it has also a much better browsing quality when only a part of the bit stream is decompressed. Finally, the possibility of hybrid lossy/lossless compression is presented using ultrasound images. As with other compression algorithms, considerable gain can be obtained if only the regions of interest are compressed losslessly.
Engineering of a mammalian O-glycosylation pathway in the yeast Saccharomyces cerevisiae: production of O-fucosylated epidermal growth factor domains (2008)

Development of a heterologous system for the production of homogeneous sugar structures has the potential to elucidate structure-function relationships of glycoproteins. In the current study, we used an artificial O-glycosylation pathway to produce an O-fucosylated epidermal growth factor (EGF) domain in Saccharomyces cerevisiae. The in vivo O-fucosylation system was constructed via expression of genes that encode protein O-fucosyltransferase 1 and the EGF domain, along with genes whose protein products convert cytoplasmic GDP-mannose to GDP-fucose. This system allowed identification of an endogenous ability of S. cerevisiae to transport GDP-fucose. Moreover, expression of EGF domain mutants in this system revealed the different contribution of three disulfide bonds to in vivo O-fucosylation. In addition, lectin blotting revealed differences in the ability of fucose-specific lectin to bind the O-fucosylated structure of EGF domains from human factors VII and IX. Further introduction of the human fringe gene into yeast equipped with the in vivo O-fucosylation system facilitated the addition of N-acetylglucosamine to the EGF domain from factor IX but not from factor VII. The results suggest that engineering of an O-fucosylation system in yeast provides a powerful tool for producing proteins with homogenous carbohydrate chains. Such proteins can be used for the analysis of substrate specificity and the production of antibodies that recognize O-glycosylated EGF domains.
The role of protein phosphorylation and cytoskeletal reorganization in microparticle formation from the platelet plasma membrane (1994)

Platelets activated by various agonists produce vesicles (microparticles; MPs) from the plasma membrane. However, the mechanism of this MP formation remains to be elucidated. To investigate the possible involvement of protein phosphorylation and cytoskeletal reorganization in MP formation, the effects of various inhibitors on MP formation were investigated. Flow cytometry was employed to detect the amount of MP formation by using monoclonal antibodies against glycoprotein (GP) IIb-IIIa (NNKY 1-32) or GPIIb (Tab). The relationship between changes in cytoskeletal architecture and MP formation in the platelets activated by thrombin plus collagen was observed by scanning electron microscopy (SEM). MPs were observed in the vicinity of the terminals of pseudopods, suggesting that MPs may be related by budding of the pseudopods. Cytochalasin D (10 microM) inhibited MP formation from the activated platelets almost completely. Moreover, SEM of the cytochalasin D-treated platelets revealed the absence of shape change, pseudopod formation and MPs. These findings suggest that cytoskeletal reorganization is necessary for MP formation. Since cytoskeletal reorganization is considered to be regulated by a dynamic phosphorylation-dephosphorylation process, we investigated the effects of the protein phosphatase inhibitors, calyculin A (CLA) and okadaic acid (OA), on MP formation. Flow cytometry showed that these two inhibitors doubled MP formation in activated platelets. SEM of the platelets treated with CLA or OA demonstrated more prominent shape change and pseudopod formation in these platelets than in those without inhibitor. From these results, we conclude that cytoskeletal reorganization, which is controlled by phosphorylation, is involved in MP formation.
Novel Hybrid Conjugates with Dual Suppression of Estrogenic and Inflammatory Activities Display Significantly Improved Potency against Breast Cancer (2018)

In this work, we developed a small library of novel OBHS-RES hybrid compounds with dual inhibition activities targeting both the estrogen receptor α (ERα) and NF-κB by incorporating resveratrol (RES), a known inhibitor of NF-κB, into a privileged indirect antagonism structural motif (OBHS, oxabicycloheptene sulfonate) of estrogen receptor (ER). The OBHS-RES conjugates could bind well to ER and showed remarkable ERα antagonistic activity, and they also exhibited excellent NO inhibition in macrophage RAW 264.7 cells. Compared with 4-hydroxytamoxifen, some of them showed better antiproliferative efficacy in MCF-7 cell lines with IC<sub>50</sub> up to 3.7 μM. In vivo experiments in a MCF-7 breast cancer model in Balb/c nude mice indicated that compound 26a was more potent than tamoxifen. Exploration of the compliancy of the structure against ER specificity utilizing these types of isomeric three-dimensional ligands indicated that one enantiomer had much better biological activity than the other.
Extending the Multidimensional Data Model to Handle Complex Data (2007)

Data Warehousing and OLAP (On-Line Analytical Processing) have turned into the key technology for comprehensive data analysis. Originally developed for the needs of decision support in business, data warehouses have proven to be an adequate solution for a variety of non-business applications and domains, such as government, research, and medicine. Analytical power of the OLAP technology comes from its underlying multidimensional data model, which allows users to see data from different perspectives. However, this model displays a number of deficiencies when applied to non-conventional scenarios and analysis tasks. This paper presents an attempt to systematically summarize various extensions of the original multidimensional data model that have been proposed by researchers and practitioners in the recent years. Presented concepts are arranged into a formal classification consisting of fact types, factual and fact-dimensional relationships, and dimension types, supplied with explanatory examples from real-world usage scenarios. Both the static elements of the model, such as types of fact and dimension hierarchy schemes, and dynamic features, such as support for advanced operators and derived elements. We also propose a semantically rich graphical notation called X-DFM that extends the popular Dimensional Fact Model by refining and modifying the set of constructs as to make it coherent with the formal model. An evaluation of our framework against a set of common modeling requirements summarizes the contribution.
Compute-and-Forward: Error-Correcting Codes for Wireless Network Coding on the Physical Layer (2008)

By exploiting properties of the wireless medium, network coding may provide even larger throughput increases for wireless networks than possible for wired networks. In particular, simultaneously transmitted signals are seen as noisy linear combinations at the antennas of receivers. It is thus quite tempting to use the physical layer to directly perform network coding "on the air". However, classical communication schemes are ill-suited for carrying out these distributed computations and uncoded transmission accumulates noise with multiple transmissions. In previous work, we have developed a coding technique, computation codes, for reliable, efficient computation over noisy channels. We have also demonstrated how to use these codes to run a network code on finite-field and Gaussian multiple-access networks. In this note, we survey our recent work on reliable computation over channels and show how it can be applied to perform network coding.
Fluorescence enhancement of asCP595 is due to consecutive absorbance of two photons (2004)

Colored proteins are widely used as gene markers in biotechnology. Chromophores result from autocatalytic posttranslational reactions involving several amino acids. The protein asCP595 was isolated for the first time from the coral as a weakly fluorescent chromoprotein with a fluorescence maximum at 595 nm. Strong illumination in the blue wing of the low energy absorption band results in a superlinear increase of the fluorescence yield and shifts its fluorescence spectrum by about 10 nm to the red. Time resolved fluorescence measurements using excitation pulses with 10 ps duration revealed a multiexponential decay pattern with time constants in the range from 20 ps to 2.1 ns. The ratio of amplitudes related to the different time constants depends on the intensity of illumination favoring the ns component at high intensities. Transient absorption measurements using ultrashort excitation pulses (150 fs, 1 kHz repetition rate) did not reveal excited states with nanosecond lifetimes as observed in fluorescence upon excitation using 10 ps pulses. This observation leads to the notion that within 10 ps a second photon is absorbed by a state not yet populated within 150 fs. As a consequence we propose two different excited singlet states operative in asCP595, one with low fluorescence quantum yield peaking at 595 nm and one with high fluorescence quantum yield peaking at 605 nm which is populated via the consecutive absorption of two photons at high excitation intensities.
Synthesis of Terpenyl β-D-Glucopyranosides from Terpene Alcohols and Tetra-O-acetyl-α-D-glucopyranosyl Bromide with Silver Carbonate Supported on Silica Gel (1994)

Terpenyl β-D-glucopyranosides (3 a-e) were prepared from terpene alcohols (2 a-e) and tetra-O-acetyl-a-u-glucopyranosyl bromide (1) by a modification of Koenigs-Knorr procedure in the presence of silver carbonate supported on silica gel or alumina, followed by deacetylation. In this study terpenyl β-D-glucopyranosides (3 a-e) were obtained from geraniol (2 a), nerol (2 b), citronellol (2 c), cis-3-hexenol (2 d), menthol (2 e) and all-trans-retinol (2 f) in relatively good yields. All-trans-retinyl β-D-glucuronide (5) was prepared in a similar manner from methyl 2, 3, 4-triacetyl-1-bromo-D-glucuronate (4) and all-trans-retinol (2 f) in 28% yield
Depth image based gait tracking and analysis via robotic walker (2015)

In this paper, we propose a gait tracking and analysis method using a depth image sensor installed on robotic walker. Nowadays, robotic walker not only can assist elders who have suffered deteriorating mobility but also help to provide rehabilitating function to people who have crippled walking ability. This approach is meant to be sufficiently accurate, non-intrusive, and low-cost. The goal of this research is to enable the robotic walker to become more active in terms of walker control and comfortable user experiences thorough gait analysis. In experiment, the accuracy of the proposed 3D leg pose tracking method was evaluated by a motion capture system and the result is quite promising. After actual trials, the proposed method has the potential to be used in a safer and more reliable application such as those assisting elders and specific group of patient subjects.
Why do arms extract less oxygen than legs during exercise? (2005)

To determine whether conditions for O2 utilization and O2 off-loading from the hemoglobin are different in exercising arms and legs, six cross-country skiers participated in this study. Femoral and subclavian vein blood flow and gases were determined during skiing on a treadmill at approximately 76% maximal O2 uptake (V(O2)max) and at V(O2)max with different techniques: diagonal stride (combined arm and leg exercise), double poling (predominantly arm exercise), and leg skiing (predominantly leg exercise). The percentage of O2 extraction was always higher for the legs than for the arms. At maximal exercise (diagonal stride), the corresponding mean values were 93 and 85% (n = 3; P < 0.05). During exercise, mean arm O2 extraction correlated with the P(O2) value that causes hemoglobin to be 50% saturated (P50: r = 0.93, P < 0.05), but for a given value of P50, O2 extraction was always higher in the legs than in the arms. Mean capillary muscle O2 conductance of the arm during double poling was 14.5 (SD 2.6) ml.min(-1).mmHg(-1), and mean capillary P(O2) was 47.7 (SD 2.6) mmHg. Corresponding values for the legs during maximal exercise were 48.3 (SD 13.0) ml.min(-1).mmHg(-1) and 33.8 (SD 2.6) mmHg, respectively. Because conditions for O2 off-loading from the hemoglobin are similar in leg and arm muscles, the observed differences in maximal arm and leg O2 extraction should be attributed to other factors, such as a higher heterogeneity in blood flow distribution, shorter mean transit time, smaller diffusing area, and larger diffusing distance, in arms than in legs.
Gaseous products from the reaction of XeF2 with silicon (1983)

XeF2 was reacted with silicon, and the gaseous products were detected using modulation techniques which made the experiments sensitive only to products which had not collided with a wall. In agreement with previous experiments, SiF4 was found to be the major reaction product. Radicals such as SiF and SiF2 were observed at a much lower level. However, SiF2 was not found to be the dominant species as might have been suspected on the basis of experiments by other workers with atomic fluorine. Bombardment with 2000-eV argon ions enhanced the rate of product formation and decreased the fraction of the products that was SiF4. Production of radical species, in particular SiF2, was enhanced. Collisions of SiF2 with fluorinated, stainless-steel vacuum chamber walls were investigated in order to determine whether the SiF2 radical was converted to SiF4 as suggested by others. Wall reactions were found to be important in some circumstances and not important in others.
The probiotic bacterium Lactobacillus plantarum species 299 reduces intestinal permeability in experimental biliary obstruction (2005)

This study provides insight to direct further work into the modulation of intestinal barrier function by probiotic bacteria.
Synthesis of optically active teleocidins B-3 and B-4. (1989)

The potent tumor promoters, optically active teleocidins B-3 (3) and B-4 (4), were totally synthesized mostly using our synthetic pathway for the teleocidin A series. The key reaction, the BF3·Et2 O-catalyzed intramolecular Friedel-Crafts cyclization, was applied at the final stage of the synthesis to the acetates (18a and 18b) to form the teleocidin B framework.
Determination of the in-plane elastic tensor of crystalline decanol monolayers on water by x-ray diffraction (1997)

We show how high-resolution x-ray studies associated with surface tension measurements allow a determination of the elastic constants of crystalline 1-decanol monolayers at the water-air interface. The shape and position of the power-law diffraction peak yield, respectively, the shear and compression elastic constants. At low temperature, rotation scans of the liquid surface around a vertical axis exhibit six sharp peaks, proving the existence of the long-range order of bond orientations, as expected for a hexagonal two-dimensional (2D) crystal. We find a shear elastic constant of (210\ifmmode\pm\else\textpm\fi{}30) mN/m and a compression modulus of (2500\ifmmode\pm\else\textpm\fi{}500) mN/m. These values are compatible with the existence of a 2D solid, according to the Nelson-Halperin melting theory. Between \ensuremath{\sim}12 \ifmmode^\circ\else\textdegree\fi{}C and melting (${\mathrm{T}}_{\mathrm{m}}$=14.3 \ifmmode^\circ\else\textdegree\fi{}C), the drastic broadening of the diffraction line can be interpreted either as the occurrence of a hexatic phase or as a strong decrease of the shear modulus, as expected in the framework of the weak crystallization theory.
Microvascular architecture of experimental colon tumors in the rat. (1990)

Tumor cell proliferation is dependent upon concurrent growth of a supporting vasculature. This study aims to characterize the structural features of the microvasculature within a primary tumor model. There were 22 colon tumors induced in 16 rats by repeated administration of dimethylhydrazine. A cast of the microvessels was prepared by intraarterial administration of acrylic resin (Mercox). After corrosion of the tissue, the cast was examined by scanning electron microscopy. Tumors 2.6 to 12.0 mm in diameter were examined. Within polypoid carcinomas up to 5.7 mm in diameter, there were two distinct vascular zones, a luminal vascular zone continuous with the vasculature of normal mucosa and a central zone continuous with the normal submucosa and muscularis propria vessels. Within both vascular zones, the organization of microvessels had the same general pattern as in normal mucosa. However, in tumors with diameters greater than 5.7 mm, the vasculature was seen to be disorganized and of a greater density than normal. In the smallest tumors, few morphological changes were seen in the individual microvessels when compared to normal. However, with tumor growth, there was elongation and increased diameters of the microvessels within the tumor. Microvessels within the luminal zone of the tumors which could definitely be traced to veins had diameters of 50 to 100 microns (compared to 12 to 30 microns for normal venules). Individual microvessels varied in diameter along their course forming saccular dilations in places. Networks of frequently anastomosing microvessels were formed. Extravasation of resin occurred from some microvessels. Elongated vessels of uniform diameter which travel distances up to 2 mm without branching were seen and were probably arterioles. These appearances indicate that there are two distinct stages of development of the vasculature within primary tumors, an early phase where the tumor is supplied by the preexisting host microvessels, followed by a phase of proliferation of new vessels with abnormal morphological characteristics.
Decline Curve Analysis Using Type Curves — Evaluation of Well Performance Behavior in a Multiwell Reservoir System (2001)

Abstract In this paper we present a new multiwell reservoir solution and an associated analysis methodology to analyze single well performance data in a multiwell reservoir system. The key to this approach is the use of FIELD cumulative production data and individual well flowrate and pressure data. Our new solution and analysis methodology "couples" the single well and multiwell reservoir models — and permits the estimation of total reservoir volume and flow properties within the drainage area of an individual well — where the analysis is performed using a SINGLE WELL reservoir model (type curve). This "multiwell analysis" using a "single well model" is made possible by a "coupling" of the single well and multiwell solutions based on a total material balance of the system. The data required for this approach are readily available in practice: basic reservoir properties, fluid properties, well completion data, and well rate (and pressure) data and cumulative production data for the entire field. Currently, ALL existing decline type curve analyses assume a single well in closed system (or single well with constant pressure or prescribed influx at outer boundary). In many cases a well produces in association with other wells in the same reservoir — and unless all wells are produced at the same constant rate or the same constant bottomhole flowing pressure, non-uniform drainage systems will form during boundary-dominated flow conditions. Further, it is well established that new wells "steal" reserves from older wells, and this behavior is commonly observed in the production behavior. Our new approach accounts for the ENTIRE production history of the well and the reservoir, and eliminates the influence of "well interference" effects. This approach provides much better estimates of the in-place fluids in a multiwell system, AND the methodology also provides a consistent and straightforward analysis of production data where "well interference" effects are observed. This work provides the following deliverables: A new solution for a multiwell reservoir where the formulation of this solution yields a simplified form for an arbitrary (individual) well during boundary-dominated flow conditions. A complete analysis methodology for oil and gas reservoir systems based on conventional production data (on a per well basis) as well as the cumulative production of the entire field. A systematic validation of this approach using a numerical reservoir simulator for cases of homogeneous, regionally heterogeneous, and randomly heterogeneous reservoirs. An application to a large gas field (Arun Field, Indonesia). This analysis provides very consistent estimates of in-place fluids and reservoir properties. All of these analyses (simulated and field data) clearly demonstrate that the effects of "well interference" on individual wells have been eliminated as a result of this analysis methodology.
Overproduction, purification and characterization of FgaPT2, a dimethylallyltryptophan synthase from Aspergillus fumigatus (2005)

A putative dimethylallyltryptophan synthase gene, fgaPT2, was identified in the genome sequence of Aspergillus fumigatus. fgaPT2 was cloned and overexpressed in Saccharomyces cerevisiae. The protein FgaPT2 was purified to near homogeneity and characterized biochemically. This enzyme was found to convert L-tryptophan to 4-dimethylallyltryptophan, a reaction known to be the first step in ergot alkaloid biosynthesis. FgaPT2 is a soluble, dimeric protein with a subunit size of 52 kDa, and contains no putative prenyl diphosphate binding site (N/D)DXXD. Km values for L-tryptophan and dimethylallyl diphosphate (DMAPP) were determined as 8 and 4 microM, respectively. Metal ions, such as Mg2+ and Ca2+, enhance the reaction velocity, but are not essential for the enzymic reaction. FgaPT2 showed a relatively strict substrate specificity for both tryptophan and DMAPP. FgaPT2 is the first enzyme in the biosynthesis of ergot alkaloids to be purified and characterized in homogeneous form after heterologous overproduction.