gebhart/patrepeval huggingface dataset:
Osteopontin: An intrinsic inhibitor of inflammation in cartilage (2001)

The data indicate that one of the functions of intraarticular OPN, which is overexpressed in OA cartilage, is to act as an innate inhibitor of IL-1, NO, and PGE2 production. These findings suggest that the production of pleiotropic mediators of inflammation that influence cartilage homeostasis, such as NO and PGE2, is regulated by the interaction of chondrocytes with differentially expressed proteins within the extracellular matrix.
Multi-view face detection using support vector machines and eigenspace modelling (2002)

An approach to multi-view face detection based on head pose estimation is presented in this paper. Support vector regression is employed to solve the problem of pose estimation. Three methods, the eigenface method the support vector machine (SVM) based method, and a combination of the two methods, are investigated. The eigenface method, which seeks to estimate the overall probability distribution of patterns to be recognised, is fast but less accurate because of the overlap of confidence distributions between face and non-face classes. On the other hand, the SVM method, which tries to model the boundary of two classes to be classified is more accurate but slower as the number of support vectors is normally large. The combined method can achieve an improved performance by speeding up the computation and keeping the accuracy to a preset level. It can be used to automatically detect and track faces in face verification and identification systems.
Processivity of the DNA helicase activity of Escherichia coli recBCD enzyme. (1992)

A fluorescence assay was used to measure the processivity of Escherichia coli recBCD enzyme helicase activity. Under standard conditions, recBCD enzyme unwinds an average of 30 +/- 3.2 kilobase pairs (kb)/DNA end before dissociating. The average processivity (P obs) of DNA unwinding under these conditions is 0.99997, indicating that the probability of unwinding another base pair is 30,000-fold greater than the probability of dissociating from the double-stranded DNA. The average number of base pairs unwound per binding event (N) is sensitive to both mono- and divalent salt concentration and ranges from 36 kb at 80 mM NaCl to 15 kb at 280 mM NaCl. The processivity of unwinding increases in a hyperbolic manner with increasing ATP concentration, yielding a KN value for ATP of 41 +/- 9 microM and a limiting value of 32 +/- 1.8 kb/end for the number of base pairs unwound. The importance of the processivity of recBCD enzyme helicase activity to the recBCD enzyme-dependent stimulation of recombination at Chi sites observed in vivo is discussed.
Immunochemical Study of Human Immunoglobulin G Fc Region (1996)

Fifteen murine monoclonal antibodies (mAb) were produced that reacted with conformational epitopes present on the Fc portion of all human IgG subclasses (PAN-Fc). Inhibition and sandwich ELISA were used to elucidate overlapping and distinct epitopes. The epitopes were aligned to form a continuous "chain" of overlapping determinants from the CH2-CH3 interface to the direction of hinge. The five more hinge-proximal epitopes demonstrated high lability both in competitive and sandwich assays, being completely or partially destroyed when any of these 15 other mAb bound the IgG first. Heat-inactivation of IgG caused full disruption of these epitopes. In contrast, epitopes situated at the opposite distal of the "chain" were more stable and mAb binding could only be affected by occupying an overlapping epitope. Under heat-inactivation these epitopes were affected, but not completely destroyed. Human IgG class anti-DNA autoantibodies were bound to insolubilized dsDNA and their reaction with PAN-Fc mAb was studied. mAb titration plots on IgG and dsDNA-IgG were compared. Five epitopes proved to be altered by antigen (dsDNA) binding. Two of these were the labile hinge-proximal epitopes and the other three were situated near the CH2-CH3 interface. Cross-reactivity of mAb with xenogeneic IgG was also studied. An "epitope map" of the crystallographic model of human IgG Fc portion drawn was based on these experimental data and printed matter, concerning the location of subclass-specific amino acids and homology regions of human and animal IgG.
Primary and secondary metabolism of pentamidine by rats (1992)

The antiprotozoal drug pentamidine [1,5-bis(4'-amidinophenoxy)pentane] has been previously shown to be metabolized by rat liver microsomes, and five of the seven putative primary metabolites have been identified. With the synthesis and identification of 5-(4'-amidinophenoxy)pentanoic acid and 5-(4'-amidinophenoxy)-1-pentanol as the remaining two metabolites, the primary metabolism of pentamidine in rats appears fully characterized. Use of [14C]pentamidine with rat liver microsomes confirms this conclusion, since no unidentified radioactive peaks were detected by high-performance liquid chromatography (HPLC). Isolated, perfused rat livers were used with [14C]pentamidine to identify secondary metabolites. Only two novel radioactive peaks were detected by HPLC analysis of perfused liver samples. The treatment of liver samples with sulfatase or beta-glucuronidase resulted in the reduction or elimination of these peaks and gave rise to peaks identified as para-hydroxybenzamidine and 5-(4'-amidinophenoxy)pentanoic acid. It was concluded from these results that only these two primary metabolites were conjugated with sulfate or glucuronic acid. After 4 h of incubation in the perfused liver system, approximately 15% of the recovered radiolabel was pentamidine. These results suggest that pentamidine metabolism can be rapid and extensive in rats.
Energy Balance and Ovarian Follicle Development Prior to the First Ovulation Postpartum in Dairy Cows Receiving Three Levels of Dietary Fat (1997)

The objectives of this study were to characterize early postpartum (PP) follicular development in dairy cows and to evaluate the influence of energy balance (EB) and the level of dietary fat on dominant follicle development and function. Forty-five multiparous Holstein cows were fed either low (LF, 3.3%), moderate (MF, 5.2%), or high (HF, 7.1%) total dietary fat beginning at parturition, and daily EB was determined for all cows. Follicular development was monitored by ultrasonography, and blood plasma was analyzed for metabolites, metabolic hormones, progesterone, estradiol, and FSH. After an increase (p < 0.01) in mean plasma FSH during Days 1-5, all cows experienced a wave of follicular development during the second week PP regardless of diet or EB. Feeding the MF (p < 0.05) or HF (p < 0.06) diet resulted in a greater number of class IV (> 15 mm) follicles on Day 14 PP as compared to the LF diet. Cows fed the MF diet had higher (p < 0.05) peak plasma estradiol during the first follicular wave and a shorter (p < 0.05) interval to first ovulation than both LF and HF cows. Follicular development prior to first ovulation was characterized by either ovulation of the first dominant follicle (OV, n = 19), one or more waves of nonovulatory dominant follicles (NOV, n = 18), or the formation of a follicular cyst (CYST, n = 8). Ovulation failure during the first follicular wave PP was accompanied by lower (p < 0.001) peak plasma estradiol (0.96 +/- 0.36 vs. 5.0 +/- 0.35 pg/ml), a smaller (p < 0.01) maximum follicle diameter (16.0 +/- 0.9 vs. 20.0 +/- 1.0 mm), lower (p < 0.09) levels of plasma insulin-like growth factor-I (IGF-I; 73.5 +/- 10.1 vs. 102.9 +/- 9.9 ng/ml), and a longer (p < 0.02) interval to the EB nadir (14.6 +/- 1.9 vs. 6.4 +/- 1.9 days). The number of days to first ovulation was positively correlated with days to the EB nadir (r = 0.55), with dominant follicles that emerged after the EB nadir exhibiting enhanced (p < 0.01) production of estradiol and greater (p < 0.01) ovulatory success. The development of large (> 10 mm) dominant follicles was not a limiting factor in PP reproductive recovery, and moderate dietary fat shortened the interval to first ovulation. Follicular competence early PP was associated with higher plasma IGF-I and a shorter interval to the EB nadir.
Cytochemical identification of the regulatory subunit of the cAMP-dependent protein kinase by use of fluorescently labeled catalytic subunit. Examination of protein kinase dissociation in hepatoma cells responding to 8-Br-cAMP stimulation. (1986)

Homogeneous catalytic subunit from the cAMP-dependent protein kinase, when derivatized with a fluorophore, was used as a cytochemical probe to locate intracellular sites of the protein kinase regulatory subunit. After conjugation, the fluoresceinated catalytic subunit (F:C), derivatized to a stoichiometry of approximately 1 mol/mol, retained near full activity as judged by specific activity and by titration against either regulatory subunit or Inhibitor Protein of the protein kinase. With this molecular probe the dissociated regulatory subunit was localized by direct cytochemistry in Reuber H-35 hepatoma cells that had been exposed, while intact, for 0-120 min to 10(-4) M 8-Br-cAMP. After stimulation, cultures were fixed and washed and then incubated for 16 h with F:C. Following 8-Br-cAMP stimulation, extensive binding of the probe to both cytoplasmic and nucleolar sites was observed. This binding was diminished but not eliminated when 50 microM cAMP was present during the incubation of the fixed cells with F:C that was eliminated by a 40-fold molar excess of underivatized catalytic subunit but not by heat-denatured catalytic subunit, and was not reduced by a 20-fold molar excess of cGMP-dependent protein kinase, examined plus or minus cGMP. Collectively, the results allow the conclusion that the F:C probe binds free regulatory subunit. The time course of its change with 8-Br-cAMP (measured as the difference between binding in the presence or absence of cAMP during the postfixation treatment) mirrors that previously reported for changes in the catalytic subunit in these cells, also identified cytochemically (Byus, C. V., and Fletcher, W.H. (1982) J. Cell Biol. 93, 727-734). The binding of the F:C probe, detected when cAMP is present during postfixation treatment, may possibly represent binding to free Inhibitor Protein of the cAMP-dependent protein kinase. If so, it was at a level of approximately 20% of the maximal level of detectable regulatory subunit, and it also showed cytosolic and nucleolar localization.
N-Cyanoimidazole and Diimidazole Imine: Water-Soluble Condensing Agents for the Formation of the Phosphodiester Bond (1989)

The reaction of BrCN with imidazole results in the formation of N-cyanoimidazole and diimidazole imine. These compounds were shown to be useful condensing agents for the formation of the phosphodiester bound in aqueous solution.
The alkyl group is a –I + R substituent (2017)

Electronic substituent effects are usually classified as inductive (through σ-bonds) and resonance effects (via π-bonds). The alkyl group has been usually regarded as aσ -electron donor substituent (+I effect, according to the Ingold’s classification). However, a σ-withdrawing, π-donor effect (-I + R pattern) allows explaining the actual electron-withdrawing behavior of alkyl groups when bound to sp³ carbon atoms as well as their well-known electron-releasing properties when attached to sp² or sp atoms. Alkyl substitution effects on several molecular properties (dipole moments, NMR, IR, and UV spectra, reactivity in gas phase and solution) are discussed.
RyR1-targeted drug discovery pipeline integrating FRET-based high-throughput screening and human myofiber dynamic Ca2+ assays (2020)

Elevated cytoplasmic [Ca<sup>2+</sup>] is characteristic in severe skeletal and cardiac myopathies, diabetes, and neurodegeneration, and partly results from increased Ca<sup>2+</sup> leak from sarcoplasmic reticulum stores via dysregulated ryanodine receptor (RyR) channels. Consequently, RyR is recognized as a high-value target for drug discovery to treat such pathologies. Using a FRET-based high-throughput screening assay that we previously reported, we identified small-molecule compounds that modulate the skeletal muscle channel isoform (RyR1) interaction with calmodulin and FK506 binding protein 12.6. Two such compounds, chloroxine and myricetin, increase FRET and inhibit [<sup>3</sup>H]ryanodine binding to RyR1 at nanomolar Ca<sup>2+</sup>. Both compounds also decrease RyR1 Ca<sup>2+</sup> leak in human skinned skeletal muscle fibers. Furthermore, we identified compound concentrations that reduced leak by > 50% but only slightly affected Ca<sup>2+</sup> release in excitation-contraction coupling, which is essential for normal muscle contraction. This report demonstrates a pipeline that effectively filters small-molecule RyR1 modulators towards clinical relevance.
Clotho: Transparent Data Versioning at the Block I/O Level. (2004)

Recently storage management has emerged as one of the main problems in building cost effective storage infrastructures. One of the issues that contribute to management complexity of storage systems is maintaining previous versions of data. Up till now such functionality has been implemented by high-level applications or at the filesystem level. However, many modern systems aim at higher scalability and do not employ such management entities as filesystems. In this paper we propose pushing the versioning functionality closer to the disk by taking advantage of modern, block-level storage devices. We present Clotho, a storage block abstraction layer that allows transparent and automatic data versioning at the block level. Clotho provides a set of mechanisms that can be used to build flexible higher-level version management policies that range from keeping all data modifications to version capturing triggered by timers or other system events. Overall, we find that our approach is promising in offloading significant management overhead and complexity from higher system layers to the disk itself and is a concrete step towards building self-managed storage devices. Our specific contributions are: (i) We implement Clotho as a new layer in the block I/O hierarchy in Linux and demonstrate that versioning can be performed at the block level in a transparent manner. (ii) We investigate the impact on I/O path performance overhead using both microbenchmarks as well as SPEC SFS V3.0 over two real filesystems, Ext2FS and ReiserFS. (iii) We examine techniques that reduce the memory and disk space required for metadata information. 1.
Synergistic effects of different bone morphogenetic protein type I receptors on alkaline phosphatase induction (2001)

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor-beta superfamily, which regulate the differentiation of osteoprogenitor cells. Here we show that among members of the BMP family, BMP-4 and growth/differentiation factor 5 (GDF-5) induce osteoblast differentiation through the activation of three receptor-regulated Smads (i.e. Smad1, Smad5 and Smad8). By contrast, BMP-6 and BMP-7 induce alkaline phosphatase activity through Smad1 and Smad5, but not through Smad8. Consistent with these findings, BMP-4 induced phosphorylation and nuclear translocation of Smad1, Smad5 and Smad8, but BMP-6 activated only Smad1 and Smad5. BMP-4 and GDF-5 are known to bind to activin receptor-like kinase 3 (ALK-3) and/or ALK-6 (also termed BMP type IA and type IB receptors, respectively), whereas BMP-6 and BMP-7 preferentially bind to ALK-2. Compared with the effects induced by only one of the type I receptors, the combination of constitutively active forms of ALK-2 and ALK-3 (or ALK-6) more strongly induced alkaline phosphatase activity in C2C12 cells. Moreover, addition of BMP-4 and BMP-6 to C2C12 cells resulted in higher alkaline phosphatase activity than that of only one of these BMPs. The combination of ALK-2 and ALK-3 also induced higher transcriptional activity than either receptor alone. Thus, ALK-2 and ALK-3 (or ALK-6) might synergistically induce osteoblast differentiation of C2C12 cells, possibly through efficient activation of downstream signaling pathways.
Cyclophilin A is overexpressed in human pancreatic cancer cells and stimulates cell proliferation through CD147 (2006)

The expression of CypA and CD147 was significantly increased in both pancreatic cancer cell lines and tissues. Exogenous CypA promotes pancreatic cancer cell growth, which may be mediated through the interaction with CD147 and the activation of ERK1/2 and p38 MAPKs.
Development of a Zinc Ion-Selective Luminescent Lanthanide Chemosensor for Biological Applications (2004)

Detection of chelatable zinc (Zn(2+)) in biological studies has attracted much attention recently, because chelatable Zn(2+) plays important roles in many biological systems. Lanthanide complexes (Eu(3+), Tb(3+), etc.) have excellent spectroscopic properties for biological applications, such as long luminescence lifetimes of the order of milliseconds, a large Stoke's shift of >200 nm, and high water solubility. Herein, we present the design and synthesis of a novel lanthanide sensor molecule, [Eu-7], for detecting Zn(2+). This europium (Eu(3+)) complex employs a quinolyl ligand as both a chromophore and an acceptor for Zn(2+). Upon addition of Zn(2+) to a solution of [Eu-7], the luminescence of Eu(3+) is strongly enhanced, with high selectivity for Zn(2+) over other biologically relevant metal cations. One of the important advantages of [Eu-7] is that this complex can be excited with longer excitation wavelengths (around 340 nm) as compared with previously reported Zn(2+)-sensitive luminescent lamthanide sensors, whose excitation wavelength is at too high an energy level for biological applications. The usefulness of [Eu-7] for monitoring Zn(2+) changes in living HeLa cells was confirmed. This novel Zn(2+)-selective luminescent lanthanide chemosensor [Eu-7]should be an excellent lead compound for the development of a range of novel luminescent lanthanide chemosensors for biological applications.
Contrast‐enhanced MR imaging of liver and spleen: First experience in humans with a new superparamagnetic iron oxide (1994)

The aim of this prospective study was to obtain the first human safety and magnetic resonance (MR) imaging results with a new formulation of superparamagnetic iron oxide (SPIO) (SHU 555 A). The SPIO was tested at four iron doses, from 5 to 40 mumol/kg. Laboratory tests and clinical measurements were done in 32 healthy volunteers for up to 3 weeks after administration. MR imaging at 1.5 T was performed before and 8 hours to 14 days after fast intravenous injection (500 mumol Fe/min) of the SPIO (six subjects per dose). Results of this phase I study demonstrate that SHU 555 A at a concentration of 0.5 mol Fe/L was well tolerated. A dose-dependent minor increase in activated partial thromboplastin time, which remained within the normal range, was seen. All doses of SPIO caused a signal loss in both liver and spleen (P < .05) with a spin-echo sequence (TR = 2,300 msec, TE = 45 msec). The signal losses in the liver 8 hours after contrast agent injection were 58%, 79%, 82%, and 87% for the 5, 10, 20, and 40 mumol Fe/kg doses, respectively. The corresponding signal losses in the spleen were 23%, 45%, 65%, and 78%, respectively. The doses that reduced signal intensity by half were 3.1 mumol Fe/kg for the liver and 12.8 mumol Fe/kg for the spleen. The results suggest that the new SPIO formulation is a safe and efficient MR contrast agent.
Mechanism of liver-selective thyromimetic activity of SK&F L-94901: evidence for the presence of a cell-type-specific nuclear iodothyronine transport process (2000)

The thyromimetic compound SK&F L-94901 shows more potent thyromimetic activity in the liver than in the pituitary gland or heart when administered to rats. The mechanisms of liver-selectivity of SK&F L-94901 were examined using cultured rat hepatoma cells (dRLH-84) and rat pituitary tumor cells (GH3), both of which showed saturable cellular uptake of tri-iodothyronine (T(3)). When isolated nuclei with partial disruption of the outer nuclear membrane were used, SK&F L-94901 competed for [(125)I]T(3) binding to nuclear receptors almost equally in dRLH-84 and GH3 cells. SK&F L-94901 also did not discriminate thyroid hormone receptors (TR) alpha1 and beta1 in terms of binding affinity and activation of the thyroid hormone responsive element. In intact cells, however, SK&F L-94901 was a more potent inhibitor of nuclear [(125)I]T(3) binding in dRLH-84 cells than in GH3 cells at an early phase of the nuclear uptake process and after binding equilibrium. These data suggest that SK&F L-94901 is more effectively transported to nuclear TRs in hepatic cells than in pituitary cells and therefore shows liver-selective thyromimetic activity. In conclusion, SK&F L-94901 discriminates hepatic cells and pituitary cells at the nuclear transport process. The cellular transporters responsible for this discrimination were not evident.
Dynamic Time Warp Pattern Matching Using an Integrated Multiprocessing Array (1983)

Dynamic time warping is a well-established technique for time alignment and comparison of speech and image patterns. This paper decribes the architecture, algorithms, and design of a CMOS integrated processing array used for computing the dynamic time warp algorithm. Emphasis is placed on speech recognition applications because of the real-time constraints imposed by isolated and continuous speech recognition.
Mechanisms of Thermochemical Biomass Conversion Processes. Part 1: Reactions of Pyrolysis (2008)

Abstract The present work is a study on the pyrolysis mechanisms of biomass structural constituents. Biomass resources include wood and wood wastes, agricultural crops and their waste byproducts, municipal solid waste, animal wastes, waste from food processing, and aquatic plants and algae. The major organic components of biomass can be classified as cellulose, hemicelluloses, and lignin. The pyrolysis is thermal degradation of biomass by heat in the absence of oxygen, which results in the production of charcoal (solid), bio-oil (liquid), and fuel gas products. Thermal degradation of cellulose proceeds through two types of reaction: a gradual degradation, decomposition, and charring on heating at lower temperatures; and a rapid volatilization accompanied by the formation of levoglucosan on pyrolysis at higher temperatures. The hemicelluloses reacted more readily than cellulose during heating. Of the hemicelluloses, xylan is the least thermally stable, because pentosans are most susceptible to hydrolysis and dehydration reactions. Dehydration reactions around 473 K are primarily responsible for thermal degradation of lignin. Between 423 K and 573 K, cleavage of α- and β-aryl-alkyl-ether linkages occurs. Around 573 K, aliphatic side chains start splitting off from the aromatic ring.
Land Use Rights in China (2004)

China is a socialist country and all land in China belongs to Chinese citizens as a whole. Article 10 of the 1982 Constitution upholds the Chinese land policy that reflects the traditional view of socialism - land of the country must be owned by the country (State) or its agricultural Collectives. State-owned enterprises or other organizations, which cannot own land themselves, may use land with permission from the State.\nWith the development of the Chinese economy and increasing economic reforms, the need for both residential and commercial space has grown rapidly. This emerging real estate demand led to an amendment to the Constitution o f the People’s Republic o f China in 1988. Under this amendment, private investors may obtain land use rights from the government and the holder can retransfer these land use rights to a third party subject to certain conditions. This article extensively discusses this important amendment, the current system of land use rights in China and its application to the booming Chinese private real estate market.