gebhart/patrepeval huggingface dataset:
Differential Expression of Lumican and Fibromodulin Regulate Collagen Fibrillogenesis in Developing Mouse Tendons (2000)

Collagen fibrillogenesis is finely regulated during development of tissue-specific extracellular matrices. The role(s) of a leucine-rich repeat protein subfamily in the regulation of fibrillogenesis during tendon development were defined. Lumican-, fibromodulin-, and double-deficient mice demonstrated disruptions in fibrillogenesis. With development, the amount of lumican decreases to barely detectable levels while fibromodulin increases significantly, and these changing patterns may regulate this process. Electron microscopic analysis demonstrated structural abnormalities in the fibrils and alterations in the progression through different assembly steps. In lumican-deficient tendons, alterations were observed early and the mature tendon was nearly normal. Fibromodulin-deficient tendons were comparable with the lumican-null in early developmental periods and acquired a severe phenotype by maturation. The double-deficient mice had a phenotype that was additive early and comparable with the fibromodulin-deficient mice at maturation. Therefore, lumican and fibromodulin both influence initial assembly of intermediates and the entry into fibril growth, while fibromodulin facilitates the progression through growth steps leading to mature fibrils. The observed increased ratio of fibromodulin to lumican and a competition for the same binding site could mediate these transitions. These studies indicate that lumican and fibromodulin have different developmental stage and leucine-rich repeat protein specific functions in the regulation of fibrillogenesis.
Markers of Pancreatic Cancer: Working Toward Early Detection (2011)

Because early detection of pancreatic cancer is the best way to cure this disease, investigators continue to try to identify accurate markers of early pancreatic cancer. Because early-stage pancreatic cancer is generally asymptomatic, the only reliable way to detect it is by targeting individuals at increased risk for pancreatic screening.
The S Segment of Rift Valley Fever Phlebovirus ( Bunyaviridae ) Carries Determinants for Attenuation and Virulence in Mice (2000)

Unlike all the other Rift Valley fever virus strains (Bunyaviridae, Phlebovirus) studied so far, clone 13, a naturally attenuated virus, does not form the filaments composed of the NSs nonstructural protein in the nuclei of infected cells (R. Muller, J. F. Saluzzo, N. Lopez, T. Drier, M. Turell, J. Smith, and M. Bouloy, Am. J. Trop. Med. Hyg. 53:405-411, 1995). This defect is correlated with a large in-frame deletion in the NSs coding region of the S segment of the tripartite genome. Here, we show that the truncated NSs protein of clone 13 is expressed and remains in the cytoplasm, where it is degraded rapidly by the proteasome. Through the analysis of reassortants between clone 13 and a virulent strain, we localized the marker(s) of attenuation in the S segment of this attenuated virus. This result raises questions regarding the role of NSs in pathogenesis and highlights, for the first time in the Bunyaviridae family, a major role of the S segment in virulence and attenuation, possibly associated with a defect in the nonstructural protein.
Evaluation of Methods to Detect and Characterize Antibodies against Recombinant Human Erythropoietin (2004)

We recommend the use of the biosensor immunoassay followed by a bioassay to best identify and characterize anti-rHuEPO antibodies. The biosensor immunoassay allows for identification of all classes and subclasses of immunoglobulins and is a preferred method for the identification of lower-affinity antibodies. The bioassay is needed to determine if the antibodies identified have the capacity to neutralize a biological effect of the drug in a cell-based system.
Mechanical sensorless maximum power tracking control for direct-drive PMSG wind turbines (2010)

Wind turbine generators (WTGs) are usually equipped with mechanical sensors to measure wind speed and rotor position for system control, monitoring, and protection. The use of mechanical sensors increases the cost and hardware complexity and reduces the reliability of the WTG systems. This paper proposes a mechanical sensorless maximum power tracking control for wind turbines directly driving permanent magnetic synchronous generators (PMSGs). In the proposed algorithm, the PMSG rotor position is estimated from the measured stator voltages and currents by using a sliding mode observer (SMO). The wind turbine shaft speed is estimated from the PMSG back electromotive force (EMF) using a model adaptive reference system (MRAS) observer. A back propagation artificial neural network (BPANN) is designed to generate the optimal shaft speed reference in real time by using the estimated turbine shaft speed and the measured PMSG electrical power. A control system is developed for the PMSG wind turbine to continuously track the optimal shaft speed reference to generate the maximum electrical power without using any wind speed or rotor position sensors. The validity of the proposed control algorithm is shown by simulation studies on a 3-kW PMSG wind turbine and experimental results on a practical 300-W PMSG wind turbine.
Solute Distribution in front of an Ice/Water Interface during Directional Growth of Ice Crystals and Its Relationship to Interfacial Patterns (1997)

Directional growth experiments in a water−KCl solution were carried out using a new experimental apparatus combined with an optical system of a Mach−Zehnder interferometer, and the solute distribution in the solution in front of the ice/water interface, as well as the interfacial patterns, was observed in situ. This is the first study in which the solute diffusion field was obtained by analyzing the interference fringes. It was found that the solute distribution is strongly affected by the pattern of interface (i.e., the diffusion field of solute varies greatly with the development of interfacial patterns). On the other hand, observations of interference fringes inside the ice crystal showed that the crystal shape develops in three dimensions even in a thin growth cell. Interaction between the diffusion field and the interfacial pattern is closely related to the three-dimensional structure of the ice/water interface.
COI1 : An Arabidopsis Gene Required for Jasmonate-Regulated Defense and Fertility (1998)

The coi1 mutation defines an Arabidopsis gene required for response to jasmonates, which regulate defense against insects and pathogens, wound healing, and pollen fertility. The wild-type allele, COI1, was mapped to a 90-kilobase genomic fragment and located by complementation of coi1-1 mutants. The predicted amino acid sequence of the COI1 protein contains 16 leucine-rich repeats and an F-box motif. It has similarity to the F-box proteins Arabidopsis TIR1, human Skp2, and yeast Grr1, which appear to function by targeting repressor proteins for removal by ubiquitination.
Accelerating slow excited state proton transfer (2012)

Visible light excitation of the ligand-bridged assembly [(bpy)(2)Ru(a)(II)(L)Ru(b)(II)(bpy)(OH(2))(4+)] (bpy is 2,2'-bipyridine; L is the bridging ligand, 4-phen-tpy) results in emission from the lowest energy, bridge-based metal-to-ligand charge transfer excited state (L(-•))Ru(b)(III)-OH(2) with an excited-state lifetime of 13 ± 1 ns. Near-diffusion-controlled quenching of the emission occurs with added HPO(4)(2-) and partial quenching by added acetate anion (OAc(-)) in buffered solutions with pH control. A Stern-Volmer analysis of quenching by OAc(-) gave a quenching rate constant of k(q) = 4.1 × 10(8) M(-1) • s(-1) and an estimated pK(a)* value of ~5 ± 1 for the [(bpy)(2)Ru(a)(II)(L(•-))Ru(b)(III)(bpy)(OH(2))(4+)]* excited state. Following proton loss and rapid excited-state decay to give [(bpy)(2)Ru(a)(II)(L)Ru(b)(II)(bpy)(OH)(3+)] in a H(2)PO(4)(-)/HPO(4)(2-) buffer, back proton transfer occurs from H(2)PO(4)(-) to give [(bpy)(2)Ru(a)(II)(L)Ru(b)(bpy)(OH(2))(4+)] with k(PT,2) = 4.4 × 10(8) M(-1) • s(-1). From the intercept of a plot of k(obs) vs. [H(2)PO(4)(-)], k = 2.1 × 10(6) s(-1) for reprotonation by water providing a dramatic illustration of kinetically limiting, slow proton transfer for acids and bases with pK(a) values intermediate between pK(a)(H(3)O(+)) = -1.74 and pK(a)(H(2)O) = 15.7.
CloudSpider: Combining Replication with Scheduling for Optimizing Live Migration of Virtual Machines across Wide Area Networks (2011)

A virtual machine (VM), during its lifecycle, can be scheduled for execution at geographically disparate cloud locations depending upon the cost of computation and the load at these locations. However, trans-locating a live VM across high-latency low-bandwidth wide area networks (WAN) within 'reasonable' time is nearly impossible due to the large size of the VM image. In this paper, we deal with this problem by combining VM scheduling strategies with VM replication strategies. In particular, we propose to replicate a VM image selectively across different cloud sites, choose a replica of the VM image to be the primary copy and propagate the incremental changes at the primary copy to all the remaining replicas of the VM image. The replica placement strategies are based on factors that influence long-term costs such as the average per-unit cost of storage and the average per-unit cost of computation at different cloud sites besides the 'end-user' latency requirements associated with the VMs. We propose to compensate the additional storage requirements due to replication by exploring commonality that naturally exists amongst different VM images using de-duplication techniques. A key issue that naturally arises in this integrated replication and scheduling context for minimizing migration latencies associated with live migration of VMs across WAN is the design of a good replica placement algorithm that minimizes additional storage requirements. In this paper we address this issue as part for our integrated replication and scheduling architecture, called Cloud Spider. We discuss the trade-offs involved in the design of a replica placement algorithm and propose an algorithm that factors in deduplication ratios amongst pairs of VM images while deciding on the question of replica placement of the VM images. Preliminary experiments show extremely promising results.
Pre-clinical evaluation of [111In]-benzyl-DOTA-ZHER2:342, a potential agent for imaging of HER2 expression in malignant tumors (2007)

Imaging of expression of human epidermal growth factor receptor type 2 (HER2) in breast carcinomas may help to select patients eligible for trastuzumab therapy. The Affibody molecule Z(HER2:342) is a small (7-kDa) non-immunoglobulin affinity protein, which binds to HER2 with a picomolar affinity. Previously, a benzyl-DTPA conjugate of Z(HER2:342) was labeled with 111In and demonstrated good targeting in murine xenografts. We considered that the use of the macrocyclic chelator DOTA could increase the label stability and enhance a choice of nuclides, which could be used as a label for Z(HER2:342). The goal of this study was the preparation and pre-clinical evaluation of the indium-111- labeled DOTA-derivative of Z(HER2:342). Isothiocyanate-benzyl-DOTA was coupled to recombinant Z(HER2:342), and the conjugate was efficiently labeled with 111In at 60 degrees C. The specificity of 111In-benzyl-DOTA-Z(HER2:342) binding to HER2 was confirmed in vitro using HER2-expressing breast carcinoma BT474 and ovarian carcinoma SKOV-3 cell lines. Biodistribution of 111In-benzyl-DOTA-Z(HER2:342) was performed in nude mice bearing LS174T xenografts and compared directly with the biodistribution of 111In-benzyl-DTPA-Z(HER2:342). In vivo, 111In-benzyl-DOTA-Z(HER2:342) demonstrated quick clearance from blood and non-specific organs except the kidneys. Four hours post injection (pi), the tumor uptake of 111In-benzyl-DOTA-Z(HER2:342) (4.4+/-1.0% IA/g) was specific and the tumor-to-blood ratio was 23. The use of benzyl-DTPA provided higher tumor-to-blood and tumor-to-liver ratios. gamma-camera imaging showed clear visualization of HER2-expressing xenografts using 111In-benzyl-DOTA-Z(HER2:342). 111In-benzyl-DOTA-Z(HER2:342) has a potential for imaging of HER2 expression in malignant tumors.
The influence of dietary whey protein on tissue glutathione and the diseases of aging. (1989)

This study compared the effects of a whey-rich diet (20 g/100 g diet), with that of Purina mouse chow or casein-rich diet (20 g/100 g diet), on the liver and heart glutathione content and on the survival of old male C57BL/6NIA mice. The study was performed during a limited observation period of 6.3 months. In mice fed the whey protein-rich diet between 17 months and 20 months of age, the heart tissue and liver tissue glutathione content were enhanced significantly above the corresponding values of the casein diet-fed and Purina-fed mice. Mice fed the whey protein diet at the onset of senescence at 84 weeks, exhibited increased longevity as compared to mice fed Purina mouse chow over the 6.3 month observation period extending from the age of 21 months (corresponding to a human age of 55 years) to 26-27 months of age (corresponding to a human age of 80 years), during which time 55% mortality was observed. The corresponding mean survival time of mice fed the defined casein diet is almost identical to that of Purina-fed controls. Body weight curves were similar in all three dietary groups. Hence a whey protein diet appears to enhance the liver and heart glutathione concentration in aging mice and to increase longevity over a 6.3 month observation period.
Finding clusters in VLSI circuits (2002)

Circuit partitioning plays a fundamental role in hierarchical layout systems. Identifying the strongly connected subcircuits, the clusters, of the logic can significantly reduce the delay of the circuit and the total interconnection length. Finding such a cluster partition however, is NP-complete. The authors propose a fast heuristic algorithm based on a simple, local criterion. They are able to prove that for highly structured circuits the clusters found by this algorithm correspond with high probability to the 'natural' clusters. An application to large scale real world circuits shows that by this method the number of nets cut is reduced by up to 46% compared to the standard mincut approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria (1990)

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationships among selected species of mycobacteria and related organisms. The phylogeny inferred reflects the traditional classification, with major branches of the phylogenetic tree in general correspondence to the four Runyon groups and with numerical classification analyses. All the mycobacterial species compared, with the exception of M. chitae, are closely related (average similarity values greater than 95%). The slow growers form a coherent line of descent, distinct from the rapid growers, within which the overt pathogens are clustered. The distant relationship between M. chitae and the remaining mycobacteria suggests that this organism is incorrectly classified with the mycobacteria. M. paratuberculosis 18 was indistinguishable from M. avium-M. intracellulare-M. scrofulaceum serovar 1 by this analysis.
Novel roles of protease inhibitors in infection and inflammation (2001)

The local balance between proteinase inhibitors and proteinases determines local proteolytic activity. Various studies have demonstrated the importance of serine proteinase inhibitors in regulating the activity of serine proteinases that are released by leucocytes during inflammation. Recently it has been shown that these inhibitors may also display functions that are distinct from those associated with the inhibition of leucocyte-derived proteinases. In this review the results of selected studies focusing on three inhibitors of neutrophil elastase, i.e. α1-proteinase inhibitor, secretory leucocyte proteinase inhibitor and elafin, are presented, with the aim of illustrating their possible involvement in the regulation of inflammation, host defence against infection, tissue repair and extracellular matrix synthesis.
CHARMM: The biomolecular simulation program (2009)

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
Synthesis and analgetic activity of some 5-aryl-2-azabicyclo[3.2.1]octanes (1978)

A series of 5-aryl-2-azabicyclo[3.2.1]octanes II has been synthesized and evaluated for analgetic agonist-antagonist activity. These compounds can be regarded as five-membered, conformationally more rigid analogues of the potent agonist-antagonist (-)-5-(3-hydroxyphenyl)-2-methylmorphan (I). Several of these compounds have demonstrated marked analgesic potency comparable to morphine in the mouse writhing assay. Structure-activity correlations, generated by varying N-substitution and O-acetylation of the phenolic function, seem to indicate that optimum activity is associated with an arylethyl side chain attached to the basic nitrogen. Among the most interesting compounds in this series are the phenethyl analogue 31 and its O-acetate 39; the former shows the profile of a well-balanced analgetic-antagonist virtually devoid of physical dependence liability as demonstrated in the rat infusion test.
Identification of a STAT6 domain required for IL-4-induced activation of transcription (1997)

Tyrosine phosphorylation of STAT6 in response to IL-4 results in the formation of STAT6 homodimers that bind specific DNA elements. Although binding sites for STAT6 have been shown to be important for the function of several IL-4-inducible promoters, the role of STAT6 in this activation has not been defined. To determine whether STAT6 is a transcriptional activator, different portions of the carboxyl terminus of STAT6 were fused to the yeast Gal4 protein DNA binding domain. Analysis of these chimeric Gal4-STAT6 proteins demonstrates that a 140-amino-acid proline-rich region of the carboxyl terminus of STAT6 contains a region that activates transcription. Truncation mutants of STAT6 that lack this domain cannot activate transcription and are capable of repressing transcription stimulated by a wild-type STAT6 protein. Strikingly, the ability of IL-4 to induce transcription from the Ig germline epsilon promoter is suppressed by overexpression of a carboxyl-terminal deletion mutant of STAT6. These studies demonstrate that the carboxyl terminus of STAT6 contains an activating domain required for the induction of genes by IL-4.
Survivin expression and its relation with proliferation, apoptosis, and angiogenesis in brain gliomas (2005)

Survivin is overexpressed in brain gliomas, which may play an important role in malignant proliferation, antiapoptosis, and angiogenesis of brain gliomas.
Mass spectrometry of purified amyloid beta protein in Alzheimer's disease. (1992)

The amyloid beta-protein (A beta) that is progressively deposited in Alzheimer's disease (AD) arises from proteolysis of the integral membrane protein, beta-amyloid precursor protein (beta APP). Although A beta formation appears to play a seminal role in AD, only a few studies have examined the chemical structure of A beta purified from brain, and there are discrepancies among the findings. We describe a new method for the rapid extraction and purification of A beta that minimizes artifactual proteolysis. A beta purified by two-dimensional reverse-phase HPLC was analyzed by combined amino acid sequencing and mass spectrometry after digestion with a lysylendopeptidase. The major A beta peptide in the cerebral cortex of all five AD brains examined was aspartic acid 1 to valine 40. A minor species beginning at glutamic acid 3 but blocked by conversion to pyroglutamate was also found in all cases. A species ending at threonine 43 was detected, varying from approximately 5 to 25% of total A beta COOH-terminal fragments. Peptides ending with valine 39, isoleucine 41, or alanine 42 were not detected, except for one brain with a minor peptide ending at valine 39. Our findings suggest that A beta 1-40 is the major species of beta-protein in AD cerebral cortex. A beta 1-40 and A beta 1-43 peptides could arise independently from beta APP, or A beta 1-43 could be the initial excised fragment, followed by digestion to yield A beta 1-40. These analyses of native A beta in AD brain recommend the use of synthetic A beta 1-40 peptide to model amyloid fibrillogenesis and toxicity in vitro.
Inappropriate vasopressin secretion in severe alcohol withdrawal (1992)

Forty-one male alcoholics suffering from alcohol withdrawal syndrome were investigated to assess the relationship between vasopressin (ADH), water homeostasis and alcohol withdrawal. During 10 d, we found a significant decrease in serum vasopressin, from 3.08 +/- 0.61 to 1.71 +/- 0.22 pg/nl. There were no concomitant changes in osmolality, so that a general dysregulatory state of vasopressin secretion during alcohol withdrawal cannot be assumed. Only patients with delirium tremens (8/41) had higher vasopressin levels despite lowered serum osmolalities. These findings support the hypothesis of an inappropriate rebound secretion of vasopressin in severe alcohol withdrawal. Furthermore, they may contribute to the pathogenesis of focal alcoholic brain damage, because rapid and/or profound changes in osmolality are suspected to cause circumscribed cerebral demyelinization.
Real-time particle-based simulation on GPUs (2007)

As physical laws govern the motion of objects around us, a physically-based simulation plays an important role in computer graphics. For instance, the motion of a fluid, which is difficult to generate by hand, can be produced by solving the governing equations. Acceleration of a simulation is one of the most important research themes because the speed and stability of a simulation are essential for real-time applications.
Simplified MSK Signaling Technique (1977)

Modulation and demodulation in the minimum (frequency)-shift keying (MSK) format are reduced to the form of coherent biphase keying. Considerable simplification of circuitry is thus effected without sacrifice of performance. When the ratio of the carrier frequency to the bit rate is high, then the technique described here does not require the precise relative phasing of any pair of oscillators in the transmitter. Experimental results demonstrate the feasibility of synthesizing the one filter that is unique to this signaling scheme. In the present instance, the filter is realized as a surface acoustic wave device.