gebhart/patrepeval huggingface dataset:
Fractalkine Cleavage from Neuronal Membranes Represents an Acute Event in the Inflammatory Response to Excitotoxic Brain Damage (2000)

Fractalkine is a recently identified chemokine that exhibits cell adhesion and chemoattractive properties. It represents a unique member of the chemokine superfamily because it is located predominantly in the brain in which it is expressed constitutively on specific subsets of neurons. To elucidate the possible role of neuronally expressed fractalkine in the inflammatory response to neuronal injury, we have analyzed the regulation of fractalkine mRNA expression and protein cleavage under conditions of neurotoxicity. We observed that mRNA encoding fractalkine is unaffected by experimental ischemic stroke (permanent middle cerebral artery occlusion) in the rat. Similarly, in vitro, levels of fractalkine mRNA were unaffected by ensuing excitotoxicity. However, when analyzed at the protein level, we found that fractalkine is rapidly cleaved from cultured neurons in response to an excitotoxic stimulus. More specifically, fractalkine cleavage preceded actual neuronal death by 2-3 hr, and, when evaluated functionally, fractalkine represented the principal chemokine released from the neurons into the culture medium upon an excitotoxic stimulus to promote chemotaxis of primary microglial and monocytic cells. We further demonstrate that cleavage of neuron-derived, chemoattractive fractalkine can be prevented by inhibition of matrix metalloproteases. These data strongly suggest that dynamic proteolytic cleavage of fractalkine from neuronal membranes in response to a neurotoxic insult, and subsequent chemoattraction of reactive immune cells, may represent an early event in the inflammatory response to neuronal injury.
A Method of Advertisement Selection in Multiple RFID-Tags Sensor Network for a Ubiquitous Wide-Area Advertising Service (2008)

As the ubiquitous society grows in maturity, RFID is expected to be widely used. However, they still cost more than bar codes. To make them cost-effective, it is necessary to develop applications that make secondary use of them. As such an application, we consider a wide-area advertising system, and propose an algorithm that selects advertisement to be displayed based on the people's interest information extracted from RFID tags they carry. We propose to use the "relevance rate" as a criterion for that selection, and show that the proposed algorithm selects an effective advertisement for display.
Eating Disorders: Progress and Problems (1998)

Recent research on Anorexia Nervosa and Bulimia Nervosa has yielded an increasingly detailed understanding of the range of biological and psychological abnormalities associated with these eating disorders. Inherited vulnerabilities, cultural pressures, and adverse individual and family experiences all appear to contribute to the onset of extreme dieting, binge eating, and purging. Once initiated, these behaviors give rise to multiple physiological disturbances, some of which may serve to perpetuate the illness. Although there have been substantial advances in the management of Bulimia Nervosa, the goal of offering effective treatment to all individuals with eating disorders remains elusive. This article reviews current thinking on the etiology and treatment of the two major eating disorders and a related syndrome, Binge Eating Disorder.
Fine level feature editing for subdivision surfaces (1999)

In many industrial design modeling scenarios the designer wishes to edit small feature lines-such as variable width and height creases--on otherwise smooth surface patches. When the path of such a feature does not align with an iso-parameter line or crosses patch boundaries it becomes increasingly difficult to maintain good editing semantics of the underlying surface. In this paper we describe an algorithm and implementation allowing the interactive creation and manipulation of fine scale feature curves on subdivision surfaces. In particular, our approach addresses the problem of defining the path of such feature curves independent of the location of surface iso-parameter lines and global patch boundaries. The feature lines are modeled as swept displacement curves with variable profiles, providing a rich toolbox of shapes. Furthermore, the hierarchical editing semantics of subdivision surface based representations carry through to our extended setting, ensuring "good" behavior of the feature lines under coarse scale surface edits.
Modeling of Chemical Mechanical Polishing for Shallow Trench Isolation (2002)

Chemical mechanical polishing (CMP) is a key process enabling shallow trench isolation (STI), which is used in current integrated circuit manufacturing processes to achieve device isolation. Excessive dishing and erosion in STI CMP processes, however, create device yield concerns. This thesis proposes characterization and modeling techniques to address a variety of concerns in STI CMP. Three major contributions of this work are: characterization and modeling of STI CMP processes, both conventional and nonconventional; layout optimization to reduce pattern-dependent dishing and erosion; and modeling of wafer nanotopography impact on STI CMP yield. An STI CMP characterization method is combined with a chip-scale pattern-dependent model to create a methodology that enables tuning of STI CMP process models and prediction of post-CMP dishing, erosion, and clearing times on arbitrary layouts. Model extensions enable characterization of STI CMP processes that use nonconventional consumable sets, including fixed
Upregulation of MUC8 and Downregulation of MUC5AC by Inflammatory Mediators in Human Nasal Polyps and Cultured Nasal Epithelium (2002)

Polyps are believed to be the source of mucus hypersecretion in chronic inflammation of the sinus. However, it is not clear which mucins are responsible for the hypersecretion of mucus by nasal polyps. We describe the over-expression of MUC8 mRNA in nasal polyps and the upregulation of MUC8 mRNA expression and downregulation of MUC5AC mRNA expression by inflammatory mediators. We found that the level of MUC8 mRNA, but not the level of MUC5AC mRNA, increased in nasal polyps. We also found that there was an increase in intracellular mucin in nasal polyps, compared to the normal nasal inferior turbinate. A mixture of inflammatory mediators increased MUC8 mRNA expression and decreased MUC5AC mRNA expression in cultured normal human nasal epithelial cells. Among inflammatory mediators, IL-4 is responsible for the decrease in MUC5AC mRNA and MUC5AC mucin secretion. These results indicate that MUC8 may be one of the major mucins secreted from the polyp epithelium and that it may play an important role in the pathogenesis of mucus hypersecretion in chronic sinusitis with polyps.
High Frequency PMN-PT 1-3 Composite Transducer for Ultrasonic Imaging Application (2010)

Development of PMN-PT single crystal/epoxy 1-3 composites for high-frequency ultrasonic transducers application is presented. The composite was fabricated by using a DRIE dry etching process with a 45% volume fraction of PMN-PT. A 35 MHz ultrasound flat transducer was fabricated with the composite, which was found to have an effective electromechanical coupling coefficient of 0.81, an insertion loss of 18 db, and a −6 dB bandwidth as high as 100%. Tungsten wire phantom image shows that the transducer had an axial resolution of 30 μm, which was in good agreement with the theoretical expectation. The initial results showed that the PMN-PT/epoxy 1-3 composite has many attractive properties over conventional piezoelectric materials for medical imaging applications.
Cytosine methylation alters DNA mechanical properties (2011)

DNA methylation plays an essential role in transcriptional control of organismal development in epigenetics, from turning off a specific gene to inactivation of entire chromosomes. While the biological function of DNA methylation is becoming increasingly clear, the mechanism of methylation-induced gene regulation is still poorly understood. Through single-molecule force experiments and simulation we investigated the effects of methylation on strand separation of DNA, a crucial step in gene expression. Molecular force assay and single-molecule force spectroscopy revealed a strong methylation dependence of strand separation. Methylation is observed to either inhibit or facilitate strand separation, depending on methylation level and sequence context. Molecular dynamics simulations provided a detailed view of methylation effects on strand separation, suggesting the underlying physical mechanism. According to our study, methylation in epigenetics may regulate gene expression not only through mechanisms already known but also through changing mechanical properties of DNA.
Viruses, bacterioplankton, and phyloplankton in the southeastern Gulf of Mexico: distribution and contribution to oceanic DNA pools (1993)

Little is known concerning the factors which might control the distribution of viral abundance in oceanic environments and the relationship of viruses to the oceanic DNA pool. We have measured the distribution of viruses, bacterioplankton and phytoplankton in the subtropical southeastern Gulf of Mexico and related these parameters to the distribution of DNA (dissolved and particulate) in these waters. Viral direct counts were 4.6 to 27 X 106ml-' in Tampa Bay (Florida, USA), 3.8 to 8.5 X 105 ml-' in all oceanic euphotic zone samples and 1.4 to 4.7 X 104 ml-' in deep (200 to 2500 m) waters, and were highly correlated with chlorophyll a concentrations (r = 0.97), particulate DNA (r = 0.96) and bacterial direct counts (BDC, r = 0.94). A vertical profile indicated a subsurface euphotic zone maximum in viral direct counts that corresponded with maxima for particulate and dissolved DNA, and picocyanobacterial direct counts. For all stations, the vertical distribution of viruses most closely followed the distribution of particulate DNA. Bacterioplankton made the largest contnbution ( z 50 %) to the particulate (> 0.2 pm) DNA pool while phytoplankton averaged 8 %. A predictive model for particulate DNA was determined to be: Particulate DNA (pg 1-') = 4.94 X 10-"BDC I-') + 2.31 [chlorophyll a (pg I-')] + 2.77. DNA in viral particles was estimated to comprise only ca 4 % of the dissolved DNA pool.
Monodisperse Magnetic Single‐Crystal Ferrite Microspheres (2005)

Ungewöhnlich einheitlich: Monodisperse Ferrit-Mikrokugeln mit Durchmessern von rund 200–800 nm (TEM-Bild, links) wurden hergestellt. Gemäß Hochauflösungs-TEM-Analyse (Bild rechts und Einschub) ist jede Mikrokugel ein Einzelkristall. Wegen ihrer hydrophilen und magnetischen Eigenschaften sollten die Mikropartikel für viele Anwendungen in der Elektronik und der Biomedizin von Interesse sein. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z462551_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Everolimus (2010)

Everolimus, an orally administered rapamycin analog, has recently been approved by the U.S. Food and Drug Administration for treatment of renal cell carcinoma (RCC) refractory to inhibitors of vascular endothelial growth factor (VEGF) receptor signaling. Everolimus significantly increased progression-free survival (median PFS for the everolimus treated group was 4.0 months versus 1.9 months for the placebo group), although tumor regressions were observed only infrequently. Although the target for everolimus, [the serine-threonine kinase mammalian target of rapamycin (mTOR)] is well established, the mechanism by which this agent retards tumor growth is not well defined. Further, biomarkers that predict tumor sensitivity are still elusive. The mechanism of action, preclinical antitumor activity, and clinical activity of everolimus against RCC are reviewed.
A Simple and Specific Assay for Real‐Time Colorimetric Visualization of β‐Lactamase Activity by Using Gold Nanoparticles (2008)

The last sentence in the left column on page 8802 of this Communication should read: “These two β-lactam-resistant bacterial cells contained different kinds of β-lactamases (TEM-1 in plasmid encoded E. coli Bl21 and ESBL; SHV-18 in K. pneumoniae).” In the Supporting Information on page 1, the enzyme activity was not indicated correctly. The third sentence should read: “β-lactamases were obtained from Biologics Process Development, Inc, CA, USA and Sigma–Aldrich (6–18 units/mg corresponds to the amount of enzyme which hydrolyzes 1 μmol of benzylpenicillin per minute at pH 7.0 and 25 °C or 50–150 units/mg protein by using cephaloridine).”
A Cross-Layer Approach for an Efficient Delivery of TCP/RTP-Based Multimedia Applications in Heterogeneous Wireless Networks (2008)

Recent trends in the telecommunication industry have been moving toward the development of ubiquitous information systems, where the provision of a plethora of advanced multimedia services should be possible, regardless of time and space limitations. An efficient and seamless delivery of multimedia services over various types of wireless networks is still a challenging task. The underlying difficulty consists of the disparity in the bandwidth availability over each network type. Indeed, the fundamental challenge upon a handoff phenomenon in a heterogeneous wireless network consists of an efficient probing of the bandwidth availability of the new network, followed by a prompt adjustment of the data delivery rate. This paper presents a cross-layer approach that involves five layers, namely, physical, data link, application, network, and transport layers. The three former layers are used to anticipate the handoff occurrence and to locate the new point of attachment to the network. Based on their feedback, the transport layer is used then to probe the resources of the new network using low-priority dummy packets. Being the most widely used protocol for multimedia delivery, this paper addresses multimedia applications based on the Transmission Control Protocol (TCP) and the Real-time Transport Protocol (RTP). The design of the whole cross-layer architecture is discussed, and enhancements to the two protocols are proposed. The performance of the enhanced TCP and the RTP are evaluated and compared against existing schemes through extensive simulations. The obtained results are encouraging and promising for the delivery of multimedia services in heterogeneous wireless networks.
Pseudonocardia spinosispora sp. nov., isolated from Korean soil. (2002)

A new strain of the genus Pseudonocardia, which was isolated from a Korean soil sample, is described. The organism shows distinct cultural characteristics in that it forms well-developed aerial mycelium that fragments into rod-shaped, spiny spores, and grows only in standing culture but not in shake culture. Substrate mycelium is sparse or absent in most media used. Phylogenetic analyses based on 16S rDNA sequences reveal that this isolate forms a distinct clade within the radiation encompassing the genera Pseudonocardia and Actinobispora of the family Pseudonocardiaceae. The affiliation to the genus Pseudonocardia is also supported by the cell chemistry, which is represented by the presence of meso-diaminopimelic acid, arabinose and galactose in the cell wall, tetrahydrogenated menaquinone with eight isoprene units as a predominant menaquinone, and phosphatidylcholine as a diagnostic phospholipid. The levels of 16S rDNA sequence similarity found between the isolate and the type strain of validly described species in the genus Pseudonocardia ranged from 94.8 to 96.3%. The organism is also readily differentiated from all of the validated species of the genus Pseudonocardia by means of a battery of phenotypic tests. The name proposed for the new species is Pseudonocardia spinosispora sp. nov. The type strain is LM 141T (= IMSNU 50581T = KCTC 9991T = NRRL B-24156T).
[The phytohemagglutinins and soybean agglutinin in diagnosis of endometrial adenocarcinoma]. (1993)

The distribution of PHA and SBA receptors was studied by ABC immunoperoxidase method in 30 cases of endometrial adenocarcinoma (EA), 10 cases of normal endometrium (NE) and 20 cases of cystic glandular hyperplastic endometrium (CGH). The results showed that the positive rate of PHA and SBA in EA was 46.67% and 73.33% respectively, but negative and low in NE and CGH (P < 0.05). PHA and SBA showed a progressive rising tendency along with the changes of NE to CGH and EA (P < 0.01). It is suggested that both PHA and SBA may be used as differentiated markers in EA and may be helpful in clinical diagnosis.
A mechanistic model of developing immunity to <i>Teladorsagia circumcincta</i> infection in lambs (2010)

Acquired immunity influences the severity of parasitic disease, but modelling the effects of acquired immunity in helminth infections has proved challenging. This may be due to a lack of suitable immunological data, or to the perceived complexity of modelling the immune response. We have developed a model of T. circumcincta infection in domestic sheep that incorporates the effects of acquired immunity on parasite establishment and fecundity. A large data set from commercially managed populations of Scottish Blackface sheep was used, which included relationships between IgA activity and worm length, and between worm length and fecundity. Use was also made of a recently published meta-analysis of parasite establishment rates. This realistic but simple model of nematode infection emulates observed patterns of faecal egg counts. The end-of-season faecal egg counts are remarkably robust to perturbations in the majority of the parameters, possibly because of priming of the immune system early in the season, reducing parasite establishment and growth and, therefore, faecal egg counts. Lowering the amount of early infection leads to higher end-of-season egg counts. The periparturient rise in egg counts in ewes appears to have an important role in supplying infection for the priming of the immune response. This feedback in the immune priming suggests that nematode infections may be difficult to eliminate.
Augmenting Breath Regulation Using a Mobile Driven Virtual Reality Therapy Framework (2013)

This paper presents a conceptual framework of a virtual reality therapy to assist individuals, especially lung cancer patients or those with breathing disorders to regulate their breath through real-time analysis of respiration movements using a smartphone. Virtual reality technology is an attractive means for medical simulations and treatment, particularly for patients with cancer. The theories, methodologies and approaches, and real-world dynamic contents for all the components of this virtual reality therapy (VRT) via a conceptual framework using the smartphone will be discussed. The architecture and technical aspects of the offshore platform of the virtual environment will also be presented.
The Extended Resolution Digital Differential Analyzer: A New Computing Structure for Solving Differential Equations (1970)

In conventional digital differential analyzers (DDA), the word length used for the transmission of information between integrators is restricted to at most a single magnitude bit and a sign bit. This restriction seriously limits integrator frequency response and has to a large extent been responsible for the failure of DDAs to achieve widespread acceptance as general purpose differential analyzers. In this paper it is shown that DDA speed and accuracy can be greatly improved by using increment word lengths which are approximately one-half the length of integrand registers providing that integration formulas more accurate than Euler integration are used. The programming of such machines for the solution of both linear and nonlinear differential equations is discussed and a quantitative evaluation of performance improvement is presented. At the same time, an effort is made to isolate the principal difficulties in hardware implementation which result from extending the integrator increment resolution.
A JAK2 Interdomain Linker Relays Epo Receptor Engagement Signals to Kinase Activation (2009)

JAK2 (Janus kinase 2) is essential for cytokine receptor signaling, and several lines of evidence support a causal role of an activating JAK2 mutation in myeloproliferative disorders. JAK2 activity is autoinhibited by its pseudokinase domain in the basal state, and the inhibition is released by cytokine stimulation; how engagement of the cognate receptor triggers this release is unknown. From a functional screen for gain-of-function JAK2 mutations, we discovered 13 missense mutations, nine in the pseudokinase domain and four in the Src homology 2 (SH2)-pseudokinase domain linker. These mutations identified determinants for autoinhibition and inducible activation in JAK2. Two of the mutants, K539I and N622I, resulted in erythrocytosis in mice. Scanning mutagenesis of the SH2-pseudokinase domain linker indicated that its N-terminal part was essential for interaction of JAK2 with the Epo receptor, whereas certain mutations in the C-terminal region conferred constitutive activation. We further showed that substitutions for Glu(543)-Asp(544) in this linker or Leu(611), Arg(683), or Phe(694) in the hinge proximal region of the pseudokinase domain resulted in activated JAK2 mutants that could not be further stimulated by Epo. These results suggest that the SH2-pseudokinase domain linker acts as a switch that relays cytokine engagement to JAK2 activation by flexing the pseudokinase domain hinge.
UV Resonance Raman-Selective Amide Vibrational Enhancement:  Quantitative Methodology for Determining Protein Secondary Structure (1998)

We have directly determined the amide band resonance Raman spectra of the "average" pure alpha-helix, beta-sheet, and unordered secondary structures by exciting within the amide pi-->pi* transitions at 206.5 nm. The Raman spectra are dominated by the amide bands of the peptide backbone. We have empirically determined the average pure alpha-helix, beta-sheet, and unordered resonance Raman spectra from the amide resonance Raman spectra of 13 proteins with well-known X-ray crystal structures. We demonstrate that we can simultaneously utilize the amide I, II, and III bands and the Calpha-H amide bending vibrations of these average secondary structure spectra to directly determine protein secondary structure. The UV Raman method appears to be complementary, and in some cases superior, to the existing methods, such as CD, VCD, and absorption spectroscopy. In addition, the spectra are immune to the light-scattering artifacts that plague CD, VCD, and IR absorption measurements. Thus, it will be possible to examine proteins in micelles and other scattering media.
The role of phosphorylation in the elasticity of the tethers that connect telomeres of separating anaphase chromosomes (2020)

Elastic tethers, connecting telomeres of all separating anaphase chromosome pairs, lose elasticity when they lengthen during anaphase. Treatment with phosphatase inhibitor CalyculinA causes anaphase chromosomes to move backwards after they reach the poles, suggesting that dephosphorylation causes loss of tether elasticity. We added 50nM CalyculinA to living anaphase crane-fly spermatocytes with different length tethers. When tethers were short, almost all partner chromosomes moved backwards after nearing the poles. When tethers were longer, fewer chromosomes moved backwards. With yet longer tethers none moved backward. This is consistent with tether elasticity being lost by dephosphorylation. 50nM CalyculinA blocks both PP1 and PP2A. To distinguish between PP1 and PP2A we treated cells with short tethers with 50nM okadaic acid which blocks solely PP2A, or with 1µM okadaic acid which blocks both PP1 and PP2A. Only 1µM okadaic acid caused chromosomes to move backward. Thus, tether elasticity is lost because of dephosphorylation by PP1.