gebhart/patrepeval huggingface dataset:
Analysis of Droplet Evaporation on a Superhydrophobic Surface (2005)

The evaporation process for small, 1-2-mm-diameter droplets of water from patterned polymer surfaces is followed and characterized. The surfaces consist of circular pillars (5-15 microm diameter) of SU-8 photoresist arranged in square lattice patterns such that the center-to-center separation between pillars is 20-30 microm. These types of surface provide superhydrophobic systems with theoretical initial Cassie-Baxter contact angles for water droplets of up to 140-167 degrees, which are significantly larger than can be achieved by smooth hydrophobic surfaces. Experiments show that on these SU-8 textured surfaces water droplets initially evaporate in a pinned contact line mode, before the contact line recedes in a stepwise fashion jumping from pillar to pillar. Provided the droplets of water are deposited without too much pressure from the needle, the initial state appears to correspond to a Cassie-Baxter one with the droplet sitting upon the tops of the pillars. In some cases, but not all, a collapse of the droplet into the pillar structure occurs abruptly. For these collapsed droplets, further evaporation occurs with a completely pinned contact area consistent with a Wenzel-type state. It is shown that a simple quantitative analysis based on the diffusion of water vapor into the surrounding atmosphere can be performed, and estimates of the product of the diffusion coefficient and the concentration difference (saturation minus ambient) are obtained.
Head Up Games: combining the best of both worlds by merging traditional and digital play (2009)

Current pervasive games are mostly location-aware applications, played on handheld computing devices. Considering pervasive games for children, it is argued that the interaction paradigm existing games support limits essential aspects of outdoor play like spontaneous social interaction, physical movement, and rich face-to-face communication. We present a new genre of pervasive games conceived to address this problem, that we call “Head Up Games” (HUGs) to underline that they liberate players from facing down to attend to screen-based interactions. The article discusses characteristics of HUG and relates them to existing genres of pervasive games. We present lessons learned during the design and evaluation of three HUG and chart future challenges.
Biological Markers of Exposure to Chemical Warfare Agents (2007)

This chapter contains sections titled: Introduction Biological Reactions of CW Agents Free Metabolites as Biological Markers Protein and DNA Adducts as Biological Markers Analytical Methods Sulphur Mustard Nitrogen Mustards Lewisite Nerve Agents Quinuclidinyl Benzilate, BZ Phosgene Hydrogen Cyanide Riot Control Agents CS CN CR Summary References
Enhancement of the characteristics of LCDs by doping nanoparticles: reduction of the operating voltage, viscosity, and response times (2006)

Herein, we report that liquid crystal displays (LCDs) such as TN (twisted nematic)-mode, TB (tunable birefringence)-mode, VAN (vertically aligned nematic)-mode, BN (bent nematic)-mode, and so forth, exhibit the reduction in the operating voltage and response times by doping the nanoparticles of inorganic substances such as MgO. These effects may be attributed to the modification of the physical properties of the liquid crystal host media in these LCD cells.
Interaction of Shc with Adaptor Protein Adaptins (1996)

The role of Shc as a substrate of receptors for growth factors and cytokines is well established. To gain further insight into the function of Shc in signal transduction, we used an affinity method to identify potential Shc-binding proteins. Incubation of bovine brain lysates with a glutathione S-transferase (GST)-Shc fusion protein immobilized on glutathione-Sepharose beads resulted in the binding of cellular proteins of approximately 115, 110, and 100 kDa as well as those of 50 and 17 kDa. Amino acid sequencing of tryptic peptides revealed that the 100-kDa protein was almost identical to beta-adaptin and that the 110- and 115-kDa proteins were almost identical to alphaA-adaptin. Using immunoblot analysis, anti-alpha-adaptin antibody recognized several proteins of 100 approximately 115 kDa, and anti-beta-adaptin antibody recognized a 100-kDa protein, suggesting that alphaA-, alphaC-, and beta-adaptins are bound to the GST-Shc fusion protein. Immunoblot analysis with anti-alpha-adaptin antibody revealed that alpha-adaptin was coimmunoprecipitated with Shc from PC12, KB, and COS cell lysates, suggesting a specific interaction of Shc and adaptins in intact cells. A binding study using mutant GST-Shc fusion proteins revealed that the collagen homologous region (amino acids 233-377) of Shc was required for adaptin binding. Conversely, the collagen homologous region of Shc inhibited the binding of adaptins to GST-Shc. In addition, adaptin was able to bind mutant fusion proteins containing amino acids 233-369, 233-355, 346-369, and 346-355 of Shc, but failed to bind a mutant containing amino acids 233-345, suggesting that amino acids 346-355 (RDLFDMKPFE) in the collagen homologous region of Shc are required for adaptin binding. Thus, this study indicates the specific interaction of Shc with alpha- and beta-adaptin components of plasma membrane adaptor proteins that are thought to be involved in receptor endocytosis.
Modulation of Bone Morphogenetic Protein-9 Expression and Processing by Insulin, Glucose, and Glucocorticoids: Possible Candidate for Hepatic Insulin-Sensitizing Substance (2008)

Bone morphogenetic protein 9 (BMP-9), a member of the TGF-beta superfamily predominantly expressed in nonparenchymal liver cells, has been demonstrated to improve glucose homeostasis in diabetic mice. Along with this therapeutic effect, BMP-9 was proposed as a candidate for the hepatic insulin-sensitizing substance (HISS). Whether BMP-9 plays a physiological role in glucose homeostasis is still unknown. In the present study, we show that BMP-9 expression and processing is severely reduced in the liver of insulin-resistant rats. BMP-9 expression and processing was directly stimulated by in situ exposition of the liver to the combination of glucose and insulin and oral glucose in overnight fasted rats. Additionally, prolonged fasting (72 h) abrogated refeeding-induced BMP-9 expression and processing. Previous exposition to dexamethasone, a known inductor of insulin resistance, reduced BMP-9 processing stimulated by the combination of insulin and glucose. Finally, we show that neutralization of BMP-9 with an anti-BMP-9 antibody induces glucose intolerance and insulin resistance in 12-h fasted rats. Collectively, the present results demonstrate that BMP-9 plays an important role in the control of glucose homeostasis of the normal rat. Additionally, BMP-9 is expressed and processed in an HISS-like fashion, which is impaired in the presence of insulin resistance. BMP-9 regulation according to the feeding status and the presence of diabetogenic factors reinforces the hypothesis that BMP-9 might exert the role of HISS in glucose homeostasis physiology.
Neuronal Transcription Factors Induce Conversion of Human Glioma Cells to Neurons and Inhibit Tumorigenesis (2012)

Recent findings have demonstrated that the overexpression of lineage-specific transcription factors induces cell fate changes among diverse cell types. For example, neurons can be generated from mouse and human fibroblasts. It is well known that neurons are terminally differentiated cells that do not divide. Therefore, we consider how to induce glioma cells to become neurons by introducing transcription factors. Here, we describe the efficient generation of induced neuronal (iN) cells from glioma cells by the infection with three transcription factors: Ascl1, Brn2 and Ngn2 (ABN). iN cells expressed multiple neuronal markers and fired action potentials, similar to the properties of authentic neurons. Importantly, the proliferation of glioma cells following ABN overexpression was dramatically inhibited in both in vitro and in vivo experiments. In addition, iN cells that originated from human glioma cells did not continue to grow when they were sorted and cultured in vitro. The strategies by which glioma cells are induced to become neurons may be used to clinically study methods for inhibiting tumor growth.
Homophilic synaptic target recognition mediated by immunoglobulin-like cell adhesion molecule Fasciclin III (1997)

We demonstrate that the cell adhesion molecule Fasciclin III (FAS3) mediates synaptic target recognition through homophilic interaction. FAS3 is expressed by the RP3 motoneuron and its target muscles during synaptic target recognition. The RP3 growth cone can form synapses on muscles that ectopically express FAS3. This mistargeting is dependent on FAS3 expression in the motoneurons. In addition, when the FAS3-negative aCC and SNa motoneuron growth cones ectopically express FAS3, they gain the ability to recognize FAS3-expressing muscles as alternative targets. We propose that homophilic synaptic target recognition serves as a basic mechanism of neural network formation.
Effects of the novel alphav integrin antagonist SM256 and cis-platinum on growth of murine squamous cell carcinoma PAM LY8. (2000)

Increased density of proliferating and migrating tumor cells and neovascular endothelial cells has been associated with tumor progression and poor prognosis in patients with squamous cell carcinoma (SCC). Tumor and neovascular endothelial cells in squamous cell carcinoma have been reported to express integrin heterodimers containing the alphav subunit, which binds to vitronectin and other extracellular matrix proteins that contain the amino acid recognition sequence Arg-Gly-Asp (RGD). In the present study, we examined the effect of the novel non-peptide alphav integrin antagonist SM256 on growth of SCC line PAM LY8 in BALB/c SCID mice, and determined whether SM256 has direct inhibitory effects on growth of murine endothelial and PAM LY8 SCC cells in vitro. SM256 inhibits cell adhesion of murine cells expressing alphavbeta3 and alphavbeta5 integrins in vitro with an IC50 of 35 nM and 30 nM, respectively. Growth of Pam LY8 tumors in vivo was inhibited with 14-day continuous administration of SM256 by subcutaneous osmotic diffusion pump, during which a mean serum concentration of 56 nM was detected. While both murine aortic endothelial cells and PAM LY8 were found to express alphav integrins by fluorescence cytofluorometry, SM256 at 50 nM in MTT assay completely inhibited growth of endothelial cells, but had no significant direct effect on growth of PAM LY8 cells. We compared the effect on growth of PAM LY8 of SM256 infusion versus single agent or combination chemotherapy with a maximally tolerated dose of cis-platinum, which is used as a standard chemotherapy for SCC. When treatment was initiated at either 7 or 21 days following establishment of tumor, 14-day infusion of SM256 had an inhibitory effect on growth that was similar to that obtained with single dose cis-platinum, but no additive effect of concurrent therapy with SM256 and cis-platinum was observed. These results demonstrate the activity and feasibility of use of alphav antagonists such as SM256 for therapy of SCC.
Deacetoxycephalosporin C hydroxylase of Streptomyces clavuligerus. Purification, characterization, bifunctionality, and evolutionary implication. (1991)

Deacetoxycephalosporin C hydroxylase from cell-free extracts of Streptomyces clavuligerus was stabilized partially and purified to near homogeneity by three anion-exchange chromatographies, ammonium sulfate fractionation, and two gel filtrations. The hydroxylase was a monomer with a Mr of 35,000-38,000. alpha-Ketoglutarate, ferrous iron, and molecular oxygen were required for the enzyme activity. The hydroxylase was optimally active between pH 7.0 and 7.4 in a 3-(N-morpholino)propanesulfonic acid buffer and at 29 degrees C. It was stimulated by a reducing agent, particularly dithiothreitol or reduced glutathione, and ATP. The requirement for ferrous ion was specific, and at least one sulfhydryl group was apparently essential for the enzymatic hydroxylation. The Km values of the hydroxylase for deacetoxycephalosporin C and alpha-ketoglutarate were 59 and 10 microM, respectively, and the Ka for ferrous ion was 20 microM. In addition to its known hydroxylation of deacetoxycephalosporin C to deacetylcephalosporin C, the hydroxylase catalyzed effectively an analogous hydroxylation of 3-exomethylenecephalosporin C to deacetoxycephalosporin C. Surprisingly, the hydroxylase also mediated slightly a novel ring-expansion of penicillin N to deacetoxycephalosporin C. The substrate specificity of the hydroxylase is overlapping with but distinguishable from that of deacetoxycephalosporin C synthase, the enzyme which normally mediates the ring-expansion reaction (Dotzlaf, J. E., and Yeh, W. K. (1989) J. Biol. Chem. 264, 10219-10227). Furthermore, the hydroxylase exhibited an extensive sequence similarity to the synthase. Thus, the two enzymes catalyzing the consecutive reactions for cephamycin C biosynthesis in S. clavuligerus represent apparent products from a divergent evolution.
Effect of electrical energy on the efficacy of biofilm treatment using the bioelectric effect (2015)

Our results demonstrate that the energy of the electrical signal, and not the type of electrical signal (AC or DC or SP), is the key to determine the efficacy of the BE treatment. We anticipate that this observation will pave the way for further understanding of the mechanism of action of the BE treatment method and may open new doors to the use of electric fields in the treatment of bacterial biofilms.
New sensor principle based on Barkhausen noise (2007)

More than 85 years after its discovery, the Barkhausen effect remains one of the basic principles involved in the characterization of magnetic and metallic materials, e.g. to measure their residual stresses and hardness. Reliable testing results can be obtained quickly and nondestructively for a large range of industrial applications using micro-magnetic parameters. This paper summarizes the physical principles and demonstrates applications important for today's nondestructive testing procedures.
Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells (2010)

Coordination of cellular processes through the establishment of tissue-specific gene expression programs is essential for lineage maturation. The basic helix-loop-helix hemopoietic transcriptional regulator TAL1 (formerly SCL) is required for terminal differentiation of red blood cells. To gain insight into TAL1 function and mechanisms of action in erythropoiesis, we performed ChIP-sequencing and gene expression analyses from primary fetal liver erythroid cells. We show that TAL1 coordinates expression of genes in most known red cell-specific processes. The majority of TAL1's genomic targets require direct DNA-binding activity. However, one-fifth of TAL1's target sequences, mainly among those showing high affinity for TAL1, can recruit the factor independently of its DNA binding activity. An unbiased DNA motif search of sequences bound by TAL1 identified CAGNTG as TAL1-preferred E-box motif in erythroid cells. Novel motifs were also characterized that may help distinguish activated from repressed genes and suggest a new mechanism by which TAL1 may be recruited to DNA. Finally, analysis of recruitment of GATA1, a protein partner of TAL1, to sequences occupied by TAL1 suggests that TAL1's binding is necessary prior or simultaneous to that of GATA1. This work provides the framework to study regulatory networks leading to erythroid terminal maturation and to model mechanisms of action of tissue-specific transcription factors.
Pathogenesis of Infectious Diarrhea (2001)

A brief overview of some of the main features involved in normal physiological bi-directional absorption and secretion of fluid in the gut is given, including the nature and cellular location of key enzymes, ion pumps, symports, antiports and diffusion channels; the microanatomy of intestinal villous vasculature and the dynamics of villus blood flow, which together generate hypertonic zones in villus tip regions; and the production, differentiation, escalator movement (from crypt to villus tip) and subsequent shedding of intestinal epithelial cells. (Neural and hormonal mechanisms that regulate normal mucosal ion transport are not discussed.) The manner in which Vibrio cholerae, several pathotypes of Escherichia coli, several Salmonella serotypes, rotavirus, Campylobacter species, Shigella dysenteriae, Yersinia species and Clostridium difficile perturb these mechanisms and cause diarrhea, is discussed. Throughout the article, the main emphasis is on experimental studies designed to elucidate biological mechanisms and (where relevant) the microbial determinants responsible for diarrheal disease. Allusions are also made to the involvement of host responses such as the inflammatory response, the production and release of potent cytokines and accelerated homeostatic responses (such as increased rates of crypt cell division seen in some infections), and the role that they play in pathophysiological fluid secretion.
Design, synthesis, and cyclization of 4-aminobutyric acid derivatives: potential candidates as self-immolative spacers (2011)

Self-immolative spacers have gained significant interest in recent years due to their utility in numerous prodrug, sensor and drug delivery systems. However, there are a very limited number of spacers that are capable of undergoing spontaneous and rapid reactions under mild conditions. To address this need, 4-aminobutyric acid derivatives were explored as a potential class of self-immolative spacers. Using a modular approach, eleven N- and α-substituted derivatives of 4-aminobutyric acid were synthesized, and their intramolecular cyclizations to γ-lactams were studied. Kinetics experiments were carried out at physiological pH and temperature, and the observed half-lives for the spacers ranged from 2 to 39 s, depending on the molecular structure. In addition, the pH dependence of the cyclization rate was also explored and it was found that cyclization still occurred rapidly at mildly acidic pH. Therefore, this class of compounds exhibits promise for incorporation into a variety of self-immolative systems where rapid cyclization reactions are desired.
A new image reconstruction algorithm for real-time monitoring of conductivity and permeability changes in Magnetic Induction Tomography (2012)

A linear image reconstruction algorithm for solving the Magnetic Induction Tomography inverse problem is presented. It's an optimization process to determine a reconstruction matrix that does the best mapping between a set of training parameter vectors and their respective measurements dictated by a forward model. It allows the simultaneous 3D reconstructions of the electric conductivity, electric permittivity and magnetic permeability. The results were compared with the ones obtained from a single-step regularized Gauss-Newton method and a reduction of 15% in the image error was verified. The behavior of the developed algorithm in a simulated clinical environment was also assessed using a realistic bio-impedance model of the human head, derived from a high resolution magnetic resonance image.
Annotating Large Email Datasets for Named Entity Recognition with Mechanical Turk (2010)

Amazon&amp;apos;s Mechanical Turk service has been successfully applied to many natural language processing tasks. However, the task of named entity recognition presents unique challenges. In a large annotation task involving over 20,000 emails, we demonstrate that a competitive bonus system and interannotator agreement can be used to improve the quality of named entity annotations from Mechanical Turk. We also build several statistical named entity recognition models trained with these annotations, which compare favorably to similar models trained on expert annotations. 1
Mechanisms of activation of tissue procollagenase by matrix metalloproteinase 3 (stromelysin) (1990)

The mechanism of activation of tissue procollagenase by matrix metalloproteinase 3 (MMP-3)/stromelysin was investigated by kinetic and sequence analyses. MMP-3 slowly activated procollagenase by cleavage of the Gln80-Phe81 bond to generate a fully active collagenase of Mr = 41,000. The specific collagenolytic activity of this species was 27,000 units/mg (1 unit = 1 microgram of collagen digested in 1 min at 37 degrees C). Treatment of procollagenase with plasmin or plasma kallikrein gave intermediates of Mr = 46,000. These intermediates underwent rapid autolytic activation, via cleaving the Thr64-Leu65 bond, to give a collagenase species of Mr = 43,000 that exhibited only about 15% of the maximal specific activity. Similarly, (4-aminophenyl)mercuric acetate (APMA) activated procollagenase by intramolecular cleavage of the Val67-Met68 bond to generate a collagenase species of Mr = 43,000, but with only about 25% of the maximal specific activity. Subsequent incubation of the 43,000-Mr species with MMP-3 resulted in rapid, full activation and generated the 41,000-Mr collagenase by cleaving the Gln80-Phe81 bond. In the case of the proteinase-generated 43,000-Mr species, the action of MMP-3 was approximately 24,000 times faster than that on the native procollagenase. This indicates that the removal of a portion of the propeptide of procollagenase induces conformational changes around the Gln80-Phe81 bond, rendering it readily susceptible to MMP-3 activation. Prolonged treatment of procollagenase with APMA in the absence of MMP-3 also generated a 41,000-Mr collagenase, but this species had only 40% of the full activity and contained Val82 and Leu83 as NH2 termini. Thus, cleavage of the Gln80-Phe81 bond by MMP-3 is crucial for the expression of full collagenase activity. These results suggest that the activation of procollagenase by MMP-3 is regulated by two pathways: one with direct, slow activation by MMP-3 and the other with rapid activation in conjunction with tissue and/or plasma proteinases. The latter event may explain an accelerated degradation of collagens under certain physiological and pathological conditions.
'An Unfinished Mourning': Echo Poems from Pietermaritzburg (1991)

Between January 1987 and June 1989 some 1400 people were killed in incidents of politically-motivated violence in an area of 374 square kilometres around Pietermaritzburg in the Natal Midlands in South Africa1 • In the same area an estimated 1000 houses were destroyed, some 10,000 people moved house permanently, and another 10 to 15 thousand had to flee their homes for some part of the period in question. The South African State, represented by Cabinet Ministers and South African Police (SAP) spokesmen in particular, made consistent efforts to downplay the conflict until it suddenly became an excuse for not lifting the State of Emergency. Despite the denials, it was all too clear that a major political conflict of mounting intensity, amounting in effect to a civil war, was raging in the Natal Midlands, despite the draconian measures for the suppression of political dissent embodied in the Internal Security Act and the Emergency Regulations. The consequences for the several hundred thousand black inhabitants of the area were devastating.
Is otitis media with effusion a biofilm infection? (2004)

Recent attention has focused on the possibility that otitis media with effusion (OME) may represent a chronic infective state such as those evidenced in conditions secondary to biofilms or small colony variants. This review discusses the evidence suggesting that this may indeed be the case and explains why this may prove to be important in the future management of this condition by discussing recent advances in understanding these bacterial phenotypic variants.