gebhart/patrepeval huggingface dataset:
Self -aligned radial contour mode micromechanical disk resonators for wireless communications. (2006)

A new fabrication methodology that allows self-alignment of a micromechanical structure to its anchor(s) has been developed to achieve vibrating radial contour mode polysilicon micromechanical disk resonators with resonance frequencies up to 1.156 GHz and measured <italic>Q</italic>'s at this frequency 2,650 in both vacuum and air. For these resonators, self-alignment of the stem to exactly the center of the disk it supports allows balancing of the resonator far superior to that achieved by previous versions, allowing the present devices to retain high <italic>Q</italic> while achieving frequencies in the gigahertz range for the first time. Furthermore, via design strategies that merge different materials at critical locations, this work has demonstrated micromechanical resonators in chemical vapor deposited (CVD) nanocrystalline diamond with record frequencies up to 1.89 GHz and with order of magnitude increases in <italic> Q</italic> at this frequencies to values >10,000, At 498 MHz, <italic>Q</italic>'s up to 55,300 in vacuum and 35,550 in air have been demonstrated, both of which sets frequency-<italic>Q</italic> product record at 2.75 x 10<super> 13</super> in vacuum, and 1.77 x 10<super>13</super> in air, both of which now exceeds the 1 x 10<super>13</super> of some of the best quartz crystals. In addition, closed-form analytical models for the <italic>Q</italic>-limiting anchor losses have been developed and verified by the experimental data, providing valuable guidance on geometrical and material-centric design of radial contour mode disk resonators. Finally, a mixing-based measurement setup and an electrically accessible substrate ground plane have been employed to characterize micromechanical resonators in the ultra-high frequency (UHF) range, both of which prove instrumental in suppressing feedthrough noises to allow clean measurement of gigahertz vibrating resonator frequency characteristics.
Gastrointestinal urease in man. I. Activity of mucosal urease. (1966)

EDITORIAL SYNOPSIS Mucosal estimations of urease show that it is highest in the gastric mucosa and lowest in the large intestine. It seems that bacterial urease activity may be limited to the colon.
Identification and functional characterization of DR6, a novel death domain‐containing TNF receptor (1998)

Tumor nectosis factor (TNF) receptors are key players in inflammation and immune regulation. A new member of this family, termed death receptor-6 (DR6), has been identified. Like other death receptors, DR6 is a type I transmembrane receptor, possesses four extracellular cysteine-rich motifs and a cytoplasmic death domain. DR6 is expressed in most human tissues and abundant transcript was detected in heart, brain, placenta, pancreas, thymus, lymph node and several non-lymphoid cancer cell lines. DR6 interacts with TRADD, which has previously been shown to associate with TNFR1. Furthermore, ectopic expression of DR6 in mammalian cells induces apoptosis and activation of both NF-kappaB and JNK.
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates (2007)

Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as microRNAs. We have constructed the TranspoGene database, which covers TEs located inside protein-coding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TEs were classified according to location within the gene: proximal promoter TEs, exonized TEs (insertion within an intron that led to exon creation), exonic TEs (insertion into an existing exon) or intronic TEs. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. In addition, we created microTranspoGene: a database of human, mouse, zebrafish and nematode TE-derived microRNAs. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. Publicly available query interfaces to TranspoGene and microTranspoGene are available at http://transpogene.tau.ac.il/ and http://microtranspogene.tau.ac.il, respectively. The entire database can be downloaded as flat files.
Coupling of Angiogenesis and Neurogenesis in Cultured Endothelial Cells and Neural Progenitor Cells after Stroke (2007)

Angiogenesis and neurogenesis are coupled processes. Using a coculture system, we tested the hypothesis that cerebral endothelial cells activated by ischemia enhance neural progenitor cell proliferation and differentiation, while neural progenitor cells isolated from the ischemic subventricular zone promote angiogenesis. Coculture of neural progenitor cells isolated from the subventricular zone of the adult normal rat with cerebral endothelial cells isolated from the stroke boundary substantially increased neural progenitor cell proliferation and neuronal differentiation and reduced astrocytic differentiation. Conditioned medium harvested from the stroke neural progenitor cells promoted capillary tube formation of normal cerebral endothelial cells. Blockage of vascular endothelial growth factor receptor 2 suppressed the effect of the endothelial cells activated by stroke on neurogenesis as well as the effect of the supernatant obtained from stroke neural progenitor cells on angiogenesis. These data suggest that angiogenesis couples to neurogenesis after stroke and vascular endothelial growth factor likely mediates this coupling.
Metal‐Mediated Cross‐Linking in the Generation of a Marine‐Mussel Adhesive (2004)

Iron muscles into mussels: Marine mussels adhere to rocks with a protein-based glue. An iron complex is the key curing agent in this adhesive, and the iron center is coordinated by three DOPA residues (see picture). These studies present the first identified case in which a transition-metal center is integral to forming a noncrystalline biological material. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z52759_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.
Chemokine Expression in the Monocytic Cell Line THP-1 in Response to Purified Shiga Toxin 1 and/or Lipopolysaccharides (2004)

Infections with Shiga toxin (Stx)-producing bacteria are associated with bloody diarrhea and postdiarrheal sequelae, including hemolytic uremic syndrome and central nervous system (CNS) abnormalities. Stx-induced intestinal, renal, and CNS vascular lesions may involve a localized production of proinflammatory cytokines in target organs, as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) up-regulate Stx receptor globotriaosylceramide (Gb(3)) expression on vascular endothelial cells. However, leukocyte recruitment to injured sites may also exacerbate vascular damage. A cytokine macroarray analysis of transcripts derived from macrophage-like THP-1 cells treated with Stx1, lipopolysaccharides (LPS), or both demonstrated a consistent up-regulation of TNF-alpha, IL-1beta, and four genes encoding the chemokines interleukin-8 (IL-8), macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, and growth-related oncogene beta (GRO-beta). Real-time PCR analysis verified the macroarray results. Northern blot analyses after the addition of the transcriptional inhibitor actinomycin D revealed increased IL-8 mRNA stability in THP-1 cells treated with Stx1 or Stx1 plus LPS. Finally, enzyme-linked immunosorbent assay data for Stx1- plus LPS-treated cells demonstrated a poor correlation between IL-8, MIP-1alpha, MIP-1beta, and GRO-beta mRNA levels and protein production, indicating a posttranscriptional regulatory effect. Our data suggest that in response to Stx1 and LPS, macrophages may be a source of chemokines that promote tissue damage through leukocyte recruitment and activation.
Wound Care Selecting the Right Dressing (1995)

1Manager of Enterostomal Therapy (ET) Nursing and director of ET Nursing Education, Cleveland, OH 2Assistant director of ET Nursing Education at the Cleveland Clinic Foundation, Cleveland, OH
Commercial human albumin preparations for clinical use are immunosuppressive in vitro (2006)

DA-DKP was present in significant concentrations in all HSA sources tested and was partially responsible for the immunosuppressive effects of HSA on activated PBMCs and T-lymphocytes in vitro. In view of these findings, administering HSA to immunocompromised critically ill patients might be reevaluated.
Tendon and pressure actuation for a bio-inspired manipulator based on an antagonistic principle (2015)

This paper proposes a soft, inflatable manipulator that is antagonistically actuated by tendons and pneumatics. The combination of the two actuation mechanisms in this antagonistic robot structure is inspired by the octopus which uses its longitudinal and transversal muscles to steer, elongate, shrink and also stiffen its continuum arms. By “activating” its antagonistic muscle groups at the same time, the octopus can achieve multiple motion patterns as well as stiffen their arms. Being organized in a similar fashion, our robot manipulator uses, on the one hand, pneumatic actuation and, on the other hand, tendon-based actuation - one opposing the other, achieving an overall antagonistic actuation framework. Controlling the pressure inside the robot while at the same time controlling the tendons' displacements, the robot can be moved into a wide range of configurations while simultaneously controlling the arm's stiffness. This paper builds on earlier work by the authors: Here, we present a new conic-shaped manipulator structure and the control architecture. Using a constant curvature model, we have derived an approach suitable for controlling the robot manipulator. The manipulator's reachable workspace is analyzed and proof-of-concept experiments were conducted to show the robot's stiffness control and motion abilities.
Clinical Importance of Identifying Coagulase-Negative Staphylococci Isolated from Blood Cultures: Evaluation of MicroScan Rapid and Dried Overnight Gram-Positive Panels versus a Conventional Reference Method (1998)

ABSTRACT We evaluated the clinical usefulness of species identification of blood isolates of coagulase-negative staphylococci as a predictor of the clinical significance of the isolates. In addition, we compared results of species identification obtained with MicroScan Rapid Gram-Positive Identification panels and Dried Overnight (Conventional) Gram-Positive Identification panels with those obtained by a tube reference method. Two hundred eighty-five blood isolates were tested, including 92 judged to represent true bacteremia and 193 judged to represent contamination. The most common species detected were Staphylococcus epidermidis , Staphylococcus hominis , and Staphylococcus haemolyticus . These three species accounted for nearly 98% of the clinically significant isolates and 89% of the contaminants. The isolation of other species almost always represented contamination. However, identification of the three most common species did not help distinguish pathogens from contaminants. Both the Rapid and the Dried Overnight Gram-Positive panels identified S. epidermidis strains accurately, but the panels performed less well for the other species. Analysis revealed that S. hominis was frequently misidentified due to the presence of a previously unknown subspecies. Based on the initial results, revised investigational Dried Overnight Gram-Positive Identification panels (CPID-2) were prepared and tested. The CPID-2 panels identified 85 to 95% of S. epidermidis strains, 76 to 86% of S. hominis strains, and 88 to 92% of S. haemolyticus strains with high probability (&gt;85%) and, overall, represented a significant improvement over the other panels for identification of these staphylococcal species.
The NCBI: Publicly Available Tools and Resources on the Web (2003)

As computing technology advances and new sources of valuable biological information are collected the numbers of database and the tools that are used to analyze the data they contain will change. From the time this article was originally written to the time (about 6 months) this summary was put together another 4 releases of Genbank have been made available, two new BLAST search engines, PHI-BLAST and organism-specific BLAST, a database of Human Genetic Variation (dbSNP), and a new version of Cn-3D. The NCBI will, for the forseeable future, provide the research community with a wealth of information and computing tools. made a number of other tools available for molecular biologists.
ARDS-like lung injury produced by endotoxin in platelet-activating factor-primed rats (1993)

We recently reported that the combined administration of lipopolysaccharide (LPS) and platelet-activating factor (PAF) in rats, at doses that are completely devoid of any effect when given alone, caused lung injury characterized by neutrophil adhesion to lung capillaries and postcapillary venules, neutrophil accumulation in the lung parenchyma, platelet-fibrin deposits in postcapillary venules, and pulmonary edema. A marked increase in lung myeloperoxidase activity and an elevation of serum tumor necrosis factor-alpha and thromboxane B2, along with leukopenia and thrombocytopenia, were also noticed. The present study aimed to examine whether repeated LPS-PAF stimulus can cause progressive lung injury reminiscent of adult respiratory distress syndrome (ARDS). A second LPS-PAF challenge, 4 h (n = 11) after the original challenge, induced mortality (69% at 24 h, P < 0.01) and some of the pathological changes seen in clinical ARDS, including severe pulmonary edema, alveolar proteinaceous exudates, monocytic infiltration, and a further increase in lung myeloperoxidase activity (700%, P < 0.01). Repeated LPS-PAF dosing also resulted in sustained increased serum tumor necrosis factor-alpha levels (1,610 +/- 470 pg/ml, P < 0.01) and further exacerbation of the leukopenia (-68 +/- 6%, P < 0.01) and thrombocytopenia (-65 +/- 8%, P < 0.01). These data suggest that repeated LPS-PAF actions are sufficient to elicit pathophysiology of ARDS-like lung injury.
CD26: an expanding role in immune regulation and cancer. (2002)

In this review, we highlight major aspects of the biology of CD26, a dipeptidyl peptidase IV (DPPIV)-containing surface glycoprotein with multiple functions. In particular, we discuss findings demonstrating that CD26/DPPIV has an essential role in immune regulation as a T cell activation molecule and a regulator of chemokine function. We also review recent studies that identify key cellular molecules that physically associate with CD26 and the potential consequences of their interaction, including those with clinically-related implications. Furthermore, we present work suggesting a role for CD26 in the pathogenesis and behavior of selected human cancers, both solid tumors and hematological malignancies. We present recent studies that investigate the potential role of CD26 as a molecular target for novel treatment modalities for T cell lymphoid malignancies and possibly other hematological malignancies, with work involving the use of anti-CD26 monoclonal antibody, CD26-transfected cells as well as soluble CD26 molecules.
Evolutionary Algorithms in Engineering and Computer Science: Recent Advances in Genetic Algorithms, Evolution Strategies, Evolutionary Programming, GE (1999)

From the Publisher:
Genetic algorithms (GA) and evolution strategies (ES) are relatively new stochastic based techniques for solving engineering problems on computers. GA and ES are based on a loose biological analogy: evolutionary theory (mutation, crossover, selection, survival of the fittest). Evolutionary algorithms encompass all adaptive and computational models of natural evolutionary systems - genetic algorithms, evolution strategies, evolutionary programming and genetic programming. In addition, they work well in the search for global solutions to optimization problems, allowing the production of optimization software that is robust and easy to implement. This book presents state of the art lectures delivered by international academic and industrial experts in the field of evolutionary computing. It bridges artificial intelligence and scientific computing with a particular emphasis on real-life problems encountered in application-oriented sectors, such as aerospace, electronics, telecommunications, energy and economics.
Antibody-Mediated versus Nontargeted Delivery in a Human Small Cell Lung Carcinoma Model (1998)

The uptake of macromolecular agents in tumor cells (LX-1, human small cell lung carcinoma) and in corresponding tumor xenografts was compared in a parallel study utilizing a long-circulating biocompatible graft copolymer, MPEGs-PL-DTPA [Bogdanov, A., Jr., et al. (1995) Adv. Drug Delivery Rev. 16, 335-348; Bogdanov, A., Jr., et al. (1996) Bioconjugate Chem. 7, 144-149] and a tumor-specific chimeric monoclonal antibody, BR96 [Hellstrom, I., et al. (1990) Cancer Res. 50, 2183-2190; Garrigues, J., et al. (1993) Am. J. Pathol. 142, 607-622]. Covalent grafted conjugates of methoxy-(polyethylene glycol)succinate and polylysine and BR96 were modified with DTPA, biotinyl, or rhodamine-X-residues. Using radionuclide and fluorescent labeled derivatives of the copolymer and the antibody, we established that (1) the copolymer does not associate with the plasma membrane in N-ethylmaleimide-treated cells and is slowly internalized by live cells at 37 degrees C; (2) the antibody binds rapidly to the surface of LX-1 cells and shows active internalization in vesicles with a subsequent slow decrease in the cell-associated antibody concentration; (3) LX-1 cells bear more than 1 million BR96 binding sites/cell (with an apparent Kd of 4.5 x 10[-7] M); and (4) intravesicular fluorescence intensity in LX-1 cells was linearly dependent on copolymer concentration, suggesting fluid phase endocytosis. Tumor localization by nuclear imaging, biodistribution, microdistribution by histology, and determination of tumor cell fraction uptake was performed in LX-1 tumor xenografts. In vivo study showed that MPEGs-PL-DTPA progressively accumulates in the tumor, yielding from 2.8+/-1.5% injected dose per gram of tissue (ID/g) at 24 h to 5.2+/-1.7% ID/g of tissue at 48 h. The antibody accumulation peaked at 24 h (6.0+/-3.2% ID/g) and decreased thereafter. We determined that at 24 h 43.9+/-11.29% of the polymer accumulated in the tumor was associated with tumor cell fraction with the remainder of the accumulated dose localized in the interstitium. Accumulation of the biotinylated graft copolymer and the antibody in LX-1 xenografts and their uptake in cells were confirmed by histology using avidin-peroxidase staining. Our study demonstrates that, although BR96 is highly specific in vitro, tumoral drug delivery in vivo can be equally high with long-circulating graft copolymers because of slow extravasation at the tumor site.
Ca2+ oscillations induced by a cytosolic sperm protein factor are mediated by a maternal machinery that functions only once in mammalian eggs (2000)

At fertilization in mammals, the sperm activates the egg by inducing a series of oscillations in the intracellular free Ca(2+) concentration. There is evidence showing that this oscillatory event is triggered by a sperm-derived protein factor which diffuses into egg cytoplasm after gamete membrane fusion. At present the identity of this factor and its precise mechanism of action is unknown. Here, we studied the specificity of action of the sperm factor in triggering Ca(2+) oscillations in mammalian eggs. In doing so, we examined the patterns of Ca(2+) signaling in mouse eggs, zygotes, parthenogenetic eggs and maturing oocytes following the stimulation of bovine sperm extracts which contain the sperm factor. It is observed that the sperm factor could induce Ca(2+) oscillations in metaphase eggs, maturing oocytes and parthenogenetically activated eggs but not in the zygotes. We present evidence that Ca(2+) oscillations induced by the sperm factor require a maternal machinery. This machinery functions only once in mammalian oocytes and eggs, and is inactivated by sperm-derived components but not by parthenogenetic activation. In addition, it is found that neither InsP(3) receptor sensitivity to InsP(3) nor Ca(2+) pool size are the determinants that cause the fertilized egg to lose its ability to generate sperm-factor-induced Ca(2+) oscillations at metaphase. In conclusion, our study suggests that the orderly sequence of Ca(2+) oscillations in mammalian eggs at fertilization is critically dependent upon the presence of a functional maternal machinery that determines whether the sperm-factor-induced Ca(2+) oscillations can persist.
Cangrelor: a novel P2Y12receptor antagonist (2009)

Antiplatelet therapy is critical in the prevention of thrombotic complications of acute coronary syndrome and percutaneous coronary interventions. Current antiplatelet agents (aspirin, clopidogrel and glycoprotein IIb/IIIa antagonists) have demonstrated the capacity to reduce major adverse cardiac events. However, these agents have limitations that compromise their clinical utility. The platelet P2Y12 receptor plays a central role in platelet function and is a focus in the development of antiplatelet therapies. Cangrelor is a potent, competitive inhibitor of the P2Y12 receptor that is administered by intravenous infusion and rapidly achieves near complete inhibition of ADP-induced platelet aggregation. This investigational drug has been studied for use during coronary procedures and the management of patients experiencing acute coronary syndrome and is undergoing evaluation for use in the prevention of perioperative stent thrombosis.