gebhart/patrepeval huggingface dataset:
Low profile phased array of dielectric resonator antennas (2002)

A novel high gain, C-Band, low profile phased array is being developed with electronic beam steering capability in the azimuth plane. The radiating elements consist of dielectric resonator antennas (DRAs) of rectangular cross-section, fed from a microstrip line by proximity coupling. Challenging issues in this research project, include achieving wide bandwidth performance, low sidelobe levels, and wide angle scan coverage. Preliminary results on sub-array performance will be presented.
Implantable Nanosensors: Toward Continuous Physiologic Monitoring (2013)

Continuous physiologic monitoring would add greatly to both home and clinical medical treatment for chronic conditions. Implantable nanosensors are a promising platform for designing continuous monitoring systems. This Feature reviews design considerations and current approaches toward such devices.
Hericenones and erinacines: stimulators of nerve growth factor (NGF) biosynthesis inHericium erinaceus (2010)

This review surveys the chemical and biological literature dealing with the isolation, structural elucidation and bioactivity of hericenones and erinacines from the fruiting body and mycelium of Hericium erinaceus, concentrating on work that has appeared in the literature up to December 2009.
Noninvasive Electrocardiographic Imaging of Arrhythmogenic Substrates in Humans (2013)

Cardiac excitation is determined by interactions between the source of electric activation (membrane depolarization) and the load that cardiac tissue presents. This relationship is altered in pathology by remodeling processes that often create a substrate favoring the development of cardiac arrhythmias. Most studies of arrhythmia mechanisms and arrhythmogenic substrates have been conducted in animal models, which may differ in important ways from the human pathologies they are designed to represent. Electrocardiographic imaging is a noninvasive method for mapping the electric activity of the heart in humans in real-world conditions. This review summarizes results from electrocardiographic imaging studies of arrhythmogenic substrates associated with human clinical arrhythmias. Examples include heart failure, myocardial infarction scar, atrial fibrillation, and abnormal ventricular repolarization.
[A new technique of extracting effective components from Chinese herb and natural plant--microwave assisted extraction, MAE]. (2004)

The extraction and separation of effective components from Chinese herb and natural plant is one of the most important processes of natural medicine production. Recently, more and more advanced techniques have been used in the field of modern Chinese medicines, for example, microwave-assisted extraction (MAE). Developed on the base of traditional extracting technology using by organic solvents, MAE is of higher extraction rate and efficiency and better extract quality, as well as few investment, simple equipment, wide adaptability, high selectivity, good fidelity and no pollution. This paper mainly reviews the action principle and characteristic of MAE and its application in the extraction of natural products such as flavonoids, glycosides, polysaccharides, terpenoids and essence. Otherwise, the developing foreground of MAE is also prospected here.
Cdk5-mediated regulation of the PIKE-A-Akt pathway and glioblastoma cell invasion (2008)

Isoform A of phosphatidylinositol 3-kinase enhancer (PIKE-A) is a newly identified prooncogenic factor that has been implicated in cancer cell growth. How PIKE-A activity is regulated in response to growth signal is poorly understood. Here, we demonstrate that cyclin dependent kinase 5 (Cdk5), a protein known to function mainly in postmitotic neurons, directly phosphorylates PIKE-A at Ser-279 in its GTPase domain in glioblastoma cells. This phosphorylation event stimulates PIKE-A GTPase activity and the activity of its downstream effector Akt. Growth signal activates Cdk5 and results in a Cdk5-dependent accumulation of phosphorylated PIKE-A and activation of Akt in the nucleus. Furthermore, PIKE-A phosphorylation and Cdk5 are increased in human glioblastoma specimens. Phosphorylation of PIKE-A by Cdk5 mediates growth factor-induced migration and invasion of human glioblastoma cells. Together, these findings identify PIKE as the first Cdk5 target in cancer cells, revealing a previously undescribed regulatory mechanism that mediates growth signal-induced activation of PIKE-A/Akt and tumor invasion.
In vitro actions on hemopoietic cells of recombinant murine GM‐CSF purified after production in Escherichia coli: Comparison with purified native GM‐CSF (1986)

Recombinant murine GM-CSF produced in Escherichia coli was purified to homogeneity and tested in parallel with purified native GM-CSF. Both recombinant and native GM-CSF stimulated granulocyte and/or macrophage colony formation by adult and fetal mouse progenitor cells, and with adult marrow cells the specific activity of the recombinant GM-CSF (25 X 10(8) U/mg) was similar to that of the native form (15 X 10(8) U/mg). At high concentrations (greater than 200 U/ml), both forms of GM-CSF also stimulated eosinophil colony formation by adult marrow cells and, at very high concentrations (greater than 800 U/ml), megakaryocyte and some erythroid and mixed-erythroid colony formation. Recombinant GM-CSF was as effective in stimulating the proliferation of the GM-CSF-dependent cell line FD as the native molecule. Both recombinant and native GM-CSF were able to induce partial differentiation in colonies of WEHI-3B myeloid leukemic cells. Recombinant GM-CSF competed effectively for the binding of 125I-labeled native GM-CSF to hemopoietic cells, and antiserum to recombinant GM-CSF also neutralized the biological activity of native GM-CSF. The bacterially synthesized GM-CSF was a slightly more effective stimulus for megakaryocyte colony formation than the native molecule. The demonstration that purified bacterially synthesized GM-CSF is biologically active in vitro now permits studies to be undertaken on the in vivo effects of this material.
Complexes of Greatly Enhanced Thermodynamic Stability and Metal Ion Size-Based Selectivity, Formed by the Highly Preorganized Non-Macrocyclic Ligand 1,10-Phenanthroline-2,9-dicarboxylic Acid. A Thermodynamic and Crystallographic Study (2006)

The metal ion-complexing properties of 1,10-phenanthroline-2,9-dicarboxylic acid (PDA) are reported. The protonation constants (pK1 = 4.75, pK2 = 2.53) and formation constants (log K(1)) for PDA with Mg(II) (3.53), Ca(II) (7.3), Sr(II) (5.61), Ba(II) (5.43), La(III) (13.5), Gd(III) (16.1), Zn(II) (11.0), Cd(II) (12.8), Pb(II) (11.4), and Cu(II) (12.8) were determined by UV-vis spectroscopy in 0.1 M NaClO4 at 25 degrees C. The log K(1) values for most of these metal ions were high enough that they were not displaced from their PDA complexes even at pH 2. The log K(1) values were determined using the UV spectra to monitor the competition with EDTA (or DTPA; EDTA = ethylendiamine tetraacetic acid, DTPA = diethylenetriamine pentaacetic acid) as a function of pH according to the equilibrium: M(EDTA) + PDA + nH+ = M(PDA) + EDTAHn. The log K1 values indicate that the rigid extended aromatic backbone of PDA leads to high levels of ligand preorganization and selectivity toward large metal ions (e.g., Ca(II), Cd(II), Gd(III)) with an ionic radius of about 1.0 A and greatly enhanced thermodynamic stability as compared to similar ligands without the reinforcing aromatic backbone. The structure of [Ca(PDA)(H2O)2].2H2O (1) is reported: orthorhombic, Fdd2, a = 44.007(9) A, b = 18.945(4) A, c = 7.2446(14) A, V = 6040(2) A(3), Z = 16, R = 0.0882. The Ca(II) ion has a coordination number of eight, lying in the plane of the tetradentate PDA, with Ca-N bonds averaging 2.55 A and Ca-O bonds to the two acetate groups of PDA averaging 2.45 A. These are very close to the normal Ca-L bonds of this type, supporting the idea that a metal ion the size of Ca(II) (ionic radius approximately 1.0 A) will fit into PDA in a low-strain manner. The remaining four coordination sites on Ca(II) in 1 come from two coordinated water molecules and a chelating carboxylate bridging from an adjacent [Ca(PDA)(H2O)2].2H2O complex. Potential applications of PDA as a ligand in biomedical applications such as Gd(III) contrast agents in MRI are discussed.
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome (2004)

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here.
KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading (2010)

Krüppel-associated box domain-zinc finger proteins (KRAB-ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic repressor assay, allowing the study of KRAB-mediated transcriptional regulation at hundreds of different transcriptional units. By targeting a drug-controllable KRAB-containing repressor to gene-trapping lentiviral vectors, we demonstrate that KRAB and its corepressor KAP1 can silence promoters located several tens of kilobases (kb) away from their DNA binding sites, with an efficiency which is generally higher for promoters located within 15 kb or less. Silenced promoters exhibit a loss of histone H3-acetylation, an increase in H3 lysine 9 trimethylation (H3K9me3), and a drop in RNA Pol II recruitment, consistent with a block of transcriptional initiation following the establishment of silencing marks. Furthermore, we reveal that KRAB-mediated repression is established by the long-range spreading of H3K9me3 and heterochromatin protein 1 beta (HP1beta) between the repressor binding site and the promoter. We confirm the biological relevance of this phenomenon by documenting KAP1-dependent transcriptional repression at an endogenous KRAB-ZFP gene cluster, where KAP1 binds to the 3' end of genes and mediates propagation of H3K9me3 and HP1beta towards their 5' end. Together, our data support a model in which KRAB/KAP1 recruitment induces long-range repression through the spread of heterochromatin. This finding not only suggests auto-regulatory mechanisms in the control of KRAB-ZFP gene clusters, but also provides important cues for interpreting future genome-wide DNA binding data of KRAB-ZFPs and KAP1.
Contribution of toxin A and elastase to virulence of Pseudomonas aeruginosa in chronic lung infections of rats (1982)

A chronic pulmonary infection model in rats was employed to assess the role of individual Pseudomonas aeruginosa exoproducts in disease due to this organism. Groups of rats were inoculated transtracheally with agar beads in which were embedded approximately 10(4) colony-forming units of P. aerugijnosa PAO and the PAO derivatives PR1, T1, E64, and a mixture of T1 and E64 in equal numbers (10(4)). Eight animals from each group were sacrificed at 3, 9, and 30 days after challenge, and their lungs were examined for histopathological changes, bacterial numbers, and the presence of P. aeruginosa exoproducts. The Tox- mutant T1 and the PR1 mutant, which produces enzymatically inactive toxin A, were both found to be less virulent in the rat lung model than was the toxigenic parental strain PAO. Pathological changes seen in animals infected with these mutants were restricted to intra- and peribronchial inflammation, whereas the toxigenic parental strain caused parenchymal changes, including a dense mononuclear-cell infiltration in the alveolar spaces in addition to intra- and peribronchial inflammation. Additionally, mutant E64, which produces a temperature-sensitive elastase, was also found to be less virulent in the rat lung model than was the parental strain. These data demonstrate that both active toxin A and elastase are required for maximum virulence of P. aeruginosa in this model.
The Drosophila gene coding for the alpha subunit of a stimulatory G protein is preferentially expressed in the nervous system. (1989)

In mammals, the alpha subunit of the stimulatory guanine nucleotide-binding protein (Gs alpha) functions to couple a variety of extracellular membrane receptors to adenylate cyclase. Activation of Gs alpha results in the stimulation of adenylate cyclase and an increase in the second messenger cAMP. A 1.7-kilobase cDNA has been identified and characterized from Drosophila that codes for a protein 71% identical to bovine Gs alpha. The similarity is most striking in the regions thought to be responsible for the interactions with receptors and effectors, suggesting that the basic components of this signal-transduction pathway have been conserved through evolution. RNA blot hybridization and DNA sequence analysis suggest that a single transcript, expressed predominantly in the head, is present in Drosophila. In situ hybridization studies indicate that the Drosophila Gs alpha transcript is localized primarily in the cells of the central nervous system and in the eyes.
Microfluidics: Applications for analytical purposes in chemistry and biochemistry (2008)

In this review, we present recent advancements and novel developments in fluidic systems for applied analytical purposes in chemistry, biochemistry, and life science in general that employ and reflect the full benefits of microfluidics. A staggering rise in publications related to integrated, all-in-one microfluidic chips capable of separation, reaction, and detection have been observed, all of which realise the principal of micro total analysis systems or lab-on-a-chip. These integrated chips actively adopt the scaling law concepts, utilising the highly developed fabrication techniques. Their aim is to multi-functionalise and fully automate devices believed to assist the future advancements of point-of-care, clinical, and medical diagnostics.
The relation between optical duobinary modulation and spectral efficiency in WDM systems (1999)

We study the relation between optical duobinary modulation and spectral efficiency in wavelength-division-multiplexed systems. We show that in spite of the fact that duobinary modulation reduces the optical bandwidth of near-rectangular signals, it offers no advantages over binary modulation in terms of the average high-frequency spectral content. This is true as long as the same basic pulse shapes are used in both cases. An improvement in the spectral efficiency can only be achieved by using narrow-band pulses in the duobinary case. This is enabled by the fact that the duobinary code is more robust to narrow-band filtering.
Increased expression of acidic and basic fibroblast growth factors in chronic pancreatitis. (1994)

Acidic fibroblast growth factor (aFGF) and basic fibroblast growth factor (bFGF) belong to a family of mitogenic polypeptides that are involved in cellular proliferation and differentiation. In this study we investigated the potential role of aFGF and bFGF in chronic pancreatitis (CP), a fibrotic condition associated with acinar cell dedifferentiation and atrophy, and fibroblastic proliferation. By immunohistochemistry, aFGF and bFGF were abundant in pancreatic ductal and acinar cells in pancreatic tissues from CP patients. Immunoblotting with the same highly specific monoclonal antibodies demonstrated a marked increase in aFGF and bFGF in pancreatic homogenates from CP patients by comparison with the normal pancreas. Northern blot analysis indicated that, by comparison with normal controls, 16 of 21 CP tissues exhibited a 14-fold increase in aFGF mRNA levels, and 19 of 21 CP tissues exhibited a 15-fold increase in bFGF mRNA levels. In situ hybridization confirmed that this overexpression occurred in ductal and acinar cells, and indicated that both mRNA moieties colocalized with their respective proteins. These findings suggest that aFGF and bFGF may either be involved in the pathobiological mechanisms that occur in CP, or that their overexpression may be the consequence of other perturbations that occur in this disorder.
Endocrine and metabolic adaptation following caesarean section or vaginal delivery. (1996)

The endocrine profile (umbilical venous plasma) of three groups of infants was compared. Samples were taken after eight vaginal deliveries, 11 emergency caesarean sections during labour, and 13 elective caesarean sections before labour. Mean umbilical plasma concentrations of thyroxine and triiodothyronine were significantly higher and cortisol concentration were lower after elective caesarean section compared with the two labour groups. Mean umbilical plasma thyroid stimulating hormone (TSH) concentration was significantly lower after vaginal delivery compared with elective caesarean section. These results suggest that labour reduces plasma thyroid hormone concentrations at birth in association with a rise in cortisol. These adaptations may be the stimulus for the subsequent surge in triiodothyronine previously reported to occur over the first few hours after birth in vaginally delivered infants.
Phase II trial of the Hsp90 inhibitor tanespimycin (Tan) + trastuzumab (T) in patients (pts) with HER2-positive metastatic breast cancer (MBC) (2008)

1027 Background: Tan (17-AAG) inhibits Hsp90 activity, resulting in degradation of client proteins including the HER2 receptor. A phase 1 trial demonstrated clinical activity of T + Tan in pts with HER2+ MBC (1 PR + 4 MRs in 15 pts with median of 2 prior T-based regimens; Modi et al, JCO 2007). Tan was initially a Cremophor-based product; a suspension became available and was substituted in this phase 2 trial. Methods: Eligible pts have HER2+ MBC and either PD within 3m following adjuvant T or PD following 1-line of T-based therapy for MBC. Pts receive standard weekly doses of T followed by Tan (450 mg/m2). Early pts received a Cremophor-based Tan product with antihistamine/steroid premeds. Later pts received the suspension Tan product without premeds. Primary endpoint: ORR by RECIST, disease status assessed every 8w. Results: As of 19Dec07, 29 pts enrolled (mean age 54 yrs, range 31–71; median KPS 90). 21 pts received Cremophor product; 8 pts received suspension product (4 pts crossed-over to the suspension product). 21 pts are evaluable for efficacy. Drug-related toxicity: fatigue (39%), diarrhea (33%), dizziness (24%) and headache (19%). Grade 3 drug-related toxicity in 3 pts (headache/fatigue; ↑ LFTs; and unsteady gait/euphoria, diarrhea), all reversible; 1 pt withdrawn for toxicity. Toxicities common to cytotoxic chemotherapy noticeably absent (alopecia, myelosuppression, peripheral neuropathy). Activity: 5 pts have a confirmed PR (1) 75% decrease in liver metastases, 8 months (m) on study; (2) 45% decrease in hilar node, 15+m/active; (3) 33% decrease in right breast lesion, 7+m /active; (4) 57% decrease in lymph nodes, liver, and left breast lesions, on study 7m; (5) 37% decrease in lymph nodes, 5+m/active. All 4 active pts maintained PR when cross-over to the new formulation. Two additional pts had MR with ↓ tumor markers (6 and 5 m); 5 pts had SD for 4, 4, 4+, 7 and 8 m. Conclusions: The combination of T + Tan is active in pts with HER2+ MBC with progression on T-based therapy (response rate of 24% and clinical benefit rate of 57%). Toxicity is very manageable. The newer suspension product produces a similar safety profile with responses maintained upon cross-over. Accrual continues on the suspension product. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Kosan Biosciences Kosan Biosciences Kosan Biosciences Kosan Biosciences
Studies on Transfer Ribonucleic Acid-Ribosome Complexes (1972)

Abstract The effect of several antibiotics on peptidyl-puromycin synthesis by native polyribosomes was studied. As previously reported, sparsomycin was a competitive inhibitor of the reaction. The inhibition of transpeptidation by a single molecule of sparsomycin per ribosome monomer was consistent with a Hill plot of the kinetic data. In addition, for sparsomycin the Ki was equal to 1.6 x 10-7 m. Inhibition by althiomycin appeared to be noncompetitive. Chloramphenicol, amicetin, gougerotin, and blasticidin S showed both competitive and noncompetitive phases as inhibitors of transpeptidation. The two phases of inhibition by these antibiotics suggested that peptidyl-tRNA on the ribosome may exist in two distinct states with respect to reactivity with puromycin and the action of these antibiotics. These observations are interpreted in terms of models for ribosome function. Furthermore, it is clear from these studies that many antibiotics previously considered to be inhibitors of peptide bond synthesis do not inhibit peptidyl-puromycin formation on native polyribosomes. Thus, some antibiotics which are strong inhibitors of formylmethionly-, acetylphenylalanyl-, or polylysyl-puromycin synthesis produced little or no inhibition of peptidyl-puromycin synthesis on native polyribosomes. These antibiotics include macrolides (erythromycin, oleandomycin, niddamycin, carbomycin, tylosin, and spiramycin III), lincomycin, and streptogramins A (vernamycin A, PA114A). Since these antibiotics cannot inhibit peptide bond synthesis on polyribosomes, the mechanism of their inhibition of peptide bond synthesis with washed ribosomes and synthetic donors remains to be clarified; effects on such model systems for peptide bond synthesis cannot necessarily be extrapolated to their mode of action in intact cells.
Solution Structure of an ABC Collagen Heterotrimer Reveals a Single-register Helix Stabilized by Electrostatic Interactions (2009)

Collagen, known for its structural role in tissues and also for its participation in the regulation of homeostatic and pathological processes in mammals, is assembled from triple helices that can be either homotrimers or heterotrimers. High resolution structural information for natural collagens has been difficult to obtain because of their size and the heterogeneity of their native environment. For this reason, peptides that self-assemble into collagen-like triple helices are used to gain insight into the structure, stability, and biochemistry of this important protein family. Although many of the most common collagens in humans are heterotrimers, almost all studies of collagen helices have been on homotrimers. Here we report the first structure of a collagen heterotrimer. Our structure, obtained by solution NMR, highlights the role of electrostatic interactions as stabilizing factors within the triple helical folding motif. This addresses an issue that has been actively researched because of the predominance of charged residues in the collagen family. We also find that it is possible to selectively form a collagen heterotrimer with a well defined composition and register of the peptide chains within the helix, based on information encoded solely in the collagenous domain. Globular domains are implicated in determining the composition of several collagen types, but it is unclear what their role in controlling register may be. We show that is possible to design peptides that not only selectively choose a composition but also a specific register without the assistance of other protein constructs. This mechanism may be used in nature as well.