gebhart/patrepeval huggingface dataset:
An intracellular lamellar–nonlamellar phase transition rationalizes the superior performance of some cationic lipid transfection agents (2006)

Two cationic phospholipid derivatives with asymmetric hydrocarbon chains were synthesized: ethyl esters of oleoyldecanoyl-ethylphosphatidylcholine (C18:1/C10-EPC) and stearoyldecanoyl-ethylphosphatidylcholine (C18:0/C10-EPC). The former was 50 times more effective as a DNA transfection agent (human umbilical artery endothelial cells) than the latter, despite their similar chemical structure and virtually identical lipoplex organization. A likely reason for the superior effectiveness of C18:1/C10-EPC relative to C18:0/C10-EPC (and to many other cationic lipoids) was suggested by the phases that evolved when these lipoids were mixed with negatively charged membrane lipid formulations. The saturated C18:0/C10-EPC remained lamellar in mixtures with biomembrane-mimicking lipid formulations [e.g., dioleoyl-phosphatidylcholine/dioleoyl-phosphatidylethanolamine/dioleoyl-phosphatidylserine/cholesterol at 45:20:20:15 (wt/wt)]; in contrast, the unsaturated C18:1/C10-EPC exhibited a lamellar-nonlamellar phase transition in such mixtures, which took place at physiological temperatures, approximately 37 degrees C. As is well known, lipid vehicles exhibit maximum leakiness and contents release in the vicinity of phase transitions, especially those involving nonlamellar phase formation. Moreover, nonlamellar phase-forming compositions are frequently highly fusogenic. Indeed, FRET experiments showed that C18:1/C10-EPC exhibits lipid mixing with negatively charged membranes that is several times more extensive than that of C18:0/C10-EPC. Thus, C18:1/C10-EPC lipoplexes are likely to easily fuse with membranes, and, as a result of lipid mixing, the resultant aggregates should exhibit extensive phase coexistence and heterogeneity, thereby facilitating DNA release and leading to superior transfection efficiency. These results highlight the phase properties of the carrier lipid/cellular lipid mixtures as a decisive factor for transfection success and suggest a strategy for the rational design of superior cationic lipid carriers.
Recovering the Basic Structure of Human Activities from a Video-Based Symbol String (2007)

In recent years stochastic context-free grammars have been shown to be effective in modeling human activities because of the hierarchical structures they represent. However, most of the research in this area has yet to address the issue of learning the activity grammars from a noisy input source, namely, video. In this paper, we present a framework for identifying noise and recovering the basic activity grammar from a noisy symbol string produced by video. We identify the noise symbols by finding the set of non-noise symbols that optimally compresses the training data, where the optimality of compression is measured using an MDL criterion. We show the robustness of our system to noise and its effectiveness in learning the basic structure of human activity, through an experiment with real video from a local convenience store.
Cloning and Expression of the Klebsiella pneumoniae Galactose Operon1 (1992)

The entire galactose (gal) operon of Klebsiella pneumoniae was isolated and functionally analyzed in Escherichia coli. The genes encoding galactokinase (galK), galactose-1-phosphate uridyltransferase (galT), and UDP-galactose-4-epimerase (galE) were mapped by complementation analysis. The gene order E-T-K was found to be identical to that of Salmonella spp. and E. coli. Analysis of the nucleotide sequence in the control region revealed significant homology with that of E. coli. Two major sites for transcriptional initiation, both mapped to a cytosyl residue, were identified by primer extension. When the operon is expressed in E. coli, the K. pneumoniae gal gene products make up about 30% of the total cellular proteins. The presence of a powerful promoter responsible for high level synthesis of the gal proteins was also demonstrated using beta-galactosidase as reporter.
Simultaneous sorting of multiple bacterial targets using integrated Dielectrophoretic–Magnetic Activated Cell Sorter (2009)

The ability to rapidly and accurately sort multiple types of biological targets-such as molecules, viruses, bacteria or mammalian cells-from complex sample mixtures is an essential component for a wide range of diagnostic and therapeutic strategies. However, most current selection methods for cell separation are either limited with regard to throughput, as is the case for Fluorescence Assisted Cell Sorting (FACS), or else only allow binary separation of targets that have been labeled via a single parameter, such as Magnetic Activated Cell Sorting (MACS). We report here the integrated Dielectrophoretic-Magnetic Activated Cell Sorter (iDMACS), an integrated platform that combines two different force fields in a single microfluidic device for highly efficient multi-target separation. We describe the underlying physics and design of the iDMACS device and demonstrate approximately 900-fold enrichment of multiple bacterial target cell types with over 95% purity after a single round of separation.
Stimulatory Effect of Melanin-Concentrating Hormone on Luteinising Hormone Release (1997)

Alpha-melanocyte-stimulating hormone (alpha-MSH) and melanin-concentrating hormone (MCH) are two peptide neurotransmitters widely distributed in the mammalian brain, the former originating mainly from cell bodies in the arcuate nucleus and the latter from cell bodies in the zona incerta and lateral hypothalamus. Within the hypothalamus they innervate the pre-optic area, median eminence (ME) and ventromedial nucleus (VMN). Both peptides stimulate sexual behaviour and in this report we have investigated their effect on another gonadal steroid-dependent function, luteinising hormone (LH) release. alpha-MSH, MCH or a combination of the two were injected bilaterally (100 ng/side) into either the medial pre-optic area (MPOA), ME, or VMN of anaesthetised (Saffan 3 ml/kg i.p.) rats that had previously been ovariectomised and adrenalectomised (O+A) and then primed with 5 microg/rat s.c. oestradiol benzoate (OB), 48 h before peptide administration. MCH stimulated LH release when applied to the MPOA and ME; alpha-MSH was inhibitory in the ME and in this model was ineffective in the MPOA. Neither peptide was effective in the VMN. The two peptides were then injected into the MPOA of O+A rats primed with OB followed 48 h later by 0.5 mg/rat s.c. progesterone, which normally induces an LH surge. alpha-MSH, but not MCH, inhibited this induced rise in LH. Administration of anti-MCH antiserum (0.5 microg/side neat serum) also had an inhibitory effect on LH release in this model. These results show that MCH has a stimulatory effect on LH release when administered into the ME and MPOA. In the MPOA, this may be physiologically significant since blocking endogenous MCH with an anti-MCH antiserum inhibits LH release. On the other hand, alpha-MSH has an inhibitory effect on LH release in the MPOA and ME. In the teleost skin these two peptides are functionally antagonistic; it seems that a similar antagonism exists between their effects on LH release.
Effect of Stimulation of the Sphenopalatine Ganglion on Cortical Blood Flow in the Rat (1988)

The effects of electrical stimulation of the sphenopalatine ganglion on cortical blood flow and gas partial pressures (PO2 and PCO2) were studied in the anesthetized rat. Tissue PO2, PCO2, and local CBF were measured simultaneously in both parietal cortices by means of mass spectrometry. Stimulation of the sphenopalatine ganglion increased CBF and tissue PO2 by approximately 50 and 20%, respectively, in the ipsilateral parietal cortex. Smaller but significant increases in CBF and tissue PO2 were simultaneously seen in the contralateral parietal cortex. These variations were also accompanied by small decreases in PCO2 in both parietal cortices and a 5% increase in mean arterial pressure, whereas cortical electrical activity did not change. We conclude that the cholinergic (and vasoactive intestinal polypeptidergic) innervation of the cerebral blood vessels, arising from the sphenopalatine ganglion has significant vasomotor potential and that this system may be of functional importance.
Computerized detection of clustered microcalcifications in digital mammograms using a shift‐invariant artificial neural network (1994)

A computer-aided diagnosis (CAD) scheme has been developed in our laboratory for the detection of clustered microcalcifications in digital mammograms. In this study, we apply a shift-invariant neural network to eliminate false-positive detections reported by the CAD scheme. The shift-invariant neural network is a multilayer back-propagation neural network with local, shift-invariant interconnections. The advantage of the shift-invariant neural network is that the result of the network is not dependent on the locations of the clustered microcalcifications in the input layer. The neural network is trained to detect each individual microcalcification in a given region of interest (ROI) reported by the CAD scheme. A ROI is classified as a positive ROI if the total number of microcalcifications detected in the ROI is greater than a certain number. The performance of the shift-invariant neural network was evaluated by means of a jackknife (or holdout) method and ROC analysis using a database of 168 ROIs, as reported by the CAD scheme when applied to 34 mammograms. The analysis yielded an average area under the ROC curve (Az) of 0.91. Approximately 55% of false-positive ROIs were eliminated without any loss of the true-positive ROIs. The result is considerably better than that obtained in our previous study using a conventional three-layer, feed-forward neural network. The effect of the network structure on the performance of the shift-invariant neural network is also studied.
Effect of CO 2 Pressure on the Reaction with CaO (1979)

The effect of temperature and CO 2 pressure on the kinetics of the reaction CaO + CO 2 °CaCO 3 was studied. The reaction rapidly becomes diffusion‐controlled as CaCO 3 builds up on the surface of CaO. The pressure dependence of the diffusion‐controlled reaction approximated that expected for a Langmuir adsorption isotherm. Temperature affected the extent of CO 2 adsorption through θ, the fraction of surface sites covered, as well as the diffusion coefficient, D. The relation Rate =θ KD describes the reaction where K is a constant containing geometrical factors, etc. The diffusion activation energy equals 29±6 kcal/mol.
Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana (2000)

We investigated the potential of double-stranded RNA interference (RNAi) with gene activity in Arabidopsis thaliana. To construct transformation vectors that produce RNAs capable of duplex formation, gene-specific sequences in the sense and antisense orientations were linked and placed under the control of a strong viral promoter. When introduced into the genome of A. thaliana by Agrobacterium-mediated transformation, double-stranded RNA-expressing constructs corresponding to four genes, AGAMOUS (AG), CLAVATA3, APETALA1, and PERIANTHIA, caused specific and heritable genetic interference. The severity of phenotypes varied between transgenic lines. In situ hybridization revealed a correlation between a declining AG mRNA accumulation and increasingly severe phenotypes in AG (RNAi) mutants, suggesting that endogenous mRNA is the target of double-stranded RNA-mediated genetic interference. The ability to generate stably heritable RNAi and the resultant specific phenotypes allows us to selectively reduce gene function in A. thaliana.
The Highly Stereoselective Oxidation of Polyunsaturated Fatty Acids by Cytochrome P450BM-3 (1996)

Cytochrome P450BM-3 catalyzes NADPH-dependent metabolism of arachidonic acid to nearly enantiomerically pure 18(R)-hydroxyeicosatetraenoic acid and 14(S), 15(R)-epoxyeicosatrienoic acid (80 and 20% of total products, respectively). P450BM-3 oxidizes arachidonic acid with a rate of 3.2 +/- 0.4 micromol/min/nmol at 30 degrees C, the fastest ever reported for an NADPH-dependent, P450-catalyzed reaction. Fatty acid, oxygen, and NADPH are utilized in an approximately 1:1:1 molar ratio, demonstrating efficient coupling of electron transport to monooxygenation. Eicosapentaenoic and eicosatrienoic acids, two arachidonic acid analogs that differ in the properties of the C-15-C-18 carbons, are also actively metabolized by P450BM-3 (1.4 +/- 0.2 and 2.9 +/- 0.1 micromol/min/nmol at 30 degrees C, respectively). While the 17,18-olefinic bond of eicosapentaenoic acid is epoxidized with nearly absolute regio- and stereochemical selectivity to 17(S),18(R)-epoxyeicosatetraenoic acid (>/=99% of total products, 97% optical purity), P450BM-3 is only moderately regioselective during hydroxylation of the eicosatrienoic acid omega-1, omega-2, and omega-3 sp3 carbons, with 17-, 18-, and 19-hydroxyeicosatrienoic acid formed in a ratio of 2.4:2.2:1, respectively. Based on the above and on a model of arachidonic acid-bound P450BM-3, we propose: 1) the formation by P450BM-3 of a single oxidant species capable of olefinic bond epoxidation and sp3 carbon hydroxylation and 2) that product chemistry and, thus, catalytic outcome are critically dependent on active site spatial coordinates responsible for substrate binding and productive orientation between heme-bound active oxygen and acceptor carbon bond(s).
Augmented acetylcholine‐induced translocation of RhoA in bronchial smooth muscle from antigen‐induced airway hyperresponsive rats (2001)

Acetylcholine (ACh)-induced translocation of RhoA in bronchial smooth muscle of repeatedly antigen-challenged rats that have a marked airway hyperresponsiveness (AHR) was examined. ACh induced time- and concentration-dependent translocation of RhoA to the plasma membrane, indicating an activation of RhoA in bronchial smooth muscle. The level of ACh-induced RhoA translocation was further increased markedly in the AHR group as compared to that in the control group. It is suggested that the augmented activation of RhoA observed in the hyperresponsive bronchial smooth muscle might be responsible for the enhanced ACh-induced Ca(2+) sensitization of bronchial smooth muscle contraction associated with AHR.
Contact Printing Beyond Surface Roughness: Liquid Supramolecular Nanostamping (2007)

Liquid supramolecular nanostamping (LiSuNS) is an efficient stamping technique that replicates various DNA features with no need of solid surface contact. LiSuNS is based on the specific interaction of complementary DNA strands. An original pattern composed of multiple DNA strands on a rough surface can be copied onto a liquid prepolymer that is subsequently hardened, leading to a solid surface that displays the mirror image of the master used. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c1068_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.
SUMO-1 targets RanGAP1 to kinetochores and mitotic spindles (2002)

RanGAP1 was the first documented substrate for conjugation with the ubiquitin-like protein SUMO-1. However, the functional significance of this conjugation has not been fully clarified. We sought to examine RanGAP1 behavior during mitosis. We found that RanGAP1 associates with mitotic spindles and that it is particularly concentrated at foci near kinetochores. Association with kinetochores appeared soon after nuclear envelope breakdown and persisted until late anaphase, but it was lost coincident with nuclear envelope assembly in telophase. A mutant RanGAP1 protein lacking the capacity to be conjugated to SUMO-1 no longer associated with spindles, indicating that conjugation was essential for RanGAP1's mitotic localization. RanBP2, a nuclear pore protein that binds SUMO-1-conjugated RanGAP1 during interphase, colocalized with RanGAP1 on spindles, suggesting that a complex between these two proteins may be involved in mitotic targeting of RanGAP1. This report shows for the first time that SUMO-1 conjugation is required for mitotic localization of RanGAP1, and suggests that a major role of SUMO-1 conjugation to RanGAP1 may be the spatial regulation of the Ran pathway during mitosis.
Primary Structure and Tissue Distribution of FRZB, a Novel Protein Related to Drosophila Frizzled, Suggest a Role in Skeletal Morphogenesis (1996)

Articular cartilage extracts were prepared to characterize protein fractions with in vivo chondrogenic activity (Chang, S., Hoang, B., Thomas, J. T., Vukicevic, S., Luyten, F. P., Ryba, N. J. P., Kozak, C. A., Reddi, A. H., and Moos, M. (1994) J. Biol. Chem. 269, 28227-28234). Trypsin digestion of highly purified chondrogenic protein fractions allowed the identification of several unique peptides by amino acid sequencing. We discovered a novel cDNA encoding a deduced 36-kDa protein by using degenerate oligonucleotide primers derived from a 30-residue peptide in reverse transcription polymerase chain reactions. Its N-terminal domain showed approximately 50% amino acid identity to the corresponding region of the Drosophila gene frizzled, which has been implicated in the specification of hair polarity during development. Hydropathy and structural analyses of the open reading frame revealed the presence of a signal peptide and a hydrophobic domain followed by multiple potential serine/threonine phosphorylation sites and a serine-rich C terminus. Cell fractionation studies of primary bovine articular chondrocytes and transfected COS cells suggested that the protein is membrane-associated. In situ hybridization and immunostaining of human embryonic sections demonstrated predominant expression surrounding the chondrifying bone primordia and subsequently in the chondrocytes of the epiphyses in a graded distribution that decreased toward the primary ossification center. Transcripts were present in the craniofacial structures but not in the vertebral bodies. Because it is expressed primarily in the cartilaginous cores of developing long bones during embryonic and fetal development (6-13 weeks) and is homologous to the polarity-determining gene frizzled, we believe that this gene, which we named frzb, is involved in morphogenesis of the mammalian skeleton.
The long noncoding RNA HOTAIR has tissue and cell type-dependent effects on HOX gene expression and phenotype of urothelial cancer cells (2015)

Our data indicate that HOTAIR overexpression may affect differentiation state and aggressiveness of UC cells, but in a cell-type dependent manner. Our functional studies and the comparison of our expression data sets with those from other cancer cell types, which revealed minimal overlaps, indicate that effects of HOTAIR are strongly tissue-dependent and can even differ within one cancer type. Thus, HOTAIR functions and target genes cannot simply be transferred from one cancer type to the other.
Peptidomimetics via modifications of amino acids and peptide bonds (2014)

Peptidomimetics represent an important field in chemistry, pharmacology and material science as they circumvent the limitations of traditional peptides used in therapy. Self-structural organizations such as turns, helices, sheets and loops can be accessed by chemical modifications of amino acids or peptides. In-depth structural and conformational analysis and structure-activity relationships (SAR) offer a way to establish peptidomimetic libraries. Herein, we review recent developments in peptidomimetics that are formed via heteroatom replacement within the native amino acid backbone. Each sub-section describes structural features, utility and preparative methods.
Oxygen therapy in chronic lung disease (1998)

### Oxygen in first aid

Oxygen can be used in acute situations where there is hypoxia because of acute lung injury or reduced ventilation, when there is underlying chronic lung disease, or when it is important to maintain oxygen delivery to certain tissues. Maintaining oxygen delivery may help tissue survival when there is cardiac failure with pulmonary oedema, ischaemic tissue (such as after an infarction), or a cerebrovascular accident. Oxygen saturation should be monitored by pulse oximetry. If oxygen saturation is low additional inspired oxygen should be used to maintain saturation near 100%.



Paramedics giving oxygen after a skiing accident



Oxygen can be used empirically in acute situations if a patient is cyanosed or has a raised respiratory rate. Generally it is safe to use a high inspired oxygen concentration as long as there is no suggestion that the patient has chronic obstructive pulmonary disease. The main danger of acute oxygen is that carbon dioxide retention may occur in some patients with chronic obstructive pulmonary disease. If this is suspected the oxygen should be given by a high flow 24% or 28% mask until arterial blood gases can be measured. Oxygen increases the fire hazard at the scene of an accident.



Small oxygen cylinders



In emergency situations lack of availability of oxygen and an appropriate delivery system may prevent early treatment. Ambulances carry oxygen and paramedical staff are trained to use the equipment in acute situations. Some general practitioners also carry small cylinders that can deliver 2 l/min for two hours, which avoids the need to wait for an ambulance.

### Occasional oxygen in chronic lung disease

Breathlessness in chronic lung conditions or in carcinoma of the bronchus may be intermittent. It is likely to increase on exertion, and simple everyday tasks such as washing, dressing, or eating may cause problems. Some patients feel that a short period on oxygen before or …
Derivation of Coupled Power Equations (1972)

The modes of a multimode dielectric waveguide are coupled by imperfections of the waveguide structure. The propagation of the coupled modes is described by coupled wave equations involving the wave amplitudes. If the coupling functions are random variables the interaction between the modes can be described more easily by coupled power equations. The derivation of the coupled power equations from the coupled wave equations is accomplished with the help of perturbation theory.
HmSearch (2013)

Hamming distance measures the number of dimensions where two vectors have different values. In applications such as pattern recognition, information retrieval, and databases, we often need to efficiently process Hamming distance query, which retrieves vectors in a database that have no more than k Hamming distance from a given query vector. Existing work on efficient Hamming distance query processing has some of the following limitations, such as only applicable to tiny error threshold values, unable to deal with vectors where the value domain is large, or unable to attain robust performance in the presence of data skew.
THE CHEMICAL REACTIVITY AND MODIFICATION OF KERATIN FIBRES (1975)

(1975). THE CHEMICAL REACTIVITY AND MODIFICATION OF KERATIN FIBRES. Textile Progress: Vol. 7, No. 1, pp. 1-70.
Gould-Jacob Type of Reaction in the Synthesis of Thieno[3,2-e]pyrimido[1,2-c]pyrimidines: A Comparison of Classical Heating vs Solvent-Free Microwave Irradiation (1999)

Gould-Jacob type of reaction for the synthesis of thieno[3,2e]pyrimido[l,Z-~Jpyrimidines (5) has been carried out conventionally by the condensation between 4-aminothieno[2,3qpyrimidines (3 and diethyl ethoxymethylenemdonate (2) via acyclic intermediates diethyl N-[5,6-disubstituted thieno[2,3-