gebhart/patrepeval huggingface dataset:
Principles of Surface-Directed Liquid Flow in Microfluidic Channels (2002)

To direct liquid flow inside microchannels, surface free energies were patterned by use of self-assembled monolayers (SAMs) in combination with either multistream laminar flow or photolithography. For the photolithographic method, two photocleavable SAMs were designed and synthesized. Carboxylic acid-terminated monolayers were obtained by photodeprotection, which was confirmed by contact angle and X-ray photoelectron spectroscopy. Using either of these patterning methods, we show that aqueous liquids flow only along the hydrophilic pathways when the pressure is maintained below a critical value; the liquids are referred to as being confined by virtual walls. Several principles of liquid flow in surface-patterned channels were derived analytically and verified experimentally. These principles include the maximum pressure that virtual walls can withstand, the critical width of the hydrophilic pathway that can support spontaneous flow, the smallest width of the liquid streams under an external pressure, the critical radius of curvature of turns that can be introduced into the hydrophilic pathway without liquid crossing the hydrophilic-hydrophobic boundary, and the minimal distance for two liquid streams to remain separated under the maximum pressure. Experimental results are in good agreement with the analytical predictions.
Towards a New Regime for the Protection of Outer Space as the "Province of All Mankind" (2000)

In the year 2004, the planned $60 billion International Space Station (ISS) is scheduled to be completed, extending over an area almost as large as three football fields, and its laboratory and living modules will have as much room as two Boeing 747 jumbojets. The ISS will usher in a multinational human presence in space and will be a world community living and working together in space. As science progresses in leaps and bounds, international law governing the exploration and use of outer space limps forlornly behind. As we move to colonize the "province of all mankind," the accompanying dangers become more apparent. It has often been questioned whether international law can contribute more than lofty aspirations, general principles, or broad frameworks. This Article argues that international law must replace its language of normativity, and a vocabulary of treaty rules and customary norms, with a new rhetoric of cooperation and implementation in building a new regime for the protection of the outer-space environment in the new millennium.
Electrodeposition of Al-Mo-X (X: Mn or Ni) Ternary Alloys from Lewis Acidic AlCl3-EtMeImCl Molten Salts (2004)

The electrodeposition of Al-Mo-X (X: Mn or Ni) ternary alloys was examined in the Lewis acidic 66.7-33.3 percent mole fraction aluminum chloride-1-ethyl-3-methylimidazolium chloride (AlCl3-EtMeImCl) molten salt. The electrodeposition of Al-Mo-Mn was investigated in solutions containing Mo(II) and Mn(II). By adjusting CMn(II)/CMo(II) in the plating solution and employing different current densities, it was possible to prepare alloys with very different compositions and surface morphologies. All Al-Mo-Mn alloys were dense, compact, and adhered well to the substrate surface. The addition of small amounts of Mn to the Al-Mo alloy resulted in an improvement in its chloride pitting corrosion resistance and metallic brightness. For example, Al90.1Mo9.9 displayed a pitting potential of +725 mV versus Al, whereas Al88.8Mo10.0Mn1.2 exhibited a pitting potential of +868 mV versus Al. Al-Mo-Mn alloys that contained more than about 10 a/o Mo+Mn exhibited a metallic glass structure. Al-Mo-Ni alloys that were electrodeposited from solutions of Ni(II) and Mo(II) in the AlCl3-EtMeImCl molten salt were fragile and powdery.
Electron-induced crosslinking of aromatic self-assembled monolayers: Negative resists for nanolithography (1999)

We have explored the interaction of self-assembled monolayers of 1,1′-biphenyl-4-thiol (BPT) with low energy electrons. X-ray photoelectron, infrared, and near edge x-ray absorption fine structure spectroscopy showed that BPT forms well-ordered monolayers with the phenyl rings tilted ∼15° from the surface normal. The films were exposed to 50 eV electrons and changes were monitored in situ. Even after high (∼10 mC/cm2) exposures, the molecules maintain their preferred orientation and remain bonded on the gold substrate. An increased etching resistance and changes in the infrared spectra imply a crosslinking between neighboring phenyl groups, which suggests that BPT can be utilized as an ultrathin negative resist. This is demonstrated by the generation of patterns in the underlying gold.
Mitochondrial medicine--molecular pathology of defective oxidative phosphorylation. (2001)

Different tissues display distinct sensitivities to defective mitochondrial oxidative phosphorylation (OXPHOS). Tissues highly dependent on oxygen such as the cardiac muscle, skeletal and smooth muscle, the central and peripheral nervous system, the kidney, and the insulin-producing pancreatic beta-cell are especially susceptible to defective OXPHOS. There is evidence that defective OXPHOS plays an important role in atherogenesis, in the pathogenesis of Alzheimer's disease, Parkinson's disease, diabetes, and aging. Defective OXPHOS may be caused by abnormal mitochondrial biosynthesis due to inherited or acquired mutations in the nuclear (n) or mitochondrial (mt) deoxyribonucleic acid (DNA). For instance, the presence of a mutation of the mtDNA in the pancreatic beta-cell impairs adenosine triphosphate (ATP) generation and insulin synthesis. The nuclear genome controls mitochondrial biosynthesis, but mtDNA has a much higher mutation rate than nDNA because it lacks histones and is exposed to the radical oxygen species (ROS) generated by the electron transport chain, and the mtDNA repair system is limited. Defective OXPHOS may be caused by insufficient fuel supply, by defective electron transport chain enzymes (Complexes I - IV), lack of the electron carrier coenzyme Q10, lack of oxygen due to ischemia or anemia, or excessive membrane leakage, resulting in insufficient mitochondrial inner membrane potential for ATP synthesis by the F0F1-ATPase. Human tissues can counteract OXPHOS defects by stimulating mitochondrial biosynthesis; however, above a certain threshold the lack of ATP causes cell death. Many agents affect OXPHOS. Several nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit or uncouple OXPHOS and induce the 'topical' phase of gastrointestinal ulcer formation. Uncoupled mitochondria reduce cell viability. The Helicobacter pylori induces uncoupling. The uncoupling that opens the membrane pores can activate apoptosis. Cholic acid in experimental atherogenic diets inhibits Complex IV, cocaine inhibits Complex I, the poliovirus inhibits Complex II, ceramide inhibits Complex III, azide, cyanide, chloroform, and methamphetamine inhibit Complex IV. Ethanol abuse and antiviral nucleoside analogue therapy inhibit mtDNA replication. By contrast, melatonin stimulates Complexes I and IV and Gingko biloba stimulates Complexes I and III. Oral Q10 supplementation is effective in treating cardiomyopathies and in restoring plasma levels reduced by the statin type of cholesterol-lowering drugs.
Aspartic acid 85 in bacteriorhodopsin functions both as proton acceptor and negative counterion to the Schiff base. (1992)

In bacteriorhodopsin Asp85 has been proposed to function both as a negative counterion to the Schiff base and as proton acceptor in the early stages of the photocycle. To test this proposal further, we have replaced Asp85 by His. The rationale for this replacement is that although His can function as a proton acceptor, it cannot provide a negative charge at residue 85 to serve as a counterion to the protonated Schiff base. We show here that the absorption spectrum of the D85H mutant is highly sensitive to the pH of the external medium. From spectroscopic titrations, we have determined the apparent pK for deprotonation of the Schiff base to be 8.8 +/- 0.1 and the apparent pK for protonation of the His85 side chain to be approximately 3.5. Between pH 3.5 and 8.8, where the Schiff base is protonated, and the His side chain is deprotonated, the D85H mutant is completely inactive in proton transport. Time-resolved studies show that there is no detectable formation of an M-like intermediate in the photocycle of the D85H mutant. These experiments show that the presence of a neutral proton-accepting moiety at residue 85 is not sufficient for carrying out light-driven proton transport. The requirements at residue 85 are therefore for a group that serves both as a negatively charged counterion and as a proton acceptor.
A chimeric saporin‐transferrin conjugate compared to ricin toxin: role of the carrier in intracellular transport and toxicity (1995)

Human transferrin (Tf) and saporin-6 (Sap), a ribosome inactivating protein from Saponaria officinalis, were chemically conjugated: the reaction generated two chimeras (called Tf-Sap) that proved to be cytotoxic to HepG2 cells. Electrophoretic and chromatographic analysis revealed that the two conjugates contained saporin and Tf in a 2:1 or 1:1 molar ratio (140 and 110 KDa, respectively). Free saporin is essentially nontoxic, whereas Tf-Sap efficiently kills HepG2 cells, although its ID50 (= 6 nM) is 1000-fold greater than that of ricin. Intracellular transport of these toxins was followed by in vivo fluorescence video microscopy, preparing the conjugates starting from rhodamine isothiocyanate-labeled saporin. Image analysis of living HepG2 cells exposed to fluorescent Tf-Sap revealed that the endocytotic pathway involving passage through secondary endosomes is dictated by Tf and is different from that of ricin (the dimeric toxin from Ricinus communis), which is delivered to the Golgi apparatus, the probable site of activation. We discuss whether differences in toxicity between ricin and Tf-Sap can be attributed to the different mechanisms of transport and activation.
Implementation of a 20‐nm pore‐size filter in the plasma‐derived Factor VIII manufacturing process (2006)

The virus-clearance efficiency of the FVIII product, CROSS EIGHT M, was markedly increased, in particular against small non-enveloped viruses, by changing the virus filter pore size from 35 nm to 20 nm. It was possible to implement the 20-nm pore-size filter without variation of the biochemical properties or a serious loss of FVIII.
Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti (2009)

The data support the argument that HGT between Wolbachia endosymbiotic bacteria and their hosts has produced evolutionary innovation.
Integrating Semantic and Visual Facets for Browsing Digital Photo Collections. (2009)

Managing photos by using low-level visual features is a powerful, yet imprecise, organization paradigm. The same is true if only keywords (or tags) are used. In this paper we present a new browsing and search system, named Scenique, that allows the user to manage her photo collections by using both visual features and tags, all homogeneously organized into a set of (visual and semantic, respectively) hierarchical facets. We present the basic principles of Scenique, describe the building blocks of its software architecture, and provide evidence of its effectiveness, as evaluated by a set of real users.
Two Forms of Aryl Hydrocarbon Receptor Type 2 in Rainbow Trout (Oncorhynchus mykiss) (1999)

Two aryl hydrocarbon receptors (AhRs), rtAhR2alpha and rtAhR2beta, were cloned from rainbow trout (rt) cDNA libraries. The distribution of sequence differences, genomic Southern blot analysis, and the presence of both transcripts in all individual rainbow trout examined suggest that the two forms of rtAhR2 are derived from separate genes. The two rtAhR2s have significant sequence similarity with AhRs cloned from mammalian species, especially in the basic helix-loop-helix and PAS functional domains located in the amino-terminal 400 amino acids of the protein. In contrast, the Gln-rich transactivation domain found in the carboxyl-terminal half of mammalian AhRs is absent from both rtAhR2s. Both clones were expressed by in vitro transcription/translation and proteins of approximately 125 kDa were produced. These proteins bind 2,3,7, 8-tetrachlorodibenzo-p-dioxin (TCDD) and are able to bind dioxin response elements in gel shift assays. rtAhR2alpha and rtAhR2beta are expressed in a tissue-specific manner with the highest expression of rtAhR2beta in the heart. Expression of rtAhR2alpha and rtAhR2beta mRNAs is positively regulated by TCDD. Both rtAhR2alpha and rtAhR2beta produced TCDD-dependent activation of a reporter gene driven by dioxin response elements. Surprisingly, the two receptors showed distinct preferences for different enhancer sequences. These results suggest that the two receptor forms may regulate different sets of genes, and may play different roles in the toxic responses produced by AhR agonists such as TCDD.
(S)-Spiro[(1,3-diazacyclopent-1-ene)-5,2‘-(7‘-methyl-1‘,2‘,3‘,4‘- tetrahydronaphthalene)]:  Resolution, Stereospecific Synthesis, and Preliminary Pharmacological Characterization as a Partial α-Adrenergic Agonist (1997)

Recently, we reported on the design, synthesis, and structure-activity relationships of a series of spiroimidazolines endowed with alpha-adrenergic agonist activities. Among the compounds described, (R,S)-spiro(1,3-diazacyclopent-1-ene)-[5,2'](7'-methyl-1'2',3', 4',-tetrahydronaphthalene) fumarate (5RS) was chosen for further development as a venotonic agent. The resolution of this compound, as well as the pharmacological characterization of the enantiomers, stereospecific synthesis of eutomer (5S, S 18149), and determination of absolute configuration by single-crystal X-ray diffraction analysis, are described.
Determination of fractional flow reserve (FFR) based on scaling laws: a simulation study (2008)

Fractional flow reserve (FFR) provides an objective physiological evaluation of stenosis severity. A technique that can measure FFR using only angiographic images would be a valuable tool in the cardiac catheterization laboratory. To perform this, the diseased blood flow can be measured with a first pass distribution analysis and the theoretical normal blood flow can be estimated from the total coronary arterial volume based on scaling laws. A computer simulation of the coronary arterial network was used to gain a better understanding of how hemodynamic conditions and coronary artery disease can affect blood flow, arterial volume and FFR estimation. Changes in coronary arterial flow and volume due to coronary stenosis, aortic pressure and venous pressure were examined to evaluate the potential use of flow and volume for FFR determination. This study showed that FFR can be estimated using arterial volume and a scaling coefficient corrected for aortic pressure. However, variations in venous pressure were found to introduce some error in FFR estimation. A relative form of FFR was introduced and was found to cancel out the influence of pressure on coronary flow, arterial volume and FFR estimation. The use of coronary flow and arterial volume for FFR determination appears promising.
Cloning, expression, and characterization of the unique bovine A1 adenosine receptor. Studies on the ligand binding site by site-directed mutagenesis. (1992)

The bovine brain A1 adenosine receptor (A1AR) is distinct from other A1ARs in that it displays the unique agonist potency series of N6-R-phenylisopropyladenosine (R-PIA) greater than N6-S-phenylisopropyladenosine (S-PIA) greater than 5'-N-ethylcarboxamidoadenosine and has a 5-10-fold higher affinity for both agonists and antagonists. The cDNA for this receptor has been cloned from a size-selected (2-4-kb) bovine brain library and sequenced. The 2.0-kb cDNA encodes a protein of 326 amino acid residues with a molecular mass of 36,570 daltons. The amino acid sequence fits well into the seven-transmembrane domain motif typical of G protein-coupled receptors. Northern analysis in bovine tissue using the full length cDNA demonstrates mRNAs of 3.4 and 5.7 kb with a tissue distribution consistent with A1AR binding. Subcloning of the cDNA in a pCMV5 expression vector with subsequent transfection into both COS7 and Chinese hamster ovary cells revealed a fully functional A1AR which could inhibit adenylylcyclase and retained the unique pharmacologic properties of the bovine brain A1AR. The A1AR was found to have a single histidine residue in each of transmembrane domains 6 and 7. Histidine residues have been postulated by biochemical studies to be important for ligand binding. Mutation of His-278 to Leu-278 (seventh transmembrane domain) dramatically decreased both agonist and antagonist binding by greater than 90%. In contrast, mutation of His-251 to Leu-251 decreased antagonist affinity and the number of receptors recognized by an antagonist radioligand. In contrast, agonist affinity was not perturbed but the number of receptors detected by an agonist radioligand was also reduced. These data suggest that both histidines are important for both agonist and antagonist binding, but His-278 appears critical for ligand binding to occur.
Structural Requirement of Heparan Sulfate for Interaction with Herpes Simplex Virus Type 1 Virions and Isolated Glycoprotein C (1997)

Cell surface heparan sulfates mediate primary attachment of herpes simplex virus type 1, the first step in virus invasion of the cells. Removal of the host cell heparan sulfate results in a significantly diminished susceptibility of the cell to virus infection. On the virus envelope, glycoprotein C has been identified as the major binding site for heparan sulfate in the primary attachment of the virus to host cells. Using selectively desulfated heparins and metabolically labeled host cell heparan sulfate, we have analyzed the structural requirements of heparan sulfate to provide binding sites for glycoprotein C and the whole virus. Employing glycoprotein C affinity chromatography and a virus binding assay, we subfractionated oligosaccharides derived from heparan sulfate and partially desulfated heparin into selectively bound and unbound pools. These were chemically depolymerized and analyzed at the disaccharide level. The shortest glycoprotein C-binding fragment consisted of 10-12 monosaccharide units containing at least one 2-O- and one 6-O-sulfate group that have to be localized in a sequence-specific way, based on the finding that bound and unbound HS fragments do not differ in charge or composition. The binding sequence is found within N-sulfated blocks of heparan sulfate, although several N-acetyl groups can be tolerated within the minimal binding sequence. These minimal requirements for herpes simplex virus type 1 binding to heparan sulfate are clearly distinct from other identified protein binding sites.
PARTICLE SWARM OPTIMIZATION (2004)

In this paper, we introduce a new parameter, called inertia weight, into the original particle swarm optimizer. Simulations have been done to illustrate the signilicant and effective impact of this new parameter on the particle swarm optimizer. 1.
The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits (2013)

The 38-residue SBP-Tag binds to streptavidin more tightly (K(d) -/= 2.5-4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12-14) and a C-terminal HPQ sequence (residues 31-33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17-28) adopts a regular α-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1-10 and 35-38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11-34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of β-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag-streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.
A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1 (2015)

Adenosine deaminases acting on RNA (ADARs) are RNA-editing enzymes responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. ADAR1 and ADAR2 are two members of the family that have been shown to be catalytically active. Earlier, we reported a phenotypic screen for the study of human ADAR2 using budding yeast S. cerevisiae as the host system. While this screen has been successfully applied to the study of ADAR2, it failed with ADAR1. Here, we report a new reporter that uses a novel editing substrate and is suitable for the study of ADAR1. We screened plasmid libraries with randomized codons for two important residues in human ADAR1 (G1007 and E1008). The screening results combined with in vitro deamination assays led to the identification of mutants that are more active than the wild type protein. Furthermore, a screen of the ADAR1 E1008X library with a reporter construct bearing an A•G mismatch at the editing site suggests one role for the residue at position 1008 is to sense the identity of the base pairing partner for the editing site adenosine. This work has provided a starting point for future in vitro evolution studies of ADAR1 and led to new insight into ADAR's editing site selectivity.
Production of Human Papillomavirus Type 16 Virus-Like Particles in Transgenic Plants (2003)

Cervical cancer is linked to infection with human papillomaviruses (HPV) and is the third most common cancer among women worldwide. There is a strong demand for the development of an HPV preventive vaccine. Transgenic plants expressing the HPV major capsid protein L1 could be a system to produce virus-like particles for prophylactic vaccination or could even be used as edible vaccines to induce an L1-specific prophylactic immune response. Here, we describe the generation of transgenic tobacco and potato plants carrying the HPV type 16 major structural gene L1 under the control of the cauliflower mosaic virus 35S promoter. All attempts to express either the original, unmodified L1 gene or an L1 gene with a codon usage optimized for expression in plants failed. Surprisingly, small amounts of the protein were detected using an L1 gene optimized for expression in human cells. However, Northern blot analysis revealed that most of the L1 transcripts were degraded. Introduction of the translational enhancer Omega derived from the tobacco mosaic virus strongly increased transcript stability and resulted in accumulation of L1 protein to approximately 0.5 to 0.2% of total soluble protein in transgenic tobacco and potato plants, respectively. The plant-derived L1 protein displayed conformation-specific epitopes and assembled into virus-like particles. Furthermore, we did not find any indications of protein modification of the L1 protein produced in plants. Plant-derived L1 was as immunogenic as L1 expressed in baculovirus-infected insect cells. Feeding of tubers from transgenic potatoes to mice induced an anti-L1 antibody response in 3 out of 24 mice, although this response was only transient in two of the mice. Our data, however, indicate that an anti-L1 response was primed in about half of the 24 animals.