gebhart/patrepeval huggingface dataset:
Precise and reliable gene expression via standard transcription and translation initiation elements (2013)

An inability to reliably predict quantitative behaviors for novel combinations of genetic elements limits the rational engineering of biological systems. We developed an expression cassette architecture for genetic elements controlling transcription and translation initiation in Escherichia coli: transcription elements encode a common mRNA start, and translation elements use an overlapping genetic motif found in many natural systems. We engineered libraries of constitutive and repressor-regulated promoters along with translation initiation elements following these definitions. We measured activity distributions for each library and selected elements that collectively resulted in expression across a 1,000-fold observed dynamic range. We studied all combinations of curated elements, demonstrating that arbitrary genes are reliably expressed to within twofold relative target expression windows with ∼93% reliability. We expect the genetic element definitions validated here can be collectively expanded to create collections of public-domain standard biological parts that support reliable forward engineering of gene expression at genome scales.
The cardiovascular physiologic actions of urocortin II: Acute effects in murine heart failure (2004)

Corticotropin-releasing factor (CRF) and its paralogues urocortin (Ucn)I, -II, and -III signal by activating their receptors, CRF receptors (CRFR)1 and -2, to maintain homeostasis through endocrine, autonomic, and behavioral responses. CRFR2 is found in cardiomyocytes and in endothelial and smooth muscle cells of the systemic vasculature. Echocardiography and cardiac catheterization were used in mice to assess the physiologic effects of i.v. UcnII and CRFR2 deficiency on left ventricular function and the systemic vasculature. UcnII treatment augmented heart rate, exhibited potent inotropic and lusitropic actions on the left ventricle, and induced a downward shift of the diastolic pressure-volume relation. UcnII also reduced systemic arterial pressure, associated with a lowering of systemic arterial elastance (end-systolic pressure/stroke volume) and systemic vascular resistance. CRFR2-deficient mice showed no alteration in cardiac contractility or blood pressure in response to UcnII administration, suggesting that the effects of UcnII are specific to CRFR2 function. Pretreatment with a beta-adrenergic receptor antagonist, esmalol, had no effect on the inotropic or lusitropic effects of UcnII in vivo, indicating that its actions are independent of beta-adrenergic receptors. Single i.v. bolus administration of UcnII to a heart failure model (muscle-specific LIM protein-deficient mice) produced significant enhancement of inotropic and lusitropic effects on left ventricular function and improved cardiac output. These results demonstrate the potent cardiovascular physiologic actions of UcnII in both wild-type and cardiomyopathic mice and support a potential beneficial use of this peptide in therapy of congestive heart failure.
A Novel Fully Differential Biopotential Amplifier With DC Suppression (2004)

Fully differential amplifiers yield large differential gains and also high common mode rejection ratio (CMRR), provided they do not include any unmatched grounded component. In biopotential measurements, however, the admissible gain of amplification stages located before dc suppression is usually limited by electrode offset voltage, which can saturate amplifier outputs. The standard solution is to first convert the differential input voltage to a single-ended voltage and then implement any other required functions, such as dc suppression and dc level restoring. This approach, however, yields a limited CMRR and may result in a relatively large equivalent input noise. This paper describes a novel fully differential biopotential amplifier based on a fully differential dc-suppression circuit that does not rely on any matched passive components, yet provides large CMRR and fast recovery from dc level transients. The proposed solution is particularly convenient for low supply voltage systems. An example implementation, based on standard low-power op amps and a single 5-V power supply, accepts input offset voltages up to +/-500 mV, yields a CMRR of 102 dB at 50 Hz, and provides, in accordance with the AAMI EC38 standard, a reset behavior for recovering from overloads or artifacts.
Rotational interference in vibrational ladder climbing in NO by chirped infrared laser pulses (1999)

Results from experiments and model calculations on rotational interference in vibrational ladder climbing in the $X{}^{2}{\ensuremath{\Pi}}_{1/2}$ state of NO are presented. In the low-fluence limit, the population in excited vibrational states shows an oscillatory behavior as a function of the chirp of the IR laser pulse. The interference is due to the accumulated phase difference of pathways involving different intermediate rotational states. The theoretical results match the experiments on an absolute scale.
The innovative Osmotic Membrane Bioreactor (OMBR) for reuse of wastewater (2011)

An innovative osmotic membrane bioreactor (OMBR) is currently under development for the reclamation of wastewater, which combines activated sludge treatment and forward osmosis (FO) membrane separation with a RO post-treatment. The research focus is FO membrane fouling and performance using different activated sludge investigated both at laboratory scale (membrane area of 112cm2) and at on-site bench scale (flat sheet membrane area of 0.1 m2). FO performance on laboratory-scale (i) increased with temperature due to a decrease in viscosity and (ii) was independent of the type of activated sludge. Draw solution leakage increased with temperature and varied for different activated sludge. FO performance on bench-scale (i) increased with osmotic driving force, (ii) depended on the membrane orientation due to internal concentration polarization and (iii) was invariant to feed flow decrease and air injection at the feed and draw side. Draw solution leakage could not be evaluated on bench-scale due to experimental limitation. Membrane fouling was not found on laboratory scale and bench-scale, however, partially reversible fouling was found on laboratory scale for FO membranes facing the draw solution. Economic assessment indicated a minimum flux of 15L.m-2 h-1 at 0.5M NaCl for OMBR-RO to be cost effective, depending on the FO membrane price.
Vascular endothelial growth factor induces VE-cadherin tyrosine phosphorylation in endothelial cells (1998)

Interendothelial junctions play an important role in the regulation of endothelial functions, such as vasculogenesis, angiogenesis, and vascular permeability. In this paper we show that vascular endothelial growth factor (VEGF), a potent inducer of new blood vessels and vascular permeability in vivo, stimulated the migration of endothelial cells after artificial monolayer wounding and induced an increase in paracellular permeability of human umbilical vein endothelial cells (HUVECs). Furthermore, VEGF increased phosphotyrosine labeling at cell-cell contacts. Biochemical analyses revealed a strong induction of VEGF-receptor-2 (flk-1/KDR) tyrosine-autophosphorylation by VEGF which was maximal after 5 minutes and was followed by receptor downregulation. 15 minutes to 1 hour after VEGF stimulation the endothelial adherens junction components VE-cadherin, beta-catenin, plakoglobin, and p120 were maximally phosphorylated on tyrosine, while alpha-catenin was not modified. PECAM-1/CD31, another cell-cell junctional adhesive molecule, was tyrosine phosphorylated with similar kinetics in response to VEGF. In contrast, activation of VEGF-receptor-1 (Flt-1) by its specific ligand placenta growth factor (PlGF) had no effect on the tyrosine phosphorylation of cadherins and catenins. Despite the rapid and transient receptor activation and the subsequent tyrosine phosphorylation of adherens junction proteins the cadherin complex remained stable and associated with junctions. Our results demonstrate that the endothelial adherens junction is a downstream target of VEGFR-2 signaling and suggest that tyrosine phosphorylation of its components may be involved in the the loosening of cell-cell contacts in established vessels to modulate transendothelial permeability and to allow sprouting and cell migration during angiogenesis.
Rod and cone visual cycle consequences of a null mutation in the 11-cis-retinol dehydrogenase gene in man (2000)

Vertebrate vision starts with photoisomerization of the 11-cis-retinal chromophore to all-trans-retinal. Biosynthesis of 11-cis-retinal is required to maintain vision. A key enzyme catalyzing the oxidation of 11-cis-retinol is 11-cis-retinol dehydrogenase (11-cis-RDH), which is encoded by the RDH5 gene. 11-cis-RDH is expressed in the RPE and not in the neural retina. The consequences of a lack of 11-cis-RDH were studied in a family with fundus albipunctatus. We identified the causative novel RDH5 mutation, Arg157Trp, that replaces an amino acid residue conserved among short-chain alcohol dehydrogenases. Three-dimensional structure modeling and in vitro experiments suggested that this mutation destabilizes proper folding and inactivates the enzyme. Studies using RPE membranes indicated the existence of an alternative oxidizing system for the production of 11-cis-retinal. In vivo visual consequences of this null mutation showed complex kinetics of dark adaptation. Rod and cone resensitization was extremely delayed following full bleaches; unexpectedly, the rate of cone recovery was slower than rods. Cones showed a biphasic recovery with an initial rapid component and an elevated final threshold. Other unanticipated results included normal rod recovery following 0.5% bleach and abnormal recovery following bleaches in the 2-12% range. These intermediate bleaches showed rapid partial recovery of rods with transitory plateaux. Pathways in addition to 11-cis-RDH likely provide 11-cis-retinal for rods and cones and can maintain normal kinetics of visual recovery but only under certain constraints and less efficiently for cone than rod function.
Vehicle-Infrastructure Integration-Enabled Plug-in Hybrid Electric Vehicles for Optimizing Energy Consumption (2011)

As the market share of hybrid electric vehicles (HEVs) increases to reduce the dependency on fossil fuels and there is an increased interest in real-time communication between vehicles and infrastructure, the integration of these two technologies has become an important research topic. Such an integrative paradigm, envisioned in the Vehicle-Infrastructure Integration (VII) or IntelliDrive systems, can improve mobility and increase safety. In this paper, a VII-HEV framework is proposed for utilization for both conventional HEVs and Plug-in Hybrid Electric Vehicles (PHEV). The data collection and communication capability of these VII’s permits the prediction of speed profiles at the vehicle level within a reasonable error rate. Once predicted, the speed profile is sent from roadside units (RSUs) to VII-HEV/PHEVs for optimization. The authors describe the use of the Equivalent Consumption Minimization Strategy (ECMS), which optimizes energy usage of PHEVs and HEVs with the predicted speed profile obtained through the VII system. A simulation analysis of the framework with 65 driving cycles shows improvement of energy consumption of 2% to 12% with an average of 6% for PHEVs and 1% to 3.5% with an average of 2.2% for HEVs.
Efficient and targeted delivery of siRNA in vivo (2010)

RNA interference (RNAi) has been regarded as a revolutionary tool for manipulating target biological processes as well as an emerging and promising therapeutic strategy. In contrast to the tangible and obvious effectiveness of RNAi in vitro, silencing target gene expression in vivo using small interfering RNA (siRNA) has been a very challenging task due to multiscale barriers, including rapid excretion, low stability in blood serum, nonspecific accumulation in tissues, poor cellular uptake and inefficient intracellular release. This minireview introduces major challenges in achieving efficient siRNA delivery in vivo and discusses recent advances in overcoming them using chemically modified siRNA, viral siRNA vectors and nonviral siRNA carriers. Enhanced specificity and efficiency of RNAi in vivo via selective accumulations in desired tissues, specific binding to target cells and facilitated intracellular trafficking are also commonly attempted utilizing targeting moieties, cell-penetrating peptides, fusogenic peptides and stimuli-responsive polymers. Overall, the crucial roles of the interdisciplinary approaches to optimizing RNAi in vivo, by efficiently and specifically delivering siRNA to target tissues and cells, are highlighted.
The development and implementation of high-speed laser welding in the can-making industry (1986)

This paper describes the development and implementation of laser side seam welding for the production of food and aerosol cans from 0.008″ tinplate. The project was initiated by Stoffel Welding Systems in 1974 and the first “laser bodymakers” went on line in multiple shift operation in 1983. The project required the development of new high speed welding techniques and hardware to overcome fundamental problems of weld instability. The maximum welding speed previously reported before the onset of instability was 22 m/min (866 ins/min). This figure was more than doubled as a result of our development work. As the project progressed it became apparent that if the process was to succeed in production an ultra-reliable, CO2 laser would be required. Testing of eight different lasers from five different suppliers revealed that there was no commercially available laser with the required performance or reliability. A new laser was, therefore, designed and built specifically for this application by PRC Corporation. This laser was the first of what are now referred to as “corporate lasers”; that is, lasers built to meet the specific standards and specifications of the end user. Bodymakers incorporating this laser have been operating multiple shift since 1983.
Macromolecular Drug Conjugates II. Metronidazole-Dextran Prodrugs (1993)

The antimicrobial drug metronidazole was attached to dextran. Two methods of dextran-metronidazole synthesis were studied: (1) the reaction of metronidazole with chloroacetylated derivatives of crosslinked dextran microparticles in basic aprotic solvents, and (2) the reaction of metronidazole chloroacetic acid ester with crosslinked dextran microparticles in basic media. The release of metronidazole from the two types of macromolecular prodrugs was compared.
Fracture testing of bulk silicon microcantilever beams subjected to a side load (1996)

A custom experimental system was developed to fracture silicon microcantilever beams in side loading (i.e., the load was applied in the noncompliant direction), and the resulting force/deflection (stiffness) characteristics were obtained. A finite element model of these structures was analyzed using ABAQUS, and the resulting model stiffness correlated well with the experimental data. Fracture types were divided into two categories, {111} and {110}, according to the type of silicon crystalline plane along which fracture occurred. The initiation location of each fracture type was identified. The fracture stress (strength) in the beam was obtained from the stress produced in the model at the fracture initiation site for a load equivalent to the experimental fracture force. Numerous beams were tested, and the statistical results were compiled. The distributions and statistical data from each of the fracture types were compared to each other and to previously acquired results from front/back loading (i.e., loading in the compliant direction) of these same structures. Side-loading results indicated that the {110} fracture type had a greater fracture strength than the {111} type. Based on a comparison of the side loading data with the front/back loading data, it was concluded that side wall roughness and especially the edge roughness greatly affected the fracture strength of the silicon micromechanical structures.
Optical Nanosensors for Chemical Analysis inside Single Living Cells. 2. Sensors for pH and Calcium and the Intracellular Application of PEBBLE Sensors (1999)

Optical nanosensors, or PEBBLEs (probes encapsulated by biologically localized embedding), have been produced for intracellular measurements of pH and calcium. Five varieties of pH-sensitive sensors and three different calcium-selective sensors are presented and discussed. Each sensor combines an ion-selective fluorescent indicator and an ion-insensitive internal standard entrapped within an acrylamide polymeric matrix. Calibrations and linear ranges are presented for each sensor. The photobleaching of dyes incorporated into PEBBLEs is comparable to that of the respective free dye that is incorporated within the matrix. These PEBBLE sensors are fully reversible over many measurements. The leaching of fluorescent indicator from the polymer is less than 50% over a 48-h period (note that a typical application time is only a few hours). The PEBBLE sensors have also been applied to intracellular analysis of the calcium flux in the cytoplasm of neural cells during the mitochondrial permeability transition. Specifically, a distinct difference is noted between cells of different types (astrocyte vs neuron-derived cells) with respect to their response to the toxicant m-dinitrobenzene (DNB). Use of PEBBLE sensors permits the quantitative discrimination of subtle differences between the ability of human SY5Y neuroblastoma and C6 glioma to respond to challenge with DNB. Specifically, measurement of intracellular calcium, the precursor to cell death, has been achieved.
Layout and Language: Challenges for Table Understanding on the Web (2001)

In this paper, we consider the table understanding task and present a catalogue of particular issues that arise when the tables are those found on the web. In addition, we consider what happens when processes commonly associated with web pages are applied to those bearing tables.
The observation of the sedation effects of intranasal methods of dexmedetomidine for magnetic resonance imaging in children (2017)

purpose: To compare the sedation effects of two intranasal methods of dexmedetomidine for magnetic resonance imaging (MRI) in children. Method: 40 children for MRI were randomly divided into two groups, namely 20 cases for each group: nasal drip group(group A)and nasal spray group(group B). Group A and group B received intranasal dexmedetomidine of 1.5 ug/kg by two methods. Monitoring the HR, SpO2, RR and inspection time of the two groups so as to observe the sedation effects and Ramsay sedation score while recording the adverse reactions. Results: There was no significant difference in the HR, SpO2, RR between the two groups at the same time point (P>0.05). Compared with group A, the time-to-fall-asleep in group B was shorter and the adverse reactions significantly decreased (P<0.05). Conclusion: Compared with nasal drip, nasal spray dexmedetomidine by MAD can shorten the time-to-fall-asleep and reduce adverse reactions for MRI in children.
Human Cytomegalovirus Infection of Langerhans-Type Dendritic Cells Does Not Require the Presence of the gH/gL/UL128-131A Complex and Is Blocked after Nuclear Deposition of Viral Genomes in Immature Cells (2013)

Human cytomegalovirus (CMV) enters its host via the oral and genital mucosae. Langerhans-type dendritic cells (LC) are the most abundant innate immune cells at these sites, where they constitute a first line of defense against a variety of pathogens. We previously showed that immature LC (iLC) are remarkably resistant to CMV infection, while mature LC (mLC) are more permissive, particularly when exposed to clinical-strain-like strains of CMV, which display a pentameric complex consisting of the viral glycoproteins gH, gL, UL128, UL130, and UL131A on their envelope. This complex was recently shown to be required for the infection of immature monocyte-derived dendritic cells. We thus sought to establish if the presence of this complex is also necessary for virion penetration of LC and if defects in entry might be the source of iLC resistance to CMV. Here we report that the efficiency of LC infection is reduced, but not completely abolished, in the absence of the pentameric complex. While virion penetration and nuclear deposition of viral genomes are not impaired in iLC, the transcription of the viral immediate early genes UL122 and UL123 and of the delayed early gene UL50 is substantially lower than that in mLC. Together, these data show that the UL128, UL130, and UL131A proteins are dispensable for CMV entry into LC and that progression of the viral cycle in iLC is restricted at the step of viral gene expression.
Monoclonal Antibodies of Predetermined Specificity for Fibrin: A Rational Approach to Monoclonal Antibody Production (1986)

Three monoclonal antibodies (MAbs) (55D10, 59D8, and 64C5) have been produced by an immunization strategy that uses a synthetic heptapeptide from the amino terminus of the beta-chain in human fibrin. These MAbs bind to human fibrin in the presence of 4 mg/ml human fibrinogen in solid-phase radioimmunoassay. Ligand specificity studies demonstrate that antifibrin immunoreactivity is completely inhibited by a series of synthetic fibrin-like beta-peptides that bear the position-2 histidyl residue. Although the presence of this residue on the epitope is necessary for its recognition by a fibrin-specific antibody, the presence of the histidyl residue alone is not sufficient for antibody recognition.
Lymphocyte Sequestration Through S1P Lyase Inhibition and Disruption of S1P Gradients (2005)

Lymphocyte egress from the thymus and from peripheral lymphoid organs depends on sphingosine 1-phosphate (S1P) receptor-1 and is thought to occur in response to circulatory S1P. However, the existence of an S1P gradient between lymphoid organs and blood or lymph has not been established. To further define egress requirements, we addressed why treatment with the food colorant 2-acetyl-4-tetrahydroxybutylimidazole (THI) induces lymphopenia. We found that S1P abundance in lymphoid tissues of mice is normally low but increases more than 100-fold after THI treatment and that this treatment inhibits the S1P-degrading enzyme S1P lyase. We conclude that lymphocyte egress is mediated by S1P gradients that are established by S1P lyase activity and that the lyase may represent a novel immunosuppressant drug target.
Nickel(0)-catalyzed Synthesis of Diaryl Sulfides from Aryl Halides and Aromatic Thiols (1987)

Abstract Facile and selective syntheses of various diaryl sulfides from aryl halides and aromatic thiols by the aid of an in situ generated nickel(0) catalyst are reported. The nickel(0) induces a C–S cleavage, as well.