gebhart/patrepeval huggingface dataset:
Effect of the ET(B) receptor agonist, IRL-1620, on paclitaxel plasma pharmacokinetics of breast tumor rats. (2006)

Endothelin (ET)-B receptors are expressed in human breast carcinoma. We previously demonstrated that intravenous administration of the ET(B) receptor agonist, IRL-1620, to tumor-bearing rats, increased blood perfusion and enhanced delivery of paclitaxel to breast tumor tissue. The present study was conducted to determine whether IRL-1620 alters the pharmacokinetics of paclitaxel. Breast tumor-bearing rats were given 0.3 ml/kg saline or 3 nmol/kg IRL-1620 by intravenous (iv) administration. Fifteen minutes after saline or IRL-1620, 40 microCi/rat 3H-Paclitaxel was administered iv and serial plasma samples were collected until 24 hrs. 3H-Paclitaxel radioactivity in the plasma samples was measured by liquid scintillation counting. Data were fit to a three-compartment model and pharmacokinetic parameters were generated using WinNonlin software. IRL-1620 did not produce any change in the plasma paclitaxel pharmacokinetics of tumor-bearing rats. The AUC(0-infinity) (9.43 +/- 3.18 microg-hr/ml), clearance (0.69 +/- 0.17 l/hr/kg), volume of distribution (10.31 +/- 4.54 l/kg), and half-life (1.0 +/- 0.32 hrs) of paclitaxel were similar between rats treated with saline or IRL-1620. In conclusion, the ET(B) receptor agonist, IRL-1620, does not alter paclitaxel plasma pharmacokinetics and, therefore, could be used to augment the delivery of paclitaxel to the tumor tissue.
Engineering of Phosphotriesterase to Detoxify Organophosphates in Extreme Environments (2003)

Acknowledgements PJB is grateful to the National Science Foundation for supporting his research under a GK-12 Fellows grant 0741714. We also thank AFOSR and DURIP for their financial support. Phosphotriesterase (PTE) is a well-studied naturally occurring enzymes capable of degrading and detoxifying organophosphates. Detailed kinetic analysis of the wild-type enzyme has shown a decreased activity in extreme environments such as high temperatures, low pH and in the presence of organic solvents. An enzyme which is functional in these environments has a great potential for bioremediation and antiterrorism applications. Here we describe the residue specific incorporation of p-fluorophenylalanine into PTE and the effects on its thermostability and thermoactivity. .
Hashing Methods and Relational Algebra Operations (1984)

This paper present algorithms for relational algebra and set operations based on hashing. Execution times are computed and performance is compared to standard methods based on nested loop and sort-merge. The algorithms are intended for use on a monoprocessor computer with standard disks for data base storage. It is indicated however that hashing methods are well suited to multi processor or especially multi machine database machines. The relational algebra operatrons described in this paper are under implementation In TECHRA (TECHBC), a database system especially designed to meet the needs of technical applications, like CAD systems, utility maps, oil field exploration, etc.
Sedum plumbizincicola, A New Species of the Crassulaceae from Zhejiang, China (2006)

Sedum plumbizincicola X. H. Guo et S. B. Zhou sp. nov. was described as a new species from China.
Single Molecule Activity Measurements of Cytochrome P450 Oxidoreductase Reveal the Existence of Two Discrete Functional States (2013)

Electron transfer between membrane spanning oxidoreductase enzymes controls vital metabolic processes. Here we studied for the first time with single molecule resolution the function of P450 oxidoreductase (POR), the canonical membrane spanning activator of all microsomal cytochrome P450 enzymes. Measurements and statistical analysis of individual catalytic turnover cycles shows POR to sample at least two major functional states. This phenotype may underlie regulatory interactions with different cytochromes P450 but to date has remained masked in bulk kinetics. To ensure that we measured the inherent behavior of POR, we reconstituted the full length POR in "native like" membrane patches, nanodiscs. Nanodisc reconstitution increased stability by ∼2-fold as compared to detergent solubilized POR and showed significantly increased activity at biologically relevant ionic strength conditions, highlighting the importance of studying POR function in a membrane environment. This assay paves the way for studying the function of additional membrane spanning oxidoreductases with single molecule resolution.
Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein (2006)

Many cellular proteins exist as homo-oligomers. The mechanism of the assembly process of such proteins is still poorly understood. We have previously observed that Hsp16.3, a protein exhibiting chaperone-like activity, undergoes stepwise disassembly and nonstepwise reassembly. Here, the disassembly and reassembly of a nonchaperone protein RbsD, from Escherichia coli, was studied in vitro. The protein was found to mainly exist as decamers with a small portion of apparently larger oligomeric forms, both of which are able to refold/reassemble effectively in a spontaneous way after being completely unfolded. Disassembly RbsD intermediates including pentamers, tetramers, trimers, dimers, and monomers were detected by using urea-containing pore gradient polyacrylamide gel electrophoresis, while only pentamers were detected for its reassembly. The observation of stepwise disassembly and apparent nonstepwise reassembly for both a chaperone protein (Hsp16.3) and a nonchaperone protein (RbsD) strongly suggests that such a feature is most likely general for homo-oligomeric proteins.
Role of Amine Type in CO2 Separation Performance within Amine Functionalized Silica/Organosilica Membranes: A Review (2018)

Various types of amine-functionalized silica/organosilica membranes have been developed due to their potentially superior CO2 separation performance. This article reviews the progress made in this field and special attention is paid to elucidating the role of amine type in CO2 separation performance within amine-functionalized silica/organosilica membranes. This review includes a systematic comparison of various organosilica membranes with either unhindered or sterically hindered amines developed in our previous studies. Herein, we thoroughly discuss the structural characterizations and CO2 adsorption/desorption properties of amine-functionalized xerogel powders and CO2 transport/separation performance across the relevant membranes. Future directions for the design and development of high-performance CO2 separation membranes are suggested, and particular attention is paid to the future of activation energies for gas permeation.
Oleoylethanolamide Stimulates Lipolysis by Activating the Nuclear Receptor Peroxisome Proliferator-activated Receptor α (PPAR-α) (2004)

Amides of fatty acids with ethanolamine (FAE) are biologically active lipids that participate in a variety of biological functions, including the regulation of feeding. The polyunsaturated FAE anandamide (arachidonoylethanolamide) increases food intake by activating G protein-coupled cannabinoid receptors. On the other hand, the monounsaturated FAE oleoylethanolamide (OEA) reduces feeding and body weight gain by activating the nuclear receptor PPAR-alpha (peroxisome proliferator-activated receptor alpha). In the present report, we examined whether OEA can also influence energy utilization. OEA (1-20 microm) stimulated glycerol and fatty acid release from freshly dissociated rat adipocytes in a concentration-dependent and structurally selective manner. Under the same conditions, OEA had no effect on glucose uptake or oxidation. OEA enhanced fatty acid oxidation in skeletal muscle strips, dissociated hepatocytes, and primary cardiomyocyte cultures. Administration of OEA in vivo (5 mg kg(-1), intraperitoneally) produced lipolysis in both rats and wild-type mice, but not in mice in which PPAR-alpha had been deleted by homologous recombination (PPAR-alpha(-/-)). Likewise, OEA was unable to enhance lipolysis in adipocytes or stimulate fatty acid oxidation in skeletal muscle strips isolated from PPAR-alpha mice. The synthetic PPAR-alpha agonist Wy-14643 produced similar effects, which also were dependent on the presence of PPAR-alpha. Subchronic treatment with OEA reduced body weight gain and triacylglycerol content in liver and adipose tissue of diet-induced obese rats and wild-type mice, but not in obese PPAR-alpha(-/-) mice. The results suggest that OEA stimulates fat utilization through activation of PPAR-alpha and that this effect may contribute to its anti-obesity actions.
A peptide pair coordinates regular ovule initiation patterns with seed number and fruit size (2019)

Abstract Ovule development in Arabidopsis thaliana involves pattern formation which ensures that ovules are regularly arranged in the pistils to reduce competition for nutrients and space. Mechanisms underlying pattern formation in plants, such as phyllotaxis, flower morphogenesis or lateral root initiation, have been extensively studied, and genes controlling the initiation of ovules have been identified. However, how a regular spacing of ovules is achieved is not known. Using natural variation analysis combined with quantitative trait locus analysis, we found that the spacing of ovules in the developing fruits is controlled by two secreted peptides, EPFL2 and EPFL9 (also known as Stomagen), and their receptors from the ERECTA (ER) family that act from the carpel wall and the placental tissue. We found that a signalling pathway controlled by EPFL9 acting from the carpel wall through the LRR-receptor kinases ER, ERL1 and ERL2 promotes fruit growth. Regular spacing of ovules depends on EPFL2 expression in the carpel wall and in the inter-ovule spaces, where it acts through ERL1 and ERL2. Loss of EPFL2 signalling results in shorter fruits and irregular spacing of ovules or even ovule twinning. The EPFL2 expression pattern between ovules is under negative-feedback regulation by auxin, which accumulates in the arising ovule primordia. We propose that the auxin-EPFL2 signalling module evolved to control the initiation and regular, equidistant spacing of ovule primordia, which serves to minimise competition between developing seeds. Together, EPFL2 and EPFL9 coordinate ovule patterning and thereby seed number with fruit growth through a set of shared receptors.
Nε‐carboxymethyllysine‐modified proteins are unable to bind to RAGE and activate an inflammatory response (2008)

Advanced glycation endproducts (AGEs) containing carboxymethyllysine (CML) modifications are generally thought to be ligands of the receptor for AGEs, RAGEs. It has been argued that this results in the activation of pro-inflammatory pathways and diseases. However, it has not been shown conclusively that a CML-modified protein can interact directly with RAGE. Here, we have analyzed whether beta-lactoglobulin (bLG) or human serum albumin (HSA) modified chemically to contain only CML (10-40% lysine modification) can (i) interact with RAGE in vitro and (ii) interact with and activate RAGE in lung epithelial cells. Our results show that CML-modified bLG or HSA are unable to bind to RAGE in a cell-free assay system (Biacore). Furthermore, they are unable to activate pro-inflammatory signaling in the cellular system. Thus, CML probably does not form the necessary structure(s) to interact with RAGE and activate an inflammatory signaling cascade in RAGE-expressing cells.
A system for integrative and post-planned analysis of 2-DE/MS centered proteomics data (2005)

Summary Proteomic analysis is intrinsically an iterative, incremental process. Information is usually acquired gradually by researchers, and in different projects. At the same time, there are relatively few examples of biological data management systems which take into account this reality, most of them usually treat the experiment generated data as static and unchangeable: data are never reconsidered, or seldom, whereas technology becomes more powerful or that other researchers have brought information on data correction. And yet, post-planned analysis [21] which involves multiple iterations and subsequent re-investigations of previously prepared data might bring tremendous benefits. Named PARIS (Proteomic Analysis and Resources Indexation System), the system we developed here seeks to address this requirement. Compliant with the majority of 2-DE analysis and MALDI-TOF based protein identification softwares, it automatically takes data from them and stores the raw and processed data in a relational database suitable for advanced exploration. Taking into account the standards proposed by PSI (Proteomics Standard Initiative), the system exports the stored data in XML format for data exchange and knowledge sharing. PARIS also manages information about experiments and their biological contexts, and allows the user to search and analyze a large data collection in a global manner. It provides tools for data integration and advanced, cross multi-experiment, multi-experimenter data exploration, and supports visual verification and correction of the analysis results. Implemented in Java, the system is platform independent, accessible to multiple users through Internet. It is also scalable for use for one or many laboratories, and therefore suitable to inter-institute collaborative work. PARIS can be tested and downloaded at http://genome.jouy.inra.fr/paris
RESPONSE OF THE AMERICAN LOBSTER TO THE STRESS OF SHELL DISEASE (2005)

Shell disease is a problem affecting lobsters in eastern Long Island Sound causing disfiguration of the shell, decreasing the lobsters' value, and whereas mild and medium levels of the disease are not lethal, ultimately, severe cases result in mortality. Levels of the molting hormone, ecdysone, were quantitated, using a radioimmunoassay (RIA), in hemolymph of animals exhibiting shell disease. Our results indicate that levels of ecdysone were increased in the hemolymph of shell-diseased lobsters, with a medium level of expression of the disease to 89 ± 32 ng/mL (n = 76), whereas unaffected, presumably healthy ones had 57 ± 16 ng/mL (n = 210). In 7 of 10 months of the year shell-diseased animals had higher ecdysone levels in their hemolymph than unaffected animals. In addition, ecdysone levels were abnormally high, 165 ± 53 ng/mL (n = 5), in shell-diseased ovigerous lobsters, whereas normal unaffected ovigerous ones had low levels of this hormone, 13 ± 4 ng/mL (n = 7). These results indicate that shell disease may induce lobsters to alter the systemic levels of ecdysone, possibly serving as a defensive measure, allowing the animals to ward off the effects of shell disease through induced molting.
Significance of Patent Foramen Ovale in Patients with GOLD Stage II Chronic Obstructive Pulmonary Disease (COPD) (2014)

<b>Background:</b> Patent foramen ovale (PFO) is a common finding in adults. A PFO is associated with right to left shunting but its importance in the aetiology of hypoxia in early COPD remains uncertain, although it has not proved possible to demonstrate a role for PFOs in the aetiology of hypoxia in patients with Global Initiative for chronic Obstructive Lung Disease (GOLD) stage III/IV disease. We compared the characteristics of GOLD stage II patients with or without a PFO and assessed its impact on exercise performance. <b>Methods:</b> In 22 GOLD stage II COPD patients we measured exercise performance, arterial oxygen tension and lung function and used contrast transcranial Doppler ultrasonography (TCD) to assess the presence of a PFO. Patients (n=20) underwent TCD measurements during incremental cycle ergometry with respiratory pressures measured using an esophageal balloon catheter (n=13). <b>Results:</b>Twelve individuals (54%) had a PFO. Patients with a PFO were more hypoxic; mean(SD) partial pressure of oxygen in arterial blood (PaO<sub>2</sub>)10.2(1.1) kilopascals (kPa) <i>vs.</i> 11.7(0.9)kPa (p<0.01), but the presence of a PFO was not associated with reduced exercise performance either on cycle ergometry or a 6 Minute Walk Test (6MWT). A strong relationship was noted between the esophageal pressure swing (P<sub>SwingEs</sub>) and the degree of shunting observed during exercise (r=0.7; p<0.001). <b>Conclusions:</b>The presence of a PFO in GOLD stage II COPD patients does not appear to influence exercise performance despite increased right-to-left shunting.
From robotic hands to human hands: a visualization and simulation engine for grasping research (2005)

Purpose Robotic hands are still a long way from matching the grasping and manipulation capability of their human counterparts, but computer simulation may help us understand this disparity. We present our publicly available simulator, and describe our research projects involving the system including the development of a human hand model derived from experimental measurements. Design/methodology/approach Unlike other simulation systems, our system was built specifically to analyze grasps. It can import a wide variety of robot designs by using standard descriptions of the kinematics and link geometries. Various components support the analysis of grasps, visualization of results, dynamic simulation of grasping tasks, and grasp planning. Findings The simulator has been used in several grasping research problems and can be used to plan grasps for an actual robot. With the aid of a vision system, we have shown that these grasps can be executed by a robot. Research limitations/implications We are currently developing methods to handle deformable surfaces, tendon driven models, and non‐ideal joints in order to better model human grasping. Practical implications This work is part of our current project to create a biomechanically realistic human hand model to better understand what features are most important to mimic in the designs of robotic hands. Such a model will also help clinicians better plan reconstructive hand surgeries. Originality/value We describe our publicly available grasping simulator and review experiments performed with it. The paper demonstrates the usefulness of this system as a tool for grasping research.
Renal vein reconstruction with interposition allografts in cadaveric renal transplantation (1988)

The short or injured renal vein in cadaveric transplantation is a surgical challenge. Over a 2-year period, we have performed ex vivo renal vein lengthening with an interposition vascular allograft in 17 recipients of cadaveric kidneys. Indications for renal vein extension allografts were a short right renal vein (N = 12), procurement injury to the vein (N = 4), and double renal vein (N = 1). In six cases (35.3%), ex vivo renal artery reconstruction was performed in combination with the venous repair. Our preferred approach is to employ allograft material in ex vivo reconstruction under cold storage conditions. Bench surgery ranged from 10 to 30 min, and the mean in situ anastomosis time was 20 min. The mean length of renal vein prior to reconstruction was 12 mm, and the mean length of venous interposition allograft after revascularization was 27 mm. There were no episodes of vascular thrombosis or primary nonfunction. Three patients (17.6%) required postoperative hemodialysis for acute tubular necrosis, which was subsequently resolved. The mean serum creatine at 1 month post-transplant was 1.7 mg/dl. These preliminary results suggest that ex vivo renal vein reconstruction with an interposition allograft is a safe and effective modality which should be added to the transplant surgeon's armamentarium in select cases.
GPS Ephemeris Verification for Local Area Augmentation System (LAAS) Ground Stations (1999)

Certain types of satellite failures, such as broadcast
ephemeris messages that do not correspond to true
satellite locations, can be difficult to detect by a Local
Area Augmentation System (LAAS) ground facility (LGF)
because satellites are observed from reference antennas
that are very close together. Although ephemeris failures
large enough to threaten LAAS user integrity should be
very rare, a combination of monitors in the LGF is
needed. This paper analyzes the combined effectiveness
of several monitoring techniques and proposes solutions
for all phases of LAAS operations.
The first solution is the combination of the GPS
Operational Control Segment (OCS) and monitors
included in the existing Category I LGF prototypes.
Built-in LGF checks confirm that broadcast range and
range-rate corrections have reasonable values and also
compare computed satellite positions based on the current
and previous ephemeris messages as well as the current
almanac message. OCS monitoring by itself is insufficient
for LAAS because OCS alerts are not guaran-teed to meet
the minimum time-to-alert requirement of 6 seconds for
precision approaches. However, the combi-nation of OCS
and existing LGF monitoring is sufficient to meet the
allocated per-approach probability of an undetected
ephemeris error for Category I operations.
For Category II and III operations, the integrity
requirement is 200 times tighter than for Category I; thus
the monitors described above may be insufficient. This
paper introduces new algorithms for validating
ephemerides in three dimensions that can provide the
needed improvement. The Differential Pseudorange
Residual method (DPR) is used to detect ephemeris errors
parallel to the LGF – satellite line of sight, and the
Double Phase Difference with Ambiguity Search method
(DPDAS) is used to detect ephemeris errors perpendicular
to the line of sight (and thus very difficult to observe).
Unlike RAIM, these two methods need only one other
already-approved GPS satellite in view. These two methods can detect all ephemeris failures in three
dimensions. This paper develops these algorithms in
detail and presents experimental results from the Stanford
LAAS Integrity Monitor Testbed (IMT).
An Open-source Tool for Simplifying Computer and Assistive Technology Use (2021)

Computer access is increasingly critical for all aspects of life from education to employment to daily living, health and almost all types of participation. The pandemic has highlighted our dependence on technology, but the dependence existed before and is continuing after. Yet many face barriers due to disability, literacy, or digital literacy. Although the problems faced by individuals with disabilities have received focus for some time, the problems faced by people who just have difficulty in using technologies has not, but is a second large, yet less understood problem. Solutions exist but are often not installed, buried, hard to find, and difficult to understand and use. To address these problems, an open-source extension to the Windows and macOS operating systems has been under exploration and development by an international consortium of organizations, companies, and individuals. It combines auto-personalization, layering, and enhanced discovery, with the ability to Install on Demand (IoD) any assistive technologies a user needs. The software, called Morphic, is now installed on all of the computers across campus at several major universities and libraries in the US and Canada. It makes computers simpler to use, and allows whichever features or assistive technologies a person needs to appear on any computer they encounter (that has Morphic on it) and want to use at school, work, library, community center, etc. This demonstration will cover both the basic and advanced features as well as how to get free copies of the open-source software and configure it for school, work or personal use. It will also highlight lessons learned from the placements.