gebhart/patrepeval huggingface dataset:
Two channel switched reluctance starter/generator results (2002)

Measured data and simulation results for a two channel experimental switched reluctance motor (SRM) based aircraft engine starter/generator system is presented. The two channels of the system provide power to two separate and independent loads. The results presented here document the performance capability of this system from load step response to output ripple voltage. Both measured and predicted system performance is presented and compared. In addition, operating characteristics that are unique to this SRM-based system are described. Of particular interest is the interaction between the two separate channels when one channel experiences a load transient and the other does not. The source of channel interactions is described and measured data are provided. The issue of clearing load faults is also addressed. Design results for adding this capability to the experimental system are described.
Increased Phosphorylation of Protein Kinase B and Related Substrates after Traumatic Brain Injury in Humans and Rats (2005)

Activation of protein kinase B (PKB, also known as Akt) by phosphorylation at serine-473 and threonine-308 promotes cell survival in multiple in vitro and in vivo models where neuronal death is seen, including traumatic brain injury (TBI); however, whether PKB is activated in humans after TBI was heretofore unknown. Activated PKB inhibits apoptogenic factors and is involved in the regulation of several transcription factors. Accordingly, we examined phosphorylation of the PKB signaling pathway in humans as well as rats after TBI using phosphospecific antibodies. Increased phosphorylation of PKB and PKB substrates was detected in injured brain from both humans and rats. In humans, increased phosphorylation of the PKB signaling pathway-related proteins Bad and forkhead transcription factor (FKHR) was detected in patients with TBI versus controls. In rats, increased phosphorylation of FKHR, inhibitor of kappaBalpha, and cyclic adenosine monophosphate responsive element binding protein (CREB) was detected after TBI versus controls. The deoxyribonucleic acid-binding activity of CREB was also enhanced after TBI in rats. Increased phosphorylation of PKB and PKB substrates was identified in neurons and other cell types by immunohistochemistry in both humans and rats. These data show increased phosphorylation of PKB, PKB substrates, and related proteins after both experimental and clinical TBI, suggesting either activation of the PKB signaling pathway or reduced phosphatase activity in both species.
MicroRNA binding site polymorphisms as biomarkers in cancer management and research (2014)

MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression. They have been implicated in a broad range of biological processes, and miRNA-related genetic alterations probably underlie several human diseases. Single nucleotide polymorphisms of transcripts may modulate the posttranscriptional regulation of gene expression by miRNAs and explain interindividual variability in cancer risk and in chemotherapy response. On the basis of recent association studies published in the literature, the present review mainly summarizes the potential role of miRNAs as molecular biomarkers for disease susceptibility, diagnosis, prognosis, and drug-response prediction in tumors. Many clues suggest a role for polymorphisms within the 3' untranslated regions of KRAS rs61764370, SET8 rs16917496, and MDM4 rs4245739 as SNPs in miRNA binding sites highly promising in the biology of human cancer. However, more studies are needed to better characterize the composite spectrum of genetic determinants for future use of markers in risk prediction and clinical management of diseases, heading toward personalized medicine.
PRMT1 Is the Predominant Type I Protein Arginine Methyltransferase in Mammalian Cells (2000)

Type I protein arginine methyltransferases catalyze the formation of asymmetric omega-N(G),N(G)-dimethylarginine residues by transferring methyl groups from S-adenosyl-L-methionine to guanidino groups of arginine residues in a variety of eucaryotic proteins. The predominant type I enzyme activity is found in mammalian cells as a high molecular weight complex (300-400 kDa). In a previous study, this protein arginine methyltransferase activity was identified as an additional activity of 10-formyltetrahydrofolate dehydrogenase (FDH) protein. However, immunodepletion of FDH activity in RAT1 cells and in murine tissue extracts with antibody to FDH does not diminish type I methyltransferase activity toward the methyl-accepting substrates glutathione S-transferase fibrillarin glycine arginine domain fusion protein or heterogeneous nuclear ribonucleoprotein A1. Similarly, immunodepletion with anti-FDH antibody does not remove the endogenous methylating activity for hypomethylated proteins present in extracts from adenosine dialdehyde-treated RAT1 cells. In contrast, anti-PRMT1 antibody can remove PRMT1 activity from RAT1 extracts, murine tissue extracts, and purified rat liver FDH preparations. Tissue extracts from FDH(+/+), FDH(+/-), and FDH(-/-) mice have similar protein arginine methyltransferase activities but high, intermediate, and undetectable FDH activities, respectively. Recombinant glutathione S-transferase-PRMT1, but not purified FDH, can be cross-linked to the methyl-donor substrate S-adenosyl-L-methionine. We conclude that PRMT1 contributes the major type I protein arginine methyltransferase enzyme activity present in mammalian cells and tissues.
A Survey of Anomaly Detection Methods in Networks (2009)

Despite the advances reached along the last 20 years, anomaly detection in networks is still an immature technology, Nevertheless, the benefits which could be obtained from a better understanding of the problem itself as well as the improvement of these methods. Therefore, in this paper we present a survey on anomaly detection in networks. In order to distinguish between the different approaches used for anomaly detection in networks in a structured way, we have classified those methods into four categories: statistical anomaly detection, classifier based anomaly detection, anomaly detection using machine learning and finite state machine anomaly detection. We describe each method in details and give examples for its applications in networks.
Role of the Carboxyl-Terminal Lectin Domain in Self-Association of Galectin-3 (1998)

Galectin-3 is a member of a large family of beta-galactoside-binding animal lectins and is composed of a carboxyl-terminal lectin domain connected to an amino-terminal nonlectin part. Previous experimental results suggest that, when bound to multivalent glycoconjugates, galectin-3 self-associates through intermolecular interactions involving the amino-terminal domain. In this study, we obtained evidence suggesting that the protein self-associates in the absence of its saccharide ligands, in a manner that is dependent on the carboxyl-terminal domain. This mode of self-association is inhibitable by the lectin's saccharide ligands. Specifically, recombinant human galectin-3 was found to bind to galectin-3C (the carboxyl-terminal domain fragment) conjugated to Sepharose 4B and the binding was inhibitable by lactose. In addition, biotinylated galectin-3 bound to galectin-3 immobilized on plastic surfaces and the binding could also be inhibited by various saccharide ligands of the lectin. A mutant with a tryptophan to leucine replacement in the carboxyl-terminal domain, which exhibited diminished carbohydrate-binding activity, did not bind to galectin-3C-Sepharose 4B. Furthermore, galectin-3C formed covalent homodimers when it was treated with a chemical cross-linker and the dimer formation was completely inhibited by lactose. Therefore, galectin-3 can self-associate through intermolecular interactions involving both the amino- and the carboxyl-terminal domains and the relative contribution of each depends on whether the lectin is bound to its saccharide ligands.
Identification, Classification and Zooarchaeology (2011)

Identification of preserved biological materials is often regarded as a skill which has little to do with analysis and interpretation. This paper argues that in zooarchaeological studies―here with particular reference to vertebrate remains―identification procedures deserve more detailed consideration, because these procedures have a significant effect on the results of faunal studies. It is suggested that most identifications are made within a system of usually unspecified rules which vary from one analyst to another. Improvements in comparability between faunal studies will result if these rules are considered before beginning an analysis, and if the rules are made explicit in publications.
Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from<i>Clostridium botulinum</i>in the presence of its substrate pyruvate (2009)

In this paper, the crystallization and preliminary X-ray diffraction analysis to near-atomic resolution of DHDPS from Clostridium botulinum crystallized in the presence of its substrate pyruvate are presented. The enzyme crystallized in a number of forms using a variety of PEG precipitants, with the best crystal diffracting to 1.2 A resolution and belonging to space group C2, in contrast to the unbound form, which had trigonal symmetry. The unit-cell parameters were a = 143.4, b = 54.8, c = 94.3 A, beta = 126.3 degrees . The crystal volume per protein weight (V(M)) was 2.3 A(3) Da(-1) (based on the presence of two monomers in the asymmetric unit), with an estimated solvent content of 46%. The high-resolution structure of the pyruvate-bound form of C. botulinum DHDPS will provide insight into the function and stability of this essential bacterial enzyme.
Association of XK and Kell Blood Group Proteins (1998)

A disulfide bond links Kell and XK red cell membrane proteins. Kell, a type II membrane glycoprotein, carries over 20 blood group antigens, and XK, which spans the membrane 10 times, is lacking in rare individuals with the McLeod syndrome. Kell is classified in the neprilysin family of zinc endopeptidases, and XK has structural features that suggest it is a transport protein. Kell has 15 extracellular cysteines, and XK has one in its fifth extracellular loop. Five of the extracellular cysteine residues in Kell are not conserved in the other members of the neprilysin family, and based on the hypothesis that one of the nonconserved cysteines is linked to XK, cysteines 72 and 319 were mutated to serine. The single extracellular cysteine 347 of XK was also mutated. Co-expression of combinations of wild-type and mutant proteins in transfected COS-1 cells showed that Kell C72S did not form a Kell-XK complex with wild-type XK, while wild-type Kell and Kell C319S did. XK C347S was also unable to form a complex with wild-type Kell, indicating that Kell cysteine 72 is linked to XK cysteine 347. Kell C72S was transported to the cell surface, indicating that linkage to XK is not required. In addition, chemical cross-linking of red cell membranes with dithiobispropionimidate indicated that glyceraldehyde-3-phosphate dehydrogenase is a near neighbor of Kell.
Look-ahead Control of Heavy Trucks utilizing Road Topography (2007)

The power to mass ratio of a heavy truck causes even moderate slopes to have a significant influence on the motion. The velocity will inevitable vary within an interval that is primarily determined by the ratio and the road topography. If further variations are actuated by a controller, there is a potential to lower the fuel consumption by taking the upcoming topography into account. This possibility is explored through theoretical and simulation studies as well as experiments in this work. Look-ahead control is a predictive strategy that repeatedly solves an optimization problem online by means of a tailored dynamic programming algorithm. The scenario in this work is a drive mission for a heavy diesel truck where the route is known. It is assumed that there is road data on-board and that the current heading is known. A look-ahead controller is then developed to minimize fuel consumption and trip time. The look-ahead control is realized and evaluated in a demonstrator vehicle and further studied in simulations. In the prototype demonstration, information about the road slope ahead is extracted from an on-board database in combination with a GPS unit. The algorithm calculates the optimal velocity trajectory online and feeds the conventional cruise controller with new set points. The results from the experiments and simulations confirm that look-ahead control reduces the fuel consumption without increasing the travel time. Also, the number of gear shifts is reduced. Drivers and passengers that have participated in tests and demonstrations have perceived the vehicle behavior as comfortable and natural. i ii
<i>In Vitro</i> Activity of a Novel Glycopolymer against Biofilms of Burkholderia cepacia Complex Cystic Fibrosis Clinical Isolates (2019)

<i>Burkholderia cepacia</i> complex (Bcc) lung infections in cystic fibrosis (CF) patients are often associated with a steady decline in lung function and death. The formation of biofilms and inherent multidrug resistance are virulence factors associated with Bcc infection and contribute to increased risk of mortality in CF patients. New therapeutic strategies targeting bacterial biofilms are anticipated to enhance antibiotic penetration and facilitate resolution of infection. Poly (acetyl, arginyl) glucosamine (PAAG) is a cationic glycopolymer therapeutic being developed to directly target biofilm integrity. In this study, 13 isolates from 7 species were examined, including <i>Burkholderia multivorans</i>, <i>Burkholderia cenocepacia</i>, <i>Burkholderia gladioli</i>, <i>Burkholderia dolosa</i>, <i>Burkholderia vietnamiensis</i>, and <i>B. cepacia</i> These isolates were selected for their resistance to standard clinical antibiotics and their ability to form biofilms <i>in vitro</i> Biofilm biomass was quantitated using static tissue culture plate (TCP) biofilm methods and a minimum biofilm eradication concentration (MBEC) assay. Confocal laser scanning microscopy (CLSM) visualized biofilm removal by PAAG during treatment. Both TCP and MBEC methods demonstrated a significant dose-dependent relationship with regard to biofilm removal by 50 to 200 μg/ml PAAG following a 1-h treatment (<i>P</i> < 0.01). A significant reduction in biofilm thickness was observed following a 10-min treatment of Bcc biofilms with PAAG compared to that with vehicle control (<i>P</i> < 0.001) in TCP, MBEC, and CLSM analyses. PAAG also rapidly permeabilizes bacteria within the first 10 min of treatment. Glycopolymers, such as PAAG, are a new class of large-molecule therapeutics that support the treatment of recalcitrant Bcc biofilm.
EZH2 Depletion Blocks the Proliferation of Colon Cancer Cells (2011)

The Enhancer of Zeste 2 (EZH2) protein has been reported to stimulate cell growth in some cancers and is therefore considered to represent an interesting new target for therapeutic intervention. Here, we investigated a possible role of EZH2 for the growth control of colon cancer cells. RNA interference (RNAi)-mediated intracellular EZH2 depletion led to cell cycle arrest of colon carcinoma cells at the G1/S transition. This was associated with a reduction of cell numbers upon transient transfection of synthetic EZH2-targeting siRNAs and with inhibition of their colony formation capacity upon stable expression of vector-borne siRNAs. We furthermore tested whether EZH2 may repress the growth-inhibitory p27 gene, as reported for pancreatic cancer. However, expression analyses of colon cancer cell lines and colon cancer biopsies did not reveal a consistent correlation between EZH2 and p27 levels. Moreover, EZH2 depletion did not re-induce p27 expression in colon cancer cells, indicating that p27 repression by EZH2 may be cell- or tissue-specific. Whole genome transcriptome analyses identified cellular genes affected by EZH2 depletion in colon cancer cell lines. They included several cancer-associated genes linked to cellular proliferation or invasion, such as Dag1, MageD1, SDC1, Timp2, and Tob1. In conclusion, our results demonstrate that EZH2 depletion blocks the growth of colon cancer cells. These findings might provide benefits for the treatment of colon cancer.
Expression of Envelope Protein (E2) of Bovine Viral Diarrhea Virus in Insect Cells. (1997)

The gene encoding the envelope glycoprotein (E2) of bovine viral diarrhea virus (BVDV) was expressed in a baculovirus. The expressed protein was detected on the surface of infected cells by immunofluorescence. Western blotting analysis showed the presence of the expressed protein of a similar molecular size to the E2 protein. The antigenicity of expressed protein were tested in guinea pigs and cattle. The immunized animals developed neutralizing antibodies against BVDV.
Monoterpenoid Synthesis by Transition Metal Catalyzed Coupling of Enediylmagnesium with C5-Organic Halides (1980)

Abstract A series of isoprene coupling dimers bonded at 1-2, 1-3, 1-4, 2-4, 3-4, or 4-4 position was prepared by regiocontrolled catalysis of trasition metals or without catalysts in the reaction of 2-methyl-2-butene-1,4-diylmagnesium or 3-methyl-2-butenylmagnesium chloride with C5-alkenyl halides.
Exploiting Adaptive Data Compression to Improve Performance and Energy-Efficiency of Compute Workloads in Multi-GPU Systems (2019)

Graphics Processing Unit (GPU) performance has relied heavily on our ability to scale of number of transistors on chip, in order to satisfy the ever-increasing demands for more computation. However, transistor scaling has become extremely challenging, limiting the number of transistors that can be crammed onto a single die. Manufacturing large, fast and energy-efficient monolithic GPUs, while growing the number of stream processing units on-chip, is no longer a viable solution to scale performance. GPU vendors are aiming to exploit multi-GPU solutions, interconnecting multiple GPUs in the single node with a high bandwidth network (such as NVLink), or exploiting Multi-Chip-Module (MCM) packaging, where multiple GPU modules are integrated in a single package. The inter-GPU bandwidth is an expensive and critical resource for designing multi-GPU systems. The design of the inter-GPU network can impact performance significantly. To address this challenge, in this paper we explore the potential of hardware-based memory compression algorithms to save bandwidth and improve energy efficiency in multi-GPU systems. Specifically, we propose an adaptive inter-GPU data compression scheme to efficiently improve both performance and energy efficiency. Our evaluation shows that the proposed optimization on multi-GPU architectures can reduce the interGPU traffic up to 62%, improve system performance by up to 33%, and save energy spent powering the communication fabric by 45%, on average.
Strategy Escalation: An emerging paradigm for safe clinical development of T cell gene therapies (2010)

Gene therapy techniques are being applied to modify T cells with chimeric antigen receptors (CARs) for therapeutic ends. The versatility of this platform has spawned multiple options for their application with new permutations in strategies continually being invented, a testimony to the creative energies of many investigators. The field is rapidly expanding with immense potential for impact against diverse cancers. But this rapid expansion, like the Big Bang, comes with a somewhat chaotic evolution of its therapeutic universe that can also be dangerous, as seen by recently publicized deaths. Time-honored methods for new drug testing embodied in Dose Escalation that were suitable for traditional inert agents are now inadequate for these novel "living drugs". In the following, I propose an approach to escalating risk for patient exposures with these new immuno-gene therapy agents, termed Strategy Escalation, that accounts for the molecular and biological features of the modified cells and the methods of their administration. This proposal is offered not as a prescriptive but as a discussion framework that investigators may wish to consider in configuring their intended clinical applications.
<i>De Novo</i> Production of Metabolites by Fungal Co-culture of <i>Trichophyton rubrum</i> and <i>Bionectria ochroleuca</i> (2013)

The co-cultivation of fungi has recently been described as a promising strategy to induce the production of novel metabolites through possible gene activation. A large screening of fungal co-cultures in solid media has identified an unusual long-distance growth inhibition between Trichophyton rubrum and Bionectria ochroleuca. To study metabolite induction in this particular fungal interaction, differential LC-MS-based metabolomics was performed on pure strain cultures and on their co-cultures. The comparison of the resulting fingerprints highlighted five de novo induced compounds, which were purified using software-oriented semipreparative HPLC-MS. One metabolite was successfully identified as 4″-hydroxysulfoxy-2,2″-dimethylthielavin P (a substituted trimer of 3,5-dimethylorsellinic acid). The nonsulfated form, as well as three other related compounds, were found in the pure strain culture of B. ochroleuca.
A Systems Approach to Downhole Adjustable Stabilizer Design and Application (1994)

ABSTRACT This paper discusses the applications where existing downhole adjustable diameter stabilizers have proven to be beneficial, then identifies additional applications where improved features or capabilities will increase the utility of adjustable stabilizers. Using a systems design approach, those features and capabilities have been incorporated into a new adjustable stabilizer, which is currently under development. Capabilities include a greater range of diameter adjustment, multiple positions, and verifiable twoway communication. The design and construction which makes those improved features possible is discussed. The benefits of those features are demonstrated through computer modeling. Finally, lab and field test results are presented.
Biosynthesis of the angiogenesis inhibitor borrelidin: directed biosynthesis of novel analogues (2006)

We report the directed biosynthesis of borrelidin analogues and their selective anti-proliferative activity against human cancer cell lines.
Inhibition of human factor IXa by human antithrombin (1975)

A procedure is presented for the purification of Factor IX from human plasma. The final product is homogeneous as judged by disc gel electrophoresis and sodium dodecyl sulfate gel electrophoresis. Furthermore, it is completely free of other coagulation component activities. Factor IX is converted to its enzymatically active form by the addition of small quantities of Factor IXa in the presence of calcium ions. This activated species is added to purified antithrombin-heparin cofactor and the interaction is studied in the presence and absence of heparin. Antithrombin-heparin cofactor is found to be a progressive, time-dependent inhibitor of Factor IXa and neutralizes approximately 57% of this enzyme's proteolytic activity within 30 min. The addition of heparin dramatically accelerates the rate of this interaction with virtually complete inhibition of Factor IXa occurring within 15 s. Sodium dodecyl sulfate gel electrophoresis of reduced and nonreduced proteins indicates that antithrombin-heparin cofactor functions as a potent inhibitor of Factor IXa by forming an undissociable complex with the enzyme which is stable in the presence of denaturing or reducing agents (or both). This complex represents a 1:1 stoichiometric combination of enzyme and inhibitor. Heparin increases the rate of formation of this complex without affecting its dissociability or stoichiometry.