gebhart/patrepeval huggingface dataset:
Uptake of Phenylalanine into Isolated Barley Vacuoles Is Driven by Both Tonoplast Adenosine Triphosphatase and (1988)

The uptake of phenylalanine was studied with vacuole isolated from barley mesophyll protoplasts. The phenylalanine transport exhibited saturation kinetics with apparent Km-values of 1.2 to 1.4 millimolar for ATP- or PPi-driven uptake; Vmax pp was 120 to 140 nanomoles Phe per milligram of chlorophyll per hour (1 milligram of chlorophyll corresponds to 5 x 106 vacuoles). Half-maximal transport rates driven with ATP or PPi were reached at 0.5 millimolar ATP or 0.25 millimolar PPi. ATP-driven transport showed a distinct pH optimum at 7.3 while PPi-driven transport reached maximum rates at pH 7.8. Direct measurement of the H translocating enzyme activities revealed Km app values of 0.45 millimolar for ATPase (EC 3.6.1.3) and 23 micromolar for pyrophosphatase (PPase) (EC 3.6.1.1). In contrast to the coupled amino acid transport, ATPase and PPase activities had relative broad pH optima between 7 to 8 for ATPase and 8 to 9 for PPase. ATPase as well as ATP-driven transport was markedly inhibited by nitrate while PPase and PPi-coupled transport was not affected. The addition of ionophores inhibited phenylalanine transport suggesting the destruction of the electrochemical proton potential difference A ,uH while the rate of ATP and PPi hydrolysis was stimulated. The uptake of other lipophilic amino acids like LTrp, L-Leu, and L-Tyr was also stimulated by ATP. They seem to compete for the same carrier system. L-Ala, L-Val, D-Phe, and DLeu did not influence phenylalanine transport suggesting a stereospecificity of the carrier system for L-amino acids having a relatively high hydrophobicity. Vacuoles are the largest organelles of differentiated plant cells occupying up to 90% of the total cell volume. As reviewed by Boller and Wiemken (4), they fulfill a series of functions. Active transport into this compartment has been demonstrated for metabolic intermediates as well as inorganic ions. Phenylalanine, the major aromatic amino acid synthesized in chloroplasts (3), is transiently stored in the vacuole. Up to 95% of all free cellular phenylalanine is found in this compartment (2; and E Martinoia, personal communication). Transport is an active. ATP consuming nrocess which is
Visualization of forced air flows over a populated printed circuit board and their impact on convective heat transfer (2003)

A detailed characterization of the airflow patterns around Printed Circuit Board (PCB)-mounted electronic components has been undertaken using three different, but complementary flow visualization techniques. Uniform airflows of 2 m/s, 4 m/s and 5.5 m/s were directed over Plastic Quad Flat Pack (PQFP) components mounted on a double Euro-Card PCB. The complexity of PCB topology and resulting flow phenomena, was increased in three stages from just one, centrally placed component, to seven components and finally to the most complex case consisting of a symmetrical in-line array of fifteen components. Traditional smoke- and paint-flow visualization techniques, as well as a novel paint-film evaporation technique, were applied to help identify the sensitivity of the flow phenomena and its impact on convective heat transfer, to both air velocity and PCB topology. Combined, these techniques not only helped characteristic features of these flows such as separation/reattachment points, re-circulation zones and horseshoe vortices to be identified, but also showed in a qualitative way, using the evaporation technique, how these flow phenomena impact on PCB/component surface heat transfer. Linking the flow phenomena with the surface heat transfer in this way also provides, in the early design phase, a means of identifying both an appropriate numerical flow modeling strategy for the flow phenomena present, and the locations of high aerodynamic disturbance on the PCB, where temperature prediction accuracy must be viewed with caution.
Synthesis and Biological Activity of Novel 1<i>H</i>,3<i>H</i>-Thiazolo[3,4-<i>a</i>]Benzimidazoles: Non-nucleoside Human Immunodeficiency Virus Type 1 Reverse Transcriptase Inhibitors (1999)

Using a known human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitor (NNRTI), 1-(2,6-difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole (TBZ NSC 625487) as the lead structure for drug design, a series of novel 1H,3H-thiazolo[3,4-a]benzimidazole derivatives substituted on the benzene-fused ring was prepared. Their in vitro anti-HIV-1 activity, as well as their inhibitory effects on the viral reverse transcriptase, were evaluated. The structure-activity relationships for these compounds are described and the results suggest that the apolar binding pocket of RT, into which the NNRTIs must fit, can accommodate only groups with a limited size and shape.
Collective acceleration of electrons using an autoacceleration process (1980)

A means of collectively accelerating an intense electron beam is demonstrated. A long pulse (800 ns) electron beam is propagated through cavity structures which redistributed the energy in the beam such that most of the beam energy is transferred to a short segment (6 ns) in the tail of the beam. Electrons are accelerated in a two cavity system from 200 keV to energies of 2.4–3.0 MeV at a beam current of ∼8 kA. The extension of this principle to larger number of cavities appears feasible.
Activation of Mitogen-activated Protein Kinase Cascade Regulates Pituitary Tumor-transforming Gene Transactivation Function (2000)

Pituitary tumor-transforming gene (PTTG) is a recently characterized oncogene that can act as a transcriptional activator. In this study, we have characterized the transactivation domain of PTTG. Transient transfection of fusion constructs containing GAL4 DNA-binding domain and different parts of PTTG indicated the transactivation domain of PTTG is located between amino acids 119 and 164. Mitogen-activated protein (MAP) kinase cascade is important in the regulation of cell growth, apoptosis, and differentiation. Therefore, we have explored the possibility that this kinase cascade plays a role in regulating PTTG transactivation function. Activation of the MAP kinase cascade by epidermal growth factor or an expression vector for a constitutively active form of the MAP kinase kinase (MEK1) led to stimulation of PTTG transactivation activity. We showed that PTTG is phosphorylated in vitro on Ser(162) by MAP kinase and that this phosphorylation site plays an essential role in PTTG transactivation function. We demonstrated that PTTG interacts directly with MEK1 through a putative SH3 domain-binding site located between amino acids 51 and 54 and that this interaction is crucial for PTTG transactivation function. In addition, we showed that activation of MAP kinase phosphorylation cascade resulted in nuclear translocation of PTTG. Together, our data establish that a growth factor-stimulated MAP kinase plays an important role in modulating PTTG function.
Emulation of TPM on Raspberry Pi (2015)

The Trusted Platform Module (TPM) is a dedicated microprocessor designed to secure hardware by integrating cryptographic keys into the non-volatile memory of the module. TPM is specified by the Trusted Computing Group (TCG). TCG is an initiative started in 2003 by several multinational semiconductor and IT-companies. The initiative is an effort to develop standards for Trusted Computing where hardware is used to provide security support to software. The TPM is typically connected to the LPC bus on the motherboard of a PC and can be used to create and store cryptographic keys, generate random numbers, hash values and encrypt data. The purpose of this thesis is to develop a TPM learning environment and a laboratory manual for introductory courses in computer security where the students are able to learn about the functionalities of the TPM as a means to secure hardware. The functions of the TPM will be emulated on the ARM based single board computer Raspberry Pi developed by the Raspberry Pi foundation. The TPM commands will be executed from a PC which will connect to the Raspberry Pi remotely through TCP. Several exercises related to TPM and its functionalities are provided as an appendix to this report. The exercises are intended for students or others interested in Trusted Computing. This report also provides exercises related to the creation of TPM applications using TSS (Trusted Computing Software Stack).
Three-Dimensional In Vivo Measurement of Lumbar Spine Segmental Motion (2006)

Complex coupled motions were measured due to external torsion and could be indicative of instability chronic patients with low back pain. The presented data provide baseline segmental motions for future comparisons to symptomatic subjects.
Use of Genomics To Identify Bacterial Undecaprenyl Pyrophosphate Synthetase: Cloning, Expression, and Characterization of the Essential <i>uppS</i> Gene (1999)

The prenyltransferase undecaprenyl pyrophosphate synthetase (di-trans,poly-cis-decaprenylcistransferase; EC 2.5.1.31) was purified from the soluble fraction of Escherichia coli by TSK-DEAE, ceramic hydroxyapatite, TSK-ether, Superdex 200, and heparin-Actigel chromatography. The protein was labeled with the photolabile analogue of the farnesyl pyrophosphate analogue (E, E)-[1-3H]-(2-diazo-3-trifluoropropionyloxy)geranyl diphosphate and was detected on a sodium dodecyl sulfate-polyacrylamide gel as a protein with an apparent molecular mass of 29 kDa. This protein band was cut out from the gel, trypsin digested, and subjected to matrix-assisted laser desorption ionization mass spectrometric analysis. Comparison of the experimental data with computer-simulated trypsin digest data for all E. coli proteins yielded a single match with a protein of unassigned function (SWISS-PROT Q47675; YAES_ECOLI). Sequences with strong similarity indicative of homology to this protein were identified in 25 bacterial species, in Saccharomyces cerevisiae, and in Caenorhabditis elegans. The homologous genes (uppS) were cloned from E. coli, Haemophilus influenzae, and Streptococcus pneumoniae, expressed in E. coli as amino-terminal His-tagged fusion proteins, and purified over a Ni2+ affinity column. An untagged version of the E. coli uppS gene was also cloned and expressed, and the protein purified in two chromatographic steps. We were able to detect Upp synthetase activity for all purified enzymes. Further, biochemical characterization revealed no differences between the recombinant untagged E. coli Upp synthetase and the three His-tagged fusion proteins. All enzymes were absolutely Triton X-100 and MgCl2 dependent. With the use of a regulatable gene disruption system, we demonstrated that uppS is essential for growth in S. pneumoniae R6.
MRAM-on-FDSOI Integration: A Bit-Cell Perspective (2018)

In this paper we discuss the potential foundry announced hybrid integration of magnetic random access memory (MRAM) on fully depleted silicon-on-insulator (FD-SOI) technology. The spin transfer torque magnetic tunnel junction (STT-MTJ) and the next generation voltage-controlled magnetic anisotropy (VCMA) MTJ are separately integrated into a 28 nm FD-SOI process. Circuit-level design strategies are explored that use FD-SOI leverage and spin-device characteristic to realize writing and reading power-delay efficiency, robust and reliable performance in a 1-transistor 1-MTJ (1T1M) bit cell. Process variation aware strategies for MTJ-FDSOI integration are proposed to compensate failure operations, by using the dynamic step-wise back-bias and the flip-well back-bias. A qualitative summary demonstrates that the MRAM-on-FDSOI integration offers attractive performance for future non-volatile CMOS integration.
Pseudomonas aeruginosa, Candida albicans, and device-related nosocomial infections: implications, trends, and potential approaches for control (2005)

For many years, device-associated infections and particularly device-associated nosocomial infections have been of considerable concern. Recently, this concern was heightened as a result of increased antibiotic resistance among the common causal agents of nosocomial infections, the appearance of new strains which are intrinsically resistant to the antibiotics of choice, and the emerging understanding of the role biofilms may play in device-associated infections and the development of increased antibiotic resistance. Pseudomonas aeruginosa and Candida albicans are consistently identified as some of the more important agents of nosocomial infections. In light of the recent information regarding device-associated nosocomial infections, understanding the nature of P. aeruginosa and C. albicans infections is increasingly important. These two microorganisms demonstrate: (1) an ability to form biofilms on the majority of devices employed currently, (2) increased resistance/tolerance to antibiotics when associated with biofilms, (3) documented infections noted for virtually all indwelling devices, (4) opportunistic pathogenicity, and (5) persistence in the hospital environment. To these five demonstrated characteristics, two additional areas of interest are emerging: (a) the as yet unclear relationship of these two microorganisms to those species of highly resistant Pseudomonas spp and Candida spp that are of increasing concern with device-related infections, and (b) the recent research showing the dynamic interaction of P. aeruginosa and C. albicans in patients with cystic fibrosis. An understanding of these two opportunistic pathogens in the context of their ecosystems/biofilms also has significant potential for the development of novel and effective approaches for the control and treatment of device-associated infections.
6. Dryden’s Absalom and Achitophel, 745-746 (1961)

(1961). 6. Dryden’s Absalom and Achitophel, 745-746. The Explicator: Vol. 20, No. 1, pp. 10-11.
<title>Fast finite-state codebook design algorithm for vector quantization</title> (1991)

The Linde-Buzo-Gray (LBG) algorithm is usually used to design a codebook for encoding images in the vector quantization. In each iteration of this algorithm, we must search the full codebook in order to assign the training vectors to their corresponding codewords. Therefore, the LBG algorithm needs large computation effort to obtain a good codebook from the training set. In this paper, we propose a finite-state LBG (FSLBG) algorithm for reducing the computation time. Instead of searching the whole codebook, we search only those codewords that are close to the codeword for a training vector in its previous iteration. In general, the number of these possible codewords can be very small without sacrificing performance. Because of searching only a small part of the codebook, the computation time is reduced. In our experiment, the performance of the FSLBG algorithm in terms of the signal-to-noise ratio is very close to that of the LBG algorithm. However, the computation time of the FSLBG algorithm is only about 10 percent of the time required by the LBG algorithm.
Ferroelectric lyo-mesophase of banana-shaped molecules (2001)

Preliminary results are reported on the first ferroelectric 'lyo-mesophases' of banana-shaped molecules. We studied the effect of the non-polar solvents p-xylene and m-xylene on the macroscopic properties of banana-shaped molecules having a B7 phase. It was observed that by adding only 15% of solvent the isotropic-B7 transition temperature was lowered from 130°C to 70°C and the ferroelectric electro-optical switching range was extended from 1-2°C to more than 50°C, thus maintaining the switching even at room temperature. The xylene molecules act as spacers, maintaining larger separations between the banana-molecules, thus reducing the polar packing order. These observations provide unique opportunities for tuning the intermolecular interactions of banana-shaped molecules and modifying their macroscopic properties.
Role of β-Oxidation Enzymes in γ-Decalactone Production by the Yeast <i>Yarrowia lipolytica</i> (2001)

Some microorganisms can transform methyl ricinoleate into gamma-decalactone, a valuable aroma compound, but yields of the bioconversion are low due to (i) incomplete conversion of ricinoleate (C(18)) to the C(10) precursor of gamma-decalactone, (ii) accumulation of other lactones (3-hydroxy-gamma-decalactone and 2- and 3-decen-4-olide), and (iii) gamma-decalactone reconsumption. We evaluated acyl coenzyme A (acyl-CoA) oxidase activity (encoded by the POX1 through POX5 genes) in Yarrowia lipolytica in lactone accumulation and gamma-decalactone reconsumption in POX mutants. Mutants with no acyl-CoA oxidase activity could not reconsume gamma-decalactone, and mutants with a disruption of pox3, which encodes the short-chain acyl-CoA oxidase, reconsumed it more slowly. 3-Hydroxy-gamma-decalactone accumulation during transformation of methyl ricinoleate suggests that, in wild-type strains, beta-oxidation is controlled by 3-hydroxyacyl-CoA dehydrogenase. In mutants with low acyl-CoA oxidase activity, however, the acyl-CoA oxidase controls the beta-oxidation flux. We also identified mutant strains that produced 26 times more gamma-decalactone than the wild-type parents.
Calculating A Helicopter Pilot's Instrument Scan Pattern from Discrete, 60-Hz Measures of the Line-of-Sight: The Evaluation of an Algorithm (1998)

Abstract : In order obtain data to develop and evaluate theories relating instrument scanning to flight performance we recorded the line of sight (LOS) of student naval helicopter pilots as they flew prescribed maneuvers in a motion-based, high fidelity, instrument training simulator. These LOS data were discrete, 60 Hz samples of eye pointing. For some types of analysis it is helpful to think of a scan pattern as a sequence of fixations and to use an averaging algorithm to transform the 60 Hz data into such a sequence, a scan path. An appropriate algorithm was identified, developed and evaluated. As part of this evaluation, we developed a String Similarity measure, SS, a measure of the similarity between two scan paths. The evaluation of the algorithm, consisting of observing the algorithm's output as a function of the algorithm's parameter values, showed that the algorithm behaved in a sensible fashion, logically consistent with the input data. This increased our confidence in our implementation of the fixation algorithm. The SS metric proved to be an informative, useful tool that may have addition uses in the analysis scanning behavior and flight performance.
DéjàVu: a map of code duplicates on GitHub (2017)

Previous studies have shown that there is a non-trivial amount of duplication in source code. This paper analyzes a corpus of 4.5 million non-fork projects hosted on GitHub representing over 428 million files written in Java, C++, Python, and JavaScript. We found that this corpus has a mere 85 million unique files. In other words, 70% of the code on GitHub consists of clones of previously created files. There is considerable variation between language ecosystems. JavaScript has the highest rate of file duplication, only 6% of the files are distinct. Java, on the other hand, has the least duplication, 60% of files are distinct. Lastly, a project-level analysis shows that between 9% and 31% of the projects contain at least 80% of files that can be found elsewhere. These rates of duplication have implications for systems built on open source software as well as for researchers interested in analyzing large code bases. As a concrete artifact of this study, we have created DéjàVu, a publicly available map of code duplicates in GitHub repositories.
Synthesis and Structure of a 1,1‘-Diphospha[2]ferrocenophane (2001)

A four-step sequence allows us to transform 1-phenyl-3,4-dimethylphosphole-2-carboxaldehyde (1) into the bis(phosphole) 5 with a CH2CH2 bridge between the two α-carbons. The cleavage of the two P−phenyl bonds of 5 by lithium, followed by the reaction of the bis(phospholide) thus formed with FeCl2, gives the corresponding 1,1‘-diphospha[2]ferrocenophane 7, which displays a tilt angle of 20°.
The 'Real Experience' industry: Student development projects and the depoliticisation of poverty (2013)

Participation in development projects in the Global South has become one of the most sought-after activities among American and British high school graduates and college students. In the United States this often takes the form of Alternative Spring Break trips, while in Britain students typically pursue development work during their 'gap years'. Development projects offer students a way to craft themselves in an alternative mould, to have a 'real experience' that marks them off from the cultural mainstream as 'authentic' individuals. The student development craze represents an impulse to resist consumerist individualism, but this impulse has been appropriated and neutralised by a new logic of consumption, transforming a profoundly political urge for change into a form of 'resistance' compatible with neoliberal capitalism. In the end, students' pursuit of self-realisation through development has a profoundly depoliticising effect, shifting their attention away from substantive problems of extraction and exploitation to the state of the inner self.
External Fracture Fixation—the Analysis and Design of a New System (1979)

External skeletal fixation of long bone fractures is the procedure of choice for the treatment of certain clearly established types of fracture. In particular, it is appropriate when the skin and soft tissue at the site of the fracture is at risk and requires careful management. For sound bone union to be achieved correct orientation and stability of the fracture is needed. A rigid fixation method is therefore required, and this rigidity determines the degree of post-operative mobility that the patient can exercise during the healing phase. A single-sided fixation system when applied, for example, to the medial aspect of the tibia, which gives adequate skeletal support, would be preferred to a double-sided unit as it would not inhibit the action of muscles, would reduce the number of pin holes, and be more convenient for the patient. From experience with existing equipment available for this surgical technique, a specification to meet the performance criteria needed was drawn up, and from this a design emerged giving priority to aspects of stiffness and convenience. The report concludes with three case studies of patients treated with this fixator. A separate paper gives the results of practical tests on this fixator, with a theoretical analysis of the factors which influence stiffness in single-sided fixators, and of the strength which can be expected.
Synthesis and Characterization of a Ruthenium(II)-Based Redox Conjugate for Reagentless Biosensing (2001)

Synthesis of a novel sulfhydryl-specific, tetraammine Ru(II)polypyridyl complex, [Ru(II)(NH3)4(1,10-phenanthroline-5-maleimide)](PF6)2, which exhibits environment-sensitive electrochemical properties is described. When conjugated to an allosteric site in a genetically engineered mutant of maltose binding protein, the formal potential of the conjugated redox probe is shifted to higher potential upon maltose binding. The magnitude of this potential shift was used to measure maltose affinity of the protein-redox conjugate complex and to monitor maltose concentration in solution. These results are presented in context of reagentless biosensing.