gebhart/patrepeval huggingface dataset:
A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry (2005)

There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited reproducibility and low throughput make this a challenging task. A new LC-MS-based platform is able to generate complex peptide patterns from the analysis of proteolyzed protein samples at high throughput and represents a promising approach for quantitative proteomics. A crucial component of the LC-MS approach is the accurate evaluation of the abundance of detected peptides over many samples and the identification of peptide features that can stratify samples with respect to their genetic, physiological, or environmental origins. We present here a new software suite, SpecArray, that generates a peptide versus sample array from a set of LC-MS data. A peptide array stores the relative abundance of thousands of peptide features in many samples and is in a format identical to that of a gene expression microarray. A peptide array can be subjected to an unsupervised clustering analysis to stratify samples or to a discriminant analysis to identify discriminatory peptide features. We applied the SpecArray to analyze two sets of LC-MS data: one was from four repeat LC-MS analyses of the same glycopeptide sample, and another was from LC-MS analysis of serum samples of five male and five female mice. We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics.
Fatty Acid Synthase Gene Is Up-regulated by Hypoxia via Activation of Akt and Sterol Regulatory Element Binding Protein-1 (2008)

The fatty acid synthase (FAS) gene is significantly up-regulated in various types of cancers, and blocking the FAS expression results in apoptosis of tumor cells. Therefore, FAS is considered to be an attractive target for anticancer therapy. However, the molecular mechanism by which the FAS gene is up-regulated in tumor cells is poorly understood. We found that FAS was significantly up-regulated by hypoxia, which was also accompanied by reactive oxygen species (ROS) generation in human breast cancer cell lines. The FAS expression was also activated by H(2)O(2), whereas N-acetyl-L-cystein, a ROS inhibitor, suppressed the expression. We also found that the hypoxia significantly up-regulated sterol regulatory-element binding protein (SREBP)-1, the major transcriptional regulator of the FAS gene, via phosphorylation of Akt followed by activation of hypoxia-inducible factor 1 (HIF1). Moreover, our results of reporter assay and chromatin immunoprecipitation analysis indicate that SREBP-1 strongly bound to the SREBP binding site/E-box sequence on the FAS promoter under hypoxia. In our xenograft mouse model, FAS was strongly expressed in the hypoxic regions of the tumor. In addition, our results of immunohistochemical analysis for human breast tumor specimens indicate that the expressions of both FAS and SREBP-1 were colocalized with hypoxic regions in the tumors. Furthermore, we found that hypoxia-induced chemoresistance to cyclophosphamide was partially blocked by a combination of FAS inhibitor and cyclophosphamide. Taken together, our results indicate that FAS gene is up-regulated by hypoxia via activation of the Akt and HIF1 followed by the induction of the SREBP-1 gene, and that hypoxia-induced chemoresistance is partly due to the up-regulation of FAS.
Single-site glycine-specific labeling of proteins (2019)

Labeling of native proteins invites interest from diverse segments of science. However, there remains the significant unmet challenge in precise labeling at a single site of a protein. Here, we report the site-specific labeling of natural or easy-to-engineer N-terminus Gly in proteins with remarkable efficiency and selectivity. The method generates a latent nucleophile from N-terminus imine that reacts with an aldehyde to deliver an aminoalcohol under physiological conditions. It differentiates N-Gly as a unique target amongst other proteinogenic amino acids. The method allows single-site labeling of proteins in isolated form and extends to lysed cells. It administers an orthogonal aldehyde group primed for late-stage tagging with an affinity tag, <sup>19</sup>F NMR probe, and a fluorophore. A user-friendly protocol delivers analytically pure tagged proteins. The mild reaction conditions do not alter the structure and function of the protein. The cellular uptake of fluorophore-tagged insulin and its ability to activate the insulin-receptor mediated signaling remains unperturbed.
Single-Intersection Evaluation of Real-Time Adaptive Traffic Signal Control Algorithms (2004)

Adaptive traffic signal control systems present the potential to significantly reduce delay, travel time, stops, and fuel consumption relative to current arterial traffic management practices. However, this technology—now referred to as adaptive-control software (ACS) by FHWA—has not been widely deployed in the United States, in part because traffic engineers are unconvinced of the incremental benefits of ACS over those of well-maintained time-of-day plans. This study identifies three specific deficiencies in the current generation of adaptive-control algorithms. Primarily, the inability to optimize timing in general multiring configurations prevents current adaptive-control algorithms from consistently out-performing properly calibrated dual-ring vehicle-actuated controllers. Limitations in real-time computational capabilities are identified as the main roadblock to overcoming this and other deficiencies. This limitation motivates a novel simulation study focused on real-time computational capabilities of adaptive-control algorithms used in OPAC, PRODYN, ALLONS-D, and COP, the intersection control algorithm of RHODES. The goal is to determine which algorithmic techniques are best suited for extension or reformulation to overcome the identified deficiencies. Benchmarks for vehicle delay performance include Webster's optimized fixed-time control, vehicle-actuated control, and an adaptive fixed-time policy derived from SCOOT. In conclusion, certain aspects of algorithmic techniques from OPAC, PRODYN, and ALLONS-D are unsuitable for much more computationally demanding tasks, including future extension to full optimization of a multiring controller. Also, specific features of the COP-97 and ALLONS-D algorithms present significant advantages in computational complexity and reduced traffic delay, respectively.
Spin-dependent tunneling between ferromagnetic metals in a new type of tunnel junction (abstract) (1997)

We report on tunneling experiments in tunnel junctions with ferromagnetic electrodes (cobalt or permalloy) separated by a relatively thick (15 nm) Al2O3 layer in which small cobalt clusters are embedded. Electron transport is, thus, by successive tunnelings from electrode to cluster and from cluster to cluster. This structure for multichannel and multistep tunneling is less liable to metallic bridging by pinholes than junctions with an unique thin layer of insulator, and also makes easier the control of the total tunnel resistance. Layers of Al2O3 and discontinuous ultrathin layers of cobalt (“cluster layers”) are alternately deposited by sputtering through masks. The structure is characterized by transmission electron microscopy (Co clusters of 3 nm typical diameter, with about 2 nm of Al2O3 between successive cluster layers and between clusters and electrode). The total tunnel resistance can reach 25 kΩ at 4.2 K. Its variation with magnetic field reflects the magnetization reversal of the electrodes and cobalt clusters, with a maximum fractional change of about 21% at room temperature.
A Bisphosphonate Monoamide Analogue of DOTA:  A Potential Agent for Bone Targeting (2005)

A new macrocyclic DOTA-like ligand (BPAMD) for bone imaging and therapy containing a monoamide bis(phosphonic acid) bone-seeking group was designed and synthesized. Its lanthanide(III) complexes were prepared and characterized by 1H and 31P NMR spectroscopy. The Gd(III)-BPAMD complex was investigated in detail by 1H and 17O relaxometric studies to inspect parameters relevant for its potential application as an MRI contrast agent. Sorption experiments were conducted with Gd(III) and Tb(III) complexes using hydroxyapatite (HA) as a model of bone surface. Very effective uptake of the Gd-BPAMD complex by the HA surface was observed in NMR experiments. Radiochemical studies with the (160Tb-BPAMD)-HA system proved the sorption to be remarkably fast and strong on one hand and fully reversible on the other hand. The strong (Gd-BPAMD)-HA interaction was also supported by 1H NMRD measurements in the presence of a hydroxyapatite slurry, which showed an increase of the rotational correlation time upon adsorption of the complex on the HA surface, resulting in a significant relaxivity enhancement. The amide-bis(phosphonate) moiety is the only factor responsible for the binding of the complex to HA.
Origins of perpendicular magnetic anisotropy in Ni/Pd multilayer films (1999)

Room-temperature perpendicular magnetic anisotropy (PMA) was observed in Ni/Pd multilayer films having 5.1–11 Å Ni and constant 5.7 Å Pd sublayer thicknesses, prepared by dc magnetron sputtering at 7 mTorr Ar sputtering pressure. The magnetoelastic anisotropy determined from delicate in situ stress and ex situ magnetostriction coefficient measurements was found to contribute positively to the observed PMA in those samples and its magnitude was nearly comparable to the surface anisotropy.
Millimeter-wave and optoelectronic applications of heterostructure integrated circuits (1991)

The properties are reviewed of heterostructure devices for microwave-monolithic-integrated circuits (MMICs) and optoelectronic integrated circuits (OICs). Specific devices examined include lattice-matched and pseudomorphic InAlAs/InGaAs high-electron mobility transistors (HEMTs), mixer/multiplier diodes, and heterojunction bipolar transistors (HBTs) developed with a number of materials. MMICs are reviewed that can be employed for amplification, mixing, and signal generation, and receiver/transmitter applications are set forth for OICs based on GaAs and InP heterostructure designs. HEMTs, HBTs, and junction-FETs can be utilized in combination with PIN, MSM, and laser diodes to develop novel communication systems based on technologies that combine microwave and photonic capabilities.
Success factors for collaborative product development: a study of suppliers of information and communication technology (1995)

Abstract It is apparent that more and more organizations are embarking on collaborative ventures to develop products. This is particularly evident in Information and Communication Technology (ICT) sectors, so much so that part of the ‘received wisdom’ of ICT companies is that collaboration is the preferred route for product development. The benefits of collaboration have been well documented and are linked to the complexity and costliness of product development and the need for inputs from wide and varied areas of expertise as well as shorter lead times for product development. But the risks and costs of collsborative product development have been less well defined. In this paper, it is argued that the alleged rewards of collaboration may not be experienced in practice and that collaboration can lengthen the product development process, add to the cost of product development and prove difficult to control. However, management practice can facilitate the effective outcome of collaborative product development and the critical factors affecting the likelihood of successful management practice are presented here.
Relationships between Parts A and B of the Trail Making Test (1987)

Two measures of relationship between Parts A and B of the Trail Making Test (TMT) were examined in a large, acute rehabilitation population (N = 497). A difference (B-A) and a ratio (B/A) score were calculated and compared to other neuropsychological measures. The difference score was found to be correlated highly with intelligence and severity of impairment and, to a lesser degree, with age, education, and memory functioning. The ratio measure was correlated moderately or showed no significant relationship with other variables. This finding supported the curvilinear nature of the relationship between the ratio measure and cerebral impairment, as suggested by Golden, Osmon, Moses, and Berg (1981). Both measures were examined for their ability to distinguish between right and left cerebral damage. Only a trend toward differentiating lateralized damage was found; the ratio measure and a geometric transformation of the ratio showed greater sensitivity than did the difference measure. Results are discussed in terms of the potential usefulness of TMT relationship measures in neuropsychological inference.
Study of Liquid Crystal Lens with Focus Movable in Focal Plane by Wave Front Analysis (2006)

The phase transformation of a liquid crystal lens with its focus movable not only along but also off the lens axis is discussed. A lateral translation of the phase transformation is found. The wave front of an incident light wave in the exit pupil of the lens is observed by the interference method. It is found that the focusing ability of the lens is preserved even when the focus is away from the lens axis. From the obtained wave front, the focus position and the appropriate voltage for maintaining the focus in the focal plane are determined.
High-order velocity structure functions in turbulent shear flows (1984)

Measurements are presented of the velocity structure function on the axis of a turbulent jet at Reynolds numbers R λ ≤ 852 and in a turbulent duct flow at R λ = 515. Moments of the structure function up to the eighteenth order were calculated, primarily with a view to establish accurately the dependence on the order of the inertial range power-law exponent and to draw conclusions about the distribution of energy transfer in the inertial range. Adequate definition of the probability density of the structure function was achieved only for moments of order n ≤ 10. It is shown, however, that, although the values of moments of n > 10 diverges from their true values, the dependence of the moment of the structure function on the separation r is still given to a fair accuracy for moments up to n ≈ 18. The results demonstrate that the inertial-range power-law exponent is closely approximated by a quadratic dependence on the power which for lower-order moments ( n [lsim ] 12) would be consistent with a lognormal distribution. Higher-order moments diverge, however, from a lognormal distribution, which gives weight to Mandelbrot's (1971) conjecture that ‘Kolmogorov's third hypothesis’ is untenable in the strict sense. The intermittency parameter μ, appearing in the power-law exponent, has been determined from sixth-order moments 〈(δμ) 6 〉 ∼ r 2−μ to be μ = 0.2 ± 0.05. This value coincides with that determined from non-centred dissipation correlations measured in identical conditions.
Stable human standing with lower‐limb muscle afferents providing the only sensory input. (1994)

1. This study investigated the sources of sensory information upon which normal subjects' ability to stand depends. 2. An 'equivalent body' was used to simulate the physical properties of each subject's body during standing. The modulation of ankle torque required to support the equivalent body in an upright position was similar to that required to support the subject's own body when standing. However, when balancing the equivalent body, vestibular inputs were excluded from directing the appropriate changes in ankle torque. Thus, stability of stance could be studied with (normal stance) and without (balancing equivalent body) modulation by vestibular inputs. Vision could be excluded by closing the eyes. Sensory input from the feet and ankles could be removed by local anaesthesia from prolonged ischaemia, induced by occluding blood flow with inflated pneumatic cuffs just above the ankles. With vestibular, visual and peripheral sensory inputs negated, standing could rely only upon remaining sensory inputs, notably those from sensory receptors in the leg muscles. 3. Unlike the human body, the equivalent body used to negate vestibular inputs is not segmented. Therefore, the effects on stability of having a segmented body were determined by splinting subjects during standing so that only ankle movement was possible. This was done in the presence and absence of visual stabilization. 4. For each experimental task, either standing or balancing the equivalent body, sway was recorded while posture was unperturbed. Root mean square values of sway amplitude and power spectra were used to compare conditions. 5. Every subject could balance the equivalent body in a stable way when the eyes were closed, and when the feet were anaesthetized.(ABSTRACT TRUNCATED AT 250 WORDS)
Analysis-by-Synthesis Sinusoidal Model without an Overlapping Scheme (2008)

A new sinusoidal modeling approach for the analysis-by-synthesis (AbS) of parameters that characterize a linear combination of damped sinusoids is proposed. In addition to the typical sinusoidal parameters, two different damping factors, which represent the time-varying nature of speech, were used to efficiently reduce the modeling error. Even though the proposed model does not employ the overlap-adding synthesis or smoothly interpolative synthesis scheme, it shows substantially better modeling performance in the synthesis of voiced and transient segments.
AIDS Knowledge in Three Sites in Bas-Zaire (1992)

This study surveyed 5,494 women in one urban and two rural sites of Bas-Zaire on their knowledge, attitudes, and practices regarding AIDS. The AIDS Risk Reduction Model (ARRM) was used to analyze the results to better understand factors that may be related to motivation for behavior change. The results show that there are considerable barriers to achieving the first stage of the 3-stage model. Most notably, only a third of the women believed they were at risk of getting AIDS. Those aged 25-29, educated, and married felt themselves to be most at risk. Results are compared to other knowledge, attitudes, and practices studies conducted in Zaire. Policy implications of these results are discussed.
Scalable P2P search (2003)

Although the traditional client-server model first established the Web's backbone, it tends to underuse the Internet's bandwidth and intensify the burden that dedicated servers face as their load increases.' Peer-to-peer computing relies on individual computers' computing power and storage capacity to better utilize bandwidth and distribute this load in a self-organizing manner. In P2P, nodes (or peers) act as both clients and servers, form an application-level network, and route messages (such as requests to locate a resource). The design of these routing protocols is of paramount importance to a P2P application's efficiency: naive approaches - such as Gnutella's flood routing, for example - can add traffic. P2P systems that exhibit the "small world" property - in which most peers have few links to other peers, but a few of them have many - are robust to random attacks, but can be highly vulnerable to targeted ones. P2P computing also has the potential to enhance reliability and fault tolerance because it doesn't rely on dedicated servers.' Each peer maintains a local directory with entries to the resources it manages. It can also cache other peers' directory entries. Important applications of P2P technologies include distributed directory systems, new e-commerce models, and Web service discovery, all of which require efficient resource-location mechanisms.
Kinetic characterisation of arylamine N-acetyltransferase from Pseudomonas aeruginosa (2007)

Arylamine N-acetyltransferases (NATs) are important drug- and carcinogen-metabolising enzymes that catalyse the transfer of an acetyl group from a donor, such as acetyl coenzyme A, to an aromatic or heterocyclic amine, hydrazine, hydrazide or N-hydroxylamine acceptor substrate. NATs are found in eukaryotes and prokaryotes, and they may also have an endogenous function in addition to drug metabolism. For example, NAT from Mycobacterium tuberculosis has been proposed to have a role in cell wall lipid biosynthesis, and is therefore of interest as a potential drug target. To date there have been no studies investigating the kinetic mechanism of a bacterial NAT enzyme. We have determined that NAT from Pseudomonas aeruginosa, which has been described as a model for NAT from M. tuberculosis, follows a Ping Pong Bi Bi kinetic mechanism. We also describe substrate inhibition by 5-aminosalicylic acid, in which the substrate binds both to the free form of the enzyme and the acetyl coenzyme A-enzyme complex in non-productive reaction pathways. The true kinetic parameters for the NAT-catalysed acetylation of 5-aminosalicylic acid with acetyl coenzyme A as the co-factor have been established, validating earlier approximations. This is the first reported study investigating the kinetic mechanism of a bacterial NAT enzyme. Additionally, the methods used herein can be applied to investigations of the interactions of NAT enzymes with new chemical entities which are NAT ligands. This is likely to be useful in the design of novel potential anti-tubercular agents.
The Effect of Conformational Rigidity on Several Physical Properties of Polymers (1998)

The phenomenological dependences of several physical properties such as the softening temperature, friction coefficient, elasticity modulus, fire-resistance parameters and quantum luminescence yield on the conformational rigidity of a polymeric chain are revealed for polyheteroarylenes. The contribution of the conformational rigidity of a polymer chain to the physical properties of this class of polymers is shown to be significant. It should be taken into account in estimation of the above-mentioned properties together with the contribution of intermolecular interactions.
Temperature sensitive diphtheria toxin confers conditional male‐sterility in <i>Arabidopsis thaliana</i> (2002)

A gene encoding a temperature-sensitive diphtheria toxin A chain (DTA) polypeptide was fused to the Arabidopsis thaliana tapetum-specific A9 promoter. Expression of the chimaeric gene in transgenic A. thaliana lines resulted in plants that were male-sterile, but female-fertile, when grown at 18 degrees C, and fully self fertile at 26 degrees C. No pollen grains were found on the anthers of transgenic plants grown at 18 degrees C, although aggregated pollen grains were found inside the anthers. Electron microscopy revealed discrete alterations in the tapetal cells of the male-sterile transgenic plants. The strength of the phenotype observed in segregants correlated with the level of expression of the gene and the copy number. The low frequency at which fully male-sterile plants were generated suggests that the temperature-sensitive DTA protein is disabled as a cytotoxin, relative to the wild-type protein activity.