gebhart/patrepeval huggingface dataset:
Selection of a Carbohydrate-Binding Domain with a Helix−Loop−Helix Structure (2008)

We obtained a novel carbohydrate-binding peptide having a helix-loop-helix scaffold from a random peptide library. The helix-loop-helix peptide library randomized at five amino acid residues was displayed on the major coat protein of a filamentous phage. Affinity selection with a ganglioside, Galbeta1-3GalNAcbeta1-4(Neu5Acalpha2-3)Galbeta1-4Glcbeta1-1'Cer (GM1), gave positive phage clones. Surface plasmon resonance spectroscopy showed that a corresponding 35-mer synthetic peptide had high affinity for GM1 with a dissociation constant of 0.24 microM. This peptide preferentially binds to GM1 rather than asialo GM1 and GM2, suggesting that a terminal galactose and sialic acid are required for the binding as for cholera toxin. Circular dichroism spectroscopic studies indicated that a helical structure is important for the affinity and specificity. Furthermore, alanine scanning at randomized positions showed that arginine and phenylalanine play an especially important role in the recognition of carbohydrates. Such a de novo helix-loop-helix peptide would be available for the design of carbohydrate-binding proteins.
Modeling and control system design of reel-to-reel tape drives (2002)

The control system design for a reel-to-reel type tape drive system is presented. Such a system is a multiple-input-multiple-output (MIMO) 2-input 2-output system. The paper presents the control system modeling of a general tape drive system and then develops a frequency response method to validate the model. Control system design techniques are presented using a decoupled transfer function approach as well as a state space linear quadratic regulator technique. Finally, test results are presented to illustrate the design techniques.
Multiple Binding Sites in Fibrinogen for Integrin αMβ2 (Mac-1) (2004)

The leukocyte integrin alphaMbeta2 (Mac-1) is a multiligand receptor that mediates a range of adhesive reactions of leukocytes during the inflammatory response. This integrin binds the coagulation protein fibrinogen providing a key link between thrombosis and inflammation. However, the mechanism by which alphaMbeta2 binds fibrinogen remains unknown. Previous studies indicated that a model in which two fibrinogen gammaC domain sequences, P1 (gamma190-202) and P2 (gamma377-395), serve as the alphaMbeta2 binding sites cannot fully account for recognition of fibrinogen by integrin. Here, using surface plasmon resonance, we examined the interaction of the ligand binding alphaMI-domain of alphaMbeta2 with the D fragment of fibrinogen and showed that this ligand is capable of associating with several alphaMI-domain molecules. To localize the alternative alphaMI-domain binding sites, we screened peptide libraries covering the complete sequences of the gammaC and betaC domains, comprising the majority of the D fragment structure, for alphaMI-domain binding. In addition to the P2 and P1 peptides, the alphaMI-domain bound to many other sequences in the gammaC and betaC scans. Similar to P1 and P2, synthetic peptides derived from gammaC and betaC were efficient inhibitors of alphaMbeta2-mediated cell adhesion and were able to directly support adhesion suggesting that they contain identical recognition information. Analyses of recognition specificity using substitutional peptide libraries demonstrated that the alphaMI-domain binding depends on basic and hydrophobic residues. These findings establish a new model of alphaMbeta2 binding in which the alphaMI-domain interacts with multiple sites in fibrinogen and has the potential to recognize numerous sequences. This paradigm may have implications for mechanisms of promiscuity in ligand binding exhibited by integrin alphaMbeta2.
Self-aligning microfluidic interconnects for glass- and plastic-based microfluidic systems (2001)

In this work, we present novel self-aligning fluidic interconnection techniques with low dead volume and pressure drop for generic microfluidic systems and capillary electrophoresis chips. We have successfully designed, fabricated and characterized two self-aligning fluidic interconnection techniques in this work, both resulting in low dead volume and low pressure drop across the interconnects. The first technique is a serial assembly technique, in which each fluidic interconnect is assembled individually, exhibiting a pressure drop of 977 Pa (0.14 psi) at a flow rate of 100 µl min-1. The second technique is a parallel assembly technique that is suitable for high-density interconnects with multi-stacked generic microfluidic systems, which has a pressure drop of 1024 Pa (0.15 psi) at a flow rate of 100 µl min-1. Furthermore, the parallel assembly technique is ideally suited for plastic-based microfluidic systems. We have simulated the flow characteristics of these interconnection schemes and, based in part on the simulation results, we have designed the above interconnection schemes. We have also characterized these interconnects in terms of the physical robustness of the interconnection scheme. The serial interconnection scheme can theoretically withstand 2.6 MPa and the parallel interconnection scheme can withstand a theoretical maximum pressure of 6.6 MPa.
Lyotropic and Thermotropic Phase Transitions in Films of Ionene−Alkyl Sulfate Complexes (2005)

Five [X,Y]-ionenes [(CH2)(X)N+(CH3)2(CH2)(Y)N+(CH3)2]nBr-(2n) were prepared (X = 3, 5; Y = 10, 12, 22). Using new preparation methods, dry, salt-free complexes with three n-alkyl sulfates (octyl, decyl, and dodecyl) were obtained. The ionenes and their complexes were characterized in methanol solution by light scattering, viscometry, and fluorescent probe studies. The solid materials were investigated by means of DSC, TG, and ATR-IR. Transparent films were formed from stoichiometric [3,10], [3,12], and [5,10]-ionene complexes with decyl and dodecyl sulfate. In the films, mesogenic phase transitions could be induced: dry films were optically isotropic; when exposed to elevated humidity, the films slowly became optically anisotropic because of a lyotropic transition to a hexagonal mesogenic phase. The relative humidity, at which the hexagonal phase developed, was distinct for each complex. The anisotropic phases were converted to isotropic in a thermotropic transition under controlled relative humidity at specific clearing temperatures, which were higher for dodecyl complexes than for decyl complexes. This thermotropic isotropic-anisotropic transition could be cycled several times, but partial hydrolysis of the alkyl sulfates reduced the reproducibility of transition points.
'Conserved hypothetical' proteins: prioritization of targets for experimental study (2004)

Comparative genomics shows that a substantial fraction of the genes in sequenced genomes encodes 'conserved hypothetical' proteins, i.e. those that are found in organisms from several phylogenetic lineages but have not been functionally characterized. Here, we briefly discuss recent progress in functional characterization of prokaryotic 'conserved hypothetical' proteins and the possible criteria for prioritizing targets for experimental study. Based on these criteria, the chief one being wide phyletic spread, we offer two 'top 10' lists of highly attractive targets. The first list consists of proteins for which biochemical activity could be predicted with reasonable confidence but the biological function was predicted only in general terms, if at all ('known unknowns'). The second list includes proteins for which there is no prediction of biochemical activity, even if, for some, general biological clues exist ('unknown unknowns'). The experimental characterization of these and other 'conserved hypothetical' proteins is expected to reveal new, crucial aspects of microbial biology and could also lead to better functional prediction for medically relevant human homologs.
A hitchhiker's guide to diffusion tensor imaging (2013)

Diffusion Tensor Imaging (DTI) studies are increasingly popular among clinicians and researchers as they provide unique insights into brain network connectivity. However, in order to optimize the use of DTI, several technical and methodological aspects must be factored in. These include decisions on: acquisition protocol, artifact handling, data quality control, reconstruction algorithm, and visualization approaches, and quantitative analysis methodology. Furthermore, the researcher and/or clinician also needs to take into account and decide on the most suited software tool(s) for each stage of the DTI analysis pipeline. Herein, we provide a straightforward hitchhiker's guide, covering all of the workflow's major stages. Ultimately, this guide will help newcomers navigate the most critical roadblocks in the analysis and further encourage the use of DTI.
Identification and Characterization of a Novel Cap-binding Protein from Arabidopsis thaliana (1998)

Cap-binding proteins specifically bind to the 7-methyl guanosine (m7G) functional group at the 5' end of eukaryotic mRNAs. A novel Arabidopsis thaliana protein has been identified that has sequence similarity to cap-binding proteins but is clearly a different form of the protein. The most obvious primary sequence difference is the substitution of two of the eight conserved tryptophan residues with other aromatic amino acids in the novel protein. Analogous forms of this novel protein appear to be present in other higher eukaryotes but not in yeast. Analysis of the native and recombinant forms of the novel protein by retention on m7GTP-Sepharose indicate that it is a functional cap-binding protein. Measurements of the dissociation constant for this protein indicate that it binds m7GTP 5-20-fold tighter than eukaryotic initiation factor (eIF)(iso)4E. The novel protein also supports the initiation of translation of capped mRNA in vitro. Biochemical analysis and yeast two-hybrid data indicate that it interacts with eIF(iso)4G to form a complex. Based on these observations, this protein appears to be able to function as a cap-binding protein and is given the designation of novel cap-binding protein (nCBP).
A signal design without co-channel interference for approximately synchronized CDMA systems (1994)

A signal design is proposed for a CDMA system that is approximately synchronized. The signals are called pseudoperiodic sequences. The set of pseudoperiodic polyphase sequences are introduced from a set of periodic polyphase sequences with ideal autocorrelation for small shifts and zero cross correlation for all shifts. The system works without cochannel interference, even when the signals are modulated by data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Understanding What They Do with What They Know (Short Paper) (2012)

This work seeks to understand what “they” (Web advertisers) actually do with the information available to them. We analyze the ads shown to users during controlled browsing as well as examine the inferred demographics and interests shown in Ad Preference Managers provided by advertisers. In an initial study of ad networks and a focused study of the Google ad network, we found many expected contextual, behavioral and location-based ads along with combinations of these types of ads. We also observed profile-based ads. Most behavioral ads were shown as categories in the Ad Preference Manager (APM) of the ad network, but we found unexpected cases where the interests were not visible in the APM. We also found unexpected behavior for the Google ad network in that non-contextual ads were shown related to induced sensitive topics regarding sexual orientation, health and financial matters. In a smaller study of Facebook, we did not find clear evidence that a user’s browsing behavior on non-Facebook sites influences the ads shown to the user on Facebook, but we did observe such influence when the Facebook Like button is used to express interest in content. We did observe Facebook ads appearing to target users for sensitive interests with some ads even asserting such sensitive information, which appears to be a violation of Facebook’s stated policy.
CD23 antigen regulation and signaling in chronic lymphocytic leukemia. (1992)

B lymphocytes from patients with chronic lymphocytic leukemia (B-CLLs), strongly express the CD23 antigen, a surface marker with significant prognostic importance in this disease. Because we previously reported that IL-4 shows a poor capacity for CD23 expression on B-CLLs, we first examined the possible mechanisms underlying CD23 overexpression on B-CLLs and found that mitogen-activated CLL T cells release soluble factors that are capable, in synergy with IL-4, of strongly inducing CD23. Using neutralizing Abs, we noticed that the T-cell-derived enhancing activity is entirely ascribed to the combined effects of IFN gamma (potent inhibitor of CD23 on normal B cells), TNF alpha (which has no effect on normal B cells), and IL-2 (which has a slight enhancing effect on both CLL and normal B cells). Furthermore, recombinant IFN gamma as well as IFN alpha, TNF alpha, and IL-2 (but not IL-3, IL-5, IL-6, IL-7, and lymphotoxin) significantly enhance CD23 protein and mRNA expression on B-CLLs, in the presence or absence of IL-4. Inasmuch as optimal CD23 expression absolutely requires the combination of IFN gamma, IL-2, TNF alpha (the production of which is increased in CLL disease), and IL-4, it was relevant to show that IL-4 mRNA is indeed expressed in fresh T-CLL cells. We next examined the possible role of CD23 in the regulation of B-CLL proliferation. Signaling through CD23 via ligation of the antigen by F(ab')2 anti-CD23 MAb but not Fab fragments inhibits the cytokine-induced B-CLL DNA synthesis. It is concluded that the CD23 gene is abnormally regulated in B-CLL disease and that cross-linking of CD23 molecule delivers a negative growth signal to the leukemic B cells.
A transgenic mouse model for the simultaneous monitoring of ANF and BNP gene activity during heart development and disease (2013)

A genomic region sufficient to regulate the developmental pattern and stress response of Nppa and Nppb has been defined. The double reporter mice can be used for the functional imaging and investigation of cardiac hypertrophy and myocardial infarction in vivo.
Sams Teach Yourself SQL in 10 Minutes, Third Edition (2004)

Sams Teach Yourself SQL in 10 Minutes has established itself as the gold standard for introductory SQL books, offering a fast-paced accessible tutorial to the major themes and techniques involved in applying the SQL language. Fortai??s examples are clear and his writing style is crisp and concise. As with earlier editions, this revision includes coverage of current versions of all major commercial SQL platforms. New this time around is coverage of MySQL, and PostgreSQL. All examples have been tested against each SQL platform, with incompatibilities or platform distinctives called out and explained.
Control of Solid‐State Dye‐Sensitized Solar Cell Performance by Block‐Copolymer‐Directed TiO<sub>2</sub> Synthesis (2010)

Abstract Hybrid dye‐sensitized solar cells are typically composed of mesoporous titania (TiO 2 ), light‐harvesting dyes, and organic molecular hole‐transporters. Correctly matching the electronic properties of the materials is critical to ensure efficient device operation. In this study, TiO 2 is synthesized in a well‐defined morphological confinement that arises from the self‐assembly of a diblock copolymer—poly(isoprene‐ b ‐ethylene oxide) (PI‐ b ‐PEO). The crystallization environment, tuned by the inorganic (TiO 2 mass) to organic (polymer) ratio, is shown to be a decisive factor in determining the distribution of sub‐bandgap electronic states and the associated electronic function in solid‐state dye‐sensitized solar cells. Interestingly, the tuning of the sub‐bandgap states does not appear to strongly influence the charge transport and recombination in the devices. However, increasing the depth and breadth of the density of sub‐bandgap states correlates well with an increase in photocurrent generation, suggesting that a high density of these sub‐bandgap states is critical for efficient photo‐induced electron transfer and charge separation.
Effect of X-ray Tube Parameters, Iodine Concentration, and Patient Size on Image Quality in Pulmonary Computed Tomography Angiography: A Chest-Phantom-Study (2008)

Low kVp protocols for pulmonary embolism are potentially advantageous especially in thin and, to a lesser extent, in intermediate patients. Thin patients profit from low voltage protocols preserving a good CNR at a lower exposure. The use of 80 kVp in obese patients may be problematic because of the limitation of the tube current available, reduced CNR, and high skin dose. The high CNR of the 400 mg iodine/mL contrast medium together with lower tube energy and/or current can be used for exposure reduction.
Visualization (2004)

article Share on Visualization: a quickly emerging field Author: Kwan-Liu Ma University of California, Davis, CA University of California, Davis, CAView Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 38Issue 1February 2004 pp 4–7https://doi.org/10.1145/1012272.1012281Online:01 February 2004Publication History 3citation962DownloadsMetricsTotal Citations3Total Downloads962Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Pressure Effects of Foreign Gases on the Absorption Lines of Cesium. VI. Intensity Measurements of the Cesium Resonance Lines and Their Associated Satellites in the Presence of Various Foreign Gases (1969)

The intensity contours of the pressure-broadened Cs resonance lines and their associated satellites in the presence of He, Ne, Ar, Kr, Xe, and C${\mathrm{F}}_{4}$ are studied. The total integrated intensity of the lines and satellites in the presence of these gases is found to decrease exponentially with the relative density (rd) of foreign gas. For the range of foreign-gas pressures studied (0 to \ensuremath{\sim}50 rd), the ratio of the integrated intensity of the $^{2}P_{\frac{3}{2}}$ component to that of the $^{2}P_{\frac{1}{2}}$ component is found to be close to the theoretical value of 2 for all rd's only when the integrated intensity of the satellites is included with the parent lines. These ratios (1.90 \ifmmode\pm\else\textpm\fi{} 0.03 for Ar, 2.00 \ifmmode\pm\else\textpm\fi{} 0.03 for Kr, and 2.06 \ifmmode\pm\else\textpm\fi{} 0.04 for Xe) indicate that satellites are part of the lines. The integrated intensity of the violet satellites associated with the $^{2}P_{\frac{3}{2}}$ component in the presence of these gases is found to be proportional to the cube of the low-energy collision diameter of the particular foreign gas. A violet satellite associated with the $^{2}P_{\frac{1}{2}}$ component is observed in the presence of C${\mathrm{F}}_{4}$.
Histograms of oriented optical flow and Binet-Cauchy kernels on nonlinear dynamical systems for the recognition of human actions (2009)

System theoretic approaches to action recognition model the dynamics of a scene with linear dynamical systems (LDSs) and perform classification using metrics on the space of LDSs, e.g. Binet-Cauchy kernels. However, such approaches are only applicable to time series data living in a Euclidean space, e.g. joint trajectories extracted from motion capture data or feature point trajectories extracted from video. Much of the success of recent object recognition techniques relies on the use of more complex feature descriptors, such as SIFT descriptors or HOG descriptors, which are essentially histograms. Since histograms live in a non-Euclidean space, we can no longer model their temporal evolution with LDSs, nor can we classify them using a metric for LDSs. In this paper, we propose to represent each frame of a video using a histogram of oriented optical flow (HOOF) and to recognize human actions by classifying HOOF time-series. For this purpose, we propose a generalization of the Binet-Cauchy kernels to nonlinear dynamical systems (NLDS) whose output lives in a non-Euclidean space, e.g. the space of histograms. This can be achieved by using kernels defined on the original non-Euclidean space, leading to a well-defined metric for NLDSs. We use these kernels for the classification of actions in video sequences using (HOOF) as the output of the NLDS. We evaluate our approach to recognition of human actions in several scenarios and achieve encouraging results.
Species variation in the response of the cytochrome P-450-dependent monooxygenase system to inducers and inhibitors (1990)

1. In the safety evaluation of drugs and other chemicals it is important to evaluate their possible inducing and inhibitory effects on the enzymes of drug metabolism. 2. While many similarities exist between species in their response to inducers and inhibitors, there are also important differences. Possible mechanisms of such variation are considered, with particular reference to the cytochrome P-450 system. 3. Differences in inhibition may be due to differences in inhibitory site of the enzyme involved, which is not always the active site of the enzyme, in competing pathways or in the pharmacokinetics of the inhibitor. 4. Differences in induction could be due to differences in the nature of the induction mechanism, in the isoenzyme induced, in tissue- or age-dependent regulation, in competing pathways for the substrate or its products, or in the pharmacokinetics of the inducing agent. 5. Examples of each of these possible differences are considered, often from our own work on the P450 IA subfamily, and results in animals are compared with those in humans, where possible. 6. At present, the differences between species in their response to inducers and inhibitors make extrapolation to humans from the results of animal studies difficult, so that ultimately such effects should be studied in the species of interest, humans.
Transforming Growth Factor-β (TGF-β) and TGF-β–Associated Kinase 1 Are Required for R-Ras–Mediated Transformation of Mammary Epithelial Cells (2008)

Transforming growth factor-beta (TGF-beta) cooperates with oncogenic members of the Ras superfamily to promote cellular transformation and tumor progression. Apart from the classic (H-, K-, and N-) Ras GTPases, only the R-Ras subfamily (R-Ras, R-Ras2/TC21, and R-Ras3/M-Ras) has significant oncogenic potential. In this study, we show that oncogenic R-Ras transformation of EpH4 cells requires TGF-beta signaling. When murine EpH4 cells were stably transfected with a constitutively active R-Ras(G38V) mutant, they were no longer sensitive to TGF-beta-mediated growth inhibition and showed increased proliferation and transformation in response to exogenous TGF-beta. R-Ras/EpH4 cells require TGF-beta signaling for transformation to occur and they produce significantly elevated levels of endogenous TGF-beta, which signals in an autocrine fashion. The effects of TGF-beta are independent of Smad2/3 activity and require activation of TGF-beta-associated kinase 1 (TAK1) and its downstream effectors c-Jun NH(2)-terminal kinase and p38 mitogen-activated protein kinase as well as the phosphoinositide 3-kinase/Akt and mammalian target of rapamycin pathways. Thus, TAK1 is a novel link between TGF-beta signaling and oncogenic R-Ras in the promotion of tumorigenesis.