gebhart/patrepeval huggingface dataset:
Identification of a protein, YneA, responsible for cell division suppression during the SOS response in Bacillus subtilis (2003)

A knock-out mutant of the dinR gene that encodes the SOS regulon repressor in Bacillus subtilis was constructed. The yneA, yneB and ynzC genes transcribed divergently from the dinR gene were strongly induced in mutant cells. Northern hybridization analyses revealed that these genes collectively form an operon and belong to the SOS regulon. The simultaneous deletion of dinR and yneA suppressed the filamentous phenotype of the dinR mutant. Furthermore, although yneA is suppressed in the wild-type cell in the absence of SOS induction, artificial expression of the YneA protein using an IPTG-inducible promoter resulted in cell elongation. Disruption of yneA significantly reduced cell elongation after the induction of the SOS response by mitomycin C in dinR+ cells. These results indicate that the YneA protein is responsible for cell division suppression during the SOS response in B. subtilis. Localization of the FtsZ protein to the cell division site was reduced in dinR-disrupted or yneA-expressing cells, further suggesting that the YneA protein suppresses cell division through the suppression of FtsZ ring formation. Interestingly, the B. subtilis YneA protein is structurally and phylogenetically unrelated to its functional counterpart in Escherichia coli, SulA.
Photoforming applied to fine machining (2002)

Photoforming refers to optical forming methods such as stereolithography, photomask layering, and the 1H process. In these processes, a special liquid resin is used as forming material and solidified by light exposure. The authors applied this method to making micromachines. A theoretical analysis including computer simulation of photon behavior in the liquid resin shows that sharp focusing is not required to achieve high precision, but controlling of light amount is important for a good result. It is proved that resolution can be within a few micrometers. Results of experimental forming demonstrate the possibility of making such precise structures. Some microscopic models with a resolution of 8 mm and some movable models were formed. It is suggested that this process can be applied to the construction of three-dimensional fine structures and precise mechanisms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abandoning Objectives: Evolution Through the Search for Novelty Alone (2010)

In evolutionary computation, the fitness function normally measures progress toward an objective in the search space, effectively acting as an objective function. Through deception, such objective functions may actually prevent the objective from being reached. While methods exist to mitigate deception, they leave the underlying pathology untreated: Objective functions themselves may actively misdirect search toward dead ends. This paper proposes an approach to circumventing deception that also yields a new perspective on open-ended evolution. Instead of either explicitly seeking an objective or modeling natural evolution to capture open-endedness, the idea is to simply search for behavioral novelty. Even in an objective-based problem, such novelty search ignores the objective. Because many points in the search space collapse to a single behavior, the search for novelty is often feasible. Furthermore, because there are only so many simple behaviors, the search for novelty leads to increasing complexity. By decoupling open-ended search from artificial life worlds, the search for novelty is applicable to real world problems. Counterintuitively, in the maze navigation and biped walking tasks in this paper, novelty search significantly outperforms objective-based search, suggesting the strange conclusion that some problems are best solved by methods that ignore the objective. The main lesson is the inherent limitation of the objective-based paradigm and the unexploited opportunity to guide search through other means.
35-nm gate-length and ultra low-voltage (0.45 V) operation Bulk Thyristor-SRAM/DRAM (BT-RAM) cell with Triple selective Epitaxy Layers (TELs) (2008)

We have successfully developed an alternative SRAM cell using a bulk thyristor-RAM (BT-RAM), which has a 35-nm gate-length with triple selective epitaxy layers (TELs) for the anode, the n-base, and the cathode. The TEL BT-RAM reads and writes at an ultra low voltage of 0.45 V at 900 ps and reads and writes at a high speed of 100 ps at 0.9 V. It also has excellent scalability, a high I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ratio, and good thermal stability even at 125degC. The TEL BT-RAM is therefore a promising alternative SRAM cell for the 35-nm gate length generation and beyond.
Kerma Factors for Neutron Energies below 30 MeV (1980)

Kerma factors for neutrons have been calculated from thermal neutron energies to 30 MeV. In addition to a point at 0.0253 eV, there are 116 contiguous energy bins extending from 0.026 eV to 30 MeV. Values are given for 19 elements or nuclides: H, ${}^{6}{\rm Li}$ , ${}^{7}{\rm Li}$ , B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, and Fe. The chief source of nuclear data is the Evaluated Nuclear Data File ENDF/B-4. The basis of the calculations is discussed, and comparison is made with some other tabulations.
Arginine-rich peptides and their internalization mechanisms (2007)

As the versatility and use of CPPs (cell-penetrating peptides) as intracellular delivery vectors have been widely accepted, the cellular uptake mechanisms that enable their efficient internalization have become the subject of much interest. Arginine-rich peptides, including HIV-1 Tatp (transactivator of transcription peptide), are regarded as a representative class of CPPs. Evidence suggests that macropinocytosis plays a crucial role in the cellular uptake of these peptides. We have recently shown that treatment of cells with arginine-rich peptides induces activation of Rac protein leading to F-actin (filamentous actin) organization and macropinocytosis. We have also shown that depletion of membrane-associated proteoglycans results in the failure of this signalling pathway, suggesting that membrane-associated proteoglycans may act as a potential receptor for the induction of macropinocytic uptake of arginine-rich peptides. However, when the macropinocytic pathway is inhibited at a low temperature or by cholesterol depletion, these peptides can be internalized by alternative mechanisms, one of which appears to be direct translocation of the peptides through the plasma membrane. This review summarizes the current theories on both endocytic and non-endocytic aspects of internalization of arginine-rich peptides.
High-affinity AKAP7δ–protein kinase A interaction yields novel protein kinase A-anchoring disruptor peptides (2006)

PKA (protein kinase A) is tethered to subcellular compartments by direct interaction of its regulatory subunits (RI or RII) with AKAPs (A kinase-anchoring proteins). AKAPs preferentially bind RII subunits via their RII-binding domains. RII-binding domains form structurally conserved amphipathic helices with unrelated sequences. Their binding affinities for RII subunits differ greatly within the AKAP family. Amongst the AKAPs that bind RIIalpha subunits with high affinity is AKAP7delta [AKAP18delta; K(d) (equilibrium dissociation constant) value of 31 nM]. An N-terminally truncated AKAP7delta mutant binds RIIalpha subunits with higher affinity than the full-length protein presumably due to loss of an inhibitory region [Henn, Edemir, Stefan, Wiesner, Lorenz, Theilig, Schmidtt, Vossebein, Tamma, Beyermann et al. (2004) J. Biol. Chem. 279, 26654-26665]. In the present study, we demonstrate that peptides (25 amino acid residues) derived from the RII-binding domain of AKAP7delta bind RIIalpha subunits with higher affinity (K(d)=0.4+/-0.3 nM) than either full-length or N-terminally truncated AKAP7delta, or peptides derived from other RII binding domains. The AKAP7delta-derived peptides and stearate-coupled membrane-permeable mutants effectively disrupt AKAP-RII subunit interactions in vitro and in cell-based assays. Thus they are valuable novel tools for studying anchored PKA signalling. Molecular modelling indicated that the high affinity binding of the amphipathic helix, which forms the RII-binding domain of AKAP7delta, with RII subunits involves both the hydrophobic and the hydrophilic faces of the helix. Alanine scanning (25 amino acid peptides, SPOT technology, combined with RII overlay assays) of the RII binding domain revealed that hydrophobic amino acid residues form the backbone of the interaction and that hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction.
Single amino acid substitutions in the hemagglutinin can alter the host range and receptor binding properties of H1 strains of influenza A virus (1991)

We have previously characterized an influenza A (H1N1) virus which has host-dependent growth and receptor binding properties and have shown that a mutation which removes an oligosaccharide from the tip of the hemagglutinin (HA) by changing Asn-129 to Asp permits this virus to grow to high titer in MDBK cells, (C. M. Deom, A. J. Caton, and I. T. Schulze, Proc. Natl. Acad. Sci. USA 83:3771-3775, 1986). We have now isolated monoclonal antibodies specific for the mutant HA and have used escape mutants to identify alterations in HA sequence which reduce virus yields from MDBK cells without reducing those from chicken embryo fibroblasts. Two types of escape mutants which grow equally well in chicken embryo fibroblasts were obtained. Those with the parent phenotype contain Asn at residue 129 and are glycosylated at that site. Those with the mutant phenotype are unchanged at residue 129 but have a Gly to Glu substitution at residue 158, which is close to residue 129 on the HA1 subunit. Binding assays with neoglycoproteins containing N-acetylneuraminic acid in either alpha 2,3 or alpha 2,6 linkage to galactose showed that the MDBK-synthesized oligosaccharides at Asn-129 reduce binding to both of these receptors, leaving the HA's preference for alpha 2,6 linkages unchanged. Glu at residue 158 greatly reduces binding to both receptors without reducing virus yields from MDBK cells. We conclude that changes in the receptor binding properties of the HA can result either from direct alteration of the HA protein by host cell glycosylation or from mutations in the HA gene and that these changes generate heterogeneity that can contribute to the survival of influenza A virus populations in nature.
Robust Real-Time Needle Tracking in 2-D Ultrasound Images Using Statistical Filtering (2016)

Percutaneous image-guided tumor ablation is a minimally invasive surgical procedure for the treatment of malignant tumors using a needle-shaped ablation probe. Automating the insertion of a needle by using a robot could increase the accuracy and decrease the execution time of the procedure. Extracting the needle tip position from the ultrasound (US) images is of paramount importance for verifying that the needle is not approaching any forbidden regions (e.g., major vessels and ribs), and could also be used as a direct feedback signal to the robot inserting the needle. A method for estimating the needle tip has previously been developed combining a modified Hough transform, image filters, and machine learning. This paper improves that method by introducing a dynamic selection of the region of interest in the US images and filtering the tracking results using either a Kalman filter or a particle filter. Experiments where a biopsy needle has been inserted into a phantom by a robot have been conducted, guided by an infrared tracking system. The proposed method has been accurately evaluated by comparing its estimations with the needle tip’s positions manually detected by a physician in the US images. The results show a significant improvement in precision and more than 85% reduction of 95th percentile of the error compared with the previous automatic approaches. The method runs in real time with a frame rate of 35.4 frames/s. The increased robustness and accuracy can make our algorithm usable in autonomous surgical systems for needle insertion.
Analysis of Immune Surveillance of Sequentially Derived Cell Lines That Differ in Their Tumorigenic Potential<xref ref-type="fn" rid="FN2">2</xref> (1985)

The immune surveillance hypothesis suggests that cancer evolves as a multistage process. Further, it predicts that cells intermediate on the pathway to cancer are susceptible to host protective mechanisms, and only those variants that are able to escape the protective mechanisms are able to grow as tumors. We have isolated, as lineages, fibroblast lines that express phenotypes predicted by the surveillance hypothesis. The lineages were derived by treating nontransformed cells (N-cells) with chemical carcinogens and by isolating transformed variants in vitro. From the transformants that are tumorigenic in immune-depressed ATXFL mice but rejected by normal mice (I-cells), variants were selected in vivo that had escaped the rejection mechanism(s) and had grown as tumors in normal mice (C-cells). Thus lineages were established comprised of sequentially derived cell lines with the following phenotypes: nontransformed, transformed but susceptible to host protective mechanisms, transformed and resistant to host protective mechanisms (i.e., N----I----C). With the use of in vivo cross-protection experiments, two independently derived I-cell lines were shown to express non-cross-reactive antigens that are not expressed by the parental nontransformed N-cells (i.e., transformation-associated antigens). The transformation-associated antigens are expressed at an equivalent level on the cells that are susceptible to rejection (i.e., I-lines) and those that have escaped rejection (i.e., C-lines). In addition, although the transformation-associated antigens expressed by I-cells induce an effective immune response capable of rejecting both the I-line and C-line, the expression of these antigens on C-cells does not induce an effective immune response. The role of host defense mechanisms in the rejection of these chemically transformed I-cells and the possible mechanisms by which C-cells escape rejection are discussed.
200/spl deg/C, 96-nm wavelength range, continuous-wave lasing from unbonded GaAs MOVPE-grown vertical cavity surface-emitting lasers (1995)

We report record temperature and wavelength range attained using MOVPE-grown AlGaAs vertical cavity surface-emitting lasers (VCSEL's). Unbonded continuous-wave lasing is achieved at temperatures up to 200/spl deg/C from these top-emitting VCSEL's and operation over a 96-nm wavelength regime near 850 nm is also achieved from the same nominal design. Temperature and wavelength insensitive operation is also demonstrated; threshold current is controlled to within a factor of 2 (2.5-5 mA) for a wavelength range exceeding 50 nm and to within /spl plusmn/30% (5-10 mA) for a temperature range of 190/spl deg/C at 870 nm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Common Motif of Eukaryotic Glycosyltransferases Is Essential for the Enzyme Activity of Large Clostridial Cytotoxins (1998)

A fragment of the N-terminal 546 amino acid residues of Clostridium sordellii lethal toxin possesses full enzyme activity and glucosylates Rho and Ras GTPases in vitro. Here we identified several amino acid residues in C. sordellii lethal toxin that are essential for the enzyme activity of the active toxin fragment. Exchange of aspartic acid at position 286 or 288 with alanine or asparagine decreased glucosyltransferase activity by about 5000-fold and completely blocked glucohydrolase activity. No enzyme activity was detected with the double mutant D286A/D288A. Whereas the wild-type fragment of C. sordellii lethal toxin was labeled by azido-UDP-glucose after UV irradiation, mutation of the DXD motif prevented radiolabeling. At high concentrations (10 mM) of manganese ions, the transferase activities of the D286A and D288A mutants but not that of wild-type fragment were increased by about 20-fold. The exchange of Asp270 and Arg273 reduced glucosyltransferase activity by about 200-fold and blocked glucohydrolase activity. The data indicate that the DXD motif, which is highly conserved in all large clostridial cytotoxins and also in a large number of glycosyltransferases, is functionally essential for the enzyme activity of the toxins and may participate in coordination of the divalent cation and/or in the binding of UDP-glucose.
Analysis of cellular structure by light scattering measurements in a new cytometer design based on a liquid-core waveguide (2004)

The results of applying a novel microfluidic optical cytometer to generate and observe the light scattered from biological cells over a wide range of angles are presented. This cytometer incorporates a waveguide that increases the intensity of the scattered light to the extent that an inexpensive digital camera can be used to detect the light over a large solid angle. This device was applied to yeast cells and latex beads and experimental data were compared with the results of a finite difference time-domain (FDTD) method of simulation. The simulated scattering patterns were calculated from reported values of optical parameters and are in good qualitative agreement with experiment. It is demonstrated that this system could be used to acquire information on the microstructure and potentially the nanostructure of cells.
Interactions of histidine and other imidazole derivatives with transition metal ions in chemical and biological systems (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleInteractions of histidine and other imidazole derivatives with transition metal ions in chemical and biological systemsRichard J. Sundberg and R. Bruce MartinCite this: Chem. Rev. 1974, 74, 4, 471–517Publication Date (Print):August 1, 1974Publication History Published online1 May 2002Published inissue 1 August 1974https://pubs.acs.org/doi/10.1021/cr60290a003https://doi.org/10.1021/cr60290a003research-articleACS PublicationsRequest reuse permissionsArticle Views7788Altmetric-Citations977LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Common LISP. The language (1984)

The defacto standard - a must-have for all LISP programmers. In this greatly expanded edition of the defacto standard, you'll learn about the nearly 200 changes already made since original publication - and find out about gray areas likely to be revised later. Written by the Vice- Chairman of X3J13 (the ANSI committee responsible for the standardization of Common Lisp) and co-developer of the language itself, the new edition contains the entire text of the first edition plus six completely new chapters. They cover: - CLOS, the Common Lisp Object System, with new features to support function overloading and object-oriented programming, plus complete technical specifications * Loops, a powerful control structure for multiple variables * Conditions, a generalization of the error signaling mechanism * Series and generators * Plus other subjects not part of the ANSI standards but of interest to professional programmers. Throughout, you'll find fresh examples, additional clarifications, warnings, and tips - all presented with the author's customary vigor and wit.
Stoichiometric and Catalytic Conversion of Alkynes to Conjugated (Z,Z)-Dienes and Cyclopentadienes via Palladacyclopentadienes and 1,3-Dienylpalladium(II) Halide and Triorganopalladium(IV) Halide Compounds Containing Chelating Nitrogen Ligands (1998)

Palladacyclo-2,4-pentadiene compounds containing a chelating bidentate nitrogen ligand Pd{(C(E)C(E)-C(E)C(E)}(NN) 1a−f (E = CO2Me, NN = Ph-bip, Ar-bian, bpy, dcm-bpy, bpym) and 2a,b (E = CF3, NN = Ph-bip, (p-tol)-bian) have been prepared from Pd(dba)2, the appropriate bidentate N-ligand, and electron-deficient acetylenes dimethyl 2-butynedioate or hexafluorobutyne. X-ray crystal structures were obtained for compounds 1a (NN = Ph-bip) and 1d (NN = 2,2‘-bpy). In solution, an equilibrium between the monomer and a dimer exists for compounds 1d and 1e (NN = bipyrimidine); in the solid state, 1d is a monomer. The dimeric form of 1d is of the same type as the zerovalent palladium compound [(μ-3,3‘-dicarbomethoxy-2,2‘-bipyridine)Pd(tcne)]2 in which the two bipyridine derivatives bridge between the two palladium centers, as determined from the X-ray crystal structure of this compound (7). The palladacycles 1 undergo oxidative addition of methyl iodide, benzyl bromide, or iodobenzene. Subsequent reductive elimination gives rise to the formation of 4-functionalized 1,3-dienylpalladium(II) halide compounds 3−5 (cis arrangement of the ester functions at the double bonds). In the reaction with an excess of 1,4-chloro-2-butyne, a trimerization took place forming 1-(1‘-chloroethenyl)-1,2,3,4,5-pentakis(chloromethyl)-2,4-cyclopentadiene (6). Employing the established kinetic compatibility of the formation of the palladacycles with a successive oxidative addition/reductive elimination of organic halides and subsequent transmetalation with tetramethyltin, a catalytic cycle for the three-component synthesis of (Z,Z)-dienes of the type R−C(E)C(E)C(E)C(E)CH3 (8, R = alkyl, aryl; E = CO2CH3) has been conceived, e.g., from dimethyl 2-butynedioate, an organic halide, and tetramethyltin employing 1% of 1b as the catalyst in DMF. This constitutes the first catalytic synthesis of conjugated dienes from alkynes. Pd(phosphine) compounds do not catalyze this reaction.