gebhart/patrepeval huggingface dataset:
Membrane curvature at a glance (2015)

Membrane curvature is an important parameter in defining the morphology of cells, organelles and local membrane subdomains. Transport intermediates have simpler shapes, being either spheres or tubules. The generation and maintenance of curvature is of central importance for maintaining trafficking and cellular functions. It is possible that local shapes in complex membranes could help to define local subregions. In this Cell Science at a Glance article and accompanying poster, we summarize how generating, sensing and maintaining high local membrane curvature is an active process that is mediated and controlled by specialized proteins using general mechanisms: (i) changes in lipid composition and asymmetry, (ii) partitioning of shaped transmembrane domains of integral membrane proteins or protein or domain crowding, (iii) reversible insertion of hydrophobic protein motifs, (iv) nanoscopic scaffolding by oligomerized hydrophilic protein domains and, finally, (v) macroscopic scaffolding by the cytoskeleton with forces generated by polymerization and by molecular motors. We also summarize some of the discoveries about the functions of membrane curvature, where in addition to providing cell or organelle shape, local curvature can affect processes like membrane scission and fusion as well as protein concentration and enzyme activation on membranes.
Structural ambiguity and lexical relations (1990)

From a certain (admittedly narrow) perspective, one of the annoying features of natural language is the ubiquitous syntactic ambiguity. For a computational model intended to assign syntactic descriptions to natural language text, this seem like a design defect. In general, when context and lexical content are taken into account, such syntactic ambiguity can be resolved: sentences used in context show, for the most part, little ambiguity. But the grammar provides many alternative analyses, and gives little guidance about resolving the ambiguity.
Data-Oriented Programming: On the Expressiveness of Non-control Data Attacks (2016)

As control-flow hijacking defenses gain adoption, it is important to understand the remaining capabilities of adversaries via memory exploits. Non-control data exploits are used to mount information leakage attacks or privilege escalation attacks program memory. Compared to control-flow hijacking attacks, such non-control data exploits have limited expressiveness, however, the question is: what is the real expressive power of non-control data attacks? In this paper we show that such attacks are Turing-complete. We present a systematic technique called data-oriented programming (DOP) to construct expressive non-control data exploits for arbitrary x86 programs. In the experimental evaluation using 9 programs, we identified 7518 data-oriented x86 gadgets and 5052 gadget dispatchers, which are the building blocks for DOP. 8 out of 9 real-world programs have gadgets to simulate arbitrary computations and 2 of them are confirmed to be able to build Turing-complete attacks. We build 3 end-to-end attacks to bypass randomization defenses without leaking addresses, to run a network bot which takes commands from the attacker, and to alter the memory permissions. All the attacks work in the presence of ASLR and DEP, demonstrating how the expressiveness offered by DOP significantly empowers the attacker.
Carbanion mechanisms. 6. Metalation of arylmethanes by potassium hydride/18-crown-6 ether in tetrahydrofuran and the acidity of hydrogen (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbanion mechanisms. 6. Metalation of arylmethanes by potassium hydride/18-crown-6 ether in tetrahydrofuran and the acidity of hydrogenErwin Buncel and Balachandran MenonCite this: J. Am. Chem. Soc. 1977, 99, 13, 4457–4461Publication Date (Print):June 1, 1977Publication History Published online1 May 2002Published inissue 1 June 1977https://doi.org/10.1021/ja00455a040RIGHTS & PERMISSIONSArticle Views584Altmetric-Citations61LEARN 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 InReddit PDF (641 KB) Get e-Alerts Get e-Alerts
Molecular Radiotherapy Using Cleavable Radioimmunoconjugates That Target EGFR and γH2AX (2013)

Many anticancer therapies, including ionizing radiation (IR), cause cytotoxicity through generation of DNA double-strand breaks (DSB). Delivery of therapeutic radionuclides to DNA DSB sites can amplify this DNA damage, for additional therapeutic gain. Herein, we report on two radiopharmaceuticals, radiolabeled with the Auger electron emitter (111)In, with dual specificity for both the intranuclear, DNA damage repair signaling protein γH2AX and the EGF receptor (EGFR). The EGFR ligand EGF was conjugated to a fluorophore- or (111)In-labeled anti-γH2AX antibody, linked via a nuclear localization sequence (NLS) to ensure nuclear translocation. EGF conjugation was achieved either through a noncleavable PEG linker (PEO6) or a cleavable disulfide bond. Both conjugates selectively bound EGFR on fixed cells and γH2AX in cell extracts. Both compounds enter EGFR-expressing cells in an EGF/EGFR-dependent manner. However, only the cleavable compound was seen to associate with γH2AX foci in the nuclei of irradiated cells. Intracellular retention of the cleavable compound was prolonged in γH2AX-expressing cells. Clonogenic survival was significantly reduced when cells were exposed to IR (to induce γH2AX) plus (111)In-labeled cleavable compound compared to either alone and compared to nonspecific controls. In vivo, uptake of (111)In-labeled cleavable compound in MDA-MB-468 xenografts in athymic mice was 2.57 ± 0.47 percent injected dose/g (%ID/g) but increased significantly to 6.30 ± 1.47%ID/g in xenografts where γH2AX was induced by IR (P < 0.01). This uptake was dependent on EGF/EGFR and anti-γH2AX/γH2AX interactions. We conclude that tumor-specific delivery of radiolabeled antibodies directed against intranuclear epitopes is possible using cleavable antibody-peptide conjugates.
Calcium-Promoted Protein Phosphorylation in Plants (1984)

Phosphorylation of several polypeptides in corn coleoptiles was promoted by adding calcium. Chlorpromazine, a calmodulin inhibitor, reduced calcium-promoted phosphorylation, suggesting that the phosphorylation was modulated by calmodulin. This is evidence for the role of calcium in protein phosphorylation in plants and could serve as an experimental approach to understanding the molecular mechanism by which calcium modulates various physiological processes in plants.
Synthesis of micro and nanostructures in microfluidic systems (2010)

In this critical review, we present an overview of the current progress in synthesis of micro and nanostructures by using microfluidics techniques. Emphasis is placed on processes that can be realized on chip, such as polymerization, precipitation, sol-gel, thermolysis and multistep processes. Continuous flow, microfluidic systems show particular promise in controlling size, shape and size distribution of synthesized micro and nanoparticles. Moreover, the use of microfluidics expands the synthesis space (e.g., temperature, pressure, reagents) to conditions not easily accessed in conventional batch procedures and thus, opens new methods for the realization of complex engineered nanostructures and new materials systems. (187 references).
Combining the power of Internal and External denoising (2013)

Image denoising methods can broadly be classified into two types: “Internal Denoising” (denoising an image patch using other noisy patches within the noisy image), and “External Denoising” (denoising a patch using external clean natural image patches). Any such method, whether Internal or External, is typically applied to all image patches. In this paper we show that different image patches inherently have different preferences for Internal or External de-noising. Moreover, and surprisingly, the higher the noise in the image, the stronger the preference for Internal De-noising. We identify and explain the source of this behavior, and show that Internal/External preference of a patch is directly related to its individual Signal-to-Noise-Ratio (“PatchSNR”). Patches with high PatchSNR (e.g., patches on strong edges) benefit much from External Denoising, whereas patches with low PatchSNR (e.g., patches in noisy uniform regions) benefit much more from Internal Denoising. Combining the power of Internal or External denoising selectively for each patch based on its estimated PatchSNR leads to improvement in denoising performance.
Monoclonal antibody cetuximab binds to and down-regulates constitutively activated epidermal growth factor receptor vIII on the cell surface. (2007)

These data suggest that cetuximab may be a potential candidate for the treatment of tumors that also express EGFRvIII.
Singular value decomposition for genome-wide expression data processing and modeling (2000)

We describe the use of singular value decomposition in transforming genome-wide expression data from genes x arrays space to reduced diagonalized "eigengenes" x "eigenarrays" space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.
An initial investigation of L1 and L2 discourse speech planning in English (2010)

A perceptually-based hierarchy of prosodic phrase group (HPG) framework was used in this study to investigate similarities and differences in the size and strategy of discourse-level speech planning across L1 and L2 English speaker groups. While both groups appear to produce similar configurations of acoustic contrasts to signal discourse boundaries, L1 speakers were found to produce these cues more robustly in English. Differences were also found between L1 English and L1 Taiwan Mandarin speaker groups with respect to the distribution of prosodic break levels and break locations. These differences in L1 and L2 organization of discourse speech prosody in English can be largely attributed to between-group differences in speech planning and chunking strategies whereby L2 speakers use more intermediate chunking units and fewer larger-scale planning units in their prosodic discourse organization. Through more understanding of prosody transfer, we believe that technology developed on the basis of L1 Mandarin spoken language processing may be applied to L2 English produced by the same speaker population, with little modification.
Clinical aspects of a phase I trial of 5,6-dimethylxanthenone-4-acetic acid (DMXAA), a novel antivascular agent (2003)

The antitumour action of 5,6-dimethylxanthenone-4-acetic acid (DMXAA) is mediated through tumour-selective antivascular effects and cytokine induction. This clinical phase I trial was conducted to examine its toxicity, maximum tolerated dose, pharmacokinetics (PK) and pharmacodynamics (PD). A secondary objective was to assess its antitumour efficacy. DMXAA was administered every 3 weeks as a 20-min i.v. infusion. Dose escalation initially followed a modified Fibonacci schema but was also guided by PK and toxicity. A total of 63 patients received 161 courses of DMXAA over 19 dose levels ranging from 6 to 4900 mg m(-2). DMXAA was well tolerated at lower doses and no drug-related myelosuppression was seen. Rapidly reversible dose-limiting toxicities were observed at 4900 mg m(-2), including confusion, tremor, slurred speech, visual disturbance, anxiety, urinary incontinence and possible left ventricular failure. Transient prolongation of the corrected cardiac QT interval was seen in 13 patients evaluated at doses of 2000 mg m(-2) and above. A patient with metastatic cervical carcinoma achieved an unconfirmed partial response at 1100 mg m(-2), progressing after eight courses. The results of PK and PD studies are reported separately. DMXAA has antitumour activity at well-tolerated doses.
Comparison of skin color detection and tracking methods under varying illumination (2005)

When skin areas such as faces and hands are imaged under natural environments their color appearance is frequently affected by variations in illumination intensity and chromaticity. In color-based skin tracking and detection, changing intensity is often dismissed either with the use of normalized, intensity-invariant color coordinates or by additionally modeling possible skin intensities. Chromaticity variations are rarely considered, although they are common in practice. In most approaches considering chromaticity, the experiments are done with a small or undefined variation range. It is difficult to compare different approaches and assess their applicability range for this reason. To improve the situation, we evaluate the performance of four state-of-the-art methods under drastic but practically common illumination changes. The effect of illumination chromaticity for skin is clearly defined, and based on it we draw conclusion about the performance of these approaches.
Convenient and Efficient Tosylation of Oligoethylene Glycols and the Related Alcohols in Tetrahydrofuran–Water in the Presence of Sodium Hydroxide (1990)

Abstract Oligoethylene glycols and some related alcohols were efficiently tosylated with p-toluenesulfonyl chloride in a tetrahydrofuran–water (1:1) mixture in the presence of excess sodium hydroxide. This method is advantageous over the conventional tosylation in pyridine both regarding the work-up procedure, the yield, and the purity of the product, and may be potentially useful for the tosylation of certain acid-labile alcohols.
Evidence of Bacterial Biofilms in Human Chronic Sinusitis (2004)

The purpose of this study was to evaluate whether bacterial biofilms exist on the sinus mucosa surfaces of human subjects with recalcitrant chronic sinusitis. Scanning electron microscopy was used to evaluate patients with continued symptoms of chronic sinusitis despite prior appropriate medical and surgical management. Morphologic structures that confirm the presence of bacterial biofilms were identified on the sinus mucosa of patients infected with Pseudomonas aeruginosa, a known biofilm former. The presence of bacterial biofilms may explain the recalcitrant nature of some forms of chronic sinusitis.
Polar Substituent Effects in the Solvolysis of Primary and Tertiary Alkyl Halides. Polar Effect IX (1980)

Abstract When the Hammett‐Taft equation log ( k/k o )=ρ q · σ is applied to the solvolysis of the 3‐substituted propyl bromides 6a‐6i in ethanol/water 4:1 (v/v) log k correlates linearly with σ except in cases where R exerts an anchimeric effect. The reaction constant ρ q for 6 is − 0.12 and is typical for a nucleophilic solvent‐assisted k s process at a primary C‐atom. The tertiary halides 1 and 3 , however, which react with little or no nucleophilic solvent assistance, i.e. by k c processes, lead to larger ρ q values of −0.71 and −1.14, respectively. The reaction constant p q is therefore a sensitive gauge for charge development in the transition state for solvolysis of saturated compounds.
CD4+ Cells Regulate Fibrosis and Lymphangiogenesis in Response to Lymphatic Fluid Stasis (2012)

Lymphedema and lymphatic stasis result in CD4+ cell inflammation and infiltration of mature T-helper cells. Loss of CD4+ but not CD8+ or CD25+ cell inflammation markedly decreases the pathological changes associated with lymphedema. In addition, CD4+ cells regulate lymphangiogenesis during wound repair and inflammatory lymphangiogenesis.
Enhanced corrosion resistance of NdFeB type permanent magnet coated by a dual layer of either Ti/Al or Ni/Al intermetallics (1997)

NdFeB magnets were coated with a dual layer of either Ti/Al or Ni/Al by thermal evaporation. When the coated samples were annealed at 400/spl deg/C, intermetallic reactions occurred within these coatings, between Ti and Al, and between Ni and Al. When the samples were annealed at 500/spl deg/C, the reaction were extended to the matrix of the magnet forming Al/sub 36/Ti/sub 43/Fe/sub 17/Nd/sub 4/ in the sample coated with Ti/Al, but forming Ni/sub 2/AlFe/sub 0.1/ in the Ni/Al coated sample. The presence of these intermetallics were confirmed by leaching the coated magnets in NaOH. We had observed that the annealed Ti/Al coated sample had a smooth surface, while that of the Ni/Al was porous with microcracks as a result of the volume contraction of the Ni/Al layer. It was also found that Nd in the Nd-rich grain boundaries of the magnet tended to react actively with the dual layers. The areas involved would be extended as the annealing temperature and time increased. This shows that the quality of the resultant intermetallic coating depends upon the microstructure of the NdFeB magnet. Furthermore, the adhesion between the coating and the magnet can be improved greatly by the appropriate heat treatment.
A realistic brain tissue phantom for intraparenchymal infusion studies (2004)

Agarose gel (0.6%) is a useful surrogate for in vivo brain in exploratory studies of convection-enhanced delivery.
Link quality based association mechanism in IEEE 802.11 h compliant wireless LANs (2005)

Abstract — When deploying IEEE 802.11 LANs, it is important from the performance perspective to associate the users to the available access points in an efficient way. The efficiency of an association relates to the average rates that the users can achieve with the particular association. Current implementations of 802.11 LANs do not take into account physical channel information in making association decisions. This usually results in much lower user rates than what can be ideally achieved. In this paper, we propose a new user association control framework for infrastructure-based wireless LANs compliant with the IEEE 802.11h specification in light of these issues. By using the new information that is implicitly provided by 802.11h specifications, our framework, takes into account the channel conditions when associating stations with the access points. Simulation results show that the proposed schemes improve the throughput of the network, compared with the static allocation without channel quality information. This improvement is significant, especially in an environment where external interference is present. I.
CVD110, an attenuated Vibrio cholerae O1 El Tor live oral vaccine strain (1993)

The recent expansion of the seventh cholera pandemic into South America emphasizes the need for a safe, long-lasting, protective, and nonreactogenic vaccine for this disease. Since the predominant Vibrio cholerae O1 strains in the world today are of the El Tor biotype, a bivalent vaccine containing both classical and El Tor biotypes may be desirable. We have constructed a new oral vaccine candidate, V. cholerae CVD110 El Tor, Ogawa, from which all toxin genes so far identified in V. cholerae have been deleted. Three of these genes, those encoding cholera toxin (ctx), zonula occludens toxin (zot), and accessory cholera enterotoxin (ace), are located on a 4.5-kb virulence cassette flanked by repetitive sequences (RS1 elements). Homologous recombination between these RS1 elements resulted in the deletion of this virulence cassette to yield V. cholerae CVD109. Insertion of genes encoding mercury resistance (mer) and the cholera toxin B subunit (ctxB) into the hemolysin locus (hlyA) produced CVD110. This insertion serves three purpose. (i) It genetically tags the vaccine strain so as to distinguish it from wild-type V. cholerae O1. (ii) It produces cholera toxin B subunit in order to elicit antitoxic immunity. (iii) It inactivates the hemolysin gene, rendering the strain nonhemolytic on sheep erythrocyte plates. Supernatants from V. cholerae CVD110 cultures are nonreactogenic when assayed in Ussing chambers.
Thermometry and Thermal Transport in Micro/Nanoscale Solid-State Devices and Structures (2001)

We review recent advances in experimental methods for high spatial-resolution and high time-resolution thermometry, and the application of these and related methods for measurements of thermal transport in low-dimensional structures. Scanning thermal microscopy (SThM) achieves lateral resolutions of 50 nm and a measurement bandwidth of 100 kHz; SThM has been used to characterize differences in energy dissipation in single-wall and multi-wall carbon nanotubes. Picosecond thermoreflectance enables ultrahigh time-resolution in thermal diffusion experiments and characterization of heat flow across interfaces between materials; the thermal conductance G of interfaces between dissimilar materials spans a relatively small range, 20&lt;G&lt;200 MW m−2K−1 near room temperature. Scanning thermoreflectance microscopy provides nanosecond time resolution and submicron lateral resolution needed for studies of heat transfer in microelectronic, optoelectronic and micromechanical systems. A fully-micromachined solid immersion lens has been demonstrated and achieves thermal-radiation imaging with lateral resolution at far below the diffraction limit, &lt;2 μm. Microfabricated metal bridges using electrical resistance thermometry and joule heating give precise data for thermal conductivity of single crystal films, multilayer thin films, epitaxial superlattices, polycrystalline films, and interlayer dielectrics. The room temperature thermal conductivity of single crystal films of Si is strongly reduced for layer thickness below 100 nm. The through-thickness thermal conductivity of Si-Ge and GaAs-AlAs superlattices has recently been shown to be smaller than the conductivity of the corresponding alloy. The 3ω method has been recently extended to measurements of anisotropic conduction in polyimide and superlattices. Data for carbon nanotubes measured using micromachined and suspended heaters and thermometers indicate a conductivity near room temperature greater than diamond.