gebhart/patrepeval huggingface dataset:
Relationship between amide proton chemical shifts and hydrogen bonding in amphipathic .alpha.-helical peptides (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRelationship between amide proton chemical shifts and hydrogen bonding in amphipathic .alpha.-helical peptidesNian E. Zhou, Bing Yan Zhu, Brian D. Sykes, and Robert S. HodgesCite this: J. Am. Chem. Soc. 1992, 114, 11, 4320–4326Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/ja00037a042https://doi.org/10.1021/ja00037a042research-articleACS PublicationsRequest reuse permissionsArticle Views1099Altmetric-Citations127LEARN 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
The Importance of Fungi to Man (1997)

Completion of the Saccharomyces cerivisiae genome sequence and that of several bacterial genomes has led to a great rallying around the cause for sequencing of other small genomes. This has been most apparent in bacteria where sequencing projects are either complete or under way for no fewer than 38 different species. In contrast, the sequencing of small eukaryotic genomes lags far behind. The only large-scale public sequencing efforts currently under way in microbial eukaryotes are for the fission yeast Schizosaccharomyces pombe and for the protozoan parasite Plasmodium falciparum. Completion of these genomes is sure to yield greater insights into the general functions required for eukaryotic life and will permit researchers to address a number of fundamental questions. However, even coupled with the genome sequences from humans and other animals, the genome sequences from this small number of eukaryotes will not be sufficient to describe life with a nucleus. The primary purpose of this article is to point out the merits of sequencing the genomes of additional microbial eukaryotes, in particular the genetically amenable filamentous fungi. There are an estimated >1 million filamentous fungal species and some members of this diverse group of organisms can be found in virtually every ecosystem. These organisms conduct a variety of processes not seen in yeast, many of which have significant impacts on man (Table 1). For instance, some filamentous fungi
An efficient implementation of SELF a dynamically-typed object-oriented language based on prototypes (1989)

We have developed and implemented techniques that double the performance of dynamically-typed object-oriented languages. Our SELF implementation runs twice as fast as the fastest Smalltalk implementation, despite SELF's lack of classes and explicit variables.
Generating sub-30-nm polysilicon gates using PECVD amorphous carbon as hardmask and anti-reflective coating (2003)

A PECVD deposited carbon hardmask is combined with dielectric anti-reflective coating (DARC) for the patterning of sub-90nm lines with 248nm lithography. Using this CVD dual layer stack, <1% reflectivity control is demonstrated for both 248nm and 193nm lithography. The film stack is tested with an etch integration scheme to reduce polysilicon gate critical dimension (CD). The dual layer stack can be defined with less than 100nm thick photoresist. Because of the minimal resist required to open the stack, this film stack enables an integration scheme that extends conventional photoresist trim processes up to 70% of the starting line width. In addition to conventional trim process, a resistless carbon mask trim process is investigated to further shrink the gate critical dimension. The results show that the carbon hardmask has greater than 6:1 etch selectivity to polysilicon, enabling the extension of the resist trimming technique to generate sub-30nm structures using 248nm lithography.
A concentrically corrugated near-field plate (2010)

We present a concentrically corrugated near-field plate which can form a subwavelength near-field focus. The experimental plate consists of a coaxial aperture surrounded by non-periodic concentric corrugations. The measured subwavelength patterns are compared to those created by a coaxial probe with similar dimensions and are shown to be narrower. Excellent agreement between measurements and simulated results is observed. Finally, the frequency response of the plate is experimentally studied. The presented near-field plate will find applications in near-field probing.
Person-on-person violence detection in video data (2003)

We address the problem of detecting human violence in video, such as fist fighting, kicking, hitting with objects, etc. To detect violence we rely on motion trajectory information and on orientation information of a person's limbs. We define an Acceleration Measure Vector (AMV) composed of direction and magnitude of motion and we define jerk to be the temporal derivative of AMV We present results from several data sequences involving multiple types of violent activities.
Translation of Sindbis virus mRNA: effects of sequences downstream of the initiating codon (1994)

One incentive for developing the alphavirus Sindbis virus as a vector for the expression of heterologous proteins is the very high level of viral structural proteins that accumulates in infected cells. Although replacement of the structural protein genes by a heterologous gene should lead to an equivalent accumulation of the heterologous protein, the Sindbis virus capsid protein is produced at a level 10- to 20-fold higher than that of any foreign protein. Chimeric mRNAs which contain the first 275 nucleotides of the Sindbis virus 26S mRNA fused to the lacZ gene are also translated at the higher level. The enhancing sequences, located downstream of the AUG codon that initiates translation of the capsid protein, have a predicted hairpin-like structure; deletions in this region destroy the activity. These sequences enhance translation in infected cells but have the opposite effect in uninfected cells. Furthermore, translation of this RNA in infected cells is suppressed by a second viral RNA lacking the hairpin-like structure, but translation of the latter RNA is not affected. We propose that the hairpin-like structure presents a barrier to the movement of the ribosomes during translation of mRNA. In infected cells, under conditions in which this mRNA is essentially the only RNA being translated, a slowdown in the transit of the ribosomes gives factors present at low concentrations a chance to bind to the translation complex and permits a high level of functional complexes to be formed. In uninfected cells and in infected cells translating two different viral subgenomic mRNAs, a pause in the movement of the ribosomes along the RNA is no longer an advantage, because the required factors are now usurped by other translation complexes.
A history of innovation in marine seismic data acquisition (1991)

In the summer of 1989 the geophysical contractor Geco, working in Dutch waters of the North Sea, collected approximately 60 000 line-km of 3-D seismic data in a 70 day period. Just a few years ago, this would have represented about five crew-years of effort. Geco claims a record of 2057.7 line-km collected in a single day during the course of that survey.
Seed-mediated growth method to prepare cubic copper nanoparticles (2000)

A new and simple method has been reported here which can be applied to control simultaneously the shape and size of the copper nanoparticles, without using any ca p ping agent or template. By this method, cube -shaped copper nanoparticles in the size range ~ 75 –250 nm were formed from smaller spherical co p-per particles. At the first stage, 5–6 nm spherical co p per particles were prepared from aqueous copper sulphate solution by borohydride reduction. In the second stage, these small particles were mixed with ap propriate amount of copper sulphate and sodium ascorbate, which resulted in the production of larger size cu bic copper particles. In the latter step, the new grown larger particles acted as seed and grew larger due to the reduction of copper ions by ascorbate ion on their surfaces. Thus cubic copper nanoparticles of varied size regime were produced by ascorbate ion by var ying the ratio of copper seed particles to copper ion concentrations in solution. M
Automatic discovery of groups of objects for scene understanding (2012)

Objects in scenes interact with each other in complex ways. A key observation is that these interactions manifest themselves as predictable visual patterns in the image. Discovering and detecting these structured patterns is an important step towards deeper scene understanding. It goes beyond using either individual objects or the scene as a whole as the semantic unit. In this work, we promote "groups of objects". They are high-order composites of objects that demonstrate consistent spatial, scale, and viewpoint interactions with each other. These groups of objects are likely to correspond to a specific layout of the scene. They can thus provide cues for the scene category and can also prime the likely locations of other objects in the scene. It is not feasible to manually generate a list of all possible groupings of objects we find in our visual world. Hence, we propose an algorithm that automatically discovers groups of arbitrary numbers of participating objects from a collection of images labeled with object categories. Our approach builds a 4-dimensional transform space of location, scale and viewpoint, and efficiently identifies all recurring compositions of objects across images. We then model the discovered groups of objects using the deformable parts-based model. Our experiments on a variety of datasets show that using groups of objects can significantly boost the performance of object detection and scene categorization.
Encapsidation of Viral DNA Requires the Adenovirus L1 52/55-Kilodalton Protein (1998)

Previous work demonstrated that the adenovirus L1 52/55-kDa protein is required for assembly of viral particles, although its exact role in the assembly process is unclear. The 52/55-kDa protein's early expression, however, suggests that it might have other roles at earlier times during infection. To uncover any role the 52/55-kDa protein might have at early times and to better characterize its role in assembly, a mutant adenovirus incapable of expressing the 52/55-kDa protein was constructed (H5pm8001). Analysis of the onset and extent of DNA replication and late protein synthesis revealed that H5pm8001-infected 293 cells entered the late stage of infection at the same time as did adenovirus type 5 (Ad5)-infected cells. Interestingly, H5pm8001-infected cells displayed slightly lower levels of replicated viral DNA and late proteins, suggesting that although not required, the 52/55-kDa protein does augment these activities during infection. Analysis of transcripts produced from the major late and IVa2 promoters indicated a slight reduction in H5pm8001-infected compared to Ad5-infected cells at 18 h postinfection that was not apparent at later times. Analysis of particles formed in H5pm8001 cells revealed that empty capsids could form, suggesting that the 52/55-kDa protein does not function as a scaffolding protein. Subsequent characterization of these particles demonstrated that they lacked any associated viral DNA. These findings indicate that the 52/55 kDa-protein is required to mediate stable association between the viral DNA and empty capsid and suggest that it functions in the DNA encapsidation process.
Pyridylalanine‐Containing Hydroxamic Acids as Selective HDAC6 Inhibitors (2008)

We synthesized hydroxamic acids with a pyridylalanine substructure and identified them as selective inhibitors of human recombinant HDAC6. The in vitro selectivity was up to 25-fold for HDAC6 over HDAC1 and was confirmed by Western blotting to assess tubulin versus histone acetylation in cancer cells. Docking studies with an HDAC6 homology model suggested that the hydrophobic cap group of the inhibitors interacts with aromatic residues that form a sub-pocket near the entrance of the substrate binding channel. The HDAC6-selective compounds have less cytotoxicity toward cancer cells than do pan-HDAC inhibitors. The synergistic antiproliferative activity we showed with the proteasome inhibitor bortezomib suggests the potential for combination anticancer therapy with less general toxicity.
Rational Design of a Potent Anticoagulant Thrombin (2000)

Thrombin acts as a procoagulant when it cleaves fibrinogen and promotes the formation of a fibrin clot and functions as an anticoagulant when it activates protein C with the assistance of the cofactor thrombomodulin. The dual function of thrombin in the blood poses the challenge to turn the enzyme into a potent anticoagulant by selectively abrogating fibrinogen cleavage. Using functional and structural data, we have rationally designed a thrombin mutant, W215A/E217A, that cleaves fibrinogen with a value of k(cat)/K(m) about 20,000-fold slower than wild-type but activates protein C in the presence of thrombomodulin with a specificity comparable with wild-type. This mutant demonstrates for the first time that the relative specificity of thrombin toward fibrinogen and protein C can be completely reversed.
Reactions of 5-substituted 3-alkyl- and 3-aryl-isoxazoles with tetrasulfur tetranitride antimony pentachloride complex (S4N4·SbCl5): complete regioselective formation of 4-substituted 3-acyl- and 3-aroyl-1,2,5-thiadiazoles and their mechanism of formation (1998)

The reactions of 3-alkyl- 5a–f, 3-aryl- 5g–m, 3-acylamido- 5n,p, 3-benzamido- 5o and 3-arylamino- 5q -5-alkyl- and -5-aryl-isoxazoles with tetrasulfur tetranitride antimony pentachloride complex (S4N4·SbCl5) in toluene at 90 °C to reflux temperature give 3-acyl- 6a–c, e, n–q and 3-aroyl-4-substituted-1,2,5-thiadiazoles 6d, f–m in 13 to 61% yields as single isomers. The same reactions of 3,4-dimethyl- 5s, 5v, 4-ethyl-3-methyl- 5t -5-alkyl- and/or 5-aryl-isoxazoles under the same conditions give 3-(1-acetyl-1-chloroethyl)- 8a, 3-(1-benzoyl-1-chloropropyl)- 8b, 3-(1-benzoyl-1-chloroethyl)- 8d, or 3-(1-benzoyl-1-chloroethyl)-4-methyl-1,2,5-thiadiazoles 8c, which are a new type of 1,2,5-thiadiazole derivatives. In addition the reactions with 5-aryl-4-bromoisoxazoles (5,w,y,z) having an electron-donating substituent such as methyl, 4-methylphenyl, and 4-methoxyphenyl groups at C3 under the same conditions afford 3-aroyl-4-substituted-1,2,5-thiadiazoles 6d, 6j and 6k, whereas the starting isoxazoles are recovered from the reactions with 5-aryl-4-bromoisoxazoles 5x,z′ having a phenyl or a 4-chlorophenyl group at C3. A plausible mechanism is proposed for the formation of the products.
Physico-Chemical Properties of Synthetic Hydrotalcites in Relation to Composition (1980)

Abstract Hydrotalcite solid solutions were prepared by coprecipitation followed by hydrothermal treatment between 150° and 250°C. Based on the structural formula [Mg 1−x Al x (OH) 2 ] x+ [(CO 3 ) x/2 • mH 2 O] x− , pure solid solutions were formed in the range A1/(A1 + Mg) = 0.2 to 0.33, where m = (1 − 3x/2). Maximum crystallite size was achieved by hydrothermal treatment between 180° and 200°C, with x = 0.337 to 0.429. Crystal strain was also minimized at these values of x. The adsorption capacity for Naphthol Yellow S increased as x increased and reached a maximum (1.56 × 10 −6 moles/m 2 ) when x = 0.287, a value eight times larger than that of Mg(OH) 2 . A weak endothermic DTA peak at about 350°C is probably due to the loss of structural water in the main layer of the structure. On calcination between 400° and 700°C, only periclase was detected, probably containing Al in solid solution. Hydration of the calcined product resulted in the reconstruction of the original hydrotalcite structure.
Proliferating cell nuclear antigen immunohistochemistry in rat aorta after balloon denudation. Comparison with thymidine and bromodeoxyuridine labeling. (1992)

The authors compared detection of proliferating vascular smooth muscle cells (SMC) in vitro and in vivo with proliferating cell nuclear antigen (PCNA) immunohistochemistry and two established methods: [3H]thymidine autoradiography and bromodeoxyuridine immunohistochemistry. Labeling with [3H]thymidine and bromodeoxyuridine of rat vascular SMC in culture stained 11% +/- 2% and 11% +/- 1% of cells, and PCNA immunohistochemistry 22% +/- 2% of cells. Proliferation in the media of the denuded rat aortae was highest 3 days after denudation: 4.2%, 3.8%, and 4.7% of labeled cells with [3H]thymidine, bromodeoxyuridine, and PCNA, respectively. In the intima, proliferation was highest 7 days after denudation with 42% [3H]thymidine, 40% bromodeoxyuridine, and 46% PCNA-positive cells. With double labeling, all [3H]thymidine-positive cells were PCNA positive, whereas some cells were only positive for PCNA. The authors conclude that PCNA immunohistochemistry compares favorably with [3H]thymidine autoradiography, and bromodeoxyuridine immunohistochemistry.
Heterogeneity of the Surfactant Layer in Organically Modified Silicates and Polymer/Layered Silicate Composites (2006)

Dynamics and microstructure of the surfactant layer in organically modified silicates and their composites with polystyrene were studied as a function of surfactant loading and temperature in the range relevant for melt intercalation. Site selectivity was achieved by using specifically headgroup- and tail-labeled surfactant EPR spin probes and by applying 31P MAS NMR to phosphonium surfactants. Bimodal dynamics is observed over a broad range of surfactant loadings and temperatures in both the absence and presence of polymers and correlates with a bimodal distribution of surfactant headgroup distances from the silicate surface. Excess surfactant with respect to the cation exchange capacity of the silicate plasticizes the surfactant layer. Electron spin echo envelope modulation on nanocomposites with ammonium surfactant and deuterated polystyrene demonstrates close contact between the polymer and surfactant tail ends. Surfactant dynamics changes strongly during microcomposite formation, i.e., by embedding stacks of organoclay platelets in a polymer matrix, even if no intercalation takes place.
Refrigeration Lubricants - Current Practice and Future Development (1996)

Manufacturers of refrigeration and air-conditioning compressors and systems have had to re-evaluate the requirements for lubricants.The HFC (hydro:fluorocarbon) refrigerants that are replacing chlorofluorocarbon (CFC) refrigerants have a different influence on lubricants which effects both compressor durability and system performance.Other types of refrigerants such as ammonia and hydrocarbons are also alternatives to CFCs, and new lubricants are being evaluated to improve performance in these systems.This paper provides an overview of several types of synthetic lubricants currently supported by equipment manufacturers.Practical examples are provided to improve the understanding of these new lubricants, how they are used, and suggested application guidelines.Also described are lubricants currently being developed.
Adenovirus-Mediated Atrial Natriuretic Protein Expression in the Lung Protects Rats from Hypoxia-Induced Pulmonary Hypertension (2001)

Endogenous as well as exogenous atrial natriuretic peptide (ANP) attenuates the development of chronic hypoxic pulmonary hypertension (CHPH) in rats. We built a recombinant adenovirus type 5 containing ANP cDNA under the control of the Rous sarcoma virus long terminal repeat (Ad.ANP). The efficiency of this vector in delivering the ANP gene was first examined in rat primary cultures of pulmonary vessel smooth muscle cells (SMCs) in comparison with Ad.beta GAL. Conditioned medium collected from Ad.ANP-infected cells (1000 TCID(50)/cell) contained 5 x 10(9) M immunoreactive ANP and elicited relaxation of isolated rat pulmonary arteries preconstricted with phenylepinephrine. To examine the effects of adenovirus-mediated ANP expression in the CHPH rat lung, Ad.ANP or Ad.beta GAL was administered via the tracheal route. Immunoreactive ANP was detected in bronchoalveolar fluid as early as 4 days and until 10-17 days after Ad.ANP administration (5 x 10(8) TCID(50)). Lung ANP immunostaining was mainly localized in bronchial and alveolar epithelial cells. As compared with Ad.beta GAL-treated controls, rats given Ad.ANP (5 x 10(8) TCID(50)) on the day before a 2-week exposure to hypoxia (10% O(2)) had lower values for pulmonary artery pressure (32.1 +/- 1.93 vs. 35.5 +/- 2 mmHg, p < 0.01) and Fulton's index (0.52 +/- 0.089 vs. 0.67 +/- 0.12, p < 0.001) and less severe right ventricular hypertrophy and distal vessel muscularization. These results suggest that induction of ANP expression in the lung may hold promise in the treatment of pulmonary hypertension.
An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy (2000)

Even the best optical microscopes available on the market exhibit chromatic aberrations to some extent. In some types of study, chromatic aberrations of current optics cannot be neglected and a software correction is highly desirable. This paper describes a novel method of chromatic aberration measurement and software correction using sub-resolution bead imaging and computer image analysis. The method is quick, precise and enables the determination of both longitudinal and lateral chromatic aberrations. Correction function can be computed in about half an hour, including image acquisition. Using this approach, chromatic aberrations can be reduced to 10-20 nm laterally and 10-60 nm axially depending on the type of optical set-up. The method is especially suitable for fluorescence microscopy, where a limited number of wavelengths are observed.
miR-612 suppresses the invasive-metastatic cascade in hepatocellular carcinoma (2013)

MicroRNAs (miRNAs) play a critical role in tumor metastasis. In this study, we identified a set of 32 miRNAs involved in hepatocellular carcinoma (HCC) metastasis. Among them, miR-612 was shown for the first time to have inhibitory effects on HCC proliferation, migration, invasion, and metastasis. AKT2 was verified to be one of the direct targets of miR-612, through which the epithelial-mesenchymal transition (EMT) and metastasis were inhibited. The level of miR-612 in HCC patients was inversely associated with tumor size, stage, EMT, and metastasis. Of particular importance, miR-612 is involved in both the initial and final steps of the metastatic cascade, by suppressing local invasion and distant colonization. The pleiotropic roles of miR-612 in the HCC metastatic cascade suggest that it could be an effective target for both early and advanced HCC.
Joining of long double-stranded RNA molecules through controlled overhangs (2004)

We describe two methods for creating long (>1 kb) dsRNA molecules with specific, user-controlled overhangs for efficient hybridization and ligation. The two methods create double-stranded RNA (dsRNA) molecules with 5' overhangs or with 3' overhangs using T7 RNA polymerase (T7 RNAP) in transcription reactions of carefully designed PCR products. Primers utilized in the PCR reactions provide the template for the desired dsRNA overhangs. These methods provide complete control of the length and the sequence of the overhangs. This supplies a tool which is particularly lacking in dsRNA biochemistry given the absence of restriction endonucleases active on these substrates.