gebhart/patrepeval huggingface dataset:
Design of Sequence-Specific DNA Binding Molecules for DNA Methyltransferase Inhibition (2014)

The CpG dyad, an important genomic feature in DNA methylation and transcriptional regulation, is an attractive target for small molecules. To assess the utility of minor groove binding oligomers for CpG recognition, we screened a small library of hairpin pyrrole-imidazole polyamides targeting the sequence 5'-CGCG-3' and assessed their sequence specificity using an unbiased next-generation sequencing assay. Our findings indicate that hairpin polyamide of sequence PyImβIm-γ-PyImβIm (1), previously identified as a high affinity 5'-CGCG-3' binder, favors 5'-GCGC-3' in an unanticipated reverse binding orientation. Replacement of one β alanine with Py to afford PyImPyIm-γ-PyImβIm (3) restores the preference for 5'-CGCG-3' binding in a forward orientation. The minor groove binding hairpin 3 inhibits DNA methyltransferase activity in the major groove at its target site more effectively than 1, providing a molecular basis for design of sequence-specific antagonists of CpG methylation.
Extracellular Matrix Gene Expression by Human Bone Marrow Stroma and by Marrow Fibroblasts (1993)

In the marrow space hemopoietic progenitors interact with stromal cells allowing homing, migration and the expression of developmental programs. Some of these interactions are mediated by extracellular matrix molecules (ECM) which are produced by marrow stromal cells. In the murine system the nature of these interactions and its biological significance have been studied in vitro by using indistinctly, either whole stroma (obtained from long-term marrow cultures) or isolated stromal (fibroblast-like) cells. In an attempt to analyze whether in the human system both sources of stromal cells are equivalent in terms of production of ECM components, we measured the expression of genes encoding for several ECM proteins. The results obtained show that whole stroma as well as marrow fibroblasts express genes for collagen types I, III, IV, V and VI as well as for fibronectin and laminin. However, the relative abundance of mRNA transcripts for some of these proteins was higher in marrow fibroblasts as compared to whole stroma. The latter was further supported by an increased collagen synthesis observed in marrow fibroblasts as compared to whole stroma.
Bioinformatics-based strategies for rapid microorganism identification by mass spectrometry (2004)

We review approaches for microorganism identification that exploit the wealth of information in constantly expanding proteome databases. Masses of an organism’s protein biomarkers are experimentally determined and matched against sequence-derived masses of proteins, found together with their source organisms in proteome databases. The source organisms are ranked according to the matches, resulting in microorganism identifi cation. Statistical analysis of proteome uniqueness across organisms in a database enables evaluation of the probability of false identifications based on protein mass assignments alone. Biomarkers likely to be observed can be identified based solely on microbial genome sequence information. Protein identification methodologies allow assignment of detected proteins to specific microorganisms and, by extension, allow identification of the microorganism from which those proteins originate.
A succinct N-gram language model (2009)

Efficient processing of tera-scale text data is an important research topic. This paper proposes lossless compression of N-gram language models based on LOUDS, a succinct data structure. LOUDS succinctly represents a trie with M nodes as a 2M + 1 bit string. We compress it further for the N-gram language model structure. We also use 'variable length coding' and 'block-wise compression' to compress values associated with nodes. Experimental results for three large-scale N-gram compression tasks achieved a significant compression rate without any loss.
Multi-touch authentication on tabletops (2010)

The introduction of tabletop interfaces has given rise to the need for the development of secure and usable authentication techniques that are appropriate for the co-located collaborative settings for which they have been designed. Most commonly, user authentication is based on something you know, but this is a particular problem for tabletop interfaces, as they are particularly vulnerable to shoulder surfing given their remit to foster co-located collaboration. In other words, tabletop users would typically authenticate in full view of a number of observers. In this paper, we introduce and evaluate a number of novel tabletop authentication schemes that exploit the features of multi-touch interaction in order to inhibit shoulder surfing. In our pilot work with users, and in our formal user-evaluation, one authentication scheme - Pressure-Grid - stood out, significantly enhancing shoulder surfing resistance when participants used it to enter both PINs and graphical passwords.
Split-Voxel: A Simple Discontinuity-Preserving Voxel Representation for Volume Rendering (2010)

The most common representation of volumetric models is a regular grid of cubical voxels with one value each, from which a smooth scalar field is reconstructed. However, common real-world situations include cases in which volumes represent physical objects with well defined boundaries separating different materials, giving rise to models with quasi-impulsive gradient fields. In our split-voxel representation, we replace blocks of N 3 voxels by one single voxel that is split by a feature plane into two regions with constant values. This representation has little overhead over storing precomputed gradients, and has the advantage that feature planes provide minimal geometric information about the underlying volume regions that can be effectively exploited for volume rendering. We show how to convert a standard mono-resolution representation into a out-of-core multiresolution structure, both for labeled and continuous scalar volumes. We also show how to interactively explore the models using a multiresolution GPU raycasting framework. The technique supports real-time transfer function manipulation and proves particularly useful for fast multiresolution rendering, since accurate silhouettes are preserved even at very coarse levels of detail.
The Prefix Design and Performance Analysis of DFT-based Overlapped Frequency Division Multiplexing (OvFDM-DFT) System (2007)

This paper propose the theoretical analysis of the DFT based overlapped frequency division multiplexing (OvFDM)/non-orthogonal frequency division multiplexing(NOFDM) communication system, and investigates the impact of conventional cyclic-prefix and zero-padding cyclic-prefix respectively for the OvFDM-DFT system in the time-variant frequency-selective fading channels. The sub-carriers of the DFT based OvFDM/NOFDM communication system are overlapped together and the bandwidth can be larger than the frequency coherence bandwidth, so a kind of implicit frequency diversity will be exploited by the MLSD receiver, which will improve the system performance. Theoretical analysis and simulation results show that zero-padding cyclic-prefix has a much better performance than the conventional cyclic-prefix. The implicit frequency diversity ability of the OvFDM-DFT symbols is also verified by the simulations.
Enantio-, Diastereo-, and Regioselective Iridium-Catalyzed Asymmetric Allylic Alkylation of Acyclic β-Ketoesters (2013)

The first regio-, diastereo-, and enantioselective allylic alkylation of acyclic β-ketoesters to form vicinal tertiary and all-carbon quaternary stereocenters is reported. Critical to the successful development of this method was the employment of iridium catalysis in concert with N-aryl-phosphoramidite ligands. Broad functional group tolerance is observed at the keto-, ester-, and α-positions of the nucleophile. Various transformations demonstrating the utility of this method for rapidly accessing complex enantioenriched compounds are reported.
Intramembrane cavitation as a unifying mechanism for ultrasound-induced bioeffects (2011)

The purpose of this study was to develop a unified model capable of explaining the mechanisms of interaction of ultrasound and biological tissue at both the diagnostic nonthermal, noncavitational (<100 mW · cm(-2)) and therapeutic, potentially cavitational (>100 mW · cm(-2)) spatial peak temporal average intensity levels. The cellular-level model (termed "bilayer sonophore") combines the physics of bubble dynamics with cell biomechanics to determine the dynamic behavior of the two lipid bilayer membrane leaflets. The existence of such a unified model could potentially pave the way to a number of controlled ultrasound-assisted applications, including CNS modulation and blood-brain barrier permeabilization. The model predicts that the cellular membrane is intrinsically capable of absorbing mechanical energy from the ultrasound field and transforming it into expansions and contractions of the intramembrane space. It further predicts that the maximum area strain is proportional to the acoustic pressure amplitude and inversely proportional to the square root of the frequency (ε A,max ∝ P(A)(0.8f - 0.5) and is intensified by proximity to free surfaces, the presence of nearby microbubbles in free medium, and the flexibility of the surrounding tissue. Model predictions were experimentally supported using transmission electron microscopy (TEM) of multilayered live-cell goldfish epidermis exposed in vivo to continuous wave (CW) ultrasound at cavitational (1 MHz) and noncavitational (3 MHz) conditions. Our results support the hypothesis that ultrasonically induced bilayer membrane motion, which does not require preexistence of air voids in the tissue, may account for a variety of bioeffects and could elucidate mechanisms of ultrasound interaction with biological tissue that are currently not fully understood.
A Landscape Ecological Classification based on Watershed Focusing Landcover Types (2007)

The purpose of this study is to evaluate landscape characteristics of watersheds in the Nakdong River Basin for identifying the groups of watershed with similar landcover patterns by using Geographic Information System and statistical technique. According to the results based on the cluster analysis using cluster analysis tool in the ArcGIS 8.3 program, 22 sub-watersheds were classified into three types; Forest Agriculture and Urban watershed. In the forest watershed that has the least potential of ecological disturbances by human, a forest management approach based on geographic conditions and coverage types, etc., should be developed to sustain the ecological and environmental functions of forest. For the agriculture watershed, environmental-friendly agricultural techniques should be performed in the particular enhancement of riparian buffer zone to the prevent direct inflow of soils, fertilizers, and other chemicals into the stream network. Finally, in the urban watershed, an environmental-friendly plan that may increase the ratio of pervious surface and amount of green-space to should be reserved.
An RFDC Converter with Wide DynamicRange Input Matching For Power RecoveryApplications (2014)

3 ABSTRACT: An improved RF-dc converter based on a class-E rectifier with wide-dynamic-range input matching is presented. The input impedance is controlled by two varactor diodes to compensate for impedance changes with RF input power and dc loading conditions. The RF-dc converter achieved a peak efficiency of 60% and an S11 less than −20 dB over an input RF power range of 12 dB and an operating battery voltage of 2.5-4.2 V at 800 MHz. An analytical model for input impedance and efficiency was developed and shown to match simulation and measurement results.
Gα16 Mimics Vasoconstrictor Action to Induce Smooth Muscle α-Actin in Vascular Smooth Muscle Cells through a Jun-NH2-terminal Kinase-dependent Pathway (1997)

Prolonged exposure of vascular smooth muscle cells (VSMC) to vasoconstrictors such as vasopressin or angiotensin II induces hypertrophy and increases expression of muscle-specific genes including smooth muscle alpha-actin (SM-alpha-actin). These vasoconstrictors signal through G-proteins, including members of the Gq family. To further investigate the role of Gq family members, VSMC were transfected with a constitutively active mutant of a Gq family member, Galpha16 (Galpha16Q212L). Stable expression of Galpha16Q212L persistently stimulated phospholipase C, resulting in increased basal levels of inositol phosphates. These cells were hypertrophied and expressed elevated levels of SM-alpha-actin compared with wild-type VSMC or cells transfected with a control plasmid (Neo). SM-alpha-actin promoter activity was markedly increased in cells stably or transiently expressing Galpha16Q212L. Basal c-Jun-NH2-terminal kinase (JNK) activity was increased 3-9-fold in cells stably expressing Galpha16Q212L, while basal activity of the p42/44 mitogen-activated protein kinases (ERKs) was unaffected. Transient expression of a kinase inactive JNK kinase partially inhibited induction of SM-alpha-actin promoter activity in response to vasoconstrictors or expression of Galpha16Q212L. These results indicate that expression of constitutively active Galpha16 in VSMC mimics the effects of vasoconstrictors on hypertrophy and muscle-specific gene expression, and activation of JNK may play a role in these responses.
Concurrent chemoradiation with capecitabine and weekly irinotecan as preoperative treatment for rectal cancer: results from a phase I/II study (2006)

The aim of this study was to investigate the efficacy and safety of chemoradiation using capecitabine and irinotecan as neoadjuvant therapy for patients with rectal cancer. Conventional radiation was given at daily fractions of 1.8 Gy on 5 days a week for a total dose of 55.8 (50.4 + 5.4) Gy. Concurrently, irinotecan 40 mg m(-2) once weekly and capecitabine continuously at dose levels of 500, 650, 750 and 825 mg m(-2) twice daily were administered. Surgery was performed 4-6 weeks following completion of chemoradiation. A total of 28 patients (3 UICC II, 25 UICC III) were enrolled and all received treatment. Dose-limiting toxicity was diarrhoea grade IV and hand-foot syndrome at the 825 mg m(-2) dose level. The maximum tolerated dose of capecitabine was 750 mg m(-2). Diarrhoea was the most common toxicity: grade III in nine patients. Two patients died, one due to pneumonia and one due to sudden cardiac death. A complete response and only microfocal residual tumour disease was achieved in four and three patients (27%). In all, 25 of 28 patients undergoing surgery, 24 (96%) had R0 resection. Preoperative chemoradiation based on continuous daily capecitabine and weekly irinotecan appears to tolerated and effective in patients with rectal cancer.
Nitrogen balance on a restricted caloric intake. (1945)

Abstract In dogs on restricted isoealoric intake, positive nitrogen balance can be maintained when the proportion of protein to carbohydrate is 4 to 1 but not 1 to 4, respectively. The practical implications of these findings in regard to the desirability in restricted diets of giving priority to protein over caloric needs are discussed.
Expulsion Reduction in Resistance Spot Welding by Controlling of welding Current Waveform (2011)

There is a welding problem such as expulsion in resistance spot welding of high strength steel. This is due to overheating induced by increase of total heat input. Recently, many studies are carried out to solve the problems using electrode force control and current control. In this study, we tried to achieve expulsion reduction through controlling welding current. Steel sheet coated by Al-Si that has strength of 1500 MPa was selected as a base material. The control results were compared with conventional welding method. Also, it is characterized how the variation of the heating and cooling by pulse current waveform control have an effect on expulsion.
Augmenting Tactile Interaction with Pressure-Based Input (2015)

The application of pressure (or force) through the fingers is an inherent part of investigative and interactive touch and yet re-mains underutilized in the field of Human Computer Interaction (HCI). To highlight the potential usefulness of pressure as an in-put or information channel, this paper includes example imple-mentations and uses for pressure-based input in a variety of do-mains. These include the active application of force for the pur-poses of interacting with or controlling devices as well as passive detection of force as a means of monitoring behaviour in safety or healthcare scenarios. The use of pressure would allow for easier, more varied and more engaging interaction with devices, provid-ing opportunities for new applications and services to be devel-oped beyond what is currently possible.
Occupational Phenoxyethanol Neurotoxicity: A Report of Three Cases (1990)

2-Phenoxyethanol, used as an anesthetic for handling small fish at a salmon hatchery, caused three women to experience headache and symptoms of intoxication during use, followed by diminished sensation and strength of hands and fingers, worse in the preferred hand. Persistent neuropathy did not develop in any of them. After 1 to 2 years of exposure, the women manifested gradual onset of symptoms of cognitive impairment with an inability to work. Neuropsychologic testing verified that all three had focal cognitive impairments that persisted. One also had documented labyrinthine hypofunction, which originated during this exposure. The immediate and delayed effects of 2-phenoxyethanol on the central nervous system resemble those of the other organic solvents.
Retinal image registration based on salient feature regions (2009)

Retinal image registration is essential and crucial for ophthalmologists to diagnose various diseases. A great number of methods have been developed to solve this problem, however, fast and accurate retinal image registration is still a challenging problem since the great content complexity and low image quality of the unhealthy retina. This paper provides a new retinal image registration method based on salient feature regions (SFR). We first extract the SFR in each image based on a well defined region saliency metric. Next, SFR are matched by using an innovative local feature descriptor. Then we register those matched SFR using local rigid transformation. Finally, we register the two images adopting global second order polynomial transformation with locally rigid registered region centers as control points. Experimental results prove that our method is very fast and accurate, especially quite effective for the low quality retinal images registration.
A simple and mild esterification method for carboxylic acids using mixed carboxylic-carbonic anhydrides (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA simple and mild esterification method for carboxylic acids using mixed carboxylic-carbonic anhydridesSunggak Kim, Jae In Lee, and Youn Chul KimCite this: J. Org. Chem. 1985, 50, 5, 560–565Publication Date (Print):March 1, 1985Publication History Published online1 May 2002Published inissue 1 March 1985https://pubs.acs.org/doi/10.1021/jo00205a004https://doi.org/10.1021/jo00205a004research-articleACS PublicationsRequest reuse permissionsArticle Views5527Altmetric-Citations121LEARN 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
Manipulation of Host Gene Expression by Root-Knot Nematodes (1996)

Root-knot nematodes (Meloidogyne spp.) establish elaborate feeding sites in their host. Unique patterns of gene expression are induced in root cells, resulting in formation of a novel cell type called a giant cell. Based on analysis of approximately 220 giant cell expressed genes, key elements of giant cell function and regulation have been identified; examples are discussed in the context of giant cell biology and ontogeny. The potential to effect nematode control by manipulating these genes in transgenic host plants is considered, and models for giant cell induction are presented.
High gain in hybrid transistors with BAlq3∕Alq3 isotype heterostructure emitter (2008)

We report the fabrication of permeable metal-base transistors based on bis(2-methyl-8-quinolinolato-N1,O8)-(1,1’-biphenyl-4-olato) aluminum (BAlq3)/tri(8-hydroxyquinoline) aluminum (Alq3) isotype heterostructure as emitter layer. In this transistor, n-Si was used as the collector, LiF∕Al as the emitter electrode, and Au∕Al bilayer metal as the base. We show that the leakage current is greatly reduced in Al∕n-Si∕Au∕Al∕BAlq3∕Alq3∕LiF∕Al devices with respect to Al∕n-Si∕Au∕Al∕Alq3∕LiF∕Al devices due to the utilization of BAlq3∕Alq3 isotype heterostructure emitter, leading to high common-base and common-emitter current gains at low driving voltages.
A simplified synthesis of (.+-.)-4-hydroxy-N-methylmorphinan-6-one (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA simplified synthesis of (.+-.)-4-hydroxy-N-methylmorphinan-6-oneArnold Brossi, Fu Lian Hsu, and Kenner C. RiceCite this: J. Org. Chem. 1982, 47, 26, 5214–5216Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://pubs.acs.org/doi/10.1021/jo00147a039https://doi.org/10.1021/jo00147a039research-articleACS PublicationsRequest reuse permissionsArticle Views97Altmetric-Citations4LEARN 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