gebhart/patrepeval huggingface dataset:
Coordinate suppression of <i>Sdpr</i> and <i>Fhl1</i> expression in tumors of the breast, kidney, and prostate (2008)

The Src tyrosine kinase associates with the focal adhesion adaptor protein Cas (Crk-associated substrate) to suppress the expression of potential tumor suppressor genes. For example, Src utilizes Cas to suppress the expression of the LIM-only protein Fhl1 (four and a half LIM domains 1), in order to promote non-anchored tumor-cell growth and migration. Here, we report that the promoter region of the Fhl1 gene was methylated more in Src-transformed cells than non-transformed cells. In addition, global expression analysis indicates that Fhl1 induced expression of serum deprivation response factor (Sdpr) in Src-transformed cells. Moreover, Fhl1 and Sdpr was expressed in approximately 87% and 40% of samples obtained from non-transformed breast, 100% of samples obtained from non-transformed kidney, and over 60% of samples obtained from non-transformed prostate. In contrast, Fhl1 and Sdpr was detected in approximately 40% and 7% of matched samples from mammary carcinoma, less than 11% of matched samples from kidney carcinoma, and in less than 22% of matched samples from prostate carcinoma. These data indicate that Fhl1 and Sdpr expression was significantly reduced in tumors of the breast (P < 0.02 and P < 0.001), kidney (P < 0.01), and prostate (P < 0.05). In addition, although Src can activate mitogen-activated protein kinase (MAPK) to promote tumor-cell growth, our data indicate that Src did not rely on MAPK activity to suppress the expression of Fhl1 and Sdpr in transformed cells. Thus, Src induced methylation of the promoter region of the Fhl1 gene; Src suppressed Fhl1 and Sdpr expression independent of mitogen-activated protein kinase (MAPK) activity; Fhl1 induced the expression of Sdpr in Src-transformed cells; and Fhl1 and Sdpr expression was suppressed in tumors of the breast, kidney, and prostate.
Exploring the Cellulose/Xylan Specificity of the β-1,4-Glycanase Cex from <i>Cellulomonas fimi</i> through Crystallography and Mutation<sup>,</sup> (1998)

The retaining beta-1,4-glycanase Cex from Cellulomonas fimi, a family 10 glycosyl hydrolase, hydrolyzes xylan 40-fold more efficiently than cellulose. To gain insight into the nature of its preference for xylan, we determined the crystal structure of the Cex catalytic domain (Cex-cd) trapped as its covalent 2-deoxy-2-fluoroxylobiosyl-enzyme intermediate to 1.9 A resolution. Together with the crystal structure of unliganded Cex-cd [White, A., et al. (1994) Biochemistry 33, 12546-12552] and the previously determined crystal structure of the covalent 2-deoxy-2-fluorocellobiosyl-Cex-cd intermediate [White, A., et al. (1996) Nat. Struct. Biol. 3, 149-154], this structure provides a convincing rationale for the observed substrate specificity in Cex. Two active site residues, Gln87 and Trp281, are found to sterically hinder the binding of glucosides and must rearrange to accommodate these substrates. Such rearrangements are not necessary for the binding of xylobiosides. The importance of this observation was tested by examining the catalytic behavior of the enzyme with Gln87 mutated to Met. This mutation had no measurable effect on substrate affinity or turnover number relative to the wild type enzyme, indicating that the Met side chain could accommodate the glucoside moiety as effectively as the wild type Gln residue. Subsequent mutagenesis studies will address the role of entropic versus enthalpic contributions to binding by introducing side chains that might be more rigid in the unliganded enzyme.
Interaction sensing in dynamic force microscopy (2000)

A first-order perturbative theory of the motion of a harmonic oscillator interacting with a weak arbitrary force field is presented, as it pertains to dynamic force microscopy. In essence the theory corresponds to a Born approximation for the scattering of standing waves trapped in a perturbed parabolic potential. In particular, it is shown that the scattering amplitudes are related to corresponding moments, involving Chebyshev polynomials and associated metrics of the conservative interaction force, and of a generalized friction coefficient accounting for irreversible interactions. Implications for dynamic force microscopy are discussed.
Robocodes: Towards Generative Street Addresses from Satellite Imagery (2017)

We describe our automatic generative algorithm to create street addresses (Robocodes) from satellite images by learning and labeling regions, roads, and blocks. 75% of the world lacks street addresses [12]. According to the United Nations, this means 4 billion people are 'invisible'. Recent initiatives tend to name unknown areas by geocoding, which uses latitude and longitude information. Nevertheless settlements abut roads and such addressing schemes are not coherent with the road topology. Instead, our algorithm starts with extracting roads and junctions from satellite imagery utilizing deep learning. Then, it uniquely labels the regions, roads, and houses using some graph- and proximity-based algorithms. We present our results on both cities in mapped areas and in developing countries. We also compare productivity based on current ad-hoc and new complete addresses. We conclude with contrasting our generative addresses to current industrial and open solutions.
Tn7 transposition as a probe of cis interactions between widely separated (190 kilobases apart) DNA sites in the Escherichia coli chromosome (1996)

We have used the bacterial transposon Tn7 to examine communication between widely separated DNA sites in the Escherichia coli chromosome. Using Tn7 target immunity, a regulatory feature of transposition which influences target selection, we have evaluated (i) how the presence of Tn7 sequences at one DNA site affects Tn7 insertion into another site in the same DNA molecule and (ii) the nucleotide distances over which the two sites are able to communicate. We demonstrate that Tn7 sequences at one chromosomal site act at a distance to inhibit insertion of Tn7 elsewhere in that DNA as far away as 190 kb, reflecting effective long-range cis interactions. We have found that while target immunity is effective over a substantial region of the chromosome, insertion of Tn7 into a more distant site 1.9 Mb away in the same DNA is not inhibited; this observation provides evidence that target immunity relies on DNA spacing. We also find that within the region of the chromosome affected by target immunity, the magnitude of the immune effect is greater at close DNA sites than DNA sites farther away, suggesting that target immunity is distance dependent. We also extend the characterization of the Tn7 end-sequences involved in transposition and target immunity and describe how Tn7 target immunity can be used as a tool for probing bacterial chromosome structure.
Inkjet Printing Based Mono-layered Photonic Crystal Patterning for Anti-counterfeiting Structural Colors (2016)

Photonic crystal structures can be created to manipulate electromagnetic waves so that many studies have focused on designing photonic band-gaps for various applications including sensors, LEDs, lasers, and optical fibers. Here, we show that mono-layered, self-assembled photonic crystals (SAPCs) fabricated by using an inkjet printer exhibit extremely weak structural colors and multiple colorful holograms so that they can be utilized in anti-counterfeit measures. We demonstrate that SAPC patterns on a white background are covert under daylight, such that pattern detection can be avoided, but they become overt in a simple manner under strong illumination with smartphone flash light and/or on a black background, showing remarkable potential for anti-counterfeit techniques. Besides, we demonstrate that SAPCs yield different RGB histograms that depend on viewing angles and pattern densities, thus enhancing their cryptographic capabilities. Hence, the structural colorations designed by inkjet printers would not only produce optical holograms for the simple authentication of many items and products but also enable a high-secure anti-counterfeit technique.
Excimer laser desorption mass spectrometry of biomolecules at 248 and 193 nm (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExcimer laser desorption mass spectrometry of biomolecules at 248 and 193 nmB. Spengler, M. Karas, U. Bahr, and F. HillenkampCite this: J. Phys. Chem. 1987, 91, 26, 6502–6506Publication Date (Print):December 1, 1987Publication History Published online1 May 2002Published inissue 1 December 1987https://pubs.acs.org/doi/10.1021/j100310a016https://doi.org/10.1021/j100310a016research-articleACS PublicationsRequest reuse permissionsArticle Views168Altmetric-Citations41LEARN 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 options Get e-Alerts
The Availability of a Recombinant Anti-SNAP Antibody in VHH Format Amplifies the Application Flexibility of SNAP-Tagged Proteins (2010)

Antibodies are indispensable reagents in basic research, and those raised against tags constitute a useful tool for the evaluation of the biochemistry and biology of novel proteins. In this paper, we describe the isolation and characterization of a single-domain recombinant antibody (VHH) specific for the SNAP-tag, using Twist2 as a test-protein. The antibody was efficient in western blot, immunoprecipitation, immunopurification, and immunofluorescence. The sequence corresponding to the anti-SNAP has been subcloned for large-scale expression in vectors that allow its fusion to either a 6xHis-tag or the Fc domain of rabbit IgG2 taking advantage of a new plasmid that was specifically designed for VHH antibodies. The two different fusion antibodies were compared in immunopurification and immunofluorescence experiments, and the recombinant protein SNAP-Twist2 was accurately identified by the anti-SNAP Fc-VHH construct in the nuclear/nucleolar subcellular compartment. Furthermore, such localization was confirmed by direct Twist2 identification by means of anti-Twisit2 VHH antibodies recovered after panning of the same naïve phage display library used to isolate the anti-SNAP binders. Our successful localization of Twist2 protein using the SNAP-tag-based approach and the anti-Twist2-specific recombinant single-domain antibodies opens new research possibilities in this field.
Histopathologic Features Aid in Predicting Risk for Progression of IgA Nephropathy (2010)

Baseline histopathologic parameters are independent predictors of adverse outcomes in IgAN even after taking into consideration clinical characteristics. Relatively small degrees of interstitial fibrosis confer an increased risk for progressive IgAN.
Data Science for Business: What You Need to Know about Data Mining and Data-Analytic Thinking (2013)

Written by renowned data science experts Foster Provost and Tom Fawcett, Data Science for Business introduces the fundamental principles of data science, and walks you through the data-analytic thinking necessary for extracting useful knowledge and business value from the data you collect. This guide also helps you understand the many data-mining techniques in use today. Based on an MBA course Provost has taught at New York University over the past ten years, Data Science for Business provides examples of real-world business problems to illustrate these principles. Youll not only learn how to improve communication between business stakeholders and data scientists, but also how participate intelligently in your companys data science projects. Youll also discover how to think data-analytically, and fully appreciate how data science methods can support business decision-making.Understand how data science fits in your organizationand how you can use it for competitive advantage Treat data as a business asset that requires careful investment if youre to gain real value Approach business problems data-analytically, using the data-mining process to gather good data in the most appropriate way Learn general concepts for actually extracting knowledge from data Apply data science principles when interviewing data science job candidates
The Synthetic Elicitor 3,5-Dichloroanthranilic Acid Induces<i>NPR1</i>-Dependent and<i>NPR1</i>-Independent Mechanisms of Disease Resistance in Arabidopsis     (2009)

Immune responses of Arabidopsis (Arabidopsis thaliana) are at least partially mediated by coordinated transcriptional up-regulation of plant defense genes, such as the Late/sustained Up-regulation in Response to Hyaloperonospora parasitica (LURP) cluster. We found a defined region in the promoter of the LURP member CaBP22 to be important for this response. Using a CaBP22 promoter-reporter fusion, we have established a robust and specific high-throughput screening system for synthetic defense elicitors that can be used to trigger defined subsets of plant immune responses. Screening a collection of 42,000 diversity-oriented molecules, we identified 114 candidate LURP inducers. One representative, 3,5-dichloroanthranilic acid (DCA), efficiently induced defense reactions to the phytopathogens H. parasitica and Pseudomonas syringae. In contrast to known salicylic acid analogs, such as 2,6-dichloroisonicotinic acid (INA), which exhibit a long-lasting defense-inducing activity and are fully dependent on the transcriptional cofactor NPR1 (for Nonexpresser of Pathogenesis-Related genes1), DCA acts transiently and is only partially dependent on NPR1. Microarray analyses revealed a cluster of 142 DCA- and INA-responsive genes that show a pattern of differential expression coinciding with the kinetics of DCA-mediated disease resistance. These ACID genes (for Associated with Chemically Induced Defense) constitute a core gene set associated with chemically induced disease resistance, many of which appear to encode components of the natural immune system of Arabidopsis.
BMP stimulation of bone response adjacent to titanium implants <i>in vivo</i> (1999)

The objective of this study was to evaluate the effect of bone morphogenetic protein (BMP) on the bond strength of titanium (Ti) implants at the bone-implant interface. Thirty-six Brånemark screw implants (3.75 mm diameter by 15 mm long) were implanted for 3 and 12 weeks. At 3 weeks after implantation, the mean reverse torque value for implants stimulated with BMP delivered using an atelopeptide type-I collagen carrier (74.2 +/- 5.2 N cm) was observed to be statistically greater (P < 0.000016) than the mean reverse torque value for control Ti implants (32.8 +/- 1.1 N cm). Similarly, at 12 weeks after implantation, the mean reverse torque value for implants stimulated with BMP (89.2 +/- 2.7 N cm) was statistically greater (P < 0.0042) than the mean reverse torque value for control Ti implants (75.8 +/- 2.4 N cm). In addition, histomorphometric evaluations indicated more bone contact with the BMP stimulated implant surfaces compared to the controls after 3 weeks implantation. It was concluded from this study that the use of BMP-atelopeptide type-I collagen mixture is an effective means of obtaining greater bond strength at the bone implant interface within a shorter time period than Ti implants without BMP.
Strain in the Human Medial Collateral Ligament During Valgus Loading of the Knee (2001)

The medial collateral ligament is one of the most frequently injured ligaments in the knee. Although the medial collateral ligament is known to provide a primary restraint to valgus and external rotations, details regarding its precise mechanical function are unknown. In this study, strain in the medial collateral ligament of eight knees from male cadavers was measured during valgus loading. A material testing machine was used to apply 10 cycles of varus and valgus rotation to limits of +/- 10.0 N-m at flexion angles of 0 degrees, 30 degrees, 60 degrees, and 90 degrees. A three-dimensional motion analysis system measured local tissue strain on the medial collateral ligament surface within 12 regions encompassing nearly the entire medial collateral ligament surface. Results indicated that strain is significantly different in different regions over the surface of the medial collateral ligament and that this distribution of strain changes with flexion angle and with the application of a valgus torque. Strain in the posterior and central portions of the medial collateral ligament generally decreased with increasing flexion angle, whereas strain in the anterior fibers remained relatively constant with changes in flexion angle. The highest strains in the medial collateral ligament were found at full extension on the posterior side of the medial collateral ligament near the femoral insertion. These data support clinical findings that suggest the femoral insertion is the most common location for medial collateral ligament injuries.
Correction of distortion in US images caused by subcutaneous tissues: results in tissue phantoms and human subjects. (1995)

The forward-propagation technique compensates for refraction at subcutaneous fat-muscle interfaces.
Low-Temperature Growth of ZnO Nanowire Array by a Simple Physical Vapor-Deposition Method (2003)

Well-aligned single-crystalline wurzite zinc oxide (ZnO) nanowire array was successfully fabricated on an Al2O3 substrate by a simple physical vapor-deposition method at a low temperature of 450 °C. The diameter and growth rate of ZnO nanowires increased as a function of growth temperature. TEM observation showed that the ZnO nanowires were synthesized along the c-axial direction of the hexagonal crystal structure. We demonstrate that ZnO nanowires followed the self-catalyzed growth mechanism on the ZnO nuclei. Besides high-quality ZnO nanowires, sometimes a fascinating hierarchically ordered ZnO structure was also observed.
Direct C-2 Arylation of Alkyl 4-Thiazolecarboxylates: New Insights in Synthesis of Heterocyclic Core of Thiopeptide Antibiotics (2008)

The Pd(0)-catalyzed regioselective C-2 (hetero)arylation of tert-butyl 4-thiazolecarboxylate with a broad (hetero)aryl halide is reported, including the direct coupling of pyridinyl halides. The process has allowed the preparation of valuable 2-pyridynyl-4-thiazolecarboxylates which are components of the complex heterocyclic core of thiopeptides antibiotics. As a first application, a synthesis of a tert-butyl sulfomycinamate thio-analogue from tert-butyl 4-thiazolecarboxylate is here described through a three-step direct pyridinylation, halogenation, and Stille cross-coupling sequence.
A new semantic segmentation model for remote sensing images (2017)

Semantic segmentation for remote sensing images is a critical process in the workflow of object-based image analysis. Recently, convolutional neural networks(CNNs) are powerful visual models that yield hierarchies of features. In this paper, we propose a deep convolutional encoder-decoder model for remote sensing images segmentation. Specifically, we rely on the encoder network to extract the high-level semantic feature of ultra-high resolution images and the decoder network is employed to map the low resolution encoder feature maps to full input resolution feature maps for pixel-wise labeling. Also the fully connected conditional random field (CRF) is integrated into the model so that the network can be trained end-to-end. Experiments on the Vaihingen dataset demonstrate that our model can make promising performance.
A similarity metric for edge images (2003)

The performance of several discrepancy measures for the comparison of edge images is analyzed and a novel similarity metric aimed at overcoming their problems is proposed. The algorithm finds an optimal matching of the pixels between the images and estimates the error produced by this matching. The resulting Pixel Correspondence Metric (PCM) can take into account edge strength as well as the displacement of edge pixel positions in the estimation of similarity. A series of experimental tests shows the new metric to be a robust and effective tool in the comparison of edge images when a small localization error of the detected edges is allowed.
Surface Chemistry in the Atomic Layer Deposition of TiN Films from TiCl<sub>4</sub> and Ammonia (2006)

The surface chemistry of atomic layer depositions (ALD) of titanium nitride films using alternate doses of TiCl4 and NH3 was characterized by using X-ray photoelectron spectroscopy. The nature of the species deposited by each half-reaction was explored first. Evidence was obtained for the partial loss of chlorine atoms and the reduction of the metal during the adsorption of the TiCl4. Subsequent ammonia treatment removes most of the remaining chlorine and leads to the formation of a nitride. Both half-reactions were proven self-limited, stopping after the deposition of submonolayer quantities of the materials. Repeated ALD cycles were shown to lead to the buildup of thick films. However, those films display a Ti3N4 layer on top of the expected TiN. The data suggest that the reduction of the Ti4+ species may therefore occur during the TiCl4, not NH3, dosing step. The incorporation of impurities in the films was also investigated. Chlorine is only deposited on the surface, and in negligible quantities. This Cl appears to originate from readsorption of the HCl byproduct, and could be removed by light sputtering, heating, or further ammonia treatment. Oxygen incorporation, on the other hand, was unavoidable and was determined to possibly come from diffusion from the underlying substrate.
Smart Control of Monodisperse Stöber Silica Particles:  Effect of Reactant Addition Rate on Growth Process (2004)

Control over the synthesis of monodisperse silica particles up to mesoscopic scale is generally made difficult due to intrinsic limitation to submicrometric dimensions and secondary nucleation in seeded experiments. To investigate this issue and overcome these difficulties, we have implemented single step processing by quantifying the effects of the progressive addition of a diluted tetraethyl orthosilicate solution in ethanol on the size and monodispersity of silica particles. Contrary to particles grown in seeded polymerization, monodisperse particles with size up to 2 microm were synthesized. Moreover, the particles exhibit a final diameter (d(f)), which varies with V(-1/3) over more than 2 orders of magnitude in rate of addition (V). On the basis of a kinetic study in the presence of addition showing that particle growth is limited by the diffusion of monomer species, we developed a diffusion-limited growth model to theoretically explain the observed d(f)(V) behavior and quantitatively retrieve the measured amplitude and exponent. Using a single parameter procedure, we can therefore predict and generate in the room temperature range, monodisperse particles of a targeted size by simply adjusting the rate of addition.