gebhart/patrepeval huggingface dataset:
Measuring the Formaldehyde Protein–DNA Cross-Link Reversal Rate (2014)

Protein-DNA binding interactions play critical roles in important cellular processes such as gene expression, cell division, and chromosomal organization. Techniques to identify and characterize these interactions often utilize formaldehyde cross-linking for stabilization of the complexes. Advantages of formaldehyde as a cross-linking reagent include cell permeability, relatively fast cross-linking kinetics, and short cross-linker length. In addition, formaldehyde cross-links are reversible, which has the advantage of allowing complexes to be dissociated if desired but may also present a problem if undesired dissociation occurs in the course of an experiment. While the kinetics of formaldehyde cross-link formation have been well-established in numerous studies, there have been no reports of the rate of cross-link dissociation, even though it is clearly a critical variable when developing a biochemical protocol involving formaldehyde cross-linking. We present here a method for measurement of the rate of formaldehyde cross-link reversal based upon the Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) procedure and use it to determine the rate of cross-link reversal for cross-linked protein-DNA complexes from yeast cell lysate. The half-life of the protein-DNA cross-links varies from 179 h at 4 °C to 11.3 h at 47 °C, with a rate that increases exponentially with temperature and is independent of salt concentration.
On the removal of shadows from images (2006)

This paper is concerned with the derivation of a progression of shadow-free image representations. First, we show that adopting certain assumptions about lights and cameras leads to a 1D, gray-scale image representation which is illuminant invariant at each image pixel. We show that as a consequence, images represented in this form are shadow-free. We then extend this 1D representation to an equivalent 2D, chromaticity representation. We show that in this 2D representation, it is possible to relight all the image pixels in the same way, effectively deriving a 2D image representation which is additionally shadow-free. Finally, we show how to recover a 3D, full color shadow-free image representation by first (with the help of the 2D representation) identifying shadow edges. We then remove shadow edges from the edge-map of the original image by edge in-painting and we propose a method to reintegrate this thresholded edge map, thus deriving the sought-after 3D shadow-free image.
Essential role of MALT1 protease activity in activated B cell-like diffuse large B-cell lymphoma (2009)

A key element for the development of suitable anti-cancer drugs is the identification of cancer-specific enzymatic activities that can be therapeutically targeted. Mucosa-associated lymphoid tissue transformation protein 1 (MALT1) is a proto-oncogene that contributes to tumorigenesis in diffuse large B-cell lymphoma (DLBCL) of the activated B-cell (ABC) subtype, the least curable subtype of DLBCL. Recent data suggest that MALT1 has proteolytic activity, but it is unknown whether this activity is relevant for tumor growth. Here we report that MALT1 is constitutively active in DLBCL lines of the ABC but not the GCB subtype. Inhibition of the MALT1 proteolytic activity led to reduced expression of growth factors and apoptosis inhibitors, and specifically affected the growth and survival of ABC DLBCL lines. These results demonstrate a key role for the proteolytic activity of MALT1 in DLBCL of the ABC subtype, and provide a rationale for the development of pharmacological inhibitors of MALT1 in DLBCL therapy.
Functionalization of Silica Surface with UV-Active Molecules by Multivalent Organosilicon Spacer (2016)

Immobilization of active molecules by attachment onto solid surfaces is a well-established practice in many processes and applications. Silica micro- and nano-particles are attractive candidates as support for active molecules as a result of a combination of desirable properties. The present study deals with grafting of a functional UV active molecule onto silica surfaces via hydrosilylation reactions using multivalent organosilicon spacers. Different types of organosilicon precursors based on dimethylsiloxysilanes containing multiple SiH groups were used as spacers between vinyl-modified silica surface and the benzotriazole UV-absorber (UVA). Firstly, the surface of silica was modified with vinyltrimetoxsisilane coupling agent. The UVA molecules were attached to the silica-vinyl by a two-step procedure involving hydrosilylation reaction. The successful grafting was confirmed by FTIR, TGA and UV-Vis characterization. More than fivefold increase in UVA loading was found for the MH30 multifunctional spacer, which contains approximately 75 SiH groups per molecule, when compared to a four-functional spacer. Furthermore a branched, bulky six-functional spacer is preferred over a linear spacer of the same functionality. UV activity of functionalized silica was studied by UV-Vis spectroscopy, indicating that the immobilization of UVA onto silica surface has not altered its UV absorbance properties.
Multi-stages hybrid ARQ with conditional frame skipping and reference frame selecting scheme for real-time video transport over wireless LAN (2004)

This paper proposes a multi-stages hybrid ARQ/FEC scheme with frame skipping, reference frame selecting and intra-frame refreshing techniques for H.26L real-time video streaming over WLAN. In this paper, adaptive ARQ/FEC is adopted to save unnecessary FEC overhead; conditional frame skipping is adopted to avoid ETE delay inflation due to MAC ARQ/FEC error recovery; reference frame selecting is adopted to save bandwidth; intra-frame refreshing is adopted to prevent residual error propagation among consecutive frames. Through analysis and simulation, we show that multi-stages hybrid ARQ scheme has the following key properties: (1) high error recovery rate for real-time video frames, (2) excellent sea/ability, (3) high transmission efficiency. In case of severe unreliable channel, which causes losing a lot of IP packets, we obtain a peak signal-to-noise ratio improvement up to about 10 dB compared to the hybrid ARQ proposed in [A. Majumdar et al., June 2002].
Human IgA1 half-molecules: clinical and immunologic features in a patient with multiple myeloma (1979)

Abnormal IgA1 half-molecules consisting of one heavy and one light chain were found in a patient (N.N.) with typical multiple myeloma. The serum and the urine of this patient contained both 7.0S and 3.9S IgA myeloma proteins. The IgA half-molecules (3.9S) were found to have a molecular weight of 59,000 daltons and were composed of one alpha1 chain of about 40,000 daltons and one light chain of 22,000 daltons. Furthermore, enzymatic degradation suggested that the alpha chain of the N.N. half-molecules had a large deletion in its Fc portion. We suggest that its heavy and light chains were probably bound noncovalently, since the interchains connecting the heavy and light chains of these IgA half-molecules were easily dissociated with 1% SDS and 8 M urea. Cytologic studies identified at least two types of myeloma cells, and it is possible that half-molecule IgA production might result from mutation among the myeloma cells producing whole- molecule IgA.
PNA interference mapping demonstrates functional domains in the noncoding RNA <i>Xist</i> (2001)

The noncoding RNA Xist has been shown to be essential for X-chromosome inactivation and to coat the inactive X-chromosome (Xi). Thus, an important question in understanding the formation of Xi is whether the binding reaction of Xist is necessary for X-chromosome inactivation. In this article, we demonstrate the failure of X-chromosome silencing if the association of Xist with the X-chromosome is inhibited. The chromatin-binding region was functionally mapped and evaluated by using an approach for studying noncoding RNA function in living cells that we call peptide nucleic acid (PNA) interference mapping. In the reported experiments, a single 19-bp antisense cell-permeating PNA targeted against a particular region of Xist RNA caused the disruption of the Xi. The association of the Xi with macro-histone H2A is also disturbed by PNA interference mapping.
Highly selective epoxidation of alkenes and styrenes with H2O2 and manganese complexes of the cyclic triamine 1,4,7-trimethyl-1,4,7-triazacyclononane (1996)

In acetone and at subambient temperature, manganese complexes of 1,4,7-trimethyl-1,4,7-triazacyclononane-catalyse the selective oxidation of many alkenes and styrenes to epoxides with an efficient use of H2O2; the regio- and chemo-selectivity resemble those of manganese-porphyrin catalysts.
Direct Asymmetric <i>a</i><i>nti</i>-Mannich-Type Reactions Catalyzed by a Designed Amino Acid (2006)

The development of catalysts for Mannich-type reactions that afford anti-products with excellent diastereo- and enantioselectivities under mild conditions and low catalyst loadings (1-5 mol %) is reported. Based on principles gained from the study of (S)-proline-catalyzed Mannich-type reactions that afford enantiomerically enriched syn-products, (3R,5R)-5-methyl-3-pyrrolidinecarboxylic acid (RR35) has been designed to catalyze the direct enantioselective anti-selective Mannich-type reactions. Computational studies of the above reaction using HF/6-31G* level of theory suggested that this design would be highly effective. The catalyst was subsequently synthesized and studied in organocatalytic Mannich-type reactions between unmodified aldehydes and N-PMP-protected alpha-imino esters. In accord with the design principles and in quantitative agreement with the theoretical predictions, reactions catalyzed by this catalyst afforded anti-products in good yields with excellent diastereo- and enantioselectivities (anti:syn 94:6 to 98:2, >97 to >99% ee).
Statistical Analysis-Based Error Models for the Microsoft KinectTM Depth Sensor (2014)

The stochastic error characteristics of the Kinect sensing device are presented for each axis direction. Depth (z) directional error is measured using a flat surface, and horizontal (x) and vertical (y) errors are measured using a novel 3D checkerboard. Results show that the stochastic nature of the Kinect measurement error is affected mostly by the depth at which the object being sensed is located, though radial factors must be considered, as well. Measurement and statistics-based models are presented for the stochastic error in each axis direction, which are based on the location and depth value of empirical data measured for each pixel across the entire field of view. The resulting models are compared against existing Kinect error models, and through these comparisons, the proposed model is shown to be a more sophisticated and precise characterization of the Kinect error distributions.
Amino Acid Derived Nickelacycles:  Intermediates in Nickel-Mediated Polypeptide Synthesis (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAmino Acid Derived Nickelacycles: Intermediates in Nickel-Mediated Polypeptide SynthesisTimothy J. DemingView Author Information Departments of Materials and Chemistry University of California, Santa Barbara Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 1998, 120, 17, 4240–4241Publication Date (Web):April 16, 1998Publication History Received28 January 1998Published online16 April 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ja980313ihttps://doi.org/10.1021/ja980313irapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2167Altmetric-Citations111LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Ligands,Metallacycles,Monomers,Peptides and proteins,Reactivity Get e-Alerts
Structure at 2.5 Å of a Designed Peptide that Maintains Solubility of Membrane Proteins (1993)

A 24-amino acid peptide designed to solubilize integral membrane proteins has been synthesized. The design was for an amphipathic alpha helix with a "flat" hydrophobic surface that would interact with a transmembrane protein as a detergent. When mixed with peptide, 85 percent of bacteriorhodopsin and 60 percent of rhodopsin remained in solution over a period of 2 days in their native forms. The crystal structure of peptide alone showed it to form an antiparallel four-helix bundle in which monomers interact, flat surface to flat surface, as predicted.
Haplotype diversity in the human red and green opsin genes: evidence for frequent sequence exchange in exon 3 (1993)

We studied polymorphisms in the coding sequences of the human red and green opsin genes of 133 Caucasian males. Eleven polymorphic sites were discovered in the red opsin gene, seven of which were in exon 3, three in exon 4 and one in exon 5. Polymorphisms at 8 of these sites resulted in amino acid substitutions which generated a total of 18 unique red opsins in the population. The substitutions at three (S180A, I230T, and A233S) of the 8 sites involve hydroxyl-bearing to non-polar amino acid residues, and are therefore likely to alter spectral characteristics of the red pigment. Eight polymorphic sites were observed in the green opsin coding sequences, six of which were in exon 3, one in exon 2 and one in exon 5. Five of the eight involved amino acid substitutions which generated 15 unique green opsins in the population. Substitutions at two of these sites involve hydroxyl-bearing vs. non-polar residues. Six polymorphisms, all of which are located in exon 3, are shared between the red and green opsin genes, essentially making it difficult to assign this exon to either of these genes. Markers in exon 3 are in partial linkage disequilibrium with those in exons 4 and 5, whereas the latter two are in strong linkage disequilibrium with each other. Furthermore, markers in the 5' region of exon 3 are also in only partial (54%) disequilibrium with those in the 3' region. The above results strongly suggest a history of frequent gene conversion, mainly localized to exon 3, in the lineages leading to the human red and green opsin genes.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficient operation of an Yb-sensitised Er fibre laser at 1.56 μm (1988)

We report operation of a high-efficiency Yb : Er single-mode fibre laser. Pumping at wavelengths of 1064 nm and at 820 nm has shown low pump power thresholds (&lt;7 and 4 mW) and high slope efficiencies (4.2 and 7.0%).
3D Hybrid Mesh Generation for Reservoir Flow Simulation. (2004)

A great challenge for flow simulators of new generation is to gain more accuracy at well proximity within complex geological structures. For this purpose, a new approach based on hybrid mesh modeling was proposed in 2D in [1]. In this hybrid mesh, the reservoir is described by a structured quadrilateral mesh and drainage areas around wells are represented by radial circular meshes. In order to generate a global conforming mesh, unstructured transition meshes constituted by convex polygonal elements satisfying finite volume properties are used to connect together these two structured meshes. Thus, the resulting mesh allows us to take full advantages of simplicity and practical aspects of structured meshes while complexity inherent to unstructured meshes is introduced only where strictly needed.
Vitamin K2 supplementation improves hip bone geometry and bone strength indices in postmenopausal women (2007)

Vitamin K(2) helps maintaining bone strength at the site of the femoral neck in postmenopausal women by improving BMC and FNW, whereas it has little effect on DXA-BMD.
Tarantula: a vector extension to the alpha architecture (2003)

Tarantula is an aggressive floating point machine targeted at technical, scientific and bioinformatics workloads, originally planned as a follow-on candidate to the EV8 processor. Tarantula adds to the EV8 core a vector unit capable of 32 double-precision flops per cycle. The vector unit fetches data directly from a 16 MByte second level cache with a peak bandwidth of sixty four 64-bit values per cycle. The whole chip is backed by a memory controller capable of delivering over 64 GBytes/s of raw bandwidth. Tarantula extends the Alpha ISA with new vector instructions that operate on new architectural state. Salient features of the architecture and implementation are: (1) it fully integrates into a virtual-memory cache-coherent system without changes to its coherency protocol, (2) provides high bandwidth for non-unit stride memory accesses, (3) supports gather/scatter instructions efficiently, (4) fully integrates with the EV8 core with a narrow, streamlined interface, rather than acting as a co-processor (5) can achieve a peak of 104 operations per cycle, and (6) achieves excellent "real-computation" per transistor and per watt ratios. Our detailed simulations show that Tarantula achieves an average speedup of 5X over EV8, out of a peak speedup in terms of flops of 8X. Furthermore, performance on gather/scatter intensive benchmarks such as Radix Sort is also remarkable: a speedup of almost 3X over EV8 and 15 sustained operations per cycle. Several benchmarks exceed 20 operations per cycle.
Widespread long-term gene transfer to mouse skeletal muscles and heart. (1992)

Successful treatment of muscular disorders awaits an adapted gene delivery protocol. The clinically applicable technique used for hematopoietic cells which is centered around implantation of retrovirally modified cells may not prove sufficient for a reversal of phenotype when muscle diseases are concerned. We report here efficient, long-term in vivo gene transfer throughout mouse skeletal and cardiac muscles after intravenous administration of a recombinant adenovirus. This simple, direct procedure raises the possibility that muscular degenerative diseases might one day be treatable by gene therapy.
Preparation of Highly Immunogenic Ribosomal Fractions of<i>Mycobacterium tuberculosis</i>by Use of Sodium Dodecyl Sulfate (1966)

Youmans, Anne S. (Northwestern University Medical School, Chicago, Ill.), and Guy P. Youmans. Preparation of highly immunogenic ribosomal fractions of Mycobacterium tuberculosis by use of sodium dodecyl sulfate. J. Bacteriol. 91:2139-2145. 1966.-Ribosomal fractions of Mycobacterium tuberculosis, strain H37Ra, were prepared by treatment of the intracellular particulate fraction with 0.25 or 0.5% sodium dodecylsulfate (SDS) followed by centrifugation at 144,700 x g for 3 hr. This procedure has greatly simplified the preparation of ribosomal fractions and has given fractions composed of approximately 50% ribonucleic acid (RNA) and 15 to 20% protein. When incorporated into Freund's incomplete adjuvant and injected intraperitoneally into CF-1 mice, the SDS ribosomal fractions were more immunogenic than the particulate fractions from which they were prepared. They were as much as 100 times more immunogenic than ribosomal fractions prepared by differential centrifugation, 1 mug (dry weight) per mouse being sufficient for the induction of some immunity. However, none of these ribosomal preparations, in comparable doses, was as immunogenic as the living cells from which they were prepared. It was also shown that the addition of 10(-4)m MgCl(2) to the final diluent increased immunogenic activity, whereas larger concentrations (10(-3)m) reduced immunogenic activity. Preparation of the ribosomal fraction from ruptured cells in one continuous process during the course of 1 day increased the activity. Two-week-old H37Ra cells contained more RNA and were more immunogenic than the older cultures which have been used in the past.
Hypophosphatasia and the risk of atypical femur fractures: a case–control study (2016)

Clinicaltrials.gov number NCT01360099 . Prospectively registered May 20, 2011. First patient enrolled June 14, 2011.
Mesh integration based on co-measurements (2002)

An algorithm for the integration of meshes derived from range data is presented. All of the triangles from either mesh which have sampled the same surface patch of the object are identified as co-measurements and only the most confidently acquired one is kept. Co-measurement identification is based on the position and orientation of the range scanner when each triangle was sampled. Once the redundant triangles have been removed what remains is a patchwork of unconnected non-intersecting meshes which cover the sampled areas of the object. Neighborhood relationships established between the edge points of each patch are used to seam them together. The final mesh is guaranteed to be plausible in the sense that each triangle represents a surface which could have been scanned given the positions and orientations of the range scanner and 2-manifold with the exception that a vertex may be incident to two triangles that are connected only through that vertex. The algorithm performs equally well in areas of low and high curvature.
Productivity of Frac Stimulations in the German Rotliegend: Theoretical Consideration and Practical Results (2005)

Abstract The main production of German gas fields is from sandstones of Upper Rotliegend age (Permian period). The Upper Rotliegend is characterised by a sequence of sandstones, siltstones and shale beds. Most of the present gas fields produce from low permeability layers (mainly 0.1-20mD) in a high pressure and high temperature environment. Hydraulic fracture stimulation has been developed to a regular completion concept in the last 15 years. Fracture stimulations, if applicable, are planned in all new drilling projects as a standard procedure to enhance the productivity of a well. Due to the nature of the Upper Rotliegend depositional environment, a vertical to horizontal permeability anisotropy of about 1/10 can occur within the sandstones. Hydraulic fracture stimulations, in comparison to perforations, have proven to (i) bridge vertical flow barriers within sandstone/ siltstone sequences as well as (ii) to improve the connectivity of the stimulated layers horizontally. The result is an overall permeability capacity increase, vertically as well as horizontally. In addition, the effective productivity index enhancement pre and post frac, the fold of increase (FOI), is usually higher than theoretically expected from hydraulic fracturing. Based on an "effective wellbore radius concept" to calculate the inflow performances of a fractured well, sensitivity studies were carried out to investigate the stimulation treatment results under different reservoir conditions. The main parameters, which have an impact on the fold of increase, are discussed. Based on transient well test analysis, 20 fracture treatments are compared with a theoretical radial inflow model with respect to their expected and observed productivity enhancement.