gebhart/patrepeval huggingface dataset:
Functional engineered channels and pores (Review) (2004)

Significant progress has been made in membrane protein engineering over the last 5 years, based largely on the re-design of existing scaffolds. Engineering techniques that have been employed include direct genetic engineering, both covalent and non-covalent modification, unnatural amino acid mutagenesis and total synthesis aided by chemical ligation of unprotected fragments. Combinatorial mutagenesis and directed evolution remain, by contrast, underemployed. Techniques for assembling and purifying heteromeric multisubunit pores have been improved. Progress in the de novo design of channels and pores has been slower. But, we are at the beginning of a new era in membrane protein engineering based on the accelerating acquisition of structural information, a better understanding of molecular motion in membrane proteins, technical improvements in membrane protein refolding and the application of computational approaches developed for soluble proteins. In addition, the next 5 years should see further advances in the applications of engineered channels and pores, notably in therapeutics and sensor technology.
Definition and Redesign of the Extended Substrate Specificity of Granzyme B (1998)

Granzyme B is a protease involved in the induction of rapid target cell death by cytotoxic lymphocytes. Definition of the substrate specificity of granzyme B allows for the identification of in vivo substrates in this process. By using the combinatorial methods of synthetic substrate libraries and substrate-phage display, an optimal substrate for granzyme B that spans over six subsites was determined to be Ile-Glu-Xaa-(Asp downward arrowXaa)-Gly, with cleavage of the Asp downward arrowXaa peptide bond. Granzyme B proteolysis was shown to be highly dependent on the length and sequence of the substrate, supporting the role of granzyme B as a regulatory protease. Arginine 192 was identified as a determinant of P3-Glu and P1-Asp substrate specificity. Mutagenesis of arginine 192 to glutamate reversed the preference for negatively charged amino acids at P3 to positively charged amino acids. The preferred substrate sequence matches the activation sites of caspase 3 and caspase 7 and thus is consistent with the role of granzyme B in activation of these proteases during apoptosis. The caspase substrate poly(ADP)-ribose polymerase is cleaved by granzyme B in a cell-free assay at two sites that resemble the granzyme B specificity determined by the combinatorial methods. Many caspase substrates contain granzyme B cleavage sites and are proposed as potential granzyme B targets, suggesting a redundant function with certain caspases.
Ribosomal −1 Frameshifting during Decoding ofBacillus subtilis cddOccurs at the Sequence CGA AAG (1999)

During translation of the Bacillus subtilis cdd gene, encoding cytidine deaminase (CDA), a ribosomal -1 frameshift occurs near the stop codon, resulting in a CDA subunit extended by 13 amino acids. The frequency of the frameshift is approximately 16%, and it occurs both when the cdd gene is expressed from a multicopy plasmid in Escherichia coli and when it is expressed from the chromosomal copy in B. subtilis. As a result, heterotetrameric forms of the enzyme are formed in vivo along with the dominant homotetrameric species. The different forms have approximately the same specific activity. The cdd gene was cloned in pUC19 such that the lacZ' gene of the vector followed the cdd gene in the -1 reading frame immediately after the cdd stop codon. By using site-directed mutagenesis of the cdd-lacZ' fusion, it was shown that frameshifting occurred at the sequence CGA AAG, 9 bp upstream of the in-frame cdd stop codon, and that it was stimulated by a Shine-Dalgarno-like sequence located 14 bp upstream of the shift site. The possible function of this frameshift in gene expression is discussed.
Twitinfo (2011)

Microblogs are a tremendous repository of user-generated content about world events. However, for people trying to understand events by querying services like Twitter, a chronological log of posts makes it very difficult to get a detailed understanding of an event. In this paper, we present TwitInfo, a system for visualizing and summarizing events on Twitter. TwitInfo allows users to browse a large collection of tweets using a timeline-based display that highlights peaks of high tweet activity. A novel streaming algorithm automatically discovers these peaks and labels them meaningfully using text from the tweets. Users can drill down to subevents, and explore further via geolocation, sentiment, and popular URLs. We contribute a recall-normalized aggregate sentiment visualization to produce more honest sentiment overviews. An evaluation of the system revealed that users were able to reconstruct meaningful summaries of events in a small amount of time. An interview with a Pulitzer Prize-winning journalist suggested that the system would be especially useful for understanding a long-running event and for identifying eyewitnesses. Quantitatively, our system can identify 80-100% of manually labeled peaks, facilitating a relatively complete view of each event studied.
Pediatric Parenteral Amino Acid Mixture in Low Birth Weight Infants (1988)

A mixture of amino acids designed to maintain normal plasma amino acid concentrations in infants and children requiring parenteral nutrition was evaluated in 28 low birth weight (LBW) infants (birth weight, 750 to 1750 g; postnatal age, 1 to 4 weeks) who required parenteral nutrients for optimal nutritional management. Sixteen babies received only parenteral nutrients for five to 21 days. Ten of these received a typical regimen by peripheral vein (1.91 +/- 0.16 g/kg/d of amino acids and 44.7 +/- 4.4 kcal/kg/d) and six received a typical regimen through a central vein (2.39 +/- 0.11 g/kg/d of amino acids and 95.9 +/- 14.5 kcal/kg/d). Mean weight gain of the peripheral vein subgroup was 10.3 +/- 10.6 g/kg/d; mean nitrogen balance was 230 +/- 66 mg/kg/d. Both the mean rate of weight gain (17.2 +/- 5.1 g/kg/d) and the mean rate of nitrogen retention (267 +/- 49 g/kg/d) of the central vein subgroup were similar to intrauterine rates. In these two subgroups as well as the total population, plasma concentrations of all amino acids except phenylalanine were within the 95% confidence limits of the plasma concentrations observed in LBW infants fed sufficient amounts of human milk to result in a rate of weight gain similar to the intrauterine rate. However, although plasma tyrosine and cyst(e)ine concentrations were within the 95% confidence limits of the plasma concentrations goals, the LBW infant's ability to use N-acetyl-L-tyrosine and cysteine HCl appears to be even less than that of the term infant and older child. In toto, these data support the efficacy of the amino acid mixture evaluated for LBW infants. Of equal importance, they suggest that the LBW infant's ability to use parenterally delivered amino acids is not as limited as commonly thought.
Diamond-Based Molecular Platform for Photoelectrochemistry (2008)

Boron doped diamond (BDD) thin film was found to exhibit higher photocurrent conversion efficiencies and photostability compared to commonly used transparent conducting oxides (ITO and FTO) owing to the matching energy levels and strong C-C bonding at the organic/diamond interface.
Maximum-likelihood estimation of OFDM carrier frequency offset for fading channels (2002)

In OFDM systems, significant performance degradation can result from a small carrier frequency offset, which may occur due to drift after an initial frequency acquisition. We consider the estimation of the frequency offset in the tracking mode, using demodulation decisions rather than training sequences. Both maximum-likelihood estimation and a simpler, iterative technique are considered. For a system with 128 subchannels, coherent QPSK modulation, and an exponentially decaying multipath-fading channel, our simulation results show that unbiased estimation with a standard deviation of less than 1% can be achieved within three iterations if the frequency offset is less than 15%. After the correction using the estimated frequency offset, the bit error rate of the demodulation decisions is no different from that without a frequency offset.
Large-scale semantic mapping and reasoning with heterogeneous modalities (2012)

This paper presents a probabilistic framework combining heterogeneous, uncertain, information such as object observations, shape, size, appearance of rooms and human input for semantic mapping. It abstracts multi-modal sensory information and integrates it with conceptual common-sense knowledge in a fully probabilistic fashion. It relies on the concept of spatial properties which make the semantic map more descriptive, and the system more scalable and better adapted for human interaction. A probabilistic graphical model, a chaingraph, is used to represent the conceptual information and perform spatial reasoning. Experimental results from online system tests in a large unstructured office environment highlight the system's ability to infer semantic room categories, predict existence of objects and values of other spatial properties as well as reason about unexplored space.
Multidimensional transfer functions for interactive volume rendering (2002)

Most direct volume renderings produced today employ 1D transfer functions which assign color and opacity to the volume based solely on the single scalar quantity which comprises the data set. Though they have not received widespread attention, multi-dimensional transfer functions are a very effective way to extract materials and their boundaries for both scalar and multivariate data. However, identifying good transfer functions is difficult enough in 1D, let alone 2D or 3D. This paper demonstrates an important class of 3D transfer functions for scalar data, and describes the application of multi-dimensional transfer functions to multivariate data. We present a set of direct manipulation widgets that make specifying such transfer functions intuitive and convenient. We also describe how to use modern graphics hardware to both interactively render with multidimensional transfer functions and to provide interactive shadows for volumes. The transfer functions, widgets and hardware combine to form a powerful system for interactive volume exploration.
Thyristor-Based Volatile Memory in Nano-Scale CMOS (2006)

A thyristor-based memory cell technology provides SRAM-like performance at 2times to 3times the density of conventional 6T SRAM. The technology is readily embedded into conventional nano-scale CMOS and scales into future SOI and FinFET technologies. A 19mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 0.13μm 9Mb SOI test chip has a 0.562μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> cell with a cell-R/W time <2ns
Glycoarrays—tools for determining protein–carbohydrate interactions and glycoenzyme specificity (2008)

Carbohydrate arrays (glycoarrays) have recently emerged as a high-throughput tool for studying carbohydrate-binding proteins and carbohydrate-processing enzymes. A number of sophisticated array platforms that allow for qualitative and quantitative analysis of carbohydrate binding and modification on the array surface have been developed, including analysis by fluorescence spectroscopy, mass spectrometry and surface plasmon resonance spectroscopy. These platforms, together with examples of biologically-relevant applications are reviewed in this Feature Article.
Vascular Endothelial Growth Factor Receptor-2–Induced Initial Endothelial Cell Migration Depends on the Presence of the Urokinase Receptor (2004)

The angiogenic response of endothelial cells initiated by different growth factors is accompanied by assembly of cell surface-bound proteolytic machinery as a prerequisite for focal invasion. We have shown previously how the vascular endothelial growth factor (VEGF) initiates proteolysis by activation of pro-urokinase (pro-PA) via the VEGF receptor-2 (VEGFR-2). We now show that the cell surface receptor of the uPA-system, the urokinase receptor (uPAR), is redistributed to focal adhesions at the leading edge of endothelial cells in response to VEGF. VEGF165 and VEGF-E, both interacting with VEGFR-2, but not PlGF exclusively stimulating VEGFR-1, induce within minutes internalization of uPAR via an LDL receptor-like molecule, dependent on generation of active uPA and the presence of plasminogen activator inhibitor-1 (PAI-1). uPAR seems to play a pivotal role in VEGFR-2-induced endothelial cell migration because cleavage of surface uPAR impaired the migratory response of endothelial cells toward VEGF-E, but not toward PlGF.
Angiogenesis-independent tumor growth mediated by stem-like cancer cells (2006)

In this work, highly infiltrative brain tumors with a stem-like phenotype were established by xenotransplantation of human brain tumors in immunodeficient nude rats. These tumors coopted the host vasculature and presented as an aggressive disease without signs of angiogenesis. The malignant cells expressed neural stem cell markers, showed a migratory behavior similar to normal human neural stem cells, and gave rise to tumors in vivo after regrafting. Serial passages in animals gradually transformed the tumors into an angiogenesis-dependent phenotype. This process was characterized by a reduction in stem cells markers. Gene expression profiling combined with high throughput immunoblotting analyses of the angiogenic and nonangiogenic tumors identified distinct signaling networks in the two phenotypes. Furthermore, proinvasive genes were up-regulated and angiogenesis signaling genes were down-regulated in the stem-like tumors. In contrast, proinvasive genes were down-regulated in the angiogenesis-dependent tumors derived from the stem-like tumors. The described angiogenesis-independent tumor growth and the uncoupling of invasion and angiogenesis, represented by the stem-like cancer cells and the cells derived from them, respectively, point at two completely independent mechanisms that drive tumor progression. This article underlines the need for developing therapies that specifically target the stem-like cell pools in tumors.
Selecting and Sorting Waxy Wheat Kernels Using Near‐Infrared Spectroscopy (2009)

ABSTRACT An automated single kernel near‐infrared (NIR) sorting system was used to separate single wheat ( Triticum aestivum L.) kernels with amylose‐free (waxy) starch from reduced‐amylose (partial waxy) or wild‐type wheat kernels. Waxy kernels of hexaploid wheat are null for the granule‐bound starch synthase alleles at all three Wx gene loci; partial waxy kernels have at least one null and one functional allele. Wild‐type kernels have three functional alleles. Our results demonstrate that automated single kernel NIR technology can be used to select waxy kernels from segregating breeding lines or to purify advanced breeding lines for the low‐amylose kernel trait. Calibrations based on either amylose content or the waxy trait performed similarly. Also, a calibration developed using the amylose content of waxy, partial waxy, and wild‐type durum ( T. turgidum L. var durum ) wheat enabled adequate sorting for hard red winter and hard red spring wheat with no modifications. Regression coefficients indicated that absorption by starch in the NIR region contributed to the classification models. Single kernel NIR technology offers significant benefits to breeding programs that are developing wheat with amylose‐free starches.
Polymerisation of ethylene and propene using new chiral zirconium derivatives. Crystal structure of [ZrL1Cl2][H2L1=(4S,5S)-trans-4,5-bis(1H-inden-1-ylmethyl)-2,2-dimethyl-1,3-dioxolane] (1991)

The chiral indene derivative (4S,5S)-trans-4,5-bis(1H-inden-3-ylmethyl)-2,2-dimethyl-1,3-dioxolane has been prepared and used to synthesise the bis(η-indenyl) derivatives [ML1Cl2][M = Ti, Zr or Hf; H2L1=(4S,5S)-trans-4,5-bis(1H-inden-1-ylmethyl)-2,2-dimethyl-1,3-dioxolane]. The crystal structure of the zirconium compound has been determined. Hydrogenation of the compounds [ML1Cl2] gives the corresponding bis(4,5,6,7-tetrahydroinden-1-ylmethyl) derivatives [ML2Cl2]. The ability of the new metal compounds to catalyse the polymerisation of ethylene and propene has been examined. The compounds together with methylaluminoxane [(OAIMe)n] as cocatalyst are active for polymerisation of ethylene and, for M = Zr, for propene.
Human Immunodeficiency Virus type 1 reverse transcriptase. (1996)

The Human Immunodeficiency Virus type 1 (HIV-1) is a retrovirus and a causative agent of the Acquired Immuno Deficiency Syndrome (AIDS). Retroviruses are distinct from other viruses in their ability to encode an enzyme called reverse transcriptase (RT). The RT is the enzyme mainly involved in replication. It performs RNA- as well as DNA-dependent DNA synthesis in order to convert the single-stranded viral RNA genome into double-stranded DNA. The double-stranded DNA is stably integrated into the host cell genome and is used as a template for the production of a new viral generation. The HIV-1 RT is partially encoded by the POL open reading frame of the HIV-1 genome and consists of two subunits of 66 kDa (p66) and 51 kDa (p51). The p66 polypeptide encodes the reverse transcriptase and the RNase H domain. Half of the p66 molecules are further processed to generate the p51 protein with an identical N-terminus, but lacking the C-terminus which encodes the RNase H domain. In vivo both polypeptides are found in equimolar amounts thus forming a heterodimer. This dimerization is critical for the enzymatic activity. In this review we summarize (i) the replication cycle of HIV-1, (ii) the enzymatic properties of HIV-1 RT and (iii) the structure-function relationship of the HIV-1 RT in view of the known three dimensional structure.
Analysis of NADPH supply during xylitol production by engineered Escherichia coli (2008)

Escherichia coli strain PC09 (DeltaxylB, cAMP-independent CRP (crp*) mutant) expressing an NADPH-dependent xylose reductase from Candida boidinii (CbXR) was previously reported to produce xylitol from xylose while metabolizing glucose [Cirino et al. (2006) Biotechnol Bioeng 95(6): 1167-1176]. This study aims to understand the role of NADPH supply in xylitol yield and the contribution of key central carbon metabolism enzymes toward xylitol production. Studies in which the expression of CbXR or a xylose transporter was increased suggest that enzyme activity and xylose transport are not limiting xylitol production in PC09. A constraints-based stoichiometric metabolic network model was used to understand the roles of central carbon metabolism reactions and xylose transport energetics on the theoretical maximum molar xylitol yield (xylitol produced per glucose consumed), and xylitol yields (Y(RPG)) were measured from resting cell biotransformations with various PC09 derivative strains. For the case of xylose-proton symport, omitting the Zwf (glucose-6-phosphate dehydrogenase) or PntAB (membrane-bound transhydrogenase) reactions or TCA cycle activity from the model reduces the theoretical maximum yield from 9.2 to 8.8, 3.6, and 8.0 mol xylitol (mol glucose)(-1), respectively. Experimentally, deleting pgi (encoding phosphoglucose isomerase) from strain PC09 improves the yield from 3.4 to 4.0 mol xylitol (mol glucose)(-1), while deleting either or both E. coli transhydrogenases (sthA and pntA) has no significant effect on the measured yield. Deleting either zwf or sucC (TCA cycle) significantly reduces the yield from 3.4 to 2.0 and 2.3 mol xylitol (mol glucose)(-1), respectively. Expression of a xylose reductase with relaxed cofactor specificity increases the yield to 4.0. The large discrepancy between theoretical maximum and experimentally determined yield values suggests that biocatalysis is compromised by pathways competing for reducing equivalents and dissipating energy. The metabolic role of transhydrogenases during E. coli biocatalysis has remained largely unspecified. Our results demonstrate the importance of direct NADPH supply by NADP+-utilizing enzymes in central metabolism for driving heterologous NADPH-dependent reactions, and suggest that the pool of reduced cofactors available for biotransformation is not readily interchangeable via transhydrogenase.
Joint Discriminative and Generative Learning for Person Re-identification (2019)

Person re-identification (re-id) remains challenging due to significant intra-class variations across different cameras. Recently, there has been a growing interest in using generative models to augment training data and enhance the invariance to input changes. The generative pipelines in existing methods, however, stay relatively separate from the discriminative re-id learning stages. Accordingly, re-id models are often trained in a straightforward manner on the generated data. In this paper, we seek to improve learned re-id embeddings by better leveraging the generated data. To this end, we propose a joint learning framework that couples re-id learning and data generation end-to-end. Our model involves a generative module that separately encodes each person into an appearance code and a structure code, and a discriminative module that shares the appearance encoder with the generative module. By switching the appearance or structure codes, the generative module is able to generate high-quality cross-id composed images, which are online fed back to the appearance encoder and used to improve the discriminative module. The proposed joint learning framework renders significant improvement over the baseline without using generated data, leading to the state-of-the-art performance on several benchmark datasets.
Evaluation of regional and whole gut motility using the wireless motility capsule: relevance in clinical practice (2012)

The wireless motility capsule (WMC) is an ambulatory noninvasive and nonradioactive diagnostic sensor that continuously samples intraluminal pH, temperature, and pressure as it moves through the gastrointestinal (GI) tract. This review summarizes the data obtained in clinical trials with the WMC and discusses its role in clinical practice. The United States Food and Drug Administration has approved the SmartPill GI monitoring system for the evaluation of gastric emptying time in patients with suspected gastroparesis, the evaluation of colonic transit time in patients with suspected chronic constipation, and for the characterization of pressure profiles from the antrum and duodenum. Clinical studies have shown that WMC-measured GI transit times can distinguish patients with motility abnormalities similarly to conventional testing. However, the WMC offers the advantage of providing a full GI-tract profile, enabling the detection of multiregional GI transit abnormalities in patients with suspected upper or lower GI dysmotility. The WMC also characterizes pressure profiles of the GI tract and impaired pressure profile limits are reported for the antrum and duodenum. In comparison with manometry, interpretations of pressure measurements obtained by the WMC are limited by an inability to detect a peristaltic pressure wave front, and further investigation is required to develop clinical applications. Clinical studies with the WMC indicated that it should be considered for the evaluation of regional and whole gut transit time in patients with suspected upper or lower dysmotility, particularly if there are concerns about multiregional dysmotility.