gebhart/patrepeval huggingface dataset:
A New Class of Phosphotransferases Phosphorylated on an Aspartate Residue in an Amino-terminal DXDX(T/V) Motif (1998)

When incubated with their substrates, human phosphomannomutase and L-3-phosphoserine phosphatase are known to form phosphoenzymes with chemical characteristics of an acyl-phosphate. The phosphorylated residue in phosphomannomutase has now been identified by mass spectrometry after reduction of the phosphoenzyme with tritiated borohydride and trypsin digestion. It is the first aspartate in a conserved DVDGT motif. Replacement of either aspartate of this motif by asparagine or glutamate resulted in complete inactivation of the enzyme. The same mutations performed in the DXDST motif of L-3-phosphoserine phosphatase also resulted in complete inactivation of the enzyme, except for the replacement of the second aspartate by glutamate, which reduced the activity by only about 40%. This suggests that the first aspartate of the motif is also the phosphorylated residue in L-3-phosphoserine phosphatase. Data banks contained seven other phosphomutases or phosphatases sharing a similar, totally conserved DXDX(T/V) motif at their amino terminus. One of these (beta-phosphoglucomutase) is shown to form a phosphoenzyme with the characteristics of an acyl-phosphate. In conclusion, phosphomannomutase and L-3-phosphoserine phosphatase belong to a new phosphotransferase family with an amino-terminal DXDX(T/V) motif that serves as an intermediate phosphoryl acceptor.
Information Extraction (2005)

In 2001 the U.S. Department of Labor was tasked with building a Web site that would help people find continuing education opportunities at community colleges, universities, and organizations across the country. The department wanted its Web site to support fielded Boolean searches over locations, dates, times, prerequisites, instructors, topic areas, and course descriptions. Ultimately it was also interested in mining its new database for patterns and educational trends. This was a major data-integration project, aiming to automatically gather detailed, structured information from tens of thousands of individual institutions every three months.
P<scp>LANT</scp>C<scp>ELLULAR AND</scp>M<scp>OLECULAR</scp>R<scp>ESPONSES TO</scp>H<scp>IGH</scp>S<scp>ALINITY</scp> (2000)

Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to those that regulate osmotic stress responses of yeast. There is evidence also of signaling cascades that are not known to exist in the unicellular eukaryote, some that presumably function in intercellular coordination or regulation of effector genes in a cell-/tissue-specific context required for tolerance of plants. A complex set of stress-responsive transcription factors is emerging. The imminent availability of genomic DNA sequences and global and cell-specific transcript expression data, combined with determinant identification based on gain- and loss-of-function molecular genetics, will provide the infrastructure for functional physiological dissection of salt tolerance determinants in an organismal context. Furthermore, protein interaction analysis and evaluation of allelism, additivity, and epistasis allow determination of ordered relationships between stress signaling components. Finally, genetic activation and suppression screens will lead inevitably to an understanding of the interrelationships of the multiple signaling systems that control stress-adaptive responses in plants.
Opsonising Immunoglobulins and Mannan-Binding Lectin in Chronic Lymphocytic Leukemia (1999)

We investigated the influence of plasma concentrations of immunoglobulin G (IgG), IgA, IgM, IgG subclasses and mannan-binding lectin (MBL) on susceptibility to infection in patients with chronic lymphocytic leukemia (CLL). Of 28 patients with CLL, increased susceptibility to infection was recorded in nine. Four of them (44%) had hypogammaglobulinemia as opposed to only one (5%) of the 19 patients without increased susceptibility to infection (OR 14.4; 95% CI, 1.6-130). When the effect of IgG subclasses contributing to hypogammaglobulinemia was studied, only the decreased concentrations of IgG4 and IgG2 were associated with increased susceptibility to infection. They, in turn, were intercorrelated and also highly correlated with the concentration of IgA. In fact, when these parameters were studied by a multivariable model, only the decreased concentration of IgA was shown as an independent risk factor for infection (P = 0.03). The mean concentration of MBL was significantly higher in patients with infections than in those without (6.54 mg/l and 2.75 mg/l, respectively; P = 0.001). The monitoring of its concentrations might be useful in the follow-up of infectious morbidity in CLL.
UKRN Position on COVID-19 Research (2021)

UKRN position statement on COVID-19 research. Written by the UKRN Steering Group. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA).
Hybrid Indoor Location Estimation System Using Image Processing and WiFi Strength (2009)

Recently, the service of cellular phone which is dependent on the location is spreading widely. Various techniques are suggested for the location estimation in indoor, however, indoor location estimation techniques have many subjects with a cost and an aspect of the accuracy. To deal with these subjects, we propose a quite new hybrid indoor location estimation method for paying attention to a smart phone with built-in Wi-Fi and camera. The proposal method is able to realized both highly accuracy of indoor location estimation and low cost by using the two-dimensional marker, Wi-Fi base stations, and the radio wave strength of ad hoc communications. Verified by using simulation was able to demonstrate the effectiveness.
Transcriptional Regulatory Cascade for Elastase Production in Vibrio vulnificus (2006)

Vibrio vulnificus causes diseases through actions of various virulence factors, including the elastase encoded by the vvpE gene. Through transposon mutagenesis of V. vulnificus, vvpE expression was shown to be increased by luxO mutation. Since the vvpE gene is known to be positively regulated by SmcR via direct binding to the vvpE promoter, the role of LuxO in smcR expression was investigated. The luxAB-transcriptional fusions containing different lengths of the smcR promoter region indicated that the smcR transcription was negatively regulated by LuxO and that a specific upstream region of the smcR gene was required for this repression. Since LuxO is a known member of positive regulators, the negative regulation of smcR transcription by LuxO prompted us to identify the factor(s) linking LuxO and smcR transcription. LuxT was isolated in a ligand fishing experiment using the smcR upstream region as bait, and smcR expression was increased by luxT mutation. Recombinant LuxT bound to a specific upstream region of the smcR gene, -154 to -129 relative to the smcR transcription start site. The expression of luxT was positively regulated by LuxO, and the luxT promoter region contained a putative LuxO-binding site. Mutagenesis of the LuxO-binding site in the luxT promoter region resulted in a loss of transcriptional control by LuxO. Therefore, this study demonstrates a transcriptional regulatory cascade for elastase production, where LuxO activates luxT transcription and LuxT represses smcR transcription.
Chemical synthesis and characterization of duplex DNA containing a new base pair: a nondisruptive, benzofused pyrimidine analog (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical synthesis and characterization of duplex DNA containing a new base pair: a nondisruptive, benzofused pyrimidine analogMarjorie S. Solomon and Paul B. HopkinsCite this: J. Org. Chem. 1993, 58, 8, 2232–2243Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/jo00060a045https://doi.org/10.1021/jo00060a045research-articleACS PublicationsRequest reuse permissionsArticle Views226Altmetric-Citations16LEARN 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 Get e-Alerts
Relations between the Thermal and Mechanical Properties of Cast Zr-TM-Al (TM: Cu, Ni, or Co) Bulk Glassy Alloys (2007)

Ternary Zr-TM-Al (TM: Cu, Ni or Co) bulk glassy alloys were fabricated to clarify the relations between the thermal and mechanical features. These alloy systems show the distinct ternary eutectic point, and a bulk glassy phase also forms around the ternary eutectic composition. We determine the 12 standard Zr-TM-Al bulk glassy alloys in this study. In the twelve standard Zr-TM-Al bulk glassy alloys, the glass-transition temperature has large positive correlation coefficient with Young’s modulus and Vickers hardness. The melting temperature has large negative correlation coefficient with Charpy impact value, fracture strain and volume change due to structural relaxation. Furthermore, in order to recognize the origin of ductility, Poisson’s ratio (metallic bond nature) and volume change (free volume) were also examined.
Overexpression of EphA4 gene and reduced expression of EphB2 gene: Correlation with liver metastasis in colorectal cancer (2009)

e15129 The Eph receptors, members of a large family of transmembrane receptor tyrosine kinases, play important roles in a variety of biologic functions. Recent studies have suggested that EphA4 and EphB2 participate in the growth and development of various carcinomas. This study examined the relations of EphA4 and EphB2 gene expression to clinicopathological factors, especially metastasis, in patients with colorectal cancer. We studied surgical specimens of cancer tissue and adjacent normal mucosa obtained from 205 patients with untreated colorectal cancer. The relative expression levels of EphA4 and EphB2 mRNA in the specimens were measured by quantitative real-time, reverse-transcription polymerase chain reaction. The relative expression level of EphA4 mRNA was higher in the presence than in the absence of liver metastasis, whereas the relative expression levels of EphB2 mRNA were similar. Analysis of the relations between clinicopathological features and gene expression showed that high expression of the EphA4 gene and low expression of the EphB2 gene correlated with liver metastasis. There was no correlation between EphA4 and EphB2 gene expression. Our results suggest that over-expression of the EphA4 gene and reduced expression of the EphB2 gene might promote liver metastasis in colorectal cancer. Over-expression of the EphA4 gene and reduced expression of the EphB2 gene may thus be a useful predictor of liver metastasis in patients with colorectal cancer. No significant financial relationships to disclose.
Resonant slots (1946)

This paper describes how the coupling of a resonant half-wave slot to a rectangular wave guide in the wall of which the slot is cut, came to be studied in order to solve the problem of linear microwave radiators fed from wave guides. The methods of experimental investigation are described and the results are presented in terms of a method of representing the loading of the dominant wave in the guide. The important conception is the transformation of the circle-diagram variable (w) representing the dominant wave-system in the guide.It is shown that wave guides may be coupled by resonant slots. If such a slot is cut in the wall of a wave guide and lies opposite a registering slot in a second guide in contact with the first, the wave guides are coupled if the slot can be excited by the dominant wave in both guides. The type of coupling depends on the aspect of the slot in each guide.The laws of guide coupling are explained in terms of the manner in which impedance is transferred from the position of the slot centre guide 2 into guide 1 at the same position.The coupling of variable reactances to the guide by resonant slots to produce a T-section load is described, with experimental confirmation of the transformation of impedance and phase by the load. The method of radiation coefficients is applied to deduce the law of guide-coupling in the general case; it may be applied to treat loading and coupling of two waves in the same guide. Finally, directive aerial coupling by a pair of slots is discussed.Finally, the elements of the design problem for a linear microwave array and the theory of the wave-guide feed are discussed. Both transverse and longitudinal polarization are considered, together with the effects of mutual interaction between the inclined slots cut in the narrow face of the guide in the longitudinally-polarized array. The bandwidth of arrays is treated and a broad-band array of inclined-displaced slots in the broad face is described with measurements of its performance. The principle of the microwave Yagi aerial is briefly presented.
A self‐regulating cell culture analog device to mimic animal and human toxicological responses (1996)

The overall goal of this project is the development of a new methodology for translating advances in molecular level understanding of toxicological responses into a predictive tool for dose response in whole animals and humans exposed to single compounds or mixtures of compounds. The methodology incorporates a mechanistic cellular level model into a PBPK (physiologically based pharmacokinetic) model which simultaneously guides the development of an in vitro cell culture analog (CCA) to the PBPK. Where the PBPK specifies an organ, (e.g., liver) the in vitro or CCA system contains a compartment with the appropriate cell or cell population (e.g., hepatocytes for the liver). The CCA has significant advantages over other in vitro systems and PBPK systems used independently for evaluating metabolic responses to drugs or potentially toxic chemicals where the exchange of metabolites between organs is likely to be important. The CCA system is superior to a PBPK because an a priori description of complete metabolism is not required and secondary, unexpected interactions can be detected. The CCA system, unlike other in vitro systems, gives a dynamic response that realistically simulates in vivo interactions between organs. Furthermore, the CCA allows dosing on the same basis as animal tests (e.g., milligrams per kilogram of body mass equivalent). Because the construction of a CCA is guided by a PBPK, this approach allows extrapolation to low doses and across species, including extrapolation to humans. We have constructed a prototype system and have conducted proof-of-concept experiments using naphthalene as a test chemical. These experiments clearly demonstrate the ability to generate a reactive metabolite in one compartment and detect its effects (on LDH release and glutathione depletion) in a second compartment. However, this prototype device would be expensive to replicate and requires nearly constant supervision from a trained investigator. For this concept to replace animals an inexpensive, self-regulating device is needed. An initial design to accomplish this goal is described as well as the corresponding model using naphthalene as a test compound. © 1996 John Wiley & Sons, Inc.
Characterization of α-Ketoglutarate-dependent Taurine Dioxygenase from Escherichia coli (1997)

The Escherichia coli tauD gene is required for the utilization of taurine (2-aminoethanesulfonic acid) as a sulfur source and is expressed only under conditions of sulfate starvation. The sequence relatedness of the TauD protein to the alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase of Alcaligenes eutrophus suggested that TauD is an alpha-ketoglutarate-dependent dioxygenase catalyzing the oxygenolytic release of sulfite from taurine (van der Ploeg, J. R., Weiss, M. A., Saller, E., Nashimoto, H., Saito, N., Kertesz, M. A., and Leisinger, T. (1996) J. Bacteriol. 178, 5438-5446). TauD was overexpressed in E. coli to approximately 70% of the total soluble protein and purified to apparent homogeneity by a simple two-step procedure. The apparent Mr of 81,000 of the native protein and the subunit Mr of 37,400 were consistent with a homodimeric structure. The pure enzyme converted taurine to sulfite and aminoacetaldehyde, which was identified by high pressure liquid chromatography after enzymatic conversion to ethanolamine. The reaction also consumed equimolar amounts of oxygen and alpha-ketoglutarate; ferrous iron was absolutely required for activity; and ascorbate stimulated the reaction. The properties and amino acid sequence of this enzyme thus define it as a new member of the alpha-ketoglutarate-dependent dioxygenase family. The pure enzyme showed maximal activity at pH 6.9 and retained activity on storage at -20 degrees C for several weeks. Taurine (Km = 55 microM) was the preferred substrate, but pentanesulfonic acid, 3-(N-morpholino)propanesulfonic acid, and 1,3-dioxo-2-isoindolineethanesulfonic acid were also desulfonated at significant rates. Among the cosubstrates tested, only alpha-ketoglutarate (Km = 11 microM) supported significant dioxygenase activity.
Daily Stress Recognition from Mobile Phone Data, Weather Conditions and Individual Traits (2014)

Research has proven that stress reduces quality of life and causes many diseases. For this reason, several researchers devised stress detection systems based on physiological parameters. However, these systems require that obtrusive sensors are continuously carried by the user. In our paper, we propose an alternative approach providing evidence that daily stress can be reliably recognized based on behavioral metrics, derived from the user's mobile phone activity and from additional indicators, such as the weather conditions (data pertaining to transitory properties of the environment) and the personality traits (data concerning permanent dispositions of individuals). Our multifactorial statistical model, which is person-independent, obtains the accuracy score of 72.28% for a 2-class daily stress recognition problem. The model is efficient to implement for most of multimedia applications due to highly reduced low-dimensional feature space (32d). Moreover, we identify and discuss the indicators which have strong predictive power.
Raziel: Private and Verifiable Smart Contracts on Blockchains (2018)

Raziel combines secure multi-party computation and proof-carrying code to provide privacy, correctness and verifiability guarantees for smart contracts on blockchains. Effectively solving DAO and Gyges attacks, this paper describes an implementation and presents examples to demonstrate its practical viability (e.g., private and verifiable crowdfundings and investment funds). Additionally, we show how to use Zero-Knowledge Proofs of Proofs (i.e., Proof-Carrying Code certificates) to prove the validity of smart contracts to third parties before their execution without revealing anything else. Finally, we show how miners could get rewarded for generating pre-processing data for secure multi-party computation.
Identification of Erbin Interlinking MuSK and ErbB2 and Its Impact on Acetylcholine Receptor Aggregation at the Neuromuscular Junction (2010)

Erbin, a binding partner of ErbB2, was identified as the first member of the LAP family of proteins. Erbin was shown at postsynaptic membranes of the neuromuscular junction (NMJ) or in cultured C2C12 myotubes (1) to be concentrated, (2) to regulate the Ras-Raf-Mek pathway, and (3) to inhibit TGF-beta signaling. In the CNS, Erbin interacts with PSD-95. Furthermore, agrin-MuSK signaling initiates formation of AChR aggregates at the postsynaptic membrane. In search of proteins interacting with MuSK, we identified Erbin as a MuSK binding protein. We verified the interaction of MuSK with Erbin, or both concomitantly with ErbB2 by coimmunoprecipitation, and we mapped the interacting epitopes between Erbin and MuSK. We demonstrated elevated mRNA levels of Erbin at synaptic nuclei and colocalized Erbin and MuSK at postsynaptic membranes. We identified several Erbin isoforms at the NMJ, all of which contained the MuSK binding domain. By knocking down Erbin, we observed agrin-dependent AChR aggregates on murine primary skeletal myotubes and C2C12 cells, and in the absence of agrin, microclusters, both of significantly lower density. Complementary, AChR-epsilon-reporter expression was reduced in myotubes overexpressing Erbin. We show that myotubes also express other LAP protein family members, namely Scribble and Lano, and that both affect physical dimensions of agrin-dependent AChR aggregates and density of microclusters formed in the absence of agrin. Moreover, MuSK-Erbin-ErbB2 signaling influences TGF-beta signaling. Our data define the requirement of Erbin on the cross talk between agrin and neuregulin signaling pathways at the NMJ.
Macro Testing: Unifying IC And Board Test (1986)

Historically, IC testing and board testing have been considered two separate subjects. However, today's increasing complexity in both design and technology has given rise to a number of efforts to produce a consistent test strategy that smoothly couples both types of testing. This article describes one such effort by Philips, a design for testability methodology for semicustom VLSI circuits. The methodology is based on the partitioning of a design into testable macros, hence the term "macro testing." The challenges in this approach are the partitioning itself, the selection of a test technique suited to the separate macros and the chip's architecture, the execution of a macro test independent of its environment, and the assembly of macro tests into a chip test.