gebhart/patrepeval huggingface dataset:
Two Unique Phosphorylation-Driven Signaling Pathways Crosstalk in <i>Staphylococcus aureus</i> to Modulate the Cell-Wall Charge: Stk1/Stp1 Meets GraSR (2013)

The Stk1/Stp1 and GraSR signal-transduction pathways are two distinct pathways in Staphylococcus aureus that rely on a reversible phosphorylation process in transducing external stimuli intracellularly. Stk1/Stp1 is an eukaryote-like Ser/Thr kinase phosphatase pair involved in purine biosynthesis, cell-wall metabolism, and autolysis. GraSR is a two-component system involved in resistance to cationic antimicrobial peptides. Both systems are implicated in S. aureus virulence and resistance to cell-wall inhibitors. Our study shows that the response regulator protein GraR undergoes phosphorylation by Stk1 at three threonine residues in the DNA-binding domain. Phosphorylation by Stk1 depends on the structural integrity of GraR as well as the amino acid sequences flanking the phosphorylation sites. Its homologue in Bacillus subtilis , BceR, which harbors two of the three phosphorylation sites in GraR, does not undergo Stk1-dependent phosphorylation. GraR is involved in regulation of the dltABCD operon, the gene products of which add the d-Ala on wall teichoic acid (WTA). Investigation of WTA isolated from the S. aureus RN6390 ΔgraR strain by NMR spectroscopy showed a clear negative effect that graR deletion has on the d-Ala content of WTA. Moreover, complementation of ΔgraR mutant with graR lacking the Stk1 phosphorylation sites mirrors this effect. These findings provide evidence that GraR is a target of Stk1 in vivo and suggest that modification of WTA by d-Ala is modulated by Stk1. The crosstalk between these two otherwise independent signaling pathways may facilitate S. aureus interaction with its environment to modulate processes such as cell growth and division and virulence.
ALBERTI AND THE VERNACULAR ECLOGUE IN THE QUATTROCENTO (1956)

‘Scripsitque per ea tempora animi gratia complurima opuscula: Ephebiam, de Religione, Deiphiram, et pleraque huiusmodi soluta oratione; tum et versu, Elegias, Eclogasque; atque Conciones, et eiuscemodi amatoria ….‘ So runs the Vita Anonima of L. B. Alberti, by some scholars attributed to the author himself, though in my opinion erroneously. This is not, however, the problem which interests us here, but instead the affirmation that Alberti wrote Eclogues, a statement which is further supported by the praises of Cristoforo Landino who claims: ‘Ha scritto Batista Alberti egloghe et elegie tali, che in quelle molto bene osserva e pasturali costumi et in queste è maraviglioso in exprimere, anzi quasi dipigniere tutti gli affetti et perturbazioni amatorie.’ We possess two compositions, Agiletta and Mirzia, which correspond to the description of Elegies, both written in ‘terza rima’ and dealing with love complaints. In subject they are akin to others of his works in prose, particularly the Deijira. On the other hand, only one composition of Alberti has up to the present been known with the qualification of Eclogue, his Corimbo, to which some importance has been accorded by Carrara for its ‘intenzione pastorale.’ In its form, ‘terza rima’ with a ‘ballata’ in the middle, and theme, the love lament of the ‘giovinetto averniese’ followed by the consolations of Batista, this eclogue comes nearer to the pastoral than the Elegies, but scarce qualifies for Landino's praise cited above. Certainly there is nothing here of that Virgilian imitation, which Alberti claims elsewhere to have indulged in, and Carrara had some justification for letting this contribution to the history of the pastoral, and the vernacular eclogue in particular, go at half a page. The possibility of the composition by Alberti of more than one eclogue aroused Mancini's interest but seemed ‘assai tenue’ to Carrara. It is now proved correct at least to the extent of one more by the coming to light of a truly pastoral eclogue in Italian, which may well stand at the beginning of that phenomenal vogue of the pastoral in the vernacular, which from Florence, Ferrara and Naples passed in various forms to the whole of European literature.
Triarylamine: a promising core unit for efficient photovoltaic materials (2009)

Triarylamine has been widely used in opto- and electro-active materials for its good electron donating and transporting capability, as well as its special propeller starburst molecular structure. Recently, organic photovoltaic functional materials with triarylamine as electron donor have aroused great interest and become the focus of intensive research in the field of solar cells. These materials have significantly reinforced the conversion efficiency of next-generation solar cells, especially dye sensitized solar cells. This Feature Article describes new synthetic methods and the application of starburst triarylamines, highlighting the applications in photovoltaic and optoelectrical fields.
Companion cell‐specific inhibition of the potato sucrose transporter SUT1 (1996)

ABSTRACT In many plants, translocation of sucrose from mesnsophyll to phloem for long‐distance transport is carrier‐mediated. The sucrose H + ‐symporter gene SUT1 from potato is expressed at high levels in the phloem of mature, exporting leaves and at lower levels in other organs. Inhibition of SUT1 by expression of an antisense gene in companion cells under control of the rolC promoter leads to accumulation of high amounts of soluble and insoluble carbohydrates in leaves and inhibition of photosynthesis. The distribution of in situ localized starch does not correspond with areas of reduced photosynthesis as shown by fluorescence imaging. Dissection of antisense effects on sink and source organs by reciprocal grafts shows that inhibition of transporter gene expression in leaves is sufficient to produce chlorosis in leaves and reduced tuber yield. In contrast to the arrest of plasmodesmal development found in plants that express yeast invertase in the apoplast, in mature leaves of sucrose transporter antisense plants plasmodesmata are branched and have median cavities. These data strongly support an apoplastic mode of phloem loading in potato, in which the sucrose transporter located at the plasma membrane of the sieve element/companion cell complex represents the primary route for sugar uptake into the long‐distance translocation pathway.
Distributed debugging and Tumult (2002)

A description is given of Tumult (Twente university multicomputer) and its operating system, along with considerations about parallel debugging, examples of parallel debuggers, and the proposed debugger for Tumult. Problems related to debugging distributed systems and solutions found in other distributed debuggers are discussed. The following are the main features of the debugger: it is event based, using a monitor for intercepting these events; record and reply are the main debugging techniques; preprocessing of events is done by programmable filters; the user interface is graphical, using grouping as the main abstraction mechanism. Parts of the debugger, as well as initial versions of the global and local event managers, have been implemented. A slow serial link between the front-end processor and the Tumult system has been replaced by a fast SCSI communication link. The user interface is partly textual, partly graphical. The languages used to implement the debugger are Modula-2 and C. The X Window System and OSF/Motif are used for the graphical user interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Functional Packaging of Lateral Flow Strip Allows Simple Delivery of Multiple Reagents for Multistep Assays (2016)

This paper presents a rotary device designed for facile delivery of multiple reagents to a paper strip for multistep assays. Its purpose is to allow users to easily perform multistep assays and achieve sensitive detection. While the test strip remains stationary, rotating the top piece of the device aligns the reagent and absorbent pads to each end of the paper strip and initiates fluid flow. Further incremental rotation makes an adjacent pair of pads to align simultaneously, causing fluid flow of subsequent reagent that was preloaded in the reagent pad. In this work, various porous substrates were tested to observe their effect on overall flow rate of the system and multistep assays were performed to demonstrate its simple use. As a proof of concept, enzyme-linked immunosorbent assay was carried out to detect Escherichia coli O157:H7.
Enhanced Methods of Seasonal Adjustment (2021)

The effect of the conventional model-based methods of seasonal adjustment is to nullify the elements of the data that reside at the seasonal frequencies and to attenuate the elements at the adjacent frequencies. It may be desirable to nullify some of the adjacent elements instead of merely attenuating them. For this purpose, two alternative sets of procedures are presented that have been implemented in a computer program named SEASCAPE. In the first set of procedures, a basic seasonal adjustment filter is augmented by additional filters that are targeted at the adjacent frequencies. In the second set of procedures, a Fourier transform of the data is exploited to allow the elements in the vicinities of the seasonal frequencies to be eliminated or attenuated at will. The question is raised of whether an estimated trend-cycle trajectory that is devoid of high-frequency noise can serve in place of the seasonally adjusted data.
Systemic Autoimmunity and Lymphoproliferation Are Associated with Excess IL-7 and Inhibited by IL-7Rα Blockade (2011)

Lupus is characterized by disturbances in lymphocyte homeostasis, as demonstrated by the marked accumulation of activated/memory T cells. Here, we provide evidence that proliferation of the CD8+ precursors for the accumulating CD4⁻CD8⁻ T cells in MRL-Fas(lpr) lupus-predisposed mice is, in part, driven by commensal antigens. The ensuing lymphadenopathy is associated with increased production of IL-7 due to expansion of fibroblastic reticular cells, the primary source of this cytokine. The excess IL-7 is not, however, consumed by CD4⁻CD8⁻ T cells due to permanent down-regulation of IL-7Rα (CD127), but instead supports proliferation of autoreactive T cells and progression of autoimmunity. Accordingly, IL-7R blockade reduced T cell activation and autoimmune manifestations even when applied at advanced disease stage. These findings indicate that an imbalance favoring production over consumption of IL-7 may contribute to systemic autoimmunity, and correction of this imbalance may be a novel therapeutic approach in lymphoproliferative and autoimmune syndromes.
Anatomically and Physiologically Based Guidelines for Use of the Sphenopalatine Ganglion Block Versus the Stellate Ganglion Block to Reduce Atypical Facial Pain (2001)

This literature review is designed to develop guidelines needed for the use of a sphenopalatine ganglion block versus a stellate ganglion block to reduce atypical facial pain. We have reviewed the basic anatomy of both ganglia and the physiological responses usually associated with each, and have given an opinion on appropriate use of these therapeutic modalities.
Data-Driven Based Approach to Aid Parkinson’s Disease Diagnosis (2019)

This article presents a machine learning methodology for diagnosing Parkinson’s disease (PD) based on the use of vertical Ground Reaction Forces (vGRFs) data collected from the gait cycle. A classification engine assigns subjects to healthy or Parkinsonian classes. The diagnosis process involves four steps: data pre-processing, feature extraction and selection, data classification and performance evaluation. The selected features are used as inputs of each classifier. Feature selection is achieved through a wrapper approach established using the random forest algorithm. The proposed methodology uses both supervised classification methods including K-nearest neighbour (K-NN), decision tree (DT), random forest (RF), Naïve Bayes (NB), support vector machine (SVM) and unsupervised classification methods such as K-means and the Gaussian mixture model (GMM). To evaluate the effectiveness of the proposed methodology, an online dataset collected within three different studies is used. This data set includes vGRF measurements collected from eight force sensors placed under each foot of the subjects. Ninety-three patients suffering from Parkinson’s disease and 72 healthy subjects participated in the experiments. The obtained performances are compared with respect to various metrics including accuracy, precision, recall and F-measure. The classification performance evaluation is performed using the leave-one-out cross validation. The results demonstrate the ability of the proposed methodology to accurately differentiate between PD subjects and healthy subjects. For the purpose of validation, the proposed methodology is also evaluated with an additional dataset including subjects with neurodegenerative diseases (Amyotrophic Lateral Sclerosis (ALS) and Huntington’s disease (HD)). The obtained results show the effectiveness of the proposed methodology to discriminate PD subjects from subjects with other neurodegenerative diseases with a relatively high accuracy.
Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome (2011)

Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level.
Preparation of Zeolite Catalysts for Production of Lower Olefins from Methanol (1981)

Mobil Oil 社から発表されているZSM-5ゼオライト (触媒A) の調製法を改良し, メタノールからの低級オレフィン炭化水素合成に高い選択性を有するゼオライト (触媒B) を調製した。触媒A, Bともメタノールの転化反応における活性の経時変化は少なかった。触媒AとBを比較すると, 同転化率では低級オレフィンの選択率は触媒Bの方が約1.5倍高かった。触媒Bの選択性に対するSiO2/Al2O3比の影響を検討した。SiO2/Al2O3比の増加と共に活性が低下した。また, SiO2/Al2O3比を高くすると低級オレフィンへの選択率が増加し, 芳香族炭化水素へのそれは減少する傾向を示した。
EFFECTS OF OESTRADIOL AND PROSTAGLANDIN F2α ON THE TIMING OF PARTURITION IN THE RAT (1974)

Summary. Groups of rats were treated with oestradiol or PGF2α, or both, at various times between Days 19 and 21 of pregnancy and the times of onset of parturition were recorded. On Day 20, oestradiol (10 μg/rat) appeared to delay the onset of parturition in those rats which would otherwise have littered in the early part of the normal range, so that all the rats went into labour in the later part of that range. On Day 21, oestradiol (10 μg/rat) advanced the time of littering in about half the rats, but delayed parturition in about 30%. Prostaglandin F2α (4×25 μg) on Day 19 or Day 20 caused all the rats to litter prematurely, but PGF2α (2×25 μg) on Day 21 advanced parturition only in rats which normally produced late litters. When oestradiol (10 μg/rat) was given on Day 20 or 21, following treatment with PGF2α (4×25 μg) on Day 19 or Day 20, the spread of times of onset of parturition was reduced. It is postulated that (a) the final changes in preparation for parturition in rats are initiated at different times in different animals between late evening on Day 20 and early evening on Day 21, about 45 hr before parturition; (b) these changes, once started, probably take comparable times in different animals. The spread of times of parturition normally seen is thus attributed to the variation in the time at which the preparations begin and not in the length of time required for their completion; and (c) the first phase of the preparations involves prostaglandin-mediated luteolysis, and that this is followed by a final oestrogen-dependent phase which begins when progesterone concentration falls below a critical level and that of oestrogen attains a critical level. Oestradiol on Day 20 may have a direct or indirect luteotrophic action in rats close to the onset of luteolysis at the time of dosing, thus causing retardation of luteolysis and delay of littering. The advance of littering in many rats after oestradiol treatment on Day 21 is attributed to acceleration of the final phase of preparations for parturition in those rats at advanced stages of luteolysis at the time of dosing. Rats in which parturition was delayed by oestradiol treatment on Day 21 are believed to be those in which luteolysis had not begun and in which oestradiol exerted a luteotrophic effect. The effects of exogenous PGF2α are all attributed to its luteolytic activity. An anti-inflammatory agent, fenclozic acid (50 mg/kg), given close to the time of parturition, neither delayed nor disturbed normal labour. This suggests that active prostaglandin biosynthesis at the time of parturition is not essential for the parturient activity of the uterus.
A practical semantic representation for natural language parsing (2004)

This thesis deals with the problem of building fast, accurate and portable parsers for natural language understanding. Our focus is a multi-domain dialogue system in which we need a deep linguistically-motivated parser to produce the representations of the input suitable for reasoning. In this dissertation, we are concerned with building parsers which have the wide coverage and portability offered by a general syntactic grammar without sacrificing parsing speed and accuracy. 
Our approach relies on a domain-independent deep parser and grammar which uses selectional restrictions to control parsing speed and accuracy. We develop a feature list representation as the basis for selectional restrictions, and a formal model for using selectional restrictions in a unification based framework. 
We then develop a lexicon design for multi-domain parsing and semantic interpretation. We show how the restrictions based on feature sets can be integrated with a traditional frame-based semantics, and extend our formal model to cover inheritance and defaults in the lexicon. We show that none of the existing large-scale ontologies and lexicons provide all the information necessary for parsing and semantic disambiguation, and we develop a parsing lexicon suitable for use with a wide-coverage grammar in multiple domains. 
Our domain-independent lexicon provides coverage and portability over four different application domains. To customize the representations produced by the parser for domain reasoning, we designed an architecture with mappings between our domain-independent ontology and a domain model. This architecture allows us to produce semantic representations optimally suited for different application domains. In addition, we use the mappings to specialize the lexicon for improved parsing speed and accuracy, and show that our specialization method significantly improves parsing performance. 
Finally, we develop a statistical model to learn selectional restrictions from corpora and show how it can be used to distinguish between acceptable and unacceptable verb-object pairs in data sets derived from our lexicon and from the World Street Journal corpus.
Preparation of Preforms for Fluoride Glass Fibers (1981)

Various dopants were added to 33BaF 2 -4GdF 3 -63ZrF 4 (mol%) glass to control the refractive index and some properties of the resultant glasses were investigated. It has become apparent that LiF, PbF 2 , AlF 3 and BiF 3 are useful dopants for controlling the refractive index of BaF 2 -GdF 3 -ZrF 4 glasses. Waveguide structure has been formed by casting a cladding glass melt around the core glass rod.
Fairness-aware machine learning: a perspective (2017)

Algorithms learned from data are increasingly used for deciding many aspects in our life: from movies we see, to prices we pay, or medicine we get. Yet there is growing evidence that decision making by inappropriately trained algorithms may unintentionally discriminate people. For example, in automated matching of candidate CVs with job descriptions, algorithms may capture and propagate ethnicity related biases. Several repairs for selected algorithms have already been proposed, but the underlying mechanisms how such discrimination happens from the computational perspective are not yet scientifically understood. We need to develop theoretical understanding how algorithms may become discriminatory, and establish fundamental machine learning principles for prevention. We need to analyze machine learning process as a whole to systematically explain the roots of discrimination occurrence, which will allow to devise global machine learning optimization criteria for guaranteed prevention, as opposed to pushing empirical constraints into existing algorithms case-by-case. As a result, the state-of-the-art will advance from heuristic repairing, to proactive and theoretically supported prevention. This is needed not only because law requires to protect vulnerable people. Penetration of big data initiatives will only increase, and computer science needs to provide solid explanations and accountability to the public, before public concerns lead to unnecessarily restrictive regulations against machine learning.
Hybrid bonding of Cu/Sn microbump and adhesive with silica filler for 3D interconnection of single micron pitch (2015)

This paper describes hybrid bonding technology of Cu/Sn microbumps and adhesive with silica filler for three-dimensional (3D) interconnection of single-micron pitch. We fabricated bonding structure composed of 8-µm pitch Cu/Sn bumps and uncured adhesive with by using combination process of resin-chemical mechanical polishing (CMP) and O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> /CHF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> plasma etching. Adhesive with silica filler is conventionally used for reduction of mechanical stress around microbumps by lowering CTE of underfill. With the bonding structure, the Cu/Sn microbumps and the adhesive were simultaneously bonded in N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> atmospheric pressure after surface treatment of Ar/H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> plasma irradiation. Results of scanning electron microscope (SEM) and scanning ion microscope (SIM) analyses show that Sn of microbumps was properly wetted on Cu film without resin and silica filler trapping. The adhesive was also bonded on Cu film in 6-µm gap between chips. The shear strength was 17.85 MPa. Therefore, proposed method is highly effective for hybrid bonding of single-micron pitch aimed at future ultra-high density 3D interconnection.
Flavonoid Complexes as Promising Anticancer Metallodrugs (2017)

Flavonoid metal complexes commonly exhibit an improvement of biological activity compared to the parent ligands. This chapter is focused on the antioxidant and anticanc-cer properties of flavonoid metal complexes, in correlation with their binding ability to vital macromolecules such as nucleic acids and serum proteins. Perspectives for an adequate formulation of these complexes were also discussed.