gebhart/patrepeval huggingface dataset:
The plant signal salicylic acid shuts down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium (2007)

Agrobacterium tumefaciens is capable of transferring and integrating an oncogenic T-DNA (transferred DNA) from its tumor-inducing (Ti) plasmid into dicotyledonous plants. This transfer requires that the virulence genes (vir regulon) be induced by plant signals such as acetosyringone in an acidic environment. Salicylic acid (SA) is a key signal molecule in regulating plant defense against pathogens. However, how SA influences Agrobacterium and its interactions with plants is poorly understood. Here we show that SA can directly shut down the expression of the vir regulon. SA specifically inhibited the expression of the Agrobacterium virA/G two-component regulatory system that tightly controls the expression of the vir regulon including the repABC operon on the Ti plasmid. We provide evidence suggesting that SA attenuates the function of the VirA kinase domain. Independent of its effect on the vir regulon, SA up-regulated the attKLM operon, which functions in degrading the bacterial quormone N-acylhomoserine lactone. Plants defective in SA accumulation were more susceptible to Agrobacterium infection, whereas plants overproducing SA were relatively recalcitrant to tumor formation. Our results illustrate that SA, besides its well known function in regulating plant defense, can also interfere directly with several aspects of the Agrobacterium infection process.
Control of Leishmania major by a Monoclonal αβ T Cell Repertoire (1998)

Abstract Little is known regarding the diversity of the host T cell response that is required to maintain immunologic control of microbial pathogens. Leishmania major persist as obligate intracellular parasites within macrophages of the mammalian host. Immunity is dependent upon activation of MHC class II-restricted T cells to an effector state capable of restricting growth and dissemination of the organisms. We generated α-β Leishmania-specific (ABLE) TCR transgenic mice with MHC class II-restricted T cells that recognized an immunodominant Leishmania Ag designated LACK. Naive T cells from ABLE mice proliferated in vitro after incubation with recombinant LACK or with Leishmania-parasitized macrophages and in vivo after injection into infected mice. Infected ABLE mice controlled Leishmania infection almost as well as wild-type mice despite a drastic reduction in the T cell repertoire. ABLE mice were crossed to mice with disruption of the TCR constant region α gene to create animals with a single αβ T cell repertoire. Although mice deficient in all αβ T cells (TCR-Cαo mice) failed to control L. major, mice with a monoclonal αβ T cell repertoire (ABLE TCR-Cαo mice) displayed substantial control. The immune system is capable of remarkable efficiency even when constrained to recognition of a single epitope from a complex organism.
Dancing on a Fullerene Surface: Isomerization of Y3N@(N‐Ethylpyrrolidino‐C80) from the 6,6 to the 5,6 Regioisomer (2006)

Dancing partners: Density functional calculations have been used to unravel the different reactivity of endohedral metallofullerenes M3N@C80 (M=Sc or Y) with respect to 1,3-dipolar N-ethylazomethine cycloaddition. The mechanism for the isomerization of Y3N@(N-ethylpyrrolidino-C80) from the 6,6 to the 5,6 regioisomer during thermalization of the kinetically favored product is proposed to involve a “dancing” of the pyrrolidine on the fullerene surface.
Calibration of Schlieren Systems (1965)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Jurgen R. Meyer-Arendt and Eric P. Shettle, "Calibration of Schlieren Systems," Appl. Opt. 4, 757-757 (1965) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Phonon annihilation and excited-state absorption processes inSm2+:BaClF (1984)

Using selective pulsed laser excitation into the first metastable excited state $^{5}D_{0}$ of the ${\mathrm{Sm}}^{2+}$:BaClF system, we have observed an anti-Stokes fluorescence originating from the $^{5}D_{1}$ multiplet located at 1339 ${\mathrm{cm}}^{\ensuremath{-}1}$ above $^{5}D_{0}$ at temperatures ranging from 295 to 650 K. At long times after the laser pulse, the $^{5}D_{1}$ and $^{5}D_{0}$ fluorescences decay exponentially with the same time constant. At shorter times, the $^{5}D_{1}$ emission exhibits either an initial rise or a fast decay depending on the laser beam intensity, the $^{5}D_{0}$ fluorescence decay remaining purely exponential in any case. Under the same excitation conditions but at low temperature, we have also observed the anti-Stokes fluorescence from the $^{5}D_{2}$ multiplet located at 3280 ${\mathrm{cm}}^{\ensuremath{-}1}$ above the $^{5}D_{0}$ pumping state, in addition to that originating from $^{5}D_{1}$. These new experiments give direct evidence of phonon annihilation and excited-state absorption processes in the ${\mathrm{Sm}}^{2+}$:BaClF system.
Analyzing the Capacity of Distributed Vector Representations to Encode Spatial Information (2020)

Vector Symbolic Architectures belong to a family of related cognitive modeling approaches that encode symbols and structures in high-dimensional vectors. Similar to human subjects, whose capacity to process and store information or concepts in short-term memory is subject to numerical restrictions, the capacity of information that can be encoded in such vector representations is limited and one way of modeling the numerical restrictions to cognition. In this paper, we analyze these limits regarding information capacity of distributed representations. We focus our analysis on simple superposition and more complex, structured representations involving convolutive powers to encode spatial information. In two experiments, we find upper bounds for the number of concepts that can effectively be stored in a single vector only depending on the dimensionality of the underlying vector space.
Modeling bias sputter planarization of metal films using a ballistic deposition simulation (1991)

A simulation by ballistic deposition model (SIMBAD) has been developed to predict thin-film microstructures of films deposited over topography. In order to study the radio frequency (rf) bias planarization process, this model has been extended to include film resputtering, redeposition, ion reflection, and ion-induced diffusion. To test the resulting SIMBAD simulations, tungsten was bias sputter deposited over high aspect ratio grooves. The resulting films exhibited increased sidewall coverage and planarity. Ion milling effects were also observed. These features were qualitatively matched by SIMBAD predictions as were microstructural details, such as column orientations and void locations. This preliminary success shows that such SIMBAD simulations can be useful in understanding and optimizing the rf bias planarization process.
Regulatory domains of erythrocyte ankyrin. (1987)

This report provides evidence for regulatory domains of erythrocyte ankyrin that modulate associations of this protein with the anion transporter and spectrin. Two domains have been identified that are located at opposite ends of the polypeptide chain. One domain (Mr = 20,000), which is released by calpain, is primarily involved in regulation of the association of ankyrin with the anion transporter. The Mr = 195,000 fragment remaining after calpain cleavage binds to ankyrin-depleted inside-out vesicles with a 8-fold reaction in affinity, although with a 2-fold increase in number of high affinity sites. Cleavage of ankyrin by calpain induces a reduction in the frictional ratio from 1.55 to 1.33 suggesting either that the calpain-sensitive domain is present as a tail extending from a globular domain, or that upon cleavage ankyrin undergoes a major change in conformation. The other proposed regulatory domain is missing in protein 2.2, a form of ankyrin present in human erythrocytes that has a molecular weight about 29,000 smaller than ankyrin. Protein 2.2 is distinct from the calpain fragment based on peptide maps and reaction with domain-specific antibodies. The activity of the domain deleted from protein 2.2 has been inferred by comparison of ankyrin and protein 2.2, with the assumption that differences between these proteins are due to the missing domain. Protein 2.2 is an activated form of ankyrin that has a 3-fold higher affinity for spectrin and binds to twice the number of high affinity anion transporter sites. These observations suggested that removal of terminal domains of ankyrin may have a physiological role in modulation of ankyrin activity.
CFS Biomarkers in Parkinson’s Disease (2011)

In the recent years increasing attention on biomarkers for neurodegenerative diseases, including Parkinson's disease (PD), has been paid. The reasons of this growing tendency are several: (i) PD is one of the most common neurodegenerative diseases, affecting approximately 1% of people over 60 years of age Diagnosis of PD is based on clinical criteria, relying on motor features: rigidity, bradykinesia, resting tremor and in the late stages postural instability However, clinical diagnosis especially in the early stages of disease can be challenging owing to the difficult differential diagnosis with essential tremor and atypical parkinsonism, namely multiple system atrophy (MSA), progressive sopranuclear palsy (PSP), and corticobasal degeneration (CBD). Although in movement disorder specialized settings the diagnostic accuracy is satisfactory (80%), almost one third of the clinical diagnoses in patients with parkinsonism is revised in the first five years of disease Diagnostic accuracy in the early stages of disease is important, in view of forthcoming disease-modifying therapies In this perspective, diagnostic biomarkers are urgently needed. (ii) Also, there is the need for progression biomarkers, ie, parameters reflecting a feature associated with disease-severity (iii) Finally, PD per se is a heterogeneous disease, with different clinical phenotypes (the akinetic-rigid type vs. the tremor dominant variant) and different etiologies (genetic vs. sporadic form), which might have different progression rate, prognosis, thus requiring different therapeutic approaches. PD is not merely a motor disorder. Recently, great attention has been drawn to non-motor symptoms, namely cognitive decline, behavioural changes, sleep disorders and autonomic dysfunction, due to their relevant impact on quality of life of parkinsonian patients Both in early and in advanced stages, these symptoms represent a challenge in the clinical management of PD
MVH in piRNA processing and gene silencing of retrotransposons (2010)

VASA is an evolutionarily conserved RNA helicase essential for germ cell development. The mouse PIWI family proteins MILI and MIWI2 are involved in production of Piwi-interacting RNAs (piRNAs) in fetal male germ cells through a ping-pong amplification cycle. Expression of retrotransposons is elevated in MILI- and MIWI2-deficient male germ cells due to defective de novo DNA methylation, which is presumably caused by impaired piRNA expression. Here, we report that essentially the same abnormalities are observed in MVH (mouse VASA homolog)-deficient mice. Comprehensive analysis of piRNAs in MVH-deficient fetal male germ cells showed that MVH plays crucial roles in the early phase of the ping-pong amplification cycle.
Protein Tyrosine Phosphatase-μ Differentially Regulates Neurite Outgrowth of Nasal and Temporal Neurons in the Retina (2002)

Cell adhesion molecules play an important role in the development of the visual system. The receptor-type protein tyrosine phosphatase, PTPmu is a cell adhesion molecule that mediates cell aggregation and may signal in response to adhesion. PTPmu is expressed in the chick retina during development and promotes neurite outgrowth from retinal ganglion cell (RGC) axons in vitro (Burden-Gulley and Brady-Kalnay, 1999). The axons of RGC neurons form the optic nerve, which is the sole output from the retina to the optic tectum in the chick. In this study, we observed that PTPmu expression in RGC axons occurs as a step gradient, with temporal axons expressing the highest level of PTPmu. PTPmu expression in the optic tectum occurred as a smooth descending gradient from anterior to posterior regions during development. Because temporal RGC axons innervate anterior tectal regions, PTPmu may regulate the formation of topographic projections to the tectum. In agreement with this hypothesis, a differential response of RGC neurites to a PTPmu substrate was also observed: RGCs of temporal retina were unable to extend neurites on PTPmu compared with neurites of nasal retina. When given a choice between PTPmu and a second substrate, the growth cones of temporal neurites clustered at the PTPmu border and stalled, thus avoiding additional growth on the PTPmu substrate. In contrast, PTPmu was permissive for growth of nasal neurites. Finally, application of soluble PTPmu to retinal cultures resulted in the collapse of temporal but not nasal growth cones. Therefore, PTPmu may specifically signal to temporal RGC axons to cease their forward growth after reaching the anterior tectum, thus allowing for subsequent innervation of deeper tectal layers.
A 155 MHz clock recovery delay- and phase-locked loop (2003)

The authors describe a completely monolithic delay-locked loop (DLL) which may be used either by itself as a deskewing element or in conjunction with an external voltage-controlled crystal oscillator (VCXO) for a delay- and phase-locked loop (D/PLL) that enables jitter-peaking-free clock recovery by removing the zero from the forward path. The voltage-controlled phase shifter (VCPS) shifts incoming data under loop control to align the data with the clock. The loop amplifier is an integrator so that the DLL is first order. The bandwidth of the loop determines the frequencies over which input jitter may be tracked out. The phase detector is a pattern-and duty-cycle insensitive implementation. The higher-order poles provide additional filtering of phase-detector output ripple to further improve jitter accommodation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stream Power Application for Bridge-Damage Probability Mapping Based on Empirical Evidence from Tropical Storm Irene (2017)

On August 28, 2011, Tropical Storm Irene hit the state of Vermont with a severity that deposited 100–200 mm (4–8 in.) of rain across the state and resulted in damage or failure of over 300 bridges. The analysis of available data sets helped identify a set of 313 bridges (with a span greater than 6 m) damaged in a single state from a single extreme flood event that caused a 12-h rainfall recurrence interval that exceeded 500 years in some areas and 100 years throughout most of the affected areas. Based on available damage reports and photographs, the observed bridge damage was grouped into four levels of severity. This paper links watershed stream power to the observed bridge damage, develops a process for quantifying the hazard at bridges both as a case study and for future storms, and uses stream power as a hazard metric to produce probabilistic predictions of bridge vulnerability. The analysis also offers a comparison between damaged bridges and bridges that were not damaged in Tropical Storm Irene. Specific stream power (SSP) and the event-based Irene-specific stream power (ISSP) were computed and found to be both statistically significant at discriminating between damaged and nondamaged bridges, as well as between damage levels. The application of the empirical fragility curve analysis for SSP and ISSP produces a probability of damage generated from the results collected from Tropical Storm Irene. Spatially mapping the bridge-damage probability from an extreme event like Tropical Storm Irene enables the hazard to be effectively displayed over a broad range of scales (e.g., stream reaches, select watershed, statewide). The methodology presented here can be applied to other geographic settings and storm events of interest, and to the best of the authors’ knowledge, this is the first investigation comparing site-specific stream power to observed bridge damage at a network level.
Rate of hydrogen evolution by immobilized resting cells of Enterobacter aerogenes. (1988)

Resting cells of E. aerogenes strain E. 82005 evolved hydrogen at a speed of 28 ml / (g-dry cell.h) from glucose. The evolution rate of the resting cells was stabilized by immobilization with calcium alginate in a wide range of pH from 4.5 to 7.5. Since the rate (ca. 58 ml/ (g-dry cell. h)) was greater than that of growing cells below pH 5 and above pH 7, hydrogen evolution under these particular conditions could be enhanced by immobilizing the cells.
Understanding each other (2000)

Although natural language is ambiguous, various linguistic and extra-linguistic factors often help determine a preferred reading. In this paper, we show that model generation can be used to model this process in the case of reciprocal statements. The proposed analysis builds on insights from Dalrymple et al. 98 and is shown to provide an integrated, computational account of the interplay between model theoretic interpretation, knowledge-based reasoning and preferences that characterises the interpretation of reciprocals.
Alternative techniques for the efficient acquisition of haptic data (2001)

Immersive environments are those that surround users in an artificial world. These environments consist of a composition of various types of immersidata: unique data types that are combined to render a virtual experience. Acquisition, for storage and future querying, of information describing sessions in these environments is challenging because of the real-time demands and sizeable amounts of data to be managed. In this paper, we summarize a comparison of techniques for achieving the efficient acquisition of one type of immersidata, the haptic data type, which describes the movement, rotation, and force associated with user-directed objects in an immersive environment. In addition to describing a general process for real-time sampling and recording of this type of data, we propose three distinct sampling strategies: fixed, grouped, and adaptive. We conducted several experiments with a real haptic device and found that there are tradeoffs between the accuracy, efficiency, and complexity of implementation for each of the proposed techniques. While it is possible to use any of these approaches for real-time haptic data acquisition, we found that an adaptive sampling strategy provided the most efficiency without significant loss in accuracy. As immersive environments become more complex and contain more haptic sensors, techniques such as adaptive sampling can be useful for improving scalability of real-time data acquisition.
Selection of Radioresistant Cells by Vitamin A Deficiency in a Small Cell Lung Cancer Cell Line (1990)

Radiation sensitivity of a human small cell lung cancer cell line, Lu-134-B cells, cultured in serum-supplemented medium and of cells transferred to and cultured in delipidized serum-supplemented (vitamin A-deficient) medium was studied. The cells cultured in serum-supplemented medium showed the phenotype of classic small cell lung cancer sensitive to radiation, while cells transferred to delipidized serum-supplemented medium showed partial squamous cell differentiation and became resistant to radiation. These results suggest that some small cell lung cancer cells in vitro change their morphology and radiosensitivity depending on the culture conditions. The change in radiosensitivity was reproducible, and was not reversible by culture of the radioresistant cells in delipidized serum-supplemented medium with addition of retinoic acid (vitamin A-sufficient medium) for two months, although squamous cells disappeared. Acquisition of radioresistancy was considered to occur as the result of clonal selective growth in delipidized medium of a minor cell population in the original cell culture, based on a study of chromosome number. It was also found that there was no association of myc-family oncogenes with the changes of radiosensitivity in this cell line.
Transcriptional regulation of precore and pregenomic RNAs of hepatitis B virus (1992)

Hepatitis B virus (HBV) infection, either acute or chronic, has been one of the leading health problems in the world. To understand the HBV life cycle and disease process, we set out to study the regulation of viral gene expression. In this paper, we report the characterization of the HBV core promoter: two 3.5-kb transcripts, precore and pregenomic, are made from it. The latter is itself a template for viral genome replication and also encodes viral proteins essential for both viral replication and virion assembly. We identify a short sequence (from nucleotides [nt] 1744 to 1851, referred to as the basic core promoter [BCP]) that is sufficient to direct correct initiation of both precore and pregenomic messages. In addition, the two appear to be regulated in a coordinate manner. Sequences upstream of the BCP (from nt 1636 to 1744, referred to as the core upstream regulatory sequence [CURS]), have a strong stimulating effect on the BCP. Addition of the CURS to the BCP leads to a dramatic increase in both the transcription of two 3.5-kb messages and the production of 42-nm virions from transiently transfected hepatoma cells. The CURS stimulates the BCP in a position- and orientation-dependent manner. Therefore, it is unlikely that the effect is mediated through enhancer II, which has been localized to the same sequence. Deletion analysis of the CURS suggests that it contains multiple regulatory elements that control the BCP in an interactive manner. In accord with this hypothesis, the CURS is found to be bound with many distinct protein factors in footprinting experiments. Among these elements, box alpha (from nt 1646 to 1668) and box gamma delta (from nt 1671 to 1703) are two regulatory elements which individually stimulate promoter activity more than 100-fold.
Searching for BRCA3 by exome sequencing (2012)

The current paradigm suggests that some non-BRCA1/2 multiple case breast cancer families are caused by rare mutations in high-risk genes. We are using exome sequencing to identify putative ‘BRCA3’ genes in a small number of kConFab families. We selected five non-BRCA1/2 families containing 5-9 breast cancer cases (of which 0-4 per family were affected under the age of 40) who have had extensive analysis of BRCA1 and BRCA2, and for which germline DNA was available from two distant relatives (at least 4th degree) affected with breast cancer between 30 and 56 years of age. In first stage we isolated the exomes of two pairs of affected individuals (4th and 5th degree relatives, from two families) diagnosed with breast cancer between the age of 30 and 39, using the SeqCap EZ exome capture kit (NimbleGen) and then sequenced the libraries on the GAIIx and HiSeq (Illumina) platforms with a paired-end protocol. The sequences were aligned to the human genome with BWA and we then compared several pipelines for processing the sequences and calling variants. The best results were obtained with the Picard/GATK pipeline after local re-alignment and re-calibration of the base quality. The samples from the remaining three families will be sequenced by Axeq Inc. and the results of the analysis will be presented.