gebhart/patrepeval huggingface dataset:
(p)ppGpp: Still Magical? (2008)

The fundamental details of how nutritional stress leads to elevating (p)ppGpp are questionable. By common usage, the meaning of the stringent response has evolved from the specific response to (p)ppGpp provoked by amino acid starvation to all responses caused by elevating (p)ppGpp by any means. Different responses have similar as well as dissimilar positive and negative effects on gene expression and metabolism. The different ways that different bacteria seem to exploit their capacities to form and respond to (p)ppGpp are already impressive despite an early stage of discovery. Apparently, (p)ppGpp can contribute to regulation of many aspects of microbial cell biology that are sensitive to changing nutrient availability: growth, adaptation, secondary metabolism, survival, persistence, cell division, motility, biofilms, development, competence, and virulence. Many basic questions still exist. This review tries to focus on some issues that linger even for the most widely characterized bacterial strains.
H2AX: tailoring histone H2A for chromatin-dependent genomic integrity (2005)

During the last decade, chromatin research has been focusing on the role of histone variability as a modulator of chromatin structure and function. Histone variability can be the result of either post-translational modifications or intrinsic variation at the primary structure level: histone variants. In this review, we center our attention on one of the most extensively characterized of such histone variants in recent years, histone H2AX. The molecular phylogeny of this variant seems to have run in parallel with that of the major canonical somatic H2A1 in eukaryotes. Functionally, H2AX appears to be mainly associated with maintaining the genome integrity by participating in the repair of the double-stranded DNA breaks exogenously introduced by environmental damage (ionizing radiation, chemicals) or in the process of homologous recombination during meiosis. At the structural level, these processes involve the phosphorylation of serine at the SQE motif, which is present at the very end of the C-terminal domain of H2AX, and possibly other PTMs, some of which have recently started to be defined. We discuss a model to account for how these H2AX PTMs in conjunction with chromatin remodeling complexes (such as INO80 and SWRI) can modify chromatin structure (remodeling) to support the DNA unraveling ultimately required for DNA repair.
The Potential for Real-Time Traffic Crash Prediction (2005)

The development of freeway crash prediction models using intelligent transportation systems (ITS) archived data could be a substantial advancement in the field of real-time traffic management. Such models not only are expected to improve safety but also may go a long way to improve freeway operations by reducing incident-related congestion. Because there is a need to use real-time traffic data emanating from loop detectors, the approach differs distinctly from previous studies estimating crash frequencies or rates on a certain freeway section through aggregate measures of flow (such as average daily traffic or hourly volumes). Although the authors try to establish a relationship between the patterns in precrash data from detectors surrounding the crash location, it is imperative that the time of the historical crashes is known with precision. This feature proposes a shockwave and rule-based methodology to estimate the time of the crash and then identifies how much time and distance ahead of crash occurrence loop data may be used to predict the impending hazard. The final objective is to predict the possibility of crashes on freeways using real-time loop data.
Mapping Netrin Receptor Binding Reveals Domains of Unc5 Regulating Its Tyrosine Phosphorylation (2004)

Netrin and its receptors Unc5 and deleted in colorectal carcinoma (DCC) regulate axon guidance and cell migration. We defined domains involved in the interactions between netrin-1, DCC, and Unc5c. We show that Unc5 requires both Ig domains to interact with netrin. DCC binds through the fourth fibronectin type III domain, whereas netrin binds through multiple domains to both receptors. We examined the functional consequences of removing the netrin binding and nonbinding domains from Unc5 in vitro and in vivo. In human embryonic kidney 293 cells, removal of the netrin binding second Ig domain causes an increase in basal tyrosine phosphorylation, whereas removal of the netrin nonbinding thrombospondin domains decreases tyrosine phosphorylation. Moreover, experiments in Caenorhabditis elegans indicate that both netrin binding and nonbinding domains are necessary for phenotypic rescue of an unc-5 loss of function mutation.
Climate Change and Water Resources: The Role of Risk Management Methods (1998)

Risk management methods in water resources in theUnited States and elsewhere have been applied within thecontext of highly developed sets of planning criteria. Inconsidering these methods, many of which are listed here,it is helpful to distinguish between the use of thesetechniques to assess risk and to manage risk. While theuse of risk assessment and management methods forwater resources planning varies widely among agencies,the robustness and resiliency of existing methods for riskmanagement in water planning have the potential to serveeffectively as the basis for adapting to changes in thesupply and demand for water resulting from climatechange. There are, however, substantial research,application, and technology transfer issues to beconfronted.
Transformation of diploid human fibroblasts by DNA transfection with the v‐<i>sis</i> oncogene (1986)

The simian sarcoma virus (SSV) oncogene (v-sis) has a high degree of homology to the cellular gene coding for the B peptide of human platelet-derived growth factor (PDGF), a potent fibroblast mitogen. The cellular homolog of v-sis is activated in some mesenchymal human tumors and cell lines derived from them. To determine the phenotype produced by v-sis in diploid human fibroblasts, we constructed plasmids containing the SSV provirus and drug-resistance markers and transfected them into early-passage human cells. Fibroblasts that had integrated the plasmid were selected for drug resistance and shown to contain and express the v-sis oncogene by DNA and RNA hybridization. The v-sis-expressing cells grew to higher saturation densities than control cells transfected with the vector plasmid alone and formed large, well defined foci. This allowed selection of transfectants directly for focus formation. The v-sis transformed cells continued to grow well in the absence of serum, whereas age-matched, vector-transfected control cells ceased replicating under these conditions so that the final difference in density between the two populations was tenfold. Incorporation of thymidine in serum-free medium by the v-sis-transformed cells was independent of exogenous PDGF. In contrast, PDGF increased thymidine incorporation in such medium by the control cells to the level found in the v-sis-transformed cells with or without added PDGF. These results suggest that expression of the v-sis oncogene in diploid human fibroblasts causes sufficient endogenous synthesis of the B chain of PDGF to allow transformants to grow to abnormally high cell densities. When individual v-sis-transformed cells were grown on a background of normal cells, this higher cell density at confluence could be visualized as a focus.
Are trials of intravascular infusions of autologous mesenchymal stem cells in patients with multiple system atrophy currently justified, and are they effective? (2012)

Peer Reviewed
Consideration of corona onset from awater drop as afunction of air pressure (1996)

The paper identifies three different corona onset mechanisms for a water drop attached to the underside of a conductor as a function of air pressure. The three different corona onset mechanisms are a result of two different corona onset processes: water drop instability and ionisation of the surrounding air. Both processes are considered in the paper. A model which determines the corona onset potential as a function of air pressure for a water drop attached to a conductor is presented. The model identifies the three onset mechanisms and accounts for the previously unexplained transition between the ionisation and instability modes. The corona onset potential is determined by modelling both the stability of the drop and the ionisation of the surrounding air as a function of the potential applied to the conductor. This is done over a range of air pressures resulting in an ‘onset versus air pressure’ curve. The entire model is then verified by experimentation. The model accounts for changes in the drop shape with changes in applied potential and the influence of this on the E-field distribution and hence the ionisation processes. Drop volume, conductor surface conditions and applied E-field divergency are accounted for.
Reactive adsorption of hydrogen sulfide by a solution of sulfur dioxide in poly(glycol ether): effect of a volatile dissolved reactant on mass-transfer enhancement (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactive adsorption of hydrogen sulfide by a solution of sulfur dioxide in poly(glycol ether): effect of a volatile dissolved reactant on mass-transfer enhancementR. Marshall Hix and Scott LynnCite this: Ind. Eng. Chem. Res. 1991, 30, 5, 930–939Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ie00053a016https://doi.org/10.1021/ie00053a016research-articleACS PublicationsRequest reuse permissionsArticle Views121Altmetric-Citations7LEARN 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-Alertsclose Get e-Alerts
Compressed biodegradable matrices of spray-dried PLGA microspheres for the modified release of ketoprofen (2003)

A spray-drying technique was used to prepare poly(lactide-co-glycolide) (PLGA) drug loaded microspheres. Ketoprofen was chosen as a model NSAID drug. The microspheres were characterized in terms of morphology, drug content and release behaviour. The spray-dried particles were subject to a direct compression process for the preparation of biodegradable matrix tablets. The spray-dried powders were found to have good compaction properties. Tablets were also prepared from a mixture of microspheres and microcrystalline cellulose, mannitol and hydroxypropylmethylcellulose or sodium alginate. The release of ketoprofen in phosphate buffer (pH 7.4) was significantly sustained, indicating the suitability of using tabletted spray-dried PLGA microspheres for controlled drug delivery. The results show that spray-dried PLGA particles have promising properties as direct compression and release controlling excipients in matrix tablets for oral administration.
The structure of shared forests in ambiguous parsing (1989)

The Context-Free backbone of some natural language analyzers produces all possible CF parses as some kind of shared forest, from which a single tree is to be chosen by a disambiguation process that may be based on the finer features of the language. We study the structure of these forests with respect to optimality of sharing, and in relation with the parsing schema used to produce them. In addition to a theoretical and experimental framework for studying these issues, the main results presented are:- sophistication in chart parsing schemata (e.g. use of look-ahed) may reduce time and space efficiency instead of improving it,- there is a shared forest structure with at most cubic size for any CF grammar,- when O(n3) complexity is required, the shape of a shared forest is dependent on the parsing schema used.Though analyzed on CF grammars for simplicity, these results extend to more complex formalisms such as unification based grammars.
YBa/sub 2/Cu/sub 3/O/sub 7/(-δ) a-axis films and planar junctions (1995)

In order to prepare planar junctions, multilayers were sputtered, using YBa/sub 2/Cu/sub 3/O/sub 7-/spl delta// as superconductor and PrBa/sub 2/Cu/sub 3/O/sub 7/(-/spl delta/) as barrier material. The sandwiches are a-axis oriented. Out of these, single junctions were etched, planarized with CeO/sub 2/. Finally gold contacts were sputtered. The junctions are squares of size 20/spl times/20 to 100/spl times/100 /spl mu/m/sup 2/. A prerequisite for successful preparation of junctions from a-axis oriented multilayers is a study of such films. Films deposited by RF off-axis sputtering were characterized electrically, Their morphology was investigated by XRD, AFM and TEM. The films are very smooth and have a grain size of below 100/spl times/100 nm/sup 2/. To improve T/sub c/ and crystal quality, template layers were used. The T/sub c/ of a single film is about 62 K; by using a template layer up to 78 K can be reached. For a-axis oriented growth not only a reduction of the deposition temperature is important, but also the growth rate must be high enough. Best results were obtained at rates higher than 150 nm/h. The first planar junctions show a supercurrent, but otherwise rounded I-V curves.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Subcool, Fluid Productivity, and Liquid Level Above a SAGD Producer (2013)

Summary Thermodynamic steam-trap control, or subcool control, in a typicalsteam-assisted gravity-drainage (SAGD) production is essential to the stabilityand longevity of the operation. It is achieved commonly through the control offluid production. The goal of such control is to maintain a steady and healthyliquid production without allowing steam from the injector to bypass to theproducer. Therefore, it is effectively a control of the liquid level above theproducer. Unfortunately, it is not practical to monitor this liquid level. Arule-of-thumb subcool-per-metre estimation of 10°C/m of liquid level is popularin the industry; however it does not prove to hold in many situations. Thispaper presents a study of the dynamics of SAGD-production control with aresulting algebraic equation that relates subcool, fluid productivity, andwellbore drawdown to the liquid level above a producer. The main conclusions ofthis study include There is no minimum subcool value for a pure-gravity-drainage scenario;however, as the wellbore drawdown is considered, there is a minimum subcoolvalue in order to maintain the stability of fluid flow. For a given productivity, the liquid level increases as subcool increasesor as wellbore drawdown decreases. For each given set of operating parameters, there exists a criticalproductivity below which SAGD operation would halt. Before the steam chamber reaches the top of the reservoir, the fluidproductivity is limited by the vertical distance between the injector and theproducer; the larger the distance, the higher the fluid production rate canbe. A verification of this analysis was conducted by a series of numericalreservoir simulations. Although limited to two dimensions, we expect that thisanalysis captures the main physics amid the dynamic complexity ofSAGD-production control. The resulting algebraic equation can be used forbetter understanding of the dynamics of subcool control and for determiningoperation strategies.
Research report. DataSpace: 3-D visualizations of large databases (2002)

DataSpace is a system for interactive 3-D visualization and analysis of large databases. DataSpace utilizes the display space by placing panels of information, possibly generated by different visualization applications, in a 3-D graph layout, and providing continuous navigation facilities. Selective rearrangements and transparency can be used to reduce occlusion or to compare or merge a set of images (e.g. line graphs or scatter plots) that are aligned and stacked in depth. A prototype system supporting the basic 3-D graphic operations (layout, zoom, rotation, translation, transparency) has been implemented. We provide several illustrative examples of DataSpace displays taken from the current system. We present the 3-D display paradigm, describe the query, layout and rendering steps required to create a display, and discuss some performance issues.
A cryptic miniplasmid from the hyperthermophilic bacterium Thermotoga sp. strain RQ7 (1994)

An 846-bp cryptic plasmid has been discovered in the hyperthermophilic bacterium Thermotoga sp. strain RQ7. This is the first plasmid described for an organism from this ancient bacterial lineage and the smallest plasmid described to date for any organism. Nucleotide sequencing revealed a single open reading frame possibly encoding a 25,460-Da basic protein (212 amino acids). Upstream of the putative promoter lie five 11-bp direct repeats, each separated by 1 to 4 bp, while between the promoter and the open reading frame lies an 11-bp palindromic sequence. Its mode of replication is unknown, but its sequence bears similarities to those of plasmids which replicate by a rolling-circle mechanism.
Spinstand demonstration of areal density enhancement using two-dimensional magnetic recording (invited) (2015)

Exponential growth of the areal density has driven the magnetic recording industry for almost sixty years. But now areal density growth is slowing down, suggesting that current technologies are reaching their fundamental limit. The next generation of recording technologies, namely, energy-assisted writing and bit-patterned media, remains just over the horizon. Two-Dimensional Magnetic Recording (TDMR) is a promising new approach, enabling continued areal density growth with only modest changes to the heads and recording electronics. We demonstrate a first generation implementation of TDMR by using a dual-element read sensor to improve the recovery of data encoded by a conventional low-density parity-check (LDPC) channel. The signals are combined with a 2D equalizer into a single modified waveform that is decoded by a standard LDPC channel. Our detection hardware can perform simultaneous measurement of the pre- and post-combined error rate information, allowing one set of measurements to assess the absolute areal density capability of the TDMR system as well as the gain over a conventional shingled magnetic recording system with identical components. We discuss areal density measurements using this hardware and demonstrate gains exceeding five percent based on experimental dual reader components.
The clinical value of using chloroquine or hydroxychloroquine as autophagy inhibitors in the treatment of cancers (2018)

This meta-analysis showed that autophagy-inhibitor-based therapy has better treatment response compared to chemotherapy or radiation therapy without inhibiting autophagy, which may provide a new strategy for the treatment of cancers.
Silica Spheres Coated with YVO<sub>4</sub>:Eu<sup>3+</sup> Layers via Sol−Gel Process:  A Simple Method To Obtain Spherical Core−Shell Phosphors (2005)

Spherical SiO2 particles have been successfully coated with YVO4:Eu3+ phosphor layers through a Pechini sol−gel process. The resulted YVO4:Eu3+@SiO2 core−shell phosphors were characterized by X-ray diffraction (XRD), Fourier-transform IR spectroscopy, scanning electron microscopy, X-ray photoelectron spectra, transmission electron microscopy, UV/vis absorption spectra, general and time-resolved photoluminescence spectra, as well as kinetic decays. The XRD results demonstrate that the YVO4:Eu3+ layers begin to crystallize on the SiO2 particles after annealing at 400 °C, and the crystallinity increases with raising the annealing temperature. The obtained core−shell phosphors have perfect spherical shape with narrow size distribution (average size ca. 500 nm), nonagglomeration, and smooth surface. The thickness of the YVO4:Eu3+ shells on SiO2 cores could be easily tailored by varying the number of deposition cycles (60 nm for two deposition cycles). The Eu3+ shows a strong photoluminescence (PL) (dominated by 5D0−7F2 red emission at 617 nm) due to an efficient energy transfer from vanadate groups to Eu3+. The energy transfer process was further studied by the time-resolved emission spectra as well as kinetic decay curves of Eu3+ upon excitation into the VO43- ion. The PL intensity of Eu3+ increases with raising the annealing temperature and the number of coating cycles, and optimum polyethylene glycol concentration in the precursor solution was determined to be 0.08 g/mL for obtaining the strongest emission of Eu3+.
Therapeutic Effects of Oral Nutritional Supplements during Haemodialysis: Physician's Experience. (2014)

Predialytic oral supplementation with NEPRO HP improves nutritional status of CKD patients on MHD.
Two-layer optical model of skin for early, non-invasive detection of wound development on the diabetic foot (2010)

Foot ulceration is a debilitating comorbidity of diabetes that may result in loss of mobility and amputation. Optical detection of cutaneous tissue changes due to inflammation and necrosis at the preulcer site could constitute a preventative strategy. A commercial hyperspectral oximetry system was used to measure tissue oxygenation on the feet of diabetic patients. A previously developed predictive index was used to differentiate preulcer tissue from surrounding healthy tissue with a sensitivity of 92% and specificity of 80%. To improve prediction accuracy, an optical skin model was developed treating skin as a two-layer medium and explicitly accounting for (i) melanin content and thickness of the epidermis, (ii) blood content and hemoglobin saturation of the dermis, and (iii) tissue scattering in both layers. Using this forward model, an iterative inverse method was used to determine the skin properties from hyperspectral images of preulcerative areas. The use of this information in lowering the false positive rate was discussed.
Activated murine macrophages induce apoptosis in tumor cells through nitric oxide-dependent or -independent mechanisms. (1994)

Work reported here investigated aspects of macrophage-mediated tumor cell death, in particular the role of apoptosis as a mechanism for nitric oxide (NO)-mediated macrophage tumor cytotoxicity. Nitric oxide induced apoptosis in P815 cells in macrophage P815 cocultures where fragmentation of tumor cell [3H]thymidine-labeled DNA preceded cell lysis (as measured by 51Cr release), paralleled nitrite accumulation, and was prevented by a specific inhibitor of NO synthase, N-MMA. DNA from P815 cells separated from macrophages in culture by a cell-impermeable membrane or exposed to authentic NO gas showed the pattern of internucleosomal cleavage that is characteristic of apoptosis. Additionally, culture of P815 cells with the NO donor sodium nitroprusside was followed by DNA fragmentation. Macrophages also induced apoptosis in L929 cells but, in this case, apoptosis was NO independent and partially inhibited in cocultures by an antitumor necrosis factor alpha monoclonal antibody. The anti-tumor necrosis factor alpha monoclonal antibody fully prevented apoptosis when macrophages and L929 were separated by a cell-impermeable membrane. Exposure of L929 cells to NO gas or sodium nitroprusside did not result in their apoptotic death. Like other immune cytotoxic cells, macrophages can determine tumor cell death through the induction of apoptosis and do so through more than one effector mechanism.