gebhart/patrepeval huggingface dataset:
Analogs of the Autoinducer 3-Oxooctanoyl-Homoserine Lactone Strongly Inhibit Activity of the TraR Protein of <i>Agrobacterium tumefaciens</i> (1998)

The TraR and TraI proteins of Agrobacterium tumefaciens mediate cell-density-dependent expression of the Ti plasmid tra regulon. TraI synthesizes the autoinducer pheromone N-(3-oxooctanoyl)-L-homoserine lactone (3-oxo-C8-HSL), while TraR is an 3-oxo-C8-HSL-responsive transcriptional activator. We have compared the abilities of 3-oxo-C8-HSL and 32 related compounds to activate expression of a TraR-regulated promoter. In a strain that expresses wild-type levels of TraR, only 3-oxo-C8-HSL was strongly stimulatory, four compounds were detectably active only at high concentrations, and the remaining 28 compounds were inactive. Furthermore, many of these compounds were potent antagonists. In contrast, almost all of these compounds were stimulatory in a congenic strain that overexpresses TraR and no compound was a potent antagonist. We propose a model in which autoinducers enhance the affinity of TraR either for other TraR monomers or for DNA binding sites and that overexpression of TraR potentiates this interaction by mass action. Wild-type A. tumefaciens released a rather broad spectrum of autoinducers, including several that antagonize induction of a wild-type strain. However, under all conditions tested, 3-oxo-C8-HSL was more abundant than any other analog, indicating that other released autoinducers do not interfere with tra gene induction. We conclude that (i) in wild-type strains, only 3-oxo-C8-HSL significantly stimulates tra gene expression, while many autoinducer analogs are potent antagonists; (ii) TraR overexpression increases agonistic activity of autoinducer analogs, allowing sensitive biodetection of many autoinducers; and (iii) autoinducer stimulatory activity is potentiated by TraR overproduction, suggesting that autoinducers may shift an equilibrium between TraR monomers and dimers or oligomers. When autoinducer specificities of other quorum-sensing proteins are tested, care should be taken not to overexpress those proteins.
A multilevel computing architecture for embedded multimedia applications (2004)

We have designed a new architecture that simplifies integration of heterogeneous IP for multimedia and streaming applications. The multilevel computing architecture (MLCA) is a template architecture featuring multiple processing units. This template architecture for SOC systems uses superscalar techniques to exploit task-level parallelism among different processing units. It supports a natural programming model that relieves programmers from explicitly synchronizing tasks and communicating data. code transformations that improve application performance are easy to incorporate in compilers for this architecture.
Single flux quantum circuit technology and CAD overview (2018)

Single Flux Quantum (SFQ) electronic circuits originated with the advent of Rapid Single Flux Quantum (RSFQ) logic in 1985 and have since evolved to include more energy-efficient technologies such as ERSFQ and eSFQ. SFQ logic circuits, based on the manipulation of quantized flux pulses, have been demonstrated to run at clock speeds in excess of 120 GHz, and with bit-switch energy below 1 aJ. Small SFQ microprocessors have been developed, but characteristics inherent to SFQ circuits and the lack of circuit design tools have hampered the development of large SFQ systems. SFQ circuit characteristics include fan-out of one and the subsequent demand for pulse splitters, gate-level clocking, susceptibility to magnetic fields and sensitivity to intra-gate and inter-gate inductance. Superconducting interconnects propagate data pulses at the speed of light, but suffer from reflections at vias that attenuate transmitted pulses. The recently started IARPA SuperTools program aims to deliver SFQ Computer-Aided Design (CAD) tools that can enable the successful design of 64 bit RISC processors given the characteristics of SFQ circuits. A discussion on the technology of SFQ circuits and the most modern SFQ fabrication processes is presented, with a focus on the unique electronic design automation CAD requirements for the design, layout and verification of SFQ circuits.
High‐resolution physical mapping in <i>Arabidopsis thaliana</i> and tomato by fluorescence <i>in situ</i> hybridization to extended DNA fibres (1996)

A technique to detect DNA sequences on extended DNA fibres (EDF) prepared from interphase nuclei from tomato ( Lycopersicon esculentum ) and Arabidopsis thaliana leaves by fluorescence in situ hybridization (FISH) is described. Three nuclear lysis procedures have been tested for their ability to decondense chromatin and to generate highly extended intact DNA fibres on microscopic slides. DNA probes of various sizes have been used in FISH experiments to EDFs to establish the resolution and sensitivity of the technique. The fluorescent signals of a 5S rDNA probe hybridized to tomato EDFs revealed continuous strings of about 200 µm, that corresponded to a molecular size of about 660 kb. In A. thaliana , a contig of three cosmids spanning a genomic region with a total length of about 89 kb was analysed. By means of multi‐colour hybridization the physical positions of the cosmids were visualized as red and green fluorescence strings with overlapping regions in yellow. Comparison of the length of the fluorescent signals with the molecular data revealed a stretching degree of the DNA fibres at 3.27 kb µm −1 , which is close to the Watson‐Crick DNA length estimate of 2.9 kb µm −1 . Other experiments on small size molecular probes with both lambda clones (13.5–17 kb insert sizes) and plasmids (4.2 and 5 kb) in a contig of A. thaliana , and the 5S rDNA region in tomato showed close agreement with molecular data. The lower limit of the detection, which was established in a hybridization experiment with two DNA probes from the 45S ribosomal gene on extended fibres of tomato, was about 0.7 kb. Consistent patterns of alternating fluorescent red and green spots were obtained reflecting the tandemly repeated arrangement of the 18S and 25S ribosomal sequences. On the basis of the microscopic distance between these hybridization spots the size of the ribosomal unit was estimated at 8.2 kb. This implies a drastic improvement of high‐resolution physical mapping of DNA sequences by FISH on plant DNA.
Thermal Stability and Electrical Properties of (La<sub>2</sub>O<sub>3</sub>)<sub>1-x</sub>(Al<sub>2</sub>O<sub>3</sub>)<sub>x</sub> Composite Films (2005)

(La 2 O 3 ) 1- x (Al 2 O 3 ) x composite films (La 2 O 3 :Al 2 O 3 = 100:0, 80:20, 67:33, 50:50) were synthesized using pulsed laser deposition. We investigated their thermal stability and electrical properties as high dielectric constant gate dielectric films. La 2 O 3 (an Al 2 O 3 content of 0%) films were uniformly crystallized as La-silicate after rapid thermal annealing (RTA) at 1000°C for 15 s in an N 2 ambient. We found that the addition of Al 2 O 3 suppresses crystallization, and amorphous structures are retained in the samples with an Al 2 O 3 content of 33% or greater. Furthermore, Al 2 O 3 addition suppresses diffusion of Si into upper composite films during RTA. The smallest capacitance equivalent oxide thickness of 1.2 nm was achieved for a sample with an Al 2 O 3 content of 20% and with leakage current density of 3.9×10 -3 A/cm 2 at + 1 V relative to the flat band voltage.
Effect of different rootstock on plant growth, yield and quality of watermelon (2003)

This study was conducted in Department of Horticulture, Faculty of Agriculture, University of Cukurova in 1999 and 2000. Watermelon [C itrullus lanatus (Thunb.) Matsum and Nakai] cultivar Crimson Tide was grafted onto 10 different rootstocks. Cucurbita moschata , Cucurbita maxima and Lagenaria siceraria were open pollinated cultivars, and Strong Tosa, Gold Tosa, P360 ( Cucurbita maxima × Cucurbita moschata ), Skopje, Emphasis, 216 and FRG ( Lagenaria spp.) were hybrid cultivars. The ungrafted Crimson Tide watermelon cultivar was used as the control. Plants were grown under low tunnel conditions until the outdoor temperature was suitable (22–25°C) for watermelon growth. Our results showed that while survival rate was low (65%) in Cucurbita type rootstocks, it was high (95%) in Lagenaria type rootstocks. Grafted plants flowered about 10 days earlier and showed more vigorous vegetative growth than the control plants. Grafted plants had up to 148% higher fresh weights than control plants. Similarly, grafted plants showed 42–180% higher dry weight, 58–100% more leaves and larger leaf area as compared with the control. In total yield, Lagenaria type rootstocks produced a higher yield but Cucurbita type rootstocks produced a lower yield than the control. While control plants had 6.43 kg/m2 yield, Lagenaria type rootstocks produced 27–106% higher yield than the control. In contrast, Cucurbita type rootstocks had 127–240% less yield than the control. This could be attributed to incompatibility of Cucurbita rootstocks because some of the plants died before harvest. The study showed that rootstock choices influence plant growth as well as yield and quality of scion fruit, suggesting an important consideration in the potential use of grafting applications in watermelon.
An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose (2021)

D614G genotype of SARS-CoV-2 virus is highly infectious and responsible for almost all infection for 2nd wave. However, there are currently no reports with D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine with D614G variant and characterization in animal model. We have used special mRNA-architecture and formulation that provides suitable response of the product. The surface plasmon resonance (SPR) data with spike protein (S) revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice neutralized SARS-CoV-2-pseudoviruses in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, single-dose immunization protected mice-lungs from homotypic-pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+ cells with a Th1 bias. The data suggested great promise for immediate translation of the technology to the clinic.
Formation and Destruction of Silicon Monoxide in SN 1987A (1996)

We present a new chemistry model for the silicon monoxide molecules in SN 1987A. It incorporates an enhanced rate of formation by radiative association and an enhanced rate of destruction through charge transfer between SiO and Ar`and Ne`, which is more efficient than the energetic electron impact ionization and dissociation in a previous model. The conclusion is unchanged that the of SiO observed in SN 1987A can be produced by chemistry models in which there is no 10~410~3 M _ microscopic mixing of helium into the silicon-oxygen region of the ejecta.
Receptor for Advanced Glycation End Products and Its Ligands: A Journey from the Complications of Diabetes to Its Pathogenesis (2005)

Many studies have suggested that the expression of RAGE (receptor for advanced glycation end products) is upregulated in human tissues susceptible to the long-term complications of diabetes. From the kidneys to the macrovessels of the aorta, RAGE expression is upregulated in a diverse array of cell types, from glomerular epithelial cells (podocytes) to endothelial cells, vascular smooth muscle cells, and inflammatory mononuclear phagocytes and lymphocytes. Although RAGE was first described as a receptor for advanced glycation end products (AGEs), the key finding that RAGE was also a signaling receptor for proinflammatory S100/calgranulins and amphoterin, led to the premise that even in euglycemia, ligand-RAGE interaction propagated inflammatory mechanisms linked to chronic cellular perturbation and tissue injury. Indeed, such considerations suggested that RAGE might even participate in the pathogenesis of type 1 diabetes. Our studies have shown that pharmacological and/or genetic deletion/mutation of the receptor attenuates the development of hyperglycemia in NOD mice; in mice with myriad complications of diabetes, interruption of ligand-RAGE interaction prevents or delays the chronic complications of the disease in both macro- and microvessel structures. Taken together, these findings suggest that RAGE is "at the right place and time" to contribute to the pathogenesis of diabetes and it complications. Studies are in progress to test the premise that antagonism of this interaction is a logical strategy for the prevention and treatment of diabetes.
Crohn disease–associated adherent-invasive E. coli bacteria target mouse and human Peyer’s patches via long polar fimbriae (2011)

Crohn disease (CD) is a multifactorial disease in which an abnormal immune response in the gastrointestinal (GI) tract leads to chronic inflammation. The small intestine, particularly the ileum, of patients with CD is colonized by adherent-invasive E. coli (AIEC)--a pathogenic group of E. coli able to adhere to and invade intestinal epithelial cells. As the earliest inflammatory lesions are microscopic erosions of the epithelium lining the Peyer's patches (PPs), we investigated the ability of AIEC bacteria to interact with PPs and the virulence factors involved. We found that AIEC bacteria could interact with mouse and human PPs via long polar fimbriae (LPF). An LPF-negative AIEC mutant was highly impaired in its ability to interact with mouse and human PPs and to translocate across monolayers of M cells, specialized epithelial cells at the surface of PPs. The prevalence of AIEC strains harboring the lpf operon was markedly higher in CD patients compared with controls. In addition, increased numbers of AIEC, but not LPF-deficient AIEC, bacteria were found interacting with PPs from Nod2(-/-) mice compared with WT mice. In conclusion, we have identified LPF as a key factor for AIEC to target PPs. This could be the missing link between AIEC colonization and the presence of early lesions in the PPs of CD patients.
AVO helps seismic imaging in deepwater environments (1997)

Amplitude and frequency variations related to offset should be analyzed routinely during interpretation of seismic data acquired in deepwater environments. Amplitude variation with offset (AVO) in three dimensions is the key exploration tool in deep waters of the Gulf of Mexico. But application of the tool requires special care. Three-dimensional AVO helps the interpreter understand stratigraphy and the meaning of amplitude anomalies. Used in conjunction with well log data, it can help the interpreter distinguish amplitudes related to the presence of hydrocarbons from those that result from, for example, rock-property changes within a non-hydrocarbon-bearing layer, such as a shale, or residual gas (fizz water) in high-porosity sands. The paper discusses examples from the Gulf of Mexico, will control application, improving detail, and frequency-dependent analysis.
Normal tubular regeneration and differentiation of the post-ischemic kidney in mice lacking vimentin. (1997)

Proliferation and dedifferentiation of tubular cells are the hallmark of early regeneration after renal ischemic injury. Vimentin, a class III intermediate filament expressed only in mesenchymal cells of mature mammals, was shown to be transiently expressed in post-ischemic renal tubular epithelial cells. Vimentin re-expression was interpreted as a marker of cellular dedifferentiation, but its role in tubular regeneration after renal ischemia has also been hypothesized. This role was evaluated in mice bearing a null mutation of the vimentin gene. Expression of vimentin, proliferating cell nuclear antigen (a marker of cellular proliferation), and villin (a marker of differentiated brush-border membranes) was studied in wild-type (Vim+/+), heterozygous (Vim+/-), and homozygous (Vim-/-) mice subjected to transient ischemia of the left kidney. As expected, vimentin was detected by immunohistochemistry at the basal pole of proximal tubular cells from post-ischemic kidney in Vim+/+ and Vim+/- mice from day 2 to day 28. The expression of the reporter gene beta-galactosidase in Vim+/- and Vim-/- mice confirmed the tubular origin of vimentin. No compensatory expression of keratin could be demonstrated in Vim-/- mice. The intensity of proliferating cell nuclear antigen labeling and the pattern of villin expression were comparable in Vim-/-, Vim+/- and Vim+/+ mice at any time of the study. After 60 days, the structure of post-ischemic kidneys in Vim-/- mice was indistinguishable from that of normal non-operated kidneys in Vim+/+ mice. In conclusion, 1) the pattern of post-ischemic proximal tubular cell proliferation, differentiation, and tubular organization was not impaired in mice lacking vimentin and 2) these results suggest that the transient tubular expression of vimentin is not instrumental in tubular regeneration after renal ischemic injury.
A pair of adjacent glucocorticoid response elements regulate expression of two mouse metallothionein genes (1997)

Synthesis of mouse metallothionein (MT)-I and MT-II is transcriptionally induced by the synthetic glucocorticoid, dexamethasone (DEX) or both in vivo as well as in numerous cell lines. However, the location(s) of a glucocorticoid response element (GRE) has not been described. The observation that a marked MT-I gene, as well as heterologous genes, when placed in the context of 17 kb of flanking sequence from the MT locus, are inducible by DEX and lipopolysaccharide in transgenic mice renewed the search for the GRE. Analysis of a series of deletion constructs from this 17-kb region in cultured cells identified a single 455-bp region that conferred DEX induction on a reporter gene. This 455-bp region contains two GREs that bind to the glucocorticoid receptor as assessed by gel mobility shift. Deletion of this fragment from the 17-kb flanking region eliminates the DEX responsiveness of reporter genes. The two GREs, which are located ≈1 kb upstream of the MT-II gene and ≈7 kb upstream of the MT-I gene, are necessary for induction of both genes and can function independently of elements within the proximal promoter region of either gene.
Simultaneous distribution of multichannel analog and digital video channels to multiple terminals using high-density WDM and a broad-band in-line erbium-doped fiber amplifier (1990)

The simultaneous amplification of 16 distributed feedback (DFB) lasers over a 34-nm spectral range in an erbium-doped fiber amplifier is reported. Sixteen DFB lasers spaced at approximately 2-nm intervals and covering 34 nm in the 1.55- mu m band were modulated with a total of 100 studio-quality analog FM-TV channels and six 622-Mb/s channels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
RESISTANCE AND DESIGN CHS X AND T-JOINTS UNDER TENSION (1984)

Past test results indicated that tubular X and T-joints under tensile brace loading sustained greater deformation than the same joints under compression, without losing the overall stability. It has been proposed in the past by several investigators to calculate the ultimate strengths of these joints under tension only by multiplying the capacities of the same joints under compression by a constant value greater than 1.0. Additional test results recently obtained, however, evidenced that the capacity of the joints in tension did not vary propotionally with the capacity in compression. Further, the observed ultimate strengths in tension were subjected to greater than those in compression, because the ultimate strengths were governed by separation of a tension brace from the chord and, therefore, were influenced by welding conditions, weld defects, material propeties, and so forth. This paper presents presents results of analysis of all the test results available for tubular X and T-joints under tension. Comparison is also made with the capacity of simple model rings, on which the ultimate strength formulae are based. The following conclusions are drawn : (1) The nonlinear finite element analysis is found to interpret well responses of model rings to concentrated brace forces. Many similarities are found between the behaviors of tubular X-joints and model rings. (2) The ultimate and the yield strengths of tubular joints are defined basing them on the load-deformation curves. It is assumed that the yield strength can be used as a measure of a serviceability limit state. (3) A multiple regression analysis is carried out to obtain new prediction equations for both the ultimate and the yield strengths of the X and T-joints under tension. Greater scatter is observed in these equations as compared with the joints under compression. (4) The resistance factors for serviceability and ultimate limit states are calculated using simple LRFD formats. The serviceability limit state can be more critical than the ultimate limit state, although this statement varies with the probability distributions of loads.
Standardized Visual Estimation of Blood Loss during Vaginal Delivery with its Correlation Hematocrit Changes—A Descriptive Study (2009)

ABSTRACT Introduction Postpartum hemorrhage is a leading cause of maternal morbidity and mortality. Traditionally, visual method with variations in accuracy is followed, because it is quick, simple and noninvasive. To rely on this method accuracy is of vital importance. This study was aimed to improve accuracy of visual estimation of blood loss during vaginal delivery by standardizing (using similar sized mops and a fixed container) and correlating with hematocrit changes. Methods design A descriptive study. Sample size 250 women. Single fixed collecting container and similar sized mops were used in the third stage of labor. Blood was drained into the container and was visually calibrated by a single trained observer. The soaking characteristics of the mops were used to estimate total blood loss. Blood spillage on delivery table, garments and floor were approximately assessed. Total blood loss was calculated from the above three sources. Hemoglobin and hematocrit measurements were done at the time of admission and, at 24 and 72 hours postpartum and its correlation was done with blood loss. Analysis By paired and unpaired ‘t’ test. Results 250 out of 269 women completed the study. Incidence of PPH (> 500 ml) was 11.2%. The estimated blood loss correlated well with the hemoglobin and hematocrit changes postpartum. Conclusion Standardized visual method (fixed container and mops) with trained observer improves the accuracy of estimation. This may assist clinicians to accurately estimate blood loss thus preventing hemorrhage related complications.
Use of cryogenic fluids for environmental drilling in unconsolidated formations (1994)

A novel method is being developed to drill and support horizontal boreholes in loose, unconsolidated formations such as sands or gravels. It consists of drilling using supercooled air as the flushing medium in order to freeze the surrounding soil. The method is suited to drilling near surface holes for environmental monitoring and remediation because no additional polluting substances are introduced into the hole and there is little permanent alteration of the surrounding soil. In addition, subsurface pollutants adjacent to the borehole will be frozen in place, preventing them from spreading along the borehole or returning to the surface and endangering workers. Laboratory drilling tests have demonstrated that sands with as little as 2.5% water content (11% saturation), subjected to pressures simulating 60 meters (200 ft.) of overburden may be drilled without collapse, and that the freezing is sufficiently rapid to allow penetration rates up to 9 m/hr. (30 ft./hr,) under some conditions. Observed borehole collapse pressures agree with those predicted from measured strengths of frozen sand samples. Preliminary work suggests that conventional air drilling equipment may be used with minimal modifications.