gebhart/patrepeval huggingface dataset:
Exploring the transcriptome of luxI- and ΔainS mutants and the impact of N-3-oxo-hexanoyl-L- and N-3-hydroxy-decanoyl-L-homoserine lactones on biofilm formation in Aliivibrio salmonicida (2018)

Background. The marine bacterium A. salmonicida uses the quorum sensing (QS) systems, AinS/R and LuxI/R to produce eight acyl-homoserine lactones (AHLs) in a cell density dependent manner . Biofilm formation is one of the QS regulated phenotypes, which requires the expression of exopolysaccharides (EPS) . We previously demonstrated that inactivation of LitR, the master regulator of QS in A. salmonicida resulted in biofilm formation, which was, similar to the biofilm formed by the AHL deficient mutant ΔainSluxI - . In this work, we have identified genes regulated by AinS and LuxI using RNA sequensing (RNA-Seq), and studied their role in biofilm formation, colony morphology and motility. We have also studied the effect of two AHLs on the biofilm formation. Results. The transcriptome profiling of ΔainS and luxI - mutants allowed us to identify essential genes regulated by QS in A. salmonicida . Relative to the wild-type, the ΔainS and luxI - mutants revealed 40 and 500 differentially expressed genes (DEGs), respectively. The functional analysis demonstrated that the most pronounced DEGs were involved in bacterial motility and chemotaxis, exopolysaccharide production, and surface structures related to adhesion. Inactivation of luxI but not ainS genes resulted in wrinkled colony morphology. While inactivation of both genes ( ΔainSluxI - ) resulted in strains able to form wrinkled colonies and mushroom structured biofilm. Moreover, when the ΔainSluxI - mutant was supplemented with N-3-oxo-hexanoyl-L- homoserine lactone (3OC6-HSL) and N-3-hydroxy-decanoyl-L-homoserine lactone(3OHC10-HSL), the biofilm did not develop. We also show that LuxI is needed for motility and repression for EPS production, where repression of EPS is likely operated through the RpoQ-sigma factor. Conclusion. These findings imply that LuxI and AinS synthases have a critical contribution to the QS-dependent regulation on gene expression and the phenotypic traits related to it.
Detection of residual B precursor lymphoblastic leukemia by uniform gating flow cytometry (2009)

Thus, FC with preset uniform gating at day 15 predicts PCR-detectable MRD in B precursor ALL. Presented data may be used to define new polychromatic cytometric diagnostics of MRD including semiautomatic assessment. Pediatr Blood Cancer 2010; 54:62-70. (c) 2009 Wiley-Liss, Inc.
Micromagnetic simulation of spin transfer torque switching by nanosecond current pulses (2006)

Magnetization reversal by spin transfer torque due to current flowing in magnetic tunnel junction nanopillar with 200nm×125nm elliptical cross section is studied by micromagnetic simulation assuming the Slonczewski model for spin transfer torque. The magnetization dynamics during the switching is found to be highly inhomogeneous with formation of complex domain structure and spin wave generation even for artificially increased exchange length. The Oersted field influence on onset of precession leading to switching is described in terms of spin wave generation. The switching time as a function of current is found to have nonmonotonic behavior, which is not completely understood but is found to be related to the presence of Oersted field.
Metabolic Stone Risk Factors Associated with Papillary Calcification on Unenhanced Spiral Computed Tomography (2006)

Purpose: Increasing evidence suggests that Randalls plaque contributes to the pathogenesis of urinary stone formation. The purpose of our study is to compare the incidence of the abnormal metabolic stone risk factors between the calcium stone former with papillary calcification and the calcium stone former without papillary calcification on unenhanced spiral computed tomography (CT). Materials and Methods: A series of patients with calcium stones (n=49) underwent unenhanced spiral CT and complete metabolic evaluation after they consumed a random diet for 1 month after stone removal. Of the 49 patients, 38 patients showed papillary calcification on unenhanced spiral CT and 11 patients did not. Their blood was evaluated by using a multichannel analysis sequential multichannel autoanalyzer (SMA)-20 and PTH tests. The 24-hour urinary constituents were assayed for calcium, oxalate, citrate, total volume, phosphorus and sodium. We compared the incidence of abnormal metabolic risk factors between the two groups. Statistical analysis was performed by chi-square tests. Results: The incidences of hyperuricemia were 27.3% in the patients without papillary calcification and 31.6% in the patients with papillary calcification. The incidences of hypernatriuria were 18.2% versus 42.1%, the incidences of hypercalciuria were 36.4% versus 26.3%, the incidences of hyperuricosuria were 18.2% versus 18.4%, the incidences of hyperoxaluria were zero versus 28.9%, and the incidences of hypocitraturia were 45.5% versus 44.7%, respectively. The difference between the two groups was statistically significant only for hyperoxaluria (p=0.043). Conclusions: Hyperoxaluria is the only metabolic risk factor that more frequently occurred in the patients with papillary calcification. Our date suggest that hyperoxaluria may be an important factor in the pathogenesis of papillary calcification. (Korean J Urol 2006;47:507-511)
Complete Blood Count and Retinal Vessel Calibers (2014)

These associations show that elevated levels of hematological indices can have adverse effects on the microcirculation.
Loss of T cell CD98hc specifically ablates T cell clonal expansion and protects from autoimmunity. (102.16) (2011)

Abstract CD98hc (CD98 heavy chain, 4F2 antigen, Slc3a2) is a lymphocyte activation antigen with unclear function in T cells. Deletion of CD98hc in B cells leads to complete failure of B cell proliferation, plasma cell formation, and antibody secretion. Here we examined the role of T cell CD98 in protective and auto- immune responses by specifically deleting it in mouse T cells. Deletion of T cell CD98 prevented experimental autoimmune diabetes associated with reduced T cell clonal expansion. However, initial T cell homing to pancreatic islets was unimpaired. In contrast to B cells, CD98-null T cells showed only moderately impaired antigen-driven proliferation in vitro and nearly normal homeostatic proliferation. Furthermore, these cells were activated by antigen and produced cytokines (CD4) and efficiently killed targets (CD8). The integrin binding domain of CD98hc was necessary and sufficient for full clonal expansion, highlighting the role of adhesive signaling in T cell proliferation and autoimmune disease. When CD98-null T cells were pre-expanded in vitro, they adoptively transferred diabetes, establishing that impaired clonal expansion was responsible for protection from disease. The integrin binding domain of CD98hc is thus required for antigen-driven T cell clonal expansion in the pathogenesis of an autoimmune disease and may represent a useful therapeutic target.
Convenient Method for the Preparation of Weinreb Amides via Pd‐Catalyzed Aminocarbonylation of Aryl Bromides at Atmospheric Pressure. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Corrosion Resistance Test of Stainless Steels in the Biofuel Environment (2019)

The oxidation degradation characteristics of four types of bioethanol fuel and one type of biodiesel fuel were investigated. It was found that rape methyl ester (RME) was the fuel that was most susceptive to oxidative degradation, whereas bioethanol fuels were resistant. Oxidative degradation of the fuels promoted the formation of fatty acids in the water phase. Once all formic and acetic acid contained in the oxidized RME was distributed in 0.1 vol% of the water phase, its pH was estimated to be ~1.6. Of the different stainless steel variants in the corrosion tests, which simulated the most severe conditions, SUS436L and SUS444 exhibited excellent corrosion resistance
Isolation and characterization of Streptomyces sp. KACC 91027 against Plasmodiophora brassicae (2004)

Club root caused by Plasmodiophora brassicae is found in crucifers. Among the over hundreds of Streptomyces isolated from soil in Korea. One strain showed prominent activity against P. brassicae. The strain was identified based on 16S rDNA sequencing and the morphology by a method of scanning electron microscopy. An active compound in the fermented broth obtained from the strain was separated. Even though the complete assignments of the compound remain for future work, the results regarding the isolation and characterization of the strain with a certain activity against P. brassicae are shown in this paper.
Photonic Microbricks: Fabrication of Photonic Microbricks via Crack Engineering of Colloidal Crystals (Adv. Funct. Mater. 26/2020) (2020)

In article number 1908242, Ling Li and co-workers provide a mechanistic understanding of crack formations during the evaporation-induced self-assembly of colloidal crystals, which allows for rational controlling of the location and orientation of cracks for fabricating photonic microstructures with controlled geometries and sizes.
Infrared Streak Camera (1997)

An atomic streak camera has been constructed with a spectral range from 1 to 100 μm and a 2 ps time resolution. Gas-phase Rydberg atoms are used as a infrared sensitive photocathode. Prompt electron emission from the autoionizing Rydberg atoms is obtained when a red Stark states are selected.
Inheritance of congenital myasthenia gravis in smooth fox terrier dogs (1984)

The phenotypes with respect to congenital myasthenia gravis of 132 smooth fox terrier dogs from 25 matings were analyzed. These included both prospective and retrospective matings. It was determined that congenital myasthenia gravis in the smooth fox terrier dog breed is inherited in an autosomal recessive manner with complete penetrance. We propose the symbol mg for the gene for congenital myasthenia gravis in the smooth fox terrier. Attempts to maintain live affected dogs to adulthood were unsuccessful and it is concluded that this is a lethal trait.
Modeling of resistance in FinFET local interconnect (2014)

We present an innovative and comprehensive approach to model the resistance of local interconnect used in finFET technologies. Our parasitic resistance formulas for finFET source/drain regions cover both merged and unmerged fin processes. They have been verified with field solver simulation results, and are found to be accurate over a wide range of parameter values. Our local interconnect resistance model has been used in 14nm finFET technology, and is a critical part of compact models used in both extraction flow and schematic/pre-layout flow.
Bone marrow hypocellularity does not affect tolerance or efficacy of azacitidine in patients with higher-risk myelodysplastic syndromes (2014)

The efficacy and tolerance of azacitidine in higher-risk myelodysplasia with hypocellular bone marrow (BM) are unknown. This post hoc AZA-001 trial analysis assessed whether baseline BM cellularity affected the overall survival (OS) advantage demonstrated with azacitidine versus conventional care regimens (CCR). Baseline BM biopsies of <30% cellularity were considered hypocellular with data evaluable from 299 patients (azacitidine n = 154, CCR n = 145); 13% (n = 39) hypocellular, 87% (n = 260) non-hypocellular. Patient characteristics were balanced between cellularity and treatment groups. Most patients (90-100%) had 2-3 cytopenias at baseline. Median (range) azacitidine treatment cycle lengths were 35·5 (28-54) and 33·0 (15-75) d in hypocellular and non-hypocellular groups, respectively. At 33 months, median OS was not reached (NR) [95% confidence interval (CI): 19·2, NR] in hypocellular patients receiving azacitidine versus 16·9 months (95% CI: 11·1, 19·3) with CCR (P = 0·001); and in non-hypocellular patients, it was 21·1 months (95% CI: 16·2, 34·7) versus 15·3 months (95% CI: 9·3, 17·6) (P = 0·012). Azacitidine tolerance was similar regardless of cellularity. Grade 3-4 thrombocytopenia and neutropenia occurred similarly in hypocellular patients treated with azacitidine versus CCR (80% vs. 92% and 88% vs. 75%). Azacitidine OS results are consistent with those from AZA-001, regardless of cellularity, and demonstrate its safety and efficacy in higher-risk myelodysplasia with hypocellular BM.
In-Cylinder Soot Deposition Rates Due to Thermophoresis in a Direct Injection Diesel Engine (1992)

&lt;div class="htmlview paragraph"&gt;An investigation of the mechanism causing in-cylinder soot deposition in a direct injection diesel engine was carried out. First, an analytical study was undertaken to determine which of following possible deposition mechanisms, thermophoresis, Brownian diffusion, turbulent diffusion, inertial impingement, or electrophoresis were responsible for the deposition of the soot on the combustion chamber walls. Based on a series of numerical models comparing each mechanism under conditions typical of diesel engine combustion, thermophoresis was singled out as the most likely cause of in-cylinder soot deposition.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Second, an experiment was performed to test the hypothesis that the soot deposition was caused by thermophoresis. An optical probe was designed to fit an access port in the cylinder head of a Cummins NH250 single cylinder test engine. The probe was designed such that a sapphire optical access window was positioned flush with the combustion chamber surface when the probe was installed. The probe incorporated the capability of changing the temperature of the window surface approximately 100øC when the engine was operating at: 1300 rpm, an equivalence ratio of 0.3, and an intake pressure of 27 psi.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A thermocouple was placed near the window to measure the temperature. A fiber optic cable carried the combustion radiation signal, transmitted through the window, to a photodiode detector. The photodiode signal was amplified and then recorded by a high speed data acquisition system. In the testing sequence, the engine was first motored at 1300 rpm and then the fuel was turned on. The radiation signal was then recorded for the next 1600 cycles and was observed to attenuate as soot accumulated on the window. The transmittance of the soot layer on the window, &lt;img class="article-image inline" src="921629_fig0001.jpg" alt=""/&gt;, was calculated by assigning the initial peak voltage radiation signal recorded to I&lt;sub&gt;o&lt;/sub&gt; and the signal measured subsequent to this to I&lt;sub&gt;&lt;i&gt;[&lt;/i&gt;&lt;/sub&gt;. Using light scattering theory, the transmittance was then applied to the calculation of the mass deposited on the window. The results from the experimental study show that the soot deposition rate was, on average, 46.9% higher when the window was cooled versus uncooled. These results were consistant with the earlier predictions that thermophoresis is a main contributor to the soot deposits on the in-cylinder surfaces.&lt;/div&gt;
Sparse Regression Driven Mixture Importance Sampling for Memory Design (2017)

In this paper, we present a sparse regression (SpaRe) model-based yield analysis methodology and apply it to memory designs with state-of-the-art write-assist circuitry. At the core of its engine is a mixture importance sampling technique which consists of a uniform sampling stage and an importance sampling stage. The proposed methodology allows for fast and accurate statistical analysis of rare fail events. In our approach, a SpaRe model is built using the uniform sampling stage data points obtained via circuit simulation (CktSim). Along with the model, an optimal threshold value is determined for proper pass/fail predict capability. The model and the threshold value are then used to predict the response in the importance sampling stage. This alleviates the need for CktSims in the latter stage and introduces significant speedup compared to fully CktSim-based approaches. The SpaRe model-based yield analysis is tested on a 14-nm FinFET SRAM design, and the results corroborate well with that of full CktSim-based yield analysis. The methodology is used to compare multiple state-of-the-art SRAM designs including selective boost and write-assist designs. The operating Vmin ranges and trends corroborate well with hardware measurements.
Efficient transcription and replication of simian immunodeficiency virus in the absence of NF-kappaB and Sp1 binding elements (1996)

Ten mutants of the simian immunodeficiency virus (SIV) SIVmac239 bearing deletions (delta) or substitutions (subst) in the NF-kappaB and/or Sp1 binding elements were created, and the replicative capacities of the mutants were analyzed. All mutants, including one extensively mutagenized strain entirely missing the NF-kappaB and four Spl binding elements, replicated with wild-type kinetics and to a wild-type level in peripheral blood mononuclear cell cultures in 50 to 100% of the experiments. One group of mutants replicated very similarly to SIVmac239 in kinetics and yield in CEMxl74 cells (2xNFKappaB > or = SlVmac239 approximately deltaNFkappaB approximately deltaSpl234 approximately substNFkappaB approximately substSpl2 approximately substSp23), while a second group replicated with delayed or slightly delayed kinetics in CEMxl74 cells (SIVmac239 > substSp34 > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSp1 > substSpl234). Reversions or additional mutations were not detected in the U3 and R regions of proviral DNA from CEMxl74 cells infected with the SIVmac239 mutants. Similar results were obtained when mutants of SIVmacMER (a macrophage-competent derivative of SIVmac239) were tested in peripheral blood mononuclear cell and CEMx174 cultures. However, the growth of most mutated viruses was suppressed in primary rhesus monkey alveolar macrophages (SIVmacMER approximately 2xNFkappaB approximately substNFkappaB > deltaNFkappaB > deltaNFkappaBdeltaSpl234 approximately deltaNFkappaBdeltaSpl > deltaSpl234 approximately substSpl2 > substSp23 approximately substSp34 approximately substSpl234 > or = SIVmac239). Thus, changes in the Sp1 binding sites had the most dramatic effects on SIVmac replication in primary macrophage cultures. Analysis of long terminal repeat-driven secreted alkaline phosphatase activity in transient assays showed that, unlike human immunodeficiency virus type 1, the SIV long terminal repeat possesses an enhancer region just upstream of the NF-kappaB element which maintains significant levels of basal transcription in the absence of NF-kappaB and Sp1 sites. This region is responsive to transactivation by Tat. In addition, the SIV TATA box was shown to be stronger than that of human immunodeficiency virus type 1. Therefore, the surprisingly high replicative capacity of NF-kappaB and Sp1 binding site mutants of SIVmac is due to unique features or the enhancer/promoter region.
Phycoerythrin and interfertility patterns inCallithamnion(Rhodophyta) isolates (1981)

Ten sexually reproducing strains of Callithamnion have been used in a comparison of phycoerythrin, interfertility and morphology. Four isolates of C. byssoides Harvey from North America (Massachusetts, New York, North Carolina and Georgia) are all interfertile and they also hybridize with C. halliae Collins (UTEX LB1411) from Texas. Norwegian C. byssoides and C. roseum (Roth) Lyngbye (sensu Harvey) isolates are not interfertile with any North American strain. Phycoerythrins were compared by absorption spectroscopy, SDS gel electrophoresis and Ouchterlony double diffusion techniques. The absorption spectrum of phycoerythrin from the Massachusetts C. roseum is different from that of the R-phycoerythrin typical of all other strains. The subunits of phycoerythrin from all cultures showed very similar mobilities in SDS gels. Phycoerythrin from all C. byssoides and C. halliae reacted identically in Ouchterlony plates. Antigenic identity with C. byssoides was also seen with one strain (an unidentified species from Vera Cruz, Mexico) which is not crossable with C. byssoides. Immunological reactions of partial identity were observed with other North Atlantic strains as well as Pacific isolates and members of other genera. These results indicate that the basic protein structure of Callithamnion phycoerythrin is highly conserved. The ability to detect differences among Callithamnion species using immunology provides a valuable taxonomic indicator at that level.
Epidermal Growth Factor and Acute Radiation Damage in CDF1 Mice in Vivo (1997)

The aim was to investigate if extent and time course of acute radiation damage to epidermis and intestine could be moderated by epidermal growth factor (EGF). Twelve-to-sixteen weeks old female CDF1 mice were treated either by single dose local irradiation to the right hind leg or total body irradiation (TBI). The endpoints were skin score and lethality, respectively. Human recombinant EGF was given s.c. or i.p. at a dose of 5-10 microg/day either before or after irradiation. Body weight was significantly higher for EGF treated animals compared with controls treated with saline. However, EGF did not reduce the median skin score following local irradiation and did not increase LD50 (days 1-6) following TBI. Further studies using more specific assays are necessary to determine if radiation damage to less toxic levels can be ameliorated by EGF.
Field emission from silicon and molybdenum tips coated with diamond powder by dielectrophoresis (1996)

Thin diamond layers have been formed on molybdenum and single-crystal silicon field emitters using a dielectrophoresis coating method from a suspension of diamond powder in a nonconducting fluid. Transmission and scanning electron microscopy observation revealed a significant amount of diamond on the tips. The average thickness of the deposited diamond layer depended on the applied bias and the immersion time. Field emission from these diamond-coated emitters exhibited significant enhancement compared to the pure emitters.
Electrically switchable third-harmonic generation in photonic crystals (2005)

We demonstrate electrically switchable third-harmonic generation in low refractive index contrast one-dimensional photonic crystals pumped by a near-infrared laser beam. A dramatic enhancement of the third-harmonic signal is observed on the short wavelength side of the photonic crystal stop band. The enhancement of the third-harmonic generation disappears when an electric field is applied, revealing the electrical switchability of the third-harmonic generation. The observed phenomenon of enhancement is explained theoretically with a coupled-mode model. We also show that up to a modulation frequency of 10 kHz the switching properties are supported in the photonic crystal.