gebhart/patrepeval huggingface dataset:
Depth of field extension with spherical optics (2008)

The introduction of spherical aberration in a lens design can be used to extend the depth of field while preserving resolution up to half the maximum diffraction-limited spatial frequency. Two low-power microscope objectives are shown that achieve an extension of +/- 0.88 lambda in terms of wavefront error, which is shown to be comparable to alternative techniques but without the use of special phase elements. The lens performance is azimuth-independent and achromatic over the visible range.
MyVox—Device for the communication between people: blind, deaf, deaf-blind and unimpaired (2014)

Humans are social creatures. We learn by connecting with those around us, through communication. While people with hearing or visual impairments alone can find a way to share their thoughts with others and understand them, deaf-blind people face a much more difficult communication task. Here, appropriate technology can play a decisive role. The small size and low power consumption of ARM-based computers, such as the Raspberry Pi, have opened the door for many embedded applications, including a heart monitoring method and an assistive navigation system for the blind. Some estimates place the number of deaf-blind people in the U.S. at around 40,000 individuals. While a commercial view considers this a small market, thus making communication devices not commercially viable; from a humanitarian view, this is a significant number of people who would greatly benefit from a technological means of communication. This paper presents the design, prototype and testing of a portable keyboard and speaker device with a braille refreshable display for the communication between two people (either being deaf-blind) that has both, a comparatively low cost, and many possibilities for further development on the ARM-based computer system.
Detection of Mycoplasma genitalium in urogenital specimens by real-time PCR and by conventional PCR assay (2004)

A real-time LightCycler PCR (LC-PCR) with hybridization probes for detection of Mycoplasma genitalium in endocervical and first void urine specimens was developed and compared to a conventional PCR. The primers for both assays were identical and designed to amplify a 427 bp fragment of the 16S rRNA gene of M. genitalium. The LC-PCR assay had a detection limit of < 5 bacterial genomes per reaction when dilutions of genomic DNA from a type strain of M. genitalium were tested. First void urine from 398 men and first void urine and endocervical specimens from 301 women attending an STD clinic were analysed by LC-PCR and by the conventional PCR. Using the conventional PCR as reference, the LC-PCR had a specificity of 99.7 % and a sensitivity of 72.2 % for the detection of M. genitalium in first void urine samples from men. There was no significant difference in the performance of the LC-PCR assay compared to the conventional PCR when endocervical swabs were considered (58 and 65 %, respectively) or with a set of endocervical swab/urine specimens for which the LC-PCR assay detected 73 % of the infections (specificity = 98.6 % and sensitivity = 68.2 %) while the conventional PCR detected 85 % of the infections. With female urine specimens there was a significant difference between the two assays (38 and 73 %, respectively; P = 0.01 McNemar's test). This illustrates the need to analyse both endocervical and urine specimens, because M. genitalium DNA was detected in only one of the two specimens in a great number of the M. genitalium-infected women. The lower sensitivity of the LC-PCR assay was probably caused by a combination of inhibition and limitations regarding the amount of template DNA. The LC-PCR assay was easy to perform and the simultaneous amplification and detection eliminated the need for further handling of PCR products. With improvement in sample preparation methods and increased volumes of the template DNA, the LC-PCR assay could be a useful routine diagnostic method.
Mechanistic Role of Cytochrome P450 Monooxygenases in Oxidized Low-Density Lipoprotein–Induced Vascular Injury (2003)

Oxidized low-density lipoprotein (oxLDL) is an important risk factor for vascular injury. Its role on coronary vasoconstriction remains speculative. Endothelial monooxygenases (cytochrome P450s [CYPs]) are regulators of vascular tonus through production of epoxy fatty acids. We investigated the effects of oxLDL on CYP monooxygenases in human arterial coronary endothelial cells and explanted healthy and atherosclerotic aortae. We found oxLDL to induce radical oxygen species production via the action of NADPH oxidase NOX4. Intracellular radical oxygen species production prompted reduced protein expression of the transcriptional regulator nuclear factor 1 (NF-1). We identified novel DNA binding sites for NF-1 in promoter regions of CYPs. DNA binding of NF-1 was confirmed by electromobility shift assays. OxLDL repressed DNA binding of NF-1 and diminished transcript level of CYP genes targeted by this factor. The production of endothelial-derived hyperpolarization factor, a key regulator of vascular tonus, was also reduced. Repression of CYP monooxygenases was reversed, and production of endothelial-derived hyperpolarization factor was normalized after treatment of endothelium with the lectin-like oxLDL receptor antagonist kappa-carrageenan or blocking of LOX-1 with a specific antibody. This suggests a mechanistic role of CYP monooxygenases in oxLDL-induced vascular injury. Therapy of endothelial dysfunction through LOX-1 receptor antagonism will be an interesting avenue to explore. The full text of this article is available online at http://www.circresaha.org.
Experimental study and numerical simulation of the injection stretch/blow molding process (1998)

Abstract The injection stretch/blow molding process of PET bottles is a complex process, in which the performance of the bottles depends on various processing parameters. Experimental work has been conducted on a properly instrumented stretch/blow molding machine in order to characterize these processing parameters. The objective being a better understanding of the pressure evolution, preform free inflation has been processed and compared with a simple thermodynamic model. In addition, a numerical model for the thermomechanical simulation of the stretch/blow molding process has been developed. At each time step, mechanical and temperature balance equations are solved separately on the current deformed configuration. Then, the geometry is updated. The dynamic equilibrium and the Oldroyd B constitutive equations are solved separately using an iterative procedure based on a fixed‐point method. The heat transfer equation is discretized using the Galerkin method and approximated by a Crank‐Nicholson's scheme over the time increment. Successful free blowing simulations as well as stretch/blow molding simulations have been performed and compared with experiments.
Mini-Review: Antifouling Natural Products from Marine Microorganisms and Their Synthetic Analogs (2017)

Biofouling causes huge economic loss and generates serious ecological issues worldwide. Marine coatings incorporated with antifouling (AF) compounds are the most common practices to prevent biofouling. With a ban of organotins and an increase in the restrictions regarding the use of other AF alternatives, exploring effective and environmentally friendly AF compounds has become an urgent demand for marine coating industries. Marine microorganisms, which have the largest biodiversity, represent a rich and important source of bioactive compounds and have many medical and industrial applications. This review summarizes 89 natural products from marine microorganisms and 13 of their synthetic analogs with AF EC<sub>50</sub> values ≤ 25 μg/mL from 1995 (the first report about marine microorganism-derived AF compounds) to April 2017. Some compounds with the EC<sub>50</sub> values < 5 μg/mL and LC<sub>50</sub>/EC<sub>50</sub> ratios > 50 are highlighted as potential AF compounds, and the preliminary analysis of structure-relationship (SAR) of these compounds is also discussed briefly. In the last part, current challenges and future research perspectives are proposed based on opinions from many previous reviews. To provide clear guidance for the readers, the AF compounds from microorganisms and their synthetic analogs in this review are categorized into ten types, including fatty acids, lactones, terpenes, steroids, benzenoids, phenyl ethers, polyketides, alkaloids, nucleosides and peptides. In addition to the major AF compounds which targets macro-foulers, this review also includes compounds with antibiofilm activity since micro-foulers also contribute significantly to the biofouling communities.
Long‐term in vitro persistence of magnetic properties after magnetic bead‐based cell separation of T cells (2020)

Magnetic-activated cell sorting (MACS) using magnetic nanoparticles coated with specific antibodies is commonly used in immunology research. For in vitro isolation purposes, it is important to know to what extent the magnetic properties remain present in the isolated cell populations and whether it has consequences for sequential isolations. We hypothesized that only upon cell division, cells will lose their magnetic properties via dilution of the particles in/on their daughter cells. We analysed residual magnetic properties of cells that divided vs cells that did not divide after magnetic bead-based cell separation. As a model, we isolated T cells using beads targeting the non-modulating surface molecule CD45RO. Cells were labelled with the cell division tracking dye PKH and cultured under different conditions to induce variable degrees of cell division. We demonstrate that T cells that underwent no, or only minimal, cell divisions after MACS retained magnetic properties for up to at least 2 weeks of in vitro culture. The presence of nanoparticles was detected on their cell surface and intracellularly using Labeling Check reagent. These results have important consequences for procedures requiring repetitive isolation rounds after in vitro culture.
Efficient Laser-Driven Proton Acceleration from a Cryogenic Solid Hydrogen Target (2019)

We report on the successful implementation and characterization of a cryogenic solid hydrogen target in experiments on high-power laser-driven proton acceleration. When irradiating a solid hydrogen filament of 10 μm diameter with 10-Terawatt laser pulses of 2.5 J energy, protons with kinetic energies in excess of 20 MeV exhibiting non-thermal features in their spectrum were observed. The protons were emitted into a large solid angle reaching a total conversion efficiency of several percent. Two-dimensional particle-in-cell simulations confirm our results indicating that the spectral modulations are caused by collisionless shocks launched from the surface of the the high-density filament into a low-density corona surrounding the target. The use of solid hydrogen targets may significantly improve the prospects of laser-accelerated proton pulses for future applications.
A Cell Line Derived from the Fin of Japanese Flounder, Paralichthys olivaceus. (1991)

A cell line, designated as FF-11, was developed from Japanese flounder (Paralichthys olivaceus) fin. This epithelioid cell has been passed 45 times in a period of 2 years in Leibovitz's L-15 medium supplemented with 20% fetal bovine serum (FBS) at 20deg;C. A modal number of chromosomes at passage 42 was 48, which is the same as that of normal flounder somatic cells. The temperature range from 20 to 28deg;C supported the growth of FF-11 cell and optimal growth occurred at 25 to 28deg;C, but 37deg;C was lethal. Cells were able to be stored at a -80deg;C with 10% dimethyl sulphoxide for at least 12 months and no mycoplasmal, bacterial or fungal contaminations were detected. The FF-11 cell line was susceptible to yellowtail ascites virus (YAV) and Rhabdovirus olivaceus (HRV), but the susceptibility was lower than those of established fish cell lines (FHM, EPC, CHSE-214, RTG-2). It was tried to isolate flounder herpesvirus (FHV), the causative agent of epidermal hyperplasia of flounder larvae, by FF-11 cell, but to no avail.
Do what I mean: online shopping with a natural language search agent (2001)

Ineffective search engines on e-catalog sites are driving away potential customers. Natural-language querying improves precision and parsing capability, and with advances in the technology, it can also meet these shopping sites' performance demands.
Another Geotech Import: Deep Soil Mixing (1987)

A technique called deep soil mixing (DSM), imported from Japan, has been used to stabilize an existing dam foundation. When the Bureau of Reclamation discovered that Jackson Lake Dam had been built (in 1916) on soils that subject to liquefaction, they lowered the lake and decided to remove the 50 ft high hydraulic fill embankment and replaced it wwith an engineered compacted fill. Dynamic compaction was used to treat shallow parts of the foundation, but the very deep, loose soils were treated with DSM, which differs from jet grouting in two ways. The equipment is not high pressure, and the soil is mixed in situ, without excavation, by special paddles on the drilling auger. DSM columns were placed continuously to form an upstream cutoff wall and then in a hexagonal pattern to stabilize the foundation. DSM can also be used to prevent migration of contaminated groundwater, stabilize soils under water and create structural walls.
Highly Efficient White Organic Electroluminescence from a Double-Layer Device Based on a Boron Hydroxyphenylpyridine Complex (2002)

Electroluminescence from 400 to 700 nm (see right picture) is exhibited by an organic electroluminescent device based on (mdppy)BF (left picture) as emitter and a 1,1′-biphenyl-4,4′-diamine derivative as a hole-transporting material. The device emits white light with high efficiency and good color purity.
Characterization of <i>cis-</i> Acting Sites Controlling Arginine Deiminase Gene Expression in <i>Streptococcus gordonii</i> (2006)

The arginine deiminase system (ADS) is responsible for the production of ornithine, CO2, ammonia, and ATP from arginine. The ADS of the oral bacterium Streptococcus gordonii plays major roles in physiologic homeostasis, acid tolerance, and oral biofilm ecology. To further our understanding of the transcriptional regulation of the ADS (arc) operon, the binding of the ArcR transcriptional activator, which governs expression of the ADS in response to arginine, was investigated by DNase I protection and gel mobility shift assays. An ArcR binding sequence was found that was 27 bp in length and had little sequence similarity to binding sites of other arginine metabolism regulators. The presence of arginine at physiologically relevant concentrations enhanced the binding of ArcR to its target. Using cat fusions, various deletion and substitution mutations within the putative ArcR footprint were shown to cause dramatic reductions in expression from the arcA promoter in vivo, confirming that the 27-bp sequence is required for optimal expression and induction of the ADS by arginine. Mutation of two putative catabolite response elements (CREs) within the arc promoter region showed that both CREs contribute to catabolite repression. A thorough understanding of the regulation of the ADS in S. gordonii and related organisms is needed to develop ways to exploit arginine catabolism for the control of oral diseases. Identification of the ArcR and CcpA binding sites lays the foundation for a more complete understanding of the complex interactions of multiple regulatory proteins with elements in the arc promoter region.
Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis (2009)

Structural genomics (SG) is an international effort that aims at solving three-dimensional shapes of important biological macro-molecules with primary focus on proteins. One of the main bottlenecks in SG is the ability to produce dif-fraction quality crystals for X-ray crystallogra-phy based protein structure determination. SG pipelines allow for certain flexibility in target selection which motivates development of in- silico methods for sequence-based prediction/ assessment of the protein crystallization pro-pensity. We overview existing SG databanks that are used to derive these predictive models and we discuss analytical results concerning protein sequence properties that were discov-ered to correlate with the ability to form crystals. We also contrast and empirically compare mo- dern sequence-based predictors of crystalliza-tion propensity including OB-Score, ParCrys, XtalPred and CRYSTALP2. Our analysis shows that these methods provide useful and compli-mentary predictions. Although their average ac- curacy is similar at around 70%, we show that application of a simple majority-vote based en-semble improves accuracy to almost 74%. The best improvements are achieved by combining XtalPred with CRYSTALP2 while OB-Score and ParCrys methods overlap to a larger extend, although they still complement the other two predictors. We also demonstrate that 90% of the protein chains can be correctly predicted by at least one of these methods, which suggests that more accurate ensembles could be built in the future. We believe that current protein crystalli-zation propensity predictors could provide useful input for the target selection procedures utilized by the SG centers.
<sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N NMR assignments of phenazopyridine derivatives (2004)

Phenazopyridine hydrochloride (1), a drug in clinical use for many decades, and some derivatives were studied by one- and two-dimensional (1)H, (13)C and (15)N NMR methodology. The assignments, combined with DFT calculations, reveal that the preferred protonation site of the drug is the pyridine ring nitrogen atom. The chemoselective acetylation of phenazopyridine (2) and its influence on the polarization of the azo nitrogen atoms were evidenced by the (15)N NMR spectra. Molecular calculations of the phenazopyridines 2-4 show that the pyridine and phenyl groups are oriented in an antiperiplanar conformation with intramolecular hydrogen bonding between the N-b atom and the C-2 amino group preserving the E-azo stereochemistry.
Troglitazone Inhibits Cell Growth and Induces Apoptosis of B-Cell Acute Lymphoblastic Leukemia Cells with t(14;18) (2006)

Peroxisome proliferator-activated receptor-gamma (PPARgamma), a member of the nuclear receptor superfamily, has been detected in several human leukemia cells. Recent studies reported that PPARgamma ligands inhibit cell proliferation and induce apoptosis in both normal and malignant B-lineage cells. We investigated the expression of PPARgamma and the effects of PPARgamma ligands on UTree-O2, Bay91 and 380, three B-cell acute lymphoblastic leukemia (B-ALL) cell lines with t(14;18), which show a poor prognosis, accompanying c-myc abnormality. Western blot analysis identified expression of PPARgamma protein and real-time PCR that of PPARgamma mRNA on the three cell lines. Troglitazone (TGZ), a synthetic PPARgamma ligand, inhibited cell growth in these cell lines in a dose-dependent manner, which was associated with G(1) cell cycle arrest and apoptosis. We also found this effect PPARgamma independent since PPARgamma antagonists failed to reverse this effect. We assessed the expression of c-myc, an apoptosis-regulatory gene, since c-myc abnormality was detected in most B-ALL cells with t(14;18). TGZ was found to dose-dependently downregulate the expression of c-myc mRNA and c-myc protein in the three cell lines. These results suggest that TGZ inhibits cell growth via induction of G(1) cell cycle arrest and apoptosis in these cell lines and that TGZ-induced apoptosis, at least in part, may be related to the downregulation of c-myc expression. Moreover, the downregulation of c-myc expression by TGZ may depend on a PPARgamma-independent mechanism. Further studies indicate that PPARgamma ligands may serve as a therapeutic agent in B-ALL with t(14;18).
False-Positive Results for Immunoglobulin M Serologic Results: Explanations and Examples (2013)

Scenario
Identification and characterization of IL-10/IFN-γ–producing effector-like T cells with regulatory function in human blood (2009)

Two subsets of natural and adaptive regulatory T (T reg) cells have been described, but the identity of adaptive type 1 regulatory (Tr1)-like cells in humans is unclear. We analyzed a subset of human blood CD4(+) T cells--CD45RA(-)CD25(-)interleukin (IL)-7 receptor (R)(-) cells--that rapidly secreted high levels of IL-10 together with interferon gamma, but produced little IL-2. These IL-7R(-) T cells were rare, anergic, and largely Foxp3(-). They expressed low levels of Bcl-2 but high levels of Ki-67 and ICOS, suggesting that they have been recently activated in vivo. Consistently, they responded selectively to persistent foreign and self-antigens under steady-state conditions. Unlike natural CD25(+) T reg cells, IL-7R(-) cells suppressed naive and memory T cell proliferation in an IL-10-dependent fashion, and they required strong T cell receptor stimulation for suppression. To our knowledge, this is the first report that identifies Tr1-like cells in human blood. These IL-10-secreting cells have characteristics of chronically activated Th1 effector cells and are distinct from CD25(+) T reg cells.
Empirical Study on Factors Influencing Farmland Circulation in Economically Developed Areas (2013)

Farmland circulation is the foundation of development of regional farmland market. With the aid of survey data of Jiangsu Province and using Heckman two-stage method, this paper analyzed factors influencing farmland circulation from supply and demand of land. Results showed that non-agricultural employment, social security level, and regional economic development level are key factors. In view of these factors, it is recommended to improve rural labor quality, establish perfect rural social security system, and constantly improve rural security level, which are fundamental ways to promoting farmland circulation and improve circulation market.
Phase‐Field Relaxation of Topology Optimization with Local Stress Constraints (2006)

We introduce a new relaxation scheme for structural topology optimization problems with local stress constraints based on a phase‐field method. In the basic formulation we have a PDE‐constrained optimization problem, where the finite element and design analysis are solved simultaneously. The starting point of the relaxation is a reformulation of the material problem involving linear and 0‐1 constraints only. The 0‐1 constraints are then relaxed and approximated by a Cahn–Hilliard‐type penalty in the objective functional, which yields convergence of minimizers to 0‐1 designs as the penalty parameter decreases to zero. A major advantage of this kind of relaxation opposed to standard approaches is a uniform constraint qualification that is satisfied for any positive value of the penalization parameter. The relaxation scheme yields a large‐scale optimization problem with a high number of linear inequality constraints. We discretize the problem by finite elements and solve the arising finite‐dimensional programming problems by a primal‐dual interior point method. Numerical experiments for problems with local stress constraints based on different criteria indicate the success and robustness of the new approach.
RND type efflux pump system MexAB-OprM of pseudomonas aeruginosa selects bacterial languages, 3-oxo-acyl-homoserine lactones, for cell-to-cell communication (2012)

This work demonstrated that MexAB-OprM does not control the binding of LasR to 3-oxo-Cn-HSLs but rather accessibility of non-cognate acyl-HSLs to LasR in P. aeruginosa. MexAB-OprM not only influences multidrug resistance, but also selects acyl-HSLs and regulates QS in P. aeruginosa. The results demonstrate a new QS regulation mechanism via the efflux system MexAB-OprM in P. aeruginosa.