gebhart/patrepeval huggingface dataset:
Advancing biomaterials towards biological complexity (2018)

3D printing has the potential for on-demand, patient-specific devices with high structural complexity. However, the tools and biomaterials most widely available for 3D printing are largely limited to fused deposition modelling (FDM) with commodity plastics that lack cell-scale resolution and biological cues. The lack of biologically active materials, also called 'bioinks,' is a key issue that limits the ability to produce engineered tissues, tissue interfaces and functional organs. While advances are being made in the field of biomaterials, current technologies can be combined into hybrid systems that overcome the limitations of a single technique or material, as described in this article.
Cutting Edge: DNA Immunization with Minigenes of Carbohydrate Mimotopes Induce Functional Anti-Carbohydrate Antibody Response (2000)

To date, the generation of anti-carbohydrate Th1 immune responses, which would be useful for both tumor immunotherapy as well as in pathogen vaccine strategies, has been elusive. To augment Th1 immune responses to carbohydrate Ags, we describe results of DNA vaccination studies in mice using plasmids encoding designed peptide mimotopes (minigenes) of the neolactoseries Ag Lewis Y (LeY). In contrast to LeY immunization, immunization with mimotope-encoded plasmids induced LeY cross-reactive IgG2a Abs. Minigene immunization primed for a LeY-specific response that is rapidly activated upon encounter with nominal Ag upon subsequent boost. The resulting IgG2a response mediated complement-dependent cytotoxicity of a LeY-expressing human tumor cell line in the presence of human complement. These studies establish that peptide mimotopes of carbohydrate Ags encoded as DNA plasmids are novel immunogens providing a means to manipulate carbohydrate cross-reactive Th1 responses.
Size-Tailored Biocompatible FePt Nanoparticles for Dual T1/T2 Magnetic Resonance Imaging Contrast Enhancement (2019)

The development of new contrast agents (CAs) for magnetic resonance imaging (MRI) is of high interest, especially because of the increased concerns of patient safety and quick clearance of clinically used gadolinium and iron oxide-based CAs, respectively. Here, a two-step synthesis of superparamagnetic water-soluble iron platinum (FePt) nanoparticles (NPs) with core sizes between 2 and 8 nm for use as CAs in MRI is reported. First, wet-chemical organometallic NPs are synthesized by thermal decomposition in the presence of stabilizing oleic acid and oleylamine. Second, the hydrophobic NPs are coated with an amphiphilic polymer and transferred into aqueous media. Their magnetization values and relaxation rates exceed those published for CAs already used for clinical application. Their saturation magnetization increases with the core size to approximately 82 A·m<sup>2</sup>/kg<sub>Fe</sub>. For 8 nm NPs, the <i>T</i><sub>2</sub> relaxivity of approximately 221 (mM·s)<sup>-1</sup> is 5 times larger than that for the ferumoxides, and for 6 nm NPs, the <i>T</i><sub>1</sub> relaxivity of approximately 12 (mM·s)<sup>-1</sup> is slightly higher than that of ultrasmall gadolinium oxide NPs. The 6 nm FePt NPs are identified as excellent CAs for both <i>T</i><sub>1</sub> and <i>T</i><sub>2</sub> imaging. Most importantly, because of their coating, significantly low cytotoxicity is achieved. FePt NPs prove to be a promising alternative to gadolinium and iron oxide NPs showing high-quality CA characteristics for both <i>T</i><sub>1</sub>- and <i>T</i><sub>2</sub>-weighted images.
The fate of not sensing phosphate (2012)

&lt;br&gt;Comment on: Crépin S, et al. Infect Immun 2012; 80:2802-15; PMID:22665376;&#13;\nhttp://dx.doi.org/10.1128/IAI.00162-12&lt;/br&gt;
A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals (2016)

The pathogenic yeast Cryptococcus neoformans causes cryptococcosis, a life-threatening fungal disease. C. neoformans has multiple virulence mechanisms that are non-host specific, induce damage and interfere with immune clearance. Microarray analysis of C. neoformans strains serially passaged in mice associated a small gene (CNAG_02591) with virulence. This gene, hereafter identified as HVA1 (hypervirulence-associated protein 1), encodes a protein that has homologs of unknown function in plant and animal fungi, consistent with a conserved mechanism. Expression of HVA1 was negatively correlated with virulence and was reduced in vitro and in vivo in both mouse- and Galleria-passaged strains of C. neoformans. Phenotypic analysis in hva1Δ and hva1Δ+HVA1 strains revealed no significant differences in established virulence factors. Mice infected intravenously with the hva1Δ strain had higher fungal burden in the spleen and brain, but lower fungal burden in the lungs, and died faster than mice infected with H99W or the hva1Δ+HVA1 strain. Metabolomics analysis demonstrated a general increase in all amino acids measured in the disrupted strain and a block in the TCA cycle at isocitrate dehydrogenase, possibly due to alterations in the nicotinamide cofactor pool. Macrophage fungal burden experiments recapitulated the mouse hypervirulent phenotype of the hva1Δ strain only in the presence of exogenous NADPH. The crystal structure of the Hva1 protein was solved, and a comparison of structurally similar proteins correlated with the metabolomics data and potential interactions with NADPH. We report a new gene that modulates virulence through a mechanism associated with changes in fungal metabolism.
On the Convex Properties of Wireless Power Transfer With Nonlinear Energy Harvesting (2020)

The convex property of a nonlinear wireless power transfer (WPT) is characterized in this work. Following a nonlinear energy harvesting model, we express the relationship between the harvested direct current (DC) power and the power of the received radio-frequency signal via an implicit function, based on which the convex property is further proved. In particular, for a predefined rectifier`s input signal distribution, we show that the harvested DC power of the nonlinear model is convex in the reciprocal of the rectifier's input signal power. Finally, we provide an example to show the advantages of applying the convex property in WPT network designs.
On the Possibility of Identifying Nonlinear Constitutive Laws by Back Analysis (2006)

Back analysis of a ground deformational behavior involving nonlinear behavior is discussed. It is of primary importance to make reliable prediction of deformational behavior for shallow tunnels in soft ground. However, predictions made often prove to be incorrect due to complexity of constitutive law and other relevant factors. Back analysis therefore becomes more important, for it may be used to interpret measured displacement to derive non-linear material characteristics. The paper shows some example in which a deformational mechanism is studied in the light of inhomogeneous distribution of Young's module, from which a logic is derived to identify two different types of non-linear constitutive relationships.
A high precision 24-GHz FMCW radar based on a fractional-N ramp-PLL (2003)

A 24-GHz FMCW radar system is presented using a fractional-N phase-locked loop ramp generator. This fractional-N ramp generator achieves relative ramp nonlinearities below 10/sup -8/. Among others linear frequency ramps are important tools in high precision FMCW radar systems. Highly linear frequency ramps make post measurement error correction feasible. Other important aspects of the high performance FMCW radar system are the design of the microwave circuit and the digital signal processing of the IF signals. Furthermore, a large RF bandwidth of more than 3 GHz obtained by thorough simulations results in a high range resolution and a good potential measurement accuracy. To maintain this high potential accuracy, a phase slope algorithm is used to calculate the precise range value leading to a significantly better precision with absolute range errors below 0.8 mm, compared to the commonly used spectral center algorithm.
Expression and purification of immunologically reactive DPPD, a recombinantMycobacterium tuberculosisskin test antigen, usingMycobacterium smegmatisandEscherichia colihost cells (2004)

DPPD is a Mycobacterium tuberculosis recombinant antigen that elicits specific delayed type hypersensitivity reactions similar in size and morphological aspects to that elicited by purified protein derivative, in both guinea pigs and humans infected with M. tuberculosis. In addition, earlier clinical studies with DPPD suggested that this molecule could improve the specificity of the tuberculin skin test, which is used as an important aid for the diagnosis of tuberculosis. However, these studies could only be performed with DPPD engineered as a fusion molecule with another Mycobacterium spp. protein because no expression of DPPD could be achieved as a single molecule or as a conventional fusion protein in any commercial system. Although recombinant fusion proteins are in general suitable for several biological studies, they are by definition not ideal for studies involving highly purified and defined polypeptide sequences. Here, we report two alternative approaches for the expression of immunologically reactive recombinant genuine DPPD. The first approach used the rapidly growing, nonpathogenic Mycobacterium smegmatis as host cells transformed with the pSMT3 plasmid vector containing the full-length DPPD gene. The second approach used Escherichia coli transformed with the pET-17b plasmid vector containing the DPPD gene engineered in a three-copy fusion manner in tandem with itself. Though at low levels, expression and purification of immunologically reactive DPPD in M. smegmatis could be achieved. More abundant expression and purification of DPPD as a homo-trimer molecule was achieved in E. coli (> or =2 mg/L of bacterial broth cultures). Interestingly, expression could only be achieved in host cells transformed with the DPPD gene containing its leader peptide. However, the expressed proteins lacked the leader sequence, which indicates that processing of the M. tuberculosis DPPD gene was accurately achieved and necessary in both M. smegmatis and E. coli. More importantly, the delayed type hypersensitivity reactions elicited by purified molecules in guinea pigs infected with M. tuberculosis were indistinguishable from that elicited by purified protein derivative. Because the DPPD gene is present only in the tuberculosis-complex organisms of the Mycobacterium genus, these highly purified molecules should be helpful in identifying individuals sensitized with tubercle bacilli.
MANAGEMENT OF ENDOPHTHALMITIS IN A SILICONE OIL-FILLED EYE (1997)

Aggressive management of endophthalmitis in an eye requiring silicone oil tamponade may salvage useful vision.
Sulfur‐containing polymers by the reaction of diphenyl sulfide with sulfur chlorides (1992)

Abstract The electrophilic reaction of sulfur dichloride with diphenyl sulfide proceeds efficiently at room temperature to yield oligo(phenylene sulfide) in the presence of a catalytic amount of Fe powder. Sulfur dichloride shows higher reactivity than sulfur monochloride. The reaction is promoted through the activation of sulfur dichloride by Fe powder. The polymeric product contains a linear structure linked by disulfide and sulfide bonds.
The management of stable angina. (1997)

Symptoms of chronic stable angina are easily identifiable and indicate that a patient is at increased risk of heart attack and death. In patients with less severe angina, medical treatments are as effective as more invasive treatments and produce better survival rates. There is little evidence that the main types of medical treatment differ in effectiveness. For patients at higher risk, invasive revascularisation procedures--coronary artery bypass grafting (CABG) and angioplasty--are more appropriate. CABG is slightly more effective than angioplasty. A high proportion of patients receiving angioplasty require re-treatment. The risk of recurrence and coronary events is reduced if patients who receive invasive procedures also have long-term low dose aspirin and cholesterol-lowering therapy. There is no clear evidence that intracoronary stents are more cost-effective than standard angioplasty. There is a need for evidence-based guidance to help determine referral thresholds for further investigation, and revascularisation procedures. There is evidence of inequality of access to testing and treatment, by gender, ethnic group and social class. Access should be monitored in order to promote equity.
CCD Inner Workings: Residual Bulk Image: Cause and Cure (2011)

Understanding the subtleties of your CCD camera will help you create better images and scientific data.
Unique dispersion properties of photonic crystal fibers (2004)

In conventional photonic crystal fibers (PCFs), the cladding structure is usually formed by air holes with the same diameter arrayed in a regular triangular lattice. However, in index-guiding PCFs, the periodicity in the cladding region is not essential to confine the guiding light into the high-index core region. In this paper, we report that it is possible to control chromatic dispersion of index-guiding PCFs in wide wavelength range by varying the hole diameter of each air-hole ring along the radius. Using this design principle, a PCF with ultra-low and ultra-flattened dispersion is designed through a full-vector finite element method with anisotropic perfectly matched layers. Effective mode areas and leakage loss properties are also investigated.
Raw materials: Chemical and biochemical changes occurring during the traditional Madagascan vanilla curing process - Effects on the sensory qualities of cured beans (2007)

During the past few years, several reviews have been published on specific aspects of vanilla research and in particular on chemical changes that happen during the traditional curing process. This labor- and time-intensive process is of utmost importance in determining the ultimate sensory quality of the cured beans. The final product of this process is the cured, dry bean that has not only become shelf-stable but has also developed the familiar vanilla flavor, the latter having been formed as a result of very many chemical and enzymatic reactions that occur concurrently during the curing process Every vanilla-growing country has developed its own specific curing process, but all of these generally consist of four main steps, namely killing/blanching, sweating, drying and conditioning. Killing is very often achieved by submerging the freshly picked green beans in hot water for a short time (e.g. 55-60 degrees for about 3 min) during which the vegetative phase is stopped. - In the sweating step, the hot beans are kept wrapped in blankets, thus maintaining a temperature of about 45-50 degrees C for one or two days. During this period endogenous enzymes are active and the beans develop their characteristic brown color. - During the remaining months of the process, the beans undergo passive drying until they have a dry substance level of about 70-75%, thereby becoming microbiologically shelf-stable. Many (bio)chemical reactions take place in the course of this long production process, some of which result in the formation of low molecular weight, flavor-active compounds that together contribute toward the final flavor of the cured bean. - The main biochemical reaction occurring during the curing process is the hydrolysis of the glucovanillin (the beta-glucoside of vanillin), which is catalyzed by the beta-glucosidase endogenously present in the green bean. A certain amount of hydrolysis can also occur before the green bean is picked from the vine, whereby the degree of hydrolysis depends upon how ripe the bean actually is before being picked. -The fate of glucovanillin and vanillin have been studied during the various steps of the traditional curing process as performed on the island of Reunion. In this present publication, the findings made during the traditional curing process performed during the 2005 season in Madagascar are described, and, in particular, an attempt is made to explain how some of the vanillin losses occur during the process.
Influence of inhomogeneous magnetic field on the characteristics of very high frequency capacitively coupled plasmas (2010)

The effect of inhomogeneous magnetic field on the spatial structure of very high frequency (VHF) plasmas is investigated for different coil configurations, gas pressures, high frequency bias powers, and degrees of electronegativity. The simulation results show that the electron density peaks in the center of the chamber for VHF plasmas due to the standing electromagnetic wave effect. On application of a magnetic field, the density increases near the wafer edge and decreases at the chamber center. The radial magnetic field component is found to limit electron loss to the electrodes and locally enhance the electron density. The axial magnetic field component limits plasma diffusion in the radial direction helping preserve the effect of improved electron confinement by the radial magnetic field. The peak electron density decreases with increasing magnetic field as the plasma moves toward the electrode edge occupying a larger volume. The effect of magnetic field becomes weaker at higher pressure due to the increased electron-neutral collisions which reduce the effectiveness of electron confinement around the magnetic field lines. The impact of magnetic field on plasma profile is somewhat weaker in an electronegative Ar/CF4 plasma because of the presence of less mobile and unmagnetized negative ions.
Fuzzy Logic Control For Lane Change Maneuvers In Lateral Vehicle Guidance (1995)

This paper investigates the feasibility of a fuzzy logic control (FLC) algorithm for lateral control in a lane change maneuver in an automated highway system (AHS). The lane change maneuver takes the vehicle from lane following control in one lane to lane following control in an adjacent lane. A lateral accelerometer is the only sensor used for feedback during the maneuver. The rules of the FLC are developed based on human driving experience.
Background scene classification robust to the influence of human regions (2013)

We propose a background scene classification method robust to the influence of human regions. Conventional methods classify scene of an image by using image features extracted from entire region in the image. Therefore, in these methods, the influence of the human region such as color of the skin and the clothes reduces classification accuracy of the background scene. Our method classifies background scene of an image by using image features extracted from only background region except detected human regions. The experimental results show that the proposed method improves average of the rate at the balance point between recall rate and precision rate in almost all background scenes compared to the conventional method.
Holographic storage in electrooptic crystals. i. steady state (1978)

The non-linear theory of the self-diffraction on the light induced grating of refractive index in electrooptic crystals is developed. The intensities of the diffracted beams, the diffraction efficiency, and the shape of the surfaces of equal index change are calculated analytically for saturation holograms.Holographic storage in nominally pure reduced crystals of LiNbO3 is studied experimentally. It is shown that the developed theory in diffusion approximation satisfactorily describes the experimental data.
Low-Wavelengths SOI CMOS Photosensors for Biomedical Applications (2011)

Biological agents may be characterized (in terms of quantity (or concentration), purity, nature) using optical ways like spectrometry, fluorometry and real-time PCR for example. Most of these techniques are based on absorbance or fluorescence. Indeed, many biological molecules can absorb the light when excited at wavelengths close to blue and ultraviolet (UV). For example, DNA, RNA and proteins feature an absorption peak in the deep UV, more precisely around 260 and 280 nm (Karczemska & Sokolowska, 2001). This work is widely focused on those wavelengths. A biological sample concentration measurement method can be based on UV light absorbance or transmittance, as already known and realized with high-cost and large-size biomedical apparatus. But, often, the difficulties come from the limitation for measuring very small concentrations (close to a few ng/μL or lower) since themeasurement of such small light intensity variations at those low wavelengths requires a precise light source, and very efficient photodetectors. Reducing the dimensions of such a characterization system further requires a small light source, a miniaturized photosensor and a processing system with high precision to reduce the measurement variations. Some light-emitting diodes (LED) performing at those UV wavelengths have recently appeared and may be used to implement the light source. Concerning the optical sensor, while accurate but high-cost photosensors in technologies such as AlGaN and SiC provide high sensitivities in UV lowwavelengths thanks to their semiconductor bandgap (Yotter & Wilson, 2003), the silicon-on-insulator (SOI) layers absorb the photons in that specific range thanks to an appropriate thickness of the silicon. Adding excellent performances of low power consumption, good temperature behavior and high speed (Flandre et al., 1999; 2001), the SOI technology allows the designers for integrating a specific signal processing integrated CMOS circuit to transform the photocurrent into a digital signal for example. This opens the possibility to build a low-cost, complete and portable microsystem, including the light source, the photodetector and a recipient for the sample to characterize. For this chapter, we start with a state-of-the-art describing the current DNA quantification methods with their advantages and disadvantages. Since we will work at low optical wavelengths, we review different ultraviolet light sources that are used in laboratories or in biomedical fields. A description of different photodetectors in various technologies, more especially in SOI, suitable for DNA quantification will then be presented. Afterwards, we 14
An Integrated Phosphoproteomics Work Flow Reveals Extensive Network Regulation in Early Lysophosphatidic Acid Signaling (2010)

Lysophosphatidic acid (LPA) induces a variety of cellular signaling pathways through the activation of its cognate G protein-coupled receptors. To investigate early LPA responses and assess the contribution of epidermal growth factor (EGF) receptor transactivation in LPA signaling, we performed phosphoproteomics analyses of both total cell lysate and protein kinase-enriched fractions as complementary strategies to monitor phosphorylation changes in A498 kidney carcinoma cells. Our integrated work flow enabled the identification and quantification of more than 5,300 phosphorylation sites of which 224 were consistently regulated by LPA. In addition to induced phosphorylation events, we also obtained evidence for early dephosphorylation reactions due to rapid phosphatase regulation upon LPA treatment. Phosphorylation changes induced by direct heparin-binding EGF-like growth factor-mediated EGF receptor activation were typically weaker and only detected on a subset of LPA-regulated sites, indicating signal integration among EGF receptor transactivation and other LPA-triggered pathways. Our results reveal rapid phosphoregulation of many proteins not yet implicated in G protein-coupled receptor signaling and point to various additional mechanisms by which LPA might regulate cell survival and migration as well as gene transcription on the molecular level. Moreover, our phosphoproteomics analysis of both total lysate and kinase-enriched fractions provided highly complementary parts of the LPA-regulated signaling network and thus represents a useful and generic strategy toward comprehensive signaling studies on a system-wide level.