gebhart/patrepeval huggingface dataset:
Death by protein damage in irradiated cells (2011)

A founding concept of radiobiology that deals with X-rays, γ-rays and ultraviolet light is that radiation indiscriminately damages cellular macromolecules. Mounting experimental evidence does not fit into this theoretical framework. Whereas DNA lesion-yields in cells exposed to a given dose and type of radiation appear to be fixed, protein lesion-yields are highly variable. Extremely radiation resistant bacteria such as Deinococcus radiodurans have evolved extraordinarily efficient antioxidant chemical defenses which specifically protect proteins and the functions they catalyze. In diverse prokaryotes, the lethal effects of radiation appear to be governed by oxidative protein damage, which inactivates enzymes including those needed to repair and replicate DNA. These findings offer fresh insight into the molecular mechanisms of radiation resistance and present themselves as new opportunities to study and control oxidative stress in eukaryotes, including mammalian cells and their cancer cell counterparts.
Notch Signaling Pathway (2006)

Notch is a receptor that mediates intercellular signaling through a pathway conserved across the metazoa. It is involved in cell fate assignation and pattern formation during development. The receptor acts as a membrane-tethered transcription factor and is activated by members of the Delta, Serrate, Lag-2 family of Notch ligands, which trigger two successive proteolytic cleavages of the receptor. The second cleavage releases the intracellular domain of Notch, which translocates to the nucleus, where it interacts with the CSL family of transcriptional regulators and forms part of a Notch target gene-activating complex. In the absence of signaling, CSL [CBF1, Su(H), Lag-1] regulators repress Notch target genes through interactions with several transcriptional co-repressors that recruit histone deacetylases and other chromatin-modifying enzymes. After forming, the transcription-activating binary Notch intracellular domain-CSL complex recruits several proteins that facilitate transcription, among them the coactivator MAM and histone acetylases. Transcription of target genes is terminated when the Notch intracellular domain is degraded in a proteasome-dependent manner.
Systemic autoimmune disease arises from polyclonal B cell activation. (1987)

The number of B cells producing antibodies reactive with any of seven autoantigens or two conventional antigens was compared at the single-cell level to the total number of Ig-secreting B cells present in the spleens of NZB, MRL lpr/lpr, and BXSB autoimmune mice. The proportion of lymphocytes producing antibodies of each specificity, expressed as a percentage of the total B cell repertoire, was virtually identical among autoimmune and congenic nonautoimmune animals. Furthermore, B cells and serum antibodies reactive with conventional antigens increased commensurately with those reactive with autoantigens. These results indicate that systemic autoimmune diseases arise from polyclonal B cell activation.
Mono-oxigenase-like dioxygen activation leading to alkane hydroxylation and olefin epoxidation by an Mn<sup>III</sup>(porphyrin)–ascorbate biphasic system (1983)

A biphasic H2O–C6H6 system, which has MnIII(tetraphenylporphyrin)(Cl) and a phase transfer agent as catalysts and ascorbate as a reducing agent, activates dioxygen leading to selective epoxidation of olefins and hydroxylation of alkanes under mild conditions.
Self‐renaturing enzymes: Design of an enzyme‐chaperone chimera as a new approach to enzyme stabilization (2009)

Molecular chaperones in aqueous-organic mixtures can broaden the utility of biocatalysis by stabilizing enzymes in denaturing conditions. We have designed a self-renaturing enzyme-chaperone chimera consisting of penicillin amidase and a thermophilic chaperonin that functions in aqueous-organic mixtures. The flexible linker separating the enzyme and chaperone domains was optimized and the design was extended to incorporate a chitin binding domain to facilitate immobilization of the chimera to a chitin support. The initial specific activity of penicillin amidase was not compromised by the enzyme-chaperone fusion or by immobilization. The total turnover number of immobilized chimera for amoxicillin synthesis in aqueous-methanol mixtures was 2.8 times higher after 95 h than the total turnover number of the immobilized penicillin amidase lacking a chaperone domain. Similarly, in 32% methanol the soluble chimera was active for over three times longer than the enzyme alone. This approach could easily be extended to other enzyme systems.
Phosphatidylcholine’s functions beyond that of a membrane brick (2015)

Since its discovery in the 19th century, phosphatidylcholine (PC) has been regarded primarily as a structural lipid. However, more recent evidence, much of it in the last five years, strongly suggests that PC has other roles. Here, we explore some of that new evidence and consider the possibility that the ultimate role of phosphatidylcholine may not be predictable.
Quantitative Comparison of the Transient Rescue Effects of Neurotrophic Factors on Axotomized Motoneurons In Vivo (1995)

A reproducible neuronal degeneration induced by nerve lesion in neonatal rats or mice provides a convenient in vivo assay for testing the survival-promoting activity of putative growth factors on motoneurons. The goal of this study was to compare the rescue effects of the four known neurotrophins [nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3) and neurotrophin-4 (NT-4)] and two of the cytokines [ciliary neurotrophic factor (CNTF) and leukaemia inhibitory factor (LIF)] in one particular experimental model of spinal motoneuron degeneration at two different survival times. The sciatic nerve was cut in neonatal rats and the factors were applied onto the nerve stump; bovine serum albumin was used in controls. Simultaneous application of the retrograde tracer fluoro-gold made it possible to count motoneurons specifically in the sciatic pool. One week after lesion, the neurotrophins BDNF, NT-3 and NT-4, but not NGF, equally enhanced motoneuron survival compared to controls; their effects were significantly better than those of the cytokines. However, the rescue from cell death was only transitory because a great number of the motoneurons died during the second week after nerve lesion. Additional BDNF and/or CNTF supplied by repeated subcutaneous injections (1 mg/ml) over 2 weeks could not prevent this delayed motoneuron loss. These results suggest that still other factors or alternative routes of administration may be required for permanent rescue of the lesioned immature motoneurons.
Effective-exposure-dose monitoring technique in EUV lithography (2010)

EUV lithography is a promising candidate for 2x-nm-node device manufacturing. Management of effective dose is important to meet the stringent requirements for CD control. Test pattern for a lithography tool evaluation, the effective dose monitor (EDM), shows good performance in the dose monitoring for optical lithography, for example, KrF lithography. The EDM can measure an exposure dose with no influence on defocus, because the image of an EDM pattern is produced by the zero-th-order ray in diffraction only. When this technique is applied to EUV lithography, the mask shadowing effect should be taken into consideration. We calculated the shadowing effect as a function of field position and applied it to correction of the experimental dose variation. We estimated the dose variation in EUV exposure field to be 2.55 % when corrected by the shadowing effect. We showed that the EDM is useful for EUV lithography.
A Mechanical Methodology of Improved Proppant Transport in Low-Viscosity Fluids: Application of a Fiber-Assisted Transport Technique in East Texas (2004)

Abstract Several different hydraulic fracturing treatment design methodologies have been adopted and used with varying success in East Texas and, specifically, in the Cotton Valley Sand Formation. Treatment designs have ranged from massive hydraulic fractures using crosslinked polymer fluids to low proppant concentration slickwater treatments (waterfracs) using only water plus a friction reducer. Operators have varying opinions regarding the benefits of the various design approaches, with the only common conclusion being that hydraulic fracturing must be employed to commercially produce hydrocarbons from these tight formations. The major design challenges include the need for long fractures, relatively limited height growth, good proppant coverage over the entire fracture surface, and low proppant pack damage. Neither conventional fracturing treatments nor slickwater fracturing treatments address all of these issues. To meet the challenging design requirements, a new design methodology in which fibers are added to the fracturing fluid has resulted in added benefits for operators. The fibers assist in the transport of proppant based on a mechanical suspension mechanism and prevent proppant settling during fracture closure. As a result, the fluid viscosity is no longer the main factor in proppant transport and significantly lower polymer concentrations can be used without compromising proppant transport. For example, the polymer concentration used in several successful treatments at BHST in excess of 250°F has been reduced by about 50% when used in conjunction with the fibers. The lower fluid viscosity allows for the creation of the desired fracture geometry with controlled fracture height growth. In addition, reducing the polymer concentration has largely been accepted as a means to increase fracture conductivity. The use of fibers in conjunction with the polymer fluid is a new approach that has allowed for additional reduction in polymer loadings while still maintaining excellent proppant transport in over 90 jobs pumped to date. The purpose of this paper is to share the fracture design methodology incorporated for several operators completing wells in East Texas. Typical job designs with fluid rheology and laboratory conductivity data are presented in conjunction with the placement success when using the fiber assisted transport design methodology. Initial production results are reviewed and compared to offset wells that have been stimulated using conventional methods.
Beta-agonist aerosol distribution in respiratory syncytial virus bronchiolitis in infants. (2002)

Poor total aerosol deposition in infants may be related as much to their small conducting airways as to the disease state. There is considerable room for improvement in aerosol delivery in this age group, with greater emphasis on targeting narrowed peripheral airways with superfine aerosols.
Carbon Black Morphology: I. Particle Microstructure. II. Automated EM Analysis of Aggregate Size and Shape (1969)

Abstract Carbon black particle and aggregate microstructure were studied in detail by means of high resolution electron microscopy. Improved instrumental and environmental conditions have enabled more detailed studies on the size, orientation, and spacing of graphite layers in carbon black particles than heretofore possible. The layers form continuous networks about particle growth centers and between adjoining particles and show a paracrystalline orientation rather than individual crystallites. Based on this type of orientation carbon black primary aggregates are now defined as single graphite paracrystals exhibiting either a fibrous (furnace and channel blacks) or spheroidal (thermal blacks) shape.
Structural changes accompanying chloroform-induced contraction of the filamentous phage fd (1993)

Contact with a chloroform/water interface at 2 degrees C induces contraction of fd filamentous phage into rodlike I-forms; this contraction is accompanied by a decrease in the magnitude of circular dichroism spectral intensity near 222 nm and an increase near 210 nm. Comparisons with circular dichroism spectra of 100% helical poly-L-lysine and N-bromosuccinimide-oxidized fd phage indicate that the spectral change accompanying the fd to I-forms transition is due primarily to a change in the contributions from the single tryptophan (W26) of the major coat protein, with probably no significant change in the alpha-helix content. Further contraction of the rodlike I-forms to spherical S-forms at 25 degrees C is accompanied by a substantial general decrease in the magnitude of the ellipticity throughout the 230-210-nm region, which is indicative of a decrease in the alpha-helix content of the major coat protein. The similarity of the circular dichroism spectrum of S-forms with that of coat protein in detergents suggests that the S-form coat protein resembles the coat protein in lipid bilayers. The intrinsic fluorescence of W26 is quenched without red-shift (but perhaps a barely detectable blue-shift) following fd contraction to I-forms and S-forms. The accessibility of W26 to aqueous quenchers does not change significantly upon contraction. However, interaction with hydrophobic quenchers is dramatically altered in the contracted forms in a manner suggesting that the environment surrounding the tryptophan changes from native-protein-like in the fd filament to molten globule-like in the I-form rods and S-form spheroids. As discussed herein, certain features of these data support previous suggestions that chloroform-induced filamentous phage contraction may provide information about phage penetration and assembly in vivo.
Determination of twelve heparin- and heparan sulfate-derived disaccharides as 2-aminoacridone derivatives by capillary zone electrophoresis using ultraviolet and laser-induced fluorescence detection (2002)

In quest for high sensitivities, we developed an ultrahigh capillary electrophoresis (CE) method for the structural analysis of heparin and heparan sulfate (HS) in biologic samples. Heparin and HS were digested with an equi-unit mixture of heparin lyases I, II and III and the obtained Delta-disaccharides were derivatized with the fluorophore 2-aminoacridone. All known twelve non-, mono-, di- and trisulfated Delta-disaccharides were completely resolved in a single run, using 50 mM phosphate buffer, pH 3.5, and reversed polarity at 30 kV. Relative standard deviation in migration times and peak areas as well as day-to-day variance ranged from 0.9 to 2.4%, suggesting a reproducible and precise method. Detection of 2-aminoacridone (AMAC)-derivatives of Delta-disaccharides by UV at 255 nm showed 2.8 and 10 times higher sensitivity than that of derivatized and non-derivatized ones at 232 nm. Laser-induced fluorescence detection with an Ar-ion laser source showed an approximately 100 times higher sensitivity than that obtained at 232 nm of the non-derivatized species. Application of this method to quantitative analysis of Delta-disaccharides derived from porcine intestinal mucosa heparin and bovine kidney HS showed excellent agreement with previously published methods, suggesting an accurate method. The developed method can be easily applied for the disaccharide analysis of heparin/HS at the attomole level with high accuracy, for distinguishing between heparin and HS and may be of value for studying their interactions with matrix effective molecules.
Monoclonal Antibodies to Polioviruses (1981)

Murine lymphocyte hybridomas which produce neutralizing or non-neutralizing monoclonal antibodies to different type 1, 2 or 3 poliovirus strains were isolated. The majority of these monoclonal antibodies reacted with antigenic determinants present on different poliovirus strains of the same type. However, hybridomas producing monoclonal antibodies specific for each of the three Sabin vaccine strains were also generated.
Diseño y Moderación de Entornos Virtuales de aprendizaje, Juan Silva Quiroz. Prólogo de Begoña Gros Salvat: 1 º edición en lengua castellana, Editorial UOC, Diciembre de 2011. 157 páginas, ISBN 978-84-9788-936-6. Impreso en Barcelona, España (2012)

Esta publicacion presenta y trabaja el concepto de diseno de entorno virtual de aprendizaje, enfatiza en la importancia del entorno y el contexto para el aprendizaje. El libro aporta orientaciones para los profesores que deseen integrar un espacio virtual en alguna de las modalidades: apoyo a la presencial, sistemas hibridos (b-learning) y tambien e-learning
A microtool for in vitro cell array manipulation (2003)

This paper reports on the fabrication of a transparent micro-post array with supporting pillars for in-vitro cell array manipulation. The capability to manipulate and apply mechanical force to an array of cells will enable the engineering of living neural networks having defined connectivity. The micro-tool described in this paper was designed to achieve this goal. Its transparency permits visual access through a light microscope. When the microtool is placed on top of a cell culture, the tips of the posts are 3-5 /spl mu/m microns above the surface due to the differential height between the posts and the supporting pillars. This small gap prevents the cells from being damaged when the microtool is translated with respect to the cells, while allowing them to touch and adhere to the posts. The micro-tool was tested by using it to apply force to non-arrayed embryonic chick forebrain cells in vitro. The array was moved at a constant speed of 36 /spl mu/m/hour during one hour. In response, several neurite-like cytoplasmic processes initiated from cells that had formed adhesions to posts, and these processes elongated in response to further translation. This is the first reported microarray designed to apply mechanical forces to cells.
Inducible Heat-Shock Protein 70 Is Involved in the Radioadaptive Response (2000)

Park, S-H., Lee, S-J., Chung, H-Y., Kim, T-H., Cho, C-K., Yoo, S-Y. and Lee, Y-S. Inducible Heat-Shock Protein 70 Is Involved in the Radioadaptive Response. The thermoresistant (TR) clone of radiation-induced fibrosarcoma (RIF) cells showed an adaptive response, i.e. a reduced effect, after exposure to a higher challenging dose (4 Gy) when the priming dose (1 cGy) was given 4 or 7 h earlier, but RIF cells did not. Since inducible Hsp70 expression was different in cells of these two cell lines, the role of inducible Hsp70 in the adaptive response was examined. When inducible Hsp70 was transfected into RIF cells, the adaptive response was acquired. Transfection of inducible Hsp70 to NIH 3T3 mouse embryo cells also conferred radioresistance to the cells as assayed by clonogenic survival, [(3)H]thymidine incorporation, and an ELISA cell death detection kit. An increased tendency for the induction of an adaptive response was also observed. Interestingly, basal levels of Ca(2+)-dependent and independent Pkc activities were increased by transfection with inducible Hsp70 compared to those of control vector cells. Irradiation with gamma rays induced activation of Pkc within minutes in control vector cells, while transfection with inducible Hsp70 did not. Cellular redistribution to particulate fractions of Pkca, d and z after exposure gamma rays also was not detected. Furthermore, radioresistance by transfection with inducible Hsp70, as tested by clonogenic survival, disappeared after pretreatment with Pkc inhibitors, 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H7), prolonged treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA), and GF109203X. Taken together, these data suggest that radioresistance inducible by Hsp70 is associated with an elevated level of Pkc activity.
Silica‐Immobilized NHC–Cu<sup>I</sup> Complex: An Efficient and Reusable Catalyst for A<sup>3</sup>‐Coupling (Aldehyde–Alkyne–Amine) under Solventless Reaction Conditions (2008)

Abstract A novel silica‐immobilized NHC–Cu I complex was developed and used as a highly efficient catalyst in the three‐component coupling reactions of aldehydes, alkynes and amines (A 3 ‐coupling). The reactions were applicable to aromatic and aliphatic aldehydes, alkynes and amines, and generated the corresponding propargylamines in good yields only in the presence of SiO 2 –NHC–Cu I (2 mol‐%) at room temp. under solvent‐free reaction conditions. Moreover, the catalyst was quantitatively recovered from the reaction mixture by a simple filtration and reused for ten cycles with almost consistent activity.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Construction of spider genomic DNA Cosmid library and cloning of dragline silk gene (2001)

The genomic DNA Cosmid library was constructed from Nephila clavipes spider muscle using SuperCos 1 Cosmid as a vector.The title of library was 5×10 4 cfu/μg ligated DNA.On the basis of published sequence from a partial cDNA sequence of the 3′end of the dragline silk gene, we designed and synthesized 3 oligonucleotides.Oligonucleotides were labeled with non radioactive digoxigenin dUTP and detected with chemilluminescent substrate.56 positive recombinants were screen from the Cosmid library using DIG Oligo 2 as a probe.DNA dot hybridization using DIG Oligo 1 and DIG Oligo 3 as the probes, respectively, 3 positive signals were identified from 56 colonies.They were appeared the same pattern when DNA from the colones digested by restriction enzymes.The spider dragline silk gene was confirmed again by Southern blot hybridization.
Bluetooth based home automation system using cell phone (2011)

Technology is a never ending process. To be able to design a product using the current technology that will be beneficial to the lives of others is a huge contribution to the community. This paper presents the design and implementation of a low cost but yet flexible and secure cell phone based home automation system. The design is based on a stand alone Arduino BT board and the home appliances are connected to the input/ output ports of this board via relays. The communication between the cell phone and the Arduino BT board is wireless. This system is designed to be low cost and scalable allowing variety of devices to be controlled with minimum changes to its core. Password protection is being used to only allow authorised users from accessing the appliances at home.
Gaze Tracking by Using Factorized Likelihoods Particle Filtering and Stereo Vision (2006)

This paper describes a non-intrusive method to estimate the gaze direction of a person by using stereo cameras. First, facial features are tracked with an adapted particle filtering algorithm using factorized likelihoods to estimate the 3D head pose. Next the 3D gaze vector is calculated by estimating the eyeball center and the cornea center of both eyes. For the intended application of visual perception research, we also propose a new screen registration scheme to accurately locate a planar screen in world coordinates within 2 mm error. We combine the 3D screen location with the 3D gaze vectors from both eyes to establish a point of focus on the screen. The experimental results indicate that an average error of the gaze direction of about 4.6deg can be achieved and an average error of about 4 mm for the focus point location at a viewing distance of 50 cm.