gebhart/patrepeval huggingface dataset:
Accumulation of Werner protein at DNA double-strand breaks in human cells (2005)

Werner syndrome is an autosomal recessive accelerated-aging disorder caused by a defect in the WRN gene, which encodes a member of the RecQ family of DNA helicases with an exonuclease activity. In vitro experiments have suggested that WRN functions in several DNA repair processes, but the actual functions of WRN in living cells remain unknown. Here, we analyzed the kinetics of the intranuclear mobilization of WRN protein in response to a variety of types of DNA damage produced locally in the nucleus of human cells. A striking accumulation of WRN was observed at laser-induced double-strand breaks, but not at single-strand breaks or oxidative base damage. The accumulation of WRN at double-strand breaks was rapid, persisted for many hours, and occurred in the absence of several known interacting proteins including polymerase beta, poly(ADP-ribose) polymerase 1 (PARP1), Ku80, DNA-dependent protein kinase (DNA-PKcs), NBS1 and histone H2AX. Abolition of helicase activity or deletion of the exonuclease domain had no effect on accumulation, whereas the presence of the HRDC (helicase and RNaseD C-terminal) domain was necessary and sufficient for the accumulation. Our data suggest that WRN functions mainly at DNA double-strand breaks and structures resembling double-strand breaks in living cells, and that an autonomous accumulation through the HRDC domain is the initial response of WRN to the double-strand breaks.
Solubilization of Protein from Human Hair in Aqueous Solutions of Surfactants (1979)

Some proteins which construct human hair were solubilized in aqueous solutioons of surfactants generally applied for shampoos. 1) The aqueous solution of sodium dodecylpoly (oxyethylene) sulfate solubilized smaller amounts of proteins from the hair than that of other surfactants used in this experiment. 2) The amount of solubilized proteins had the relationship with the degree of damage in hair. The higher damaged hair gave larger amounts of solubilized proteins. 3) Solubilization of proteins was influenced with pH of the solution. The minimum amount of solubilized proteins was obtained at pH 56 corresponding to the isoelectric point of human hair. 4) The hair of which proteins was extracted with an aqueous solution of the surfactant had poor water holding capacity and gave much splitted hair caused by combing. These facts have provided valuable imformation on the effect of surfactants on human hair.
When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values (2010)

As repositories of chemical molecules continue to expand and become more open, it becomes increasingly important to develop tools to search them efficiently and assess the statistical significance of chemical similarity scores. Here, we develop a general framework for understanding, modeling, predicting, and approximating the distribution of chemical similarity scores and its extreme values in large databases. The framework can be applied to different chemical representations and similarity measures but is demonstrated here using the most common binary fingerprints with the Tanimoto similarity measure. After introducing several probabilistic models of fingerprints, including the Conditional Gaussian Uniform model, we show that the distribution of Tanimoto scores can be approximated by the distribution of the ratio of two correlated Normal random variables associated with the corresponding unions and intersections. This remains true also when the distribution of similarity scores is conditioned on the size of the query molecules to derive more fine-grained results and improve chemical retrieval. The corresponding extreme value distributions for the maximum scores are approximated by Weibull distributions. From these various distributions and their analytical forms, Z-scores, E-values, and p-values are derived to assess the significance of similarity scores. In addition, the framework also allows one to predict the value of standard chemical retrieval metrics, such as sensitivity and specificity at fixed thresholds, or receiver operating characteristic (ROC) curves at multiple thresholds, and to detect outliers in the form of atypical molecules. Numerous and diverse experiments that have been performed, in part with large sets of molecules from the ChemDB, show remarkable agreement between theory and empirical results.
Photoaffinity labelling of human poly(ADP-ribose) polymerase catalytic domain (1997)

Photoaffinity labelling of the human poly(ADP-ribose) polymerase (PARP) catalytic domain (40 kDa) with the NAD+ photoaffinity analogue 2-azido-[alpha-32P]NAD+ has been used to identify NAD+-binding residues. In the presence of UV, photo-insertion of the analogue was observed with a stoichiometry of 0.73 mol of 2-azido-[alpha-32P]NAD+ per mol of catalytic domain. Competition experiments indicated that 3-aminobenzamide strongly protected the insertion site. Residues binding the adenine ring of NAD+ were identified by trypsin digestion and boronate affinity chromatography in combination with reverse-phase HPLC. Two major NAD+-binding residues, Trp1014 of peptide Thr1011-Trp1014 and Lys893 of peptide Ile979-Lys893, were identified. The site-directed mutagenesis of these two residues revealed that Lys893, but not Trp1014, is critical for activity. The close positioning of Lys893 near the adenine ring of NAD+ has been confirmed by the recently solved crystallographic structure of the chicken PARP catalytic domain [Ruf, Menissier-de Murcia, de Murcia and Schulz (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 7481-7485].
Lightweight Directory Access Protocol (LDAP): Technical Specification Road Map (2006)

The Lightweight Directory Access Protocol (LDAP) is an Internet protocol for accessing distributed directory services that act in accordance with X.500 data and service models. This document provides a road map of the LDAP Technical Specification.
Development of a Personalized Intestinal Fibrosis Model Using Human Intestinal Organoids Derived From Induced Pluripotent Stem Cells (2021)

We demonstrate the feasibility of utilizing iPSC-HIO technology to model intestinal fibrotic responses in vitro. This now permits the generation of near unlimited quantities of patient-specific cells that could be used to reveal cell- and environmental-specific mechanisms underpinning intestinal fibrosis.
[Effect of acetyl-CoA synthase gene overexpression on physiological function of Saccharomyces cerevisiae]. (2010)

The results presented here demonstrated that the overexpression of acetyl-CoA synthase can enhance the carbon flux into mevalonate pathway and improve the tolerance of S. cerevisiae to high content of ethanol, which is the main byproduct of the fermentation process with the yeast.
Bootstrapped leakage suppression switch for switched capacitor circuits with zero input common mode (2017)

This paper proposes a bootstrapped sub-threshold leakage suppression switch for switched capacitor (SC) circuits that operate from a single supply voltage and acquire analog input that have zero common mode. The design is implemented using AMS 0.35 μm, 3.3 V CMOS process. The proposed switch gives best combination of linearity, leakage and swing. It improves the linearity of switched capacitor circuits, when compared to the existing leakage suppression switches. Simulations using simple unity gain sampling circuit shows that this technique will achieve a dynamic range of more than 96 dB across all corners.
Hysteresis modeling of magnetic devices using dipole distribution (2005)

A new modeling method based on the normal distribution of dipoles is used to represent the B-H loop of magnetic materials. The dipole representation can be expressed either in 2-orientation or 4-orientation. Depending on the accuracy required, the modeling method typically requires only magnetic saturation parameters, the critical H-field, and a few control parameters. Experimental results show that the method can be used to represent the B-H loop of materials very accurately.
Holographic acoustic microscopy for quantitative velocity profile imaging (1989)

In this letter, a new approach is reported for the quantitative measurement of the acoustic velocity profile with the scanning laser acoustic microscope operating in the holographic mode. Due to the addition of a quadrature detector, the acoustic microscope is now capable of holographic recording of the complex wave field. As a result, it enables one to estimate the velocity profile with superior resolving capability directly from the wave field distribution instead of from the interferometry fringe patterns of the conventional methods.
Supplementary Table 5. from Cell-Free DNA Modification Dynamics in Abiraterone Acetate-Treated Prostate Cancer Patients (2023)

&lt;p&gt;List of significant AA-DVPs.&lt;/p&gt;
Clinical features of a toddler with bilateral bullous retinoschisis with a novel RS1 mutation (2016)

We report the detailed retinal structure in a genetically identified case of bullous retinoschisis. The notable finding was that the cavity of bullous retinoschisis contained a number of fiber-like strands as observed in the cavity of typical retinoschisis.
Thermodynamics of CeSiO4: Implications for Actinide Orthosilicates (2020)

Zircon (ZrSiO<sub>4</sub>, <i>I</i>4<sub>1</sub>/<i>amd</i>) can accommodate actinides, such as thorium, uranium, and plutonium. The zircon structure has been determined for several of the end-member compositions of other actinides, such as plutonium and neptunium. However, the thermodynamic properties of these actinide zircon structure types are largely unknown due to the difficulties in synthesizing these materials and handling transuranium actinides. Thus, we have completed a thermodynamic study of cerium orthosilicate, stetindite (CeSiO<sub>4</sub>), a surrogate of PuSiO<sub>4</sub>. For the first time, the standard enthalpy of formation of CeSiO<sub>4</sub> was obtained by high temperature oxide melt solution calorimetry to be -1971.9 ± 3.6 kJ/mol. Stetindite is energetically metastable with respect to CeO<sub>2</sub> and SiO<sub>2</sub> by 27.5 ± 3.1 kJ/mol. The metastability explains the rarity of the natural occurrence of stetindite and the difficulty of its synthesis. Applying the obtained enthalpy of formation of CeSiO<sub>4</sub> from this work, along with those previously reported for USiO<sub>4</sub> and ThSiO<sub>4</sub>, we developed an empirical energetic relation for actinide orthosilicates. The predicted enthalpies of formation of AnSiO<sub>4</sub> are then determined with a discussion of future strategies for efficiently immobilizing Pu or minor actinides in the zircon structure.
Instrument engineers' handbook: process measurement and analysis (1995)

This third edition of the Instrument Engineers' Handbook-most complete and respected work on process instrumentation and control-helps you:
Synthesis of Glycocluster−Tumor Antigenic Peptide Conjugates for Dendritic Cell Targeting (2007)

The use of dendritic cells (DC) for the development of therapeutic cancer vaccines is attractive because of their unique ability to present tumor epitopes via the MHC class I pathway to induce cytotoxic CD8+ T lymphocyte responses. C-Type membrane lectins, DC-SIGN and the mannose receptor (MR), present on the DC surface, recognize oligosaccharides containing mannose and/or fucose and mediate sugar-specific endocytosis of synthetic oligolysine-based glycoclusters. We therefore asked whether a glycotargeting approach could be used to induce uptake and presentation of tumor antigens by DC. To this end, we designed and synthesized glycocluster conjugates containing a CD8+ epitope of the Melan-A/Mart-1 melanoma antigen. These glycocluster-Melan-A conjugates were obtained by coupling glycosynthons: oligosaccharyl-pyroglutamyl-beta-alanine derivatives containing either disaccharides, a dimannoside (Manalpha-6Man) or lactoside, or a Lewis oligosaccharide, to Melan-A 16-40 peptide comprising the 26-35 HLA-A2 restricted T cell epitope, extended with an oligolysine stretch at the C-terminal end. We showed by confocal microscopy and flow cytometry that fluorescent-labeled Melan-A glycoclusters containing either dimannoside or Lewis oligosaccharide were taken up by DC and concentrated in acidic vesicles; conversely lactoside glycopeptides were not at all taken up. Furthermore, using surface plasmon resonance, we showed that dimannoside and Lewis-Melan-A conjugates bind MR and DC-SIGN with high affinity. DC loaded with these conjugates, but not with the lactose-Melan-A conjugate, led to an efficient presentation of the Melan-A epitope eliciting a CD8+ T-lymphocyte response. These data suggest that synthetically designed glycocluster-tumor antigen conjugates may induce antigen cross-presentation by DC and represent a promising tool for the development of tumor vaccines.
Dielectric Spectrscopy Analysis Behavior of low Density Polyethylene (2008)

Dielectric spectroscopy is a powerful tool in the investigation of dipolar and conduction in electrical insulating materials. In particular, the localisation of space charges at crystalline - amorphous interfaces in a semicrystalline polymer, such as low density polyethylene LDPE, provides on internal field which could be unfavourable to the insulating properties of the polymer. A physical displacement of space charges through the clusters and structural defects can be detected in the low frequency region. Changes in the real and imaginary parts of the complex permittivity correspond ot changes in the bulk capacitance and conductance of the polymer. In this work we have presented results of dielectric studies in semicristalline polyethylene low density by means of dielectric relaxation spectroscopy (DRS) in frequency range 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> - 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> Hz and temperature between -60 and 70degC In this study a relaxation is observed at high frequencies as a large peak in the domain 1 Hz - 10 kHz in the plot of the imaginary part of dielectric permittivity epsiv* (omega) and in the plot of the loss factor Tandelta(omega). An important increasing in values of epsiv" and Tandelta at low frequencies and high temperature is observed. Also it was noted that the effect of electrical conductivity causes an important increasing in the index of losses epsiv"(omega). The dielectric permittivity epsiv' presents a gradual decrease with increasing frequency and increasing temperature. This feature is masked by high index losses epsiv" values due to DC conductivity.These results confirm that the step in the permittivity epsiv'(omega) is due to conductivity current relaxation.
The stage-specific expression of TEC-1, -2, -3, and -4 antigens on bovine preimplantation embryos (1998)

The preimplantation developmental period is associated with constant changes within the embryo, and some of these changes are apparent on the embryo cell surface. For example, during transition from maternal to embryonic genome control and the compaction and differentiation of embryonic cells, the cell surface undergoes morphologic alterations that reflect changes in gene control. In order to gain insight into the events occurring during embryonic development and cellular differentiation, monoclonal antibodies specific for cell surface antigens (TEC antigens) of embryonic cells have been generated previously and shown to recognise either the carbohydrate moiety of embryoglycan or a developmentally regulated protein epitope. The TEC antigens have been identified on mouse preimplantation embryos, and their expression is specific to particular developmental stages. To determine whether these antigens are conserved in higher mammals, we examined the expression of four TEC antigens (TEC-1 to TEC-4) on in vitro-derived bovine and murine embryos during the preimplantation stage of development. It was found that bovine oocytes and embryos derived from in vitro maturation (IVM) and in vitro fertilisation (IVF) showed stage-specific expression of each of the TEC antigens investigated, with the pattern of expression overlapping but not identical to that seen in the mouse. Immunoprecipitation together with Western blot analysis showed that the TEC monoclonal antibodies recognised a single glycoprotein band with an apparent molecular weight of 70 kDa. Confocal microscopy of immunofluorescence staining of the bovine cells showed this protein to be located on the cell surface. The apparent negative expression of these TEC antigens by immunohistochemistry and immunoprecipitation at particular stages of development appears to be due to the epitopes being inaccessible to the TEC antibodies, since Western blotting revealed the TEC antigens to be present at all stages of development examined. Antibodies identifying stage-specific antigens will provide useful markers to characterise early embryonic cells, monitor normal embryonic development in vitro, and identify cell surface structures having a function in cell-cell interactions during embryogenesis and differentiation.
Laser Resurfacing: Usual and Unusual Complications (1999)

The use of the carbon dioxide laser for skin resurfacing was initially described in 1989. 1 Since that time, several reports have shown it to be highly effective in the treatment of photodamaged skin and acne scarring. 2,3,4,5 Advances in laser technology have simplified the procedure and minimized adverse sequelae. Laser skin resurfacing has become a very popular technique, and recently several patient series have been published on the use of different resurfacing lasers to treat photodamaged skin. 3,4 However, very little has been written about its complications. Adequate patient selection, sound medical judgement, proper training with experience and knowledge of skin physiology and wound care are important factors for successful outcomes. Interested physicians across a broad range of subspecialties have expressed concern about the rate of adverse outcomes and management of complications. We report seven representative cases of complications referred to our dermatology clinics from outside physicians, in the hope of educating clinicians regarding the usual and unusual side effects of this procedure.
Reducing sampling intensity in order to investigate spatial variability of soil pH, organic matter and available phosphorus using co-kriging techniques. A case study of acid soils in Eastern Croatia (2017)

Soil pH, hydrolytic acidity (HA), organic matter (OM) and plant available phosphorus (AP) are factors controlling the environmental-friendly soil management in agroecosystems. These parameters are highly variable in space. The objective of this work is to study spatial variability of pH, HA, OM and AP using several interpolation methods in Eastern Croatia. A total of 1004 (0–30 cm) soil samples were collected, and several univariate and multivariate interpolation performances were tested. The results showed that soils of the study area had high HA and AP, while pH and OM were low. The variogram analysis revealed different spatial structures among studied soil properties and demonstrate a need for variable-rate management. Soil pH and OM had lower spatial variability compared to AP and HA. Ordinary kriging was the most accurate method to estimate the studied variables. The incorporation of auxiliary variables increased the precision of the estimations for HA. Soil AP and OM showed different results for spatial prediction obtained by co-kriging. Overall, the incorporation of pH as auxiliary variable increased the prediction of the models. However, more co-variates should be incorporated in further models, in order to identify with more precision areas that need to be restored.
Structural basis for selectin mechanochemistry (2009)

Selectins are adhesion molecules that resist large tensile forces applied by hydrodynamic forces to leukocytes binding to vessel walls. In crystals, the liganded (high-affinity) and unliganded (low-affinity) conformations differ in orientation between their tandem lectin and EGF domains. I examine how tensile force exerted on a selectin-ligand complex in vivo could favor the more extended, high-affinity conformation. Allostery is transmitted from the EGF-lectin domain interface to the ligand-binding interface on the lectin domain, 30 A away. Trp-1 of the lectin domain and the long axis of the EGF domain form an L-shaped prybar that is welded together by hydrogen bonds to the Trp-1 alpha-amino group. Pivoting of the prybar induced by force demolishes an interface between the Trp-1 side chain and the lectin domain at a switch1 region. These changes are transmitted by rigid body movement of the switch2 region to rearrangements in the switch3 region at the ligand binding site. Another switch region corresponds to a single residue in the EGF domain with large effects on ligand binding and rolling adhesion. Allostery in selectins, and the alignment of tensile force on a selectin-ligand complex with the transition pathway for conformational change, explain much of the structural basis for selectin mechanochemistry.
Environmental assessment for the satellite power system concept development and evaluation program-electromagnetic systems compatibility (1981)

The EMC analysis addressed only the direct effects of electromagnetic emissions from the SPS on other technological systems. Emissions were defined quite broadly, including not only those from the microwave system, but also thermal blackbody emission and scattered sunlight from the satellite. The analysis is based on the design for an SPS as described in the Reference System Report and some quantitative conclusions, e.g., ranges from rectenna sites at which effects are expected are specific to that design. The methodology and qualitative conclusions, however, apply to an SPS concept using microwave power transmission. Quantitative conclusions have been obtained parametrically and can be adjusted as SPS designs change. The electromagnetic environment that the Reference System would produce, and in which other systems would have to function, is described. As an early part of the EMC Assessment, the problems expected for a hypothetical rectenna site, in the Mojave Desert of southern California, were analyzed in detail. This effort provided an initial quantitative indication of the scope of potential EMC problems and indicated the importance of EMC considerations in rectenna site selection. The results of this analysis are presented. The effects of SPS microwave emissions on important categories of electronic systems and equipment are summarized, with many examples of test results and demonstrated techniques for mitigation of problems encountered. SPS effects on other satellite systems are presented. Astronomical research frequently involves measurement of extremely low levels of electromagnetic radiation and is thus very susceptible to interference. The concerns of both radio astronomy with microwave emissions from SPS and optical astronomy with sunlight scattered from SPS spacecraft are discussed. Summaries of mitigation techniques, cost estimates, and conclusions are presented. (WHK)