gebhart/patrepeval huggingface dataset:
Hematopoietic Stem Cells Are Dependent On Homologous Recombination Only During Active Cell Cycle in Nuclease-Mutant Exonuclease1mut mice (2012)

Abstract Abstract 1225 Hematopoietic stem cell (HSC) maintenance and self-renewal is crucial for long term tissue repopulation and immune function. HSC populations require functional DNA repair pathways in order to maintain their reconstitution capabilities but the pathways involved and the mechanisms of regulation are still being elucidated. It has been proposed that quiescent HSCs rely on the error prone non homologous end joining pathway for DNA double strand break (DSB) repair while HSCs in cycle use both NHEJ and the high fidelity homologous recombination (HR), but functional in vivo studies have not yet been completed. Exonuclease 1 participates in homologous recombination. We used Exo1mut fibroblasts to demonstrate that loss of Exo1 function results in a defective HR response, increased sensitivity to DSB inducing agents, and aberrant DNA damage signaling. However, Exo1mut mice did not appear to require HR to maintain quiescent HSCs at steady state or to respond to DNA damage. Exo1mutmice were able to sustain long term serial repopulation, displayed no defect in competitive repopulation or quiescence maintenance, and did not display increased sensitivity to whole body ionizing radiation (IR). In contrast, when Exo1mut HSCs were pushed into cell cycle with 5-Fluorouracil, the hematopoietic population and HSCs became hypersensitive to IR stress relative to WT B6 mice, as shown by decreased bone marrow cellularity, colony forming unit defects, loss of the HSC population, and finally animal death. Thus, loss of Exo1, and in turn fully functional HR, in quiescent HSC is not critical to stem cell function, survival, or recovery after DNA damage, whereas HR mediated repair of DNA damage is essential for HSC maintenance after cell cycle entry. In HSCs, DNA damage repair response, and sensitivity is dependent on cell cycle. Disclosures: No relevant conflicts of interest to declare.
Spectrally stable Er-fiber laser for application in phase-sensitive optical time-domain reflectometry (2003)

A high degree of frequency stability in an Er-fiber laser with the Fabry-Perot configuration was achieved using a long (25-km) optical-feedback loop. The frequency-drift rate was determined to be <1 MHz/min by observing temporal fringes in an unbalanced Mach-Zehnder interferometer. Instantaneous linewidth measured with a delayed self-heterodyne interferometer was less than the 3-kHz resolution limit. The laser was utilized in an optical time-domain reflectometry experiment to detect and locate a time-varying phase perturbation applied to an optical fiber.
Structural and Thermodynamic Aspects of the Interaction between Heparan Sulfate and Analogues of Melittin (2006)

Melittin is an amphipathic cationic peptide derived from honeybee venom with well-known cytolytic and antimicrobial properties. When coupled to cationic polymers or lipid molecules, it forms conjugates with high transfection efficiency and low toxicity with promising applications in gene therapy. A first step in the internalization of melittin and its conjugates is their binding to the cell surface, a reaction likely to involve heparan sulfate proteoglycans (HSPG). In the present work, we characterize the binding equilibrium of heparan sulfate (HS) with two melittin analogues, [Cys(1)]melittin (mel-SH) and retro-inverso [Cys(1)]melittin (ri-mel-SH). The terminal cysteine found in these peptides replaces the N-terminal glycine present in native melittin and allows covalent binding to other molecules. Isothermal titration calorimetry (ITC) reveals a high affinity of each melittin analogue to HS. Association constants of 4.7 x 10(4) and 3.5 x 10(5) M(-)(1) are found at physiological ionic strength and 15 degrees C for ri-mel-SH and mel-SH, respectively. The reaction enthalpy measured under these conditions is DeltaH(degrees)pep= 4.2 kcal/mol for ri-mel-SH and DeltaH(degrees)pep= 1.1 kcal/mol for mel-SH. The peptide-to-HS stoichiometry is approximately 20 for ri-mel-SH and approximately 14 for mel-SH under the same conditions. Temperature dependence studies using ri-mel-SH (mel-SH) show that DeltaH(degrees)pep decreases in magnitude upon increase in temperature, which results in a molar heat capacity of DeltaH(degrees)pep= -322 cal mol(-)(1) K(-)(1) (-45 cal mol(-)(1) K(-)(1)). Such a negative heat capacity change is not expected for a purely electrostatic interaction and indicates that hydrophobic and other interactions are also involved in the binding equilibrium. Salt dependence studies of the binding constants confirm that nonelectrostatic forces are an important component of the HS-melittin interaction. Binding to HS induces conformational changes in both peptides, with ri-mel-SH showing a 6-fold increase of the alpha-helix content when incubated with HS under saturation conditions.
Cold Staining And Ziehl - Neelsen Staining For Acid Fast Bacilli (1997)

The cold staining was compared with Ziehl-Neelsen (Z-N) method for detection of acid fast bacilli (AFB) in sputum in 1500 sputum smears. In cold staining method 72.1% cases were reported positive for AFB and 27.9% negative, while in Z-N method 75% were reported positive and 25% negative and the difference was not statistically significant (P>0.05).
Evaluation of the Safety and Efficacy of a Novel Home-Use Device with Diode Arrays and Contact Heating for Facial Skin Rejuvenation (2011)

Background: Phototherapy of photoaged skin has been attempted by lasers or intense pulsed light at the visible or near-infrared part of the spectrum. The use of red Light-Emitting Diodes (LED) delivering a low dose energy to the skin has been described for office and home use. Methods: In the present study, a portable home-use device is presented that combines fractional non-thermal red LED with mild contact heating. Forty subjects aged 30 - 55 presenting with facial lax skin, large pores, fine lines, wrinkles and brown pigmentation received 8 bi-weekly treatments for 4 weeks, using the Silk’n Reju/FaceFX device (Home Skinovations, Yokneam, Israel). Skin condition was evaluated before and 1, 2, and 3 months following the last treatment session. Grading of outcome was done according to an independent blinded evaluator and patient satisfaction. Results: Facial skin improvement of wrinkling and skin texture were apparent immediately and scored clinically after 3 months as excellent and considerable by >90% of patients. Pigmentation improvement was less apparent. Overall facial skin improvement was noted by 77% of patients. Conclusions: The combination of fractional red LED and mild contact heating, using an at home portable device, proved to be safe and effective method to improve the quality of photoaged skin.
Inheritance of Cold Hardiness and Dehydrin Genes in Diploid Mapping Populations of Blueberry (2004)

Summary Studies of herbaceous plants suggest that cold hardiness is a complex, quantitatively inherited trait. Although development of cold hardiness is an integral part of the life cycle of woody perennial plants, studies on the genetic control of cold hardiness in woody perennials are scarce. A better understanding of the genetic control of cold hardiness would be valuable for developing more effective strategies to increase cold hardiness and, hence, climatic adaptation of woody perennial crops. In blueberry, three major dehydrins of 65, 60, and 14 kDa have been found to increase with cold acclimation and decrease with deac-climation. A comparison of these dehydrin levels among various blueberry cultivars and selections has revealed their level of accumulation to be closely associated with cold hardiness level. Efforts are underway to isolate and map the dehydrin genes of blueberry utilizing blueberry populations that segregate for cold hardiness in order to determine if the dehydrin genes map to or co-segregate with QTLs controlling cold hardiness. Progress has been made toward this goal. Cold hardiness levels were determined for a portion of the blueberry mapping populations (derived from testcrosses of Vaccinium darrowi Camp X V. caesariense Mackenz. F1s to another V. darrowi and another V. caesariense) using a laboratory controlled freeze-thaw regime, followed by visual assessment of injury to floral buds. As expected, the V. darrowi and V. caesariense parents were found to differ significantly in terms of cold hardiness levels (LT50s of -13°C and -20°C, respectively). Mean cold hardiness level of F1s (LT50 of -14.7°C) was skewed toward the V. darrowi parents suggesting that cold hardiness is a partially recessive trait. The sequence of a 2.0 kb cDNA clone, which encodes the 60 kDa blueberry dehydrin, was used to map a dehydrin-related gene to current linkage group 12 of the V. caesariense testcross population. A preliminary comparison of the segregation pattern of the dehydrin-related gene to that of the cold hardiness trait suggests that the marker does not segregate with cold hardiness.
Docile Bodies of (Im)Material Girls: The Fairy-Tale Construction of Jon-Benet Ramsey and Princess Diana (1999)

The sediments of classic fairy tales continue to be imbricated in contemporary discourses of gender, power, and consumption, reflecting and shaping deeper ideological tendencies. Nowhere is this more emphatically presented than in women’s magazines and tabloids. This article analyzes the news and tabloid presentation of the stories of JonBenet Ramsey and Princess Diana in the larger context of narratives about fairy-tale princesses, arguing that in order to understand the pervasiveness of the images of JonBenet and Diana, we must locate them within the nexus of traditional fairy-tale princess narratives, the social construction of gender, and the historical trajectory of women’s magazines in their visual ordering of femininity and female desire.
Non-invasive assessment of liver fibrosis. (2012)

The presence and degree of hepatic fibrosis is crucial in order to make therapeutic decisions and predict clinical outcomes. Currently, the place of liver biopsy as the standard of reference for assessing liver fibrosis has been challenged by the increasing awareness of a number of drawbacks related to its use (invasiveness, sampling error, inter-/intraobserver variability). In parallel with this, noninvasive assessment of liver fibrosis has experienced explosive growth in recent years and a wide spectrum of noninvasive methods ranging from serum assays to imaging techniques have been developed. Some are validated methods, such as the Fibrotest/ Fibrosure and transient elastography in Europe, and are gaining a growing role in routine clinical practice, especially in chronic hepatitis C. Large-scale validation is awaited in the setting of other chronic liver diseases. However, noninvasive tests used to detect significant fibrosis and cirrhosis, the two major clinical endpoints, are not yet at a level of performance suitable for routine diagnostic tests, and there is still no perfect surrogate or method able to completely replace an optimal liver biopsy. This article aims to review current noninvasive tests for the assessment of liver fibrosis and the perspectives for their rational use in clinical practice.
Production of Nonbitter, Desalted Milk Hydrolysate for Fortification of Soft Drinks and Fruit Juices (1983)

ABSTRACT A simpler and less expensive process than the process of Helbig et al. (1980) for preparation of a nonbitter, desalted milk hydrolysate is presented. Skim milk was hydrolyzed with Alcalase (subtilisin Carlsberg) at 50°C in 3 hr. The resin in OH form was added to milk batchwise to simultaneously raise the pH to 8.5 for optimum proteolysis and exchange the anions in milk which contributed to saltiness. These modifications resulted in a shorter hydrolysis time and a more economical resin regeneration than those of the Helbig process. The dried milk hydrolysate was added to soft drinks and fruit juices at solids concentrations up to 10% (3% protein) without adverse effects on their taste, color, viscosity and clarity.
Molecular characterization of <i>pcp</i>, the structural gene encoding the pyrrolidone carboxylyl peptidase from <i>Streptococcus pyogenes</i> (1992)

This paper describes the cloning of a gene (pcp) coding for pyrrolidone carboxylyl peptidase (PYRase), an enzyme which selectively removes N-terminal pyroglutamic acid residues from polypeptides. This gene was isolated from Streptococcus pyogenes by construction of a gene library with a bacteriophage lambda-derived cosmid-Escherichia coli host system. Nucleotide sequence determination of a 1.3 kb restriction fragment revealed a 645 bp open reading frame encoding a 215-amino-acid product of M(r) 23,135 consistent with the 26 kDa polypeptide obtained from in vivo overexpression in E. coli. Southern hybridization confirmed that pcp is a single-copy gene on the S. pyogenes chromosome. 5' and 3' endpoint mapping of the 0.7 kb specific transcript observed by Northern analysis permitted the identification of transcriptional initiation and termination signals. Structural features of the pcp gene product from S. pyogenes are discussed and compared with that from Bacillus subtilis. The lack of sequence identity with any other known protein or nucleotide sequence suggests that this enzyme belongs to a new class of peptidase.
Task description, decomposition, and allocation in a distributed autonomous multi-agent robot system (2002)

In this paper a new intelligent control architecture for autonomous multi-robot systems is presented. Furthermore, the paper deals with task description, task distribution, task allocation and coordination of the system components. The main advantage of the new control architecture is the distributed execution of tasks or subtasks by components of the multi-robot system. The components are able to build teams dynamically thereby avoiding the bottle neck problem of the information flow in centralized controlled architectures. The communication and cooperation between components to achieve distributed organized control architectures is studied. The described intelligent control architecture is to replace the former control architecture of the autonomous robot KAMRO.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Highly efficient biallelic genome editing of human ES/iPS cells using a CRISPR/Cas9 or TALEN system (2017)

Genome editing research of human ES/iPS cells has been accelerated by clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALEN) technologies. However, the efficiency of biallelic genetic engineering in transcriptionally inactive genes is still low, unlike that in transcriptionally active genes. To enhance the biallelic homologous recombination efficiency in human ES/iPS cells, we performed screenings of accessorial genes and compounds. We found that RAD51 overexpression and valproic acid treatment enhanced biallelic-targeting efficiency in human ES/iPS cells regardless of the transcriptional activity of the targeted locus. Importantly, RAD51 overexpression and valproic acid treatment synergistically increased the biallelic homologous recombination efficiency. Our findings would facilitate genome editing study using human ES/iPS cells.
Optimization of global production scheduling with deep reinforcement learning (2018)

Industrie 4.0 introduces decentralized, self-organizing and self-learning systems for production control. At the same time, new machine learning algorithms are getting increasingly powerful and solve real world problems. We apply Google DeepMind’s Deep Q Network (DQN) agent algorithm for Reinforcement Learning (RL) to production scheduling to achieve the Industrie 4.0 vision for production control. In an RL environment cooperative DQN agents, which utilize deep neural networks, are trained with user-defined objectives to optimize scheduling. We validate our system with a small factory simulation, which is modeling an abstracted frontend-of-line semiconductor production facility.
Current Concepts and Correction in the Valgus Foot (1970)

Deceased (1/30/69). Address requests for reprints to: Dr. Jean-Francois LeLievre, 130, Rue Du Faubourg St. Honore, Paris 8, France.
Single-Molecule Approach to Enzymology (2001)

Recent advances in single-molecule enzymology are reviewed. The theoretical underpinning of sincle-molecule enzymatic behaviors is discussed and exemplified by experiements and statistical analyses. In particular, the manifestations of the Michaelis-Menten mechanism, the kinetic scheme with sequential intermediates, and dynamic disorder in single molecule data are presented. A survey of current methods for single molecule enzymatic assays, especially those based on fluorescence detection, is presented as well.
Site-directed mutational analysis of a membrane guanylate cyclase cDNA reveals the atrial natriuretic factor signaling site. (1991)

Natriuretic peptides are structurally related hormones that regulate hemodynamics of the physiological processes of diuresis, water balance, and blood pressure. One of the second messengers of these hormones is cGMP, and the type of receptor that is involved in the generation of cGMP is also a guanylate cyclase. Recent genetic evidence has revealed such a receptor family; two family members, GC-A and GC-B, have been cloned. We now describe the molecular cloning, sequencing, and expression of a cDNA clone from rat adrenal gland that encodes a membrane guanylate cyclase, GC alpha, that, with the exception of two amino acids, is structurally identical to GC-A and conforms to the purported topographical model of GC-A. The two amino acid changes are the substitutions Gln338----His338 and Leu364----Pro364, involving single nucleotide changes, CAG----CAC and CTG----CCG, respectively. Expression studies indicate that GC alpha cyclase activity is independent of the known natriuretic peptides, and direct binding studies demonstrate that GC alpha is not an ANF receptor. To determine the importance of Gln338 and Leu364 in ANF signaling, the GC alpha cDNA regions encoding amino acid residues 338 and 364 were remodeled by oligonucleotide-directed mutagenesis. A double mutant encoding Gln338 and Leu364, and a single-substitution mutant encoding Leu364 expressed both ANF binding and ANF-dependent cyclase activities, but the mutant encoding Gln338 and a deletion mutant lacking residue 364 did not express either of the above activities. These results define the critical role of Leu364 in ANF signal transduction.
Statically equivalent serial chains for modeling the Center of Mass of humanoid robots (2008)

This paper proposes a method for modeling the center of mass (CoM) of humanoid robots. The method is based on the statically equivalent serial chain (SESC) model, a serial chain representation of any multi-link branched chain. An algorithm is presented to automatically construct the SESC of a symmetric anthropomorphic architecture. We also show the use of SESC modeling in the projection of the CoM when the kinematic chain is not positioned on a horizontal plane. Finally, after validating these developments on the HOAP-3 experimental humanoid robot platform, we discuss the interest of this modeling in other areas of research.
Increasing error tolerance in biometric systems (2010)

Using biometrics for authentication or cryptosystems would require tolerance of errors of the order of 40%. Most of the proposed techniques either use the reliable bits of a biometric or good quality biometric which does not have such a large variation. However, biometric authentication can be viewed as a design of error correcting codes wherein the redundancy provides the tolerance to errors. This paper explores addition of redundancy to support variations as high as 40% in biometrics. We investigated the error characteristics of biometric templates and found that some blocks within the template tend to produce errors higher than the mean error. To handle this behavior we propose a two level correction. We extensively tested our proposed method using iris images from the commercial Bath dataset [13] and found that the proposed method can tolerate the errors with a success rate of 99.07%, while not accepting any imposters.
Autoimmune diseases as stem cell disorders: normal stem cell transplant for their treatment (Review). (1998)

Using various animal models for autoimmune diseases, we have found that autoimmune diseases are stem cell disorders. The transplantation of normal hemopoietic stem cells (HSCs) can be used to treat autoimmune diseases, whereas the transplantation of abnormal HSCs from autoimmune-prone mice to normal mice leads to the induction of autoimmune diseases in recipients. To elucidate the differences between normal and abnormal HSCs, we have established a new method for purifying pluripotent-HSCs (P-HSCs), and have compared the qualitative differences. Although normal P-HSCs cannot proliferate under major histocompatibility complex (MHC)-incompatible microenvironments (stromal cells), abnormal P-HSCs can proliferate under such conditions. In addition, the proliferation of abnormal P-HSCs is much faster than that of normal P-HSCs. These findings indicate that abnormal P-HSCs are more resilient than normal P-HSCs. Therefore, we propose that allogeneic bone marrow transplantation (BMT) (not autologous BMT) should be applied to the treatment of autoimmune diseases. human data on BMT in autoimmune diseases is reviewed, and the conditions essential for successful BMT, including tolerance induction, are discussed.
<title>Combined spectroscopic ellipsometry and reflectometry for advanced semiconductor fabrication metrology</title> (1996)

Spectroscopic reflectometry has been a mainstay of optical semiconductor metrology for many years, as has single wavelength ellipsometry performed at a fixed angle of incidence. More recently, spectroscopic ellipsometry has been employed to provide film thickness and optical constant measurements with greater precision and accuracy. In this work we demonstrate the combined use of spectroscopic ellipsometry (performed from 420 - 720 nm at 75 degree angle of incidence) and spectroscopic reflectometry (performed from 200 to 800 nm at normal incidence) for the characterization of thin films and multilayer stacks commonly encountered in semiconductor device fabrication. By employing sophisticated parametric dispersion models and simultaneously fitting both the reflectance and ellipsometric spectra, we are able to perform accurate and precise characterization of many structures that cannot be characterized with either technique alone or with combined reflectometry and single wavelength ellipsometry.
Engineering of the Curie temperature of epitaxial Sr1−xBaxTiO3 films via strain (2016)

The impact of strain on the structural and electrical properties of epitaxial Sr1−xBaxTiO3 films grown on single crystalline DyScO3 (110), TbScO3 (110), and GdScO3 (110) substrates is presented. X-ray diffraction measurements demonstrate that all films are grown epitaxially. The tensile in-plane strain is only partially compensated by a contraction of the out-of-plane lattice parameter. As a result, the volume of the unit cell of the Sr1−xBaxTiO3 film increases due to the tensile strain, and the resulting Poisson ratio of the film is ν ≈ 0.33, which is larger than but still close to the literature values of ν ≈ 0.23 for unstrained defect-free SrTiO3. The Curie temperature derived from the temperature dependence of the in-plane dielectric response leads to a strain-temperature phase diagram for the epitaxial Sr1−xBaxTiO3 films. The experimental data show a deviation from the linear dependence predicted by the Landau thermodynamic theory for large strain (&gt;1.2%). However, using the equilibrium thermodynamic analysis, we can demonstrate that this deviation arises from the relaxation of the strain due to defect formation in the film. The result reveals that in addition to the nominal misfit strain, the defect formation strongly affects the effective strain and, thus, the dielectric response of epitaxially grown ferroelectric films.