gebhart/patrepeval huggingface dataset:
Salt causes ion disequilibrium‐induced programmed cell death in yeast and plants (2002)

Programmed cell death (PCD) is a fundamental cellular process conserved in metazoans, plants and yeast. Evidence is presented that salt induces PCD in yeast and plants because of an ionic, rather than osmotic, etiology. In yeast, NaCl inhibited growth and caused a time-dependent reduction in viability that was preceded by DNA fragmentation. NaCl also induced the cytological hallmarks of lysigenous-type PCD, including nuclear fragmentation, vacuolation and lysis. The human anti-apoptotic protein Bcl-2 increased salt tolerance of wild-type yeast strain and calcineurin-deficient yeast mutant (cnb1Delta) that is defective for ion homeostasis, but had no effect on the NaCl or sorbitol sensitivity of the osmotic hypersensitive hog1Delta mutant -- results that further link PCD in the response to the ion disequilibrium under salt stress. Bcl-2 suppression of cnb1Delta salt sensitivity was ENA1 (P-type ATPase gene)-dependent, due in part to transcriptional activation. Salt-induced PCD (TUNEL staining and DNA laddering) in primary roots of both Arabidopsis thaliana wild type (Col-1 gl1) and sos1 (salt overly sensitive) mutant seedlings correlated positively with treatment lethality. Wild-type plants survived salt stress levels that were lethal to sos1 plants because secondary roots were produced from the shoot/root transition zone. PCD-mediated elimination of the primary root in response to salt shock appears to be an adaptive mechanism that facilitates the production of roots more able to cope with a saline environment. Both salt-sensitive mutants of yeast (cnb1Delta) and Arabidopsis (sos1) exhibit substantially more profound PCD symptoms, indicating that salt-induced PCD is mediated by ion disequilibrium.
N-Myristoyltransferase 1 Is Essential in Early Mouse Development (2005)

N-Myristoyltransferase (NMT) transfers myristate to an amino-terminal glycine of many eukaryotic proteins. In yeast, worms, and flies, this enzyme is essential for viability of the organism. Humans and mice possess two distinct but structurally similar enzymes, NMT1 and NMT2. These two enzymes have similar peptide specificities, but no one has examined the functional importance of the enzymes in vivo. To address this issue, we performed both genetic and biochemical studies. Northern blots with RNA from adult mice and in situ hybridization studies of day 13.5 embryos revealed widespread expression of both Nmt1 and Nmt2. To determine whether the two enzymes are functionally redundant, we generated Nmt1-deficient mice carrying a beta-galactosidase marker gene. beta-Galactosidase staining of tissues from heterozygous Nmt1-deficient (Nmt1+/-) mice and embryos confirmed widespread expression of Nmt1. Intercrosses of Nmt1+/- mice yielded no viable homozygotes (Nmt1-/-), and heterozygotes were born at a less than predicted frequency. Nmt1-/- embryos died between embryonic days 3.5 and 7.5. Northern blots revealed lower levels of Nmt2 expression in early development than at later time points, a potential explanation for the demise of Nmt1-/- embryos. To explore this concept, we generated Nmt1-/- embryonic stem (ES) cells. The Nmt2 mRNA could be detected in Nmt1-/- ES cells, but the total NMT activity levels were reduced by approximately 95%, suggesting that Nmt2 contributes little to total enzyme activity levels in these early embryo cells. The Nmt1-/- ES cells were functionally abnormal; they yielded small embryoid bodies in in vitro differentiation experiments and did not contribute normally to organogenesis in chimeric mice. We conclude that Nmt1 is not essential for the viability of mammalian cells but is required for development, likely because it is the principal N-myristoyltransferase in early embryogenesis.
Fast exoskeleton optimization (2017)

An algorithm optimizes exoskeleton walking assistance in 1 hour
Species B adenovirus serotypes 3, 7, 11 and 35 share similar binding sites on the membrane cofactor protein CD46 receptor (2007)

We recently characterized the domains of the human cofactor protein CD46 involved in binding species B2 adenovirus (Ad) serotype 35. Here, the CD46 binding determinants are mapped for the species B1 Ad serotypes 3 and 7 and for the species B2 Ad11. Ad3, 7 and 11 bound and transduced CD46-positive rodent BHK cells at levels similar to Ad35. By using antibody-blocking experiments, hybrid CD46-CD4 receptor constructs and CD46 single point mutants, it is shown that Ad3, 7 and 11 share many of the Ad35-binding features on CD46. Both CD46 short consensus repeat domains SCR I and SCR II were necessary and sufficient for optimal binding and transgene expression, provided that they were positioned at an appropriate distance from the cell membrane. Similar to Ad35, most of the putative binding residues of Ad3, 7 and 11 were located on the same glycan-free, solvent-exposed face of the SCR I or SCR II domains, largely overlapping with the binding surface of the recently solved fiber knob Ad11-SCR I-II three-dimensional structure. Differences between species B1 and B2 Ads were documented with competition experiments based on anti-CD46 antibodies directed against epitopes flanking the putative Ad-binding sites, and with competition experiments based on soluble CD46 protein. It is concluded that the B1 and B2 species of Ad engage CD46 through similar binding surfaces.
Medication noncompliance in patients with chronic disease: issues in dialysis and renal transplantation. (2003)

For many chronic conditions, poor patient compliance with prescribed medications and other aspects of medical treatment can adversely affect the treatment outcome. Compliance with long-term treatment for chronic asymptomatic conditions such as hypertension is on the order of 50%. Although drugs with a longer therapeutic half-life may ease the burden of repeated daily dosing, the efficacy of any self-administered medication depends to a large extent on patient compliance. This article addresses the compliance issues in patients undergoing renal replacement therapy and in those with a successful renal transplant. A focused discussion of compliance in dialysis and renal transplant patients is followed by a general review of the literature on patient compliance. Many factors associated with poor compliance in this patient population are identified via a review of the recent literature. The difficulties in monitoring medication compliance and the methods used are discussed. Among factors associated with poor compliance, the following have been identified in several studies: frequent dosing, patient's perception of treatment benefits, poor patient-physician communication, lack of motivation, poor socioeconomic background, lack of family and social support, and younger age. Many strategies have been suggested to improve medication compliance, most without scientific validation. Strategies to improve compliance in dialysis and transplant patients are similar to those described for other chronic conditions and include simplifying the treatment regimen, establishing a partnership with the patient, and increasing awareness through education and feedback.
One-shot learning of object categories (2006)

Learning visual models of object categories notoriously requires hundreds or thousands of training examples. We show that it is possible to learn much information about a category from just one, or a handful, of images. The key insight is that, rather than learning from scratch, one can take advantage of knowledge coming from previously learned categories, no matter how different these categories might be. We explore a Bayesian implementation of this idea. Object categories are represented by probabilistic models. Prior knowledge is represented as a probability density function on the parameters of these models. The posterior model for an object category is obtained by updating the prior in the light of one or more observations. We test a simple implementation of our algorithm on a database of 101 diverse object categories. We compare category models learned by an implementation of our Bayesian approach to models learned from by Maximum Likelihood (ML) and Maximum A Posteriori (MAP) methods. We find that on a database of more than 100 categories, the Bayesian approach produces informative models when the number of training examples is too small for other methods to operate successfully.
Overexpression of the C-type natriuretic peptide (CNP) is associated with overgrowth and bone anomalies in an individual with balanced t(2;7) translocation (2007)

Longitudinal bone growth is determined by the process of endochondral ossification in the cartilaginous growth plate, which is located at both ends of vertebrae and long bones and involves many systemic hormones and local regulators. We report the molecular characterization of a de novo balanced t(2;7)(q37.1;q21.3) translocation in a young female with Marfanoid habitus and skeletal anomalies. The translocation was characterized by fluorescence in situ hybridization (FISH), checked for other abnormalities by array-comparative genomic hybridization (CGH), and finally, the breakpoints were cloned, sequenced, and compared. Biochemical dosage was applied to study the possible mechanisms that may cause the proposita's phenotype. The breakpoint on chromosome 2 disrupts the hypothetical gene MGC42174 (HUGO-approved symbol DIS3L2) and is located in the proximity of the NPPC gene coding for C-type natriuretic peptide (CNP), a molecule that regulates endochondral bone growth. CNP plasma concentration was doubled in the proband compared to five normal controls, while NPPC was substantially overexpressed in her fibroblasts. A transgenic mouse generated to target NPPC overexpression in bone showed a phenotype highly reminiscent of the patient's phenotype. The breakpoint on chromosome 7 is localized proximally at about 75 kb from the COL1A2 gene. The COL1A2 allele on the derivative chromosome was strongly underexpressed in fibroblasts, but total collagen was not significantly different from controls. Several evidences support the conclusion that the proband's abnormal phenotype is associated with C-type natriuretic peptide overexpression.
Engineering Lysosome-Targeting BODIPY Nanoparticles for Photoacoustic Imaging and Photodynamic Therapy under Near-Infrared Light (2016)

Developing lysosome-targeting organic nanoparticles combined with photoacoustic imaging (PAI) and photodynamic therapy (PDT) functions toward personalized medicine are highly desired yet challenging. Here, for the first time, lysosome-targeting BODIPY nanoparticles were engineered by encapsulating near-infrared (NIR) absorbed BODIPY dye within amphiphilic DSPE-mPEG5000 for high-performing lysosomal PAI and acid-activatable PDT against cancer cells under NIR light.
Rational Design and Enhanced Biocompatibility of a Dry Adhesive Medical Skin Patch (2011)

A new type of medical skin patch is developed that contains high-density, mushroom-like micropillars. Such dry-adhesive micropillars are highly biocompatible, have minimized side effects, and provide reasonable normal adhesion strength. To arrive at optimal conditions for the dry adhesive skin patch, the proper design of various structural and material parameters of micropillars is investigated.
Nutritional and Physiological Responses of Young Growing Rats to Diets Containing Raw Cowpea Seed Meal, Protein Isolate (Globulins), or Starch (2002)

The nutritional and physiological effects of raw cowpea (Vigna unguiculata (L) Walp.) seed meal, protein isolate (globulins), or starch on the metabolism of young growing rats have been evaluated in 14-day trials. Wet and dry weight gain, feed conversion efficiency, and lipid and protein accretion were significantly reduced as a result of inclusion of seed meal, globulins, or starch in the diet, with growth retardation being most marked with the seed meal. The proportional weights of the small intestine and pancreas were increased by meal diets, and serum cholesterol levels were slightly reduced. The globulins and raw starch also increased relative small intestine weights but had no effect on the pancreas or serum constituents. The effects of cowpeas on rats appeared to be due primarily to the combined actions of globulins, resistant starches, protease inhibitors, and possibly fiber and non-starch polysaccharides on intestinal and systemic metabolism.
Differential Cross-Section Measurement for the10B(n,α)7Li Reaction (2002)

The differential cross sections of the 10B(n, α)7Li reaction were measured at 4.17, 5.02, 5.74, and 6.52 MeV by using a gridded ionization chamber. Neutrons were produced through the D(d,n)3He reaction. The absolute neutron flux was determined through the 238U(n,f) reaction. The experiment shows that as the neutron energy increases from 4.17 to 6.52 MeV, the differential cross section changes from almost 90-deg symmetry to obviously backward peaked in the center-of-mass reference system.
Role of breast regression protein 39 (BRP-39)/chitinase 3-like-1 in Th2 and IL-13–induced tissue responses and apoptosis (2009)

Mouse breast regression protein 39 (BRP-39; Chi3l1) and its human homologue YKL-40 are chitinase-like proteins that lack chitinase activity. Although YKL-40 is expressed in exaggerated quantities and correlates with disease activity in asthma and many other disorders, the biological properties of BRP-39/YKL-40 have only been rudimentarily defined. We describe the generation and characterization of BRP-39(-/-) mice, YKL-40 transgenic mice, and mice that lack BRP-39 and produce YKL-40 only in their pulmonary epithelium. Studies of these mice demonstrated that BRP-39(-/-) animals have markedly diminished antigen-induced Th2 responses and that epithelial YKL-40 rescues the Th2 responses in these animals. The ability of interleukin13 to induce tissue inflammation and fibrosis was also markedly diminished in the absence of BRP-39. Mechanistic investigations demonstrated that BRP-39 and YKL-40 play an essential role in antigen sensitization and immunoglobulin E induction, stimulate dendritic cell accumulation and activation, and induce alternative macrophage activation. These proteins also inhibit inflammatory cell apoptosis/cell death while inhibiting Fas expression, activating protein kinase B/AKT, and inducing Faim 3. These studies establish novel regulatory roles for BRP-39/YKL-40 in the initiation and effector phases of Th2 inflammation and remodeling and suggest that these proteins are therapeutic targets in Th2- and macrophage-mediated disorders.
REDUCTION IN GOUT FLARES AND TOPHUS SIZE IN THE 52-WEEK FEBUXOSTAT ALLOPURINOL CONTROLLED TRIAL (FACT) (2006)

s: XIVth Congress of the Pan-American League of Associations for Rheumatology: CATEGORY: Gout and Other Crystal Diseases
5,6-Saturated thymine lesions in DNA: production by ultraviolet light or hydrogen peroxide (1982)

Thymine analogs with saturated 5-6 bonds are important types of DNA damage that are recognized by the DNA N-glycosylase activity of E. coli endonuclease III. Seeking agents which could preferentially form 5,6-hydrated thymine residues in duplex DNA both in vivo and in vitro, we exposed purified duplex DNA to 325- or 313-nm light; however, after such exposure pyrimidine dimers greatly predominated over 5,6-hydrated thymine. Hydrogen peroxide, on the other hand, formed significant numbers of endonuclease III-sensitive sites in vitro which were not apurinic/apyrimidinic lesions and thus were likely to be 5,6-hydrated thymines.
The physics basis for ignition using indirect-drive targets on the National Ignition Facility (2004)

The 1990 National Academy of Science final report of its review of the Inertial Confinement Fusion Program recommended completion of a series of target physics objectives on the 10-beam Nova laser at the Lawrence Livermore National Laboratory as the highest-priority prerequisite for proceeding with construction of an ignition-scale laser facility, now called the National Ignition Facility (NIF). These objectives were chosen to demonstrate that there was sufficient understanding of the physics of ignition targets that the laser requirements for laboratory ignition could be accurately specified. This research on Nova, as well as additional research on the Omega laser at the University of Rochester, is the subject of this review. The objectives of the U.S. indirect-drive target physics program have been to experimentally demonstrate and predictively model hohlraum characteristics, as well as capsule performance in targets that have been scaled in key physics variables from NIF targets. To address the hohlraum and hydrodynamic constraints on indirect-drive ignition, the target physics program was divided into the Hohlraum and Laser–Plasma Physics (HLP) program and the Hydrodynamically Equivalent Physics (HEP) program. The HLP program addresses laser–plasma coupling, x-ray generation and transport, and the development of energy-efficient hohlraums that provide the appropriate spectral, temporal, and spatial x-ray drive. The HEP experiments address the issues of hydrodynamic instability and mix, as well as the effects of flux asymmetry on capsules that are scaled as closely as possible to ignition capsules (hydrodynamic equivalence). The HEP program also addresses other capsule physics issues associated with ignition, such as energy gain and energy loss to the fuel during implosion in the absence of alpha-particle deposition. The results from the Nova and Omega experiments approach the NIF requirements for most of the important ignition capsule parameters, including drive temperature, drive symmetry, and hydrodynamic instability. This paper starts with a review of the NIF target designs that have formed the motivation for the goals of the target physics program. Following that are theoretical and experimental results from Nova and Omega relevant to the requirements of those targets. Some elements of this work were covered in a 1995 review of indirect-drive [J. D. Lindl, “Development of the indirect-drive approach to inertial confinement fusion and the target physics basis for ignition and gain,” Phys. Plasmas 2, 3933 (1995)]. In order to present as complete a picture as possible of the research that has been carried out on indirect drive, key elements of that earlier review are also covered here, along with a review of work carried out since 1995.
Pre-echo control using an improved post-filter in the frequency domain (2014)

In this paper, we propose a post-filter using warped linear prediction (WLP) in the frequency domain to suppress pre-echo artifacts. Conventional post-filter in the frequency domain are derived from linear prediction (LP) coefficients. The proposed method is simply implemented by the WLP coefficients instead of the LP coefficients. Since the time domain signal could be adjusted by WLP analysis in the frequency domain, we analyzed the onset position of the transient signal and set the appropriate warping factor to emphasize the resolution of the time domain signal. A subjective listening test was performed for transient signals and it was confirmed that the proposed method offers better subjective quality.
Cell cycle-regulated generation of single-stranded G-rich DNA in the absence of telomerase (1996)

Current models of telomere replication predict that due to the properties of the polymerases implicated in semiconservative replication of linear DNA, the two daughter molecules have one end that is blunt and one end with a short 3' overhang. Telomerase is thought to extend the short 3' overhang to produce long single-stranded overhangs. Recently, such overhangs, or TG1-3 tails, were shown to occur on both telomeres of replicated linear plasmids in yeast. Moreover, indirect evidence suggested that the TG1-3 tails also occurred in a yeast strain lacking telomerase. We report herein a novel in-gel hybridization technique to probe telomeres for single-stranded DNA. Using this method, it is shown directly that in yeast strains lacking the TLC1 gene encoding the yeast telomerase RNA, TG1-3 single-stranded DNA was generated on chromosomal and plasmid telomeres. The single-stranded DNA only appeared in S phase and was sensitive to digestion with a single-strand-specific exonuclease. These data demonstrate that during replication of telomeres, TG1-3 tails can be generated in a way that is independent of telomerase-mediated strand elongation. In wild-type strains, these TG1-3 tails could subsequently serve as substrates for telomerase and telomere binding proteins on all telomeres.
Ras Proteins Induce Senescence by Altering the Intracellular Levels of Reactive Oxygen Species (1999)

Human diploid fibroblasts eventually lose the capacity to replicate in culture and enter a viable but nonproliferative state of senescence. Recently, it has been demonstrated that retroviral-mediated gene transfer into primary fibroblasts of an activated ras gene (V12ras) rapidly accelerates development of the senescent phenotype. Using this in vitro system, we have sought to define the mediators of Ras-induced senescence. We demonstrate that expression of V12Ras results in an increase in intracellular and in particular, mitochondrial reactive oxygen species. The ability of V12Ras to induce growth arrest and senescence is shown to be partially inhibited by coexpression of an activated rac1 gene. A more dramatic rescue of V12Ras-expressing cells is demonstrated when the cells are placed in a low oxygen environment, a condition in which reactive oxygen species production is inhibited. In addition, in a 1% oxygen environment, Ras is unable to trigger an increase in the level of the cyclin-dependent kinase inhibitor p21 or to activate the senescent program. Under normoxic (20% O2) conditions, the V12Ras senescent phenotype is demonstrated to be unaffected by scavengers of superoxide but rescued by scavengers of hydrogen peroxide. These results suggest that in normal diploid cells, Ras proteins regulate oxidant production and that a rise in intracellular H2O2 represents a critical signal mediating replicative senescence.
Multiple quantum wells for ring and linear lasers with long lifetime gain (2005)

Various solid state lasers such as Cr:LISAF, Yb:YAG, Nd:Vanadate, Ti:sapphire and Nd:YAG have in common a long lifetime of the laser level, which results in a tendency to Q-switching rather than pure mode-locking. These lasers are being used in a linear or ring cavity for intracavity sensing applications (displacements, rotation, electric and magnetic fields), and for applications in spectroscopy. The requirements for these applications are that the pulses be centered at a specific wavelength, and be of a specific pulse duration. Multiple Quantum Wells (MQW) typically used for ultrashort pulse generation have often a high defect concentration which causes losses incompatible with the large number of intracavity elements required by the applications. We have established for all these lasers a composition curve for the MQW, that enables one to tune to a specific wavelength. These saturable absorbers have excellent optical quality both in reflection and transmission. The approach to prevent Q-switching has generally been to use very low loss modulation (single quantum wells). With a large number of intracavity elements, a larger loss modulation is desirable, hence the use of multiple QW (4 to 100). We have successfully demonstrated stable continuous model-locked operation by using passive energy limiters in the cavity. Two-photon generated carriers induce lensing in the cavity, resulting in power dependent losses through an aperture in the cavity. We show that the attenuation is proportional to the square of pulse intensity, resulting in a steep energy limiter. We demonstrate theoretically and experimentally that the presence of two intracavity pulses required for sensor applications can be satisfied with multiple quantum wells appropriately positioned in the cavity. Examples of applications include rotation sensors (ring cavity) or acceleration sensors (linear cavity), magnetic filed sensor, displacement sensors.