gebhart/patrepeval huggingface dataset:
Reliability and Processing Effects of Bandgap Engineered SONOS (BE-SONOS) Flash Memory (2007)

The reliability properties of BE-SONOS (Lue et al., 2005) are extensively studied. BE-SONOS employs a multi-layer O1/N1/O2/N2/O3 stack, where O1/N1/O2 serves as a bandgap engineered tunneling barrier that provides an efficient hole tunneling erase but eliminates the direct tunneling leakage. BE-SONOS can overcome the fundamental limitation of the conventional SONOS, for which fast erase speed and good data retention cannot be simultaneously achieved. This work provides a comprehensive understanding of the reliability of BE-SONOS. Various processes to form the critical O1/N1/O2 barrier, the trapping layer (N2), and the top blocking oxide (O3) are investigated. The results of this work provide design and processing guidelines for optimizing the performance and reliability of BE-SONOS flash memory devices.
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses (2007)

Recent experimental evidence has demonstrated that bacteria acquire resistance to viruses by incorporation of short transcribed nucleotide sequences into regions of clustered regularly interspaced short palindromic repeats (CRISPR). We have analysed community genomic data from acidophilic microbial biofilms and discovered that evolution of the CRISPR regions in two distinct Leptospirillum group II bacteria occurs fast enough to promote individuality in otherwise nearly clonal populations. Comparative genomics strongly indicates very recent lateral transfer of the CRISPR locus between these populations, followed by significant loss of spacer sequences and locus expansion by unidirectional heterogeneous addition of new spacer sequences. Diversification of the CRISPR region is inferred to be a population-level response to the rapidly changing selective pressure of phage predation. Results reinforce the importance of phage-host interactions in shaping microbial ecology and evolution over very short time scales.
Mechanisms Underlying Ubiquitination (2001)

The conjugation of ubiquitin to other cellular proteins regulates a broad range of eukaryotic cell functions. The high efficiency and exquisite selectivity of ubiquitination reactions reflect the properties of enzymes known as ubiquitin-protein ligases or E3s. An E3 recognizes its substrates based on the presence of a specific ubiquitination signal, and catalyzes the formation of an isopeptide bond between a substrate (or ubiquitin) lysine residue and the C terminus of ubiquitin. Although a great deal is known about the molecular basis of E3 specificity, much less is known about molecular mechanisms of catalysis by E3s. Recent findings reveal that all known E3s utilize one of just two catalytic domains--a HECT domain or a RING finger--and crystal structures have provided the first detailed views of an active site of each type. The new findings shed light on many aspects of E3 structure, function, and mechanism, but also emphasize that key features of E3 catalysis remain to be elucidated.
Cell-Free Translation of Messenger RNA Extracted from a Human Insulinoma* (1978)

Total nucleic acid has been extracted from a human pancreatic insulinoma. Purification of the messenger RNA (mRNA) fraction by oligo-dT cellulose chromatography yielded 200 μg poly(A)-rich mRNA. This mRNA produced a 2-fold stimulation of protein synthesis in a wheat germ cell-free system. Analysis of the translation products by gel filtration chromatography (Biogel P-30) revealed nothing smaller than an acid-alcohol-soluble protein larger than bovine proinsulin. In contrast, insulinoma slices incubated with labeled amino acids synthesized smaller proteins which comigrated with bovine proinsulin and insulin.[3H]Leucine-labeled cell-free proteins were electrophoresed on NaDodSO4-urea polyacrylamide slab gels. In the presence of insulinoma mRNA, discrete proteins of 25,000 and 11,500 mol wt were synthesized. The 11,500 mol wt protein was specifically immunoprecipitated with antiinsulin serum. Thus, cell-free translation of human insulinoma mRNA yields an immunoreactive insulin larger than proinsulin, which is the same size as fish and rat preproinsulins recently described.
SIK3 is essential for chondrocyte hypertrophy during skeletal development in mice (2012)

Chondrocyte hypertrophy is crucial for endochondral ossification, but the mechanism underlying this process is not fully understood. We report that salt-inducible kinase 3 (SIK3) deficiency causes severe inhibition of chondrocyte hypertrophy in mice. SIK3-deficient mice showed dwarfism as they aged, whereas body size was unaffected during embryogenesis. Anatomical and histological analyses revealed marked expansion of the growth plate and articular cartilage regions in the limbs, accumulation of chondrocytes in the sternum, ribs and spine, and impaired skull bone formation in SIK3-deficient mice. The primary phenotype in the skeletal tissue of SIK3-deficient mice was in the humerus at E14.5, where chondrocyte hypertrophy was markedly delayed. Chondrocyte hypertrophy was severely blocked until E18.5, and the proliferative chondrocytes occupied the inside of the humerus. Consistent with impaired chondrocyte hypertrophy in SIK3-deficient mice, native SIK3 expression was detected in the cytoplasm of prehypertrophic and hypertrophic chondrocytes in developing bones in embryos and in the growth plates in postnatal mice. HDAC4, a crucial repressor of chondrocyte hypertrophy, remained in the nuclei in SIK3-deficient chondrocytes, but was localized in the cytoplasm in wild-type hypertrophic chondrocytes. Molecular and cellular analyses demonstrated that SIK3 was required for anchoring HDAC4 in the cytoplasm, thereby releasing MEF2C, a crucial facilitator of chondrocyte hypertrophy, from suppression by HDAC4 in nuclei. Chondrocyte-specific overexpression of SIK3 induced closure of growth plates in adulthood, and the SIK3-deficient cartilage phenotype was rescued by transgenic SIK3 expression in the humerus. These results demonstrate an essential role for SIK3 in facilitating chondrocyte hypertrophy during skeletogenesis and growth plate maintenance.
Sustained release of doxorubicin from zeolite–magnetite nanocomposites prepared by mechanical activation (2006)

Nanocomposites consisting of magnetite and FAU zeolite with a high surface area and adsorption capacity have been prepared by mechanical activation using high-energy milling at room temperature. FTIR results, as well as HRTEM, EFTEM, and XPS measurements, show that the resulting magnetic nanoparticles are covered by a thin aluminosilicate coating. A saturation magnetization as high as 16 emu g(-1) and 94.2 Oe of coercivity were observed for the obtained composites. The main advantages of this synthesis procedure are (i) simplicity of the preparation procedure, (ii) prevention of agglomeration of the magnetite nanoparticles to a large extent, and (iii) absence of free magnetite outside the zeolitic matrix. In addition, in vitro experiments revealed that the nanoparticles prepared were able to store and release substantial amounts of doxorubicin. In view of these advantages, these magnetic nanoparticles can be considered as potential candidates for drug-delivery applications.
Surface Transfer Doping of Diamond (100) by Tetrafluoro-tetracyanoquinodimethane (2007)

Surface transfer doping is demonstrated on hydrogenated diamond (100) by the electron acceptor, tetrafluoro-tetracyanoquinodimethane (F4-TCNQ). Synchrotron-based photoemission spectroscopy reveals that electrons are transferred from diamond to adsorbed F4-TCNQ, leaving a diamond surface p-type doped with a high areal density of holes of about 1.6 × 1013 cm-2.
Osteogenic Differentiation of Mesenchymal Stem Cells on Pregenerated Extracellular Matrix Scaffolds in the Absence of Osteogenic Cell Culture Supplements (2009)

This study utilized a full-factorial design to investigate the effect of four factors: presence of whole bone marrow cells, presence of in vitro-generated mineralized extracellular matrix (ECM), presence of dexamethasone, and variations in culture duration, on the proliferation and osteogenic differentiation of mesenchymal stem cells (MSCs) cultured on a polymer scaffold. Electrospun poly(epsilon-caprolactone) (PCL) fiber mesh scaffolds were seeded with rat MSCs and cultured in complete osteogenic medium for 12 days to generate constructs containing mineralized ECM. MSCs or MSCs and whole bone marrow cells were seeded onto decellularized ECM constructs (PCL/ECM) or plain PCL scaffolds and cultured statically for 4, 8, and 16 days in medium either with or without dexamethasone. After each culture period, the cell number was determined by DNA analysis, and the osteogenic differentiation state of the cells was determined by alkaline phosphatase activity and calcium assays. MSCs seeded onto PCL/ECM constructs and cultured in medium either with or without dexamethasone demonstrated similar amounts of calcium deposition after 16 days. A significant increase in cell number over time compared with all other groups was observed when whole bone marrow cells were cocultured with MSCs on PCL scaffolds in medium without dexamethasone. This study establishes that the osteogenic differentiation of MSCs seeded onto ECM-containing constructs is maintained even in the absence of dexamethasone and that the coculture of MSCs and whole bone marrow cells without dexamethasone and ECM enhances the proliferation of a cell population (or populations) present in the whole bone marrow.
Effect of plant extracts and formic acid on the intestinal equilibrium of early-weaned pigs1 (2004)

We evaluated the effects of a plant extracts mixture (XT) standardized in 5% (wt/wt) carvacrol, 3% cinnamaldehyde, and 2% capsicum oleoresin (oregano, cinnamon and Mexican pepper), alone or in combination with formic acid (FA), on the productive performance and the intestinal ecosystem of the early-weaned pig. Pigs weaned at 20 +/- 1 d of age (n = 216) were allocated in 24 pens and fed a standard medicated prestarter diet for 12 d. Twelve days after weaning, a stress management system based on social and dietary stress factors was applied to the animals, after which, each group was allocated to one of six dietary treatments, which followed a factorial arrangement, with three levels (as-fed basis) of the XT (0, 150, and 300 mg/kg) and two levels of FA (0 and 0.5%). On d 24 and 25 after the stress episode, eight pigs per treatment were killed to examine variables describing some aspects of the gastrointestinal ecology. Two days after the stress episode, an Escherichia coli K88 diarrhea episode occurred, and five casualties were registered. Four of the five deaths occurred in pens of pigs not fed the XT. The FA resulted in better G:F (P = 0.040) in coincidence with shorter villous height (P = 0.073) and lower rectal total microbial mass (P = 0.078). Both XT and FA addition increased stomach content (P = 0.006 and 0.003, respectively) and percentage of DM (P = 0.089 and 0.010, respectively), suggesting an increased gastric retention time; consequently, pH was also increased (P = 0.005 and 0.060, respectively). The XT decreased ileum total microbial mass (P = 0.025) and increased the lactobacilli:enterobacteria ratio (P = 0.002). The VFA profile in the cecum and colon was modified by XT inclusion, increasing the proportion of acetate (P = 0.018 and 0.025, respectively) and diminishing the proportion of butyrate (P = 0.096 and 0.040, respectively) and valerate (P = 0.001 and 0.039, respectively). Both XT and FA were shown to be effective in modifying the gastrointestinal ecosystem, stomach contents, and stomach emptying rate, which are proposed as important aspects in the mechanisms of action for these additives.
Application of the 5′ Fluorogenic Exonuclease Assay (TaqMan) for Quantitative Ribosomal DNA and rRNA Analysis in Sediments (2001)

In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of Geobacter spp. and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or < or =2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated, amended aquifer sediments were significantly lower (P < 0.0002) than traces for the external standard curve. We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (P < 0.0001). If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (C(t)) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation. Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples.
User speed estimation and dynamic channel allocation in hierarchical cellular system (2002)

The huge amount of handoffs generated by microcells creates a problem for the future PCN. To alleviate the problem, we propose a hierarchical cellular system which comprises cells of different sizes. Ideally, one would like to use large cells to serve high-mobility users. A challenging issue is to obtain a good estimate of the user speed. A simple speed estimation is proposed and based on this estimate one can implement a number of dynamic channel allocation algorithms on such a hierarchical network. A comparative study of these algorithms will be presented based on a detailed simulation model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of Residues in α-Macroglobulins Important for Binding to the α2-Macroglobulin Receptor/Low Density Lipoprotein Receptor-related Protein (1996)

Variants of the receptor binding domain of both human alpha2-macroglobulin and the corresponding domain of hen egg white ovomacroglobulin have been expressed in Escherichia coli and refolded in vitro. Competition experiments with methylamine-treated alpha2-macroglobulin for binding to the multifunctional alpha2-macroglobulin receptor identify two Lys residues (residues 1370 and 1374 in human alpha2-macroglobulin) spaced by three amino acid residues as crucial for receptor binding. From this result and mutational evidence from other ligands for the alpha2-macroglobulin receptor, a tentative sequence motif for receptor binding is proposed.
Thyroid Peroxidase Activity-Inhibiting Immunoglobulins in Patients with Autoimmune Thyroid Disease (1989)

The thyroid microsomal antibody (M-Ab) has been found to be an antibody against thyroid peroxidase (TPO), and such antibodies have been reported not only to bind TPO but also to directly inhibit TPO activity. In this study we investigated the relationship between TPO activity-inhibiting immunoglobulin (TPII) and thyroid function in 55 untreated patients with hyperthyroidism due to Graves' disease and 35 untreated patients with Hashimoto's disease. TPO partially purified from the microsomal fraction of Graves' thyroid tissue by Sephacryl S-300 gel filtration was incubated with immunoglobulin (Ig) fractions of serum prepared by precipitation with 15% polyethylene glycol. At the end of incubation, TPO activity was measured by a guaiacol assay. The TPII level was expressed as the TPII index, defined as the inhibition of TPO activity by patient Ig divided by inhibition produced by a known positive Ig. We also measured serum free T4, free T3, and TSH concentrations and anti-M-Ab titers, the latter by a microenzyme-linked immunosorbent assay. When a positive TPII index was defined as more than the mean + 2 SD of the TPII index (0.38) for 15 normal subjects, 13 patients with Graves' disease and 14 patients with Hashimoto's disease had positive TPII index values. There was a positive correlation between the TPII index values and the M-Ab titers in patients with either Graves' disease (r = 0.38; P less than 0.01) or Hashimoto's disease (r = 0.52; P less than 0.01). The mean TPII index in patients with Hashimoto's disease was significantly higher than that in patients with Graves' disease [0.38 +/- 0.42 (+/- SD) vs. 0.19 +/- 0.41; P less than 0.05]. The slope of the regression line between the TPII index values and the M-Ab titers for patients with Hashimoto's disease was steeper than that for patients with Graves' disease. The mean serum free T4 concentration was significantly lower in those patients with Hashimoto's disease who had positive TPII index values than in those with negative TPII index values (14.0 +/- 5.0 vs. 9.6 +/- 3.7 pmol/L; P less than 0.01). There was no significant difference in thyroid function between the patients with Graves' disease with positive and negative TPII index values. TPII appears to inhibit thyroid function in some patients, but no simple relationship between TPII and thyroid function in autoimmune thyroid disease was demonstrated. Understanding the factors that control access of anti-TPO antibody to its antigen may help to elucidate the significance of circulating anti-TPO antibody.
Development of biomechanical properties and morphogenesis of in vitro tissue engineered cartilage (1995)

Neocartilage was engineered by culturing bovine chondrocytes on poly(glycolic acid) (PGA) fibrous nonwoven scaffolds. The biomechanical properties and morphologies of the PGA-chondrocyte constructs were studied over 12 weeks of in vitro culture. PGA scaffolds without cells lost their mechanical strength and structural integrity between week 2 and week 3 in culture. The thickness of the PGA-chondrocyte constructs decreased by 35% during the first 3 weeks, but the thickness increased from week 3 to week 9 to a thickness 42% higher than that of the starting scaffolds, which was then maintained. Safranin O staining of PGA-chondrocyte constructs revealed increasing proteoglycan formation over time. The compressive modules of PGA-chondrocyte constructs increased with in vitro culture time, and reached the same order of magnitude as that of normal bovine cartilage at week 9. The aggregate modulus of the PGA-chondrocyte constructs decreased by 57% over the first 2 weeks but then increased, reaching the same order of magnitude as normal bovine cartilage at week 12. The apparent permeability of the PGA-chondrocyte constructs, which was initially four orders of magnitude above that of normal cartilage, decreased between weeks 1 and 3 and thereafter remained the same order of magnitude as that measured for normal cartilage.
Roles of FGF receptors in mammalian development and congenital diseases (2003)

Four fibroblast growth factor receptors (FGFR1-4) constitute a family of transmembrane tyrosine kinases that serve as high affinity receptors for at least 22 FGF ligands. Gene targeting in mice has yielded valuable insights into the functions of this important gene family in multiple biological processes. These include mesoderm induction and patterning; cell growth, migration, and differentiation; organ formation and maintenance; neuronal differentiation and survival; wound healing; and malignant transformation. Furthermore, discoveries that mutations in three of the four receptors result in more than a dozen human congenital diseases highlight the importance of these genes in skeletal development. In this review, we will discuss recent progress on the roles of FGF receptors in mammalian development and congenital diseases, with an emphasis on signal transduction pathways.
Characterization of human rhinoviruses displaced by an anti-receptor monoclonal antibody (1988)

The attachment of rhinoviruses to cellular receptors was studied by displacing bound virus particles with an anti-receptor monoclonal antibody. The two serotypes studied differed significantly with respect to the temperature dependence of displacement and the nature of the particles displaced. Binding was shown to be a two-step process, the first of which is reversible and is seen when viruses are bound either to isolated cell membranes or to cells at lower than physiological temperatures. Second-stage binding was seen with serotype 14 when bound to intact cells. Viral particles released from such cells by incubation at 37 degrees C or by anti-receptor antibody exhibited altered physical changes in the capsid and a loss of infectivity. In contrast, serotype 67 bound efficiently to cells at 37 degrees C and did not elute spontaneously but could be displaced by anti-receptor antibody to produce complete, infectious particles. Rhinoviruses labeled with [3H]myristic acid or with [35S]methionine were displaced similarly from cells or membranes by anti-receptor antibody, indicating that the majority of VP4 of rhinoviruses does not enter or remain attached to cells during either the first or second stage of virus binding. These data support the conclusion that the myristic acid moiety of VP4 is not involved in the initial viral interaction with cellular receptors.
Subband coding of images (1986)

Subband coding has become quite popular for the source encoding of speech. This paper presents a simple yet efficient extension of this concept to the source coding of images. We specify the constraints for a set of two-dimensional quadrature mirror filters (QMF's) for a particular frequency-domain partition, and show that these constraints are satisfied by a separable combination of one-dimensional QMF's. Bits are then optimally allocated among the subbands to minimize the mean-squared error for DPCM coding of the subbands. Also, an adaptive technique is developed to allocate the bits within each subband by means of a local variance mask. Optimum quantization is employed with quantizers matched to the Laplacian distribution. Subband coded images are presented along with their signal-to-noise ratios (SNR's). The SNR performance of the subband coder is compared to that of the adaptive discrete cosine transform (DCT), vector quantization, and differential vector quantization for bit rates of 0.67, 1.0, and 2.0 bits per pixel for 256 × 256 monochrome images. The adaptive subband coder has the best SNR performance.
O4‐03‐04: Tomm40 is Associated with Gray Matter Volume in Middle‐aged Persons with Apoe ε3/ε3 Genotype (2010)

Apolipoprotein E (APOE) genotypes are associated with variable risk of developing late onset Alzheimer's disease (LOAD), with APOE ε4 having higher risk. A variable poly-T length polymorphism at rs10524523, within intron 6 of the TOMM40 gene has very recently been shown to influence age of onset in LOAD, where very long poly-T length was associated with earlier disease onset, and short poly-T length associated with later onset. In this study, we tested the hypothesis that brain changes antedating symptomatic LOAD may be associated with this TOMM40 polymorphism. Among healthy APOE ε3 homozygous adults (mean age 57), we compared those homozygous for very long (VL/VL; n = 33) TOMM40 poly-T lengths (who are presumably at higher risk) to those homozygous for short (S/S; n = 37) poly-T lengths on structural brain imaging. Voxel-based morphometry was used to assess gray matter volume using the software SPM8. Gray matter probability maps were entered into a voxel-wise ANCOVA where Age and Intracranial volume were covariates Results were that the VL/VL TOMM40 group had significantly less gray matter volume in the ventral posterior cingulate and precuneus, a region of the brain affected early in LOAD. To our knowledge, this is the first study to associate TOMM40 523 genotypes to brain imaging in people at risk for AD. These findings suggest that the group with very long TOMM40 poly-T lengths may be experiencing incipient LOAD-related cognitive and brain changes. The participants in this study are being followed over time to determine genetic and other factors that predict cognitive decline and dementia.