gebhart/patrepeval huggingface dataset:
Macromol. Chem. Phys. 9/2014 (2014)

Front Cover: Novel highly aligned, single-layered hollow fibrous membranes from PU/silica (SiO2) blend are fabricated using two-fluid coaxial electrospinning (ES). Various polymer complex concentrations and ES parameters, including the applied voltage and inner-to-outer flow rate ratio (FRRi/o), substantially affect the fiber alignment degree and hollow fibrous area. This study demonstrates that novel, highly aligned PU/SiO2 hollow fibrous membranes can be used as advanced guide conduits for nerves and vascular scaffolds. Further details can be found in the article by Y.-S. Huang, C.-C. Kuo,* Y.-C. Shu, S.-C. Jang, W.-C. Tsen, F.-S. Chuang, and C.-C. Chen on page 879.
Structure-activity relationships of cyclic opioid peptide analogs containing a phenylalanine residue in the 3-position (1987)

Ten analogues of the highly mu-receptor selective cyclic opioid peptide H-Tyr-D-Orn-Phe-Asp-NH2 (1) were synthesized by the solid phase method and were characterized in vitro in mu- and delta-receptor representative binding assays and bioassays. These cyclic analogues are structurally related to the linear opioid peptides dermorphin and beta-casomorphin (morphiceptin), which also contain a phenylalanine residue in the 3-position of the peptide sequence. The obtained results indicate that analogous structural modifications (configurational inversion at positions 2, 3, and 4 or N alpha-methylation of Phe3) in cyclic peptide 1 and in dermorphin-related peptides had qualitatively the same effect on opioid activity, whereas the corresponding modifications in beta-casomorphins had the opposite effect. These findings can be interpreted to indicate that the mode of receptor binding of H-Tyr-D-Orn-Phe-Asp-NH2 is identical with that of dermorphin, but differs from that of beta-casomorphins. The side-chain length of the aromatic residue in position 3 of cyclic analogue 1 was shown to be critical for receptor affinity and selectivity, suggesting that mu- and delta-receptors differ from one another in the relative topographical disposition of the binding sites for the Tyr1 tyramine moiety and the Phe3 aromatic ring. Cyclic lactam analogue H-Tyr-D-Asp-Phe-A2bu-NH2, containing a reduced-size (12-membered) ring structure, showed increased mu-receptor selectivity, whereas the more flexible, cystine-containing analogue H-Tyr-D-Cys-Phe-Cys-NH2 (11-membered ring) was less selective. The latter results indicate that both ring size and ring flexibility affect receptor affinity and selectivity.
Practical VTI RTM (2010)

In this abstract we describe a production implementation of 3D anisotropic VTI RTM using a finite-difference scheme on production cluster. Our end-to-end code is about four times faster than a blade that consists of dual Intel quadcore Harpertown running a similar VTI RTM code, including vectorization. It is interesting to note that in the final implementation disk IO is the bottleneck. This means that faster compute nodes (increased FLOPS per core) will not improve performance. What is needed is more disk bandwidth (&gt;200MB/s per processor) to make it run faster, and/or more computationally intensive versions of RTM to generate better images.
ADP-ribosyltransferase-specific Modification of Human Neutrophil Peptide-1 (2006)

Epithelial cells lining human airways and cells recruited to airways participate in the innate immune response in part by releasing human neutrophil peptides (HNP). Arginine-specific ADP-ribosyltransferases (ART) on the surface of these cells can catalyze the transfer of ADP-ribose from NAD to proteins. We reported that ART1, a mammalian ADP-ribosyltransferase, present in epithelial cells lining the human airway, modified HNP-1, altering its function. ADP-ribosylated HNP-1 was identified in bronchoalveolar lavage fluid (BALF) from patients with asthma, idiopathic pulmonary fibrosis, or a history of smoking (and having two common polymorphic forms of ART1 that differ in activity), but not in normal volunteers or patients with lymphangioleiomyomatosis. Modified HNP-1 was not found in the sputum of cystic fibrosis patients or in leukocyte granules of normal volunteers. The finding of ADP-ribosyl-HNP-1 in BALF but not in leukocyte granules suggests that the modification occurred in the airway. Most of the HNP-1 in the BALF from individuals with a history of smoking was, in fact, mono- or di-ADP-ribosylated. ART1 synthesized in Escherichia coli, glycosylphosphatidylinositol-anchored ART1 released with phosphatidylinositol-specific phospholipase C from transfected NMU cells, or ART1 expressed endogenously on C2C12 myotubes modified arginine 14 on HNP-1 with a secondary site on arginine 24. ADP-ribosylation of HNP-1 by ART1 was substantially greater than that by ART3, ART4, ART5, Pseudomonas aeruginosa exoenzyme S, or cholera toxin A subunit. Mouse ART2, which is an NAD:arginine ADP-ribosyltransferase, was able to modify HNP-1, but to a lesser extent than ART1. Although HNP-1 was not modified to a significant degree by ART5, it inhibited ART5 as well as ART1 activities. Human beta-defensin-1 (HBD1) was a poor transferase substrate. Reduction of the cysteine-rich defensins enhanced their ability to serve as ADP-ribose acceptors. We conclude that ADP-ribosylation of HNP-1 appears to be primarily an activity of ART1 and occurs in inflammatory conditions and disease.
Structural and functional aspects of basic helix-loop-helix protein folding by heat-shock protein 90. (1994)

The assembly and folding of nascent polypeptides are mediated in vivo by molecular chaperones, many of which are members of the heat-shock family of proteins. We have shown previously that heat-shock protein 90 (HSP90) folds an inactive fraction of a recombinant basic helix-loop-helix (bHLH) protein generated in Escherichia coli (MyoD) into its active conformation. We show here that HSP90 also folds another bHLH protein (E12) and heterodimers of E12/MyoD into their active conformations. By purifying inactive heterodimers of E12/MyoD and subsequently rendering them active in binding DNA by treatment with HSP90, we show that one folding step mediated by HSP90 occurs after oligomerization of the bHLH protein monomers. A series of deletion mutants is used to identify the 48-amino acid region of HSP90 that confers bHLH folding activity, which lies near the COOH terminus. This region is required for activation of DNA binding of MyoD and E12 homodimers and E12/MyoD heterodimers.
Fluorescence energy transfer between the primer and the beta subunit of the DNA polymerase III holoenzyme. (1992)

We report here our initial success in using fluorescence energy transfer to map the position of the subunits of the DNA polymerase III holoenzyme within initiation complexes formed on primed DNA. Using primers containing a fluorescent derivative 3 nucleotides from the 3'-terminus and acceptors of fluorescence energy transfer located on Cys333 of the beta subunit, a donor-acceptor distance of 65 A was measured. Coupling this distance with other information enabled us to propose a model for the positioning of beta within initiation complexes. Examination of the fluorescence properties of a labeled primer with the unlabeled beta subunit and other assemblies of DNA polymerase III holoenzyme subunits allowed us to distinguish all of the known intermediates of the holoenzyme-catalyzed reaction. Specific fluorescence changes could be assigned for primer annealing, Escherichia coli single-stranded DNA-binding protein binding, 3'----5' exonucleolytic hydrolysis of the primer, DNA polymerase III* binding, initiation complex formation upon the addition of beta in the presence of ATP, and DNA elongation. These fluorescence changes are sufficiently large to support future detailed kinetic studies. Particularly interesting was the difference in fluorescence changes accompanying initiation complex formation as compared to binding of DNA polymerase III holoenzyme subunit assemblies. Initiation complex formation resulted in a strong fluorescence enhancement. Binding of DNA polymerase III* led to a fluorescence quenching, and transfer of beta to primed DNA by the gamma delta complex did not change the fluorescence. This demonstrates a rearrangement of subunits accompanying initiation complex formation. Monitoring fluorescence changes with labeled beta, we have determined that beta binds with a stoichiometry of one monomer/primer terminus.
Repeated evaluation of human papillomavirus 16 status in cervical swabs of young women with a history of normal Papanicolaou smears (1993)

This study was designed to compare single-point prevalence estimates with a cumulative prevalence estimate of human papillomavirus (HPV) type 16 in cervical smears. The influence of the menstrual cycle and the long-term effect of HPV 16 positivity on the development of cervical intraepithelial neoplasia (CIN) were monitored. We examined 21 women (median age 23.6 years) every 5 weeks for 1 year. All women had a history of negative Papanicolaou smears for at least 5 years before enrollment. Cervical swabs were collected at each visit for Papanicolaou smears and HPV 16 detection by the polymerase chain reaction. Five years after completion of the last visit, self-reported information regarding cervical neoplasia was obtained. Human papillomavirus type 16 point-prevalence estimates per visit varied between 14.3-33.3%. The cumulative prevalence was 66.7%; 14 women were positive at least once and seven women were continuously negative for HPV 16. Detection of HPV 16 was significantly higher in the luteal phase. Repeated positivity for HPV 16 by Southern blot and polymerase chain reaction preceded and accompanied CIN in one patient, whereas in the remaining patients, positivity for HPV 16 by polymerase chain reaction alone was not associated with CIN during a 5-year follow-up. Single-point measurements of HPV 16 in cervical smears by polymerase chain reaction are of limited value for assessment of an individual's HPV status. This should be kept in mind when HPV testing for screening programs is considered.
Notch-4 contributes to the metastasis of salivary adenoid cystic carcinoma (2010)

The Notch signaling pathway is important for cell-cell communication; it is involved in gene regulation mechanisms that control multiple cell differentiation processes during embryonic and adult life. Notch is present in all metazoans, and vertebrates possess four different Notch receptors: Notch-1, Notch-2, Notch-3, and Notch-4. The aim of the present study was to identify the role of Notch protein in the metastasis of salivary adenoid cystic carcinoma (SACC). Real-time PCR results showed that Notch-1, Notch-2, and Notch-4 were upregulated in the highly metastatic SACC cell line ACC-M, compared to ACC-2, a SACC cell line with low metastatic ability. Knockdown of Notch-4 by small interfering RNA efficiently inhibited the invasion of ACC-M cells. Notch-4 expression was significantly higher in the clinical samples with metastasis and recurrence compared to that in control (p<0.05), shown by immunohistochemistry analysis. These results indicate that Notch-4 may play an important role in SACC metastasis.
A Planter and His Slaves in Eighteenth-Century Jamaica (1979)

The British West Indian sugar colonies of the eighteenth century were marked by the institution of slavery to a degree which has never been matched elsewhere. The sugar plantations established a virtual monoculture and they worked most profitably on a large scale, with hundreds of black slaves supervised by a handful of white men. So in all of these islands by the middle of the century the white colonists were a minority, often a very small minority, among their slaves. They accounted for about a quarter of the population in Barbados, and about a tenth in the Leeward Islands and Jamaica. How then did they maintain their authority? What measures did they take and what effects did they have? We must answer such questions if we are to understand these societies, but reliable information that might allow us to do so is scarce. There are many surviving collections of plantation papers, but these are concerned mainly with business matters — so much sugar made and sold, so many supplies bought — and they have little to say about the relations of the masters with their slaves. Most contemporary descriptions of West Indian society are those of travellers or casual visitors to the islands, and even if they observed and wrote dispassionately they were outsiders, likely to record what was striking or curious, but uncertain guides to the daily routine. In any case, most visitors were not dispassionate: by the later eighteenth century the ethics of slavery had become controversial and most reporters came with strong preconceptions, sometimes in favour of the slave-owners, but usually against them. On the other hand, what little was written by the white West Indians themselves is open to suspicion as self-exculpation and special pleading.
Pluripotent Stem Cells – Model of Embryonic Development, Tool for Gene Targeting, and Basis of Cell Therapy (2002)

Embryonic stem (ES) cells are pluripotent cell lines with the capacity of self-renewal and a broad differentiation plasticity. They are derived from pre-implantation embryos and can be propagated as a homogeneous, uncommitted cell population for an almost unlimited period of time without losing their pluripotency and their stable karyotype. Murine ES cells are able to reintegrate fully into embryogenesis when returned into an early embryo, even after extensive genetic manipulation. In the resulting chimeric offspring produced by blastocyst injection or morula aggregation, ES cell descendants are represented among all cell types, including functional gametes. Therefore, mouse ES cells represent an important tool for genetic engineering, in particular via homologous recombination, to introduce gene knock-outs and other precise genomic modifications into the mouse germ line. Because of these properties ES cell technology is of high interest for other model organisms and for livestock species like cattle and pigs. However, in spite of tremendous research activities, no proven ES cells colonizing the germ line have yet been established for vertebrate species other than the mouse (Evans and Kaufman, 1981; Martin, 1981) and chicken (Pain et al., 1996). The in vitro differentiation capacity of ES cells provides unique opportunities for experimental analysis of gene regulation and function during cell commitment and differentiation in early embryogenesis. Recently, pluripotent stem cells were established from human embryos (Thomson et al., 1998) and early fetuses (Shamblott et al., 1998), opening new scenarios both for research in human developmental biology and for medical applications, i.e. cell replacement strategies. At about the same time, research activities focused on characteristics and differentiation potential of somatic stem cells, unravelling an unexpected plasticity of these cell types. Somatic stem cells are found in differentiated tissues and can renew themselves in addition to generating the specialized cell types of the tissue from which they originate. Additional to discoveries of somatic stem cells in tissues that were previously not thought to contain these kinds of cells, they also appear to be capable of developing into cell types of other tissues, but have a reduced differentiation potential as compared to embryo-derived stem cells. Therefore, somatic stem cells are referred to as multipotent rather than pluripotent. This review summarizes characteristics of pluripotent stem cells in the mouse and in selected livestock species, explains their use for genetic engineering and basic research on embryonic development, and evaluates their potential for cell therapy as compared to somatic stem cells.
Olfactory Neuron Loss in Adult Male CD Rats Following Subchronic Inhalation Exposure to Hydrogen Sulfide (2000)

Dysosmia and anosmia are reported to occur following human exposure to hydrogen sulfide (H2S) gas. The clinical association between H2S exposure and olfactory dysfunction in humans necessitates evaluation of the nasal cavity and olfactory system in experimental animals used to study H2S toxicity. The purpose of this study was to subchronically expose 10-week-old male CD rats to relatively low concentrations of H2S and to histologically evaluate the nasal cavity for exposure-related lesions. Rats (n = 12/group) were exposed via inhalation to 0, 10, 30, or 80 ppm H2S 6 h/d and 7 d/wk for 10 weeks. Following exposure to 30 and 80 ppm H2S, a significant increase in nasal lesions limited to the olfactory mucosa was observed. The lesions, which consisted of olfactory neuron loss and basal cell hyperplasia, were multifocal, bilaterally symmetrical, and had a characteristic rostrocaudal distribution pattern. Regions of the nasal cavity affected included the dorsal medial meatus and the dorsal and medial portions of the ethmoid recess. The no observed adverse effect level for olfactory lesions in this study was 10 ppm. For perspective, the American Conference of Governmental Industrial Hygienists threshold limit value (TLV) recommendation for H2S is currently 10 ppm (proposed revision: 5 ppm), so the concentrations employed in the present study were 3 and 8 times the TLV. These findings suggest that subchronic inhalation exposure to a relatively low level of H2S (30 ppm) can result in olfactory toxicity in rats. However, because of differences in the breathing style and nasal anatomy of rats and humans, additional research is required to determine the significance of these results for human health risk assessment.
Large assist feature phase-shift mask for sub-quarter-micrometer window pattern formation (1997)

To improve the depth of focus of isolated windows, large assist feather technique has been proposed. This large assist method uses the assist features having almost the same size as main patterns, and the quartz substrate was vertically etched at the assist features. These large assist features were not printed on a wafer by mask topography effect; that is, the light intensity at large assist feature was decreased by the scattering effect of the vertical quartz edges. In this large assist feature masks, the phase shift angle of an assist feature has large effect on focus latitude. We chose two phase shift angles: 180 degrees for small sigma illumination and 360 degrees for annular illumination. The performances of two large assist feature masks were evaluated by using a 0.55 NA, valuable sigma, and KrF excimer laser stepper. Moreover, we applied surface insoluble layer to the assist feature method. Large assist features having the same size as main patterns were not printed on resist surface for 0.16 - 0.2 micrometer windows. Wide DOF (0.8 micrometer) of 0.16 micrometer window was obtained by using this method.
Human Pituitary Growth Hormone Isolation and Properties of Two Biologically Active Fragments from Plasmin Digests (1974)

Two biologically active fragments have been isolated from plasmic digests of human pituitary growth hormone. It was shown that these two fragments were derived from the cleavage of the Arg-Thr (positions 134-135) and the Lys-Gln (positions 140-141) bonds of the hormone: one has 134 amino acids and the other 51 amino acids, respectively. The two fragments were active in the rat tibia and pigeon crop-sac tests, as well as in complement fixation experiments.
Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans (2003)

More than 5 million single-nucleotide polymorphisms (SNPs) with minor-allele frequency greater than 10% are expected to exist in the human genome. Some of these SNPs may be associated with risk of developing common diseases. To assess the power of currently available SNPs to detect such associations, we resequenced 50 genes in two ethnic samples and measured patterns of linkage disequilibrium between the subset of SNPs reported in dbSNP and the complete set of common SNPs. Our results suggest that using all 2.7 million SNPs currently in the database would detect nearly 80% of all common SNPs in European populations but only 50% of those common in the African American population and that efficient selection of a minimal subset of SNPs for use in association studies requires measurement of allele frequency and linkage disequilibrium relationships for all SNPs in dbSNP.
A study on hydroxyapatite formation on/in the hydroxyl groups-bearing nonionic hydrogels (1999)

Using the biomimetic method, we formed a hydroxyapatite (HAp) layer on/in certain types of nonionic hydrogels that contain hydroxyl groups. The hydrogels used were poly(vinyl alcohol) (PVA), poly(2-hydroxyethyl methacrylate) (PHEMA), poly(glucosyloxyethyl methacrylate) (PGEMA), and agarose. Under an optical microscope, we observed a thin, continuous HAp layer on the top surface of the PVA, PHEMA, and PGEMA gels. On the other hand, we only observed an intermittent HAp layer on the surface of the agarose gel. The swelling ratio and the bound water content of these hydrogels were measured as an essential character in HAp formation. There was some relation among the HAp formation, the swelling ratios, and the bound water content.
The Development of a Metabolic Disease Phenotype in CTP:Phosphoethanolamine Cytidylyltransferase-deficient Mice (2009)

Phosphatidylethanolamine (PE) is an important inner membrane phospholipid mostly synthesized de novo via the PE-Kennedy pathway and by the decarboxylation of phosphatidylserine. CTP:phosphoethanolamine cytidylyltransferase (Pcyt2) catalyzes the formation of CDP-ethanolamine, which is often the rate regulatory step in the PE-Kennedy pathway. In the current investigation, we show that the reduced CDP-ethanolamine formation in Pcyt2(+/-) mice limits the rate of PE synthesis and increases the availability of diacylglycerol. This results in the increased formation of triglycerides, which is facilitated by stimulated de novo fatty acid synthesis and increased uptake of pre-existing fatty acids. Pcyt2(+/-) mice progressively accumulate more diacylglycerol and triglycerides with age and have modified fatty acid composition, predominantly in PE and triglycerides. Pcyt2(+/-) additionally have an inherent blockage in fatty acid utilization as energy substrate and develop impaired tolerance to glucose and insulin at an older age. Accordingly, gene expression analyses demonstrated the up-regulation of the main lipogenic genes and down-regulation of mitochondrial fatty acid beta-oxidation genes. These data demonstrate for the first time that to preserve membrane PE phospholipids, Pcyt2 deficiency generates compensatory changes in triglyceride and energy substrate metabolism, resulting in a progressive development of liver steatosis, hypertriglyceridemia, obesity, and insulin resistance, the main features of the metabolic syndrome.
Intracranial Applications of MR Imaging–Guided Focused Ultrasound (2016)

Initially used in the treatment of prostate cancer and uterine fibroids, the role of focused ultrasound has expanded as transcranial acoustic wave distortion and other limitations have been overcome. Its utility relies on focal energy deposition via acoustic wave propagation. The duty cycle and intensity of focused ultrasound influence the rate of energy deposition and result in unique physiologic and biomechanical effects. Thermal ablation via high-intensity continuous exposure generates coagulative necrosis of tissues. High-intensity, pulsed application reduces temporally averaged energy deposition, resulting in mechanical effects, including reversible, localized BBB disruption, which enhances neurotherapeutic agent delivery. While the precise mechanisms remain unclear, low-intensity, pulsed exposures can influence neuronal activity with preservation of cytoarchitecture. Its noninvasive nature, high-resolution, radiation-free features allow focused ultrasound to compare favorably with other modalities. We discuss the physical characteristics of focused ultrasound devices, the biophysical mechanisms at the tissue level, and current and emerging applications.