gebhart/patrepeval huggingface dataset:
KL-6, a Human MUC1 Mucin, Is Chemotactic for Human Fibroblasts (1997)

KL-6 in serum and bronchoalveolar lavage fluid has been reported to be a sensitive marker indicating the activity of fibrosing lung diseases. The molecule is clustered in MUC1 mucin according to the findings of immunohistochemical and cytometric studies. To elucidate the pathogenic role of KL-6 in fibrosing lung disease, we characterized its biochemical properties and examined whether purified KL-6 is chemotactic for human fibroblasts in vitro using modified Boyden chambers. Biochemical properties of purified KL-6 were similar to those of other MUC1 mucins previously reported. KL-6 promoted the migration of 5 of 5 human lung fibroblasts and 3 of 4 human skin fibroblasts. Checkerboard analysis revealed that KL-6 was chemotactic as well as chemokinetic. Though platelet-derived growth factor, fibroblast growth factor, or fibronectin were also chemotactic for fibroblasts in the experimental system, only fibronectin augmented KL-6-induced chemotaxis. These observations indicate that KL-6 is one of the chemotactic factors for most fibroblasts and that the increased KL-6 in the epithelial lining fluid in small airways may cause the intra-alveolar fibrosis in fibrosing lung diseases.
Distributions of the Two-Dimensional DCT Coefficients for Images (1983)

For a two-dimensional discrete cosine transform (DCT) image coding system, there have been different assumptions concerning the distributions of the transform coefficients. This paper presents results of distribution tests that indicate that for many images the statistics of the coefficients are best approximated by a Gaussian distribution for the DC coefficient and a Laplacian distribution for the other coefficients. Furthermore, from a simulation of the DCT coding System it is shown that the assumption that the coefficients are Laplacian yields a higher actual output signal-to-noise ratio and a much better agreement between theory and simulation than the Gaussian assumption.
Differential Regulation of Estrogen Receptor Subtypes α and β in Human Aortic Smooth Muscle Cells by Oligonucleotides and Estradiol (2004)

We investigated the mechanisms regulating estrogen receptor (ER) expression in human aortic smooth muscle cells (HASMCs) and the mechanisms by which estradiol inhibits HASMC growth. The autologous down-regulation pathway involves binding of liganded ER to the ER gene, thus suppressing transcription. Blockade of this pathway with sense and AS-OLIGOs to ERs up-regulated the expression of ERalpha but not ERbeta. Activation of the autologous down-regulation pathway with ER agonists down-regulated the expression of ERalpha but not ERbeta. The proteasomal degradation pathway entails ubiquination of liganded ER, followed by proteasome-mediated degradation. Blockade of the proteasomal degradation pathway increased the expression of ERbeta. Up-regulation of ERalpha by AS-OLIGOs did not increase the antimitogenic effects of estradiol on HASMCs; the estradiol metabolites 2-hydroxyestradiol and 2-methoxyestradiol were more potent inhibitors of HASMC growth, compared with estradiol; and blockade of metabolism of estradiol to hydroxyestradiols and methoxyestradiols abrogated the inhibitory effects of estradiol on HASMC growth. We conclude that, in HASMCs: 1) the expression of ERalpha is regulated by the autologous downregulation pathway; 2) the expression of ERbeta is governed by the proteasomal degradation pathway; and 3) the antigrowth effects of estradiol are not mediated by ERalpha, but rather by metabolism of estradiol to methoxyestradiols.
Catalytic Reductive Transformations of Carboxylic and Carbonic Acid Derivatives Using Molecular Hydrogen (2012)

A comprehensive overview on homogeneous catalytic hydrogenation of carboxylic acids and its derivatives as well as carbonic acid derivatives with transition metal-based molecular catalysts is described. Despite the tremendous potential in the hydrogenation of these less electrophilic carbonyl compounds using molecular hydrogen in synthetic organic chemistry, their reduction still relies mostly on the stoichiometric use of metal hydride reagents, such as LiAlH4, NaBH4, and their derivatives. For the past decade, a significant and rapid progress in particularly ester hydrogenation has been achieved by utilization of conceptually new bifunctional molecular catalysts originating from the metal–ligand cooperation effects. The bifunctional-catalyst-promoted hydrogenation using molecular hydrogen is now realized to be a practical tool in synthetic organic chemistry in both academia and industry. The industrial outlook for the present hydrogenation is bright because of its operational simplicity, scope, economic viability, and growing awareness of the need for green chemistry.
An Annular Corrugated-Surface Antenna (1952)

The far-zone pattem of the symmetrically excited annular corrugated-surface antenna is shown to be uniform in the azimuthal direction and polarized in a direction perpendicular to the antenna surface, and to have the major lobe directed slightly above the plane of the antenna. An analysis of the antenna immersed in an infinite ground plane is presented and compared with experimental results on the antenna in a finite ground plane.
Human UDP-Glucuronosyltransferases: Metabolism, Expression, and Disease (2000)

In vertebrates, the glucuronidation of small lipophilic agents is catalyzed by the endoplasmic reticulum UDP-glucuronosyltransferases (UGTs). This metabolic pathway leads to the formation of water-soluble metabolites originating from normal dietary processes, cellular catabolism, or exposure to drugs and xenobiotics. This classic detoxification process, which led to the discovery nearly 50 years ago of the cosubstrate UDP-glucuronic acid (19), is now known to be carried out by 15 human UGTs. Characterization of the individual gene products using cDNA expression experiments has led to the identification of over 350 individual compounds that serve as substrates for this superfamily of proteins. This data, coupled with the introduction of sophisticated RNA detection techniques designed to elucidate patterns of gene expression of the UGT superfamily in human liver and extrahepatic tissues of the gastrointestinal tract, has aided in understanding the contribution of glucuronidation toward epithelial first-pass metabolism. In addition, characterization of the UGT1A locus and genetic studies directed at understanding the role of bilirubin glucuronidation and the biochemical basis of the clinical symptoms found in unconjugated hyperbilirubinemia have uncovered the structural gene polymorphisms associated with Crigler-Najjar's and Gilbert's syndrome. The role of the UGTs in metabolism and different disease states in humans is the topic of this review.
Cytokine expression in the alkali-burned cornea (1997)

IL-1 alpha and IL-6 levels in the cornea are dramatically elevated in the regenerated epithelium during the early stages of alkali burn, and may play an important role in associated corneal damage and repair.
Microstructure evolution in magnetorheological suspensions governed by Mason number (2003)

The spatiotemporal evolution of field-induced structures in very dilute polarizable colloidal suspensions subject to rotating magnetic fields has been experimentally studied using video microscopy. We found that there is a crossover Mason number (ratio of viscous to magnetic forces) above which the rotation of the field prevents the particle aggregation to form chains. Therefore, at these high Mason numbers, more isotropic clusters and isolated particles appear. The same behavior was also found in recent scattering dichroism experiments developed in more concentrated suspensions, which seems to indicate that the dynamics does not depend on the volume fraction. Scattering dichroism experiments have been used to study the role played by the volume fraction in suspensions with low concentration. As expected, we found that the crossover Mason number does not depend on the volume fraction. Brownian particle dynamics simulations are also reported, showing good agreement with the experiments.
Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms (2003)

Acidophilic micro-organisms inhabit some of the most metal-rich environments known, including both natural and man-made ecosystems, and as such are ideal model systems for study of microbial metal resistance. Although metal resistance systems have been studied in neutrophilic micro-organisms, it is only in recent years that attention has been placed on metal resistance in acidophiles. The five metal resistance mechanisms identified in neutrophiles are also present in acidophiles, in some cases utilizing homologous proteins, but in many cases the degree of resistance is greater in acidophiles. This review summarizes the knowledge of acidophile metal resistance and presents preliminary in silico studies on a few known metal resistance systems in the sequenced acidophile genomes.
Laminar-specific distribution and infrastructural detail of amyloid in the Alzheimer disease cortex visualized by computer-enhanced imaging of epitopes recognized by monoclonal antibodies. (1988)

Monoclonal antibodies to the A4 amyloid polypeptide were used in immunocytochemical staining of the Alzheimer disease prefrontal cortex. Analysis of the resulting staining patterns allowed us to evaluate the amounts and distribution of amyloid-protein deposits exclusive of other senile-plaque components. Previously unappreciated infra-structural details of amyloid in the Alzheimer disease brain became accessible through computer-enhanced imaging procedures. Four discrete morphologic classes of amyloid deposits were observed and classified as punctate, macular, ring, and ring-with-core configurations. Computer imaging indicated that all four classes of immunostained deposits contain internal gradients of density. The classes were nonuniformly distributed with regard to size and location within cortical laminae. Our results support two separate but complementary hypotheses concerning the molecular neuropathology of Alzheimer disease in the prefrontal cortex. (i) Irrespective of cortical layer or morphology, density-gradient analyses suggest that amyloid deposits are elaborated through molecular and cellular events that may involve diffusion or coalescence of the A4 polypeptide. (ii) The distribution and morphology of prefrontal cortical amyloid deposits may be dependent upon underlying laminar-specific structures of the neocortex.
Gossypol Prototype of Inhibitors Targeted to Dinucleotide Folds (2000)

Gossypol, a disesquiterpene from cottonseed, exhibits multiple biological properties, including male antifertility activity and anticancer activity. Gossypol also inhibits the growth of numerous parasitic organisms and shows antiviral activity against a number of enveloped viruses, including the AIDS virus. Derivatives of gossypol, in which the aldehyde functional groups that contribute to toxicity have been modified, retain or even show enhanced biological activity. Ring substituted 2,3-dihydroxy-1-naphthoic acids, which are structural analogs of gossypol, share with gossypol the ability to complex with dehydrogenases at the dinucleotide fold (Rossmann fold) with selectivity, suggesting that gossypol may be considered the prototype of a new class of drugs targeted to dehydrogenases. Most of the biological activities of gossypol and related compounds may result from inhibition of dehydrogenases.
A Response to Professor Fox (1988)

In this Comment, Professors Weiss and White respond to a critique by Professor Merritt Fox of their earlier article Of Econometrics and Indeterminacy: A Study of Investors' Reactions to Changes in Corporate Law. In that article, the Authors conducted an econometric study of investors' reactions to seven recent Delaware court decisions. The results of that study led them to reassess the seven decisions and to question arguments that have been advanced by contract-oriented Professor Fox has criticized this work, stating that the Authors'primary evidenceabsence of market fluctuations following the courts' decisions-demonstrates only the inadequacy of market studies for this form of analysis. In this Comment, the Authors defend the use of market models and take exception to Fox's characterization of their methodology and conclusions. They conclude, however, that notwithstanding its undue formalism, Professor Fox's critique is not inconsistent with their own conclusions about the significance of their work for contract-oriented commentators.
Characterization of Regulatory Elements on the Promoter Region of p16INK4a That Contribute to Overexpression of p16 in Senescent Fibroblasts (2001)

Cyclin-dependent kinase inhibitor p16(INK4a) is implicated in replicative senescence, cell immortalization, and tumor generation. However, the mechanism regulating its overexpression in senescent cells is unknown. We used the enhanced green fluorescent protein reporter system to scan regulatory elements in the upstream region of p16(INK4a). The results of 5'-deletion studies indicated that the transcription regulatory elements contributing to overexpression of p16(INK4a) in senescent cells were located in the region of the p16(INK4a) promoter from -622 to -280 bp. According to the results of in vitro DNase I footprinting, EMSA, and Southwestern blotting, we found a novel negative regulatory element, the INK4a transcription silence element (ITSE), at -491 to -485 bp of the p16(INK4a) promoter. A 24-kDa protein that was highly expressed in young cells may inhibit the expression of p16(INK4a) by interacting with the ITSE. The activity of the p16(INK4a) promoter increased significantly in young cells when the ITSE was deleted. The GC-rich region of the p16(INK4a) promoter from -466 to -451 was a positive transcription regulatory element. Deletion of this region showed 91.4% loss of p16(INK4a) promoter activity in senescent cells, and the promoter activity decreased by 41.2% in young cells comparably.
An end-middle-end approach to connection establishment (2007)

The current model for flow establishment in the Internet: DNS Names, IP addresses, and transport ports, is inadequate. Not all of the problem is due to the small IPv4 address space and resulting NAT boxes. Even where global addresses exist, firewalls cannot glean enough information about a flow from packet headers, and so often err, typically by being over-conservative: disallowing flows that might otherwise be allowed. This paper presents a novel architecture, protocol design, and implementation, for flow establishment in the Internet. The architecture, called NUTSS, takes into account the combined policies of endpoints and network providers. While NUTSS borrows liberally from other proposals (URI-like naming, signaling to manage ephemeral IPv4 or IPv6 data flows), NUTSS is unique in that it couples overlay signaling with data-path signaling. NUTSS requires no changes to existing protocol stacks, and combined with recent NAT traversal techniques, works with IPv4 and existing NAT/firewalls. This paper describes NUTSS and shows how it satisfies a wide range of "end-middle-end"network requirements, including access control, middlebox steering, multi-homing, mobility, and protocol negotiation.
Evidence for Dispensable Sequences Inserted into a Nucleotide Fold (1987)

Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.
Infection with Vancomycin-ResistantStaphylococcus aureusContaining thevanAResistance Gene (2003)

Vancomycin-resistant S. aureus was cultured from the exit site of a temporary dialysis catheter of a patient with diabetes, peripheral vascular disease, and persistent foot ulcers. The organism carried the vanA resistance gene, which may have come from the vancomycin-resistant Enterococcus faecalis that was also isolated from the patient, who had received vancomycin for several weeks.
Instrument for measuring the misalignments of ocular surfaces (2006)

A compact and robust instrument for measuring the alignment of ocular surfaces has been designed and used in living eyes. It is based on recording Purkinje images (reflections of light at the ocular surfaces) at nine different angular fixations. A complete analysis on the causes of misalignments of Purkinje images and its relations with those physical variables to be measured (global eye tilt, lens decentration and lens tilt) is presented. A research prototype based on these ideas was built and tested in normal and pseudophakic eyes (after cataract surgery). The new analysis techniques, together with the semicircular extended source and multiple fixation tests that we used, are significant improvements towards a robust approach to measuring the misalignments of the ocular surfaces in vivo. This instrument will be of use in both basic studies of the eye's optics and clinical ophthalmology.
It's Time to Reframe the Savior Sibling Debate (2011)

The creation of savior siblings has been the subject of intense ethical debate over the past decade. While ethical concerns might provide clinicians with valid reasons for not providing these clinical services, we suggest that it is more difficult to make a case for physicians not disclosing to the parents of sick children under their care the option of creating a savior sibling. We “test” the ethical objections to savior siblings empirically and conclude that they rely heavily on unsound theoretical or speculative arguments and inappropriately scrutinize parental motives for having children. We contend that empirical evidence makes this moral frame increasingly tendentious, and that debate about savior siblings should be reframed as debate about the ethics of nondisclosure.
Expression of the c-ret proto-oncogene during mouse embryogenesis (1993)

The c-ret proto-oncogene encodes a receptor tyrosine kinase whose normal function has yet to be determined. To begin to investigate the potential role of this gene in vertebrate development, we have isolated cDNA clones representing the murine c-ret gene, and have analyzed the pattern of expression during mouse embryogenesis, using northern blotting, in situ hybridization to histological sections and whole-mount hybridization histochemistry. c-ret transcripts were detected beginning at day 8.5 of embryogenesis, and were observed in a number of cell lineages in the developing peripheral and central nervous systems, as well as in the excretory system. In the cranial region at day 8.5-9.5, c-ret mRNA was restricted to a population of neural crest cells migrating from rhombomere 4 and forming the anlage of the facioacoustic ganglion, as well as to a closely associated domain of surface ectoderm and pharyngeal endoderm. At later stages (10.5-14.5 days), c-ret mRNA was observed in all cranial ganglia. In the peripheral nervous system of the trunk, c-ret was expressed in the autonomic ganglia and in subsets of cells in the dorsal root ganglia. In the enteric nervous system, c-ret was expressed in the presumptive enteric neuroblasts of the vagal crest (day 9.0-11.5), and in the myenteric ganglia of the gut (day 13.5-14.5). c-ret mRNA was observed in several regions of the central nervous system, including the undifferentiated neuroepithelial cells of the ventral neural tube (8.5 days), the motor neurons in the spinal cord and the hindbrain (10.5-14.5 days), the embryonic neuroretina (day 13.5) and the layers of the postnatal retina containing ganglion, amacrine and horizontal cells. Outside the nervous system, c-ret was expressed in the nephric (Wolffian) duct at day 8.5-10.5, the ureteric bud epithelium (but not the surrounding metanephric mesenchyme) at day 11.0-11.5, and the growing tips of the renal collecting ducts (but not the previously formed, subcortical portions of the collecting ducts, or the mesenchyme-derived renal vesicles) at day 13.5-17.5. Our results suggest that the c-ret gene may encode the receptor for a factor involved in the proliferation, migration, differentiation or survival of a variety of neuronal cell lineages, as well as in inductive interactions during organogenesis of the kidney.
Polarization of porous PE foil (2003)

Piezoelectric properties of polyethylene porous foil submitted to a polarization in high electric fields is described in the paper. It was confirmed that partial discharges in DC fields lead to an activation of piezoelectric properties of porous dielectrics. It was also shown, that the value and time stability of the piezo-coefficient d/sub 33/ can be seriously affected by polarization conditions and that for commercial polyethylene foil may be on the level of 50 pC/N or higher.
FREAD revisited: Accurate loop structure prediction using a database search algorithm (2009)

Loops are the most variable regions of protein structure and are, in general, the least accurately predicted. Their prediction has been approached in two ways, ab initio and database search. In recent years, it has been thought that ab initio methods are more powerful. In light of the continued rapid expansion in the number of known protein structures, we have re-evaluated FREAD, a database search method and demonstrate that the power of database search methods may have been underestimated. We found that sequence similarity as quantified by environment specific substitution scores can be used to significantly improve prediction. In fact, FREAD performs appreciably better for an identifiable subset of loops (two thirds of shorter loops and half of the longer loops tested) than the ab initio methods of MODELLER, PLOP, and RAPPER. Within this subset, FREAD's predictive ability is length independent, in general, producing results within 2A RMSD, compared to an average of over 10A for loop length 20 for any of the other tested methods. We also benchmarked the prediction protocols on a set of 212 loops from the model structures in CASP 7 and 8. An extended version of FREAD is able to make predictions for 127 of these, it gives the best prediction of the methods tested in 61 of these cases. In examining FREAD's ability to predict in the model environment, we found that whole structure quality did not affect the quality of loop predictions.
Pyrene-Fused Porphyrins: Annulation Reactions of meso-Pyrenylporphyrins (2003)

Abstract We prepared novel pyrene-fused porphyrins via the oxidative intramolecular ring closure reactions of meso-pyrenylporphyrin. The excitation energies and the oxidation potentials of the isolated dark-colored pyrene-fused porphyrins were significantly low compared with those of the corresponding precursors.