gebhart/patrepeval huggingface dataset:
Fast distance queries with rectangular swept sphere volumes (2002)

We present new distance computation algorithms using hierarchies of rectangular swept spheres. Each bounding volume of the tree is described as the Minkowski sum of a rectangle and a sphere, and fits tightly to the underlying geometry. We present accurate and efficient algorithms to build the hierarchies and perform distance queries between the bounding volumes. We also present traversal techniques for accelerating distance queries using coherence and priority directed search. These algorithms have been used to perform proximity queries for applications including virtual prototyping, dynamic simulation, and motion planning on complex models. As compared to earlier algorithms based on bounding volume hierarchies for separation distance and approximate distance computation, our algorithms have achieved significant speedups on many benchmarks.
The Endothelial Biology of Sickle Cell Disease: Inflammation and a Chronic Vasculopathy (2004)

A single amino acid substitution in hemoglobin comprises the molecular basis for sickle cell anemia, but evolution of the corresponding clinical disease is extraordinarily complicated and likely involves multiple pathogenic factors. Sickle disease is fundamentally an inflammatory state, with activation of the endothelium, probably through proximate effects of reperfusion injury physiology and chronic molestation by adherent red cells and white cells. The disease also involves enhanced angiogenic propensity, activation of coagulation, disordered vasoregulation, and a component of chronic vasculopathy. Sickle cell anemia is truly an endothelial disease, and it is likely that genetic differences in endothelial function help govern its astonishing phenotypic diversity.
Effects of Exogenous NUB1 Expression in the Striatum of HDQ175/Q7 Mice (2016)

Findings suggest that increasing NUB1 protein in striatal neurons of HDQ175/Q7 mice in vivo may be relatively safe but is ineffective in reducing mHTT. Increased NUB1 expression in HD striatum alters PDE10A and P62 which are known to be influenced by mHTT.
Nanocrystals Modified with Peptide Nucleic Acids (PNAs) for Selective Self-Assembly and DNA Detection (2003)

Gold nanocrystals modified with peptide nucleic acids (PNAs) have been prepared and applied to self-assembly and DNA sensing. Experiments with different PNA structural motifs show that (1). the versatility in PNA synthetic design can be used to modulate the electrostatic surface properties of nanocrystals, presenting an opportunity to control assembly rate and aggregate size, (2). short (6 base) PNAs can hybridize effectively while attached to nanoparticles, providing a route to generating materials with small interparticle spacings, and (3). the superior base pair mismatch selectivity of PNAs is further enhanced on nanosurfaces, enabling PNA-modified nanoparticles to act as highly selective nanoscale sensors, as well as synthons for defect-free self-assembly. This last feature was coupled with a substantial change in colloidal stability upon DNA hybridization to develop a novel colorimetric DNA assay that detects the presence of single base imperfections within minutes. Various modes of PNA hybridization, including the first practical application of PNA-PNA interactions, were used to direct the assembly of nanoparticles into macroscopic arrangements. Shorter duplex interconnects and greater specificity in assembly were obtained compared to similar experiments with DNA-modified nanocrystals.
The Large Subunit of the DNA Replication Complex C (DSEB/RF-C140) Cleaved and Inactivated by Caspase-3 (CPP32/YAMA) during Fas-induced Apoptosis (1997)

We report the identification of the large subunit of the DNA replication factor, DSEB/RF-C140, as a new substrate for caspase-3 (CPP32/YAMA), or a very closely related protease activated during Fas-induced apoptosis in Jurkat T cells. DSEB/RF-C140 is a multifunctional DNA-binding protein with sequence homology to poly(ADP-ribose) polymerase (PARP). This similarity includes a consensus DEVD/G cleavage site for caspase-3. Cleavage of DSEB/RF-C140 is predicted to occurs between Asp706 and Gly707, generating 87-kDa and 53-kDa fragments. An antiserum raised against the amino-terminal domain of DSEB/RF-C140 detects a new 87-kDa protein in Jurkat T cells in which apoptosis is activated by a monoclonal antibody to Fas. This cleavage occurs shortly after PARP cleavage. In vitro translated DSEB/RF-C140 is specifically cleaved into the predicted fragments when incubated with a cytoplasmic extract from Fas antibody-treated cells. Proteolytic cleavage was prevented by substituting Asp706 by an alanine in the DEVD706/G caspase-3 cleavage site. The cleavage of DSEB/RF-C140 is prevented by iodoacetamide and the specific caspase-3 inhibitor, tetrapeptide aldehyde Ac-DEVD-CHO, but not by the specific ICE (interleukin-1-converting enzyme) inhibitors: CrmA and Ac-YVAD-CHO, indicating that the protease responsible for the cleavage of DSEB/RF-C140 during Fas-induced apoptosis in Jurkat cells is caspase-3, or a closely related protease. This conclusion is reinforced by the fact that recombinant caspase-3 but not caspase-1 reproduced the "in vivo" cleavage. Inasmuch as the cleavage of DSEB/RF-C140 separates its DNA binding from its association domain, required for replication complex formation, we propose that such a cleavage will impair DNA replication. Recent in vitro mutagenesis support this proposal (Uhlmann, F., Cai, J., Gibbs, E., O'Donnel, M., and Hurwitz, J. (1997) J. Biol. Chem. 272, 10058-10064).
Versatile and Facile Synthesis of Diverse Semisynthetic Tetracycline Derivatives via Pd-Catalyzed Reactions (2003)

A diverse collection of tetracycline derivatives has been synthesized utilizing Heck, Suzuki, and other palladium-coupling reactions via tetracycline arenediazonium and iodoarene salts. Large numbers of tetracyclines are now possible via these reactions, including numerous upper periphery derivatives of doxycycline, minocycline, sancycline, and methacycline modified at positions C7, C9, and C6-C13 on the tetracycline naphthacene ring. Application of palladium-coupling reactions to the tetracyclines has yielded new tetracycline classes with differing structural attributes, greatly increasing the structural diversity of this family of antibiotics, one of the last of the early antibiotic families to be expanded by organic and medicinal chemistry.
Hsp70 and Hsp40 chaperones can inhibit self-assembly of polyglutamine proteins into amyloid-like fibrils (2000)

The deposition of protein aggregates in neurons is a hallmark of neurodegenerative diseases caused by polyglutamine (polyQ) proteins. We analyzed the effects of the heat shock protein (Hsp) 70 chaperone system on the aggregation of fragments of huntingtin (htt) with expanded polyQ tracts. In vitro, Hsp70 and its cochaperone Hsp40 suppressed the assembly of htt into detergent-insoluble amyloid-like fibrils in an ATP-dependent manner and caused the formation of amorphous, detergent-soluble aggregates. The chaperones were most active in preventing fibrillization when added during the lag phase of the polymerization reaction. Similarly, coexpression of Hsp70 or Hsp40 with htt in yeast inhibited the formation of large, detergent-insoluble polyQ aggregates, resulting in the accumulation of detergent-soluble inclusions. Thus, the recently established potency of Hsp70 and Hsp40 to repress polyQ-induced neurodegeneration may be based on the ability of these chaperones to shield toxic forms of polyQ proteins and to direct them into nontoxic aggregates.
Process monitor gratings (2007)

Despite the increasing use of advanced imaging methods to pattern chip features, process windows continue to shrink with decreasing critical dimensions. Controlling the manufacturing process within these shrinking windows requires monitor structures designed to maximize both sensitivity and robustness. In particular, monitor structures must exhibit a large, measurable response to dose and focus changes over the entire range of the critical features process window. Any process variations present fundamental challenges to the effectiveness of OPC methods, since the shape compensation assumes a repeatable process. One particular process parameter which is under increasing scrutiny is focus blur, e.g. from finite laser bandwidth, which can cause such OPC instability, and thereby damage pattern fidelity. We introduce a new type of test target called the Process Monitor Grating (PMG) which is designed for extreme sensitivity to process variation. The PMG design principle is to use assist features to zero out higher diffraction orders. We show via simulation and experiment that such structures are indeed very sensitive to process variation. In addition, PMG targets have other desirable attributes such as mask manufacturability, robustness to pattern collapse, and compatibility with standard CD metrology methods such as scatterometry. PMG targets are applicable to the accurate determination of dose and focus deviations, and in combination with an isofocal grating target, allow the accurate determination of focus blur. The methods shown in this paper are broadly applicable to the characterization of process deviations using test wafers or to the control of product using kerf structures.
Human GM-CSF primes neutrophils for enhanced oxidative metabolism in response to the major physiological chemoattractants (1987)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a T cell-derived lymphokine which induces hematopoietic precursor cells to proliferate in vitro and differentiate to neutrophils and macrophages. GM-CSF also inhibits the motility of mature neutrophils (NIF-T activity), and primes neutrophils to enhance oxidative metabolism in response to the bacterial chemoattractant, N-formyl-methionyl-leucyl-phenylalanine (f-MLP). The present study was designed to determine whether this lymphokine also enhances neutrophil oxidative metabolism in response to the other major physiological chemoattractants which include complement-derived C5a, and the 5-lipoxygenation product of arachidonic acid, leukotriene B4 (LTB4). Superoxide anion production was measured as superoxide dismutase-inhibitable cytochrome C reduction. Purified biosynthetic GM-CSF enhanced superoxide anion production by neutrophils in response to f-MLP, C5a desArg, and LTB4. In contrast to several other factors which prime neutrophils, GM-CSF did not prime for an enhanced oxidative response to phorbol myristate acetate (PMA). These results suggest that GM-CSF may be an endogenous regulator of neutrophil inflammatory responses induced by the major physiological chemoattractants.
Analysis of upstream glucokinase promoter activity in transgenic mice and identification of glucokinase in rare neuroendocrine cells in the brain and gut. (1994)

A transgene consisting of an upstream glucokinase (GK) promoter fragment linked to coding sequences of the human growth hormone gene was expressed in certain neuroendocrine cells of the pancreas, pituitary, brain, gut, thyroid, and lungs of mice. In pancreas, the transgene was expressed in a nonuniform manner among beta cells and in a variable but substantial fraction of the other islet cell types. In pituitary, it was expressed in corticotropes, and in brain, it was expressed in cells of the medial hypothalamus. Within the gut transgene expression was detected in a subset of enteroendocrine cells of the stomach and duodenal epithelium, some of which also exhibited glucagon-like polypeptide-1 immunoreactivity. In thyroid, transgene expression was observed in C cells of neonatal animals, whereas in the lung, it was expressed among rare endocrine cells of the bronchopulmonary mucosa. RNA polymerase chain reaction analysis of human growth hormone mRNA corroborated the tissue-specific transgene expression pattern. Prompted by the finding of transgene expression in specific neuroendocrine cells, we sought to determine whether GK mRNA and GK itself was also expressed in the brain and gut, tissues not previously associated with the expression of this enzyme. Using rat tissues, GK mRNA was detected by RNA polymerase chain reaction in both the brain and intestine and was localized to specific cells in the hypothalamus and enteric mucosa by in situ hybridization. A high Km glucose phosphorylating activity was detected from isolated rat jejunal enterocytes that displayed a chromatographic elution profile identical to hepatic GK. GK immunoreactivity was detected in cells of the medial hypothalamus with many of the same cells also displaying GLUT2 immunoreactivity. Together, these studies provide evidence for upstream GK promoter activity, GK mRNA, and GK itself in certain neuroendocrine cells outside the pancreatic islet and lead us to suggest that GK may play a broader role in glucose sensing by neuroendocrine cells than was thought previously.
Recombinant Human Growth Hormone Promotes Hematopoietic Reconstitution after Syngeneic Bone Marrow Transplantation in Mice (1998)

Recombinant human growth hormone (rhGH) was administered to mice after syngeneic bone marrow transplantation (BMT) to determine its effect on hematopoietic reconstitution. BALB/c mice were given 10 microg intraperitoneal injections of rhGH every other day for a total of 10 injections following syngeneic BMT. Mice that received rhGH exhibited significant increases in total hematopoietic progenitor cell content (colony-forming unit-culture) in both bone marrow and spleen. Erythroid cell progenitor content (burst-forming unit-erythroid) was also significantly increased after rhGH treatment. Analysis of peripheral blood indicated that administration of rhGH resulted in significant increases in the rate of white blood cell and platelet recovery. Granulocyte marker 8C5+ cells were also increased in the bone marrow and spleens of treated mice. Red blood cell, hematocrit, and hemoglobin levels were increased at all time points after rhGH treatment. No significant pathologic effects or weight gain were observed in mice receiving repeated injections of 10 microg rhGH. Thus, rhGH administration after syngeneic BMT promoted multilineage hematopoietic reconstitution and may be of clinical use for accelerating hematopoiesis after autologous BMT.
Molecular-Level Processing of Conjugated Polymers. 1. Layer-by-Layer Manipulation of Conjugated Polyions (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular-Level Processing of Conjugated Polymers. 1. Layer-by-Layer Manipulation of Conjugated PolyionsM. Ferreira and M. F. RubnerCite this: Macromolecules 1995, 28, 21, 7107–7114Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ma00125a012https://doi.org/10.1021/ma00125a012research-articleACS PublicationsRequest reuse permissionsArticle Views995Altmetric-Citations315LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The National Survey of Stroke. Incidence. (1981)

The following estimates were made, based on data from The National Survey of Stroke: 1. About 297,000 persons were hospitalized annually for an initial stroke in the conterminous U.S. during the two-year baseline period 1975-76, an annual incidence rate of 140.7 per 100,000 population; 2. Incidence rates of initial strokes escalate rapidly with advancing age. Between the ages of 45 to 85, the average rates of increase in age-specific rates doubles from one 10-year age group to the next; and 3. Among persons over 45, the age-specific incidence rates are markedly higher for men than for women. After adjusting the crude incidence rates for men and women due to differences in their age composition, the average risk of an initial stroke is about 44 percent higher for men than for women. However, this statistic primarily represents the fact that males have a 60 percent higher age-adjusted incidence rate than do females for infarction strokes; whereas, the age-adjusted incidence rate for hemorrhagic strokes is 53 percent higher for females than for males.
0.15-μm buried-channel p-MOSFETs with ultrathin boron-doped epitaxial Si layer (1998)

We demonstrated silicon MOSFETs with a counter-doped ultrathin epitaxial channel grown by low-temperature UHV-CVD; this allows the channel region to be doped with boron with high precision. The boron concentration and epitaxial layer thickness can be chosen independently, and so it is easy to adjust the threshold voltage of the buried-channel p-MOSFETs with n-type polysilicon gates. It was confirmed that choosing an ultrathin epitaxial layer at 10 nm leads to suppression of the short-channel effects in buried-channel p-MOSFETs with gate length down to 0.15 /spl mu/m, while maintaining an appropriate value of threshold voltage.
Functional Characterization of an Aminotransferase Required for Pyoverdine Siderophore Biosynthesis in Pseudomonas aeruginosa PAO1 (2004)

The fluorescent dihydroxyquinoline chromophore of the pyoverdine siderophore in Pseudomonas is a condensation product of D-tyrosine and l-2,4-diaminobutyrate. Both pvdH and asd (encoding aspartate beta-semialdehyde dehydrogenase) knockout mutants of Pseudomonas aeruginosa PAO1 were unable to synthesize pyoverdine under iron-limiting conditions in the absence of l-2,4-diaminobutyrate in the culture media. The pvdH gene was subcloned, and the gene product was hyperexpressed and purified from P. aeruginosa PAO1. PvdH was found to catalyze an aminotransferase reaction, interconverting aspartate beta-semialdehyde and l-2,4-diaminobutyrate. Steady-state kinetic analysis with a novel coupled assay established that the enzyme adopts a ping-pong kinetic mechanism and has the highest specificity for alpha-ketoglutarate. The specificity of the enzyme toward the smaller keto acid pyruvate is 41-fold lower. The enzyme has negligible activity toward other keto acids tested. Homologues of PvdH were present in the genomes of other Pseudomonas spp. These homologues were found in the DNA loci of the corresponding genomes that contain other pyoverdine synthesis genes. This suggests that there is a general mechanism of l-2,4-diaminobutyrate synthesis in Pseudomonas strains that produce the pyoverdine siderophore.
Saturation Mutagenesis of the WSXWS Motif of the Erythropoietin Receptor (1996)

The WSXWS motif in the extracellular domain defines members of the cytokine receptor family, yet its role in receptor structure and function remains unresolved. To address this question we have generated a panel of 100 mutants within the WSXWS motif of the erythropoietin receptor, which represents all single amino acid substitutions of these five amino acids. All mutants were synthesized at the same level; however, their passage from the endoplasmic reticulum to the Golgi apparatus differed. Because of this, expression of mutant receptors at the cell surface varied more than 300-fold. The tolerance of the tryptophan and serine residues to substitution was quite narrow; as a result, most of these mutants were retained in the endoplasmic reticulum and showed no cell surface expression or reduced cell surface expression. Although many mutants with substitutions at the middle residue of the motif reached the cell surface, it was notable that one mutant, A234E, was processed more efficiently than the wild type receptor and was expressed in elevated numbers at the cell surface. Despite this variation, all mutant receptors that reached the cell surface appeared able to bind erythropoietin and transduce a proliferative signal normally. These results are discussed in terms of a general model for WSXWS function in which the motif contributes to efficient receptor folding.
Regulation of brain water during acute glucose-induced hyperosmolality in ovine fetuses, lambs, and adults (2004)

We tested the hypothesis that, during acute glucose-induced hyperosmolality, the brain shrinks less than predicted on the basis of an ideal osmometer and that brain volume regulation is present in fetuses, premature and newborn lambs. Brain water responses to glucose-induced hyperosmolality were measured in the cerebral cortex, cerebellum, and medulla of fetuses at 60% of gestation, premature ventilated lambs at 90% of gestation, newborn lambs, and adult sheep. After exposure of the sheep to increases in osmolality with glucose plus NaCl, brain water and electrolytes were measured. The ideal osmometer is a system in which impermeable solutes do not enter or leave in response to an osmotic stress. In the absence of volume regulation, brain solute remains constant as osmolality changes. The osmotically active solute demonstrated direct linear correlations with plasma osmolality in the cerebral cortex of the fetuses at 60% of gestation (r = 0.72, n = 24, P = 0.0001), premature lambs (r = 0.58, n = 22, P = 0.005), newborn lambs (r = 0.57, n = 24, P = 0.004), and adult sheep (r = 0.70, n = 18, P = 0.001). Similar findings were observed in the cerebellum and medulla. Increases in the quantity of osmotically active solute over the range of plasma osmolalities indicate that volume regulation was present in the brain regions of the fetuses, premature lambs, newborn lambs, and adult sheep during glucose-induced hyperosmolality. We conclude that, during glucose-induced hyperosmolality, the brain shrinks less than predicted on the basis of an ideal osmometer and exhibits volume regulation in fetuses at 60% of gestation, premature lambs, newborn lambs, and adult sheep.
Chaos, Dynamics, and Fractals (1993)

This book develops deterministic chaos and fractals from the standpoint of iterated maps, but the emphasis makes it very different from all other books in the field. It provides the reader with an introduction to more recent developments, such as weak universality, multifractals, and shadowing, as well as to older subjects like universal critical exponents, devil's staircases and the Farey tree. The author uses a fully discrete method, a 'theoretical computer arithmetic', because finite (but not fixed) precision cannot be avoided in computation or experiment. This leads to a more general formulation in terms of symbolic dynamics and to the idea of weak universality. The connection is made with Turing's ideas of computable numbers and it is explained why the continuum approach leads to predictions that are not necessarily realized in computation or in nature, whereas the discrete approach yields all possible histograms that can be observed or computed.