gebhart/patrepeval huggingface dataset:
Near-Infrared Optical Characteristics of Chalcogenide-Bound Nd<sup>3+</sup> Molecules and Clusters (2007)

The optical properties of the nanoscale neodymium ceramic cluster (THF)8Nd8O2Se2(SePh)16 (Nd8) and molecular (DME)2Nd(SC6F5)3 (Nd1) were studied by optical absorption, photoluminescence, and time-resolved spectroscopy. Both complexes exhibited emission characteristic of solid-state materials with bands centered at 927, 1078, 1360, and 1843 nm for Nd8 and 897, 1071, 1347, and 1824 nm for Nd1. The observed red-shift in the absorption and emission bands of Nd8 is attributed to the increased covalency and nephelauxetic effect. Using the calculated radiative decay time, the quantum efficiency of the 4F3/2 → 4I11/2 transition is calculated to be 16% in Nd8 and 9% in Nd1 with corresponding stimulated emission cross sections of 3.04 × 10-20 cm2 in Nd8 and 1.61 × 10-20 cm2 in Nd1 that are comparable to those of solid-state inorganic systems. This efficiency is the highest reported value for “molecular” neodymium compounds. This finding, along with the novel 1.8 μm emission, is attributed to the absence of direct Nd3+ coordination with fluorescence quenching vibrational groups such as hydrocarbon or hydroxide groups. The direct coordination of S, Se, and F accounts for the improved fluorescence spectral properties, because these heavy anions facilitate a low phonon energy host environment for neodymium. Monte Carlo simulation permitted analysis of energy transfer processes to show the primary source of fluorescence quenching. Cross relaxation is responsible for the quenching of the 4F3/2 → 4I15/2 emission whereas excitation migration quenches the 4F3/2 → 4I9/2 emission. These processes are mediated by a dipole−dipole interaction for Nd8 and a quadrupole−quadrupole interaction for Nd1.
Dendritic Cell Populations in<i>Leishmania major</i>-Infected Skin and Draining Lymph Nodes (2004)

Using a metacyclic promastigote ear infection model of cutaneous leishmaniasis, we examined the phenotype, parasite load, and cytokine production of dendritic cells in the skin and draining lymph nodes of resistant C57BL/6J and susceptible BALB/c mice. Five dendritic cell populations were isolated from the skin and lymph nodes, and the main difference between the groups of mice was an increased number of plasmacytoid dendritic cells in the lymph nodes of the susceptible mice. Although similar cell types were present in the skin emigrants of both strains, there was a 10-fold larger number of cells in BALB/c mouse skin early in infection than in C57BL/6J mouse skin. None of the dendritic cells in the lymph nodes harbored parasites until 3 weeks after infection, with the Langerhans cells having the largest load and the plasmacytoid dendritic cells having the smallest load but the longest lasting infection. Although parasites could be detected in the lymph nodes a few hours after infection, none of the skin emigrants harbored parasites, indicating that they are not the vehicle that ferries the parasites from the skin to the lymph nodes. The presence of larger numbers of plasmacytoid cells in infected BALB/c mice, the more protracted infection of these cells, and their production of alpha interferon point to a complex and important role for the plasmacytoid cells in leishmaniasis.
HMGA1 Protein Overexpression in Human Breast Carcinomas (2004)

We measured, by immunohistochemistry, HMGA1 protein expression in 212 breast tissue specimens: 6 normal samples, 28 hyperplastic lesions (13 with cellular atypia), 11 fibroadenomas, 10 in situ ductal carcinomas, 144 ductal carcinomas, and 13 lobular carcinomas. HMGA1 was not expressed in normal breast tissue; HMGA1 staining was intense in 40% of hyperplastic lesions with cellular atypia and in 60% of ductal carcinomas and weak in fibroadenomas and in hyperplastic lesions without cellular atypia. Because HMGA1 expression was similar among ductal breast carcinomas with different histologic grading, we evaluated the association between HMGA1 expression and that of other markers of breast carcinoma invasion (estrogen and progesterone receptors, Ki-67 antigen, and ErbB2) in 21 cases of grade 3 breast ductal carcinomas and 7 cases of breast lobular carcinomas. We found that HMGA1 expression tended to be associated only with c-erbB-2 expression (Spearman rho: 0.36; P=0.065). Taken together, these results suggest that HMGA1 expression might be a novel indicator for the diagnosis and prognosis of human breast cancer.
OPTIMAL FAST MULTIPOLE METHOD DATA STRUCTURES (2012)

The Fast Multipole Method (FMM) has been identified as one of the ten most significant numerical algorithms discovered in the 20th century. The FMM guarantees finding fast solutions to many problems in science, such as calculating Coulomb potentials among large number of particles by reducing memory footprint and runtime while attaining very high accuracy levels. One important practical issue that we have to solve in implementing a FMM algorithm is organizing large amounts of data, also called data structuring. The non-adaptive FMM is appropriate when the particles are uniformly distributed while the adaptive FMM is most efficient when the distribution is non-uniform. In practice, we typically encounter highly non-uniform 3D particle distributions. This paper summarizes our implementation of a 3D adaptive FMM algorithm data structure setup for non- uniform particle distributions.
A comparative study of static and profile-based heuristics for inlining (2000)

In this paper, we present a comparative study of static and profile-based heuristics for inlining. Our motivation for this study is to use the results to design the best inlining algorithm that we can for the Jalapeño dynamic optimizing compiler for Java [6]. We use a well-known approximation algorithm for the KNAPSACK problem as a common “meta-algorithm” for the inlining heuristics studied in this paper. We present performance results for an implementation of these inlining heuristics in the Jalapeño dynamic optimizing compiler. Our performance results show that the inlining heuristics studied in this paper can lead to significant speedups in execution time (up to 1.68x) even with modest limits on code size expansion (at most 10%).
Isolation of carcinogen-induced diploid rat hepatocytes by centrifugal elutriation. (1986)

The majority of hepatocytes isolated from rats treated with carcinogens (diethylnitrosamine plus 2-acetylaminofluorene) were found to be diploid, whereas most of the hepatocytes from normal rats are tetraploid. The carcinogen-induced diploid hepatocytes were only one-half the size (protein content) of the tetraploid hepatocytes, and could therefore be separated from the latter by centrifugal elutriation. The elutriation technique thus makes it possible to isolate a relatively pure fraction of carcinogen-induced cells. The diploid cells had the same liver-specific enzymatic and functional properties as the tetraploid cells and were thus undoubtedly of hepatocytic origin.
Angiotensin II AT<sub>2</sub> receptor inhibits smooth muscle cell migration via fibronectin cell production and binding (2002)

To explore the vascular function of the angiotensin II (ANG II) AT(2) receptor subtype (AT(2)R), we generated a vascular smooth muscle cell (SMC) line expressing the AT(2)R (SMC-vAT(2)). The involvement of AT(2)R in the motility response of SMCs was examined in SMC-vAT(2) cells and their controls (SMC-v) cultured on either laminin or fibronectin matrix proteins with the agarose drop technique. All experiments were conducted in the presence of a saturating concentration of losartan to inactivate the AT(1)R subtype. Under basal conditions, both cell lines migrated outside drops, but on laminin only. Treatment with ANG II significantly inhibited the migration of SMC-vAT(2) but not SMC-v cells, and this effect was prevented by the AT(2)R antagonist CGP-42112A. The decreased migration of SMC-vAT(2) was not associated with changes in cell growth, cytoskeleton stiffness, or smooth muscle actin, desmin, and tenascin expression. However, it was correlated with increased synthesis and binding of fibronectin. Both responses were prevented by incubation with selective AT(2)R antagonists. Addition of GRGDTP peptide, which prevents cell attachment of fibronectin, reversed the AT(2)R inhibitory effect on SMC-vAT(2) migration. These results suggest that activated ANG II AT(2)R inhibits SMC migration via cellular fibronectin synthesis and associated cell binding.
Strukturaufklärung und Totalsynthese von Kulkenon (2014)

Abstract Die beeindruckenden biologischen Aktivitäten von Sekundärmetaboliten, die von Myxobakterien der Stämme von Sorangium cellulosum isoliert wurden, haben uns veranlasst, das ebenfalls aus Sorangium cellulosum isolierte Kulkenon zu synthetisieren. In unserer Synthese waren die von uns entwickelte syn ‐selektive vinyloge Kobayashi‐Aldolreaktion und eine Ringschluss‐Heck‐Kupplung die entscheidenden Transformationen. Allerdings mussten wir nach der Synthese beim Vergleich der Spektren von authentischer und synthetischer Probe feststellen, dass es sich nicht um identische Verbindungen handelte. Mithilfe einer Kombination aus computergestützten Modellierungen und NOE‐Experimenten gelang es uns schließlich, einen überarbeiteten Strukturvorschlag für Kulkenon zu machen und mit einer erneuten Synthese zu bestätigen.
Clinical and Genomic Implications of Luminal and Basal Subtypes Across Carcinomas (2018)

This first pan-carcinoma luminal/basal subtyping across epithelial tumors reveals global similarities across carcinomas in the transcriptome, genome, clinical outcomes, and drug sensitivity, emphasizing the biological and translational importance of these luminal versus basal subtypes.
2D SOI photonic crystal slab and line-defect waveguide (2002)

We fabricate 2D Si photonic crystal slabs having large photonic band gap (PBG) by using SOI substrate, and investigate various types of line defect waveguides. We demonstrate successful structural tuning of defects to obtain desired waveguiding modes within PBG and experimentally show that they have extremely large group dispersion and the speed of light is slowed down to 1/100 of that in air.
The intragenic enhancer of human immunodeficiency virus type 1 contains functional AP-1 binding sites (1991)

An intragenic enhancer in the pol gene of human immunodeficiency virus type 1 has previously been identified (Verdin et al., Proc. Natl. Acad. Sci. USA 87:4874-4878, 1990). This element is composed of two subdomains both exhibiting phorbol ester-inducible enhancing activity on the viral thymidine kinase promoter in HeLa cells. Examination of the nucleotide sequence of one of these domains (nucleotides 4079 to 4342, HXB2 isolate) revealed the presence of three short DNA regions highly homologous to the recognition site for cellular transcription factor AP-1. Two short oligonucleotides containing these AP-1 sites each functioned as a phorbol ester-inducible enhancer when cloned upstream of the thymidine kinase promoter and transfected into HeLa cells. Gel mobility shift assays and competition experiments using the same two oligonucleotides demonstrated that they bound affinity-purified AP-1 or AP-1 present in uninduced and 12-O-tetradecanoylphorbol-13-acetate-induced HeLa nuclear extracts. Footprinting experiments confirmed that all three predicted sites bound purified AP-1. These results suggest that the AP-1 factor could play a role in the transcriptional regulation of human immunodeficiency virus type 1 gene expression.
Transannular rearrangement of activated 2,5-diketopiperazines: a key route to original scaffolds (2008)

An efficient and original stereocontrolled transannular rearrangement starting from activated 2,5-diketopiperazines has been developed, an opportunity for the medicinal chemistry field, which requests access to novel biological scaffolds. This powerful ring contraction, which can be related to a stereoselective aza-version of the Chan rearrangement, allows for example the one-step synthesis of various tetramic acids, access to 2-disubstituted statins, or the synthesis of relevant lactam-constrained dipeptide mimetics using a TRAL-RCM sequence.
Differential sensitivity of epidermal cell subpopulations to β-catenin-induced ectopic hair follicle formation (2010)

Wnt signalling is required for hair follicle development and for the growth phase (anagen) of postnatal follicles. When the pathway is activated at high levels in adult mouse epidermis, ectopic follicles form from existing follicles, interfollicular epidermis (IFE) and sebaceous glands, revealing a remarkable ability of the tissue to be reprogrammed. To compare the competence of different epidermal cell populations to form ectopic follicles, we expressed a 4-hydroxy-tamoxifen (4OHT) inducible, stabilised beta-catenin transgene (DeltaNbeta-cateninER) under the control of two different promoters. We targeted the reservoir of stem cells in the hair follicle bulge via the keratin 15 (K15) promoter and targeted the sebaceous glands and base of the follicle (bulb) with a truncated K5 promoter (DeltaK5). No ectopic follicles formed in the IFE in either model, establishing the autonomy of the IFE stem cell compartment in undamaged epidermis. Activation of beta-catenin in the bulge stimulated proliferation and bulge expansion. Existing hair follicles entered anagen, but no ectopic follicles formed. DeltaK5DeltaNbeta-cateninER expressing hair follicles also entered anagen on 4OHT treatment. In addition, a subpopulation of cells at the base of the sebaceous gland readily formed ectopic follicles, resulting in complete and reversible conversion of sebaceous glands into hair follicles. Combined activation of beta-catenin and the vitamin D receptor enhanced differentiation of sebaceous gland-derived hair follicles and stimulated ectopic follicle formation in the hair follicle bulb, but not in the bulge. Our results suggest that the bulge and sebaceous gland are, respectively, non-permissive and permissive niches for Wnt induced hair follicle differentiation.
Ignition Capsules with Aerogel-Supported Liquid DT Fuel For The National Ignition Facility (2011)

\nFor high repetition-rate fusion power plant applications, capsules with aerogel-supported liquid DT fuel can have much reduced fill time compared to β-layering a solid DT fuel layer. The melting point of liquid DT can be lowered once liquid DT is embedded in an aerogel matrix, and the DT vapor density is consequently closer to the desired density for optimal capsule design requirement. We present design for NIF-scale aerogel-filled capsules based on 1-D and 2-D simulations. An optimal configuration is obtained when the outer radius is increased until the clean fuel fraction is within 65 – 75% at peak velocity. A scan (in ablator and fuel thickness parameter space) is used to optimize the capsule configurations. The optimized aerogel-filled capsule has good low-mode robustness and acceptable high-mode mix.\n
High atom efficient and environment-friendly preparation of herbicides bromoxynil and ioxynil (2010)

The use of 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil) I and 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) II are well established as herbicides 1 . Certain esters of bromoxynil, especially the octanoate, have been used extensively as herbicides in the control of broad-leafed weeds, particularly in crop growing areas 2 . Although the esters have been shown to be highly effective, they have been produced only by incurring productivity penalties, which are aggravated by the expensive and cumbersome purifications that have till now been required.
Defective B cell responses in the absence of SH2D1A (2005)

More than half of patients with X-linked lympho-proliferative disease, which is caused by a defect in the intracellular adapter protein SH2D1A, suffer from an extreme susceptibility to Epstein-Barr virus. One-third of these patients, however, develop dysgammaglobulenemia without an episode of severe mononucleosis. Here we show that in SH2D1A(-/-) mice, both primary and secondary responses of all Ig subclasses are severely impaired in response to specific antigens. Because germinal centers were absent in SH2D1A(-/-) mice upon primary immunization, and because SH2D1A was detectable in wt germinal center B cells, we examined whether SH2D1A(-/-) B cell functions were impaired. Using the adoptive cotransfer of B lymphocytes from hapten-primed SH2D1A(-/-) mice with CD4(+) T cells from primed wt mice into irradiated wt mice provided evidence that signal transduction events controlled by SH2D1A are essential for B cell activities resulting in antigen specific IgG production. Defects in naive SH2D1A(-/-) B cells became evident upon cotransfer with non-primed wt CD4(+) cells into Rag2(-/-) recipients. Thus, both defective T and B cells exist in the absence of SH2D1A, which may explain the progressive dysgammaglobulinemia in a subset of X-linked lympho-proliferative disease patients without involvement of Epstein-Barr virus.
New Rotavirus Vaccines (2006)

From Sanofi Pasteur and the Department of Pediatrics, University of Pennsylvania, Doylestown, PA. Accepted for publication March 8, 2006. Dr. Plotkin is coholder of a patent for the WC-3 rotavirus strain and its reassortants. Address for correspondence: Stanley A. Plotkin, MD, Emeritus Professor of Pediatrics, University of Pennsylvania, 4650 Wismer Road, Doylestown, PA 18901; E-mail: [email protected].
Rotational and translational components of motion parallax: Observers' sensitivity and implications for three-dimensional computer graphics. (1995)

The motion of objects during motion parallax can be decomposed into 2 observer-relative components: translation and rotation. The depth ratio of objects in the visual field is specified by the inverse ratio of their angular displacement (from translation) or equivalently by the inverse ratio of their rotations. Despite the equal mathematical status of these 2 information sources, it was predicted that observers would be far more sensitive to the translational than rotational component. Such a differential sensitivity is implicitly assumed by the computer graphics technique billboarding, in which 3-dimensional (3-D) objects are drawn as planar forms (i.e., billboards) maintained normal to the line of sight. In 3 experiments, observers were found to be consistently less sensitive to rotational anomalies. The implications of these findings for kinetic depth effect displays and billboarding techniques are discussed.
Sulfur modifies the chemisorption of carbon monoxide on rhodium/alumina model catalysts. Technical report (1980)

The effect of D/sub 2/S on the chemisorption of CO on supported rhodium is examined with tunneling spectroscopy. It is seen that for low concentrations, D/sub 2/S decreases the density of species with two CO molecules per Rh atom and increases the density of species with one CO molecule per Rh atom. At higher concentrations D/sub 2/S decreases the density of all types of adsorbed CO.
Development of an automated high accuracy pH measuring instrument with full audit reporting facility (1997)

Scientific laboratories should now comply with Good Laboratory Practice (GLP) and the requirement of full auditing. Current pH instrumentation can not fully provide for this due to the lack of automation. Automation will mean that the instrument will be able to maintain its calibration and work to Standard Operating Procedures without deviation. This paper shows how a design specification for an automated pH instrument has been developed to create a new market in pH measurement. It outlines the control and signal conditioning electronics which are needed for highly accurate pH measurement. The GLP audit reporting functions shows how it is now possible to produce full working history reports of the instrument. The strict design requirements needed for cost effectiveness in manufacture, build/service time and for modularity, are also dealt with.
Distribution and Kinetics of Ethanol Metabolism in Rat Brain (1998)

It was found that the accumulation of acetaldehyde produced from 50 mM ethanol in rat brain homogenates takes place in all major brain regions. The velocity varied between 3.5 to 7.1 nmol/mg of protein/hr. The rate increased in the following order: brain hemispheres, striatum, brainstem, hypothalamus, and cerebellum. Significant regional differences in this process were found: in the initial period of incubation (5 min), acetaldehyde accumulation was maximal in the brain hemispheres; but, in the 30- to 60-min period, it became significantly higher in the cerebellum. Inhibition of this process by the catalase inhibitor, 3-amino-1,2,4-triazole (8 mM), was minimal in the brainstem (27%) and maximal (57%) in the cerebellum, despite nearly complete inhibition of catalase. This would indicate that processes other than catalase activity must contribute to acetaldehyde accumulation.
Excitotoxic neurodegeneration induced by deprivation of oxygen and glucose in isolated retina. (1998)

The isolated retina provided a convenient system to characterize quantitatively ischemic cell death. Retinal ischemic neurodegeneration is an excitotoxic process that involves overactivation of NMDA and non-NMDA glutamate receptors. Blockade of both of these receptor subtypes was necessary for complete neuroprotection. Receptor desensitization played a protective role. If even low concentrations of glucose were delivered to an ischemic retina in vitro, substantial neuroprotection could be achieved. This may have implications for the management of acute retinal ischemic episodes.