gebhart/patrepeval huggingface dataset:
Lipid Nanocarriers of a Lipid-Conjugated Estrogenic Derivative Inhibit Tumor Growth and Enhance Cisplatin Activity against Triple-Negative Breast Cancer: Pharmacokinetic and Efficacy Evaluation (2015)

Breast cancer is the leading cause of malignancies among women globally. The triple negative breast cancer (TNBC) subtype is the most difficult to treat and accounts for 15% of all cases. Targeted therapies have been developed for TNBC but come short of clinical translation due to acquired tumor resistance. An effective therapy against TNBC must combine properties of target specificity, efficient tumor killing, and translational relevance. The objective of this study was to formulate a nontoxic, cationic, lipid-conjugated estrogenic derivative (ESC8), with demonstrated anticancer activity, for oral delivery in mice bearing triple negative breast cancer (TNBC) as xenograft tumors. The in vitro cell viability, Caco-2 permeability, and cell cycle dynamics of ESC8-treated TNBC cells were investigated. ESC8 was formulated as liposomes, solid lipid nanoparticles (SLNs), and nanostructured lipid carriers (NLCs) and characterized for size, zeta potential, entrapment efficiency, size stability, and tumor biodistribution. Pharmacokinetic modeling of plasma concentration-time course data was carried out following intravenous and oral administration in Sprague-Dawley rats. In vivo efficacy investigation of ESC8-SLNC was carried out in Nu/Nu mice bearing MDA-MB-231 TNBC as xenograft tumors, and the molecular dynamics modulating tumor growth inhibition was analyzed by Western blot. In vitro ESC8 inhibited TNBC and non-TNBC cell viability with IC50 ranging from 1.81 to 3.33 μM. ESC8 was superior to tamoxifen and Cisplatin in inhibiting MDA-MB-231 cell viability; and at 2.0 μM ESC8 enhanced Cisplatin cytotoxicity 16-fold. Intravenous ESC8 (2.0 mg/kg) was eliminated at a rate of 0.048 ± 0.01 h(-1) with a half-life of 14.63 ± 2.95 h in rats. ESC8 was orally bioavailable (47.03%) as solid lipid nanoparticles (ESC8-SLN). ESC8-SLN (10 mg/kg/day, ×14 days, p.o.) inhibited breast tumor growth by 74% (P < 0.0001 vs control) in mice bearing MDA-MB-231 cells as xenografts; and when given in combination with Cisplatin (2.0 mg/kg/biweekly, ×2 weeks, IV), tumor growth was inhibited by 87% (P = 0.0002, vs ESC8-SLN; 10 mg/kg/day, ×14 days, p.o). ESC8-SLN tumor growth inhibition was associated with increased expression of p21 and Caspase-9; as well as by inhibition of EGFR, Slug, p-Akt1, Vimentin, NFkβ, and IKKγ. These results show the promise of ESC8 as an oral adjuvant or neoadjuvant against triple negative breast cancer.
Role of histidine 42 in ascorbate peroxidase (2002)

To examine the role of the distal His42 residue in the catalytic mechanism of pea cytosolic ascorbate peroxidase, two site-directed variants were prepared in which His42 was replaced with alanine (H42A) or glutamic acid (H42E). Electronic spectra of the ferric derivatives of H42A and H42E (pH 7.0, mu = 0.10 m, 25.0 degrees C) revealed wavelength maxima [lambda(max) (nm): 397, 509, approximately equal to 540(sh), 644 (H42A); 404, 516, approximately equal to 538(sh), 639 (H42E)] consistent with a predominantly five-co-ordinate high-spin iron. The specific activity of H42E for oxidation of L-ascorbate (8.2 +/- 0.3 U.mg(-1)) was approximately equal to 30-fold lower than that of the recombinant wild-type enzyme (rAPX); the H42A variant was essentially inactive but activity could be partially recovered by addition of exogenous imidazoles. The spectra of the Compound I intermediates of H42A [lambda(max) (nm) = 403, 534, 575(sh), 645] and H42E [lambda(max) (nm) = 404, 530, 573(sh), 654] were similar to those of rAPX. Pre-steady-state data for formation of Compound I for H42A and H42E were consistent with a mechanism involving accumulation of a transient enzyme intermediate (K(d)) followed by conversion of this intermediate into Compound I (k'(1)). Values for k'(1) and K(d) were, respectively, 4.3 +/- 0.2 s(-1) and 30 +/- 2.0 mM (H42A) and 28 +/- 1.0 s(-1) and 0.09 +/- 0.01 mM (H42E). Photodiode array experiments for H42A revealed wavelength maxima for this intermediate at 401 nm, 522 nm and 643 nm, consistent with the formation of a transient [H42A-H(2)O(2)] species. Rate constants for Compound I formation for H42A were independent of pH, but for rAPX and H42E were pH-dependent [pKa = 4.9 +/- 0.1 (rAPX) and pK(a) = 6.7 +/- 0.2 (H42E)]. The results provide: (a) evidence that His42 is critical for Compound I formation in APX; (b) confirmation that titration of His42 controls Compound I formation and an assignment of the pK(a) for this group; (c) mechanistic and spectroscopic evidence for an intermediate before Compound I formation; (d) evidence that a glutamic acid residue at position 42 can act as the acid-base catalyst in ascorbate peroxidase.
New Value for the Metastability Exchange Cross Section in Helium (1971)

We have investigated the angular aspect of metastability exchange collisions between ground-state and $2^{3}S_{1}$ metastable $^{3}\mathrm{He}$ atoms theoretically and experimentally. Coupling between the orientations of the two $2^{3}S_{1}$ hyperfine levels and partial coherence survival after a collision are shown to be important. We propose a different interpretation of previous experiments, and we suggest a new value of the metastability exchange cross section: $\ensuremath{\sigma}=(7.6\ifmmode\pm\else\textpm\fi{}0.4)\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}16}$ ${\mathrm{cm}}^{2}$. The case of $^{3}\mathrm{He}$-$^{4}\mathrm{He}$ mixtures is also studied.
The protein structure initiative structural genomics knowledgebase (2008)

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities.
Introduction to the supplement on velocity estimation for depth imaging (2008)

Abstract In the last decade, much of 3D seismic signal processing has been replaced by the single imaging process called prestack depth migration. Rapid advances in resolution and illumination have changed the way we explore, delineate, and monitor reservoirs. We now see more attention turning to the velocity models that make such depth imaging possible. For this supplement to the September-October 2008 issue of GEOPHYSICS, we invited summaries of existing practices, descriptions of new approaches, and case studies that illustrate the practical aspects of building and updating velocity models. Velocities are implicit in every imaging or moveout-sensitive processing step. Velocities still consume the most hours of human labor and interpretation during seismic processing. We cannot simply delegate the geologic implications of a velocity model to a later interpretive step. We need velocities for a seismic image, an image for interpretation, and interpretation velocities.
Microfluidic Synthesis of Photoresponsive Spool-Like Block Copolymer Nanoparticles: Flow-Directed Formation and Light-Triggered Dissociation (2015)

We demonstrate flow-directed production of nanoparticles of the photoresponsive block copolymer poly(o-nitrobenzyl acrylate)-b-polydimethylacrylamide in a gas–liquid microfluidic reactor. Microfluidic formation produced a variety of morphologies dependent on flow rate, with spheres and short cylinders, then large compound micelles, then unique spooled cylinders appearing as flow rate increased. The higher excess free energy of spooled cylinders relative to the quiescent equilibrium state is evidenced by their faster off-chip relaxation times (∼1 day) as compared to other flow-directed structures. Comparison of light-triggered dissociation of flow-directed nanoparticles prepared at two different flow rates shows faster disruption of nanoparticles prepared at the higher flow rate. The application of variable flow to direct both structure and responsivity suggests interesting possibilities for controlled microfluidic manufacturing of “smart” polymeric colloids.
Homeobox gene repertoires: implications for the evolution of diversity (2005)

Abstract Homeobox genes are key regulators of morphogenetic processes in developing organisms, and are involved in the formation and differentiation of multiple tissues and cell types. The strong conservation of homeobox gene sequences indicates that many species share a common repertoire of homeobox genes. Experimental evidence provides support for conserved as well as divergent functions, raising the question how homeobox genes evolved in distinct species and in which way they contributed to the evolution of different morphologies. This article examines the composition of homeobox gene repertoires in diverse animals at the whole‐genome level, with the aim to understand the underlying mechanisms of evolution in this multigene family.
Down regulation of the Rabphillin-3A-Like gene, located on 17p 13.3, is associated with the metastasis of colorectal adenocarcinoma. (2008)

334 Background: Our previous studies have demonstrated that frequent allelic loss (60%) of Rabphillin-3A-Like gene (RPH3AL) was associated with nodal metastasis, early recurrence and patient poor survival in colorectal adenocarcinoma (CRC). In this study, we analyzed gene expression profiles of CRCs based on nodal metastasis to identify the involvement of RPH3AL in tumor progression.  Methods: Gene expression studies were performed on mRNAsamples extracted from fresh frozen CRCs and their matching control samples. TheAffymetrix Human Genome U133 Plus 2.0 arrays, which consistover 47,000 transcripts including wereused for these studies. Additionally, the gene chip data wereprocessed by using the Affymetrix Microarray Suite (MAS 5.0). The regulated genes were then classified using gene ontologyannotation and KEGG pathway. We estimated mRNA levels of RPH3AL by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Phenotypic expression of RPH3AL was detected in 103 CRC tissues by immunohistochemistry (IHC) using polyclonal antibodies. We also performed cell migration assays in RPH3AL stably over expressing colon cancer cell lines.  Results: Microarray analysis based on nodal status has identified a distinct gene expression pattern. The list of 262 genes which are down-regulated in node positive CRCs includes RPH3AL , Protein Kinase C-beta1, Adenyl Succinate Synthase-Like 1, Cyclin-Dependent Kinase Inhibitor 1a , Glutathione S Transferase a1 and others. The list of 245 genes which are up-regulated in node positive CRCs includes Laminin Gamma 2, Glutathione Peroxidase 2, MAP Kinase Kinase Kinase 4, Matrix Metallo Peptidase 7, Matrix Metalloproteinase 11, Axin 2, Claudins 2 and 4, and others. Genes that were significantly down-regulated (≥ 4 folds change) were validated by estimating their mRNA levels. For examples, mRNA expression of RPH3AL was significantly reduced in CRCs with nodal metastasis (mean=0.20, range 0.012-0.98) when compared to their matching control tissues (2.36, 0.15-10.32) (p
Isolation and Characterization of <i>o</i> -Xylene Oxygenase Genes from <i>Rhodococcus opacus</i> TKN14 (2005)

o-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here Rhodococcus genes mediating oxygenation in the first step of o-xylene degradation. Rhodococcus opacus TKN14, isolated from soil contaminated with o-xylene, was able to utilize o-xylene as the sole carbon source and to metabolize it to o-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in Escherichia coli. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert o-xylene into o-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (nidABCD) that had been isolated from Rhodococcus sp. strain I24. Complementation studies, using E. coli expressing various combinations of individual open reading frames, revealed that a gene (named nidE) for rubredoxin (Rd) and a novel gene (named nidF) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of o-xylene, in addition to the dioxygenase iron-sulfur protein genes (nidAB). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding cis-dihydrodiols. All the nidABEF genes were transcriptionally induced in R. opacus TKN14 by the addition of o-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by Rhodococcus species as the first key enzyme.
Radiometric detection of the metabolic activity of Mycobacterium tuberculosis. (1975)

A radiometric test capable of detecting the metabolic rate of M. tuberculosis within 18 hr after inoculation has been developed. The technique is based on the measurement of 14CO2 produced by the bacterial metabolism of 14C-U-glycerol of 14C-U-acetate. The test is an important first step in the development of rapid radiometric techniques for clinical study of Mycobacterium tuberculosis.
Induction of Apoptosis in Human Corneal and HeLa Cells by Mutated BIGH3 (2003)

Overexpression of mutated BIGH3 induces apoptosis in HeLa and HCE cells through activation of a pathway that uses the PDI domain of the fourth internal Fas domain and activation of caspase-3. Because DI is a known site of interaction with alpha 3 beta 1 integrins, it suggests that integrins play a role in mediating apoptosis in the system used in the current study. This work suggests that apoptosis is a key element in the pathophysiology of BIGH3-related corneal dystrophies.
Advancing Treatment of Metastatic Cancers: From Research to Communication – Where Do we Need to Go? (2014)

Bruce Zetter* speaks to Francesca Lake, Managing Commissioning Editor: Bruce Zetter is the Charles Nowiszewski Professor of Cancer Biology at Harvard Medical School in Boston (MA, USA). Dr Zetter received a BA degree in anthropology from Brandeis University in Waltham (MA, USA) and a PhD from the University of Rhode Island in Kingston (RI, USA). He completed fellowships at Massachusetts Institute of Technology in Cambridge (MA, USA) and at the Salk Institute in San Diego (CA, USA). Subsequently, he was an assistant research biochemist at the University of California in San Francisco (CA, USA) before joining the faculty at Harvard Medical School. At Harvard, he directed the course in human physiology taken by all medical students. He further served as the Chief Scientific Officer at Boston Children's Hospital (MA, USA), where he directed the research efforts for the hospital. Dr Zetter has made major discoveries on the mechanisms underlying tumor metastasis and on the detection and treatment of late-stage tumors. As an internationally recognized expert in the field of tumor metastasis, Dr Zetter has chaired multiple international research conferences and grant review panels for agencies such as the US NIH and the US Department of Defense. He also chaired the NASA committee that selects scientific projects for the space shuttle. Dr Zetter has a strong interest in the interactions of academic and corporate institutions and has served as an advisor to more than 30 biotechnology and pharmaceutical companies, as well as to venture firms and investment companies.
Autopía control automático de automóviles. Resultados conseguidos y actualidad del proyecto cooperativo ISAAC (2003)

Trabajo presentado en el IV Workshop de Agentes Fisicos, celebrado en Alicante (Espana), en marzo de 2003
Two strategies for spare capacity placement in mesh restorable networks (2002)

Because the problem of optimal spare capacity placement in a mesh-restorable network is NP-hard, the authors consider two heuristic strategies to solve the spare capacity placement problem in a near-optimal way within reasonable time constraints. The spare link placement algorithm (SLPA) is based on the principle of iterative link addition to produce the greatest incremental change in network restorability. SLPA is shown theoretically and experimentally to have polynomial time complexity. The iterated cutsets heuristic (ICH) formulates spare capacity placement as a linear programming problem subject to constraints based on a subset of cutsets of the network. Iteration and heuristic rules are used to develop the constraint set required by ICH. Theoretical time complexities are assessed for both SLPA and ICH. Comparative experimental tests on 36 trial networks are discussed. ICH network designs require slightly less redundant capacity. On average, SLPA placed 5% more spare capacity than ICH.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Er:YAG laser ablation of epiretinal membranes in perfluorocarbon fluid-filled eyeballs: a preliminary report (1998)

Purpose: The Er:YAG laser emitting radiation at a wavelength of 2.94 micrometer has been shown to produce precise tissue ablation because of the high water absorption at this wavelength. These studies evaluated the effects of the Er:YAG laser on pig retina utilizing a perfluoro-carbon/retina interphase with the goal to precisely ablate epiretinal membranes. Method: Various laser pulse energies were applied to the surface of pig retinas in perfluorocarbon filled enucleated eyes using a specially designed rotating sample holder. Free running ((tau) equals 250 microseconds) Er:YAG laser pulses were transmitted through a zirconium fluoride (ZrF<SUB>4</SUB>) fiber guarded by a low OH-quartz fiber at its distal tip. The tip diameters measured 400 micrometers and 1 mm. The fiber probe was elevated 1 mm above the retinal surface. The laser energy was applied in a systematic fashion while alternating energy settings and probe diameters. Radiant exposures were set to 1 J/cm<SUP>2</SUP>, 3 J/cm<SUP>2</SUP>, 5 J/cm<SUP>2</SUP>, and 10 J/cm<SUP>2</SUP>. Results: Eight of ten eyes were treated with concentric circles of 3.5 mm, 6.5 mm, and 9.5 mm radius. The remaining two eyes were treated with a hand held probe. Tissue ablation increased with radiant exposure in a linear fashion. At a radiant exposure of 1 J/cm<SUP>2</SUP>, tissue ablation was minimal with a maximum tissue ablation depth of 10 micrometers and minimal thermal damage to adjacent tissue. A radiant exposure of 10 J/cm<SUP>2</SUP> produced an ablation depth of 30 - 50 micrometers. As the ablation was performed under perfluorcarbon fluid, used as transmitting medium, no laser- induced pressure transients have been measured. Conclusion: The Er:YAG laser in combination with perfluorocarbon fluid produced precise and homogeneous tissue ablation of the pig retina. Such precise tissue ablation needs to be achieved in order to safely ablate epiretinal membranes in close proximity to the retina surface. Further in-vivo experiments will be done to examine the functionality of the retina after laser treatment.
Optimal Bell Tests Do Not Require Maximally Entangled States (2005)

Any Bell test consists of a sequence of measurements on a quantum state in spacelike separated regions. Thus, a state is better than others for a Bell test when, for the optimal measurements and the same number of trials, the probability of existence of a local model for the observed outcomes is smaller. The maximization over states and measurements defines the optimal nonlocality proof. Numerical results show that the required optimal state does not have to be maximally entangled.
Reconstituted High-Density Lipoproteins Inhibit the Acute Pro-Oxidant and Proinflammatory Vascular Changes Induced by a Periarterial Collar in Normocholesterolemic Rabbits (2005)

Infusion of rHDL, apoA-I, and phospholipid-SUVs inhibits the early pro-oxidant and proinflammatory changes induced by a periarterial collar in normocholesterolemic rabbits.
Solid Solubilities in Supercritical Phases : New Apparatus, Measurements and Modeling (2000)

International audience
High speed printing with polygon scan heads (2016)

To reduce and in many cases eliminate the costs associated with high volume printing of consumer and industrial products, this paper investigates and validates the use of the new generation of high speed pulse on demand (POD) lasers in concert with high speed (HS) polygon scan heads (PSH). Associated costs include consumables such as printing ink and nozzles, provisioning labor, maintenance and repair expense as well as reduction of printing lines due to high through put. Targets that are applicable and investigated include direct printing on plastics, printing on paper/cardboard as well as printing on labels. Market segments would include consumer products (CPG), medical and pharmaceutical products, universal ID (UID), and industrial products. In regards to the POD lasers employed, the wavelengths include UV(355nm), Green (532nm) and IR (1064nm) operating within the repetition range of 180 to 250 KHz.
MPEG-2 Compressed-Domain Algorithms for Video Analysis (2006)

This paper presents new algorithms for extracting metadata from video sequences in the MPEG-2 compressed domain. Three algorithms for efficient low-level metadata extraction in preprocessing stages are described. The first algorithm detects camera motion using the motion vector field of an MPEG-2 video. The second method extends the idea of motion detection to a limited region of interest, yielding an efficient algorithm to track objects inside video sequences. The third algorithm performs a cut detection using macroblock types and motion vectors.
Spatial Distribution of Trapped Magnetic Flux in the High T<sub>c</sub> Superconductor Y<sub>1</sub>Ba<sub>2</sub>Cu<sub>3</sub>O<sub>7-δ</sub> (1987)

Spatial distribution of the trapped magnetic flux density in Y 1 Ba 2 Cu 3 O 7-δ is measured at T =4.2 K and 77 K with the GaAs Hall device as a magnetic sensor. Experimental results show that the magnetic flux density inside the sample is almost constant spatially, and suggest that superconducting grains are coupled with each other very weakly in the present sample.
Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis (2018)

We describe a syndrome of BF, gas and bloating, possibly related to probiotic use, SIBO, and D-lactic acidosis in a cohort without short bowel. Patients with BF exhibited higher prevalence of SIBO and D-lactic acidosis. Symptoms improved with antibiotics and stopping probiotics. Clinicians should recognize and treat this condition.