gebhart/patrepeval huggingface dataset:
Adsorption Behavior of Hydrophobin and Hydrophobin/Surfactant Mixtures at the Air–Water Interface (2011)

The adsorption of the surface-active protein hydrophobin, HFBII, and the competitive adsorption of HFBII with the cationic, anionic, and nonionic surfactants hexadecyltrimethylammonium bromide, CTAB, sodium dodecyl sulfate, SDS, and hexaethylene monododecyl ether, C(12)E(6), has been studied using neutron reflectivity, NR. HFBII adsorbs strongly at the air-water interface to form a dense monolayer ∼30 Å thick, with a mean area per molecule of ∼400 Å(2) and a volume fraction of ∼0.7, for concentrations greater than 0.01 g/L, and the adsorption is independent of the solution pH. In competition with the conventional surfactants CTAB, SDS, and C(12)E(6) at pH 7, the HFBII adsorption totally dominates the surface for surfactant concentrations less than the critical micellar concentration, cmc. Above the cmc of the conventional surfactants, HFBII is displaced by the surfactant (CTAB, SDS, or C(12)E(6)). For C(12)E(6) this displacement is only partial, and some HFBII remains at the surface for concentrations greater than the C(12)E(6) cmc. At low pH (pH 3) the patterns of adsorption for HFBII/SDS and HFBII/C(12)E(6) are different. At concentrations just below the surfactant cmc there is now mixed HFBII/surfactant adsorption for both SDS and C(12)E(6). For the HFBII/SDS mixture the structure of the adsorbed layer is more complex in the region immediately below the SDS cmc, resulting from the HFBII/SDS complex formation at the interface.
10 Small Vibrations about Equilibrium (2011)

Abstract This chapter focuses on the one or more essentially stable equilibrium configurations of mechanical systems. When disturbed slightly, they vibrate about equilibrium in characteristic patterns called normal modes. The Lagrangian theory of these small vibrations is presented here for the simple case of systems with a finite number of degrees of freedom. The chapter defines equilibrium by using the example of a marble. A marble placed at rest at the bottom of a spherical bowl will remain there forever. A marble placed at rest, and very carefully, on the top of a sphere will also remain there so long as no forces other than gravity act, as will a marble placed on a flat, level tabletop. These examples illustrate the three types of equilibrium point. The first is called stable; the second, unstable; and the third, conditional.
Identification of hematopoietic progenitor cells in human amniotic fluid before the 12th week of gestation. (1993)

Due to technical difficulties in performing amniocentesis before the 12th week of pregnancy, very little is known about the components of human amniotic fluid before that time. Amniocentesis was performed between the 7th-11th week of gestation in 25 informed and consenting patients, who had to undergo therapeutic interruption of pregnancy. The cells from the amniotic fluid were stained, counted on a hemocytometer, and checked for vitality. The origin of these cells was determined from cellular cultures the intracellular content of the hemoglobin and the chloroacetate esterase content of the hemoglobin and the chloroacetate esterase contents were also studied. Taking advantage of the "in vitro" adhesive properties of these cells to the bone marrow stromal feeder layer, we obtained clonal growth of an erythroid nature from 18 out of 33 samples. At the 17th week of gestation, an increased number of cells and a decrease in their vitality was found. Between the 7th and 12th week, the cellular composition of the fluid was totally different from that found later in the pregnancy. Small nucleated, round cells were identified as hematopoietic progenitor cells. At the beginning of the 11th week, a cellular population, typically used to perform prenatal diagnosis of chromosomal abnormalities from the 14th week of pregnancy appeared. Since hematopoietic progenitor cells were found in the amniotic fluid before the 12th week of gestation, these cells most probably come from the hematopoietic cells of the yolk sac through the thin membrane of the yolk sac at this time.
Medial prefrontal cortex and self-referential mental activity: Relation to a default mode of brain function (2001)

Medial prefrontal cortex (MPFC) is among those brain regions having the highest baseline metabolic activity at rest and one that exhibits decreases from this baseline across a wide variety of goal-directed behaviors in functional imaging studies. This high metabolic rate and this behavior suggest the existence of an organized mode of default brain function, elements of which may be either attenuated or enhanced. Extant data suggest that these MPFC regions may contribute to the neural instantiation of aspects of the multifaceted "self." We explore this important concept by targeting and manipulating elements of MPFC default state activity. In this functional magnetic resonance imaging (fMRI) study, subjects made two judgments, one self-referential, the other not, in response to affectively normed pictures: pleasant vs. unpleasant (an internally cued condition, ICC) and indoors vs. outdoors (an externally cued condition, ECC). The ICC was preferentially associated with activity increases along the dorsal MPFC. These increases were accompanied by decreases in both active task conditions in ventral MPFC. These results support the view that dorsal and ventral MPFC are differentially influenced by attentiondemanding tasks and explicitly self-referential tasks. The presence of self-referential mental activity appears to be associated with increases from the baseline in dorsal MPFC. Reductions in ventral MPFC occurred consistent with the fact that attention-demanding tasks attenuate emotional processing. We posit that both self-referential mental activity and emotional processing represent elements of the default state as represented by activity in MPFC. We suggest that a useful way to explore the neurobiology of the self is to explore the nature of default state activity.
The Prophylactic Use of Antibiotic Impregnated Beads in Open Fractures (1990)

Four hundred four compound fractures were reviewed in 339 patients treated between August 1983 and November 1987. The 252 males and 87 females had a mean age of 33 years (range, 14-86). One hundred twenty-seven (31.4%) fractures were classified as Grade I, 153 (38.9%) as Grade II, and 124 (30.7%) as Grade III by Gustilo's classification. The mean Injury Severity Score was 15 (range, 9-57). Three hundred thirty-four of the open fractures (82.7%) were managed with antibiotic-impregnated bead chains (tobramycin) and systemic antibiotic prophylaxis (cefazolin, tobramycin, and penicillin). Seventy open fractures (17.3%) received systemic antibiotic prophylaxis (cefazolin, tobramycin, and penicillin) without supplemental use of the antibiotic beads. All open fractures underwent acute irrigation and debridement. In the 404 fractures 46.5% of wounds were closed primarily, 12.9% underwent delayed primary closure, 7.9% were left open, and 32.7% were temporized by the antibiotic bead pouch technique until definitive flap coverage and skin grafting were performed. Of the 404 fractures evaluated, 17 (4.2%) developed an acute wound infection. Of these wound infections, eight (11.4%) were in the group managed with systemic antibiotics alone. By comparison, nine (2.7%) of open fractures treated with combined systemic antibiotics and antibiotic-impregnated beads developed an infection. Chronic osteomyelitis developed in 18 of 404 open fractures (4.5%). Ten (14.3%) open fractures which developed osteomyelitis were managed with systemic antibiotics whereas eight (2.4%) fractures managed with systemic antibiotics and antibiotic-impregnated beads developed a chronic infection.(ABSTRACT TRUNCATED AT 250 WORDS)
Transitional cells in the regenerating pancreas (1994)

We examined the spectrum of intermediate cell types in the regenerating pancreas as duct epithelial cells progressed through their differentiation pathway to become mature endocrine cells. The model used was transgenic mice in which the pancreatic islets continue to grow during adulthood, unlike normal mice whose islet cell formation ceases early in life. Because the intermediate cells migrated into islet-like clusters at specific locations, we propose a specific pathway for islet development. Endocrine cells are derived from duct cells co-expressing a duct cell antigen, carbonic anhydrase II (CA II) and an exocrine enzyme, amylase. The CA II/amylase cells become amylase/endocrine intermediate cells as they exited from their lumenal location. The abluminal amylase/endocrine cells continue to differentiate to multihormone-bearing young endocrine cells, which migrated to form clusters with other differentiating endocrine cells.
Microchip Flow Cytometry Using Electrokinetic Focusing (1999)

Flow cytometry of fluorescently labeled and unlabeled latex particles is demonstrated on a microfabricated device. The latex particles were detected and counted using laser light scattering and fluorescence coincidence measurements. Sample confinement was accomplished using electrokinetic focusing at a cross intersection, and detection occurred 50 μm downstream from the intersection. Particles with diameters of 1 and 2 μm were analyzed and distinguished from each other based on their light scattering intensity and fluorescence. A maximum sample throughput of 34 particles/s was achieved. Sample mixtures with varying proportions of fluorescently labeled and unlabeled particles were also analyzed and found to be within experimental error of the expected ratios.
Building Muscle: Molecular Regulation of Myogenesis (2012)

The genesis of skeletal muscle during embryonic development and postnatal life serves as a paradigm for stem and progenitor cell maintenance, lineage specification, and terminal differentiation. An elaborate interplay of extrinsic and intrinsic regulatory mechanisms controls myogenesis at all stages of development. Many aspects of adult myogenesis resemble or reiterate embryonic morphogenetic episodes, and related signaling mechanisms control the genetic networks that determine cell fate during these processes. An integrative view of all aspects of myogenesis is imperative for a comprehensive understanding of muscle formation. This article provides a holistic overview of the different stages and modes of myogenesis with an emphasis on the underlying signals, molecular switches, and genetic networks.
Synthetic Gene Transfer Vectors II: Back to the Future. (2012)

The discovery of RNA interference has given a new lease on life to both the chemistry of oligonucleotides and chemical approaches for the intracellular delivery of nucleic acids. In particular, delivery of siRNA, whether in vitro for screening and target validation purposes or in humans as a new class of drugs, may revolutionize our approach to therapy. Their impact could equal that of the bioproduction and various uses of monoclonal antibodies today. Unfortunately, global pharmaceutical companies again seem to be waiting to buy the next Genentech or Genzyme of gene silencing rather than investing research and development into this promising area of research. Gene silencing encounters barriers similar to gene addition and hence may benefit from the extra decade of experience brought by gene therapy. "Chemical" transfection of cells in culture has become routine, and this Account discusses some of the reasons this success has not extended to nonviral gene therapy trials, most of which do not progress beyond the phase 2 stage. The author also discusses a (much debated) mechanism of nucleic acid cell entry and subsequent release of the polycationic particles into the cytoplasm. Both topics should be useful to those interested in delivery of siRNA. The move from gene therapy toward siRNA as an oligonucleotide-based therapy strategy provides a much wider range of druggable targets. Even though these molecules are a hundredfold smaller than a gene, they are delivered via similar cellular mechanisms. Their complexes with cationic polymers are less stable than those with a higher number of phosphate groups, which may be compensated by siRNA concatemerization or by chemical conjugation with the cationic carrier. Thus chemistry is again desperately needed.
Molecular markers of early Parkinson's disease based on gene expression in blood (2007)

Parkinson's disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular multigene marker here identified is associated with risk of PD in 66 samples of the training set comprising healthy and disease controls [third tertile cross-validated odds ratio of 5.7 (P for trend 0.005)]. It is further validated in 39 independent test samples [third tertile odds ratio of 5.1 (P for trend 0.04)]. Insights into disease-linked processes detectable in peripheral blood are offered by 22 unique genes differentially expressed in patients with PD versus healthy individuals. These include the co-chaperone ST13, which stabilizes heat-shock protein 70, a modifier of alpha-synuclein misfolding and toxicity. ST13 messenger RNA copies are lower in patients with PD (mean +/- SE 0.59 +/- 0.05) than in controls (0.96 +/- 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD.
Enantioselectivity of muscarinic antagonists. Isomeric 2-cyclohexyl-2-phenyl-5-[(dimethylamino)methyl]-1,3-oxathiolane 3-oxide methiodides (1989)

The eight isomers of 2-cyclohexyl-2-phenyl-5-[(dimethylamino)methyl]-1, 3-oxathiolane 3-oxide methiodides were prepared and their absolute configurations were attributed by synthesis and by X-ray crystallography. The compounds were tested on guinea pig bladder, ileum, and heart and their antimuscarinic potency was evaluated and expressed as pA2. The absolute configuration of the most potent isomer [(+)-(2R,3R,5R)-7] is identical with that of the corresponding agonist [(2R,3R,5R)-c-2-methyl-r-5-[(dimethylamino)methyl]-1,3-oxathiolane t-e-oxide methiodide],3 which further supports our previous hypothesis that muscarinic agonists and antagonists of this series recognize a common binding site. While some of the racemates (3,4) show different enantioselectivity on the different tissues, the most potent and the most enantioselective one (7) does not discriminate between muscarinic receptors as it shows eudismic ratios of the same order for all tissues examined.
Detection of Fetal Subchromosomal Abnormalities by Sequencing Circulating Cell-Free DNA from Maternal Plasma (2015)

The limit of detection for any given MD syndrome is constrained by 4 factors: fetal fraction, MD size, coverage, and biological and technical variability of the event region. Our algorithm takes these factors into account and achieved 94.4% sensitivity and 99.4% specificity.
Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival (2009)

Metastasis underlies the majority of cancer-related deaths. Thus, furthering our understanding of the molecular mechanisms that enable tumor cell dissemination is a vital health issue. Epithelial-to-mesenchymal transitions (EMTs) endow carcinoma cells with enhanced migratory and survival attributes that facilitate malignant progression. Characterization of EMT effectors is likely to yield new insights into metastasis and novel avenues for treatment. We show that the presence of the receptor tyrosine kinase Axl in primary breast cancers independently predicts strongly reduced overall patient survival, and that matched patient metastatic lesions show enhanced Axl expression. We demonstrate that Axl is strongly induced by EMT in immortalized mammary epithelial cells that establishes an autocrine signaling loop with its ligand, Gas6. Epiallelic RNA interference analysis in metastatic breast cancer cells delineated a distinct threshold of Axl expression for mesenchymal-like in vitro cell invasiveness and formation of tumors in foreign and tissue-engineered microenvironments in vivo. Importantly, in two different optical imaging-based experimental breast cancer models, Axl knockdown completely prevented the spread of highly metastatic breast carcinoma cells from the mammary gland to lymph nodes and several major organs and increased overall survival. These findings suggest that Axl represents a downstream effector of the tumor cell EMT that is required for breast cancer metastasis. Thus, the detection and targeted treatment of Axl-expressing tumors represents an important new therapeutic strategy for breast cancer.
Advances in the chemistry of metal–organic frameworks (2002)

An extensive body of research results currently exists from the synthesis of metal–organic frameworks (MOFs), an area that has attracted widespread attention due to the facility with which well-defined molecular building blocks can be assembled into periodic frameworks and the promise that such a process holds for the logical design of materials. The synthesis of MOFs generally involves the copolymerization of organic links and metal ions in a polar solvent under mild temperatures (up to 200 °C) and autogenous pressures (up to 100 atm). Since most products can be considered kinetically driven and lie on local thermodynamic minima, factors such as solubility of the organic link and metal salt, solvent polarity, ionic strength of the medium, temperature and pressure play critical roles in determining the character of products. Indeed, slight perturbations in synthetic parameters have been the basis for the preparation of what seems to be a flood of new MOF compounds.
Spherical Nucleic Acids (2012)

A historical perspective of the development of spherical nucleic acid (SNA) conjugates and other three-dimensional nucleic acid nanostructures is provided. This Perspective details the synthetic methods for preparing them, followed by a discussion of their unique properties and theoretical and experimental models for understanding them. Important examples of technological advances made possible by their fundamental properties spanning the fields of chemistry, molecular diagnostics, gene regulation, medicine, and materials science are also presented.
Fatty acids activate a chimera of the clofibric acid-activated receptor and the glucocorticoid receptor. (1992)

Peroxisome proliferators such as clofibric acid, nafenopin, and WY-14,643 have been shown to activate PPAR (peroxisome proliferator-activated receptor), a member of the steroid nuclear receptor superfamily. We have cloned the cDNA from the rat that is homologous to that from the mouse [Issemann, I. & Green, S. (1990) Nature (London) 347, 645-650], which encodes a 97% similar protein with a particularly well-conserved putative ligand-binding domain. To search for physiologically occurring activators, we established a transcriptional transactivation assay by stably expressing in CHO cells a chimera of rat PPAR and the human glucocorticoid receptor that activates expression of the placental alkaline phosphatase reporter gene under the control of the mouse mammary tumor virus promoter. Testing of compounds related to lipid metabolism or peroxisomal proliferation revealed that 150 microM concentrations of arachidonic or linoleic acid but not of dehydroepiandrosterone, cholesterol, or 25-hydroxy-cholesterol, activate the receptor chimera. In addition, saturated fatty acids induce the reporter gene. Shortening the chain length to n = 6 or introduction of an omega-terminal carboxylic group abolished the activation potential of the fatty acid. In conclusion, the present results indicate that fatty acids can regulate gene expression mediated by a member of the steroid nuclear receptor superfamily.
Suppressive effect of basic fibroblast growth factor on transendothelial emigration of CD4(+) T-lymphocyte. (1994)

The effect of basic fibroblast growth factor (b-FGF), one of the commonest angiogenic factors in various cancer types, on lymphocyte adhesion and transmigration across the endothelial cell monolayer was investigated using human umbilical vein-derived endothelial cells (HUVEC) and type I collagen gel. Forty-eight h exposure of HUVEC with 2 ng/ml b-FGF significantly decreased the basal adhesion of lymphocytes to endothelial cells. The decrease ratio is further enhanced by the addition of shear stress in this assay system. When HUVEC was stimulated for the last 24 h with optimal conditions of recombinant interleukin 1 beta, the percentages of transmigration as well as adhesion were also decreased significantly by the presence of b-FGF. The expression of intercellular adhesion molecule 1 and vascular cell adhesion molecule 1 was down-regulated by b-FGF exposure in both resting and activated conditions by recombinant interleukin 1 beta, supposedly the main reason for this phenomenon. The migrating cells across b-FGF-stimulated HUVEC contained a markedly lower percentage of CD4(+) T-cells than those across non-treated HUVEC, although the 4B4(+)/2H4(+) ratio in CD4(+) T-cell populations did not differ significantly. These facts suggest that the presence of b-FGF in the angiogenic area suppresses lymphocyte emigration, especially that of CD4(+) T-cells, and thus causes insufficient helper function in local immune response. This effect of b-FGF was possibly one of the critical mechanisms by which cancer cells escape from the host immune reactions in the angiogenic stage of tumor development.
Intracellular Reactive Oxygen Species Mediate the Linkage of Na+/K+-ATPase to Hypertrophy and Its Marker Genes in Cardiac Myocytes (1999)

We showed before that in cardiac myocytes partial inhibition of Na+/K+-ATPase by nontoxic concentrations of ouabain causes hypertrophy and transcriptional regulations of growth-related marker genes through multiple Ca2+-dependent signal pathways many of which involve Ras and p42/44 mitogen-activated protein kinases. The aim of this work was to explore the roles of intracellular reactive oxygen species (ROS) in these ouabain-initiated pathways. Ouabain caused a rapid generation of ROS within the myocytes that was prevented by preexposure of cells to N-acetylcysteine (NAC) or vitamin E. These antioxidants also blocked or attenuated the following actions of ouabain: inductions of the genes of skeletal alpha-actin and atrial natriuretic factor, repression of the gene of the alpha3-subunit of Na+/K+-ATPase, activation of mitogen-activated protein kinases, activation of Ras-dependent protein synthesis, and activation of transcription factor NF-kappaB. Induction of c-fos and activation of AP-1 by ouabain were not sensitive to NAC. Ouabain-induced inhibition of active Rb+ uptake through Na+/K+-ATPase and the resulting rise in intracellular Ca2+ were also not prevented by NAC. A phorbol ester that also causes myocyte hypertrophy did not increase ROS generation, and its effects on marker genes and protein synthesis were not affected by NAC. We conclude the following: (a) ROS are essential second messengers within some but not all signal pathways that are activated by the effect of ouabain on Na+/K+-ATPase; (b) the ROS-dependent pathways are involved in ouabain-induced hypertrophy; (c) increased ROS generation is not a common response of the myocyte to all hypertrophic stimuli; and (d) it may be possible to dissociate the positive inotropic effect of ouabain from its growth-related effects by alteration of the redox state of the cardiac myocyte.