gebhart/patrepeval huggingface dataset:
Fetal ovarian cysts: an early manifestation of McCune–Albright syndrome? (2012)

We demonstrate for the first time that voluminous fetal unilateral ovarian cysts may be suggestive of MAS. Systematic search for the Gsα mutation should be performed in all newborns with voluminous fetal unilateral ovarian cysts requiring percutaneous cyst aspiration, because early diagnosis of MAS prevents unnecessary oophorectomy to eliminate questions of malignancy and imposes long-term clinical, biological, and imaging follow-up to detect other early manifestations of MAS.
Parthenolide inhibits ERK and AP-1 which are dysregulated and contribute to excessive IL-8 expression and secretion in cystic fibrosis cells (2011)

In addition to NFκB MAPKs ERK, JNK and p38 and the transcription factor AP-1 are also dysregulated in CF epithelial cells. Parthenolide inhibited both NFκB and MAPK/AP-1 pathways contributing to the inhibition of IL-8 production.
Effect of phospholipid on the formation of volatile heterocyclic compounds in heated aqueous solutions of amino acids and ribose (1988)

Abstract The concentrations of 68 heterocyclic compounds produced by heating a series of amino acid—ribose and lecithin—amino acid—ribose reaction mixtures at 140°Cfor 1 h were measured, after headspace collection on Tenax GC, by capillary gas chromatography—mass spectrometry. The amino acids studied were glycine, lysine and cysteine, and the classes of heterocyclic compounds quantified were pyrazines (14), pyridines (7), furans (14), thiophenes (26) and thiazoles (7). The studies showed that the addition of lecithin to the simple Maillard reaction mixtures led to a reduction in the concentrations of many of the heterocyclic compounds formed in these reactions. These findings support an earlier observation that phospholipids in foodstuffs, such as meat products, could exert a quenching effect on the amount of heterocyclic compounds formed in Maillard reactions during the cooking of food. A number of volatile compounds formed by the reaction of lipid degradation products with Maillard reaction intermediates were also identified.
DIVERGENT OPERONS AND THE GENETIC STRUCTURE OF THE MALTOSE B REGION IN ESCHERICHIA COLI K12 (1974)

Complementation and polarity suppression data are interpreted in terms of the genetic structure of the maltose B region. It is proposed that this region comprises two divergent operons. One operon includes malK, a cistron involved in maltose permeation, and lamB the only known cistron specifically involved in lambda receptor synthesis. The other operon includes malJ(1) and malJ(2) which are most probably two different cistrons, both involved in maltose permeation*. It is further assumed that expression of the two operons is controlled by malT, the positive regulatory gene of the maltose system, located in the malA region. The target(s) for the action of the malT product is (are) most likely to be located between malJ(1) and malK. There is an indication that the two operons might overlap in the region of their promoters. The structure of such an overlap as well as the possible function of the products of the different cistrons in malB are briefly discussed.
Prediction of Liver Fibrosis According to Serum Collagen VI Level in Children with Cystic Fibrosis (1997)

To the Editor: Chronic fibrotic liver disease accounts for virtually all nonpulmonary causes of mortality in patients with cystic fibrosis. Therefore, along with lung disease and nutritional status...
PRODUCTION OF ACETIC ACID FROM HYDROGEN AND CARBON DIOXIDE BY CLOSTRIDIUM SPECIES ATCC 29797 (1986)

Abstract Clostridium sp. ATCC 29797 converts H2 and CO2 to acetic acid in stationary phase in almost 100% yield. The resting cells are stable for up to 300 h and produce acetate to a final product concentration of 221 mM. The specific productivity of acetate during the stationary phase appears limited by the specific activity of hydrogenase. A high pressure fermentor was constructed to investigate the use of pressure, as a general strategy, for increasing the rates of microbial syngas conversions. Fermentations were conducted at pressures up to 1000 psig using various mixtures of H2 and CO2. The use of high pressure proved to be an effective method for eliminating gas transfer resistances and increasing the volumetric productivity. Hydrostatic pressure had little effect on the specific productivity of acetate, however, high partial pressures of hydrogen caused the specific productivity and total acetate accumulated to decrease. High pressures of hydrogen also caused a decrease in the specific activity of hydrogenase. These results suggest that Clostridium sp. ATCC 29797 attempts to control the input of reducing power by regulating the activity of hydrogenase.
Mitochondrial dysfunction and Parkinson’s disease genes: insights from Drosophila (2009)

Parkinson's disease (PD), one of the most common neurodegenerative disorders worldwide, currently lacks a cure. Although most PD cases occur sporadically, studies from rare genetic mutations give significant insights into addressing the pathological mechanism of not only familial PD, but also sporadic PD. Recent PD research focuses on generating genetic mutant animal models that recapitulate the features of human PD patients. Significant advances in PD research have resulted from studying Drosophila mutants of several identified PD-associated genes because they show strikingly visible phenotypes. In particular, previous studies with the Drosophila mutants parkin and PINK1, which are two common causative genes among PD familial forms, have suggested strongly that mitochondrial dysfunction is the prominent cause for the PD pathogenesis and that these two PD genes are in a common pathway, with Parkin downstream of PINK1. Recent genetic studies have revealed that the PINK1-Parkin pathway is involved in regulating the mitochondrial remodeling process. In addition, PINK1 was recently found to regulate the localization of Parkin through direct phosphorylation. Here, we briefly review these new and exciting findings in Drosophila PD models and discuss how using these models can further advance PD studies.
Estrogen-receptor-α exchange and chromatin dynamics are ligand- and domain-dependent (2006)

We report a mammalian-based promoter chromosomal array system developed for single-cell studies of transcription-factor function. Designed after the prolactin promoter-enhancer, it allows for the direct visualization of estrogen receptor alpha (ERalpha) and/or Pit-1 interactions at a physiologically regulated transcription locus. ERalpha- and ligand-dependent cofactor recruitment, large-scale chromatin modifications and transcriptional activity identified a distinct fingerprint of responses for each condition. Ligand-dependent transcription (more than threefold activation compared with vehicle, or complete repression by mRNA fluorescent in situ hybridization) at the array correlated with its state of condensation, which was assayed using a novel high throughput microscopy approach. In support of the nuclear receptor hit-and-run model, photobleaching studies provided direct evidence of very transient ER-array interactions, and revealed ligand-dependent changes in k(off). ERalpha-truncation mutants indicated that helix-12 and interactions with co-regulators influenced both large-scale chromatin modeling and photobleaching recovery times. These data also showed that the ERalpha DNA-binding domain was insufficient for array targeting. Collectively, quantitative observations from this physiologically relevant biosensor suggest stochastic-based dynamics influence gene regulation at the promoter level.
Fast and Reliable Stream Processing over Wide Area Networks (2007)

We present a replication-based approach that enables both fast and reliable stream processing over wide area networks. Our approach replicates stream processing operators in a manner where operator replicas compete with each other to make the earliest impact. Therefore, any processing downstream from such replicas can proceed by relying on the fastest replica without being held back by slow or failed ones. Furthermore, our approach allows replicas to produce output in different orders so as to avoid the cost of forcing an identical execution across replicas, without sacrificing correctness. We first consider semantic issues for correct replicated stream processing and, based on a formal foundation, extend common stream-processing primitives. Next, we discuss strategies for deploying replicas. Finally, we present preliminary results obtained from experiments on Planet-Lab that substantiate the potential benefits of our approach.
Treatment of Recurrent Clostridium difficile Diarrhea. (2006)

Treatment of recurrent <i>Clostridium difficile</i>-associated diarrhea can be challenging. Once patients develop recurrent disease, further episodes are common and can continue for months or even a year or more. Treatment begins with a repeat standard 10-day course of antibiotics, followed by tapering and/or pulsing of the antibiotic dose. Probiotics can also be useful, particularly the nonpathogenic yeast <i>Saccharomyces boulardii</i>. Stool reconstitution via fecal enemas, colonoscopy, and nasogastric tubes have been performed to restore normal colonic flora. Additional approaches under investigation, such as vaccination against <i>C. difficile</i>, show encouraging preliminary results.
A National Survey of Severe Group B Streptococcal Infections in Neonates and Young Infants in Denmark, 1978–83 (1985)

During a six-year period, 1978-83, 80 cases of culture proven group B streptococcal (GBS) bacteraemia and meningitis were identified in neonates and young infants up to 12 weeks of age in a national retrospective survey. Two thirds (68%) were early onset disease (EOD) while one third was late onset disease (LOD) occurring later than the seventh day of life. The overall incidence for the period was 0.24 per 1,000 live-born with a trend towards decline through the period. EOD was associated with low birthweight, twin delivery and congenital anomalies as well as with obstetric risk factors like premature or prolonged rupture of membranes and intrapartum fever. The overall case fatality rate was 23%, both in EOD and LOD. Seven (11%) of the surviving infants, six of whom had had meningitis, developed neurological sequelae. Newborns that showed signs of infection with 12 hours of delivery were at a significantly higher risk of running a fulminant course than newborns whose infections developed later (p = 0.02). Nosocomial transmission of GBS seemed limited and most hospital-acquired cases were unconnected.
Abstract 4584: Pre-clinical studies of a novel antibody to treat pancreatic and colorectal cancers (2011)

Abstract Introduction: NPC-1C is a chimeric monoclonal antibody being developed as a novel biological treatment for pancreatic and colorectal cancers. NPC-1C appears to recognize a variant form of MUC5AC expressed specifically by human pancreatic and colorectal tumor tissues and cell lines. Here we show pre-clinical studies in preparation for testing this therapeutic for a Phase I clinical trial. Methods: The NPC-1C antibody was selected from a panel of hybridomas generated from mice immunized with semi-purified membrane-associated proteins derived from biologically screened, pooled human allogeneic colon cancer tissues. In vitro assays and in vivo studies were performed to characterize the GMP-grade antibody. Results: Here we show that NPC-1C reacts with colorectal and pancreatic tumor tissues, but does not cross-react with normal human tissues, except for occasional, weak binding to certain GI tract tissues, which may indicate a pre-malignant state. The NPC-1C antibody exhibits cell-specific binding and ADCC activity against human colorectal and pancreatic tumor cells, but not against control tumor cell lines. In vivo, the anti-tumor efficacy of NPC-1C was tested using pre-established subcutaneous human tumor xenograft models. The data showed significant, and reproducible, anti-tumor action, including some complete tumor regressions. The pre-clinical toxicity profile of NPC-1C in normal BALB/c mice demonstrated little, if any, toxicity following single or multiple intravenous injections. The bio-distribution of radiolabeled NPC-1C in mice with pre-established human tumors revealed specific accumulation of NPC-1C at the tumor site, with little or no binding or accumulation in several major organ systems. Finally, the cytokine and antibody responses to NPC-1C were studied in the pre-clinical mouse model. Although anti-NPC-1C antibodies were detected (as expected) in a time-dependent fashion, there were no changes detect in Type I and Type II cytokines either 3 days or 14 days after intravenous administration. Conclusions: The pre-clinical development of NPC-1C indicates that it is safe and efficacious, and suggests that it may have clinical activity in patients whose tumor expresses the variant MUC5AC epitope. The potential clinical application for this antibody was bolstered by showing approximately 50-70% of human pancreatic and colon tumor tissues stained positively with NPC-1C. The therapeutic antibody is now being tested in a Phase I clinical trial in patients with advanced pancreatic and colorectal cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4584. doi:10.1158/1538-7445.AM2011-4584
N-Type Conjugated Materials Based on 2-Vinyl-4,5-dicyanoimidazoles and Their Use in Solar Cells (2007)

The high-yield syntheses of a new class of n-type conjugated materials based on the Heck coupling of 2-vinyl-4,5-dicyanoimidazole with selected dibromoaromatics is reported. The resultant materials have tunable HOMO−LUMO levels and photoluminescence ranging from deep blue to red. Solution-processed organic solar cells with external quantum efficiencies exceeding 14% could be prepared by blending selected novel materials with poly-(3-hexylthiophene) (P3HT).
Tomato Transcription Factors Pti4, Pti5, and Pti6 Activate Defense Responses When Expressed in Arabidopsis (2002)

The Pti4, Pti5, and Pti6 proteins from tomato were identified based on their interaction with the product of the Pto disease resistance gene, a Ser-Thr protein kinase. They belong to the ethylene-response factor (ERF) family of plant-unique transcription factors and bind specifically to the GCC-box cis element present in the promoters of many pathogenesis-related (PR) genes. Here, we show that these tomato ERFs are localized to the nucleus and function in vivo as transcription activators that regulate the expression of GCC box-containing PR genes. Expression of Pti4, Pti5, or Pti6 in Arabidopsis activated the expression of the salicylic acid-regulated genes PR1 and PR2. Expression of jasmonic acid- and ethylene-regulated genes, such as PR3, PR4, PDF1.2, and Thi2.1, was affected differently by each of the three tomato ERFs, with Arabidopsis-Pti4 plants having very high levels of PDF1.2 transcripts. Exogenous application of salicylic acid to Arabidopsis-Pti4 plants suppressed the increased expression of PDF1.2 but further stimulated PR1 expression. Arabidopsis plants expressing Pti4 displayed increased resistance to the fungal pathogen Erysiphe orontii and increased tolerance to the bacterial pathogen Pseudomonas syringae pv tomato. These results indicate that Pti4, Pti5, and Pti6 activate the expression of a wide array of PR genes and play important and distinct roles in plant defense.
Free Energy Perturbation Simulation on Transition States and High-Activity Mutants of Human Butyrylcholinesterase for (−)-Cocaine Hydrolysis (2010)

A unified computational approach based on free energy perturbation (FEP) simulations of transition states has been employed to calculate the mutation-caused shifts of the free energy change from the free enzyme to the rate-determining transition state for (-)-cocaine hydrolysis catalyzed by the currently most promising series of mutants of human butyrylcholinesterase (BChE) that contain the A199S/A328W/Y332G mutations. The FEP simulations were followed by Michaelis-Menten kinetics analysis determining the individual k(cat) and K(M) values missing for the A199S/F227A/A328W/Y332G mutant in this series. The calculated mutation-caused shifts of the free energy change from the free enzyme to the rate-determining transition state are in good agreement with the experimental kinetic data, demonstrating that the unified computational approach based on the FEP simulations of the transition states may be valuable for future computational design of new BChE mutants with a further improved catalytic efficiency against (-)-cocaine.
Noncovalent Modulation of the Inverse Temperature Transition and Self-Assembly of Elastin-b-Collagen-like Peptide Bioconjugates (2015)

Stimuli-responsive nanostructures produced with peptide domains from the extracellular matrix offer great opportunities for imaging and drug delivery. Although the individual utility of elastin-like (poly)peptides and collagen-like peptides in such applications has been demonstrated, the synergistic advantages of combining these motifs in short peptide conjugates have surprisingly not been reported. Here, we introduce the conjugation of a thermoresponsive elastin-like peptide (ELP) with a triple-helix-forming collagen-like peptide (CLP) to yield ELP-CLP conjugates that show a remarkable reduction in the inverse transition temperature of the ELP domain upon formation of the CLP triple helix. The lower transition temperature of the conjugate enables the facile formation of well-defined vesicles at physiological temperature and the unexpected resolubilization of the vesicles at elevated temperatures upon unfolding of the CLP domain. Given the demonstrated ability of CLPs to modify collagens, our results not only provide a simple and versatile avenue for controlling the inverse transition behavior of ELPs, but also suggest future opportunities for these thermoresponsive nanostructures in biologically relevant environments.
Exclusion of Golgi Residents from Transport Vesicles Budding from Golgi Cisternae in Intact Cells (2000)

A central feature of cisternal progression/maturation models for anterograde transport across the Golgi stack is the requirement that the entire population of steady-state residents of this organelle be continuously transported backward to earlier cisternae to avoid loss of these residents as the membrane of the oldest (trans-most) cisterna departs the stack. For this to occur, resident proteins must be packaged into retrograde-directed transport vesicles, and to occur at the rate of anterograde transport, resident proteins must be present in vesicles at a higher concentration than in cisternal membranes. We have tested this prediction by localizing two steady-state residents of medial Golgi cisternae (mannosidase II and N-acetylglucosaminyl transferase I) at the electron microscopic level in intact cells. In both cases, these abundant cisternal constituents were strongly excluded from buds and vesicles. This result suggests that cisternal progression takes place substantially more slowly than most protein transport and therefore is unlikely to be the predominant mechanism of anterograde movement.
Parallel Alignment of Carbon Nanotubes Induced with Inorganic Molecules (2005)

In this work, a new strategy is presented to form ordered multiwalled carbon nanotube (MWNT) arrays. The MWNTs are aligned horizontally and parallel in (3-aminopropyl)triethoxysilane (3-APTES) sol films on the surface of mica and glassy carbon (GC). 3-APTES is ready to form charged rodlike micelles, which play a key role in fabricating orderly MWNT arrays. Moreover, we prepare MWNT arrays on the surfaces of solid electrodes and detect the electrochemical response of the microarray electrodes for the Fe(CN)(6)3-/Fe(CN)6(4-) couple.
Space Fresnel lens concentrator modules with triple-junction solar cells (2005)

The work presented in this paper is concerned with fabrication of an improved concentrator module based on linear Fresnel lenses and photoreceivers with GalnP/GaAs/Ge triple junction (TJ) cells. The manufactured module consists of: four linear Fresnel lenses with focal distance of 30 mm and dimensions of 2.5/spl times/10 cm/sup 2/ each; four linear photoreceivers of 10 cm in length with 12 TJ solar cells each; heat sink made of thin copper metallized dielectric plate. Linear Fresnel lenses with optical efficiency of 82-84% were made of silicone formed on shockproof radiation-resistant UV-protective glass 0.2 mm thick. The solar cells intended for use in linear receivers have efficiencies of 23-24% (AM0, 25 /spl deg/C) at geometrical sunlight concentration of 6-9/spl times/. The estimated module efficiency is about 21% (AM0).
Role of colony stimulating factor-1 in the establishment and regulation of tissue macrophages during postnatal development of the mouse (1994)

Colony stimulating factor-1 (CSF-1) regulates the survival, proliferation and differentiation of mononuclear phagocytes. The osteopetrotic (op/op) mutant mouse is devoid of CSF-1 due to an inactivating mutation in the CSF-1 gene and is deficient in several mononuclear phagocyte subpopulations. To analyze more fully the requirement for CSF-1 in the establishment and maintenance of mononuclear phagocytes, the postnatal development of cells bearing the macrophage marker antigens F4/80 and MOMA-1, in op/op mice and their normal (+/op or +/+) littermates, were studied during the first three months of life. In normal mice, maximum expression of tissue F4/80+ cells was generally correlated with the period of maximum organogenesis and/or cell turnover. Depending on the tissue, the F4/80+ cell density either decreased, transiently increased or gradually increased with age. In op/op mice, tissues that normally contain F4/80+ cells could be classified into those in which F4/80+ cells were absent and those in which the F4/80+ cell densities were either reduced, normal or initially normal then subsequently reduced. To assess which F4/80+ populations were regulated by circulating CSF-1 in normal mice, op/op mice in which the circulating CSF-1 concentration was restored to above normal levels by daily subcutaneous injection of human recombinant CSF-1 from day 3 were analyzed. These studies suggest that circulating CSF-1 exclusively regulates both the F4/80+ cells in the liver, spleen and kidney and the MOMA-1+ metallophilic macrophages in the spleen. Macrophages of the dermis, bladder, bone marrow and salivary gland, together with a subpopulation in the gut, were partially restored by circulating CSF-1, whereas macrophages of the muscle, tendon, periosteum, synovial membrane, adrenals and the macrophages intimately associated with the epithelia of the digestive tract, were not corrected by restoration of circulating CSF-1, suggesting that they are exclusively locally regulated by this growth factor. Langerhans cells, bone marrow monocytes and macrophages of the thymus and lymph nodes were not significantly affected by circulating CSF-1 nor decreased in op/op mice, consistent with their regulation by other growth factors. These results indicate that important differences exist among mononuclear phagocytes in their dependency on CSF-1 and the way in which CSF-1 is presented to them. They also suggest that the prevalent role of CSF-1 is to influence organogenesis and tissue turnover by stimulating the production of tissue macrophages with local trophic and/or scavenger (physiological) functions. Macrophages involved in inflammatory and immune (pathological) responses appear to be dependent on other factors for their ontogenesis and function.(ABSTRACT TRUNCATED AT 400 WORDS)