gebhart/patrepeval huggingface dataset:
12 Trophoblast Stem Cells (2001)

THE TROPHOBLAST LINEAGE AND PLACENTAL DEVELOPMENT In the mammalian embryo, the formation of the extraembryonic lineages, the trophectoderm and primitive endoderm, precedes the differentiation of cells that will contribute to the fetus itself. The precocious differentiation of these lineages in mammals is related to their essential roles in promoting survival of the embryo in the uterine environment. Cells of the primitive endoderm give rise to the endoderm layers of the yolk sacs, whereas descendants of the trophectoderm will form the trophoblast portion of the placenta (Fig. 1). The development of both extraembryonic lineages has been reviewed previously (Rossant 1986Rossant 1995). The scope of the following discussion is to provide an overview of trophectoderm development in the preimplantation embryo and of the trophoblast lineage and placenta in postimplantation stages, as the basis for the study of trophoblast stem cells. The trophectoderm is the first cell type to differentiate in the mammalian embryo. In the mouse, it is morphologically distinguishable by the blastocyst stage (3.5 days post coitum [dpc]), where it forms an outer monolayer of cells surrounding the blastocoelic cavity and the inner cell mass (ICM) (Fig. 1A). The trophectoderm cells are characterized by their flattened epitheloid-like appearance, with apical tight junction complexes. In addition, trophectoderm cells harbor sodium pumps (Na + , K + -ATPase) whose activity leads to accumulation of fluid within the blastocoel cavity, resulting in blastocoel expansion. This process is thought to facilitate hatching from the zona pellucida, a thick protein coat surrounding the embryo (Wiley et al. 1990). The distinction...
Template-Directed Synthesis of Shape-Persistent Macrocyclic Amphiphiles with Convergently Arranged Functionalities (1999)

Macrocyclic structures such as 1 and rings with different polar substituents pointing inwards can be prepared by the intramolecular Glaser coupling of tetraacetylenes held covalently in position around a temporary template.
Developmental changes of cardiac function and mass assessed with MRI in neonatal, juvenile, and adult mice (2000)

Cardiovascular transgenic mouse models with an early phenotype or even premature death require noninvasive imaging methods that allow for accurate visualization of cardiac morphology and function. Thus the purpose of our study was to assess the feasibility of magnetic resonance imaging (MRI) to characterize cardiac function and mass in newborn, juvenile, and adult mice. Forty-five C57bl/6 mice from seven age groups (3 days to 4 mo after birth) were studied by MRI under isoflurane anesthesia. Electrocardiogram-gated cine MRI was performed with an in-plane resolution of (78-117 microm)(2). Temporal resolution per cine frame was 8.6 ms. MRI revealed cardiac anatomy in mice from all age groups with high temporal and spatial resolution. There was close correlation between MRI- and autopsy-determined left ventricular (LV) mass (r = 0.95, SE of estimate = 9.5 mg). The increase of LV mass (range 9.6-101.3 mg), cardiac output (range 1.1-14.3 ml/min), and stroke volume (range 3. 2-40.2 microl) with age could be quantified by MRI measurements. Ejection fraction and cardiac index did not change with aging. However, LV mass index decreased with increasing age (P < 0.01). High-resolution MRI allows for accurate in vivo assessment of cardiac function in neonatal, juvenile, and adult mice. This method should be useful when applied in transgenic mouse models.
Synthetic Glycopeptides for the Construction of Anticancer Vaccines (2008)

Glycopeptides of the tandem repeat region of the tumor-associated epithelial mucin MUCl containing tumor-associated saccharide antigens have been synthesized and conjugated to carrier proteins or T-cell epitope peptides. The T, sialyl TN, 2,6- and 2,3-sialyl T antigen amino acid building blocks were obtained by biomimetic syntheses starting from the monosaccharide TN antigen conjugate. To synthesize the MUCl glycopeptides solid-phase methods with varied anchors were applied. Conjugation of synthetic glycopeptides to bovine serum albumin were achieved by selective reactions at squaric esters. Solid-phase fragment condensation proved successful for constructions of MUCl glycopeptide-T-cell epitope conjugates. Immunization of mice with a synthetic vaccine consisting of a MUCl glycopeptide and a T-cell epitope from ovalbumin induced a specific immune response. The elicited antibody only reacted with the glycopeptide. Neither its peptide nor the glycan in a different peptide were recognized. This precise differentiation by antibodies induced by chemically pure vaccines is considered promising for the development of antitumor vaccines.
Powdery Mildew Resistance in the U.S. National Plant Germplasm System Cucumber Collection (2005)

Nine hundred and seventy-seven (977) cucumber ( Cucumis sativus L.) accessions from the U.S. National Plant Germplasm System (NPGS) collection were tested for resistance to powdery mildew, caused by the fungus Podosphaera xanthii (Castagne) Braun and Shishkoff, formerly known as Sphaerotheca fuliginea (Schlecht.) Poll. Plants from each accession were evaluated in the greenhouse following inoculation with field isolates of P. xanthii . Each plant was placed into one of three susceptibility classes based on the amount of fungal growth and sporulation on the hypocotyl, stem, petioles and leaves - susceptible (S), intermediate (I) or resistant (R). Of the 977 accessions (9.6%), 94 contained at least one I or R-type plant. Seventeen of the 20 most-resistant accessions came from Asian sources, including China (PIs 418962, 418964, 432860, and 432870), India (PIs 197085, 197088, and 605930), Japan (PIs 279465, 288238, 390258, and 390266), Pakistan (PI 330628), the Philippines (PIs 426169 and 426170), and Taiwan (PIs 321006, 321009, and 321011). A quantitative study was conducted to compare mildew reproduction on S, I, and R-type cucumbers in the greenhouse and under field conditions in Ames, Iowa. Leaf disks were removed weekly and microscopic counts made of spore populations. The leaf disk method was superior to visual rating for ranking and differentiating intermediate from resistant accessions. Both the intermediate (moderately resistant) and highly resistant accessions provided excellent protection against powdery mildew in the field.
Acute γ-Secretase Inhibition Improves Contextual Fear Conditioning in the Tg2576 Mouse Model of Alzheimer's Disease (2005)

Transgenic mice (Tg2576) overexpressing the Swedish mutation of the human amyloid precursor protein display biochemical, pathological, and behavioral markers consistent with many aspects of Alzheimer's disease, including impaired hippocampal function. Impaired, hippocampal-dependent, contextual fear conditioning (CFC) is observed in mice as young as 20 weeks of age. This impairment can be attenuated after treatment before training with the phosphodiesterase-4 inhibitor rolipram (0.1 mg/kg, i.p.). A rolipram-associated improvement is also observed in the littermate controls, suggesting that the effect of rolipram is independent of beta-amyloid. Acute treatment before training (but not after training or before testing) with the gamma-secretase inhibitor (GSI) N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine-t-butylester (DAPT), at a dose that reduces brain concentrations of beta-amyloid (100 mg/kg), attenuates the impairment in 20- to 65-week-old Tg2576 mice. Importantly, DAPT had no effect on performance of control littermates. These data are supportive of a role of beta-amyloid in the impairment of CFC in Tg2576 mice. Furthermore, they suggest that acute treatment with GSI may provide improved cognitive functioning as well as disease-modifying effects in Alzheimer's disease.
Enhancing Chemotherapy Efficacy in Pten-Deficient Prostate Tumors by Activating the Senescence-Associated Antitumor Immunity (2014)

Prosenescence therapy has recently emerged as a novel therapeutic approach for treating cancer. However, this concept is challenged by conflicting evidence showing that the senescence-associated secretory phenotype (SASP) of senescent tumor cells can have pro- as well as antitumorigenic effects. Herein, we report that, in Pten-null senescent tumors, activation of the Jak2/Stat3 pathway establishes an immunosuppressive tumor microenvironment that contributes to tumor growth and chemoresistance. Activation of the Jak2/Stat3 pathway in Pten-null tumors is sustained by the downregulation of the protein tyrosine phosphatase PTPN11/SHP2, providing evidence for the existence of a novel PTEN/SHP2 axis. Importantly, treatment with docetaxel in combination with a JAK2 inhibitor reprograms the SASP and improves the efficacy of docetaxel-induced senescence by triggering a strong antitumor immune response in Pten-null tumors. Altogether, these data demonstrate that immune surveillance of senescent tumor cells can be suppressed in specific genetic backgrounds but also evoked by pharmacological treatments.
Platelets: bridging hemostasis, inflammation, and immunity (2013)

Summary Although the function of platelets in the maintenance of hemostasis has been studied in great detail, more recent evidence has highlighted a central role for platelets in the host inflammatory and immune responses. Platelets by virtue of their large numbers and their ability to rapidly release a broad spectrum of immunomodulatory cytokines, chemokines, and other mediators act as circulating sentinels. Upon detection of a pathogen, platelets quickly activate and begin to drive the ensuing inflammatory response. Platelets have the ability to directly modulate the activity of neutrophils (phagocytosis, oxidative burst), endothelium (adhesion molecule and chemokine expression), and lymphocytes. Due to their diverse array of adhesion molecules and preformed chemokines, platelets are able to adhere to leukocytes and facilitate their recruitment to sites of tissue damage or infection. Furthermore, platelets directly participate in the capture and sequestration of pathogens within the vasculature. Platelet–neutrophil interactions are known to induce the release of neutrophil extracellular traps ( NET s) in response to either bacterial or viral infection, and platelets have been shown to internalize pathogens, sequestering them in engulfment vacuoles. Finally, emerging data indicate that platelets also participate in the host immune response by directly killing infected cells. This review will highlight the central role platelets play in the initiation and modulation of the host inflammatory and immune responses.
Inhibitors of Ketohexokinase: Discovery of Pyrimidinopyrimidines with Specific Substitution that Complements the ATP-Binding Site (2011)

Attenuation of fructose metabolism by the inhibition of ketohexokinase (KHK; fructokinase) should reduce body weight, free fatty acids, and triglycerides, thereby offering a novel approach to treat diabetes and obesity in response to modern diets. We have identified potent, selective inhibitors of human hepatic KHK within a series of pyrimidinopyrimidines (1). For example, 8, 38, and 47 exhibited KHK IC50 values of 12, 7, and 8 nM, respectively, and also showed potent cellular KHK inhibition (IC50 < 500 nM), which relates to their intrinsic potency vs KHK and their ability to penetrate cells. X-ray cocrystal structures of KHK complexes of 3, 8, and 47 revealed the important interactions within the enzyme's adenosine 5'-triphosphate (ATP)-binding pocket.
Correlation between rhodamine 123 accumulation and azole sensitivity in Candida species: possible role for drug efflux in drug resistance (1996)

A wide variety of prokaryotic and eukaryotic cells exhibit a multidrug resistance (MDR) phenotype, indicating that resistance to potentially toxic compounds is mediated by their active efflux from the cell. We have sought to determine whether resistance to azoles in some strains of Candida species may be due in part to active drug efflux. Rhodamine 123 (Rh123) is a fluorescent compound that is transported by a wide variety of MDR cell types. We have shown that certain azole-resistant strains of Candida albicans, C. glabrata, and C. krusei accumulate less Rh123 than azole-susceptible ones. In C. albicans, Rh123 accumulation was growth phase and temperature dependent and was increased by proton uncouplers and by reserpine, an MDR modulator. This is consistent with an energy-dependent efflux mechanism for Rh123, mediated by an MDR transporter. In C. glabrata, but not in C. albicans, there was competition between Rh123 and fluconazole for efflux. Thus, in C. glabrata, Rh123 and fluconazole appear to be transported via a common MDR-like transporter, whereas in C. albicans, the Rh123 transporter does not appear to transport azoles.
Joint sentiment/topic model for sentiment analysis (2009)

Sentiment analysis or opinion mining aims to use automated tools to detect subjective information such as opinions, attitudes, and feelings expressed in text. This paper proposes a novel probabilistic modeling framework based on Latent Dirichlet Allocation (LDA), called joint sentiment/topic model (JST), which detects sentiment and topic simultaneously from text. Unlike other machine learning approaches to sentiment classification which often require labeled corpora for classifier training, the proposed JST model is fully unsupervised. The model has been evaluated on the movie review dataset to classify the review sentiment polarity and minimum prior information have also been explored to further improve the sentiment classification accuracy. Preliminary experiments have shown promising results achieved by JST.
p75 neurotrophin receptor signaling regulates hepatic myofibroblast proliferation and apoptosis in recovery from rodent liver fibrosis† (2008)

NGF species have a differential effect on hepatic myofibroblast survival. Our data suggest that cleavage of proNGF by MMP7 during the early phase of recovery from liver fibrosis alters the pro/mature NGF balance to facilitate hepatic myofibroblast loss. Whereas fibrosis develops in the absence of p75(NTR) signaling, the dominant effects of loss of p75(NTR) ligand-mediated events are the retardation of liver fibrosis resolution via regulation of hepatic myofibroblast proliferation and apoptosis, and the reduction of hepatocyte and oval cell proliferation.
CPG ODN allows lower dose of antigen against hepatitis B surface antigen in BALB/c mice (2003)

We have evaluated alum, immunostimulatory cytosine guanine dinucleotide-containing oligodeoxy-nucleotides (CPG ODN), and an alum/CPG ODN combination as adjuvants with hepatitis B surface antigen, to compare their potential to allow lower doses of antigen to be used for induction of humoral responses. BALB/c mice were immunized by intramuscular injection with 0.01, 0.1 or 1.0 micro g recombinant hepatitis B surface antigen without adjuvant or with alum and/or CPG ODN added. When given without adjuvant or with alum, each 10-fold decrease in amount of antigen resulted in a similarly reduced titre of antibody against hepatitis B surface antigen. In contrast, CPG ODN, on its own or combined with alum, allowed high anti-hepatitis B surface antigen titres even with a 1000-fold reduction in amount of antigen. These findings may have important immunological and economical consequences for vaccine development.
The Identification of Two New ABCB11 Gene Mutations and the Treatment Outcome in a Young Adult with Benign Recurrent Intrahepatic Cholestasis: A Case Report (2017)

Introduction: Benign recurrent intrahepatic cholestasis (BRIC) is a rare autosomal recessive disease characterized by recurrent episodes of severe pruritus and jaundice. Although the disease symptom will relieve spontaneously without leaving any hepatic injury, the ceaseless attacks would reduce the life quality of patients. However, there is not a validated treatment for BRIC yet. Considering the limited cases and the unpredictability of this disease, the publications of well-described case reports are necessary for the investigation of disease development and treatment efficacy. Case Presentation: A 26-year-old Chinese male, with clinical approved and genetic diagnosis of BRIC, experienced 3 attacks of recurrent intrahepatic cholestasis from 2010 to 2016. During hospitalizations, he received symptomatic treatments and plasmapheresis therapies. Both plasma exchange (PE) and plasma bilirubin adsorption (PBA) were conducted for him. The whole-exome sequencing revealed several single nucleotide polymorphisms (SNPs) as well as 2 novel mutations in ABCB11 (c.70A > T, p.Lys24*, exon2 and c.1417G > A, p.Asp473Asn, exon13). These SNPs and mutations might be associated with the BRIC development. Conclusions: Both medications and plasmapheresis interventions could relieve the patientâs symptoms, however, neither could shorten the natural process of the disease. The 2 mutations (c.70A > T and c.1417G > A) in ABCB11 were first reported in a BRIC patient.
Electron and hole mobility enhancement in strained SOI by wafer bonding (2002)

N- and p-MOSFETs have been fabricated in strained Si-on-SiGe-on-insulator (SSOI) with high (15-25%) Ge content. Wafer bonding and H-induced layer transfer techniques enabled the fabrication of the high Ge content SiGe-on-insulator (SGOI) substrates. Mobility enhancement of 50% for electrons (with 15% Ge) and 15-20% for holes (with 20-25% Ge) has been demonstrated in SSOI MOSFETs. These mobility enhancements are commensurate with those reported for FETs fabricated on strained silicon on bulk SiGe substrates.
Synthesis of Well-Defined Environmentally Responsive Polymer Brushes by Aqueous ATRP (2004)

Functionalized anionic polystyrene latex particles with ATRP initiators were synthesized by surfactant-free shell-growth emulsion polymerization of styrene and 2-(2‘-chloropropionato)ethyl acrylate (HEA-Cl). N-Isopropylacrylamide (NIPAM) was polymerized from these particles by surface-initiated aqueous ATRP using PMDETA/CuCl and HMTETA/CuCl catalysts to synthesize poly(N-isopropylacrylamide) (PNIPAM) brushes. The grafted latexes were characterized for molecular weight of the PNIPAM chains, grafting density, and hydrodynamic thickness of the grafted polymer layer. Molecular weights of the grafted PNIPAM chains depended on the monomer concentration, concentration of copper(II) complex, and the presence of external initiator in the reaction medium. Mn of the grafted chains increases with increase in the monomer concentration and decreases with addition of copper(II) complex and external initiator. The HMTETA/CuCl catalyst produces higher molecular weight chains than PMDETA/CuCl. Molecular weights from ∼50 000 to 800 000 with low polydispersities, between 1.25 and 1.4, were achieved. The grafting density of PNIPAM on the surface increases with increasing monomer concentration and decreases with addition of copper(II) catalyst and external initiator. Block copolymerization of N,N-dimethylacrylamide from PNIPAM-grafted latex demonstrated that the chains are terminated with a chlorine atom, and the grafting reactions are taking place by the ATRP mechanism. The hydrodynamic thickness (HT) of the grafted PNIPAM layer scales as DP0.66 (where DP = degree of polymerization) at constant grafting density (chains/nm2). The HT values for PNIPAM brushes are sensitive to temperature and salt concentration. Since the transition from extended coil to collapsed structure occurs over a range of temperature and salt concentration, it follows a second-order transition, as predicted by theory. The thickness of the collapsed brush is sensitive to the type of stimulus used to induce the phase transition.
Proton NMR assignment and secondary structure of the cell adhesion type III module of fibronectin (1992)

The secondary structure of the tenth type III module from human fibronectin has been determined using NMR. This type of module appears many times in a wide variety of proteins. The type III module described here contains an Arg-Gly-Asp sequence known to be involved in cell-cell adhesion. The module was expressed in yeast and characterized by amino acid sequencing and mass spectrometry. 2D and 3D NMR spectroscopy of 15N-labeled protein was used to perform sequence-specific assignment of the spectrum. The secondary structure was defined by patterns of nuclear Overhauser effects, 3JNH-alpha CH spin-spin coupling constants, and amide proton solvent exchange rates. The molecule consists of seven beta-strands in two antiparallel beta-sheets with an immunoglobulin-like fold similar to that predicted for homologous modules in the cytokine receptor super family [Bazan, J. F. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6934-6938]. The Arg-Gly-Asp sequence is located on a loop between the beta-strands F and G.
Development of Herceptin resistance in breast cancer cells (2003)

Herceptin binds effectively to Her-2 on the cell surface of Herceptin-resistant cell lines and the level of Her-2 expression on the cell surface is not downregulated. Herceptin resistance is not due to downregulation of levels of AKT protein expression, although, phosphorylation of AKT is enhanced in resistant lines and could have a role in resistance. Resistance appears to correlate with the loss of nuclear expression of the cyclin-dependent kinase inhibitor, p27, as defined by immunofluorescence and flow cytometry studies and cdk-2 binding studies.
Ventilator-associated Lung Injury Decreases Lung Ability to Clear Edema in Rats (1999)

Ventilator-associated lung injury (VALI) is caused by high tidal volume (VT) excursions producing microvascular leakage and pulmonary edema. However, the effects of VALI on lung edema clearance and alveolar epithelial cells' Na,K-ATPase function have not been elucidated. We studied lung edema clearance in the isolated-perfused rat lung model after ventilation for 25, 40, and 60 min with high VT (peak airway opening pressure [Pao] of approximately 35 cm H2O) and compared them with low VT ventilation (Pao approximately 8 cm H2O), moderate VT ventilation (Pao approximately 20 cm H2O), and nonventilated rats. Lung edema clearance in control rats was 0.50 +/- 0.02 ml/h and decreased after 40 and 60 min of high VT to 0.26 +/- 0.03 and 0.11 +/- 0.08 ml/h, respectively (p < 0.01), but did not change after low VT and moderate VT ventilation at any time point. Lung permeability to small (22Na+, [3H]mannitol) and large solutes (fluorescein isothiocyanate-tagged albumin [FITC-albumin]) increased significantly in rats ventilated for 60 min with high VT, compared with low VT, moderate VT, and control rats (p < 0.01). Paralleling the impairment in lung edema clearance we found a decrease in Na,K-ATPase activity in alveolar type II (ATII) cells isolated from rats ventilated with moderate VT and high VT for 40 min without changes in alpha1 Na,K-ATPase mRNA. We reason that VALI decreases lung ability to clear edema by inhibiting active sodium transport and Na,K-ATPase function in the alveolar epithelium.
Experience With Elemental Diet in the Treatment of Inflammatory Bowel Disease (1973)

Thirteen patients with inflammatory bowel disease were treated 17 times for an average of 22 days with elemental diet. The diet was well tolerated in all but one patient. All but one demonstrated weight gain and positive nitrogen balance, without apparent irritation of the inflamed gut. Nine patients were considered to have indications for surgery and seven underwent operation, approaching it in an improved nutritional state and withstanding it well. Elemental diet is able to provide nutrition while allowing bowel rest, without the risks of intravenous hyperalimentation. Occasionally indications for surgery resolve during the period of nutritional improvement. Whether this represents a primary therapeutic effect of elemental diet or the natural course of the disease remains to be examined by controlled studies.