gebhart/patrepeval huggingface dataset:
Computer Simulations of Alzheimers Amyloid &#946;-Protein Folding and Assembly (2006)

Pathological folding and aggregation of the amyloid β-protein (Aβ) are widely perceived as central to understanding Alzheimers disease (AD) at the molecular level. Experimental approaches to study Aβ self-assembly are limited, because most relevant aggregates are quasi-stable and inhomogeneous. In contrast, simulations can provide significant insights into the problem, including specific sites in the molecule that would be attractive for drug targeting and details of the assembly pathways leading to the production of toxic assemblies. Here we review computer simulation approaches to understanding the structural biology of Aβ. We discuss the ways in which these simulations help guide experimental work, and in turn, how experimental results guide the development of theoretical and simulation approaches that may be of general utility in understanding pathologic protein folding and assembly.
CTC-mRNA (AR-V7) Analysis from Blood Samples—Impact of Blood Collection Tube and Storage Time (2017)

Circulating tumour cells (CTCs) are an emerging resource for monitoring cancer biomarkers. New technologies for CTC isolation and biomarker detection are increasingly sensitive, however, the ideal blood storage conditions to preserve CTC-specific mRNA biomarkers remains undetermined. Here we tested the preservation of tumour cells and CTC-mRNA over time in common anticoagulant ethylene-diamine-tetra-acetic acid (EDTA) and acid citrate dextrose solution B (Citrate) blood tubes compared to preservative-containing blood tubes. Blood samples spiked with prostate cancer cells were processed after 0, 24, 30, and 48 h storage at room temperature. The tumour cell isolation efficiency and the mRNA levels of the prostate cancer biomarkers androgen receptor variant 7 (AR-V7) and total AR, as well as epithelial cell adhesion molecule (EpCAM) were measured. Spiked cells were recovered across all storage tube types and times. Surprisingly, tumour mRNA biomarkers were readily detectable after 48 h storage in EDTA and Citrate tubes, but not in preservative-containing tubes. Notably, AR-V7 expression was detected in prostate cancer patient blood samples after 48 h storage in EDTA tubes at room temperature. This important finding presents opportunities for measuring AR-V7 expression from clinical trial patient samples processed within 48 h-a much more feasible timeframe compared to previous recommendations.
Endostatin-induced tyrosine kinase signaling through the Shb adaptor protein regulates endothelial cell apoptosis (2000)

Endostatin, which corresponds to the C-terminal fragment of collagen XVIII, is a potent inhibitor of angiogenesis. Fibroblast growth factor-2 (FGF-2)-induced angiogenesis in the chicken chorioallantoic membrane was inhibited by endostatin, but not by an endostatin mutant R158/270A, lacking heparin-binding ability. Endostatin was internalized by endothelial cells, but not by mouse fibroblasts. Treatment of murine brain endothelial (IBE) cells with endostatin reduced the proportion of cells in S phase, whereas growth-arrested IBE cells in collagen gels treated with endostatin displayed enhanced tubular morphogenesis. IBE cells overexpressing Shb, an adaptor protein implicated in angiostatin-induced apoptosis, displayed elevated apoptosis and decreased tubular morphogenesis in collagen gels in response to endostatin when added together with FGF-2. Induction of apoptosis was dependent on the heparin-binding ability of endostatin and the expression of Shb with a functional Src homology 2 (SH2)-domain. Endostatin treatment for 10 minutes or 24 hours induced tyrosine phosphorylation of Shb and formation of multiprotein complexes. An Shb SH2 domain fusion protein precipitated a 125-kd phosphotyrosyl protein in endostatin-treated cells. The 125-kd component either contained intrinsic tyrosine kinase activity or occurred in complex with a tyrosine kinase. In conclusion, our data show that endostatin induces tyrosine kinase activity and enhanced apoptosis in FGF-treated endothelial cells.
Saliva and Dental Pellicle-A Review (2000)

The acquired enamel pellicle is an organic film covering the surfaces of teeth. When this film was first discovered, it was thought to be of embryologic origin. Only in the middle of this century did it become clear that it was acquired after tooth eruption. Initially, the small amounts of material that could be obtained have virtually limited the investigation of pellicle proteins to amino acid analysis. Nevertheless, this technique revealed that the pellicle is mainly proteinaceous and is formed by selective adsorption of salivary proteins on tooth enamel. Later, immunologic techniques allowed for the identification of many salivary and fewer non-salivary proteins as constituents of pellicle. However, to this date, isolation and direct biochemical characterization of in vivo pellicle protein have not been possible, because only a few micrograms can be obtained from a single donor. Therefore, the composition and structure of the acquired enamel pellicle are still essentially unknown. Information on the functions of pellicle has been obtained mainly from in vitro experiments carried out with saliva-coated hydroxyapatite and enamel discs. It was found that pellicle protects enamel by reducing demineralization upon acid challenge. Improved pellicle harvesting procedures and analysis by state-of-the-art proteomics with mass spectroscopy approaches promise to make major inroads into the characterization of enamel pellicle.
Induction of Self-Rolerance in T Cells But Not B Cells of Transgenic Mice Expressing Little Self Antigen (1991)

Self-tolerance to a transgene-encoded protein, hen egg lysozyme, was examined in the T and B cell repertoires of a series of lines of transgenic mice that expressed different serum concentrations of soluble lysozyme. T cells were tolerant in all lines in which lysozyme was expressed irrespective of the antigen concentration, whereas B cell tolerance did not occur when the serum lysozyme concentration was less than 1.5 nanograms per milliliter (0.1 nM). Induction of elevated transgene expression could restore B cell tolerance. These findings support the hypothesis that autoimmune disease may in some instances arise through a bypass of T cell tolerance.
Selective agonist of group II glutamate metabotropic receptors, LY354740, inhibits tolerance to analgesic effects of morphine in mice (2000)

1. Antagonists of glutamate N-methyl-D-aspartate (NMDA) subtype receptor inhibit the development of tolerance to the antinociceptive effects of opioids. Another way to inhibit the function of glutamate receptors is the stimulation of presynaptic metabotropic group II (mGluRII) receptors. Because LY354740 ((+)-2-aminobicyclo [3,1,0] hexane-2,6-dicarboxylic acid) is the first systemically active agonist of group II mGlu receptors, we investigated if this compound might inhibit the development of tolerance to antinociceptive effects of morphine and fentanyl. 2. As assessed by cumulative dose-response approach in the tail-flick test, administration of 10 mg kg(-1) morphine bid s.c. to male Albino Swiss mice for 6 days, right-shifted morphine dose-response curve by approximately 4 fold. In a separate group of mice, 12 injections of 0.04 mg kg(-1) of fentanyl over 3 days, right-shifted fentanyl dose-response curve by approximately 3.3 fold. 3. In experiment 1, LY354740 (1 and 10, but not 0.1 mg kg(-1)) as well as the reference compound, an uncompetitive NMDA receptor antagonist memantine (7.5 mg kg(-1)) inhibited the development of morphine tolerance. Neither LY354740 (10 mg kg(-1)) nor memantine (7.5 mg kg(-1)) affected the development of tolerance to fentanyl. In experiment 2, neither LY354740 (1 and 10 mg kg(-1)) nor memantine (7.5 mg kg(-1)) affected the tail-flick antinociceptive response, or the acute antinociceptive effect of morphine. 4. The present results are the first to suggest that the development of antinociceptive morphine tolerance may be inhibited by metabotropic group II glutamate agonist.
Transforming growth factor β1 mediates cell-cycle arrest of primitive hematopoietic cells independent of p21Cip1/Waf1or p27Kip1 (2001)

The regulation of stem cell proliferation is a poorly understood process balancing rapid, massive blood cell production in times of stress with maintenance of a multipotent stem cell pool over decades of life. Transforming growth factor beta 1 (TGF-beta 1) has pleiotropic effects on hematopoietic cells, including the inhibition of primitive cell proliferation. It was recently demonstrated that the cyclin-dependent kinase inhibitors, p21(Cip1/Waf1) (p21) and p27(Kip1) (p27), can inhibit the proliferation of hematopoietic stem cells and progenitor cells, respectively. The relation of TGF-beta 1 stimulation to p21 and p27 was examined using a fine-mapping approach to gene expression in individual cells. Abundant TGF-beta 1 expression and p21 expression were documented in quiescent, cytokine-resistant hematopoietic stem cells and in terminally differentiated mature blood cells, but not in proliferating progenitor cell populations. TGF-beta 1 receptor (T beta R II) was expressed ubiquitously without apparent modulation. Cell- cycle-synchronized 32D cells exposed to TGF-beta 1 demonstrated a marked antiproliferative effect of TGF-beta 1, yet neither the level of p21 mRNA nor the protein level of either p21 or p27 was altered. To corroborate these observations in primary cells, bone marrow mononuclear cells derived from mice engineered to be deficient in p21 or p27 were assessed. Progenitor and primitive cell function was inhibited by TGF-beta 1 equivalently in -/- and +/+ littermate controls. These data indicate that TGF-beta 1 exerts its inhibition on cell cycling independent of p21 and p27 in hematopoietic cells. TGF-beta 1 and p21 or p27 participate in independent pathways of stem cell regulation, suggesting that targeting each may provide complementary strategies for enhancing stem or progenitor cell expansion and gene transduction.
Peer Reviewed: Plastic Advances Microfluidic Devices (2002)

ADVERTISEMENT RETURN TO ISSUEPREVFeaturesNEXTPeer Reviewed: Plastic Advances Microfluidic DevicesThe devices debuted in silicon and glass, but plastic fabrication may make them hugely successful in biotechnology applicationsTravis D. Boone, Z. Hugh Fan, Herbert H. Hooper, Antonio J. Ricco, Hongdong Tan, and Stephen J. WilliamsCite this: Anal. Chem. 2002, 74, 3, 78 A–86 APublication Date (Web):February 1, 2002Publication History Published online1 February 2002Published inissue 1 February 2002https://pubs.acs.org/doi/10.1021/ac021943chttps://doi.org/10.1021/ac021943cnewsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2614Altmetric-Citations121LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (78 MB) Get e-Alertsclose SUBJECTS:Microfluidic devices,Plastics Get e-Alerts
Midgut bacteria required for Bacillus thuringiensis insecticidal activity (2006)

Bacillus thuringiensis is the most widely applied biological insecticide and is used to manage insects that affect forestry and agriculture and transmit human and animal pathogens. This ubiquitous spore-forming bacterium kills insect larvae largely through the action of insecticidal crystal proteins and is commonly deployed as a direct bacterial spray. Moreover, plants engineered with the cry genes encoding the B. thuringiensis crystal proteins are the most widely cultivated transgenic crops. For decades, the mechanism of insect killing has been assumed to be toxin-mediated lysis of the gut epithelial cells, which leads to starvation, or B. thuringiensis septicemia. Here, we report that B. thuringiensis does not kill larvae of the gypsy moth in the absence of indigenous midgut bacteria. Elimination of the gut microbial community by oral administration of antibiotics abolished B. thuringiensis insecticidal activity, and reestablishment of an Enterobacter sp. that normally resides in the midgut microbial community restored B. thuringiensis-mediated killing. Escherichia coli engineered to produce the B. thuringiensis insecticidal toxin killed gypsy moth larvae irrespective of the presence of other bacteria in the midgut. However, when the engineered E. coli was heat-killed and then fed to the larvae, the larvae did not die in the absence of the indigenous midgut bacteria. E. coli and the Enterobacter sp. achieved high populations in hemolymph, in contrast to B. thuringiensis, which appeared to die in hemolymph. Our results demonstrate that B. thuringiensis-induced mortality depends on enteric bacteria.
Acute Coronary Syndrome Caused by Coronary Artery Mycotic Aneurysm Due to Late Stent Infection Localized With Radiolabeled Autologous Leukocyte Imaging (2009)

Mycotic coronary artery aneurysm presenting as acute coronary syndrome is an uncommon but fatal condition. The diagnosis of mycotic aneurysm can be very challenging and difficult. Therefore, a high index of suspicion along with the use of multimodality imaging may help to diagnose this condition in patients with a prior history of coronary artery bypass grafting or percutaneous coronary intervention with persistent bacteremia with no identifiable source of infection. This case highlights a possibility of late stent infection and its association to drug eluting stents.
“Cures Pal·liatives: un dret, una necessitat”: avaluació d’un projecte col·laboratiu de difusió i divulgació de les cures pal·liatives a les Illes Balears (2020)

catalaEs presenta el projecte col·laboratiu de difusio i divulgacio de les Cures Pal·liatives dirigit a la ciutadania amb el titol: “Cures Pal·liatives: un dret, una necessitat” que des del Centre Coordinador del programa de Cures Pal·liatives de les Illes Balears (CCPCPIB), conjuntament amb la Societat Balear de Cures Pal·liatives (IllesPal), l’Associacio Espanyola Contra el Cancer (AECC), l’associacio de voluntaris de cures pal·liatives de les Illes Balears (DIME) i l’associacio Angeles sin Alas, van posar en marxa. L’objectiu de l’esmentat projecte es donar a coneixer l’atencio pal·liativa com un dret i una necessitat que te tota persona que es troba en un proces de final de vida. S’ha estructurat mitjancant sessions a diferents pobles de les illes, dirigits a la ciutadania, amb la participacio de representants de les entitats citades. Es presenten els resultats d’aquest programa, amb la conclusio que la satisfaccio percebuda dels assistents ha estat molt bona. EnglishA collaborative project to divulge palliative care to the citizen with the title: “Palliative Care: a right, a necessity” was implemented by the Palliative Care Program Coordinating Center of the Balearic Islands, jointly with the Balearic Society of Palliative Care, the Spanish Association Against Cancer, the association of volunteers of palliative care of the Balearic Islands (DIME) and the association Angeles sin Alas. The aim of this project is to make people to be aware of palliative care as right and necessity that all people have at the end of life. They organized meetings in different Balearic villages, directed at the citizenry, with the participation of representatives of the quoted entities. The results of this program are presented, with the conclusion that the attendee satisfaction has been very hight.
Tuning the focus of a plasmonic lens by the incident angle (2006)

We report the experimental realization of tuning the focus position of a plasmonic lens by adjusting the angle of the incident light similar to conventional lenses. A circular slit in silver film acts as both a surface plasmon polariton coupler and a plasmonic focusing lens. At small incident angles, the plasmonic lens has a very good focus with the position depending only on the angle of the incident beam. Numerical simulations of the focusing properties, including polarization dependence, agree well with experimental observations. This tunable plasmonic lens can be used in nanoscale photonics, biological sensing, and manipulation.
Autophagy protects LNCaP cells under androgen deprivation conditions (2008)

Androgen plays a critical role in the development and progression of prostate cancer. However, the regulatory role of androgen in the autophagic process and the function of the increased autophagosomes following androgen deprivation remain poorly understood. We found that autophagosomes, which were induced upon serum deprivation in LNCaP cells, can be significantly suppressed by dihydrotestosterone (DHT). Pharmacological inhibition of autophagy by 3-methyladenine led to increased apoptosis of LNCaP cells in serum-free medium compared to the medium with DHT or serum. Additionally, depletion of Beclin 1 to inhibit autophagy by small interfering RNA resulted in a slower proliferation of LNCaP cells in the medium depleted of serum than in the medium with DHT. Altogether, these findings suggested that LNCaP cells can resort to the autophagic pathway to survive under androgen deprivation conditions, which can be a novel mechanism involved in the transition of prostate cancer cells from an androgen-dependent to an androgen-independent cell type.
Oxidized LDL Binds to CD36 on Human Monocyte-Derived Macrophages and Transfected Cell Lines (1995)

Accumulating evidence strongly implicates oxidized LDL (Ox-LDL) in the pathogenesis of atherosclerosis. Several receptors have been identified that bind and internalize Ox-LDL, but their relative importance in vivo is unclear. CD36 is an 88-kD transmembrane glycoprotein expressed on monocytes/macrophages, platelets, and microvascular endothelium that has been implicated as a putative receptor for Ox-LDL. We demonstrate that an anti-CD36 monoclonal antibody inhibited 50% of the specific binding and 26% of the specific degradation of Ox-LDL by human monocyte-derived macrophages. To characterize more completely this binding we evaluated interactions between CD36 and Ox-LDL in murine NIH-3T3 cells stably transfected with human CD36 cDNA. Ox-LDL bound to CD36-transfected 3T3 cells in a saturable manner. Specific binding, internalization, and degradation of Ox-LDL were increased fourfold in CD36-transfected cell lines compared with 3T3 cells transfected with vector alone. Binding of Ox-LDL to CD36-transfected 3T3 cells was inhibited by a panel of anti-CD36 antibodies and by soluble CD36 but not by thrombospondin. Specificity of binding was demonstrated by the equivalent binding of LDL and acetylated LDL to control and CD36-transfected 3T3 cells. The epitope or epitopes on Ox-LDL recognized by CD36 are undefined. Two observations suggest that CD36 recognizes a lipid moiety or that the lipid portion of the lipoprotein is essential for apoprotein recognition. The first is that the increased binding of Ox-LDL to CD36-transfected 3T3 cells is abrogated by delipidation of the lipoprotein, and the second is that oleic acid competes for the binding of Ox-LDL to CD36-transfected 3T3 cells.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficient backsplicing produces translatable circular mRNAs (2014)

While the human transcriptome contains a large number of circular RNAs (circRNAs), the functions of most circRNAs remain unclear. Sequence annotation suggests that most circRNAs are generated from splicing in reversed orders across exons. However, the mechanisms of this backsplicing are largely unknown. Here we constructed a single exon minigene containing split GFP, and found that the pre-mRNA indeed produces circRNA through efficient backsplicing in human and Drosophila cells. The backsplicing is enhanced by complementary introns that form double-stranded RNA structure to bring splice sites in proximity, but such structure is not required. Moreover, backsplicing is regulated by general splicing factors and cis-elements, but with regulatory rules distinct from canonical splicing. The resulting circRNA can be translated to generate functional proteins. Unlike linear mRNA, poly-adenosine or poly-thymidine in 3' UTR can inhibit circular mRNA translation. This study revealed that backsplicing can occur efficiently in diverse eukaryotes to generate circular mRNAs.
Influence of Maternal Antibody on Efficacy of Embryo Vaccination with Cell-Associated and Cell-Free Marek's Disease Vaccine (1982)

Vaccination with turkey herpesvirus (HVT) of 18-day-old chicken embryos from a commercial source or from a cross (15 X 7) of two inbred lines induced better protection against early post-hatch challenge with virulent Marek's disease virus (MDV) than vaccination at hatch, despite the presence in embryos of maternally derived antibodies to HVT or to HVT and MDV. However, 50%-protective-dose (PD50) assays revealed that maternal antibodies in embryos reduced vaccine efficacy. The PD50 assays were conducted by vaccinating 15 X 7 embryos with serial dilutions of HVT at the 18th day of incubation. Embryonally vaccinated and unvaccinated chicks were challenged with MDV on the day of hatch. In the absence of maternal antibodies, the PD50 values in plaque-forming units for cell-associated and cell-free HVT were 57 and 328, respectively. In the presence of maternal antibodies, PD50 values for cell-associated and cell-free HVT were 105 and greater than 4,000, respectively.