gebhart/patrepeval huggingface dataset:
Neurotrophin and neurotrophin receptors in vascular smooth muscle cells. Regulation of expression in response to injury. (1995)

The neurotrophins, a family of related polypeptide growth factors including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-3 and NT-4/5 promote the survival and differentiation of distinctive sets of embryonic neurons. Here we define a new functional role for neurotrophins, as autocrine or local paracrine mediators of vascular smooth muscle cell migration. We have identified neurotrophins, and their cognate receptors, the trk tyrosine kinases, in human and rat vascular smooth muscle cells in vivo. In vitro, cultured human smooth muscle cells express BDNF; NT-3; and trk A, B, and C. Similarly, rat smooth muscle cells expressed all three trk receptors as well as all four neurotrophins. Moreover, NGF induces cultured human smooth muscle cell migration at subnanomolar concentrations. In the rat aortic balloon deendothelialization model of vascular injury, the expression of NGF, BNDF, and their receptors trk A and trk B increased dramatically in the area of injury within 3 days and persisted during the formation of the neointima. In human coronary atherosclerotic lesions, BDNF, NT-3, and NT-4/5, and the trk B and trk C receptors could be demonstrated in smooth muscle cells. These findings suggest that neurotrophins play an important role in regulating the response of vascular smooth muscle cells to injury.
Mismatch Amplification Mutation Assay-Based Real-Time PCR for Rapid Detection of Neisseria gonorrhoeae and Antimicrobial Resistance Determinants in Clinical Specimens (2018)

Molecular methods are often used for <i>Neisseria gonorrhoeae</i> detection, but complete definition of antimicrobial resistance (AMR) patterns still requires phenotypic tests. We developed an assay that both identifies <i>N. gonorrhoeae</i> and detects AMR determinants in clinical specimens. We designed a mismatch amplification mutation assay (MAMA)-based SYBR green real-time PCR targeting one <i>N. gonorrhoeae</i>-specific region (<i>opa</i>); mosaic <i>penA</i> alleles (Asp345 deletion [Asp345del], Gly545Ser) associated with decreased susceptibility to cephalosporins; and alterations conferring resistance to ciprofloxacin (GyrA Ser91Phe), azithromycin (23S rRNA A2059G and C2611T), and spectinomycin (16S rRNA C1192T). We applied the real-time PCR to 489 clinical specimens, of which 94 had paired culture isolates, and evaluated its performance by comparison with the performance of commercial diagnostic molecular and phenotypic tests. Our assay exhibited a sensitivity/specificity of 93%/100%, 96%/85%, 90%/91%, 100%/100%, and 100%/90% for the detection of <i>N. gonorrhoeae</i> directly from urethral, rectal, pharyngeal, cervical, and vaginal samples, respectively. The MAMA strategy allowed the detection of AMR mutations by comparing cycle threshold values with the results of the reference <i>opa</i> reaction. The method accurately predicted the phenotype of resistance to four antibiotic classes, as determined by comparison with the MIC values obtained from 94 paired cultures (sensitivity/specificity for cephalosporins, azithromycin, ciprofloxacin, and spectinomycin resistance, 100%/95%, 100%/100%, 100%/100%, and not applicable [NA]/100%, respectively, in genital specimens and NA/72%, NA/98%, 100%/97%, and NA/96%, respectively, in extragenital specimens). False-positive results, particularly for the <i>penA</i> Asp345del reaction, were observed predominantly in pharyngeal specimens. Our real-time PCR assay is a promising rapid method to identify <i>N. gonorrhoeae</i> and predict AMR directly in genital specimens, but further optimization for extragenital specimens is needed.
In vivo administration of lentiviral vectors triggers a type I interferon response that restricts hepatocyte gene transfer and promotes vector clearance (2006)

Liver gene transfer is a highly sought goal for the treatment of inherited and infectious diseases. Lentiviral vectors (LVs) have many desirable properties for hepatocyte-directed gene delivery, including the ability to integrate into nondividing cells. Unfortunately, upon systemic administration, LV transduces hepatocytes relatively inefficiently compared with nonparenchymal cells, and the duration of transgene expression is often limited by immune responses. Here, we investigated the role of innate antiviral responses in these events. We show that administration of LVs to mice triggers a rapid and transient IFNalphabeta response. This effect was dependent on functional vector particles, and in vitro challenge of antigen-presenting cells suggested that plasmacytoid dendritic cells initiated the response. Remarkably, when LVs were administered to animals that lack the capacity to respond to IFNalphabeta, there was a dramatic increase in hepatocyte transduction, and stable transgene expression was achieved. These findings indicate that, even in the setting of acute delivery of replication-defective vectors, IFNs effectively interfere with transduction in a cell-type-specific manner. Moreover, because disabling a single component of the innate/immune network was sufficient to establish persistent xenoantigen expression, our results raise the hope that the immunologic barriers to gene therapy are less insurmountable than expected.
Study of Excimer Laser Electrochemical Etching Silicon (2007)

To further understand the behavior of laser-induced electrochemical etching process, the experiments of micromachining silicon by laser-induced electrochemical etching were carried out. 248nm excimer laser as light source is adopted in this work with the power of 109W/cm2 for the first time and KOH solution is used as electrolyte. Based on the experiment results, the surface images and etching rate are analyzed in detail. It is verified that the compound technique is a combination of laser etching, electrochemical etching and coupling etching, and laser etching is dominating in the compound process. Besides, both liquid-enhanced pressure and jet shock pressure can preferably improve the etching rate. At the same time, the anisotropic etching stop of silicon in alkaline solution is solved in this study. As a result, this process can be applied to transfer pattern without mask, and it possesses the ability of machining large aspect ratio microstructures.
Mouse whey acidic protein is a novel member of the family of ‘four-disulfide core’ proteins (1982)

Unlike in other mammalian species, the major whey protein in mouse is not alpha-lactalbumin, but a cysteine rich, acidic protein with a molecular weight of 14.0 kDa. We have deduced the amino acid sequence of this mouse acidic of whey protein from the nucleotide sequence of cloned cDNA. The positions of the half cysteines suggest that mouse whey acidic protein (WAP) is a two domain protein, very similar in structure to the plant lectin wheat germ agglutinin and the hypothalamic carrier protein neurophysin.
Beam tracing polygonal objects (1984)

Ray tracing has produced some of the most realistic computer generated pictures to date. They contain surface texturing, local shading, shadows, reflections and refractions. The major disadvantage of ray tracing results from its point-sampling approach. Because calculation proceeds ab initio at each pixel it is very CPU intensive and may contain noticeable aliasing artifacts. It is difficult to take advantage of spatial coherence because the shapes of reflections and refractions from curved surfaces are so complex.
Zhou et al 2019 - Normal 2 Cell Population Migration Dataset (2019)

Videos to accompany Zhou et al 2019. Please see publication for details: Motion Sensing Superpixels (MOSES) is a systematic, computational framework to quantify and discover cellular motion phenotypes Felix Y. Zhou, Carlos Ruiz-Puig, Richard P. Owen, Michael J. White, Jens Rittscher, Xin Lu eLife 2019
The Prevalence of Refractive Errors Among Adults in the United States,Western Europe, and Australia (2004)

Refractive errors affect approximately one third of persons 40 years or older in the United States and Western Europe, and one fifth of Australians in this age group.
High mobility group proteins 1 and 2 stimulate transcription in vitro by RNA polymerases II and III. (1986)

We have used specific in vitro transcription as a functional assay to study the effects of the major chromosomal proteins, histones and high mobility group (HMG) proteins 1 and 2, on transcription by RNA polymerases II and III. HMG proteins 1 and 2 can stimulate transcription by both RNA polymerases II and III; maximal stimulation (up to 20-fold) is seen when HMG proteins 1 and 2 are mixed with template DNA prior to the addition of whole cell transcription lysate. HMG proteins 1 and 2 are also able to overcome inhibition of transcription caused by histones; maximal enhancement of transcription (at least 60-fold) is seen when histones and then HMG proteins 1 and 2 are added to DNA before addition of transcription lysate. This suggests that stimulation of transcription by HMG proteins 1 and 2 in the presence of histones is not due to a simple competition between histones and HMG proteins for binding to DNA. It appears likely that HMG proteins 1 and 2 stimulate transcription in a nonspecific manner, perhaps altering the template in such a way as to allow increased accessibility of transcription factors or rate of elongation for both RNA polymerases II and III.
Differential Expression of PCSK9 Modulates Infection, Inflammation, and Coagulation in a Murine Model of Sepsis (2016)

These findings demonstrate that PCSK9 deficiency confers protection against systemic bacterial dissemination, organ pathology, and tissue inflammation, particularly in the lungs and liver, while PCSK9 overexpression exacerbates multi-organ pathology as well as the hypercoagulable and pro-inflammatory states in early sepsis.
Tumor-Derived Microvesicles and the Cancer Microenvironment (2012)

Tumor cells release microvesicles (MVs) that may remain in the extracellular space in proximity to the cell of origin, or that may migrate to distant sites by entering biological fluids. Increasing evidence indicates that MVs are mediators of cell-to-cell communication which are able to deliver specific signals, both within the tumor microenvironment and in the long-range. MVs are able to transfer bioactive lipids and proteins, including oncogene products and receptors, from the cell of origin to recipient cell. In addition, MVs may induce epigenetic changes in recipient cells by transferring genetic information in the form of mRNA, microRNA and oncogenes. Several changes in the phenotype and function that occur in stromal cells within the cancer microenvironment have been ascribed to tumor cell-derived MVs. In this review we discuss the various biological actions of tumor-derived MVs and their potential role in tumor biology.
Insulin expression and C-peptide in type 1 diabetes subjects implanted with stem cell-derived pancreatic endoderm cells in an encapsulation device (2021)

These preliminary data from an ongoing first-in-human phase 1/2, open-label study provide proof-of-concept that pluripotent stem cell-derived pancreatic endoderm cells (PEC-01) engrafted in type 1 diabetes patients become islet cells releasing insulin in a physiologically regulated fashion. In this study of 17 subjects aged 22-57 with type 1 diabetes, PEC-01 cells were implanted subcutaneously in VC-02 macroencapsulation devices, allowing for direct vascularization of the cells. Engraftment and insulin expression were observed in 63% of VC-02 units explanted from subjects at 3-12 months post-implant. Six of 17 subjects (35.3%) demonstrated positive C-peptide as early as 6 months post-implant. Most reported adverse events were related to surgical implant or explant procedures (27.9%) or to side-effects of immunosuppression (33.7%). Initial data suggest that pluripotent stem cells, which can be propagated to the desired biomass and differentiated into pancreatic islet-like tissue, may offer a scalable, renewable alternative to pancreatic islet transplants.
PIK3CA Mutations and Copy Number Gains in Human Lung Cancers (2008)

We investigated the frequency and function of mutations and increased copy number of the PIK3CA gene in lung cancers. PIK3CA mutations are one of the most common gene changes present in human cancers. We analyzed the mutational status of exons 9 and 20 and gene copy number of PIK3CA using 86 non-small cell lung cancer (NSCLC) cell lines, 43 small cell lung cancer (SCLC) cell lines, 3 extrapulmonary small cell cancer (ExPuSC) cell lines, and 691 resected NSCLC tumors and studied the relationship between PIK3CA alterations and mutational status of epidermal growth factor receptor (EGFR) signaling pathway genes (EGFR, KRAS, HER2, and BRAF). We also determined PIK3CA expression and activity and correlated the findings with effects on cell growth. We identified mutations in 4.7% of NSCLC cell lines and 1.6% of tumors of all major histologic types. Mutations in cell lines of small cell origin were limited to two ExPuSC cell lines. PIK3CA copy number gains were more frequent in squamous cell carcinoma (33.1%) than in adenocarcinoma (6.2%) or SCLC lines (4.7%). Mutational status of PIK3CA was not mutually exclusive to EGFR or KRAS. PIK3CA alterations were associated with increased phosphatidylinositol 3-kinase activity and phosphorylated Akt expression. RNA interference-mediated knockdown of PIK3CA inhibited colony formation of cell lines with PIK3CA mutations or gains but was not effective in PIK3CA wild-type cells. PIK3CA mutations or gains are present in a subset of lung cancers and are of functional importance.
Aminolevulinic Acid (ALA) as a Prodrug in Photodynamic Therapy of Cancer (2011)

Aminolevulinic acid (ALA) is an endogenous metabolite normally formed in the mitochondria from succinyl-CoA and glycine. Conjugation of eight ALA molecules yields protoporphyrin IX (PpIX) and finally leads to formation of heme. Conversion of PpIX to its downstream substrates requires the activity of a rate-limiting enzyme ferrochelatase. When ALA is administered externally the abundantly produced PpIX cannot be quickly converted to its final product - heme by ferrochelatase and therefore accumulates within cells. Since PpIX is a potent photosensitizer this metabolic pathway can be exploited in photodynamic therapy (PDT). This is an already approved therapeutic strategy making ALA one of the most successful prodrugs used in cancer treatment.
The extended hinge region of IgG3 is not required for high phagocytic capacity mediated by Fcγ receptors, but the heavy chains must be disulfide bonded (1993)

Fc gamma receptor (Fc gamma R) phagocytosis and respiratory burst were induced by chimeric mouse-human anti-(4-hydroxy-5-iodo-3-nitrophenyl) acetyl IgG3 antibodies with mutations in hinge and/or in CH1 region. IgG3 mutants with different hinge length ranging from 47 to 0 amino acids, an IgG3 molecule with an artificial hinge of just one cysteine residue (HM-1), and two hybrid IgG3 molecules with IgG4 hinge or IgG4 CH1-hinge were tested. Using the monocytic cell line U937 as effector cells, the mutated IgG3 molecules were very similar, revealing high activity, while the IgG3/IgG4 hybrids revealed a slightly reduced activity. However, the hingeless (0-h) mutant was negative, except after interferon-gamma stimulation when it became slightly positive. Interestingly, HM-1 was as active as the IgG3 mutants. With polymorphonuclear leucocytes (PMN) as effector cells we obtained some day-to-day variations, but all the IgG3 mutants were highly active, with the two shortest hinge mutants somewhat less active. The IgG3/IgG4 hybrid molecules revealed an intermediate activity, while IgG4 wild-type and the 0-h mutant were negative. However, the HM-1 molecule revealed an activity similar to that of the IgG3 mutants. The phagocytic activity of U937 was inhibited by monomeric IgG, indicating the importance of Fc gamma RI. In contrast, with PMN both blockage of Fc gamma RII and cleavage of Fc gamma RIII were required to significantly reduce the phagocytosis and respiratory burst, thus showing that both receptors contribute to the effect. These results demonstrate that the extended IgG3 hinge region is not necessary for a high phagocytic activity and that the major structural importance of the hinge is to connect the two heavy chains in this region.
Recruitment of Single-Stranded Recombinant Adeno-Associated Virus Vector Genomes and Intermolecular Recombination Are Responsible for Stable Transduction of Liver In Vivo (2000)

Recombinant adeno-associated virus (rAAV) vectors stably transduce hepatocytes in experimental animals. Following portal-vein administration of rAAV vectors in vivo, single-stranded (ss) rAAV genomes become double stranded (ds), circularized, and/or concatemerized concomitant with a slow rise and, eventually, steady-state levels of transgene expression. Over time, at least some of the stabilized genomes become integrated into mouse chromosomal DNA. The mechanism(s) of formation of stable ds rAAV genomes from input ss DNA molecules has not been delineated, although second-strand synthesis and genome amplification by a rolling-circle model has been proposed. To begin to delineate a mechanism, we produced rAAV vectors in the presence of bacterial PaeR7 or Dam methyltransferase or constructed rAAV vectors labeled with different restriction enzyme recognition sites and introduced them into mouse hepatocytes in vivo. A series of molecular analyses demonstrated that second-strand synthesis and rolling-circle replication did not appear to be the major processes involved in the formation of stable ds rAAV genomes. Rather, recruitment of complementary plus and minus ss genomes and subsequent random head-to-head, head-to-tail, and tail-to-tail intermolecular joining were primarily responsible for the formation of ds vector genomes. These findings contrast with the previously described mechanism(s) of transduction based on in vitro studies. Understanding the mechanistic process responsible for vector transduction may allow the development of new strategies for improving rAAV-mediated gene transfer in vivo.
An open-label, phase II study of tipifarnib for the treatment of HRAS mutant solid tumors, including squamous cell carcinomas of the head and neck. (2017)

TPS2618 Background: Tipifarnib is a potent and highly selective inhibitor of farnesyltransferase (FT). FT catalyzes the post-translational attachment of farnesyl groups to signaling proteins that are requisite for localization to the inner cell membrane. While all RAS isoforms (KRAS/NRAS/HRAS) are FT substrates, only HRAS is exclusively dependent upon farnesylation for membrane localization and signaling activation, making HRAS mutant tumors uniquely susceptible to tipifarnib mediated inhibition of FT. Tipifarnib has demonstrated robust activity in HRAS mutant head and neck squamous cell carcinoma (HNSCC) and HRAS mutant squamous non-small cell lung cancer (NSCLC) patient derived xenograft (PDX) models resistant to standard therapies. Methods: This is a multi-institutional, open-label Phase II trial evaluating the efficacy and safety of tipifarnib for pts with HRAS mutant solid tumors. Pts must have either unresectable, locally advanced or metastatic non-hematological malignancies that harbor a missense HRAS mutation. The primary endpoint of the study is overall response rate. Secondary endpoints include safety and tolerability, PFS, duration of response. Two cohorts (N = 18 each) are enrolling, each being evaluated with a Simon two-stage design. Cohort 1 is for patients with malignant thyroid tumors of any histology. Cohort 2 was originally designated for pts with any other solid tumor. The prespecified activity goal for the first stage of accrual in Cohort 2 was met. Based on data observed in the first stage of this group, enrollment to the second stage of Cohort 2 has been limited to HRAS mutant HNSCC since August 2016. Enrolled patients are treated with tipifarnib 900 mg administered orally twice daily on days 1-7 and 15-21 of 28-day treatment cycles until progression of disease or unacceptable toxicity. Clinical trial information: NCT02383927.
Rotational dynamics of the Fc.epsilon. receptor on mast cells monitored by specific monoclonal antibodies and IgE (1991)

The rotational motions of the type I receptor for the Fc epsilon domains (Fc epsilon RI) present on mast cells were investigated by measuring the phosphorescence emission and anisotropy decay kinetics of erythrosin (Er) covalently bound to several Fc epsilon RI-specific macromolecular ligands. The latter consisted of three murine monoclonal antibodies (IgG class) raised against the Fc epsilon RI of rat mast cells (RBL-2H3 line), their Fab fragments, and a murine monoclonal IgE. Different anisotropy decay patterns were observed for the three monovalent Er-Fab fragments bound to the Fc epsilon RI, reflecting the rotational motion of the Fe epsilon RI reported by each specific macromolecular probe bound to its particular epitope. Internal motions of the tethered Er-labeled ligands may also contribute to the observed anisotropy decay, particularly in the case of cell-bound IgE. The results corroborate an earlier study with rat Er-IgE in which the Fc epsilon RI-IgE complex was shown to be mobile throughout the temperature range examined (5-37 degrees C). The anisotropy decays of the three Er-labeled, Fc epsilon RI-specific intact mAbs bound to cells also differed markedly. Whereas the decay curves of one mAb (H10) were characterized by temperature-dependent positive amplitudes and rather short rotational correlation times, the decay of a second mAb (J17) showed complex qualitative variations with temperature, and in the case of the third antibody (F4), there was no apparent decay of anisotropy over the time and temperature ranges examined.(ABSTRACT TRUNCATED AT 250 WORDS)
Peptide immobilisation on porous silicon surface for metal ions detection (2011)

In this work, a Glycyl-Histidyl-Glycyl-Histidine (GlyHisGlyHis) peptide is covalently anchored to the porous silicon PSi surface using a multi-step reaction scheme compatible with the mild conditions required for preserving the probe activity. In a first step, alkene precursors are grafted onto the hydrogenated PSi surface using the hydrosilylation route, allowing for the formation of a carboxyl-terminated monolayer which is activated by reaction with N-hydroxysuccinimide in the presence of a peptide-coupling carbodiimide N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide and subsequently reacted with the amino linker of the peptide to form a covalent amide bond. Infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy are used to investigate the different steps of functionalization.The property of peptides to form stable complexes with metal ions is exploited to achieve metal-ion recognition by the peptide-modified PSi-based biosensor. An electrochemical study of the GlyHisGlyHis-modified PSi electrode is achieved in the presence of copper ions. The recorded cyclic voltammograms show a quasi-irreversible process corresponding to the Cu(II)/Cu(I) couple. The kinetic factors (the heterogeneous rate constant and the transfer coefficient) and the stability constant of the complex formed on the porous silicon surface are determined. These results demonstrate the potential role of peptides grafted on porous silicon in developing strategies for simple and fast detection of metal ions in solution.