gebhart/patrepeval huggingface dataset:
An efficient cone beam filtered back-projection (CB-FBP) reconstruction algorithm for a circle-plus-two-arc orbit (2002)

The circle-plus-are orbit surpasses other 'circle-plus' orbits for the application of X-ray cone beam (CB) volume CT in image-guided interventional procedures requiring intraoperative imaging, in which movement of a patient table is to be avoided. A CB circle-plus-two-arc orbit satisfying the data sufficiency condition (DSC) and a filtered back projection (FBP) algorithm to reconstruct longitudinally unbounded objects is presented here. In the circle sub-orbit, the algorithm employs Feldkamp's formula and another FBP implementation. In the arc sub-orbits, an FBP solution is obtained originating from Grangeat's formula, and the reconstruction computation cost is significantly reduced using a window function to exclude the redundancy in the Radon domain. The performance of the algorithm has been evaluated through computer simulation using the Disc and Shepp phantoms, showing that the algorithm can regionally reconstruct longitudinally unbounded objects efficiently, and is stable with X-ray quantum noise.
[Treatment of facial spasm with botulin A toxin]. (1990)

The authors use injections of botulinum A toxin in treatment of facial spasms. 105 patients (70 patients with blepharospasm, 35 patients with hemispasm) were treated during 4 years. The toxin Wisconsin relieved spasms for an average of 10 weeks. Local complications such as ptosis and diplopia appeared in less than 1/5 of the cases. No general complications were observed. Repeated treatments are necessary. The authors noted a decrease of lacrimal secretion on the treated side in hemifacial spasm and concluded that botulinum A toxin injections could be used as a treatment of epiphora.
Modulation of gap junction mediated intercellular communication in TM3 Leydig cells (2003)

Long-term modulation of intercellular communication via gap junctions was investigated in TM3 Leydig cells, under low and high confluence states, and upon treatment of the cells for different times with activators of protein kinase A (PKA) and protein kinase C (PKC). Cells in low confluence were readily coupled, as determined by transfer of the dye Lucifer Yellow; on reaching confluence, the cells uncoupled. Western blots and RT-PCR revealed that connexin 43 (Cx43) was abundantly expressed in TM3 Leydig cells and its expression was decreased after the cells achieved confluence. Stimulation of PKA or PKC induced a decrease in cell-cell communication. Staurosporin, an inhibitor of protein kinases, increased coupling and was able to prevent and reverse the uncoupling actions of dibutyryl cAMP and 12-O-tetradecanoyl-phorbol-13-acetate (TPA). Under modulation by confluence, Cx43 was localized to the appositional membranes when cells were coupled and was mainly in the cytoplasm when they were uncoupled. In addition, cAMP and TPA reduced the surface membrane labeling for Cx43, whereas staurosporin increased it. These data show a strong correlation between functional coupling and the membrane distribution of Cx43, implying that this connexin has an important role in intercellular communication between TM3 cells. Furthermore, increased testosterone secretion in response to luteinizing hormone was accompanied by a decrease in intercellular communication, suggesting that gap junction mediated coupling may be a modulator of hormone secretion in TM3 cells.
Identification and characterization of the blood vessels of solid tumors that are leaky to circulating macromolecules. (1988)

The tumor microvasculature is hyperpermeable to plasma proteins, but the specific vessels that leak have not been identified. To investigate this question, the extravasation of circulating tracers of varying size was studied by fluorescence, light, and electron microscopy in animals bearing solid transplantable carcinomas. In all five tumors studied, 70 and 150 kD fluoresceinated (FITC)-dextrans and colloidal carbon leaked extensively from the prominent vascular plexus that was induced around individual tumor nodules and at the tumor-host interface. Leaky vessels were mature veins or venules, lined by a continuous endothelium; most had closed interendothelial cell junctions. Immature interface vessels and tumor-penetrating vessels did not leak these macromolecular tracers significantly. Three kD of FITC-dextran leaked from peripherally situated tumor veins or venules but also extravasated from tumor-penetrating vessels and capillaries supplying normal tissues. These data correlate the functional and anatomic heterogeneity of tumor vessels and provide a rationale for the distribution of circulating molecules such as monoclonal antibodies and tumoricidal drugs in solid tumors.
High-sensitivity DNA detection with a laser-excited confocal fluorescence gel scanner. (1991)

A high-sensitivity, laser-excited confocal fluorescence gel scanner has been developed and applied to the detection of fluorescently labeled DNA. An argon ion laser (1-10 mW at 488 nm) is focused in the gel with a high-numerical aperture microscope objective. The laser-excited fluorescence is gathered by the objective and focused on a confocal spatial filter, followed by a spectral filter and photodetector. The gel is placed on a computer-controlled scan stage, and the scanned image of the gel fluorescence is stored and analyzed in a computer. This scanner has been used to detect DNA separated on sequencing gels, agarose mapping gels and pulsed field gels. Sanger sequencing gels were run on M13mp18 DNA using a fluoresceinated primer. The 400-microns-thick gels, loaded with 30 fmol of DNA fragments in 3-mm lanes, were scanned at 78-microns resolution. The high resolution of our scanner coupled with image processing allows us to read up to approximately 300 bases in four adjacent sequencing lanes. The minimum band size that could be detected and read was approximately 200 microns. This instrument has a limiting detection sensitivity of approximately 10 amol of fluorescein-labeled DNA in a 1 x 3-mm band. In applications to agarose mapping gels, we have exploited the fact that DNA can be prestained with ethidium homodimer, followed by electrophoresis and fluorescence detection to achieve picogram sensitivity. We have also developed methods using both ethidium homodimer and thiazole orange staining which permit two-color detection of DNA in one lane.(ABSTRACT TRUNCATED AT 250 WORDS)
Gene targeting technology for creating transgenic models of lymphopoiesis. (1993)

Naturally occurring immunodeficient mouse strains express a variety of genetic defects in myeloid and/or lymphoid cell development. These strains have served as valuable animal models for studying immune cell differentiation and mechanisms of transplant rejection. Some of the most commonly used strains carry mutations at the nude, scid, beige, and/or xid loci. Gene targeting technology can now be used to directly modify endogenous alleles via homologous recombination with exogenous DNA. By performing DNA targeting in embryonic stem (ES) cells, germline transmission of these modifications can be obtained by breeding chimeras generated from cloned ES cells. This approach can be used to target the inactivation, modification, or replacement of specific genes and has been used to examine the role of several alleles in hematopoiesis. This review describes the use of this technology to generate mutations that influence the development and function of T and B lymphocytes.
Green Fluorescent Protein Is Lighting Up Fungal Biology (2001)

Prasher ([42][1]) cloned a cDNA for the green fluorescent protein (GFP) gene from the jellyfish Aequorea victoria in 1992. Shortly thereafter, to the amazement of many investigators, this gene or derivatives thereof were successfully expressed and conferred fluorescence to bacteria and
Thiol-capped gold: from planar to irregular surfaces (2008)

Thiol-capped metals, in particular gold, have a wide range of technological applications, especially for building systems by bottom-up methods.In most cases, stability of the organic film during exposure to ambient conditions and/or to electrolyte solutions is a crucial requirement.In this work we discuss the stability of butanethiol self-assembled monolayers (SAMs) on planar, nanocurved and irregular Au surfaces against both air exposure and electrodesorption in aqueous media.We have found a slower rate of air oxidation and increased stability against electrodesorption for butanethiol monolayers on highly irregular Au surfaces as compared to those on planar surfaces.The increased stability of SAMs on highly irregular surfaces is promising because desorption and degradation seriously limit their application in nanotechnology.
Efficient generation of narrow-bandwidth picosecond pulses by frequency doubling of femtosecond chirped pulses (1998)

We demonstrate efficient generation of picosecond narrow-bandwidth pulses by frequency mixing of broadband opposite chirped pulses in a type I doubling crystal. This procedure allows us to produce picosecond pulses that are perfectly synchronized with femtosecond pulses. The experiment shows a decrease of the initial bandwidth by a factor of more than 30, while a high conversion efficiency is maintained.
Liposome-mediated Transfection ofLactobacillus caseiSpheroplasts (1984)

Journal Article Liposome-mediated Transfection of Lactobacillus casei Spheroplasts Get access Mariko Shimizu-Kadota, Mariko Shimizu-Kadota Yakult Central Institute for Microbiological Research, Kunitachi, Tokyo 186, Japan Search for other works by this author on: Oxford Academic Google Scholar Satoshi Kudo Satoshi Kudo Yakult Central Institute for Microbiological Research, Kunitachi, Tokyo 186, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 48, Issue 4, 1 April 1984, Pages 1105–1107, https://doi.org/10.1080/00021369.1984.10866279 Published: 01 April 1984 Article history Received: 15 December 1983 Published: 01 April 1984
How nucleation affects the aggregation of nanoparticles (2007)

Using the conducting polymer, polyaniline, as a prime example, this article highlights the important role of nucleation on the aggregation of nanoparticles. We demonstrate that during synthesis, irreversible aggregation of nanoparticles can be triggered by heterogeneous nucleation on pre-formed particles. Aggregation can be prevented by mediating the nucleation behavior via experimental conditions including mechanical agitation, reaction temperature and the use of additives. These findings may provide a valuable guide in the synthesis of many other nanostructures.
Selective activation of mechanosensitive ion channels using magnetic particles (2007)

This study reports the preliminary development of a novel magnetic particle-based technique that permits the application of highly localized mechanical forces directly to specific regions of an ion-channel structure. We demonstrate that this approach can be used to directly and selectively activate a mechanosensitive ion channel of interest, namely TREK-1. It is shown that manipulation of particles targeted against the extended extracellular loop region of TREK-1 leads to changes in whole-cell currents consistent with changes in TREK-1 activity. Responses were absent when particles were coated with RGD (Arg-Gly-Asp) peptide or when magnetic fields were applied in the absence of magnetic particles. It is concluded that changes in whole-cell current are the result of direct force application to the extracellular loop region of TREK-1 and thus these results implicate this region of the channel structure in mechano-gating. It is hypothesized that the extended loop region of TREK-1 may act as a tension spring that acts to regulate sensitivity to mechanical forces, in a nature similar to that described for MscL. The development of a technique that permits the direct manipulation of mechanosensitive ion channels in real time without the need for pharmacological drugs has huge potential benefits not only for basic biological research of ion-channel gating mechanisms, but also potentially as a tool for the treatment of human diseases caused by ion-channel dysfunction.
Lung Function and Bronchial Hyperresponsiveness in Adults Born Prematurely. A Cohort Study (2015)

In a population-derived, cross-sectional study, we confirmed previous reports that adults 21 or 22 years of age who were born prematurely with neonatal bronchopulmonary dysplasia are more likely to have airflow obstruction, bronchial hyperresponsiveness, and pulmonary gas trapping than subjects born prematurely without bronchopulmonary dysplasia or at term. Clinicians who care for adults need to be better informed of the long-term respiratory consequences of premature birth to assist young patients in maintaining lung function and health.
Engineering the 3D microenvironment of embryonic stem cells undergoing differentiation (2008)

Embryonic stem (ES) cells are pluripotent cells that may be used for regenerative medicine treatmentsfor a variety of degenerative diseases and traumatic injuries because of their ability to differentiate into allsomatic cell types. In order to translate the potential of ES cells into viable cellular therapies, enhancedmethods for controlled differentiation
Homocysteine and Marginal Vitamin Deficiency (1993)

Apart from calcium and iron requirements, nutrition in general (and vitamins in particular) has traditionally rated only a passing nod in medical school. Physicians in training are typically taught that a "balanced" diet is sufficient and that hardly anyone really needs vitamin supplements. Although frank vitamin deficiency is now uncommon in the United States, many investigators have long suspected that large segments of the US population are consuming suboptimal levels of several micronutrients; in recent years, compelling evidence has emerged that supports this contention. In national surveys, a substantial proportion of the US population consumes levels of several vitamins that are well below recommended intakes,<sup>1</sup>and recent evidence strongly indicates that such low intakes are associated with serious health consequences. The most striking recent example is the finding that folic acid supplements can reduce the risk of neural tube defects by approximately 70%. That relationship See also p 2693.
Effect of baseline carbohydrate antigen 19-9 (CA19-9) level on overall survival (OS) in NAPOLI-1 trial: A phase III study of MM-398 (nal-IRI), with or without 5-fluorouracil and leucovorin (5-FU/LV), versus 5-FU/LV in metastatic pancreatic cancer (mPAC) previously treated with gemcitabine-based therapy. (2016)

425 Background: CA19-9 has been shown to correlate with response to therapy and OS in patients with mPAC. NAPOLI-1, a randomized phase 3 study evaluated nal-IRI, a nanoliposomal formulation of irinotecan, with or without 5-FU/LV vs 5-FU/LV in patients with mPAC previously treated with gemcitabine-based therapy. Nal-IRI+5-FU/LV significantly improved OS (primary endpoint) vs 5-FU/LV (6.1 mo vs 4.2 mo; unstratified hazard ratio [HR] = 0.67; P = 0.012). CA19-9 response (≥50% decline from baseline) was superior with nal-IRI+5FU/LV compared with 5-FU/LV (29% vs 9%; P=0.0006). Nal-IRI alone did not show a statistical improvement in survival. Methods: Patients with a recorded baseline CA19-9 measurement were divided into quartiles to evaluate the treatment effect pattern of CA19-9 from nal-IRI+5-FU/LV and 5-FU/LV arms. Quartile ranges were based on 404 available CA19-9 values from randomized patients (N=417). Unstratified Cox proportional hazards regression was used to estimate HRs and corresponding 95% CIs. Effect of baseline CA19-9 on time to response, progression-free survival, and response will be presented. Results: Of patients randomized to receive nal-IRI+5-FU/LV (n = 117) or 5-FU/LV enrolled contemporaneously (n = 119), 218 received study drug and had a baseline CA19-9 measurement. Results show a greater treatment effect on OS with higher CA19-9 level relative to 5-FU/LV. Conclusions: In patients with mPAC previously treated with gemcitabine-based therapy, nal-IRI+5-FU/LV significantly improved OS supported by progression free survival and objective response rate. The CA19-9 serum level can provide important information with regards to overall survival. Clinical trial information: NCT01494506. [Table: see text]
Peptide binding predictions for HLA DR, DP and DQ molecules (2010)

We found that 1) prediction methodologies developed for HLA DR molecules perform equally well for DP or DQ molecules. 2) Prediction performances were significantly increased compared to previous reports due to the larger amounts of training data available. 3) The presence of homologous peptides between training and testing datasets should be avoided to give real-world estimates of prediction performance metrics, but the relative ranking of different predictors is largely unaffected by the presence of homologous peptides, and predictors intended for end-user applications should include all training data for maximum performance. 4) The recently developed NN-align prediction method significantly outperformed all other algorithms, including a naïve consensus based on all prediction methods. A new consensus method dropping the comparably weak ARB prediction method could outperform the NN-align method, but further research into how to best combine MHC class II binding predictions is required.
BI 885578, a Novel IGF1R/INSR Tyrosine Kinase Inhibitor with Pharmacokinetic Properties That Dissociate Antitumor Efficacy and Perturbation of Glucose Homeostasis (2015)

Inhibition of the IGF1R, INSRA, and INSRB receptor tyrosine kinases represents an attractive approach of pharmacologic intervention in cancer, owing to the roles of the IGF1R and INSRA in promoting cell proliferation and survival. However, the central role of the INSRB isoform in glucose homeostasis suggests that prolonged inhibition of this kinase could result in metabolic toxicity. We describe here the profile of the novel compound BI 885578, a potent and selective ATP-competitive IGF1R/INSR tyrosine kinase inhibitor distinguished by rapid intestinal absorption and a short in vivo half-life as a result of rapid metabolic clearance. BI 885578, administered daily per os, displayed an acceptable tolerability profile in mice at doses that significantly reduced the growth of xenografted human GEO and CL-14 colon carcinoma tumors. We found that treatment with BI 885578 is accompanied by increases in circulating glucose and insulin levels, which in turn leads to compensatory hyperphosphorylation of muscle INSRs and subsequent normalization of blood glucose within a few hours. In contrast, the normalization of IGF1R and INSR phosphorylation in GEO tumors occurs at a much slower rate. In accordance with this, BI 885578 led to a prolonged inhibition of cell proliferation and induction of apoptosis in GEO tumors. We propose that the remarkable therapeutic window observed for BI 885578 is achieved by virtue of the distinctive pharmacokinetic properties of the compound, capitalizing on the physiologic mechanisms of glucose homeostasis and differential levels of IGF1R and INSR expression in tumors and normal tissues.
Metalloproteinases in tumor progression: the contribution of MMP-9. (1995)

Many enzymes capable of proteolytic degradation of extracellular matrix and basement membranes have been implicated in tumor progression, including the matrix metalloproteinases, cathepsins, plasminogen activators, and heparanase. Matrix metalloproteinases, a family of zinc-dependent proteases, participate in several steps in tumor progression, including invasion, metastasis, and angiogenesis. In this review, we will give a brief overview of this protease family, and we will review in vitro and in vivo evidence implicating a particular metalloproteinase, the 92-kD type IV collagenase/gelatinase (MMP-9 or gelatinase B), as well as other metalloproteinases, in cancer progression. Finally, using recent studies from our laboratory, we will demonstrate the importance of both tumor cell and host stromal cell production of MMP-9 in tumor progression.
Role of corticosterone in the murine enteric nervous system during fasting (2014)

Food intake depends on a tightly controlled interplay of appetite hormones and the enteric (ENS) and central nervous system. Corticosterone (CORT) levels, which are mainly studied with regard to stress, are also increased during fasting. However, the role of CORT in the ENS remains elusive. Therefore, we investigated whether CORT modulates activity of enteric neurons and whether its intracellular regulator, 11β-hydroxysteroid dehydrogenase (HSD) type 1, is present in the myenteric plexus, using immunohistochemistry and RT-qPCR. Effects of CORT on neuronal activity and expression of neuronal markers in the myenteric plexus were assessed via Ca(2+) imaging and RT-qPCR, respectively, whereas modulations in mixing behavior were measured by video imaging. 11β-HSD-1 was present in enteric neurons along the gastrointestinal tract, and its expression increased after fasting (control: 0.58 ± 0.09 vs. fasted: 1.5 ± 0.23; P < 0.05). CORT incubation significantly reduced neuronal Ca(2+) transients in tissues stimulated by electrical pulses (control: 1.31 ± 0.01 vs. CORT: 1.27 ± 0.01, P < 0.01) and in cultured neurons (control: 1.85 ± 0.03 vs. CORT: 1.76 ± 0.03, P < 0.05). CORT decreased small intestinal mixing (P < 0.05). Incubation of muscle myenteric plexus preparations with CORT induced an increase in cannabinoid receptor 1 (CB1, P < 0.05) and synaptobrevin (P < 0.05) but not in 11β-HSD-1 mRNA expression. In addition, fasting induced significant elevations in synaptobrevin (P < 0.05) and CB1 (P < 0.01) mRNA expression. In conclusion, we suggest CORT to be a downstream factor in a feeding state-related pathway that modulates important proteins in the fine tuning of enteric neurotransmission and gastrointestinal motility.
Primary structure of two-chain botrocetin, a von Willebrand factor modulator purified from the venom of Bothrops jararaca. (1993)

The complete amino acid sequence and location of the disulfide bonds of two-chain botrocetin, which promotes platelet agglutination in the presence of von Willebrand factor, from venom of the snake Bothrops jararaca are presented. Sequences of the alpha and beta subunits were determined by analysis of peptides generated by digestion of the S-pyridylethylated protein with Achromobacter protease I or alpha-chymotrypsin and by chemical cleavage with cyanogen bromide or 2-(2'-nitrophenylsulfenyl)-3-methyl-3-bromoindolenine. Two-chain botrocetin is a heterodimer composed of the alpha subunit (consisting of 133 amino acid residues) and the beta subunit (consisting of 125 amino acid residues) held together by a disulfide bond. Seven disulfide bonds link half-cystine residues 2 to 13, 30 to 128, and 103 to 120 of the alpha subunit; 2 to 13, 30 to 121, and 98 to 113 of the beta subunit; and 80 of the alpha subunit to 75 of the beta subunit. In terms of amino acid sequence and disulfide bond location, two-chain botrocetin is homologous to echinoidin (a sea urchin lectin) and other C-type (Ca(2+)-dependent) lectins.
Compiled instruction set simulation (1991)

Abstract An efficient method for simulating instruction sets is described. The method allows for compiled instruction set simulation using the macro expansion capabilities found in many languages. Additionally, we show how the semantics of the C case statement allows instruction branching to be incorporated in an efficient manner. The method is compared with conventional interpreted techniques and is shown to offer considerable performance benefits.