gebhart/patrepeval huggingface dataset:
Expression of the GLP-1 Receptor in Mouse, Rat, and Human Pancreas (2008)

We studied the intra-islet localization of the glucagon-like peptide 1 receptor (GLP-1R) by colocalization studies of the GLP-1R mRNA and protein with islet cell hormones in mice, rats, and humans. In contrast to previous reports, we show that the GLP-1R is selectively located on the beta cells. The localization of GLP-1R in islets and ducts was studied using ISH and double and triple fluorescence microscopy. In normal pancreatic tissue from mice and rats, GLP-1R mRNA was only detectable in the beta cells. Double and triple immunofluorescence using two different GLP-1R antisera and combinations of insulin, glucagon, pancreatic polypeptide, and somatostatin showed that GLP-1R protein is almost exclusively colocalized with insulin. The same pattern was observed in human pancreas, but the GLP-1R expression was more heterogeneous, with populations of insulin immunoreactive cells with high and low expression. This is the first time that the GLP-1R has been localized in human islets. Furthermore, GLP-1R immunoreactivity was found in the pancreatic ducts in mouse, rat, and human pancreas. As an important confirmation of the specificity of our methods, we found no signals for GLP-1R mRNA or protein in pancreatic tissue from gene-targeted GLP-1R-deficient mice. In conclusion, our data suggest that the GLP-1 receptor is restricted to the pancreatic beta cells and the lack of receptor immunoreactivity on delta cells cannot be explained suitably to correspond with published in vivo and in vitro data. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.
Sinogram bow‐tie filtering in FBP PET reconstruction (2009)

Low-pass filtering of sinograms in the radial direction is the most common practice to limit noise amplification in filtered back projection (FBP) reconstruction of positron emission tomography studies. Other filtering strategies have been proposed to prevent the loss in resolution due to low-pass radial filters, although results have been diverse. Using the well-known properties of the Fourier transform of a sinogram, the authors defined a binary mask that matches the expected shape of the support region in the Fourier domain of the sinogram ("bow tie"). This mask was smoothed by a convolution with a ten-point Gaussian kernel which not only avoids ringing but also introduces a pre-emphasis at low frequencies. A new filtering scheme for FBP is proposed, comprising this smoothed bow-tie filter combined with a standard radial filter and an axial filter. The authors compared the performance of the bow-tie filtering scheme with that of other previously reported methods: Standard radial filtering, angular filtering, and stackgram-domain filtering. All the quantitative data in the comparisons refer to a baseline reconstruction using a ramp filter only. When using the smallest size of the Gaussian kernel in the stackgram domain, the authors achieved a noise reduction of 33% at the cost of degrading radial and tangential resolutions (14.5% and 16%, respectively, for cubic interpolation). To reduce the noise by 30%, the angular filter produced a larger degradation of contrast (3%) and tangential resolution (46% at 10 mm from the center of the field of view) and showed noticeable artifacts in the form of circular blurring dependent on the distance to the center of the field of view. For a similar noise reduction (33%), the proposed bow-tie filtering scheme yielded optimum results in resolution (gain in radial resolution of 10%) and contrast (1% increase) when compared with any of the other filters alone. Experiments with rodent images showed noticeable image quality enhancement when using the proposed bow-tie filtering scheme.
Frequent mutations of the β- catenin gene in mouse colon tumors induced by azoxymethane (2000)

The beta-catenin gene is frequently mutated at codons 33, 41 and 45 of the glycogen synthase kinase-3beta phosphorylation motif in human colon cancers in patients without APC mutations. Frequent mutations at codons 32 and 34, as well as 33 and 41, have been detected in rat colon tumors induced by azoxymethane (AOM), with the second G of CTGGA sequences being considered as a mutational hot-spot. In the present study, exon 3 of the beta-catenin gene in mouse colon tumors induced by AOM was amplified by PCR and mutations were detected by the single strand conformation polymorphism method, restriction enzyme fragment length polymorphism and direct sequencing. All 10 colon tumors tested were found to have beta-catenin mutations, four in codon 34, three in codon 33, two in codon 41 and one in codon 37, nine being G:C-->A:T transitions. However, no mutations were found in codon 32 of the mouse beta-catenin gene. On immmunostaining, beta-catenin was observed in the cytoplasm and nucleus of the tumor cells. The cytoplasmic staining was homogeneous, while both homogeneous and heterogeneous patterns were noted for the nuclei. Highly frequent mutations of the beta-catenin gene in AOM-induced mouse colon tumors suggest that consequent alterations in the stability and localization of the protein may play an important role in this colon carcinogenesis model.
Simulation of optical coupling from surface emitting LEDs (1983)

A general computer simulation analysis of the coupling efficiency between surface emitting LEDs and optical fibers has been carried out using ray tracing techniques. Coupling efficiencies were evaluated as a function of both the fiber numerical aperture (N.A.) and the ratio of the fiber core diameter dF to the LED emission diameter dE for a spherical lens positioned between the LED and fiber. Coupling efficiencies near the theoretical maximum values were obtained for dF/dE ≤ 5 for 0.20-N.A. fibers and for dF/dE ≤ 2.5 for 0.40-N.A. fibers by optimizing the lens’s index of refraction and the LED-to-lens spacing.
A polyvalent inactivated rhinovirus vaccine is broadly immunogenic in rhesus macaques (2016)

As the predominant aetiological agent of the common cold, human rhinovirus (HRV) is the leading cause of human infectious disease. Early studies showed that a monovalent formalin-inactivated HRV vaccine can be protective, and virus-neutralizing antibodies (nAb) correlated with protection. However, co-circulation of many HRV types discouraged further vaccine efforts. Here, we test the hypothesis that increasing virus input titres in polyvalent inactivated HRV vaccine may result in broad nAb responses. We show that serum nAb against many rhinovirus types can be induced by polyvalent, inactivated HRVs plus alhydrogel (alum) adjuvant. Using formulations up to 25-valent in mice and 50-valent in rhesus macaques, HRV vaccine immunogenicity was related to sufficient quantity of input antigens, and valency was not a major factor for potency or breadth of the response. Thus, we have generated a vaccine capable of inducing nAb responses to numerous and diverse HRV types.
A manifesto for model merging (2006)

If a modeling task is distributed, it will frequently be necessary to merge models developed by different team members. Existing approaches to model merging make assumptions about the types of model to be merged, and the nature of the relationship between them. This makes it hard to compare approaches. In this paper, we present a manifesto for research on model merging. We propose a framework for comparing different approaches to merging, by treating merge as an algebraic operator over models and model relationships. We specify the algebraic properties of an idealized merge operator, as well as related operators such as match, diff, split, and slice. We then show how our framework can be used to compare existing approaches by applying it to two of our own research projects on model merging. We show how this analysis permits a detailed comparison of approaches, reveals the key features of each, and identifies weaknesses that require further research. Most importantly, the framework emphasizes the need to make explicit all assumptions about the relationships between models, and indeed to treat model relationships as first class objects.
Changes of defect and active-dopant concentrations induced by annealing of highly Si-doped GaAs (1998)

We identified point defects and dopant atoms and measured their concentrations in as-grown and post-growth annealed highly Si-doped GaAs by scanning tunneling microscopy. The annealing under As atmosphere reduces the concentration of Si atoms incorporated into Si pairs and clusters by cluster dissolution, while the concentrations of Si donors, Si donor--Ga vacancy complexes, and Si donor--As vacancy complexes increase. For the dissolution of the Si clusters during heat treatment, a Ga-vacancy-mediated mechanism is suggested.
A Causal-based Framework for Multimodal Multivariate Time Series Validation Enhanced by Unsupervised Deep Learning as an Enabler for Industry 4.0 (2020)

An advanced conceptual validation framework for multimodal multivariate time series defines a multi-level contextual anomaly detection ranging from an univariate context definition, to a multimodal abstract context representation learnt by an Autoencoder from heterogeneous data (images, time series, sounds, etc.) associated to an industrial process. Each level of the framework is either applicable to historical data and/or live data. The ultimate level is based on causal discovery to identify causal relations in observational data in order to exclude biased data to train machine learning models and provide means to the domain expert to discover unknown causal relations in the underlying process represented by the data sample. A Long Short-Term Memory Autoencoder is successfully evaluated on multivariate time series to validate the learnt representation of abstract contexts associated to multiple assets of a blast furnace. A research roadmap is identified to combine causal discovery and representation learning as an enabler for unsupervised Root Cause Analysis applied to the process industry.
Expression of drug metabolizing enzymes in transgenic animals and heterologous expression systems (1992)

Article Expression of drug metabolizing enzymes in transgenic animals and heterologous expression systems was published on July 1, 1992 in the journal Journal of Basic and Clinical Physiology and Pharmacology (volume 3, issue Supplement).
Differential endocytosis and signaling dynamics of insulin receptor variants IR-A and IR-B (2012)

Retraction of: J. Cell Sci. 124, 801–811.The authors wish to retract this paper after it has come to their attention that the constructs of insulin receptor (IR) isoform A were of isoform B. This was discovered when the constructs were subcloned into retroviral vectors to be used in a different study. Thus the significant differences reported between IR-A and IR-B must be assumed to be erroneous and, in agreement with the Journal of Cell Science editorial policies, the paper must be retracted. A detailed comparison between certified IR-A and IR-B is being conducted and will be reported.The authors apologise for not having detected the cloning error prior to publication and for any inconvenience caused.
Activation of the cyclin D1 Gene by the E1A-associated Protein p300 through AP-1 Inhibits Cellular Apoptosis (1999)

The adenovirus E1A protein interferes with regulators of apoptosis and growth by physically interacting with cell cycle regulatory proteins including the retinoblastoma tumor suppressor protein and the coactivator proteins p300/CBP (where CBP is the CREB-binding protein). The p300/CBP proteins occupy a pivotal role in regulating mitogenic signaling and apoptosis. The mechanisms by which cell cycle control genes are directly regulated by p300 remain to be determined. The cyclin D1 gene, which is overexpressed in many different tumor types, encodes a regulatory subunit of a holoenzyme that phosphorylates and inactivates PRB. In the present study E1A12S inhibited the cyclin D1 promoter via the amino-terminal p300/CBP binding domain in human choriocarcinoma JEG-3 cells. p300 induced cyclin D1 protein abundance, and p300, but not CBP, induced the cyclin D1 promoter. cyclin D1 or p300 overexpression inhibited apoptosis in JEG-3 cells. The CH3 region of p300, which was required for induction of cyclin D1, was also required for the inhibition of apoptosis. p300 activated the cyclin D1 promoter through an activator protein-1 (AP-1) site at -954 and was identified within a DNA-bound complex with c-Jun at the AP-1 site. Apoptosis rates of embryonic fibroblasts derived from mice homozygously deleted of the cyclin D1 gene (cyclin D1(-/-)) were increased compared with wild type control on several distinct matrices. p300 inhibited apoptosis in cyclin D1(+/+) fibroblasts but increased apoptosis in cyclin D1(-/-) cells. The anti-apoptotic function of cyclin D1, demonstrated by sub-G(1) analysis and annexin V staining, may contribute to its cellular transforming and cooperative oncogenic properties.
Magazine Cover: Sports Illlustrated, March 27, 2006 (2006)

Original Magazine Cover Image: color, 8.5 x 11 (21.6 cm x 27.9 cm); jpeg image as displayed:442 x 575 pixels
Enzymatic Synthesis of N-Acetyllactosamine (LacNAc) Type 1 Oligomers and Characterization as Multivalent Galectin Ligands (2017)

Repeats of the disaccharide unit <i>N</i>-acetyllactosamine (LacNAc) occur as type 1 (Galβ1, 3GlcNAc) and type 2 (Galβ1, 4GlcNAc) glycosylation motifs on glycoproteins and glycolipids. The LacNAc motif acts as binding ligand for lectins and is involved in many biological recognition events. To the best of our knowledge, we present, for the first time, the synthesis of LacNAc type 1 oligomers using recombinant β1,3-galactosyltransferase from <i>Escherichia coli</i> and β1,3-<i>N</i>-acetylglucosaminyltranferase from <i>Helicobacter pylori</i>. Tetrasaccharide glycans presenting LacNAc type 1 repeats or LacNAc type 1 at the reducing or non-reducing end, respectively, were conjugated to bovine serum albumin as a protein scaffold by squarate linker chemistry. The resulting multivalent LacNAc type 1 presenting neo-glycoproteins were further studied for specific binding of the tumor-associated human galectin 3 (Gal-3) and its truncated counterpart Gal-3∆ in an enzyme-linked lectin assay (ELLA). We observed a significantly increased affinity of Gal-3∆ towards the multivalent neo-glycoprotein presenting LacNAc type 1 repeating units. This is the first evidence for differences in glycan selectivity of Gal-3∆ and Gal-3 and may be further utilized for tracing Gal-3∆ during tumor progression and therapy.
Text Mining and Automation for Processing of Patient Referrals (2018)

This pilot study successfully demonstrated that there is potential for automating the assignment of reasons for referrals and provides a foundation for further work to build on. This study also outlined a potential application of text mining and NLP to automating a manual task in hospitals to save time of human resources.
Subtypes of Drug Abuse With Psychosis (1982)

Hospital records of 72 drug abusers with psychoses (DAP) were analyzed to clarify the relationship between drug abuse and psychosis. Comparison groups included schizophrenics and atypical schizophrenics without drug abuse and drug abusers without psychoses (DA). Compared with DAP in whom psychoses lasted less than six months before admission (DAP-short), drug abusers with psychoses of a longer duration (DAP-long) had more symptoms, more premorbid personality disorders, and greater familial risks of schizophrenia and affective disorder. The DAP-long group resembled atypical schizophrenia for clinical features and family history, whereas the DAP-short group resembled DA for some clinical features and family history. The results indicate that there are several subgroups of DAP. The importance of clinical features and family history in identifying subgroups of DAP was stressed.
Microwave-optical mixing in LiNbO/sub 3/ modulators (1993)

An investigation study of microwave-optical mixing in different configurations of LiNbO/sub 3/ Mach-Zehnder interferometric modulators is presented. In each case, models that describe mixer performance are developed and are shown to be in good agreement with measurements. For antenna remoting applications, a technique to down-convert RF signals is demonstrated by cascading in series a pair of Mach-Zehnder interferometric modulators. In general, it is shown that by virtue of their truly broadband characteristics, interferometric modulators can also by employed as microwave mixers at frequencies up to 40 GHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Geologic model building in SEAM Phase II — Land seismic challenges (2017)

Three digital earth models were designed and constructed during SEAM Phase II to study exploration challenges at the scale of modern land seismic surveys. Although built as generic models, each was based on one or more related geologic type areas. The Barrett model represents the seismic anisotropy of complex laminated and fractured shale reservoirs, based on the Woodford and Eagle Ford formations and set below a stratigraphic overburden and near surface of a North American midcontinent basin. The Arid model features the extreme property contrasts of desert terrains in a 500 m thick near surface that juxtaposes hard carbonate bedrock and soft sediments filling karsts, typical of the Saudi Arabian Peninsula. The Foothills model contains sharp surface topography and alluvial fan-like sediments above complex fold-and-thrust structures based on the compressive tectonics of the Llanos Foothills of South America. All three models were built in workflows that combined automated steps with a large measure of manual model building, which represents the current state of the art in geologic modeling for large-scale geophysical simulations. The Barrett and Arid models each contain about 1.5 billion grid cells representing regions 10 × 10 × 3.75 km in physical size. The Foothills model has about 2 billion cells representing a region about 14.5 × 12.5 × 11 km. Full elastic-wave simulations with these models were run for a combined total of about 170,000 shots, usually with millions of recorded channels per shot, generating several petabytes of seismic data in standard and novel shot-receiver geometries. Selected shots from these simulations show that large, detailed earth models can reproduce features of land seismic surveys that continue to challenge the best modern seismic data processing and imaging techniques.
Mirror fusion vacuum technology developments (1983)

Magnetic Mirror Fusion experiments, such as MFTF-B+T (Mirror Fusion Test Facility-B, Tritium Upgrade) and foreseeable follow-on devices, have operational and maintenance requirements that have not yet been fully demonstrated. Among those associated with vacuum technology are the very-high continuous-pumping speeds, 10/sup 7/ to 10/sup 8/ l/s for D/sub 2/, T/sub 2/ and, to a lesser extent, He; the early detection of water leaks from the very-high heat-flux neutral-beam dumps and the detection and location of leaks in the superconducting magnets not protected by guard vacuums. Possible solutions to these problems have been identified and considerable progress has been made toward successfully demonstrating their feasibility.
Medications Acting on the Dopaminergic System in the Treatment of Alcoholic Patients (2010)

An extensive literature supports the role of dopamine in the development and maintenance of alcohol dependence. Yet the organization of brain dopamine is complex, with multiple dopamine receptor subtypes and distinct effects on reinforcement, craving, motivation and behavior. Several modestly effective pharmacological treatments for alcoholism, including naltrexone, baclofen and ondansetron, affect dopaminergic systems indirectly. Direct dopamine antagonists, including tiapride, quetiapine, ondansetron and clozapine have been shown to be somewhat effective in reducing alcohol consumption in controlled clinical trials. The partial dopamine agonist, aripiprazole has shown mixed efficacy. Dopaminergic medications can have significant side effects. A better understanding of how dopamine affects the various aspects of addictive behavior may lead to more effective medications.
NOD2 (CARD15) mutations in Crohn’s disease are associated with diminished mucosal α-defensin expression (2004)

As alpha defensins are important in the mucosal antibacterial barrier, their diminished expression may explain, in part, the bacterial induced mucosal inflammation and ileal involvement of Crohn's disease, especially in the case of NOD2 mutations.
A MODEL OF FOOD SPREADABILITY FROM FLUID MECHANICS (1982)

Subjective spreadability was predicted through understanding of psychophysical mechanisms involved during the back and forth spreading action of foods on crackers. Transient complex Theology of food products is incorporated into mass and momentum balances used to model the spreading action. Furthermore, because the consumer is in contact with the food product through a knife, it is assumed that the inverse of the torque needed to generate the deformation is assessed as spreadability. Torque is assumed to be equal to the shear stress on the knife multiplied by the distance the knife traueled across the cracker. Because this distance is constant, the final form for the psychophysical model is: image Using magnitude estimation, subjective spreadability scores ranged from 0.13 for marshmallow cream to 5.23 for squeeze margarine. When these scores were plotted versus the model on log‐log coordinates, the best slope was 0.85 with a correlation coefficient of 0.95. The results strongly support the assumption that shear stresses generated on the knife are assessed as spreadability by the consumer.
Tip–sample distance feedback control in a scanning evanescent microwave microscope (1999)

We have developed a means of tip–sample distance regulation for a scanning evanescent microwave microscope over conductive samples. Changes in resonant frequency and quality factor are measured, where changes in resonant frequency are related to the tip–sample capacitance and changes in quality factor are related to microwave absorption. With the analytical expression of the tip–sample capacitance as a function of tip–sample distance, we can quantitatively regulate the tip–sample separation. We demonstrated simultaneous noncontact imaging of topography and surface resistance with high spatial resolution.
RETRACTED ARTICLE: RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail (2019)

N6-Methyladenosine (m<sup>6</sup>A) modification has been implicated in the progression of several cancers. We reveal that during epithelial-mesenchymal transition (EMT), one important step for cancer cell metastasis, m<sup>6</sup>A modification of mRNAs increases in cancer cells. Deletion of methyltransferase-like 3 (METTL3) down-regulates m<sup>6</sup>A, impairs the migration, invasion and EMT of cancer cells both in vitro and in vivo. m<sup>6</sup>A-sequencing and functional studies confirm that Snail, a key transcription factor of EMT, is involved in m<sup>6</sup>A-regulated EMT. m<sup>6</sup>A in Snail CDS, but not 3'UTR, triggers polysome-mediated translation of Snail mRNA in cancer cells. Loss and gain functional studies confirm that YTHDF1 mediates m<sup>6</sup>A-increased translation of Snail mRNA. Moreover, the upregulation of METTL3 and YTHDF1 act as adverse prognosis factors for overall survival (OS) rate of liver cancer patients. Our study highlights the critical roles of m<sup>6</sup>A on regulation of EMT in cancer cells and translation of Snail during this process.