gebhart/patrepeval huggingface dataset:
Intraductal Papillary Mucinous Neoplasm of the Pancreas: Can Benign Lesions Be Differentiated from Malignant Lesions with Multidetector CT? (2005)

Intraductal papillary mucinous neoplasm (IPMN) of the pancreas is a distinct clinicopathologic entity that is being recognized with increasing frequency. In 25%-44% of IPMNs treated with surgical resection, associated invasive carcinoma has been reported. Surgical resection is the treatment of choice for most IPMNs. Preoperative determination of the presence or absence of associated invasive carcinoma is crucial. The prognosis is worse if there is associated invasive carcinoma; when invasive carcinoma is present, the surgical procedure may be modified to include resection of regional lymph nodes. The spectrum of appearances of IPMN, which includes adenoma, borderline lesion, and lesions with associated carcinoma in situ or invasive carcinoma, was studied with 16-section multidetector computed tomography (CT) and histologic correlation. CT was performed with dual-phase acquisition; the reconstructed images were reviewed on a workstation with axial scrolling and interactive multiplanar reformation and three-dimensional reformation techniques. Features predictive of invasive carcinoma in IPMN at CT and other imaging studies include involvement of the main pancreatic duct, marked dilatation of the main pancreatic duct, diffuse or multifocal involvement, the presence of a large mural nodule or solid mass, large size of the mass, and obstruction of the common bile duct.
Community Inference From Partially Observed Graph Signals: Algorithms and Analysis (2022)

This paper considers community inference methods for finding communities on a graph. We treat the setting where the edges are not fully observed. Instead, inference is based on partially observed filtered graph signals where observations from some nodes are missing. Under this setup, we treat two related tasks: <inline-formula><tex-math notation="LaTeX">$\mathsf{A}$</tex-math></inline-formula>) <i>blind</i> inference which recovers the inherited communities on the sub-graph; <inline-formula><tex-math notation="LaTeX">$\mathsf{B}$</tex-math></inline-formula>) <i>semi-blind</i> inference which recovers communities on the full graph with additional partial topology information. For task <inline-formula><tex-math notation="LaTeX">$\mathsf{A}$</tex-math></inline-formula>, we suggest a spectral method which analyzes the principal components of the data covariance matrix. We prove that it succeeds in finding the &#x2018;true&#x2019; communities if the graph filter is low-pass and the nodes are uniformly sampled. For task <inline-formula><tex-math notation="LaTeX">$\mathsf{B}$</tex-math></inline-formula>, we propose a method using spectral interpolation with a Nystr&#x00F6;m extension. The latter approach is proven to succeed in finding the &#x2018;true&#x2019; communities for modular graphs and low-pass graph filters. Numerical experiments on synthetic and real data corroborate our results.
ChemInform Abstract: Synthesis of Oligoferrocenylenearylenes and the X‐Ray Structure of 1,4‐Bis(tricarbonylmethyltungstentetramethylcyclopentadienyl)benzene. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Do Smartphones Hurt Our Eyes by Causing Shortsightedness? (2021)

Shortsightedness is caused by the eye growing too long, which results in faraway objects, such as the board in school, appearing blurry. People who are shortsighted wear glasses or contact lenses to see better. But would not it be incredible to figure out and avoid whatever causes shortsightedness, so we could wave goodbye to our never-clean, always-lost, forever-slipping-down-our-face glasses? Well, scientists have already started to solve the puzzle of shortsightedness and have discovered that time spent doing close-up tasks, such as reading, may put us at risk of shortsightedness. But now there is another near task we must consider, our ground-breaking, picture-taking, TikTok-making smartphones! We therefore carried out the first ever study looking at shortsightedness and smartphone data use and discovered that young people growing up with smartphones appear to be at greater risk of shortsightedness.
Silicon microchannel plates: initial results for photon counting detectors (2000)

The emergence of Silicon based microchannel plates (MCP's) has been awaited for a number of years, with many proposed advantages over standard glass MCPs for space-based detectors. Si should have a very low inherent background (&lt; 0.01 events sec<SUP>-1</SUP> cm<SUP>-2</SUP>), as well as being a low Z element with low stopping power for x, gamma and cosmic rays. The surface is oxidized and can be baked to very high temperatures (&gt; 800 degrees Celsius), and will not react with photocathodes deposited on the surface. This could potentially allow opaque photocathodes, with their higher resolution and efficiency, to be used in the near UV/optical bands. Since the microchannel positions are determined photolithographically, the pattern will be uniform and coherent, resulting in more uniform flat fields and less differential non-linearity in the spatial response. Microchannel spacing could decrease to the micron regime, while size formats could increase. The potential advantages of Si MCPs encompass increased gain, stability, longevity, event rate, and QE. However, glass MCPs have a strong and successful heritage in space-based detector systems and the advantages of Si MCP's must be demonstrated in the laboratory before being considered for flight applications. We have tested some newly developed silicon (Si) MCP's provided by Nanosciences Corp. Although these are still in the developmental stage we have achieved a number of significant results. The gain, pulse height, response and gain uniformity, and quantum detection efficiency are very similar to glass MCP's. However the Si MCP background is approximately 0.02 events sec<SUP>-1</SUP> cm<SUP>-2</SUP> without shielding, a significant improvement over even low noise MCP's. The small samples we have tested are 25 mm format with 8 micrometer pore spacing, but they are taken from a 75 mm substrate, which offers the possibility of large MCP's in the near future. More testing and process development are underway to probe other operational parameters and optimize the manufacturing process.
Medial plantar nerve compression by a tibial artery schwannoma (2007)

The authors describe the case of a patient with a novel cause of medial plantar symptoms due to extrinsic compression by a schwannoma arising within the adventitia of the tibial artery in the ankle region. Additionally they provide the operative, histological, and imaging findings.
Acoustic Propagation in Dispersions and the Geometric Theory of Diffraction (2003)

The ultrasonic characterization of emulsions relies principally upon the theory of thermoacoustic scattering. For a single spherical particle of radius a suspended in a homogeneous medium, the theory provides an exactly soluble solution to the scattering problem. Unfortunately, direct computations with this solution are often ill-conditioned for certain ranges of the acoustic wave number K and thermal wave number L. Recently the authors have developed a low frequency (i.e., $|Ka|,|La|\ll1$) approach to the theory based on a potential theory technique. This low frequency theory is rapidly convergent and overcomes computation ill-conditioning. In this paper, we pursue the single particle theory and consider the region in which $|Ka| \ll 1$ and $|La| \gg 1$, i.e., the high frequency range of the thermal wavelength. To achieve this, we employ the geometric theory of diffraction. We show that the high frequency solution agrees well with both the experimental measurements and the exact solution in the region where $|Ka| \ll 1$ and $|La| \gg 1$. As in the low frequency case, the high frequency solution may be applied to arbitrary scattering domains.
Abstract 3365: Epigenetic inactivation of PTPRT and sensitivity to STAT3 inhibition in lung cancer (2017)

Abstract Signal Transducers and Activators of Transcription-3 (STAT3), a potent oncogenic transcription factor is persistently activated in several malignancies including lung cancer. Protein Tyrosine Phosphatase Receptor-T (PTPRT) is an endogenous inhibitor of STAT3 transcriptional activity, and is methylated in many types of human cancer. Loss-of-function of PTPRT by promoter methylation contributes to STAT3 mediated growth and survival and represent one of the plausible mechanism of STAT3 hyperactivation. We report identification of hypermethylation in CpG islands of the PTPRT promoter which correlates with its transcriptional silencing as well as expression of pSTAT3 protein and STAT3 target genes in both lung cancer cell lines and primary human tumors. Analyses of the TCGA (The Cancer Genome Atlas) data revealed that PTPRT promoter is frequently hypermethylated in a subset of lung squamous cell carcinoma and approximately 25% of adenocarcinoma tumors in association with downregulation of PTPRT mRNA expression. This observation was verified in vitro using lung cancer cell lines. Out of the 7 lung cancer cell lines examined, one lung cancer cell line showed lack of methylation (only unmethylated sequences) of the PTPRT promoter region and revealed mRNA expression (H520). All 6 cell lines which showed PTPRT promoter methylation had nearly absent PTPRT mRNA and had high levels of pSTAT3Tyr705, while H520 had little or no pSTAT3Tyr705 protein expression. Silencing of PTPRT using siRNA in H520, where PTPRT was not endogenously silenced by promoter hypermethylation, resulted in the upregulation of the STAT3 target genes such as cyclin D1 and Bcl-XL mRNA and protein expression as well as increased pSTAT3Tyr705 level. Analyses of the methylation status in the PTPRT promoter region in primary lung tumor samples revealed methylation in one of the 3 tumor samples. This correlated with increased STAT3 target genes (cyclin D1 and Bcl-XL) mRNA expression. In lung cancer cell lines, PTPRT promoter methylation is associated with sensitivity to STAT3 inhibition. Our data suggests that silencing of PTPRT by promoter hypermethylation is a frequent mechanism of STAT3 hyperactivation, and targeting STAT3 may be an effective molecular targeted approach in the treatment of this subset of lung cancer. Citation Format: Malabika Sen, Audrey Kindsfather, James G. Herman. Epigenetic inactivation of PTPRT and sensitivity to STAT3 inhibition in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3365. doi:10.1158/1538-7445.AM2017-3365
Genetic Analysis of QTL for Resistance to Maize Lethal Necrosis in Multiple Mapping Populations (2019)

Maize lethal necrosis (MLN) occurs when maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) co-infect maize plant. Yield loss of up to 100% can be experienced under severe infections. Identification and validation of genomic regions and their flanking markers can facilitate marker assisted breeding for resistance to MLN. To understand the status of previously identified quantitative trait loci (QTL)in diverse genetic background, F<sub>3</sub> progenies derived from seven bi-parental populations were genotyped using 500 selected kompetitive allele specific PCR (KASP) SNPs. The F<sub>3</sub> progenies were evaluated under artificial MLN inoculation for three seasons. Phenotypic analyses revealed significant variability (<i>P</i> ≤ 0.01) among genotypes for responses to MLN infections, with high heritability estimates (0.62 to 0.82) for MLN disease severity and AUDPC values. Linkage mapping and joint linkage association mapping revealed at least seven major QTL (<i>qMLN3_130</i> and <i>qMLN3_142</i>, <i>qMLN5_190</i> and <i>qMLN5_202</i>, <i>qMLN6_85</i> and <i>qMLN6_157</i><i>qMLN8_10</i> and <i>qMLN9_142</i>) spread across the 7-biparetal populations, for resistance to MLN infections and were consistent with those reported previously. The seven QTL appeared to be stable across genetic backgrounds and across environments. Therefore, these QTL could be useful for marker assisted breeding for resistance to MLN.
Data on G-quadruplex topology, and binding ability of G-quadruplex forming sequences found in the promoter region of biomarker proteins and those relations to the presence of nuclear localization signal in the proteins (2021)

Aptamer is a nucleic acid ligand which specifically binds to its target molecule. Previously, we have designed an identification method of aptamer called "G-quadruplex (G4) promoter-derived aptamer selection (G4PAS)" [1]. In G4PAS procedure, putative G4 forming sequences (PQS) were explored in a promoter region of a target protein in human gene through computational analysis, and evaluated binding ability towards the gene product encoded in the downstream of the promoter. We investigated the topology of the obtained PQSs by circular dichroism measurement, as well as their binding ability against its target protein by surface plasmon resonance measurement and gel-shift assay. Additionally, the presence of nuclear localization signal in the target protein was predicted <i>in silico</i>. This data set summarized all the PQS sequences, their biochemical characteristics, and the presence of nuclear localization signal to address the possibility of binding of these PQS region to the target proteins <i>in vivo</i>. Those data should contribute to increase the success rate of G4PAS. Moreover, considering the G4 motifs in genomic DNA are suggested to be involved <i>in vivo</i> gene regulation [2], [3], this data set is also potentially beneficial for the cell biology field.
Characterization and Targeting of Neoplastic Stem Cells in Ph + Chronic Myeloid Leukemia (2015)

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm characterized by the presence of an oncogenic fusion gene, BCR–ABL1. This fusion gene produces a cytoplasmic protein with tyrosine kinase activity that acts as a main driver of oncogenesis and abnormal proliferation of myeloid cells in CML. Targeted therapy with BCR–ABL1 tyrosine kinase inhibitors (TKIs) such as imatinib is followed by long-term responses in most patients. However, despite continuous treatment, relapses occur, suggesting the presence of TKI-resistant neoplastic stem cells in these patients. Here, we discuss potential mechanisms and signaling molecules involved in the prosurvival and self-renewal capacity of CML neoplastic stem cells as well as antigens expressed by these cells. Several of these signaling molecules and cell surface antigens may serve as potential targets of therapy and their use may overcome TKI resistance in CML in the future.
The Antibiotic Gentamicin Inhibits Specific Protein Trafficking Functions of the Arf1/2 Family of GTPases (2010)

Gentamicin is a highly efficacious antibiotic against Gram-negative bacteria. However, its usefulness in treating infections is compromised by its poorly understood renal toxicity. Toxic effects are also seen in a variety of other organisms. While the yeast Saccharomyces cerevisiae is relatively insensitive to gentamicin, mutations in any one of ∼20 genes cause a dramatic decrease in resistance. Many of these genes encode proteins important for translation termination or specific protein-trafficking complexes. Subsequent inspection of the physical and genetic interactions of the remaining gentamicin-sensitive mutants revealed a network centered on chitin synthase and the Arf GTPases. Further analysis has demonstrated that some conditional arf1 and gea1 alleles make cells hypersensitive to gentamicin under permissive conditions. These results suggest that one consequence of gentamicin exposure is disruption of Arf-dependent protein trafficking.
Proportions in categorical and geographic data (2012)

Colorpleth maps are commonly used to display election results, either by using one distinct color for representing the winning party in each district or by showing a proportion between two parties on a bi-polar colormap, for example, from red to blue representing Republicans vs. Democrats. Showing only the largest party may disable insights into the data whereas using bipolar colormaps works only reasonably well in cases of two parties. To overcome these limitations we introduce a new technique for visualizing proportions in such categorical data. In particular, we combine bipolar colormaps with an adapted double-rendering of polygons to simultaneously visually represent the first two categories and the spatial location. Our technique enables the recognition of close election results as well as clear majorities in a scalable manner. We proof our concept by applying our technique in a prototype implementation used to display election results from the U. S. Presidential election in 2008 and elections of the German Bundestag in 2005 and 2009. Different interesting findings are presented, which would not be recognizable when visualizing only the winner. As we additionally represent the party with the second most votes, we are able to show changes in the spatial distribution of the votes as well as outlier regions with exceptional results. Our visualization technique therefore enables valuable insights into categorical data with a spatial reference.
<title>Computerized Detection Of Lung Nodules In Digital Chest Radiographs</title> (1987)

Detection of cancerous lung nodules in chest radiographs is one of the more important tasks performed by a radiologist. In addition, the &quot;miss rate&quot; associated with the radiographic detection of lung nodules is approximately 30%. A computerized scheme that alerts the radiologist to possible locations of lung nodules should allow this number of false-negative diagnoses to be reduced. We are developing a computer-aided nodule detection scheme based on a difference image approach. We attempt to eliminate the camouflaging background structure of the normal lung anatomy by creating, from a single-projection chest image, two images: one in which the signal-to-noise ratio (SNR) of the nodule is maximized and another in which that SNR is suppressed while the processed background remains essentially the same. Thus, the difference between these two processed images should consist of the nodule superimposed on a relatively uniform background in which the detection task may be simplified. This difference image approach is fundamentally different from conventional subtraction techniques (e.g., temporal or dual-energy subtraction) in that the two images which are subtracted arise from the same single-projection chest radiograph. Once the difference image is obtained, thresholding is performed along with tests for circularity, size and growth in order to extract the nodules. It should be noted that once an original chest image is input to the computer the nodule detection process is totally automated.
Cdebp, a site-specific dna-binding protein of the ‘app-like’ family, is required during the early development of the mouse (1995)

A murine protein, termed CDEBP, was previously shown to bind the double-stranded DNA motif GTCACATG, identical to the yeast centromeric element CDEI. The cDNA sequence showed three domains with extensive similarities to the amyloid beta precursor protein (APP). The protein is homologous over its entire length to the human protein designated APPH. In situ immunofluorescence assays using antibodies raised against distinct parts of CDEBP detected discrete sites of accumulation inside the interphase nucleus, and the bulk of the protein was not associated with mitotic chromosomes. One of the complexes with double-stranded CDEI oligonucleotides detected by gel shift assay was not present when the protein had been selectively removed from nuclear extracts by immunoprecipitation. We reported previously that microinjection into one-cell mouse embryos of DNA fragments including the CDEI sequence results in an early arrest of development with abnormal nuclei containing variable amounts of DNA. The same characteristic figures were observed when embryos were treated with antisense oligonucleotides complementary to parts of the CDEBP coding region. Complexes between the CDEBP protein and CDEI sites in the mouse genome thus appear to play a critical role in the replication/segregation of the embryonic genome.
Development and evaluation of copper-67 and samarium-153 labeled conjugates for tumor radioimmunotherapy (1995)

The potential of utilizing receptor-specific agents such as monoclonal antibodies (MAb), and MAb-derived smaller molecules, as carriers of radionuclides for the selective destruction of tumors has stimulated much research activity. The success of such applications depends on many factors, especially the tumor binding properties of the antibody reagent, the efficiency of labeling and in-vivo stability of the radioconjugate and, on the careful choice of the radionuclide best suited to treat the tumor under consideration. The radiolabeled antibody technique for radioimmunotherapy (RIT), however, has experienced many limitations, and its success has not matched the expectations that were raised more than a decade ago. The problems that have been identified include: (i) degradation of antibody immunoreactivity resulting from chemical manipulations required for labeling; (ii) lack of suitable radioisotopes and methods for stable attachment of the radiolabel; (iii) in-vivo instability of the radioimmunoconjugates; (iv) excessive accumulation of activity in non-target locations; and (v) lack of radioimmunoconjugate accessibility to cells internal to a tumor mass. A careful choice of the radionuclide(s) best suited to treat the tumor under consideration is one of the most important requirements for successful radioimmunotherapy. This study evaluates copper 67 and samarium 153 for tumor radioimmunotherapy.
Efficiency of Implicit Symplectic Finite-Difference Time-Domain Method for Near-Field Optics (2012)

We proposed a new method, implicit symplectic finite difference time domain (FDTD) method) which inherits the good properties from the conventional FDTD method, simplecticity and the conservation of energy. The proposed method is free from the Courant-Friedrics-Lewy condition at the same time. In this paper, we show our method is more efficient than the conventional FDTD method using a typical problem, a polarization control in optical near and far fields of the designing the shape of a metal nanostructure.
Supplementary Figure 1 from Adrenal Hyperplasia and Adenomas Are Associated with Inhibition of Phosphodiesterase 11A in Carriers of <i>PDE11A</i> Sequence Variants That Are Frequent in the Population (2023)

Supplementary Figure 1 from Adrenal Hyperplasia and Adenomas Are Associated with Inhibition of Phosphodiesterase 11A in Carriers of &lt;i&gt;PDE11A&lt;/i&gt; Sequence Variants That Are Frequent in the Population
NMR STUDIES OF IN VIVO BRAIN GLUCOSE CONCENTRATIONS AND TRANSPORT. Paulson,O., Knudsen,G.M. Moos,T. (eds.), Munksgaard, Copenhagen. (1999)

Author: Gruetter, R et al.; Genre: Journal Article; Published in Print: 1999; Title: NMR STUDIES OF IN VIVO BRAIN GLUCOSE CONCENTRATIONS AND TRANSPORT. Paulson,O., Knudsen,G.M. Moos,T. (eds.), Munksgaard, Copenhagen.
Stochastic gradient algorithm based on an improved higher order exponentiated error cost function (2014)

We propose stochastic gradient algorithm based on exponentiated cost functions that employ higher order moments of the chosen error. Recently, such algorithms based on exponential dependence of squared of the error have attracted a lot of attention. It has been felt that such algorithms have only been tested in the Gaussian noise environment. Motivated by the performance of the least-mean-fourth algorithm in sub-Gaussian environments, we make use of the same strategy to come up with a new algorithm with superior convergence and steady-state performance. Simulations show promising results.