gebhart/patrepeval huggingface dataset:
A semantic framework for the retrieval of similar radiological images based on medical annotations (2014)

Image retrieval approaches can assist radiologists by finding similar images in databases as a means to providing decision support. In general, images are indexed using low-level imaging features, and a distance function is used to find the best matches in the feature space. However, using low-level features to capture the appearance of diseases in images is challenging and the semantic gap between these features and the high-level visual concepts in radiology may impair the system performance. We present a semantic framework that enables retrieving similar images based on high-level semantic image annotations. This framework relies on (1) an automatic approach to predict the annotations as semantic terms from Riesz texture image features and (2) a distance function to compare images considering both texture-based and radiodensity-based similarities among image annotations. Experiments performed on CT images emphasize the relevance of this framework.
[Creation of a dynamic digital phantom and its application to a kinetic analysis]. (1998)

A dynamic digital brain phantom was created from the MRI to evaluate visually the relationship between the noise and the error in the parameter estimates in the PET kinetic analysis. This phantom incorporates the noise level depending on administration dose, camera efficiency and the data acquisition schedule. We simulated a serial dynamic scan with 18F-FDG or 11C-flumazenil, assuming 2-tissue 3-parameter model and 1-tissue 2-parameter model, respectively, and the sampling schedule was determined according to the clinical examination. The noise in the tissue time activity curve in FDG had a peak in the first minute and decreased thereafter, whereas the noise increased gradually in the flumazenil study after the initial peak due to radioactivity decay. We examined the relationship between the noise level and the error in the parameter estimates. Both mean absolute differences between true and estimated values and standard deviation became large, and the quality of the parametric images became poor with increasing noise level. This simulation was compared with human tissue time activity curves and parametric images, which were obtained with 100 MBq administration dose in FDG study and 430 MBq in flumazenil study. We inferred that the noise level in the human study was 10-20% in FDG, and 20-40% in flumazenil, and the error in the estimated parameter of K-complex in FDG study was about 20%, that of DV in flumazenil study was 2%.
Asymmetric Electrostatic and Hydrophobic–Hydrophilic Interaction Forces between Mica Surfaces and Silicone Polymer Thin Films (2013)

We have synthesized model hydrophobic silicone thin films on gold surfaces by a two-step covalent grafting procedure. An amino-functionalized gold surface reacts with monoepoxy-terminated polydimethylsiloxane (PDMS) via a click reaction, resulting in a covalently attached nanoscale thin film of PDMS, and the click chemistry synthesis route provides great selectivity, reproducibility, and stability in the resulting model hydrophobic silicone thin films. The asymmetric interaction forces between the PDMS thin films and mica surfaces were measured with the surface forces apparatus in aqueous sodium chloride solutions. At an acidic pH of 3, attractive interactions are measured, resulting in instabilities during both approach (jump-in) and separation (jump-out from adhesive contact). Quantitative analysis of the results indicates that the Derjaguin-Landau-Verwey-Overbeek theory alone, i.e., the combination of electrostatic repulsion and van der Waals attraction, cannot fully describe the measured forces and that the additional measured adhesion is likely due to hydrophobic interactions. The surface interactions are highly pH-dependent, and a basic pH of 10 results in fully repulsive interactions at all distances, due to repulsive electrostatic and steric-hydration interactions, indicating that the PDMS is negatively charged at high pH. We describe an interaction potential with a parameter, known as the Hydra parameter, that can account for the extra attraction (low pH) due to hydrophobicity as well as the extra repulsion (high pH) due to hydrophilic (steric-hydration) interactions. The interaction potential is general and provides a quantitative measure of interfacial hydrophobicity/hydrophilicity for any set of interacting surfaces in aqueous solution.
Canopy fuel and tree biomass data from the Interior West (2011)

This archive contains research data collected and/or funded by Forest Service Research and Development (FS R&D), U.S. Department of Agriculture. It is a resource for accessing both short and long-term FS R&D research data, which includes Experimental Forest and Range data. It is a way to both preserve and share the quality science of our researchers.
Automatic and hand guided self-registration between a robot and an optical tracking system (2009)

In this paper an self-registration method for a robot with an optical tracking system (OTS) is presented. The ability of the used KUKA lightweight robot allows to perform the registration in hand guided mode or completely automatically. The hand guidance allows the user to register the robot with the tracking system in a very fast and intuitive way. He can take the robot by hand and move it and the registration is performed automatically. The mathematical goal is to find a rotation and translation to compute the pose of the robot base and end effector in terms of the coordinate system of the OTS. At each position the pose of the rigid body as well as the TCP of the robot is determined. Since the origin of the rigid body usually is different from the TCP a simple point-to-point transformation as e.g. provided by Horn [1, 2] is not suitable. The problem was reformulated to avoid this and solved with a modified Gauss Newton algorithm.
Estimating OSNR of Equalised QPSK Signals (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. J. Ives, B. C. Thomsen, R. Maher, and S. J. Savory, "Estimating OSNR of Equalised QPSK Signals," in 37th European Conference and Exposition on Optical Communications, OSA Technical Digest (CD) (Optica Publishing Group, 2011), paper Tu.6.A.6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Damage-free surface treatment of carbon nanotubes and self-assembled monolayer devices using a neutral beam process for fusing top–down and bottom–up processes (2008)

Plasma etching processes have been used for the past 30 years to shrink the pattern size of integrated devices. However, the inherent problems of plasma processes, such as ultraviolet photon radiation damage, limit the effectiveness of etching and surface treatments of nanoscale devices. To overcome these problems, we developed a neutral beam surface treatment process. The process uses neutral beams and a defect-free surface process to fabricate carbon nanotubes and self-assemble mono-layer devices. We found that neutral beams can be used to produce atomically defect-free surfaces in carbon nanotubes and organic molecules. This technique has potential for fabricating nanodevices.
Numerical Study on Si Etching by Monatomic Br+/Cl+ Beams and Diatomic Br2 +/Cl2 +/HBr+ Beams (2009)

Classical molecular dynamics simulations revealed a new relationship between Si etching by monatomic (Br+/Cl+) beams and that by diatomic (Br2+/Cl2+/HBr+) beams. The etching characteristics by x eV Br+ (or Cl+) bombardment were identical to those by 2x eV Br2+ (or Cl2+) bombardment. This simple relationship, combined with the previous result that the effect of H in HBr+ bombardment could be neglected and that the yields of Si by HBr+ are equal to those by Br+ in the high-energy region (more than 100 eV), is beneficial for estimating total etch rates for arbitrary compositions of ions in HBr/Cl2 plasmas.
Metamaterial Broadband Angular Selectivity (2014)

We demonstrate how broadband angular selectivity can be achieved with stacks of one-dimensionally periodic photonic crystals, each consisting of alternating isotropic layers and effective anisotropic layers, where each effective anisotropic layer is constructed from a multilayered metamaterial. We show that by simply changing the structure of the metamaterials, the selective angle can be tuned to a broad range of angles; and, by increasing the number of stacks, the angular transmission window can be made as narrow as desired. As a proof of principle, we realize the idea experimentally in the microwave regime. The angular selectivity and tunability we report here can have various applications such as in directional control of electromagnetic emitters and detectors.
Measurement of k T splitting scales in W→ℓν events at $\sqrt{s} = 7\ \mathrm{TeV}$ with the ATLAS detector (2013)

A measurement of splitting scales, as defined by the <i>k</i><sub>T</sub> clustering algorithm, is presented for final states containing a <i>W</i> boson produced in proton-proton collisions at a centre-of-mass energy of 7 TeV. The measurement is based on the full 2010 data sample corresponding to an integrated luminosity of 36 pb<sup>-1</sup> which was collected using the ATLAS detector at the CERN Large Hadron Collider. Cluster splitting scales are measured in events containing <i>W</i> bosons decaying to electrons or muons. The measurement comprises the four hardest splitting scales in a <i>k</i><sub>T</sub> cluster sequence of the hadronic activity accompanying the <i>W</i> boson, and ratios of these splitting scales. Backgrounds such as multi-jet and top-quark-pair production are subtracted and the results are corrected for detector effects. Predictions from various Monte Carlo event generators at particle level are compared to the data. Overall, reasonable agreement is found with all generators, but larger deviations between the predictions and the data are evident in the soft regions of the splitting scales.
Coordinate Expression of Transforming Growth Factor-β1 and Adrenomedullin in Rodent Embryogenesis (1998)

Transforming growth factor-beta (TGFbeta) and adrenomedullin (AM) are multifunctional regulatory peptides that are secreted by a variety of normal and malignant cells. The TGFbetas are expressed in developing organs and adults, and their tissue distribution pattern has possible significance for signaling roles in many epithelial-mesenchymal interactions. AM is also expressed in a variety of embryonic and adult tissues. The present study reports a comparison of the patterns of expression of the proteins and messenger RNAs (mRNAs) for TGFbeta1 and AM in the developing mouse embryo. Immunohistochemical and in situ hybridization analyses were performed on formalin-fixed paraffin-embedded sections of developing embryonic mouse tissues using specific antibodies and complementary RNA probes for TGFbeta1 and AM. The early placenta, including the giant trophoblastic cells, showed high levels of staining and hybridization for TGFbeta1 and AM proteins and mRNAs. The heart was the first organ that showed expression of TGFbeta1 and AM during embryogenesis. The spatio-temporal patterns of expression of TGFbeta1 and AM in cardiovascular, neural, and skeletal-forming tissues as well as in the main embryonic internal organs showed striking similarities. The lung, kidney, and intestine, in which epithelial-mesenchymal interactions occur, showed similar patterns of TGFbeta1 and AM expression. These data show colocalization of TGFbeta1 and AM in specific cell types associated with several tissues in the developing mouse embryo. Additionally, RT-PCR amplification and Northern blot hybridization showed expression of TGFbeta1 and AM mRNAs in all embryonic and adult mouse and rat tissues examined. Our data show that the expression of TGFbeta1 and AM is regulated in a spatial and temporal manner such that overlapping patterns of expression of TGFbeta1 and AM occur in several tissues at the same stage of development and in the same cellular location in rodent embryogenesis.
SUN-LB51 Growth Hormone Deficiency and Resistance Result in Altered Intestinal Gross Anatomy and Morphology in Mice at Adult and Older Adult Timepoints (2020)

Abstract Growth hormone (GH) plays an important role in sustaining intestinal integrity. That is, GH has been shown to decrease intestinal permeability and bacterial translocation and alter gut functions like macronutrient absorption and immune function. To date, however, few studies have investigated how GH action – especially global knockdown of GH action - alters intestinal gross anatomy and morphology. This study characterized the intestinal gross anatomy and morphology of two mouse lines with decreased GH action (with improved health-span and insulin sensitivity): 1) GH gene disrupted (GH-/-) mice (GH deficiency) and 2) GH receptor knockout (GHR-/-) mice (GH resistance). Intestines from GH-/- and GHR-/- mice and their respective littermate controls at adult (12-13 mo.) and older adult (19 mo. and 24 mo., respectively) were used for this study. Both length and weight of small and large intestines were measured at the time of dissection. Six sections for the small intestine and four sections for the large intestine were prepared using a swill roll technique. Images were taken at 100x magnification with a Nikon Eclipse E600 microscope, and villus height, crypt depth, and muscle thickness were measured using ImageJ. All measurements were analyzed using Student t-test, and Cohen’s d effect size was used to compare the intestinal phenotype between lines. Both GHR-/- and GH-/- displayed altered intestinal gross anatomy and morphology. GHR-/- mice at 13 mo. of age had significantly shorter small and large intestines compared to controls. Morphologically, GHR-/- mice also showed significantly decreased villus height in the duodenum and decreased villus height and crypt depth in the jejunum. Likewise, GHR-/- mice at 24 mo. of age had significantly decreased intestinal length, and circumference in both small and large intestines with significantly decreased crypt depth in the ileum. Similar to GHR-/- mice, GH-/- mice at both 12 mo. and 19 mo. of age exhibited significantly shorter small and large intestines compared to controls with significantly smaller circumferences. Duodenum and jejunum of GH-/- mice also had a significant decrease in villus height in the duodenum and jejunum. In this study, decreased GH action is apparent in significantly affecting intestinal morphology and gross anatomy. GHR-/- and GH-/- mice had similar changes in gross anatomy (i.e. length and circumference) and villus height of the duodenum and jejunum. Similar changes to intestinal gross anatomy and morphology were also seen across the different ages in the mice. These findings suggest that decreased GH action influences the gross anatomy of both small and large intestines, and yet has a distinctive section-dependent impact on intestinal morphology. Research needs to be conducted to understand how these structural changes relate to gut function and assess intestinal phenotype at a younger ages in these mouse lines.
Antibiotic resistance versus small molecules, the chemical evolution (1999)

Two discovery approaches directed to addressing the problem of increasing bacterial resistance are described. The first is a program to build activity against methicillin-resistant Staphylococcus aureus (MRSA) into the cephalosporin class of antibacterials, by enhancing affinity for PBP2a, the penicilln-binding protein responsible for this resistance. Through stepwise improvement in potency, human serum binding, solubility, and betalactamase stability, a stable of new compunds with excellent potential as anti-MRSA agents was realized. From this set was chosen MC-02, 479 (RWJ-54428), which is now undergoing extensive preclinical evaluation. The second approach explores the uridyl peptide family of antibiotics, inhibitors of bacterial translocase (mraY), whose members include the pacidamycins, mureidomycins, and napsamycins. Access to a diverse set of analogs by total synthesis was catalyzed by the discovery that hydrogenation of the 4′-exoenamidofuranosyl moiety causes no loss in biological activity. Depthful exploration of SAR required (1) establishment of the absolute stereochemistry of the central diaminobutyric acid (DABA) moiety and (2) determination of the stereochemistry of the 4′-substituent on the deoxyfuranose unit. The former was accomplished by comparison of DABA derived from degradation of a natural product pacidamycin with a sample synthesized from L- threonine. The biological activity of one member of a synthesized library of possible stereoisomers of the natural product established the absolute stereochemistry of the remaining centers. A variety of analogs of the natural product were prepared utilizing the synthetic methods developed, and their biological activities provide important insights into the specificity and spectrum of the antibiotic class. © 1999 John Wiley & Sons, Inc. Med Res Rev, 19, No. 6, 521–542, 1999
IL-33 delays metastatic peritoneal cancer progression inducing an allergic microenvironment (2018)

Ovarian cancer is frequently diagnosed as peritoneal carcinomatosis. Unlike other tumor locations, the peritoneal cavity is commonly exposed to gut-breaching and ascending genital microorganisms and has a unique immune environment. IL-33 is a local cytokine that can activate innate and adaptive immunity. We studied the effectiveness of local IL-33 delivery in the treatment of cancer that has metastasized to the peritoneal cavity. Direct peritoneal administration of IL-33 delayed the progression of metastatic peritoneal cancer. Prolongation in survival was not associated with a direct effect of IL-33 on tumor cells, but with major changes in the immune microenvironment of the tumor. IL-33 promoted a significant increase in the leukocyte compartment of the tumor immunoenvironment and an allergic cytokine profile. We observed a substantial increase in the number of activated CD4<sup>+</sup> T-cells accompanied by peritoneal eosinophil infiltration, B-cell activation and activation of peritoneal macrophages which displayed tumoricidal capacity. Depletion of CD4<sup>+</sup> cells, eosinophils or macrophages reduced the anti-tumor effects of IL-33 but none of these alone were sufficient to completely abrogate its positive benefit. In conclusion, local administration of IL-33 generates an allergic tumor environment resulting in a novel approach for treatment of metastatic peritoneal malignancies, such as advanced ovarian cancer.
Microsatellite instability at AAAG repeat sequences in respiratory tract cancers (2001)

We surveyed the occurrence of novel alleles at microsatellite sequences in non-small cell lung cancers (NSCLC) using 61 tetranucleotide repeat markers. The presence of at least one new allele, consistent with microsatellite instability (MSI), was observed in 26 of 61 (43%) markers involving 30 of 47 (64%) NSCLC. Twelve of the 26 markers detected new alleles in 2 or more tumors and 11 of these 12 markers contained an AAAG repeat sequence. Using this panel of 12 markers, MSI was detected in 24 of 47 (51%) NSCLC and 10 of 18 (56%) head and neck cancers but was only observed in 8 of 38 (21%) bladder cancers and 3 of 25 (12%) kidney cancers. Our results suggested that about 50% of respiratory tract cancers exhibited microsatellite instability predominantly at AAAG sequences. This distinct type of instability was termed EMAST for elevated microsatellite alterations at selected tetranucleotide repeats. The identification of markers with EMAST should have potential application for the molecular detection of respiratory tract cancers.
ChemInform Abstract: Synthesis of 3‐Fluorodiaminopimelic Acid Isomers as Inhibitors of Diaminopimelate Epimerase: Stereocontrolled Enzymatic Elimination of Hydrogen Fluoride. (1990)

Abstract Two hydroxylated analogues (III) and (IV) and four fluorinated analogues such as (VIII) and (IX) of diaminopimelic acid are synthesized in stereochemically pure form.
Magnetic-field-induced spin polarization of AlAs two-dimensional electrons (2002)

Two-dimensional (2D) electrons in an in-plane magnetic field become fully spin polarized above a field ${B}_{P},$ which we can determine from the in-plane magnetoresistance. We perform such measurements in modulation-doped AlAs electron systems, and find that the field ${B}_{P}$ increases approximately linearly with 2D electron density. These results imply that the product $|{g}^{*}|{m}^{*},$ where ${g}^{*}$ is the effective g factor and ${m}^{*}$ the effective mass, is a constant essentially independent of density. While the deduced $|{g}^{*}|{m}^{*}$ is enhanced relative to its band value by a factor of $\ensuremath{\sim}4,$ we see no indication of its divergence as 2D density approaches zero. These observations are at odds with results obtained in Si, but qualitatively confirm spin-polarization studies of 2D GaAs carriers.
Vascular Smooth Muscle Relaxation by Nitro Compounds: Reduced Relaxation and cGMP Elevation in Tolerant Vessels and Reversal of Tolerance by Dithiothreitol (1982)

Smooth muscle preparations obtained from bovine mesenteric artery were incubated with high concentrations of nitroglycerin (NG) or nitroprusside (NP) at elevated pH. This treatment was found to make the vessels tolerant towards both the relaxant and cGMP elevating action of a challenging dose of nitrocompounds when tested on the histamine contracted vessels. Also, some cross-tolerance between NP and NG could be found since pretreatment of the vessels with NP caused a reduction in both the relaxant and the cGMP elevating action of NG. The NG induced tolerance could be partly reversed by treatment with the disulfide reducing agent dithiothreitol (DTT). These results are suggested to strengthen the evidence for cGMP as a mediator of vascular smooth muscle relaxation induced by nitrocompounds. The ability of DTT to partly reverse this tolerance indicates the existence of critical tissue sulfhydryl groups with which the nitrocompounds interact. There also seemed to exist certain differences in the mechanism of action between NG and NP since the tolerance induced against NG was much more pronounced than was the case for NP.
Towards Foundation Models for Relational Databases [Vision Paper] (2023)

Tabular representation learning has recently gained a lot of attention. However, existing approaches only learn a representation from a single table, and thus ignore the potential to learn from the full structure of relational databases, including neighboring tables that can contain important information for a contextualized representation. Moreover, current models are significantly limited in scale, which prevents that they learn from large databases. In this paper, we thus introduce our vision of relational representation learning, that can not only learn from the full relational structure, but also can scale to larger database sizes that are commonly found in real-world. Moreover, we also discuss opportunities and challenges we see along the way to enable this vision and present initial very promising results. Overall, we argue that this direction can lead to foundation models for relational databases that are today only available for text and images.