gebhart/patrepeval huggingface dataset:
An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms (2022)

Investigating the 3D structures and rearrangements of organelles within a single cell is critical for better characterizing cellular function. Imaging approaches such as soft X-ray tomography have been widely applied to reveal a complex subcellular organization involving multiple inter-organelle interactions. However, 3D segmentation of organelle instances has been challenging despite its importance in organelle characterization. Here we propose an intensity-based post-processing tool to identify and separate organelle instances. Our tool separates sphere-like (insulin vesicle) and columnar-shaped organelle instances (mitochondrion) based on the intensity of raw tomograms, semantic segmentation masks, and organelle morphology. We validate our tool using synthetic tomograms of organelles and experimental tomograms of pancreatic β-cells to separate insulin vesicle and mitochondria instances. As compared to the commonly used connected regions labeling, watershed, and watershed + Gaussian filter methods, our tool results in improved accuracy in identifying organelles in the synthetic tomograms and an improved description of organelle structures in β-cell tomograms. In addition, under different experimental treatment conditions, significant changes in volumes and intensities of both insulin vesicle and mitochondrion are observed in our instance results, revealing their potential roles in maintaining normal β-cell function. Our tool is expected to be applicable for improving the instance segmentation of other images obtained from different cell types using multiple imaging modalities.
Evaluation of ERG and SPINK1 by Immunohistochemical Staining and Clinicopathological Outcomes in a Multi-Institutional Radical Prostatectomy Cohort of 1067 Patients (2015)

Distinguishing between patients with early stage, screen detected prostate cancer who must be treated from those that can be safely watched has become a major issue in prostate cancer care. Identification of molecular subtypes of prostate cancer has opened the opportunity for testing whether biomarkers that characterize these subtypes can be used as biomarkers of prognosis. Two established molecular subtypes are identified by high expression of the ERG oncoprotein, due to structural DNA alterations that encode for fusion transcripts in approximately ½ of prostate cancers, and over-expression of SPINK1, which is purportedly found only in ERG-negative tumors. We used a multi-institutional prostate cancer tissue microarray constructed from radical prostatectomy samples with associated detailed clinical data and with rigorous selection of recurrent and non-recurrent cases to test the prognostic value of immunohistochemistry staining results for the ERG and SPINK1 proteins. In univariate analysis, ERG positive cases (419/1067; 39%) were associated with lower patient age, pre-operative serum PSA levels, lower Gleason scores (≤ 3+4=7) and improved recurrence free survival (RFS). On multivariate analysis, ERG status was not correlated with RFS, disease specific survival (DSS) or overall survival (OS). High-level SPINK1 protein expression (33/1067 cases; 3%) was associated with improved RFS on univariate and multivariate Cox regression analysis. Over-expression of either protein was not associated with clinical outcome. While expression of ERG and SPINK1 proteins was inversely correlated, it was not mutually exclusive since 3 (0.28%) cases showed high expression of both. While ERG and SPINK1 appear to identify discrete molecular subtypes of prostate cancer, only high expression of SPINK1 was associated with improved clinical outcome. However, by themselves, neither ERG nor SPINK1 appear to be useful biomarkers for prognostication of early stage prostate cancer.
Potential Involvement of LOX-1 in Functional Consequences of Endothelial Senescence (2011)

Numerous studies have described the process of senescence associated with accumulation of oxidative damage, mutations and decline in proliferative potential. Although the changes observed in senescent cells are likely to result in significant phenotypic alterations, the studies on consequences of endothelial senescence, especially in relation to aging-associated diseases, are scarce. We have analyzed effects of senescence on the functions of endothelial cells relevant to the development of atherosclerosis including angiogenesis, adhesion, apoptosis and inflammation. In the course of progressing through the passages, human umbilical vein endothelial cells (HUVECs) displayed significant increase in size (+36% passage 12 vs. passage 4 , p<0.001) and reduction in both basal and VEGF-stimulated tube formation. The analysis of a scavenger receptor LOX-1, a key molecule implicated in atherogenesis, revealed a significant decline of its message (mRNA) and protein content in senescent endothelial cells (-33%) and in aortas of 50 wk (vs. 5 wk) old mice (all p<0.01). These effects were accompanied by a marked reduction of the basal expression of VCAM-1 and ICAM-1. Compared to early cultures, late passage HUVECs also exhibited nuclear translocation of NF-κB (p65) and reciprocal shifts in BAX and BCL2 protein content resulting in almost 2-fold increase in BAX/BCL2 ratio and 3-fold increase in apoptotic response to TNFα exposure (p<0.04). These changes in senescent endothelial cells are suggestive of aberrant responses to physiological stimuli resulting in a less permissive environment for tissue remodeling and progression of diseases requiring angiogenesis and cell adhesion in elderly, possibly, mediated by LOX-1.
Orthostatic blood pressure response, carotid intima–media thickness, and plasma fibrinogen in older nondiabetic adults (2012)

In older nondiabetic adults only orthostatic hypotension seems to independently correlate with increased carotid atherosclerosis and systemic inflammation.
Towards smarter documents (2004)

Document analysis research typically focuses on document image understanding or classic problems in text classification, clustering, summarization and discovery. While that is an important aspect of document management, in practice, documents lifecycles are often determined by the context of the business process that they are relevant to. It therefore becomes necessary for the document analysis techniques to recognize and leverage the contextual information provided by a supporting schema and business process. This paper presents an intelligent document management framework with relevant document analysis, metadata extraction, and business process association algorithms and methodology. The architecture supporting this framework seamlessly integrates a runtime environment with an authoring environment by combining relational data modeling tools with document classification techniques. The runtime environment accepts incoming documents, classifies the document, extracts metadata and executes customized business logic. The authoring environment supports the association of a class of documents with a relational document schema, identification of attribute values that must be extracted automatically, generation of relevant business logic, and deployment of authoring artifacts into the runtime architecture. We demonstrate the use of this framework with representative real-world document transformative applications.
Modulation of Glial and Neuronal Migration by Lipocalin-2 in Zebrafish (2011)

Thus, LCN2 proteins secreted under diverse conditions may play an important role in CNS immune and inflammatory responses by controlling cell migration and morphology.
Size effects on metal-insulator phase transition in individual vanadium dioxide nanowires (2014)

We report the size effects on the metal-insulator phase transition of vanadium dioxide (VO2) nanowires prepared by chemical vapor deposition. The phase transition temperature can be tuned from 67 °C in the bulk VO2 to as low as 29°C by reducing the diameter of VO2 nanowires to nanoscale. Temperature-dependent Raman spectra display a clear dynamic picture on the metal-insulator phase transition process of the VO2 nanowires. Whilst, Raman study shows no remarkable strain effect on the phase transition behaviors of our samples. The increasing surface defect density with reducing nanowire size facilitates the decreasing phase transition temperature. In addition, the polarized-photocurrent effect was observed, resulting from the anisotropy of the photoresponse and also caused by the reduced dimensionality.Our results indicate that size of VO2 nanostructures can dominate their thermoelectric and photoelectrical properties.
New Insights into Structures, Stability, and Bonding of μ-Allyl Ligands Coordinated with Pd−Pd and Pd−Pt Fragments (1996)

A series of complexes of μ-allyl ligands coordinated with the Pd−Pd fragment Pd2(μ-allyl)(μ-Cl)(PPh3)2 were prepared from reactions of the corresponding allylpalladium(II) chlorides with Pd(C2H4)(PPh3)2. The μ-allyl ligands employed contained both electron-withdrawing (Cl, CN, COOMe, SO2Ph) and electron-donating (Me, Ph) substituents at either the terminal or central carbon of the allyl framework. The relative ability of a substituted allyl ligand to coordinate to the Pd(I)−Pd(I) fragment vs the mononuclear Pd(II) fragment was determined by means of an allyl ligand exchange equilibrium between the dinuclear and the mononuclear fragments. The allyl ligand bearing the more withdrawing substituent coordinated to the Pd−Pd fragment more strongly than that bearing the less withdrawing substituent. The 1-methyl, 1-phenyl, and 1-chloroallyl ligands on the Pd−Pd bond exist in an anti configuration almost exclusively. X-ray structure determinations of some of the μ-allyl Pd−Pd and Pd−Pt complexes, PdM(μ-allyl)(μ-X)(PPh3)2 (11, M = Pt, allyl = CH2C(COOMe)CH2, X = Br; 12, M = Pd, allyl = CH2C(COOMe)CH2, X = Br; 13, M = Pd, allyl = CH2CHCH(COOMe), X = SPh) were carried out. The crystal of 11 was isomorphous with that of 12. The results revealed a unique geometrical feature of the bridging allyl ligand; the dihedral angle between the allyl plane and the approximate coordination plane (M−M−X plane) is smaller than 90°. Ab initio MO calculations on the model Pd2(μ-CH2CHCH2)(μ-Br)(PH3)2 were performed to reveal important aspects of the bonding nature; the coordinate bond of the μ-allyl ligand involved not only donation from the allyl nonbonding π orbital to the unoccupied dσ−dσ antibonding orbital of the Pd2(μ-Br)(PH3)2 unit but also back-donation from the occupied dσ−dσ and dπ−dπ bonding combinations of the Pd2(μ-Br)(PH3)2 unit to the allyl π* orbital. The latter is not observed in the mononuclear palladium(II) allyl complex but is found as a characteristic interaction in the dinuclear μ-allyl complex. The above-mentioned unique geometrical and stability features of the dinuclear μ-allyl complexes arise from the back-bonding interaction.
ChemInform Abstract: SELECTIVE EPOXIDATION OF OLEFINS BY MOLYBDENUM PORPHYRIN CATALYZED PEROXY‐BOND HETEROLYSIS (1981)

Abstract Komplexe des 5,10,15,20‐Tetraphenyl‐porphyrins (TPP) mit Mo(V) vom Typ [OMo(TPP)OCH3] katalysieren bei 80°C in Benzol unter Ar die Epoxidation von Olefinen wie Cyclohexen durch tert.‐Butylhydroperoxid, wobei nach einer Induktionsperiode von 40 min innerhalb von 17 h mit gleichbleibender Geschwindigkeit das gesamte Hydroperoxid umgesetzt und das Epoxid mit einer Selektivität von 84% gebildet wird.
Deep Learning at the Physical Layer: System Challenges and Applications to 5G and Beyond (2020)

The unprecedented requirements of IoT have made fine-grained optimization of spectrum resources an urgent necessity. Thus, designing techniques able to extract knowledge from the spectrum in real time and select the optimal spectrum access strategy accordingly has become more important than ever. Moreover, 5G networks will require complex management schemes to deal with problems such as adaptive beam management and rate selection. Although deep learning (DL) has been successful in modeling complex phenomena, commercially available wireless devices are still very far from actually adopting learning-based techniques to optimize their spectrum usage. In this article, we first discuss the need for real-time DL at the physical layer, and then summarize the current state of the art and existing limitations. We conclude the article by discussing an agenda of research challenges and how DL can be applied to address crucial problems in 5G and beyond networks.
ChemInform Abstract: Synthesis of Di‐ and Tri‐Substituted Imidazole‐4‐carboxylates via PBu3‐Mediated [3 + 2] Cycloaddition (2013)

Abstract of Δ 2 ‐oxazoline generated in situ from amidoacetic acids (I) and cyanoformate (II)
A novel lesion crossing technique: Balloon deployment using FORcible Manner (BADFORM) technique (2017)

The efficacy and safety of the BADFORM technique might be acceptable. © 2017 Wiley Periodicals, Inc.
Integrated device for combined optical neuromodulation and electrical recording for chronicin vivoapplications (2011)

Studying brain function and its local circuit dynamics requires neural interfaces that can record and stimulate the brain with high spatiotemporal resolution. Optogenetics, a technique that genetically targets specific neurons to express light-sensitive channel proteins, provides the capability to control central nervous system neuronal activity in mammals with millisecond time precision. This technique enables precise optical stimulation of neurons and simultaneous monitoring of neural response by electrophysiological means, both in the vicinity of and distant to the stimulation site. We previously demonstrated, in vitro, the dual capability (optical delivery and electrical recording) while testing a novel hybrid device (optrode-MEA), which incorporates a tapered coaxial optical electrode (optrode) and a 100 element microelectrode array (MEA). Here we report a fully chronic implant of a new version of this device in ChR2-expressing rats, and demonstrate its use in freely moving animals over periods up to 8 months. In its present configuration, we show the device delivering optical excitation to a single cortical site while mapping the neural response from the surrounding 30 channels of the 6 × 6 element MEA, thereby enabling recording of optically modulated single-unit and local field potential activity across several millimeters of the neocortical landscape.
A Soluble Form of the First Extracellular Domain of Mouse Type 2β Corticotropin-releasing Factor Receptor Reveals Differential Ligand Specificity (2003)

The heptahelical receptors for corticotropin-releasing factor (CRF), CRFR1 and CRFR2, display different specificities for CRF family ligands: CRF and urocortin I bind to CRFR1 with high affinity, whereas urocortin II and III bind to this receptor with very low affinities. In contrast, all the urocortins bind with high affinities, and CRF binds with lower affinity to CRFR2. The first extracellular domain (ECD1) of CRFR1 is important for ligand recognition. Here, we characterize a bacterially expressed soluble protein, ECD1-CRFR2beta, corresponding to the ECD1 of mouse CRFR2beta. The K(i) values for binding to ECD1-CRFR2beta are: astressin = 10.7 (5.4-21.1) nm, urocortin I = 6.4 (4.7-8.7) nm, urocortin II = 6.9 (5.8-8.3) nm, CRF = 97 (22-430) nm, urocortin III = sauvagine >200 nm. These affinities are similar to those for binding to a chimeric receptor in which the ECD1 of CRFR2beta replaces the ECD of the type 1B activin receptor (ALK4). The ECD1-CRFR2beta possesses a disulfide arrangement identical to that of the ECD1 of CRFR1, namely Cys(45)-Cys(70), Cys(60)-Cys(103), and Cys(84)-Cys(118). As determined by circular dichroism, ECD1-CRFR2beta undergoes conformational changes upon binding astressin. These data reinforce the importance of the ECD1 of CRF receptors for ligand recognition and raise the interesting possibility that different ligands having similar affinity for the full-length receptor may, nevertheless, have different affinities for microdomains of the receptor.
Extraction of SPICE-type equivalent circuits of microwave components and discontinuities using the genetic algorithm optimization technique (2000)

In this paper, the genetic algorithm (GA) is employed as an efficient optimization tool to derive SPICE-type equivalent circuits of microwave components, and of discontinuities in coaxial lines, from their specified S-parameters. Nodal analysis and techniques are utilized in conjunction with the GA to extract these equivalent circuits, whose component values are the parameters optimized by the GA. Numerical examples, that demonstrate the fact that GA yields excellent results for the cases studied, are included in the paper.
Synthesis and variable-temperature magnetochemical and Moessbauer spectroscopy studies of tris(monothiocarbamato)iron(III) complexes. A new 2T .dblarw. 6A spin-equilibrium system containing the FeS3O3 core (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and variable-temperature magnetochemical and Moessbauer spectroscopy studies of tris(monothiocarbamato)iron(III) complexes. A new 2T .dblarw. 6A spin-equilibrium system containing the FeS3O3 coreKenneth R. Kunze, Dale L. Perry, and Lon J. WilsonCite this: Inorg. Chem. 1977, 16, 3, 594–599Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://pubs.acs.org/doi/10.1021/ic50169a019https://doi.org/10.1021/ic50169a019research-articleACS PublicationsRequest reuse permissionsArticle Views454Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Investigation of bearing faults in three phase induction motor using wavelet de-noising with improved Wiener filtering (2021)

Bearing fault diagnosis in an induction motor, especially at nascent stage has become inevitable and captious to avoid unexpected shut down of the industrial process. Many researchers have concentrated on various monitoring techniques including vibration, temperature, chemical and current monitoring. In this paper, an improved bearing fault detection using motor current signature analysis (MCSA) has been presented. In the proposed work, the bearing fault signature is extracted from stator current using improved Wiener filter cancellation. Performance of Wiener filter is improved using two stage process. The side band effects of filter is removed using Kaiser window and the higher order noise due to filtering process is removed with wavelet de-noising technique. Different categories of bearing failures are examined with and without de-nosing using pre-fault component cancellation (noise cancellation). Moreover, fault indexing based on standard deviation (SD) and energy (E) value of noise canceled stator current is proposed. The proposed bearing fault detection topology is examined using simulations and experiments on a 2HP induction motor under different load condition.
Supplementary Tables from Novel Inhibitors of Cyclin-Dependent Kinases Combat Hepatocellular Carcinoma without Inducing Chemoresistance (2023)

&lt;p&gt;PDF file, 227K, Suppl. table S1: IC50 values Suppl. table S2: Substrate specificity.&lt;/p&gt;
Mapping a path to the beyond-CMOS technology for computation (2012)

This paper describes a methodology for benchmarking beyond CMOS exploratory devices for computation using metrics that can provide insights about the device fundamental operation. A more detailed investigation of circuits based upon two beyond-CMOS devices is given in the paper. First tunneling FET (TFET) circuits are compared to low power CMOS circuits. Then the All-Spin Logic device (ASLD) is described and a spin circuit theory based simulator is used to show the functional transient operation of an all spin logic circuit.
Measurement of the shape of the $$ {B}_s^0\to {D}_s^{\ast -}{\mu}^{+}{\nu}_{\mu } $$ differential decay rate (2020)

A bstract The shape of the $$ {B}_s^0\to {D}_s^{\ast -}{\mu}^{+}{\nu}_{\mu } $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>B</mml:mi><mml:mi>s</mml:mi><mml:mn>0</mml:mn></mml:msubsup><mml:mo>→</mml:mo><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mrow><mml:mo>∗</mml:mo><mml:mo>−</mml:mo></mml:mrow></mml:msubsup><mml:msup><mml:mi>μ</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msub><mml:mi>ν</mml:mi><mml:mi>μ</mml:mi></mml:msub></mml:math> differential decay rate is obtained as a function of the hadron recoil parameter using proton-proton collision data at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 1.7 fb − 1 collected by the LHCb detector. The $$ {B}_s^0\to {D}_s^{\ast -}{\mu}^{+}{\nu}_{\mu } $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>B</mml:mi><mml:mi>s</mml:mi><mml:mn>0</mml:mn></mml:msubsup><mml:mo>→</mml:mo><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mrow><mml:mo>∗</mml:mo><mml:mo>−</mml:mo></mml:mrow></mml:msubsup><mml:msup><mml:mi>μ</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msub><mml:mi>ν</mml:mi><mml:mi>μ</mml:mi></mml:msub></mml:math> decay is reconstructed through the decays $$ {D}_s^{\ast -}\to {D}_s^{-}\gamma $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mrow><mml:mo>∗</mml:mo><mml:mo>−</mml:mo></mml:mrow></mml:msubsup><mml:mo>→</mml:mo><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mo>−</mml:mo></mml:msubsup><mml:mi>γ</mml:mi></mml:math> and $$ {D}_s^{-}\to {K}^{-}{K}^{+}{\pi}^{-} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>D</mml:mi><mml:mi>s</mml:mi><mml:mo>−</mml:mo></mml:msubsup><mml:mo>→</mml:mo><mml:msup><mml:mi>K</mml:mi><mml:mo>−</mml:mo></mml:msup><mml:msup><mml:mi>K</mml:mi><mml:mo>+</mml:mo></mml:msup><mml:msup><mml:mi>π</mml:mi><mml:mo>−</mml:mo></mml:msup></mml:math> . The differential decay rate is fitted with the Caprini-Lellouch-Neubert (CLN) and Boyd-Grinstein-Lebed (BGL) parametrisations of the form factors, and the relevant quantities for both are extracted.
Continuous Counteracting Chromatographic Electrophoresis (1990)

Abstract Counteracting chromatographic electrophoresis (CACE) uses opposing electric and convective fields to focus proteins at the boundary separating distinct granular gel phases. In batch operation, CACE can purify, stack, and concentrate gram quantities of proteins. This technique has been extended to continuous operation by modifying the batch column. Experiments were then used to demonstrate operation of the column. The principles underlying focusing and separation are elucidated by linear chromatography theory.