gebhart/patrepeval huggingface dataset:
Penalized maximum likelihood simultaneous longitudinal PET image reconstruction with difference‐image priors (2018)

Reconstruction of longitudinal datasets by penalizing difference images between pairs of scans from a data series allows for noise reduction in all reconstructed images. An appropriate choice of penalty term and penalty strength allows for this noise reduction to be achieved while maintaining reconstruction performance in regions of change, either in terms of quantitation of mean intensity via DE-PML, or in terms of tumor RMSE via DTV-PML. Overall, improving the image quality of longitudinal datasets via simultaneous reconstruction has the potential to improve upon currently used methods, allow dose reduction, or reduce scan time while maintaining image quality at current levels.
DYNAMIC AND STATIC DISPLACEMENT PROPERTY OF RIGID FOUNDATION ON WEATHERED ROCK BY FIELD TEST (1996)

風化岩盤上の現地で大型模型基礎を対象に静的・動的実験を実施し, 得られた変形特性の考察と, 理論解や数値解析解との比較検討を行った. 具体的には, 支持岩盤の特性や微小振幅下の実測自由振動数と力学モデルの固有値の関係, 強制振動実験での共振点の変動やばね係数と減衰定数の応答値との関係, この実験のFEMによるシュミレーション, さらに, 極度な偏心傾斜荷重下の静的繰返し載荷での応答性状とばね係数やエネルギー消費としての減衰性, そして, 静的と動的な変形特性の関係などについて述べている. 得られた結果は, この種の基礎の耐震計算法をより発展させるための基礎的な資料として, 有益なものと考えている.
Ordered Mesoporous Sb-, Nb-, and Ta-Doped SnO<sub>2</sub> Thin Films with Adjustable Doping Levels and High Electrical Conductivity (2009)

This paper describes the synthesis and electrical properties of self-organized Sb-, Nb-, and Ta-doped SnO(2) thin films with adjustable doping levels. These transparent conducting oxides (TCOs) were prepared using a poly(ethylene-co-butylene)-b-poly(ethylene oxide) diblock copolymer as well as a novel polyisobutylene-b-poly(ethylene oxide) as organic templates. All samples are highly crystalline and have ordered cubic pore-solid architectures after removal of the polymer template by calcination; however, the electrical conductivity is not identical. The films are characterized by a combination of small- and wide-angle X-ray diffraction/scattering, SEM/TEM imaging, and X-ray photoelectron spectroscopy. Resistivity measurements conducted on the mesoporous frameworks show that the electrical properties strongly depend on both the degree of crystallinity and the elemental makeup. Considerable enhancements of the electrical properties result when the films are doped with antimony and treated in N(2) at elevated temperatures. Such TCO materials show electrical resistivities which are--despite the mesoporous morphology--only 1 order of magnitude higher than reported values for dense Sb-doped SnO(2) films.
Rapid molecular assessment of the bioturbation extent in sandy soil horizons under pine using ester‐bound lipids by on‐line thermally assisted hydrolysis and methylation‐gas chromatography/mass spectrometry (2004)

Each plant species has a unique chemical composition, and also within a given plant the various tissues differ from one another in their chemistry. These different compositions can be traced back after decay of the plant parts when they are transformed into soil organic matter (SOM). As a result, the composition of SOM reflects not only the plant origin, but also the various tissues, and the composition consequently provides an estimate of the contribution of above-ground vs. below-ground litter. From the latter distribution the extent of bioturbation (mixing of above-ground litter with the mineral soil) can be assessed. Application of thermally assisted hydrolysis and methylation (THM) using tetramethylammonium hydroxide (TMAH) and subsequent analysis by gas chromatography/mass spectrometry (GC/MS) releases all typical cutin- and suberin-derived aliphatic monomers (mono-, di- and trihydroxyalkanoic acids, alpha,omega-alkanedioic acids) as their methyl esters and/or ethers in a rapid manner. Using the distribution of omega-hydroxyalkanoic acids that are present in pine needle cutin (C(12) and C(14)) and not in root suberin, and those that are present in roots but not in needles (C(20) and C(22)), the extent of bioturbation (mixing of above-ground plant litter with the mineral soil) can be assessed. Similarly, the (9,16-dihydroxyhexadecanoic acid+9,10,18-trihydroxyoctadecanoic acid)/(C(20) + C(22) alpha,omega-alkanedioic acids) ratio reflects the degree of bioturbation. Three mineral soil profiles under Corsican pine with an A horizon that exhibited extensive bioturbation phenomena, and underlying C horizons with hardly any or no bioturbation, were investigated in order to examine the applicability of such an approach. It appeared that the A horizons contained all four mentioned omega-hydroxyalkanoic acids, while the C horizons contained virtually only the C(20) and C(22) members. The results not only suggest that bioturbation occurs in the A horizons, but also that possible illuviation or other transport mechanisms of omega-hydroxyalkanoic acids seem hardly ever or never to occur, which is a prerequisite for applying this biomarker approach in assessing degrees of bioturbation.
Wave number–spiral acoustic tweezers for dynamic and reconfigurable manipulation of particles and cells (2019)

Acoustic tweezers have recently raised great interest across many fields including biology, chemistry, engineering, and medicine, as they can perform contactless, label-free, biocompatible, and precise manipulation of particles and cells. Here, we present wave number-spiral acoustic tweezers, which are capable of dynamically reshaping surface acoustic wave (SAW) wavefields to various pressure distributions to facilitate dynamic and programmable particle/cell manipulation. SAWs propagating in multiple directions can be simultaneously and independently controlled by simply modulating the multitone excitation signals. This allows for dynamic reshaping of SAW wavefields to desired distributions, thus achieving programmable particle/cell manipulation. We experimentally demonstrated the multiple functions of wave number-spiral acoustic tweezers, among which are multiconfiguration patterning; parallel merging; pattern translation, transformation, and rotation; and dynamic translation of single microparticles along complex paths. This wave number-spiral design has the potential to revolutionize future acoustic tweezers development and advance many applications, including microscale assembly, bioprinting, and cell-cell interaction research.
Effect of Taxol and Taxotere on Gene Expression in Macrophages: Induction of the Prostaglandin H Synthase-2 Isoenzyme (1999)

Induction of genes encoding cytokines or other, unidentified proteins may contribute to the pharmacological effects of taxol. We hypothesized that prostaglandin H synthase-2 (PGHS-2) was one of the unidentified genes induced by taxol. Taxol alone or taxol plus IFN-gamma increased PGE2 formation, PGHS-2 protein expression, and PGHS-2 mRNA expression in RAW 264.7 murine macrophages. The kinetics for mRNA induction, protein expression, and catalysis were self-consistent. A selective inhibitor of PGHS-2 blocked PGE2 formation by cells incubated with taxol; a selective inhibitor of PGHS-1 had no effect. A glucocorticoid blocked the induction of mRNA, the expression of PGHS-2 protein, and the formation of PGE2. Neither taxol alone nor taxol plus IFN-gamma altered the expression of the PGHS-1 isoenzyme in RAW 264.7 cells. Taxotere, an analogue that stabilizes microtubules as potently as taxol, did not alter the expression of PGHS-2, implying that its induction in RAW 264.7 murine macrophages did not originate from microtubule stabilization. Taxol and taxotere each induced PGHS-2 expression in human monocytes suspended in 10% human serum. However, human monocytes suspended in 10% bovine serum responded only to LPS, not to taxol or taxotere, implying that they act independently of the LPS-mimetic process that is prominent in mice. Taxol induced PGHS-2 in human and murine monocytes via a p38 mitogen-associated protein kinase pathway. The inclusion of PGHS-2 among the early response genes induced in leukocytes may be relevant to the beneficial and adverse effects encountered during taxol administration.
Scale and Rotation Invariant Approach to Tracking Human Body Part Regions in Videos (2013)

We propose a novel scale and rotation invariant method to track a human subject's body part regions in cluttered videos. The proposed method optimizes the assembly of body part region proposals with the spatial and temporal constraints of a human body plan. This approach is invariant to the object scale and rotation changes. To enable scale and rotation invariance, the human body part graph of the proposed method has to be loopy, efficiently optimizing the body part region assembly is a great challenge. We propose a dynamic programming method to solve the problem. We devise a method that finds N-best whole body configurations from loopy structures in each video frame using dynamic programming. The N-best configurations are then used to construct trellises with which we track human body part regions by finding shortest paths on the trellises. Our experiments on a variety of videos show that the proposed method is efficient, accurate and robust against object appearance variations, scale and rotation changes and background clutter.
Overexpression of Jagged‐1 combined with blockade of CD40 pathway prolongs allograft survival (2014)

Dendritic cells (DCs) have the tolerogenic potential to regulate adaptive immunity and induce allografts acceptance. Here we investigated whether blockade of the CD40 pathway could enhance the immune tolerance induced by DC2.4 cells modified to express Jagged-1 (JAG1-DC) in heart transplantation. Results showed that JAG1-DC treatment combined with anti-CD40L monoclonal antibody (mAb) administration significantly prolonged cardiac allograft survival in mice, with long-term survival (>110 days) of 50% of the allografts in the recipients. The therapy specifically inhibited the immune response, induced alloantigen-specific T-cell hyporesponsiveness, upregulated transforming growth factor-β synthesis and increased the population of regulatory T cells (Tregs) driven by Jagged-1-Notch activation. These results highlight the potential application of gene therapy to induce alloantigen-specific Tregs effectively by providing the Jagged-1 stimulation.
Functional Phosphodiesterase 11A Mutations May Modify the Risk of Familial and Bilateral Testicular Germ Cell Tumors (2009)

Inactivating germline mutations in phosphodiesterase 11A (PDE11A) have been implicated in adrenal tumor susceptibility. PDE11A is highly expressed in endocrine steroidogenic tissues, especially the testis, and mice with inactivated Pde11a exhibit male infertility, a known testicular germ cell tumor (TGCT) risk factor. We sequenced the PDE11A gene-coding region in 95 patients with TGCT from 64 unrelated kindreds. We identified 8 nonsynonymous substitutions in 20 patients from 15 families: four (R52T, F258Y, G291R, and V820M) were newly recognized, three (R804H, R867G, and M878V) were functional variants previously implicated in adrenal tumor predisposition, and one (Y727C) was a known polymorphism. We compared the frequency of these variants in our patients to unrelated controls that had been screened and found negative for any endocrine diseases: only the two previously reported variants, R804H and R867G, known to be frequent in general population, were detected in these controls. The frequency of all PDE11A-gene variants (combined) was significantly higher among patients with TGCT (P = 0.0002), present in 19% of the families of our cohort. Most variants were detected in the general population, but functional studies showed that all these mutations reduced PDE activity, and that PDE11A protein expression was decreased (or absent) in TGCT samples from carriers. This is the first demonstration of the involvement of a PDE gene in TGCT, although the cyclic AMP signaling pathway has been investigated extensively in reproductive organ function and their diseases. In conclusion, we report that PDE11A-inactivating sequence variants may modify the risk of familial and bilateral TGCT.
Brain-Imaging Detection of Visual Scene Encoding in Long-term Memory for TV Commercials (2001)

<h3>ABSTRACT</h3> The authors report on experimental research using a new brain imaging technique (steady-state probe topography or SSPT) to investigate whether patterns of brain activity in the left or right frontal hemispheres could identify which frames from new TV commercials would be recognised by consumers one week later. The research revealed that video scenes held on screen for 1.5 seconds or longer were better recognised, and that scenes that elicited the fastest brain activity in the left frontal hemisphere were better recognised. The authors conclude that visual content that stimulates left-brain activity would create memorable advertising - and suggest a new method of pre-testing commercials.
Activation of Influenza A Viruses by Host Proteases from Swine Airway Epithelium (2013)

Pigs are important natural hosts of influenza A viruses, and due to their susceptibility to swine, avian, and human viruses, they may serve as intermediate hosts supporting adaptation and genetic reassortment. Cleavage of the influenza virus surface glycoprotein hemagglutinin (HA) by host cell proteases is essential for viral infectivity. Most influenza viruses, including human and swine viruses, are activated at a monobasic HA cleavage site, and we previously identified TMPRSS2 and HAT to be relevant proteases present in human airways. We investigated the proteolytic activation of influenza viruses in primary porcine tracheal and bronchial epithelial cells (PTEC and PBEC, respectively). Human H1N1 and H3N2 viruses replicated efficiently in PTECs and PBECs, and viruses containing cleaved HA were released from infected cells. Moreover, the cells supported the proteolytic activation of HA at the stage of entry. We found that swine proteases homologous to TMPRSS2 and HAT, designated swTMPRSS2 and swAT, respectively, were expressed in several parts of the porcine respiratory tract. Both proteases cloned from primary PBECs were shown to activate HA with a monobasic cleavage site upon coexpression and support multicycle replication of influenza viruses. swAT was predominantly localized at the plasma membrane, where it was present as an active protease that mediated activation of incoming virus. In contrast, swTMPRSS2 accumulated in the trans-Golgi network, suggesting that it cleaves HA in this compartment. In conclusion, our data show that HA activation in porcine airways may occur by similar proteases and at similar stages of the viral life cycle as in human airways.
Induced Pluripotent Stem Cell Reprogramming by Integration-Free Sendai Virus Vectors from Peripheral Blood of Patients with Craniometaphyseal Dysplasia (2013)

Studies of rare genetic bone disorders are often limited due to unavailability of tissue specimens and the lack of animal models fully replicating phenotypic features. Craniometaphyseal dysplasia (CMD) is a rare monogenic disorder characterized by hyperostosis of craniofacial bones concurrent with abnormal shape of long bones. Mutations for autosomal dominant CMD have been identified in the ANK gene (ANKH). Here we describe a simple and efficient method to reprogram adherent cells cultured from peripheral blood to human induced pluripotent stem cells (hiPSCs) from eight CMD patients and five healthy controls. Peripheral blood mononuclear cells (PBMCs) were separated from 5-7 mL of whole blood by Ficoll gradient, expanded in the presence of cytokines and transduced with Sendai virus (SeV) vectors encoding OCT3/4, SOX2, KLF4, and c-MYC. SeV vector, a cytoplasmic RNA vector, is lost from host cells after propagation for 10-13 passages. These hiPSCs express stem cell markers, have normal karyotypes, and are capable of forming embryoid bodies in vitro as well as teratomas in vivo. Further differentiation of these patient-specific iPSCs into osteoblasts and osteoclasts can provide a useful tool to study the effects CMD mutations on bone, and this approach can be applied for disease modeling of other rare genetic musculoskeletal disorders.
Real-time unobtrusive program execution trace compression using branch predictor events (2010)

Unobtrusive capturing of program execution traces in real-time is crucial in debugging cyber-physical systems. However, tracing even limited program segments is often cost-prohibitive, requiring wide trace ports and large on-chip trace buffers. This paper introduces a new cost-effective technique for capturing and compressing program execution traces in real time. It uses branch predictor-like structures in the trace module to losslessly compress the traces. This approach results in high compression ratios because it only has to transmit misprediction events to the software debugger. Coupled with an effective variable encoding scheme, our technique requires merely 0.036 bits/instruction of trace port bandwidth (a 28-fold improvement over the commercial state-of-the-art) at a cost of roughly 5,200 logic gates.
Alkaline decomposition of organic disulfides. II. Alternative pathways as determined by structure (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkaline decomposition of organic disulfides. II. Alternative pathways as determined by structureJames P. Danehy and Wood Eugene HunterCite this: J. Org. Chem. 1967, 32, 7, 2047–2053Publication Date (Print):July 1, 1967Publication History Published online1 May 2002Published inissue 1 July 1967https://pubs.acs.org/doi/10.1021/jo01282a001https://doi.org/10.1021/jo01282a001research-articleACS PublicationsRequest reuse permissionsArticle Views509Altmetric-Citations50LEARN 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
Photochemistry of Colloidal Metal Sulfides. 5. Fluorescence and Chemical Reactions of ZnS and ZnS/CdS Co‐Colloids (1983)

Abstract Small colloidal particles of ZnS were obtained by precipitation of Zn 2+ with SH − in the presence of colloidal silicon dioxide. Co‐colloids were prepared by simultaneously precipitating ZnS and CdS. Colloidal ZnS fluoresces at 425 nm. 90% of the fluorescence decays within 30 ns. The fluorescence is partly quenched by oxygen, chloroethanol and chloralhydrate. It can be completely quenched by methyl viologen and sulfide anions at low concentrations. The quenching actions are attributed to the scavenging of electrons or positive holes which are photo‐generated in ZnS. The onset of the absorption and the maximum of the fluorescence band are shifted towards shorter wavelengths with increasing Zn/Cd ratio of the co‐colloid. – ZnS in deaerated solution undergoes a slow photo‐anodic dissolution (quantum yield ø = 2 · 10 −3 ZnS molecules/photon), the products being H 2 , Zn 2+ (aq), sulfur and SO (aq). In the presence of air, a rapid decomposition with ø = 0.32 ZnS/photon takes place. In deaerated solutions, chloroorganic compounds promote the dissolution of ZnS. The chloroorganic compounds are decomposed, too. In the presence of sulfite, zinc metal is photo‐deposited onto the colloidal particles until hydrogen production takes over with ø = 0.18 H 2 /photon. In the presence of both sulfite and carbon dioxide, formic acid is produced with ø = 0.2 HCOOH/photon.
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway (2017)

Immunoglobulin G (IgG) is a major effector molecule of the human immune response, and aberrations in IgG glycosylation are linked to various diseases. However, the molecular mechanisms underlying protein glycosylation are still poorly understood. We present a data-driven approach to infer reactions in the IgG glycosylation pathway using large-scale mass-spectrometry measurements. Gaussian graphical models are used to construct association networks from four cohorts. We find that glycan pairs with high partial correlations represent enzymatic reactions in the known glycosylation pathway, and then predict new biochemical reactions using a rule-based approach. Validation is performed using data from a GWAS and results from three in vitro experiments. We show that one predicted reaction is enzymatically feasible and that one rejected reaction does not occur in vitro. Moreover, in contrast to previous knowledge, enzymes involved in our predictions colocalize in the Golgi of two cell lines, further confirming the in silico predictions.
Ensemble of binary tree structured deep convolutional network for image classification (2017)

In this paper, we propose an ensemble of tree- structured learning architecture to improve the discriminative capability of deep convolutional neural network (DCNN) for image classification. In the proposed technique, the path from the root node to a leaf node represents a classification rule. Thus, to maximize the classification accuracy, each internal node needs to make an optimal binary decision to the left or the right child node. To this aim, we develop a tree-CNN as a randomized tree to embed a DCNN into each internal node and train the model to determine the best traversing path to predict a class. Classification of some images with similar statistical properties yet belonging to different classes are difficult with the conventional DCNN architecture. Thus, to resolve the problem, we use a coarse-to-fine approach where subsequent networks in children nodes are hierarchically and randomly organized to discriminate smaller sets of classes than those in a parent node. The results from all the individual tree-CNNs are ensembled to make the final decision in classification. The proposed technique is implemented with the state-of-the-art deep network model, i.e., Wide Residual Network DCNN model [19], and is demonstrated with experimental results to outperform the classification performance over the anchor.
Two-component signal-transducing systems involved in stress responses and vancomycin susceptibility in Lactobacillus sakei (1998)

Fragments of five rrp genes encoding response regulators (RRs) in Lactobacillus sakei were amplified by PCR using degenerate oligonucleotide primers. The five rrp genes were part of distinct loci that also comprised hpk genes encoding histidine protein kinases (HPKs). The putative RRs belonged to the OmpR-PhoB subclass of response regulators that consist of N-terminal receiver and C-terminal DNA-binding domains. The putative HPKs were members of the EnvZ-NarX family of orthodox histidine protein kinases which possess two transmembrane segments in a non-conserved N-terminal domain and a C-terminal cytoplasmic kinase domain. Insertional inactivation of the rrp genes indicated that the RRs are implicated in susceptibility to the glycopeptide antibiotic vancomycin, and to extreme pH, temperature and oxidative conditions.