gebhart/patrepeval huggingface dataset:
Using integrated omics to assess the effects of rhinovirus infection in children with Cystic Fibrosis (CF) (2020)

<b>Introduction/Aim:</b> Children with Cystic Fibrosis (CF) typically exhibit prolonged and severe symptoms during rhinovirus (RV) infection compared to healthy children. Here, we studied the host-rhinovirus interaction signature after infection, integrating two omics: (1) Whole transcriptome sequencing (WTS) to determine the viral load and host’s gene expression, and (2) metabolomics to profile the metabolites associated with the viral infection of primary tracheal epithelial cells obtained from healthy children (H) and those with CF. <b>Methods:</b> WTS and hydrophilic interaction liquid chromatography (HILIC) coupled to mass spectrometry, were used to identify the differences in transcripts/metabolites and RV coverage produced by H (3.9 ± 1.5 years; n=8) and CF (2.6 ± 1.8 years; n=8; all p.Phe508del/p.Phe508del) primary epithelial cells at 24 hours post-infection with human rhinovirus 1B. Univariate and multivariate analyses were then performed to identify the infection hallmark. <b>Results:</b> RV coverage in uninfected cells (Mock) was less than 0.5X, whereas, infected cells presented 44.4X and 101.6X of RV in children with and without CF respectively. Global RV infection was associated with 14 metabolites and 1713 genes differential expressed. From these, several metabolic pathways were found dysregulated including inositol metabolism and glycerophospholipid biosynthesis. <b>Conclusion:</b> Metabolic host-derived pathways associated with RV infection were identified. Although functional analysis is still required, these pathways could be used as potential biomarkers of RV infection in CF. Future analysis will help to understand whether these compounds can be targeted for antiviral purposes.
Toward ultralow-power computing at exteme with silicon carbide (SiC) nanoelectromechanical logic (2014)

Growing number of important application areas, including automotive and industrial applications as well as space, avionics, combustion engine, intelligent propulsion systems, and geo-thermal exploration require electronics that can work reliable at extreme conditions - in particular at a temperature > 250°C and at high radiation (1-30 Mrad), where conventional electronics fail to work reliably. Traditionally, existing wideband-gap semiconductors, e.g., silicon carbide (SiC) transistor-based electronics have been considered most viable for high temperature and high radiation applications. However, the large-size, high threshold voltage, low switching speed and high leakage current make logic design with these devices unattractive. Additionally, the leakage current markedly increases at high temperature (in the range of 10 μA for a 2-input NAND gate), which induces self-heating effect and makes power delivery at high temperature very challenging. To address these issues, in this paper we present a computing platform for low-power reliable operation at extreme environment using SiC electromechanical switches. We show that a device-circuit-architecture co-design approach can provide reliable long-term operation with virtually zero leakage power.
Tris DBA palladium overcomes hypoxia-mediated drug resistance in multiple myeloma (2015)

Despite recent progress in novel and targeted therapies, multiple myeloma (MM) remains a therapeutically challenging incurable disease. The regulation of important cellular processes and its link to cancer presented Src as an attractive target for MM. We suggest a novel strategy to improve the treatment of MM and overcome the drug resistance for the current therapeutic agents by specific inhibition of Src in MM cells by Tris (Dibenzylideneacetone) dipalladium (Tris DBA). Tris DBA reduces proliferation, induces G1 arrest and apoptosis in MM cells. Tris DBA showed additive effect with proteasome inhibitors reducing proliferation, cell cycle signaling, and increasing apoptosis more than each drug alone. Tris DBA overcame hypoxia-induced effects such as enhanced chemotaxis or drug resistance to proteasome inhibitors by inhibition of HIF1α expression. Moreover, we found that Tris DBA is an effective anti-myeloma agent alone or in combination with other targeted drugs and that it reverses hypoxia-induced drug resistance in myeloma.
Nonlinear Multigrid Optical Diffusion Tomography (2000)

We propose a nonlinear multigrid technique for computing the maximum a posteriori (MAP) reconstruction in the optical diffusion tomography problem. The multigrid approach improves reconstruction quality and it dramatically reduces computation.
Trusted-HB: a low-cost version of HB+ secure against Man-in-The-Middle attacks (2008)

Since the introduction at Crypto'05 by Juels and Weis of the protocol HB+, a lightweight protocol secure against active attacks but only in a detection based-model, many works have tried to enhance its security. We propose here a new approach to achieve resistance against Man-in-The-Middle attacks. Our requirements - in terms of extra communications and hardware - are surprisingly low.
Exciton Dynamics in Bundled and Unbundled (6,5) Carbon Nanotubes (2006)

We present a pump-probe study of exciton dynamics in semiconducting (6,5) single-wall carbon nanotubes (SWNTs). Optical transients from individual tubes and small bundles (ntubes≤7) shed new light onto the dynamics of singlet and triplet excitons.
A review of recent developments in electrical machine design optimization methods with a permanent magnet synchronous motor benchmark study (2011)

The paper systematically covers the significant developments of the last decade, including surrogate modelling of electrical machines, direct and stochastic search algorithms for both single- and multi- objective design optimization problems. The specific challenges and the dedicated algorithms for electric machine design are discussed, followed by benchmark studies comparing Response Surface (RS) and Differential Evolutionary (DE) algorithms on a permanent magnet synchronous motor (PMSM) design with 5 independent variables and a strong non-linear multi-objective Pareto front and on a function with 11 independent variables. The results show that RS and DE are comparable when the optimization employs only a small number of design candidates and DE performs better when more candidates are included.
Towards exploiting the full adaptation potential of cloud applications (2014)

Current technology for cloud application adaptation fails to capture two fundamental aspect of cloud environments: multiple adaptation options and interferences and dependencies among these multiple mechanisms. Addressing these aspects requires a significant extension of existing cloud tools and frameworks for engineering and executing cloud application adaptations. They should explicitly take into account: all entities of the cloud environment relevant for adaptation decisions; the concrete adaptation actions that these cloud entities may perform; and the mutual dependencies between those entities and actions. In this paper we provide the first insights towards such novel technology. As main contribution, we systematically elicit the key entities related to adaptations inside a cloud environment and explicitly document those in a conceptual model. To build this model we surveyed the literature, discussed with industrial partners with experience in cloud computing, and analyzed commercial solutions. We also provide a case study based on Amazon Web Services solutions, to show how our conceptual model can be instantiated and help developers to identify possible cloud application adaptation strategies.
Phase I trial of PN401, an oral prodrug of uridine, to prevent toxicity from fluorouracil in patients with advanced cancer. (1997)

Oral PN401 is well tolerated and total doses of 6 g every 6 hours yield sustained levels of URD in the target range of 50 mumol/L. The MTD of FU with PN401 rescue is 1,000 mg/m2 and the recommended dose for phase II trials is 800 mg/m2 given weekly for 6 weeks with dose escalation. Further studies to define better the appropriate interval for PN401 rescue and the appropriate dose of FU when given with biochemical modulation, such as with leucovorin, are indicated.
Photo‐patterning of smart light‐modulation gel (2006)

Abstract A novel method for fabricating desired patterns of smart light‐modulation gels, which consist of thermoresponsive N ‐isopropylacrylamide (NIPAM) gel particles containing pigment, was developed. The patterns were fabricated by photo‐patterning of dispersion of colored NIPAM gel particles in photosensitive poly(vinylalcohol)‐styrylpyridinium solution. The pattern showed drastic color changes in response to the surrounding temperature changes. By repeated cycles of the patterning method, several independent patterns that contained different color particles were fabricated. In addition, a thermosensor array was also fabricated, which was constructed with independent patterns containing colored NIPAM gel having different color‐changing temperatures. The patterning method studied here is considered to have strong potential to extend the application field of the smart light‐modulation gels. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 5351–5357, 2006
Single particle detection in CMOS compatible photonic crystal nanobeam cavities (2013)

We report the label-free detection of single particles using photonic crystal nanobeam cavities fabricated in silicon-on-insulator platform, and embedded inside microfluidic channels fabricated in poly-dimethylsiloxane (PDMS). Our system operates in the telecommunication wavelength band, thus leveraging the widely available, robust and tunable telecom laser sources. Using this approach, we demonstrated the detection of polystyrene nanoparticles with dimensions down to 12.5nm in radius. Furthermore, binding events of a single streptavidin molecule have been observed.
Changes of Periodontal Tissues Because of Orthodontic Treatment: A Retrospective Study (2021)

Aim: To evaluate the periodontal status before and after orthodontic treatment and to analyze the confounding factors associated with it. Materials and Methods: The present retrospective study analyzed pre- and posttreatment records of a total of 60 patients. Intraoral digital photographs before and after the orthodontic treatment were used to measure the following three periodontal variables: (a) width of the keratinized gingiva, (b) gingival recession, and (c) the status of interdental papilla. The ImageJ 46 software imaging program was used to perform the required measurements. The clinical data were then analyzed in an association with the participants’ demographic data, the type of orthodontic tooth movement, and other confounding factors. The data obtained were manually entered into the statistical package and analyzed using a significance level set at P &lt; .05. Descriptive statistics, paired t -tests, and Pearson’s correlation analysis were used to identify differences among the studied variables. Results: Among the 60 patients, the majority (66.7%) were females. Most cases of the treated malocclusion were Class II, and most patients underwent intrusion and retrusion movements. The width of keratinized gingiva increased for most sites of upper teeth. In contrast, the lower teeth showed a mix of improvement and compromised width of keratinized gingiva. As a measure of gingival recession, the difference of clinical crown height revealed the tendency toward a reduced clinical crown height for most sites. Upper left lateral incisors and canines showed significant values with regard to keratinized gingival width measurements and tooth movements such as extrusion and intrusion movements. Likewise, with regard to the clinical crown height, upper right central incisors showed significant differences when correlated with the interincisal angle, lower incisors to the mandibular plane, and upper incisors to the NA line. The upper lateral incisors also showed significant correlations to certain cephalometric measurements. Conclusions: The orthodontic treatment was found to exert a significantly positive impact on the surrounding periodontium, particularly in the upper canine areas. Likewise, various types of tooth movement were found to positively affect the periodontium.
Association of lipocalin-type prostaglandin D synthase with disproportionately enlarged subarachnoid-space in idiopathic normal pressure hydrocephalus (2014)

Our data support the diagnostic value of L-PGDS as a CSF biomarker for iNPH and suggest a possible interaction between L-PGDS and tau protein. In addition, L-PGDS might work as a surrogate marker for DESH features, white matter damage, and frontal lobe dysfunction.
Differentiation Therapy by Epigenetic Reconditioning Exerts Antitumor Effects on Liver Cancer Cells (2018)

Primary liver tumors are mainly represented by hepatocellular carcinoma (HCC), one of the most aggressive and resistant forms of cancer. Liver tumorigenesis is characterized by an accumulation of epigenetic abnormalities, leading to gene extinction and loss of hepatocyte differentiation. The aim of this work was to investigate the feasibility of converting liver cancer cells toward a less aggressive and differentiated phenotype using a process called epigenetic reconditioning. Here, we showed that an epigenetic regimen with non-cytotoxic doses of the demethylating compound 5-azacytidine (5-AZA) promoted an anti-cancer response by inhibiting HCC cell tumorigenicity. Furthermore, epigenetic reconditioning improved sorafenib response. Remarkably, epigenetic treatment was associated with a significant restoration of differentiation, as attested by the increased expression of characteristic hepatocyte markers in reconditioned cells. In particular, we showed that reexpression of these epigenetically silenced liver genes following 5-AZA treatment or after knockdown of DNA methyltransferase 1 (DNMT1) was the result of regional CpG demethylation. Lastly, we confirmed the efficacy of HCC differentiation therapy by epigenetic reconditioning using an in vivo tumor growth model. In summary, this work demonstrates that epigenetic reconditioning using the demethylating compound 5-AZA shows therapeutic significance for liver cancer and is potentially attractive for the treatment of solid tumors.
Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid (2020)

Central nervous system atypical teratoid/rhabdoid tumors (ATRTs) are rare and aggressive tumors with a very poor prognosis. Current treatments for ATRT include resection of the tumor, followed by systemic chemotherapy and radiation therapy, which have toxic side effects for young children. Gene expression analyses of human ATRTs and normal brain samples indicate that ATRTs have aberrant expression of epigenetic markers including class I histone deacetylases (HDAC's) and lysine demethylase (LSD1). Here, we investigate the effect of a small molecule epigenetic modulator known as Domatinostat (4SC-202), which inhibits both class I HDAC's and Lysine Demethylase (LSD1), on ATRT cell survival and single cell heterogeneity. Our findings suggest that 4SC-202 is both cytotoxic and cytostatic to ATRT in 2D and 3D scaffold cell culture models and may target cancer stem cells. Single-cell RNA sequencing data from ATRT-06 spheroids treated with 4SC-202 have a reduced population of cells overexpressing stem cell-related genes, including <i>SOX2</i>. Flow cytometry and immunofluorescence on 3D ATRT-06 scaffold models support these results suggesting that 4SC-202 reduces expression of cancer stem cell markers SOX2, CD133, and FOXM1. Drug-induced changes to the systems biology landscape are also explored by multi-omics enrichment analyses. In summary, our data indicate that 4SC-202 has both cytotoxic and cytostatic effects on ATRT, targets specific cell sub-populations, including those with cancer stem-like features, and is an important potential cancer therapeutic to be investigated in vivo.
Improving Processor Performance by Dynamically Pre-Processing the Instruction Stream (1998)

Improving Processor Performance by Dynamically PreProcessing the Instruction Stream by James David Dundas Chairman: Trevor Mudge The exponentially increasing gap between processors and off-chip memory, as measured in processor cycles, is rapidly turning memory latency into a major processor performance bottleneck. Traditional solutions, such as employing multiple levels of caches, are expensive and do not work well with some applications. We evaluate a technique, called runahead pre-processing, that can significantly improve processor performance. The basic idea behind runahead is to use the processor pipeline to pre-process instructions during cache miss cycles, instead of stalling. The pre-processed instructions are used to generate highly accurate instruction and data stream prefetches, while all of the pre-processed instruction results are discarded after the cache miss has been serviced: this allows us to achieve a form of very aggressive speculation with a simple in-order...
Erythropoietin mediated bone formation is regulated by mTOR signaling (2011)

The role of erythropoietin (Epo) and Epo/Epo receptor (EpoR) signaling pathways for production of red blood cells are well established. However, little is known about Epo/EpoR signaling in non-hematopoietic cells. Recently, we demonstrated that Epo activates JAK/STAT signaling in hematopoietic stem cells (HSCs), leading to the production of bone morphogenetic protein 2 (BMP2) and bone formation and that Epo also directly activates mesenchymal cells to form osteoblasts in vitro. In this study, we investigated the effects of mTOR signaling on Epo-mediated osteoblastogenesis and osteoclastogenesis. We found that mTOR inhibition by rapamycin blocks Epo-dependent and -independent osteoblastic phenotypes in human bone marrow stromal cells (hBMSCs) and ST2 cells, respectively. Furthermore, we found that rapamycin inhibits Epo-dependent and -independent osteoclastogenesis in mouse bone marrow mononuclear cells and Raw264.7 cells. Finally, we demonstrated that Epo increases NFATc1 expression and decreases cathepsin K expression in an mTOR-independent manner, resulting in an increase of osteoclast numbers and a decrease in resorption activity. Taken together, these results strongly indicate that mTOR signaling plays an important role in Epo-mediated bone homeostasis.
Dynamic simulation of first pass myocardial perfusion MR with a novel perfusion phantom (2011)

To describe a novel hardware MR-perfusion phantom to model first-pass of a bolus of contrast in the cardiac cavities and large thoracic vessels (arterial input function, AIF) and in the myocardium, allowing for the acquisition of dynamic first-pass MR-perfusion data and for a precise control of cardiac output and myocardial perfusion for true validation of perfusion quantification.
Ultrasound Signal Processing: From Models to Deep Learning (2023)

Medical ultrasound imaging relies heavily on high-quality signal processing to provide reliable and interpretable image reconstructions. Conventionally, reconstruction algorithms have been derived from physical principles. These algorithms rely on assumptions and approximations of the underlying measurement model, limiting image quality in settings where these assumptions break down. Conversely, more sophisticated solutions based on statistical modeling or careful parameter tuning or derived from increased model complexity can be sensitive to different environments. Recently, deep learning-based methods, which are optimized in a data-driven fashion, have gained popularity. These model-agnostic techniques often rely on generic model structures and require vast training data to converge to a robust solution. A relatively new paradigm combines the power of the two: leveraging data-driven deep learning and exploiting domain knowledge. These model-based solutions yield high robustness and require fewer parameters and training data than conventional neural networks. In this work we provide an overview of these techniques from the recent literature and discuss a wide variety of ultrasound applications. We aim to inspire the reader to perform further research in this area and to address the opportunities within the field of ultrasound signal processing. We conclude with a future perspective on model-based deep learning techniques for medical ultrasound.
Illuminating Permeable Mineral Soil Groundwater Seepage Pathways Feeding Peatland Pools Using Thermal and Electrical Conductivity Signatures (2023)

Wetland environments are well documented to contain unique hydrogeomorphic subsystems that benefit from nutrient and temperature regimes provided by upwelling groundwater sources. Matrix seepage and preferential flow can both serve as groundwater inputs that control carbon-cycling within these environments. Recent work in a northern boreal peatland of Maine illuminates parallel dynamics to other wetland environments, with matrix seepage and preferential flow pathways (PFPs) identified and quantified proximal to peatland pools. PFPs around the peatland pools have been interpreted as peat pipes, known to transport nutrients within the peat matrix. Thermal signatures surrounding the peatland pool sources were mapped using point temperature measurements, handheld thermal imagery, and airborne thermal infrared mapping. Electrical geophysical methods were deployed to image the structure and stratigraphy of the underlying mineral sediments to delineate the source of focused upwelling around the peatland pools. Ground-penetrating radar (GPR) surveys show discontinuities in the impermeable glacio-marine clay controlling the hydrogeomorphic development of the peatlands studied. These mineral soil discontinuities in the GPR surveys, interpreted to be regional glacial esker deposits, are located proximal to the overlying peatland pools. Electromagnetic induction surveys were deployed to map the bulk electrical conductivity structures associated with the near-surface geology beneath the peatland pools. Point specific conductance measurements were taken at identified zones of thermal anomalies to further validate contrasts between peat pore water and mineral soil groundwater in the peatlands. Water samples were collected at the seepage sites and analyzed for iron and manganese trace elements to support the hypothesis that upwelling occurs from permeable glacial esker deposits. Focused groundwater inputs into peatlands may define a key hydrogeomorphic development process for peatland pool systems and the surrounding ecology. Further, these inputs could have implications for carbon-cycling, building on the established regional relationship between groundwater flow and carbon transport. Illuminating the focused groundwater flowpaths and interpreting their hydrogeologic origins may serve as a basis for future carbon-cycling exploration within peatlands at novel, fine-scales.
Synthesis and structural study of 3-phenyl-6,7,8,9-tetrahydrocyclopenta[a]naphthalene-containing ansa-complexes of zirconium (2017)

The zirconium rac- and meso-complexes of the ansa-type that contain a 3-phenyl-6,7,8,9-tetrahydrocyclopenta[a]naphthalene fragment and a dimethylsilylene bridge are synthesized. The compounds obtained are characterized by NMR spectroscopy; the structure of rac-complex is studied by X-ray diffraction, which maked it possible to evaluate the steric availability of the zirconium center in the corresponding catalysts for the olefin polymerization.