gebhart/patrepeval huggingface dataset:
Advancing Relative Permeability Estimation Through Data-Driven Modeling (2020)

Abstract Availability of large amounts of data helps in developing data-driven models using state of the art Artificial intelligence (AI) methodologies. Relative permeability is an important parameter used by reservoir engineers and are usually accurately obtained from laboratory experiments, which are relatively expensive. Therefore, AI can play an important role in developing models to predict relative permeability accurately without extensive lab procedures. Accordingly, this work presents application of two AI algorithms namely, Artificial Neural Network (ANN) and Adaptive Neuro-Fuzzy Inference System (ANFIS). Furthermore, two novel mathematical correlations are extracted from the ANN model to predict relative permeability of oil/water in oil- and water-wet environments. The input data, obtained from literature, for the development of AI models include porosity, rock absolute permeability, initial water saturation, residual oil saturation, wettability index and water saturation. A customized workflow is applied to ensure proper data is fed into the AI models. In addition, a rigorous sensitivity analysis is performed within the framework of this workflow. This analysis involves running multiple realizations with varying number of neurons, resulting in various weights and bias for the ANN model. Moreover, ANFIS model is tuned using various cluster sizes to result in the most optimum value. Finally, the optimized ANN and ANFIS models are compared using the Root Mean Squared Error (RMSE) and correlation coefficient (R2) analysis when applied to a blind dataset comprising of more than 300 data points. The analysis illustrates that the ANN model is relatively better in predicting relative permeability values to both, oil, and water. On the other hand, analysis of the ANFIS model shows that it yields high error values when tested on unseen dataset. Also, unlike the ANN mode, it does not provide an actual mathematical correlation. This work presents alternate data-driven artificial intelligence models which will lead to quicker and cheaper relative permeability estimates.
Joint Reconstruction Of Correlated Images From Compressed Images (2012)

Publication in the conference proceedings of EUSIPCO, Bucharest, Romania, 2012
Thermo-electrical property measurement by a laser based micro ZT-meter of nanostructured oxide thin films (2014)

Communication Orale
Ultrabright fluorescent OLEDS using triplet sinks (2023)

A first device is provided. The first device further comprises an organic light emitting device. The organic light emitting device further comprises an anode, a cathode, and an emissive layer disposed between the anode and the cathode. The emissive layer further comprises an organic host compound, an organic emitting compound capable of fluorescent emission at room temperature, and an organic dopant compound. The triplet energy of the dopant compound is lower than the triplet energy of the host compound. The dopant compound does not strongly absorb the fluorescent emission of the emitting compound.
Unnatural tetradeoxy echinocandins produced by gene cluster design and heterologous expression (2023)

The hydroxyl groups in the amino acid residues of echinocandin B were related to the biological activity, the instability, and the drug resistance. The modification of hydroxyl groups was expected to obtain the new lead compounds for next generation of echinocandin drug development. In this work one method for heterologous production of the tetradeoxy echinocandin was achieved. A reconstructed biosynthetic gene cluster for tetradeoxy echinocandins composed of <i>ecdA</i>/<i>I</i>/<i>K</i> and <i>htyE</i> was designed and successfully hetero-expressed in <i>Aspergillus nidulans</i>. The target product of echinocandin E (1) together with one unexpected derivative echinocandin F (2), were isolated from the fermentation culture of engineered strain. Both of compounds were unreported echinocandin derivatives and the structures were identified on the basis of mass and NMR spectral data analysis. Compared with echinocandin B, echinocandin E demonstrated superior stability and comparable antifungal activity.
Eupatilin Improves Cilia Defects in Human CEP290 Ciliopathy Models (2023)

The photoreceptor outer segment is a highly specialized primary cilium that is essential for phototransduction and vision. Biallelic pathogenic variants in the cilia-associated gene <i>CEP290</i> cause non-syndromic Leber congenital amaurosis 10 (LCA10) and syndromic diseases, where the retina is also affected. While RNA antisense oligonucleotides and gene editing are potential treatment options for the common deep intronic variant c.2991+1655A>G in <i>CEP290</i>, there is a need for variant-independent approaches that could be applied to a broader spectrum of ciliopathies. Here, we generated several distinct human models of <i>CEP290</i>-related retinal disease and investigated the effects of the flavonoid eupatilin as a potential treatment. Eupatilin improved cilium formation and length in CEP290 LCA10 patient-derived fibroblasts, in gene-edited <i>CEP290</i> knockout (CEP290 KO) RPE1 cells, and in both CEP290 LCA10 and CEP290 KO iPSCs-derived retinal organoids. Furthermore, eupatilin reduced rhodopsin retention in the outer nuclear layer of CEP290 LCA10 retinal organoids. Eupatilin altered gene transcription in retinal organoids by modulating the expression of rhodopsin and by targeting cilia and synaptic plasticity pathways. This work sheds light on the mechanism of action of eupatilin and supports its potential as a variant-independent approach for <i>CEP290</i>-associated ciliopathies.
Secondary cell wall polysaccharides from Bacillus cereus strains G9241, 03BB87 and 03BB102 causing fatal pneumonia share similar glycosyl structures with the polysaccharides from Bacillus anthracis (2011)

Secondary cell wall polysaccharides (SCWPs) are important structural components of the Bacillus cell wall and contribute to the array of antigens presented by these organisms in both spore and vegetative forms. We previously found that antisera raised to Bacillus anthracis spore preparations cross-reacted with SCWPs isolated from several strains of pathogenic B. cereus, but did not react with other phylogenetically related but nonpathogenic Bacilli, suggesting that the SCWP from B. anthracis and pathogenic B. cereus strains share specific structural features. In this study, SCWPs from three strains of B. cereus causing severe or fatal pneumonia (G9241, 03BB87 and 03BB102) were isolated and subjected to structural analysis and their structures were compared to SCWPs from B. anthracis. Complete structural analysis was performed for the B. cereus G9241 SCWP using NMR spectroscopy, mass spectrometry and derivatization methods. The analyses show that SCWPs from B. cereus G9241 has a glycosyl backbone identical to that of B. anthracis SCWP, consisting of multiple trisaccharide repeats of: →6)-α-d-GlcpNAc-(1 → 4)-β-d-ManpNAc-(1 → 4)-β-d-GlcpNAc-(1→. Both the B. anthracis and pathogenic B. cereus SCWPs are highly substituted at all GlcNAc residues with α- and β-Gal residues, however, only the SCWPs from B. cereus G9241 and 03BB87 carry an additional α-Gal substitution at O-3 of ManNAc residues, a feature lacking in the B. anthracis SCWPs. Both the B. anthracis and B. cereus SCWPs are pyruvylated, with an approximate molecular mass of ≈12,000 Da. The implications of these findings regarding pathogenicity and cell wall structure are discussed.
Deregulated expression of human c-jun transforms primary rat embryo cells in cooperation with an activated c-Ha-ras gene and transforms rat-1a cells as a single gene. (1989)

While the ability of the retroviral oncogene V-jun to transform chicken cells led to its discovery, the oncogenic potential of its cellular homologue, c-jun, which encodes a transcription factor, is unknown. We isolated a 1070-base-pair cDNA clone containing the unmutated entire open reading frame of c-jun from a human small cell lung cancer line. This cDNA as well as a 5.6-kilobase normal human genomic DNA fragment containing the c-jun gene were placed under the control of retroviral long terminal repeats and introduced into primary rat embryo cells (RECs), with or without other oncogenes, and into an immortal rat fibroblast cell line, Rat-1a, as a single gene. In Rat-1a cells the expression of human c-jun mRNA was associated with the ability to clone in soft agarose and form tumors in nude mice. When the c-jun cDNA or genomic DNA constructs were introduced into RECs, no foci of transformed cells were seen with c-jun alone or c-jun cotransfected with deregulated c-myc or L-myc protooncogenes. However, cotransfection of the c-jun constructs with an activated human c-Ha-ras gene led to foci of transformed cells which gave rise to immortalized cell lines that cloned in soft agarose and formed tumors in nude mice. Furthermore, formation of foci of transformed RECs by the c-jun/ras combination was augmented 3-fold by the tumor promoter phorbol 12-tetradecanoate 13-acetate. We conclude that deregulated expression of human c-jun can participate in malignant transformation of normal mammalian cells.
3.6 A CMOS Resistor-Based Temperature Sensor with a 10fJ·K2 Resolution FoM and 0.4°C (30) Inaccuracy From −55°C to 125°C After a 1-point Trim (2020)

Energy efficiency and accuracy are important specifications of CMOS temperature sensors. BJT -based sensors achieve state-of-the-art accuracy [1], while Wheatstone-bridge (WhB) sensors achieve lower accuracy but state-of-the-art energy efficiency [2], [3]. This paper presents a WhB sensor that is read out by an energy-efficient continuous-time delta-sigma modulator (CTDSM). Compared to [2], [3], the modulator achieves better energy efficiency with the help of a return-to-CM (RCM) DAC and an OTA with a tail-resistor linearization scheme. Moreover, better accuracy is achieved by embedding the DAC in the bridge and by using more sensitive silicided-diffusion resistors instead of silicided-poly resistors. Compared to the state-of-the-art [3], the proposed sensor achieves a 2× improvement in resolution FoM (10fJ.K2), and a 2× improvement in inaccuracy (0.4° C(3σ) from -55° C to 125°C after a 1-point trim).
Fast 1H spectroscopic imaging using a multi‐element head‐coil array (1998)

Fast proton magnetic resonance spectroscopic imaging (MRSI) using a multi-element head-coil array is examined with respect to three aspects: the coil design, the use of an appropriate signal combination method, and the design of the MRSI pulse sequence itself. An eight-element head-coil array has been developed to increase the signal-to-noise ratio (SNR) of MRSI in the human brain. The flexible wraparound design optimally fits different head sizes and thus provides high sensitivity. The signal combination of the individual coil elements is based on the approach proposed by Roemer et al. (Magn. Reson. Med. 16, 192 (1990)). An additional short prescan is performed to provide a good estimate of the complex coil sensitivity profiles, which are used in the signal combination procedure to correct the spectroscopic imaging data for the spatially varying intensity. The use of coil arrays in MRSI has some effect on the requirements for both water and lipid suppression. These techniques and a MRSI pulse sequence that provides a high spectroscopic resolution are described and discussed. Experimental results at 1.5 T show that metabolite maps of N-acetylaspartate (NAA), choline (Cho), phosphocreatine (PCr)/creatine (Cr) can be obtained within a 5-min acquisition time.
Data from Whole-Genome and Transcriptional Analysis of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer Demonstrates Intraclass Heterogeneity (2023)

&lt;div&gt;Abstract&lt;p&gt;Therapeutic resistance in metastatic castration-resistant prostate cancer (mCRPC) can be accompanied by treatment-emergent small-cell neuroendocrine carcinoma (t-SCNC), a morphologically distinct subtype. We performed integrative whole-genome and -transcriptome analysis of mCRPC tumor biopsies including paired biopsies after progression, and multiple samples from the same individual. t-SCNC was significantly less likely to have amplification of &lt;i&gt;AR&lt;/i&gt; or an intergenic &lt;i&gt;AR-&lt;/i&gt;enhancer locus, and demonstrated lower expression of &lt;i&gt;AR&lt;/i&gt; and its downstream transcriptional targets. Genomic and transcriptional hallmarks of t-SCNC included biallelic loss of &lt;i&gt;RB1&lt;/i&gt;, elevated expression levels of &lt;i&gt;CDKN2A&lt;/i&gt; and &lt;i&gt;E2F&lt;/i&gt;1, and loss of expression of the &lt;i&gt;AR&lt;/i&gt; and &lt;i&gt;AR&lt;/i&gt;-responsive genes including &lt;i&gt;TMPRSS2&lt;/i&gt; and &lt;i&gt;NKX3-1&lt;/i&gt;. We identified three tumors that converted from adenocarcinoma to t-SCNC and demonstrate spatial and temporal intrapatient heterogeneity of metastatic tumors harboring adenocarcinoma, t-SCNC, or mixed expression phenotypes, with implications for treatment strategies in which dual targeting of adenocarcinoma and t-SCNC phenotypes may be necessary.&lt;/p&gt;Implications:&lt;p&gt;The t-SCNC phenotype is characterized by lack of &lt;i&gt;AR&lt;/i&gt; enhancer gain and loss of &lt;i&gt;RB1&lt;/i&gt; function, and demonstrates both interindividual and intraindividual heterogeneity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Visual Overview:&lt;/b&gt; &lt;a href="http://mcr.aacrjournals.org/content/molcanres/17/6/1235/F1.large.jpg" target="_blank"&gt;http://mcr.aacrjournals.org/content/molcanres/17/6/1235/F1.large.jpg&lt;/a&gt;.&lt;/p&gt;&lt;/div&gt;
Mortality after myocardial infarction in HIV-infected patients who have initiated HAART (2007)

We identified all Danish HIV patients registered with myocardial infarction (MI) when on HAART (44 patients) and compared their mortality with that of matched patients with MI and no HIV and patients with HIV and no MI. Mortality in HIV-infected MI patients was not significantly different to that of MI only patients in the first 90 days post-MI and thereafter was not significantly different to that of HIV patients without MI.
Two-photon absorption and multi-exciton generation in lead salt quantum dots (2010)

Understanding the nonlinear optical processes in semiconductor nanostructures leads to possible applications in areas including laser amplifiers, optical switches, and solar cells. Here we present a study of the frequency degenerate two-photon absorption (2PA) spectrum of a series of PbS and PbSe quantum dots (QDs). The influence of the quantum confinement is analyzed using a four-band model which considers the mixing of valence and conduction bands. In contrast to our observations of CdSe QDs, the present results point to an increase of the 2PA cross-section (normalized by the QD volume) as the quantum dot size is made smaller. This is explained by the symmetry between the valence and conduction bands which allows the density of states to remain high even for small QDs. A study of the ultrafast carrier dynamics of the PbS quantum dots is also presented. Through nondegenerate femtosecond pump-probe experiments we show evidence of multi-exciton generation with quantum yield (number of excitons generated per absorbed photon) up to 170% for excitation with <i>h&omega;</i>&gt; 3 <i>E<sub>g</sub></i> (where <i>E<sub>g</sub></i> is the bandgap energy).
Nitric oxide synthase in the JGA of the SHR: expression and role in tubuloglomerular feedback (1999)

The spontaneously hypertensive rat (SHR) has an enhanced tubuloglomerular feedback (TGF) and a diminished buffering by juxtaglomerular apparatus (JGA)-derived NO. We examined the hypothesis that these effects are due to decreases in nitric oxide synthase (NOS) expression or limited availability of L-arginine or tetrahydrobiopterin (BH(4)). SHR had significantly (P < 0.05) greater mRNA abundance (by RT-PCR) or protein (by Western analysis) for neuronal NOS (nNOS, or type I) and endothelial cell NOS (ecNOS, or type III) in renal cortex or isolated glomeruli, respectively. There was prominent expression of ecNOS in glomerular endothelium and nNOS in macula densa. Maximal TGF responses, assessed from changes in proximal stop-flow pressure during orthograde loop of Henle (LH) perfusion, were greater in SHR [Wistar-Kyoto (WKY), 8.1 +/- 0.3 (n = 46) vs. SHR, 10.3 +/- 0.3 mmHg (n = 57); P < 0.001]. Unlike WKY, TGF responses of SHR were unresponsive to microperfusion of the nNOS inhibitor, 7-nitroindazole (7-NI, 10(-4) M) [WKY, 9.5 +/- 0.5 to 13.2 +/- 0.7 (n = 13, P < 0.001) vs. SHR, 11.8 +/- 0.7 to 12.5 +/- 0.6 mmHg (n = 19, not significant)], or to L-arginine (10(-3) M) [WKY, 7.7 +/- 0.8 to 6.3 +/- 0.4 (n = 10, P < 0.05) vs. SHR, 10.4 +/- 0.7 to 10.6 +/- 0.7 mmHg (n = 10, not significant)]. Neither BH(4) (10(-4) M) nor sepiapterin (10(-4) M), its stable precursor, modified TGF responses in WKY or in SHR, nor did they restore a response to microperfusion of 7-NI in SHR. In conclusion, there is a diminished role for NO from nNOS in blunting of TGF in SHR which cannot be ascribed to limited NOS expression or availability of substrate or BH(4).
Flow-based Medium Access Algorithm on Optical Access Node (2003)

This work concentrates on new flow concept and mechanism especially for QoS-guaranteed communication systems over optical access networks. To explain those, first I mentioned a need of 'label' in protocol over optical access networks and some technical issues. The structure of a label and the parameters would be described at an optical access network on which the protocol is implemented. After showing network architecture and configuration, I would explain a flow-handling mechanism over optical Access networks. There are some advantages and disadvantages of that. Finally I would conclude the whole abstraction of a flow-based access technology in networks.
FunState-an internal design representation for codesign (2001)

In this paper, an internal design model called FunState (functions driven by state machines) is presented that enables the representation of different types of system components and scheduling mechanisms using a mixture of functional programming and state machines. It is shown how properties relevant for scheduling and verification of specification models such as Boolean dataflow, cyclostatic dataflow, synchronous dataflow, marked graphs, and communicating state machines as well as Petri nets can be represented in the FunState model of computation. Examples of methods suited for FunState are described, such as scheduling and verification. They are based on the representation of the model's state transitions in the form of a periodic graph. The feasibility of the novel approach is shown with an asynchronous transfer mode switch example.
Convergent Evolution of Sugar Donor Specificity of Glycosyltransferases in Plant Specialized Metabolisms (2012)

自然界は多様な植物二次代謝産物で溢れているが，それらの多くは糖が付加された配糖体として蓄積されている．配糖体化は反応性の高いアグリコンを安定化し，代謝物の細胞内輸送や貯蔵を司る重要な反応である．その配糖体化反応を触媒するUDP糖依存型配糖体化酵素の機能解析を通じて明らかになってきた酵素機能の可塑性と二次代謝産物の構造多様性について解説する．
Thyroid Dysfunction in 281 Patients with Metastatic Melanoma or Renal Carcinoma Treated with Interleukin-2 Alone (1995)

The purpose of this prospective study was to determine the incidence of thyroid dysfunction in cancer patients receiving immunotherapy with interleukin-2 (IL-2) alone, and to assess the relationship of hypothyroidism to clinical response. A cohort of 281 consecutive patients with metastatic melanoma or renal carcinoma were treated with IL-2 alone from July 1, 1989 until June 30, 1993. The majority (n = 216) received high-dose IL-2 and the remainder (n = 65) received low-dose therapy. Thyroid function was measured before, during, and after immunotherapy. Forty-one percent of initially euthyroid patients developed thyroid dysfunction after starting high-dose IL-2-alone therapy. The most common abnormality was hypothyroidism, occurring in 35% of patients, although moderate or severe hypothyroidism requiring thyroid hormone replacement occurred in 9% of patients. Hypothyroidism was related to duration of IL-2 therapy and was not associated with clinical response. Hyperthyroidism developed in 7% of previously euthyroid patients receiving high-dose IL-2. Overall, the incidence of thyroid dysfunction was similar in the high- and low-dose IL-2 regimens. In conclusion, thyroid dysfunction is a common sequela of IL-2 therapy. Thyroid function should be measured routinely in cancer patients receiving IL-2-based treatment. It is recommended that thyroid hormone replacement be given to patients with moderate or severe hypothyroidism.
Robust State Estimation under False Data Injection in Distributed Sensor Networks (2010)

Distributed sensor networks have been widely employed to monitor and protect critical infrastructure assets. The network status can be estimated by centralized state estimation using coordinated data aggregation or by distributed state estimation, where nodes only exchange information locally to achieve enhanced scalability and adaptivity to network dynamics. One important property of state estimation is robustness against false data injection from sensors compromised by attackers. Different from most existing works in the literature that focus on centralized state estimation, we propose two novel robust distributed state estimation algorithms against false data injection. They are built upon an existing distributed Kalman filtering algorithm. In the first algorithm, we use variational Bayesian learning to estimate attack parameters and achieve performance similar to a centralized majority voting rule, without causing extra communication overhead. In the second algorithm, we introduce heterogeneity into the network by utilizing a subset of pre-trusted nodes to achieve performance better than majority voting. We show that as long as there is a path connecting each node to some of the pre-trusted nodes, the attackers can not subvert the network. Experimental results demonstrate the effectiveness of our proposed schemes.