gebhart/patrepeval huggingface dataset:
Finite element beam propagation method for nonlinear optical waveguides (1999)

A new beam propagation method based on the finite element method (FE-BPM) has been developed for the analysis of nonlinear optical waveguides. A formulation for the FE-BPM that is applicable not only to the TE mode but also to the TM mode is presented. Various techniques for enhancing the performance of the FE-BPM are introduced, including the Padé equation of wide-angle beam propagation, the transparent boundary condition, the perfect matched layer condition for prevention of spurious reflection from the edge of the analysis region, and an algorithm for adaptive updating of the reference index of refraction and the finite-element grids. Beam propagation analysis of spatial soliton emission in a nonlinear optical waveguide is performed in order to investigate the performance of the new FE-BPM. © 1999 Scripta Technica, Electron Comm Jpn Pt 2, 82(4): 47–53, 1999
Nitrogen fixation at passivated Fe nanoclusters supported by an oxide surface: Identification of viable reaction routes using density functional calculations (2009)

Using density-functional calculations, we investigate the possibility of ammonia synthesis at supported Fe nanoclusters along catalytic routes closely resembling those in biological nitrogen fixation. To achieve similar catalytic conditions as at the active site of the enzyme nitrogenase, the clusters are passivated with either S or N atoms. From calculated potential-energy profiles for the ${\text{N}}_{2}$ hydrogenation, we find that low-temperature synthesis of ammonia is viable at the clusters passivated by N atoms due to the strong binding energy of the ${\text{N}}_{2}$ molecule in the initial adsorption step.
Developmental regulation of creatine kinase activity in cells of the epiphyseal growth cartilage (1992)

During the process of endochondral bone formation, the maturing chondrocyte exhibits profound changes in energy metabolism. To explore the mechanism of energy conservation in cartilage we examined the expression of creatine kinase, an enzyme that catalyzes the formation of ATP in tissues under oxygen stress. Measurement of creatine kinase activity and cytochemical assessment of enzyme distribution clearly showed that the level of enzyme activity was related to chondrocyte maturation. Thus, as the cells hypertrophied, there was a progressive increase in creatine kinase activity. Similarly, an elevation in creatine kinase activity was noted in chondrocyte cultures as the cells assumed an hypertrophic state. When cartilage calcification was disturbed by rickets, there was a decrease in enzyme activity in the hypertrophic region. Studies were performed to examine the creatine kinase isozyme profile of cells of the epiphysis. In resting and proliferating cartilage, the isoform was MM. In hypertrophic cartilage, the predominant isoforms were MB and BB. In terms of the creatine phosphate content, the highest values were seen in the proliferative region; lower amounts were present in hypertrophic and resting cartilage; and no creatine phosphate was detected in calcified cartilage. These data suggest that turnover of creatine phosphate is greatest in the mineralized region of the epiphysis. The results of these investigations point to creatine kinase as being under developmental control. The activity of the enzyme in cartilage cells should serve as a marker of developmental events associated with chondrocyte proliferation, hypertrophy, and mineralization.
Expression of Activation-induced Cytidine Deaminase in Malignant Lymphomas Infiltrating the Bone Marrow (2008)

Somatic hypermutation of immunoglobulin genes and class switch recombination are pivotal processes in the germinal center (GC) reaction and have been implicated in the development of malignant B-cell lymphoma. Both processes require the enzyme activation-induced cytidine deaminase (AID). Expression of AID is largely restricted to GC B cells and B cells that undergo class switch recombination outside the GC. AID is also expressed in many B-cell lymphomas. This study investigates the expression of AID of malignant lymphomas infiltrating the bone marrow. Bone marrow trephines (n=130) with infiltration of Hodgkin lymphoma and non-Hodgkin lymphoma of B cell and T-cell type and trephines with reactive lymphoid follicles (n=16) were analyzed immunohistochemically for AID protein. AID is expressed in bone marrow infiltrates of malignant lymphomas. AID was generally detected in lymphomas of GC origin. Tumor cells of hairy cell leukemia are mostly AID. There is apparently no different expression of AID found in bone marrow infiltrates of malignant lymphomas compared with a control group with nodal malignant lymphoma infiltrates (n=105). These results suggest that the expression pattern of AID in lymphoma infiltrates in the bone marrow reflects that of extramedullary lymphoma infiltrates.
Developing a benchmarking tool for minimizing wastewater utility greenhouse gas footprints (2011)

Growing voluntary and regulatory pressures require the performance evaluation of urban wastewatertreatment systems to extend beyond the traditional scope of effluent quality and operational cost, to includegreenhouse gas emissions (carbon footprint). To address this, the IWA Task Group on “the use of waterquality and process models for minimizing wastewater utility greenhouse gas footprints” (Task GroupGHG) includes a subgroup that is developing a benchmark simulation model that includes a plant-widemodel and rising main sewer model for testing mitigation strategies to reduce the system’s GHG footprint.The sewer model was run to predict methane emissions and its output used for the plant-wide model input.The latest nitrous oxide (N2O) models from literature were implemented within the plant-wide model topredict nitrification and denitrification pathway N2O emissions, in addition to electric consumption andproduction (from anaerobic digestion methane). Different scenarios were tested to assess the relativeimpacts of various process parameters and simple control strategies. Methane predicted in the sewersgenerally accounted for 8% of the total sewer and plant-wide GHG emissions, while N2O emissions fromdenitrification and nitrification accounted for approximately 25% of the total GHG emissions. Aerationcontrol played a clear role in N2O emissions, which in some cases increased the net GHG emissions whensignificantly reducing aeration electricity use to reduce CO2 emissions. The best among the few controllersstudied reduced the GHG footprint by 7%, the operating costs by 10% and improved effluent quality by2%. Finally, noteworthy, steady state simulation results were found to be 11% below the average of theequivalent dynamic simulation, stressing the importance of dynamic interactions in the system. As theGHG models used are not mature and some have yet to be validated, these results may not be accurate;however, they served to fulfill the objective of this study - demonstrate the potential of a dynamic systemwidemodelling and benchmarking approach for balancing water quality, operational costs, and GHGemissions.
Supplementary File 4 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes (2023)

&lt;p&gt;Components of tumor progression TAp63 (4.1) and Î"Np63 (4.2) signatures used in this study. Pathways enriched in TAp63 (4.3) and Î"Np63 (4.4) tumor progression signatures.&lt;/p&gt;
Revealing skype traffic (2007)

Skype is a very popular VoIP software which has recently attracted the attention of the research community and network operators. Following a closed source and proprietary design, Skype protocols and algorithms are unknown. Moreover, strong encryption mechanisms are adopted by Skype, making it very difficult to even glimpse its presence from a traffic aggregate. In this paper, we propose a framework based on two complementary techniques to reveal Skypetraffic in real time. The first approach, based on Pearson'sChi-Square test and agnostic to VoIP-related trafficcharacteristics, is used to detect Skype's fingerprint from the packet framing structure, exploiting the randomness introduced at the bit level by the encryption process. Conversely, the second approach is based on a stochastic characterization of Skype traffic in terms of packet arrival rate and packet length, which are used as features of a decision process based on Naive Bayesian Classifiers.In order to assess the effectiveness of the above techniques, we develop an off-line cross-checking heuristic based on deep-packet inspection and flow correlation, which is interesting per se. This heuristic allows us to quantify the amount of false negatives and false positives gathered by means of the two proposed approaches: results obtained from measurements in different networks show that the technique is very effective in identifying Skype traffic. While both Bayesian classifier and packet inspection techniques are commonly used, the idea of leveraging on randomness to reveal traffic is novel. We adopt this to identify Skype traffic, but the same methodology can be applied to other classification problems as well.
Achilles’ Lead: Will Pacemakers Break Free? (2015)

Pacemaker leads, which connect the chest-wall generator of a pacemaker to the pacing electrode in the heart, are the “Achilles’ heel” of pacing and defibrillation systems. Over time, they wear out, which often necessitates their risky removal and replacement. In addition, transvenous leads provide a portal into the vascular space, which increases the risk of infection. Patients with traditional pacemakers and defibrillators are also susceptible to hematomas and pocket infections in the chest wall where the generators lie. Thus, a self-contained leadless pacemaker that can be placed directly into the heart is an appealing prospect.Reports of two recent nonrandomized, . . .
The Role of Direct Air Capture in Mitigation of Anthropogenic Greenhouse Gas Emissions (2019)

In recent years Direct Air Capture (DAC) has established itself as one promising approache to Atmospheric Carbon dioxide Removal (CDR) also referred to as Negative Emissions. However due to the amounts likely needed to be removed CDR Technologies (CDRTs) like DAC will only become climate relevant if they reach gigaton scale fast, around the middle of this century. The paper will give a brief insight into DAC and in particular, the modular low temperature DAC technology developed by Climeworks of Switzerland. It will discuss potential co benefits, in particular in relation to the Sustainable Development Goals (SDGs) of the United Nations and conclude by suggesting some policy approaches on how a climate relevant scale could be achieved in time.
ChemInform Abstract: Replacement of Nitrogen by Fluorine (in Organic Molecules) (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Mutation of Bacillus firmus OF4 to duramycin resistance results in substantial replacement of membrane lipid phosphatidylethanolamine by its plasmalogen form (1989)

Mutant strains of alkalophilic Bacillus firmus OF4 that were selected for resistance to duramycin had greatly reduced levels of membrane diacylphosphatidylethanolamine, as had been found in studies of such mutants of Bacillus subtilis. In the B. firmus strains, however, substantial levels of plasmenylethanolamine were found. This is an unusual membrane component for an aerobic eubacterium, but the presence of trace amounts even in the wild type was confirmed in experiments with 32Pi-labeled growth medium. The membrane lipid composition of the duramycin-resistant strains had several other changes that also left alkalophilic growth unimpaired.
RETRACTED: Gait Analysis of Pedestrians with the Aim of Detecting Disabled People (2018)

Gait classification is an effective and non-intrusive method for human identification and it has received significant attention in the recent years due to its applications in visual surveillance and monitoring systems. In this project, we analysed gait signatures using spatio-temporal motion characteristics of a person to answer the question ``is there a discriminating feature in gait signal that can help to categorise disable person from healthy''. The procedure has three steps. detection of a pedestrian using YOLO followed by the silhouette extraction using the Gaussian Mixture Model (GMM). Finally, skeletonization from the silhouette image to estimate head and torso locations and their angles with the vertical axis. Furthermore, velocity and acceleration signals were recorded to look for accelerating behaviour of person walking with a limp.
Mutation of 3' splice sites in two different class I genes results in different usage of cryptic splice sites. (1989)

To determine the pattern of alternative splicing at the 5' end of class I genes, the 3' splice sites bordering exon 2 of the H-2Dd and H-2Kd genes were mutated from AG to GG (H-2Dd) or CG (H-2Kd). The mutant genes were transfected into L cells, and RNA from clones expressing these Ag was used for analysis by RNase and S1 nuclease mapping techniques. The first intervening sequence of both class I genes contains several potential 3' splice acceptor sites. However, a clear preference for only one site was detected in each of the H-2Dd and H-2Kd mRNA. Examination of the endogenous H-Dd and H-2Kd class I transcripts in normal murine tissues and in tumors demonstrated that the alternatively spliced mRNAs were produced, but at a low frequency. Infection of transfected L cells or tumor lines with vesicular stomatitis virus altered the level of differentially spliced message in these cells.
Enteral glutamine stimulates protein synthesis and decreases ubiquitin mRNA level in human gut mucosa (2003)

Effects of glutamine on whole body and intestinal protein synthesis and on intestinal proteolysis were assessed in humans. Two groups of healthy volunteers received in a random order enteral glutamine (0.8 mmol.kg body wt(-1)x h(-1)) compared either to saline or isonitrogenous amino acids. Intravenous [2H5]phenylalanine and [13C]leucine were simultaneously infused. After gas chromatography-mass spectrometry analysis, whole body protein turnover was estimated from traced plasma amino acid fluxes and the fractional synthesis rate (FSR) of gut mucosal protein was calculated from protein and intracellular phenylalanine and leucine enrichments in duodenal biopsies. mRNA levels for ubiquitin, cathepsin D, and m-calpain were analyzed in biopsies by RT-PCR. Glutamine significantly increased mucosal protein FSR compared with saline. Glutamine and amino acids had similar effects on FSR. The mRNA level for ubiquitin was significantly decreased after glutamine infusion compared with saline and amino acids, whereas cathepsin D and m-calpain mRNA levels were not affected. Enteral glutamine stimulates mucosal protein synthesis and may attenuate ubiquitin-dependent proteolysis and thus improve protein balance in human gut.
Inverse modelling of atmospheric tracers: non-Gaussian methods and second-order sensitivity analysis (2008)

For a start, recent techniques devoted to the reconstruction of sources of an atmospheric tracer at continental scale are introduced. A first method is based on the principle of maximum entropy on the mean and is briefly reviewed here. A second approach, which has not been applied in this field yet, is based on an exact Bayesian approach, through a maximum a posteriori estimator. The methods share common grounds, and both perform equally well in practice. When specific prior hypotheses on the sources are taken into account such as positivity, or boundedness, both methods lead to purposefully devised cost-functions. These cost-functions are not necessarily quadratic because the underlying assumptions are not Gaussian. As a consequence, several mathematical tools developed in data assimilation on the basis of quadratic cost-functions in order to establish a posteriori analysis, need to be extended to this non-Gaussian framework. Concomitantly, the second-order sensitivity analysis needs to be adapted, as well as the computations of the averaging kernels of the source and the errors obtained in the reconstruction. All of these developments are applied to a real case of tracer dispersion: the European Tracer Experiment [ETEX]. Comparisons are made between a least squares cost function (similar to the so-called 4D-Var) approach and a cost-function which is not based on Gaussian hypotheses. Besides, the information content of the observations which is used in the reconstruction is computed and studied on the application case. A connection with the degrees of freedom for signal is also established. As a by-product of these methodological developments, conclusions are drawn on the information content of the ETEX dataset as seen from the inverse modelling point of view.
Superconducting Time-of-flight Mass Spectrometry Systems for Biomolecules using Superconducting Digital Circuits (2017)

We have been developing superconducting time-of-flight mass spectrometry (TOF-MS) systems that utilize a superconducting strip particle detector (SSPD) and a single-flux-quantum (SFQ) time-to-digital converter (TDC). The SSPD has high time resolution and constant detection efficiency even for high-mass molecules. The SFQ TDC can measure the time intervals between multiple input signals with extremely high time resolution and directly convert them into binary data. In this paper, we review recent developments on the superconducting TOF-MS systems in our group.
Gastrointestinal Uptake of Nasunin, Acylated Anthocyanin in Eggplant (2006)

We previously showed that nasunin, acylated anthocyanins in eggplant peel, comprises two isomers, cis-nasunin and trans-nasunin. In this study, gastrointestinal absorption of cis- and trans-nasunins was studied in rats. Orally administered nasunins were quickly absorbed in their original acylated forms and maximally appeared in blood plasma after 15 min. When the maximum plasma concentration and area under the plasma concentration curve were normalized by orally administered dose (micromoles per kilogram), there was no significant difference in the uptake efficiency between two isomers and both exhibited a plasma level almost identical to that of delphinidin 3-O-beta-D-glucopyranoside. However, metabolites such as 4'-O-methyl analogues and extended glucuronides which were observed for delphinidin 3-O-beta-D-glucopyranoside and cyanidin 3-O-beta-D-glucopyranoside metabolisms were not detected in urine or blood plasma. Moreover, deacylated and glycolytic products of nasunins such as delphinidin 3-O-beta-D-glucopyranoside or delphinidin (aglycone) were also not detected in blood plasma even after oral administration for 8 h. These results indicated that nasunins were absorbed in their original acylated forms and exhibit a bioavailability almost identical to that of nonacylated anthocyanins.
EBI3 regulates the NK cell response to mouse cytomegalovirus infection (2017)

Natural killer (NK) cells are key mediators in the control of cytomegalovirus infection. Here, we show that Epstein-Barr virus-induced 3 (EBI3) is expressed by human NK cells after NKG2D or IL-12 plus IL-18 stimulation and by mouse NK cells during mouse cytomegalovirus (MCMV) infection. The induction of EBI3 protein expression in mouse NK cells is a late activation event. Thus, early activation events of NK cells, such as IFNγ production and CD69 expression, were not affected in EBI3-deficient (<i>Ebi3</i><sup><i>-/-</i></sup> ) C57BL/6 (B6) mice during MCMV infection. Furthermore, comparable levels of early viral replication in spleen and liver were observed in MCMV-infected <i>Ebi3</i><sup><i>-/-</i></sup> and wild-type (WT) B6 mice. Interestingly, the viral load in salivary glands and oral lavage was strongly decreased in the MCMV-infected <i>Ebi3</i><sup><i>-/-</i></sup> B6 mice, suggesting that EBI3 plays a role in the establishment of MCMV latency. We detected a decrease in the sustained IL-10 production by NK cells and lower serum levels of IL-10 in the MCMV-infected <i>Ebi3</i><sup>-/-</sup> B6 mice. Furthermore, we observed an increase in dendritic cell maturation markers and an increase in activated CD8<sup>+</sup> T cells. Thus, EBI3 dampens the immune response against MCMV infection, resulting in prolonged viral persistence.
Abstract 1044: Establishment and characterization of rare breast patient-derived xenograft models as a potential resource for personalized medicine (2018)

Abstract Breast cancer (BC) exhibits a wide range of morphologic phenotypes and gene expression profiles. Most of the studies that led to the identification of intrinsic molecular subtypes in BC were limited to invasive ductal carcinomas of the breast and did not take rare histopathologic subtypes into account. Rare histopathologic BC subtypes (collectively less than 2% of all breast cancer) have particular prognostic and clinical characteristics. There is no current established treatment that takes into account the specificity of rare BC subtypes. This is mainly due to the absence of clinical trials to determine the optimal management of these rare pathologies. The establishment of relevant preclinical models and molecular characterization of rare BC subtypes is essential for identifying directed and suitable therapeutic regimens for BC patients diagnosed with these rare histopathologic variants. Patient-derived xenograft (PDX) has been recognized as a valuable method to evaluate the clinical diversity of breast cancer. These models were shown to be predictive of clinical outcomes and are being used for preclinical drug evaluation, biomarker identification, and personalized medicine strategies. We developed a cohort of eight BC rare histopathologic subtypes, including four metaplastic, one adenoid cystic, one IDC pleomorphic, one neuroendocrine, and one mucinous BC subtype. These PDXs and their primary tumors were submitted to whole-genome sequencing (WGS) and RNA sequencing. We also evaluated a total of 255 proteins by reverse phase protein array (RPPA) in these PDX samples. We are currently performing conditional reprogramming experiments to generate cell lines from these rare BC PDXs. Our preliminary results indicate that pathways related to PI3K/AKT, ERK/MAPK, mTOR, HGF, ERBB, AMPK and IL3 signaling are disrupted in rare BC subtypes. Several genes belonging to these pathways are dysregulated in rare BC tumors, and therefore represent potential therapeutic targets for personalized treatment. Citation Format: Hellen Kuasne, Paul Savage, Constanza Martinez Ramirez, Leah Liu, Valentina Muñoz-Ramos, Virginie Pilon, Anie Monast, Radia Johnson, Nicholas Bertos, Jamil Asselah, Nathaniel Bouganim, Kevin Petrecca, Sarkis Meterissian, Atilla Omeroglu, Mark Basik, Morag Park. Establishment and characterization of rare breast patient-derived xenograft models as a potential resource for personalized medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1044.