gebhart/patrepeval huggingface dataset:
Altered expression of prostaglandin synthases in NSCLC: Therapeutic strategies and targets for intervention (2007)

18083 Background: Prostacyclin Synthase (PGIS) and Thromboxane synthase (TXS) metabolize PGH(2) into prostacyclin and thromboxane respectively. PGIS over-expression inhibits cancer growth in a mouse model, while over-expression of TXS caused opposite effects. TXS is expressed in a variety of tumours, associated with poor prognosis and increased metastasis. The aim of this study was to examine the expression of PGIS and TXS in NSCLC, the effect of targeted TXS inhibition, and the mechanisms regulating these effects. Methods: A panel of resected human lung tumours were stained for PGIS and TXS expression by IHC and by western analysis. A 170- core tissue microarray was stained for TXS and intensity correlated with tumour grade. Cell survival was examined by BrdU assay in A-549 (adenocarcinoma) and SKMES-1 (squamous cell carcinoma) cells following 24h selective TXS inhibition with Ozagrel (500nM) alone, or in combination with chemotherapy. Multi-parameter apoptosis signalling was examined after TXS inhibition using In Cell Analyser and confirmed by DNA laddering and cell death ELISA. PCR arrays were used to examine genes involved in tumourigenesis following TXS inhibition. Results: PGIS was absent in lung cancer sections. TXS was over-expressed in lung cancer relative to matched normal, with significantly increased expression in lower grade tumours. PGIS was down-regulated or absent, while TXS expression was up-regulated in tumours v’s normal tissue. Ozagrel significantly reduced cell survival and induced apoptosis, determined by both DNA laddering and Cell Death ELISA. Multi-parameter apoptosis analysis revealed enlarged nuclei, decreased f-actin staining and decreased mitochondrial mass potential, while PCR arrays confirmed upregulation of the pro-apoptotic gene BAX following TXS inhibition. Ozagrel in combination with Doxorubicin (10nM) showed greatest efficacy compared to a number of other chemotherapy drugs. Conclusions: Expression of PGIS and TXS are altered in NSCLC. Overexpression of TXS may regulate tumour survival as its inhibition induces apoptosis, potentially through upregulation of pro- apoptotic proteins. Targeting TXS, alone or in combination with chemotherapy is a potential therapeutic strategy for the treatment of NSCLC. No significant financial relationships to disclose.
Abstract 6221: Tandem use of multi-omics and artificial intelligence identified novel prognostic and therapeutic biomarkers for head and neck squamous cell carcinoma (2022)

Abstract Introduction: Head and neck squamous cell carcinoma (HNSCC) is categorized into Human Papilloma Virus positive (HPV+ve) and negative (HPV-ve) tumors, with the latter being more aggressive and displaying poor overall survival (OS). There is a need to identify aggressive biomarkers for patient stratification and improved patient care. Materials and Methods: Using the multi-omics data, including somatic mutations, copy number alterations, RNA sequencing, miRNA sequencing, and methylation from 513 HNSCC patients, we performed an integrative clustering analysis to differentiate HPV+ve and HPV-ve tumors and identify novel prognostic biomarkers for survival and treatment response. Using artificial intelligence (AI) based machine learning approach by implementing scikit-learn, we developed a model to predict the patient's OS. Results: Our clustering analysis robustly segregated HNSCC patients into HPV+ve and HPV-ve tumors. Artificial intelligence-based machine learning model identified a 30 gene signature panel specific to HPV-ve tumors precisely predicting poor OS with an accuracy of 90.5±0.8% (95% CI) and AUC of 80.2%. Furthermore, the multivariate Cox regression survival model identified 12 genes as independent prognostic biomarkers in HPV-ve tumors, including overexpression of novel genes NT5E and TRIML2. Interestingly, higher expression of NT5E and TRIML2 due to promoter hypomethylation predicted therapy resistance in 62.8% and 65.1% of HNSCC patients, respectively. The prognostic signature panel of 30 genes was further validated using three additional expression data sets (n = 450) of HNSCC. Conclusion: Our multi-omics and AI analysis revealed a novel HPV-ve molecular cluster with implications for predicting disease aggressiveness, therapeutic response, and OS in HNSCC patients. Citation Format: Ajaz A. Bhat, Tariq Masoodi, Deepika Mishra, Mayank Singh, Sabah Nisar, Sheema Hashem, Sana K. Baba, Puneet Bagga, Ravinder Reddy, Davide Bedognetti, Shahab Uddin, Wael El-Rifai, Muzafar A. Macha, Mohammad Haris. Tandem use of multi-omics and artificial intelligence identified novel prognostic and therapeutic biomarkers for head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6221.
ChemInform Abstract: Tris(trimethylsilyl)methanetellurenyl Halides (Me3Si)3CTeX (X: Cl, Br, I): Synthesis of Stable Alkanetellurenyl Halides. (1989)

Abstract By halogenolysis of (I) the first stable and isolable alkanetellurenyl halides (IV) are obtained.
Polariton chemistry: Thinking inside the (photon) box (2019)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Enslaved [Editorial] (2014)

Presents the editorial for this issue of the publication.
Combined information and performance optimization of linear MIMO modulations (2002)

Information maximal and performance optimal linear MIMO modulations are constructed. A recursive closed form expression of mutual information is used to find optimal bases for linear MIMO-modulations. The symmetry group of mutual information is decomposed. Performance is optimized by (possibly matrix valued) constellation rotations in orthogonally encoded directions.
Broadband antireflection sub-wavelength structure of InGaP/InGaAs/Ge triple junction solar cell with composition-graded SiNx (2015)

This work reports a fabrication strategy to improve the antireflective ability of a InGaP/GaAs/Ge triple-junction solar cell, by combining a nano-templating technique and a chemical-synthesis approach. SiH4 and N2 were used as ammonia-free reaction gases in a plasma-enhanced chemical vapor deposition (PECVD) to prepare Si3N4 as an original antireflective coating (ARC) layer with better chemical stability. Composition-graded SiNx was successfully integrated with sub-wavelength structure by modulating SiH4/N2 ratio during PECVD deposition, and followed by a controllable gold-nanoparticle masking technique on top of the solar cell. Finite-difference time-domain solution was employed to simulate and optimize the aspect-ratio of the ARC, under the condition of variable refractive index over a broad wavelength window, and followed by the masking technique to obtain the desired ARC dimension. This enabled a low light reflectance (<10%) over a broad spectral bandwidth (300–1800 nm) for the solar cell with excellent stability, because of the triple advantages of structural optimization, better chemical stability and graded refractive index of the ARC. The solar cell's performance was tested and showed great competitiveness to those of forefront studies, suggesting the feasibility of the proposed technology.
Pigmented skin lesion segmentation on macroscopic images (2010)

Several pigmented skin lesion segmentation methods have been proposed for dermoscopy images, however skin lesion segmentation on macroscopic images have not received much attention. Despite the fact that dermoscopy is a very specialized technique, in some practical situations, patients do not have a fast access to an specialist. In this situations, pre-screening systems can be used to evaluate a suspect skin lesion by a non-specialist, and lesion segmentation is very important for the success of such systems. This paper proposes a new method for segmenting pigmented skin lesions on macroscopic images acquired with standard cameras. Our method is simpler than comparable methods proposed for dermoscopy, and our experiments based on publicly available datasets of pigmented skin lesion images show promising results. Our approach can achieve an average segmentation error of 24.85%, which is better than the accuracy of comparable methods available in the literature (even for illumination corrected images).
Effect on Cell Surface Markers following Allergen-Induced Desensitization of Human Whole-Blood Basophils (2010)

We have established a protocol for basophil desensitization. By mimicking the updosing phase of immunotherapy we raised the allergen threshold for basophil activation and obtained efficient desensitization for all donors. We showed that conditions leading to desensitization affect histamine release and expression of different basophil markers alike.
1P-093 Stochastic and dynamic pathways detected by quasi-static mechanical unzipping of single-base pair of DNA and MD simulations(Nucleic acid:Structure & Property, The 47th Annual Meeting of the Biophysical Society of Japan) (2009)

LxprLs"on "stem usmg E celi ExprLssion wds tested at 37℃ and 20℃ the lalter condition ]ed to the good }ield ot igN and 'iCt
Glucocorticoid Treatment at Moderate Doses of SIV mac251 -Infected Rhesus Macaques Decreases the Frequency of Circulating CD14 + CD16 ++ Monocytes But Does Not Alter the Tissue Virus Reservoir (2014)

Subsets of CD16-positive monocytes produce proinflammatory cytokines and expand during chronic infection with the human immunodeficiency virus type 1 (HIV). HIV-infected macrophage in tissues may be long lived and contribute to the establishment and maintenance of the HIV reservoir. We found that the (intermediate) CD14(++)CD16(+) and (nonclassical) CD14(+)CD16(++) monocyte subsets are significantly expanded during infection of Rhesus macaques with pathogenic SIV(mac251) but not during infection of sooty mangabeys with the nonpathogenic isolate SIVSM. In vitro glucocorticoid (GC) treatment of peripheral blood mononuclear cells (PBMCs) from uninfected or SIV(mac251)-infected Rhesus macaques and HIV-infected patients treated or not with antiretroviral therapy (ART) resulted in a significant decrease in the frequency of both CD16-positive monocyte subsets. Short-term in vivo treatment with high doses of GC of chronically SIV(mac251)-infected macaques resulted in a significant decrease in the CD14(+)CD16(++) population and, to a lesser extent, in the CD14(++)CD16(+) monocytes, as well as a significant decrease in the number of macrophages in tissues. Surprisingly, treatment of SIV(mac251)-infected macaques with ART significantly increased the CD14(++)CD16(+) population and the addition of GC resulted in a significant decrease in only the CD14(+)CD16(++) subset. No difference in SIV DNA levels in blood, lymph nodes, gut, and spleen was found between the groups treated with ART or ART plus GC. Thus, it appears that high doses of GC treatment in the absence of ART could affect both CD16-positive populations in vivo. Whether the efficacy of this treatment at higher doses to decrease virus levels outweighs its risks remains to be determined.
Pendeteksi Sinyal Jual/Beli Saham dengan Fuzzy Rule-Based Evidential Reasoning dan C-means Clustering (2018)

Stocks are securities indicating the share of ownership of a company. In stock market, most of traded stocks fluctuate in price at all times and traders take an advantage for taking profit. Traders often use technical analysis to determine the trend of stock price movements. The problem is on how traders take positions (buying/selling stocks) with minimal trading decision so they can maximize profits. Fuzzy rule-based evidential reasoning approach can map the conditions of stock movements. Clustering can help the mapping conducted with a high degree of equality with each other. One of the clustering methods is fuzzy C-means clustering. This method is used to determine the number of membership functions for each attribute. To increase profit/Return of Investment (ROI), verification of output decision is required to analyze stock trends when placing buy or sell. From the results experimented, an ROI of 83.80% profit is obtained
The Relationship of Complement Consumption to Immune Fever (1971)

Abstract The administration of cobra venom factor or soluble human serum albumin (HSA)-anti-HSA complexes in antigen excess to rabbits resulted in a lowering of total hemolytic complement and C3 titers which persisted more than 24 hr. When such animals were challenged with complexes made up in 10 times antigen excess, the consumption of complement, febrile and thrombocytopenic responses were significantly diminished from those seen in untreated controls, and the duration of post-challenge leukopenia was shortened. These observations suggest a role for complement consumption, particularly of components C3-9, in the manifestation of these responses. Pyrogenic tolerance to complexes could not be explained by their more rapid removal from the circulation or a failure of the thermoregulatory centers to respond to preformed leukocytic pyrogen, suggesting that impairment in complement consumption either by depletion of C3 or interference with the activation of C1 might be responsible for this state. In contrast to these findings using complexes in 10 times antigen excess, similar prior treatment of immunized rabbits given HSA or of normal rabbits that received a mixture of soluble and insoluble complexes in 3 times antibody excess failed to suppress febrile or hematologic responses. If the formation of antigen-antibody complexes is essential for the production of these responses in immunized animals challenged with specific antigen, it appears that the large, rapidly-cleared complexes formed near equivalence are most likely involved in producing these biologic activities. Whereas some of the properties of these complexes make them more able to fix complement in vitro, it seems unlikely that complement-mediated mechanisms are significantly involved in the pathogenesis of the in vivo responses measured in these investigations.
A Color Image Analysis Method for Assessment of Germination Based on Differential Fluorescence Staining of Bacterial Spores and Vegetative Cells Using Acridine Orange (1995)

Color fluorescence image analysis of acridine orange (AO) stained germinating Bacillus subtilis var. niger bacteria revealed a cell population initially dominated by small green spores followed by the emergence of at least three additional discernible subpopulations in response to stimulation with D-glucose. These subpopulations were small, round or oblong red cells; intermediate to large metachromatic cells; and large red rods. Large green rods were rarely observed. An increase in red emissions (i.e., putative RNA synthesis) was sometimes seen as early as 90 min after exposure to D-glucose and uptake of AO at room temperature. This may represent either metabolic recovery from quiescence or RNA synthesis associated with germination. In the absence of D-glucose, or using autoclaved bacteria in the presence of glucose, no relative increase in the red signal was observed despite hours of observation. Digital image analysis was used for relative measurement of red, green and blue signals and to correlate the size of various subpopulations with their fluorescence color emissions over time. Image analysis demonstrated a trend toward increasing size and red emission in the presence of glucose. The average red emission was found to be a good discriminator of the various subpopulations, while the average green emission was approximately equal among the subpopulations making it a poor discriminator. These data suggest that AO staining might be used for rapid computer-assisted discrimination of spores vs. vegetative cells.
SoK: Beyond IoT MUD Deployments -- Challenges and Future Directions (2020)

Due to the advancement of IoT devices in both domestic and industrial environments, the need to incorporate a mechanism to build accountability in the IoT ecosystem is paramount. In the last few years, various initiatives have been started in this direction addressing many socio-technical concerns and challenges to build an accountable system. The solution that has received a lot of attention in both industry and academia is the Manufacturer Usage Description (MUD) specification. It gives the possibility to the IoT device manufacturers to describe communications needed by each device to work properly. MUD implementation is challenging not only due to the diversity of IoT devices and manufacturer/operator/regulators but also due to the incremental integration of MUD-based flow control in the already existing Internet infrastructure. To provide a better understanding of these challenges, in this work, we explore and investigate the prototypes of three implementations proposed by different research teams and organisations, useful for the community to understand which are the various features implemented by the existing technologies. By considering that there exist some behaviours which can be only defined by local policy, we propose a MUD capable network integrating our User Policy Server(UPS). The UPS provides network administrators and endusers an opportunity to interact with MUD components through a user-friendly interface. Hence, we present a comprehensive survey of the challenges.
Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle (2016)

The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.
Three novel thiopurine S-methyltransferase allelic variants (TPMT*20, *21, *22) – association with decreased enzyme function (2006)

The genetic polymorphism of the thiopurine S-methyltransferase, TPMT, comprises at least 21 alleles causing three distinct drug metabolism phenotypes termed normal/high, intermediate, and deficient methylators. In consequence, adverse drug reactions may occur if standard doses of thiopurines are applied routinely. Genetic prediction of the methylator phenotype as a basis for dose selection requires the extensive knowledge of single nucleotide polymorphisms occurring naturally in the population. Here we describe three novel missense variants in the TPMT gene which were associated with an intermediate red blood cell TPMT activity in three Caucasians. The following alleles were designated: TPMT*20 (c.712A>G), *21 (c.205C>G), and *22 (c.488G>C). No further genetic variations in remaining coding regions as well as the 5'flanking region of TPMT were identified. These sequence variants are present in highly conserved nucleotide positions of the TPMT gene throughout various mammalian species and in zebra fish, and are predicted to be intolerant when the functional consequences of variations were analyzed using SIFT (Sorting Intolerant From Tolerant) algorithm. In Caucasians the occurrence of these genetic variants appears to be extremely rare since none of these alleles were identified in a randomly selected control population of 1048 individuals.
Mutable Codesign for Embedded Protocol Processing (2005)

This paper addresses exploitation of the capabilities of platform FPGAs to implement embedded networking for systems on chip. In particular, a methodology for exploring trade-offs between the placement of protocol handling functions in programmable logic and on an embedded processor is demonstrated. This is facilitated by two new design tool capabilities: first, being able to describe programmable logic based functions in a more software-like manner; and second, being able automatically to generate efficient interfaces between a programmable logic fabric and an embedded processor. The methodology is illustrated by an example of a simple Web server, targeted at Xilinx Virtex-II Pro and Virtex-4 platform FPGAs. Trade-offs both of complete protocol placement and of within-protocol placement are systematically investigated in terms of resources used and packet handling latency. The work points the way to highly fluid allocation of functions to implementations, beyond conventional static codesign.
Invited Paper The Application Of Coherent Optical Techniques To Broadband Networks (1986)

The potential advantages of applying coherent optical fibre techniques to broadband networks are reviewed and a number of system types are described which illustrate the operating principles. In this instance particular consideration is given to networks which rely on the use of optically tunable lasers to define either a source frequency or to select a channel from a frequency multiplexed transmission using the heterodyne receiver technique.
Modelling and management of mortality risk: a review (2008)

In the first part of the paper, we consider the wide range of extrapolative stochastic mortality models that have been proposed over the last 15–20 years. A number of models that we consider are framed in discrete time and place emphasis on the statistical aspects of modelling and forecasting. We discuss how these models can be evaluated, compared and contrasted. We also discuss a discrete-time market model that facilitates valuation of mortality-linked contracts with embedded options. We then review several approaches to modelling mortality in continuous time. These models tend to be simpler in nature, but make it possible to examine the potential for dynamic hedging of mortality risk. Finally, we review a range of financial instruments (traded and over-the-counter) that could be used to hedge mortality risk. Some of these, such as mortality swaps, already exist, while others anticipate future developments in the market.
An audio-visual approach to learning salient behaviors in couples' problem solving discussions (2013)

We present a method for characterizing salient behavioral events from audio-visual data of dyadic human interactions. This behavioral signal processing work is aimed at supporting observational analysis of domain experts such as psychologists and clinicians. We extract prosodic and spectral speech features as well as visual motion vector features on overlapping windows from a multimodal corpus. We then apply a technique called multiple instance learning to detect salient audio and visual instances for predicting human expert annotated behavior ratings. We demonstrate the performance gains achieved through multimodal fusion in characterizing complex behavior patterns of interest such as blame and acceptance in recordings of couples' problem solving discussions during marital therapy.
The Impact of Student Opt-Out on Educational Predictive Models (2019)

Privacy concerns may lead people to opt-in or opt-out of having their educational data collected. These decisions may impact the performance of educational predictive models. To understand this, we conducted a survey to determine the propensity of students to withhold or grant access to their data for the purposes of training predictive models. We simulated the effects of opt-out on the accuracy of educational predictive models by dropping a random sample of data over a range of increments, and then contextualize our findings using the survey results. We find that grade predictive models are fairly robust and that kappa scores do not decrease unless there is signiicant opt-out, but when there is, the deteriorating performance disproportionately affects certain subpopulations.