gebhart/patrepeval huggingface dataset:
Online Nonlinear System Identification with Evolving Spatial-Temporal Filters (2018)

Identifying nonlinear models is a challenging problem. In this paper, we present an efficient online identification methodology with a composite local model structure. We introduce the concept of evolving spatial-temporal filters (STF) that dynamically decompose an incoming input-output data stream into a nonlinear combination of local models. The local models are weighed by a set of weights corresponding to the compatibility of the input-output data to a set of clusters of general shape that partition the input-output space. The filters exploit ellipsoidal-shape evolving clusters as function bases and a distance metric defined as a combination of Mahalanobis distance and local model prediction error. Parameters of the filters and local models are updated simultaneously online. The proposed identification methodology has a versatile structure that can work with arbitrary combinations of local models, e.g., a single point, linear model, Markov chain, and neural network. A detailed identification algorithm for an STF with local linear models is presented. A numerical example and a real-world fuel consumption prediction model are demonstrated to illustrate the efficacy of the proposed method.
Copy number alterations of DNA mismatch repair (MMR) genes as novel prognostic markers in localised prostate cancer (CaP). (2016)

96 Background: To investigate the prognostic significance of CNA of genes involved in the MMR pathway in localised CaP. Methods: We studied CNA of genes involved in MMR, namely MSH2, MSH3, MSH6, MLH1, PMS2, in 284 patients with intermediate-risk CaP (Toronto cohort), and compared our findings against three public databases (MSKCC and Cambridge cohorts) that included 375 low- to high-risk CaP. The Toronto cohort comprised of 143 and 141 individuals who underwent image-guided radiotherapy (IGRT) and radical prostatectomy (RadP), respectively, while all patients from the public databases underwent RadP. Information on genome-wide copy number alterations (Toronto) was obtained using Affymetrix Oncoscan array. Biochemical relapse-free survival (bRFS) was assessed for clinical outcome. Results: CNA of MSH2, MSH3, MSH6, MLH1, PMS2 were observed in 3.9% (n = 11), 7.7% (n = 22), 3.9% (n = 11), 4.6% (n = 13) and 13.0% (n = 37) of the Toronto cohort, respectively. Distinct patterns of allelic gain and loss were observed for the gene set; gains only for MLH1 and PMS2, and losses only, in all but 1 case, for MSH2, MSH3 and MSH6. In the Toronto cohort, allelic losses of MSH2, MSH3 and MSH6 were determined to be prognostic for poorer bRFS in IGRT patients (HR 2.04, 95% CI 1.01, 4.12, p = 0.048), but not for patients who underwent RadP (HR 1.08, 95% CI 0.49, 2.39, p = 0.84); while gains in MLH1 and PMS2 were not prognostic in either IGRT or RadP patients. A pooled analysis of these genes for all RadP patients from the Toronto and public databases (n = 516) did however indicate that allelic losses of MSH2, MSH3 and MSH6 were significant predictors of poorer bRFS (HR 2.48, 95% CI 1.64-3.77, p &lt; 0.001), but not MLH1 and PMS2 gains. On multi-variable modelling that includes percent genome aberration and pre-treatment PSA levels, allelic losses of MSH2, MSH3 and MSH6remained significant predictors of bRFS for the pooled RadP cohort (HR 1.96, 95% CI 1.27, 3.01, Wald's p &lt; 0.001), but not for IGRT patients (HR 1.50, 95% CI 0.72, 3.12, p = 0.28). Conclusions: We identified a distinct pattern of copy number loss of MSH2, MSH3 and MSH6 genes in localised CaP that appears to be a novel biomarker of failure to definitive treatment.
Outdoor Wideband Channel Measurements and Modeling in the 3–18 GHz Band (2018)

Fifth generation cellular systems will operate in a wide range of frequencies, covering both the traditional cellular bands, and mm-wave frequency bands, either selecting a specific band or operating in multiple bands simultaneously. For the design of such systems, a detailed understanding of the frequency dependence of the propagation channel is essential. While many channel measurements exist in either microwave bands (< 6 GHz) or near mm-wave bands (> 20 GHz), the results are not easily comparable, and furthermore the transition between these bands is not well studied. This paper aims to bridge the gap by providing the results from a channel measurement campaign conducted in urban macro and micro-cellular environments, over the continuous frequency band of 3–18 GHz. We characterize the pathloss, shadow fading, root-mean-square (RMS) delay spreads, Ricean factor and coherence bandwidth in urban macro-cellular and urban micro-cellular environments. Measurements were taken in both line-of-sight (LOS) and non-line-of-sight (NLOS) environments. The pathloss exponents and the RMS delay spreads increase with the base station height in NLOS environment; but not much dependency is observed in the LOS environment. By dividing the wideband channel transfer function into subbands of 1 GHz each, we study the frequency dependence of pathloss, shadow fading, Ricean factor, delay spread, and coherence bandwidth in the 3–18 GHz band. The pathloss exponents vary significantly with frequency, but not-monotonically. The shadow fading and the Ricean factor increase with frequency. The RMS delay spreads decrease with frequency in the LOS environments, but they do not change significantly in the NLOS environments. The coherence bandwidth values do not change significantly with frequency in either environment.
Manipulating the morphology of colloidal particles via ion beam irradiation: A route to anisotropic shaping (2022)

Ion beam irradiation of spherical colloidal particles is a viable route to induce particle deformation, especially to get anisotropic shapes. Even though less common in comparison with dry etching techniques, different types of morphological changes can be attained depending on the process parameters (angle of incidence, energy, fluence of the ion beam, type of ion, temperature) and on particle material and initial particle arrangement (crystalline or disordered, made up of isolated or closely-packed particles). The technique can be harnessed to get anisotropic deformation of spherical colloidal particles into an ellipsoidal shape, but also to tailor the interstices between closely-packed colloidal particles, to get particle necking and coalescence as well as particle rearrangement. As such, particle deformation based on ion irradiation can find diverse applications from synthesis of ellipsoidal particles to modified templates for colloidal lithography. In this review, we examine in detail the principles and models of colloidal particle shaping via ion beam irradiation, the influence of process parameters on particle morphology and the applications of irradiated particles.
Regulation of the Gene for Estrogenic 17-Ketosteroid Reductase Lying on Chromosome 17cen→q25 (1989)

17-Ketosteroid reductase (17KSR), also known as 17 beta-hydroxysteroid dehydrogenase, catalyzes the reversible interconversion of estradiol to estrone and of androstenedione to testosterone. Using a recently cloned human placental 17KSR cDNA, we show that the 1.4-kilobase mRNA for this enzyme is detected only in tissues producing estrogens, and a 2.4-kilobase mRNA is detected in some estrogenic tissues and some androgenic tissues. This tissue distribution suggests that the interconversion of androstenedione and testosterone may be mediated by a different enzyme. Southern blotting studies show that the mRNA for this estrogenic 17KSR is encoded by two very similar genes localized to chromosome 17cen----q25 by analysis of DNA from mouse/human somatic hybrid cell lines. 8-Br-cAMP increases the abundance of estrogenic 17KSR mRNA as well as mRNAs for other steroidogenic enzymes in JEG-3 choriocarcinoma cells. By contrast, cAMP decreases estrogenic 17KSR mRNA in primary cultures of human cytotrophoblasts and human granulosa cells, a pattern of tropic regulation that differs from other steroidogenic enzyme mRNAs.
A peer-support lifestyle intervention for preventing type 2 diabetes in India: A cluster-randomized controlled trial of the Kerala Diabetes Prevention Program (2018)

Australia and New Zealand Clinical Trials Registry ACTRN12611000262909.
Modulation of experimental hypersensitivity pneumonitis by Sendai virus. (1993)

To evaluate the potential role of viruses in the pathogenesis of hypersensitivity pneumonitis (HP), we looked at the effect of challenging normal versus Sendai-injected mice with Saccharopolyspora rectivirgula (SR). In this model of HP, mice are nasally instilled with SR antigen three consecutive days per week of study. For this study virus was given after 3 weeks of SR. Two positive (SR alone, virus alone) and a negative (saline) control groups were done in parallel with the viral plus SR group. Lung response to these different conditions was evaluated by lung index, bronchoalveolar lavage (BAL) cell populations, lung histopathology, and BAL fluid fibronectin levels. SR challenge resulted in an increase in BAL cells, lung index, and BAL fibronectin levels and in a peribronchial inflammatory reaction. The virus alone produced a transient increase in BAL cells. The cellular response to SR, in virus-injected animals, was greater than the added effects of the virus and SR. Virus alone had no persistent effect on the other measured parameters and did not change the effect of SR on these variables. We conclude that the Sendai virus enhances the cellular response of the mouse lungs to an SR antigenic challenge.
Clozapine blood level assessment using a point-of-care device: feasibility and reliability (2022)

The point-of-care device offers an accessible and satisfactory measurement of clozapine blood levels. Both patients and healthcare providers reported preference for capillary sampling as well as for the in-office TDM procedure. The immediate results provided by the device can facilitate rapid and informed clinical decisions and therefore improve clozapine treatment outcomes.
Optimization of anti-reflection coatings for bifacial solar cells with upconversion layers (2014)

Upconversion is an optical process in which two or more low-energy photons are converted to one high-energy photon. Placing layers capable of performing this process at the rear face of a standard bifacial solar cell allows for utilization of sub-bandgap photons that would be otherwise lost. Optimization of antireflection coatings for devices using upconversion is particularly important as it needs to take into account the normally neglected sub-bandgap part of the spectrum. In this paper we study the optimization of antireflection coatings for bifacial silicon solar cells for upconversion applications. A 3- layer stack of MgF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> /TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> shows the lowest weighted reflectance with 88.6% transmission at 1520 nm as compared to 78% transmission for 1-layer ARC. Minimizing reflection losses results in greater number of photons reaching the upconverter layer resulting in a potential enhancement of 28% in the short-circuit current due to upconversion.
Characterization of highly stable liposomal and immunoliposomal formulations of vincristine and vinblastine (2009)

These results demonstrate that active targeting of solid tumors with liposomal formulations of vincristine is possible when the resulting immunoliposomes are sufficiently stabilized.
Figure S2 from Microparticle Encapsulation of a Prostate-targeted Biologic for the Treatment of Liver Metastases in a Preclinical Model of Castration-resistant Prostate Cancer (2023)

&lt;p&gt;Fig. S2&lt;/p&gt;
Generalized support constraint for three-dimensional reconstruction from incomplete Fourier spectra (1997)

Many imaging systems involve a loss of information that requires the incorporation of prior knowledge in the restoration/reconstruction process. We focus on the typical case of 3D reconstruction from an incomplete set of projections. An approach based on constrained optimization is introduced. This approach provides a powerful mathematical framework for selecting a specific solution from the set of feasible solutions; this is done by minimizing some criteria depending on prior densitometric information that can be interpreted through a generalized support constraint. We propose a global optimization scheme using a deterministic relaxation algorithm based on Bregman's algorithm associated with half-quadratic minimization techniques. When used for 3D vascular reconstruction from 2D digital subtracted angiography (DSA) data, such an approach enables the reconstruction of a well-contrasted 3D vascular network in comparison with results obtained using standard algorithms.
Trimethyloxonium-mediated methylation strategies for the rapid and simultaneous analysis of chlorinated phenols in various soils by electron impact gas chromatography–mass spectrometry (2022)

The efficient methylation of a panel of five industrial and environmentally-relevant chlorophenols (CPs) employing trimethyloxonium tetrafluoroborate (TMO) for their qualitative detection and identification by electron impact gas chromatography-mass spectrometry (EI-GC-MS) is presented. The protocol's execution is simple and smoothly converts the phenols into their O-methylated counterparts conveniently at ambient temperature. The efficiency of two versions of the protocol was successfully tested in their ability to simultaneously derivatize five CPs (2-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, pentachlorophenol and triclosan) in six distinct, separate soil matrices (Nebraska EPA standard soil, Virginia Type A soil, Ottawa sand, Baker sand, Silt and Georgia EPA standard soil) when present at low levels (~ 10 μgg<sup>-1</sup>). The first version involves the direct derivatization of the spiked soils with the methylating salt while the second one involves an initial soil extraction step of the CPs followed by methylation. The MDL values for each methylated CP were determined and lower values were found (4.1-13.2 ng<sup>.</sup>mL<sup>-1</sup>) for both sand matrices (Ottawa and Baker) as well as for the Georgia EPA standard soil, while larger values (8.2-21.8 ng<sup>.</sup>mL<sup>-1</sup>) were found for the Virginia Type soil, Nebraska EPA standard soil and Silt. The presented protocol offers a safer and more practical alternative to the universally employed diazomethane method and can be readily applicable to matrices other than soils. Furthermore, the protocols described herein may find applicability to the methylation of other analytes bearing acidic protons.
The helical nanofilament phase as a host for creation of aligned, nanostructured composites (Presentation Recording) (2015)

The helical nanofilament (HNF) liquid crystal phase is a member of an unusual class of thermotropic phases with lamellar structures dominated by a tendency towards developing negative Gaussian curvature of the layers. Members of this family are sometimes termed “dark conglomerates,” due to their behavior in polarized light microscopy. These include a fluid phases - the high temperature dark conglomerate phase, which is a kind of sponge phase, and the low temperature dark conglomerate phase, also seemingly a sponge phase with structural details currently under investigation. The HNF phase, also a “dark conglomerate,” seems to be unique in the family, since slow conformational dynamics indicate a quasi-crystalline structure within layers, but no long range positional correlations across layers. We have been exploring possible applications of the HNF phase, which is highly porous, as a host for the formation of alignable composites for photovoltaics and other organic semiconductor applications. Recent results regarding the structure of these composites, including data suggesting a remarkably elegant nanostructure for HNF-chiral nematic composites, will be discussed.
The utilization of telephone follow-up in the advanced cancer population: a review of the literature (2012)

Telephone follow-up is a feasible alternative to traditional hospital follow-ups for assessment of symptom palliation. There are fewer burdens on the patient, allowing for a better maintenance of quality of life and lower rates of attrition in clinical trials. Patients had an overall positive opinion of the use of this alternative approach with no common disadvantages. A combination of follow-up strategies, such as clinic follow-up and telephone contact for those not attending, may result in a more comprehensive assessment.
Supplementary Materials and Methods, Table 1 from p53 Regulates the Ras Circuit to Inhibit the Expression of a Cancer-Related Gene Signature by Various Molecular Pathways (2023)

Supplementary Materials and Methods, Table 1 from p53 Regulates the Ras Circuit to Inhibit the Expression of a Cancer-Related Gene Signature by Various Molecular Pathways
ChemInform Abstract: Peptidomimetic Therapeutic Agents Targeting the Protease Enzyme of the Human Immunodeficiency Virus and Hepatitis C Virus (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Abstract 1004: Impact of genetic polymorphisms on colorectal adenoma recurrence and toxicity in a COX-2 inhibitor trial (Celecoxib): Results from a pilot study (2012)

Abstract Background: Chemoprevention trials have shown that Celecoxib, a selective COX-2 inhibitor can reduce adenoma recurrence but can also increase risk of cardiac toxicity. Therefore, in this pilot study, we evaluated the associations between genetic variation in several candidate pathways (e.g. prostaglandin, arachidonic acid and leukotriene synthesis), the incidence of adenoma recurrence as well as toxicity (any, gastrointestinal, cardiac, and non-gastrointestinal/non-cardiac toxicities). Methods: This analysis includes 119 Israeli patients with colorectal adenoma who participated in the Prevention of Colorectal Sporadic Adenomatous Polyps (PreSAP) trial. Reassessment followed after ∼3 years on Celecoxib, followed by 2 years off drug. Incidence of colorectal adenomas was measured by colonoscopy at years 1, 3, and 5. The presence of any, gastrointestinal, cardiac and non-gastrointestinal/non-cardiac toxicities was assessed by investigators for the on-treatment period and collected by patient self-report after treatment. A linkage-disequilibrium-based tagSNP selection algorithm (r2≥0.90, MAF≥4%) identified tagSNPs in candidate pathways. Genotyping was performed using IlluminaTM GoldenGate bead-based genotyping technology. Results: Multiple variants were associated with adenoma recurrence and toxicities. Variability, particularly in COX-1 (rs10306164, rs1236913, rs1330344, rs3119773), COX- 2 (rs4648268), and ALOX12 (rs2073438, rs2292350) played a major role in adenoma recurrence risk among patients on placebo compared to patients on Celecoxib. The highest risk was observed for the COX-1 rs3119773 variant (1890 G&amp;gt;A intron 2) (HR=4.65, 95%CI 1.71-12.64, p=0.0026). Variants in COX2 (rs2206593, rs2745557), EGFR (rs1558544, rs17336919), ALOX15 (rs2619112, rs2619118, rs4796535), SRC (rs6018027, rs7269342), SEPP1 (rs230819, rs230820), and WNT6 (rs6747776, rs6754599) genes were associated with any toxicity. In contrast to gastrointestinal toxicity, a larger number of gene variants (especially variants in PGES, CRP, SRC and GPX3) were associated with increased risk of cardiac toxicity. The increased risk of cardiac toxicity associated with the SRC gene variants (rs6017996, rs6018256, rs6018257) ranged from 7- to 11-fold. Conclusion: Genetic polymorphisms in multiple inflammation-related genes appear to mediate the effect of Celecoxib on adenoma recurrence and the resultant toxicity, particularly cardiac toxicity. Identification of these genetic variants can potentially help in the provision of tailored and optimum care for colorectal adenoma patients. Larger studies validating these pharmacogenetic relationships are warranted. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1004. doi:1538-7445.AM2012-1004
Definition and solution of the memory packing problem for field-programmable systems (1994)

This paper defines a new optimization problem that arises in the use of a Field-Programmable System (FPS). An FPS consists of a set of Field-Programmable Gate Arrays and memories, and is used both for emulation of ASICs and computation. In both cases the application circuits will include a set of memories which may not match the number and aspect ratio of the physical memories available on the FPS. This can often require that the physical memories be time-multiplexed to implement the required memories, in a circuit we call a memory organizer.We give a precise definition of the packing optimization problem and present an algorithm for its solution. The algorithm has been implemented in a CAD tool that automatically produces a memory organizer circuit ready for synthesis by a commercial FPGA tool set.
Unsupervised domain adaptation method for segmenting cross-sectional CCA images (2022)

The results show that it is feasible to first train a neural network on simulated data, and then apply model-based domain adaptation to further improve segmentation performance by training on unlabeled in-vivo data. This overcomes the limitation of conventional deep learning approaches to require large amounts of manually labeled in-vivo data. Since the proposed domain adaptation method only requires prior knowledge on the shape of the segmentation mask, performance can be explored in various domains and applications in future research.
Quality of shelf-stable low-acid vegetables processed using pressure–ohmic–thermal sterilization (2014)

Pressure ohmic thermal sterilization (POTS) involves ohmic heating of foods by applying an electric field under elevated pressure. Experiments were conducted using a custom made POTS apparatus using carrot as the model food. The samples were processed at a target temperature of 105 °C at 600 MPa and treated for 0, 1, 3, and 5 min by regulating the electric field (30 V/cm). POTS treated carrot sample quality attributes were compared against those processed using ohmic heating (0.12 MPa, 30 V/cm, 105 °C) and pressure-assisted thermal processing (PATP; 600 MPa, 0 V/cm, 105 °C). Within the experimental conditions of the study, the thermal come-up time of the POTS, Ohmic and PATP were 1.45 min, 3.58 min and 6.84 min respectively. PATP come-up time also included the pre-heating time (≈6 min). Results indicate the POTS samples had the least textural damage due to minimal thermal exposure. POTS samples had higher crunchiness index (CI) of 0.76 compared to PATP (CI = 0.57) and ohmic heated (CI = 0.62) carrots. All the technologies investigated had minimal impact on product color. This study demonstrates the potential to produce high quality shelf stable low-acid vegetable products using POTS.