gebhart/patrepeval huggingface dataset:
Attenuation and mode profile determination of leaky/lossy modes in multilayer planar waveguides by a coupling simulation method (2009)

Leaky planar waveguides are critically important to the operation of present day and future integrated photonic circuits. However, to incorporate these waveguides successfully into practical photonic circuits requires an accurate knowledge of their attenuation and mode profile in operation. In contrast with previous numerical methods for obtaining leaky waveguide characteristics, which usually involve complicated algorithms to solve for the complex roots of boundary conditions, the transverse transmission/reflection (TTR) method presented here provides a straightforward and simple approach by simulating the corresponding coupled-waveguide structure. By adding a high-index layer adjacent to the cover to enable the coupling, the transmission/reflection coefficients are shown to be definitively expressed in the form of a Lorentzian that is directly related to the complex propagation constant of leaky/lossy mode. The TTR method simultaneously determines the mode profile of the leaky/lossy mode via the angle of incidence for resonant transmission/reflection. In the present work, the TTR method is applied to an antiresonant reflection optical waveguide (ARROW), a lossy waveguide structure, and a waveguide structure that is simultaneously leaky and lossy.
Deterministic Boltzmann machine VLSI can be scaled using multi-chip modules (2003)

Describes a special purpose, very high speed, digital deterministic Boltzmann neural network VLSI chip. Each chip has 32 physical neural processors, which can be apportioned into an arbitrary topology (input, multiple hidden and output layers) of up to 160 virtual neurons total. Under typical conditions, the chip learns at approximately 5*10/sup 8/ connection updates/second (CUPS). Through relatively minor (subsequent) modifications, the authors' chips can be 'tiled' in multi-chip modules, to make multi-layer networks of arbitrary size suffering only slight communications delays and overhead. In this way, the number of CUPS can be made arbitrarily large, limited only by the number of chips tiled. The chip's high speed is due to massively parallel array computation of the inner products of connection weights and neural activations, limited (but adequate) precision for weights and activations (5 bits), high clock rate (180 MHz), as well as several algorithmic and design insights.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Visual Reconciliation of Alternative Similarity Spaces in Climate Modeling (2014)

Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses additional challenges. In this paper we define visual reconciliation as the problem of reconciling multiple alternative similarity spaces through visualization and interaction. We derive this problem from our work on model comparison in climate science where climate modelers are faced with the challenge of making sense of alternative ways to describe their models: one through the output they generate, another through the large set of properties that describe them. Ideally, they want to understand whether groups of models with similar spatio-temporal behaviors share similar sets of criteria or, conversely, whether similar criteria lead to similar behaviors. We propose a visual analytics solution based on linked views, that addresses this problem by allowing the user to dynamically create, modify and observe the interaction among groupings, thereby making the potential explanations apparent. We present case studies that demonstrate the usefulness of our technique in the area of climate science.
Enamel Pathology Resulting from Loss of Function in the Cystic Fibrosis Transmembrane Conductance Regulator in a Porcine Animal Model (2011)

Cystic fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR), a phosphorylation- and ATP-regulated anion channel. CFTR expression and activity is frequently associated with an anion exchanger (AE) such as AE2 coded by the Slc4a2 gene. Mice null for Cftr and mice null for Slc4a2 have enamel defects, and there are some case reports of enamel anomalies in patients with CF. In this study we demonstrate that both Cftr and AE2 expression increased significantly during the rat enamel maturation stage versus the earlier secretory stage (5.6- and 2.9-fold, respectively). These qPCR data im- ply that there is a greater demand for Cl(-) and bicarbonate (HCO₃⁻) transport during the maturation stage of enamel formation, and that this is, at least in part, provided by changes in Cftr and AE2 expression. In addition, the enamel phenotypes of 2 porcine models of CF, CFTR-null, and CFTR-ΔF508 have been examined using backscattered electron microscopy in a scanning electron microscope. The enamel of newborn CFTR-null and CFTR-ΔF508 animals is hypomineralized. Together, these data provide a molecular basis for interpreting enamel disease associated with disruptions to CFTR and AE2 expression.
Generation of Multiple Choice Questions Including Panoramic Information using Linked Data (2019)

In recent years, just about all subjects require students to learn panoramic information. Because the need exists for cross-curriculum learning aimed at relating subject areas, it is useful for multiple-choice questions to include panoramic information for learners. A question including panoramic information refers to content that includes transverse related information and makes respondents grasp the whole knowledge. However, it is costly to manually generate and collect appropriate multiple-choice questions for questioners and learners. Therefore, in this research, we propose a method for the automatic generation of multiple-choice questions including panoramic information using Linked Data. Linked Data is graphical data that can link structured data, and it is used as a technology for data integration and utilization. Some attempts have been made to use Linked Data as a resource for creating teaching material, and the possibility of using Semantic Web technology in education has been verified. In this paper, we aim to realize a system for automatically generating two types of multiple-choice questions by implementing an approach to generating questions and choices. An evaluation method for the generation of questions and choices involves setting indicators for each evaluation item, such as validity and the degree of the inclusion of panoramic information.
Development and Validation of a High-Throughput Sequencing Test for Mitogenome and rDNA Assembly and Annotation, and Its Use in Support of Nematode Identification of Regulatory Concern (2022)

Nematoda is a diverse phylum, and representatives are found in most habitats, including in and on animals and plants. Nematodes are regarded as the most abundant group in terms of individuals in marine and terrestrial sediments. Plant-parasitic nematodes are globally responsible for an annual yield loss of $125 billion. Reliable species identification is essential to take appropriate phytosanitary measures. The introduction of validated Sanger sequencing of 18S, 28S, and cox1 barcode loci represented a powerful tool in support of nematode identification. However, technical challenges associated with PCR and Sanger sequencing and the need for additional loci for identification hamper the efficient use of sequence data. To overcome these challenges, we developed an automated bioinformatic pipeline for the assembly and annotation of mitochondrial genomes and ribosomal DNAs, and we defined and validated a standardized test protocol including controls for routine diagnostics (i.e., high-throughput sequencing [HTS] test). The HTS test can be performed on single nematode specimens and outperforms the Sanger-based sequencing by producing less ambiguous consensus sequences and by yielding additional sequence data offering additional diagnostic resolution when needed. Compared with Sanger sequencing, the HTS test represents a reduction in hands-on time. The HTS test is regarded as fit for the purpose of the molecular identification of single nematode specimens in support of nematode diagnostics of regulatory concern. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
ChemInform Abstract: Efficient Synthesis of Lactosaminylated Core‐2 O‐Glycans. (2002)

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.
Curing Losses: Lab Developments and Best Practices (2022)

Abstract Moderate to severe loss circulation problem encountered while drilling is a major economic burden that increases the total well construction cost dramatically in some cases. This study will focus on best practices to mitigate curing losses in terms of prevention of potential loss by pre-treatment, locating and identifying the losses, identify the mechanism of losses and severity, curing losses strategies and their best drilling practices. In addition, the study will detail typical curing losses materials and their limitations. Finally, selected examples of recent developments in curing losses materials are detailed. The examples are activated nanoparticles dispersed fluid, Epoxy polymer resins, and sodium acid soluble cement solutions. Pre-treatment of loss circulation zone with proper size of bridging materials can reduce and eliminate mud losses into porous formations. The choice of bridging agents will depend on the formation characteristics. The moment of the occurrence (while drilling, circulating or tripping), the severity of the loss (seeping, partial or complete) and the exposed formations are the key factors to identify the best remedy for loss circulation. Losses to reservoir zones are handled differently than non-reservoir zones, wherein only acid soluble or non-damaging material is used in the pay-zone. Seepage losses occur in any formation type when the particle size distribution of the bridging agents is not optimum enough to create an effective seal. This paper describes three different types of novel loss circulation materials to control moderate to severe losses. The paper describes the development of a novel nanoparticle-based chemical treatment composition for its potential use as a loss circulation material. The gelation times were evaluated at different temperatures up to 300°F. The effects of pH and different concentration of activators on gelation times of the new treatment fluid has also been studied. Second example of LCM described in this paper is a novel resin composition comprising an epoxy resin and chemical activator to treat moderate to severe losses. The effect of the chemical activator concentration on the setting time of the resin composition was investigated to accomplish a controlled and delayed polymerization. The third example of LCM described in this paper involves a formulation consisting of an acid soluble cement and a sodium silicate gel that has a high potential to control moderate to severe loss circulation problem. The objective of this acid soluble loss circulation system technology was to design a solution to cure lost circulation in reservoir zones. This is the first study to discuss and detail such topics related to curing losses.
Transmitted Virus Fitness and Host T Cell Responses Collectively Define Divergent Infection Outcomes in Two HIV-1 Recipients (2015)

Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/founder (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.
Eigenrhythms: Drum Pattern Basis Sets For Classification And Generation. (2004)

[TODO] Add abstract here.
ALS Associated Mutations in Matrin 3 Alter Protein-Protein Interactions and Impede mRNA Nuclear Export (2017)

Mutations in Matrin 3 have recently been linked to ALS, though the mechanism that induces disease in these patients is unknown. To define the protein interactome of wild-type and ALS-linked MATR3 mutations, we performed immunoprecipitation followed by mass spectrometry using NSC-34 cells expressing human wild-type or mutant Matrin 3. Gene ontology analysis identified a novel role for Matrin 3 in mRNA transport centered on proteins in the TRanscription and EXport (TREX) complex, known to function in mRNA biogenesis and nuclear export. ALS-linked mutations in Matrin 3 led to its re-distribution within the nucleus, decreased co-localization with endogenous Matrin 3 and increased co-localization with specific TREX components. Expression of disease-causing Matrin 3 mutations led to nuclear mRNA export defects of both global mRNA and more specifically the mRNA of TDP-43 and FUS. Our findings identify a potential pathogenic mechanism attributable to MATR3 mutations and further link cellular transport defects to ALS.
An interdisciplinary and application-oriented approach to teach microfluidics (2021)

Microfluidics is a relatively novel interdisciplinary research area with broad applications in chemistry, physics, material science, and biology. Despite the rapid growth of the field, students' exposure to microfluidic technologies is still limited and often insufficient to appreciate the advantages over other commonly used technologies. To this end, we designed a five-day course, "Microfluidics for microbial ecology," in which students with very different backgrounds learn the basics of microfluidic technologies and sample a range of applications in microbial ecology. The course was created for Master and Ph.D. students interested in applying microfluidics to their research and, therefore, followed an application-oriented approach. The presentation of critical aspects of fluid flow phenomena at the microscale and an outline of the advantages and constraints of the technology provide students with the background to design and perform microfluidics-based experiments. In order to improve the effectiveness of learning in a class with diverse interests and backgrounds, two active learning exercises were implemented. The first comprised the design of an individualized microfluidics experiment in parallel with the lectures: students were guided to apply each module to their personalized application and discuss it in groups. The second was a group experimental activity, in which students jointly set up, performed, analyzed, and presented a microfluidics-based experiment. Given the multidisciplinary teaching context, the course was able to foster common conceptual ground and promote discussion among students. This application-oriented approach built upon experimental activities and in-class discussion is well suited to promote learning in a technology-related subject such as microfluidics.
Green Chemistry and Sustainable Development (2008)

Bioline International is an archived version of the "Bioline International" website that functioned as a not-for-proft scholarly publishing cooperative. This archived site contains web content, including text, images and URLs for internal links from the "http://www.bioline.org.br" domain The "Bioline International" website was a platform for hosting peer-reviewed and open access journals published in developing countries in fields such as public health, tropical medicine, international development, food and nutritional security, and biodiversity. The platform was conceived as a way of reducing the South to North kowledge gap, improving the visibility of essential research and knowledge from local and regional sources in developing countries across the world, and supporting the progress of science to develop a gobal-scale knowledge base in its fields of concern. Bioline International was launched in 1993 as a joint project between the Tropical Database (now, The Reference Center on Environmental Information) in Barzil and The Electronic Publishing Trust for Development in the United Kingdom. The CRIA provided server hosting, administration and development, which The EPT oversaw content management, project development and research. In 2000, The UTSC Library and UTSC's Department of Social Sciences took over the role previously occupied by The Electronic Publishing Trust for Development.
SHP2 blockade enhances anti-tumor immunity via tumor cell intrinsic and extrinsic mechanisms (2021)

SHP2 is a ubiquitous tyrosine phosphatase involved in regulating both tumor and immune cell signaling. In this study, we discovered a novel immune modulatory function of SHP2. Targeting this protein with allosteric SHP2 inhibitors promoted anti-tumor immunity, including enhancing T cell cytotoxic function and immune-mediated tumor regression. Knockout of SHP2 using CRISPR/Cas9 gene editing showed that targeting SHP2 in cancer cells contributes to this immune response. Inhibition of SHP2 activity augmented tumor intrinsic IFNγ signaling resulting in enhanced chemoattractant cytokine release and cytotoxic T cell recruitment, as well as increased expression of MHC Class I and PD-L1 on the cancer cell surface. Furthermore, SHP2 inhibition diminished the differentiation and inhibitory function of immune suppressive myeloid cells in the tumor microenvironment. SHP2 inhibition enhanced responses to anti-PD-1 blockade in syngeneic mouse models. Overall, our study reveals novel functions of SHP2 in tumor immunity and proposes that targeting SHP2 is a promising strategy for cancer immunotherapy.
GRAND for Rayleigh Fading Channels (2022)

Guessing Random Additive Noise Decoding (GRAND) is a code-agnostic decoding technique for short-length and high-rate channel codes. GRAND attempts to guess the channel-induced noise by generating Test Error Patterns (TEPs), and the sequence of TEP generation is the primary distinction between GRAND variants. In this work, we extend the application of GRAND to multipath frequency non-selective Rayleigh fading communication channels, and we refer to this GRAND variant as Fading-GRAND. The proposed Fading-GRAND adapts its TEP generation to the fading conditions of the underlying communication channel, outperforming traditional channel code decoders in scenarios with L spatial diversity branches as well as scenarios with no diversity. Numerical simulation results show that the Fading-GRAND outperforms the traditional Berlekamp-Massey (B-M) decoder for decoding BCH code (127, 106) and BCH code (127, 113) by $0.5\sim 6.5\mathrm{dB}$ at a target FER of $10^{-7}$. Similarly, Fading-GRAND outperforms GRANDAB, the hard-input variation of GRAND, by $0.2\sim 8\mathbf{d B}$ at a target FER of $10^{-7}$ with CRC (128, 104) code and RLC (128,104). Furthermore the average complexity of Fading-GRAND, at $\frac{E_{b}}{N_{0}}$ corresponding to target FER of $10^{-7}$, is $\frac{1}{2}\times\sim\frac{1}{46}\times$ the complexity of GRANDAB.
RIP140 increases APC expression and controls intestinal homeostasis and tumorigenesis (2014)

Deregulation of the Wnt/APC/β-catenin signaling pathway is an important consequence of tumor suppressor APC dysfunction. Genetic and molecular data have established that disruption of this pathway contributes to the development of colorectal cancer. Here, we demonstrate that the transcriptional coregulator RIP140 regulates intestinal homeostasis and tumorigenesis. Using Rip140-null mice and mice overexpressing human RIP140, we found that RIP140 inhibited intestinal epithelial cell proliferation and apoptosis. Interestingly, following whole-body irradiation, mice lacking RIP140 exhibited improved regenerative capacity in the intestine, while mice overexpressing RIP140 displayed reduced recovery. Enhanced RIP140 expression strongly repressed human colon cancer cell proliferation in vitro and after grafting onto nude mice. Moreover, in murine tissues and human cancer cells, RIP140 stimulated APC transcription and inhibited β-catenin activation and target gene expression. Finally, RIP140 mRNA and RIP140 protein levels were decreased in human colon cancers compared with those in normal mucosal tissue, and low levels of RIP140 expression in adenocarcinomas from patients correlated with poor prognosis. Together, these results support a tumor suppressor role for RIP140 in colon cancer.
Light reflection of broadband nonlinear optical pulses from narrowband fiber Bragg gratings (2007)

We compute nonlinear light reflection from fiber gratings using the coupled mode equations and an undepleted pump approximation. Our simulations show features similar to measurements of light reflection from fiber Bragg gratings during continuum generation.