gebhart/patrepeval huggingface dataset:
Argonaute-2-dependent rescue of a Drosophila model of FXTAS by FRAXE premutation repeat (2007)

Fragile X Syndrome is the most common form of hereditary mental retardation. It is caused by a large expansion of the CGG trinucleotide repeat (>200 repeats) in the 5'-untranslated region (UTR) of the FMR1 gene that leads to silencing of its transcript. Individuals with CGG repeat expansions approximately between 60 and 200 are referred to as premutation carriers. Fragile X-associated tremor and ataxia syndrome (FXTAS), an RNA-mediated neurodegenerative disease has been described in up to 50% of males carrying premutation alleles. FRAXE, the most common form of non-syndromic X-linked mental retardation, is caused by expansion of a CCG trinucleotide repeat (>200) in the 5'-UTR of the FMR2 gene. While the FRAXE premutation length repeat is observed in the general population, there has not yet been a report of a neurodegenerative phenotype associated with these alleles. In this study, we show that the CCG premutation length repeat leads to an RNA-mediated neurodegenerative phenotype in a Drosophila model. Furthermore, we show that co-expression of both the CCG and CGG-containing RNAs suppresses their independent toxicity and is dependent on the RNAi pathway. These data support the concept that RNA toxicity is the mechanism of neuronal toxicity and suggests potential reversal of RNA-mediated phenotypes with complementary RNA molecules.
The antibody response to Plasmodium falciparum Merozoite Surface Protein 4: comparative assessment of specificity and growth inhibitory antibody activity to infection-acquired and immunization-induced epitopes (2011)

The panel of MSP4-specific Mabs produced were found to recognize six distinct epitopes that are also targeted by human antibodies during natural malaria infection. Antibodies directed to more than three epitope regions spread across MSP4 are likely to be required for P. falciparum growth inhibition in vitro.
Quantitative evaluation in embedded system design (2008)

In the design process of an (embedded) computer system there are several important attributes the developer has to take care of: first of all, the final product should do the right thing, we then speak of functional correctness. Second, the performance should be adequate, expressed in measures such as throughput, delay or loss probability. Third, when relying on a battery as power source, it becomes increasingly important that the system behaves in an energy-aware manner. We could assess any of the three attributes in isolation, using completely different sets of models and tools. However, since the alteration of one of the attributes most surely also affects the other two, an integrated framework where all aspects can be evaluated and balanced is definitely desirable. We present such an integrated approach, but focus on the evaluation of battery lifetime. The system under consideration is represented by a stochastic workload model which then is combined with a battery model. In doing so, several design alternatives in the behaviour of the system can be compared early in the design process and the optimum with respect to functionality, performance and energy-consumption can be chosen.
Successful treatment of vitamin D unresponsive hypoparathyroidism with multipulse subcutaneous infusion of teriparatide (2008)

Vitamin-D unresponsiveness leads to uncontrolled hypocalcemia when postsurgical hypoparathyroidism occurs; in situations of no response to usual or higher doses of vitamin-D and s.c. injections of rhPTH, treatment with teriparatide multipulse s.c. infusor is an effective and safe alternative.
Differential susceptibility of mice humanized for peroxisome proliferator-activated receptor α to Wy-14,643-induced liver tumorigenesis (2005)

Peroxisome proliferators, such as lipid-lowering fibrate drugs, are agonists for the peroxisome proliferator-activated receptor alpha (PPARalpha). Sustained activation of PPARalpha leads to the development of liver tumors in rodents. Paradoxically, humans appear to be resistant to the induction of peroxisome proliferation and development of liver tumors by peroxisome proliferators. To examine the species differences in response to peroxisome proliferators, a PPARalpha humanized mouse (hPPARalpha) was generated, in which the human PPARalpha was expressed in liver under control of the Tet-OFF system. To evaluate the susceptibility of hPPARalpha mice to peroxisome proliferator-induced hepatocarcinogenesis, a long-term feeding study of Wy-14,643 was carried out. hPPARalpha and wild-type (mPPARalpha) mice were fed either a control diet or one containing 0.1% Wy-14,643 for 44 and 38 weeks, respectively. Gene expression analysis for peroxisomal and mitochondrial fatty acid metabolizing enzymes revealed that both hPPARalpha and mPPARalpha were functional. However, the incidence of liver tumors including hepatocellular carcinoma was 71% in Wy-14,643-treated mPPARalpha mice, and 5% in Wy-14,643-treated hPPARalpha mice. Upregulation of cell cycle regulated genes such as cd1 and Cdks were observed in non-tumorous liver tissue of Wy-14,643-treated mPPARalpha mice, whereas p53 gene expression was increased only in the livers of Wy-14,643-treated hPPARalpha mice. These findings suggest that structural differences between human and mouse PPARalpha are responsible for the differential susceptibility to the peroxisome proliferator-induced hepatocarcinogenesis. This mouse model will be useful for human cancer risk assessment of PPARalpha ligands.
Structural and electronic properties of Si3P4 (2004)

Physical Review B - Condensed Matter and Materials Physics
Simplification of Antiretroviral Therapy with Tenofovir‐Emtricitabine or Abacavir‐Lamivudine: A Randomized, 96‐Week Trial (2009)

In this population, TDF-FTC and ABC-3TC had similar virological efficacy, but ABC-3TC was associated with more serious non-AIDS events, particularly cardiovascular events. Clinical trials registration. NCT00192634 .
Games for training (2007)

DARPA simulations teach habits of thought so soldiers respond on the first day of combat as if they had been there a week. More often than not, it's don't shoot, talk instead.
Expression of fractalkine (CX3CL1) and its receptor, CX3CR1, during acute and chronic inflammation in the rodent CNS (2002)

In this study, we investigate the expression of fractalkine (CX3CL1) and the fractalkine receptor (CX3CR1) in the naive rat and mouse central nervous system (CNS). We determine if the expression of this chemokine and its receptor are altered during chronic or acute inflammation in the CNS. In addition, we determine if CX3CL1, which has been reported to be chemoattractant to leukocytes in vitro, is capable of acting as a chemoattractant in the CNS in vivo. Immunohistochemistry was performed using primary antibodies recognizing soluble and membrane-bound CX3CL1 and the N-terminus of the CX3CR1. We found that neurons in the naive rodent brain are immunoreactive for CX3CL1 and CX3CR1, both showing a perinuclear staining pattern. Resident microglia associated with the parenchyma and macrophages in the meninges and choroid plexus constituitively express CX3CR1. In a prion model of chronic neurodegeneration and inflammation, CX3CL1 immunoreactivity is upregulated in astrocytes and CX3CR1 expression is elevated on microglia. In surviving neurons, expression of CX3CL1 appears unaltered relative to normal neurons. There is a decrease in neuronal CX3CR1 expression. Acute inflammatory responses in the CNS, induced by stereotaxic injections of lipopolysaccharide or kainic acid, results in activation of microglia and astrocytes but no detectable changes in the glial expression of CX3CL1 or CX3CR1. The expression of CX3CL1 and CX3CR1 by glial cells during inflammation in the CNS may be influenced by the surrounding cytokine milieu, which has been shown to differ in acute and chronic neuroinflammation.
Comparison of Yeasts as Hosts for Recombinant Protein Production (2018)

Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria <i>Escherichia coli</i> to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, <i>Saccharomyces cerevisiae</i> was the dominant yeast host for heterologous protein production. Lately, other yeasts such as <i>Komagataella</i> sp., <i>Kluyveromyces lactis</i>, and <i>Yarrowia lipolytica</i> have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.
Transmission Planning for an Evolving Local Switched Digital Network (1979)

This paper examines the major issues associated with transmission planning for an evolving local switched digital network. Three general topics are discussed. First is the need to establish various "receive" levels within the digital switch in order to maintain existing toll loss and level plans. These are required because the integration of the interface between digital switching and transmission facilities has eliminated the channel bank, traditional location of the pad which controls trunk losses. The second area examined is the inherent fourwire nature of a digital switch. In order to maintain existing loss-noise grade of service, a nominal 0 dB cross office loss has been proposed for the switch. The 0 dB loss operation must be attained while experiencing little or no degradation due to singing or near-singing distortion. Acceptable listener echo performance can be obtained in a zero loss office with existing outside plant if an appropriate impedance balance technique, such as segregation of balance networks for loaded and nonloaded loops, is adopted. The third topic is the increasing use of remote vehicles in a local digital network. The basic rule of thumb applied is that transmission performance for customers at a "remote" location should be equivalent to transmission performance for customers at the "host" office. Transmission plans can then be applied accordingly.
Environmental Enrichment Therapy for Autism: Outcomes with Increased Access (2016)

We have previously shown in two randomized clinical trials that environmental enrichment is capable of ameliorating symptoms of autism spectrum disorder (ASD), and in the present study, we determined whether this therapy could be effective under real-world circumstances. 1,002 children were given daily Sensory Enrichment Therapy, by their parents, using personalized therapy instructions given over the Internet. Parents were asked to assess the symptoms of their child every 2 weeks for up to 7 months. An intention-to-treat analysis showed significant overall gains for a wide range of symptoms in these children, including learning, memory, anxiety, attention span, motor skills, eating, sleeping, sensory processing, self-awareness, communication, social skills, and mood/autism behaviors. The children of compliant caregivers were more likely to experience a significant improvement in their symptoms. The treatment was effective across a wide age range and there was equal progress reported for males and females, for USA and international subjects, for those who paid and those who did not pay for the therapy, and for individuals at all levels of initial symptom severity. Environmental enrichment, delivered via an online system, therefore appears to be an effective, low-cost means of treating the symptoms of ASD.
Ghrelin promotes thymopoiesis during aging (2007)

The decline in adaptive immunity, T lymphocyte output, and the contraction of the TCR repertoire with age is largely attributable to thymic involution. The loss of thymic function with age may be due to diminished numbers of progenitors and the loss of critical cytokines and hormones from the thymic microenvironment. We have previously demonstrated that the orexigenic hormone ghrelin is expressed by immune cells and regulates T cell activation and inflammation. Here we report that ghrelin and ghrelin receptor expression within the thymus diminished with progressive aging. Infusion of ghrelin into 14-month-old mice significantly improved the age-associated changes in thymic architecture and thymocyte numbers, increasing recent thymic emigrants and improving TCR diversity of peripheral T cell subsets. Ghrelin-induced thymopoiesis during aging was associated with enhanced early thymocyte progenitors and bone marrow-derived Lin(-)Sca1(+)cKit(+) cells, while ghrelin- and growth hormone secretagogue receptor-deficient (GHS-R-deficient) mice displayed enhanced age-associated thymic involution. Leptin also enhanced thymopoiesis in aged but not young mice. Our findings demonstrate what we believe to be a novel role for ghrelin and its receptor in thymic biology and suggest a possible therapeutic benefit of harnessing this pathway in the reconstitution of thymic function in immunocompromised subjects.
Case study of Lykke exchange: architecture and outlook (2017)

Purpose: This paper aims to explain the architecture and design choices of the exchange. Lykke is a FinTech company based in Zurich that has launched the global marketplace for all asset classes and instruments digitized on the blockchain. The authors discuss how the exchange will evolve over time. They explore the macroeconomic benefits of the new blockchain technology. The Lykke exchange is compatible with any type of public blockchain. Design/methodology/approach: The authors present the architecture of an exchange for colored coins. By colored coins, they mean issuer-backed securities on the Bitcoin blockchain. Orders are collected and matched by a semi-trusted exchange. Matched orders are settled on the Bitcoin blockchain, where each successful trade between parties appears as a set atomic-colored coins swap transactions. Unfilled and expired orders are discarded. The exchange does not take possession of the traded coins, but needs to be trusted to match trades correctly. Findings: Lykke has launched the exchange initially for the main currencies, cryptocurrencies and Lykke coin (entitlement to the shares of Lykke company). Perspective asset classes include futures and options on digital assets, crowd-funded loans for retail and private equity financing for small and medium-sized enterprises, contracts for difference, zero coupon bonds and other fixed income and natural capital bonds. Originality/value: Lykke exchange and all its tools and services are open source; the transparency of technology is ideal for research. The paper provides a high-level overview of the exchange and concludes with a research agenda.
Evaluating KNN, LDA and QDA classification for embedded online feature fusion (2008)

In this paper we evaluate k-nearest neighbor (KNN), linear and quadratic discriminant analysis (LDA and QDA, respectively) for embedded, online feature fusion which poses strong limitations on computing resources and timing. These algorithms are implemented on our multisensor data fusion (MSDF) architecture and are applied to traffic monitoring, i.e., classifying vehicles using distributed image, acoustic and laser sensors. We performed several tests of the algorithms on our embedded platform and evaluated CPU performance and memory consumption for training as well as classification. The results obtained are very promising for further use, especially of LDA and QDA for embedded online fusion at feature-level.
Temporary Intramolecular Generation of Pyridine Carbenes in Metal‐Free Three‐Component CH Bond Functionalisation/Aryl‐Transfer Reactions (2013)

Nucleophilic addition of pyridines to benzyne generates zwitterionic adducts that evolve by a rapid intramolecular proton shift to produce the corresponding pyridine carbenes, N-phenyl pyrid-2-ylidenes. In the presence of electrophilic ketones (isatin derivatives), the pyridylidenes can further react by an original bis-arylation reaction of the carbonyl compounds involving a formal pyridine C-H bond functionalisation. The overall transformation is an unprecedented three-component reaction featuring a carbene intermediate. The mechanism of this transformation was examined in detail by using both experimental and theoretical approaches. It was found that the generation of N-phenyl pyrid-2-ylidene from pyridine and benzyne is energetically favoured, and that the corresponding carbene dimer can also form easily. Under the three-component reaction conditions, the pyridylidene preferentially adds to the ketone group of the isatin derivative to produce a zwitterionic adduct amenable to an intramolecular aryl transfer reaction by a concerted nucleophilic aromatic substitution. This peculiar reactivity for a carbene was compared to possibly competitive known reactions of stable carbenes with carbonyl compounds, and the reaction was found to be under thermodynamic control. The reported method of generation of N-phenyl pyrid-2-ylidenes and their reactivity with carbonyl compounds unlock new perspectives in organic synthesis.
Planar gradient-index glass waveguide and its applications to a 4-port branched circuit and star coupler (1984)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Eiji Okuda, Ichiro Tanaka, and Tetsuya Yamasaki, "Planar gradient-index glass waveguide and its applications to a 4-port branched circuit and star coupler," Appl. Opt. 23, 1745-1748 (1984) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
VLC-Based Positioning System for an Indoor Environment Using an Image Sensor and an Accelerometer Sensor (2016)

Recently, it is believed that lighting and communication technologies are being replaced by high power LEDs, which are core parts of the visible light communication (VLC) system. In this paper, by taking advantages of VLC, we propose a novel design for an indoor positioning system using LEDs, an image sensor (IS) and an accelerometer sensor (AS) from mobile devices. The proposed algorithm, which provides a high precision indoor position, consists of four LEDs mounted on the ceiling transmitting their own three-dimensional (3D) world coordinates and an IS at an unknown position receiving and demodulating the signals. Based on the 3D world coordinates and the 2D image coordinate of LEDs, the position of the mobile device is determined. Compared to existing algorithms, the proposed algorithm only requires one IS. In addition, by using an AS, the mobile device is allowed to have arbitrary orientation. Last but not least, a mechanism for reducing the image sensor noise is proposed to further improve the accuracy of the positioning algorithm. A simulation is conducted to verify the performance of the proposed algorithm.
1995 Merck Frosst Award Lecture Quinone methides: relevant intermediates in organic chemistry (1996)

ortho and para-Quinone methides (2-methylene-3,5-cyclohexadien-1-one and 4-methylene-2,5-cyclohexadien-1-one, respectively) are intermediates in a variety of important chemical systems. In particular, o-quinone methides are useful in synthesis for the construction of chroman ring systems. A brief account of the relevance of quinone methide chemistry will be provided. This is followed by a review of recent studies from our laboratory on efficient methods for the photogeneration of quinone methides, concentrating on the use of hydroxy-substituted benzyl alcohols in aqueous media. It is shown that this method is general since it provides access to o-, m-, and p-quinone methide isomers. When appropriately substituted, all of these quinone methide isomers have been spectroscopically characterized by laser flash photolysis, making this technique the one of choice for studying the dynamics of these reactive intermediates. The mechanism of photochemical generation from hydroxybenzyl alcohols and extensions of the reaction to photogeneration of fluorenyl and biphenyl quinone methides will also be presented. Key words: quinone methide, biphenyl quinone methide, carbocation, photosolvolysis, photodehydroxylation, hetero-Diels–Alder reaction.
Risk score predicts high‐grade prostate cancer in DNA‐methylation positive, histopathologically negative biopsies (2016)

Low DNA-methylation levels in PCa-negative biopsies led to a NPV of 96% for high-grade cancer. The risk score, comprising DNA-methylation intensity and traditional clinical risk factors, improved the identification of men with high-grade cancer, with a maximum avoidance of unnecessary repeat biopsies. This risk score resulted in better patient risk stratification and significantly outperformed current risk prediction models such as PCPTRC and PSA. The risk score could help to identify patients with histopathologically negative biopsies harboring high-grade PCa. Prostate 76:1078-1087, 2016. © 2016 The Authors. The Prostate Published by Wiley Periodicals, Inc.
Emx2 Regulates Mammalian Reproduction by Altering Endometrial Cell Proliferation (2005)

The molecular mechanisms that underlie embryo implantation are poorly understood. Under the control of sex steroids, uterine endometrium undergoes tremendous, yet tightly controlled, proliferation in each estrous cycle to facilitate implantation; disorders of endometrial proliferation underlie several uterine diseases. We have previously identified the Emx2 gene as a transcriptional target of HOXA10 regulation in the reproductive tract. Here we report the function of Emx2 in murine implantation and regulation of endometrial proliferation. We transfected mice on d 2 post coitus with pcDNA3.1/Emx2, Emx2 antisense, or respective controls consisting of empty pcDNA3.1 or a random order oligonucleotide by intrauterine lipofection. Increased expression of Emx2 reduced average implantation rate by approximately 40% (P = 0.00006) resulting in an average number of implanted embryos per litter of 13.7 in the control group to 8.2 in the pcDNA3.1/Emx2-treated group. Neither treatment altered the number of mice attaining pregnancy with at least one embryo. Decreased Emx2 expression did not alter litter size. Neither treatment affected the birth weight of the pups. To elucidate potential mechanisms through which Emx2-regulated reproduction, markers of endometrial differentiation, proliferation, and apoptosis were assessed. Increased Emx2 expression significantly decreased endometrial cell proliferating cell nuclear antigen expression and 5'-bromo-2' deoxyuridine incorporation. Markers of stromal cell differentiation (IGF binding protein-1, prolactin), epithelial differentiation (calcitonin), and apoptosis (activated caspase3) were unchanged. In human endometrial epithelial cells in vitro, Emx2 reduced cell number indicating diminished proliferation. Emx2 controls mammalian reproduction by adjusting endometrial cell proliferation without effecting differentiation. Regulated uterine Emx2 expression is necessary during reproduction for maximal implantation and litter size.
Carbamazepine-Induced Toxic Effects and HLA-B*1502 Screening in Taiwan (2011)

The identification of subjects carrying the HLA-B*1502 allele and the avoidance of carbamazepine therapy in these subjects was strongly associated with a decrease in the incidence of carbamazepine-induced SJS-TEN. (Funded by the National Science Council of Taiwan and the Taiwan Drug Relief Foundation.).