gebhart/patrepeval huggingface dataset:
Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components (2007)

Pre-mRNA splicing not only removes introns and joins exons to generate spliced mRNA but also results in remodeling of the spliced messenger ribonucleoprotein, influencing various downstream events. This remodeling includes the loading of an exon-exon junction complex (EJC). It is unclear how the spliceosome recruits the EJC onto the mRNA and whether EJC formation or EJC components are required for pre-mRNA splicing. Here we immunodepleted the EJC core component eIF4A3 from HeLa cell nuclear extract and found that eIF4A3 is dispensable for pre-mRNA splicing in vitro. However, eIF4A3 is required for the splicing-dependent loading of the Y14/Magoh heterodimer onto mRNA, and this activity of human eIF4A3 is also present in the Drosophila ortholog. Surprisingly, the loading of six other EJC components was not affected by eIF4A3 depletion, suggesting that their binding to mRNA involves different or redundant pathways. Finally, we found that the assembly of the EJC onto mRNA occurs at the late stages of the splicing reaction and requires the second-step splicing and mRNA-release factor HRH1/hPrp22. The EJC-dependent and -independent recruitment of RNA-binding proteins onto mRNA suggests a role for the EJC in messenger ribonucleoprotein remodeling involving interactions with other proteins already bound to the pre-mRNA, which has implications for nonsense-mediated mRNA decay and other mRNA transactions.
Abstract 1625: Crosstalk between breast cancer and stromal cells occurs via exosomes and gap junctions in bone metastatic breast cancer. (2013)

Abstract Breast cancer preferentially metastasizes to the bone, where the five-year relative survival rate falls from 90% to &lt;10%. Although the precise mechanism underlying preferential metastasis is unknown, the bone likely provides a hospitable environment that both attracts breast cancer cells and allows them to colonize and grow. Besides affects osteoblast and osteoclast properties, we have evidence that metastatic breast cancer cells further create a unique bone niche by orchestrating extensive crosstalk with osteoblasts that may be involved in creating a niche permissive for breast cancer cell dormancy. MC3T3-E1 murine osteoblasts were grown to confluence, then MDA-MB-231 human breast cancer cells added at a ratio of 1 breast cancer cell to 10 osteoblasts. Co-cultures were subsequently fixed and stained for Cx43 expression. Next, MC3T3-E1 cells and MDA-MB-231 cells were grown to confluence. Culture supernatants were removed and processed through a series of ultra-centrifugation, purification, and concentration steps to purify for exosomes. Finally, MC3T3-E1 cells were grown to various stages of maturity: 4 (growth) and 10 days (early differentiation) and incubated with conditioned medium from human MDA-MB-231 cells. qPCR was used to assay for changes in osteoblast-derived inflammatory cytokine expression. Expression of the gap junction protein Cx43 was localized between breast cancer cells and osteoblasts. Both MC3T3-E1 and MDA-MB-231 cells expressed exosomes, which were visualized using a transmission electron microscope. Osteoblast-derived cytokines increased in the presence of MDA-MB-231 breast cancer cell conditioned medium included MCP-1 (CCL2), LIX (CXCL5), LIF, and NFATc2. Overall, these data suggest that suggest there is extensive crosstalk directly between osteoblasts and breast cancer cells, and that osteoblasts are an important source of cytokines in breast cancer bone metastasis. Thus, these findings implicate the bone microenvironment and cancer cell manipulation thereof in orchestrating metastatic tumor cell dormancy, colonization, and survival. Supported in part by the National Institutes of Health; 1RC1 CA146381, 1R01NS06994, P50 CA083639 for FCM; Ruth L. Kirschstein Institutional Research Service Award (NRSA) T32 CA079448 for KMB. Citation Format: Karen M. Bussard, Frank C. Marini. Crosstalk between breast cancer and stromal cells occurs via exosomes and gap junctions in bone metastatic breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1625. doi:10.1158/1538-7445.AM2013-1625
Ciliary disorder of the skeleton (2012)

In the last 10 years, the primary cilia machinery has been implicated in more than a dozen disorders united as ciliopathies, including skeletal dysplasias, such as Jeune syndrome and short rib-polydactyly type III. Indeed, primary cilia play a vital role in transduction of signals in the hedgehog pathway that is especially important in skeletal development. In this review, we focus on skeletal conditions belonging to the ciliopathy group: the short rib-polydactyly group (SRPs) that includes Verma-Naumoff syndrome (SRP type III), Majewski syndrome (SRP type II), Jeune syndrome (ATD), as well as Ellis-van Creveld syndrome (EVC), the Sensenbrenner syndrome, and, finally, Weyers acrofacial dysostosis. Today, 10 different genes have been identified as responsible for seven "skeletal" ciliopathies. Mutations have been identified in dynein motor (DYNC2H1), in intraflagellar transport (IFT) complexes (IFT80, IFT122, IFT43, WDR35, WDR19, and TTC21B) as well as in genes responsible for the basal body (NEK1, EVC, and EVC2). The wide clinical variability observed for an individual ciliopathy gene supports the development of exome strategy specifically dedicated to cilia genes to identify mutations in this particularly heterogeneous group of disorders.
MUSCLE NERVE SYMPATHETIC ACTIVITY IN HYPERTEXSIVE SUBJECTS (1981)

In summary there is no difference between MSA in normotensive and hypertensive subjects that is likely to be of pathogenetic importance. We may also conclude that when high blood pressure develops slowly (irrespective of the underlying reason) baroreflex mechanisms exerted via muscle sympathetic activity are not able to counteract the blood pressure rise.
Cleaning graphene: comparing heat treatments in air and in vacuum (2017)

Surface impurities and contamination often seriously degrade the properties of two-dimensional materials such as graphene. To remove contamination, thermal annealing is commonly used. We present a comparative analysis of annealing treatments in air and in vacuum, both ex situ and "pre-situ", where an ultra-high vacuum treatment chamber is directly connected to an aberration-corrected scanning transmission electron microscope. While ex situ treatments do remove contamination, it is challenging to obtain atomically clean surfaces after ambient transfer. However, pre-situ cleaning with radiative or laser heating appears reliable and well suited to clean graphene without undue damage to its structure.
CHAPTER 8: Snack Foods, Meats, and Other Applications (1997)

Cereals & Grains Association is a nonprofit organization dedicated to advancing the knowledge and understanding of cereal grain science through research leadership, education, superior technical service, and advocacy.
Taui, A high-resolution metabolic imaging biomarker for myocardium (2014)

Background Contrast-enhanced H2O T1-weighted cardiovascular MRI is usually interpreted using tracer paradigms; e.g., the extra-/intravascular contrast agent (CA) partition coefficient. However, the signal molecule is water, not CA. Consequently, the myocardial extracellular volume fraction (ECV) is underestimated in proportion to its magnitude. Even more importantly, intercompartmental water exchange kinetics are inaccessible. The mean intracellular water molecule lifetime [taui] is assumed effectively 0; though it is a fraction of a second. For cylindrical myocytes with mean cytolemmal water permeability coefficient PW and diameter d: taui = 4(PW/d). taui -1 is linearly related to PW and to d . However, PW dominates and is itself dominated by active trans-membrane water cycling. Thus, taui -1 is proportional to the driving cytolemmal ATPase ion pump activity.
MeSOD-the metric spatial object data model for a multimedia application: hyperbook (2003)

A data model for multimedia applications, called MeSOD (metric spatial object data model), is proposed. This model maps entities in the real world onto metric spaces. The MeSOD is motivated by an electronic book system, called the hyperbook system, that enables users to interact with the system using multimedia information. The hyperbook system is introduced and the problems in implementing multimedia communications is indicated. Then the concept and the advantage of the MeSOD are discussed, and an informal definition of the MeSOD is given. The design of the MeSOD's applications development environment, MADE, is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hard X-ray Photoelectron spectroscopy (HX-PES) study on chemical binding states of ultra shallow plasma-doped silicon layer for the application of advanced ULSI devices (2006)

We took HX-PES measurement (Si 1s) on silicon samples doped by plasma doping (PD) for the first time before and after annealing using either spike RTA or flash lamp anneal (FLA) in SPring-8. After PD, the carrier density of n-Si substrate decreased to intrinsic Si level due to defect induced carrier traps. After annealing, the results revealed that the chemical binding states of the doped samples were well recovered showing high impurity activation.
DESIGN OF EXPERIMENTS IN NON-LINEAR SITUATIONS (1959)

DESIGN OF EXPERIMENTS IN NON-LINEAR SITUATIONS Get access G. E. P. BOX, G. E. P. BOX Statistical Techniques Research Group, Princeton University and Institute of Statistics, North Carolina State College Search for other works by this author on: Oxford Academic Google Scholar H. L. LUCAS H. L. LUCAS Statistical Techniques Research Group, Princeton University and Institute of Statistics, North Carolina State College Search for other works by this author on: Oxford Academic Google Scholar Biometrika, Volume 46, Issue 1-2, June 1959, Pages 77–90, https://doi.org/10.1093/biomet/46.1-2.77 Published: 01 June 1959
Migrating from planar to FinFET for further CMOS scaling: SOI or Bulk? (2009)

The multi-gate architecture is considered as a key enabler for further CMOS scaling. FinFETs can readily be manufactured on SOI or bulk substrates. We report for the first time an extensive benchmark of their critical electrical figures of merit. Both alternatives show better scalability than PLANAR CMOS and exhibit similar intrinsic device performance. Introducing SOI substrates and low doped fins results in lower junction capacitance, higher mobility and voltage gain with reduced mismatch. Using an optimized integration to minimize parasitics we demonstrate high-performing FinFET ring-oscillators with delays down to 10ps/stage for both SOI and bulk FinFETs and working SRAM cells at VDD=1.0V.
An Application of the Piecewise Autoregressive Model in Lossless Audio Coding (2006)

The paper is focused on the prediction stage for lossless audio coding. We rely on the piecewise autoregressive model to design a compressor dubbed PAR for which the complexity of the decoder is low such that to be easily implemented on economic devices. The performances of the new coder are evaluated for two data sets of monaural audio signals sampled at 44.1 KHz and recorded with 16 bits/sample. The results obtained with PAR compares favorably with the popular MAC Audio Coder.
Flexible Robot Platform For Autonomous Research (2005)

The field of mobile robotics is receiving increasing levels of research. However, the simulation tools which are utilised in the creation of new mobile robot algorithms can produce algorithms which do not work in the real world. In order to try and minimise this problem a flexible robot platform has been created which allows the testing of a variety of algorithms. The platform facilitates the testing of algorithms normally only simulated by allowing algorithms to be easily tested in the real world. Utilising the flexible robot platform for testing algorithms allows higher quality research, as algorithms can be assessed with physical evidence.
A SIMPLE QUANTIFICATION METHOD OF GRAIN SHAPE OF GRANULAR MATERIALS SUCH AS SAND (1993)

砂粒子の形状が, せん断強さなどの工学的性質に影響を与えることは周知の事実である. しかし, 砂は個々の粒子が小さく, しかも形状の定量化の作業がかなり煩雑であるために工学的性質に与える粒子形状の影響に関する系統的な研究を阻害してきた. 本論文では粒状体の粒子形状を評価する凹凸係数FUを提案し, 種々の砂およびこれまで形状の評価に用いられてきた視覚印象図の定量化例について述べている.
Maps of Meaning (1996)

Maps enable us to gain a sense of our place in the world, to orient ourselves. In this way they are like all socio-cultural frameworks: 'cultures are maps of meaning through which the world is made intelligible.'2 As Edmund Leach suggests: 'Our whole social environment is map-like. Whenever human beings construct a dwelling or lay out a settlement they do so in a geometrically ordered way. This seems to be as "natural" to Man [sic] as his capacity for language. We need order in our surroundings.'3 Without maps, life can be difficult and even dangerous. The protagonists of Ian McEwan's novel The Comfort of Strangers (1982), for example, find their lives under threat while on holiday in Venice after venturing out at night and getting lost without their tourist maps. The text implies that they are also without the appropriate cultural maps, failing to pick up clues or to recognize the approach of danger in the form of the characters Robert and Caroline who cross their path. In the film adaptation we see a reproduction of Jacopo de Barbari's map hanging in Robert and Caroline's apartment, symbolizing perhaps their greater control of the territory. Robert's attitudes towards sexuality — both his sadistic practices and his belief that women should be kept in 'their place' — certainly demonstrate such a concern for rigid control at the cultural level.
Clinical Q&A (2007)

The NLH Question and Answering Service was set up for primary care practitioners to ask any question related to their clinical practice. Below are two recent questions asked. For full answers and references please refer to website at www.clinicalanswers.nhs.uk .
Growth of Lactobacillus paracasei ATCC 334 in a cheese model system: A biochemical approach (2011)

Growth of Lactobacillus paracasei ATCC 334, in a cheese-ripening model system based upon a medium prepared from ripening Cheddar cheese extract (CCE) was evaluated. Lactobacillus paracasei ATCC 334 grows in CCE made from cheese ripened for 2 (2mCCE), 6 (6mCCE), and 8 (8mCCE) mo, to final cell densities of 5.9×10(8), 1.2×10(8), and 2.1×10(7)cfu/mL, respectively. Biochemical analysis and mass balance equations were used to determine substrate consumption patterns and products formed in 2mCCE. The products formed included formate, acetate, and D-lactate. These data allowed us to identify the pathways likely used and to initiate metabolic flux analysis. The production of volatiles during growth of Lb. paracasei ATCC 334 in 8mCCE was monitored to evaluate the metabolic pathways utilized by Lb. paracasei during the later stages of ripening Cheddar cheese. The 2 volatiles detected at high levels were ethanol and acetate. The remaining detected volatiles are present in significantly lower amounts and likely result from amino acid, pyruvate, and acetyl-coenzyme A metabolism. Carbon balance of galactose, lactose, citrate, and phosphoserine/phosphoserine-containing peptides in terms of D-lactate, acetate, and formate are in agreement with the amounts of substrates observed in 2mCCE; however, this was not the case for 6mCCE and 8mCCE, suggesting that additional energy sources are utilized during growth of Lb. paracasei ATCC 334 in these CCE. This study provides valuable information on the biochemistry and physiology of Lb. paracasei ATCC 334 in ripening cheese.
Hemin-induced modifications of the antigenicity and hemin-binding capacity of Porphyromonas gingivalis lipopolysaccharide (1996)

Previous studies have shown that the physical, biochemical, and antigenic properties of the bacterial outer membrane are profoundly influenced by the growth environment. In the present study, the effects of growth in hemin-replete (H+) and hemin-depleted (H-) media on the lipopolysaccharide (LPS) of the oral pathogen Porphyromonas gingivalis were investigated. Our studies show that LPS from P. gingivalis cultured in H+ media (H+LPS) expressed additional low-molecular-mass antigens, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analysis. Particularly evident was a 26-kDa antigen (26 LPSC) that was lost from the LPS upon transfer of P. gingivalis into H- media. The loss of the 26 LPSC was accompanied by a marked reduction in the hemin-binding capacity of the LPS. The 26 LPSC was refractory to Coomassie blue staining and proteinase K digestion. H+LPS from strain W50/BE1, a nonpigmented pleiotropic strain, lacked the 26 LPSC and did not bind hemin. Polyclonal antiserum raised to whole-cell antigens of P. gingivalis A7436, W83, and HG405 grown in H+ media, but not in H- media, recognized the 26 LPSC in the purified H+LPS from any of the three strains. The immunoreactivities of sera from humans with (n = 24) or without (n = 25) periodontitis to the 26 LPSC and other H+LPS determinants were analyzed by Western blot. Overall, 75% of adult periodontitis patient sera reacted with multiple bands in the H+LPS stepladder, particularly in the range of 14 to 27 kDa. In contrast, only 20% of control sera reacted faintly with H+LPS bands in the range 27 to 34 kDa. The 26 LPSC was recognized by over 40% of sera from adult patients with periodontitis and none of the healthy control sera. Taken together, these results suggest that the antigenicity and hemin-binding properties of P. gingivalis LPS can be modified by growth in H+ media.
Vapor-Induced Luminescence Switching in Crystals of the<i>Syn</i>Isomer of a Dinuclear (Bipyridine)platinum(II) Complex Bridged with Pyridine-2-Thiolate Ions (2002)

Remarkable vapochromic effects are observed in a dinuclear platinum(II) complex, where changes in luminescence are facilitated in the presence of solvated organic molecules, such as acetonitrile and ethanol (see scheme). Supporting information for this article is available on the WWW under http://www.angewandte.org or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The <i>enhancer of zeste homolog 2</i> gene contributes to cell proliferation and apoptosis resistance in renal cell carcinoma cells (2008)

The enhancer of zeste homolog 2 (EZH2) gene has been recently linked to human malignancies where it may serve as a new target for cancer therapy. Here, we analyzed EZH2 expression in primary renal cell carcinoma (RCC) specimens and in nontumorous tissue samples from adult kidney. EZH2 transcripts were detectable in all RCC specimens examined. Expression levels were significantly higher in tumor tissue (p < or = 0.0001) than in samples from normal adult kidney. Moreover, inhibition of endogenous EZH2 expression in RCC cell lines by RNA interference (RNAi) led to reduced proliferation and increased apoptosis in RCC cells. These data show that EZH2 is overexpressed in RCC. Furthermore, they indicate that the EZH2 gene plays a role for both the proliferation and the apoptosis resistance of RCC cells. Targeted inhibition of EZH2 could therefore represent a novel strategy to improve the therapeutic response of RCC.
Mice with a Conditional Deletion of the Neurotrophin Receptor TrkB Are Dwarfed, and Are Similar to Mice with a MAPK14 Deletion (2013)

Long bone growth results from ordered chondrocyte development within the cartilagenous growth plate. Chondrocytes are recruited from a resting pool to proliferate along the long axis of the bone, until various signals trigger differentiation and hypertrophy. We have shown previously that the neurotrophin receptor TrkB is expressed in growth plate chondrocytes, where the tyrosine kinase receptor regulates the pace of hypertrophic differentiation by modulating the activities of ERK and p38 MAP kinases. To investigate the physiological relevance of TrkB to bone growth in vivo, we generated mice with a targeted disruption of the receptor, and compared them to mice targeted for MAPK14, the gene for p38α. The TrkB mutant and p38α mutant mice showed a similar degree of dwarfism and delayed hypertrophic differentiation. To extend these findings, we showed that both the TrkB and p38α mutant mice have altered expression of Runx2 and Sox9, two key transcription factors required for skeletogenesis. The data provides in vivo evidence for the role of TrkB in bone growth, supports the role of p38 downstream of TrkB, and suggests that Runx2 and Sox9 expression is regulated by this pathway at the growth plate.
CARTOON: A Biologically Motivated Edge Detection Algorithm (1982)

Caricatures demonstrate that only a few significant "edges" need to be captured to convey the meaning of a complex pattern of image intensities. The most important of these "edges" are image intensity changes arising from surface discontinuities or occluding boundaries. The CARTOON algorithm is an attempt to locate these special intensity changes using a modification of the zero-crossing coincidence scheme suggested by Marr and Hildreth (1980).
Single-mode fiber and few-mode fiber photonic lanterns performance evaluated for use in a scalable real-time photon counting ground receiver (2019)

Photonic lanterns provide an efficient way of coupling light from a single large-core fiber to multiple small-core fibers. This capability is of interest for space to ground communication applications. In these applications, the optical ground receivers require high-efficiency coupling from an atmospherically distorted focus spot to multiple fiber coupled single pixel super-conducting nanowire detectors. This paper will explore the use of photonic lanterns in a real-time ground receiver that is scalable and constructed with commercial parts. The number of small-core fibers (i.e. an array of single or few-mode cores) that make a photonic lantern determines the number of spatial modes that they couple at the larger multimode fiber core end. For instance, lanterns made with n number of single-mode fibers can couple n number of spatial modes. Although the laser transmitted from a spacecraft originates as a Gaussian shape, the atmosphere distorts the beam profile by scrambling the phase and scattering energy into higher-order spatial modes. Therefore, if a ground receiver is sized for a target data rate with n number of detectors, the corresponding lantern made with single-mode fibers will couple n number of spatial modes. Most of the energy of the transmitted beam scattered into spatial modes higher than n will be lost. This paper shows this loss may be reduced by making lanterns with few-mode fibers instead of single-mode fibers, increasing the number of spatial modes that can be coupled and therefore increasing the coupling efficiency to single pixel, single photon detectors. The free space to fiber coupling efficiency of these two types of photonic lanterns are compared over a range of the free-space coupling numerical apertures and mode field diameters. Results indicate the few mode fiber lantern has higher coupling efficiency for telescopes with longer focal lengths under higher turbulent conditions. Also presented is analysis of the jitter added to the system by the lanterns, showing the few-mode fiber photonic lantern adds more jitter than the single-mode fiber lantern, but less than a multimode fiber.