gebhart/patrepeval huggingface dataset:
Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (2017)

Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV<sup>+</sup>) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. <i>Cancer Res; 77(23); 6538-50. ©2017 AACR</i>.
Processing-Microstructure Relationships From 3D Characterization of Additively Manufactured Metals (2019)

Journal Article Processing-Microstructure Relationships From 3D Characterization of Additively Manufactured Metals Get access Andrew T Polonsky, Andrew T Polonsky Materials Department, University of California Santa Barbara, Santa Barbara, CA, USA Corresponding author: polonsky@ucsb.edu Search for other works by this author on: Oxford Academic Google Scholar Narendran Raghavan, Narendran Raghavan Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar McLean P Echlin, McLean P Echlin Materials Department, University of California Santa Barbara, Santa Barbara, CA, USA Search for other works by this author on: Oxford Academic Google Scholar William C Lenthe, William C Lenthe Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Michael M Kirka, Michael M Kirka Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Ryan R Dehoff, Ryan R Dehoff Oak Ridge National Laboratory, Oak Ridge, TN, USA Search for other works by this author on: Oxford Academic Google Scholar Tresa M Pollock Tresa M Pollock Materials Department, University of California Santa Barbara, Santa Barbara, CA, USA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 25, Issue S2, 1 August 2019, Pages 2582–2583, https://doi.org/10.1017/S1431927619013643 Published: 01 August 2019
Investigating the Downstream Impact of Grapheme-Based Acoustic Modeling on Spoken Utterance Classification (2018)

Automatic speech recognition (ASR) and natural language understanding are critical components of spoken language understanding (SLU) systems. One obstacle to providing services with SLU systems in multiple languages is the cost associated with acquiring all of the language-specific resources required for ASR in each language. Modeling graphemes eliminates the need to obtain a pronunciation dictionary which maps from speech sounds to words and is one way to reduce ASR resource dependencies when rapidly developing ASR in new languages. However, little is known about the downstream impact on SLU task performance when selecting graphemes as the acoustic modeling unit. This work investigates acoustic modeling for the ASR component of an SLU system using grapheme-based approaches together with convolutional and recurrent neural network architectures. We evaluate both ASR word accuracy and spoken utterance classification (SUC) accuracy for English, Italian and Spanish language tasks and find that it is possible to achieve SUC accuracy that is comparable to conventional phoneme-based systems which leverage a pronunciation dictionary.
Targeted delivery of fluorogenic peptide aptamers into live microalgae by femtosecond laser photoporation at single-cell resolution (2018)

Microalgae-based metabolic engineering has been proven effective for producing valuable substances such as food supplements, pharmaceutical drugs, biodegradable plastics, and biofuels in the past decade. The ability to accurately visualize and quantify intracellular metabolites in live microalgae is essential for efficient metabolic engineering, but remains a major challenge due to the lack of characterization methods. Here we demonstrate it by synthesizing fluorogenic peptide aptamers with specific binding affinity to a target metabolite and delivering them into live microalgae by femtosecond laser photoporation at single-cell resolution. As a proof-of-principle demonstration of our method, we use it to characterize Euglena gracilis, a photosynthetic unicellular motile microalgal species, which is capable of producing paramylon (a carbohydrate granule similar to starch). Specifically, we synthesize a peptide aptamer containing a paramylon-binding fluorescent probe, 7-nitrobenzofurazan, and introduce it into E. gracilis cells one-by-one by suppressing their mobility with mannitol and transiently perforating them with femtosecond laser pulses at 800 nm for photoporation. To demonstrate the method's practical utility in metabolic engineering, we perform spatially and temporally resolved fluorescence microscopy of single live photoporated E. gracilis cells under different culture conditions. Our method holds great promise for highly efficient microalgae-based metabolic engineering.
Polymersolarzellen: Fortschritt, Herausforderungen und Perspektiven (2018)

Abstract Polymersolarzellen mit Heteroübergangsarchitektur (“bulk‐heterojunction polymer solar cell”, BHJ‐PSC) wurden zwei Jahrzehnte lang vor allem auf solche Materialmischungen hin untersucht, bei denen der Elektronendonor ein Polymer und der Elektronenakzeptor ein Fulleren ist. Dies änderte sich erst in neuerer Zeit mit der Einführung von PSCs ohne Fullerenakzeptor. Innerhalb kürzester Zeit haben sich diese fullerenfreien PSCs rasant weiterentwickelt. Fullerenfreie BHJ‐PSCs erreichen mittlerweile einen weit höheren Wirkungsgrad von über 15 % als die effizientesten Fulleren‐PSCs. Vor allem die reinen Polymersolarzellen (“all‐polymer solar cells”, APSCs), bei denen der Heteroübergang aus einem Polymer als Donor und einem Polymer als Akzeptor gebildet wird, finden steigendes Interesse. Sie bieten: 1) eine einstellbare hohe Lichtabsorption durch das Polymer‐Donor/Polymer‐Akzeptor‐Paar; 2) robuste Morphologien des BHJ‐Films; 3) Kompatibilität mit großformatiger und großflächiger Fertigung; 4) eine gute Langzeitstabilität der Zelle gegenüber Umwelt‐ und mechanischer Beanspruchung. Dieser Kurzaufsatz beschreibt die Möglichkeiten und Chancen der APSCs. Er zeigt auf, welche Polymere sich als Bauelemente eignen und wie sich deren Leistungsfähigkeit noch weiter optimieren lässt. Herausforderungen, die für kommerzielle Anwendungen weiter bestehen, werden ebenfalls erörtert.
Antibodies to Human Milk Fat Globule Molecules (1989)

Since the development of the first polyclonal antiserum to human milk fat globule (HMFG) membranes (1), this immunogen has been used by numerous workers to produce polyclonal and monoclonal antibodies. These reagents have been extremely useful in identifying markers of breast epithelial differentiation and have had a number of clinical applications. In addition, monoclonal antibodies to HMFG and to many tumour-associated antigens have brought into focus a group of highly immunogenic glycoproteins which have the characteristics of mucins and are expressed by many carcinomas. In this review we will discuss mainly work which has been done with the human milk fat globule, but it should be borne in mind that the same membranes and their components have been extensively studied in rodents and in the cow.
Herpesvirus saimiri-transformed human CD4+ T cells can provide polyclonal B cell help via the CD40 ligand as well as the TNF-alpha pathway and through release of lymphokines (1996)

We have developed human CD4+ T cell lines from the PBL of normal donors by infection with Herpesvirus saimiri (HVS), to evaluate functional properties of these immortalized lymphocytes. In this report, we characterize two such CD4+ T cell lines, CHCD4 and MHCD4, which were derived from two different donors. These cells grew independent of exogenous IL-2 stimulation for over 1 yr, and expressed surface markers (CD25+, CD69+, HLA-DR+, and B7+) associated with an activated T cell phenotype. Both lines constitutively produced and released IFN-gamma, but no IL-2 or IL-4. However, the surface expression of the two cell lines differed in that CHCD4 constitutively expressed CD40 ligand (CD40L) and membrane TNF-alpha, but MHCD4 did not. Also, CHCD4, but not MHCD4, potently induced polyclonal B cell activation and differentiation in the absence of PWM, in an MHC-unrestricted fashion. The B cell help afforded by CHCD4 included contact-dependent and soluble components. Contact-dependent help was strongly inhibited by mAb against CD40L (5C8) and to a lesser extent, by anti-TNF-alpha Ab. The CD40L-dependent helper function of CHCD4 contrasts with the recent description of other HVS-transformed CD4+ T cells that provide B cell help primarily via the membrane TNF-alpha and TNF-alphaR pathways. Furthermore, CHCD4 cells also secreted soluble factors that could mediate CD40-linked B cell differentiation into Ab-producing cells. Interestingly, this factor is not likely to be IL-2, IL-4, IL-6, IL-10, IL-15, TNF-alpha, or IFN-gamma as Abs against these cytokines were not able to inhibit the contact-independent B cell help by CHCD4. These results indicate that HVS-immortalization of CD4+ lymphocytes may produce T cell clones with a spectrum of important contact-dependent, as well as contact-independent, B cell helper function capacities.
Message from the Editors to our Reviewers (2016)

Between April 1, 2016, and September 30, 2016, Neurology ® received 2,565 new and 650 revised manuscripts (compared to 2,366 new and 646 revised manuscripts during this same period in 2015). We received 4,461 peer reviews (compared to 4,645 during the same period in 2015) for these papers. We can accept only a minority of submitted manuscripts and must often make extremely difficult decisions regarding which articles we believe will most benefit readers and improve patient care. Your thoughtful comments regarding uniqueness of study populations, novel methods, studies that are especially educational, or new strategies for diagnosing and treating neurologic disease are highly appreciated. We thank you also for your cooperation in returning reviews in a timely manner.
Convolutional codes and matrix control theory (1999)

A general description of convolutional codes is provided by a set of linear equations called discrete-time state-space equations in control theory. We discuss how the notions of controllability, observability and minimality in control, are applied to convolutional code design. The notion of output-observability is used to ensure minimality of a convolutional code. Without concatenation, searching for good trellis codes requires examining one code within each group of range-equivalent encoders (i.e. equivalent in Forney&amp;apos;s sense [1]). So it is sufficient to restrict attention within a set of canonical encoders. However, turbo code constituent encoders are optimized under specific input to output mappings. We describe this class of encoders as &amp;quot;inputHamming weight equivalent&amp;quot; and identify the canonical structures for the constituent encoder search space. In many cases of practical interest, the optimal structure for these constituent encoders connects the memory elements in a single row. ...
60 GHz board-to-board optical interconnection using polymer optical buses in conjunction with microprism couplers (1992)

We have demonstrated for the first time 60 GHz wide-band board-to-board optical interconnection with a signal-to-noise ratio of 22 dB. The total interconnection distance is 55 cm from the input coupling prism to the detector. Board-to-board optical interconnection was realized using microprisms which had a measured coupling bandwidth of more than 250 nm. The graded index of the polymer waveguide allows us to implement such an interconnection scheme on an array of substrates. The elimination of backplane interconnection greatly enhances the interconnection speed. The implementation of a high-speed on-board transceiver in connection with a polymer waveguide lens will generate a fully on-board optical interconnect involving modulation/demodulation.
Dynamic reconfiguration of coordinated multi-point transmission in high density small cell network using centralized wavelength switching in DWDM PON (2016)

We proposed DWDM-PON architecture, which utilize wavelength selective switch with tunable OLT for dynamic reconfiguration of coordinated multi-point transmission in high density small cell network. We successfully demonstrated the dynamic routing and monitoring behavior employing pilot tone scheme.
A one pot three-step process for the synthesis of an array of arylated benzimidazoribosyl nucleosides (2011)

A three-step one pot reaction/purification protocol was developed to facilitate rapid access to benzimidazole-based nucleosides, for which benzoylated benzimidazoribosyl nucleosides incorporating boronic esters were key reaction intermediates.
Cyclic AMP, a nonessential regulator of the cell cycle. (1975)

Flow-microfluorimetric analysis has been carried out on populations of exponentially growing S49 mouse lymphoma cells treated with dibutyryl cyclic AMP. The drug produces a specific concentration-dependent block in the G-1 phase of the cell cycle while other phases of the cycle are not perceptibly altered. The cell cycle of a line of mutant cells lacking the cyclic AMP-dependent protein kinase is not affected by the drug. Since these mutant cells have been shown to maintain a normal cell cycle, even in the presence of high levels of cyclic AMP, periodic fluctuations in the levels of the cyclic nucleotide cannot be required for or determine progression through the cell cycle.
SPARC is a VCAM-1 counter-ligand that mediates leukocyte transmigration (2006)

VCAM-1 is a cell surface molecule, which has been shown to mediate leukocyte adhesion to the endothelium and subsequent transmigration. Although VCAM-1 regulates adhesion through its interaction with VLA-4, VLA-4 does not play a role in VCAM-1-dependent diapedesis, an observation suggesting the presence of a second ligand for VCAM-1. We now report a novel interaction between VCAM-1 and secreted protein acidic and rich in cysteine (SPARC), which induces actin cytoskeletal rearrangement and intercellular gaps, physiological processes known to be important for leukocyte transmigration. The binding of leukocyte-derived SPARC to VCAM-1 was demonstrated to be necessary for leukocyte transmigration through endothelial monolayers (diapedesis) in vitro, and furthermore, SPARC null mice have abnormalities in leukocyte recruitment to the inflamed peritoneum in vivo. These findings provide new insight into the mechanisms of transendothelial leukocyte migration and suggest a potential, targetable interaction for therapeutic intervention.
Microalloy Precipitation at the Glass–Steel Interface Enabling Adherence of Porcelain Enamel (2015)

The adherence of vitreous enamels on steel plates is studied clarifying the mechanisms taking place at the interface during firing. Evidence is provided from electron microprobe analysis for an iron alloy precipitation at the interface, which results from oversaturation of ferrous iron in the enamel glass. Subsequent coalescence of the alloy particles is observed but only after their bonding to the base metal adherence after cupping is achieved. The formation of microalloys requires Co 2+ , Ni 2+ , and Cu 2+ ions in the enamel glass. A selective dissolution of the base metal by the latter cations does not occur.
Morphologie mitochondriale : fonctions et dysfonctions de la dynamine humaine OPA1 (2004)

Les mitochondries sont des organelles impliques dans la production d'energie et participent au a la mort cellulaire programmee ou apoptose. La structure et la dynamique de ces organelles a double membrane sont regulees par fusion ou fission membranaire. La fusion et la fission de la membrane externe sont respectivement assurees par la GTPase Fzo1/Mfn1-2 et la dynamine Dnm1/DRP. La dynamique de la membrane interne mitochondriale n'est pas encore connue. Toutefois, chez S. Cerevisiae, Mgm1p, et chez S. Pombe, Msp1 sont impliquees dans la dynamique du reseau mitochondrial. Leur localisation intra-mitochondriale suggere un role dans la dynamique de la membrane interne. OPA1, homologue humain de Msp1/Mgm1p, complemente la deletion du gene msp1 chez S. Pombe. Par une combinaison d'approches cytologiques et biochimiques nous avons montre en outre qu'OPA1 est une proteine fortement associee a la membrane interne mitochondriale, faisant face a l'espace inter-membranaire. J'ai analyse l'effet de l'inhibition de l'expression de OPA1 par interference ARN. L'invalidation d'OPA1 provoque une fragmentation du reseau mitochondrial, une dissipation du potentiel de membrane DYm et est suivie de la mort des cellules par apoptose par relargage du cytochrome c. Par des approches de surexpression ou d'interference ARN selective des variant d'epissage d'OPA1, j'ai pu montrer que l'epissage alternatif permet de dissocier les fonctions d'OPA1 impliquees dans la morphologie du reseau mitochondrial de celles responsables de la mort cellulaire. Des mutations du gene codant pour OPA1 sont responsables de l'atrophie optique dominante de type 1 (ADOA, MIM 165500) conduisant a une neuro-degenerescence des cellules ganglionnaires de la retine (RGC) suivie d'une atrophie du nerf optique aboutissant a la cecite. J'ai caracterise deux mutants pathogenes d'OPA1, et montre que la pathogenicite associee aux mutations d'OPA1 pourrait resulter aussi bien d'effets dominants negatifs que d'haplo-insuffisance
OTAGen: A Tunable Ontology Generator for Benchmarking Ontology-Based Agent Collaboration (2008)

On the one hand, agent-based software platforms are commonly used these days, while on the other hand Semantic Web technologies are also maturing. It is obvious that the combination of these two technologies can bring added value through the creation of Semantic Agent-based frameworks. However, it is also known that these Semantic Web technologies, and the reasoning on ontologies in particular, can rapidly become resource intensive. In order to get a clear view on this problem, we have developed OTAGen, a highly tunable tool to generate customized ontologies and corresponding queries. The generated ontologies can then be used to evaluate at design-time the performance of the Semantic Agent-based platform as a function of the number of ontologies, users and queries.
Shoe traction and surface compliance affect performance of soccer-related movements (2014)

Purpose: To determine how shoe-surface interaction, specifically traction and compliance, affects performance and biomechanics of soccer-related movements.Methods: Third generation artificial turf was installed in the laboratory to allow for kinetic and kinematic data collection both on the turf and on a laboratory surface (Pulastic sports surface). Twelve male athletes performed five 5 m sprint accelerations and five 180° sprint turns in three different shoe-surface conditions (indoor soccer shoe on the laboratory surface, indoor soccer shoe on the turf surface, soccer cleat on turf surface). Comparisons between the indoor shoe across surfaces indicated compliance effects and comparisons between the cleat and indoor shoe on turf indicated traction effects.Results: Performance increased for the sprint acceleration in the indoor shoe on the turf compared to the laboratory (1.04 s vs. 1.08 s); however, no further increase in acceleration performance occurred with the soccer cleat. For the turn movement, no change in performance occurred comparing the indoor shoe across surfaces however an increase in turn performance was seen when using the soccer cleat on turf compared to the indoor shoe (2.67 s vs. 2.56 s). The cleat had both increased utilised translational and rotational traction compared to the indoor shoe on turf for the turn movement. The cleat also resulted in increased ankle eversion moments as well as increased knee abduction and external rotation moments compared to the indoor shoe on the turf surface for the turn movement.Conclusion: Both compliance and traction shoe-surface characteristics affect performance; however, the effects of the different characteristics are different depending on the movement type.
Craniofacial and TMJ Effects after Glutamate and TRH Microsphere Implantation in Proximity to Trigeminal Motoneurons of Growing Rats (1997)

The sequelae of sustained, in vivo delivery of two important neurotransmitter substances, glutamate and thyrotropin-releasing hormone (TRH), upon craniofacial growth and development have previously not been investigated. Our purpose was to document and compare the relative effects of glutamate and TRH microspheres stereotactically placed in proximity to trigeminal motoneurons within the trigeminal motor nucleus. The following null hypotheses were tested: (1) TRH microspheres in proximity to trigeminal motoneurons have no significant effect upon the craniofacial skeleton, and (2) there are no significant differences between the relative effects of chronic, long-term delivery of glutamate and TRH upon the neuromusculoskeletal system of growing rats. Forty male Sprague-Dawley rats were divided into 4 experimental groups (glutamate microspheres, TRH microspheres, blank microspheres, sham surgeries) and underwent stereotactic neurosurgery at 35 days; 5 rats of each group were killed at 14 and 21 days for data collection. Histology revealed that implants were clustered in the pontine reticular formation, close to the ventrolateral tegmental nucleus. Both glutamate and TRH rats had implant-side deviation of their facial skeleton and snout regions; 4 x 2 ANOVA and post hoc t-tests revealed significant (P < or = 0.05, 0.01) differences between groups and sides for motoneuron count, muscle weight, and osteometric data. TRH rats also demonstrated larger implant-side TMJ discs and mandibular fossae in comparison with the other groups. The stated null hypotheses were therefore rejected.
Explaining Reinforcement Learning to Mere Mortals: An Empirical Study (2019)

We present a user study to investigate the impact of explanations on non-experts? understanding of reinforcement learning (RL) agents. We investigate both a common RL visualization, saliency maps (the focus of attention), and a more recent explanation type, reward-decomposition bars (predictions of future types of rewards). We designed a 124 participant, four-treatment experiment to compare participants? mental models of an RL agent in a simple Real-Time Strategy (RTS) game. Our results show that the combination of both saliency and reward bars were needed to achieve a statistically significant improvement in mental model score over the control. In addition, our qualitative analysis of the data reveals a number of effects for further study.