gebhart/patrepeval huggingface dataset:
The Adaptor Protein ARH Escorts Megalin to and through Endosomes (2003)

Megalin is an endocytic receptor that binds multiple ligands and is essential for many physiological processes such as brain development and uptake of proteins by the kidney tubule, yolk sac, and thyroid. The cytoplasmic tail of megalin contains two FXNPXY motifs. Autosomal recessive hypercholesterolemia (ARH) is an adaptor protein that binds to the FXNPXY motif of the low-density lipoprotein receptor as well as clathrin and AP-2. We found that ARH also binds to the first FXNPXY motif of megalin in two-hybrid, pull-down and coimmunoprecipitation assays. ARH colocalizes with megalin in clathrin coated pits and in recycling endosomes in the Golgi region. When cells are treated with nocodazole, the recycling endosomes containing megalin and ARH disperse. On internalization of megalin, ARH and megalin are first seen in clathrin coated pits followed by sequential localization in early endosomes and tubular recycling endosomes in the pericentriolar region followed by their reappearance at the cell surface. Expression of ARH in Madin-Darby canine kidney cells expressing megalin mini-receptors enhances megalin-mediated uptake of 125I-lactoferrin, a megalin ligand. These results show that ARH facilitates endocytosis of megalin, escorts megalin along its endocytic route and raise the possibility that transport through the endosomal system is selective and requires interaction with specific adaptor proteins.
Chromatin Remodeling and Leukemia: New Therapeutic Paradigms (1999)

L OCAL REMODELING OF chromatin is a key step in the transcriptional activation of genes. Dynamic changes in the nucleosomal packaging of DNA must occur to allow transcriptional proteins contact with the DNA template. The realization that the proteins that regulate the modification of chromatin are
Building a Delay-Tolerant Cloud for Mobile Data (2013)

Mobile data usage is on a tremendous rise, due not only to increasing number of users but also to an increase in the number of applications that transfer data over the network. Moreover, applications for sharing, sensing, and collaboration have become more popular, causing significant amounts of data to be generated on devices. Managing this data -syncing it to the cloud, or with other users or devices- is a crucial and often challenging part of writing mobile apps and services. In spite of plenty of good advice and best practices from OS vendors and network operators, storing and transferring mobile data is fraught with issues. On the one hand, an app developer needs to worry about the semantics of data storage and synchronization, while on the other, about the end-user experience, which maybe impacted by poor and intermittent network connectivity. To address the needs of the app developers and the end-users, we have built Izzy: a platform to rapidly develop and deploy data-centric mobile apps. Izzy provides well-defined and easy to use semantics for accessing local storage and for synchronizing data with a remote, scalable, global store. Izzy also provides global store access to the cloud-resident part of the applications (if any) through a similar server API. Last but not least, Izzy is designed to be frugal: it conserves mobile device resources by applying delay-tolerance and data reduction techniques (message coalescing and compression) across applications on a mobile device. In this paper we present the design of Izzy and our early experiences with using it.
The tetraspanin superfamily in insects (2000)

We describe four members of the tetraspanin/TM4SF superfamily of proteins that were identified in expressed sequence tag projects on the antennae of Manduca sexta moths and Apis mellifera honey bees. The three moth genes are expressed in the sensillar epithelium of male antennae, and some are expressed in female antennae, haemocytes, wing scale cell primordia and/or embryonic tissues. These proteins are probably involved in diverse cellular processes, much like their vertebrate homologues. A phylogenetic analysis of all known tetraspanins, including thirty-seven members of the superfamily revealed by the Drosophila melanogaster genome and twenty in the nematode Caenorhabditis elegans genome, reveals some phylum-specific gene amplification, in particular a contiguous array of eighteen genes in the D. melanogaster genome.
Purified Cas9 Fusion Proteins for Advanced Genome Manipulation (2017)

The CRISPR/Cas9 system (CRISPR = clustered regularly interspaced short palindromic repeats) has rapidly become one of the most versatile genome manipulation technologies, and different methods to introduce the Cas9 nuclease activity into cells have been developed. The direct delivery of purified Cas9 protein complexed with a guide RNA as a ribonucleoprotein (RNP) has emerged as an advantageous approach, as it provides instant, but limited activity of the enzyme, thereby reducing off‐target cleavage. The usefulness of the CRISPR/Cas9 system has recently been extended by the generation of Cas9 or dead (d)Cas9 fusion genes. However, these systems have so far been mainly explored when delivered by expression plasmids. Here, a variety of purified Cas9 fusion proteins are generated, and their utility is tested in a number of assays. This work illustrates that Cas9 fused to green‐ or red‐fluorescent proteins can be usefully employed to increase the frequency of targeted cells when transfected as RNPs. Furthermore, it is demonstrated that purified dCas9 fused to a dual transactivation domain can potently activate gene expression when transfected as an RNP into embryonic stem cells. The results show that purified Cas9 fusion proteins are versatile and efficient reagents that facilitate advanced genome manipulation.
NoC Switch with Credit Based Guaranteed Service Support Qualified for GALS Systems (2010)

In this paper we present a scalable wormhole switch architecture with a credit based guaranteed service implementation. By means of credits for a service guarantee the architecture is also able to deal with mesochronous GALS systems. We extended a regular wormhole switch architecture with a control unit for service configuration during run-time and modified the arbitration policy. These changes result in a marginal area overhead per switch of approximately 4\%. Thus our new architecture provides a simple solution to implement service guarantees without limitation to a fully synchronous system. We synthesized our design with a 65nm technology and achieved a clock frequency of 1GHz. Due to the high clock frequency we are able to get a channel throughput of more than 4GB/sec whereas the total design complexity is 30k gate equivalents.
Dicyclomine, an M1 Muscarinic Antagonist, Reduces Biomarker Levels, But Not Neuronal Degeneration, in Fluid Percussion Brain Injury (2008)

Recent studies indicate that alphaII-spectrin breakdown products (SBDPs) have utility as biological markers of traumatic brain injury (TBI). However, the utility of SBDP biomarkers for detecting effects of therapeutic interventions has not been explored. Acetylcholine plays a role in pathological neuronal excitation and TBI-induced muscarinic cholinergic receptor activation may contribute to excitotoxic processes. In experiment I, regional and temporal changes in calpain-mediated alpha-spectrin degradation were evaluated at 3, 12, 24, and 48 h using immunostaining for 145-kDa SBDP. Immunostaining of SBDP-145 was only evident in the hemisphere ipsilateral to TBI and was generally limited to the cortex except at 24 h when immunostaining was also prominent in the dentate gyrus and striatum. In Experiment II, cerebral spinal fluid (CSF) samples were analyzed for various SBDPs 24 h after moderate lateral fluid percussion TBI. Rats were administered either dicyclomine (5 mg/kg i.p.) or saline vehicle (n = 8 per group) 5 min prior to injury. Injury produced significant increases (p < 0.001) of 300%, 230%, and >1000% in SBDP-150, -145, and -120, respectively in vehicle-treated rats compared to sham. Dicyclomine treatment produced decreases of 38% (p = 0.077), 37% (p = 0.028), and 63% (p = 0.051) in SBDP-150, -145, and -120, respectively, compared to vehicle-treated injury. Following CSF extraction, coronal brain sections were processed for detecting degenerating neurons using Fluoro-Jade histofluorescence. Stereological techniques were used to quantify neuronal degeneration in the dorsal hippocampus CA2/3 region and in the parietal cortex. No significant differences were detected in numbers of degenerating neurons in the dorsal CA2/3 hippocampus or the parietal cortex between saline and dicyclomine treatment groups. The percent weight loss following TBI was significantly reduced by dicyclomine treatment. These data provide additional evidence that, as TBI biomarkers, SBDPs are able to detect a therapeutic intervention even in the absence of changes in neuronal cell degeneration measured by Fluoro-jade.
Synthesis, properties and photopolymerization of liquid crystalline dioxetanes (2004)

The synthesis and photopolymerization of various liquid crystalline dioxetanes is described. The effects of the spacer length, structure of the mesogenic group and oxetane group on the liquid crystalline properties, polymerization behaviour and optical properties (birefringence) of the oriented and crosslinked network formed in photo-polymerization are discussed. Thermally stable films with birefringence values up to 0.13 can be formed from these materials. The dioxetanes show significantly lower polymerization shrinkage than do structurally related diacrylates.
The acidosis of chronic renal failure activates muscle proteolysis in rats by augmenting transcription of genes encoding proteins of the ATP-dependent ubiquitin-proteasome pathway. (1996)

Chronic renal failure (CRF) is associated with negative nitrogen balance and loss of lean body mass. To identify specific proteolytic pathways activated by CRF, protein degradation was measured in incubated epitrochlearis muscles from CRF and sham-operated, pair-fed rats. CRF stimulated muscle proteolysis, and inhibition of lysosomal and calcium-activated proteases did not eliminate this increase. When ATP production was blocked, proteolysis in CRF muscles fell to the same level as that in control muscles. Increased proteolysis was also prevented by feeding CRF rats sodium bicarbonate, suggesting that activation depends on acidification. Evidence that the ATP-dependent ubiquitin-proteasome pathway is stimulated by the acidemia of CRF includes the following findings: (a) An inhibitor of the proteasome eliminated the increase in muscle proteolysis; and (b) there was an increase in mRNAs encoding ubiquitin (324%) and proteasome subunits C3 (137%) and C9 (251%) in muscle. This response involved gene activation since transcription of mRNAs for ubiquitin and the C3 subunit were selectively increased in muscle of CRF rats. We conclude that CRF stimulates muscle proteolysis by activating the ATP-ubiquitin-proteasome-dependent pathway. The mechanism depends on acidification and increased expression of genes encoding components of the system. These responses could contribute to the loss of muscle mass associated with CRF.
Sequence Analysis of Insecticidal Genes from <i>Xenorhabdus nematophilus</i> PMFI296 (2001)

Three strains of Xenorhabdus nematophilus showed insecticidal activity when fed to Pieris brassicae (cabbage white butterfly) larvae. From one of these strains (X. nematophilus PMFI296) a cosmid genome library was prepared in Escherichia coli and screened for oral insecticidal activity. Two overlapping cosmid clones were shown to encode insecticidal proteins, which had activity when expressed in E. coli (50% lethal concentration [LC(50)] of 2 to 6 microg of total protein/g of diet). The complete sequence of one cosmid (cHRIM1) was obtained. On cHRIM1, five genes (xptA1, -A2, -B1, -C1, and -D1) showed homology with up to 49% identity to insecticidal toxins identified in Photorhabdus luminescens, and also a smaller gene (chi) showed homology to a putative chitinase gene (38% identity). Transposon mutagenesis of the cosmid insert indicated that the genes xptA2, xptD1, and chi were not important for the expression of insecticidal activity toward P. brassicae. One gene (xptA1) was found to be central for the expression of activity, and the genes xptB1 and xptC1 were needed for full activity. The location of these genes together on the chromosome and therefore present on a single cosmid insert probably accounted for the detection of insecticidal activity in this E. coli clone. Although multiple genes may be needed for full activity, E. coli cells expressing the xptA1 gene from the bacteriophage lambda P(L) promoter were shown to have insecticidal activity (LC(50) of 112 microg of total protein/g of diet). This is contrary to the toxin genes identified in P. luminescens, which were not insecticidal when expressed individually in E. coli. High-level gene expression and the use of a sensitive insect may have aided in the detection of insecticidal activity in the E. coli clone expressing xptA1. The location of these toxin genes and the chitinase gene and the presence of mobile elements (insertion sequence) and tRNA genes on cHRIM1 indicates that this region of DNA represents a pathogenicity island on the genome of X. nematophilus PMFI296.
A case of cancerous epidermal cystoma. (1989)

55歳男性の右肩背面に生じた巨大粉瘤腫壁の一部に悪性変化が認められた。病理組織学的には, 異形性のないepidermal keratinizationを示す薄い嚢腫壁に連続して, 一部に内腔への乳頭状増殖が認められた。この部分に一致して有棘細胞癌が存在し,表皮嚢腫壁の癌化と推察した。
Single-Leg Air-Cargo Revenue Management (2007)

We consider a cargo booking problem on a single-leg flight with the goal of maximizing expected contribution. Each piece of cargo is endowed with a random volume and a random weight whose precise values are not known until just before the flight's departure. We formulate the problem as a Markov decision process (MDP). Exact solution of the formulation is impractical, because of its high-dimensional state space; therefore, we develop six heuristics. The first four heuristics are based on different value-function approximations derived from two computationally tractable MDPs, each with a one-dimensional state space. The remaining two heuristics are obtained from solving related methematical programming problems. We also compare the heuristics with the first-come, first-served (FCFS) policy. Simulation experiments suggest that the value function approximation derived from separate “volume” and “weight” problems offers the best approach. Comparisons of the expected contribution under the heuristic to an upper bound show that the heuristic is typically close to optimal.
A novel fiber-optic torsion sensor based on a CO/sub 2/-laser-induced long-period fiber grating (2003)

In this letter, we propose and demonstrate a fiber-optic torsion sensor based on a novel long period fiber grating (LPFG) written by high-frequency CO/sub 2/ laser pulses. Such a sensor can be easily embedded into a structure and can determine both the twist rate and the twist direction simultaneously.
The Hallucinogen <i>N,N</i> -Dimethyltryptamine (DMT) Is an Endogenous Sigma-1 Receptor Regulator (2009)

The sigma-1 receptor is widely distributed in the central nervous system and periphery. Originally mischaracterized as an opioid receptor, the sigma-1 receptor binds a vast number of synthetic compounds but does not bind opioid peptides; it is currently considered an orphan receptor. The sigma-1 receptor pharmacophore includes an alkylamine core, also found in the endogenous compound N,N-dimethyltryptamine (DMT). DMT acts as a hallucinogen, but its receptor target has been unclear. DMT bound to sigma-1 receptors and inhibited voltage-gated sodium ion (Na+) channels in both native cardiac myocytes and heterologous cells that express sigma-1 receptors. DMT induced hypermobility in wild-type mice but not in sigma-1 receptor knockout mice. These biochemical, physiological, and behavioral experiments indicate that DMT is an endogenous agonist for the sigma-1 receptor.
A New Method for Multi-view Face Clustering in Video Sequence (2008)

In the problem of face clustering with multi-views, the similarity between faces of different persons with similar pose is usually greater than the similarity between multi-view faces of the same person. This may exert a tremendous impact on the clustering result that sent back to the user. To solve this problem, we should do pose clustering first and then within each dasiapose grouppsila, clustering images of different individuals. Gabor filters have been used to detect the eyes in the face image. The coordinate of the eyes have been extracted as an input feature for the dasiapose clusteringpsila. After doing this, images of the similar pose will be in the same cluster. PCA/ LBP and kmeans algorithms have been used in each pose cluster for clustering of different individuals. The precision of face classification with clustering is enhanced. The proposed clustering algorithms can be applied to and face indexing or face recognition system.
Organic single-crystal complementary inverter (2006)

The authors demonstrate the operation of an organic single-crystal complementary circuit in the form of a simple inverter. The device is constructed from a high mobility p-type organic single-crystal transistor of tetramethylpentacene (TMPC) and a n-type single-crystal transistor of N,N′-di[2,4-difluorophenyl]-3,4,9,10-perylenetetracarboxylic diimide (PTCDI). Field-effect mobilities of up to 1.0cm2∕Vs are reported for TMPC devices, while a mobility of 0.006cm2∕Vs is reported for a n-type PTCDI single-crystal device. Considering that organic single-crystal inverters have not yet been explored, they are representative of potential candidates for use in high-performance complementary circuits.
Behavioral synthesis for FPGA-based computing (2002)

We describe how a behavioral synthesis system can be used to create designs for FPGA-based computing systems directly from a specification of the desired algorithm. This higher level of specification reduces design times and design errors. Our target hardware is called the Rasa Board and is composed of three Xilinx FPGAs interconnected with Aptix Field Programmable Interconnect Chips. We address two significant challenges in this research effort: the synthesis of multiple FPGA designs, and the improvement of the design through designer interaction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Robustness of continuous-time adaptive control algorithms in the presence of unmodeled dynamics (1985)

This paper examines the robustness properties of existing adaptive control algorithms to unmodeled plant high-frequency dynamics and unmeasurable output disturbances. It is demonstrated thai there exist two infinite-gain operators in the nonlinear dynamic system which determines the time-evolution of output and parameter errors. The pragmatic implication of the existence of such infinite-gain operators is that 1) sinusoidal reference inputs at specific frequencies and/or 2) sinusoidal output disturbances at any frequency (including dc), can cause the loop gain to increase without bound, thereby exciting the unmodeled high-frequency dynamics, and yielding an unstable control system. Hence, it is concluded that existing adaptive control algorithms as they are presented in the literature referenced in this paper, cannot be used with confidence in practical designs where the plant contains unmodeled dynamics because instability is likely to result. Further understanding is required to ascertain how the currently implemented adaptive systems differ from the theoretical systems studied here and how further theoretical development can improve the robustness of adaptive controllers.
Allergic rhinitis and asthma: the link, the new ARIA classification and global approaches to treatment (2004)

Department of Otolaryngology, Nippon Medical School, Tokyo, Japan Correspondence to Prof. Ruby Pawankar, MD, PhD, Department of Otolaryngology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo 113-8603, Japan Tel/fax: +81 48 597 2861; e-mail: Pawankar_Ruby/[email protected]
Ozonation of Water: Role of Hydroxyl Radicals as Oxidizing Intermediates (1975)

Hydroxyl radicals are the main oxidants formed in the decomposition of ozone in water. This is demonstrated by measuring the relative rates at which different substrates are consumed and comparing them with known reaction rate constants. Knowledge accumulated by radiation chemists and biologists on the reactions of hydroxyl radicals can therefore be used to describe oxidations succeeding ozone decomposition.
On Stereo Confidence Measures for Global Methods: Evaluation, New Model and Integration into Occupancy Grids (2015)

Stereo confidence measures are important functions for global reconstruction methods and some applications of stereo. In this article we evaluate and compare several models of confidence which are defined at the whole disparity range. We propose a new stereo confidence measure to which we call the Histogram Sensor Model (HSM), and show how it is one of the best performing functions overall. We also introduce, for parametric models, a systematic method for estimating their parameters which is shown to lead to better performance when compared to parameters as computed in previous literature. All models were evaluated when applied to two different cost functions at different window sizes and model parameters. Contrary to previous stereo confidence measure benchmark literature, we evaluate the models with criteria important not only to winner-take-all stereo, but also to global applications. To this end, we evaluate the models on a real-world application using a recent formulation of 3D reconstruction through occupancy grids which integrates stereo confidence at all disparities. We obtain and discuss our results on both indoors' and outdoors' publicly available datasets.
Preparation and Hydrolysis of Aluminum Based Composites for Hydrogen Production in Pure Water (2014)

A series of Al based composites were prepared using mechanical milling method in this paper. Effects of additives including CaO, NaCl salt and low melting point metals (Ga, In, and Sn) on the hydrolysis activity of Al based composites were evaluated in pure water. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) techniques were used for the microstructure analysis of as-prepared samples and their hydrolysis products. The results showed that the addition of CaO, NaCl salt and low melting point metals can effectively improve the hydrolysis properties of Al based composites. Especially, Al alloys-CaO–NaCl composites exhibited a higher hydrogen yields than Al–CaO and Al–CaO–NaCl materials. The SEM images displayed that NaCl salt particles were homogeneously distributed on the surface of Al based composites and inserted into Al matrix, which may damage the surface oxide layer of Al. Furthermore, the size of NaCl salt particles was much smaller in Al alloys-CaO–NaCl composites than that in Al–CaO–NaCl composites. The XRD patterns identified that the hydrolysis products were mainly composed of AlO(OH) and Al(OH)3. The microstructure-related hydrolysis reaction mechanism of Al based composites was proposed finally.
Transforming XML schemas into Java swing GUIs (2004)

one usually has to define and maintain two separate entities just for the editorial part: the database schemes (in form of XML Schema instances) on the one hand and the graphical user interfaces (GUIs) for data maintenance on the other hand. In this paper we present a method for generating the GUIs automatically from the XML Schema instances, thus the GUI can be specified in a declarative, implicit way. The target platform is Java Swing. Our transformation is based on compile-time generated templates and the XML persistence feature of Java 2. 1