gebhart/patrepeval huggingface dataset:
Direct mass spectrometry analysis of untreated samples of ultralow amounts using extraction nano-electrospray (2013)

Direct mass spectrometry analysis of untreated samples of volumes as low as 0.2 µL were achieved using fast extraction and nanoESI (electrospray ionization) in a combined fashion. The analytes in dried samples on paper substrates were extracted by organic solvent in a nanoESI tube and ionized with a high voltage applied for generating a spray. The ionization source produced stable signals for different atmospheric pressure interfaces of triple quadrupole instruments. Analysis time more than 20 minutes were available with 10 µL solvent consumed for the entire analysis process. The performance in qualitative and quantitative analysis was characterized with a wide variety of samples. Limits of detection as low as 0.1 ng/mL (corresponding to an absolute amount of 0.05 pg) were obtained for analysis of atrazine in river water, thiabendazole in orange homogenate, and methamphetamine in blood.
Three Arabidopsis Fatty Acyl-Coenzyme A Reductases, FAR1, FAR4, and FAR5, Generate Primary Fatty Alcohols Associated with Suberin Deposition (2010)

Suberin is a protective hydrophobic barrier consisting of phenolics, glycerol, and a variety of fatty acid derivatives, including C18:0-C22:0 primary fatty alcohols. An eight-member gene family encoding alcohol-forming fatty acyl-coenzyme A reductases (FARs) has been identified in Arabidopsis (Arabidopsis thaliana). Promoter-driven expression of the beta-glucuronidase reporter gene indicated that three of these genes, FAR1(At5g22500), FAR4(At3g44540), and FAR5(At3g44550), are expressed in root endodermal cells. The three genes were transcriptionally induced by wounding and salt stress. These patterns of gene expression coincide with known sites of suberin deposition. We then characterized a set of mutants with T-DNA insertions in FAR1, FAR4, or FAR5 and found that the suberin compositions of roots and seed coats were modified in each far mutant. Specifically, C18:0-OH was reduced in far5-1, C20:0-OH was reduced in far4-1, and C22:0-OH was reduced in far1-1. We also analyzed the composition of polymer-bound lipids of leaves before and after wounding and found that the basal levels of C18:0-C22:0 primary alcohols in wild-type leaves were increased by wounding. In contrast, C18:0-OH and C22:0-OH were not increased by wounding in far5-1 and far1-1 mutants, respectively. Heterologous expression of FAR1, FAR4, and FAR5 in yeast confirmed that they are indeed active alcohol-forming FARs with distinct, but overlapping, chain length specificities ranging from C18:0 to C24:0. Altogether, these results indicate that Arabidopsis FAR1, FAR4, and FAR5 generate the fatty alcohols found in root, seed coat, and wound-induced leaf tissue.
The Quality of Health Care Delivered to Adults in the United States (2003)

The deficits we have identified in adherence to recommended processes for basic care pose serious threats to the health of the American public. Strategies to reduce these deficits in care are warranted.
Pustular psoriasis: pathophysiology and current treatment perspectives (2016)

Psoriasis vulgaris is a chronic inflammatory disease that classically affects skin and joints and is associated with numerous comorbidities. There are several clinical subtypes of psoriasis including the uncommon pustular variants, which are subdivided into generalized and localized forms. Generalized forms of pustular psoriasis include acute generalized pustular psoriasis, pustular psoriasis of pregnancy, and infantile and juvenile pustular psoriasis. Localized forms include acrodermatitis continua of Hallopeau and palmoplantar pustular psoriasis. These subtypes vary in their presentations, but all have similar histopathologic characteristics. The immunopathogenesis of each entity remains to be fully elucidated and some debate exists as to whether these inflammatory pustular dermatoses should be classified as entities distinct from psoriasis vulgaris. Due to the rarity of these conditions and the questionable link to the common, plaque-type psoriasis, numerous therapies have shown variable results and most entities remain difficult to treat. With increasing knowledge of the pathogenesis of these variants of pustular psoriasis, the development and use of biologic and other immunomodulatory therapies holds promise for the future of successfully treating pustular variants of psoriasis.
Application of Coandă Jet for Generating Lift of Micro Air Vehicles - Preliminary Design Considerations (2014)

Coandă effect, which has been widely utilized in many engineering applications for circulation control, is here reviewed for the design of Coandă Micro-Air-Vehicles (MAVs). Based on the review, a basic spherical configuration is analyzed to obtain the relationship between relevant parameters to the lift that can be produced based on fundamental principles. The results can be used for preliminary design purposes and are discussed in view of existing literature.
Manipulator and object tracking for in-hand 3D object modeling (2011)

Recognizing and manipulating objects is an important task for mobile robots performing useful services in everyday environments. While existing techniques for object recognition related to manipulation provide very good results even for noisy and incomplete data, they are typically trained using data generated in an offline process. As a result, they do not enable a robot to acquire new object models as it operates in an environment. In this paper we develop an approach to building 3D models of unknown objects based on a depth camera observing the robot’s hand while moving an object. The approach integrates both shape and appearance information into an articulated Iterative Closest Point approach to track the robot’s manipulator and the object. Objects are modeled by sets of surfels, which are small patches providing occlusion and appearance information. Experiments show that our approach provides very good 3D models even when the object is highly symmetric and lacks visual features and the manipulator motion is noisy. Autonomous object modeling represents a step toward improved semantic understanding, which will eventually enable robots to reason about their environments in terms of objects and their relations rather than through raw sensor data.
Discovery and Preclinical Profile of Saxagliptin (BMS-477118):  A Highly Potent, Long-Acting, Orally Active Dipeptidyl Peptidase IV Inhibitor for the Treatment of Type 2 Diabetes (2005)

Efforts to further elucidate structure-activity relationships (SAR) within our previously disclosed series of beta-quaternary amino acid linked l-cis-4,5-methanoprolinenitrile dipeptidyl peptidase IV (DPP-IV) inhibitors led to the investigation of vinyl substitution at the beta-position of alpha-cycloalkyl-substituted glycines. Despite poor systemic exposure, vinyl-substituted compounds showed extended duration of action in acute rat ex vivo plasma DPP-IV inhibition models. Oxygenated putative metabolites were prepared and were shown to exhibit the potency and extended duration of action of their precursors in efficacy models measuring glucose clearance in Zucker(fa/fa) rats. Extension of this approach to adamantylglycine-derived inhibitors led to the discovery of highly potent inhibitors, including hydroxyadamantyl compound BMS-477118 (saxagliptin), a highly efficacious, stable, and long-acting DPP-IV inhibitor, which is currently undergoing clinical trials for treatment of type 2 diabetes.
Pulmonary Vein Stenosis After Radiofrequency Ablation of Atrial Fibrillation (2003)

V/Q scans are useful to assess the functional significance of PV stenosis. Mild and moderate degrees of PV narrowing are not associated with development of symptoms and seem to have no or minimal detrimental effect on pulmonary flow. The incidence of severe PV stenosis seems to be declining with better imaging techniques to ensure ostial isolation and to guide power titration. Mild narrowing 3 months after ablation does not preclude future development of severe stenosis and should be assessed with repeat imaging studies.
Nosocomial fungal infections: epidemiology, diagnosis, and treatment (2007)

Invasive fungal infections are increasingly common in the nosocomial setting. Furthermore, because risk factors for these infections continue to increase in frequency, it is likely that nosocomial fungal infections will continue to increase in frequency in the coming decades. The predominant nosocomial fungal pathogens include Candida spp., Aspergillus spp., Mucorales, Fusarium spp., and other molds, including Scedosporium spp. These infections are difficult to diagnose and cause high morbidity and mortality despite antifungal therapy. Early initiation of effective antifungal therapy and reversal of underlying host defects remain the cornerstones of treatment for nosocomial fungal infections. In recent years, new antifungal agents have become available, resulting in a change in standard of care for many of these infections. Nevertheless, the mortality of nosocomial fungal infections remains high, and new therapeutic and preventative strategies are needed.
Reduction of Inner Ear Inflammation by Treatment with Anti-ICAM-1 Antibody (1997)

The in vivo effect of systemic administration of monoclonal antibody (mAb) against ICAM-1 (alphaICAM-1) in experimental immune-mediated labyrinthitis was evaluated. The alphaICAM-1-treated rats showed reduced inflammatory cell infiltration in the scala tympani and the perisaccular tissue of the endolymphatic sac. However, with this experimental paradigm, labyrinthitis could not be completely abolished. These findings suggest that ICAM-1-dependent pathways play an important role in the series of immunologic events occurring in the inner ear, and that the use of ICAM-1 antagonist may be a possible therapeutic approach to labyrinthitis.
Galectin-3 regulates myofibroblast activation and hepatic fibrosis (2006)

Central to fibrogenesis and the scarring of organs is the activation of fibroblasts into matrix-secreting myofibroblasts. We demonstrate that Galectin-3 expression is up-regulated in established human fibrotic liver disease and is temporally and spatially related to the induction and resolution of experimental hepatic fibrosis. Disruption of the Galectin-3 gene blocks myofibroblast activation and procollagen (I) expression in vitro and in vivo, markedly attenuating liver fibrosis. Addition of exogenous recombinant Galectin-3 in vitro reversed this abnormality. The reduction in hepatic fibrosis observed in the Galectin-3(-/-) mouse occurred despite equivalent liver injury and inflammation, and similar tissue expression of TGF-beta. TGF-beta failed to transactivate Galectin-3(-/-) hepatic stellate cells, in contrast with WT hepatic stellate cells; however, TGF-beta-stimulated Smad-2 and -3 activation was equivalent. These data suggest that Galectin-3 is required for TGF-beta mediated myofibroblast activation and matrix production. Finally, in vivo siRNA knockdown of Galectin-3 inhibited myofibroblast activation after hepatic injury and may therefore provide an alternative therapeutic approach to the prevention and treatment of liver fibrosis.
Thinning and Shaping Solid Films into Functional and Integrative Nanomembranes (2012)

Conventional solid films on certain substrates play a crucial role in various applications, for example in flat panel displays, silicon technology, and protective coatings. Recently, tremendous attention has been directed toward the thinning and shaping of solids into so-called nanomembranes, offering a unique and fantastic platform for research in nanoscience and nanotechnology. In this Review, a conceptual description of nanomembranes is introduced and a series of examples demonstrate their great potential for future applications. The thinning of nanomembranes indeed offers another strategy to fabricate nanomaterials, which can be integrated onto a chip and exhibit valuable properties (e.g. giant persistent photoconductivity and thermoelectric property). Furthermore, the stretching of nanomembranes enables a macroscale route for tuning the physical properties of the membranes at the nanoscale. The process by which nanomembranes release from a substrate presents several approaches to shaping nanomembranes into three-dimensional architectures, such as rolled-up tubes, wrinkles, and the resulting channels, which can provide fascinating applications in electronics, mechanics, fluidics, and photonics. Nanomembranes as a new type of nanomaterial promise to be an attractive direction for nanoresearch.
14. Semi-autonomous avatars: A new direction for expressive user embodiment (2008)

Computer animated characters are rapidly becoming a regular part of our lives.They are starting to take the place of actors in films and television and are now an integral part of most computer games.Perhaps most interestingly in on-line games and chat rooms they are representing the user visually in the form of avatars, becoming our on-line identities, our embodiments in a virtual world.Currently online environments such as "Second Life" are being taken up by people who would not traditionally have considered playing games before, largely due to a greater emphasis on social interaction.These environments require avatars that are more expressive and that can make on-line social interactions seem more like face-toface conversations.Computer animated characters come in many different forms.Film characters require a substantial amount of off-line animator effort to achieve high levels of quality; these techniques are not suitable for real time applications and are not the focus of this chapter.Non-player characters (typically the bad guys) in games use limited artificial intelligence to react autonomously to events in real time.However avatars are completely controlled by their users, reacting to events solely through user commands.This chapter will discuss the distinction between fully autonomous characters and completely controlled avatars and how the current differentiation may no longer be useful, given that avatar technology may need to include more autonomy to live up to the demands of mass appeal.We will firstly discuss the two categories and present reasons to combine them.We will then describe previous work in this area and finally present our own framework for semi-autonomous avatars.
Replicative Senescence of Mesenchymal Stem Cells: A Continuous and Organized Process (2008)

Mesenchymal stem cells (MSC) comprise a promising tool for cellular therapy. These cells are usually culture expanded prior to their application. However, a precise molecular definition of MSC and the sequel of long-term in vitro culture are yet unknown. In this study, we have addressed the impact of replicative senescence on human MSC preparations. Within 43 to 77 days of cultivation (7 to 12 passages), MSC demonstrated morphological abnormalities, enlargement, attenuated expression of specific surface markers, and ultimately proliferation arrest. Adipogenic differentiation potential decreased whereas the propensity for osteogenic differentiation increased. mRNA expression profiling revealed a consistent pattern of alterations in the global gene expression signature of MSC at different passages. These changes are not restricted to later passages, but are continuously acquired with increasing passages. Genes involved in cell cycle, DNA replication and DNA repair are significantly down-regulated in late passages. Genes from chromosome 4q21 were over-represented among differentially regulated transcripts. Differential expression of 10 genes has been verified in independent donor samples as well as in MSC that were isolated under different culture conditions. Furthermore, miRNA expression profiling revealed an up-regulation of hsa-mir-371, hsa-mir-369-5P, hsa-mir-29c, hsa-mir-499 and hsa-let-7f upon in vitro propagation. Our studies indicate that replicative senescence of MSC preparations is a continuous process starting from the first passage onwards. This process includes far reaching alterations in phenotype, differentiation potential, global gene expression patterns, and miRNA profiles that need to be considered for therapeutic application of MSC preparations.
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence (1997)

We describe a program, tRNAscan-SE, which identifies 99–100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ∼30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudo-genes.
Moses: Open Source Toolkit for Statistical Machine Translation (2007)

Koehn, Philipp; Hoang, Hieu; Birch, Alexandra; Callison-Burch, Chris; Federico, Marcello; Bertoldi, Nicola; Cowan, Brooke; Shen, Wade; Moran, Christine; Zens, Richard; Bojar, Ondrej; Constantin, Alexandra; Herbst, Evan
High‐Throughput Carbohydrate Microarray Analysis of 24 Lectins (2006)

Tempo, Tempo: Lectine sind an einer Vielzahl biologischer Prozesse beteiligt und werden in Grundlagen- wie angewandter Forschung häufig als Reagentien verwendet. Mithilfe eines Kohlenhydrat-Mikroarrays wurde eine Hochdurchsatzanalyse der Lectinspezifität an 24 verschiedenen Lectinen durchgeführt. Viele der dabei identifizierten Lectin-Kohlenhydratliganden waren aufgrund früherer Informationen nicht erwartet worden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z600591_s.pdf 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.
Direct Anonymous Attestation. (2004)

This paper describes the direct anonymous attestation scheme (DAA). This scheme was adopted by the Trusted Computing Group as the method for remote authentication of a hardware module, called trusted platform module (TPM), while preserving the privacy of the user of the platform that contains the module. Direct anonymous attestation can be seen as a group signature without the feature that a signature can be opened, i.e., the anonymity is not revocable. Moreover, DAA allows for pseudonyms, i.e., for each signature a user (in agreement with the recipient of the signature) can decide whether or not the signature should be linkable to another signature. DAA furthermore allows for detection of &amp;quot;known&amp;quot; keys: if the DAA secret keys are extracted from a TPM and published, a verifier can detect that a signature was produced using these secret keys. The scheme is provably secure in the random oracle model under the strong RSA and the decisional Di#e-Hellman assumption.
Joint Timing Epoch Tracking and Channel Estimation for Alamouti Space-Time Coding in Rayleigh Fading MIMO Channels (2006)

e analyze the performance of a joint timing epoch tracking and PSAM-based channel estimation system in a frequency-flat Rayleigh fading MIMO channel. The receiver tracks a random timing drift via a timing error detector developed for n <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> = 2 orthogonal space-time block coded MPSK systems with an arbitrary number of receive antennas. The detector's S-curve has recently been shown to be independent of the channel state, resulting in system very robust in poor channel conditions. We evaluate the receiver's tracking capabilities in conjunction with channel estimation and study the effects of the delay inherent to PSAM interpolation systems. Symbol error rate performance for a QPSK system is presented, with the results showing negligible performance degrad.
Comparison of the effects of Mg–6Zn and Ti–3Al–2.5V alloys on TGF-β/TNF-α/VEGF/b-FGF in the healing of the intestinal tractin vivo (2014)

To evaluate the different effects of Mg-6Zn alloy and Ti-3Al-2.5V alloy implants in intestinal tract healing, we compared these two different alloys with respect to their effect on a rat's intestinal tract, using serum magnesium, radiology, pathology and immunohistochemistry in vivo. It was found using the scanning electron microscope that the Mg-6Zn alloy began to degrade during the first week and that the Ti-3Al-2.5V alloy was non-degradable throughout the process. The Mg-6Zn alloy did not have an impact on serum magnesium. Superior to the Ti-3Al-2.5V alloy, the Mg-6Zn alloy enhanced the expression of transforming growth factor-β1 in healing tissue, and promoted the expression of both the vascular endothelial growth factor and the basic fibroblast growth factor, which helped angiogenesis and healing. The Mg-6Zn alloy reduced the expression of the tumor necrosis factor (TNF-α) at different stages and decreased inflammatory response, which may have been related to the zinc inhibiting TNF-α. In general, the Mg-6Zn alloy performed better than Ti-3Al-2.5V at promoting healing and reducing inflammation. The Mg-6Zn alloy may be a promising candidate for use in the pins of circular staplers for gastrointestinal reconstruction in medicine.
The Case for Shared Nothing. (1985)

There are three dominent themes in building high transaction rate multiprocessor systems, namely shared memory (e.g. Synapse, IBM/AP configurations), shared disk (e.g. VAX/cluster, any multi-ported disk system), and shared nothing (e.g. Tandem, Tolerant). This paper argues that shared nothing is the preferred approach.
Monodispersed Sulfur Nanoparticles for Lithium–Sulfur Batteries with Theoretical Performance (2014)

While Li-S batteries are poised to be the next generation high-density energy storage devices, low sulfur utilization and slow rate performance have limited their practical applications. Here, we report the synthesis of monodispersed S8 nanoparticles (NPs) with different diameter and the nanosize dependent kinetic characteristics of the corresponding Li-S batteries. Most remarkably, 5 nm S NPs display the theoretical discharging/charging capacity of 1672 mAh g(-1) at 0.1 C rate and a discharge capacity of 1089 mAh g(-1) at 4 C.
Silencing Prion Protein in HT29 Human Colorectal Cancer Cells Enhances Anticancer Response to Fucoidan (2016)

Combination of fucoidan with silencing of PrP(c) has a synergic effect on the inhibition of HT29 colon cancer cell growth. Furthermore, we provide evidence for the therapeutic application of PrP(c) silencing with other anticancer drugs for cancer.
The Chronological and Spatial Relationships of Ceremonial Architecture: Seriation of Marae (1998)

&lt;p&gt;In 1933 Kenneth Emory, one of the pre-eminent archaeologists in the Pacific, published "Stone Remains in the Society Islands." Here Emory presented data on several hundred stone structures, called &lt;em&gt;marae&lt;/em&gt; that were located across the Society archipelago in the center of the Pacific. Emory's research opened the door to the archaeological study of stone architecture (e.g., Cristino et al. 1988; Descantes 1990, 1993; Emory 1933, 1943, 1970; Emory and Sinoto 1965; Garanger 1969; Graves and Cachola-Abad 1996; Graves and Ladefoged 1995; Graves and Sweeney 1993; Green et al. 1967; Kirch 1990; Kolb 1992; Martinsson-Wallin 1994; Sinoto 1996; Stokes 1991; Verin 1961; Wallin 1993) and archaeologists have spent the last 60 years analyzing the &lt;em&gt;marae&lt;/em&gt; complex in the Society Islands.&lt;/p&gt;