gebhart/patrepeval huggingface dataset:
Colonic transit times and behaviour profiles in children with defecation disorders. (2004)

Commentary on the paper by Benninga et al 

When the editorial committee discussed whether to accept the paper by Benninga et al for publication,1 some members raised concerns over the propriety of undertaking rectal manometry on children with abdominal pain. In response, the authors promptly provided their correspondence with the appropriate ethical committee (institutional review board). These revealed that the authors had properly obtained approval for the investigation in constipated children, their siblings (following fully informed consent), and those undergoing endoscopy for other conditions.

We accepted the authors’ explanation that the children with a prime complaint of abdominal pain had been referred to their …
In vitro comparison and evaluation of seven gastric closure modalities for natural orifice transluminal endoscopic surgery (NOTES) (2008)

The Eagle Claw VIII, Resolution clips, flexible stapler and flexible Endostitch produced noninferior closures in comparison with surgical closure in this model. These techniques seem to be the prime candidates for further testing in animal experiments before human trials can be initiated.
Widgets to Facilitate Service Integration in a Pervasive Environment (2010)

In pervasive environments, end-users have heterogeneous devices to access their different services. These services are usually distributed over different devices and each service should be able to run in the most appropriate device. However, current technologies do not address the integration between these services and as a consequence the end user does not have the possibility to access the services in an optimal way. In this paper, we define and implement new mechanisms that enable a seamless integration of a service in the end-user pervasive environment. First, these mechanisms enable the end-user to personalize his/her pervasive environment by running each functionality in the most suited (preferred) device, and then to make these services communicate with each other. The specificity of our approach is that we split each application into independent functionalities, and then, we define and implement on the end-user devices a distributed mechanism that detects automatically semantic compatibilities between these functionalities.
Flexible business transaction composition in service-oriented environments (2005)

Reliability and clear semantics in the presence of errors are of key importance for automated execution of business processes. Consequently, transaction support is a major ingredient for business process automation in a Service-Oriented Computing (SOC) environment. As automated business processes become more complex, different parts of\nbusiness processes have different transaction requirements. This implies that no single transaction model can accommodate for all possible transactional requirements. Therefore, we propose the Business Transaction Framework (BTF), catering for flexible composition of a variety of transaction models. Composition is supported in both a hi-\nerarchical and a choreographed way and is governed by composition rules, including inherent transaction constraints and application domain specific rules. Transaction models are represented by Abstract Transactional Constructs, which can be parameterized to tune the desired transactional behavior. Multiple composed transactions can be\nassociated to a business process type, such that precise transaction semantics can be selected per process instance. The BTF is supported by a three-level architecture, laying the basis for flexible, transactional intra- and inter-organizational business process execution on a web service based platform.
Convergence of Transforming Growth Factor-β and Vitamin D Signaling Pathways on SMAD Transcriptional Coactivators (1999)

Cell proliferation and differentiation are regulated by growth regulatory factors such as transforming growth factor-beta (TGF-beta) and the liphophilic hormone vitamin D. TGF-beta causes activation of SMAD proteins acting as coactivators or transcription factors in the nucleus. Vitamin D controls transcription of target genes through the vitamin D receptor (VDR). Smad3, one of the SMAD proteins downstream in the TGF-beta signaling pathway, was found in mammalian cells to act as a coactivator specific for ligand-induced transactivation of VDR by forming a complex with a member of the steroid receptor coactivator-1 protein family in the nucleus. Thus, Smad3 may mediate cross-talk between vitamin D and TGF-beta signaling pathways.
Precision of light scattering techniques for measuring optical parameters of microspheres (1991)

This experimental and theoretical study of light scattering techniques addresses the questions of deconvolution of light scattering data (phase functions and optical resonance spectra) from droplets and the uniqueness of that deconvolution for the measurement of size and refractive index of microspheres. Theory and experiment are compared for single component and multicomponent microdroplets and for layered microspheres levitated in electrodynamic balances. Size changes of the order of 1 A have been measured by tracking resonance shifts of slowly evaporating single component droplets. For multicomponent droplet evaporation, which involves simultaneous size and refractive index changes, and for rapid evaporation, precision is reduced to approximately 1 part in 10(4) for each parameter.
Clinical experience with <sup>13</sup>C MRS <i>in vivo</i> (2003)

13C MRS was installed on a clinical scanner at 1.5 T in order to facilitate integrated MR examinations of human brain disorders. Using a simplified protocol, (1-(13)C) glucose and/or (1-(13)C) acetate were administered orally or by intravenous infusion. (13)C spectra of diagnostic quality were acquired in more than 100 consecutive studies. Novel (13)C neurochemical data contributed to the understanding of Alzheimer's, Canavan's, mitochondrial and hepatic encephalopathy, epilepsy and normal brain development. (13)C MRS uncovered hitherto unknown disorders of NAA-synthesis, glutamate neurotransmission, TCA-cycle and glycolysis. Despite low inherent signal-to-noise, natural abundance (13)C MRS showed diagnostic promise. (13)C MRS is feasible in a clinical setting, at reasonable cost in neonates, children, adults and elderly patients.
HDP—A Novel Heme Detoxification Protein from the Malaria Parasite (2008)

When malaria parasites infect host red blood cells (RBC) and proteolyze hemoglobin, a unique, albeit poorly understood parasite-specific mechanism, detoxifies released heme into hemozoin (Hz). Here, we report the identification and characterization of a novel Plasmodium Heme Detoxification Protein (HDP) that is extremely potent in converting heme into Hz. HDP is functionally conserved across Plasmodium genus and its gene locus could not be disrupted. Once expressed, the parasite utilizes a circuitous "Outbound-Inbound" trafficking route by initially secreting HDP into the cytosol of infected RBC. A subsequent endocytosis of host cytosol (and hemoglobin) delivers HDP to the food vacuole (FV), the site of Hz formation. As Hz formation is critical for survival, involvement of HDP in this process suggests that it could be a malaria drug target.
Improvement of Thermotropic Liquid Crystallinity by Incorporation of Unsaturated Fatty Alcohol Tail Units (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImprovement of Thermotropic Liquid Crystallinity by Incorporation of Unsaturated Fatty Alcohol Tail UnitsDaniel J. Dyer and David M. WalbaCite this: Chem. Mater. 1994, 6, 8, 1096–1098Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/cm00044a004https://doi.org/10.1021/cm00044a004research-articleACS PublicationsRequest reuse permissionsArticle Views103Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
An optimality analysis of sensor-target geometries for signal strength based localization (2009)

In this paper we characterize the bounds on localization accuracy in signal strength based localization. In particular, we provide a novel and rigorous analysis of the relative receiver-transmitter geometry and the effect of this geometry on the potential localization performance. We show that uniformly spacing sensors around the target is not optimal if the sensor-target ranges are not identical and is not necessary in any case. Indeed, we show that in general the optimal sensor-target geometry for signal strength based localization is not unique.
Chemical Dimerizers in Three-Hybrid Systems for Small Molecule–Target Protein Profiling (2016)

The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
THE EPIDEMIOLOGY OF PAGET'S DISEASE OF BONE (1984)

Journal Article THE EPIDEMIOLOGY OF PAGET'S DISEASE OF BONE Get access D J P BARKER, PhD MD FRCP D J P BARKER, PhD MD FRCP MRC Environmental Epidemiology Unit University of Southampton Search for other works by this author on: Oxford Academic PubMed Google Scholar British Medical Bulletin, Volume 40, Issue 4, 1984, Pages 396–400, https://doi.org/10.1093/oxfordjournals.bmb.a072011 Published: 01 December 1984
Nonlinear-optical coherent combining of supercontinua from multiple filaments (2012)

The coherent combining of supercontinuum radiation from multiple filaments induced by an ultrashort laser pulse is demonstrated by supercomputer simulations. Four-wave mixing of supercontinuum field waveforms with an ultrashort reference pulse is shown to retrieve the coherent components from multiple supercontinua and combine them into a beam whose spatial and temporal coherence is much higher than those of supercontinua in multiple filaments.
Rationally designed squaryldiamides – a novel class of sugar-nucleotide mimics? (2010)

Sugar-nucleotides such as GDP-mannose, GDP-fucose and UDP-glucose are important biomolecules with a central role in carbohydrate and glycoconjugate biosynthesis, metabolism and cell signalling. Analogues and mimics of naturally occurring sugar-nucleotides are sought after as chemical tools and inhibitor candidates for sugar-nucleotide-dependent enzymes including glycosyltransferases. Many sugar-nucleotides bind to their target glycosyltransferases via coordination of the diphosphate group to a divalent metal cofactor in the active site. The identification of uncharged, chemically stable surrogates for the diphosphate group, with the ability to coordinate to a divalent metal, is therefore an important design criteria for the development of sugar-nucleotide mimics. Here, we describe the rational design and synthesis of a novel class of sugar-nucleotide mimics based on a squaryldiamide scaffold, an uncharged phosphate isostere. We demonstrate by comprehensive NMR titration experiments that the new sugar-nucleotide mimics coordinate efficiently to Mg(2+), and provide results from biological studies with a therapeutically relevant mannosyltransferase from Trypanosoma brucei. Our findings suggest that squaryldiamides are a promising template for the development of sugar-nucleotide mimics, and illustrate the considerable potential of the squarylamide group as a fragment for inhibitor design.
Fast semi-analytical solution of Maxwell’s equations in Born approximation for periodic structures (2016)

We propose a fast semi-analytical approach for solving Maxwell's equations in Born approximation based on the Fourier modal method (FMM). We show that, as a result of Born approximation, most matrices in the FMM algorithm become diagonal, thus allowing a reduction of computational complexity from cubic to linear. Moreover, due to the analytical representation of the solution in the vertical direction, the number of degrees of freedom in this direction is independent of the wavelength. The method is derived for planar illumination with two basic polarizations (TE/TM) and an arbitrary 2D geometry infinitely periodic in one horizontal direction.
Urokinase‐derived peptides regulate vascular smooth muscle contraction <i>in vitro</i> and <i>in vivo</i> (2000)

We examined the effect of urokinase (uPA) and its fragments on vascular smooth muscle cell contraction. Single-chain uPA inhibits phenylepherine (PE) -induced contraction of rat aortic rings, whereas two-chain uPA exerts the opposite effect. Two independent epitopes mediating these opposing activities were identified. A6, a capped peptide corresponding to amino acids 136-143 (KPSSPPEE) of uPA, increased the EC(50) of PE-induced vascular contraction sevenfold by inhibiting the release of calcium from intracellular stores. A6 activity was abolished by deleting the carboxyl-terminal Glu or by mutating the Ser corresponding to position 138 in uPA to Glu. A single-chain uPA variant lacking amino acids 136-143 did not induce vasorelaxation. A second epitope within the kringle of uPA potentiated PE-induced vasoconstriction. This epitope was exposed when single-chain uPA was converted to a two-chain molecule by plasmin. The isolated uPA kringle augmented vasoconstriction, whereas uPA variant lacking the kringle had no procontractile activity. These studies reveal previously undescribed vasoactive domains within urokinase and its naturally derived fragments.
Catching CO<sub>2</sub> in a Bowl (2009)

Increased concentrations of CO(2) in the atmosphere contribute to global climate change. Improved methods are needed for removing CO(2) from the flue gas of power plants and/or directly from the atmosphere. A macrocyclic amidourea recently synthesized by Brooks et al., when dissolved in DMSO along with tetrabutyl ammonium fluoride, removes CO(2) from the atmosphere to form a complex in which a CO(3) group is held by a number of O-H-N bonds within the bowl-shaped cavity of the macrocycle. We have calculated the structure, stability, and vibrational spectra of this complex, using density functional techniques and polarized double-zeta basis sets. Both basis set superposition errors and polarizable continuum effects on the complex geometry and stability have been evaluated. The calculated structure is in good agreement with experiment. We predict that this CO(3)(-2) complex (and its HCO(3)(-) analogue) have larger formation constants by several orders of magnitude than the analogue complex of the amidourea macrocycle with Cl(-) (particularly in DMSO solution compared to aqueous solution). Our calculations also indicate that the CO(3)(-2) and HCO(3)(-) complexes can be distinguished by (13)C NMR. The CO(3)(-2) complex also has a distinctive H-N stretch, perturbed by the H-bonding to the CO(3) group. We also calculate the CO(3)(-2) complex to absorb within the visible region, unlike the free macrocycle or typical metal carbonates. Macrocycles of this type may provide a useful route to the absorption of atmospheric CO(2). Our calculations also indicate that changing the solvent from DMSO to water and/or heating the complex will be an efficient way to decompose it to release CO(2).
The Oncolytic Activity of Newcastle Disease Virus NDV-HUJ on Chemoresistant Primary Melanoma Cells Is Dependent on the Proapoptotic Activity of the Inhibitor of Apoptosis Protein Livin (2009)

Patients with advanced melanoma usually do not benefit from conventional chemotherapy treatment. There is therefore a true need for a new kind of therapy for melanoma. One factor responsible for the poor prognosis of melanoma is the inhibitor of apoptosis protein (IAP) family member Livin. In this study, we applied a novel approach for the treatment of melanoma, using a unique strain of the oncolytic Newcastle disease virus (NDV-HUJ). We found that, unlike chemotherapeutic drugs, NDV-HUJ, a one-cycle replicating virus, overcomes the resistance to apoptosis of melanoma primary cultures that over express the Livin protein. In contrast, melanoma tumor cells that do not express Livin are relatively resistant to NDV-HUJ treatment. Furthermore, we show that NDV-HUJ-induced oncolysis is attributed to the dual function of Livin: although Livin inhibits apoptosis through the inhibition of caspases, under the robust apoptotic stimulation of NDV-HUJ, caspases can cleave Livin to create a truncated protein with a paradoxical proapoptotic activity. Thus, NDV-HUJ is a potent inducer of apoptosis that can overcome the antiapoptotic effect of Livin and allow cleavage of Livin into the proapoptotic tLivin protein. Moreover, the results indicate that the interferon system, which is functional in melanoma, is not involved in NDV-induced oncolysis. Taken together, our data offer the possibility of a new viral oncolytic treatment for chemoresistant melanoma.
High-speed autonomous navigation of unknown environments using learned probabilities of collision (2014)

We present a motion planning algorithm for dynamic vehicles navigating through unknown environments. We focus on the scenario in which a fast-moving car attempts to navigate from a start location to a set of goal coordinates in minimum time with no prior information about the environment, building a map in real time from onboard sensor data. Whereas existing planners for exploration confine themselves to a conservative set of constraints to guarantee safety around unknown regions of the environment, we instead learn a hazard function from data, which maps the vehicle's dynamic state and current environment knowledge to a probability of collision. We perform receding horizon planning in which the objective function is evaluated in expectation over those learned probabilities of collision. Our algorithm demonstrates sensible emergent behaviors, like swinging wide around blind corners, slowing down near the map frontier, and accelerating in regions of high visibility. Our algorithm is capable of navigating from start to goal much more quickly than the conservative baseline planner without sacrificing safety. We demonstrate our algorithm on a 1:8-scale high-performance RC car equipped with a planar laser range-finder and inertial measurement unit, reaching speeds of 4m/s in unknown, indoor spaces. A video of experimental results is available at: http: //groups.csail.mit.edu/rrg/nav_learned_prob_collision.
Does mate-guarding give non-territorial birds the chance to settle? (2004)

Territory defence has been suggested to serve as a means of preventing extrapair copulations. This hypothesis predicts that territory size is largest during the fertile period, and hence at this time few new territory settlements are expected. I show that Great Tits Parus major show a peak in new territory settlements in between adjacent territories precisely at the time other pairs start egg-laying. These newly settled individuals were mostly known as floaters in the area, and did not seem to be paired before they settled. This observation is in contrast with the territory defence to prevent EPC's hypothesis. I hypothesise that males have to trade-off territory defence and mateguarding, enabling new birds to settle at the time males mate guard. [KEYWORDS: TERRITORY SIZE ; GREAT TIT ; CUCKOLDRY ; Female functions ; COMPETITION ; BEHAVIOR ; SUCCESS ; RISK]
Enhancing surface free energy and hydrophilicity through chemical modification of microstructured titanium implant surfaces (2005)

Roughness-induced hydrophobicity, well-known from natural plant surfaces and intensively studied toward superhydrophobic surfaces, has currently been identified on microstructured titanium implant surfaces. Studies indicate that microstructuring by sandblasting and acid etching (SLA) enhances the osteogenic properties of titanium. The undesired initial hydrophobicity, however, presumably decelerates primary interactions with the aqueous biosystem. To improve the initial wettability and to retain SLA microstructure, a novel surface modification was tested. This modification differs from SLA by its preparation after acid etching, which was done under protective gas conditions following liquid instead of dry storage. We hypothesized that this modification should have increased wettability due to the prevention of contaminations that occurs during air contact. The main outcome of dynamic wettability measurements was that the novel modification shows increased surface free energy (SFE) and increased hydrophilicity with initial water contact angles of 0 degrees compared to 139.9 degrees for SLA. This hydrophilization was kept even after any drying. Reduced hydrocarbon contaminations were identified to play a possible role in altered surface thermodynamics. Such surfaces aim to retain the hydrophilicity and natural high surface energy of the Ti dioxide surface until surgical implants' insertion and are compared in this in vitro study with structural surface variants of titanium to compare roughness and chemically induced wettability.
A new Method for Fast Haptoglobin Phenotyping and Hemoglobin Binding Capacity Calculation Based on Capillary Zone Electrophoresis (2000)

A capillary zone electrophoresis method was developed for haptoglobin (Hp) phenotyping in hemoglobin (Hb) supplemented serum. The method allows a complete resolution of the major haptoglobin phenotypes Hp 1-1, Hp 2-1, and Hp 2-2 based on the difference in charge-to-mass ratio of their Hb-Hp complexes. Identification of these phenotypes was achieved by their significant differences in migration times and their marked difference in electrophoretic pattern. Our method showed full agreement with starch gel electrophoresis. Furthermore, following neuraminidase treatment of the serum, the Hp subtypes Hp1-1FF, FS and SS could be resolved, based on the same criteria as the phenotyping. The new electrophoretic method allowed typing of the rare phenotypes Hp 2-1 modified (Hp 2-1M) and Hp Johnson. The calculated hemoglobin binding capacity of serum correlates well with the nephelometrically determined haptoglobin concentration. The new method for typing haptoglobin gives prospectives for fast haptoglobin typing and Hp 1-1 subtyping.