gebhart/patrepeval huggingface dataset:
Anti-nociceptive effect of a conjugate of substance P and light chain of botulinum neurotoxin type A (2013)

Neuropathic pain is a debilitating condition resulting from damage to sensory transmission pathways in the peripheral and central nervous system. A potential new way of treating chronic neuropathic pain is to target specific pain-processing neurons based on their expression of particular receptor molecules. We hypothesized that a toxin-neuropeptide conjugate would alter pain by first being taken up by specific receptors for the neuropeptide expressed on the neuronal cells. Then, once inside the cell the toxin would inhibit the neurons' activity without killing the neurons, thereby providing pain relief without lesioning the nervous system. In an effort to inactivate the nociceptive neurons in the trigeminal nucleus caudalis in mice, we targeted the NK1 receptor (NK1R) using substance P (SP). The catalytically active light chain of botulinum neurotoxin type A (LC/A) was conjugated with SP. Our results indicate that the conjugate BoNT/A-LC:SP is internalized in cultured NK1R-expressing neurons and also cleaves the target of botulinum toxin, a component-docking motif necessary for release of neurotransmitters called SNAP-25. The conjugate was next tested in a murine model of Taxol-induced neuropathic pain. An intracisternal injection of BoNT/A-LC:SP decreased thermal hyperalgesia as measured by the operant orofacial nociception assay. These findings indicate that conjugates of the light chain of botulinum toxin are extremely promising agents for use in suppressing neuronal activity for extended time periods, and that BoNT/A-LC:SP may be a useful agent for treating chronic pain.
Blind Identifiability Of Class Of Nonlinear Instantaneous Ica Models (2002)

Publication in the conference proceedings of EUSIPCO, Toulouse, France, 2002
Electron photodetachment dissociation for structural characterization of synthetic and bio‐polymer anions (2013)

Tandem mass spectrometry (MS-MS) is a generic term evoking techniques dedicated to structural analysis, detection or quantification of molecules based on dissociation of a precursor ion into fragments. Searching for the most informative fragmentation patterns has led to the development of a vast array of activation modes that offer complementary ion reactivity and dissociation pathways. Collisional activation of ions using atoms, molecules or surface resulting in unimolecular dissociation of activated ions still plays a key role in tandem mass spectrometry. The discovery of electron capture dissociation (ECD) and then the development of other electron-ion or ion/ion reaction methods, constituted a significant breakthrough, especially for structural analysis of large biomolecules. Similarly, photon activation opened promising new frontiers in ion fragmentation owing to the ability of tightly controlled internal energy deposition and easy implementation on commercial instruments. Ion activation by photons includes slow heating methods such as infrared multiple photon dissociation (IRMPD) and black-body infrared radiative dissociation (BIRD) and higher energy methods like ultra-violet photodissociation (UVPD) and electron photo detachment dissociation (EPD). EPD occurs after UV irradiation of multiply negatively charged ions resulting in the formation of oxidized radical anions. The present paper reviews the hypothesis regarding the mechanisms of electron photo-detachment, radical formation and direct or activated dissociation pathways that support the observation of odd and even electron product ions. Finally, the value of EPD as a complementary structural analysis tool is illustrated through selected examples of synthetic polymers, oligonucleotides, polypeptides, lipids, and polysaccharides.
Hip protectors for preventing hip fractures in older people (2005)

Accumulating evidence casts some doubt on the effectiveness of the provision of hip protectors in reducing the incidence of hip in older people. Acceptance and adherence by users of the protectors remain poor due to discomfort and practicality.
Instruction in physical facility construction for medical students (1982)

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Appraisal and Development of the Murta Reservoir Using Hydraulic Fracture Stimulation (1991)

Abstract This paper describes the evolution and field application of fracture stimulation techniques applied to the Murta reservoir in South Australia, where unique conditions govern fracture stimulation design. The use of a minimum viscosity pad fluid has been shown to provide effective fracture height growth constraint and provide for efficient fracture length propagation, resulting in increased productivity index improvement. Fracture stimulation has proved to be a viable technique to allow economic exploitation of this resource, while allowing its continual appraisal.
Angle-resolved photoemission study of black phosphorus: Interlayer energy dispersion (1986)

Angle-resolved photoemission measurements with synchrotron radiation (about 20--50 eV) have been carried out on a black-phosphorus single crystal to study the interlayer interaction which characterizes the essential properties of the narrow-gap semiconductor, black P. The band dispersions along the \ensuremath{\Gamma}Z (interlayer) direction have been successfully obtained and compared with the self-consistent pseudopotential calculation. It is found that the overall features obtained are in good agreement with the calculation although an overestimation of the interlayer dispersion and the valence-band width by about 0.5 and 1 eV, respectively, was observed in the calculation.
Treatment with lithium carbonate does not improve disease progression in two different strains of SOD1 mutant mice (2009)

It has been shown that chronic treatment with lithium carbonate (Li(2)CO(3)) in presymptomatic SOD1G93A transgenic male mice, a model of ALS, was able to remarkably increase their lifespan through the activation of autophagy and the promotion of mitochondriogenesis and neurogenesis. This prompted us to test the lithium effect also in female SOD1G93A mice with two phenotypes of different disease severity. Female SOD1G93A mice of C57BL/6J or 129S2/Sv genetic background were treated daily with Li(2)CO(3) 37 mg/kg (1 mEq/kg) i.p. starting from age 75 days until death. Grip strength, latency to fall on rotarod and body weight were monitored twice weekly. At the time of death the spinal cord was removed to assess the number of motor neurons and to measure the expression of a marker of autophagy (LCII) and the activity of mitochondrial complex IV. We observed a significant anticipation of the onset and reduced survival in 129Sv/G93A and no effect in C57/G93A mice treated with lithium compared to vehicle treated mice. Moreover, lithium neither exerted neuroprotective effects nor increased the expression of LCII and the activity of mitochondrial complex IV in the spinal cord. The present study does not identify any therapeutic or neuroprotective effect of lithium in SOD1G93A female mice.
Recognition and tagging of compound verb groups in Czech (2000)

In Czech corpora compound verb groups are usually tagged in word-by-word manner. As a consequence, some of the morphological tags of particular components of the verb group lose their original meaning. We present a method for automatic recognition of compound verb groups in Czech. From an annotated corpus 126 definite clause grammar rules were constructed. These rules describe all compound verb groups that are frequent in Czech. Using those rules we can find compound verb groups in unannotated texts with the accuracy 93%. Tagging compound verb groups in an annotated corpus exploiting the verb rules is described.
Cell‐Type‐Specific adhesion mechanisms mediated by fibronectin adsorbed to chemically derivatized substrata (1992)

Plasma fibronectin (pFN) adhesion mechanisms on inert substrata were evaluated for murine fibroblasts (3T3) and human neuroblastoma (Platt) cells using glass coverslips chemically derivatized with a self-assembled monolayer of aliphatic chains terminated with a specific endgroup to interact with adsorbed pFN: [CH3], [SH], [SCOCH3], [NH2], [SO3H], or underivatized glass [SiOH]. All surfaces bound similar amounts of pFN and facilitated attachment of both cell types within narrow ranges. However, spreading/differentiation responses of cells differed considerably among the surfaces. While 3T3 cells spread and developed microfilament stress fibers comparably on all surfaces, inclusion of an RGDS-containing synthetic peptide in the medium revealed variation in resistance to stress fiber formation mediated by an RGDS-recognizing integrin: [NH2] greater than [CH3] much greater than [SiOH],[SH],[SCOCH3]. Different patterns of neurite formation were observed for neuroblastoma cells: [SiOH], [SO3H] greater than [SCOCH3],[SH] much greater than [CH3] greater than [NH2]. Similarity in cell responses to both [CH3] and [NH2] surfaces argues against a pattern dependent upon the hydrophobicity of substrata. When pFN was diluted to a subsaturable concentration with albumin for adsorption, neuroblastoma responses changed significantly from those observed on pFN-saturated surfaces, for both spreading and neurite generation: [NH2],[SO3H] much greater than [SH], [SCOCH3] greater than [SiOH],[CH3]. Responses to the pFN: albumin mixture were markedly improved from responses after sequential adsorptions, demonstrating "optimization" of pFN conformation (not merely binding) by coadsorption of albumin molecules. In most cases, the [NH2] surface yielded responses distinctively different from the other surfaces. Overall, these data suggest many variations in the conformation of pFN molecules adsorbed to specific inert surfaces, as well as variations in the responses of cell surface receptors to conformationally specific pFNs. They also reveal cell-type-specific changes in differentiated cell responses on derivatized substrata, mediated by different classes of cell surface receptors for the two cell types, and provide optimism for regulating FN-dependent adhesion mechanisms in either positive or negative contexts on biomaterial surfaces derivatized with one or more of these chemical end-groups.
Feature Selection via Coalitional Game Theory (2007)

We present and study the contribution-selection algorithm (CSA), a novel algorithm for feature selection. The algorithm is based on the multiperturbation shapley analysis (MSA), a framework that relies on game theory to estimate usefulness. The algorithm iteratively estimates the usefulness of features and selects them accordingly, using either forward selection or backward elimination. It can optimize various performance measures over unseen data such as accuracy, balanced error rate, and area under receiver-operator-characteristic curve. Empirical comparison with several other existing feature selection methods shows that the backward elimination variant of CSA leads to the most accurate classification results on an array of data sets.
Synthesis and structure-activity relations of 5H,11H-[2]benzopyrano[4,3-g][1]benzopyran-9-carboxylic acids (1977)

The synthesis and properties of the title compounds 1 are described. Many of these compounds are potent inhibitors of the passive cutaneous anaphylaxis reaction of rats against egg albumin challenge. Structural variations include substitutions in the 2, 3, 4, 5, 7, and 12 position of the nucleus 1. A novel rearrangement from a compound of the related [3,4-f] series to this group is reported.
The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains (2016)

Glycoside hydrolase (GH) family 29 consists solely of α-L-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins. GH29_0940 is a monomer and its overall structure consists of an N-terminal TIM-barrel-like domain, a central β-sandwich domain and a C-terminal β-sandwich domain. The TIM-barrel-like catalytic domain exhibits a (β/α)<sub>8/7</sub> arrangement in the core instead of the typical (β/α)<sub>8</sub> topology, with the `missing' α-helix replaced by a long meandering loop that `closes' the barrel structure and suggests a high degree of structural flexibility in the catalytic core. This feature was also noted in all six other structures of GH29 enzymes that have been deposited in the PDB. Based on sequence and structural similarity, the residues Asp162 and Glu220 are proposed to serve as the catalytic nucleophile and the proton donor, respectively. Like other GH29 enzymes, the GH29_0940 structure shows five strictly conserved residues in the catalytic pocket. The structure shows two glycerol molecules in the active site, which have also been observed in other GH29 structures, suggesting that the enzyme catalyses the hydrolysis of small carbohydrates. The two binding domains are classed as family 32 carbohydrate-binding modules (CBM32). These domains have residues involved in ligand binding in the loop regions at the edge of the β-sandwich. The predicted substrate-binding residues differ between the modules, suggesting that different modules bind to different groups on the substrate(s). Enzymes that possess multiple copies of CBMs are thought to have a complex mechanism of ligand recognition. Defined electron density identifying a long 20-amino-acid hydrophilic loop separating the two CBMs was observed. This suggests that the additional C-terminal domain may have a dynamic range of movement enabled by the loop, allowing a unique mode of action for a GH29 enzyme that has not been identified previously.
Gut Microbial Flora, Prebiotics, and Probiotics in IBD: Their Current Usage and Utility (2013)

Inflammatory bowel diseases are chronic diseases affecting the gastrointestinal tract, whose major forms are represented by Crohn's disease (CD) and ulcerative colitis (UC). Their etiology is still unclear, although several factors have been identified as major determinants for induction or relapses. Among these, the role of the "forgotten organ", gut microbiota, has become more appreciated in recent years. The delicate symbiotic relationship between the gut microbiota and the host appears to be lost in IBD. In this perspective, several studies have been conducted to assess the role of prebiotics and probiotics in gut microbiota modulation. This is a minireview aimed to address in an easy format (simple questions-simple answers) some common issues about the theme. An update on the role of selected constituents of gut microbiota in the pathogenesis of IBD is presented together with the analysis of the efficacy of gut microbiota modulation by prebiotics and probiotics administration in the management of IBD.
Optical networking testbeds in China (2006)

National R&D activities on optical networking testbeds in China, including CAINONET, 3Tnet and OBS testbed, are described for investigating key technologies of next generation optical networking.
Crystallization of Amorphous Silicon Thin Films Using Self-Limiting ALD of Nickel Oxide (2007)

The crystallization of amorphous Si (a-Si) thin films was performed using atomic layer deposition (ALD) of nickel oxide. Nickel oxide layers were deposited using nickel aminoalkoxide as a precursor in Ni and water as a precursor in oxygen. The presence of nickel oxide caused significant crystallization to occur in a-Si at under a reducing atmosphere. Even one single ALD layer of nickel oxide was high enough to crystallize the a-Si thin films. Self-limiting layer controllability in ALD is useful in providing a catalytic layer for formation of polycrystalline Si thin films for application to large-scale flat panel displays.
Automatic reconfiguration of flexible robot gripping system (2010)

Typical gripping systems for industrial robots have a predefined geometry which is suitable for only a specific part. The reutilization for other parts is restricted and associated with high effort for manual changeover. The presented paper shows a flexible gripping system with the possibility of self-adaptation to different workpieces. The adaptation is based on a robot-guided gripping system having a large number of passive joints without motion drives. These passive joints are normally fixed during operation and can be released in case of reconfiguration. The robot trajectory to reconfigure the gripping system is calculated using the 3D CAD data of the part. Restraints during the robot reconfiguration will be compensated with a sensor-controlled algorithm.
High Efficiency Vehicular Gas Turbines (2005)

<div class="htmlview paragraph">Recuperated intercooled gas turbine cycles offer efficiencies in the 40% and higher range at medium to high loads. Although these cycles offer better low-load efficiency than other gas turbine cycles, the idle and low-load fuel consumption are still not good enough for satisfactory vehicle operation. In addition, response time to sudden demands for power is slow. The multi-pressure gas turbine allows the combustion air to enter the cycle at a different point, reducing the mass flow and the rating of the gas turbine for efficient operation at low power. Yet, the full power of the gas turbine is available quickly for acceleration or hill climbing.</div>
Model-driven design and deployment of service-enabled web applications (2005)

Significant effort is currently invested in application integration, enabling business processes of different companies to interact and form complex multiparty processes. Web service standards, based on WSDL (Web Service Definition Language), have been adopted as process-to-process communication paradigms. However, the conceptual modeling of applications using Web services has not yet been addressed. Interaction with Web services is often specified at the level of the source code; thus, Web service interfaces are buried within a programmatic specification.In this article, we argue that Web services should be considered first-class citizens in the specification of Web applications. Thus, service-enabled Web applications should benefit from the high-level modeling and automatic code generation techniques that have long been advocated for Web application design and implementation. To this end, we extend a declarative model for specifying data-intensive Web applications in two directions: (i) high-level modeling of Web services and their interactions with the Web applications which use them, and (ii) modeling and specification of Web applications implementing new, complex Web services.Our approach is fully implemented within a CASE tool allowing the high-level modeling and automatic deployment of service-enabled Web applications.
The relationship between tonic accommodation and ciliary muscle innervation. (1985)

Previous studies have used Badal laser optometry to demonstrate significant variance in the distribution of tonic (or "dark-focus") resting positions of accommodation (TA) for groups of observers. This study investigates whether individual differences in TA are due to individual differences in autonomic tone of the ciliary muscle by comparing separately the effects of a muscarinic receptor antagonist (Tropicamide 0.5%) and a beta receptor agonist (Isoprenaline 3%) on the distribution of TA. Ten subjects were used for each study with mean ages of 23.2 and 23.0 yr, respectively. The distribution of TA within each subject group was equivalent to the large sample distributions published in previous literature. Darkroom measurements of TA and pupil diameter were determined with a Badal laser optometer and infrared photography. Distance correction and amplitude of accommodation were determined by standard optometric techniques. Isoprenaline produced a significant hyperopic shift in TA of 0.47 D over 22 min but this was not accompanied by a significant change in standard deviation of the TA distribution. This finding was in accord with the authors' previously reported investigation using the beta receptor antagonist Timolol Maleate. Tropicamide also produced a significant hyperopic shift in TA of 1.24 D over 24 min, and this was accompanied by a significant change in standard deviation of the distribution from 0.87 to 0.17. The results indicate that the parasympathetic system plays a significant role in determining the TA position and that the variations in TA between individuals is a consequence of parasympathetic rather than sympathetic ciliary muscle tone.
Quantitative imaging of bromine‐76 and yttrium‐86 with PET: A method for the removal of spurious activity introduced by cascade gamma rays (2003)

Positron Emission Tomography of bromine-76 and yttrium-86 results in the detection of coincident events that are not strictly associated with annihilation photon pairs. Instead, these coincidences occur because prompt gamma rays emitted by these nuclides result in cascades of photons that are emitted within the timing window of the PET scanner. Pairs of detected photons from these cascades are not angularly correlated and therefore contain little information regarding the location of their source. Furthermore, these coincidences are not removed by correction procedures (e.g., randoms, scatter) routinely applied to PET data. If left uncorrected, the cascade coincidences will result in spurious apparent activity within the PET images. A correction, applied within projection space, that removes the cascade coincidence signal from septa-in (i.e., two-dimensional) datasets is proposed and tested on phantom data.
Synthesis and Visualization of Densely Grafted Molecular Brushes with Crystallizable Poly(octadecyl methacrylate) Block Segments (2003)

Densely grafted molecular brushes with AB and ABA “block−graft” architectures, i.e., pODMA-b-p(BPEM-g-nBuA) and pODMA-b-p(BPEM-g-nBuA)-b-pODMA, were synthesized by the “grafting from” approach using atom transfer radical polymerization (ATRP). The backbone macroinitiators were prepared in three steps. First, ATRP of ODMA or HEMA-TMS was carried out from mono- or difunctional initiators to form macroinitiators, followed by ATRP of HEMA-TMS or ODMA initiated from these macroinitiators to obtain pODMA-b-pHEMA-TMS or pODMA-b-pHEMA-TMS-b-pODMA macromolecular backbone precursors. Finally, these precursors were esterified to pODMA-b-pBPEM and pODMA-b-pBPEM-b-pODMA backbone macroinitiators. The pnBuA side chains were grafted from the pBPEM segments of these backbone macroinitiators by ATRP. AFM measurement of the final molecular brushes demonstrated that the backbone of the brushes, the pBPEM segment, was almost completely stretched on the mica surface. pODMA segments tended to associate, due to crystallization of the relatively long C18 chains, and form “dimers” for AB block brushes and “multimers” or “circles” for ABA block brushes.