gebhart/patrepeval huggingface dataset:
The Wnt/β-catenin Pathway (2003)

Wnts are a family of secreted glycoproteins that act as ligands to activate receptor-mediated signaling pathways. The first described Wnt pathway, and the best understood, is one that works through a cytoplasmic protein, β-catenin. Specific members of the Wnt family interact with a Frizzled receptor complex, promoting the activity of Dishevelled, which in turn enhances the stability and activity of β-catenin. β-catenin probably binds members of the T cell factor and lymphoid enhancer factor (TCF/LEF) family of transcription factors, or to various other proteins, to regulate expression of target genes in a cellular context-dependent manner. Wnt signaling through this pathway regulates cell proliferation, survival, and cell fate. Inappropriate activation of this pathway may be an initiating event in some cancers, and inhibiting this pathway in transformed cells shows promise for anticancer therapies. Conversely, activation of this pathway shows promise as a target for developing osteoporosis, neurodegenerative disease, and stem cell therapies. The Connections Map for this Pathway provides an overview of the many signals that converge on β-catenin and influence Wnt signaling. Science Viewpoint R. T. Moon, B. Bowerman, M. Boutros, and N. Perrimon, The promise and perils of Wnt signaling through β-catenin. Science 296 , 1644-1646 (2002). [ Abstract ] [ Full Text ]
Heads up! (2006)

Unlike the human face, the neck has been largely overlooked in the computer graphics literature, this despite its complex anatomical structure and the important role that it plays in supporting the head in balance while generating the controlled head movements that are essential to so many aspects of human behavior. This paper makes two major contributions. First, we introduce a biomechanical model of the human head-neck system. Emulating the relevant anatomy, our model is characterized by appropriate kinematic redundancy (7 cervical vertebrae coupled by 3-DOF joints) and muscle actuator redundancy (72 neck muscles arranged in 3 muscle layers). This anatomically consistent biomechanical model confronts us with a challenging motor control problem, even for the relatively simple task of balancing the mass of the head in gravity atop the cervical spine. Hence, our second contribution is a novel neuromuscular control model for human head animation that emulates the relevant biological motor control mechanisms. Incorporating low-level reflex and high-level voluntary sub-controllers, our hierarchical controller provides input motor signals to the numerous muscle actuators. In addition to head pose and movement, it controls the tone of mutually opposed neck muscles to regulate the stiffness of the head-neck multibody system. Employing machine learning techniques, the neural networks within our neuromuscular controller are trained offline to efficiently generate the online pose and tone control signals necessary to synthesize a variety of autonomous movements for the behavioral animation of the human head and face.
Enhanced Bone Regeneration in Beagle Dogs With Bovine Bone Mineral Coated With a Synthetic Oligopeptide (2007)

Deproteinized cancellous bovine bone coated with synthetic oligopeptides enhanced new bone formation, and it seemed to be a better material for guided bone regeneration in the beagle L-shaped defect model.
Phosphorylation of C/EBPβ at a Consensus Extracellular Signal-Regulated Kinase/Glycogen Synthase Kinase 3 Site Is Required for the Induction of Adiponectin Gene Expression during the Differentiation of Mouse Fibroblasts into Adipocytes (2004)

Stimulation of adipogenesis in mouse preadipocytes requires C/EBPbeta as well as activation of the MEK/extracellular signal-regulated kinase (ERK) signaling pathway. In this study, we demonstrate that phosphorylation of C/EBPbeta at a consensus ERK/glycogen synthase kinase 3 (GSK3) site regulates adiponectin gene expression during the C/EBPbeta-facilitated differentiation of mouse fibroblasts into adipocytes. First, we show that exposure of 3T3-L1 preadipocytes to insulin, dexamethasone (DEX), and isobutylmethylxanthine (MIX) leads to the phosphorylation of C/EBPbeta at threonine 188. Pretreating the cells with a MEK1-specific inhibitor (U0126) significantly attenuates this activity. Similarly, these effectors activate the phosphorylation of T188 within an ectopic C/EBPbeta overexpressed in Swiss mouse fibroblasts, and this event involves both MEK1 and GSK3 activity. We further show that expression of C/EBPbeta (p34kD LAP isoform) in Swiss mouse fibroblasts exposed to DEX, MIX, and insulin induces expression of peroxisome proliferator-activated receptor gamma (PPARgamma) and some adiponectin but that it does not activate expression of FABP4/aP2. In fact, complete conversion of these fibroblasts into lipid-laden adipocytes, which includes activation of FABP4 and adiponectin expression, requires their exposure to a potent PPARgamma ligand such as troglitazone. Expression of a mutant C/EBPbeta in which threonine 188 has been modified to alanine (C/EBPbeta T188A) can induce PPARgamma production in the mouse fibroblasts, but it is incapable of stimulating adiponectin expression in the absence or presence of troglitazone. Interestingly, replacement of T188 with aspartic acid creates a C/EBPbeta molecule (C/EBPbeta T188D) that possesses adipogenic activity similar to that of the wild-type molecule. The absence of adiponectin expression correlates with a reduced amount of C/EBPalpha in the adipocytes expressing the T188A mutant suggesting that C/EBPalpha is required for expression of adiponectin. In fact, ectopic expression of PPARgamma in C/EBPalpha-deficient fibroblasts (NIH 3T3 cells) produces a modest amount of adiponectin, whereas expression of both PPARgamma and C/EBPalpha in NIH 3T3 cells facilitates production of abundant quantities of adiponectin. These data demonstrate that phosphorylation of C/EBPbeta at a consensus ERK/GSK3 site is required for both C/EBPalpha and adiponectin gene expression during the differentiation of mouse fibroblasts into adipocytes.
Molecular, cellular and developmental studies of sensory hyperinnervation following neonatal skin wounding. (2000)

A close interaction exists between the nervous system and the skin during development and injury. During development target derived factors are important for patterning the neuronal elements present in later life. After injury, at critical developmental time points this patterning is subject to change for long periods, and can subsequently affect pain processing. Sensory hyperinnervation is profound in the skin of postnatal animals wounded at birth (Reynolds &amp; Fitzgerald 1995). Here I have examined the development of this sensory hyperinnervation and the neurotrophins as possible causal factors. In vitro models for this phenomenon and histochemical characterisation of neurite outgrowth has also been assessed. NGF, NT-3 and GDNF are all upregulated after skin wounding in the above circumstance. However, neither NGF nor NT-3 are solely responsible for the hyperinnervation (Reynolds et al. 1997; Alvares et al. 1999). In vitro studies have demonstrated that NT-3 may be partly responsible, although trkC IgG fusion proteins show no effect in vivo. In vitro models have also demonstrated the importance of the dermis/epidermis for determining extent of neurite outgrowth. To add a new dimension to this study, I have constructed a neonatal wounded/naive skin cDNA library. By using a differential screening approach with mPCR probes, genes regulated in the above situation have been isolated. Clones generated have been sequenced and Northerns, and in situ hybridisation studies undertaken for genes of interest. Clones of particular interest include an endoplasmic reticulum stress protein-like gene (Erp29), an alpha globin-like gene, an ephrin (EPHRIN-A4) and a guanine nucleotide releasing protein-like gene. In addition several novel clones have been isolated which have yet to be characterised. This research will provide further information and understanding to both wound healing in neonates, and the peripheral patterning of cutaneous innervation during development, and lead to the discovery of the essence of hyperinnervation a largely unexplored event.
On the Thermal Expansion Coefficient and the Temperature Coefficient of Young&rsquo;s Modulus of Iron-Platinum Alloys (1965)

The thermal expansion coefficient and the temperature coefficient of Young’s modulus of iron-platinum alloys have been determined by a vertical dilatometer previously designed by the present investigators and by a vibrator-controlled oscillator using the electrostatic transducer system, respectively. It has been found that the alloys containing about 53.5∼57.0% platinum have a negative coefficient of thermal expansion; the largest mean value in the temperature range 0∼40°C is −23.68×10−6 for the alloy containing 56.0% platinum, and that the alloys containing about 51.0∼69.0% platinum have a positive coefficient of Young’s modulus; the largest mean value in the same temperature range is +161.5×10−5 for the alloy containing 55.0% platinum.
Vector Flow Imaging by Plane Wave Speckle Tracking Based on Different Beamformers (2022)

Plane wave speckle tracking allows imaging the vector flow field in the region of interest at a very high frame rate at the cost of decreased image quality. Adaptive beamformers have been developed by researchers to improve image quality. In this study, the impact of beamformers on speckle tracking performance was investigated. Three typical coherence based beamformers were compared with the classical delay and sum beamformer. Utilizing ultrasound simulation, we constructed a synthetic wall-less vessel phantom where the scatterers moved according to a parabolic velocity profile. The results show that the mean bias of velocity estimation ranged from −5.6% to −6.4% and the mean standard deviation ranged from 2.2% to 2.8%, with the best accuracy achieved by coherence factor (CF) based speckle tracking. The angle estimation had high accuracy in all approaches, where the mean bias ranged from 0.1° to 0.5° and the mean standard deviation ranged from 0.5° to 2.3°. In conclusion, CF based speckle tracking performs best, which may help to improve the accuracy ofvelocity estimation in plane wave speckle tracking.
3-Benzyl-Hexahydro-Pyrrolo[1,2-a]Pyrazine-1,4-Dione Extracted From Exiguobacterium indicum Showed Anti-biofilm Activity Against Pseudomonas aeruginosa by Attenuating Quorum Sensing (2019)

Bacterial cell-to-cell communication promotes biofilm formation and can potentially lead to multidrug resistance development. Quorum sensing inhibition (QSI) is an effective and widely employed strategy against biofilm formation. The extract from <i>Exiguobacterium indicum</i> SJ16, a gram-positive bacterium, isolated from the rhizosphere of <i>Cyperus laevigatus</i> showed significant anti-quorum sensing activity (about 99%) against the reference <i>Chromobacterium violaceum</i> CV026 strain without exerting any antibacterial effect. The potentially active QSI compound identified in the SJ16 extract was 3-Benzyl-hexahydro-pyrrolo[1, 2-a]pyrazine-1,4-dione. The SJ16 extract containing this active compound showed significant anti-quorum sensing activity against a model quorum sensing bacterium strain <i>Pseudomonas aeruginosa</i> PAO1 and a clinical isolate <i>P. aeruginosa</i> PAH by preventing biofilm formation without attenuating the cell growth within the biofilm. More specifically, the SJ16 extract changed the topography and architecture of the biofilm, thus preventing bacterial adherence and further development of the biofilm. Furthermore, it decreased virulence factors (rhamnolipid and pyocyanin), the bacterial motility, as well as the elastase, and protease activities in <i>P. aeruginosa</i>. Microarray analysis revealed the differential expression of quorum sensing regulatory genes. Based on these results, we herein propose a hypothetical model, characterizing the role of this QSI agent in the transcriptional regulation of quorum sensing in <i>P. aeruginosa</i> PAO1, demonstrating that this compound has significant drug-development potential. Further research is required to delineate its possible applications in therapeutics in the context of biofilm forming bacterial infections.
Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5'- d(CGCXAATTYGCG)-3' (1997)

The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the fourth position from the 5'-end. Procedures for synthesis of two of the nitroazole nucleosides, 10 and 11, were developed for this study. Each of the nitroazoles was converted into a 3'-phosphoramidite for oligonucleotide synthesis by conventional automated protocols. Four oligonucleotides were synthesized for each modified nucleoside in order to obtain duplexes in which each of the four natural bases was placed opposite (position 9) the nitroazole. In order to assess the role of the nitro group on base stacking interaction, sequences were also synthesized in which the fourth base was 1-(2'-deoxy-beta-D-ribofuranosyl)pyrazole. Corresponding sequences containing an abasic site, as well as sequences containing inosine, were synthesized for comparison. Thermal melting studies yielded T m values and thermodynamic parameters. Each nucleoside analog displayed a unique pattern of base pairing preferences. The least discriminating analog was 3-nitropyrrole, for which T m values differed by 5 degrees C and Delta G 25 degrees C ranged from -6.1 to -6.5 kcal/mol. 5-Nitroindole gave duplexes with significantly higher thermal stability, with Tm values varying from 35.0 to 46.5 degrees C and -Delta G 25 degrees C ranging from 7.7 to 8.5 kcal/mol. Deoxyinosine (22), a natural analog which has found extensive use as a universal nucleoside, is far less non-discriminating than any of the nitroazole derivatives. Tm values ranged from 35.4 degrees C when paired with G to 62.3 degrees C when paired with C. The significance of the nitro substituent was determined by comparison of the base pairing properties of a simple azole nucleoside, 1-(2'-deoxy-beta-D-ribofuranosyl)pyrazole (12). The pyrazole-containing sequences melt at 10-20 degrees C lower than the corresponding nitropyrazole-containing sequences. On average, the pyrazole-containing sequences were equivalent in stability (average Delta G = -4.8 kcal/mol) to the sequences containing an abasic site (average Delta G = -4.7 kcal/mol).
Effect of Thidiazuron and Casamino Acid on Adventitious Shoot Formation from Roots of Apple prunifolia Borkh. MO-84) Plantlets Cultured In Vitro (1994)

Effects of cytokinins (N6-benzyl amino purine : BAP, thidiazuron : TDZ) and casamino acid on adventitious shoot formation from the root of plantlets regenerated in vitro were investigated to establish an efficient regeneration system for apples through adventitious shoot formation. Shoot cultures of Mains prunifolia Borkh. var. ringo Asami strain MO-84 were grown on a Murashige-Skoog medium containing 1.0 mg liter-1 BAP. Micropropagated plantlets were obtained at the end of 45 weeks of subculture on an MS medium containing 0.1 mg liter-1 indole-3-butyric acid (IBA). Intact micropropagated plantlets were placed singly on the surface of the modified MS medium supplemented with various concentrations of BAP or TDZ, plus 0.1 mg liter IBA and 0.1 mg•liter-1 GA3 at 25°C under 3, 000 lx for 16 hours per day.1. Optimum morphogenic response for adventitious shoot formation was obtained by using modified MS medium supplemented with 2.193.29 mg•liter-1 TDZ, 0.1 mg•liter-1 IBA, and 0.1 mg liter-1 GA3. Multiple and rosetted adventitious shoots on the root of intact micropropagated plantlets were observed at the concentration of 2.193.29 mg•liter-1 TDZ, whereas, single adventitious shoot formation was observed at 0.1 -1.10 mg •liter-1 TDZ or 5.0 mg•liter-1 BAP.2. Among several factors in this experiment, cytokinin (BAP, TDZ) was most effective for adventitious shoot formation; casamino acid (1, 000 mg•liter-1) had an additive effect.
Representing knowledge in requirements engineering: an empirical study of what software engineers need to know (2002)

The selection and structuring of requirements engineering data necessitates an empirical prediction about the future utility of the selected data and of the retrieval paths available in the structure. In order to investigate these predictions, the questions asked by software engineers at software requirements and preliminary design meetings are analyzed. It is assumed that the kinds of information elicited by these questions are good indicators of what data would be most useful. Results lend support to systems that focus on the developing artifact itself, and indicate the importance of user scenarios.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Experimental Investigation for Enhanced Control of Rotating Unsteady Flow Instabilities in an Unshrouded Centrifugal Compressor Impeller (2019)

Abstract Unshrouded industrial centrifugal compressor impellers operate at high rotational speeds and volume flow rates. Under such conditions, impeller blade excitation is dominated by high frequency interaction with stationary parts, i.e., vaned diffusers or inlet guide vanes. In a previous study conducted on two full compression units of the original equipment manufacturer (OEM), the authors identified, characterized, and quantified resonant blade vibration caused by the interaction of the impeller blades with rotating stall cells during severe off-design conditions. This caused significant dynamic stress in the blades. In a follow-up study, this phenomenon was reproduced successfully experimentally under representative off-design conditions in a downscaled test rig and numerically with unsteady computational fluid dynamics (CFD) and structural mechanical finite element method (FEM) analysis. The gained knowledge was translated into a new diffuser design philosophy, based on sectorwise circumferential variation of the leading edge angle. This paper presents the patented philosophy, which is experimentally verified on the same test rig configuration in terms of flow path geometry and measurement equipment that was used in the mentioned prior study to assess resonant blade interaction. The results confirm the design aims: rotating stall onset was delayed without affecting the aerodynamic performance of the stage. Resonant blade interaction with rotating stall observed in the baseline diffuser could not be avoided with the two new diffuser designs. However, with the two new diffusers, the induced mechanical stresses in the impeller and the excitability were reduced by up to 12%.
Deduced amino acid sequence of human pulmonary surfactant proteolipid: SPL(pVal) (1987)

Hydrophobic, proteolipid-like protein of Mr 6500 was isolated from ether/ethanol extracts of human, canine and bovine pulmonary surfactant. Amino acid composition of the protein demonstrated a remarkable abundance of hydrophobic residues, particularly valine and leucine. The N-terminal amino acid sequence of the human protein was determined: N-Leu-Ile-Pro-Cys-Cys-Pro-Val-Asn-Leu-Lys-Arg-Leu-Leu-Ile-Val4... An oligonucleotide probe was used to screen an adult human lung cDNA library and resulted in detection of cDNA clones with predicted amino acid sequence with close identity to the N-terminal amino acid sequence of the human peptide. SPL(pVal) was found within the reading frame of a larger peptide. SPL(pVal) results from proteolytic processing of a larger preprotein. Northern blot analysis detected in a single 1.0 kilobase SPL(pVal) RNA which was less abundant in fetal than in adult lung. Mixtures of purified canine and bovine SPL(pVal) and synthetic phospholipids display properties of rapid adsorption and surface tension lowering activity characteristic of surfactant. Human SPL(pVal) is a pulmonary surfactant proteolipid which may therefore be useful in combination with phospholipids and/or other surfactant proteins for the treatment of surfactant deficiency such as hyaline membrane disease in newborn infants.
The Blue‐LED‐Sensitive Naphthoquinone‐Imidazolyl Derivatives as Type II Photoinitiators of Free Radical Photopolymerization (2023)

Abstract In this work, new naphthoquinone‐based photoinitiators are synthesized and applied for the first time in free radical photopolymerization. In the presence of acrylate monomers, these PIs display excellent photoinitiation capabilities under blue‐light LED@405 nm irradiation in a two‐component photoinitiating system in which the additive is a common iodonium salt ( bis ‐(4‐ tert ‐butylphenyl)iodonium hexafluorophosphate ‐ Iod) or a tertiary amine (ethyl 4‐dimethylaminobenzoate ‐ EDB). In controlled tests, the polymerization performance of dye4/Iod is equal to or better than that of common commercial Type II photoinitiators (2‐isopropylthioxanthone and benzophenone). Meanwhile, only a trace amount of photoinitiator is required (as low as 0.05%) to initiate the photopolymerization. It is worth noting that some of these compounds can also be used in one‐component photoinitiating system (monocomponent Type II behavior) and exhibit high photoinitiation ability. A series of complementary characterization analyses of two new naphthoquinone dyes (i.e. dye 1 and dye 4) with very similar chemical structures are carried out to investigate the relevant photochemical mechanism. Finally, 3D printing experiments are carried out by a simple and convenient Direct Laser Write (DLW) technique.
Developments of highly proton-conductive sulfonated polymers for proton exchange membrane fuel cells (2012)

This review paper covers recent publications on the developments of highly proton-conductive sulfonated polymers for proton exchange membrane (PEM) fuel cells. The PEMs presenting proton conductivities exceeding that of Nafion membranes are especially focused on. The proton conductivities of PEMs have been correlated to their ion exchange values and morphological phase-separation. Formation of ionic channels is an effective approach to develop highly proton-conductive PEMs. The approaches could be grouped into (1) developments of microphase-separation with block copolymers, (2) side-chain and grafted sulfonated polymers, and (3) locally and densely sulfonated polymers. Formation of nanocomposites of PEMs with nanofillers has also shown great ability to increase the proton conductivities of the existed PEMs. Besides proton conductivities, the formation of nanocomposites also improves some PEM properties including mechanical strength, dimensional stability, and oxidative stability. The discussed publications have provided promising PEMs for the development of high performance fuel cells.
Novel mesoporous amorphous magnesium carbonate for the adsorption of textile dyes and heavy metal ions (2018)

Novel mesoporous amorphous magnesium carbonate for the adsorption of textile dyes and heavy metal ions
Intelligent driver safety system using fatigue detection (2017)

Driver safety systems protect driver from accidents by sensing signs of drowsiness. The main aim of this paper is to propose such technique that can detect the signs of drowsiness and make corresponding decisions to make him alert. This paper presents a technique in which the driver will be continuously monitored by a camera and his eyes, head and mouth movements will be observed. If the drowsiness signs are detected on the basis of these three movements under the predefined criteria, driver will be declared as sleepy and he will get alert with the help of alarms. Three robust techniques of drowsiness detection are combined together to make a robust system that can prevent form accident.