gebhart/patrepeval huggingface dataset:
A syntax and semantics for network diagrams (2002)

Research concerning the automated design of network diagrams is reported. A formulation of syntax and semantics for network diagrams that is used in the Automated Network Diagram Designer (ANDD) system is presented. The syntactic formulation differs from previous work in two significant ways: perceptual-organization phenomena are explicitly represented, and syntax is described in terms of constraints rather than as a grammar of term-rewriting rules. The semantic formulation is based on an application-independent model of network systems that can be used to model many applications. Examples that show how these concepts are used by ANDD to automatically design network diagrams are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fermentation of Cucumbers Brined with Calcium Chloride Instead of Sodium Chloride (2010)

Waste water containing high levels of NaCl from cucumber fermentation tank yards is a continuing problem for the pickled vegetable industry. A major reduction in waste salt could be achieved if NaCl were eliminated from the cucumber fermentation process. The objectives of this project were to ferment cucumbers in brine containing CaCl(2) as the only salt, to determine the course of fermentation metabolism in the absence of NaCl, and to compare firmness retention of cucumbers fermented in CaCl(2) brine during subsequent storage compared to cucumbers fermented in brines containing both NaCl and CaCl(2) at concentrations typically used in commercial fermentations. The major metabolite changes during fermentation without NaCl were conversion of sugars in the fresh cucumbers primarily to lactic acid which caused pH to decrease to less than 3.5. This is the same pattern that occurs when cucumbers are fermented with NaCl as the major brining salt. Lactic acid concentration and pH were stable during storage and there was no detectable production of propionic acid or butyric acid that would indicate growth of spoilage bacteria. Firmness retention in cucumbers fermented with 100 to 300 mM CaCl(2) during storage at a high temperature (45 degrees C) was not significantly different from that obtained in fermented cucumbers with 1.03 M NaCl and 40 mM CaCl(2). In closed jars, cucumber fermentations with and without NaCl in the fermentation brine were similar both in the chemical changes caused by the fermentative microorganisms and in the retention of firmness in the fermented cucumbers.
Multi-frequency PLC Networking Technology Based on Preamble Sequence (2015)

Power Line Communication (PLC) network uses the existing grid as communication bracing. The low-voltage power distribution network is the most widespread network. In the low-voltage power distribution network, the communication distance is very short, which provides the possibility to achieve the narrow band and high-speed power line communication. But, its network structure is complex, and the link length, load and network branch of different locations is different. The attenuation of PLC network channel exhibits frequency-selective. In addition, the noise exhibits the frequency selective, too. Therefore, it is difficult to find a frequency to implement communication between the master and the majority of the slave stations. Thus, we propose multifrequency networking technology based on preamble sequence. This technology can reduce the number of hops of the communication between the master and the slaves. Thereby, the delay of the network will reduce, and the network throughput will increase. Meanwhile, the station can quickly adapt to the change of the communication environment and service needs.
Cylinder Test to Assess Sensory-Motor Function in a Mouse Model of Parkinson’s Disease (2019)

Parkinson's disease is a progressive neurodegenerative movement disorder that happens due to the loss of dopaminergic neurons in the substantia nigra. The deficiency of dopamine in the basal nuclei drives cardinal motor symptoms such as bradykinesia and hypokinesia. The current protocol describes the cylinder test, which is a relatively simple behavioral assessment that evaluates the motor deficits upon unilateral degeneration of the nigrostriatal pathway in experimental models of Parkinson's disease. Since dopamine-depleted mice exhibit the preferential use of the forelimb ipsilateral to the lesion, here researchers perform the cylinder test to investigate the therapeutic effects of antiparkinsonian treatments on the performance of the contralateral (injured) limb.
Optimal Analogue Relaying with Multi-Antennas for Physical Layer Network coding (2008)

This paper considers a wireless relay network where two nodes S1 and S2 exchange their information through a relay node RL. It is assumed that both S1 and S2 are equipped with single antenna and RL is equipped with multi-antennas. Based on the principle of physical layer network coding (PNC), we study the optimal design for the analogue relaying, also known as amplify-and-forward (AF), at RL so as to maximize the sum- rate of bi-directional information exchange between S1 and S2. Optimal solution for the multi-antenna linear processing at RL is presented and low-complexity suboptimal schemes are proposed. Simulation results show that the proposed methods perform better than the conventional zero-forcing (ZF) and minimum- mean-squared-error (MMSE) -based linear relaying, and the performance gain is very significant when the two channels from S1 and S2 to RL are highly correlated.
Temperature-responsive in vitro RNA structurome of <i>Yersinia pseudotuberculosis</i> (2016)

RNA structures are fundamentally important for RNA function. Dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and RNA thermometers. By parallel analysis of RNA structures, we mapped the RNA structurome of Yersinia pseudotuberculosis at three different temperatures. This human pathogen is exquisitely responsive to host body temperature (37 °C), which induces a major metabolic transition. Our analysis profiles the structure of more than 1,750 RNAs at 25 °C, 37 °C, and 42 °C. Average mRNAs tend to be unstructured around the ribosome binding site. We searched for 5'-UTRs that are folded at low temperature and identified novel thermoresponsive RNA structures from diverse gene categories. The regulatory potential of 16 candidates was validated. In summary, we present a dynamic bacterial RNA structurome and find that the expression of virulence-relevant functions in Y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mRNAs.
Retrograde Gene Delivery to Hypoglossal Motoneurons Using Adeno-Associated Virus Serotype 9 (2012)

Retrograde viral transport (i.e., muscle to motoneuron) enables targeted gene delivery to specific motor pools. Recombinant adeno-associated virus serotype 9 (AAV9) robustly infects motoneurons, but the retrograde transport capabilities of AAV9 have not been systematically evaluated. Accordingly, we evaluated the retrograde transduction efficiency of AAV9 after direct tongue injection in 129SVE mice as well as a mouse model that displays neuromuscular pathology (Gaa(-/-)). Hypoglossal (XII) motoneurons were histologically evaluated 8 weeks after tongue injection with AAV9 encoding green fluorescent protein (GFP) with expression driven by the chicken β-actin promoter (1 × 10(11) vector genomes). On average, GFP expression was detected in 234 ± 43 XII motoneurons 8 weeks after AAV9-GFP tongue injection. In contrast, tongue injection with a highly efficient retrograde anatomical tracer (cholera toxin β subunit, CT-β) resulted in infection of 818 ± 88 XII motoneurons per mouse. The retrograde transduction efficiency of AAV9 was similar between the 129SVE mice and those with neuromuscular disease (Gaa(-/-)). Routine hematoxylin and eosin staining and cluster of differentiation (CD) immunostaining for T cells (CD3) indicated no persistent inflammation within the tongue or XII nucleus after AAV9 injection. Additional experiments indicated no adverse effects of AAV9 on the pattern of breathing. We conclude that AAV9 can retrogradely infect a significant portion of a given motoneuron pool in normal and dystrophic mice, and that its transduction efficiency is approximately 30% of what can be achieved with CT-β.
Identification of a Nuclear Gene (FMC1) Required for the Assembly/Stability of Yeast Mitochondrial F1-ATPase in Heat Stress Conditions (2001)

We have identified a yeast nuclear gene (FMC1) that is required at elevated temperatures (37 degrees C) for the formation/stability of the F(1) sector of the mitochondrial ATP synthase. Western blot analysis showed that Fmc1p is a soluble protein located in the mitochondrial matrix. At elevated temperatures in yeast cells lacking Fmc1p, the alpha-F(1) and beta-F(1) proteins are synthesized, transported, and processed to their mature size. However, instead of being incorporated into a functional F(1) oligomer, they form large aggregates in the mitochondrial matrix. Identical perturbations were reported previously for yeast cells lacking either Atp12p or Atp11p, two specific assembly factors of the F(1) sector (Ackerman, S. H., and Tzagoloff, A. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 4986--4990), and we show that the absence of Fmc1p can be efficiently compensated for by increasing the expression of Atp12p. However, unlike Atp12p and Atp11p, Fmc1p is not required in normal growth conditions (28--30 degrees C). We propose that Fmc1p is required for the proper folding/stability or functioning of Atp12p in heat stress conditions.
Structure‐guided Discovery of a Novel Non‐peptide Inhibitor of Dengue Virus NS2B–NS3 Protease (2014)

Dengue fever is a fast emerging epidemic-prone viral disease caused by dengue virus serotypes 1-4. NS2B-NS3 protease of dengue virus is a validated target to develop antiviral agents. A major limitation in developing dengue virus protease inhibitors has been the lack of or poor cellular activity. In this work, we extracted and refined a pharmacophore model based on X-ray crystal structure and predicted binding patterns, followed by a three-dimensional flexible database filtration. These output molecules were screened according to a docking-based protocol, leading to the discovery of a compound with novel scaffold and good cell-based bioactivity that has potential to be further optimized. The discovery of this novel scaffold by combination of in silico methods suggests that structure-guided drug discovery can lead to the development of potent dengue virus protease inhibitors.
Femtosecond pulse width control in microscopy by two‐photon absorption autocorrelation (1995)

Summary A technique for both the measurement and the control of the pulse width at the focal point of a high‐NA lens, based on two‐photon absorption interferometric autocorrelation, is presented. The technique is applied to measuring the pulse broadening induced on a pulse propagating through a high‐NA lens system for several objectives. It is known that the pulse width may increase by up to ≅50% of its original value by propagation through an objective which has wide field compensation for spherical and chromatic aberrations. The two‐photon absorption autocorrelation technique allows adjustment of the actual pulse width in the focus of a high‐NA lens through pre‐chirp compensation. The pulse width is shown to be almost independent of penetration depth into the sample, while the amplitude of the autocorrelation signal shows a strong decrease with depth. The ability to both measure and control the actual pulse width under strong focusing conditions is of direct importance to, among others, two‐photon absorption imaging approaches.
Overproduction of Biologically-active Human Nerve Growth Factor in<i>Escherichia coli</i> (1992)

A gene coding for human nerve growth factor (hNGF) was constructed for expression under control of the trp promoter in E. coli. The plasmid pTRSNGF contained a synthetic hNGF gene fused, in frame, to the region encoding the beta-lactamase signal peptide. The plasmid pTRLNGF contained the same coding sequence as hNGF attached downstream from the N-terminal fragment of the trp L gene. E. coli cells harboring pTRSNGF produced an amount of hNGF constituting 4% of the total cellular protein, and removed the beta-lactamase signal peptide. The mature protein hNGF was biologically active in the PC12h bioassay for neurite outgrowth. This biological activity was comparable to that of authentic mouse NGF. E. coli cells harboring pTRLNGF produced an amount of fusion protein hNGF constituting 25% of the total cellular protein. Although the fusion protein hNGF formed inclusion bodies in cells, dissolved fusion protein hNGF was active in neurite outgrowth from PC12h cells.
Adhesion characteristics of alicyclic polymers for use in ArF excimer laser lithography (1998)

We evaluate the adhesion characteristics and relationship between work of adhesion and structure of polar-alicyclic polymers we developed for use in ArF excimer laser lithography. We found that the adhesion of the polymers and resists in both the alkaline-developer and water circumstances depends on the work of adhesion in air. Stronger adhesion can be obtained with higher polarity of polymer films caused by the higher surface free energy due to hydrogen bonds. The polarity of polymers and functional groups is evaluated with their relative dielectric constants. With the standard developer (2.38% tetramethylammonium hydroxide aqueous solution), the chemically amplified resist based on poly(carboxy- tetracyclo[4.4.0.1<SUP>2,5</SUP>.1<SUP>7,10</SUP>]dodecylacrylate- co-hydroxy-tricyclo[5.2.1.0<SUP>2,6</SUP>]decylacrylate) forms a 0.18-micrometers L&S pattern by the ArF excimer laser dose.
HuR, a RNA stability factor, is expressed in malignant brain tumors and binds to adenine- and uridine-rich elements within the 3' untranslated regions of cytokine and angiogenic factor mRNAs. (2001)

Tumors of the central nervous system (CNS) often have sustained expression of labile genes, including angiogenic growth factors and immunosuppressive cytokines, which promote tumor progression. Stabilization of the RNA transcripts for these genes, such as vascular endothelial growth factor (VEGF), is an important molecular pathway for this up-regulation. HuR, a member of the Elav family of RNA-binding proteins, has been implicated in this pathway through its binding to adenine and uridine (AU)-rich stability elements (ARE) located in the 3' untranslated regions (3'-UTRs) of the mRNA. Whereas three of the Elav family members (Hel-N1, HuC, and HuD) are restricted to young and mature neurons, HuR is more broadly expressed, including proliferating cells of the developing CNS. Because RNA stabilization of labile genes may promote tumor growth, we analyzed and compared the expression pattern of HuR in 35 freshly resected and cultured CNS tumors to determine whether there was any correlation with tumor grade or histological type. We found that HuR mRNA was consistently expressed in all of the tumors, regardless of cell origin or degree of malignancy. Using a novel HuR-specific polyclonal antibody, we found that strong HuR protein expression was limited to high-grade malignancies (glioblastoma multiforme and medulloblastoma). Within the glioblastoma multiforme, prominent HuR expression was also detected in perinecrotic areas in which angiogenic growth factors are up-regulated. To further define its role as a potential RNA stabilizer, we analyzed whether HuR could bind to the stability motifs within the 3'-UTRs of cytokines and growth factors linked to brain tumor progression. We used a novel ELISA-based RNA binding assay and focused on the 3'-UTRs of angiogenic factors VEGF, COX-2, and (interleukin) IL-8 as well as the immunomodulating factors IL-6, transforming growth factor (TGF)-beta and tumor necrosis factor (TNF)-alpha as potential RNA ligands. Our results indicated overall a very high binding affinity to these RNA targets. A comparison of these ligands revealed a hierarchy of binding affinities with the angiogenic factors, and TGF-beta showing the highest (Kd of 1.8-3.4 nM), and TNF-alpha the lowest (Kd of 18.3 nM). The expression pattern of HuR, coupled with the RNA binding data, strongly suggests a role for this protein in the posttranscriptional regulation of these genes in CNS tumors.
LivDet 2015 fingerprint liveness detection competition 2015 (2015)

A spoof or fake is a counterfeit biometric that is used in an attempt to circumvent a biometric sensor. Liveness detection distinguishes between live and fake biometric traits. Liveness detection is based on the principle that additional information can be garnered above and beyond the data procured by a standard authentication system, and this additional data can be used to determine if a biometric measure is authentic. The Fingerprint Liveness Detection Competition (LivDet) goal is to compare both software-based and hardware-based fingerprint liveness detection methodologies. The competition is open to all academic and industrial institutions. The number of competitors grows at every LivDet edition demonstrating a growing interest in the area. In this edition eleven institutions have registered with twelve submissions for the software-based part and one for the hardware-based part.
Injection molding of electrical parts in today's materials (2003)

It is noted that the molding of electrical components such as bobbins, housing, and bases has become more challenging with the advent of higher heat and electrical property materials such as PET (polyethylene terephthalate), PBT (polybutylene terephthalate), PPS (polyphenylene sulfide), and others. The successful production of these parts is a combination of proper mold design and construction, preparation of molding material, processing, and monitoring of both part parameters and process parameters. Therefore, close communication between the product designer, manufacturing engineer, mold designer, moldmaker, and molder is necessary to achieve successful results. Particular attention is given to the molding of engineering resins, with emphasis on material preparation, melt temperature, mold temperature, molding machine temperature, and quality control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Towards an accurate tracking of liver tumors for augmented reality in robotic assisted surgery (2014)

This article introduces a method for tracking the internal structures of the liver during robot-assisted procedures. Vascular network, tumors and cut planes, computed from pre-operative data, can be overlaid onto the laparoscopic view for image-guidance, even in the case of large motion or deformation of the organ. Compared to current methods, our method is able to precisely propagate surface motion to the internal structures. This is made possible by relying on a fast yet accurate biomechanical model of the liver combined with a robust visual tracking approach designed to properly constrain the model. Augmentation results are demonstrated on in-vivo sequences of a human liver during robotic surgery, while quantitative validation is performed on an ex-vivo porcine liver experimentation. Validation results show that our approach gives an accurate surface registration with an error of less than 6mm on the position of the tumor.
Expression of zfh‐4, a new member of the zinc finger‐homeodomain family, in developing brain and muscle (1995)

We have identified zfh-4, a new member of a recently recognized zinc finger-homeodomain (zfh) family of putative transcription factors. Zfh-4 expression is prominent in developing muscle and brain. In both tissues, zfh-4 RNA levels are highest embryonically, then decrease gradually to barely detectable levels in adults. In myogenic cell lines, far more zfh-4 is expressed in proliferating myoblasts than in myotubes, suggesting a cellular basis for the developmental regulation observed in vivo. In contrast, zfh-4 RNA in brain is more abundant in postmitotic cells of the marginal zone than in proliferating cells of the ventricular zone. Within the brain, zfh-4 RNA is regionally localized: expression is highest in midbrain, readily detectable in hindbrain, and very low in cerebral cortex. Its patterns of expression, and its homology to known DNA binding proteins, support the idea that zfh-4 may be a regulator of gene expression in developing brain and muscle.
Neurotrophic Factors in Etiology and Treatment of Mood Disorders (2007)

Abstract Basic and clinical research has demonstrated a role for neurotrophic factors in the pathophysiology and treatment of mood disorders, contributing to a neurotrophic hypothesis of depression. Animal studies report that stress decreases the expression of brain derived neurotrophic factor (BDNF), as well as other trophic factors, in limbic brain structures, which could contribute to the atrophy and cell loss caused by stress and depression. In contrast, antidepressant treatment increases the expression of BDNF and increases the birth of newborn neurons in the adult hippocampus, effects that could block or even reverse the effects of stress. BDNF also produces antidepressant effects in behavioral models, further demonstrating the functional significance of this neurotrophic factor. The relevance of the basic research studies is supported by clinical studies demonstrating that levels of BDNF in brain and plasma of depressed patients is decreased relative to controls and that this effect is reversed by antidepressant treatments. Genetic studies are underway to identify polymorphisms of the BDNF gene that could directly contribute to depressive symptoms or increase vulnerability upon exposure to stress or other environmental factors. These findings further elucidate the cellular alterations underlying mood disorders and could lead to novel therapeutic interventions.
Adaptive optical three-dimensional measurement with structured light (2000)

The described 3-D measurement system with fringe projection applies the principle of uniform scale representation by the exclusive use of phase measurement values for the coordinates of each point. The test object is successively illuminated with a grating structure from at least three different directions with a telecentric system, where gray code is combined with five 90-deg phase shifts. A CCD camera records the intensity distribution of the fringes that appear as intersection lines on the surface of the object. This provides the linearly independent absolute phase values that are necessary for the calculation of the coordinates. Note that all coordinates (x y z) are determined with the same accuracy. To compensate the influence of specular reflections or shadowed areas up to 15 light projection directions can be used. Moreover, the object can be rotated around a second axis, yielding other views of the object. Thus we acquire different patches of the object that are transformed into a global coordinate system without any interactive user help. During this procedure, correlation methods or special points are not necessary. The calibration of the 3-D orientation of the second axis is realized with a special calibration body.
Coordinated landing of a quadrotor on a skid-steered ground vehicle in the presence of time delays (2011)

This work presents a control technique to autonomously coordinate a landing between a quadrotor UAV and a skid-steered UGV. Local controllers to feedback linearize the models are presented, and a joint decentralized controller is developed to coordinate a rendezvous for the two vehicles. The effects of time delays on closed loop stability are examined using a Retarded Functional Differential Equation (RFDE) formulation of the problem, and delay margins are determined for particular closed loop setups. Simulation results are presented, which demonstrate the feasibility of this approach for autonomous outdoor coordinated landing.