gebhart/patrepeval huggingface dataset:
Close appositions between Tyrosine hydroxylase immunoreactive boutons and respiratory neurons in the rat ventrolateral medulla (1994)

The extent of the adrenergic input to respiratory neurons in the ventrolateral medulla oblongata of rats was assessed by using a combination of intracellular recording, dye filling, and immunohistochemistry. Twenty-two neurons that displayed a pronounced respiration-related modulation of their membrane potential, and could not be antidromically activated by electrical stimulation of the superior laryngeal, vagus, or facial nerves, were labelled by intracellular injection of biocytin. Three types of respiration-related neurons were labelled: small neurons located in the Bötzinger complex between 0.5 and 1.0 mm caudal to the facial nucleus; medium-sized neurons located in the ventral respiratory group 1.0 to 2.0 mm caudal to the facial nucleus; and large motoneurons located within the nucleus ambiguus 0.5 to 2.0 mm caudal to the facial nucleus. Small Bötzinger neurons [length = 22 +/- 5 microns, width = 13 +/- 3 microns, area = 222 +/- 79 microns2; (mean +/- SD, n = 5)] had membrane potentials of -15 to -27 mV during the recording period. Four of five of these cells had profuse axonal terminations between 50 microns caudal and 450 microns rostral to their somata, suggesting that they may form part of local networks responsible for generating respiratory activity. Medium-sized ventral respiratory group neurons (length = 26 +/- 5 microns, width = 18 +/- 4 microns, area = 377 +/- 141 microns2; n = 5) were found in the vicinity of the nucleus ambiguus dorsal to the lateral reticular nucleus. Three of five of these neurons had an axon that crossed the midline and travelled caudally. One axon had a collateral with varicosities close to its soma. The somata of motoneurons (length = 29 +/- 6 microns, width = 21 +/- 4 microns, area = 485 +/- 142 microns2; n = 12) were located within the nucleus ambiguus, and had axons that could be traced to exist points from the medulla. Tyrosine hydroxylase immunoreactive cells and their terminal fibres within the medulla were localised by immunocytochemistry. Small Bötzinger neurons received the largest number of close appositions from tyrosine hydroxylase immunoreactive boutons (13 +/- 2 appositions/neuron; n = 5). Medium-sized ventral respiratory group neurons received fewer appositions (8 +/- 4 appositions/neuron; n = 5). Most motoneurons (n = 10) received few appositions from tyrosine hydroxylase immunoreactive boutons, while two received none. The average number was 3 +/- 3 appositions/neuron (n = 12).(ABSTRACT TRUNCATED AT 400 WORDS)
A synchronization scheme for multimedia annotation (2002)

Multimedia annotation is of benefit to many multimedia applications in the enhancement of presentation, instruction, and communication. In the present paper, we make use of voice and electronic pen as annotation media in the designing of a multimedia annotation and playback system. Our contributions are as follows: 1) a time-based synchronization mechanism is developed which takes care of not only voice and electronic pen movement temporal synchronization issue but also electronic pen movement spatial synchronization problem; and 2) file storage and replay mechanisms are devised to handle multimedia storage process and to facilitate interactive presentation process during replay phase. We implemented the proposed system on the Microsoft Windows 95 platforms in the Multimedia Information Networking Laboratory (MINE) at the Tamkang University.
A Neurophysiological Correlate of an Immune Responsea (1987)

In order to examine possible neurophysiological changes during an immune response, we have recorded neural activity in a conscious animal bearing chronic recording electrodes in the preoptic area/anterior hypothalamus (PO/AH) and hypothalamic paraventricular nucleus (PVN). Male rats were sensitized with sheep red blood cells (SRBC) injected intraperitoneally. Basal PO/AH multiunit activity (MUA) was recorded as 14.7 +/- 2.1 Hz prior to sensitization and was seen to increase significantly to a maximum of 33.1 +/- 6.0 Hz (p less than 0.005) five days after SRBC injection. This increase correlated with the initial appearance of anti-SRBC serum antibodies at a mean antibody titer of 1:32. Also recorded were decreases in PO/AH MUA on days 3 and 8 after the sensitization (8.2 +/- 2.4 Hz, p less than 0.005); 7.1 +/- 3.3 Hz, p less than 0.005, respectively). Basal PVN MUA was recorded as 14.7 +/- 2.4 Hz. It decreased significantly for the first three days after immunization, and then returned to a basal rate before increasing to 25.9 +/- 8.4 Hz (p less than 0.005) on day 6. On the ninth and tenth days after SRBC injection PO/AH and PVN MUA levels returned to those recorded before immunization.
Sampling and multilevel coarsening algorithms for fast matrix\n approximations (2017)

This paper addresses matrix approximation problems for matrices that are\nlarge, sparse and/or that are representations of large graphs. To tackle these\nproblems, we consider algorithms that are based primarily on coarsening\ntechniques, possibly combined with random sampling. A multilevel coarsening\ntechnique is proposed which utilizes a hypergraph associated with the data\nmatrix and a graph coarsening strategy based on column matching. Theoretical\nresults are established that characterize the quality of the dimension\nreduction achieved by a coarsening step, when a proper column matching strategy\nis employed. We consider a number of standard applications of this technique as\nwell as a few new ones. Among the standard applications we first consider the\nproblem of computing the partial SVD for which a combination of sampling and\ncoarsening yields significantly improved SVD results relative to sampling\nalone. We also consider the Column subset selection problem, a popular low rank\napproximation method used in data related applications, and show how multilevel\ncoarsening can be adapted for this problem. Similarly, we consider the problem\nof graph sparsification and show how coarsening techniques can be employed to\nsolve it. Numerical experiments illustrate the performances of the methods in\nvarious applications.\n
The A2b adenosine receptor protects against vascular injury (2008)

The A2b adenosine receptor (A2bAR) is highly abundant in bone marrow macrophages and vascular smooth muscle cells (VSMC). To examine the functional significance of this receptor expression, we applied a femoral artery injury model to A2bAR knockout (KO) mice and showed that the A2bAR prevents vascular lesion formation in an injury model that resembles human restenosis after angioplasty. While considering related mechanisms, we noted higher levels of TNF-alpha, an up-regulator of CXCR4, and of VSMC proliferation in the injured KO mice. In accordance, CXCR4, which is known to attract progenitor cells during tissue regeneration, is up-regulated in lesions of the KO mice. In addition, aortic smooth muscle cells derived from A2bAR KO mice display greater proliferation in comparison with controls. Bone marrow transplantation experiments indicated that the majority of the signal for lesion formation in the null mice originates from bone marrow cells. Thus, this study highlights the significance of the A2bAR in regulating CXCR4 expression in vivo and in protecting against vascular lesion formation.
Bioassay to Screen Pathogenesis-associated Genes in Alternaria brassicicola (2013)

Alternaria brassicicola is a necrotrophic fungus that causes black spot disease of most plants in the Brassicaceae, including cultivated Brassica species and weedy Arabidopsis species. Since the concept of transformation constructs of linear minimal elements was developed (Cho et al., 2006), we have produced over 200 strains of loss-of-function mutants with an aid of selectable marker genes. Pathogenicity assays are a time-consuming step in screening pathogenesis-associated genes among targeted gene mutants. Here we describe a method for pathogenesis assays of A. brassicicola. Using this method, we have discovered pathogenesis-associated genes and were able to further characterize the functions of selected gene (Cho et al., 2013; Cho et al., 2012; Srivastava et al., 2012).
Nitric oxide and voluntary exercise together promote quadriceps hypertrophy and increase vascular density in female 18-mo-old mice (2012)

Age-related sarcopenia reduces the size, strength, and function of muscle, and the diameter of muscle fibers. It also disrupts the dystrophin-glycoprotein complex, dislocating nitric oxide synthase 1 (NOS-1) and reducing sarcolemmal integrity. This study of quadriceps muscle in 18-mo-old mice showed that NO-donor treatment with isosorbide dinitrate (I) for 6 wk, in combination with voluntary exercise for 3 wk, increased muscle mass by 25% and stimulated cell proliferation. The resulting fiber hypertrophy was accompanied by a lower ratio of protein:DNA, consistent with myogenic-cell hyperplasia. Treatment enhanced the ratio of NOS-1:β-dystroglycan in correlation with fiber diameter, improved sarcolemmal integrity, and increased vascular density after an increase in vascular endothelial growth factor protein at 3 wk. Results demonstrate that age-related muscle refractoriness to exercise can be overcome with NO-donor treatment. Since activation of muscle stem cells and vascular perfusion are limiting factors in the maintenance, regeneration, and growth of aged muscle, results suggest the feasibility of using NO-donor drugs to combat atrophy and muscle ischemia. Improved function and quality of life from the NO-amplified effects of exercise may be useful in aging and other conditions such as disuse, insulin resistance, or microgravity.
Synthesis of Bisected Glycoforms of Recombinant IFN‐β by Overexpression of β‐1,4‐N‐Acetylglucosaminyltransferase III in Chinese Hamster Ovary Cells (1998)

Genetic engineering of oligosaccharide biosynthesis pathways in mammalian cells makes possible generation of new recombinant glycoproteins of potential importance in the biopharmaceutical industry. Most prior investigations of glycosylation engineering of secreted heterologous glycoproteins involve terminal steps of oligosaccharide biosynthesis. In particular, increasing the frequency of bisected structures within the glycoform distribution has not before been considered. A Chinese hamster ovary (CHO) cell line capable of producing bisected oligosaccharides on glycoproteins was created by overexpression of a recombinant N-acetylglucosaminyltransferase III (GnT-III). Interferon beta (IFN-beta) was chosen as a model and potential therapeutic secreted heterologous protein to demonstrate the effect of recombinant GnT-III-expression on product glycosylation. IFN-beta with bisected oligosaccharides was produced by the GnT-III-engineered CHO cells but not by the unmodified parental cell line.
Apoptosis after traumatic human spinal cord injury (1998)

These results support the hypothesis that apoptosis occurs in human SCIs and is accompanied by the activation of caspase-3 of the cysteine protease family. This mechanism of cell death contributes to the secondary injury processes seen after human SCI and may have important clinical implications for the further development of protease inhibitors to prevent programmed cell death.
<title>Fluorescence polarization sensing</title> (1999)

We describe a new approach to fluorescence sensing based on fluorescence polarization measurements. The sensing device consists of an analyte sensitive fluorescence probe and a reference fluorophore which is not affected by the analyte. Combined emission from probe and reference passes through two adjacent orthogonally oriented polarizers and is viewed with second analyzer polarizer. Changes in the probe intensity result in changes in the polarization of the combined emission. The analyzer polarizer is rotated to yield equal intensity from both sides of two orthogonally oriented polarizers. So constructed sensor earlier was used for manual visual detection of RhB in intralipid and to measure pH using 6-carboxyfluorescein. A sensor equipped with the simple electronic detection system of a dual photocell and a Watson bridge improves the accuracy. We used this device with UV hand lamp, electroluminescent light source or LED to detect pH, oxygen and calcium. This sensing method is generic and can be used with any fluorophore which displays an analyte-dependent change in intensity.
Architecture and development approach for integrated cyber-physical production-service systems (CPPSS) (2020)

Product-Service Systems (PSS) have been recognized as one of the key concepts driving product innovation and value enhancement. PSS offer of a function of integrated product-service-combinations aiming to be competitive by satisfying customer needs. At the same time Cyber-Physical Production Systems (CPPS) provide the potential to extract information from the manufacturing of technical products. Both, PSS and CPPS have shown their potential to support sustainable manufacturing. This paper provides an integrated consideration of PSS and CPPS and presents a framework in the form of an architecture and development approach. The framework will be applied for the use-case of 3D printing.
Rubisco Proteins as Plant-based Alternatives to Egg White Proteins: Characterization of Thermal Gelation Properties (2022)

RuBisCO proteins can be isolated from abundant and sustainable plant sources, such as duckweed (e.g., Lemnoideae). These plant-based globular proteins are capable of irreversibly unfolding and forming gels when heated, which means they may be able to mimic some of the functional attributes exhibited by animal globular proteins. In this study, we examined the ability of RuBisCo proteins to mimic the initial rheology and thermal gelation properties of egg white, which the aim of developing plant-based egg analogs. The impact of protein concentration (10-15% w/w), pH (7 to 9), and calcium concentration (0 to 50 mM CaCl2) on the properties of the egg white analogs was examined. The appearance (colorimetry), thermal denaturation (differential scanning calorimetry), thermal gelation (dynamic shear rheology), and texture profiles (compression testing) were measured. RuBisCO-based egg white analogs could be successfully produced at 10% protein content and pH 8 in the absence of salt. These RuBisCO protein solutions had similar apparent viscosity-shear rate profiles, shear modulus-temperature profiles, gelling temperatures, and final gel strengths as egg white. However, there were some differences. RuBisCO protein gels were slightly darker than egg white, which was attributed to the presence of some phenolic impurities. RuBisCo protein exhibited a single thermal transition temperature (~ 66 ℃) whereas egg white exhibited two (~66 and ~81 ℃). RuBisCo protein gels were more brittle but less chewy and resilient than egg white gels. This study provides valuable insights into the potential of RuBisCo protein for formulating plant-based egg white analogs, which may help improve the sustainability of the modern food supply.
The power of partial tanslation (1995)

A programming language translation framework and the implementation of the C-ification of Binary Prolog are discussed. The technique can be seen as an automatic specialization with respect to a given program of the traditional instruction folding techniques used to speed up emulators. The full details and performance analysis of the C-ification of a continuation passing Binary Prolog engine are described for which large write-mode sequences and the absence of a call-return mechanism make the framework particularly well suited.
Melatonin’s neuroprotective role in mitochondria and its potential as a biomarker in aging, cognition and psychiatric disorders (2021)

Melatonin is an ancient molecule that is evident in high concentrations in various tissues throughout the body. It can be separated into two pools; one of which is synthesized by the pineal and can be found in blood, and the second by various tissues and is present in these tissues. Pineal melatonin levels display a circadian rhythm while tissue melatonin does not. For decades now, melatonin has been implicated in promoting and maintaining sleep. More recently, evidence indicates that it also plays an important role in neuroprotection. The beginning of our review will summarize this literature. As an amphiphilic, pleiotropic indoleamine, melatonin has both direct actions and receptor-mediated effects. For example, melatonin has established effects as an antioxidant and free radical scavenger both in vitro and in animal models. This is also evident in melatonin's prominent role in mitochondria, which is reviewed in the next section. Melatonin is synthesized in, taken up by, and concentrated in mitochondria, the powerhouse of the cell. Mitochondria are also the major source of reactive oxygen species as a byproduct of mitochondrial oxidative metabolism. The final section of our review summarizes melatonin's potential role in aging and psychiatric disorders. Pineal and tissue melatonin levels both decline with age. Pineal melatonin declines in individuals suffering from psychiatric disorders. Melatonin's ability to act as a neuroprotectant opens new avenues of exploration for the molecule as it may be a potential treatment for cases with neurodegenerative disease.
Nuclear Expression of BCL10 or Nuclear Factor Kappa B Predicts Helicobacter pylori–Independent Status of Early-Stage, High-Grade Gastric Mucosa-Associated Lymphoid Tissue Lymphomas (2004)

Nuclear expression of BCL10 or NF-kappaB is highly predictive of H. pylori-independent status in high-grade gastric MALT lymphoma, and coexpression of these two markers in the nuclei is frequent.
The molecular basis for responsiveness to anti-viral therapy in hepatitis C. (2000)

Hepatitis C virus (HCV) infection is an important clinical problem, with a world-wide prevalence of approximately 1-2%. HCV infection is associated with an increased risk for the development of severe liver disease. HCV is inherently resistant to anti-viral therapy with interferon (IFN). The virus circulates in infected individuals as a mixture of related, yet genetically distinct variants, or quasispecies. Many studies have implicated HCV quasispecies in IFN responsiveness. Effective containment of HCV quasispecies mutation and selection through more aggressive therapy (e.g. daily induction), combination therapy (e.g. IFN plus ribavirin), or longer lasting therapy (e.g. pegylated IFN) is required for IFN responsiveness. Recently, several HCV proteins including the non-structural 5A and envelope gene 2-glycoprotein have been implicated in HCV anti-viral resistance. It is likely that multiple HCV genes disrupt IFN-induced anti-viral responses at many levels and that these virus-host cell interactions are associated with IFN resistance. Characterisation of HCV-encoded mechanisms of anti-viral resistance has important implications for the development of new anti-virals.
Engineering Case Report (2013)

Click to increase image sizeClick to decrease image size ACKNOWLEDGMENTS The authors thank Rebekah Bruce and Thomas Molina of the Microbiology Laboratory at NASA Johnson Space Center for their assistance in this study. This study was supported by NASA ISS funding NAS9-02078. Column Editor Michael Larrañaga
Site-Specific Fluorescent Labeling of Nucleic Acids by Genetic Alphabet Expansion Using Unnatural Base Pair Systems (2016)

Site-specific fluorescent labeling of nucleic acids is a fundamental approach for the detection of specific base sequences and the analysis of the structural dynamics of functional nucleic acids. A couple of unnatural base pairs were applied to real-time PCR and structural analysis of functional RNA molecules by site-specific fluorescent labeling. This chapter introduces unnatural base pair systems that can be practically used as a third base pair for in vitro replication and transcription, as a tool for the site-specific fluorescent labeling of functional DNA and RNA molecules. Currently, the site-specific labeling of large RNA molecules mainly relies on a laborious and time-consuming method involving chemical synthesis and enzymatic ligation. The selectivity and efficiency of the unnatural base incorporation depend on the sequence context around the unnatural base, incorporation positions, and modification species. Meanwhile, active labeling methods could confer new functionalities to RNA molecules, such as sensor systems of RNA aptamers.
On Boundary Condition Capturing for Multiphase Interfaces (2006)

This paper begins with an overview of the boundary condition capturing approach to solving problems with interfaces.Although, the authors' original motivation was to extend the ghost fluid method from compressible to incompressible flow, the elliptic nature of incompressible flow quickly quenched the idea that ghost cells could be defined and used in the usual manner.Instead the boundary conditions had to be implicitly captured by the matrix formulation itself, leading to the novel approach.We first review the work on the variable coefficient Poisson equation, noting that the simplicity of the method allowed for an elegant convergence proof.Simplicity and robustness also allowed for a quick extension to threedimensional two-phase incompressible flows including the effects of viscosity and surface tension, which is discussed subsequently.The method has enjoyed popularity in both computational physics and computer graphics, and we show some comparisons with the traditional delta function approach for the visual simulation of bubbles.Finally, we discuss extensions to problems where the velocity is discontinuous as well, as is the case for premixed flames, and show an example of multiple interacting liquids that includes all of the aforementioned phenomena.
Defending Against Universal Perturbations With Shared Adversarial\n Training (2018)

Classifiers such as deep neural networks have been shown to be vulnerable\nagainst adversarial perturbations on problems with high-dimensional input\nspace. While adversarial training improves the robustness of image classifiers\nagainst such adversarial perturbations, it leaves them sensitive to\nperturbations on a non-negligible fraction of the inputs. In this work, we show\nthat adversarial training is more effective in preventing universal\nperturbations, where the same perturbation needs to fool a classifier on many\ninputs. Moreover, we investigate the trade-off between robustness against\nuniversal perturbations and performance on unperturbed data and propose an\nextension of adversarial training that handles this trade-off more gracefully.\nWe present results for image classification and semantic segmentation to\nshowcase that universal perturbations that fool a model hardened with\nadversarial training become clearly perceptible and show patterns of the target\nscene.\n
Excitation kinetics of electronic states of hydrogen molecules in nonequilibrium discharges: Electronic ground state (2015)

This review offers an analysis of the vibrational kinetics of hydrogen molecules in the singlet ground state X 1∑ + for various gas discharges. The measured quasi-stationary vibrational-level distribution functions of a hydrogen molecule in the electronic ground state at the corresponding vibrational temperatures of the first level and those calculated in the framework of a semiempirical level collisional–radiative model of low-temperature plasma in hydrogen, developed in this study, are compared. A database of the measured and calculated characteristics of kinetic processes involving vibrational-excited hydrogen molecules, as well as macro and microparameters of hydrogen low-temperature plasma, is created.