gebhart/patrepeval huggingface dataset:
Design and Fabrication of a High-Strength Hydrogel with Ideally Homogeneous Network Structure from Tetrahedron-like Macromonomers (2008)

As a new class of high-strength hydrogels, we designed a tetra-PEG gel by combining two symmetrical tetrahedron-like macromonomers of the same size. Because the nanostructural unit of the gel network was defined by the length of the tetrahedral PEG arm, the gel had a homogeneous structure and resultant high mechanical strength comparable to that of native articular cartilage. Furthermore, since the gel was formed by mixing two biocompatible macromonomer solutions, the gelation reaction itself and the resultant gel were also biocompatible. The breaking strength had local maxima at the overlap concentration of the macromonomers (C*) and at 2C*. Dynamic light scattering measurement indicated the near absence of inhomogeneities in the network at C*. Thus, we successfully designed and fabricated a high-strength hydrogel by controlling the homogeneity of network structure for the first time, which will lead to multiplied effects, i.e., contributing to the understanding of ideal networks, providing a universal strategy for designing high-strength gels, and opening up the biomedical application of hydrogels.
Endogenous opioids contribute to insensitivity to pain in humans and mice lacking sodium channel Nav1.7 (2015)

Loss-of-function mutations in the SCN9A gene encoding voltage-gated sodium channel Nav1.7 cause congenital insensitivity to pain in humans and mice. Surprisingly, many potent selective antagonists of Nav1.7 are weak analgesics. We investigated whether Nav1.7, as well as contributing to electrical signalling, may have additional functions. Here we report that Nav1.7 deletion has profound effects on gene expression, leading to an upregulation of enkephalin precursor Penk mRNA and met-enkephalin protein in sensory neurons. In contrast, Nav1.8-null mutant sensory neurons show no upregulated Penk mRNA expression. Application of the opioid antagonist naloxone potentiates noxious peripheral input into the spinal cord and dramatically reduces analgesia in both female and male Nav1.7-null mutant mice, as well as in a human Nav1.7-null mutant. These data suggest that Nav1.7 channel blockers alone may not replicate the analgesic phenotype of null mutant humans and mice, but may be potentiated with exogenous opioids.
The new paradigm of flow cell sequencing: Table 1. (2008)

DNA sequencing is in a period of rapid change, in which capillary sequencing is no longer the technology of choice for most ultra-high-throughput applications. A new generation of instruments that utilize primed synthesis in flow cells to obtain, simultaneously, the sequence of millions of different DNA templates has changed the field. We compare and contrast these new sequencing platforms in terms of stage of development, instrument configuration, template format, sequencing chemistry, throughput capability, operating cost, data handling issues, and error models. While these platforms outperform capillary instruments in terms of bases per day and cost per base, the short length of sequence reads obtained from most instruments and the limited number of samples that can be run simultaneously imposes some practical constraints on sequencing applications. However, recently developed methods for paired-end sequencing and for array-based direct selection of desired templates from complex mixtures extend the utility of these platforms for genome analysis. Given the ever increasing demand for DNA sequence information, we can expect continuous improvement of this new generation of instruments and their eventual replacement by even more powerful technology.
PHYTOCHROME STRUCTURE AND SIGNALING MECHANISMS (2006)

Phytochromes are a widespread family of red/far-red responsive photoreceptors first discovered in plants, where they constitute one of the three main classes of photomorphogenesis regulators. All phytochromes utilize covalently attached bilin chromophores that enable photoconversion between red-absorbing (P(r)) and far-red-absorbing (P(fr)) forms. Phytochromes are thus photoswitchable photosensors; canonical phytochromes have a conserved N-terminal photosensory core and a C-terminal regulatory region, which typically includes a histidine-kinase-related domain. The discovery of new bacterial and cyanobacterial members of the phytochrome family within the last decade has greatly aided biochemical and structural characterization of this family, with the first crystal structure of a bacteriophytochrome photosensory core appearing in 2005. This structure and other recent biochemical studies have provided exciting new insights into the structure of phytochrome, the photoconversion process that is central to light sensing, and the mechanism of signal transfer by this important family of photoreceptors.
Vibration Control of Machinery Installations and Structures: Some Design Procedures and Experimental Diagnostic Techniques (1990)

A review is presented of some recent work carried out in the structural dynamics field, related to vibration control. Applications of power flow techniques in the study of machinery installations are described, the objectives being to determine the relative importance of paths between source and receiver and the establishment of improved installation design rules; both theoretical and measurement methods are discussed. Dissipative mechanisms in structures are important; the damping of composite structures and means for increasing material damping are outlined together with an appraisal of fatigue life estimation procedures with particular reference to the acoustic fatigue problem. Some active and passive vibration control techniques are reviewed and indications of future areas of study are given. An appraisal of the current status of experimental work in the field is also made.
Cuff-less PPG based continuous blood pressure monitoring — A smartphone based approach (2016)

Cuff-less estimation of systolic (SBP) and diastolic (DBP) blood pressure is an efficient approach for non-invasive and continuous monitoring of an individual's vitals. Although pulse transit time (PTT) based approaches have been successful in estimating the systolic and diastolic blood pressures to a reasonable degree of accuracy, there is still scope for improvement in terms of accuracies. Moreover, PTT approach requires data from sensors placed at two different locations along with individual calibration of physiological parameters for deriving correct estimation of systolic and diastolic blood pressure (BP) and hence is not suitable for smartphone deployment. Heart Rate Variability is one of the extensively used non-invasive parameters to assess cardiovascular autonomic nervous system and is known to be associated with SBP and DBP indirectly. In this work, we propose a novel method to extract a comprehensive set of features by combining PPG signal based and Heart Rate Variability (HRV) related features using a single PPG sensor. Further, these features are fed into a DBP feedback based combinatorial neural network model to arrive at a common weighted average output of DBP and subsequently SBP. Our results show that using this current approach, an accuracy of ±6.8 mmHg for SBP and ±4.7 mmHg for DBP is achievable on 1,750,000 pulses extracted from a public database (comprising 3000 people). Since most of the smartphones are now equipped with PPG sensor, a mobile based cuff-less BP estimation will enable the user to monitor their BP as a vital parameter on demand. This will open new avenues towards development of pervasive and continuous BP monitoring systems leading to an early detection and prevention of cardiovascular diseases.
Mitofusin-1 protein is a generally expressed mediator of mitochondrial fusion in mammalian cells (2003)

Mitochondrial fusion may regulate mitochondrial morphogenesis and underlie complementation between mitochondrial genomes in mammalian cells. The nuclear encoded mitochondrial proteins Mfn1 and Mfn2 are human homologues of the only known protein mediators of mitochondrial fusion, the Drosophila Fzo GTPase and Saccharomyces cerevisiae yFzo1p. Although the Mfn1 and Mfn2 genes were broadly expressed, the two genes showed different levels of mRNA expression in different tissues. Two Mfn1 transcripts were detected at similar levels in a variety of human tissues and were dramatically elevated in heart, while Mfn2 mRNA was abundantly expressed in heart and muscle tissue but present only at low levels in many other tissues. Human Mfn1 protein localized to mitochondria and participated in a high molecular weight, detergent extractable protein complex. Forced expression of Mfn1 in cultured cells caused formation of characteristic networks of mitochondria. Introduction of a point mutation in the conserved G1 region of the predicted GTPase domain (Mfn1K88T) dramatically decreased formation of mitochondrial networks upon Mfn1 overexpression, suggesting that network formation required completion of the Mfn1 GTPase cycle. Conversely, a protein variant carrying a point mutation in the G2 motif of the Mfn1 GTPase domain acted as a dominant negative: overexpression of Mfn1T109A resulted in fragmentation of mitochondria. We propose that Mfn1T109A interferes with fusion activity of endogenous Mfn1 protein, possibly by binding necessary cofactors, so to allow unopposed mitochondrial fission. Thus, Mfn1 appears to be a key player in mediating mitochondrial fusion and morphology in mammalian cells.
Cell-Penetrating Peptide-Mediated Therapeutic Molecule Delivery into the Central Nervous System (2013)

The blood-brain barrier (BBB), a dynamic and complex barrier formed by endothelial cells, can impede the entry of unwanted substances - pathogens and therapeutic molecules alike - into the central nervous system (CNS) from the blood circulation. Taking into account the fact that CNS-related diseases are the largest and fastest growing unmet medical concern, many potential protein- and nucleic acid-based medicines have been developed for therapeutic purposes. However, due to their poor ability to cross the BBB and the plasma membrane, the above-mentioned bio-macromolecules have limited use in treating neurological diseases. Finding effective, safe, and convenient ways to deliver therapeutic molecules into the CNS is thus urgently required. In recent decades, much effort has been expended in the development of drug delivery technologies, of which cell-penetrating peptides (CPPs) have the most promising potential. The present review covers the latest advances in CPP delivery technology, and provides an update on their use in CNS-targeted drug delivery.
Nanotechnology Applications in Cancer (2007)

Cancer nanotechnology is an interdisciplinary area of research in science, engineering, and medicine with broad applications for molecular imaging, molecular diagnosis, and targeted therapy. The basic rationale is that nanometer-sized particles, such as semiconductor quantum dots and iron oxide nanocrystals, have optical, magnetic, or structural properties that are not available from molecules or bulk solids. When linked with tumor targeting ligands such as monoclonal antibodies, peptides, or small molecules, these nanoparticles can be used to target tumor antigens (biomarkers) as well as tumor vasculatures with high affinity and specificity. In the mesoscopic size range of 5-100 nm diameter, nanoparticles also have large surface areas and functional groups for conjugating to multiple diagnostic (e.g., optical, radioisotopic, or magnetic) and therapeutic (e.g., anticancer) agents. Recent advances have led to bioaffinity nanoparticle probes for molecular and cellular imaging, targeted nanoparticle drugs for cancer therapy, and integrated nanodevices for early cancer detection and screening. These developments raise exciting opportunities for personalized oncology in which genetic and protein biomarkers are used to diagnose and treat cancer based on the molecular profiles of individual patients.
Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling (2006)

In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.
Guarded commands, nondeterminacy and formal derivation of programs (1975)

So-called “guarded commands” are introduced as a building block for alternative and repetitive constructs that allow nondeterministic program components for which at least the activity evoked, but possibly even the final state, is not necessarily uniquely determined by the initial state. For the formal derivation of programs expressed in terms of these constructs, a calculus will be be shown.
Treatment of Human Immunodeficiency Virus Infection with Saquinavir, Zidovudine, and Zalcitabine (1996)

Treatment with saquinavir, zalcitabine, and zidovudine was well tolerated. This drug combination reduced HIV-1 replication, increased CD4+ cell counts, and decreased levels of activation markers in serum more than did treatment with zidovudine and either saquinavir or zalcitabine. Studies are warranted to evaluate whether the three-drug combination will reduce morbidity and mortality.
Responses of Mosquitoes and Stable Flies to a Man in a Light-Weight Rubber Diving Suit (1962)

Journal Article Responses of Mosquitoes and Stable Flies to a Man in a Light-Weight Rubber Diving Suit Get access H. K. Gouck, H. K. Gouck Entomology Research Division, Agric. Res. Serv., U.S.D.A. Search for other works by this author on: Oxford Academic PubMed Google Scholar L. H. Gilbert L. H. Gilbert Entomology Research Division, Agric. Res. Serv., U.S.D.A. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 55, Issue 3, 1 June 1962, Pages 386–392, https://doi.org/10.1093/jee/55.3.386 Published: 01 June 1962 Article history Accepted: 06 November 1961 Published: 01 June 1962
Development and Use of Multimeric Major Histocompatibility Complex Molecules (2002)

Enumeration and analysis of antigen-specific T cells play a central role in cellular immunology.While many methodologies have been established for the analysis of humoral responses, until recently the direct analysis of antigen-specific T-cell responses was extremely difficult.Difficulty in analyzing T cells was partially due to the fact that T lymphocytes recognize cell surface peptide-major histocompatibility complex (MHC) complexes and also due to the intrinsic low affinity of T-cell receptors (TCR) for cognate ligand.In this review, we discuss some new methodologies for visualizing antigen-specific T cells and how they have impacted our understanding of cellular immune responses.In the past, several methods were used to quantitate antigenspecific T-cell responses.Traditionally, these assays were functional assays, dependent on the proliferation or lytic activity of antigen-specific T cells in vitro.To improve the sensitivity of these assays, it was necessary to expand the population of antigen-specific T cells in vitro before measuring effector functions, such as cytolysis, proliferative responses, or cytokine release.Serial limiting-dilution assays (LDA) were the old "gold standard" for quantitative analysis of antigen-specific cytotoxic T lymphocytes (CTL) (19).This assay depended on the ability of antigen-specific T cells to survive, function, and proliferate in vitro upon stimulation.Therefore, the number of antigen-specific CTL determined by LDA significantly underestimated the true number of antigen-specific CTL and also lacked further detailed information about the characteristics of antigen-specific CD8 ϩ T cells in vivo.Recently, new assays based on cytokine induction and/or release have been developed.These assays do not require in vitro proliferation of antigen-specific T cells but do depend on peptide-induced production of cytokines.Cytokine production can be detected in an ELISPOT assay (34), intracellularly (29, 31), or captured on the cell surface (8) and analyzed by flow cytometry.Analysis for cytokine-producing cells has influenced our estimate of antigen-specific T-cell precursor frequency.While these methods have been useful in visualizing cells on the basis of effector cytokine release, there is also a skewing that occurs depending on which cytokine is being assayed that is not present if one can visualize T cells solely based on TCR specificity.In addition, due to technical aspects of the assays, one cannot keep cells alive for additional studies after ELI-SPOT assay or intracellular cytokine staining.Anticlonotypic TCR-specific antibodies have also been use-
Kinetics of Nitrate Reduction by Iron at Near Neutral pH (2002)

Although considerable research has been conducted on nitrate reduction by zerovalent iron (ZVI), the process kinetics at near neutral pH has not been studied thoroughly. In this study, a kinetic model with a double-Langmuir-adsorption formulation was developed to represent site saturation effects of aqueous Fe2+ and NO3- on nitrate reduction in a ZVI system at near neutral pH. Both an analytical solution and a numerical solution of the proposed model were developed. The kinetic parameters were evaluated based on batch experiments with two types of ZVI. Sensitivity analysis indicates that it is rather difficult and unreliable to estimate the parameters of the proposed multivariable nonlinear kinetic model from a single test curve. A better strategy is to obtain reliable parameters by designing specific experiments to target one parameter each time. The results indicate that, although the values of the kinetic parameters might change with different types of iron powder, the kinetic model can fit the experimental data very well, and therefore is consistent with the proposed mechanism.
Protein Transport in Cerebral Endothelium: In Vitro Transcytosis of Transferrin (2003)

Brain capillary endothelial cells forming the blood-brain barrier (BBB) are sealed by complex tight junctions and possess few pinocytotic vesicles. These characteristics, added to a metabolic barrier, restrict the passage of most small polar molecules and macromolecules from cerebrovascular circulation to the brain. Many endothelial functions that include the diffusion or transport barrier of brain microvessels have been defined by studies in whole animals and in isolated capillaries in vitro. The ability to grow central nervous system microvascular endothelial cells in culture has opened the door to many new experimental approaches for studying the transendothelial transport of substances across the in vitro BBB. However, several lines of evidence suggest that cultured brain endothelial cells rapidly lose the characteristics of a differentiated BBB in vitro (). Furthermore, Risau and Wolburg () suggested that long-term cultures of brain endothelial cells may not provide a good model system for the BBB in vitro. Nevertheless, we have described subcultures up to the 50th generation of bovine brain capillary endothelial cells (BBCECs) that maintain both endothelial and some of the BBB markers (tight junctions, low rate of pinocytosis, and monoamine oxidase activity but a loss of γ-glutamyl transpeptidase activity) ().
Generalized Parsing and Term Rewriting: Semantics Driven Disambiguation (2003)

Generalized parsing technology provides the power and flexibility to attack real-world parsing applications. However, many programming languages have syntactical ambiguities that can only be solved using semantical analysis. In this paper we propose to apply the paradigm of term rewriting to filter ambiguities based on semantical information. We start with the definition of a representation of ambiguous derivations. Then we extend term rewriting with means to handle such derivations. Finally, we apply these tools to some real world examples, namely C and COBOL. The resulting architecture is simple and efficient as compared to semantic directed parsing.
Intercooler flow path for gas turbines: CFD design and experiments (1995)

The Advanced Turbine Systems (ATS) program was created by the U.S. Department of Energy to develop ultra-high efficiency, environmentally superior, and cost competitive gas turbine systems for generating electricity. Intercooling or cooling of air between compressor stages is a feature under consideration in advanced cycles for the ATS. Intercooling entails cooling of air between the low pressure (LP) and high pressure (BP) compressor sections of the gas turbine. Lower air temperature entering the HP compressor decreases the air volume flow rate and hence, the compression work. Intercooling also lowers temperature at the HP discharge, thus allowing for more effective use of cooling air in the hot gas flow path. The thermodynamic analyses of gas turbine cycles with modifications such as intercooling, recuperating, and reheating have shown that intercooling is important to achieving high efficiency gas turbines. The gas turbine industry has considerable interest in adopting intercooling to advanced gas turbines of different capacities. This observation is reinforced by the US Navys Intercooled-Recuperative (ICR) gas turbine development program to power the surface ships. In an intercooler system, the air exiting the LP compressor must be decelerated to provide the necessary residence time in the heat exchanger. The cooler air must subsequently be accelerated towards the inlet of the HP compressor. The circumferential flow nonuniformities inevitably introduced by the heat exchanger, if not isolated, could lead to rotating stall in the compressors, and reduce the overall system performance and efficiency. Also, the pressure losses in the intercooler flow path adversely affect the system efficiency and hence, must be minimized. Thus, implementing intercooling requires fluid dynamically efficient flow path with minimum flow nonuniformities and consequent pressure losses.