gebhart/patrepeval huggingface dataset:
Modulation of Intestinal Muscle Contraction by Interleukin-9 (IL-9) or IL-9 Neutralization: Correlation with Worm Expulsion in Murine Nematode Infections (2003)

Immune responses associated with intestinal nematode infections are characterized by the activation of T-helper 2 (Th2) cells. Previous studies demonstrated that during Trichinella spiralis infection, Th2 cells contribute to the development of intestinal muscle hypercontractility and to worm eviction from the gut, in part through signal transducer and activator of transcription factor 6 (Stat6). Interleukin-9 (IL-9), a Th2-cell-derived cytokine, has pleiotropic activities on various cells that are not mediated through Stat6. In this study, we investigated the role of IL-9 in the generation of enteric muscle hypercontractility in mice infected with the intestinal parasite T. spiralis and the cecal parasite Trichuris muris. Treatment of mice with IL-9 enhanced infection-induced jejunal muscle hypercontractility and accelerated worm expulsion in T. spiralis infection. These effects were associated with an up-regulation of IL-4 and IL-13 production from in vitro-stimulated spleen cells. In addition, increases in the level of intestinal goblet cells and in the level of mouse mucosal mast cell protease 1 (MMCP-1) in serum were observed in infected mice following IL-9 administration. However, the neutralization of IL-9 by anti-IL-9 vaccination or by anti-IL-9 antibody had no significant effect on worm expulsion or muscle contraction in T. spiralis-infected mice. In contrast, the neutralization of IL-9 significantly attenuated T. muris infection-induced colonic muscle hypercontractility and inhibited worm expulsion. The attenuated expulsion of the parasite by IL-9 neutralization was not accompanied by changes in goblet cell hyperplasia or the MMCP-1 level. These findings suggest that IL-9 contributes to intestinal muscle function and to host protective immunity and that its importance and contribution may differ depending on the type of nematode infection.
RTL emulation (1996)

Article Free Access Share on RTL emulation: the next leap in system verification Authors: Sanjay Sawant View Profile , Paul Giordano View Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996Pages 233–235https://doi.org/10.1145/240518.240561Published:01 June 1996Publication History 3citation520DownloadsMetricsTotal Citations3Total Downloads520Last 12 Months163Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Detection of 17p loss in gastric carcinoma using polymerase chain reaction. (1995)

The polymerase chain reaction and silver staining of DNA seemed to be a simple and excellent method for the evaluation of chromosomal allelic loss. The 17p LOH was frequently found in gastric carcinoma, but specific association with conventional clinicopathologic parameters was not found.
Compact and stable temporally magnified tomography using a phase-locked broadband source (2016)

The temporally magnified tomography system is further improved in terms of resolution and imaging stability. We simplify the system configuration and improve the axial resolution simultaneously by utilizing a stabilized all-fiber broadband source. The highly stable spectrum of the source assisted by a phase-locked loop guarantees an improved imaging quality. In addition, the impact of the repetition-rate fluctuation of the source to the system stability is analyzed, which also applies to other temporal imaging systems. Achieving a 90-μm in-air resolution at 89-MHz A-scan rate and improved stability, we are taking one major step toward the practical application of this new optical tomographic modality.
Sporadic amyotrophic lateral sclerosis: A hypothesis of persistent (non‐lytic) enteroviral infection (2005)

Because of recently reported reverse transcriptase polymerase chain reaction evidence of enterovirus in sporadic amyotrophic lateral sclerosis (SALS) and because of newly available anti-enteroviral drugs binding enteroviral capsids, it is reasonable to re-formulate an enteroviral hypothesis of SALS using recent advances in molecular virology. Viral persistence is non-lytic and non-cytopathic infection that evades host's immune surveillance. Enteroviruses are known to cause persistent as well as lytic infection both in vitro and in vivo. Both virion as well as host factors modulate between persistent and lytic infection. Apoptosis, or programmed cell death, is a process of active non-necrotic cell death. It has complex interplay with viruses and may be either promoted or opposed by them. Apoptosis is a major factor in motor neuron death in SALS. Viral tropism is the process by which viruses select and propagate to target cells. It is controlled by capsid conformation and surface receptors on host cells. Enteroviruses have a region on their capsids known as the canyon which docks on such receptors. Docking induces conformational changes of the capsid and genome release. Poliovirus, tropic for motor neurons, docks on the poliovirus receptor, about which much is known. The virus penetrates the motor system focally after crossing either the blood-muscle or the blood-brain barriers. It propagates bidirectionally along axons and synapses to contiguous motor neurons, upper as well as lower, which sequester infection and create avenues for spread over long distances. If chronic and persistent rather than acute and lytic, such viruses trafficking in a finite system of non-dividing cells and inducing apoptosis would cause cell death that summates linearly rather than exponentially. Taken together, these explain signature clinical features of SALS - focal onset weakness, contiguous or regional spread of weakness, confinement to upper and lower motor neurons, and linear rates of progression. The hypothesis predicts the following testable investigations: 1) viral detection may be possible by applying amplification technology to optimally acquired nervous tissue processed by laser microdissection; 2) genetic susceptibility factors such as cell surface receptor polymorphisms may combine with sporadic exposure and chance penetration of the motor system in SALS; 3) a transgenic animal model might be created by inserting such genetic factors into an animal host and inoculating intramuscularly rather than intracerebrally biochemical fractions of SALS motor neurons at vulnerable periods in the developmental life cycle of the transgenic host; and 4) continual long-term administration of anti-enteroviral agents called capsid-binding compounds which stabilize capsids and prevent genome release might be efficacious.
hBfl-1/hNOXA Interaction Studies Provide New Insights on the Role of Bfl-1 in Cancer Cell Resistance and for the Design of Novel Anticancer Agents (2016)

Upregulation of antiapoptotic Bcl-2 proteins in certain tumors confers cancer cell resistance to chemotherapy or radiations. Members of the antiapoptotic Bcl-2 proteins, including Bcl-2, Mcl-1, Bcl-xL, Bcl-w, and Bfl-1, inhibit apoptosis by selectively binding to conserved α-helical regions, named BH3 domains, of pro-apoptotic proteins such as Bim, tBid, Bad, or NOXA. Five antiapoptotic proteins have been identified that interact with various selectivity with BH3 containing pro-apoptotic counterparts. Cancer cells present various and variable levels of these proteins, making the design of effective apoptosis based therapeutics challenging. Recently, BH3 profiling was introduced as a method to classify cancer cells based on their ability to resist apoptosis following exposure to selected BH3 peptides. However, these studies were based on binding affinities measured with model BH3 peptides and Bcl-2-proteins taken from mouse sequences. While the majority of these interactions are conserved between mice and humans, we found surprisingly that human NOXA binds to human Bfl-1 potently and covalently via conserved Cys residues, with over 2 orders of magnitude increased affinity over hMcl-1. Our data suggest that some assumptions of the original BH3 profiling need to be revisited and that perhaps further targeting efforts should be redirected toward Bfl-1, for which no suitable specific inhibitors or pharmacological tools have been reported. In this regard, we also describe the initial design and characterizations of novel covalent BH3-based agents that potently target Bfl-1. These molecules could provide a novel platform on which to design effective Bfl-1 targeting therapeutics.
Subcellular localization and sequence of sea urchin kinesin heavy chain: evidence for its association with membranes in the mitotic apparatus and interphase cytoplasm [published erratum appears in J Cell Biol 1991 Aug;114(4):following 863] (1991)

Kinesin was previously immunolocalized to mitotic apparatuses (MAs) of early sea urchin blastomeres (Scholey, J.M., M.E. Porter, P.M. Grissom, and J.R. McIntosh. 1985. Nature [Lond.]. 318:483-486). Here we report evidence that this MA-associated motor protein is a conventional membrane-bound kinesin, rather than a kinesin-like protein. Our evidence includes the observation that the deduced amino acid sequence of this sea urchin kinesin heavy chain is characteristic of a conventional kinesin. In addition, immunolocalizations using antibodies that distinguish kinesin from kinesin-like proteins confirm that conventional kinesin is concentrated in MAs. Finally, our immunocytochemical data further suggest that conventional kinesin is associated with membranes which accumulate in MAs and interphase asters of early sea urchin embryos, and with vesicles that are distributed in the perinuclear region of coelomocytes. Thus kinesin may function as a microtubule-based vesicle motor in some MAs, as well as in the interphase cytoplasm.
Selective Vapor Sorption by Polymers and Cavitands on Acoustic Wave Sensors:  Is This Molecular Recognition? (1996)

Selectivity patterns for the sorption of organic vapors from the gas phase into cavitand monolayers on acoustic wave sensors are very similar to those seen for sorption of the same vapors by amorphous polymers, demonstrating that the vapor/cavitand selectivity patterns are determined primarily by solubility interactions. The amorphous polymers serve as controls demonstrating that the three-dimensional structure of a cavitand layer is not primarily responsible for the selectivity observed. Binding and selectivity in the examples cited are governed primarily by general dispersion interactions and not by specific oriented interactions that could lead to molecular recognition.
Blood flow cooling and ultrasonic lesion formation (1996)

This article examines lesion formation using focused ultrasound and demonstrates how blood flow may affect lesion dimensions using a theoretical model. The effects of blood flow on temperature distributions during ultrasonic lesioning are examined for both regional cooling by the microvasculature and localized cooling due to thermally significant vessels. Regional cooling was critically assessed using two models: the Pennes bioheat transfer equation and the scalar effective thermal conductivity equation. Localized cooling was modeled by adding an advective term in the heat diffusion equation in regions enclosed by thermally significant vessels. A finite difference approach was used to solve the basic equations of heat transfer in perfused tissues in cylindrical coordinates. The extent of the lesioned tissue was determined by the accumulated thermal dose at each location. The size of the lesion was then calculated from the boundaries of the thermal isodose curves generated by the simulations. The results were compared to published in vivo lesion data in rat liver. It was shown that even for short ultrasound exposure times (approximately 8 s), blood flow may play an important role in the thermal dose distribution.
Control of β-Cell Differentiation by the Pancreatic Mesenchyme (2007)

The importance of mesenchymal-epithelial interactions for normal development of the pancreas was recognized in the early 1960s, and mesenchymal signals have been shown to control the proliferation of early pancreatic progenitor cells. The mechanisms by which the mesenchyme coordinates cell proliferation and differentiation to produce the normal number of differentiated pancreatic cells are not fully understood. Here, we demonstrate that the mesenchyme positively controls the final number of beta-cells that develop from early pancreatic progenitor cells. In vitro, the number of beta-cells that developed from rat embryonic pancreatic epithelia was larger in cultures with mesenchyme than without mesenchyme. The effect of mesenchyme was not due to an increase in beta-cell proliferation but was due to increased proliferation of early pancreatic duodenal homeobox-1 (PDX1)-positive progenitor cells, as confirmed by bromodeoxyuridine incorporation. Consequently, the window during which early PDX1(+) pancreatic progenitor cells differentiated into endocrine progenitor cells expressing Ngn3 was extended. Fibroblast growth factor 10 mimicked mesenchyme effects on proliferation of early PDX1(+) progenitor cells and induction of Ngn3 expression. Taken together, our results indicate that expansion of early PDX1(+) pancreatic progenitor cells represents a way to increase the final number of beta-cells developing from early embryonic pancreas.
Indoor localization without infrastructure using the acoustic background spectrum (2011)

We introduce a new technique for determining a mobile phone's indoor location even when Wi-Fi infrastructure is unavailable or sparse. Our technique is based on a new ambient sound fingerprint called the Acoustic Background Spectrum (ABS). An ABS serves well as a room fingerprint because it is compact, easily computed, robust to transient sounds, and surprisingly distinctive. As with other fingerprint-based localization techniques, location is determined by measuring the current fingerprint and then choosing the "closest" fingerprint from a database. An experiment involving 33 rooms yielded 69% correct fingerprint matches meaning that, in the majority of observations, the fingerprint was closer to a previous visit's fingerprint than to any fingerprints from the other 32 rooms. An implementation of ABS-localization called Batphone is publicly available for Apple iPhones. We used Batphone to show the benefit of using ABS-localization together with a commercial Wi-Fi-based localization method. In this second experiment, adding ABS improved room-level localization accuracy from 30% (Wi-Fi only) to 69% (Wi-Fi and ABS). While Wi-Fi-based localization has difficulty distinguishing nearby rooms, Batphone performs just as well with nearby rooms; it can distinguish pairs of adjacent rooms with 92% accuracy.
Discharge-based sources of XUV-X radiations: development and applications (2003)

There is an increasing use of high energy photons in many fields of research and in industry. Where large installations such as synchrotrons or dedicated laser based source facilities can provide solutions for specific needs, they are presently unable to bring convenient solutions for on-site experiments or industrial processes. Compact discharge based devices appear to be a very interesting response to the demand in many cases. They can provide high photon fluxes in a wide spectral range, from VUV to hard x-rays, covering most of the actual needs. Certainly, they still need a lot of improvement and optimization to meet the most stringent requirements. In this paper, we will present some of the recent results we obtained in that field along with new applications. Among them, we will present our report on the performance of a novel and truly compact xenon-filled fast capillary discharge system which generates radiation mostly in the EUV region (10–16 nm) developed in the framework of an EUV lithography program. We will also present results obtained in the field of hard x-ray generation with a new source capable of producing high dose pulses in quasi-continuous or burst mode at a very high frequency developed for high speed cineradiography.
Sequence-Specific Binding of DNA to Liposomes Containing Di-Alkyl Peptide Nucleic Acid (PNA) Amphiphiles (2005)

We present a method to covalently attach peptide nucleic acid (PNA) to liposomes by conjugation of PNA peptide to charged amino acids and synthetic di-alkyl lipids ("PNA amphiphile," PNAA) followed by co-extrusion with disteroylphosphatidylcholine (DSPC) and cholesterol. Attachment of four Glu residues and two ethylene oxide spacers to the PNAA was required to confer proper hydration for extrusion and presentation for DNA hybridization. The extent of DNA oligomer binding to 10-mer PNAA liposomes was assessed using capillary zone electrophoresis. Nearly all PNAs on the liposome surface are complexed with a stoichiometric amount of complementary DNA 10-mers after 3-h incubation in pH 8.0 Tris buffer. No binding to PNAA liposomes was observed using DNA 10-mers with a single mismatch. Longer DNA showed a greatly attenuated binding efficiency, likely because of electrostatic repulsion between the PNAA liposome double layer and the DNA backbone. Langmuir isotherms of PNAA:DSPC:chol monolayers indicate miscibility of these components at the compositions used for liposome preparation. PNAA liposomes preserve the high sequence-selectivity of PNAs and emerge as a useful sequence tag for highly sensitive bioanalytical devices.
Collagen Orientation and Leather Strength for Selected Mammals (2013)

Collagen is the main structural component of leather, skin, and some other applications such as medical scaffolds. All of these materials have a mechanical function, so the manner in which collagen provides them with their strength is of fundamental importance and was investigated here. This study shows that the tear strength of leather across seven species of mammals depends on the degree to which collagen fibrils are aligned in the plane of the tissue. Tear-resistant material has the fibrils contained within parallel planes with little crossover between the top and bottom surfaces. The fibril orientation is observed using small-angle X-ray scattering in leather, produced from skin, with tear strengths (normalized for thickness) of 20-110 N/mm. The orientation index, 0.420-0.633, is linearly related to tear strength such that greater alignment within the plane of the tissue results in stronger material. The statistical confidence and diversity of animals suggest that this is a fundamental determinant of strength in tissue. This insight is valuable in understanding the performance of leather and skin in biological and industrial applications.
GC Composition of the Human Genome: In Search of Isochores (2005)

The isochore theory, proposed nearly three decades ago, depicts the mammalian genome as a mosaic of long, fairly homogeneous genomic regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five distinct isochore families: L1, L2, H1, H2, and H3, with GC contents of <37%, 37%-42%, 42%-47%, 47%-52%, and >52%, respectively. In this paper, we address the question of the validity of the isochore theory through a rigorous sequence-based analysis of the human genome. Toward this end, we adopt a set of six attributes that are generally claimed to characterize isochores and statistically test their veracity against the available draft sequence of the complete human genome. By the selection criteria used in this study: distinctiveness, homogeneity, and minimal length of 300 kb, we identify 1,857 genomic segments that warrant the label "isochore." These putative isochores are nonuniformly scattered throughout the genome and cover about 41% of the human genome. We found that a four-family model of putative isochores is the most parsimonious multi-Gaussian model that can be fitted to the empirical data. These families, however, are GC poor, with mean GC contents of 35%, 38%, 41%, and 48% and do not resemble the five isochore families in the literature. Moreover, due to large overlaps among the families, it is impossible to classify genomic segments into isochore families reliably, according to compositional properties alone. These findings undermine the utility of the isochore theory and seem to indicate that the theory may have reached the limits of its usefulness as a description of genomic compositional structures.
A Modified Borresen’s Coarse-Mesh Solution to the LRA-BWR Benchmark Problem (1983)

Computational accuracy of the modified Borresen's coarse-mesh diffusion theory scheme is investigated with the steady-state solutions of the two- and three-dimensional LRA-BWR bench-mark problem. By comparing the numerical results available for the critical eigenvalue and power distribution of the LRA-BWR, it is shown that the modified scheme is capable of predicting the power distribution of the multi-dimensional BWR problem with an improved accuracy.
Host response and outcome of sepsis in the critically ill (2017)

Sepsis is a major cause of morbidity and mortality worldwide. It is a life-threatening condition that is characterized by a dysregulated host response to infection, leading to tissue and organ damage. Important features of the septic host response include activation of the cytokine network, the vascular endothelium and the coagulation system. This thesis describes studies with specific research questions within the MARS cohort, a large prospective observational study conducted in the intensive care units of the Academic Medical Center in Amsterdam and the University Medical Center Utrecht. We studied several “external” and host factors that might influence sepsis outcome and the accompanying host response, particularly chronic medication (antiplatelet agents, calcium channel blockers, statins) and comorbidity (HIV infection). None of these factors had a major impact on the host response to sepsis, while only the use of calcium channel blockers was associated with an altered (improved) outcome. In addition, we examined the influence of hypothermia, an acute manifestation of severe infection, on sepsis outcome and the host response, revealing an independent association between hypothermia and mortality without evidence for an altered immune response. Finally, the research presented in this thesis provides evidence that a disturbed host response towards a more hyperinflammatory phenotype renders sepsis patients more vulnerable to develop a secondary infection while on the intensive care unit.