gebhart/patrepeval huggingface dataset:
Streptozotocin‐diabetes attenuates α2‐adrenoceptor agonist‐induced delay in small intestinal transit in mice* (1990)

1. The effect of alpha 2-adrenoceptor agonists on gastrointestinal motility was assessed in normoglycaemic and streptozotocin-diabetic mice. 2. The alpha 2-adrenoceptor agonists used were: clonidine (0.1, 0.3 and 1 mg kg-1, azepexole (10, 20 and 40 mg kg-1), tizanidine (1, 3 and 10 mg kg-1) and ST-91 (10, 20 and 30 mg kg-1). 3. Acute hyperglycaemia was induced by D-(+)-glucose (5 g kg-1) and chronic hyperglycaemia by streptozotocin (200 mg kg-1) injection. 4. The gut motility was quantitated using the charcoal meal test. 5. The results indicate that in normoglycaemic and acutely hyperglycaemic mice, all of the alpha 2-adrenoceptor agonists used produced significant inhibition of meal transit. 6. However, in streptozotocin-diabetic mice, the anti-transit effect of alpha 2-adrenoceptor agonists was attenuated. 7. Since streptozotocin-induced diabetes but not acute hyperglycaemia was associated with the attenuation of anti-transit effect, elevated blood sugar is not the mechanism for the observed effect. 8. As with groups treated with clonidine, azepexole or tizanidine, the anti-transit effect of a peripherally acting alpha 2-adrenoceptor agonist, ST-91, was attenuated in streptozotocin-diabetic mice. This suggests the involvement of peripheral mechanism(s) in attenuating the anti-transit effect of alpha 2-adrenoceptor agonists. 9. These results identify the need for critical evaluation of the role and efficacy of alpha 2-adrenoceptor agonists in the therapeutic management of diabetic diarrhoea.
Calcium Regulates S-Nitrosylation, Denitrosylation, and Activity of Tissue Transglutaminase (2001)

Nitric oxide (NO) and related molecules play important roles in vascular biology. NO modifies proteins through nitrosylation of free cysteine residues, and such modifications are important in mediating NO's biologic activity. Tissue transglutaminase (tTG) is a sulfhydryl rich protein that is expressed by endothelial cells and secreted into the extracellular matrix (ECM) where it is bound to fibronectin. Tissue TG exhibits a Ca(2+)-dependent transglutaminase activity (TGase) that cross-links proteins involved in wound healing, tissue remodeling, and ECM stabilization. Since tTG is in proximity to sites of NO production, has 18 free cysteine residues, and utilizes a cysteine for catalysis, we investigated the factors that regulated NO binding and tTG activity. We report that TGase activity is regulated by NO through a unique Ca(2+)-dependent mechanism. Tissue TG can be poly-S-nitrosylated by the NO carrier, S-nitrosocysteine (CysNO). In the absence of Ca(2+), up to eight cysteines were nitrosylated without modifying TGase activity. In the presence of Ca(2+), up to 15 cysteines were found to be nitrosylated and this modification resulted in an inhibition of TGase activity. The addition of Ca(2+) to nitrosylated tTG was able to trigger the release of NO groups (i.e. denitrosylation). tTG nitrosylated in the absence of Ca(2+) was 6-fold more susceptible to inhibition by Mg-GTP. When endothelial cells in culture were incubated with tTG and stimulated to produce NO, the exogenous tTG was S-nitrosylated. Furthermore, S-nitrosylated tTG inhibited platelet aggregation induced by ADP. In conclusion, we provide evidence that Ca(2+) regulates the S-nitrosylation and denitrosylation of tTG and thereby TGase activity. These data suggest a novel allosteric role for Ca(2+) in regulating the inhibition of tTG by NO and a novel function for tTG in dispensing NO bioactivity.
15-keto-prostaglandin E2 activates host peroxisome proliferator-activated receptor gamma (PPAR-γ) to promote Cryptococcus neoformans growth during infection (2019)

Cryptococcus neoformans is one of the leading causes of invasive fungal infection in humans worldwide. C. neoformans uses macrophages as a proliferative niche to increase infective burden and avoid immune surveillance. However, the specific mechanisms by which C. neoformans manipulates host immunity to promote its growth during infection remain ill-defined. Here we demonstrate that eicosanoid lipid mediators manipulated and/or produced by C. neoformans play a key role in regulating pathogenesis. C. neoformans is known to secrete several eicosanoids that are highly similar to those found in vertebrate hosts. Using eicosanoid deficient cryptococcal mutants Δplb1 and Δlac1, we demonstrate that prostaglandin E2 is required by C. neoformans for proliferation within macrophages and in vivo during infection. Genetic and pharmacological disruption of host PGE2 synthesis is not required for promotion of cryptococcal growth by eicosanoid production. We find that PGE2 must be dehydrogenated into 15-keto-PGE2 to promote fungal growth, a finding that implicated the host nuclear receptor PPAR-γ. C. neoformans infection of macrophages activates host PPAR-γ and its inhibition is sufficient to abrogate the effect of 15-keto-PGE2 in promoting fungal growth during infection. Thus, we describe the first mechanism of reliance on pathogen-derived eicosanoids in fungal pathogenesis and the specific role of 15-keto-PGE2 and host PPAR-γ in cryptococcosis.
Universal cervical‐length screening to prevent preterm birth: a cost‐effectiveness analysis (2010)

In low-risk pregnancies, universal transvaginal cervical length ultrasound screening appears to be a cost-effective strategy under a wide range of clinical circumstances (varied preterm birth rates, predictive values of a shortened cervix and costs).
Model-mediated Telemanipulation (2008)

This paper presents a user-centered, model-mediated approach to bilateral telemanipulation under large communication delays. Assuming that the environment is only slowly or infrequently changing, it mitigates user perception difficulties and allows stable motion and force interactions with the remote environment. Rather than directly sending slave sensory data to the user, the method abstracts the data to form a very simple model of the environment. The model is transmitted to the master, where it is haptically rendered for user feedback without any lag. In return, the slave only executes force or motion commands consistent with the model. This effectively mediates the master—slave interaction. Particular attention is placed on the system behavior as it adjusts to unexpected environment interactions and as the model updates. The basic principles of the approach are demonstrated on a simple one degree-of-freedom telerobotic system operating with four seconds of round-trip delay.
Optimum open eye equalizer design for nonminimum phase channels (1998)

This paper contains results on the design of optimum equalizers to eliminate intersymbol interference (ISI) in linear nonminimum phase channels conveying binary signals. The optimization is with respect to an open eye condition with a delay d. For causal stable channels with n/sub c/ nonminimum phase zeros, we argue that this problem requires only the consideration of the n/sub c/-tap FIR modified channel that has all the n/sub c/ nonminimum phase zeros of the original channel. We show that if this modified channel can be equalized to yield an equalized system that is open eye with delay d, then the optimizing equalizer is, in fact, (d-n/sub c/)-tap FIR with all zeros outside the unit circle. We also give a simple necessary and sufficient condition to determine if for a particular d, a given channel can be equalized to achieve an equalized response that is open eye with delay d.
Supplemental Table 1 from MHC Class I Loss Is a Frequent Mechanism of Immune Escape in Papillary Thyroid Cancer That Is Reversed by Interferon and Selumetinib Treatment <i>In Vitro</i> (2023)

&lt;p&gt;Supplemental Table 1. &lt;b&gt;Primer sequences for qRT-PCR.&lt;/b&gt; Forward and reverse primer sequences are shown for each gene examined, in 5' to 3' direction.&lt;/p&gt;
Analysis oftheDynamicCharacteristics ofaPowerSemiconductor Module, Considering theInfluence ofElectromagnetic Coupling Between Wiring (2005)

Thedynamic characteristics ofpowersemiconductor modules wereinvestigated. Theswitching behavior ofpowermodules isstrongly influenced byelectromagnetic coupling. Therefore todesign highly reliable powermodules, itisimportant toestablish amethodofanalyzing their dynamic characteristics whichconsiders these electromagnetic phenomena. Theparasitic parameters ofwiring inapowersemiconductor module weredetermined using three-dimensional electromagnetic field analysis andtheir dynamic characteristics wereanalyzed using these parameters. Theanalysis results showed goodagreement withtheexperimental results.
Channel Characterization for Wideband Large-Scale Antenna Systems Based on a Low-Complexity Maximum Likelihood Estimator (2018)

Wideband large-scale array systems operating at millimeter-wave bands are expected to play a key role in future communication systems. It is recommended by standardization groups to use spherical-wave models (SWMs) to characterize the channel in near-field cases because of the large array apertures and the small cell size. However, this feature is not widely reflected in channel models yet, mainly due to the high computational complexity of SWMs compared to that of the conventional plane-wave model (PWM), especially when ultrawideband signals are considered. In this paper, a maximum likelihood estimator of low computational complexity is implemented with an SWM for ultrawideband signals. The measurement data obtained from an ultrawideband large-scale antenna array system at 28-30 GHz are processed with the proposed algorithm. The power azimuth-delay profiles estimated from the SWM and the PWM are compared to those obtained from rotational horn antenna measurement, respectively. It shows that the multipath components (MPCs) are well-estimated with the proposed algorithm, and significant improvement in estimation performance is achieved with the SWM compared to the PWM. Moreover, the physical interpretation of the estimated MPCs is also given along with the estimated scatterers.
A block-Alamouti scheme for filter bank based multicarrier transmission (2010)

Filter bank based multicarrier (FBMC) is an interesting alternative to OFDM especially for spectrally agile communication waveform generation and for cognitive radio scenarios. For enhanced link performance and robustness, most of the common multi-antenna schemes can be combined with FBMC equally well as with OFDM. However, one significant shortcoming of FBMC is the difficulty of combining it with the famous transmit diversity scheme of Alamouti coding. In this paper, we present a block-wise Alamouti scheme for FBMC and test its performance.
Toward the Development of an Antidisease, Transmission‐Blocking Intranasal Vaccine for Group A Streptococcus (2005)

Infection with group A streptococcus (GAS) may result in a number of clinical conditions, including the potentially life-threatening postinfectious sequelae of rheumatic fever and rheumatic heart disease. As part of the search for a vaccine to prevent GAS infection, a conformationally constrained and minimally conserved peptide, J14, from the M protein of GAS has been defined. In the present study, J14 was formulated with bacterial outer membrane proteins (proteosomes) and then intranasally administered to outbred mice without additional adjuvant. Such immunization led to high titers of J14-specific serum immunoglobulin (Ig) G and mucosal IgA. After upper respiratory tract GAS challenge, immunized mice demonstrated increased survival and reduced GAS colonization of the throat.
Abstract 21: Stiffness-Dependent Notch1 Activation Regulates Cardiogenic Differentiation of Cardiac Progenitor Cells (2012)

Cardiac progenitor cells (CPCs) are multipotent, self-renewing cells that can regenerate the myocardium and improve cardiac function in animal models of MI by cardiogenic differentiation. However, limited survival of stem/progenitor cells, myocardial scarring and fibrosis inhibit cardiac regeneration. Notch signaling promotes early cardiac development, cardiomyocyte survival and cardiac gene expression in circulating endothelial progenitor cells, mesenchymal stem cells and CPCs. As misregulation of Notch signaling during development is lethal due to cardiovascular defects, activating this critical pathway during cell transplantation could improve the efficacy of stem cell therapy. We investigated whether self-assembling peptide nanofiber hydrogels can be used to activate Notch1 signaling. The 16 amino acid self-assembling scaffold (RAD) was modified with a 20 amino acid peptide mimicking the active site of Notch1 ligand, Jagged1 (RJAG) or with the corresponding scrambled peptide (RSCR). To determine whether scaffold stiffness regulates Notch1 activation, CHO cells with Notch1 responsive YFP expression were cultured in scaffolds of 1-3% w/v in presence of RSCR or RJAG at a 1:10 ligand: scaffold ratio in 3D. Presence of the RJAG peptide (p&lt;0.01) and % concentration of the scaffold (p&lt;0.01) increased Notch1 activation significantly (n=5) indicating that RJAG mediated Notch1 activation in 3D is scaffold stiffness-dependent. Therefore, CPCs were cultured within 3D scaffolds (1-3% w/v; empty, scaffold +RJAG or RSCR) and cardiogenic gene expression was determined by qPCR. An increase in expression of early endothelial (Flk1, Flt1, vWF) and smooth muscle (sm22α, sm αactin) genes was observed in CPCs cultured in 3D scaffolds containing RJAG but not when cultured in 2D. These data show that Notch1 activation is dependent on ligand density and scaffold stiffness. Delivery of CPCs in JAG1 containing self-assembling scaffolds could be used to enhance therapeutic angiogenesis and improve cardiac function following myocardial infarction.
EASY HANDLING AND INJECTABLE CEMENT FOAM FOR BONE TISSUE ENGINEERING (2021)

International audience
High Production of Ergothioneine in Escherichia coli using the Sulfoxide Synthase from Methylobacterium strains (2020)

We previously constructed a heterologous production system for ergothioneine (ERG) in <i>Escherichia coli</i> using five ERG biosynthesis genes (<i>egtABCDE</i>) from <i>Mycobacterium smegmatis</i>. However, significant amounts of hercynine (HER), an intermediate of ERG, as ERG were accumulated, suggesting that the reaction of EgtB catalyzing the attachment of γ-glutamylcysteine (γGC) to HER to yield hercynyl-γ-glutamylcysteine sulfoxide was a bottleneck. In this study, we searched for other EgtBs and found many <i>egtB</i> orthologs in diverse microorganisms. Among these, <i>Methylobacterium</i> strains possessed EgtBs that catalyze the direct conversion of HER into hercynylcysteine sulfoxide with l-cysteine (l-Cys) as a sulfur donor, in a manner similar to those of acidobacterial CthEgtB and fungal Egt1. An <i>in vitro</i> study with recombinant EgtBs from <i>Methylobacterium brachiatum</i> and <i>Methylobacterium pseudosasicola</i> clearly showed that both enzymes accepted l-Cys but not γGC. We reconstituted the ERG production system in <i>E. coli</i> with <i>egtB</i> from <i>M. pseudosasicola</i>; ERG productivity reached 657 mg L<sup>-1</sup>.
Protein Stabilization by Removal of Unsatisfied Polar Groups:  Computational Approaches and Experimental Tests (1996)

The role of polar and charged side chains in partially buried protein environments has been probed in a variant of Arc repressor (MYL) in which hydrophobic interactions between Met31, Tyr36, and Leu40 replace the wild-type salt-bridge interactions between Arg31, Glu36, and Arg40. In the absence of this salt-bridge triad, three additional side chains were identified by continuum electrostatic calculations as incurring larger desolvation penalties during folding than were recovered in favorable electrostatic interactions in the folded state. These side chains (Asn29, Ser44, and Glu48) were mutated singly and collectively to alanine in the MYL background, and the thermodynamic stabilities of the resulting mutant proteins were found to be increased by 0.1 to 1.3 kcal/mol of dimer. All of the mutants displayed cooperative thermal melts and appeared to have well-packed hydrophobic cores by near-UV circular dichroism spectroscopy, indicating that conformational specificity is maintained. The Arc variant (MYL-NA29/SA44/EA48) in which the entire six-residue polar network is replaced by nonpolar groups is 5.1 kcal/mol of dimer more stable than wild type, indicating that the strategy of replacing buried or partially buried charged and polar side chains with hydrophobic residues can lead to substantial stabilization.
A Nodal- and ALK4-independent signaling pathway activated by Cripto-1 through Glypican-1 and c-Src. (2003)

Human Cripto-1 (CR-1) is a member of the epidermal growth factor-Cripto FRL1 Cryptic family that has been shown to function as a coreceptor with the type I Activin serine-threonine kinase receptor ALK4 for the transforming growth factor beta-related peptide Nodal. However, CR-1 can also activate the mitogen-activated protein kinase and Akt pathways independently of Nodal and ALK4 by an unknown mechanism. Here, we demonstrate that CR-1 specifically binds to Glypican-1, a membrane-associated heparan sulfate proteoglycan, and activates the tyrosine kinase c-Src, triggering the mitogen-activated protein kinase and Akt signaling pathways. Finally, an active Src kinase is necessary for CR-1 to induce in vitro transformation and migration in mouse mammary epithelial cells.
Rapid production of large-area, transparent and stretchable electrodes using metal nanofibers as wirelessly operated wearable heaters (2017)

A rapidly growing interest in wearable electronics has led to the development of stretchable and transparent heating films that can replace the conventional brittle and opaque heaters. Herein, we describe the rapid production of large-area, stretchable and transparent electrodes using electrospun ultra-long metal nanofibers (mNFs) and demonstrate their potential use as wirelessly operated wearable heaters. These mNF networks provide excellent optoelectronic properties (sheet resistance of ~1.3 Ω per sq with an optical transmittance of ~90%) and mechanical reliability (90% stretchability). The optoelectronic properties can be controlled by adjusting the area fraction of the mNF networks, which also enables the modulation of the power consumption of the heater. For example, the low sheet resistance of the heater presents an outstanding power efficiency of 0.65 W cm−2 (with the temperature reaching 250 °C at a low DC voltage of 4.5 V), which is ~10 times better than the properties of conventional indium tin oxide-based heaters. Furthermore, we demonstrate the wireless fine control of the temperature of the heating film using Bluetooth smart devices, which suggests substantial promise for the application of this heating film in next-generation wearable electronics. A quick method to make a large-area, stretchable and transparent electrode for wearable electronics has been developed by a team in Korea. Materials that are both transparent and conducting are useful for many optoelectronic applications. Indium tin oxide is a common choice, but it lacks the flexibility required for wearable technologies. Jang-Ung Park and co-workers from the Ulsan National Institute of Science and Technology spun long metal nanofibers to create a wearable heater that can operate wirelessly. They form a conductive random network of silver nanofibers as a random network on a flexible and stretchable substrate. The high thermal conductivity of silver means a current passing through the nanofiber can quickly attain a temperature of 250 degrees Celsius on a polyimide sheet. The stretchable and transparent, large-area electrode using electrospun, ultra-long metal nanofibers (mNFs) shows excellent optoelectronic and mechanical properties. It is mass-producible because of the roll-to-roll process and its fast production speed. The optoelectronic properties can be controlled by adjusting area fraction of mNF network. The large-area heater based on the mNF network exhibits outstanding power efficiency and mechanical reliability. The wireless operation of the wearable heater using Bluetooth is demonstrated.
An echo cancellation solution for voice control devices (2009)

This paper proposes an acoustic echo control solution for voice control devices. An important property of an acoustic echo canceller is its capability to handle double-talk and be able to operate in real time. When it is applied to intelligent voice control device with interactive conversations, it is important to suppress the speech from the device and enhance the speech of the user for speech recognition, where double-talk situation is frequently occurred. The main idea is to use a robust adaptive algorithm to handle the double-talk. In order to achieve real-time adaptation, subband processing together with a hardware accelerator implemented in an FPGA fabric surrounding a Power-PC on a Xilinx XUP V2P platform.
Sarcoma Molecular Pathological Diagnosis of FFPE Tissues without Dewaxing based on Lipidomic Profiles using SpiderMass Technology (2021)

<title>Abstract</title> <bold>Background :</bold>Formalin-fixation and paraffin-embedding (FFPE) is the worldwide gold standard for tissue preservation and routine pathology for general and cancer diagnostics. Despite robust histopathology methods, accurate diagnostic remains difficult for certain cases. Overall, the entire process is time-consuming, labor-intensive and doesn’t reach the right sensitivity and specificity. Lipids are central players in cancer, but they are not routinely used in diagnostics because of the sample processing which limits their detection, and lipid analysis directly from unprocessed FFPE tissues has never been reported. <bold>Methods</bold> :We present a new method for cancer diagnostics based on tissue-lipidomic signatures through rapid screening of FFPE without dewaxing using Water-Assisted Laser Desorption Ionization Mass Spectrometry (WALDI-MS) and deep-learning. <bold>Results</bold> :We show on a cohort of canine and human sarcoma tissues that classification for sarcoma sub-typing is possible and enables diagnosing blind samples in less than five minutes, with over 95% probability to discriminate specific subtypes. <bold>Conclusion</bold>: We have revealed the possibility to create a rapid diagnostic platform to screen clinical FFPE tissues with minimal sample preparation for molecular pathology.
Peripheral Visual Field Thresholds using Humphrey Field Analyzer Program 60–4 in Normal Eyes (2011)

The areas that demonstrate the highest between-subject consistency and thus might best reveal peripheral visual abnormalities with HFA 60-4 are the inner ring, inferior and temporal zone of the middle ring, and temporal zone of the outer ring. These observations may be useful for developing strategies to detect peripheral field loss at an early stage when central vision is not yet affected.
Welcome to DARK2 (2003)

Dept of Information Technology| www.it.uu.se © Erik Hagersten| http://user.it.uu.se/~eh 2 DARK2 2006 Literature Computer Architecture A Quantitative Approach (3rd or 4th edition) Hennesey & Pattersson Lecturer Erik Hagersten gives most lectures and is responsible for the course Frederic Haziza is responsible for the laborations and the hand-ins Jakob Carlstrom guest lecturer in network processors Sverker Holmgren guest lecturer in parallel programming