gebhart/patrepeval huggingface dataset:
Tsetse Fly Saliva Accelerates the Onset ofTrypanosoma bruceiInfection in a Mouse Model Associated with a Reduced Host Inflammatory Response (2006)

Tsetse flies (Glossina sp.) are the vectors that transmit African trypanosomes, protozoan parasites that cause human sleeping sickness and veterinary infections in the African continent. These blood-feeding dipteran insects deposit saliva at the feeding site that enables the blood-feeding process. Here we demonstrate that tsetse fly saliva also accelerates the onset of a Trypanosoma brucei infection. This effect was associated with a reduced inflammatory reaction at the site of infection initiation (reflected by a decrease of interleukin-6 [IL-6] and IL-12 mRNA) as well as lower serum concentrations of the trypanocidal cytokine tumor necrosis factor. Variant-specific surface glycoprotein-specific antibody isotypes immunoglobulin M (IgM) and IgG2a, implicated in trypanosome clearance, were not suppressed. We propose that tsetse fly saliva accelerates the onset of trypanosome infection by inhibiting local and systemic inflammatory responses involved in parasite control.
Comparative Evaluation of the Translocator Protein Radioligands 11C-DPA-713, 18F-DPA-714, and 11C-PK11195 in a Rat Model of Acute Neuroinflammation (2009)

(18)F-DPA-714 appears to be an attractive alternative to (11)C-PK11195 because of its increased bioavailability in brain tissue and its reduced nonspecific binding. Moreover, its labeling with (18)F, the preferred PET isotope for radiopharmaceutical chemistry, favors its dissemination and wide clinical use. (18)F-DPA-714 will be further evaluated in longitudinal studies of neuroinflammatory conditions such as are encountered in stroke or neurodegenerative diseases.
Verifying security patches (2014)

In this paper, we introduce a formal framework for ensuring the correctness of security patches. We discuss the issues and provide a sketch of how one could implement a system that proves (in many cases) or provides robust evidence (in other cases) that a security patch fixes a bug, and changes nothing else about the semantics of a program. We make use of an analysis of "bug surfaces" the set of inputs that trigger a bug, to give a type theoretic characterization of the non-buggy surface of a program. We thus give credence to the Langsec notion that security flaws are often about input handling, and show how formal patch and bug analysis can be used to define a more correct input type for a program.
Polarized electronic absorption spectra of (n-Bu4N)2[Pt(CN)4] at 5 K (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolarized electronic absorption spectra of (n-Bu4N)2[Pt(CN)4] at 5 KCharles D. Cowman and Harry B. GrayCite this: Inorg. Chem. 1976, 15, 11, 2823–2824Publication Date (Print):November 1, 1976Publication History Published online1 May 2002Published inissue 1 November 1976https://pubs.acs.org/doi/10.1021/ic50165a051https://doi.org/10.1021/ic50165a051research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Three-dimensional branch waveguide fabricated by mask-transfer self-written method (2011)

Novel three-dimensional (3D) branch waveguide fabricated by mask-transfer self-written (MTSW) method was proposed and the optical characteristics of the fabricated V-branch waveguide are demonstrated. By controlling the irradiating angle of UV-light through the mask aperture, it is possible to fabricate V-branch waveguide having a certain branch angle.
Akt Activity Negatively Regulates Phosphorylation of AMP-activated Protein Kinase in the Heart (2003)

In the heart, insulin stimulates a variety of kinase cascades and controls glucose utilization. Because insulin is able to activate Akt and inactivate AMP-activated protein kinase (AMPK) in the heart, we hypothesized that Akt can regulate the activity of AMPK. To address the potential existence of this novel signaling pathway, we used a number of experimental protocols to activate Akt in cardiac myocytes and monitored the activation status of AMPK. Mouse hearts perfused in the presence of insulin demonstrated accelerated glycolysis and glucose oxidation rates as compared with non-insulin-perfused hearts. In addition, insulin caused an increase in Akt phosphorylation and a decrease in AMPK phosphorylation at its major regulatory site (threonine 172 of the alpha catalytic subunit). Transgenic mice overexpressing a constitutively active mutant form of Akt1 displayed decreased phosphorylation of cardiac alpha-AMPK. Isolated neonatal cardiac myocytes infected with an adenovirus expressing constitutively active mutant forms of either Akt1 or Akt2 also suppressed AMPK phosphorylation. However, Akt-dependent depression of alpha-AMPK phosphorylation could be overcome in the presence of the AMPK activator, metformin, suggesting that an override mechanism exists that can restore AMPK activity. Taken together, this study suggests that there is cross-talk between the AMPK and Akt pathways and that Akt activation can lead to decreased AMPK activity. In addition, our data suggest that the ability of insulin to inhibit AMPK may be controlled via an Akt-mediated mechanism.
3D thin film microstructures for space microrobots (1995)

Micromechanisms of locomotion and a manipulator with an external skeleton like the structure of an insect are proposed. Several micro-sized models were built on silicon wafers by using polysilicon for rigid plates and polyimide for elastic joints. Due to scale effects, friction in micromechanical components is dominant as compared to the inertial forces because friction is proportional to L(exp 2) while mass is proportional to L(exp 3). Therefore, to ensure efficient motion, rotational joint that exhibits rubbing should be avoided. In this paper, paper models of a robot leg and a micro-manipulator are presented to show structures with external skeletons and elastic joints. Then the large scale implementation using plastic plates, springs, and solenoids is demonstrated. Since the assembly technique is based on paper folding, it is compatible with thin film micro-fabrication and integrated circuit (IC) planar processes. Finally, several micromechanisms were fabricated on silicon wafers to demonstrate the feasibility of building a 3D microstructure from a single planar structure that can be used for space microrobots.
ChemInform Abstract: REACTION OF 4‐ACETOXY‐1,4‐BENZOXAZIN‐3‐ONE WITH AMINO ACID DERIVATIVES (1984)

Abstract Das N‐Acetoxy‐benzoxazinon (Ic) reagiert in unterschiedlicher Weise mit den Boa‐Aminosäureestern (II), (V) bzw. (VII) zu den Verbindungen (III) und (IV) bzw. (VI) bzw. (VIII).
Correlation between immunity and clinical outlook in a phase I trial of intranodal injection of a plasmid vaccine in patients with stage IV melanoma (2007)

A137 Purpose: Nineteen patients with stage IV melanoma were enrolled in a dose ranging, open label phase I trial of a DNA plasmid vaccine pSEM. The expression vector encompasses T cell epitopes from the differentiation antigen Melan-A/MART-1, including the major epitope 26-35. The endpoints of the trial were safety, tolerability and immune response to Melan-A/MART-1 measured by tetramer assays. Procedure: Patients received multiple infusions of the vaccine four times, every two weeks over 96 hours each in groin lymph nodes. The vaccine doses were 500, 1000 and 1500 micrograms of DNA per infusion. Disease evaluation was performed at 8 weeks after treatment initiation and specific immunity at baseline and at various intervals, by tetramer / CD8 analysis. Immune competence was evaluated by an ex vivo mitogen / ELISPOT test. Results: The vaccine was well tolerated, with only grade I/II toxicity observed and no dose limiting toxicity. Immune responses defined prospectively were seen in 4/19 patients, whereas 5 additonal patients had evidence of pre-existing immunity to Melan-A/MART-1. There was a significant correlation between time to progression (TTP) and Melan-A/MART-1 immunity (pre-existing or induced) in this trial (p=0.029). There was no correlation between TTP and immune competence assayed by ex vivo polyclonal stimulation of peripheral blood mononuclear cells. In addition, there were no objective clinical responses observed in this trial. Conclusion: The DNA plasmid vaccine pSEM was well tolerated when administered intranodally to patients with stage IV melanoma and demonstrated immunogenicity in a select group of patients. There was a significant correlation between TTP and Melan-A / MART-1 immunity, whether pre-existing or induced, that supports the potential therapeutic value of Melan-A / MART-1 and future attempts to improve on methodologies to immunize against it.
Toward Polymorphic Internet of Things Receivers Through Real-Time Waveform-Level Deep Learning (2022)

Wireless systems such as the Internet of Things (IoT) are changing the way we interact with the cyber and the physical world. As IoT systems become more and more pervasive, it is imperative to design wireless protocols that can effectively and efficiently support IoT devices and operations. On the other hand, today's IoT wireless systems are based on inflexible designs, which makes them inefficient and prone to a variety of wireless attacks. In this paper, we introduce the new notion of a deep learning-based polymorphic IoT receiver, able to reconfigure its waveform demodulation strategy itself in real time, based on the inferred waveform parameters. Our key innovation is the introduction of a novel embedded deep learning architecture that enables the solution of waveform inference problems, which is then integrated into a generalized hardware/software architecture with radio components and signal processing. Our polymorphic wireless receiver is prototyped on a custom-made software-defined radio platform. We show through extensive over-the-air experiments that the system achieves throughput within 87% of a perfect-knowledge Oracle system, thus demonstrating for the first time that polymorphic receivers are feasible.
MINING PATENTS USING MOLECULAR SIMILARITY SEARCH (2006)

Text analytics is becoming an increasingly important tool used in biomedical research. While advances continue to be made in the core algorithms for entity identification and relation extraction, a need for practical applications of these technologies arises. We developed a system that allows users to explore the US Patent corpus using molecular information. The core of our system contains three main technologies: A high performing chemical annotator which identifies chemical terms and converts them to structures, a similarity search engine based on the emerging IUPAC International Chemical Identifier (InChI) standard, and a set of on demand data mining tools. By leveraging this technology we were able to rapidly identify and index 3,623,248 unique chemical structures from 4,375,036 US Patents and Patent Applications. Using this system a user may go to a web page, draw a molecule, search for related Intellectual Property (IP) and analyze the results. Our results prove that this is a far more effective way for identifying IP than traditional keyword based approaches.
Supply-Power-Constrained Cable Capacity Maximization Using Multi-Layer Neural Networks (2020)

We experimentally solve the problem of maximizing capacity under a total supply power constraint in a massively parallel submarine cable context, i.e., for a spatially uncoupled system in which fiber Kerr nonlinearity is not a dominant limitation. By using multi-layer neural networks trained with extensive measurement data acquired from a 12-span 744-km optical fiber link as an accurate digital twin of the true optical system, we experimentally maximize fiber capacity with respect to the transmit signal's spectral power distribution based on a gradient-descent algorithm. By observing convergence to approximately the same maximum capacity and power distribution for almost arbitrary initial conditions, we conjecture that the capacity surface is a concave function of the transmit signal power distribution. We then demonstrate that eliminating gain flattening filters (GFFs) from the optical amplifiers results in substantial capacity gains per Watt of electrical supply power compared to a conventional system that contains GFFs.
A 200 &#x00B5;A duty-cycled PLL for wireless sensor nodes (2009)

A duty-cycled PLL operating in burst mode is presented. It is an essential building block of a moderately accurate low-power frequency synthesizer suitable for use in nodes for wireless sensor networks. Once in lock, the PLL's frequency error is less than 0.1% (rms). Fabricated in a baseline 65 nm CMOS process, the PLL occupies 0.19 times 0.15 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and draws 200 muA from a 1.3-V supply when generating a 1 GHz signal with a duty cycle of 10%.
Tissue-Type Transglutaminase from Red Sea Bream (Pagrus major). Sequence Analysis of the cDNA and Functional Expression in Escherichia coli (1995)

A cDNA clone encoding a tissue-type transglutaminase (TGase) was isolated from a cDNA library prepared from the liver of red sea bream (Pagrus major). The cDNA sequence had an open reading frame coding for a protein of 695 amino acids and showed 43 % identity to the sequence of guinea pig liver TGase, revealing a relatively low overall similarity. However, the 25-amino-acid sequence containing the putative active site (Cys272) of the enzyme was completely conserved between the two species, and was also identical to the corresponding regions of human and bovine endothelial cell TGases. In addition, the critical residues (His332 and Asp355) thought to form the catalytic-center triad together with Cys272, were found in the highly conserved region. The red sea bream TGase had an extension of 11 amino acids in the C-terminal region and some differences in the N-terminal region when compared with guinea pig TGase. From the cloned cDNA, a semi-synthetic TGase gene suitable for overexpression in Escherichia coli was constructed (pTTG2-22). At a reduced temperature (28°C), E. coli cells transformed with pTTG2–22 could produce soluble TGase which exhibited catalytic activity in the presence of calcium. E. coli extracts containing the recombinant red sea bream TGase induced gelation of actomyosin solutions, accompanied by a significant increase of ɛ-(γ-glutamyl)lysine bonds, which are predominantly derived from the cross-linking of myosin heavy chains. These results indicate that this fish TGase should be useful for further analysis of TGase structure/function relationships and that it could also be employed to enhance the viscoelastic properties of proteinaceous materials.
Maggot Therapy for Venous Stasis Ulcers (1996)

<h3>REPORT OF A CASE</h3> A 74-year-old man with a history of recurrent venous stasis ulcers presented to the clinic with a 1-month history of an enlarging, erythematous, tender, right pretibial wound. He recalled no trauma. Despite bedrest and oral dicloxacillin as prescribed, the patient returned to the clinic the following week with a larger wound, now described as a central black eschar with surrounding cellulitis. He was admitted for therapy with intravenous antibiotics (piperacillin and tazobactam) and frequent bedside surgical débridement. He did not tolerate a trial of hydrotherapy because of symptomatic hypotension. Plastic surgery consultants recommended split-thickness skin grafting after wound débridement; the wound was débrided two to three times weekly, limited primarily by the patient's pain and by concerns about the great depth of the wound and the patient's poor healing ability. Between débridements, his wound was dressed with hydrocolloid pads to aid in autolysis or with a
Abstract 2917: Functional protein pathway activation mapping of the progression of normal skin to squamous cell carcinoma (2011)

Abstract In order to identify important cell signaling derangements in squamous cell carcinoma (SCC) and its precursor actinic keratosis (AK) as a means to uncover important molecular targets and further characterize this disease, we analyzed two independent tissue study sets using Reverse Phase Protein Microarrays (RPMA). Set 1 served as a pilot as well as a means to generate candidate pathway alterations that could be further validated in a second independent sample set. Study Set 1 was comprised of 4 AK, 6 advanced SCC (≥ 2 cm), 7 non-advanced SCC, and 20 normal appearing skin samples [upper-inner arm, (UIA)]. Set 2 included15 AK, 5 advanced SCC, 4 non-advanced SCC and 20 UIA. LCM was used to isolate pure populations of epithelial cells. Fifty-one key signaling proteins and phosphorylated proteins were assessed for set 1 showing that the MEK-ERK pathway was activated in SCC compared to AK and normal skin, that EGFR was aberrantly activated in SCC, and that the mTOR pathway was highly activated in SCC. Unsupervised clustering revealed dramatic differences in SCC signaling architecture. Statistical analysis (p&amp;lt;0.01) found that pro-survival signaling through phosphorylation of ASK, and 4EBP1 as well as increased Bax and Bak expression were higher in AK vs UIA. We then expanded our pathway network activation mapping in set 2 to 108 key signaling proteins. We corroborated the MEK-ERK, EGFR and mTOR pathway activation and identified an expanded number of upstream and downstream signaling molecules within these pathways, and that SCC is indeed a pathway activation-driven disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2917. doi:10.1158/1538-7445.AM2011-2917
Quality and denoising in real-time fMRI neurofeedback: a methods review (2019)

Supporting information for the manuscript available at https://osf.io/xubhq
Rapid Identification of Novel Inhibitors of the Human Aquaporin‐1 Water Channel (2015)

Aquaporins (AQPs) are a family of membrane proteins that function as channels facilitating water transport in response to osmotic gradients. These play critical roles in several normal physiological and pathological states and are targets for drug discovery. Selective inhibition of the AQP1 water channel may provide a new approach for the treatment of several disorders including ocular hypertension/glaucoma, congestive heart failure, brain swelling associated with a stroke, corneal and macular edema, pulmonary edema, and otic disorders such as hearing loss and vertigo. We developed a high-throughput assay to screen a library of compounds as potential AQP1 modulators by monitoring the fluorescence dequenching of entrapped calcein in a confluent layer of AQP1-overexpressing CHO cells that were exposed to a hypotonic shock. Promising candidates were tested in a Xenopus oocyte-swelling assay, which confirmed the identification of two lead classes of compounds belonging to aromatic sulfonamides and dihydrobenzofurans with IC50 s in the low micromolar range. These selected compounds directly inhibited water transport in AQP1-enriched stripped erythrocyte ghosts and in proteoliposomes reconstituted with purified AQP1. Validation of these lead compounds, by the three independent assays, establishes a set of attractive AQP1 blockers for developing novel, small-molecule functional modulators of human AQP1.
[Expression of multiple cancer-testis antigen genes in non-small cell lung cancer treated by chemotherapy prior surgery]. (2004)

(1) Cancer vaccines with CT antigens including MAGE-3, NY-ESO-1, LAGE-1, etc, are suitable for immunotherapy of NSCLC after chemotherapy and surgery. (2) NSCLC patients at different stages of disease may be treated with vaccines of different CT antigen composition. (3) CT antigen vaccines are most attractive for patients with late stage NSCLC and/or squamous cell carcinoma of NSCLC.
Coherent terahertz communication based on DSP-aided radio-over-fiber technology (2013)

Coherent terahertz-signal transmission using an optical frequency comb and a high-speed digital signal processing (DSP) technology is successfully demonstrated. The DSP-aided radio-over-fiber technology can enhance the resilience of networks to disasters.
[Clinical evaluation of 3D delayed-enhancement MRI using parallel imaging in the assessment of myocardial viability]. (2005)

This study aimed to evaluate the efficacy of breath-hold three-dimensional (3D)delayed-enhancement MRI using parallel imaging in terms of the effect of parallel imaging on the image quality and visualization of myocardial infarction. Twenty-two patients (17 men and 5 women) with suspected myocardial infarction underwent breath-hold 3D late-enhanced viability examination at least 30 days after occurrence. All patients underwent a Tl-scintigraphy examination. First, 10 patients were examined without applying parallel imaging, then the next 12 patients were studied using parallel imaging. All 3D late-enhanced images at the short axis were acquired 10, 15, and 20 min after an injection of contrast agent, and both the long axis and the four-chamber views were acquired after 15 min. In quantitative analysis, the late-enhanced myocardial images at 10, 15, and 20 min showed higher contrast-to-noise ratios (CNR) in parallel imaging than those with no parallel imaging. During the time-intensity curve of the myocardium, no significant change was observed at 10 or 15 min; however, marked signal reduction was observed at 20 min. In diagnostic evaluation, images obtained with parallel imaging were superior to those without parallel imaging. In general, the application of parallel imaging reduces acquisition time with an expense of reduction in SNR. However, the breath-hold 3D late-enhanced images with parallel imaging showed no apparent SNR reduction. Furthermore, parallel imaging provided clear edge definition between the infarction and the normal region. The reduction of acquisition time with parallel imaging may be less susceptible to fast cardiac motion. In conclusion, breath-hold 3D delayed-enhancement MRI using parallel imaging was highly evaluated in our study and may show promise in clinical application.
Using SVMS and discriminative models for speech recognition (2002)

In speech recognition, standard MAP decoders attribute speech data to the class with the highest posterior probability. This minimises the error rate under assumptions of model correctness. This assumption is invalid for speech recognition with HMMs. Hence, an interesting question is whether extra, useful information about the speech source can be extracted from the HMMs and used to lower error rates in practical systems, In this paper additional features are extracted from HMMs and incorporated into a multi-dimensional score-space. SVMs are then used to implement a decision rule. Preliminary experiments are performed on a small speaker-independent isolated letter task. Score-spaces based on discriminative models are used with previous results based on generative models. Both score-spaces outperform standard schemes.