gebhart/patrepeval huggingface dataset:
Prostacyclin-IP signaling and prostaglandin E2-EP2/EP4 signaling both mediate joint inflammation in mouse collagen-induced arthritis (2006)

Prostaglandin (PG)I2 (prostacyclin [PGI]) and PGE2 are abundantly present in the synovial fluid of rheumatoid arthritis (RA) patients. Although the role of PGE2 in RA has been well studied, how much PGI2 contributes to RA is little known. To examine this issue, we backcrossed mice lacking the PGI receptor (IP) to the DBA/1J strain and subjected them to collagen-induced arthritis (CIA). IP-deficient (IP-/-) mice exhibited significant reduction in arthritic scores compared with wild-type (WT) mice, despite anti-collagen antibody production and complement activation similar to WT mice. IP-/- mice also showed significant reduction in contents of proinflammatory cytokines, such as interleukin (IL)-6 in arthritic paws. Consistently, the addition of an IP agonist to cultured synovial fibroblasts significantly enhanced IL-6 production and induced expression of other arthritis-related genes. On the other hand, loss or inhibition of each PGE receptor subtype alone did not affect elicitation of inflammation in CIA. However, a partial but significant suppression of CIA was achieved by the combined inhibition of EP2 and EP4. Our results show significant roles of both PGI2-IP and PGE2-EP2/EP4 signaling in the development of CIA, and suggest that inhibition of PGE2 synthesis alone may not be sufficient for suppression of RA symptoms.
Specificity of C-Reactive Protein for Choline Phosphate Residues of Pneumococcal C-Polysaccharide (1971)

C-reactive protein (CRP) is an acute phase protein appearing in the serum of man during various pathological conditions, and frequently employed as a clinical index of acute inflammation. It is precipitated from the serum by pneumococcal C-polysaccharide in the presence of Ca ions. Although this precipitation reaction, which led to the discovery of CRP, has been known for many years, there is little information about the active site(s) in the molecule of C-polysaccharide participating in the reaction with CRP. It has been recently reported that choline phosphate is a unit of the macro-molecular structure of C-polysaccharide (1, 2). In an attempt to determine the specificity of CRP for choline phosphate residues of C-polysaccharide, we conducted quantitative inhibition studies of CRP-C-polysaccharide precipitation. The substances tested for inhibitory effect included choline phosphate and a series of organic phosphate menoesters. The results of these experiments indicated that choline phosphate is the most active inhibitor of CRP-C-polysaccharide precipitation yet described, and suggested that this compound might provide the major reacting site of C-polysaccharide.A single lot of CRP-positive serum (no. 9 E.M.), obtained 2 days following surgery from a patient with an intertrochanteric fracture of the femur, was used for all the inhibition experiments described below. Tested by capillary precipitation against a commercial antiserum (Hyland Labs, Los Angeles, California), this serum gave a 4+ reaction for CRP. The results with this serum were representative of data obtained also with other CRP-positive sera. C-polysaccharide was prepared by the method of Anderson and McCarty (3) from a III R strain of pneumococcus. The following substances obtained from commerical sources were tested for inhibitory effect without further purification: Choline phosphate chloride, o-phosphoryl-ethanol-amine, DL-α-glycerophosphate, β-glycerophosphate, L-α-glycerophosphorylcholine, choline base, uridine-5′-monophosphate (UMP), adenosine-5′-monophosphate (AMP), and cytidine-5′-monophosphate (CMP).
Status report on carbapenemases: challenges and prospects (2011)

Antimicrobial resistance in hospital and community-onset bacterial infections is a significant source of patient morbidity and mortality. In the past decade, we have witnessed the increasing recovery of carbapenem-resistant Gram-negative bacteria. For many isolates, carbapenem resistance is due to the production of carbapenemases, β-lactamases that can inactivate carbapenems and frequently other β-lactam antibiotics. Currently, these enzymes are mainly found in three different β-lactamase classes (class A, B and D). Regardless of the molecular classification, there are few antimicrobials available to treat infections with these organisms and data regarding agents in development are limited to in vitro studies. This article focuses on the epidemiology of carbapenemase-producing Gram-negative bacteria. We also review available agents and those in development with potential activity against this evolving threat.
A non-replicating adenoviral vector as a potential HIV vaccine. (2003)

HIV-specific T cell immune responses will play an important role in any HIV vaccine paradigm. Studies in rhesus monkeys have shown that significant and persistent virus-specific T cell responses can be elicited with vaccines incorporating viral genetic sequences and that these responses are primarily mediated by CD8 T cells. Benefits such as stable CD4 levels and viral control have resulted. Two vaccine candidates developed by Merck and Co., Inc., including a non-replicating adenoviral vector, have been studied in animals and are now being studied in Phase I clinical trials in humans. Important considerations include cross-clade reactivity (effectiveness in diverse HIV-infected populations), tolerability, and durability of response. Ongoing studies are looking at responses in both uninfected and infected individuals. Optimal vaccine combinations as well as the development and testing of vaccines with multiple genetic targets are part of future plans investigating this vaccine strategy.
Holographic line field en-face OCT with digital adaptive optics in the retina in vivo (2018)

We demonstrate a high-resolution line field en-face time domain optical coherence tomography (OCT) system using an off-axis holography configuration. Line field en-face OCT produces high speed en-face images at rates of up to 100 Hz. The high frame rate favors good phase stability across the lateral field-of-view which is indispensable for digital adaptive optics (DAO). Human retinal structures are acquired in-vivo with a broadband light source at 840 nm, and line rates of 10 kHz to 100 kHz. Structures of different retinal layers, such as photoreceptors, capillaries, and nerve fibers are visualized with high resolution of 2.8 µm and 5.5 µm in lateral directions. Subaperture based DAO is successfully applied to increase the visibility of cone-photoreceptors and nerve fibers. Furthermore, en-face Doppler OCT maps are generated based on calculating the differential phase shifts between recorded lines.
Synthesis and spectral properties of a new luminescent europium(III) terpyridyl chelate (2000)

A new europium(III) chelate, which uses the 2,2′∶6′,2′′-terpyridyl chelating group as sensitizer, has been synthesized and its spectral properties investigated. The chelate, which can incorporate an isothiocyanate group for biological labelling, has proved useful in time resolved fluorescence studies and for delayed fluorescence resonance energy transfer (DEFRET).
Identification of a Stat3-Dependent Transcription Regulatory Network Involved in Metastatic Progression (2009)

High levels of activated Stat3 are often found in human breast cancers and can correlate with poor patient outcome. We employed an activated ErbB2 mouse model of breast cancer to investigate the in vivo role of Stat3 in mammary tumor progression and found that Stat3 does not alter mammary tumor initiation but dramatically affects metastatic progression. Four-fold fewer animals exhibited lung metastases in the absence of Stat3 and a 12-fold reduction in the number of lung lesions was observed in animals bearing Stat3-null tumors when compared with the wild-type cohort. The decreased malignancy in Stat3-deficient tumors is attributed to a reduction in both angiogenic and inflammatory responses associated with a Stat3-dependent transcriptional cascade involving CCAAT/enhancer binding protein delta.
Pressure Altitude Enhanced AGNSS Hybrid Receiver for a Mobile Terminal (2005)

The vertical positioning capability of GNSS receivers as a performance criterion will be more important in the near future due to upcoming location-based services setting stricter vertical positioning requirements. Vertical positioning accuracy particularly suffers in situations where there is poor satellite geometry, e.g., due to the low satellite elevation angle in high-rise buildings. The focus of this paper is to study ways to improve AGNSS performance in terms of vertical positioning accuracy and reliability by providing pressure altitude measurements for the GNSS positioning solution. Pressure measurements are obtained from an AGNSS receiver integrated MEMS pressure sensor. To cope with the bias and drift tendency of the pressure altitude, the reference pressure information is transmitted via a TCP/IP network. System performance was evaluated in an urban office environment both indoors and outdoors. Single-fix and navigation tests show that pressure altitude augmentation improves the vertical positioning capability and measurement geometry of the AGNSS receiver. Singlefix tests also indicated improvement on the time-to-firstfix estimates compared to the GNSS-only solution.
Tetranucleotide repeat polymorphism at the human c-fes/fps proto-oncogene (FES) (1991)

Journal Article Tetranucleotide repeat polymorphism at the human c-fes/fps proto-oncogene (FES) Get access Mihael H. Polymeropoulos, Mihael H. Polymeropoulos National Institute of Mental Health Neuroscience CenterSt. Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Denise S. Rath, Denise S. Rath National Institute of Mental Health Neuroscience CenterSt. Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Hong Xiao, Hong Xiao National Institute of Mental Health Neuroscience CenterSt. Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Carl R. Merril Carl R. Merril National Institute of Mental Health Neuroscience CenterSt. Elizabeths Hospital, Room 131, 2700 Martin Luther King Avenue, Washington, DC 20032, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 14, 25 July 1991, Page 4018, https://doi.org/10.1093/nar/19.14.4018 Published: 25 July 1991
The basics of epithelial-mesenchymal transition (2009)

The origins of the mesenchymal cells participating in tissue repair and pathological processes, notably tissue fibrosis, tumor invasiveness, and metastasis, are poorly understood. However, emerging evidence suggests that epithelial-mesenchymal transitions (EMTs) represent one important source of these cells. As we discuss here, processes similar to the EMTs associated with embryo implantation, embryogenesis, and organ development are appropriated and subverted by chronically inflamed tissues and neoplasias. The identification of the signaling pathways that lead to activation of EMT programs during these disease processes is providing new insights into the plasticity of cellular phenotypes and possible therapeutic interventions.
Intestinal Colonisation of Laboratory Rats by Anaerobic Oxalate-degrading Bacteria: Effects on the Urinary and Faecal Excretion of Dietary Oxalate (1993)

Oxalobacter formigenes, an anaerobic bacterium that degrades oxalate to CO2 and formate, colonises the intestinal tracts of man and other animals. In this study, the large intestines of laboratory rats were experimentally colonised with a strain of O. formigenes to examine effects of these bacteria on the fate of dietary oxalate. When rats (n = 6) were fed a standard rat diet plus 2 per cent sodium oxalate, urinary oxalate excretion was not significantly changed following inoculation and colonisation with O. formigenes. There was a consistent trend towards less oxalate excretion in faeces of rats after they became colonised with O. formigenes, but differences between colonised and non-colonised states were not significant. In an isotope recovery study, when rats were orally dosed with [14C]oxalate, the percentage of 14C in expired CO2 from three colonised rats was 10-fold greater than from three non-colonised rats. Although 14C excretion in faeces was decreased three-fold in the group of colonised rats, 14C activity in the urine of colonised and non-colonised rats was not significantly different. Thus, although O. formigenes colonised and degraded oxalate in the rat intestinal tract, under conditions of these experiments, this colonisation did not markedly influence urinary oxalate excretion.
Das Verhalten der Alkalimetalle zu Halbmetallen. XI. Die Kristallstruktur von NaSi und NaGe (1964)

Abstract Die Kristallstrukturen von NaSi und NaGe wurden mit Hilfe moderner Methoden bestimmt. Beide Verbindungen sind zwar analog aufgebaut, aber nicht streng isotyp (Raumgruppe C C 2/c bzw. C P 2 1 /c). Wie in den Verbindungen der höheren Alkalimetalle 1 ) werden auch hier Si 4 ‐ bzw. Ge 4 ‐Tetreader gebildet. Die Umgebung der Si‐ bzw. Ge‐Teilchen mit Alkalimetallatomen ist unregelmäßig. Die Übereinstimmung zwischen berechneten und beobachteten Strukturfaktoren ist gut: NaSi: R0,07; R′0,10 für insgesamt 125 Reflexe (h 0 l) und (h k 0); NaGe: R0,08; R′0,13 für insgesamt 1300 Reflexe (h k l).
The intrinsic signal‐to‐noise ratio in NMR imaging (1986)

The fundamental limit for NMR imaging is set by an intrinsic signal-to-noise ratio (SNR) for a particular combination of rf antenna and imaging subjects. The intrinsic SNR is the signal from a small volume of material in the sample competing with electrical noise from thermally generated, random noise currents in the sample. The intrinsic SNR has been measured for a number of antenna-body section combinations at several different values of the static magnetic field and is proportional to B0. We have applied the intrinsic and system SNR to predict image SNR and have found satisfactory agreement with measurements on images. The relationship between SNR and pixel size is quite different in NMR than it is with imaging modalities using ionizing radiation, and indicates that the initial choice of pixel size is crucial in NMR. The analog of "contrast-detail-dose" plots for ionizing radiation imaging modalities is the "contrast-detail-time" plot in NMR, which should prove useful in choosing a suitable pixel array to visualize a particular anatomical detail for a given NMR receiving antenna.
The magnetic resonance shutter speed discriminates vascular properties of malignant and benign breast tumors in vivo (2008)

The pharmacokinetic analysis of dynamic-contrast-enhanced (DCE) MRI data yields K(trans) and k(ep), two parameters independently measuring the capillary wall contrast reagent transfer rate. The almost universally used standard model (SM) embeds the implicit assumption that equilibrium transcytolemmal water exchange is effectively infinitely fast. In analyses of routine DCE-MRI data from 22 patients with suspicious breast lesions initially ruled positive by institutional screening protocols, the SM K(trans) values for benign and malignant lesions exhibit considerable overlap. A form of the shutter-speed model (SSM), which allows for finite exchange kinetics, agrees with the SM K(trans) value for each of the 15 benign lesions. However, it reveals that the SM underestimates K(trans) for each of the seven malignant tumors in this population. The fact that this phenomenon is unique to malignant tumors allows their complete discrimination from the benign lesions, as validated by comparison with gold-standard pathology analyses of subsequent biopsy tissue samples. Likewise, the SM overestimates k(ep), particularly for the benign tumors. Thus, incorporation of the SSM into the screening protocols would have precluded all 68% of the biopsy/pathology procedures that yielded benign findings. The SM/SSM difference is well understood from molecular first principles.
Towards Solar Fuels from Water and CO2 (2010)

Solar fuels from water and CO2 are a topic of current large scientific and industrial interest. Research advances on bioroutes, concentrated solar thermal and low-temperature conversion using semiconductors and a photoelectrocatalytic (PEC) approach, are critically discussed and compared in an attempt to define challenges and current limits and to identify the priorities on which focus research and development (R&D). The need to produce fuels that are easy to transport and store, which can be integrated into the existing energy infrastructure, is emphasized. The role of solar fuels produced from CO2 in comparison with solar H2 is analyzed. Solar fuels are complementary to solar to electrical energy conversion, but they still need intensified R&D before possible commercialization.
Fragmented aperture antenna design of miniaturized GPS CRPA: model and measurements (2007)

A new approach to developing miniaturized GPS antennas suitable for use in CRPA anti-jam arrays is presented. The approach leverages recent advances in fragmented aperture antenna design and manufacturing. This approach uses a combination of FDTD simulations combined with genetic optimization.
Privatizing Airports-Options and Case Studies (1996)

Traditionally, the air transport sector--airlines, airports, and air navigation services--has been in state hands. The private sector became involved in the sector only recently, beginning with the airlines. Privatization of airport infrastructure and private sector participation in air navigation are also at an early stage. The air transport sector will require large capital investments over the next fifteen years to modernize aircraft fleets, improve airport infrastructure, introduce more sophisticated air navigation systems, and meet the demand of new markets. There is no doubt that governments will be unable to fund all necessary investments, and that the private sector will therefore play an increasing role in meeting the sector's needs. Table 1 in this Note presents three options of private sector participation in airports. Table 2 presents two options most suitable for transferring airport activities to the private sector. The Note also outlines cases of airport privatization in Colombia, Jamaica, Canada, and Northern Ireland.
Identification of MAGE-1 and MAGE-4 proteins in spermatogonia and primary spermatocytes of testis. (1995)

The MAGE genes encoding tumor rejection antigens recognized by CTLs are expressed at the mRNA level in various cancers and in the testis but not in the other normal tissues. The expression of MAGE-1 or MAGE-4 protein in the testicular cells was studied immunohistochemically with the antibodies to the recombinant MAGE-1 or MAGE-4 protein. Both proteins were identified in the nucleus and cytoplasm of spermatogonia and in primary spermatocytes but not in spermatids or Sertoli's cells. Therefore, MAGE proteins are normal tissue antigens compartmentalized in particular testicular cells playing an important role in the early phase of the spermatogenesis.
Homogeneous Optical and Electronic Properties of Graphene Due to the Suppression of Multilayer Patches During CVD on Copper Foils (2013)

A synthesis method of strictly monolayer and fully homogeneous graphene across tens of centimeter squares, by chemical vapour deposition onto standard copper foils, is presented. The growth technique involves cyclic injection of a carbon precursor separated by idle times with constant hydrogen exposure. The formation of spurious multilayer patches, which accompanies the standard growth techniques based on continuous exposure to methane, is inhibited here, in a broad range of pressure and gas composition, including in two pressure regimes which are known to yield distinctive grain morphologies (dendritic versus hexagonal). Raman spectra confirm the absence of defects within the graphene films. A mechanism for growth/suppression of the multilayer patches based on the carbon storage at defective regions is proposed. The importance of multilayer suppression is highlighted in a comparative study showing the detrimental effect of patches on the performances of graphene transistors and on the optical transparency of stacked layers. The full‐layer graphene sheets are superiorly homogeneous in terms of their optical and electronic properties, and are thus suited for applications for high‐density integration as well as transparent electrodes with spatially continuous optical absorbance. Graphene transistors fabricated by the pulsed CVD method exhibit room‐temperature mobilities with a mean value of 5000 cm 2 V −1 s −1 .
An Improved Min-Cut Algonthm for Partitioning VLSI Networks (1984)

Recently, a fast (linear) heuristic for improving min-cut partitions of VLSI networks was suggested by Fiduccia and Mattheyses [6]. In this-paper we generalize their ideas and suggest a class of increasingly sophisticated heuristics. We then show, by exploiting the data structures originally suggested by them, that the computational complexity of any specific heuristic in the suggested class remains linear in the size of the network.
Advanced data mining techniques for identifying correlation between gene expression and promoters (2006)

With the genetic code unveiled, one of the major challenges in the post-genomic era is to determine the regulatory networks of cells. An intermediate goal for revealing the transcription regulatory network of cells is to determine all DNA-binding transcription factors (TFs) and their regulatory binding sites within the genomes. The initial step to achieve this goal is to find the transcription factor binding sites within the regulatory regions of clustered co-expressed genes from microarray experiments, which includes a two-step solution: gene expression clustering followed by motif discovery. Although this approach id successful applied to small datasets, it is based on the assumption that co-expression implies co-regulation, which might always hold. Besides, genes are typically regulated by a combination of several TFs, which is not considered in most motif discovery algorithms. In this dissertation, we are mainly focus on designing a new gene expression clustering algorithm as well as a new algorithm to correlate the transcription binding sites with the gene expression. 
The most popular approaches in microarray gene clustering are K-means and hierarchical clustering. While the K-means clustering algorithm is initialization dependent and may converge to a local optimum, the hierarchical clustering algorithm needs human intervention because of its nested cluster structure. We have proposed a Fast Genetic K-means Algorithm (FGKA) with a guarantee of converging to the global optimum in theory. Our experiments show that the FGKA indeed converges to the global optimum and independent from initialization. FGKA and its variance, Incremental Genetic K-means Algorithm (IGKA) and Hybrid Genetic K-means Algorithm (HGKA) have been applied to cluster gene expression data of yeast and found that it increased the enrichment of genes of similar function within the cluster. 
To understand the relationship between the motifs and gene expression changes, we proposed a new algorithm, Co-Miner (Correlation Mbiner). By using association rule mining technique, correlation rules were generated based on the expression profiles of genes with significant expression change through the time course of gene expression. In this way, we may consider the change in gene expression to be causatively associated with the transcription binding sites in the upstream sequences. By applying Co-Miner algorithm on yeast data set, the relationships between some motifs and gene expressions are confirmed in the literature.