gebhart/patrepeval huggingface dataset:
Expression of human delta-6-desaturase is associated with aggressiveness of human breast cancer (2003)

Highly unsaturated fatty acids (HUFAs) are cyto-toxic to cancer cells and generated in the body by desaturation from essential fatty acids, primarily involving delta-6-desaturase. This study, for the first time, examined the level of expression of human delta-6-desaturase as well as delta-4-desaturase in human breast cancer. Breast tumours (n=102) which comprised of 88 ductal and 14 lobular carcinomas, as well as normal breast tissues (n=31), together with breast cancer cell lines were analysed for the level of expression of delta-6- and delta-4-desaturases using RT-PCR and quantitative PCR. A lower level of delta-6-desaturase was seen in breast tumour compared with normal tissues. Tumours from patients who had a poor prognostic index and from those who died of breast cancer had the lowest level of delta-6-desaturase (median follow-up 72 months). In addition, TNM3 and TNM4 tumours had significantly lower level of delta-6-desaturase than TNM1 tumours. Interestingly, ductal tumours displayed significantly higher level of the enzyme than lobular tumours. In contrast, a stepwise increase of delta-4-desaturase was seen in tumour from patients with poor prognosis. It is concluded that aggressive breast tumours have a reduced level of delta-6-desaturase. This aberrant expression has clinical bearings to the outcome in patients with breast cancer.
Theory of light transmission through subwavelength periodic hole arrays (2000)

The existing theories which aim to explain the extraordinary optical transmission of a metallic film pierced by a two-dimensional subwavelength hole array [T.W. Ebbesen, H.J. Lezec, H.F. Ghaemi, T. Thio, and P.A. Wolff, Natural (London) 391, 667 (1998)] all have in common the following feature: instead of studying the two-dimensional crossed grating resulting from the hole array, they consider a one-dimensional grating with infinite slits. We show that such a simplification introduces an efficient channel for light transmission in lamellar gratings, which does not exist for hole arrays. Therefore in order to explain the relatively high transmission observed by Ebbesen et al., it is necessary to take into account the existence of the holes in the array. In this paper we develop a two-dimensional analysis of the experiment performed by Ebbesen et al. No simplification is introduced. This allows us to obtain theoretically the long-wavelength peak reported by Ebbesen et al. with the same grating thickness as the one used by these authors. We also review and study in detail the various contributions devoted to this very surprising effect.
Roseburia hominis: a novel guilty player in ulcerative colitis pathogenesis? (2013)

Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) or ulcerative colitis (UC) comprise the two most common forms of intestinal inflammation characterised by a chronic relapsing disease course. The aetiology of both disorders has still not yet been identified. Whereas it has been elegantly demonstrated in many studies in the last years that genetic factors are crucially involved, other so-called environmental factors are much less well defined.1 In recent years evidence was accumulating that the gut microbiota and its manipulation might constitute one of those relevant ‘environmental’ factors. Trillions of microbes compose the intestinal microbiota of healthy individuals and several studies have demonstrated in the past that IBD patients exhibit a pronounced dysbiosis. It remains, however, speculative whether observed changes are causally involved in IBD pathogenesis or reflect simply epiphenomena due to inflammation.2 

Whereas several clinical aspects strongly support a role for intestinal bacteria in CD such as improvement of inflammation after diversion of the faecal stream or improvement of disease during antibiotic therapy, similar observations are mostly not available for UC. However, other aspects are suggesting a role for bacteria in the pathogenesis of UC as, for example, abnormal mucosal secretion of IgG antibodies …
Long term survival after heart transplantation for doxorubicin induced cardiomyopathy. (1991)

A 10 year old child developed severe cardiomyopathy after combined, multicycle chemotherapy for Ewing's sarcoma and was treated by heart transplantation with good results. Long term azathioprine and cyclosporin caused only mild impairment of immune function and there were no recurrent infections, local recurrences of the tumour, or distant metastases.
High Speed Pattern Matching for Network IDS/IPS (2006)

The phenomenal growth of the Internet in the last decade and society's increasing dependence on it has brought along, a flood of security attacks on the networking and computing infrastructure. Intrusion detection/prevention systems provide defenses against these attacks by monitoring headers and payload of packets flowing through the network. Multiple string matching that can compare hundreds of string patterns simultaneously is a critical component of these systems, and is a well-studied problem. Most of the string matching solutions today are based on the classic Aho-Corasick algorithm, which has an inherent limitation; they can process only one input character in one cycle. As memory speed is not growing at the same pace as network speed, this limitation has become a bottleneck in the current network, having speeds of tens of gigabits per second. In this paper, we propose a novel multiple string matching algorithm that can process multiple characters at a time thus achieving multi-gigabit rate search speeds. We also propose an architecture for an efficient implementation on TCAM-based hardware. We additionally propose novel optimizations by making use of the properties of TCAMs to significantly reduce the memory requirements of the proposed algorithm. We finally present extensive simulation results of network-based virus/worm detection using real signature databases to illustrate the effectiveness of the proposed scheme.
Genetically based resistance to the antiinflammatory effects of methotrexate in the air‐pouch model of acute inflammation (2005)

Genetic factors contribute to the antiinflammatory efficacy of MTX, and a single locus involved in MTX-induced adenosine up-regulation is likely responsible for the observed resistance to MTX in DBA/1J mice.
Melastatin Expression and Prognosis in Cutaneous Malignant Melanoma (2001)

Downregulation of melastatin mRNA in the primary cutaneous tumor is a prognostic marker for metastasis in patients with localized malignant melanoma and is independent of tumor thickness and other variables. Used in combination, melastatin status and tumor thickness allow for the identification of subgroups of patients at high and low risk of developing metastatic disease.
Production of anti‐virus, viroid plants by genetic manipulations (2002)

Many pathogenic plant viruses are RNA viruses, which initiate production of double-stranded RNA intermediates when they replicate in host plant cells. Introduction of double-stranded RNA-specific ribonucleases such as the Schizosaccharomyces pombe derived pac I protein and animal cell derived interferon-induced 2',5'-oligoadenylate synthetase (2-5 Aase)/ribonuclease L (RNase L) system into various plants may make plants resistant to various pathogenic viruses and viroids. We have demonstrated that pac I and 2-5 Aase/RNase L transgenic tobacco plants are resistant to various viruses including tobacco mosaic virus, cucumber mosaic virus and potato virus Y. In addition, pac I transgenic potato plants are resistant to potato spindle tuber viroid. Using Agrobacterium-mediated transformation, we have established a transformation system for chrysanthemum plants and have recently developed pac I transgenic chrysanthemum (Dendranthema grandiflora cv Reagan) resistant to chrysanthemum stunt viroid and have grown them in isolated fields for an evaluation of their effects.
Isotropic “Islands” in a Cholesteric “Sea”: Patterned Thermal Expansion for Responsive Surface Topologies (2006)

A method to capture ordered and disordered regions in reactive mesogen films to take advantage of the anisotropic thermal properties and fabricate a thermally responsive patterned film is presented. The image shows white-light interferometer images of isotropic cylinders in cholesteric material. The underlying principle phenomenon observed here is well described by a finite-element simulation.
Synthesis and evaluation of n-substituted imidazole derivatives for antimicrobial activity (2011)

A series of N-substituted imidazole derivatives was synthesized. Imidazole nucleus was reacted with ethylchloroacetate to form imidazole ester. Reaction of the imidazole ester (I) with different amines yields the desired products (1a- 1e). The compounds were characterized by FT-IR, (1)H-NMR and mass spectra. The synthesized compounds were evaluated for the antimicrobial activity against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Candida albicans and Aspergillus niger by determination of MIC (minimum inhibitory concentration) using tube dilution method. Compound (1b) was found to be the most active antimicrobial compound amongst others in the series.
A model for charge transfer in buried-channel charge-coupled devices at low temperature (1991)

Charge transfer in buried-channel charge-coupled devices (CCDs) is explored with a one-dimensional numerical model which describes the capture and emission of electrons from a shallow donor level in silicon through the use of the Shockley-Read-Hall generation-recombination theory. Incorporated in the model are the three-dimensional Poole-Frenkel barrier lowering theory of A. K. Jonscher (1967) and J. L. Hartke (1968) and the low-temperature form of Poisson's equation. Reasonable agreement of the model with experimental data taken from the buried-channel CCDs of a PtSi Schottky barrier infrared image sensor is found. Moreover, the value for the capture cross section of electrons to the shallow phosphorus level in silicon inferred from the model follows the cascade theory for capture by M. Lax (1959) and agrees roughly with determinations made by other experimenters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Roxadustat (FG-4592) (2015)

Safety concerns with erythropoietin analogues and intravenous (IV) iron for treatment of anemia in CKD necessitate development of safer therapies. Roxadustat (FG-4592) is an orally bioavailable hypoxia-inducible factor (HIF) prolyl hydroxylase inhibitor that promotes coordinated erythropoiesis through HIF-mediated transcription. We performed an open-label, randomized hemoglobin (Hb) correction study in anemic (Hb≤10.0 g/dl) patients incident to hemodialysis (HD) or peritoneal dialysis (PD). Sixty patients received no iron, oral iron, or IV iron while treated with roxadustat for 12 weeks. Mean±SD baseline Hb was 8.3±1.0 g/dl in enrolled patients. Roxadustat at titrated doses increased mean Hb by ≥2.0 g/dl within 7 weeks regardless of baseline iron repletion status, C-reactive protein level, iron regimen, or dialysis modality. Mean±SEM maximal change in Hb from baseline (ΔHb(max)), the primary endpoint, was 3.1±0.2 g/dl over 12 weeks in efficacy-evaluable patients (n=55). In groups receiving oral or IV iron, ΔHb(max) was similar and larger than in the no-iron group. Hb response (increase in Hb of ≥1.0 g/dl from baseline) was achieved in 96% of efficacy-evaluable patients. Mean serum hepcidin decreased significantly 4 weeks into study: by 80% in HD patients receiving no iron (n=22), 52% in HD and PD patients receiving oral iron (n=21), and 41% in HD patients receiving IV iron (n=9). In summary, roxadustat was well tolerated and corrected anemia in incident HD and PD patients, regardless of baseline iron repletion status or C-reactive protein level and with oral or IV iron supplementation; it also reduced serum hepcidin levels.
Reliability of the Mouse Model of Choroidal Neovascularization Induced by Laser Photocoagulation (2014)

We present our recommended methods for conducting experiments with the mouse laser-induced CNV model to enhance reproducibility and minimize investigator bias.
A one-pass decoder based on polymorphic linguistic context assignment (2005)

In this study, we examine how fast decoding of conversational speech with large vocabularies profits from efficient use of linguistic information, i.e. language models and grammars. Based on a re-entrant single pronunciation prefix tree, we use the concept of linguistic context polymorphism to allow an early incorporation of language model information. This approach allows us to use all available language model information in a one-pass decoder, using the same engine to decode with statistical n-gram language models as well as context free grammars or re-scoring of lattices in an efficient way. We compare this approach to our previous decoder, which needed three passes to incorporate all available information. The results on a very large vocabulary task show that the search can be speeded up by almost a factor of three, without introducing additional search errors.
Multi-Color Laser Spectroscopy with a Dual-Wavelength Quantum Cascade Laser (2014)

A new concept of multi-color spectroscopy based on a dual-wavelength QCL is presented. The latter emits at two distinct wavelengths (5.26 and 6.25 µm), featuring simultaneous detection of two different gas species without any beam combining optics.
Function and Production of Nitric Oxide in the Coronary Circulation of the Conscious Dog During Exercise (1996)

This study determined the changes in NO production from the coronary circulation of the conscious dog during exercise. The role of endogenous NO as it relates to coronary flow, myocardial work, and metabolism was also studied. Mongrel dogs were chronically instrumented for measurements of coronary blood flow (CBF), ventricular and aortic pressure, and ventricular diameter, with catheters in the aorta and coronary sinus. Acute exercise (5 minutes at 3.6, 5.9, and 9.1 mph) was performed, and hemodynamic measurements and blood samples were taken at each exercise level. Nitro-L-arginine (NLA, 35 mg/kg IV) was given to block NO synthesis, and the exercise was repeated. Blood samples were analyzed for oxygen, plasma nitrate/nitrite (an index of NO), lactate, glucose, and free fatty acid (FFA) levels. Acute exercise caused significant elevations in NO production by the coronary circulation (46 +/- 23, 129 +/- 44, and 63 +/- 32 nmol/min at each speed respectively, P < .05). After NLA, there was no measurable NO production at rest or during exercise. Blockade of NO synthesis resulted in elevations in myocardial oxygen consumption and reductions in myocardial FFA consumption for comparable levels of CBF and cardiac work. The metabolic changes after NLA occurred in the absence of alterations in myocardial lactate or glucose consumptions. NO production by the coronary circulation is increased with exercise and blocked by NLA. The absence of NO in the coronary circulation during exercise does not affect levels of CBF, because it shifts the relationship between cardiac work and myocardial oxygen consumption, suggesting that endogenous NO modulates myocardial metabolism.
Nitroxyl gets to the heart of the matter (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Temporal resolution requirements for intensity modulated radiation therapy delivered by multileaf collimators (1999)

Intensity modulated radiation therapy may be delivered via dynamic control of a multileaf collimator by defining dynamic leaf trajectories at a series of control points which are spaced at arbitrary intervals throughout an exposure. Leaves move linearly between the positions defined at the control points and hence leaf motion is a linear approximation to the planned trajectories. When many control points are used, very complex modulations can be defined accurately. If too few are used, dose errors are introduced which depend on the complexity of the modulation and the number of control points chosen. Proposed intensity modulations, of varying complexity, have been converted to trajectory plans where the number of equally spaced control points varied between 11 and 99. In each case the fluence map generated by the resulting leaf motions was computed, and this was quantitatively compared with the desired modulation by calculating the root mean square (RMS) error. It is shown that in no case can the RMS error be significantly reduced by increasing the number of control points beyond 50. Guidelines are derived such that compensators and simple modulations may be very accurately delivered with about 20 control points, moderately complex modulations require 30-35 control points and very complex modulations 50 control points. A similar analysis of the step and shoot technique suggests that very accurate deliveries are always achieved with a maximum of 25 equally weighted static fields and reasonable accuracy with 15 fields.
Template Synthesis of Metal Nanowires Containing Monolayer Molecular Junctions (2002)

Metal nanowires containing in-wire monolayer junctions of 16-mercaptohexanoic acid were made by replication of the pores of 70 nm diameter polycarbonate track etch membranes. Au was electrochemically deposited halfway through the 6 microm long pores and a self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid was adsorbed on top. A thin layer of Au was then electrolessly grown to form a metal cap separated from the bottom part of the wire by the SAM. Electron micrographs showed that the bottom and top metal segments were separated by an approximately 2 nm thick organic monolayer. Current-voltage measurements of individual nanowires confirmed that the organic monolayer could be contacted electrically on the top and bottom by the metal nanowire segments without introducing electrical short circuits that penetrate the monolayer. The values of the electrical properties for zero-bias resistance, current density, and breakdown field strength were within the ranges expected for a well-ordered alkanethiol SAM of this thickness.
Synthesis and Properties of N-, O-, and S-Phospho Derivatives of Amino Acids, Peptides, and Protein (1984)

The literature on chemical (i.e., nonenzymic) phosphorylation of amino acids, peptides, and proteins is reviewed through 1982. The review covers synthetic methods, chemical reactions, and physical properties, with emphasis on the techniques used for separation and characterization of the products. Synthetic methods are classified by reagent rather than product, and are illustrated by experimental procedures for the most important methods. Chemical reactions are classified into four groups depending on whether the reaction site is the phospho group, the amino group, the carboxyl group, or in the case of serine the hydroxyl group. Physical data are given for all of the known N-, O-, and S-phospho derivatives of the amino acids, peptides, and proteins, within certain limitations, and are discussed in detail in the section on physical properties. Emphasis is given to the techniques used for separation of the products, such as chromatography and electrophoresis, and for characterization of the products, particularly spectroscopy. Medical and other uses of the products are mentioned.
Gusperimus: immunological mechanism and clinical applications (2014)

Gusperimus is an immunosuppressive drug with a unique mode of action. We review its effects on different arms of the immune system and the current evidence for clinical applications, particularly in the treatment of transplant rejection and ANCA-associated vasculitis.
Enamel Matrix Protein Interactions (2005)

Identifying integral membrane proteins of the secretory surface of ameloblast cells (Tomes' processes) and additional enamel matrix proteins, based on their abilities to interact with the most abundant enamel matrix proteins, will better define the molecular mechanisms of enamel formation at its most rudimentary level.
[Molecular pathogenesis of motor neuron diseases]. (2001)

Spinal and bulbar muscular atrophy (SBMA) and amyotrophic lateral sclerosis (ALS) are representative motor neuron diseases in which selective neuronal degeneration occurs. In this paper, some molecular aspects are discussed related to the pathogenesis of the neuronal degeneration. SBMA is a an X-linked neurodegenerative disease caused by the expansion of a CAG repeat in the first exon of the androgen receptor (AR) gene. To date, eight CAG repeat diseases have been identified, including spinal and bulbar muscular atrophy (SBMA), Huntington's disease (HD), dentatorubralpallidoluysian atrophy (DRPLA), and five spinocerebellar ataxias (SCAs 1, 2, 3, 6, 7). These disorders very likely share a common pathogenesis caused by the gain of a toxic function associated with the expanded polyglutamine tract. Several mechanisms have been postulated as a pathogenic process for neurodegeneration caused by the expanded polyglutamine tract. In SBMA, nuclear inclusions (NIs) containing mutant AR protein have been observed in regions of SBMA central nervous system susceptible to degenerations. Transcriptional factors or their cofactors, such as CREB or creb-binding protein (CBP) sequestrated in NIs, may alter the major intracellular transcriptional signal transduction and ultimately may result in neuronal degeneration. The components in the ubiquitin-proteasome pathway also colocalized in NIs and contribute to the path-ogenesis of SBMA. We generated two types of transgenic mice expressing 239Q under the control of human AR promoter and full-size AR containing 97Q. Marked neurological symptoms and extensive nuclear inclusions were observed in both transgenic lines, but there was no neuronal cell death, suggesting that major neurological phenotype was due to neuronal dysfunction instead of neuronal cell death. As for the therapeutic strategies, the overexpression of Hsp70 and Hsp40 chaperones acted together to protect a cultured neuronal cell model of SBMA from inclusion formation and cell death by mutant AR with expanded polyglutamine tract. In regard to ALS, we are screening the gene expression profiles of the motor neurons from the human ALS and SOD transgenic mouse spinal cord. Motor neurons were microdissected from the spinal cord samples by a lazer-captured microdissection system. Gene expression profiles were screened by cDNA microarray and molecular indexing. Several new molecules were cloned and characterized for their function and relation to neuronal cell dysfunction. Some molecules characterized in this procedure were briefly described.
Prefrontal cortex fMRI signal changes are correlated with working memory load (1997)

We investigated whether a nonspatial working memory (WM) task would activate dorsolateral prefrontal cortex (DLPFC) and whether activation would be correlated with WM load. Using functional magnetic resonance imaging we measured regional brain signal changes in 12 normal subjects performing a continuous performance, choice reaction time task that requires WM. A high WM load condition was compared with a non-WM choice reaction time control condition (WM effect) and a low WM load condition (load effect). Significant changes in signal intensity occurred in the DLPFC, frontal motor regions and the intraparietal sulcus (IPS) in both comparisons. These findings support the role of DLPFC and IPS in WM and suggest that signal changes in DLPFC correlate with WM load.