gebhart/patrepeval huggingface dataset:
Nitric oxide from neuronal nitric oxide synthase sensitises neurons to hypoxia‐induced death via competitive inhibition of cytochrome oxidase (2007)

Hypoxia/ischaemia is known to trigger neuronal death, but the role of neuronal nitric oxide synthase (nNOS) in this process is controversial. Nitric oxide (NO) inhibits cytochrome oxidase in competition with oxygen. We tested whether NO derived from nNOS synergises with hypoxia to induce neuronal death by inhibiting mitochondrial cytochrome oxidase. Sixteen hours of hypoxia (2% oxygen) plus deoxyglucose (an inhibitor of glycolysis) caused extensive, excitotoxic death of neurons in rat cerebellar granule cell cultures. Three different nNOS inhibitors (including the selective inhibitor N-4S-4-amino-5-2-aminoethyl-aminopentyl-N'-nitroguanidine) decreased this neuronal death by half, indicating a contribution of nNOS to hypoxic death. The selective nNOS inhibitor did not, however, block neuronal death induced either by added glutamate or by added azide (an uncompetitive inhibitor of cytochrome oxidase), indicating that nNOS does not act downstream of glutamate or cytochrome oxidase. Hypoxia plus deoxyglucose-induced glutamate release and neuronal depolarisation, and the nNOS inhibitor decreased this. Hypoxia inhibited cytochrome oxidase activity in the cultures, but a selective nNOS inhibitor prevented this inhibition, indicating NO from nNOS was inhibiting cytochrome oxidase in competition with oxygen. These data indicate that hypoxia synergises with NO from nNOS to induce neuronal death via cytochrome oxidase inhibition causing neuronal depolarisation. This mechanism might contribute to ischaemia/stroke-induced neuronal death in vivo.
Neural reputation models learned from passive DNS data (2017)

Blacklists and whitelists are often employed to filter outgoing and incoming traffic on computer networks. One central function of these lists is to mitigate the security risks posed by malware threats by associating a reputation (for instance benign or malicious) to end-point hosts. The creation and maintenance of these lists is a complex and time-consuming process for security experts. As a consequence, blacklists and whitelists are prone to various errors, inconsistencies and omissions, as only a tiny fraction of end-point hosts are effectively covered by the reputation lists. In this paper, we present a machine learning model that is able to automatically detect whether domain names and IP addresses are benign, malicious or sinkholes. The model relies on a deep neural architecture and is trained on a large passive DNS database. Evaluation results demonstrate the effectiveness of the approach, as the model is able to detect malicious DNS records with a F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> score of 0.96. In other words, the model is able to detect 95 % of the malicious hosts with a false positive rate of 1:1000.
On the c-Si surface passivation mechanism by the negative-charge-dielectric Al2O3 (2008)

Al 2 O 3 is a versatile high-κ dielectric that has excellent surface passivation properties on crystalline Si (c-Si), which are of vital importance for devices such as light emitting diodes and high-efficiency solar cells. We demonstrate both experimentally and by simulations that the surface passivation can be related to a satisfactory low interface defect density in combination with a strong field-effect passivation induced by a negative fixed charge density Qf of up to 1013 cm−2 present in the Al2O3 film at the interface with the underlying Si substrate. The negative polarity of Qf in Al2O3 is especially beneficial for the passivation of p-type c-Si as the bulk minority carriers are shielded from the c-Si surface. As the level of field-effect passivation is shown to scale with Qf2, the high Qf in Al2O3 tolerates a higher interface defect density on c-Si compared to alternative surface passivation schemes.
Synthesis and Photovoltaic Properties of Alternating Conjugated Polymers Derived from Indeno[1,2‐b]fluorene and Bithiophene or Thieno[3,2‐b]thiophene‐Cored Benzothiadiazole (2011)

Abstract Two narrow bandgap copolymers derived from 6,6′,12,12′‐tetraoctyl‐indeno[1,2‐ b ]fluorene and bithiophene or thieno[3,2‐ b ]thiophene‐cored benzothiadiazole are synthesized and characterized. The copolymers show broad absorption in the range 350–700 nm. The application of the copolymers as photovoltaic cells with configurations ITO/PEDOT:PSS/blend/Al and ITO/PEDOT:PSS/blend/interlayer/Al is investigated. A power conversion efficiency (PCE) of approximately 3.0% is achieved under an AM 1.5G solar simulator (80 mW cm −2 ) for the cells with ITO/PEDOT:PSS/polymer:PC 71 BM([6,6]‐phenyl‐C 71 butyric acid methyl ester) (1:4)/interlayer/Al. magnified image
Light microscopic immunolocation of thrombospondin in human tissues. (1985)

Affinity-purified antisera against thrombospondin were used to locate the presence of this glycoprotein in frozen sections of several human tissues by immunofluorescence techniques. Immunostaining was observed in the peritubular connective tissue and in basement membrane regions beneath glandular epithelium in skin and lung. Intense immunostaining was observed at the dermal-epidermal junction in skin and in small blood vessels throughout this tissue. Skeletal muscle exhibited positive staining with anti-thrombospondin antisera within interstitial areas. Immunostaining was confined to the luminal portions of large blood vessels such as aorta. In large blood vessels that contained lesions of atherosclerosis, immunostaining was observed throughout the lesion area and was especially prominent surrounding some of the lesion cells. These results indicate that thrombospondin is located within the matrix of a variety of human tissues and supports the suggestion that this glycoprotein is an endogenous component of some extracellular matrices.
Thienodolin, a New Plant Growth-regulating Substance Produced by a Streptomycete Strain: I. Taxonomy and Fermentation of the Producing Strain, and the Isolation and Characterization of Thienodolin (1993)

Thienodolin, a new plant growth-regulating substance, was isolated from the fermentation broth of a streptomycete strain identified as Streptomyces albogriseolus.The active principle was extracted with ethyl acetate and purified by silica gel column chromatography and preparative HPLC. The substance showed growth promoting activity with 1.2 × 10−6–1.2 × 10−5 M treatment to rice seedlings, and inhibitory activity with 4.0 × 10−5 M treatment.
Direct Spectroscopic Observation of the Structural Origin of Peroxide Generation from Co-Based Pyrolyzed Porphyrins for ORR Applications (2008)

Pyrolyzed transition metal based porphyrins present an attractive alternative to state of the art Pt-based electrocatalysts for fuel cell applications based on their comparatively low cost. Unfortunately, the large array of precursors and synthetic strategies has led to considerable ambiguity regarding the specific structure/property relationships that give rise to their activity for oxygen reduction. Specifically, considerable debate exists in actual chemical structure of the pyrolyzed reaction centers, and their relationship to membrane-damaging peroxide yield. In this manuscript a comprehensive electrochemical and spectroscopic study of pyrolyzed CoTMPP produced via a self-templating process is presented. The resulting electrocatalysts are not carbon-supported, but are highly porous self-supported pyropolymers. Rotating ring disk electrode measurements showed that the materials pyrolyzed at 700 °C exhibited the highest performance, whereas pyrolysis at 800 °C resulted in a significant increase in the peroxide yield. X-ray photoelectron spectroscopy and Co L and K edge extended X-ray absorption fine structure (EXAFS) studies confirm that the majority of the Co−N4 active site has broken down to Co−N2 at 800 °C. Application of Δμ analysis (an X-ray absorption near-edge structure difference technique) to the in situ Co K edge EXAFS data allowed for direct spectroscopic observation of the geometry of Oads on the pyropolymer active sites. The specific geometrical adsorption of molecular oxygen with respect to the plane of the Co−Nx moieties highly influences the oxygen reduction reaction pathway. The application of the Δμ technique to other transition metal based macrocycle electrocatalyst systems is expected to provide similarly detailed information.
Host location byAedes aegypti(Diptera: Culicidae): a wind tunnel study of chemical cues (1991)

Abstract Lactic acid, carbon dioxide and human sweat stimuli were presented singly and in combination to female Aedes aegypti (Linnaeus) within a wind-tunnel system. The take-off, flight, landing and probing responses of the mosquitoes were recorded using direct observation and video techniques. The analyses determined the nature of the response to different stimuli and the concentration ranges within which specific behaviours occurred. A threshold carbon dioxide concentration for taking-off of approximately 0.03% above ambient was detected. Lactic acid and human sweat samples did not elicit take-off when presented alone, however, when they were combined with elevated carbon dioxide, take-off rate was enhanced in most of the combinations tested. Flight activity was positively correlated with carbon dioxide level and some evidence for synergism with lactic acid was found within a narrow window of blend concentrations. The factors eliciting landing were more subtle. There was a positive correlation between landing rate and carbon dioxide concentration. At the lowest carbon dioxide concentration tested, landing occurred only in the presence of lactic acid. Within a window of low to intermediate concentrations, landing rate was enhanced by this combination. At the highest carbon dioxide concentration, landing was however inhibited by the presence of lactic acid. The sweat extract elicited landings in the absence of elevated carbon dioxide. This indicated the presence of chemical stimuli, other than lactic acid, active in the short range. Probing occurred only at low carbon dioxide concentrations and there was no probing when lactic acid alone was tested. There was however probing in the presence of combined stimuli, the level of response seemed to be positively correlated with the ratio of carbon dioxide and lactic acid concentrations.
Eotaxin (CCL11) and Eotaxin-2 (CCL24) Induce Recruitment of Eosinophils, Basophils, Neutrophils, and Macrophages As Well As Features of Early- and Late-Phase Allergic Reactions Following Cutaneous Injection in Human Atopic and Nonatopic Volunteers (2002)

Eotaxin and eotaxin-2, acting through CCR3, are potent eosinophil chemoattractants both in vitro and in animal models. In this study we examined the capacity of eotaxin and eotaxin-2 to recruit eosinophils and other inflammatory cells in vivo in human atopic and nonatopic skin. Skin biopsies taken after intradermal injection of eotaxin and eotaxin-2 were examined by immunohistochemistry. Allergen- and diluent-challenged sites were used as positive and negative controls. Eotaxin and eotaxin-2 produced a dose- and time-dependent local eosinophilia of comparable intensity in both atopic and nonatopic individuals. This was associated with an acute wheal and flare response at the site of injection and development of a cutaneous late phase reaction in a proportion of subjects. There was an accompanying decrease in mast cell numbers. Both chemokines also induced the accumulation of basophils and an unexpected early infiltration of neutrophils. Macrophages were prominent at the 24-h point. Although there was surface CCR3 expression on neutrophils in whole blood, we were unable to demonstrate any functional neutrophil responses to eotaxin in vitro. Thus, intradermal injection of eotaxin and eotaxin-2 in humans induced infiltration of eosinophils and other inflammatory cells as well as changes consistent with CC chemokine-induced mast cell degranulation.
Inhibition of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Activity by Cordatolides Isolated fromCalophyllum cordato-oblongum (1998)

Cordatolide A and B were re-isolated from Calophyllum cordato-oblongum, an endemic species of Sri Lanka, and found to inhibit HIV-1 reverse transcriptase with IC50 values of 12.3 and 19.0 microM, respectively.
BiCS Flash as a Future 3D Non-Volatile Memory Technology for Ultra High Density Storage Devices (2009)

In this presentation, recent reports on three dimensional non-volatile memories are reviewed and their pros and cons are discussed. BiCS (Bit Cost Scalable) flash technology is focused as one of the most promising candidates for the future ultra high density storage devices.
Detection and Differentiation of Chlamydia trachomatis, Chlamydia psittaci, and Chlamydia pneumoniae by DNA Amplification (1990)

The polymerase chain reaction was used to detect major outer membrane protein (MOMP) gene sequences from the three species of Chlamydia. Using three primer pairs and one restriction enzyme digestion, three distinct genotypes, corresponding to the three species, Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci, were demonstrated. C. trachomatis was amplified by all three primer pairs and the amplified fragment was digested by EcoRI. C. pneumoniae was amplified by only two of the three primer pairs, and the amplified fragment was digested by EcoRI. C. psittaci was amplified by only two of the pairs and the amplified fragment was EcoRI-resistant. C. trachomatis was detected in direct patient specimens, tissue culture specimens, and fixed specimens, and all serovars of C. trachomatis were detectable. The polymerase chain reaction can detect and differentiate the three species of Chlamydia and may prove a valuable diagnostic tool.
Adsorption of Atomic Hydrogen on Single-Walled Carbon Nanotubes (2005)

We have investigated atomic and electronic structures of hydrogen-chemisorbed single-walled carbon nanotubes (SWCNTs) by density functional calculations. We have searched for relative stability of various hydrogen adsorption geometries with coverage. The hydrogenated SWCNTs are stable with coverage of H/C, theta >/= 0.3. The circular cross sections of nanotubes are transformed to polygonal shapes with different symmetries upon hydrogen adsorption. We find that the band gap in carbon nanotubes can be engineered by varying hydrogen coverage, independent of the metallicity of carbon nanotubes. This is explained by the degree of sp(3) hybridization.
Noncovalent interactions of molecules with single walled carbon nanotubes (2006)

In this critical review we survey non-covalent interactions of carbon nanotubes with molecular species from a chemical perspective, particularly emphasising the relationship between the structure and dynamics of these structures and their functional properties. We demonstrate the synergistic character of the nanotube-molecule interactions, as molecules that affect nanotube properties are also altered by the presence of the nanotube. The diversity of mechanisms of molecule-nanotube interactions and the range of experimental techniques employed for their characterisation are illustrated by examples from recent reports. Some practical applications for carbon nanotubes involved in non-covalent interactions with molecules are discussed.
P1 site-specific recombination: nucleotide sequence of the recombining sites. (1982)

Site-specific recombination between molecules of bacteriophage P1 DNA occurs at sites called loxP and requires the action of a protein that is the product of the P1 cre gene. Although recombination between two loxP sites is very efficient, recombination between loxP and a unique site in the bacterial chromosome (loxB) is inefficient and generates two hybrid lox sites called loxR and loxL. We present here the nucleotide sequences of all four lox sites. Analysis of these sequences indicates that (i) a region of extensive homology is not present at the loxP X loxB crossover point, in contrast to the 15-base pair common-core sequence in the bacteriophage lambda att sites, and (ii) the sites contain a region of dyad symmetry with 8- to 13-base pair inverted repeats separated by an 8- to 9-base pair sequence. The loxP X loxB crossover point falls in the sequence that separates the inverted repeats, and deletions that remove either the left or the right inverted repeat of loxP inactivate the site. These two observations are consistent with the conclusion that the region of dyad symmetry is important in los recombination. We have shown further that the loxP X loxP crossover point occurs in a 63-base pair sequence containing the loxP X loxB crossover point, suggesting that, despite the great difference in efficiencies of the two reactions, the crossover points may occur at the same place in both. Explanations for the different recombination properties of the various lox sites are discussed.
Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer. (2002)

The serum of cancer patients often harbors increased free DNA levels, which can potentially be used for cancer detection. Because genetic and epigenetic alterations of the adenomatous polyposis coli (APC) gene are common events in gastrointestinal tumor development, we sought to investigate the frequency and level of aberrant APC promoter methylation in primary tumors and paired preoperative serum or plasma samples of lung cancer patients by semiquantitative methylation-specific fluorogenic real-time PCR. We detected methylation of APC in 95 of 99 (96%) primary lung cancer tissues. Forty-two of 89 (47%) available serum and/or plasma samples from these cases carried detectable amounts of methylated APC promoter DNA. In contrast, no methylated APC promoter DNA was detected in serum samples from 50 healthy controls. A highly elevated APC methylation level in lung cancer tissue was the only independent factor predicting inferior survival in this cohort (P = 0.015). APC methylation analysis appears to be promising as a prognostic factor in primary lung cancer and as a noninvasive tumor marker in plasma and/or serum DNA.
Improved J-E Characteristics and Stress Induced Leakage Currents (SILC) in Oxynitride Films Grown at 400℃ by Microwave-Excited High-Density Kr/O2/NH3 Plasma (2001)

2001 International Conference on Solid State Devices and Materials,Improved J-E Characteristics and Stress Induced Leakage Currents (SILC) in Oxynitride Films Grown at 400℃ by Microwave-Excited High-Density Kr/O2/NH3 Plasma
Adenosine A2A receptor ligand recognition and signaling is blocked by A2B receptors (2018)

The adenosine receptor (AR) subtypes A<sub>2A</sub> and A<sub>2B</sub> are rhodopsin-like G<sub>s</sub> protein-coupled receptors whose expression is highly regulated under pathological, e.g. hypoxic, ischemic and inflammatory conditions. Both receptors play important roles in inflammatory and neurodegenerative diseases, are blocked by caffeine, and have now become major drug targets in immuno-oncology. By Förster resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), bimolecular fluorescence complementation (BiFC) and proximity ligation assays (PLA) we demonstrated A<sub>2A</sub>-A<sub>2B</sub>AR heteromeric complex formation. Moreover we observed a dramatically altered pharmacology of the A<sub>2A</sub>AR when co-expressed with the A<sub>2B</sub>AR (A<sub>2B</sub> ≥ A<sub>2A</sub>) in recombinant as well as in native cells. In the presence of A<sub>2B</sub>ARs, A<sub>2A</sub>-selective ligands lost high affinity binding to A<sub>2A</sub>ARs and displayed strongly reduced potency in cAMP accumulation and dynamic mass redistribution (DMR) assays. These results have major implications for the use of A<sub>2A</sub>AR ligands as drugs as they will fail to modulate the receptor in an A<sub>2A</sub>-A<sub>2B</sub> heteromer context. Accordingly, A<sub>2A</sub>-A<sub>2B</sub>AR heteromers represent novel pharmacological targets.
Analysis of Drosophila photoreceptor axon guidance in eye-specific mosaics (2000)

During development of the adult Drosophila visual system, axons of the eight photoreceptors in each ommatidium fasciculate together and project as a single bundle towards the optic lobes of the brain. Within the brain, individual photoreceptor axons from each bundle then seek specific targets in distinct layers of the optic lobes. The axons of photoreceptors R1-R6 terminate in the lamina, while R7 and R8 axons pass through the lamina to terminate in separate layers of the medulla. To identify genes required for photoreceptor axon guidance, including those with essential functions during early development, we have devised a strategy for the simple and efficient generation of genetic mosaics in which mutant photoreceptor axons innervate a predominantly wild-type brain. In a large-scale saturation mutagenesis performed using this system, we recovered new alleles of the gene encoding the receptor tyrosine phosphatase PTP69D. PTP69D has previously been shown to function in the correct targeting of motor axons in the embryo and R1-R6 axons in the visual system. Here, we show that PTP69D is also required for correct targeting of R7 axons. Whereas mutant R1-R6 axons occasionally extend beyond their normal targets in the lamina, mutant R7 axons often fail to reach their targets in the medulla, stopping instead at the same level as the R8 axon. These targeting errors are difficult to reconcile with models in which PTP69D plays an instructive role in photoreceptor axon targeting, as previously proposed. Rather, we suggest that PTP69D plays a permissive role, perhaps reducing the adhesion of R1-R6 and R7 growth cones to the pioneer R8 axon so that they can respond independently to their specific targeting cues.
Home blood pressure monitor use in patients with chronic kidney disease (2016)

Home blood pressure monitoring (HBPM) is recommended in patients with chronic kidney disease (CKD) and hypertension (HTN). However, little is known about the use and pattern of HBPM in CKD patients. A cross-sectional study was conducted in an out-patient nephrology clinic. A total of 285 patients participated in the study. Of all patients, 66% reported using HBPM. Self-reported compliance with BP medications (93.9% vs. 85.1%, p 0.03), exercise >3 days/week (45.9 vs. 26.3%, p <0.001) and dietary sodium restriction (85.6% vs. 71.6%, p < 0.001) were more common in HBPM users vs. non-HBPM users. Most patients with HBPM used upper arm cuff (82.3%), reported receiving education on correct use of HBPM (82.5%), had perception that home BP was controlled (75.4%) and believed that HBPM is helpful in managing hypertension (85.4%). Most common reason for not using HBPM was lack of advice by a physician (43.4%). HBPM use is common in patients with CKD and HTN. HBPM users are more likely to follow life-style and dietary modifications for blood pressure control.
Direct Observation of Nucleation and Growth in Amyloid Self-Assembly (2010)

Access to native protein structure depends on precise polypeptide folding and assembly pathways. Identifying folding missteps that may lead to the nearly 40 protein misfolding diseases could feature prominently in the development of intervention strategies. Accordingly, we have investigated the earliest steps of assembly by the folding nucleus of the Alzheimer's disease Abeta peptide with real-time imaging and fluorescence correlation spectroscopy. These analyses reveal the immediate formation of large micrometer size clusters maintaining properties of intermolecular molten globules. These dynamic unstructured aggregates serve as the nucleating sites for amyloid growth and, as with native protein folding, appear important for backbone desolvation. The resulting amyloid nucleus however is able to template monomer addition from solution at rates from 2K peptides/s at millimolar peptide concentrations. This direct observation of amyloid assembly unifies several divergent models that currently exist for protein misfolding.