gebhart/patrepeval huggingface dataset:
Construction of an Expression System for Site-DirectedMutagenesis of the LantibioticMersacidin (2003)

The lantibiotic (i.e., lanthionine-containing antibiotic) mersacidin is an antimicrobial peptide of 20 amino acids which is produced by Bacillus sp. strain HIL Y-85,54728. Mersacidin inhibits bacterial cell wall biosynthesis by binding to the precursor molecule lipid II. The structural gene of mersacidin (mrsA) and the genes for the enzymes of the biosynthesis pathway, dedicated transporters, producer self-protection proteins, and regulatory factors are organized in a biosynthetic gene cluster. For site-directed mutagenesis of lantibiotics, the engineered genes must be expressed in an expression system that contains all of the factors necessary for biosynthesis, export, and producer self-protection. In order to express engineered mersacidin peptides, a system in which the engineered gene replaces the wild-type gene on the chromosome was constructed. To test the expression system, three mutants were constructed. In S16I mersacidin, the didehydroalanine residue (Dha) at position 16 was replaced with the Ile residue found in the closely related lantibiotic actagardine. S16I mersacidin was produced only in small amounts. The purified peptide had markedly reduced antimicrobial activity, indicating an essential role for Dha16 in biosynthesis and biological activity of mersacidin. Similarly, Glu17, which is thought to be an essential structure in mersacidin, was exchanged for alanine. E17A mersacidin was obtained in good yields but also showed markedly reduced activity, thus confirming the importance of the carboxylic acid function at position 17 in the biological activity of mersacidin. Finally, the exchange of an aromatic for an aliphatic hydrophobic residue at position 3 resulted in the mutant peptide F3L mersacidin; this peptide showed only moderately reduced activity.
Carbon monoxide as an endogenous vascular modulator (2011)

Carbon monoxide (CO) is produced by heme oxygenase (HO)-catalyzed heme degradation to CO, iron, and biliverdin. HO has two active isoforms, HO-1 (inducible) and HO-2 (constitutive). HO-2, but not HO-1, is highly expressed in endothelial and smooth muscle cells and in adjacent astrocytes in the brain. HO-1 is expressed basally only in the spleen and liver but can be induced to a varying extent in most tissues. Elevating heme, protein phosphorylation, Ca(2+) influx, and Ca(2+)/calmodulin-dependent processes increase HO-2 activity. CO dilates cerebral arterioles and may constrict or dilate skeletal muscle and renal arterioles. Selected vasodilatory stimuli, including seizures, glutamatergic stimulation, hypoxia, hypotension, and ADP, increase CO, and the inhibition of HO attenuates the dilation to these stimuli. Astrocytic HO-2-derived CO causes glutamatergic dilation of pial arterioles. CO dilates by activating smooth muscle cell large-conductance Ca(2+)-activated K(+) (BK(Ca)) channels. CO binds to BK(Ca) channel-bound heme, leading to an increase in Ca(2+) sparks-to-BK(Ca) channel coupling. Also, CO may bind directly to the BK(Ca) channel at several locations. Endothelial nitric oxide and prostacyclin interact with HO/CO in circulatory regulation. In cerebral arterioles in vivo, in contrast to dilation to acute CO, a prolonged exposure of cerebral arterioles to elevated CO produces progressive constriction by inhibiting nitric oxide synthase. The HO/CO system is highly protective to the vasculature. CO suppresses apoptosis and inhibits components of endogenous oxidant-generating pathways. Bilirubin is a potent reactive oxygen species scavenger. Still many questions remain about the physiology and biochemistry of HO/CO in the circulatory system and about the function and dysfunction of this gaseous mediator system.
Theory of Simulated-Skin-Effect Filters a Thin Film Approach to EMI (1964)

The theory of a new, ceramic lowpass filter, highly effective at very high frequencies, is discussed. Its excellent performance is based on simulation of the skin effect whereby the VHF, UHF and microwave currents are forced along a thin, electrically permeable resistive film deposited inside a high-ϵ dielectric tube while a large dc current may flow through the coaxial conductor. Theory and experiment are in excellent agreement. In several respects these filters are better than cascaded filters (ferrites and dielectrics combined) which were, thus far, considered the best available. The simulated-skin-effect filter shows great promise of becoming a significant means in combatting conducted electromagnetic interference.
Sulfated Hyaluronan Derivatives Modulate TGF-β1:Receptor Complex Formation: Possible Consequences for TGF-β1 Signaling (2017)

Glycosaminoglycans are known to bind biological mediators thereby modulating their biological activity. Sulfated hyaluronans (sHA) were reported to strongly interact with transforming growth factor (TGF)-β1 leading to impaired bioactivity in fibroblasts. The underlying mechanism is not fully elucidated yet. Examining the interaction of all components of the TGF-β1:receptor complex with sHA by surface plasmon resonance, we could show that highly sulfated HA (sHA3) blocks binding of TGF-β1 to its TGF-β receptor-I (TβR-I) and -II (TβR-II). However, sequential addition of sHA3 to the TβR-II/TGF-β1 complex led to a significantly stronger recruitment of TβR-I compared to a complex lacking sHA3, indicating that the order of binding events is very important. Molecular modeling suggested a possible molecular mechanism in which sHA3 could potentially favor the association of TβR-I when added sequentially. For the first time bioactivity of TGF-β1 in conjunction with sHA was investigated at the receptor level. TβR-I and, furthermore, Smad2 phosphorylation were decreased in the presence of sHA3 indicating the formation of an inactive signaling complex. The results contribute to an improved understanding of the interference of sHA3 with TGF-β1:receptor complex formation and will help to further improve the design of functional biomaterials that interfere with TGF-β1-driven skin fibrosis.
Olfactory receptor neurons exist as distinct subclasses of immature and mature cells in primary culture (1999)

The processes of neuronal differentiation and survival are key questions in neurobiology. The olfactory system possesses unique regenerative capacity, as its neurons are continually replaced throughout adulthood from a maintained population of precursor cells. Primary cultures of olfactory epithelium enriched in olfactory neurons would provide a useful model to study the processes of neurogenesis, differentiation and senescence. To determine whether immature olfactory neurons could be isolated in primary culture and to investigate the mechanisms underlying these processes, culture conditions which selectively favored the presence of immature olfactory neurons were optimized. Using low plating densities, a population of cells was identified which, by reverse transcription-polymerase chain reaction, demonstrated messages for olfactory neuronal markers, including Golf, olfactory cyclic nucleotide-gated channel and olfactory marker protein, as well as the p75 low-affinity nerve growth factor receptor. Immunocytochemical analysis showed that these putative immature olfactory neurons possessed immunoreactivity to G(olf), neuron-specific tubulin, neural cell adhesion molecule, synaptophysin and neurofilament. These neurons were defined as olfactory receptor neuron-1 cells. Under these conditions, a separate class of rarely occurring cells with different morphology demonstrated immunoreactivity to mature markers, such as adenylyl cyclase III and olfactory marker protein. Electrophysiologically, these cells displayed properties consistent with those of acutely dissociated olfactory receptor neurons. Another class of rarer cells which represented less than 2% of cells in culture demonstrated immunoreactivity to glial fibrillary acidic protein. These cultures can serve as a model for in vitro analysis of olfactory receptor neuronal development and maintenance, and provide a potential substrate for the development of cell lines.
Preparation of thioester substrates and development of continuous spectrophotometric assays for phospholipase A1 and monoacylglycerol lipase (1981)

Current assays of phospholipase A1 (EC 3.1.1.32) and monoacylglycerol lipase (EC 3.1.1.23) activities in tissues are discontinuous, laborious, and expensive. Some spectrophotometric substrates were synthesized to alleviate this problem. Thioester analogs of phosphatidylcholine and phosphatidylethanolamine. rac-1,2-S,O-didecanoyl-3-phosphocholine-1-mercapto-2,3-propanediol and rac-1,2-S,O-didecanoyl-3-phosphoethanolamine-1-mercapto-2,3-propanediol, were synthesized from the diacylglycerol analog, rac-1,2-S,O--didecanoyl-1-mercapto-2,3-propanediol. The latter was prepared from triacylmercaptoglycerol by lipolysis and separation by chromatography on silica gel. Monoacylglycerol thioester analogs, 1-S-hexadecanoyl-1-mercapto-2,3-propanediol and 1-S-decanoyl-1-mercapto-2,3-propanediol, were synthesized by selective acylation of mercaptoglycerol. All of the substrates were hydrolyzed by Rhizopus delemar lipase to release sulfhydryl groups reactive towards 4,4'-dithiobispyridine. The hydrolysis could be followed continuously in a spectrophotomer with 0.1 absorbance unit corresponding to 5 nmol product. The structure and isomeric purity of the phospholipid analogs were verified by their behavior on thin-layer chromatography, elemental analyses, infrared spectra, and by the specificity of the colorimetric reaction with lipolytic enzymes. Whereas phospholipase A1 activity hydrolyzed both phospholipid analogs to release the theoretical amount of free thiol, neither phospolipases C nor A2 promoted thio release. The pH optimum, heat stability, and Ca2+ ion dependency were determined for the hydrolysis of each substrate by R. delemar lipase. The results indicate that the phospholipase A1 and monoacylglycerol lipase activities in R. delemar lipase are due to separate enzymes, and that these enzyme specific assays will be of general utility for enzyme characterization and purification studies. These substrates are useful for sensitive, convenient, and specific spectrophotometric assays for phospholipase A1 and monoacylglycerol lipase over the pH range 3 to 8.
Shields Up! Protecting browsers, endpoints and enterprises against web-based attacks (2009)

Browser-based malware attacks have become increasingly common, and the packing of legitimate websites using techniques such as SQL injection and FTP password theft has led to a proliferation of bot-infected machines. How can users protect themselves against such threats? Virtualising the browser can help to provide detection by inserting a virtual layer between the application and the operating system. This article describes the mechanics of popular Web-based attacks, and looks at the idea of a virtual shield to help protect unwitting surfers from danger. What do security technology and Norman Britain have in common? Well, the former may have come a long way in the last 850 years, but we can still learn a thing or two from the latter, and apply it accordingly.
Transportation of mono-dispersed micro-plasma bubble in microfluidic chip under atmospheric pressure (2013)

We have successfully produced mono-dispersed micro-scale plasma bubble in microfluidic chip under atmospheric pressure, and which can be transported to the downstream of the chip. The plasma produced has characteristics of low temperature and which was generated by dielectric barrier discharge for biomedical applications. The discretized plasma phase in microfluidic chip provides high accuracy irradiation to the affected area with limited collateral damage area. This technique is closely tied to the therapeutic uses with high accuracy.
Nature and nurture, danger and delight: urban women's experiences of the natural world (1997)

Abstract In this paper, we address a research lacuna in the area of human experience of, and interaction with, nature. We focus on women in an urbanized setting, exploring their actual and desired experiences of the natural world, using Singapore as a case study. Our intention is to contribute to both the evolving theoretical and empirical discussions on this subject. Based on data collected from focus group discussions and household questionnaires, we conclude that women's relationships with nature in Singapore are underscored by a strong inclination towards nurturing: teaching, tending and caring, in a way that is not as apparent in men's relationships with nature. Women's relationships with nature may also be conceptualized in terms of ‘danger’ and ‘delight’, a fine balance between ambivalent experiences of fear and enjoyment. In comparing results based on the Singapore context with those in Britain, sources of enjoyment appear to be similar, but the different social situations have resulted in different sources of fear. We conclude by putting forward some recommendations for planning and designing green areas that may enhance women's use and enjoyment of nature areas.
Micelle Morphology and Mechanical Response of Triblock Gels (2009)

The effect of polymer concentration on mechanical response and micelle morphology of ABA and AB copolymers in B-selective solvents has been systematically studied. Micelle morphology was determined using a combination of small-angle X-ray scattering, shear, and birefringence while mechanical response at low and high strains was determined using indentation techniques. Self-consistent field theory calculations were used to determine micelle volume fraction profiles and to construct an equilibrium phase map. The transition from spherical to cylindrical micelles increases the triblock gel modulus and energy dissipation. Combining knowledge of gel relaxation time, which determines the rate at which the gel can equilibrate its micelle structure, with the equilibrium phase map allows estimation of the experimental temperatures and time scales over which kinetic trapping will arrest micelle structure evolution. Kinetic trapping enables cylindrical morphologies to be obtained at significantly lower polymer fractions than is possible in equilibrated systems.
Antibody-Targeted Chemotherapy with the Calicheamicin Conjugate hu3S193-<b> <i>N</i> </b>-Acetyl γ Calicheamicin Dimethyl Hydrazide Targets Lewisy and Eliminates Lewisy-Positive Human Carcinoma Cells and Xenografts (2004)

Hu3S193-CalichDMH can specifically eliminate Le(y+) tumors. These results support development of this conjugate for treatment of carcinomas.
Guidelines for Management of Idiopathic Normal Pressure Hydrocephalus Guidelines From the Guidelines Committee of Idiopathic Normal Pressure Hydrocephalus, the Japanese Society of Normal Pressure Hydrocephalus (2008)

With the rapid aging of Japanese society, medical care of the elderly has become an important social issue. Among various disorders manifesting dementia, gait disturbance, and urinary incontinence in the elderly population, normal pressure hydrocephalus (NPH), especially of idiopathic type (iNPH), is becoming noteworthy. The Guidelines for management of iNPH in Japan are created in compliance with the evidence-based medicine methods and published in 2004. This English version is made to show the diagnosis and treatment of iNPH with reference to the socio-medical background in Japan and to promote the international research on iNPH. They propose three diagnostic levels; possible, probable, and definite. They indicate the diagnostic importance of high convexity tightness and dilated sylvian fissure with mild to moderate ventriculomegaly on coronal magnetic resonance imaging. The cerebrospinal fluid tap test is regarded as an important diagnostic test because of its simplicity to perform and high predictability of the shunt efficacy. The use of programmable valves at shunt surgeries is recommended. Flowcharts for diagnosis, preoperative assessment, and prevention for complications of shunt surgery are made to promote a wide use of them.
Grains, Growth, and Grooving (2003)

We report the in situ investigation of grain growth and grain boundary migration, performed with a variable-temperature scanning tunneling microscope (STM) on a polycrystalline gold film. Atomic step resolution allowed us to identify the individual grains and, thus, also the grain boundaries. Our special, thermal-drift-compensated STM design made it possible to follow the same sample area over large temperature intervals. In this way, we have directly observed grain boundary migration and grain growth. In a first quantitative analysis we correlate the observed, unexpected changes in surface roughness with the evolution of the grain and grain boundary configuration.
Building energy doctors: SPC and Kalman filter-based fault detection (2011)

Buildings worldwide account for nearly 40% of global energy consumption. The biggest energy consumer in buildings is the Heating, Ventilation and Air Conditioning (HVAC) systems. HVAC also ranks top in terms of number of complaints by tenants. Maintaining HVAC systems in good conditions through early fault detection is thus a critical issue. The problem, however, is difficult since HVAC systems are large in scale, consisting of many coupling subsystems, building and equipment dependent, and operating under uncertain conditions. In this paper, a model-based and data-driven method is presented for robust system-level fault detection with potential for large-scale implementation. It is a synergistic integration of (1) Statistical Process Control (SPC) for measuring and analyzing variations; (2) Kalman filtering based on gray-box models to provide predictions and determine SPC control limits; and (3) system analysis for analyzing fault propagation. The method has been tested against a simulation model of a 420-meter-high building. It detects both sudden faults and gradual degradation, and differentiates faults within a subsystem or propagated from elsewhere. Furthermore, the method is simple and generic, and should have good replicability and scalability.
[The effect of wuto granules on the levels of excitatory amino acids in extracellullar fluid of rat hippocampus following cerebral ischemia]. (1997)

We observed the changes of excitatory amino acids (EAA) in extracellular fluid (ECLF) in rat hippocampus in case of cerebral ischemia after giving Wuto Granule compring the test groups with the control groups by microdialysis method. Results showed that there was no effect on EAA in extrcellular fluid by the drug before cerebral ischemia, but there existed staistical singnifcant changes of EAA in extracellular fluid one hour after cerebral ischemia comparing the test groups Glu and Asp with the control groups (P < 0.01). We found that there is a decrease of release of release of EAA in ECLF in case of ischemia by Wuto Granule. It could be deduced that Wuto Granule can penetrate the brain-blood barrier and this can protect the brain incse of ischemia. The application of intracerebral micrdialysis has provided a new method for the research work of pharmacology.
Alternative Splice Variants of Doublecortin-like Kinase Are Differentially Expressed and Have Different Kinase Activities (2002)

Alternative splicing of mRNA transcripts expands the range of protein products from a single gene locus. Several splice variants of DCLK (doublecortin-like kinase) have previously been reported. Here, we report the genomic organization underlying the splice variants of DCLK and examine the expression profile of two splice variants affecting the kinase domain of DCLK and CPG16 (candidate plasticity gene 16), one containing an Arg-rich domain and the other affecting the C terminus of the protein. These splice alternatives were differentially expressed in embryonic and adult brain. Both splice variants disrupted DCLK PEST domains; however, all splice variants remained sensitive to proteolysis by calpain. The adult-specific C-terminal splice variant of DCLK had reduced autophosphorylation activity, but similar kinase activity for myelin basic protein relative to the embryonic splice variant. The splice variant adding an Arg-rich domain gained an autophosphorylation site at Ser-382. Although this protein isoform was expressed mainly in the adult brain, the phosphorylated form was strongly enriched in embryonic brain and adult olfactory bulb, suggesting a possible role in migrating neurons.
Association of Preterm Birth With Long-term Survival, Reproduction, and Next-Generation Preterm Birth (2008)

In persons born in Norway in 1967-1988, preterm birth was associated with diminished long-term survival and reproduction.
The Determination of Ultrafiltrable Calcium and Magnesium in Serum (1982)

Ultrafiltrate of human serum was investigated in order to evaluate the serum content of calcium and magnesium. The acid and base concentrations and pH of the serum was altered through titration with HCl- or NaOH-solutions. The Pco2 was varied in the titrated serum using different carbon dioxide tensions. This was performed when serum was filtered in a recycling system. It is shown that the analysis of calcium and magnesium have to be done under anaerobic conditions or at standardized pH and Pco2 situations, as the concentrations vary with both pH and Pco2. The concentration ratio between ultrafiltrate and serum for calcium and magnesium was found to be 0.56 and 0.74 respectively at pH=7.41 and Pco2=40 mmHg.
Stripe-specific regulation of pair-rule genes by hopscotch, a putative Jak family tyrosine kinase in Drosophila. (1994)

We describe the characterization of the Drosophila gene, hopscotch (hop), which is required maternally for the establishment of the normal array of embryonic segments. In hop embryos, although expression of the gap genes appears normal, there are defects in the expression patterns of the pair-rule genes even-skipped, runt, and fushi tarazu, as well as the segment-polarity genes engrailed and wingless. We demonstrate that the effect of hop on the expression of these genes is stripe-specific. The hop gene encodes a putative nonreceptor tyrosine kinase of the Janus kinase family, based on an internal duplication of the catalytic domain. We present a model in which the Hop tyrosine kinase is involved in the control of pair-rule gene transcription in a stripe-specific manner. Our results provide the first evidence for stripe-specific regulation of pair-rule genes by a tyrosine kinase.
Architectural Design and Implementation of an FPGA Softcore Based Speech Recognition System (2006)

In spite of ever increasing logic capacity of FPGAs, the implementation of a large vocabulary speech recognition system encounters insufficient I/O bandwidth and internal memory capacity problems. In this paper, a speech recognition system architecture was described based on a softcore with hardware accelerators for the emission probability computation and the Viterbi beam search. The hardware accelerator for emission probability computation is equipped with the internal memory to effectively capture the access pattern of the acoustic model data which depend on the language model. The optimal memory configuration is determined by the proposed data partitioning strategy. The developed system has been implemented on a Xilinx Virtex-4 FPGA with MicroBlaze softcore processor along with various peripherals. The experimental results show that the proposed architecture speeds up the recognition by reducing the memory bandwidth requirement thereby the system is capable of performing real-time recognition for the DARPA resource management task which supports about 1000 words continuous speech recognition