gebhart/patrepeval huggingface dataset:
Solvent-exposed Residues in the Tet repressor (TetR) Four-helix Bundle Contribute to Subunit Recognition and Dimer Stability (1999)

Dimerization specificity of Tet repressor (TetR) can be altered by changes in the core of the four-helix bundle that mediates protein-protein recognition. We demonstrate here that the affinity of subunit interaction depends also on the solvent-exposed residues at positions 128 and 179'-184', which interact across the dimerization surface. TetR(B) and (D), two naturally occurring sequence variants, differ at position 128 with respect to the monomer-monomer distances in the crystal structures and the charge of the amino acids, being glutamate in TetR(B) and arginine in TetR(D). In vivo analysis of chimeric TetR(B/D) variants revealed that the single E128R exchange does not alter the dimerization specificity of TetR(B) to the one of TetR(D). When combined with specificity mutations in alpha10, it is, however, able to increase dimerization efficiency of the TetR(B/D) chimera with TetR(D). A loss of contact analysis revealed a positive interaction between Arg-128 and residues located at positions 179'-184' of the second monomer. We constructed a hyperstable TetR(B) variant by replacing residues 128 and 179-184 by the respective TetR(D) sequence. These results establish that in addition to a region in the hydrophobic core residues at the solvent-exposed periphery of the dimerization surface participate in protein-protein recognition in the TetR four-helix bundle.
Security Issues and Challenges for Cyber Physical System (2010)

In this paper, we investigate the security challenges and issues of cyber-physical systems. (1)We abstract the general workflow of cyber physical systems, (2)identify the possible vulnerabilities, attack issues, adversaries characteristics and a set of challenges that need to be addressed, (3)then we also propose a context-aware security framework for general cyber-physical systems and suggest some potential research areas and problems.
Three-Dimensional Photonic Crystal Laser-Driven Accelerator Structures (2006)

We discuss simulated photonic crystal structure designs for laser‐driven particle acceleration, focusing on three‐dimensional planar structures based on the so‐called “woodpile” lattice. We describe guiding of a speed‐of‐light accelerating mode by a defect in the photonic crystal lattice and discuss the properties of this mode, including particle beam dynamics and potential coupling methods for the structure. We also discuss possible materials and power sources for this structure and their effects on performance parameters, as well as possible manufacturing techniques and the required tolerances. In addition we describe the computational technique and possible improvements in numerical modeling that would aid development of photonic crystal structures.
Slide‐based cytometry for cytomics—A minireview (2006)

In the postgenomic era, to gain the most detailed quantitative data from biological specimens has become increasingly important in the emerging new fields of high-content and high-throughput single-cell analysis for systems biology and cytomics. Areas of research and diagnosis with the demand to virtually measure "anything" in the cell include immunophenotyping, rare cell detection and characterization in the case of stem cells and residual tumor cells, tissue analysis, and drug discovery. Systemic analysis is also a prerequisite for predictive medicine by genomics, proteomics, and cytomics. This issue of Cytometry Part A is dedicated to innovative concepts of system wide single cells analysis and manipulation, new technologies, data analysis and display, and, finally, quality assessment. The manuscripts to these chapters are provided by cutting edge experts in the fields. This overview will briefly highlight the most important aspects of this continuously developing field.
Autophagy Promotes Oligodendrocyte Survival and Function following Dysmyelination in a Long-Lived Myelin Mutant (2013)

The Long-Evans shaker (les) rat has a mutation in myelin basic protein that results in severe CNS dysmyelination and subsequent demyelination during development. During this time, les oligodendrocytes accumulate cytoplasmic vesicles, including lysosomes and membrane-bound organelles. However, the mechanism and functional relevance behind these oligodendrocyte abnormalities in les have not been investigated. Using high-magnification electron microscopy, we identified the accumulations in les oligodendrocytes as early and late autophagosomes. Additionally, immunohistochemistry and Western blots showed an increase in autophagy markers in les. However, autophagy did not precede the death of les oligodendrocytes. Instead, upregulating autophagy promoted membrane extensions in les oligodendrocytes in vitro. Furthermore, upregulating autophagy in les rats via intermittent fasting increased the proportion of myelinated axons as well as myelin sheath thickness in les and control rats. Overall, this study provides insight into the abnormalities described in les as well as identifying a novel mechanism that promotes the survival and function of oligodendrocytes.
Teleheimarbeit bei der IBM (1997)

Cet article presente la convention mise en place par la societe IBM Deutschland Informationsysteme GmbH concernant le teletravail a domicile dans le but de faire concurrence a la Deutsche Telekom AG. Cette convention est donc presentee et discutee
STUDY OF IMPACT FACTORS ON DATA ACQUISITION RATIO FOR DBF OCEAN RADAR WITH VHF BAND (2008)

The acquisition ratio of observational data by ocean radar presents a cyclic variation synchronized with tidal motion and an abrupt decreasing due to the meteorological conditions. Information relevant to the property of variation of the data acquisition and the impact factors on its variation is important for practical uses of ocean radar observation systems. The authors investigated the impact factors to the data acquisition ratio of the DBF (Digital Beam Forming) ocean radar with VHF band, central frequency 41.9MHz through long-term observation in Ariake Bay. As a result, the appearance of tidal flat along the coast off Arao mainly affected the cyclic variation of the data acquisition due to the transmission loss of radio waves. Besides, the flood from Chikugo River accompanied by heavy rainfalls and the decrease of conductivity at sea surface caused the abrupt decline of the acquisition ratio. At the term of weak wind less than 1m/s, the data acquisition also decreased by way of suppression of surface resonant wave.
Automated optimal synthesis of microresonators (2002)

The rapid layout synthesis of a microresonator from high-level functional specifications and design constraints is demonstrated. Functional parameters such as resonant frequency, quality factor, and displacement amplitude at resonance are satisfied while simultaneously minimizing an objective function. The optimal synthesis tool allows exploration of micromechanical design issues and objectives, as illustrated with a polysilicon lateral resonator example modeled in three mechanical degrees-of-freedom. Layouts for three sets of five different resonators from 3 kHz to 300 kHz are generated, with each set globally optimized to minimize either active device area, electrostatic drive voltage, or a weighted combination of area and drive voltage.
Pharmacology of novel imidazole alcohol inhibitors of primate renin (1989)

SQ 30,774 and SQ 31,844 are representatives of a novel class of renin inhibitors, the imidazole alcohols. These compounds, which contain an imidazole ring as part of their active site binding group are potent in vitro inhibitors of primate renin, but not rat, hog of dog renin. In conscious, sodium-depleted cynomolgus monkeys both compounds produced a dose-related inhibition of plasma renin activity (PRA) at doses ranging between 0.001 and 1.0 mumol/kg, intravenously, and total inhibition was observed after the highest dose. However, a reduction in blood pressure was observed only after an intravenous dose of 10 mumol/kg or when the compounds were administered by infusion. In sodium-replete monkeys, SQ 30,774 inhibited the rise in arterial pressure and PRA following administration of exogenous monkey renin. When the compounds were administered orally at 50 mumol/kg, only SQ 31,844 significantly inhibited PRA (80%). It is concluded that representatives of the imidazole alcohol class of renin inhibitors are potent inhibitors of renin in vitro and inhibit PRA and lower arterial pressure in vivo.
Inverse Flash NanoPrecipitation for Biologics Encapsulation: Nanoparticle Formation and Ionic Stabilization in Organic Solvents (2017)

Inverse Flash NanoPrecipitation, or iFNP, is a recently developed scalable, controllable, and reproducible process to produce nanoparticles highly loaded with water soluble molecules, such as biologics. The nanoparticles produced by iFNP have a hydrophilic core and hydrophobic corona, and are dispersed in organic solvents. However, most nanoparticle applications, particularly biomedical applications, require that the particle be stable in aqueous environments. Here, we demonstrate that the size of these “inverted” nanoparticles can be controlled between 40 and 300nm, and that they can be stabilized by ionically gelling the poly(acrylic acid) core with metal cations. The effect of solvent and salt on crosslinking were investigated. A method to evaluate the crosslinking efficiency was developed, and a number of metals were found to be effective at crosslinking the particle core, including Ca2+, Zn2+, and Fe3+. Once stabilized, these particles may be further processed for applications in aqueous environments.
Terrain Understanding for Robot Navigation (2007)

This paper presents a method to forecast terrain trafficability from visual appearance. During training, the system identifies a set of image chips (or exemplars) that span the range of terrain appearance. Each chip is assigned a vector tag of vehicle-terrain interaction characteristics that are obtained from on-board sensors and simple performance models, as the vehicle traverses the terrain. The system uses the exemplars to segment images into regions, based on visual similarity to the terrain patches observed during training, and assigns the appropriate vehicle-terrain interaction tag to them. This methodology will therefore allow the online forecasting of vehicle performance on upcoming terrain. Currently, we are using fuzzy c-means clustering and exploring a number of different features for characterizing the visual appearance of the terrain.
Double Circular Caching Scheme for DRAM/PRAM Hybrid Cache (2012)

DRAM is widely adopted as a cache for secondary storage due to its small access latency. Compared with DRAM, PRAM draws a lot of attention recently, since it provides higher density and has no need to refresh the capacitor charge periodically. The non-volatile nature of PRAM can even reduce compulsory miss, which cannot be avoided by DRAM cache. However, PRAM cache cannot replace DRAM cache due to its endurance issue. Thus DRAM/PRAM hybrid cache becomes a good alternative for traditional DRAM cache. Least recently used (LRU) replacement algorithm and CLOCK-Pro algorithm work well for traditional DRAM cache. But these algorithms shall not be directly applied to DRAM/PRAM hybrid cache since the characteristics of PRAM are not considered. This paper proposed a double circular caching scheme to manage DRAM/PRAM hybrid cache. In our scheme, cached data migrate between DRAM cache and PRAM cache adaptively to achieve good hit ratio while frequent writes to PRAM cache are avoided for endurance concern.
A MEMS-based Benzene Gas Sensor with a Self-heating WO3 Sensing Layer (2009)

In the study, a MEMS-based benzene gas sensor is presented, consisting of a quartz substrate, a thin-film WO(3) sensing layer, an integrated Pt micro-heater, and Pt interdigitated electrodes (IDEs). When benzene is present in the atmosphere, oxidation occurs on the heated WO(3) sensing layer. This causes a change in the electrical conductivity of the WO(3) film, and hence changes the resistance between the IDEs. The benzene concentration is then computed from the change in the measured resistance. A specific orientation of the WO(3) layer is obtained by optimizing the sputtering process parameters. It is found that the sensitivity of the gas sensor is optimized at a working temperature of 300 °C. At the optimal working temperature, the experimental results show that the sensor has a high degree of sensitivity (1.0 KΩ ppm(-1)), a low detection limit (0.2 ppm) and a rapid response time (35 s).
Characterization of the <i>vls</i> antigenic variation loci of the Lyme disease spirochaetes <i>Borrelia garinii</i> Ip90 and <i>Borrelia afzelii</i> ACAI (2003)

The vls locus of Borrelia burgdorferi B31 consists of 15 silent cassettes and one expression site (vlsE), and the presence of the encoding plasmid lp28-1 correlates with high infectivity. Recombination between the expression cassette and silent cassettes occurs in vivo, and this process may enable B. burgdorferi to evade the immune response. To determine the characteristics of the vls loci in other Borrelia strains, we have cloned and characterized the vls silent cassette loci of Borrelia garinii Ip90 and Borrelia afzelii ACAI, consisting of 11 vls silent cassettes and 14 vls silent cassettes respectively. The silent cassettes share 90-97% nucleotide sequence identity with one another within the Ip90 vls locus and 84-91% within the ACAI vls locus. In both organisms, the silent cassettes resemble the B31 Vls sequences in overall amino acid similarity (50-65%) and in the presence of six variable regions interspersed between six relatively invariant regions. The vlsE expression sites of these two strains have not been isolated, but transcripts of vlsE were detected by reverse transcriptase-polymerase chain reaction for both Ip90 and ACAI. In addition, the occurrence of sequence variation within the vlsE cassette region of these transcripts was verified. This study indicates that the vls loci present in B. garinii Ip90 and B. afzelii ACAI have characteristics similar to those found in B. burgdorferi B31.
[Expression of connexin 43 in ovarian cancer and its relationship with chemoresistance]. (2009)

Phosphorylation of Cx43 caused by PKC leads to decrease in the expression of Cx43. This effect makes ovarian cancer cells less chemosensitive. Phosphorylation of Cx43 caused by PKC can be inhibited by staurosporine.
Three-dimensional hippocampal MR morphometry with high-dimensional transformation of a neuroanatomic atlas. (1997)

The automated method estimates hippocampal volumes with less variability (ie, lower variance) than that of manual out-lining.
Retrieval of Placental Blood From the Umbilical Vein to Determine Volume, Sterility, and Presence of Clot Formation (1992)

From August 1988 to October 1989, 60 specimens of citrate-phosphate-dextrose-adenine anticoagulated blood were retrieved from the placental umbilical veins of newborns from three gestational age groups. The specimens were removed with a needle and syringe apparatus and placed directly into sterile transfusion packs. The specimens were evaluated for the volume obtained, sterility, and presence of macroscopic clots. A blood volume sufficient to provide at least one transfusion (10 mL/kg) for 87% of the premature infants studied was retrieved from the placenta. A greater blood volume per unit of birth weight was recovered from the placentas of the smaller newborns. A 12% positive culture frequency and a 7% frequency of detectable clots were identified. These rates of occurrence suggest the need for further studies to determine the origins of these complicating factors before the adoption of this technique in the clinical setting. These findings support the hypothesis that, with proper patient selection and with specimen culture and filtration, placental blood may be a viable option for the autologous transfusion of sick, premature infants.
Investigation of Pavement Light Reflection Characteristics (2011)

ABSTRACT Current road lighting standards and recommendations are based on luminance levels and luminance distributions on the road surface. The luminance of the road surface depends on the amount of light falling on it and the reflection properties of the road surface. Using light aggregate for road surface pavements, significant energy savings in road lighting could be achieved due to significantly higher reflectance properties of the surface. In this study several experimental pavement samples with light surface characteristics were manufactured and their reflection properties were measured. The results indicate that lighter pavement materials result in higher average road surface luminance values and lower average lighting energy usage costs per kilometer.
Review article: integrating budesonide‐MMX into treatment algorithms for mild‐to‐moderate ulcerative colitis (2014)

Budesonide-MMX 9 mg daily is an effective and safe treatment for induction in patients with mild-moderately active UC. At the current time, it should be considered in patients after 5-ASA failure and before systemic corticosteroids. Data are still needed to understand its role and dose beyond 8 weeks, and if it should be considered first line before 5-ASAs.
Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria (2016)

Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that Synechococcus sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.
CellularLocalization and Age-Dependent Changes in mRNA for Cyclic Adenosine 3′,5′-Monophosphate-Dependent Protein Kinases in Rat Testis1 (1987)

Gonadotropin activation of cyclic adenosine 3',5'-monophosphate (cAMP)-dependent protein kinases plays an important role in the regulation of testicular function. This study was undertaken to establish the expression of various subunits of cAMP-dependent protein kinases in different testicular cell types as well as during sexual maturation. RNA was extracted from cultured Sertoli cells, cultured peritubular cells, germ cells (pachytene spermatocytes, round spermatids), tumor Leydig cells, as well as whole testis from rats of various ages. Messenger RNA levels were studied by Northern analysis using available cDNA probes. The regulatory subunit (R) designated RII51 was found to be predominantly expressed in cAMP-stimulated Sertoli cells and tumor Leydig cells. Much lower levels were found in cultured peritubular cells and germ cells. A 2.9- and 3.2-kb mRNA for the RI subunit were found at about similar levels in all cell types, whereas the smaller 1.7-kb mRNA was expressed in high levels in germ cells. Also, the catalytic subunit (C) of cAMP-dependent protein kinase, designated C alpha, was expressed in all cell types; the highest mRNA levels for this subunit were found in germ cells and in tumor Leydig cells. The 1.7-kb mRNA for androgen-binding protein (ABP) was abundant in cAMP-stimulated Sertoli cells and was not present in other cell types of the testis. Furthermore, the cellular localization of the cAMP-dependent protein kinase subunits was also supported by developmental studies. The mRNA level of the RII51 3.2-kb species was relatively constant until Day 30, after which there was a tendency to decrease. A 1.6-kb message first appeared at greater ages. The mRNA for the smaller 1.7-kb species of RI, as well as the C alpha, showed a significant increase during development, supporting an enrichment of these mRNAs in germ cells. Messenger RNA levels for ABP were not detected in testis from 5- to 10-day-old rats but increased up to Day 30. After this age, mRNA for ABP revealed an age-dependent decrease, which parallels the relative increase of germ cells in the testis. In summary, these results demonstrate a clear pattern of cellular localization of the various mRNA species for subunits of the cAMP-dependent protein kinase in the rat testis.
O enfermeiro recém-graduado e o primeiro emprego. Percepções da formação na graduação e da atuação profissional (2008)

Concluir um curso de graduacao signifi ca muito para quem o faz, mas muitas vezes e motivo de grande angustia e ansiedade. Normalmente, o primeiro emprego e um desafi o que acompanha o profi ssional em seus primeiros meses de exercicio profi ssional. O enfermeiro recem-graduado enfrenta esse desafi o com muita inseguranca e receios, pois encontra inumeras difi culdades que se iniciam desde o processo admissional a adaptacao as normas e ao processo de trabalho da instituicao. Esse trabalho investigou junto aos enfermeiros recem-formados de Londrina-Parana, a condicao de iniciar suas atividades profi ssionais com seguranca, alem de levantar as principais difi culdades enfrentadas durante o primeiro ano de exercicio profi ssional. Como resultados observou-se que: 80% dos entrevistados sentiram difi culdades no primeiro emprego; sendo que 42,86% destes sentiram falta de experiencia em Lideranca e 21,43% na area administrativa. Todos os entrevistados disseram que procuraram auxilio frente as difi culdades, sendo que 35,72% atraves de consulta em livros, 28,57% atraves da chefi a, 28,57% com colegas de servico e 7,14% com professores. Constatou-se ainda que para 46,66% dos enfermeiros a escola forma o aluno para as necessidades da pratica profi ssional. Conclui-se que o enfermeiro recem-graduado nao e um produto acabado, precisa de treinamento, incentivo e participacao para desempenhar adequadamente sua funcao na instituicao empregadora.