gebhart/patrepeval huggingface dataset:
Effects of Sequential<i>Campylobacter jejuni</i>81-176 Lipooligosaccharide Core Truncations on Biofilm Formation, Stress Survival, and Pathogenesis (2010)

Campylobacter jejuni is a highly prevalent human pathogen for which pathogenic and stress survival strategies remain relatively poorly understood. We previously found that a C. jejuni strain 81-176 mutant defective for key virulence and stress survival attributes was also hyper-biofilm and hyperreactive to the UV fluorescent dye calcofluor white (CFW). We hypothesized that screening for CFW hyperreactive mutants would identify additional genes required for C. jejuni pathogenesis properties. Surprisingly, two such mutants harbored lesions in lipooligosaccharide (LOS) genes (waaF and lgtF), indicating a complete loss of the LOS outer core region. We utilized this as an opportunity to explore the role of each LOS core-specific moiety in the pathogenesis and stress survival of this strain and thus also constructed DeltagalT and DeltacstII mutants with more minor LOS truncations. Interestingly, we found that mutants lacking the LOS outer core (DeltawaaF and DeltalgtF but not DeltagalT or DeltacstII mutants) exhibited enhanced biofilm formation. The presence of the complete outer core was also necessary for resistance to complement-mediated killing. In contrast, any LOS truncation, even that of the terminal sialic acid (DeltacstII), resulted in diminished resistance to polymyxin B. The cathelicidin LL-37 was found to be active against C. jejuni, with the LOS mutants exhibiting modest but tiled alterations in LL-37 sensitivity. The DeltawaaF mutant but not the other LOS mutant strains also exhibited a defect in intraepithelial cell survival, an aspect of C. jejuni pathogenesis that has only recently begun to be clarified. Finally, using a mouse competition model, we now provide the first direct evidence for the importance of the C. jejuni LOS in host colonization. Collectively, this study has uncovered novel roles for the C. jejuni LOS, highlights the dynamic nature of the C. jejuni cell envelope, and provides insight into the contribution of specific LOS core moieties to stress survival and pathogenesis.
Preparation of highly oxidized nitrogen-doped carbon nanotubes (2012)

A method for the preparation of highly oxidized nitrogen-doped carbon nanotubes (N-CNTs) from KMnO(4) + H(2)SO(4) solution is described. The atomic ratio of C/O in oxidized N-CNTs is as low as 1.2. The x-ray photoelectron spectroscopy results show that about 75% of the carbon atoms are oxidized and bound to oxygen-containing functional groups. The oxidation reaction mainly occurs at the outer sidewalls, which destroys the graphene stack to an sp(3)-rich structure and helps to preserve the tubular structure of the inner N-CNTs. The oxidized N-CNTs show an energy gap of ~2.1 eV.
Follistatin and its role as an activin-binding protein. (1997)

Follistatin (FS), a specific binding protein for activin, neutralizes the diverse actions of activin by forming an inactive complex with activin. FS is a monomer derived from two polypeptide core sequences of 288 (FS-288) and 315 (FS-315) amino acids originated from alternatively spliced mRNA. We purified six molecular forms of FS from porcine ovaries. Their structural differences were caused by truncation of the COOH-terminal region and/or the presence of carbohydrate chains, resulting in the formation of FS-288, FS-315 and FS composed of 303 amino acids (FS-303) in various forms of glycosylation on the two potential Asn-linked glycosylation sites. All six molecular species have almost the same activin binding activity (Kd = 540-680 pM). By contrast, the COOH-terminal truncated form, FS-288, showed much higher affinity for heparan sulfate proteoglycans of the cell surface than FS-303, whereas the intact form of FS, FS-315, had no affinity. Furthermore, FS-288 more effectively blocked the suppression of follicle-stimulating hormone (FSH) secretion from rat pituitary cells by activin. This implies that activin binds to the cell surface through FS-288 which adheres to the cell surface. To clarify the physiological role of cell-associated FS, we then investigated the binding of activin to cell-associated FS and the fate of cell surface-bound activin and FS using primary cultured rat pituitary and ovarian granuloma cells. When the cells were incubated with 125I-activin A in the presence of FS-288 or 315, the binding of activin A to the cell surface was promoted much more markedly by FS-288 than by FS-315. The amounts of radioactivity recovered in trichloroacetic acid-soluble fractions (degraded activin) from the incubation medium were greatly increased by the addition of FS-288. This increase was abolished by heparan sulfate, monensin (an endocytosis inhibitor), chloroquine (a lysosome function inhibitor) and several lysosomal enzyme inhibitors. These results suggest that cell-associated FS-288 accelerates the internalization of activin into the cells, leading to its degradation by lysosomal enzymes, and that cell surface-associated FS therefore plays a role in the clearance system of activin.
Multi-Stage Holomorphic Embedding Method for Calculating the Power-Voltage Curve (2017)

The recently proposed non-iterative load flow method, called the holomorphic embedding method, may encounter the precision issue, i.e., the nontrivial round-off errors caused by the limited digits used in computing the power-voltage (P-V) curve for a heavily loaded power system. This letter proposes a multi-stage scheme to solve such a precision issue and calculate an accurate P-V curve. The scheme is verified on the New England 39-bus power system and benchmarked with the result from the traditional continuation power flow method.
Single Polypyrrole Nanowire Ammonia Gas Sensor (2007)

Abstract We report the synthesis, electrical characterization and ammonia gas sensing with single nanowire of conducting polypyrrole. Three hundred nanometer in diameter and 50 to 60 μm long polypyrrole nanowires were synthesized by chemical polymerization inside SiO 2 coated alumina membranes. Temperature dependent electrical resistance studies established that the chemically synthesized nanowires were more ordered compared to electrochemically synthesized nanowires. We further demonstrated that gas sensors based on single polypyrrole nanowire exhibited good sensitivity towards ammonia, and provided a reliable detection at concentration as low as approximately 40 ppm.
Enhancement and inhibition of dental plaque formation — Some old and new concepts (1991)

The presence of sucrose in the diet is a dominant factor in supragingival plaque formation. Glucosyltransferase catalyzing the formation of insoluble polysaccharide is presumably the adhesive factor binding bacteria to teeth and to each other through interaction between rigid a 1–3 linked glucose chains. Model studies concerning plaque formation should include introduction of sucrose into the media. Plaque inhibition can be achieved by use of cationic water soluble substances (chlorhexidine, certain metal ions etc.) and by certain lipid soluble antibacterial agents. Treatment of teeth with agents which give teeth hydrophobic surfaces may reduce plaque formation in vivo.
Timing and Grounding in Motor Skill Coaching Interaction: Consequences for the Information State (2015)

Hough J, de Kok I, Schlangen D, Kopp S. Timing and Grounding in Motor Skill Coaching Interaction: Consequences for the Information State. In: <em>Proceedings of the 19th SemDial Workshop on the Semantics and Pragmatics of Dialogue (goDIAL)</em>. 2015: 86-94.
Recording on perpendicular anisotropy media with ring heads (1981)

This paper reports experimental studies directed at the application of ring head structures to a perpendicular recording system. The media tested were sputter deposited films of CoCrTa alloys. Ferrite heads were studied, but the thin film head was chosen for evaluating roll-off, overwrite, and superposition. The data presented in the paper demonstrates the potential of high density recording with a single layer medium with perpendicular magnetic anistropy and a thin film head separated by 0.20 micrometers.
Lyophilized Kit for the Preparation of the PET Perfusion Agent [<sup>68</sup>Ga]-MAA (2014)

Rapid developments in the field of medical imaging have opened new avenues for the use of positron emitting labeled microparticles. The radioisotope used in our research was (68)Ga, which is easy to obtain from a generator and has good nuclear properties for PET imaging. Methods. Commercially available macroaggregated albumin (MAA) microparticles were suspended in sterile saline, centrifuged to remove the free albumin and stannous chloride, relyophilized, and stored for later labeling with (68)Ga. Labeling was performed at different temperatures and times. (68)Ga purification settings were also tested and optimized. Labeling yield and purity of relyophilized MAA microparticles were compared with those that were not relyophilized. Results. MAA particles kept their original size distribution after relyophilization. Labeling yield was 98% at 75°C when a (68)Ga purification system was used, compared to 80% with unpurified (68)Ga. Radiochemical purity was over 97% up to 4 hours after the labeling. The relyophilized MAA and labeling method eliminate the need for centrifugation purification of the final product and simplify the labeling process. Animal experiments demonstrated the high in vivo stability of the obtained PET agent with more than 95% of the activity remaining in the lungs after 4 hours.
Self adaptive filtering of noise from speech: a hearing aid application (2003)

The authors discuss and evaluate a self-adaptive filter of noise from speech. The filter uses a single microphone, and incorporates time-series identification algorithms with artificial intelligence decision procedures to discriminate between environmental noises, including babble from speech. The filter has recently been realized in a single CMOS microchip that includes digital, analog, and ADC circuits and is presently being used by seven hearing-aid manufacturers in their otherwise conventional hearing aids, of both the behind-ear and inside-ear types. Circuit and system design considerations are discussed and performance evaluation is presented, as is the relative performance as compared with conventional nonadaptive single microphone designs based on automatic gain control and ASP-type compression circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Predicting Hypoglycemia in Diabetic Patients using Machine Learning Techniques (2014)

A Master of Science thesis in Computer Engineering by Khuloud Abdel Aziz Safi Eljil entitled, "Predicting Hypoglycemia in Diabetic Patients using Machine Learning Techniques," submitted in June 2014. Thesis advisor is Dr. Ghassan Qaddah and thesis co-advisor is Dr. Michel Pasquier. Available are both soft and hard copies of the thesis.
CAKE: the intelligent knowledge modeling Web services for semantic Web (2005)

In order to solve the problems of low interconversion, interoperability and difficult rule-logic extraction in the semantic Web, based on the spiral law of knowledge evolution we discovered, we have put forward a set of unified knowledge modeling approach, accompanied in the entire cycle of knowledge application, from the primary data layer to ontology, rule and logic layer, and have defined a universal Knowledge Modeling Language - KML. We have further invented the KML-based knowledge construction, conversion and rule-logic extracting mechanism. In the end, we have designed and developed a computer aided knowledge modeling environment - CAKE, to implement a multimode intelligent Web services. Our work opens up a way to achieve the ultimate goal of semantic Web - effective and efficient global knowledge exchange.
An expandable time-division circuit switching LSI and network architecture for broadband ISDN (1996)

A broadband network architecture is proposed that integrates multimedia services, such as data, video, and telephony information, using 52-Mb/s based STM-paths at the user network interface (UNI). The user can access any new service via the STM-based access network via either synchronous transfer mode (STM) switching or asynchronous transfer mode (ATM) switching. STM circuit switching supports long duration, constant bandwidth data transfer services such as video and high-definition television (HDTV) distribution and will also be used for the crossconnect system. Circuit switching can provide transparent transmission during long connection periods. This paper also proposes an expandable time-division switch architecture, an expandable time-division switching LSI, and an expandable switching module for small to large size system applications. The proposed time-division switching LSI, module, and system handle 52-Mb/s bearer signals and have throughputs of 2.4 Gb/s, 10 Gb/s, and 40 Gb/s, respectively. The time-division switch realizes video distribution with 1:n connections. Finally, a local switching node that features an expandable 52-Mb/s time-division circuit switching network is shown for multimedia access networking.
A New Multiply-by-Two Gain-Stage with Enhanced Immunity to Capacitor-Mismatch (2005)

A new multiply-by-two gain-stage (MBT-GS)(/spl times/2) is presented in which the gain-sensitivity to the capacitors' mismatches is suppressed. Using one operational amplifier (op-amp) in three phases, a gain of two, which is not highly influenced by the mismatches between the capacitors, is achieved. An analytical study of the architecture is presented followed by some Monte-Carlo simulations using a generic 0.6 /spl mu/m CMOS technology in HSPICE. Simulations clearly show the reduction of the matching-requirements in the new architecture.
Antibiotics in critically ill patients: a systematic review of the pharmacokinetics of β-lactams (2011)

The PK of β-lactam antibiotics are heterogeneous and largely unpredictable in ICU patients. Consequently, the dosing of antibiotics should be supported by PK concepts, including data derived from studies of the PK of ICU patients and therapeutic drug monitoring.
A convergent dynamic window approach to obstacle avoidance (2005)

The dynamic window approach (DWA) is a well-known navigation scheme developed by Fox et al. and extended by Brock and Khatib. It is safe by construction, and has been shown to perform very efficiently in experimental setups. However, one can construct examples where the proposed scheme fails to attain the goal configuration. What has been lacking is a theoretical treatment of the algorithm's convergence properties. Here we present such a treatment by merging the ideas of the DWA with the convergent, but less performance-oriented, scheme suggested by Rimon and Koditschek. Viewing the DWA as a model predictive control (MPC) method and using the control Lyapunov function (CLF) framework of Rimon and Koditschek, we draw inspiration from an MPC/CLF framework put forth by Primbs to propose a version of the DWA that is tractable and convergent.
Improved MLT and Its Applications to Solar Models (2001)

Based on an improved MLT that takes the anisotropy and dissipation of the turbulence into account, we found that the dissipation of the turbulence in the solar convection zone should be fairly strong, while the turbulence anisotropy plays a less significant role.
Design and Verification of SRAM Self-Detection Repair Based on ECC and BISR Circuit (2019)

In the space radiation environment, the chip in the spacecraft is susceptible to radiation effects, which leading to the errors of the device. Therefore, the detection and repair of the errors is particularly important. Aiming at the soft and hard errors of memory cell caused by single event effect in space radiation environment, a memory architecture based on ECC circuit and BISR circuit is proposed to detect errors online, distinguish between soft and hard errors and repair them, so as to reduce the accumulation of errors. And the memory structure uses repair circuit and redundant memory to repair soft errors and hard errors respectively. The simulation results show that in normal read-write mode, the proposed memory structure not only can repair soft errors, but also can repair hard errors, and can detect unrepairable hard errors. It means that the proposed method is effective. when the memory size is 39 x 64K, the area of the ECC and the BIRA circuit is about 13.95% of the entire memory chip.
Fault Detection Based on AP Clustering and PCA (2017)

To improve the accuracy, reduce the time consumption and obtain the number of faults, a fault detection method based on AP (affinity propagation) clustering and PCA (principal component analysis) was proposed. Firstly, discontinuous points in seismic horizons were searched out by the connected component labeling method. Secondly, the AP clustering algorithm was used to cluster the discontinuous points and the points of the same cluster were used to determine a fault, meanwhile, the faults existing in a seismic section were quantified. Finally, the PCA was adopted to calculate the principal direction of the discontinuous points contained in the same cluster. As a result, the corresponding cluster center and the principal direction determined a straight line, and the part that intercepted by the clustered edge was the fault we wanted. In the proposed method, the time consumption of correlation calculation of the traditional method was reduced; the computing work was simplified and the number of the faults in the seismic section was obtained. To confirm the feasibility and advancement of the proposed method, comparative experiments were done on the seismic model data and the real seismic section. The results show that the accuracy of the proposed method was better and the time cost was greatly reduced.
Some Unusual Reactions of 1,2‐Bis(phenylethynyl)benzene with Sulfur, Carbon Monoxide and Alkyl Acetylenedicarboxylates (1992)

1,2‐Bis(phenylethynyl)benzene ( 1 ) reacts with sulfur, carbon monoxide, and acetylenedicarboxylic esters to give unusual polycyclic products. Under exclusion of air 1 adds sulfur to give 6‐phenylbenz[ b ]indeno[2,1‐ d ]thiopyran ( 3b ) and bis(6‐phenylbenz[ b ]indeno[2,1‐ d ]thiopyran‐11‐yl) disulfide ( 4 ). In the presence of air 3‐benzoyl‐2‐phenyl‐1 H ‐inden‐1‐one ( 5 ) is formed via a sulfur‐containing intermediate. Under phase‐transfer conditions [CH 3 N(C 8 H 17 ) 3 ] + [RhCl 4 (H 2 O) 2 ] − promotes reductive carbonylation of 1 to give initially the lactones 3,8‐dihydro‐ and 8,8a‐dihydro‐3‐phenyl‐8‐(phenylmethylene)‐2 H ‐indeno[2,1‐b]furan‐2‐one ( 6 and 7 ) which isomerize to 3‐phenyl‐8‐(phenylmethyl)‐2 H ‐indeno[2,1‐ b ]furan‐2‐one ( 8 ). Interaction of 1 and MeO 2 CC≡CCO 2 Me in the presence of the same rhodium catalyst results in crosscyclooligomerization in which tetramethyl 2‐(phenylethynyl)‐1,1′:2′,1′'‐terphenyl‐3′,4′,5′,6′‐tetracarboxylate ( 9 ) is obtained. The H 2 PtCl 6 ‐Aliquat‐336 catalyst promotes the reaction of 1 with equimolar amounts of RO 2 CC≡CCO 2 R (R = Me, Et, Pr) to give the corresponding ( Z )‐2‐(10‐phenylindeno[2,1‐α]inden‐5‐yl)‐2‐butendioates ( 11a–c ). The structures of 3b, 4, 5, 8 , and 11a have been determined by X‐ray diffraction analyses. Possible routes for the transformation of 1 into the polycyclic products are discussed.
Profiles in mass storage: a tale of two systems (2003)

The Los Alamos Common File System (CFS) and the NCAR (National Center for Atmospheric Research) mass storage systems (MSSs) are file-storage and file-management systems that serve heterogeneous computing networks of supercomputers, general-purpose computers, scientific workstations, and personal computers. Philosophical, implementation and performance aspects of the two MSSs storage are detailed. Areas covered include the computing environment, the user interface, storage strategies, and file-movement strategies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Flow Cytometric Analysis of the In Situ Accessibility of <i>Escherichia coli</i> 16S rRNA for Fluorescently Labeled Oligonucleotide Probes (1998)

In situ identification of whole fixed bacterial cells by hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes is often limited by low signal intensities. In addition to an impermeability of the cell periphery and a low cellular rRNA content, the three-dimensional structure of the ribosome may hinder the access of oligonucleotides to their target sites. Until now, a systematic study on the accessibility of 16S rRNA target sites had not been done. Here, we report fluorescence intensities obtained with more than 200 oligonucleotide probes (mostly 18-mers) used with whole fixed cells of Escherichia coli DSM 30083(T). Two overlapping sets of adjacent oligonucleotides, 171 in total, were designed to cover the full length of the 16S rRNA. The two sets are shifted by 5 to 13 nucleotides. The probes were labeled with carboxyfluorescein, and signal intensities of hybridized cells were quantified by flow cytometry. Care was taken that the signal intensity of cells was dependent solely on the in situ accessibility of probe target sites. The brightest signal resulted from probe Eco1482, complementary to positions 1482 to 1499. With this probe, the fluorescence was 1.7 times brighter than that of the standard bacterial probe EUB338 and 44 times brighter than that of the worst probe, Eco468. The distribution of probe-conferred cell fluorescence in six arbitrarily set brightness classes (classes I to VI; 100 to 81%, 80 to 61%, 60 to 41%, 40 to 21%, 20 to 6%, and 5 to 0% of the brightness with Eco1482, respectively) was as follows: I, 4%; II, 14%; III, 21%; IV, 29%, V, 19%; and VI, 13%. A more detailed analysis of helices 6, 18, and 23 with additional probes demonstrated that a shift of the target region by only a few bases could result in a decline of cell fluorescence from >80 to <10%. Considering the high evolutionary conservation of 16S rRNA, the in situ accessibility map of E. coli should facilitate a more rational selection of probe target sites for other species as well.
Investigating the robustness of ion beam therapy treatment plans to uncertainties in biological treatment parameters (2012)

Uncertainties in determining clinically used relative biological effectiveness (RBE) values for ion beam therapy carry the risk of absolute and relative misestimations of RBE-weighted doses for clinical scenarios. This study assesses the consequences of hypothetical misestimations of input parameters to the RBE modelling for carbon ion treatment plans by a variational approach. The impact of the variations on resulting cell survival and RBE values is evaluated as a function of the remaining ion range. In addition, the sensitivity to misestimations in RBE modelling is compared for single fields and two opposed fields using differing optimization criteria. It is demonstrated for single treatment fields that moderate variations (up to ±50%) of representative nominal input parameters for four tumours result mainly in a misestimation of the RBE-weighted dose in the planning target volume (PTV) by a constant factor and only smaller RBE-weighted dose gradients. Ensuring a more uniform radiation quality in the PTV eases the clinical importance of uncertainties in the radiobiological treatment parameters, as for such a condition uncertainties tend to result only in a systematic misestimation of RBE-weighted dose in the PTV by a constant factor. Two opposed carbon ion fields with a constant RBE in the PTV are found to result in rather robust conditions. Treatments using two ion species may be used to achieve a constant RBE in the PTV irrespective of the size and depth of the spread-out Bragg peak.