Miracle-dz/UniFAR-FTUs huggingface dataset:
The Escherichia coli Replisome Is Inherently DNA Damage Tolerant

The core DNA replication machinery of Escherichia coli has an inherent ability to squeeze past DNA damage on the leading strand. The Escherichia coli DNA replication machinery must frequently overcome template lesions under normal growth conditions. Yet, the outcome of a collision between the replisome and a leading-strand template lesion remains poorly understood. Here, we demonstrate that a single, site-specific, cyclobutane pyrimidine dimer leading-strand template lesion provides only a transient block to fork progression in vitro. The replisome remains stably associated with the fork after collision with the lesion. Leading-strand synthesis is then reinitiated downstream of the damage in a reaction that is dependent on the primase, DnaG, but independent of any of the known replication-restart proteins. These observations reveal that the replisome can tolerate leading-strand template lesions without dissociating by synthesizing the leading strand discontinuously.
THE SIGNIFICANCE AND ROLE OF TRUST IN AN ORGANIZATION WITHIN THE PROCESSES OF COMMUNICATION AND CONTROL

Today, studying trust within society is a very current topic. The significance and role, which trust plays in the post-industrial society is multi-layered. Without a doubt, trust within different institutions and trust amongst individual institutions has been at the forefront in recent time. Often the level of trust individual institutions enjoy depends on the success and efficiency of their operations. In the paper, the authors have exposed the significance and role that trust plays within organizations. The level of trust within an organization is very important for each individual who is a member of some organization. In the paper, the authors have shown the results of the empirical research on the correlation between the levels of trust within a certain organization and the impact on the form of supervision and communication in implementing tasks. They established that the greater the levels of trust within an organization, less formalized forms of delegating tasks are required and the level of informal communication is greater. These stated facts increase the efficiency of the management processes and with this the success of the organization as a whole.
[Demodex-related marginal blepharitis in Japan].

PURPOSE Some marginal blepharitis is related to demodex, but this has not yet been reported in Japan. In this study, patients with severe marginal blepharitis with cylindrical dandruff were studied to examine the number of demodex in their cilia. METHODS Ten eyes of 10 patients (7 men and 3 women, mean age: 62.9 +/- 9.0 years) with unilateral marginal blepharitis which had cylindrical dandruff in their cilia were studied. Three cilia which had the most cylindrical dandruff were removed from the eyelids for microscopic examination. After cleaning the eyelid margins for 1 week, the examination was repeated. Scoring of itching and foreign body sensation of the patients was performed both before and after the treatment. RESULTS Demodex folliculorum was detected in the cilia of 8 out of 10 eyes (80%), and 22 cilia out of 30 with cylindrical dandruff. The average number of demodex/cilia was 1.6 +/- 0.9. In all cases, the number of demodex/cillium decreased significantly with the improvement in symptoms and blepharitis. CONCLUSION An Increase in the number of demodex might be the pathogen causing blepharitis with cylindrical dandruff, and cleaning of the eyelid margin is effective as a therapeutic method.
Proteomic Analysis of Rhoptry Organelles Reveals Many Novel Constituents for Host-Parasite Interactions in Toxoplasma gondii*

Rhoptries are specialized secretory organelles that are uniquely present within protozoan parasites of the phylum Apicomplexa. These obligate intracellular parasites comprise some of the most important parasites of humans and animals, including the causative agents of malaria (Plasmodium spp.) and chicken coccidiosis (Eimeria spp.). The contents of the rhoptries are released into the nascent parasitophorous vacuole during invasion into the host cell, and the resulting proteins often represent the literal interface between host and pathogen. We have developed a method for highly efficient purification of rhoptries from one of the best studied Apicomplexa, Toxoplasma gondii, and we carried out a detailed proteomic analysis using mass spectrometry that has identified 38 novel proteins. To confirm their rhoptry origin, antibodies were raised to synthetic peptides and/or recombinant protein. Eleven of 12 of these yielded antibody that showed strong rhoptry staining by immunofluorescence within the rhoptry necks and/or their bulbous base. Hemagglutinin epitope tagging confirmed one additional novel protein as from the rhoptry bulb. Previously identified rhoptry proteins from Toxoplasma and Plasmodium were unique to one or the other organism, but our elucidation of the Toxoplasma rhoptry proteome revealed homologues that are common to both. This study also identified the first Toxoplasma genes encoding rhoptry neck proteins, which we named RONs, demonstrated that toxofilin and Rab11 are rhoptry proteins, and identified novel kinases, phosphatases, and proteases that are likely to play a key role in the ability of the parasite to invade and co-opt the host cell for its own survival and growth.
Performance Evaluation of A Testing Framework Using QuickCheck and Hadoop

Formal methods are mathematically-based techniques for specifying, developing and verifying a component or system for increasing the confidence regarding the reliability and robustness of the target. It can be used at different levels with different techniques, and one approach is to use model-oriented formal languages such as VDM languages in writing specifications. During model development, we can test executable specifications in VDM-SL and VDM++. In a lightweight formal approach, we test formal specifications to increase our confidence as we do in implementing software code with conventional programming languages. For this purpose, millions of tests may be conducted in developing highly reliable mission-critical software in a lightweight formal approach. In this paper, we introduce our approach to supporting a large volume of testing for executable formal specifications using Hadoop, an implementation of the MapReduce programming model. We are able to automatically distribute an interpretation of specifications in VDM languages by using Hadoop. We also apply a property-based data-driven testing tool, QuickCheck, over MapReduce so that specifications can be checked with thousands of tests that would be infeasible to write by hand, often uncovering subtle corner cases that wouldn't be found otherwise. We observed effect to coverage and evaluated scalability in testing large amounts of data for executable specifications in our approaches.
Analysis of Vascular Access in Intestinal Transplant Recipients Using the Miami Classification from the VIIIth International Small Bowel Transplant Symposium

Background. Loss of vascular access in patients with intestinal failure is considered an indication for intestinal transplantation. Such patients often have one or more occluded vein sites. Venous access could be classified according to the number of occluded vessels, to facilitate pre- and postoperative management. Methods. At the VIIIth International Small Bowel Transplant Symposium in September 2003, a new classification of vascular access in patients who were candidates for bowel transplant was proposed. The classification was then applied to stratify all patients that underwent intestinal transplantation at the University of Miami between 1998 and 2003. Data were collected on Doppler ultrasonography, angiography, and vein angioplasty in such patients. Results. A total of 106 cases in 91 patients were included in the study. Based on Doppler ultrasound results, 51.9% of patients fell into class I (no thrombosed vessels), 21.7% were in class II (one occluded vessel, or positive risk factors for thrombosis), 24.5% were in class III (multiple thrombosed vessels), and 1.9% were in class IV (all vessels thrombosed). Fifteen percent of the patients required preoperative angiography to better evaluate venous access. Most of the patients that required angiography were in class III or IV, and 53.3% of patients requiring angiography needed additional venous angioplasty to achieve access. Conclusions. All patients that are referred for intestinal transplantation should undergo preliminary mapping of their venous access by Doppler ultrasound and then be assigned to a vascular access class. Those patients with multiple thrombosed vessels (class III and above) should be strongly considered for additional angiographic evaluation.
Two‐dimensional electrophoresis of Cereus peruvianus (Cactaceae) callus tissue proteins

Two‐dimensional electrophoresis of Cereus peruvianus callus tissues grown in culture media containing two different 2,4‐dichlorophenoxyacetic acid (2,4‐D) and kinetin combinations was used to identify minor differences in polypeptide composition of these cell clones. Altered expression during growth in the two 2,4‐D and kinetin combinations was apparent for 13 polypeptides when calluses in the two media were compared. The number of proteins with differential expression (presence or absence of specific spots) was higher in callus tissues cultured in the 4.0 mg/L 2,4‐D and 8.0 mg/L kinetin combination than in callus tissues cultured in the 4.0 mg/L 2,4‐D and 4.0 mg/L kinetin combination. The present results show that the callus tissues maintained at 4.0 mg/L 2,4‐D and 8.0 mg/L kinetin can be used as a matrix for in vitro selection programs.
Analysis of Semantic Heterogeneity Using a New Ontological Structure Based on Description Logics

Every information system has its own domain model for its environment and efficient task operations, which results in diverse heterogeneity, especially the semantic heterogeneity. Ontology is an agreement about shared conceptualizations, which can make the meaning of the different vocabularies used explicit, and so the semantics of diverse information systems can be captured by ontology-definitions of terms. This paper constructs an ontological structure using description logic, divides the types of heterogeneity of information system into two categories from the ontological view: conceptualization conflict and term assignment conflict, and analyses approaches to solve conflict by ontology mapping. Finally, this paper construct semantic-oriented integration architecture for heterogeneous systems based on ontology mapping, and discusses data request and response under the architecture, and proposes five rules for data search.
Potentially low-cost widely tunable laser consisting of a semiconductor optical amplifier connected directly to a silica waveguide grating router

We present a widely tunable laser consisting of a semiconductor optical amplifier (SOA) glued directly to a silica waveguide grating router, that can be packaged without submicrometer alignments, air gaps, or SOA vertical spot-size conversion. However, issues regarding thermooptic power consumption and modal stability remain to be solved.
A Proposal of a Novel Cardiorespiratory Long-term Monitoring Device

Monitoring of respiratory movements is an important feature in planning of medical care. We present here a simple, portable, accelerometer-based device suitable for long term-monitoring of the breathing and heart rates, along with postural changes, during sleep and wakefulness. Recordings of respiratory frequency, heart rate, posture and voluntary cough were obtained from a group of volunteers who also participated in sleep studies (6-8 hrs). A pair of capacitive MEMS tri-axial accelerometers was positioned at the level of the 10 rib along the mid-axillary line bilaterally; simultaneous recordings of respiratory movements, heart rate and body position could be easily performed. The signal were digitized and used to detect body position and relative movement between accelerometers. Conventional spirometry was performed in parallel when appropriate. During resting breathing, qualitative analysis revealed that the accelerometric assessment of respiratory pattern correlated well with that obtained by spirometry. Values of respiratory rates were identical with the two techniques. Recordings of respiratory and cardiac activity during sleep were satisfactorily obtained except for short lasting episodes corresponding to changes in body position. These devices seem to be also suitable for detecting the motor pattern of cough.
Structure based computational assessment of channel properties of assembled ORF‐8a from SARS‐CoV

ORF 8a is a short 39 amino acid bitopic membrane protein encoded by severe acute respiratory syndrome causing corona virus (SARS‐CoV). It has been identified to increase permeability of the lipid membrane for cations. Permeability is suggested to occur due to the assembly of helical bundles. Computational models of a pentameric assembly of 8a peptides are generated using the first 22 amino acids, which include the transmembrane domain. Low energy structures reveal a hydrophilic pore mantled by residues Thr‐8, and −18, Ser‐11, Cys‐13, and Arg‐22. Potential of mean force (PMF) profiles for mono (Na+, K+, Cl−) and divalent (Ca2+) ions along the pore are calculated. The data support experimental findings of a weak cation selectivity of the channel. Calculations on 8a are compared to data derived for a pentameric bundle consisting of the M2 helices of the bacterial pentameric ligand gated ion channel GLIC (3EHZ). PMF curves of both, bundles 8a and M2, show sigmoidal shaped profiles. In comparison to the data for the M2‐GLIC model, data of the 8a bundle show lower amplitude of the PMF values between maximum and minimum and less discrimination amongst ions. Proteins 2015; 83:300–308. © 2014 Wiley Periodicals, Inc.
Antigenic determinants on bovine encephalitogenic protein. Localization of regions that induce transformation of lymph node cells from immunized rabbits

With the aid of a lymph node cell transformation test and several fragments of the bovine encephalitogenic protein, attempts have been made to examine more closely various parts of the protein that stimulate DNA‐synthesis of lymph node cells from immunized rabbits. Evidence was obtained for the presence of at least two strongly stimulating regions within residues 44–170: one resides in peptide 44–89 and the other in peptide 93–170. When parts of these regions and other oligopeptide derivatives of region 44–170 were tested, only a slight or no stimulating effect was observed, and a closer localization of all reactive sites – corresponding to that made in guinea pigs with the macrophage migration inhibition technique – could not be made unequivocally. However, peptides 44–68 and 154–170 were shown to have transformation‐inducing effects.
Integrin modulators: a patent review

Introduction: Integrins are heterodimeric cell surface receptors, which enable adhesion, proliferation, and migration of cells by recognizing binding motifs in extracellular matrix (ECM) proteins. As transmembrane linkers between the cytoskeleton and the ECM, they are able to recruit a huge variety of proteins and to influence signaling pathways bidirectionally, thereby regulating gene expression and cell survival. Hence, integrins play a key role in various physiological as well as pathological processes, which has turned them into an attractive target for pharmaceutical research. Areas covered: In this review, the latest therapeutic developments of drug candidates and recently patented integrin ligands are summarized. Expert opinion: Integrins have been proven to be valuable therapeutic targets in the treatment of several inflammatory and autoimmune diseases, where leukocyte adhesion processes are regulated by them. Furthermore, they play an important role in pathological angiogenesis and tumor metastasis, being a promising target for cancer therapy.
Unconventional cryptographic keying variable management

We present three unconventional approaches to keying variable management. The first approach is based on using a public key cryptosystem (PKC) that is breakable in short, but on average less, time than it takes to set up an ultrawide bandwidth modem that is then used to transport a keying variable for a classical cryptosystem. The second concept proposes using the characteristics of an urban UHF radio channel, determined by mutual sounding, as the cryptovariable. The third concept encourages research into ill-conditioned problems as potentially fruitful ground for PKCs not based on finite field arithmetic. >
Ultra-High-Energy Cosmic-Ray Acceleration by Magnetic Reconnection in Newborn Accretion-induced Collapse Pulsars

We here investigate the possibility that the ultra-high-energy cosmic-ray (UHECR) events observed above the Greisen-Zatsepin-Kuzmin (GZK) limit are mostly protons accelerated in reconnection sites just above the magnetosphere of newborn millisecond pulsars that are originated by accretion-induced collapse (AIC). We formulate the requirements for the acceleration mechanism and show that AIC pulsars with surface magnetic fields 1012 G < B⋆ ≲ 1015 G and spin periods 1 ms ≲ P⋆ < 60 ms are able to accelerate particles to energies ≥1020 eV. Because the expected rate of AIC sources in our Galaxy is very small (~10-5 yr-1), the corresponding contribution to the flux of UHECRs is negligible and the total flux is given by the integrated contribution from AIC sources produced by the distribution of galaxies located within the distance that is unaffected by the GZK cutoff (~50 Mpc). We find that reconnection should convert a fraction ξ ≳ 0.1 of magnetic energy into UHECRs in order to reproduce the observed flux.
EMI reduction technology in 85 kHz band 44 kW wireless power transfer system for rapid contactless charging of electric bus

A 44 kW wireless power transfer (WPT) system is being developed for rapid contactless charging in an electric bus in the 85 kHz band, the candidate frequency for a wireless charging system for light-duty vehicles that is currently undergoing standardization. For field operation of this WPT system using the 85 kHz band in Japan, permission for use as industrial facilities emitting radio waves is required under the Radio Act. A two-channel WPT system with currents of opposite phase in the two transmit pads of the channels is introduced to reduce radiated emissions to within the Radio Act limits of electromagnetic radiation disturbance by cancelling the emission from each channel. Then, the diagonal placement of the transmit pads for the two channels is proposed to avoid the interference between the two channels where the interference couplings become null. Finally, the measured emission of the 44 kW WPT system in a 10 m anechoic chamber is shown.
A Compact Octaband Printed Antenna for Mobile Handsets

A compact octaband printed antenna for mobile handsets is presented in this letter. The proposed antenna only occupies a small area of 15×28.3 mm2 on a printed circuit board (PCB) with 0.8 mm thickness. The compact antenna consists of a driven branch connected with a tuning pad and a ground branch, which are printed on the top layer and the bottom layer of a PCB, respectively. A prototype has been fabricated and measured. Two wide bands over 775-972 and 1699-2929 MHz are obtained, within which the measured reflection coefficient is better than -6 dB. Good radiation characteristics are achieved over the two bands for the proposed antenna.
Second Order Optimality in Transient and Discounted Markov Decision Chains

Abstract. The article is devoted to second order optimality in Markov decision processes. Attention is primarily focused on the reward variance for discounted models and undiscounted transient models (i.e. where the spectral radius of the transition probability matrix is less then unity). Considering the second order optimality criteria means that in the class of policies maximizing (or minimizing) total expected discounted reward (or undiscounted reward for the transient model) we choose the policy minimizing the total variance. Explicit formulae for calculating the variances for transient and discounted models are reported along with sketches of algorithmic procedures for finding second order optimal policies.
Thermosensitive core-shell particles as carriers for ag nanoparticles: modulating the catalytic activity by a phase transition in networks.

Metal nanoparticles have properties that are significantly different from the bulk properties of the metals. Moreover, their high surface-to-volume ratio renders them ideal candidates for application as catalysts. However, the pronounced tendency of nanoparticles to aggregate must be overcome by using suitable carrier systems. Recently, a number of systems have been discussed that are suitable for applications in aqueous environments. These include polymers, dendrimers, microgels, 18] and other colloidal systems. 20] In all the cases studied so far, these carrier systems only provide a suitable support for the nanoparticles and prevent them from aggregating. In this way the carrier system of, for example, dendrimers or microgels acts much in the same way as a “nanoreactor” that immobilizes the particles and leads to their more convenient handling. Here we report on the first system that allows us to modulate the activity of nanoparticles through a thermodynamic transition that takes place within the carrier system. Figure 1 displays the principle. Metallic nanoparticles are embedded in a polymeric network attached to a colloidal core particle. In all the cases discussed here the core consists of poly(styrene) (PS) while the network consists of poly(Nisopropylacrylamide) (PNIPA) cross-linked with N,N’-methylenebisacrylamide (BIS). The particles are suspended in water, which swells the PNIPA at room temperature. The PNIPA network, however, undergoes a phase transition around 30 8C, during which most of the water is expelled. Previous experiments have demonstrated that this transition is perfectly reversible and the process of shrinking and reswelling can be repeated without degradation or coagulation of the particles. Metallic nanoparticles embedded in such a network are fully accessible to reactants at low temperature. Above the phase transition, however, the marked shrinkage of the network should be followed by a concomitant slowing down of the diffusion of the reactants within the network. The rate of reactions catalyzed by the nanoparticles should thus be slowed down considerably. In this way, the network could act as a “nanoreactor” that can be opened or closed to a certain extent. Herein we demonstrate that thermosensitive core–shell networks may indeed be used as such a nanoreactor. The activity of the catalyst can be modulated by temperature over a wide range. As the model reaction we chose the reduction of 4-nitrophenol to 4-aminophenol by sodium borohydride. The reaction was repeatedly performed to check the catalytic activity of the metal nanoparticles, and the results obtained in the present study can be directly compared to literature data. The carrier particles having a PS core and a PNIPA shell were prepared as described recently. 24] Figure 2 shows a schematic representation of the silver nanoparticles being