Miracle-dz/UniFAR-FTUs huggingface dataset:
3D ENGINEERING OF VIRUS-BASED PROTEIN NANOTUBES AND RODS: A TOOLKIT FOR GENERATING NOVEL NANOSTRUCTURED MATERIALS

Title of Dissertation: 3D ENGINEERING OF VIRUS-BASED PROTEIN NANOTUBES AND RODS: A TOOLKIT FOR GENERATING NOVEL NANOSTRUCTURED MATERIALS Adam Degen Brown, Doctor of Philosophy, 2018 Dissertation directed by: Professor James N. Culver, Department of Plant Science and Landscape Architecture and the Institute for Bioscience and Biotechnology Research Technological innovation at the nanometer scale has the potential to improve a wide range of applications, including energy storage, sensing of environmental and medical signals, and targeted drug delivery. A key challenge in this area is the ability to create complex structures at the nanometer scale. Difficulties in meeting this challenge using traditional fabrication methods have prompted interest in biological processes, which provide inspiration for complex structural organization at nanometer to micrometer length scales from self-assembling components produced inexpensively from common materials. From that perspective, a system of targeted modifications to the primary amino acid structure of Tobacco mosaic virus (TMV) capsid protein (CP) has been developed that induces new self-assembling behaviors to produce nanometer-scale particles with novel architectures. TMV CPs contain several negatively charged carboxylate residues which interact repulsively with those of adjacent CP subunits to destabilize the assembled TMV particle. Here, the replacement of these negatively charged carboxylate residues with neutrally charged or positively charged residues results in the spontaneous assembly of bacterially expressed CP into TMV virus-like particles (VLPs) with a range of environmental stabilities and morphologies and which can be engineered to attach perpendicularly to surfaces and to display functional molecular patterns such as target-binding peptide chains or chemical groups for attachment of functional targets. In addition, the distinct electrostatic surface charges of these CP variants enable the higher-level coassembly of TMV and VLP into continuous rod-shaped nanoparticles with longitudinally segregated distribution of functionalities and surface properties. Furthermore, the unique, novel, environmentally responsive assembly and disassembly behaviors of the modified CPs are shown to act as simple mechanisms to control the fabrication of these hierarchically structured functional nanoparticles. 3D ENGINEERING OF VIRUS-BASED PROTEIN NANOTUBES AND RODS: A TOOLKIT FOR GENERATING NOVEL NANOSTRUCTURED MATERIALS
Sonographically Guided Infraclavicular Brachial Plexus Block in Adults

Objective. The aim of this study was to analyze our experience in 1146 cases of sonographically guided infraclavicular brachial plexus block (ICBPB) performed over 32 months. Methods. Anesthetic records of 1146 cases of sonographically guided ICBPB performed by our staff were studied retrospectively with the use of a database created by an automated anesthesia record‐keeping system. The rates of successful blocks, failed blocks necessitating conversion to general anesthesia or requiring supplementation with local anesthetics, those requiring larger‐than‐usual doses of sedation, and complications were determined. Analysis included an attempt to determine the possible causes of inadequate blocks and complications. Results. In 1138 patients (99.3%), the block was successful. Six patients had incomplete blocks requiring general anesthesia, and another 2 patients needed local anesthetic supplementation by the surgeons. Ninety‐seven percent of the blocks were performed by residents directly supervised by an attending anesthesiologist who held the ultrasound probe. The mean age ± SD of the patients was 39 ± 15 years; the mean duration of surgery was 165 ± 114 minutes; and the male‐female ratio was 4:1. More than 50% of patients were obese. There were no reported cases of nerve injury, pneumothorax, or local anesthetic toxicity. Arterial punctures occurred in 8 (0.7%) patients, but all were inconsequential. Conclusions. The data from this retrospective study suggest that sonographic guidance provides a high success rate (99.3%) and improved safety for ICBPB. The increased operator team experience virtually eliminates failure and complications.
A Re-examination of the MM Capital Structure Irrelevance Theorem: A Partial Payout Approach

Contrary to Modigliani and Miller (1958, MM hereafter), Capital Structure is not irrelevant when we consider a firm with a dividend payout policy. This article extends the MM capital structure theorem by relaxing the full payout assumption and introducing retention policy. The theoretical contribution shows that it is possible to verify the theorem when we suppose an investor who exchanges his initial holding for another portfolio composed of consumption and investment. The empirical analysis of this new approach is based on a data set of the USA Electric Utilities and Oil companies for the period 1990-1998. The results show that the relationships between leverage and firm value are significantly affected by the firm’s payout ratio. This finding is largely inconsistent with MM’s view that the division of a stream between cash dividend and retained earnings is a mere detail in dealing with the irrelevance of capital structure.
Mitotic kinase expression and colorectal cancer progression.

Loss of chromosomal integrity as well as genomic stability is considered to act as a driving force during the processes of tumorigenesis and tumor progression(1–3). Recently, two kinase genes involved in mitosis, the genes for aurora and IPL1l ike midbodyassociated protein kinase-1 (4,5) [AIM1, registered in UniGene and also known as aurora1(6) and ARK2 (7)] and for serine/threonine kinase-6 [STK6, also known as BTAK/STK15(8,9),Aik (10), aurora2(6), and ARK1 (7)], which are related to Ipl1 inSaccharomyces cerevisiae and aurora inDrosophila, have been found to be expressed at high levels in cancer cells(5,6,9). These genes encode serine/threonine protein kinases whose functional roles during chromosomal segregation processes in mitosis have been examined (4–10). In transfected human cellsin vitro, the overexpression of either AIM-1 or STK6 causes chromosomal abnormalities, which are presumably attributed to a defect in the mitotic processes (5,9). Thus, these genes may be involved in the loss of chromosomal integrity during human cancer development via mitotic subversion.
Examination of postextraction space closure speed using elastic chains and NiTi closed coil springs

Summary Introduction In everyday clinical practice, we often encounter a lack of space for placing all the teeth present into dental arch; therefore it is often recommended to extract teeth within orthodontic treatment. In clinical practice, the most commonly used methods of closing space after are elastic chains and NiTi closed spiral springs. The aim of this paper was to compare postextraction space closure speed using two different sliding mechanisms, NiTi closed coil springs and elastic chains within treatment with fixed orthodontic appliances. Material and Method The total sample in this study consisted of 46 postexstraction spaces in 23 patients indicated for the extraction of first premolars using treatment with fixed orthodontic appliances. Two sliding mechanisms, NiTi closed coil spring and elastic chains were applied to postextraction space closure. Postextraction spaces were monitored for 4 months with appointments every 4 weeks. During appointments mechanisms were activated and digital caliper was used to measure the width of the postextraction space. Results The results showed that NiTi closed coil springs method achieved greater reduction in postexstraction space (3.94 mm) while with elastic chain method the closure of 3.10 mm was achieved. The total difference between these two methods in the observed period was 0.84mm and no statistically significant difference was found (p> 0.05). The lowest value for NiTi closed springs was 2.19 mm, while for the elastic chain it was 1.29 mm. The best postextraction space closure was 5.70 mm and it was completed using NiTi closed springs while for elastic chain the best value was 4.80 mm. Conclusion: NiTi closed coil springs lead to faster closure of postextraction spaces in relation to elastic chain. Since this difference is minimal, in practice, both methods can be used equally.
Magnetic resonance techniques for the in vivo assessment of multiple sclerosis pathology: Consensus report of the white matter study group

On October 9–11, 2003, the third meeting of the White Matter Study Group of the International Society for Magnetic Resonance in Medicine was held in Venice, Italy. This article is the report of the meeting on how to use MRI in the diagnostic workup of multiple sclerosis (MS) and allied white matter disorders, and to define the nature and the extent of MS pathology in vivo. Both of these steps are central to the design of future treatment strategies aimed at limiting the functional consequences of the most disabling aspects of this disease. J. Magn. Reson. Imaging 2005;21:669–675. © 2005 Wiley‐Liss, Inc.
Examining University Students’ Self-Compassion and Compassionate Love Levels in Terms of Perceived Parental Attitudes

The aim of this research is to investigate the relationship between parental attitudes perceived by the students, self-compassion and compassionate love levels, and differences occur in parental attitudes, self-compassion and compassionate love levels according to various variables. The research was conducted with 326 university students studying in different departments of Sakarya University Faculty of Education. Parental Attitude Scale (PAS), Self-Compassion Scale (SCS), the Compassionate Love Scale (CLS) and Information Collection Form were applied in the study. The research data were analyzed by correlation, T-test and One Way (ANOVA). The results of the research revealed that the self-compassion level of the students who perceived the parents' attitudes as democratic was high, whereas the self-compassion level of the students who perceived the parental attitudes as authoritarian and protective-demanding was low. It was also found out that the students who perceived their parents' attitudes as authoritarian and protective-demanding had high compassionate love levels. The present study demonstrated the authoritarian and protective-demanding parental attitudes perceived by university students differed according to sex, the democratic parental attitude differed in terms of the number of siblings, and the compassionate love differed in terms of gender. It was revealed that there was a negative relationship between self-compassion and compassionate love.
The Ethics of IT Professionals in Japan and China

The ethical integrity and accountability of Information Technology (IT) professionals is important given our reliance on various forms of IT. We examined the applicability of Lawrence Kohlberg’s theory of Cognitive Moral Development (CMD) in non-Western contexts by investigating the ethical values of IT professionals in Asia’s two largest economies. Analysis of survey data from Japan (n=289) and China (n=290) indicates support for the basic six-stage model of CMD. The concept of abiding by universal laws and rules (termed stage 4 reasoning by Kohlberg) was widely accepted by IT professionals in both Japan and China, despite the Confucian cultural emphasis on personal relationships with particularistic obligations. However, differences between Japanese and Chinese IT professionals were found while, in direct contrast with the stage-wise theory of CMD, the respondents from Japan and especially China exhibited significant volatility, reasoning at different stages simultaneously. The implications of these findings for research and practice are discussed. significant correlation with their responses in our study.
Enabling the Definition and Enforcement of Governance Rules in Open Source Systems

Governance rules in software development projects help to prioritize and manage their development tasks, and contribute to the long-term sustainability of the project by clarifying how core and external contributors should collaborate in order to advance the project during its whole lifespan. Despite their importance, specially in Open Source Software (OSS) projects, these rules are usually implicit or scattered in the project documentation/tools (e.g., Tracking-systems or forums), hampering the correct understanding of the development process. We propose to enable the explicit definition and enforcement of governance rules for OSS projects. We believe this brings several important benefits, including improvements in the transparency of the process, its traceability and the semi-automation of the governance itself. Our approach has been implemented on top of My Lyn, a project-management Eclipse plug-in supporting most popular tracking-systems.
In vitro bactericidal effects of 405-nm and 470-nm blue light.

OBJECTIVE The aim of this study was to determine the bactericidal effect of 405- and 470-nm light on two bacteria, Staphylococcus aureus and Pseudomonas aeruginosa, in vitro. BACKGROUND DATA It is well-known that UV light kills bacteria, but the bactericidal effects of UV may not be unique since recent studies indicate that blue light produces a somewhat similar effect. The effects of blue light seem varied depending on wavelength, dose and the nature of the bacteria, hence this study. METHODS Two common aerobes, Staphylococcus aureus and Pseudomonas aeruginosa, and anaerobic Propionibacterium acnes were tested. Each organism was treated with Super Luminous Diode probes with peak emission at 405 and 470 nm. Treatment was timed to yield 1, 3, 5, 10, and 15 Jcm2 doses. Colony counts were performed and compared to untreated controls. RESULTS The 405-nm light produced a dose dependent bactericidal effect on Pseudomonas aeruginosa and Staphylococcus aureus (p < .05), achieving as much as 95.1% and nearly 90% kill rate for each, respectively. The 470-nm light effectively killed Pseudomonas aeruginosa at all dose levels, but only killed Staphylococcus aureus at 10 and 15 J cm2. With this wavelength, as much as 96.5% and 62% reduction of Pseudomonas aeruginosa and Staphylococcus aureus was achieved, respectively. Neither of the two wavelengths proved bactericidal with anaerobic Propionibacterium acnes. CONCLUSION The results indicate that, in vitro, 405- and 470-nm blue light produce dose dependent bactericidal effects on Pseudomonas aeruginosa and Staphylococcus aureus but not Propionibacterium acnes.
Mixing properties of ARCH and time-varying ARCH processes

There exist very few results on mixing for non-stationary processes. However, mixing is often required in statistical inference for non-stationary processes such as time-varying ARCH (tvARCH) models. In this paper, bounds for the mixing rates of a stochastic process are derived in terms of the conditional densities of the process. These bounds are used to obtain the $\alpha$, 2-mixing and $\beta$-mixing rates of the non-stationary time-varying $\operatorname {ARCH}(p)$ process and $\operatorname {ARCH}(\infty)$ process. It is shown that the mixing rate of the time-varying $\operatorname {ARCH}(p)$ process is geometric, whereas the bound on the mixing rate of the $\operatorname {ARCH}(\infty)$ process depends on the rate of decay of the $\operatorname {ARCH}(\infty)$ parameters. We note that the methodology given in this paper is applicable to other processes.
Marginal fit of electroplated copings before and after the coction of the porcelain.

The aim of this study was to evaluate the marginal discrepancy of electroforming copings, before and after the porcelain application, varying the cervical preparation of the crowns.Two master die were prepared with stainless steel to complete crown margin designs: chamfer and rounded shoulder. The impressions were taken with a polyvinylsiloxane by the double impression technique and, the insertion and removal axis were standardized by a dental surveyor. Ten type IV plaster dies from each cervical margin were obtained, on which a die spacer was applied before duplicate. The duplicated dies received a silver layer and connected to a copper wire to enable the gold electrodeposition. After cleaning and adjustments all specimens were examined under a microscope (magnificatio X 30). The marginal gap was measured before and after ceramic application. The results were elaborated by descriptive statistical and two-way analysis of variance (ANOVA). The ANOVA revealed no significant difference between marginal gap before and after the ceramic application (p=5%). It was concluded that the porcelain application does not influence the marginal fit of copings, therefore the two marginal endings can be used with the electroforming system.
Gene Expression Analysis Reveals Distinct Pathways of Resistance to Bevacizumab in Xenograft Models of Human ER-Positive Breast Cancer

Bevacizumab, the recombinant antibody targeting vascular endothelial growth factor (VEGF), improves progression-free but not overall survival in metastatic breast cancer. To seek further insights in resistance mechanisms to bevacizumab at the molecular level, we developed VEGF and non-VEGF-driven ER-positive MCF7-derived xenograft models allowing comparison of tumor response at different timepoints. VEGF gene (MV165) overexpressing xenografts were initially sensitive to bevacizumab, but eventually acquired resistance. In contrast, parental MCF7 cells derived tumors were de novo insensitive to bevacizumab. Microarray analysis with qRT-PCR validation revealed that Follistatin (FST) and NOTCH were the top signaling pathways associated with resistance in VEGF-driven tumors (P<0.05). Based on the presence of VEGF, treatment with bevacizumab resulted in altered patterns of metagenes and PAM50 gene expression. In VEGF-driven model after short and long-term bevacizumab treatments, a change in the intrinsic subtype (luminal to myoepithelial/basal-like) was observed in association with increased expression of genes implicated with cancer stem cell phenotype (P<0.05). Our results show that the presence or absence of VEGF expression affects the response to bevacizumab therapy and gene pathways. In particular, long-term bevacizumab treatment shifts the cancer cells to a more aggressive myoepithelial/basal subtype in VEGF-expressing model, but not in non-VEGF model. These findings could shed light on variable results to anti-VEGF therapy in patients and emphasize the importance of patient stratification based on the VEGF expression. Our data strongly suggest consideration of patient subgroups for treatment and designing novel combinatory therapies in the clinical setting.
Empirical treatment of influenza-associated pneumonia in primary care: a descriptive study of the antimicrobial susceptibility of lower respiratory tract bacteria (England, Wales and Northern Ireland, January 2007–March 2010)

Objectives To determine the susceptibility of lower respiratory tract (LRT) isolates of Streptococcus pneumoniae, Staphylococcus aureus and Haemophilus influenzae to antimicrobial agents recommended by UK guidelines for treatment of pneumonia associated with influenza-like illness. Methods Analysis of antimicrobial susceptibility data from sentinel microbiology laboratories in England, Wales and Northern Ireland was carried out. Subjects comprised patients who had an LRT specimen taken in a general practitioner surgery or hospital outpatient setting between January 2007 and March 2010. The main outcome measurements were antimicrobial susceptibility trends of LRT isolates over time, between patient age groups and in different geographical regions. Results Susceptibility to tetracyclines or co-amoxiclav was high. Of the 70 288 and 45 288 isolates with susceptibility results for tetracyclines or co-amoxiclav, 96% and 92%, respectively, were susceptible. Overall susceptibility to ciprofloxacin, ampicillin/amoxicillin and macrolides was lower than for tetracyclines or co-amoxiclav and varied markedly by organism. There were few clinically relevant variations in susceptibility to doxycycline or co-amoxiclav over time, geographically or between age groups. Conclusions The data support the use of doxycycline or co-amoxiclav as appropriate empiric treatment for LRT infection caused by the pathogens investigated, for patients in primary care.
Design of the EuCARD High Field Model Dipole Magnet FRESCA2

This paper reports on the design of FRESCA2, a dipole magnet model wound with Nb3Sn Rutherford cable. This magnet is one of the deliverables of the High Field Magnets work package of the European FP7-EuCARD project. The nominal magnetic flux density of 13 Tesla in a 100 mm bore will make it suitable for upgrading the FRESCA cable test facility at CERN. The magnetic layout is based on a block coil, with four layers per pole. The mechanical structure is designed to provide adequate pre-stress, through the use of bladders, keys and an aluminum alloy shrinking cylinder.
Conformational modulation and hydrodynamic radii of CP12 protein and its complexes probed by fluorescence correlation spectroscopy

Light/dark regulation of the Calvin cycle in oxygenic photosynthetic organisms involves the formation and dissociation of supramolecular complexes between CP12, a nuclear‐encoded chloroplast protein, and the two enzymes glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) (EC 1.2.1.13) and phosphoribulokinase (PRK) (EC 2.7.1.19). Despite the high importance of understanding the structural basis of the interaction of CP12 with GAPDH and PRK to investigate the regulation of the Calvin cycle, information is still lacking about the structural remodulation of CP12 and its complex formation. Here, we characterize the diffusion dynamics and hydrodynamic radii of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH and PRK using fluorescence correlation spectroscopy experiments. We quantify a hydrodynamic radius of 3.4 ± 0.2 nm for the CP12 protein with an increase up to 5.2 ± 0.3 nm upon complex formation with GAPDH and PRK. In addition, unfolding experiments reveal a 1.6‐ and 2.0‐fold increase respectively of the hydrodynamic radii for the N‐terminal and C‐terminal cysteine CP12 mutant proteins compared with their native folded structures. The different behavior of the CP12 mutant proteins during hydrophobic collapse transition is a direct clue to different structural orientations of the CP12 mutant proteins. These different structures are expected to facilitate the binding of either GAPDH or PRK during binary complex and ternary complex formation.
Dietarycalciumphosphate content and oat b-glucan in £ uence gastrointestinalmicrobiota , butyrate-producing bacteria and butyrate fermentation inweanedpigs

Dietarycalciumphosphate content and oat b-glucan in£uence gastrointestinalmicrobiota, butyrate-producing bacteria and butyrate fermentation inweanedpigs Barbara U. Metzler-Zebeli, Ruurd T. Zijlstra, Rainer Mosenthin & Michael G. Gänzle Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada; and Institute of Animal Nutrition (450), University of Hohenheim, Stuttgart, Germany