Miracle-dz/UniFAR-FTUs huggingface dataset:
Multilayering and loss of apical polarity in MDCK cells transformed with viral K-ras

The effects of viral Kirsten ras oncogene expression on the polarized phenotype of MDCK cells were investigated. Stable transformed MDCK cell lines expressing the v-K-ras oncogene were generated via infection with a helper-independent retroviral vector construct. When grown on plastic substrata, transformed cells formed continuous monolayers with epithelial-like morphology. However, on permeable filter supports where normal cells form highly polarized monolayers, transformed MDCK cells detached from the substratum and developed multilayers. Morphological analysis of the multilayers revealed that oncogene expression perturbed the polarized organization of MDCK cells such that the transformed cells lacked an apical--basal axis around which the cytoplasm is normally organized. Evidence for selective disruption of apical membrane polarity was provided by immunolocalization of membrane proteins; a normally apical 114-kD protein was randomly distributed on the cell surface in the transformed cell line, whereas normally basolateral proteins remained exclusively localized to areas of cell contact and did not appear on the free cell surface. The discrete distribution of the tight junction-associated ZO-1 protein as well as transepithelial resistance and flux measurements suggested that tight junctions were also assembled. These findings indicate that v-K-ras transformation alters cell-substratum and cell-cell interactions in MDCK cells. Furthermore, v-K-ras expression perturbs apical polarization but does not interfere with the development of a basolateral domain, suggesting that apical and basolateral polarity in epithelial cells may be regulated independently.
Genomics and Comparative Genomic Analyses Provide Insight into the Taxonomy and Pathogenic Potential of Novel Emmonsia Pathogens

Over the last 50 years, newly described species of Emmonsia-like fungi have been implicated globally as sources of systemic human mycosis (emmonsiosis). Their ability to convert into yeast-like cells capable of replication and extra-pulmonary dissemination during the course of infection differentiates them from classical Emmonsia species. Immunocompromised patients are at highest risk of emmonsiosis and exhibit high mortality rates. In order to investigate the molecular basis for pathogenicity of the newly described Emmonsia species, genomic sequencing and comparative genomic analyses of Emmonsia sp. 5z489, which was isolated from a non-deliberately immunosuppressed diabetic patient in China and represents a novel seventh isolate of Emmonsia-like fungi, was performed. The genome size of 5z489 was 35.5 Mbp in length, which is ~5 Mbp larger than other Emmonsia strains. Further, 9,188 protein genes were predicted in the 5z489 genome and 16% of the assembly was identified as repetitive elements, which is the largest abundance in Emmonsia species. Phylogenetic analyses based on whole genome data classified 5z489 and CAC-2015a, another novel isolate, as members of the genus Emmonsia. Our analyses showed that divergences among Emmonsia occurred much earlier than other genera within the family Ajellomycetaceae, suggesting relatively distant evolutionary relationships among the genus. Through comparisons of Emmonsia species, we discovered significant pathogenicity characteristics within the genus as well as putative virulence factors that may play a role in the infection and pathogenicity of the novel Emmonsia strains. Moreover, our analyses revealed a novel distribution mode of DNA methylation patterns across the genome of 5z489, with >50% of methylated bases located in intergenic regions. These methylation patterns differ considerably from other reported fungi, where most methylation occurs in repetitive loci. It is unclear if this difference is related to physiological adaptations of new Emmonsia, but this question warrants further investigation. Overall, our analyses provide a framework from which to further study the evolutionary dynamics of Emmonsia strains and identity the underlying molecular mechanisms that determine the infectious and pathogenic potency of these fungal pathogens, and also provide insight into potential targets for therapeutic intervention of emmonsiosis and further research.
Physical activity readiness in patient withdrawals from cardiac rehabilitation.

BACKGROUND Adherence to cardiac rehabilitation (CR) programmes may be an important element for improving and maintaining physical activity (PA) behaviour in secondary prevention. Little is known about the PA behaviour in patients who have withdrawn from CR programmes. Therefore, a study was carried out to identify the reasons for withdrawal and the stage of PA readiness in those patients previously engaged in a Leeds-based community CR programme. METHODS A cross-sectional study was conducted using a telephone questionnaire to determine causes of withdrawal. A questionnaire based on the transtheoretical model of change was used to assess changes in PA readiness in these patients. RESULTS 101 withdrawn patients (mean age = 61 years; 72% male) were identified. It was found that 20 patients had relapsed beyond baseline (preparation phase) into pre-contemplation and contemplation phases and 15 reported they were in the preparation phase. However, the majority of patients remained in the action (18) and maintenance (48) phases of the transtheoretical model. Patients reported the following reasons for withdrawal: joined other facilities (16%); injury or illness (3%); family demands (7%); work demands (14%); lack of motivation (4%); lack of enjoyment (11%); lack of transport (10%); lack of time (10%); too expensive (6%); too crowded (4%). CONCLUSION 66% of patients who had withdrawn from a phase IV CR programme remained in an advanced stage of PA readiness. Drop-out was due to a combination of financial, physical and lifestyle factors.
Recombinant Sox Enzymes from Paracoccus pantotrophus Degrade Hydrogen Sulfide, a Major Component of Oral Malodor

Hydrogen sulfide (H2S) is emitted from industrial activities, and several chemotrophs possessing Sox enzymes are used for its removal. Oral malodor is a common issue in the dental field and major malodorous components are volatile sulfur compounds (VSCs), including H2S and methyl mercaptan. Paracoccus pantotrophus is an aerobic, neutrophilic facultatively autotrophic bacterium that possesses sulfur-oxidizing (Sox) enzymes in order to use sulfur compounds as an energy source. In the present study, we cloned the Sox enzymes of P. pantotrophus GB17 and evaluated their VSC-degrading activities for the prevention of oral malodor. Six genes, soxX, soxY, soxZ, soxA, soxB, and soxCD, were amplified from P. pantotrophus GB17. Each fragment was cloned into a vector for the expression of 6×His-tagged fusion proteins in Escherichia coli. Recombinant Sox (rSox) proteins were purified from whole-cell extracts of E. coli using nickel affinity chromatography. The enzyme mixture was investigated for the degradation of VSCs using gas chromatography. Each of the rSox enzymes was purified to apparent homogeneity, as confirmed by SDS-PAGE. The rSox enzyme mixture degraded H2S in dose- and time-dependent manners. All rSox enzymes were necessary for degrading H2S. The H2S-degrading activities of rSox enzymes were stable at 25–80°C, and the optimum pH was 7.0. The amount of H2S produced by periodontopathic bacteria or oral bacteria collected from human subjects decreased after an incubation with rSox enzymes. These results suggest that the combination of rSox enzymes from P. pantotrophus GB17 is useful for the prevention of oral malodor.
Coupling element based mobile terminal antenna structures

In this paper, internal low-volume antenna structures for mobile terminals are studied. The work concentrates on the possibilities to reduce the volume of mobile terminal antenna elements by efficiently utilizing the radiation of the currents on the mobile terminal chassis. Essentially nonresonant coupling elements are used to optimally couple to the dominating char- acteristic wavemodes of the chassis. The antenna structures are tuned to resonance with matching circuits. During the last few years, the approach has achieved growing interest—also among industrial manufacturers of mobile terminals. There exist, how- ever, no systematical feasibility and performance studies of the idea. During the work, two antenna models with very low-volume coupling elements are designed and in total four prototypes are constructed. The simulation and measurement results show that the studied antenna concept is a very promising alternative for traditional antenna technologies. The presented analysis provides useful and novel information for the designs of the future low-pro- file and low-volume mobile terminal antennas.
Commonly asked questions: imaging stroke and other types of neurovascular disorders

The medical management of patients requiring imaging of the head is often complex. This is confounded by growth and development of neuroimaging technology. Summarizing established guidelines and provided answers to commonly asked questions about neurovascular imaging may aid in providing efficient medical care. Noncontrast head computed tomography (CT) is usually the first line in imaging because of its speed and wide-spread availability. More advanced techniques are reserved for more specific questions or when the CT head is non-diagnostic. MRI is the modality of choice for indications that include chronic headache, pulsatile tinnitus, and cerebrovascular diseases including stroke in the subacute or chronic setting. The imaging of stroke is evolving and many advanced techniques including CT and magnetic resonance perfusion are playing an increasing role in diagnosis. Digital subtraction angiography is widely accepted as the gold standard for evaluation of vascular pathology including aneurysm, vascular malformations, Moyamoya syndrome, carotid stenosis and dissection; and offers treatment options. Alternatives such as MR angiography, MR venography, and CT angiography offer similar sensitivity and specificity to conventional digital subtraction angiography. Safety considerations are an important concern. When using iodinated and gadolinium contrast agents, there are potential complications including allergic reactions, lactic acidosis, and nephrogenic systemic fibrosis. Impaired renal function requires modification in the use of contrast during neuroimaging. Neuroimaging during pregnancy is also discussed.
Models for Call Acceptance Based on Handoff Guarantees

Call admission control (CAC) is important for cellular wireless networks to provide quality-of-service (QoS) requirements to users. Static and adaptive CAC schemes, respectively, make unrealistic assumptions about the distributions of the handoff call arrival process and the number of users in a cell. Handoff arrivals are usually assumed to follow Poisson process in static CAC schemes for Poisson new call arrivals and exponentially distributed call holding and cell residence times. We use a simple proof to show that this assumption of Poisson handoff arrival process is not justified for a two-cell wireless network. In general, we find that the handoff process can be captured by a two-dimensional Markov chain. We propose a novel adaptive CAC scheme for the two-cell system which accepts a new call if it can guarantee, with a certain probability, that a user's call will be maintained irrespective of its (his/her) movement in the system. Then, we extend this adaptive scheme for multiple-cell network. We develop another variant of this adaptive scheme which we call fractional adaptive scheme. Both the adaptive and fractional adaptive schemes are found to outperform the guard channel scheme in controlling the handoff failure probability in a cellular wireless network.
Association of COMT Val108/158Met Genotype and Cigarette Smoking in Pregnant Women

Introduction: Smoking behaviors, including heaviness of smoking and smoking cessation, are known to be under a degree of genetic influence. The enzyme catechol O-methyltransferase (COMT) is of relevance in studies of smoking behavior and smoking cessation due to its presence in dopaminergic brain regions. While the COMT gene is therefore one of the more promising candidate genes for smoking behavior, some inconsistencies have begun to emerge. Methods: We explored whether the rs4680 A (Met) allele of the COMT gene predicts increased heaviness of smoking and reduced likelihood of smoking cessation in a large population-based cohort of pregnant women. We further conducted a meta-analysis of published data from community samples investigating the association of this polymorphism with heaviness of smoking and smoking status. Results: In our primary sample, the A (Met) allele was associated with increased heaviness of smoking before pregnancy but not with the odds of continuing to smoke in pregnancy either in the first trimester or in the third trimester. Meta-analysis also indicated modest evidence of association of the A (Met) allele with increased heaviness of smoking but not with persistent smoking. Conclusions: Our data suggest a weak association between COMT genotype and heaviness of smoking, which is supported by our meta-analysis. However, it should be noted that the strength of evidence for this association was modest. Neither our primary data nor our meta-analysis support an association between COMT genotype and smoking cessation. Therefore, COMT remains a plausible candidate gene for smoking behavior phenotypes, in particular, heaviness of smoking.
Generic torque-maximizing design methodology of surface permanent-magnet vernier machine

A surface permanent-magnet vernier machine (SPMVM) has a toothed-pole structure, and its highly nonlinear relationship between its dimensions and magnetic field makes its design cumbersome. This paper presents a generic design methodology for the machine which brings out its torque-maximizing structure in a convenient manner. Various suggestions concerning the design of the SPMVM are also set forth.
cAMP response element‐binding protein 1 is required for hydroxyurea‐mediated induction of γ‐globin expression in K562 cells

Hydroxyurea (HU) is a drug used for the treatment of haemoglobinopathies. Hydroxyurea functions by upregulating γ‐globin transcription and fetal haemoglobin (HbF) production in erythroid cells. The K562 erythroleukaemia cell line is widely used as a model system in which to study the mechanism of γ‐globin induction by HU. However, the transcription factors required for the upregulation of γ‐globin expression by HU in K562 cells have not been identified. Similarities between the HU and sodium butyrate (SB) pathways suggest cAMP response element‐binding protein (CREB) 1 as a potential candidate. Thus, the aim of the present study was to investigate the possible role of CREB1 in the HU pathway. Experiments were performed using transient and stable RNA interference (RNAi) to show that CREB1 is necessary for HU‐mediated induction of γ‐globin expression and haemoglobin production in K562 cells. Furthermore, western blot analyses demonstrated that CREB1 becomes phosphorylated in a dose‐dependent manner after HU (100–400 µmol/L) treatment of K562 cells for 72 h. We also investigated role of a Gγ promoter CREB1 response element (G‐CRE) in this pathway. Quantitative amplification refractory mutation system–polymerase chain reaction experiments were performed to demonstrate that HU induces the expression of both Gγ and Aγ in this cell line. In addition, electrophoretic mobility shift assays were used to show that levels of CREB1 complexes binding to the G‐CRE site are increased following HU treatment and are decreased in CREB1‐knockdown cells. The results suggest that CREB1 is necessary for γ‐globin induction by HU in K562 cells, a role that may be mediated, in part, through the G‐CRE element.
Global ocean carbon uptake: magnitude, variability and trends

The globally integrated sea–air anthropogenic carbon dioxide (CO 2 ) flux from 1990 to 2009 is determined from models and data-based approaches as part of the Regional Carbon Cycle Assessment and Processes (RECCAP) project. Numerical methods include ocean inverse models, atmospheric inverse models, and ocean general circulation models with parameterized biogeochemistry (OBGCMs). The median value of different approaches shows good agreement in average uptake. The best estimate of anthropogenic CO 2 uptake for the time period based on a compilation of approaches is −2.0 Pg C yr −1 . The interannual variability in the sea–air flux is largely driven by large-scale climate re-organizations and is estimated at 0.2 Pg C yr −1 for the two decades with some systematic differences between approaches. The largest differences between approaches are seen in the decadal trends. The trends range from −0.13 (Pg C yr −1 ) decade −1 to −0.50 (Pg C yr −1 ) decade −1 for the two decades under investigation. The OBGCMs and the data-based sea–air CO 2 flux estimates show appreciably smaller decadal trends than estimates based on changes in carbon inventory suggesting that methods capable of resolving shorter timescales are showing a slowing of the rate of ocean CO 2 uptake. RECCAP model outputs for five decades show similar differences in trends between approaches.
The effect of tramadol and tramadol + gabapentin combination in patients with lumbar disc herniation after epidural steroid injection.

BACKGROUND/AIM To compare the effects of tramadol-only treatment and tramadol + gabapentin treatment in patients who had received an epidural steroid injection. MATERIALS AND METHODS Forty patients with hernia disc-originated acute lumbar discogenic pain were evaluated. All patients received a single dose of steroid and local anesthesia mixture epidurally via the lumbar approach. In both groups, Group T (tramadol, n = 20) and Group TG (tramadol + gabapentin, n = 20), the injection dose was adjusted to 4 mL of triamcinolone acetonide and 0.25% bupivacaine mixture. Orally, 75 mg/day tramadol or 75 mg/day tramadol + 900 mg/day gabapentin were added to the treatment. Leukocyte, erythrocyte sedimentation rate, C-reactive protein, and urine serotonin levels were measured prior to and after treatment. The effectiveness of the treatment was evaluated byvisual analog scale (VAS), Oswestry Disability Index (ODI), and straight leg elevation test (SLET). RESULTS Similar improvements in VAS, ODI, and SLET values were observed in both groups in the second week. The inflammation markers were not different after treatment, neither within the groups nor between the groups. CONCLUSION This study revealed that tramadol + gabapentin treatment was not superior to tramadol treatment.
Judgements of a 2 × 2 Contingency Table: Sequential processing and the Learning Curve

Shanks (1985) has used a video game to investigate how subjects estimate the effect of their behaviour in a task defined by a 2×2 contingency table. The subjects were able to distinguish positive and negative contingencies from zero contingencies. In addition, they showed a learning curve and a bias to rate zero contingencies with a high outcome density higher than low-density zero contingencies. He interpreted these data as being consistent with associative models derived from animal learning. In Experiment 1 we replicated these results using a task and instructions similar to his. In a second experiment we showed that the subjects’ tendency to overestimate high-density zero contingencies did not arise because the “game” was so difficult that it interfered with processing the events. In this experiment subjects were given tables of the outcome frequencies that had been determined by the earlier subjects. These subjects were, if anything, less accurate in rating the zero contingencies. We point out several logical problems with Shanks's initial task. The task did not represent a true 2×2 contingency, and aspects of it were physically impossible. In Experiment 3 we modified the task to represent a true 2×2 contingency. Using this task, we found a similar pattern of results, except that there was no evidence of the learning curve predicted by the associative models. We conclude that there is little in our data to rule out a “rule-based” analysis of contingency judgements.
Teaching Smalltalk as a first programming language

Object-oriented programming is an emerging technology in both the research and industrial communities. At the School of Computer Science at Carleton UniversiQ, we have moved to an object-oriented paradigm to teach our introductory courses. This paradigm was chosen because it is more suitable for teaching the basic concepts of computer science such as data abstraction and encapsulation. Smalltalk has been chosen as the fundamental teaching language. In this paper, many of the experiences gained while teaching the introductory programming course are described. The structure of this course is outlined and the effects it has had on the program are identified. The problems encountered as well as a summary of students’ reactions to the course are discussed. A description of further modi~cations to the course is given.
Interference modelling and management for cognitive radio networks

Radio spectrum is becoming increasingly scarce as more and more devices go wireless. Meanwhile, studies indicate that the assigned spectrum is not fully utilised. Cognitive radio (CR) technology is envisioned to be a promising solution to address the imbalance between spectrum scarcity and spectrum underutilisation. It improves the spectrum utilisation by reusing the unused or underutilised spectrum owned by incumbent systems (primary systems). With the introduction of CR networks, two types of interference originating from CR networks are introduced. They are the interference from CR to primary networks (CR-primary interference) and the interference among spectrum-sharing CR nodes (CR-CR interference). The interference should be well controlled and managed in order not to jeopardise the operation of the primary network and to improve the performance of CR systems. This thesis investigates the interference in CR networks by modelling and mitigating the CR-primary interference and analysing the CR-CR interference channels. Firstly, the CR-primary interference is modelled for multiple CR nodes sharing the spectrum with the primary system. The probability density functions of CR-primary interference are derived for CR networks adopting different interference management schemes. The relationship between CR operating parameters and the resulting CRprimary interference is investigated. It sheds light on the deployment of CR networks to better protect the primary system. Secondly, various interference mitigation techniques that are applicable to CR networks are reviewed. Two novel precoding schemes for CR multiple-input multipleoutput (MIMO) systems are proposed to mitigate the CR-primary interference and maximise the CR throughput. To further reduce the CR-primary interference, we also approach interference mitigation from a cross-layer perspective by jointly considering channel allocation in the media access control layer and precoding in the physical layer of CR MIMO systems. Finally, we analyse the underlying interference channels among spectrum-sharing CR users when they interfere with each other. The Pareto rate region for multi-user MIMO interference systems is characterised. Various rate region convexification schemes are examined to convexify the rate region. Then, game theory is applied to the interference system to coordinate the operation of each CR user. Nash bargaining over MIMO interference systems is characterised as well. The research presented in this thesis reveals the impact of CR operation on the resulting CR-primary network, how to mitigate the CR-primary interference and how to coordinate the spectrum-sharing CR users. It forms the fundamental basis for interference management in CR systems and consequently gives insights into the design and deployment of CR networks.