Miracle-dz/UniFAR-FTUs huggingface dataset:
Current status of lung transplantation

Lung transplantation is a well-established treatment option for selected patients with end-stage lung disease, leading to improved survival and improved quality of life. The last 20 years have seen a steady growth in number of lung transplantation procedures performed worldwide. The increase in clinical activity has been associated with tremendous progress in the understanding of cellular and molecular processes that limit both short- and long-term outcomes. This review gives a comprehensive overview of the current status of lung transplantation for the referring physician. It demonstrates that careful selection of potential recipients, optimisation of their condition prior to transplant, use of carefully assessed donor organs, excellent surgery and meticulous long-term follow-up are all essential ingredients in determining a successful outcome.
Assembly of Respiratory Complexes I, III, and IV into NADH Oxidase Supercomplex Stabilizes Complex I in Paracoccus denitrificans*

Stable supercomplexes of bacterial respiratory chain complexes III (ubiquinol:cytochrome c oxidoreductase) and IV (cytochrome c oxidase) have been isolated as early as 1985 (Berry, E. A., and Trumpower, B. L. (1985) J. Biol. Chem. 260, 2458-2467). However, these assemblies did not comprise complex I (NADH:ubiquinone oxidoreductase). Using the mild detergent digitonin for solubilization of Paracoccus denitrificans membranes we could isolate NADH oxidase, assembled from complexes I, III, and IV in a 1:4:4 stoichiometry. This is the first chromatographic isolation of a complete “respirasome. ” Inactivation of the gene for tightly bound cytochrome c552 did not prevent formation of this supercomplex, indicating that this electron carrier protein is not essential for structurally linking complexes III and IV. Complex I activity was also found in the membranes of mutant strains lacking complexes III or IV. However, no assembled complex I but only dissociated subunits were observed following the same protocols used for electrophoretic separation or chromatographic isolation of the supercomplex from the wild-type strain. This indicates that the P. denitrificans complex I is stabilized by assembly into the NADH oxidase supercomplex. In addition to substrate channeling, structural stabilization of a membrane protein complex thus appears as one of the major functions of respiratory chain supercomplexes.
Socio-demographic variables and perceptual moderators related to mental health stigma

Background For many, seeking mental healthcare services remains a clandestine, shameful, or secret activity due in part, to the stigma associated with it. Aim This study examined the mental health stigma associated with mental illness within the USA as a product of differences in ethnicity, gender, perceptions of a just worldview, and individual controllability. Methods A total of 466 participants completed a questionnaire measuring perceptions of social sensitivity, likelihood of engaging in helping behaviors, perceptions of danger, and global just worldviews. Results Women were stigmatized less than men with mental illness (p = 0.0113), just worldview was not significantly correlated with the stigma, and controllability of mental health condition was positively associated with increased stigma (p < 0.0001). Finally, trends in individual perceptions of ethnicity suggest that both African Americans and Hispanics were less stigmatizing toward those with mental illness versus Asian Americans or Caucasians (p < 0.0001). Conclusion Mental health stigma, while not associated with one's just worldview, remains relevant in examining, and ultimately changing the acceptance of receiving mental health services. Implications of the findings are discussed about increasing public mental health awareness and reducing mental health stigma as a function of gender, ethnic disparity, and shared life experiences.
Polyethylene glycol (PEG) modification of granulocyte‐macrophage colony stimulating factor (GM‐CSF) enhances neutrophil priming activity but not colony stimulating activity

PEG‐modified proteins have numerous advantages over their unmodified counterparts (increased half life, reduced antigenicity, improved solubility), but, almost without exception, they show a modest to marked reduction in biological or enzymatic activity. However, while investigating a new protocol for the preparation of PEG‐proteins, we compared PEG‐modified and unmodified GM‐CSF with respect to their polymorphonuclear neutrophil granulocyte (PMN) priming activities. PEG‐GM‐CSF was unexpectedly more active than GM‐CSF in its ability to prime neutrophils to respond to the synthetic peptide n‐formyl‐methionyl‐leucyl‐phenylalanine (FMLP) with an oxidative burst (assessed both by nitroblue tetrazolium reduction and ferricytochrome c reduction). These results were in contrast to the findings for colony stimulating activity and with GM‐CSF induced thymi‐dine uptake, where the biological activity was unchanged or reduced. The enhanced neutrophil priming activity of PEG‐GM‐CSF was confirmed using FPLC fractionated PEG‐modified GM‐CSF. This showed changes in the bioactivity profile consistent with both the shift in protein elution profile and enhanced activity of the PEG‐modified material (reflected in the increased area under the bioactivity curve). We also excluded a neutrophil priming action for PEG‐modified fetal calf serum proteins, carrier proteins and‘irrelevant’cytokine, erythropoietin. The dissociation of the two bioactivities was confirmed using individual FPLC fractions. These results suggest the presence of differences in either binding, receptor/ligand processing or signal transduction for neutrophils versus progenitors, that are differentially affected by PEG‐modification of GM‐CSF. The demonstration that PEG‐modification can partially dissociate two biological activities suggests the feasibility of using PEG‐modification to produce proteins with subtly altered spectra of biological activity and hence new ranges of clinical applications.
Simultaneous transmission and reception on all elements of an array: binary code excitation

Pulse-echo arrays are used in radar, sonar, seismic, medical and non-destructive evaluation. There is a trend to produce arrays with an ever-increasing number of elements. This trend presents two major challenges: (i) often the size of the elements is reduced resulting in a lower signal-to-noise ratio (SNR) and (ii) the time required to record all of the signals that correspond to every transmit–receive path increases. Coded sequences with good autocorrelation properties can increase the SNR while orthogonal sets can be used to simultaneously acquire all of the signals that correspond to every transmit–receive path. However, a central problem of conventional coded sequences is that they cannot achieve good autocorrelation and orthogonality properties simultaneously due to their length being limited by the location of the closest reflectors. In this paper, a solution to this problem is presented by using coded sequences that have receive intervals. The proposed approach can be more than one order of magnitude faster than conventional methods. In addition, binary excitation and quantization can be employed, which reduces the data throughput by roughly an order of magnitude and allows for higher sampling rates. While this concept is generally applicable to any field, a 16-element system was built to experimentally demonstrate this principle for the first time using a conventional medical ultrasound probe.
Estimation of chaos function for the implementation of high-resolution measurement system

The use of chaotic maps as measurement system or as a signal quantisation unit in analogue to digital converters (ADC) is a fairly modern approach. Compared to existing ADC architectures, chaotic systems are advantageous because these are simple mathematical functions and can be implemented physically involving less components. Additionally, unique symbolic identities corresponding to an input value (initial condition) can be generated iteratively through the dynamics, thus simplifying the design complexities. For the application of signal measurement system, the chaotic function tent map (TM) is found to be the suitable candidate, as dense distribution of points within the state-space can be realised from the dynamics. However,a significant issue that may arise while implementing the TM electronically is that, it is difficult to maintain the parameter of the map at the ideal value due to component imprecisions. When the map parameter is reduced, the dynamics is distorted from the ideal behaviour; hence estimating the initial condition from the symbols become difficult. If the knowledge of the non-ideal parameter is available, then the actual initial condition can be recovered. Hence, it becomes essential to determine the non-ideal parameter from the available dynamics. In this work, two different approaches have been proposed for the parameter estimation of the TM. The first approach is realised from the symbolic dynamics of the TM in which the sequence corresponding to the map maximum is searched over a symbolic time series, and a difference equation is realised in terms of the map parameter. The second method is based on the identification of the map fixed-point through the noisy dynamics of the TM. It has been discovered that unique crossovers appear within the noisy samples and the information of the map fixed-point is preserved through those crossovers. The proposed methods have been broadly analysed through mathematical simulations and graphical results. The approaches deliver parameter estimates with errors below 1% and using short length trajectories as low as 200 iterations. This development can benefit accurate estimation of initial condition from the non-ideal dynamics and therefore maybe considered as a step forward in the development of chaos-based measurement systems and chaotic ADCs. The study and the proposed estimation methods can also be utilised in other areas of applications such as communication and encryption, where parameter estimation of the chaotic functions is one of the prime requirements.
E proteins regulate osteoclast maturation and survival

Osteoclasts are bone‐specific polykaryons derived from myeloid precursors under the stimulation of macrophage colony stimulating factor (M‐CSF) and receptor activator of NF‐κB ligand (RANKL). E proteins are basic helix‐loop‐helix (bHLH) transcription factors that modulate lymphoid versus myeloid cell fate decisions. To study the role of E proteins in osteoclasts, myeloid‐specific E protein gain‐of‐function transgenic mice were generated. These mice have high bone mass due to decreased osteoclast numbers and increased osteoclast apoptosis leading to overall reductions in resorptive capacity. The molecular mechanism of decreased osteoclast numbers and resorption is in part a result of elevated expression of CD38, a regulator of intracellular calcium pools with known antiosteoclastogenic properties, which increases sensitivity to apoptosis. In vivo, exogenous RANKL stimulation can overcome this inhibition to drive osteoclastogenesis and bone loss. In vitro–derived ET2 osteoclasts are more spread and more numerous with increases in RANK, triggering receptor expressed on myeloid cells 2 (TREM2), and nuclear factor of activated T cells, cytoplasmic 1 (NFATc1) compared to wild type. However, their resorptive capacity does not increase accordingly. Thus, E proteins participate in osteoclast maturation and survival in homeostatic bone remodeling. © 2012 American Society for Bone and Mineral Research
Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil.

Two gamma- and UVC-resistant bacterial strains, designated JSH3-1T and 9-2-2, were isolated from garden soil in South Korea. Cells were Gram-stain-positive, aerobic, non-motile and spherical. A polyphasic approach was used to study the taxonomic properties of strains JSH3-1T and 9-2-2. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences of strains JSH3-1T and 9-2-2 indicated highest similarity with Deinococcus radiomollis PO-04-20-132T (94.7 and 94.9 %, respectively); levels of sequence similarity with the type strains of other Deinococcus species were less than 94.0 %. Strains JSH3-1T and 9-2-2 shared relatively high 16S rRNA gene sequence similarity (98.7 %) and had a high DNA reassociation value of 81±0.5 %. Meanwhile, they showed low levels of DNA reassociation (<25 %) with other closely related species of the genus Deinococcus. The two strains showed chemotaxonomic features typical of the genus Deinococcus, with the presence of menaquinone 8 as the respiratory quinone. The predominant fatty acids were iso-C17 : 0, iso-C13 : 0 and anteiso-C13 : 0. The polar lipids comprised phosphoglycolipid, aminophospholipid, glycolipid and unknown aminolipids. The DNA G+C contents of strains JSH3-1T and 9-2-2 were 62.0 and 61.9 mol%, respectively. On the basis of their phenotypic and genotypic characteristics, and phylogenetic distinction, strains JSH3-1T (=KCTC 33790T=JCM 31311T) and 9-2-2 (=KCTC 33789=JCM 31310) should be classified within a novel species of the genus Deinococcus, for which the name Deinococcus ruber sp. nov. is proposed.
Heparan Sulfate Proteoglycan Is Associated with Amyloid Plaques and Neuroanatomically Targeted PrP Pathology throughout the Incubation Period of Scrapie-Infected Mice

Heparan sulfate proteoglycan (HSPG) has been found to be associated with amyloid deposits in a number of diseases including the cerebral amyloid plaques of Alzheimer's disease and the transmissible spongiform encephalopathies (TSEs). The role of HSPG in amyloid formation and the neurodegenerative pathology of these diseases have not been established. We have addressed these questions using a scrapie mouse model which exhibits both amyloid and nonamyloid deposition of abnormal PrP protein, the protein marker of TSE infection. The distribution of HSPG was examined throughout the course of the disease in the brains of experimentally infected mice and compared with the distribution of abnormal PrP. Abnormally high levels of HSPG were associated with most types of PrP pathology including all plaque types and diffuse neuroanatomically targeted forms. Scrapie-associated HSPG was present from 70 days after infection, the earliest time-point examined, in the same target areas as abnormal PrP. The association with amyloid plaques may indicate that HSPG is involved in amyloid plaque formation and/or persistence but involvement with early diffuse forms of PrP suggests a more fundamental role in scrapie pathogenesis.
EVALUATION OF THE SENSITIVITY AND SPECIFICITY OF AN ENZYME-LINKED IMMUNOSORBENT ASSAY FOR DIAGNOSING BRUCELLOSIS IN AFRICAN BUFFALO (SYNCERUS CAFFER)

Abstract Brucellosis is a disease of veterinary and public health importance worldwide. In sub-Saharan Africa, where the bacterium Brucella abortus has been identified in several free-ranging wildlife species, successful disease control may be dependent on accurate detection in wildlife reservoirs, including African buffalo (Syncerus caffer). We estimated the sensitivity and specificity of a commercial enzyme-linked immunosorbent assay (ELISA) (IDEXX Brucellosis Serum Ab test, IDEXX Laboratories, Westbrook, Maine, USA) for B. abortus based on a data set of 571 serum samples from 258 buffalo in the Kruger National Park, South Africa. We defined a pseudogold standard test result as those buffalo that were consistently positive or negative on two additional serologic tests, namely, the rose bengal test (RBT) and the complement fixation test (CFT). The ELISA's cutoff value was selected using receiver operating characteristics analysis, the pseudogold standard, and a threshold criterion that maximizes the total sensitivity and specificity. Then, we estimated the sensitivity and specificity of all three tests using Bayesian inference and latent class analysis. The ELISA had an estimated sensitivity of 0.928 (95% Bayesian posterior credibility interval [95% BCI] = 0.869–0.974) and specificity of 0.870 (95% BCI = 0.836–0.900). Compared with the ELISA, the RBT had a higher estimated sensitivity of 0.986 (95% BCI = 0.928–0.999), and both the RBT and CFT had higher specificities, estimated to be 0.992 (95% BCI = 0.971–0.996) and 0.998 (95% BCI = 0.992–0.999), respectively. Therefore, no single serologic test perfectly detected the antibody. However, after adjustment of cutoff values for South African conditions, the IDEXX Brucellosis Serum Ab Test may be a valuable additional screening test for brucellosis in Kruger National Park's African buffalo.
A passive revolution?: constructing a municipal alternative to carbon markets in British Columbia.

Supervisory Committee Dr. Susan Boyd (Faculty of Human and Social Development) Supervisor Dr. Michael Prince (Faculty of Human and Social Development) Departmental Member Dr. William Carroll (Department of Sociology) Outside Member Using a Foucault-inspired critical analysis of discourse within a Gramscian framework of hegemony, this thesis analyzes how patterns of international climate change policy relate to climate policy in British Columbia (BC), Canada, and explores the patterns of resistance to carbon neutrality in a single municipality. The BC Carbon Neutral Government Strategy and the Provincial Crown Corporation responsible for stimulating the growth of the BC carbon-offset market are characterized by neo-liberalism ideology and dispossession. The District of Saanich’s policy, which establishes a local and public form of carbon offset alternative, is characterized as a form of resistance. Saanich’s policy represents a passive revolution. This thesis suggests that the discourse of ecological modernization exists within both the hegemonic climate policy structure as well as the alternative found in Saanich. This thesis also suggests that municipalities represent a political space in which a Gramscian war of position may be waged. iv Table of Contents SUPERVISORY COMMITTEE . II ABSTRACT . III TABLE OF CONTENTS . IV LIST OF FIGURES . V ACKNOWLEDGMENTS . VI INTRODUCTION . 1 OUTLINE OF THIS THESIS . 5 NEO-­‐LIBERAL MOTIVATIONS IN CLIMATE CHANGE POLICY . 7 THE KYOTO MECHANISMS . 9 ECOLOGICAL MODERNIZATION . 15 POLITICAL ECONOMY OF KYOTO . 18 BRITISH COLUMBIA’S CLIMATE COMPROMISE . 25 CONCLUSION . 32 THEORY . 35 ECO-­‐SOCIALISM . 35 GRAMSCI, FOUCAULT AND POST-­‐MODERNITY . 38 GRAMSCI AND HEGEMONY . 38 FOUCAULT AND POWER . 44 IDEOLOGY, COUNTER-­‐HEGEMONY AND DISCOURSE . 47 CONCLUSION . 54 METHOD . 55 CASE STUDIES . 55 DISCOURSE, FOUCAULT, AND INTERVIEWS . 57 RESEARCH DESIGN . 61 ETHICAL CONSIDERATIONS . 65 RESULTS . 66 MOVING BC TOWARD ECO-­‐MODERNIZATION . 66 SAANICH AND THE “CARBON FUND” ALTERNATIVE . 71 THE DISCOURSE OF BC CLIMATE POLICY: . 79 CONCLUSION . 94 CONCLUSION . 95 BIBLIOGRAPHY . 102 APPENDIX 1: INTERVIEW GUIDE . 114 APPENDIX 2: PARTICIPANT CONSENT FORM . 115 APPENDIX 3: KEY INFORMANT PARTICIPANT CONSENT FORM . 117
Eye Gesture Analysis with Head Movement for Advanced Driver Assistance Systems

Road traffic accidents are a major cause of death worldwide. In an attempt to reduce accidents, some research efforts have focused on creating Advanced Driver Assistance Systems (ADAS) able to detect vehicle, driver and environmental conditions and to use this information to identify cues for potential accidents. This paper presents continued work on a novel Non-intrusive Intelligent Driver Assistance and Safety System (Ni-DASS) for assessing driver point of regard within vehicles. It uses an onboard CCD camera to observe the driver’s face. A template matching approach is used to compare the driver’s eye-gaze pattern with a set of eye-gesture templates of the driver looking at different focal points within the vehicle. The windscreen is divided into cells and comparison of the driver’s eye-gaze pattern with templates of a driver’s eyes looking at each cell is used to determine the driver’s point of regard on the windscreen. Results indicate that the proposed technique could be useful in situations where low resolution estimates of driver point of regard are adequate. For instance, To allow ADAS systems to alert the driver if he/she has positively failed to observe a hazard.
QCM Aptasensor for Rapid and Specific Detection of Avian Influenza Virus

There has been a need for rapid detection of Avian Influenza virus (AIV) H5N1 due to it being a potential pandemic threat. Most of the current methods, including culture isolation and PCR, are very sensitive and specific but require specialized laboratories and trained personnel in order to complete the tests and are time-consuming. The goal of this study was to design a biosensor that would be able to rapidly detect AIV H5N1 using aptamers as biosensing material and a quartz crystal microbalance (QCM) for transducing method. Specific DNA aptamers against AIV H5N1 were immobilized, through biotin and streptavidin conjugation, onto the gold surface of QCM sensor to capture the target virus. Magnetic nanobeads (150 nm in diameter) were then added as amplifiers considering its large surface/volume ratio which allows for faster movement and a higher target molecule binding rate. The result showed that the captured AIV caused frequency change, and more change was observed when the AIV concentration increased. The nanobead amplification was effective at the lower concentrations of AIV, however, it was not significant when the AIV concentration was 1 HA or higher. The detection limit of the aptasensor was 1 HAU with a detection time of 1 h. The capture of the target virus on to the surface of QCM sensor and the binding of magnetic nanobeads with the virus was confirmed with electron microscopy. Aptamers have unlimited shelf life and are temperature stable which allows this aptasensor to give much more consistent results specifically for in field applications.
Shuffled Multi-Track Detection for Shingled Magnetic Recording Channels With an Array of Read Heads

Shingled magnetic recording (SMR) with 2-D magnetic recording has recently emerged as a promising technology to sustain the growth of magnetic storage areal density. However, with the reduction of track pitch, the intertrack interference (ITI) becomes a major impairment. Furthermore, in SMR, the ITI is non-uniform among the top and lower tracks. A 2-D read channel which makes use of an array of read heads can effectively detect and compensate the severe ITI. In this paper, based on a read-array SMR channel model with non-uniform ITI, a shuffled multi-track detection (SMTD) detector, which shuffles and propagates the most reliable extrinsic information among the upper, lower, and middle detectors, is proposed to mitigate ITI more effectively. With the optimized non-binary low-density parity-check code, the performance of the proposed SMTD over the read-array SMR channel is evaluated.
Resource allocation in OFDMA networks with femto and macro-cells coexistence using Fractional Frequency Reuse (FFR)

Femto-cell is a recent solution that offers improved indoor coverage and enhances the system capacity. However, deploying femto-cells with macro-cells coexistence may introduce a phenomenon of interference. To remedy this problem, we propose in this paper a frequency allocation scheme for the downlink based on the Fractional Frequency Reuse (FFR). Unlike previous works in which a macro-cell is divided into two regions ( the inner and the outer regions ), our solution consists of dividing a cell into three regions, i.e, adding an intermediate region to exploit users diversity in the cell. We evaluate then the total throughput in a two-tier LTE femto-cells OFDMA network when varying the femto-cells number. The aim is to reduce interferences between both macro and femto cells and to maximize the total throughput. Simulation results show that by introducing a third region, the total throughput is considerably enhanced since the reuse factor is increased and a higher spectrum efficiency is achieved.