Miracle-dz/UniFAR-FTUs huggingface dataset:
Ex-situ and in-situ diagnostic algorithms and methods for solid oxide fuel cell systems

The EU-project “GENIUS” is targeted at the investigation of generic diagnosis methodologies for different Solid Oxide Fuel Cell (SOFC) systems. The Ph.D study presented in this thesis was integrated into this project; it aims to develop a diagnostic tool for SOFC system fault detection and identification based on validated diagnostic algorithms, through applying theSOFC stack as a sensor.In this context, three algorithms, based on the k-means clustering technique, the wavelet transform and the Bayesian method, respectively, have been developed. The first algorithm serves for ex-situ diagnosis. It works on the classification of the polarization measurements of the stack, aiming to figure out the significant response variables that are able to indicate the state of health of the stack. The parameter “Silhouette” has been used to evaluate the classification solutions in order to determine the optimal number of classes/patterns to retain from the studied database.The second algorithm allows the on-line fault detection. The wavelet transform has been used to decompose the SOFC’s voltage signals for the purpose of finding out the effective feature variables that are discriminative for distinguishing the normal and abnormal operating conditions of the system. Considering the SOFC as a sensor, its reliability must be verifiedbeforehand. Thus, the feature variables are also required to be indicative to the state of health of the stack.When the stack is found being operated improperly, the actual operating parameters should be estimated so as to identify the system fault. To achieve this goal, a Bayesian network has been proposed serving as a meta-model of the stack to accomplish the estimation. At the end, the databases originated from different SOFC systems have been used to validate these three algorithms and assess their generalizability.
Air pollution and dementia in older adults in the Ginkgo Evaluation of Memory Study

Growing evidence implicates air pollution as a risk factor for dementia, but prior work is limited by challenges in diagnostic accuracy and assessing exposures in the decades prior to disease development. We evaluated the impact of long‐term fine particulate matter (PM2.5) exposures on incident dementia (all‐cause, Alzheimer's disease [AD], and vascular dementia [VaD]) in older adults.
Nanobodies dismantle post‐pyroptotic ASC specks and counteract inflammation in vivo

Inflammasomes sense intracellular clues of infection, damage, or metabolic imbalances. Activated inflammasome sensors polymerize the adaptor ASC into micron‐sized “specks” to maximize caspase‐1 activation and the maturation of IL‐1 cytokines. Caspase‐1 also drives pyroptosis, a lytic cell death characterized by leakage of intracellular content to the extracellular space. ASC specks are released among cytosolic content, and accumulate in tissues of patients with chronic inflammation. However, if extracellular ASC specks contribute to disease, or are merely inert remnants of cell death remains unknown. Here, we show that camelid‐derived nanobodies against ASC (VHHASC) target and disassemble post‐pyroptotic inflammasomes, neutralizing their prionoid, and inflammatory functions. Notably, pyroptosis‐driven membrane perforation and exposure of ASC specks to the extracellular environment allowed VHHASC to target inflammasomes while preserving pre‐pyroptotic IL‐1β release, essential to host defense. Systemically administrated mouse‐specific VHHASC attenuated inflammation and clinical gout, and antigen‐induced arthritis disease. Hence, VHHASC neutralized post‐pyroptotic inflammasomes revealing a previously unappreciated role for these complexes in disease. VHHASC are the first biologicals that disassemble pre‐formed inflammasomes while preserving their functions in host defense.
High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing

During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies.
Persistent low rates of same‐day umbilical hernia repair in Australia over the past 20 years: is there a need to change?

Several recent reports have identified significant variations in discharge practices following umbilical hernia repair (UHR). The primary aim of this paper is to determine Australian UHR same day discharge (SDD) rates over the past two decades. Secondary aims are to analyse factors which may contribute to variation in discharge practices, compare Australian UHR SDD rates internationally and determine LOS trends.
Cost-effectiveness of a Dengue Vector Control Intervention in Colombia

ABSTRACT. Dengue is a public health problem in Colombia and in the municipality of Girardot, an area of high risk for dengue transmission. We present the results of an economic evaluation from the societal perspective and 1-year time horizon comparing the regular control program for dengue prevention versus an intervention that comprised an environmental management strategy by covering the most Aedes aegypti productive breeding sites with insecticide covers, community actions, and educational activities. The effectiveness of the intervention was measured as the reduction in probability of dengue infection obtained from a community trial. Resource use was estimated from clinical records that were validated by clinical experts; unit costs were taken from national tariffs. Patient costs were obtained from a household survey. We found that the intervention generated an additional cost of USD20.9 per household and an incremental effectiveness of 0.00173 (reduction in the probability of reported dengue cases). Overall, both alternatives generate similar effectiveness, but the new intervention was associated with increasing costs. We conclude the new intervention is a potentially cost-effective option in areas where high prevalence of dengue exists.
XIAP promotes melanoma growth by inducing tumour neutrophil infiltration

Elevated expression of the X‐linked inhibitor of apoptosis protein (XIAP) has been frequently reported in malignant melanoma suggesting that XIAP renders apoptosis resistance and thereby supports melanoma progression. Independent of its anti‐apoptotic function, XIAP mediates cellular inflammatory signalling and promotes immunity against bacterial infection. The pro‐inflammatory function of XIAP has not yet been considered in cancer. By providing detailed in vitro analyses, utilising two independent mouse melanoma models and including human melanoma samples, we show here that XIAP is an important mediator of melanoma neutrophil infiltration. Neutrophils represent a major driver of melanoma progression and are increasingly considered as a valuable therapeutic target in solid cancer. Our data reveal that XIAP ubiquitylates RIPK2, involve TAB1/RIPK2 complex and induce the transcriptional up‐regulation and secretion of chemokines such as IL8, that are responsible for intra‐tumour neutrophil accumulation. Alteration of the XIAP‐RIPK2‐TAB1 inflammatory axis or the depletion of neutrophils in mice reduced melanoma growth. Our data shed new light on how XIAP contributes to tumour growth and provides important insights for novel XIAP targeting strategies in cancer.
Physical Environment as a Tool in Caring for the Hospitalized Patient: A Qualitative Study of Nurses’ Experiences in Hospitals

Objectives: To explore how nurses experience the physical environment when caring for hospitalized patients. Background: The physical environment as part of nursing is already an embedded understanding in the earliest nursing theory. In today’s hospitals, the impact of the physical environment is important for both patients and nurses. Patients’ well-being is linked to the physical environment, which can produce both negative and positive emotions. Nurses’ work environment is affected by the physical one, which affects practice, communication, and teamwork. Methods: This study used a qualitative design to explore nurses’ experiences of the physical environment in nursing. The study complied with the Consolidated Criteria for Reporting Qualitative Research (COREQ). Individual interviews were conducted with nine nurses working in somatic hospital units. Data collection, analysis, and interpretation consisted of individual semi-structured interviews and meaning condensation as described by Kvale and Brinkmann. Results: Three themes were identified: (1) providing a place to belong, (2) offering a protective sensory shield, and (3) balancing clinical needs with the patients’ personal needs. Conclusions: Involvement of the physical environment in nursing provides an opportunity for nurses to offer the hospitalized patient a place to belong. However, the physical environment is important for nurses to maintain accessibility with, and visualization of the patient. It is a careful balancing act carried out in practice without further verbalization in nursing.
Informative presence bias in analyses of electronic health records-derived data: a cautionary note

OBJECTIVE Electronic health record (EHR)-derived data are extensively used in health research. However, the pattern of patient interaction with the healthcare system can result in informative presence bias if those who have poorer health have more data recorded than healthier patients. We aimed to determine how informative presence affects bias across multiple scenarios informed by real-world healthcare utilization patterns. MATERIALS AND METHODS We conducted an analysis of EHR data from a pediatric healthcare system as well as simulation studies to characterize conditions under which informative presence bias is likely to occur. This analysis extends prior work by examining a variety of scenarios for the relationship between a biomarker and a health event of interest and the healthcare visit process. RESULTS Using biomarker values gathered at both informative and noninformative visits when estimating the effect of the biomarker on the event of interest resulted in minimal bias when the biomarker was relatively stable over time but produced substantial bias when the biomarker was more volatile. Adjusting analyses for the number of prior visits within a fixed look-back window was able to reduce but not eliminate this bias. DISCUSSION These results suggest that bias may arise frequently in commonly encountered scenarios and may not be eliminated by adjusting for prior visit intensity. CONCLUSION Depending on the context, the estimated effect from analyses using data from all visits available may diverge from the true effect. Sensitivity analyses using only visits likely to be informative or noninformative based on visit type may aid in the assessment of the magnitude of potential bias.
Novel applications of transoesophageal echocardiography

Transoesophageal echocardiography has become a widely used diagnostic imaging technique by virtue of its ability to yield high quality images of the heart and great vessels. This thesis is based on work performed between January 1991 and July 1992 during which novel applications of transoesophageal echocardiography were investigated in the intraoperative and critical care settings. The mechanism by which closed chest cardiopulmonary resuscitation (CPR) generates forward blood flow has long been debated. Use of transoesophageal echocardiography allowed the physiology of CPR to be elucidated in 18 human subjects with cardiac arrest. These observations supported the cardiac pump theory of CPR and suggested that transoesophageal echocardiography might be utilised to monitor the efficacy of CPR. A preliminary investigation of CPR performed with the active compression-decompression device is described. The pathophysiology of the fat embolism syndrome (FES) is poorly understood. Transoesophageal echocardiography detected intraoperative fat embolism in 24 patients with traumatic injuries, three of whom subsequently developed clinical evidence of FES. Paradoxical embolism through a patent foramen ovale occurred in one subject with fulminating fat embolism. These results support the mechanical theory of the aetiology of fat emboli, and suggest that transoesophageal echocardiography might be used to identify patients at greatest risk of FES. The role of transoesophageal echocardiography in monitoring regional and global myocardial function was explored in a study of the cardioprotective properties of acadesine in patients undergoing coronary artery bypass surgery. No differences were observed between the acadesine and control groups in the incidence of new regional wall motion abnormalities or in changes in the area ejection fraction. The strengths and limitations of transoesophageal echocardiography are discusssed. Transoesophageal echocardiography was used to examine the role of transgastric imaging in the assessment of cardiac haemodynamics. This novel imaging plane facilitates assessment of aortic stenosis and estimation of cardiac output. Use of transoesophageal echocardiography for estimation of pulmonary artery systolic pressure was also examined. The role of transoesophageal echocardiography in cardiac surgical intensive care was explored. Important clinical information was obtained in the majority of patients when used for emergency diagnosis. Elective monitoring of cardiac function was shown to be feasible and gave valuable information in 12 out of 33 patients. In conclusion, transoesophageal echocardiography is a valuable imaging technique that has useful applications in a variety of clinical settings. It can provide new insights into long-recognised conditions and might provide new avenues for future research.
Wind Scenarios for Stochastic Energy Scheduling

Wind Scenarios for Stochastic Energy Scheduling Adam Greenhall Chair of the Supervisory Committee: Professor Richard Christie Electrical Engineering Large amounts of wind generation have been added to the power system in recent years. However, wind breaks many of the core assumptions in the process used to schedule energy and is particularly difficult to forecast accurately. Rather than scheduling based on a single forecast, stochastic Unit Commitment (UC) minimizes the expected cost over several wind scenarios for the next day. Stochastic UC is often held up as a solution to help alleviate the high costs related to uncertain renewables. Yet there is no widely accepted method for creating high quality stochastic scenarios. In this dissertation, we examine two wind power scenario creation methods – moment matching and analogs. Moment matching is a general technique where scenarios are synthesized to match a set of statistics or moments. We propose a method for estimating these desired moments based on historical wind data. The analogs method looks back in time to find similar forecasts and uses the matching observations from those analogous dates directly as scenarios. This work proposes and tests a simple analogs method based solely on aggregate wind power forecasts. The performance of these methods is tested on a realistic model of the Electric Reliability Council Of Texas (ERCOT) power system based on actual data from 2012. UC and dispatch simulations showed modest stochastic savings for the relatively flexible ERCOT model at 25% wind energy penetration. The scenario creation method and number of scenarios had a significant impact on these stochastic savings. Contrary to our hypothesis and the increase in perfect forecast savings, stochastic savings decreased as wind penetration increased to 30%. Stochastic savings are often largely due to a few high cost events during peak load periods; stochastic UC costs may be higher than deterministic UC for extended periods – generally when demand and marginal prices are low. Together these results paint a more nuanced picture of stochastic UC and provide a roadmap for future scenario creation research.
Shifts of SARS-CoV-2 exposure settings in the transmission clusters of 2 epidemic waves in Hong Kong

ABSTRACT Exposure setting is crucial in the formation and propagation of SARS-CoV-2 transmission clusters. In this cohort study, transmission networks of 2 waves were differentiated by exposure setting using territory-wide surveillance data with clinical and laboratory records in Hong Kong. Characteristically, the first wave had resulted from imported cases followed by local transmissions, while the second wave was constituted primarily by local infections. With a 4-fold higher caseload, the second wave featured predominance of epidemiologically linked, local, older and asymptomatic patients with higher viral loads and shorter inpatient days. The 1028 transmission clusters formed 155 cascades composing at least two clusters. Daily and social activities were exposure settings that bridged clusters while residences usually terminated transmission cascades. Regulatory restrictions on social activities extinguished cluster formation in bars, but shifted to private parties in the second wave. The results confirmed that strategic interventions targeting exposure settings could achieve effective epidemic control.
Outer membrane vesicles-transmitted virulence genes mediate the emergence of new antimicrobial-resistant hypervirulent Klebsiella pneumoniae

ABSTRACT Hypervirulent Klebsiella pneumoniae (hvKp) is a notorious clinical pathogen that is more likely to cause severe primary and metastatic abscesses. The dissemination of antimicrobial-resistant hvKp isolates has been reported worldwide, posing a great challenge and severe clinical threat. However, the mechanisms of antimicrobial-resistant hvKp isolates prevalent worldwide are not well precise. Outer membrane vesicles (OMVs) secreted from gram-negative bacteria are an important vehicle for delivering effector molecules inter- and intra-species. To explore whether OMVs as the vector of virulence genes horizontal transfer among Klebsiella pneumoniae and to explain the potential mechanism for the development of antimicrobial-resistant hvKp isolates, we isolated OMVs from hvKp and classical Klebsiella pneumoniae (cKp) by sequential differential centrifugation, respectively. Then, the characteristics and contents of hvKp-OMVs and cKp-OMVs were analyzed. These hvKp-OMVs contain virulence genes, which could be transferred from hvKp horizontally to extended-spectrum beta lactamase (ESBL)-producing cKp, leading to the production of antimicrobial-resistant hypervirulent transformants. Further experiments confirmed the transformants exhibited antimicrobial resistance and hypervirulent phenotypes in vitro and in vivo. In short, this work demonstrated that hvKp-OMVs facilitated virulence genes transfer, allowing an increase in the virulence level of ESBL-producing cKp and providing a new mechanism for the emergence of antimicrobial-resistant hvKp isolates.
Long-Term Effects of Repeated Social Defeat Stress on Brain Activity during Social Interaction in BALB/c Mice

Abstract Understanding the long-term effects of stress on brain function is crucial for understanding the mechanisms of depression. The BALB/c mouse strain has high susceptibility to stress and is thus an effective model for depression. The long-term effects of repeated social defeat stress (SDS) on BALB/c mice, however, are not clear. Here, we investigated the effects of repeated SDS in male BALB/c mice over the subsequent two weeks. Some defeated mice immediately exhibited social avoidance, whereas anxiety-like behavior was only evident at later periods. Furthermore, defeated mice segregated into two groups based on the level of social avoidance, namely, avoidant and nonavoidant mice. The characteristic of avoidance or nonavoidance in each individual was not fixed over the two weeks. In addition, we developed a semi-automated method for analyzing c-Fos expression in the mouse brain to investigate the effect of repeated SDS on brain activity more than two weeks after the end of the stress exposure. Following social interaction, c-Fos expression was reduced in several brain regions in the defeated mice compared with control mice. The correlation of c-Fos expression among these brain areas, with exception of the medial prefrontal cortex (mPFC) and central amygdala (CeA), was increased in defeated mice, suggesting increased synchrony. Notably, c-Fos expression in the lateral habenula (LHb) was different between mice that exhibited social avoidance from immediately after the repeated SDS and those that exhibited social avoidance only at later periods. These observations provide insight into the long-term effects of social stress on behavior and brain activity.
Expression of Cytochrome P450 Enzymes in Pediatric Non-Rhabdomyosarcoma Soft Tissue Sarcomas: Possible Role in Carcinogenesis and Treatment Response

The 5-year relative survival rate estimate of treated patients with non-rhabdomyosarcoma soft tissue sarcomas (NRSTS) is ∼50% since they generally present with tumor progression, relapse, metastasis, and/or chemoresistance. The expression of cytochrome P450 (CYP) enzymes in malignancies can affect the pharmacology of drugs commonly used in chemotherapy or confer susceptibility to development of chemical carcinogenesis; in addition, their specific tumor expression can be used as a therapeutic target. Using qPCR and Western blot assays, the expression of CYP1B1, CYP2E1, CYP3A4, and CYP3A5 were analyzed in a cohort of tumor tissue paired with non-malignant adjacent tissue of patients with NRSTS. The mRNA and protein expression of CYP1B1, CYP2E1, and CYP3A4 were significantly increased in tumor tissue. We propose that the expression of these isoforms is related to carcinogenesis and chemoresistance frequently observed in these neoplasms.