Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of decision support system for emergency management in water treatment plants

The occurrence of natural disasters such as floods, droughts, and earthquakes may cause water supply to stop working, which may also lead to social disasters and economic damages. Therefore, it is essential to prepare an emergency response management system to prepare disasters in water treatment infrastructures. In this study, a decision support system (DSS) responding to an emergency was proposed to systematically address possible problems in water treatment plants affected by various disasters. The DSS consists of several modules in the stages for planning, disaster sensing, and response and each module was developed based on a different approach depending on its function and purpose. The paper illustrates each module in detail and discusses the application in the proposed situation.
Comparison of Estimators for Monitoring Long-Term Population Trends in Deer Mice, Peromyscus maniculatus, on the California Channel Islands

Abstract. Capture-recapture methods are commonly used to estimate abundance and density of wild animal populations. Although a variety of sophisticated analytical techniques are available to evaluate capture-recapture data, vertebrate monitoring programs often lack the resources (e.g., time, personnel, and/or analytical expertise) to apply these methods. As an alternative, simple population indices, such as counts of unique individuals, may provide sufficient information to detect meaningful changes in population size. In this study we investigated whether a population index, easily generated from mark-recapture data under all conditions, might be used to provide valid ecological information for managers interested in long-term population trends of deer mice (Peromyscus maniculatus) on the California Channel Islands. In practice, determining the efficacy of estimating abundance from mark-recapture data and indices using empirical data (as opposed to simulated data) is difficult given the scarcity of long-term data sets that describe real populations. Using mark-recapture data that span 18 years (n = 122 trapping events, >12,000 marked individuals) for deer mice on 2 of the islands, we compared density estimates obtained from several commonly used mark-recapture models and also compared these estimates to index counts. Populations of island deer mice are extremely dynamic; estimated densities over the data period varied from 0 to >1200 mice/ha. Density estimates from models in program CAPTURE and program DENSITY, as well as from model-averaged Huggins models, were strongly correlated with each other and with the density index. Densities calculated by the models and the index showed similar patterns of population variation and trend over time for all 5 sites. For long-term population monitoring and assessment of population trends in deer mice, our findings suggest that the use of a simple index may provide adequate understanding of ecologically relevant population changes, though data collection methods that allow for more detailed analyses using advanced modeling techniques should be maintained.
Spring-loaded inverted pendulum goes through two contraction-extension cycles during the single stance phase of walking

Despite the overall complexity of legged locomotion, the motion of the center of mass (COM) itself is relatively simple, and can be qualitatively described by simple mechanical models. The spring-loaded inverted pendulum (SLIP) is one such model, and describes both the COM motion and the ground reaction forces (GRFs) during running. Similarly, walking can be modeled by two SLIP-like legs (double SLIP or DSLIP). However, DSLIP has many limitations and is unlikely to serve as a quantitative model for walking. As a first step to obtaining a quantitative model for walking, we explored the ability of SLIP to model the single stance phase of walking across the entire range of walking speeds. We show that SLIP can be employed to quantitatively model the single stance phase except for two exceptions: first, it predicts larger horizontal GRFs than empirically observed. A new model - angular and radial spring-loaded inverted pendulum (ARSLIP) can overcome this deficit. Second, even the single stance phase has active elements, and therefore a quantitative model of locomotion would require active elements. Surprisingly, the leg spring undergoes a contraction-extension-contraction-extension (CECE) during walking; this cycling is partly responsible for the M-shaped GRFs produced during walking. The CECE cycle also lengthens the stance duration allowing the COM to travel passively for a longer time, and decreases the velocity redirection between the beginning and end of a step. A combination of ARSLIP along with active mechanisms during transition from one step to the next is necessary to describe walking.
EFFECT OF OPA EXPRESSION ON TRANSMIGRATION OF NEISSERIA GONORRHOEAE ACROSS POLARIZED EPITHELIAL CELLS

Title of Document: EFFECT OF OPA EXPRESSION ON TRANSMIGRATION OF NEISSERIA GONORRHOEAE ACROSS POLARIZED EPITHELIAL CELLS. Luz Angela Adriana Le Van Doctor of Philosophy, 2013 Directed By: Professor, Daniel C Stein, Department of Cell Biology and Molecular Genetics Neisseria gonorrhoeae (GC) is a solely human pathogen that causes gonorrhea. This study examines how Opas, which are surface factors expressed by GC that undergo antigenic and phase variation can affect transmigration across epithelium. Opas are encoded by 11 different genes. A gonococcal variant that lacked all opa genes was constructed to help elucidate the role of Opa in pathogenesis. This variant retained most physical characteristics of the parent strain including growth rate and LOS profile but proved to produce a different interaction with other GC by being unable to bind LOS of adjacent GC and form microcolonies. Lack of Opa expression increased the ability of GC to transmigrate across polarized colonic epithelial cells T84. When the opa deletion variant was not expressing pili, bacteria were observed entering and crossing the polarized epithelia as early as four hours after infection. GC were observed at the bottom of the polarized epithelial monolayer demonstrated by confocal microscopy. While GC transmigrate across the monolayer, they do not appear to disrupt the integrity of tight junction proteins. Transepithelial resistance did not show a significant change and there was no leakage of FITC or HRP. Inhibitors of acid sphingomyelin and F-actin did not cause a redistribution of ZO-1 and did not increase the transmigration of GC. Only in the presence of EGTA, a calcium chelator, were Opa-expressing GC observed crossing the monolayer through visible disruption of the tight junctions. Induction of TNF-α by T84 cells was increase when infected with GC but not the production of IL-8. This study indicates that the lack of expression of Opa and pili leads to an increase in invasion into subepithelial tissues. EFFECT OF OPA EXPRESSION ON TRANSMIGRATION OF NEISSERIA GONORRHOEAE ACROSS POLARIZED EPITHELIAL CELLS
Genome-wide analysis of heptahelical protein (HHP) gene family and expression of BcHHP1 in response to stresses in Brassica rapa

Heptahelical protein (HHP) signalling pathway is involved in cold acclimation responses to low temperature and other stresses. The HHP transcription factor family is the key component regulating this signalling pathway. In this study, five HHP-like genes, BcHHP1, BcHHP2, BcHHP3, BcHHP4, and BcHHP5, were isolated from non-heading Chinese cabbage (Brassica rapa ssp. chinensis cv. Suzhouqing). Multiple sequence alignment and phylogenetic analysis showed that BcHHP proteins are highly homologous to HHP proteins from Arabidopsis thaliana, Glycine max, Oryza sativa, and Zea mays. Some of these HHP proteins might share similar functions in some aspects, which might be further proved by interaction network of BcHHP genes. Furthermore, real-time quantitative PCR showed that BcHHP1 was induced under cold and salt treatments. Besides, BcHHP1 was also accumulated in response to abscisic acid and salicylic acid, indicating that BcHHP1 gene might participate in response to hormone treatments. In addition, a BcHHP1-YFP fusion protein was localized to the nucleus and cytoplasm. These results indicated that five BcHHP genes might play important roles in a functional HHP signalling pathway responding to cold treatment. This work might be useful for future functional analysis of other HHP-like genes.
Studies on regulatory roles of the translation initiation factor 3 subunits E and H in Arabidopsis

The three protein complexes known as the PCI complexes {19S Proteasome lid, COP9 signalosome (CSN), eukaryotic translation Initiation factor 3) play important roles at the protein synthesis and protein degradation stages of gene expression. The PCI complexes are defined on the basis of sequence similarities between their paralogous subunits. Interestingly, physical biochemical interactions have been reported between all three PCI complexes but the physiological significance of those interactions is poorly understood. Two subunits of elF3, elF3e and elF3h, were confirmed to interact with both elF3 and with the subunits of the CSN. This study was conducted to define the roles of el F3e and el F3h in the regulation of translation during Arabidopsis development and to suggest further testable hypotheses regarding the interaction between elF3 and the CSN. To this end, two T-DNA insertion mutants of the e/F3h gene were isolated and characterized morphologically and biochemically. The eif3h mutant produced pleiotropic developmental defects including delayed growth, reduced meristem activities, and malformed organs such as leaves, roots, fruits, and stamens. The eif3h mutants share certain phenotypic characteristics with the csn mutants, including hypersensitivity to exogenous sucrose, reduced elongation of hypocotyls and partial opening of cotyledons in the dark condition, suggesting their participation in common developmental pathways. A regulatory role of the elF3h subunit of elF3 was suggested given that the eif3h mutation did not affect the overall efficiency of translation but differentially regulates translation of a subset of mRNAs such as those of the transcription factors ATB2 and HY5. Concerning the el F3e subunit, data presented suggest a tissue type specific nucleocytoplasmic distribution of elF3e. In light of nuclear localization and nuclear export signals present in el F3e, these results suggest that a dynamic nucleocytoplasmic transport mechanism may mediate a regulatory role of elF3e during translation. Reverse genetic approaches targeted to el F3e demonstrated a role of el F3e during the transition between cell division and differentiation phases of Arabidopsis development. Therefore it is shown that translational control of specific target mRNAs by regulatory subunits of elF3 participates in the modulation of protein synthesis in order to control development in Arabidopsis. The data further suggest a new type of functional crosstalk between the machineries of translation (elF3) and protein turnover (CSN) in Arabidopsis.
SOLUBILIZATION AND REMOVAL OF PETROLEUM HYDROCARBONS BY A NATIVE MICROBIAL BIOMASS IN A BUBBLE COLUMN REACTOR

A native-microbial biomass obtained from a contaminated site in Puebla, Mexico was evaluated to determine hydrocarbonoclastic capacities and solubilization strategies of Mayan crude oil. The biomass was able to use 13 g L-1 of Mayan crude oil as a single carbon source in a bubble column reactor during 14 days period. Gompertz model was chosen as the best fit for the profiles of growth and hydrocarbon consumption. The microbial biomass achieved removal efficiencies of 70 ± 2 % and a high maximum growth rate (μmax = 0.76 d-1). Hydrocarbon degradation increased due to solubilization strategies, mainly emulsification. In particular, a maximum emulsification index (17.7 ± 0.4 %) was reached at 12-day of cultivation increasing the solubility and dispersion of hydrocarbons. Our work contributes to understand the mechanisms of hydrocarbon-degradation in multiphasic systems and reveal the potential use of this native-microbial biomass for bioremediation purposes.
Comparison of Antihypertensive Drug Classes for Dementia Prevention

Introduction There is evidence that hypertension in midlife can increase the risk of Alzheimer’s disease and vascular dementia in late life. In addition, some treatments for hypertension have been proposed to have cognitive benefits, independent of their effect on hypertension. Consequently, there is potential to repurpose treatments for hypertension for dementia. This study systematically compared seven antihypertensive drug classes for this purpose, using data on over 849,000 patients from the Clinical Practice Research Datalink. Methods Treatments for hypertension were assessed in an instrumental variable (IV) analysis to address potential confounding and reverse causation. Physicians’ prescribing preference was used as a categorical instrument, defined by the physicians’ last seven prescriptions. Participants were new antihypertensive users between 1996-2016, aged 40 and over. Findings We analysed 849,378 patients with total follow up of 5,497,266 patient-years. Beta-adrenoceptor blockers and vasodilator antihypertensives were found to confer small protective effects – for example, vasodilator antihypertensives resulted in 27 (95% CI: 17 to 38; p=4.4e-7) fewer cases of any dementia per 1000 treated compared with diuretics. Interpretation We found small differences in antihypertensive drug class effects on risk of dementia outcomes. However, we show the magnitude of the differences between drug classes is smaller than previously reported. Future research should look to implement other causal analysis methods to address biases in conventional observational research with the ultimate aim of triangulating the evidence concerning this hypothesis. Funding This work was supported by the Perros Trust and the Integrative Epidemiology Unit. The Integrative Epidemiology Unit is supported by the Medical Research Council and the University of Bristol [grant number MC_UU_00011/1, MC_UU_00011/3]. RESEARCH IN CONTEXT Evidence before this study A recent systematic review and meta-analysis has collated the evidence for treating hypertension to prevent dementia. Seven comparable observational studies were identified that used either case-control designs with logistic regression or cohort designs with survival analysis. These studies suggested that some classes, such as angiotensin-II receptor blockers, may prevent dementia. However, conventional observational analyses, such as these, can be subject to confounding and reverse causation. Added value of this study We have provided new evidence about the potential effects of antihypertensives on risk of dementia through the novel application of instrumental variable analysis to this research question and have shown that the magnitude of the differences between drug classes is smaller than many observational studies have previously reported. Implications of all the available evidence Further research is needed to triangulate this evidence with other sources and to understand the inconsistencies between the studies conducted to date. Ultimately, this will inform the prioritization of antihypertensive drug classes for dementia prevention.
Improving employee performance by developing empowering leaders & companies

Empowerment has been a buzzword in many companies for decades, and research shows that empowerment enhances individual, team, and company performance. In practice, though, empowerment programs often fail. People who institute the programs frequently have a narrow understanding of what empowerment is, and this limited view probably helps to account for the failures. Drawing on several decades of organizational-science research, we provide a more useful, robust definition of empowerment and describe obstacles that company leaders and other employees can throw in the path of empowerment initiatives. We then provide empirically driven, practical recommendations for overcoming the obstacles and for otherwise enhancing employee empowerment, such as having leaders model empowerment and changing the company climate to align with more empowering policies and procedures.
Multi-Sensor Multi-Vehicle (MSMV) Localization and Mobility Tracking for Autonomous Driving

Vehicle localization and mobility tracking are important tasks in autonomous driving. Traditional methods either have insufficient accuracy or rely on additional facilities to reach the desired accuracy for autonomous driving. In this paper, a multi-sensor multi-vehicle localization and mobility tracking framework is developed for autonomous vehicles equipped with GPS, inertial measurement unit (IMU), and an integrated sensing system. Our algorithm fuse the information from local onboard sensors as well as the observations of other vehicles or existing intelligent transportation system infrastructure such as road side units (RSU) to improve the precision and stability of localization and mobility tracking. Specifically, this framework incorporates the dynamic model of vehicles to achieve better localization and tracking performance. The communication delays during the information sharing process are explicitly taken into account in our algorithm development. Simulations manifest that not only the accuracy of localization and mobility tracking could be greatly enhanced in general, but also the robustness can be guaranteed under circumstances where traditional localization and tracking devices fail.
Management of Innovations in Public Governance: Quality Management System, Management Controlling and Internal Auditing Appropriation

The race for performance has led some public service organizations to put in place some management innovations such as the implementation of organizational control. Organizational control is a system, a set of mechanisms and tools such as Quality management system, Management controlling, Internal auditing etc that affects all levels of the organization (strategic and operational levels), to master the decision-making processes, actions and results. Those organizational control tools don’t bring all expected effects because they are under-used. Internal auditing is used mainly for compliance procedures, management controlling for budgeting and Quality Management, a system for the prescription of procedures which is only a small percentage of the potential functionalities of these tools used punctually or inducing inappropriate behaviours. Those behaviours deprive these organizations of a significant source of synergies and performance. Those observations led to the questions of change management, learning organization, etc that can be included in a general question of appropriation of controlling tools considering Simultaneity Dimension (Simultaneous deployment of those tools), an original dimension little studied in research on appropriation and which corresponds more to the reality of those companies. Appropriation refers to two conceptions. Appropriation as a process inducing the acquisition of knowledge or behaviours concerning an object. Appropriation as a state which implies the assessment of the gap between how an object is integrated by users and its conceptual definition. Appropriation implies consistency between an object and its use. This research is a multiple case study comparing 3 companies, which allowed the enrichment of the appropriation model proposed by De Vaujany (2006) by specifying the predictive factors affecting each of the phases of this process of appropriation of control tools (Internal Auditing, Management controlling and Quality Management System) including the impact of simultaneity in the context of public service organizations in Morocco. For managerial use, those models constitute a frame or a diagnosis methodology to assess the appropriation of organizational control tools for the stimulation of their usage and therefore improve the multidimensional performance of the public service and citizen’s satisfaction.
Characterization of fungi associated with black foot disease of grapevine (Vitis vinifera L.) in Peru

Gravepine trunk diseaseas (Vitis vinifera L.) are mostly caused by fungi, which can cause serious economic losses worldwide. One of these diseases is Black Foot Disease. The most common symptoms are necrotic root lesions, reduced root biomass, under-bark black discoloration, and necrosis of xylem tissue at the base of the rootstocks. Over the last decade, the intensity and the incidence of the disease increased, causing loss of productivity and death of young grapevines. In this study were characterized a collection of 138 fungi isolated from grapevine in Peru with Black foot disease symptoms. Primarily, a genetic typing of the isolates was performed to assess the genetic diversity of the isolate collection. Identification by sequencing and analysis of the Internal Transcribed Spacer (ITS) was carried out with 38 representative isolates of the diversity. This allowed the initial identification of the genera Fusarium, Cylindrocladiella and Clonostachys. Afterwards, it was done a secondary marker analyses to allow a correct identification of the isolates to the species level. Sequences of the Translation elongation factor 1alpha (tef1-α) were obtained for all the isolates, allowing the identification of the genus Pleiocarpon, previously unidentified when using the ITS region. The partial sequence of the gene that codes for β–Tubulin (tub2) was used to differentiate the species of Clonostachys and Cylindrocladiella. The phylogenetic analyses with the combined sequences of ITS and tef1-α for the genera Cylindrocladiella and Pleiocarpon indicated the presence of the species Cylindrocladiella peruviana and Pleiocarpon strelitziae. The phylogenetic analyses of the combined sequences of ITS, tef1-α and tub2 confirmed the identity of C. peruviana. The species P. strelitziae was described for the first time in association with symptomatic grapevine. The phylogenetic analyses of genus Fusarium/Neocosmospora using tef1-α sequences allowed to group 26 isolates in three different species complexes: 12 in Neocosmospora solani species complex, 1 in Fusarium incarnatum-equiseti species complex and 13 in Fusarium fujikuroi species complex. The Fusarium/Neocosmospora species are not normally associated with grapevine Black Foot Disease. Their potential involvement in this pathology needs to be studied in the future. The phylogenetic analyses of the combined sequences of ITS and tub2 and ITS, tef1-α and tub2 of the genus Clonostachys indicated that the isolates of these genus belong to two possible new species Clonostachys viticola and Clonostachys peruviana. These species were characterized in terms of morphology and growth rates at different temperatures, and taxonomic descriptions are given for both.