Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty Quantification with Experimental Data and Complex System Models

Author(s): Russi, Trent Michael | Advisor(s): Packard, Andrew K; Frenklach, Michael | Abstract: This dissertation discusses uncertainty quantication as posed in the Data Collaboration framework. Data Collaboration is a methodology for combining experimental data and system models to induce constraints on a set of uncertain system parameters. The framework is summarized, including outlines of notation and techniques. The main techniques include polynomial optimization and surrogate modeling to ascertain the consistency of all data and models as well as propagate uncertainty in the form of a model prediction. One of the main methods of Data Collaboration is using techniques of nonconvex quadratically constrained quadratic programming to provide both lower and upper bounds on the various objectives. The Lagrangian dual of the NQCQP provides both an outer bound to the optimal objective as well as Lagrange multipliers. These multipliers act as sensitivity measures relaying the effects of changes to the parameter constraint bounds on the optimal objective. These multipliers are rewritten to provide the sensitivity to uncertainty in the response prediction with respect to uncertainty in the parameters and experimental data. It is often of interest to find a vector of parameters that is both feasible and representative of the current community work and knowledge. This is posed as the problem of finding the minimal number of parameters that must deviate from their literature value to achieve concurrence with all experimental data constraints. This problem is heuristically solved using the l1-norm in place of the cardinality function. A lower bound on the objective is provided through an NQCQP formulation. In order to use the NQCQP techniques, the system models need to have quadratic forms. When they do not have quadratic forms, surrogate models are fitted. Surrogate modeling can be difficult for complex models with large numbers of parameters and long simulation times because of the amount of evaluation-time required to make a good fit. New techniques are developed for searching for an active subspace of the parameters, and subsequently creating an experiment design on the active subspace that adheres to the original parameter constraints. The active subspace can have a dimension signicantly lower than the original parameter dimension thereby reducing the computational complexity of generating the surrogate model. The technique is demonstrated on several examples from combustion chemistry and biology. Several other applications of the Data Collaboration framework are presented. They are used to demonstrate the complexity of describing a high dimensional feasible set of parameter values as constrained by experimental data. Approximating the feasible set can lead to a simple description, but the predictive capability of such a set is significantly reduced compared to the actual feasible set. This is demonstrated on an example from combustion chemistry.
A new scheduling algorithm and performance with opportunistic beamforming

In this paper, a novel scheduling algorithm named time-fair selective scheduling (TFS) is proposed and the performance of TFS with multi-antenna opportunistic beamforming is investigated. Simulation shows that time-fair selective scheduling yields better time fairness and better system performance than proportional fair scheduling in TDM cellular system. Furthermore, time-fair scheduling can avoid the phenomena that the user on the border of the cell does not allocate slots more effectively. TFS combined with opportunistic beamforming can exploit multiuser diversity even in slow fading channel. It is shown that opportunistic beamforming with more antennas would induce larger and faster fluctuation, but the performance decreases with too much antennas. The optimal number of antennas can be determined according to the results in this paper
Comparative study on the metabolism of optical gossypol in rats.

The comparative metabolism of (+)- and (-)-gossypol in rats was studied. After oral administration of the drugs to rats, the half-lives of (+)- and (-)-gossypol in the gastrointestinal tract were found to be 18.4 h and 13.5 h, respectively. The tissue distribution of (+)-gossypol was very similar to that of (-)-gossypol. After oral administration, high drug levels were found in the liver while moderate concentrations were present in the spleen, lungs, blood, heart and kidneys. The drug levels in the testes and fat were rather low. The excretion rates of the (+)- and (-)-gossypol were quite similar. Most of the ingested drug was excreted in the feces, while only a small fraction was eliminated in the urine. After i.v. injection of the drugs to rats, the half-lives of free (+)- and (-)-gossypol were found to be 7.80 h and 3.96 h, respectively. The clearance rates of the two optical isomers were 7.81 and 29.36 ml/h, respectively.
Identification of a Novel Guanine Nucleotide Exchange Factor for the Rho GTPase*

The Rho GTPase promotes proliferation and cytoskeletal rearrangements in mammalian cells. To understand the regulation of Rho, it is important to characterize guanine nucleotide exchange factors (GEFs), which stimulate the dissociation of GDP and subsequent binding of GTP. Using Rho as an affinity ligand, we have isolated a 115-kDa protein (p115-RhoGEF) that binds specifically to the nucleotide-depleted state. A full-length cDNA encoding p115-RhoGEF was isolated, and its protein product, which exhibited sequence homology to Dbl and Lbc, catalyzed the exchange of GDP for GTP specifically on Rho and not on the Rac, Cdc42, or Ras GTPases. p115-RhoGEF is capable of regulating cell proliferation, as determined by its ability to induce the transformation of NIH 3T3 cells. Northern and Western analysis suggests that p115-RhoGEF is ubiquitously expressed. These results indicate that p115-RhoGEF may be a general regulator of Rho and its associated cellular phenotypes.
Differential Role of Ferritins in Iron Metabolism and Virulence of the Plant-Pathogenic Bacterium Erwinia chrysanthemi 3937

ABSTRACT During infection, the phytopathogenic enterobacterium Erwinia chrysanthemi has to cope with iron-limiting conditions and the production of reactive oxygen species by plant cells. Previous studies have shown that a tight control of the bacterial intracellular iron content is necessary for full virulence. The E. chrysanthemi genome possesses two loci that could be devoted to iron storage: the bfr gene, encoding a heme-containing bacterioferritin, and the ftnA gene, coding for a paradigmatic ferritin. To assess the role of these proteins in the physiology of this pathogen, we constructed ferritin-deficient mutants by reverse genetics. Unlike the bfr mutant, the ftnA mutant had increased sensitivity to iron deficiency and to redox stress conditions. Interestingly, the bfr ftnA mutant displayed an intermediate phenotype for sensitivity to these stresses. Whole-cell analysis by Mössbauer spectroscopy showed that the main iron storage protein is FtnA and that there is an increase in the ferrous iron/ferric iron ratio in the ftnA and bfr ftnA mutants. We found that ftnA gene expression is positively controlled by iron and the transcriptional repressor Fur via the small antisense RNA RyhB. bfr gene expression is induced at the stationary phase of growth. The σS transcriptional factor is necessary for this control. Pathogenicity tests showed that FtnA and the Bfr contribute differentially to the virulence of E. chrysanthemi depending on the host, indicating the importance of a perfect control of iron homeostasis in this bacterial species during infection.
Autofluorescence of normal, benign, and malignant ovarian tissues: a pilot study.

OBJECTIVE The objective of this study is to evaluate the efficacy of laser-induced fluorescence (LIF) data obtained at 325-nm pulsed laser excitation for the discrimination of normal, benign, and malignant ovarian tissues. BACKGROUND DATA Several studies have reported that the autofluorescence technique has a high specificity and sensitivity for discrimination between diseased and non-diseased tissues of various cancers, and also has the advantages of being non-invasive and producing a real-time diagnosis. When using this technique on ovarian tissues in most of the previously reported studies, multivariate statistical tools were used and classification analyses were carried out. MATERIALS AND METHODS Autofluorescence spectra of normal, benign, and malignant ovarian tissues were recorded with 325-nm pulsed laser excitation in the spectral region from 350-600 nm in vitro. The spectral analysis for discrimination between the different types of tissues was carried out using principal component analysis (PCA)-based non-parametric k-nearest neighbor (k-NN) analysis. RESULTS A total of 97 (34 normal, 33 benign, and 30 malignant) spectra were obtained from 22 subjects with normal, benign, and malignant tissues. The discrimination analysis of data using a PCA-based k-NN algorithm showed very good discrimination. The performance of the analysis was evaluated by calculating statistical parameters, specificity, sensitivity, and accuracy and were found to be 100%, 90.90%, and 94.2%, respectively. CONCLUSION The results show that the discrimination of normal, benign, and malignant ovarian conditions can be achieved quite successfully using LIF.
An aphid's Odyssey – the cortical quest for the vascular bundle

SUMMARY Sensing pH and sucrose concentration (with a preference for pH values of 7.0–7.5 and sucrose concentrations of approximately 400 mmol l–1) enables aphids to recognise sieve tubes inside vascular bundles. However, it is still unclear how aphids find their way to the vascular bundles. Membrane potentials in the cortex of Vicia faba stems were measured along a radial transect from the epidermis to the sieve elements and there was no gradient detected that could be used by aphids to guide their stylets to the sieve elements. Additionally, aphids did not demonstrate a preference between artificial diets with low or high levels of dissolved oxygen, making it unlikely that oxygen gradients in the cortex assist orientation towards the phloem. Tracks of salivary sheaths indicate that aphids search for vascular bundles in a radial direction (perpendicular from the stem surface to the vascular bundle) with regular side punctures in a pre-programmed fashion. Optical examination and electrical penetration graph (EPG) recordings suggest that aphids (Megoura viciae) probe the vacuolar sap of cortex cells. Acidic pH (5.0–5.5) and low sucrose concentrations in vacuoles, therefore, may provoke aphids to retract their stylets and probe the next cell until a favourable cell sap composition is encountered. The importance of sucrose as a cue was demonstrated by the experimental manipulation of Ricinus communis plants that cause them to transport hexoses instead of sucrose. Aphids (Aphis fabae) ingested less phloem sap of plants transporting hexoses compared with plants transporting the normal sucrose. The proposed rejection–acceptance behaviour provides a universal plant-directed mode of how aphids orientate their stylets towards the phloem.
The Earliest Phases of Star Formation (EPoS): a Herschel key program - The precursors to high-mass stars and clusters

Context. Stars are born deeply embedded in molecular clouds. In the earliest embedded phases, protostars emit the bulk of their radiation in the far-infrared wavelength range, where Herschel is perfectly suited to probe at high angular resolution and dynamic range. In the high-mass regime, the birthplaces of protostars are thought to be in the high-density structures known as infrared-dark clouds (IRDCs). While massive IRDCs are believed to have the right conditions to give rise to massive stars and clusters, the evolutionary sequence of this process is not well-characterized.Aims. As part of the Earliest Phases of Star formation (EPoS) Herschel guaranteed time key program, we isolate the embedded structures within IRDCs and other cold, massive molecular clouds. We present the full sample of 45 high-mass regions which were mapped at PACS 70, 100, and 160 μ m and SPIRE 250, 350, and 500 μ m. In the present paper, we characterize a population of cores which appear in the PACS bands and place them into context with their host molecular cloud and investigate their evolutionary stage.Methods. We construct spectral energy distributions (SEDs) of 496 cores which appear in all PACS bands, 34% of which lack counterparts at 24 μ m. From single-temperature modified blackbody fits of the SEDs, we derive the temperature, luminosity, and mass of each core. These properties predominantly reflect the conditions in the cold, outer regions. Taking into account optical depth effects and performing simple radiative transfer models, we explore the origin of emission at PACS wavelengths.Results. The core population has a median temperature of 20 K and has masses and luminosities that span four to five orders of magnitude. Cores with a counterpart at 24 μ m are warmer and bluer on average than cores without a 24 μ m counterpart. We conclude that cores bright at 24 μ m are on average more advanced in their evolution, where a central protostar(s) have heated the outer bulk of the core, than 24 μ m-dark cores. The 24 μ m emission itself can arise in instances where our line of sight aligns with an exposed part of the warm inner core. About 10% of the total cloud mass is found in a given cloud’s core population. We uncover over 300 further candidate cores which are dark until 100 μ m. These are possibly starless objects, and further observations will help us determine the nature of these very cold cores.
Fatigue in rheumatoid arthritis: from apathy to action

Fatigue is a common problem in rheumatoid arthritis (RA), experienced by the majority of patients, with fatigue scores that are often higher than pain scores. Despite this, patients feel fatigue has been largely ignored by clinicians. This article provides a personal overview of the journey of RA fatigue from ‘nonexistence’ to ‘hot topic’ and looks toward a time when fatigue might return to nonexistence because it is routinely and effectively managed.
Multi-lingual intelligent information retriever with automated ontology generator

We propose a new information retriever on the Web which: automatically classifies collected documents; and retrieves multi-lingual information (e.g., Japanese and/or English). This is attained by the mechanism of ontology processing. We set up a multi-lingual ontology as an index dictionary. The ontology manages the relations of keywords and the weights of keywords for domain categories to classify the documents. The system has the following features: users can use any keywords expressed in their native language to search for the Web documents, even if they contain multi lingual information; and the documents can be classified into specific domain categories by tuning the keyword weights up.
Catheter-Associated Urinary Tract Infections in Intensive Care Units Can Be Reduced by Prompting Physicians to Remove Unnecessary Catheters

Abstract Objective: Indwelling urinary catheters are the most common source of infections in intensive care units (ICUs). The aim of this study was to evaluate the efficacy of nurse-generated daily reminders to physicians to remove unnecessary urinary catheters 5 days after insertion. Design: A time-sequence nonrandomized intervention study. Setting: Adult ICUs (medical, surgical, cardiovascular surgical, neurosurgical, and coronary care) of a tertiary-care university medical center. Patients: All patients admitted to the adult ICUs during a 2-year period. The study consisted of a 12-month observational phase (15,960 patient-days) followed by a 12-month intervention phase (15,525 patient-days). Intervention: Daily reminders to physicians from the nursing staff to remove unnecessary urinary catheters 5 days after insertion. Results: The duration of urinary catheterization was significantly reduced during the intervention phase (from 7.0 ± 1.1 days to 4.6 ± 0.7 days; P < .001). The rate of catheter-associated urinary tract infection (CAUTI) was also significantly reduced (from 11.5 ± 3.1 to 8.3 ± 2.5 patients with CAUTI per 1,000 catheter-days; P = .009). There was a linear relationship between the monthly average duration of catheterization and the rate of CAUTI (r = 0.50; P = .01). The excess monthly cost of antibiotics for CAUTI was reduced by 69% (from $4,021 ± $1,800 to $1,220 ± $941; P = .004). Conclusion: This study demonstrated that a simple measure instituted as part of a continuous quality improvement program significantly reduced the duration of urinary catheterization, rate of CAUTI, and additional costs of antibiotics to manage CAUTI.
5 Pancreatic beta-cell failure in the pathogenesis of type 2 diabetes

As the worldwide prevalence of type 2 diabetes continues to rise, there is mounting evidence that failure of the cells which make insulin – termed pancreatic beta (or β) cells, play a fundamental role at all stages in the pathogenesis. Beta-cell defects such as loss of the initial (first) phase of insulin secretion and inefficient insulin synthesis are seen years prior to the onset of type 2 diabetes. Later, it is the failure of beta cells to adequately respond to the demand for high insulin requirements that determines the onset of hyperglycaemia leading to the clinical diagnosis of type 2 diabetes. In this chapter, we will discuss the various proposed mechanisms of beta-cell failure in type 2 diabetes and address recent controversies in this field of research.
Standardization of the AMR wideband speech codec in 3GPP and ITU-T

3GPP and ITU-T have standardized a multi-rate codec for wideband speech conversational applications. Following a competitive selection process, the adaptive multirate wideband (AMR-WB) specifications were approved in March 2001 as part of 3GPP release 5. The ITU-T Study group 16 approved the same wideband coding algorithm as Recommendation G.722. 2 and its Annexes
Temperature dependence of dark current features of CdTe thin-film solar cells

In the paper results of investigating the characteristic features of temperature dependence of electrical parameters in dark I–V measurements for CdTe thin-film PV (photovoltaic) modules are presented. The purpose of originating the second junction in this kind of PV modules is shown. The electrical behaviour of II-(III)-VI thin-film PV cells/modules is influenced mainly by the defect layers located at the buffer/absorber interface and in the bulk of depletion region as well as due to manufacturing process. Results presented in this paper were determined from fitting the large amount of data acquired in natural outdoor conditions during long term monitoring [1].
Desigualdad en el área rural de Bolivia: ¿cuán importante es la educación?

Este documento descompone la desigualdad en la distribucion de ingresos en el area rural de Bolivia durante el periodo 1999-2002. La evidencia muestra que la educacion contabiliza entre el 6 y el 8 por ciento de la desigualdad del ingreso laboral, mientras que las diferencias de ingresos entre trabajadores del sector agricola y trabajadores de otros sectores explican entre el 15 y el 20 por ciento de la desigualdad. De esta manera, la educacion resulta ser una variable fundamental en la explicacion de la desigualdad, aunque no la mas importante.
Fruit Quality Attributes of New Peach and Nectarine Varieties under Selection in the Ebro Valley Conditions (Spain)

A breeding program searching for new peach and nectarine varieties adapted to the Ebro Valley growing conditions is being developed at the Aula Dei Experimental Station (CSIC). This program evaluates 15 populations obtained by controlled crosses. Different agronomic parameters such as blooming date, yield, and ripening date were determined in these populations. Quality traits such as fruit type, weight, flesh firmness, soluble solids content (SSC), total phenolics content, antioxidant activity, and other chemical attributes were determined and evaluated. In addition, market life was tested based on chilling injury (CI) susceptibility. Several parameters studied such as yield, SSC, sugars composition, total phenolics, and CI sensibility showed a great variability within the different populations. INTRODUCTION Peach is the most important fruit tree species in the world after apple, in terms of annual production (FAOSTAT, 2005). Moreover, peach is the most dynamic species with respect to the appearance of new cultivars in the market (Byrne, 2003; Fideghelli et al., 1998). The long history of peach breeding explains the great diversification of varieties. This situation has produced a large number of available varieties. Spain is the fourth country in the world in terms of annual yield of peach and nectarine, after China, Italy, and USA (MAPA, 2006). In Spain, the main production areas, located in the Ebro Valley, are Aragon and Cataluna, followed by Murcia. The lack of experimentation with the new varieties in the fruit growing areas means that the advantages of the new varieties have not been fully explored (Carbo and Iglesias, 2002). On the other hand, European producers shipping within Europe may require three to four weeks of storage. Therefore, understanding and preventing the causes of chilling injury (CI) in peaches and nectarines is of economic, as well as scientific, interest. The peach and nectarine consumption per capita remains invariable or decreases in most of the European countries. Consumers complain about lack of flavor, problems with the texture, etc. This situation leads to the need of searching for new varieties with high fruit quality that are best adapted to the growing area (Badenes et al., 1999; Jiang et al., 2002). The main goal of this program is to obtain mid- or late-season varieties with high- medium chilling requirements, good fruit characteristics and best postharvest behaviour (Cantin et al., 2006a, b; Moreno, 2005). Also, a big diversity in fruit type and market availability period is required by international consumer tendencies.
Normalizing effects of methylphenidate on hyperactive children's vigilance performance and evoked potentials.

Evoked potentials during the × and B-X versions of the Continuous Performance Test (CPT) were evaluated in 29 hyperactive children after ingestion of placebo or methylphenidate (0.3 mg/Kg). Twenty-one age matched normal children were also assessed twice but without any drugs. In both tests, placebo-treated hyperactives made more omission and commission errors and displayed smaller late positive components (LPC) of the evoked response to salient experimental cues. Methylphenidate ameliorated hyperactives’ performance in both tasks and enlarged their LPCs in CPT-X. Several of these drug effects and diagnostic differences were absent for older hyperactive subjects, probably because some of the procedures were too easy for them. For younger patients the present tasks were sufficiently challenging, and the results reflect normalization of their deficits in sustained attention.
Low dose (1 μg) ACTH test in the evaluation of adrenal dysfunction in pre‐clinical Addison's disease

The presence of 21‐hydroxylase autoantibodies (21OHAb) is a marker of adrenal autoimmunity and can be used to identify subjects with pre‐clinical Addison's disease. The low‐dose (1 μg) ACTH test (LDT) is more sensitive than the high‐dose (250 μg) test (HDT) for the diagnosis of pituitary adrenal insufficiency, but no information is available on the use of a LDT in subjects with autoimmune adrenalitis and primary adrenal insufficiency. The aim of our study was to evaluate the clinical use of the LDT in the diagnosis of early adrenocortical dysfunction in patients with adrenal autoantibodies.