Miracle-dz/UniFAR-FTUs huggingface dataset:
Error Control for Support Vector Machines

Error Control for Support Vector Machines by Mark A. Davenport In binary classification there are two types of errors, and in many applications these may have very different costs. We consider two learning frameworks that address this issue: minimax classification, where we seek to minimize the maximum of the false alarm and miss rates, and Neyman-Pearson (NP) classification, where we seek to minimize the miss rate while ensuring the false alarm rate is less than a specified level α. We show that our approach, based on cost-sensitive support vector machines, significantly outperforms methods typically used in practice. Our results also illustrate the importance of heuristics for improving the accuracy of error rate estimation in this setting. We then reduce anomaly detection to NP classification by considering a second class of points, allowing us to estimate minimum volume sets using algorithms for NP classification. Comparing this approach with traditional one-class methods, we find that our approach has several advantages. Acknowledgements The work presented in this thesis was accomplished with a great deal of help from Clay Scott. I greatly appreciate his assistance and insight, and especially his occasional prodding. Thanks also to my advisor, Richard Baraniuk, for his enthusiastic encouragement, and to the additional members of my committee, Don Johnson and Rudolf Riedi, for their helpful feedback. I am also deeply indebted to Ryan King and Brandon Skeen who helped provide the computational resources without which this work would not have been possible. Finally, I would like to thank all of my other friends and family for their support. Thanks especially to my parents for (perhaps unwittingly) pointing me down this road, and to Kim for her constant reassurance, optimism, and encouragement.
Localization of focused-ultrasound beams in a tissue phantom, using remote thermocouple arrays

In focused-ultrasound procedures such as vessel cauterization or clot lysis, targeting accuracy is critical. To investigate the targeting accuracy of the focused-ultrasound systems, tissue phantoms embedded with thermocouples can be employed. This paper describes a method that utilizes an array of thermocouples to localize the focused ultrasound beam. All of the thermocouples are located away from the beam, so that thermocouple artifacts and sensor interference are minimized. Beam propagation and temperature rise in the phantom are simulated numerically, and an optimization routine calculates the beam location that produces the best agreement between the numerical temperature values and those measured with thermocouples. The accuracy of the method was examined as a function of the array characteristics, including the number of thermocouples in the array and their orientation. For exposures with a 3.3-MHz source, the remote-thermocouple technique was able to predict the focal position to within 0.06 mm. Once the focal location is determined using the localization method, temperatures at desired locations (including the focus) can be estimated from remote thermocouple measurements by curve fitting an analytical solution to the heat equation. Temperature increases in the focal plane were predicted to within 5% agreement with measured values using this method.
Quality of Life after Post-Prostatectomy Intensity Modulated Radiation Therapy: Pelvic Nodal Irradiation Is Not Associated with Worse Bladder, Bowel, or Sexual Outcomes

Background Limited data exist regarding toxicity and quality of life (QOL) after post-prostatectomy intensity modulated radiation therapy (IMRT) and whether pelvic nodal RT influences these outcomes. Methods 118 men were treated with curative-intent RT after radical prostatectomy. 69 men (58%) received pelvic nodal RT. QOL data and physician-assigned toxicity were prospectively collected. Changes in QOL from baseline were assessed with Wilcoxon signed-rank tests and risk factors associated with each domain were identified with generalized estimating equation (GEE) models. Late freedom from (FF) toxicity was estimated by the Kaplan-Meier method and comparisons were tested using the log-rank test. Results Urinary irritation/obstruction, bowel, and sexual domain scores declined at 2 months (all P ≤ 0.01) but were no different than baseline at subsequent visits through 4 years of follow-up. At 4 years, FF grade 2+ GI toxicity was 90% and FF grade 2+ GU toxicity was 89%. On GEE analysis, pelvic nodal RT was associated with decreased bowel function (P = 0.09) and sexual function (P = 0.01). On multivariate analysis, however, there was no significant association with either decreased bowel (P = 0.31) or sexual (P = 0.84) function. There was also no association with either FF grade 2+ GI toxicity (P = 0.24) or grade 2+ GU toxicity (P = 0.51). Conclusions Receipt of pelvic nodal RT was not associated with inferior QOL or toxicity compared to prostate bed alone RT. For the entire cohort, RT was associated with only temporary declines in patient-reported urinary, bowel, or sexual QOL.
Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum

The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the “Jekyll-and-Hyde” interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.
Panorama: extending digital libraries with topical crawlers

A large amount of research, technical and professional documents are available today in digital formats. Digital libraries are created to facilitate search and retrieval of information supplied by the documents. These libraries may span an entire area of interest (e.g., computer science) or be limited to documents within a small organization. While tools that index, classify, rank and retrieve documents from such libraries are important, it would be worthwhile to complement these tools with information available on the Web. We propose one such technique that uses a topical crawler driven by the information extracted from a research document. The goal of the crawler is to harvest a collection of Web pages that are focused on the topical subspaces associated with the given document. The collection created through Web crawling is further processed using lexical and linkage analysis. The entire process is automated and uses machine learning techniques to both guide the crawler as well as analyze the collection it fetches. A report is generated at the end that provides visual cues and information to the researcher.
Finding exact minimal polynomial by approximations

We present a new algorithm for reconstructing an exact algebraic number from its approximate value by using an improved parameterized integer relation construction method. Our result is consistent with the existence of error controlling on obtaining an exact rational number from its approximation. The algorithm is applicable for finding exact minimal polynomial of an algebraic number by its approximate root. This also enables us to provide an efficient method of converting the rational approximation representation to the minimal polynomial representation, and devise a simple algorithm to factor multivariate polynomials with rational coefficients. Compared with the subsistent methods, our method combines advantage of high efficiency in numerical computation, and exact, stable results in symbolic computation. The experimental results show that the method is more efficient than identify in Maple for obtaining an exact algebraic number from its approximation. Moreover, the Digits of our algorithm is far less than the LLL-lattice basis reduction technique in theory. In this paper, we completely implement how to obtain exact results by numerical approximate computations.
Hyperbaric Oxygen Therapy

The extent and progression of neurological impairment in traumatic brain injury depend significantly on the area of perilesional gloom, where neuronal apoptosis occurs. Inhibition of apoptosis becomes a therapeutic strategy to preserve brain tissue and promote functional recovery. Hyperbaric oxygen therapy is a treatment by which 100% oxygen is administered, with the aim of achieving a higher pressure than atmospheric pressure at sea level, to decrease ischemia and intensity of inflammatory processes triggered, compromising the viability of the tissues. For mild traumatic brain injury, studies indicate that hyperbaric oxygen therapy is no better than sham treatment. For acute treatment of moderate to severe traumatic brain injury, although the methodology is questionable in certain studies due to the complexity of the brain injury, hyperbaric oxygen therapy has been shown to be beneficial as a relatively safe adjunctive therapy. The objective of this review is to discuss aspects related to the pathophysiology of traumatic brain injury, the mechanism of action of hyperbaric oxygen therapy, and correlate these results with the use of this therapy in the prevention of neuronal injury, supported by original studies reported in the scientific literature
EACOL (Scale of Evaluation of Reading Competence by the Teacher): evidence of concurrent and discriminant validity

Aim The study aimed to provide information about the concurrent and discriminant validation of the Scale of Evaluation of Reading Competence by the Teacher (EACOL), which is composed of 27 dichotomous items concerning reading aloud (17 items) and reading silently (10 items). Samples Three samples were used in this validation study. The first was composed of 335 students with an average age of 9.75 years (SD = 1.2) from Belo Horizonte (Minas Gerais State), Brazil, where the full spectrum of reading ability was assessed. The second two samples were from São Paulo city (São Paulo State), Brazil, where only children with reading difficulties were recruited. The first São Paulo sample was labeled “SP-screening” and had n = 617, with a mean age of 9.8 years (SD = 1.0), and the other sample was labeled “SP-trial” and had n = 235, with a mean age of 9.15 years (SD = 0.05). Methods Results were obtained from a latent class analysis LCA, in which two latent groups were obtained as solutions, and were correlated with direct reading measures. Also, students’ scores on the Wechsler Intelligence Scale and on the Strengths and Difficulties Questionnaire tested the discriminant validation. Results Latent groups of readers underlying the EACOL predicted all direct reading measures, while the same latent groups showed no association with behavior and intelligence assessments, giving concurrent and discriminant validity to EACOL, respectively. Conclusion EACOL is a reliable screening tool which can be used by a wide range of professionals for assessing reading skills.
Imaging linear birefringence and dichroism in cerebral amyloid pathologies

New advances in polarized light microscopy were used to image Congo red-stained cerebral amyloidosis in sharp relief. The rotating-polarizer method was used to separate the optical effects of transmission, linear birefringence, extinction, linear dichroism, and orientation of the electric dipole transition moments and to display them as false-color maps. These effects are typically convolved in an ordinary polarized light microscope. In this way, we show that the amyloid deposits in Alzheimer's disease plaques contain structurally disordered centers, providing clues to mechanisms of crystallization of amyloid in vivo. Comparisons are made with plaques from tissues of subjects having Down's syndrome and a prion disease. In plaques characteristic of each disease, the Congo red molecules are oriented radially. The optical orientation in amyloid deposited in blood vessels from subjects having cerebral amyloid angiopathy was 90° out of phase from that in the plaques, suggesting that the fibrils run tangentially with respect to the circumference of the blood vessels. Our result supports an early model in which Congo red molecules are aligned along the long fiber axis and is in contrast to the most recent binding models that are based on computation. This investigation illustrates that the latest methods for the optical analysis of heterogeneous substances are useful for in situ study of amyloid.
A Bioacoustic Record of a Conservancy in the Mount Kenya Ecosystem

Abstract Background Environmental degradation is a major threat facing ecosystems around the world. In order to determine ecosystems in need of conservation interventions, we must monitor the biodiversity of these ecosystems effectively. Bioacoustic approaches offer a means to monitor ecosystems of interest in a sustainable manner. In this work we show how a bioacoustic record from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, was obtained in a cost effective manner. A subset of the dataset was annotated with the identities of bird species present since they serve as useful indicator species. These data reveal the spatial distribution of species within the conservancy and also point to the effects of major highways on bird populations. This dataset will provide data to train automatic species recognition systems for birds found within the Mount Kenya ecosystem. Such systems are necessary if bioacoustic approaches are to be employed at the large scales necessary to influence wildlife conservation measures. New information We provide acoustic recordings from the Dedan Kimathi University wildlife conservancy, a conservancy in the Mount Kenya ecosystem, obtained using a low cost acoustic recorder. A total of 2701 minute long recordings are provided including both daytime and nighttime recordings. We present an annotation of a subset of the daytime recordings indicating the bird species present in the recordings. The dataset contains recordings of at least 36 bird species. In addition, the presence of a few nocturnal species within the conservancy is also confirmed.
Roles of Salicylic Acid, Jasmonic Acid, and Ethylene in cpr-Induced Resistance in Arabidopsis

Disease resistance in Arabidopsis is regulated by multiple signal transduction pathways in which salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) function as key signaling molecules. Epistasis analyses were performed between mutants that disrupt these pathways (npr1, eds5, ein2, and jar1) and mutants that constitutively activate these pathways (cpr1, cpr5, and cpr6), allowing exploration of the relationship between the SA- and JA/ET–mediated resistance responses. Two important findings were made. First, the constitutive disease resistance exhibited by cpr1, cpr5, and cpr6 is completely suppressed by the SA-deficient eds5 mutant but is only partially affected by the SA-insensitive npr1 mutant. Moreover, eds5 suppresses the SA-accumulating phenotype of the cpr mutants, whereas npr1 enhances it. These data indicate the existence of an SA-mediated, NPR1-independent resistance response. Second, the ET-insensitive mutation ein2 and the JA-insensitive mutation jar1 suppress the NPR1-independent resistance response exhibited by cpr5 and cpr6. Furthermore, ein2 potentiates SA accumulation in cpr5 and cpr5 npr1 while dampening SA accumulation in cpr6 and cpr6 npr1. These latter results indicate that cpr5 and cpr6 regulate resistance through distinct pathways and that SA-mediated, NPR1-independent resistance works in combination with components of the JA/ET–mediated response pathways.
Living interfaces: the thrifty faucet

In this paper, we present a novel type of persuasive home appliance: A thrifty water faucet. Through a servo motor construction, it is enabled to move and behave in life-like manners and to step into dialogue with the user. For example about water consumption or hygiene. We sought to research the reactions of users to such an appliance, alongside possible implications for the design of future human-machine interfaces. This project is part of a larger series of experiments in the Living Interfaces project, exploring ways in which reduced and abstract life-like movements can be beneficial for Human-Machine Interaction.
Toll-like receptor–independent gene induction program activated by mammalian DNA escaped from apoptotic DNA degradation

Deoxyribonuclease (DNase) II in macrophages cleaves the DNA of engulfed apoptotic cells and of nuclei expelled from erythroid precursor cells. DNase II–deficient mouse embryos accumulate undigested DNA in macrophages, and die in feto because of the activation of the interferon β (IFN β) gene. Here, we found that the F4/80-positive macrophages in DNase II −/− fetal liver specifically produce a set of cytokines such as IFNβ, TNFα, and CXCL10. Whereas, IFN-inducible genes (2′5′-oligo(A) synthetase, IRF7, and ISG15) were expressed not only in macrophages but also in other F4/80-negative cells. When DNase II −/− macrophages or embryonal fibroblasts engulfed apoptotic cells, they expressed the IFN β and CXCL10 genes. The ablation of Toll-like receptor (TLR) 3 and 9, or their adaptor molecules (MyD88 and TRIF), had no effect on the lethality of the DNase II −/− mice. These results indicate that there is a TLR-independent sensing mechanism to activate the innate immunity for the endogenous DNA escaping lysosomal degradation.
How Did the World's Poorest Fare in the 1990s?

Drawing on data from 265 national sample surveys spanning 83 countries, the authors find that there was a net decrease in the total incidence of consumption poverty between 1987 and 1998. But it was not enough to reduce the total number of poor people, by various definitions. The incidence of poverty fell in Asia and the Middle East and North Africa, changed little in Latin America and Sub-Saharan Africa, and rose in Eastern Europe and Central Asia. The two main proximate causes of the disappointing rate of poverty reduction: too little economic growth in many of the poorest countries, and persistent inequalities (in both income and other essential measures) that kept the poor from participating in the growth that did occur.
Pioglitazone Exerts Protective Effects Against Stroke in Stroke-Prone Spontaneously Hypertensive Rats, Independently of Blood Pressure

Background and Purpose— Very recent subgroup analysis from the PROspective pioglitAzone Clinical Trial In macroVascular Events has shown that pioglitazone reduces the risk of recurrent stroke in type 2 diabetic patients. However, the underlying mechanism of stroke prevention by pioglitazone is unknown. Our aim was to examine the effect of pioglitazone on hypertension-based stroke in rats. Methods— Pioglitazone (1 mg · kg−1 · d−1) was orally administered to stroke-prone spontaneously hypertensive rats (SHRSP) to examine the effect on incidental stroke, cerebrovascular injury, brain inflammation, oxidative stress, and vascular endothelial dysfunction induced by hypertension. Results— Treatment of SHRSP with pioglitazone for 4 weeks, without affecting blood pressure and blood glucose values, improved vascular endothelial dysfunction (P<0.05), suppressed remodeling of the middle cerebral artery (P<0.05) and brain microvessels (P<0.05), and inhibited brain macrophage infiltration (P<0.05) and the upregulation of brain monocyte chemoattractant protein-1 and tumor necrosis factor-&agr; expression (P<0.01). Furthermore, pioglitazone treatment significantly delayed the onset of stroke signs and death in SHRSP (P<0.05). These beneficial effects of pioglitazone on cerebrovascular injury and stroke in SHRSP were associated with a reduction of brain and vascular superoxide via the inhibition of NADPH oxidase activity. Conclusions— Our work provides the first evidence that pioglitazone significantly protects against hypertension-induced cerebrovascular injury and stroke by improving vascular endothelial dysfunction, inhibiting brain inflammation, and reducing oxidative stress. These beneficial effects of pioglitazone were independent of blood pressure or blood sugar values. Thus, pioglitazone appears to be a potential therapeutic agent for stroke in type 2 diabetes with hypertension.
Cellular Activation, Phagocytosis, and Bactericidal Activity Against Group B Streptococcus Involve Parallel Myeloid Differentiation Factor 88-Dependent and Independent Signaling Pathways1

Group B streptococci (GBS) vigorously activate inflammatory responses. We reported previously that a secreted GBS “factor” activates phagocytes via Toll-like receptor (TLR)2 and TLR6, but that GBS cell walls activate cells independently of these receptors. We hypothesized that the phagocytic immune functions in response to GBS, such as inflammation, uptake, and elimination of bacteria, occur through a coordinated engagement of TLRs, along with the coreceptors CD14 and CD11b/CD18. Using various knockout mice we show that GBS-induced activation of p38 and NF-κB depends upon the expression of the cytoplasmic TLR adapter protein, myeloid differentiation factor 88 (MyD88), but not TLR2 and/or TLR4. Macrophages with deletions of CD14 and complement receptor 3 had a normal cytokine response to whole bacteria, although the response to GBS factor was abrogated in CD14-null cells. The intracellular formation of bactericidal oxygen species proved to be MyD88 dependent; however, uptake of GBS, a prerequisite for intracellular killing by O2 radicals, occurred independently of MyD88. While deletion of complement receptor 3 greatly diminished the uptake of opsonized GBS, it did not affect the formation of bactericidal O2 radicals or inflammatory signaling intermediates. We conclude that the inflammatory, bactericidal, and phagocytic responses to GBS occur via parallel but independent processes.
Combinatorics of the PASEP partition function

We consider a three-parameter PASEP model on N sites. A closed formula for the partition function was obtained analytically by Blythe et al. We give a new formula which generalizes the one of Blythe et al, and is proved in two combinatorial ways. Moreover the first proof can be adapted to give the moments of Al-Salam-Chihara polynomials. R´ esum´ e. Nous considun modde PASEPtrois paramsur N sites. Une formule close pour la fonction de partition a ´´