Miracle-dz/UniFAR-FTUs huggingface dataset:
Aalborg Universitet The Microbiome of Animals Implications for Conservation

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Stratigraphic Modeling and 3 D Spatial Analysis Using Photogrammetry and Octree Spatial Decomposition

The destructive nature of archaeological excavation makes the complete documentation of excavated evidence critically important to our ability to evaluate archaeological knowledge claims. Long demanded by textbooks, such complete documentation and publication have only recently become practical through the use of digital spatial technologies. These technologies open an entirely new dimension by making published evidence susceptible to independent re-analyses by the archaeological community. However, conventional stratigraphie recording methods are highly selective, and 2.5D GIS data structures do not support modeling and true 3D spatial analysis of stratigraphie volume solids. This paper presents a stratigraphie recording strategy based on oblique digital photogrammetry that is simple and inexpensive, yet comprehensive and accurate, and discusses approaches to solid modeling and 3D spatial analysis that meet the needs of archaeological stratigraphie analysis. These approaches are implemented in a custom software component under development and will be made available to the archaeological community at nominal cost.
The Pragmatism of Isaac Levi ( To appear as introductory chapter in Knowledge and Inquiry : Essays on the Pragmatism of

Isaac Levi's philosophical thinking has shown remarkable stability over the years. Basically, it all started with his first book, Gambling with Truth, which outlines a research program whose key element is the decision theoretic reconstruction of epistemology. Much of the rest of his work in epistemology has been devoted to extending and implementing this original program. With one important exception, there is little in his philosophical picture that has changed radically over the years. There have been changes, to be sure, but they have taken place at the level of detail rather than at the level of fundamental principle. The main exception is the issue of fallibilism. Starting out as a fallibilist, Levi became an infallibilist in the 70s'. The problem is that the corrigibility of our view sugge sts its fallibility: if we agree, as we must, that our view may change in the future, then it seems that we are never entitled to accept as true any claims of empirical substance now. But we do accept things as true now. Levi writes, in retrospect, that in the 60s' he unwittingly solved this problem for himself " by remaining in a fog of confusion " (Levi 1984, xiv), adding that by 1971 he had reached the conclusion that corrigibility and fallibility are best kept separate and, in particular, that endorsing corrigibilism is compatible with rejecting fallibilism. The paper " Truth, fallibility and the growth of knowledge " was the first expression of t his important revision. It was accepted for publication in 1975 but not actually published until 1983. The paper was reprinted in Levi (1984). Levi is a truly systematic philosopher. The purpose of the following text accordingly is to describe his position in a way that reveals its internal coherence. I intend to do so without diving too deeply into the technical details. I want to show how arguably most of Levi's work in epistemology rests on four cornerstones: the belief-doubt model, the injunction against roadblocks in the path of inquiry, the unity of reason thesis and the commitment-performance distinction. The first three elements undoubtedly belong to the tradition of American pragmatism. The commitment-performance distinction may have some support in Dewey's work. In any case, Levi's epistemological thinking cannot be appreciated fully unless these cornerstones of his pragmatism are kept firmly in mind. This way of describing Levi's pragmatism departs somewhat from how Levi himself usually explains …
Delivery, substantivity and clinical response of a direct application percarbonate tooth whitening film.

PURPOSE A novel overnight bleaching system containing 19% sodium percarbonate and silicone film forming agents (Crest Night Effects) is described, along with research supporting the substantivity of the product on tooth surfaces and its resulting whitening efficacy. METHODS Nine adult volunteers were enrolled in a study to determine overnight retention (substantivity) of the product. A non-reactive blue pigment was added to the product to aid in evaluating retention. The participants applied the product to their anterior dentition at night and then had digital images taken. After 7 hours of sleep, the patients were awakened and re-imaged. The percent coverage with blue pigment on the surfaces of the 12 anterior teeth was calculated from the digital images after application and after awakening. The product was also evaluated in a 2-week efficacy study with 16 adult volunteers. Each night the participants brushed their teeth before going to bed as they normally would, dried their teeth with a towel, and then applied the product to their six maxillary and mandibular anterior teeth. The product was left on the teeth overnight and then removed in the morning via toothbrushing. Color (baseline and after 2 weeks of product usage) was determined using digital imaging and the standard L*a*b* measurement scale. RESULTS In the substantivity study, 84.7% of the subject teeth surfaces were covered on average with the blue pigment-containing film immediately after application. Following overnight use, excellent retention was demonstrated as 77.4% of the initially covered surfaces still had pigment-containing film on them. These means did not differ significantly (P > 0.44). In the clinical efficacy study, there was significant (P < 0.0001) color improvement versus baseline after 2 weeks of treatment as measured by a mean (SD) delta b* of -1.71 (0.85) and mean (SD) delta L* of 1.62 (0.68). The product was well-tolerated, with the primary adverse events being oral irritation (13%) and tooth sensitivity (6%). No participants discontinued product use because of a product-related adverse event.
Democracy under High Inequality : Political Participation and Public Goods

Contrary to the view that inequality reduces turnout, political participation among low income voters is higher in democracies with very high levels of inequality and intermediate levels of state capacity. We address this puzzle by analyzing the link between political mobilization and budget allocations at di↵erent levels of inequality and state capacity. Under high inequality and low levels of capacity, parties find it optimal to mobilize low income voters via targeted goods. But as inequality decreases and capacity increases, clientelism becomes less e↵ective a tool for voters’ mobilization. To evaluate the implications of this argument we exploit a quasi-experiment, namely the anti-corruption audits by the Brazilian federal government on its municipalities. We show that an exogenous increase in monitoring e↵ort by the state breaks the clintelistic equilibrium, leading to a joint reduction in the likelihood of re-election by incumbents, the turnout rates, and the provision of targeted goods at the local level.
Transcriptional networks controlling plant development.

The rise of developmental biology to the fore of modern biology can be traced back to the efforts of three people: Ed Lewis, Christiane Nusslein-Volhard, and Eric Wieschaus. Lewis had been studying the homeotic Bithorax gene complex in fruitfly ( Drosophila melanogaster ) for several decades and
A3M: an agent architecture for automated manufacturing

This paper proposes a software architecture based on mobile agents for distributed process control applications. A set of agents is employed to handle, in a single manufacturing cell, automatic assignment of control tasks to controllers, monitoring of cell functionalities and dynamic cell reconfiguration. The agents operate in a two‐layered structure: at the highest level, the planning agents analyse the inputs of the system designer and automatically create the field agents, which operate at the lowest level and embed the control tasks to be executed. Field agents, which are mobile, are able to reach autonomously the controllers of the cell, in order to perform the control activity there. Exploiting the mobility enables a field agent to change its running device when the variation of the design parameters or a system fault requires a new task distribution. A load‐balancing algorithm is introduced, with the objective of assigning each field agent to a controller of the manufacturing cell in order to fairly distribute the computation load. The algorithm uses a branch‐and‐bound technique to explore all possible solutions and applies two heuristics to throw away non‐feasible solutions and select the best branch to analyse. The algorithm is designed to run on‐line in order to allow a fast task redistribution when a fault condition occurs in the process control environment. Copyright © 2008 John Wiley & Sons, Ltd.
Notions of Ecological Citizenship in Climate

‘This is the peer reviewed version of the following article: Star, C. (2005). Notions of ecological citizenship in climate justice campaigns. In Cassandra Star, ed. Ecopolitics XVI: Transforming Environmental Governance for the 21st Century. Brisbane, QLD: Ecopolitics Association of Australasia/Griffith University, Centre for Governance and Public Policy. Ecopolitics XVI: Transforming Environmental Governance for the 21st Century. Brisbane, QLD. Jul 2005, pp. 1-19. ,
Synthesizing Parsimonious Inexact Circuits through Probabilistic Design Techniques

The domain of inexact circuit design, in which accuracy of the circuit can be exchanged for substantial cost (energy, delay, and/or area) savings, has been gathering increasing prominence of late owing to a growing desire for reducing energy consumption of the systems, particularly in the domain of embedded and (portable) multimedia applications. Most of the previous approaches to realizing inexact circuits relied on scaling of circuit parameters (such as supply voltage) taking advantage of an application’s error tolerance to achieve the cost and accuracy trade-offs, thus suffering from acute drawbacks of considerable implementation overheads that significantly reduced the gains. In this article, two novel design approaches called Probabilistic Pruning and Probabilistic Logic Minimization are proposed to realize inexact circuits with zero hardware overhead.Extensive simulations on various architectures of critical datapath elements demonstrate that each of the techniques can independently achieve normalized gains as large as 2x--9.5x in energy-delay-area product for relative error magnitude as low as 10 − 4%--8% compared to corresponding conventional correct circuits.
Indicators of Sleepiness in an ambulatory EEG study of night driving

Driver sleepiness due to sleep deprivation is a causative factor in 1% to 3% of all motor vehicle crashes. In recent studies, the importance of developing driver fatigue countermeasure devices has been stressed, in order to help prevent driving accidents and errors. Although numerous physiological indicators are available to describe an individual's level of alertness, the EEG signal has been shown to be one of the most predictive and reliable, since it is a direct measure of brain activity. In the present study, multichannel EEG data that were collected from 20 sleep-deprived subjects during real environmental conditions of driving are presented for the first time. EEG data's annotation made by two independent Medical Doctors revealed an increase of slowing activity and an acute increase of the alpha waves 5-10 seconds before driving events. From the EEG data that were collected, the Relative Band Ratio (RBR) of the EEG frequency bands, the Shannon Entropy, and the Kullback-Leibler (KL) Entropy were estimated for each one second segment. The mean values of these measurements were estimated for 5 minutes periods. Analysis revealed a significant increase of alpha waves relevant band ratios (RBR), a decrease of gamma waves RBR, and a significant decrease of KL entropy when the first and the last 5-min periods were compared. A rapid decrease of both Shannon and K-L entropies was observed just before the driving events. Conclusively, EEG can assess effectively the brain activity alterations that occur a few seconds before sleeping/drowsiness events in driving, and its quantitative measurements can be used as potential sleepiness indicators for future development of driver fatigue countermeasure devices
DIRECT NUMERICAL SIMULATION OF THE FLOW AROUND A WING SECTION USING HIGH-ORDER PARALLEL SPECTRAL METHODS

The results of a DNS of the flow around a wing section represented by a NACA4412 profile, with Rec = 400,000 and 5◦ angle of attack, are presented in this study. The high-order spectral element code Nek5000 is used for the computations. An initial RANS simulation is used to define the velocity boundary conditions, and to design the computational mesh. The agreement between spanwiseand time-averaged fields from the DNS and the RANS simulation is excellent. The mean flow and several components of the Reynolds stress tensor at x/c = 0.4 (β = 0.53) and 0.8 (β = 4.54) are compared with the ZPG boundary layer computed by Schlatter & Örlü (2010). In both cases, the friction Reynolds number is roughly matched (330 and 450), and as expected the Reθ values from the wing (720 and 1,800) are larger than the ones from the ZPG case (612 and 1,007). The APG leads to a steeper log law, a more prominent wake region and a larger U+ e . The tangential turbulence intensity exhibits a stronger inner peak, and starts to develop an outer peak. We also show that the impact on the spanwise component is significant, and also on the wall-normal intensity and the Reynolds shear stress for stronger pressure gradients, especially in the outer region.
Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme

The panB gene from Escherichia coli, encoding the first enzyme of the pantothenate biosynthesis pathway, ketopantoate hydroxymethyltransferase (KPHMT), has been isolated by functional complementation of a panB mutant strain with an E. coli genomic library. The gene is 792 bp long, encoding a protein of 264 amino acids with a predicted M(r) of 28,179. The identity of the gene product as ketopantoate hydroxymethyltransferase was confirmed by purification of the enzyme protein, which was overexpressed approximately 50-fold in the mutant harboring the gene on a high-copy-number plasmid. The N-terminal amino acid sequence of the purified protein was found to be identical to that predicted from the gene sequence, as was its mass, determined by electrospray mass spectrometry. Upstream of the panB gene is an incomplete open reading frame encoding a protein of 220 amino acids, which shares sequence similarity to fimbrial precursor proteins from other bacteria. Northern (RNA) analysis showed that the panB gene is likely to be cotranscribed with at least one other gene but that this is not the putative fimbrial protein, since no transcripts for this gene could be detected.
Estimating a Composite Measure of Hospital Quality From the Hospital Compare Database: Differences When Using a Bayesian Hierarchical Latent Variable Model Versus Denominator-Based Weights

Background:A single composite measure calculated from individual quality indicators (QIs) is a useful measure of hospital performance and can be justified conceptually even when the indicators are not highly correlated with one another. Objective:To compare 2 basic approaches for calculating a composite measure: an extension of the most widely-used approach, which weights individual indicators based on the number of people eligible for the indicator (referred to as denominator-based weights, DBWs), and a Bayesian hierarchical latent variable model (BLVM). Methods:Using data for 15 QIs from 3275 hospitals in the Hospital Compare database, we calculated hospital ranks using several versions of DBWs and 2 BLVMs. Estimates in 1 BLVM were driven by differences in variances of the QIs (BLVM1) and estimates in the other by differences in the signal-to-noise ratios of the QIs (BLVM2). Results:There was a high correlation in ranks among all of the DBW approaches and between those approaches and BLVM1. However, a high correlation does not necessarily mean that the same hospitals were ranked in the top or bottom quality deciles. In general, large hospitals were ranked in higher quality deciles by all of the approaches, though the effect was most apparent using BLVM2. Conclusions:Both conceptually and practically, hospital-specific DBWs are a reasonable approach for calculating a composite measure. However, this approach fails to take into account differences in the reliability of estimates from hospitals of different sizes, a big advantage of the Bayesian models.
Fetal hemoglobin regulation in β-thalassemia: heterogeneity, modifiers and therapeutic approaches

ABSTRACT Introduction: Stress erythropoiesis induces fetal hemoglobin (HbF) expression in β-thalassemias, however the level of expression is highly variable. The last decade has seen dramatic advances in our understanding of the molecular regulators of HbF production and the genetic factors associated with HbF levels, leading to the promise of new methods of the clinical induction of HbF. Areas covered: This article will review the heterogeneity and genetic modifiers of HbF and HbF induction therapy in β-thalassemia. Expert commentary: One promising curative β-thalassemia therapy is to induce HbF synthesis in β-thalassemic erythrocytes to therapeutic levels before clinical symptom occurs. Further understanding of HbF level variation and regulation is needed in order to predict the response from HbF-inducing approaches.
Advances in Cytochemical Methods for Detection of Apoptosis

In an earlier article from this laboratory, the current methods developed to detect apoptosis in cells and tissues were highlighted, along with the challenges in their interpretation. Recent discoveries concerning the underlying biochemical mechanisms of apoptotic effector pathways have made possible further assays that allow a more direct measure of the activation of the apoptotic machinery in cells. This article summarizes some of these newer methods and extends the interpretation of the more classical assays of apoptosis in a defined cell system. We present data in KB and PC3 cell model culture systems induced to undergo apoptosis by the plant toxin ricin. Using a modified in situ nick translation assay (ISNT) with either Bodipy or BUdR labeling, we confirm that most cells showing altered nuclear morphology do not show reactivity with this assay until very late in the apoptotic process. We also show that only a minority of cells label with fluorescent annexin V during apoptosis but that apoptotic cells continue to internalize material from the cell surface through endocytosis after becoming reactive with annexin V. In addition, we describe the utility of a prototype of new assays for caspase substrate cleavage products, the detection of cleaved cytokeratin 18. It is these newer cleavage product assays that perhaps hold the greatest promise for specific detection of apoptosis in cells either in cell culture or in intact tissues.
Probabilistic Graphical Models PGM Prague 2018

OpenMarkov is an open-source software tool for probabilistic graphical models. It has been developed especially for medicine, but it has also been used for building applications in other fields, in a total of more than 30 countries. In this paper we explain how to use it as a pedagogical tool to teach the main concepts of Bayesian networks, such as conditional dependence and independence, d-separation, Markov blankets, explaining away, etc., and some inference algorithms: logic sampling, likelihood weighting, and arc reversal. The facilities for learning Bayesian networks interactively can be used to illustrate step by step the performance of the two basic algorithms: search-and-score and PC.
Laparoscopy for the treatment of women with endometrial cancer.

OBJECTIVE To evaluate the use of a laparoscopic approach for the management of endometrial cancer. DESIGN Retrospective study. SETTING Regional hospital, Hong Kong. SUBJECTS AND METHODS Individual medical records of patients with preoperative histological diagnosis of endometrial carcinoma from January 2000 to December 2001 were reviewed and the data analysed. MAIN OUTCOME MEASURES Success of laparoscopic-assisted surgical staging, intra-operative and postoperative morbidity, and length of hospital stay. RESULTS Laparoscopic surgery was successful for 93.3% (28 of 30) patients. Two patients were converted to laparotomy. The mean operating time was 102 minutes (standard deviation, 16 minutes) and the mean operative blood loss was 280 mL (standard deviation, 137 mL). The mean hospital stay was 5 days (standard deviation, 2.3 days). The intra-operative and postoperative complication rate was 16.7%, including vaginal tear, injury to the inferior epigastric vessel, lymphocyst, and pulmonary embolism. CONCLUSION This study illustrated that a laparoscopic approach is feasible for endometrial cancer surgery and may be considered as the primary treatment modality in skilled hands. This approach should be offered to women with endometrial cancer without contraindications for laparoscopic surgery if experienced endoscopic surgeons are available. Prophylaxis for venous thromboembolism and the use of retroperitoneal drainage may be helpful in decreasing the perioperative morbidity.
TEXT CATEGORIZATION PROBLEM

Document categorization problem gained a lot of importance in the last years due to the increase in the number of digital documents. This paper analyzes the performance of different classification algorithms on text categorization problem. Importance of parameter optimization on the performance of the algorithms is also discussed. The paper mostly focuses on the SVM (Support Vector Machines) algorithm since, according to the literature, its performance is superior to other machine learning algorithms in text categorization problem.
System of associative relationships (SOAR)

We propose a new architecture for texture classification based on pair-wise pixel associations as an extension of the multivalued recursive network (MAREN) architecture. Maybe more critically we propose a novel similarity measure and classification algorithm to be used with this network. The proposed fidelity criterion has been observed to be tightly coupled with the ubiquitous mean-square error (MSE) distance measure. Both SOAR and MAREN structures can be considered as an extension of the associative memory concept frequently used in neural networks. Our proposed similarity measure is based on the principle of directional divergence of interpixel relationships in a given texture and promises a number of advantages over the MSE measure. The SOAR is discussed within the framework of a texture classification problem, but we believe it would be very easy to extend it to other applications where the interpixel relationship is the primary focus.