Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistence of DNA in Carcasses, Slime and Avian Feces May Affect Interpretation of Environmental DNA Data

The prevention of non-indigenous aquatic invasive species spreading into new areas is a goal of many resource managers. New techniques have been developed to survey for species that are difficult to capture with conventional gears that involve the detection of their DNA in water samples (eDNA). This technique is currently used to track the invasion of bigheaded carps (silver carp and bighead carp; Hypophthalmichthys molitrix and H. nobilis) in the Chicago Area Waterway System and Upper Mississippi River. In both systems DNA has been detected from silver carp without the capture of a live fish, which has led to some uncertainty about the source of the DNA. The potential contribution to eDNA by vectors and fomites has not been explored. Because barges move from areas with a high abundance of bigheaded carps to areas monitored for the potential presence of silver carp, we used juvenile silver carp to simulate the barge transport of dead bigheaded carp carcasses, slime residue, and predator feces to determine the potential of these sources to supply DNA to uninhabited waters where it could be detected and misinterpreted as indicative of the presence of live bigheaded carp. Our results indicate that all three vectors are feasible sources of detectable eDNA for at least one month after their deposition. This suggests that current monitoring programs must consider alternative vectors of DNA in the environment and consider alternative strategies to minimize the detection of DNA not directly released from live bigheaded carps.
Blind Adaptive Channel Estimation For Decoding of Orthogonal Space-Time Block Codes

In this paper, we provide a blind adaptive channel estimation method for decoding of orthogonal space-time block codes (OSTBC), which is built on the minimizing of an unconstrained cost function. The global minima of the cost function are analyzed. Both LMS and RLS algorithm realizations are given. Our method can adaptively track the time varying channel and decode transferred symbols without pilot symbols
Public risk perceptions of ocean acidification

Ocean acidification has been called the ‘evil twin’ of climate change and has become acknowledged as a serious risk to the marine environment. This thesis aims to explore public perceptions of ocean acidification as there is limited work on how people understand this emerging risk. It is important to engage the public because ocean acidification will contribute to how carbon emissions are addressed. The mental models approach was used to compare and examine public and expert perceptions of ocean acidification to help inform future risk communications. Many of the findings were similar to those of climate change; for example, it was not seen as a personal risk but something which would impact on the environment. Results showed that ocean acidification was unfamiliar to the public with low levels of knowledge and awareness found. People could identify possible impacts of ocean acidification but they were unsure about the main cause, stating that pollution from chemicals and industrial waste was one of the main causes. Risk perceptions of ocean acidification were influenced by factors other than knowledge about the risk such as affect, place attachment and environmental identity. A key finding of this thesis was that people were concerned about ocean acidification despite this being an unfamiliar risk issue, perceiving it as a highly negative risk. This exploratory thesis will help develop more effective risk communications around ocean acidification with these findings in mind. Future work should test ocean acidification frames; whether or not it should be framed as part of climate change. The mental models approach allowed initial understandings of this unfamiliar risk to be explored using mixed methods and helped examine how ocean acidification was conceptualised through social representations theory. Public response to ocean acidification may mean that there would be greater support for policies aimed at reducing carbon emissions.
Definition of a robust modular SOC test architecture; resurrection of the single TAM daisy-chain

This paper presents a new modular SOC test architecture that uses an improved single TAM daisy-chain for scan test access to embedded modules. The architecture by definition guarantees that the total SOC test time is close to the lower bound. To make third party IP cores to fit the architecture, IP with test infrastructure 'on-demand' is introduced. An area-efficient bypass implementation for our IEEE std. 1500 compliant test wrapper is presented and results from a single TAM daisy-chain on silicon are shown
Pl-servo with state-D feedback and observer for magnetic stirrer machine

This paper presents PI-servo with a state-D feedback and observer designed for magnetic stirrer machine. Actually, the state variables cannot be directly measured that we need to feedback all state variables. Therefore, it is necessary to use an observer for the estimation of those state variables. The speed control DC motor for magnetic stirrer machine is compared between the Ogata's Method and PI-servo with State-D feedback and observer. The dynamic responses of a control system demonstrates effective the robustness and stability of a disturbance.
Effects of Cigarette Smoke Exposure on Clot Dynamics and Fibrin Structure: An Ex Vivo Investigation

Objectives—The purpose of this study was to examine the effect of cigarette smoke exposure (CSE) on clot dynamics and fibrin architecture and to isolate the relative contribution of platelets and fibrinogen to clot dynamics. Methods and Results—From young healthy males smokers (n=34) and nonsmokers (n=34) a baseline blood was drawn, and smokers had another blood draw after smoking 2 regular cigarettes. Using thromboelastography (TEG) the degree of platelet-fibrin interaction was measured. In additional experiments, abciximab (20 &mgr;g/mL) was added to the smokers samples (n=27) to reduce the effects of platelet function from the TEG parameters. The maximum clot strength (G) obtained with abciximab measured mainly the contribution of fibrinogen to clot strength (GF). By subtracting GF from G, the contribution of platelets to clot strength (GP) was presumed. A significant difference was found for all TEG parameters between nonsmokers versus postsmoking and pre- versus postsmoking samples. Postsmoking both GF and GP were significantly higher as compared to presmoking. On electron microscopy and turbidity analysis, postsmoking fibrin clots were significantly different compared to presmoking and nonsmoking samples. Conclusions—Acute CSE changes clot dynamics and alters fibrin architecture. Both functional changes in fibrinogen and platelets appear to contribute to heightened thrombogenicity after acute CSE.
Bayesian Clustering of Fuzzy Feature Vectors Using a Quasi-Likelihood Approach

Bayesian model-based classifiers, both unsupervised and supervised, have been studied extensively, and their value and versatility have been demonstrated on a wide spectrum of applications within science and engineering. A majority of the classifiers are built on the assumption of intrinsic discreteness of the considered data features or on their discretization prior to the modeling. On the other hand, Gaussian mixture classifiers have also been utilized to a large extent for continuous features in the Bayesian framework. Often, the primary reason for discretization in the classification context is the simplification of the analytical and numerical properties of the Bayesian models. However, the discretization can be problematic due to its ad hoc nature and the decreased statistical power to detect the correct classes (or clusters) in the resulting procedure. Here, we introduce an unsupervised classification approach for fuzzy feature vectors that utilizes a discrete model structure while preserving the continuous characteristics of data. This goal is achieved by replacing the ordinary likelihood by a binomial quasi-likelihood to yield an analytical expression for the posterior probability of a given clustering solution. The resulting model can also be justified from an information-theoretic perspective. Our method is shown to yield highly accurate clusterings for challenging synthetic and empirical data sets and to perform favorably compared to some alternative approaches.
The Anatomy of an Optical Biopsy Semantic Retrieval System

A case-based computer-aided diagnosis system assists physicians and other medical personnel in the interpretation of optical biopsies obtained through confocal laser endomicroscopy. Extraction in CLE images shows promising results on inferring semantic metadata from low-level features. In order to effectively ensure the interoperability with potential third-party applications, the system provides an interface compliant with the recent standards ISO/IEC 15938-12:2008 (MPEG Query Format) and ISO/IEC 24800 (JPEG Search).
Schmidt games and Markov partitions

Let T be a C2-expanding self-map of a compact, connected, C∞, Riemannian manifold M. We correct a minor gap in the proof of a theorem from the literature: the set of points whose forward orbits are nondense has full Hausdorff dimension. Our correction allows us to strengthen the theorem. Combining the correction with Schmidt games, we generalize the theorem in dimension one: given a point x0 ∊ M, the set of points whose forward orbit closures miss x0 is a winning set. Finally, our key lemma, the no matching lemma, may be of independent interest in the theory of symbolic dynamics or the theory of Markov partitions.
Tryptophan fluorescence quenching by methionine and selenomethionine residues of calmodulin: orientation of peptide and protein binding.

The two interaction surfaces of the dumbbell-shaped calcium-regulatory protein calmodulin (CaM) are rich in the amino acid Met. In this work we have used fluorescence spectroscopy to study the role of these Met residues in binding the single Trp residue that is found in many CaM-binding domain peptides. This approach is facilitated by the absence of Trp residues in CaM. In addition to the wild-type protein, we studied CaM containing the unnatural amino acid selenomethionine (SeMet), which was biosynthetically substituted for its nine Met residues. Furthermore, a CaM mutant protein in which all four Met residues in the C-terminal domain were mutated to Leu, and the N-terminal domain contained either Met or the unnatural SeMet, was studied. The Trp fluorescence quantum yield of many Trp-containing CaM-binding peptides increases upon binding to calcium-CaM. Moreover, the emission wavelength of the Trp fluorescence is blue-shifted from 353 to 325-333 nm. These parameters indicate movement of Trp from a solvent exposed to a hydrophobic environment. The fluorescence results obtained with these four CaM variants showed that Se is very effective at quenching Trp fluorescence in the calmodulin-bound peptides from myosin light chain kinase (MLCK) and CaM kinase I, while S is somewhat effective (Se > S > C). The quenching effect is markedly distance dependent, as it only influences the Trp residue of the bound peptide (<=7 A) but has little effect on the two Tyr residues in the C-terminal domain of CaM (>=10 A). Since the Trp fluorescence quenching is very dramatic, the protein containing Leu's in the C-terminal domain and SeMet's in the N-terminal domain allowed us to directly determine the orientation of the MLCK and CaM kinase I peptides bound to CaM; in both cases the Trp residue binds to the C-terminal domain of CaM. Our data indicate that SeMet quenching of Trp fluorescence could become a simple and useful tool for studies of protein folding, and protein-protein and protein-peptide interactions.
Environmental assessment of synthetic based drilling mud discharges to Bass Strait, Australia

Esso Australia Ltd. (Esso) on behalf of the Esso/BHP joint venture undertakes exploration and development drilling activities to produce oil and gas from the Gippsland Basin in eastern Bass Strait. As part of the environmental management of the operation, a field monitoring program was undertaken to verify the predicted limited effect on the seabed of the discharge of residual synthetic based mud (SBM) adhered to drill cuttings. Reservoir studies of the mature Fortescue oil field identified scope to more efficiently deplete existing reserves as well as develop undrained oil pools within the known reservoir system. As such, 18 additional wells were drilled from the Fortescue platform in 1994-1996 following the original development drilling program when 21 wells were drilled in 1983-1985. Esso's standard drilling fluid in Bass Strait is an environmentally acceptable water based mud (WBM). However, due to the high frictional forces involved the greater lubricating properties of a non-water based drilling mud were required to drill the long reach, high angle sections of seven of the additional wells. The ester SBM was chosen on the basis of its lubricity and biodegradability, to reduce any potential environmental effects from the persistence of non-water based mud in seabed sediments. A seabed monitoring program was undertaken around the Fortescue platform by taking seabed samples from August 1995 to August 1997 at sites along a transect following the predominant ocean current and at control sites, before, during and after the period in which SBM cuttings were discharged. The seabed sediments were measured for esters, barium, biological changes and grain size. Results show clearly the increase in esters concentration in sediments during drilling, then the rapid decrease after completion of cuttings discharge. After a recovery period of 11 months from completion of SBM drilling, SBM esters were not detected in sediments. Sediment barium concentration was also found to be elevated, but only after SBM had been used, indicating greater dispersion of WBM than the more cohesive SBM. The barium concentrations found generally do not have measurable effects on biota. The impact on the sediment biology was found to be limited to the sampling site 100 m from the platform discharge point with recovery evident within four months of completion of drilling. Mechanisms for recovery of the minimal zone of effect are thought to be a combination of the biodegradation of the ester SBM used and the physical seabed dispersion process evident in eastern Bass Strait generated by the continuous series of storms which pass through especially in winter.
Extended Lifted Inference with Joint Formulas

The First-Order Variable Elimination (FOVE) algorithm allows exact inference to be applied directly to probabilistic relational models, and has proven to be vastly superior to the application of standard inference methods on a grounded propositional model. Still, FOVE operators can be applied under restricted conditions, often forcing one to resort to propositional inference. This paper aims to extend the applicability of FOVE by providing two new model conversion operators: the first and the primary is joint formula conversion and the second is just-different counting conversion. These new operations allow efficient inference methods to be applied directly on relational models, where no existing efficient method could be applied hitherto. In addition, aided by these capabilities, we show how to adapt FOVE to provide exact solutions to Maximum Expected Utility (MEU) queries over relational models for decision under uncertainty. Experimental evaluations show our algorithms to provide significant speedup over the alternatives.
The Potential Role of Iron and Copper in Pediatric Obesity and Nonalcoholic Fatty Liver Disease

Obesity is a rapidly growing health problem and is paralleled by a multitude of comorbidities, including nonalcoholic fatty liver disease (NAFLD). NAFLD has become the most common chronic liver disease in both adults and children. The current understanding of NAFLD is still fragmentary. While simple steatosis is characterized by the interplay between excessive free fatty acid accumulation and hepatic insulin resistance, the progression to NASH has been related to oxidative stress and a proinflammatory state with dysbalanced adipokine, cytokine levels, and endotoxin-mediated immune response. In addition, oxidative stress has been suggested to play a central role for the sequelae leading to NASH. Trace elements are critical in regulatory, immunologic, and antioxidant functions resulting in protection against inflammation and peroxidation and consequently against the known comorbidities of obesity. Disruptions of the metal detoxification processes located in the liver are plausibly related to NAFLD development via oxidative stress. Perturbations of iron and copper (Cu) homeostasis have been shown to contribute to the pathogenesis of NAFLD. This review presents current data from pediatric studies. In addition, data from adult studies are summarized where clinical relevance may be extrapolated to pediatric obesity and NAFLD.
Spiraphase-type reflectarrays based on loaded ring slot resonators

Reflective periodic arrays based on loaded ring slot resonators are analyzed. A full-wave mathematical model is developed and numerical results are presented. It is proven that the reflection angle for the normally incident circularly polarized wave can be effectively controlled by proper positioning of reactive loads in ring slot resonators. Analysis of the reflection characteristics of the Ka band one-layer reflectarray results in a conclusion that the incident wave can be effectively redirected in the directions determined by elevation angles as high as 65/spl deg/ with conversion coefficient better than -1.5 dB. It is also shown that the usage of the multilayer reflectarray leads to a considerable improvement in the reflection characteristics when it is compared with the one-layer reflectarray. The method of the waveguide simulator has been used to verify the developed mathematical model.
Retrospective analysis of trends in current P&RM research as reflected in the 2nd ISPRM World Congress (Prague, 2003)

This special issue of Disability and Rehabilitation is dedicated to the publication of nine articles by young P&RM researchers from different countries. These works reached the final stage in a competition – the Young Scientist Award — held during the 2nd World Congress of the International Society of Physical and Rehabilitation Medicine (ISPRM; Prague, Czech Republic, May 2003). The aim of this editorial paper is to analyse current trends in P&RM research as reflected in the above congress.
Examining mobile phone text legibility while walking

In this study, alternative methods for studying legibility of text while walking with a mobile phone were examined. Normal reading and pseudo-text search were used as visual tasks in four walking conditions. Visual performance and subjective evaluation of task difficulty were used as measures of text legibility. According to the results, visual performance suffers from increasing walking speed, and the effects are greater on reading velocity for pseudo-text search. Subjects also use more homogenous strategies when reading compared to pseudo-text search, and therefore it is concluded that reading is a more useful measure of legibility. Subjective measures are found to be more sensitive to small variations in legibility than objective measures, and give additional information about task demands. Hence, without both objective and subjective measurements important information about legibility in different conditions and with different tasks will be lost.
Fibrosis Hyperhomocysteinemia in Liver Cirrhosis : Mechanisms and Role in Vascular and Hepatic

Numerous clinical and epidemiological studies have identified elevated homocysteine levels in plasma as a risk factor for atherosclerotic vascular disease and thromboembolism. Hyperhomocysteinemia may develop as a consequence of defects in homocysteine-metabolizing genes; nutritional conditions leading to vitamin B6, B12, or folate deficiencies; or chronic alcohol consumption. Homocysteine is an intermediate in methionine metabolism, which takes place mainly in the liver. Impaired liver function leads to altered methionine and homocysteine metabolism; however, the molecular basis for such alterations is not completely understood. In addition, the mechanisms behind homocysteineinduced cellular toxicity are not fully defined. In the present work, we have examined the expression of the main enzymes involved in methionine and homocysteine metabolism, along with the plasma levels of methionine and homocysteine, in the liver of 26 cirrhotic patients and 10 control subjects. To gain more insight into the cellular effects of elevated homocysteine levels, we have searched for changes in gene expression induced by this amino acid in cultured human vascular smooth muscle cells. We have observed a marked reduction in the expression of the main genes involved in homocysteine metabolism in liver cirrhosis. In addition, we have identified the tissue inhibitor of metalloproteinases-1 and 1(I)procollagen to be upregulated in vascular smooth muscle cells and liver stellate cells exposed to pathological concentrations of homocysteine. Taken together, our observations suggest (1) impaired liver function could be a novel determinant in the development of hyperhomocysteinemia and (2) a role for elevated homocysteine levels in the development of liver fibrosis. (Hypertension. 2001;38:1217-1221.)
Neuronal Activity–Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis

The mammalian brain exhibits diverse types of neural plasticity, including activity-dependent neurogenesis in the adult hippocampus. How transient activation of mature neurons leads to long-lasting modulation of adult neurogenesis is unknown. Here we identify Gadd45b as a neural activity–induced immediate early gene in mature hippocampal neurons. Mice with Gadd45b deletion exhibit specific deficits in neural activity–induced proliferation of neural progenitors and dendritic growth of newborn neurons in the adult hippocampus. Mechanistically, Gadd45b is required for activity-induced DNA demethylation of specific promoters and expression of corresponding genes critical for adult neurogenesis, including brain-derived neurotrophic factor and fibroblast growth factor. Thus, Gadd45b links neuronal circuit activity to epigenetic DNA modification and expression of secreted factors in mature neurons for extrinsic modulation of neurogenesis in the adult brain.
High accuracy WaDi image interpolation with local gradient features

In this paper, we propose a new computational method of the warped distance (WaDi) for digital image interpolation. The conventional WaDi algorithm only uses the local asymmetry features of image edges to compute the WaDi and then uses the computed WaDi in place of the interpolation operator in the linear interpolations. The local gradient features are one kind of the important features of image edges as well as the local asymmetry features. In this paper, we adopt both the local asymmetry features and the local gradient features in the WaDi computation. Experimental results show that the proposed method can obtain high accuracy interpolated images.