Miracle-dz/UniFAR-FTUs huggingface dataset:
SYNTHESIS OF COMPLEX CARBOHYDRATES IN THE GOLGI REGION, AS SHOWN BY RADIOAUTOGRAPHY AFTER INJECTION OF LABELED GLUCOSE

Biochemical work (1, 2) has shown that free glucose is incorporated into mucopolysaccharides and glycoproteins in the course of their synthesis. (The word glycoprotein is used to refer to protein-associated carbohydrates, reference 3.) Little is known, however, about the sites of these syntheses. Kumamoto (4) observed that, after injection of radioactive glucose, many cells, in particular those secreting mucus, became radioactive, presumably due to uptake of glucose into the complex carbohydrates of mucus. However, her work gave no indication of the intracellular site of this synthesis. Attention was drawn to the Golgi zone because it is often stained with the periodic acid-Schiff technique (5) (believed to be specific for glycoproteins, reference 6) and with the colloidal iron technique (7) (believed to stain acid mucopolysaccharides, reference 8). Further evidence was provided by the radioautographic finding that sulfate-S ~s was taken up into the Golgi zone of chondrocytes and of certain mucus-secreting cells (9, 10), indicating that this zone was the site of sulfation of complex carbohydrates. Was the Golgi zone also the site of synthesis of these carbohydrates? In the hope of clarifying the problem, labeled glucose was injected into rats; and radioautographs were prepared of a variety of cells, including those which are active in the elaboration of complex carbohydrates.
Biogeographic models of gene flow in two waterfowl of the Australo-Papuan tropics

There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling-duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.
Addition of Sodium Pyruvate to Stored Red Blood Cells Attenuates Liver Injury in a Murine Transfusion Model

RBCs undergo numerous changes during storage and stored RBCs may induce adverse effects, ultimately resulting in organ injury in transfusion recipients. We tested the hypothesis that the addition of SP to stored RBCs would improve the quality of the stored RBCs and mitigate liver injury after transfusion in a murine model. RBCs were harvested from C57BL/6J mice and stored for 14 days in CPDA-1 containing either a solution of SP in saline or saline alone. Haemolysis, the 24-hour posttransfusion recovery, the oxygen-carrying capacity, and the SOD activity of stored RBCs were evaluated. The plasma biochemistry, hepatic MDA level, MPO activity, IL-6, TNF-α concentrations, and histopathology were measured two hours after the transfusion of stored RBCs. Compared with RBCs stored in CPDA-1 and saline, the addition of SP to stored RBCs restored their oxygen-carrying capacity and SOD activity, reduced the AST activity, BUN concentrations, and LDH activity in the plasma, and decreased the MDA level, MPO activity, and concentrations of IL-6 and TNF-α in the liver. These data indicate that the addition of SP to RBCs during storage has a beneficial effect on storage lesions in vitro and subsequently alleviates liver injury after the transfusion of stored RBCs in vivo.
In Search of Food: Exploring the Evolutionary Link Between cGMP-DependentProtein Kinase (PKG) and Behaviour1

Abstract Despite an immense amount of variation in organisms throughout the animal kingdom many of their genes show substantial conservation in DNA sequence and protein function. Here we explore the potential for a conserved evolutionary relationship between genes and their behavioural phenotypes. We investigate the evolutionary history of cGMP-dependent protein kinase (PKG) and its possible conserved function in food-related behaviours. First identified for its role in the foraging behaviour of fruit flies, the PKG encoded by the foraging gene has since been associated with the maturation of behaviour (from nurse to forager) in honey bees and the roaming and dwelling food-related locomotion in nematodes. These parallels encouraged us to construct protein phylogenies using 32 PKG sequences that include 19 species. Our analyses suggest five possible evolutionary histories that can explain the apparent conserved link between PKG and behaviour in fruit flies, honey bees and nematodes. Three of these raise the hypothesis that PKG influences the food-related behaviours of a wide variety of animals including vertebrates. Moreover, it appears that the PKG gene was duplicated some time between the evolution of nematodes and a common ancestor of vertebrates and insects whereby current evidence suggests only the for-like PKG might be associated with food-related behaviour.
Rapid isolation of high molecular weight plant DNA.

A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.
Regime switching as an alternative early warning system of currency crises - an application to South-East Asia

In this paper we develop an early warning system of currency crises based on the Markov switching methodology. Constructed data on speculative pressure from six Asian countries indicate that currency crises are mainly captured through volatility effects. Based on an extensive survey, we test potential determinants of exiting the tranquil state and find a number of variables with significant medians across the panel. Using these candidates, we obtain final specifications using a recently proposed penalized maximum likelihood methodology. The method enables us to extract smoother transition probabilities than in the standard case, reflecting the need of policy makers to have advance warning in the medium to long term ratherthan the short term. Our forecasting results indicate that the approach is useful in the early warning of currency crises setting.
Effect of Green Tea Extract on Systemic Metabolic Homeostasis in Diet-Induced Obese Mice Determined via RNA-Seq Transcriptome Profiles

Green tea (GT) has various health effects, including anti-obesity properties. However, the multiple molecular mechanisms of the effects have not been fully determined. The aim of this study was to elucidate the anti-obesity effects of GT via the analysis of its metabolic and transcriptional responses based on RNA-seq profiles. C57BL/6J mice were fed a normal, high-fat (60% energy as fat), or high-fat + 0.25% (w/w) GT diet for 12 weeks. The GT extract ameliorated obesity, hepatic steatosis, dyslipidemia, and insulin resistance in diet-induced obesity (DIO) mice. GT supplementation resulted in body weight gain reduction than mice fed high-fat through enhanced energy expenditure, and reduced adiposity. The transcriptome profiles of epididymal white adipose tissue (eWAT) suggested that GT augments transcriptional responses to the degradation of branched chain amino acids (BCAAs), as well as AMP-activated protein kinase (AMPK) signaling, which suggests enhanced energy homeostasis. Our findings provide some significant insights into the effects of GT for the prevention of obesity and its comorbidities. We demonstrated that the GT extract contributed to the regulation of systemic metabolic homeostasis via transcriptional responses to not only lipid and glucose metabolism, but also amino acid metabolism via BCAA degradation in the adipose tissue of DIO mice.
Comparing the information seeking strategies of residents, nurse practitioners, and physician assistants in critical care settings.

OBJECTIVE Critical care environments are information-intensive environments where effective decisions are predicated on successfully finding and using the 'right information at the right time'. We characterize the differences in processes and strategies of information seeking between residents, nurse practitioners (NPs), and physician assistants (PAs). METHOD We conducted an exploratory study in the cardiothoracic intensive care units of two large academic hospitals within the same healthcare system. Clinicians (residents (n=5), NPs (n=5), and PAs (n=5)) were shadowed as they gathered information on patients in preparation for clinical rounds. Information seeking activities on 96 patients were collected over a period of 3 months (NRes=37, NNP=24, NPA=35 patients). The sources of information and time spent gathering the information at each source were recorded. Exploratory data analysis using probabilistic sequential approaches was used to analyze the data. RESULTS Residents predominantly used a patient-based information seeking strategy in which all relevant information was aggregated for one patient at a time. In contrast, NPs and PAs primarily utilized a source-based information seeking strategy in which similar (or equivalent) information was aggregated for multiple patients at a time (eg, X-rays for all patients). CONCLUSIONS The differences in the information seeking strategies are potentially a result of the differences in clinical training, strategies of managing cognitive load, and the nature of the use of available health IT tools. Further research is needed to investigate the effects of these differences on clinical and process outcomes.
Reducing the memory required to find a geodesic shortest path on a large mesh

Finding shortest paths and distances on the surface of a mesh in R3 is a well studied problem, with most research aiming to minimize computation time. However for large meshes, such as TIN terrain models in GIS, the major bottleneck is often the memory required by an algorithm. In this paper, we evaluate techniques for computing path distances (both for paths restricted to edges of the mesh and for paths traveling freely across the triangles of the mesh) that do not need to store data structure for the entire mesh in memory. In particular, we implement a novel combination of Dijkstra, A*, and MMP (aka, continuous Dijkstra) methods that, in our experiments on TINs containing millions of triangles, reduces the memory requirement by two orders of magnitude. We are also able to compare distances computed by Dijkstra, fast marching, and the MMP methods.
TerraMax Vision at the Urban Challenge 2007

This paper presents the TerraMax vision systems used during the 2007 DARPA Urban Challenge. First, a description of the different vision systems is provided, focusing on their hardware configuration, calibration method, and tasks. Then, each component is described in detail, focusing on the algorithms and sensor fusion opportunities: obstacle detection, road marking detection, and vehicle detection. The conclusions summarize the lesson learned from the developing of the passive sensing suite and its successful fielding in the Urban Challenge.
Using string similarity metrics for automated grading of SQL statements

Manual grading of structured query language (SQL) statements after an exam can be tedious and time consuming for the teaching assistant. Additionally, it can also be subjective to her current state of mind and, thus, prone to errors. In this paper we propose an automated method for grading individual SQL statements. The method uses several common and simple string similarity metrics for comparing the student devised statements against the reference statements. These are then used, along with the manually assigned grades, for building the predictive logistic regression model. The proposed method was evaluated on a dataset consisting of 314 pairs of student-reference statements, along with the discretized average grade assigned by three independent evaluators. The model achieved the expected classification accuracy of 78% on a binary class, thus exhibiting its potential for real-life application. The model can be used as is with the suggested calculated features and reported learnt parameters, or adapted to other examiners' evaluation criteria, presuming their willingness to build manually graded datasets of their own.
Automatic Syllabification with Structured SVMs for Letter-to-Phoneme Conversion

We present the first English syllabification system to improve the accuracy of letter-tophoneme conversion. We propose a novel discriminative approach to automatic syllabification based on structured SVMs. In comparison with a state-of-the-art syllabification system, we reduce the syllabification word error rate for English by 33%. Our approach also performs well on other languages, comparing favorably with published results on German and Dutch.
A Comparison of Exergaming Interfaces for Use in Rehabilitation Programs and Research

Exergames or active video games are video games with interfaces that require active involvement and the exertion of physical force by participants. These exergames are designed to track body motion and provide both fun and exercise for game players. Numerous video game console companies have designed exergaming interfaces that are becoming very popular. This paper examines the nature of the interfaces and explores the possibility of using these interfaces for rehabilitation programs and research. While many systems exist, this paper will focus on three major players: Sony PlayStation Move, Nintendo Wii, and Microsoft Xbox 360 Kinect. Comparisons include the technical specifications, the motion sensed by each interface, and the motion required in each therapeutic activity type. Discussion addresses the research implications of using these tools.
A Novel Vehicle Stationary Detection Utilizing Map Matching and IMU Sensors

Precise navigation is a vital need for many modern vehicular applications. The global positioning system (GPS) cannot provide continuous navigation information in urban areas. The widely used inertial navigation system (INS) can provide full vehicle state at high rates. However, the accuracy diverges quickly in low cost microelectromechanical systems (MEMS) based INS due to bias, drift, noise, and other errors. These errors can be corrected in a stationary state. But detecting stationary state is a challenging task. A novel stationary state detection technique from the variation of acceleration, heading, and pitch and roll of an attitude heading reference system (AHRS) built from the inertial measurement unit (IMU) sensors is proposed. Besides, the map matching (MM) algorithm detects the intersections where the vehicle is likely to stop. Combining these two results, the stationary state is detected with a smaller timing window of 3 s. A longer timing window of 5 s is used when the stationary state is detected only from the AHRS. The experimental results show that the stationary state is correctly identified and the position error is reduced to 90% and outperforms previously reported work. The proposed algorithm would help to reduce INS errors and enhance the performance of the navigation system.
Classification of research papers using citation links and citation types: Towards automatic review article generation.

We are investigating automatic generation of a review (or survey) article in a specific subject domain. In a research paper, there are passages where the author describes the essence of a cited paper and the differences between the current paper and the cited paper (we call them citing areas). These passages can be considered as a kind of summary of the cited paper from the current author's viewpoint. We can know the state of the art in a specific subject domain from the collection of citing areas. FUrther, if these citing areas are properly classified and organized, they can act 8. ', a kind of a review article. In our previous research, we proposed the automatic extraction of citing areas. Then, with the information in the citing areas, we automatically identified the types of citation relationships that indicate the reasons for citation (we call them citation types). Citation types offer a useful clue for organizing citing areas. In addition, to support writing a review article, it is necessary to take account of the contents of the papers together with the citation links and citation types. In this paper, we propose several methods for classifying papers automatically. We found that our proposed methods BCCT-C, the bibliographic coupling considering only type C citations, which pointed out the problems or gaps in related works, are more effective than others. We also implemented a prototype system to support writing a review article, which is based on our proposed method.
Downscaling temperature and precipitation using support vector regression with evolutionary strategy

In this work, we propose a hybrid algorithm combining support vector regression with evolutionary strategy (SVR-ES) in order to build successful predictive models for downscaling problems. SVR-ES uses uncorrelated mutation with p step sizes to find the optimal SVR hyper-parameters. Two downscaling forecast problems used in the WCCI-2006 contest - surface air temperature and precipitation - were tested. We used multiple linear regression (MLR) as benchmark and a variety of machine learning techniques including bootstrap-aggregated ensemble artificial neural network (ANN), SVR with hyper-parameters given by the Cherkassky-Ma estimate and random forest (RF). We also tested all techniques with using stepwise linear regression (SLR) first to screen out irrelevant predictors. We concluded that SVR-ES is an attractive approach because it tends to outperform the other techniques and can also be implemented in an almost automatic way. The Cherkassky-Ma estimate is a useful approach to minimizing the MAE error and also saves computational time related to the hyper-parameter search. The ANN and RF are also good options to outperform multiple linear regression (MLR). Finally, the use of SLR for predictor selection can dramatically reduce computational time and often help to enhance accuracy.
Comparison of fuzzy rule-based learning and inference systems

In our work we have compared various fuzzy rule based learning and inference systems. The base of the investigations was a modular system that we have implemented in C language. It contains several alternative versions of the two key elements of rule based learning – namely, the optimization algorithm and the inference method – which can be found in the literature. We obtained very different properties when combining these alternatives (changing the modules and connecting them) in all possible ways. The investigations determined the values of the quality measures (complexity and accuracy) of the obtained alternatives both analitically and experimentally where it was possible. Based on these quality measures the combinations have been ordered according to different aspects.
The interplay between social dominance orientation and intergroup contact in explaining support for multiculturalism

In contemporary societies, rights of ethnic and immigrant minorities are often questioned by national majorities. Indeed, majorities may strive to preserve their advantages, and frequently prefer that minorities pri‐ oritize local customs, language, and culture over their culture of origin (e.g., Verkuyten, 2006). In this research, we analyze factors underlying majorities’ support of multiculturalism, operationalized as support for a culturally diverse society where minority groups are allowed and en‐ couraged to preserve their culture, and where civic, social, and politi‐ cal rights are equal between citizens and immigrants (see Breugelmans & van de Vijver, 2004; Green & Staerklé, 2013; Verkuyten, 2006). Specifically, we examine whether social dominance orientation (SDO, Sidanius & Pratto, 1999)—an ideology which legitimizes group‐based hierarchies and inequalities—and intergroup contact with immigrants (Pettigrew & Tropp, 2006) jointly impact support for multicultural‐ ism in Switzerland. With two studies, we extend previous research in three ways. First, we focus on support for multiculturalism, instead of intergroup attitudes, as past research has mostly done. This is crucial because societies implementing multicultural policies strive for equal rights between nationals and immigrants, whereas high‐SDO indi‐ viduals generally reject intergroup equality. Second, we examine the interplay between SDO and intergroup contact in a specific, underex‐ plored intergroup context, Switzerland, where immigrants do not uni‐ vocally have lower status compared to Swiss nationals, but part of the immigrant population has high status and thus can represent a chal‐ lenge to the societal hierarchy. Third, we test the predicted effects both by measuring and experimentally manipulating intergroup contact.
Acquisition of a 3D audio-visual corpus of affective speech

Communication between humans deeply relies on our capability of experiencing, expressing, and recognizing feelings. For this reason, research on human-machine interaction needs to focus on the recognition and simulation of emotional states, prerequisite of which is the collection of affective corpora. Currently available datasets still represent a bottleneck because of the difficulties arising during the acquisition and labeling of authentic affective data. In this work, we present a new audio-visual corpus for possibly the two most important modalities used by humans to communicate their emotional states, namely speech and facial expression in the form of dense dynamic 3D face geometries. We also introduce an acquisition setup for labeling the data with very little manual effort. We acquire high-quality data by working in a controlled environment and resort to video clips to induce affective states. In order to obtain the physical prosodic parameters of each utterance, the annotation process includes: transcription of the corpus text into the phonological representation, accurate phone segmentation, fundamental frequency extraction, and signal intensity estimation of the speech signals. We employ a real-time 3D scanner for the recording of dense dynamic facial geometries and track the faces throughout the sequences, achieving full spatial and temporal correspondences. The corpus is not only relevant for affective visual speech synthesis or view-independent facial expression recognition, but also for studying the correlations between audio and facial features in the context of emotional speech.