Miracle-dz/UniFAR-FTUs huggingface dataset:
Multigene Phylogeny of Choanozoa and the Origin of Animals

Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.
EM algorithms of Gaussian mixture model and hidden Markov model

The HMM (hidden Markov model) is a probabilistic model of the joint probability of a collection of random variables with both observations and states. The GMM (Gaussian mixture model) is a finite mixture probability distribution model. Although the two models have a close relationship, they are always discussed independently and separately. The EM (expectation-maximum) algorithm is a general method to improve the descent algorithm for finding the maximum likelihood estimation. The EM of HMM and the EM of GMM have similar formulae. Two points are proposed in this paper. One is that the EM of GMM can be regarded as a special EM of HMM. The other is that the EM algorithm of GMM based on symbols is faster in implementation than the EM algorithm of GMM based on samples (or on observation) traditionally.
C-reactive Protein and Vein Graft Disease : Evidence for a Direct Effect on Smooth Muscle Cell Phenotype via modulation of PDGF receptor -

Plasma C-reactive protein (CRP) concentration is a biomarker of systemic atherosclerosis and may also be associated with vein graft disease. It remains unclear if CRP is also an important modulator of biologic events in the vessel wall. We hypothesized that CRP influences vein graft healing by stimulating smooth muscle cells (SMCs) to undergo a phenotypic switch. Distribution of CRP was examined by immunohistochemistry in pre-bypass human saphenous veins (HSVs) (n=21) and failing vein grafts (n=18, 25-4400 days postop). Quiescent HSVSMCs were stimulated with human CRP (5-50 gm/L). SMC migration was assessed in modified Boyden chambers with platelet derived growth factor BB (PDGF-BB; 5-10 ng/mL) as the chemoattractant. SMC viability and proliferation were assessed by trypan blue exclusion and reduction of Alamar Blue substrate, respectively. Expression of PDGF ligand and receptor (PDGFR) genes was examined at RNA and protein levels after 24-72h of CRP exposure. CRP staining was present in 13 of 18 diseased vein grafts where it localized to the deep media and adventitia, but it was minimally detectable in most pre-bypass veins. SMCs pre-treated with CRP demonstrated a dose-dependent increase in migration to PDGF-BB (p=.02), which was inhibited by a PDGF neutralizing antibody. SMCs treated with CRP showed a dose-dependent increase in PDGFRexpression and phosphorylation after 24-48h. Exogenous CRP had no effect on SMC viability or proliferation. These data suggest that CRP is detectable within the wall of most diseased vein grafts, where it may exert local effects. Clinically relevant levels of CRP can stimulate SMC migration by a mechanism that may involve upregulation and activation of PDGFR.
BDNF Promotes EGF-Induced Proliferation and Migration of Human Fetal Neural Stem/Progenitor Cells via the PI3K/Akt Pathwa

Neurogenesis is a complex process, which contributes to the ability of the adult brain to function normally and adapt to diseases. Epidermal growth factor (EGF) is known to play an important role in neurogenesis; however, the underlying mechanism is still unclear. Here, we hypothesized that brain-derived neurotrophic factor (BDNF) can enhance the effect of EGF on neurogenesis. Using in vitro cell culture of aborted human fetal brain tissues, we investigated proliferation and migration of neural stem/progenitor cells (NSPCs) after treatment with EGF and different concentrations of BDNF. EGF stimulated proliferation and migration of NSPCs, and this effect was significantly enhanced by co-incubation with BDNF. In the NSPCs treated with 50 ng/mL BDNF, BrdU incorporation was significantly increased (from 7.91% to 17.07%), as compared with that in the control. Moreover, the number of migrating cells was at least 2-fold higher than that in the control. Furthermore, phosphorylation of Akt-1 was increased by BDNF treatment, as well. By contrast, the enhancing effect of BDNF on EGF-induced proliferation and migration of NSPCs were abolished by an inhibitor of PI3K, LY294002. These findings suggest that BDNF promotes EGF-induced proliferation and migration of NSPC through the PI3K/Akt pathway, providing significant insights into not only the mechanism underlying EGF-induced neurogenesis but also potential neuronal replacement strategies to treat brain damage.
Automated Tracking of the Carotid Artery in Ultrasound Image Sequences Using a Self Organizing Neural Network

An automated method for the segmentation and tracking of moving vessel walls in 2D ultrasound image sequences is introduced. The method was tested on simulated and real ultrasound image sequences of the carotid artery. Tracking was achieved via a self organizing neural network known as Growing Neural Gas. This topology-preserving algorithm assigns a net of nodes connected by edges that distributes itself within the vessel walls and adapts to changes in topology with time. The movement of the nodes was analyzed to uncover the dynamics of the vessel wall. By this way, radial and longitudinal strain and strain rates have been estimated. Finally, wave intensity signals were computed from these measurements. The method proposed improves upon wave intensity wall analysis, WIWA, and opens up a possibility for easy and efficient analysis and diagnosis of vascular disease through noninvasive ultrasonic examination.
High Order Finite Volume Schemes for Numerical Solution of 2D and 3D Transonic Flows

The aim of this article is a qualitative analysis of two modern finite volume (FVM) schemes. First one is the so called Modified Causon's scheme, which is based on the classical MacCormack FVM scheme in total variation diminishing (TVD) form, but is simplified in such a way that the demands on computational power are much smaller without loss of accuracy. Second one is implicit WLSQR (Weighted Least Square Reconstruction) scheme combined with various types of numerical fluxes (AUSMPW+ and HLLC). Two different test cases were chosen for the comparison $-1$) two-dimensional transonic inviscid nonstationary flow over an oscillating NACA 0012 profile and 2) three-dimensional transonic inviscid stationary flow around the Onera M6 wing. Nonstationary effects were simulated with the use of Arbitrary Lagrangian–Eulerian Method (ALE). Experimental results for these regimes of flow are easily available and so the numerical results are compared both in-between and with experimental data. The obtained numerical results in all considered cases (2D and 3D) are in a good agreement with experimental data.
Dealing with Data Association in Visual SLAM

This chapter presents a stereo vision application to Mobile Robotics. In particular we deal with the problem of simultaneous localization and mapping (SLAM) (Dissanayake et al., 2001; Montemerlo et al., 2002) and propose a stereo vision-based technique to solve it (Gil et al., 2006). The problem of SLAM is of paramount importance in the mobile robotics community, since it copes with the problem of incrementally building a map of the environment while simultaneously localizing the robot within this map. Building a map of the environment is a fundamental task for autonomous mobile robots, since the maps are required for different higher level tasks, such as path planning or exploration. It is certainly an ability necessary to achieve a true autonomous operation of the robot. In consequence, this problem has received significant attention in the past two decades. The SLAM problem is inherently a hard problem, because noise in the estimate of the robot pose leads to noise in the estimate of the map and viceversa. The approach presented here is feature based, since it concentrates on a number of points extracted from images in the environment which are used as visual landmarks. The map is formed by the 3D position of these landmarks, referred to a common reference frame. The visual landmarks are extracted by means of the Scale Invariant Feature Transform (SIFT) (Lowe, 2004). A rejection technique is applied in order to concentrate on a reduced set of highly distinguishable, stable features. The SIFT transform detects distinctive points in images by means of a difference of gaussian function (DoG) applied in scale space. Next, a descriptor is computed for each detected point, based on local image information at the characteristic scale (Lowe, 2004). We track detected SIFT features along consecutive frames obtained by a stereo camera and select only those features that appear to be stable from different views. Whenever a feature is selected, we compute a more representative feature model given the previous observations. This model allows to improve the Data Association within the landmarks in the map and, in addition, permits to reduce the number of landmarks that need to be maintained in the map. The visual SLAM approach is applied within a Rao-Blackwellized particle filter (Montemerlo et al., 2002; Grisetti et al., 2005). In this chapter we propose two relevant contributions to the visual SLAM solution. First, we present a new mechanism to deal with the data association problem for the case of visual landmarks. Second, our approach actively tracks landmarks prior to its integration in the map. As a result, we concentrate on a small set of stable landmarks and incorporate them in the map. With this approach, our map typically consists of a reduced number of landmarks O pe n A cc es s D at ab as e w w w . ite ch on lin e. co m
Mitogen-activated protein kinase kinase 1/2 inhibitors and 17-allylamino-17-demethoxygeldanamycin synergize to kill human gastrointestinal tumor cells in vitro via suppression of c-FLIP-s levels and activation of CD95

Prior studies have noted that inhibitors of mitogen-activated protein kinase (MAPK) kinase 1/2 (MEK1/2) enhanced geldanamycin lethality in malignant hematopoietic cells by promoting mitochondrial dysfunction. The present studies focused on defining the mechanism(s) by which these agents altered survival in carcinoma cells. MEK1/2 inhibitors [PD184352; AZD6244 (ARRY-142886)] interacted in a synergistic manner with geldanamycins [17-allylamino-17-demethoxygeldanamycin (17AAG) and 17-dimethylaminoethylamino-17-demethoxy-geldanamycin] to kill hepatoma and pancreatic carcinoma cells that correlated with inactivation of extracellular signal-regulated kinase 1/2 and AKT and with activation of p38 MAPK; p38 MAPK activation was reactive oxygen species dependent. Treatment of cells with MEK1/2 inhibitors and 17AAG reduced expression of c-FLIP-s that was mechanistically connected to loss of MEK1/2 and AKT function; inhibition of caspase-8 or overexpression of c-FLIP-s abolished cell killing by MEK1/2 inhibitors and 17AAG. Treatment of cells with MEK1/2 inhibitors and 17AAG caused a p38 MAPK-dependent plasma membrane clustering of CD95 without altering the levels or cleavage of FAS ligand. In parallel, treatment of cells with MEK1/2 inhibitors and 17AAG caused a p38 MAPK-dependent association of caspase-8 with CD95. Inhibition of p38 MAPK or knockdown of BID, FAS-associated death domain, or CD95 expression suppressed MEK1/2 inhibitor and 17AAG lethality. Similar correlative data were obtained using a xenograft flank tumor model system. Our data show that treatment of tumor cells with MEK1/2 inhibitors and 17AAG induces activation of the extrinsic pathway and that suppression of c-FLIP-s expression is crucial in transduction of the apoptotic signal from CD95 to promote cell death. [Mol Cancer Ther 2008;7(9):2633–48]
On the Origin of Magnetospheric Line Radiation

We present a short overview of results obtained by a systematic survey of line radiation events observed by the DEMETER spacecraft at an altitude of 700 km. We find two different classes of events that can be easily distinguished by the observed frequency separation of lines forming the event - if it is 50/100 Hz or 60/120 Hz then the event is most probably caused by electromagnetic radiation from the electric power systems on the ground (Power Line Harmonic Radiation, PLHR). Other frequency separations correspond to waves generated in a completely natural way (real-Magnetospheric Line Radiation, real-MLR). We show supporting evidence and we estimate possible source locations of both PLHR and real-MLR events. We show that the source locations of PLHR with 50/100 Hz spacing lie mostly in Europe and that the source locations of PLHR with 60/120 Hz lie mostly in the United States and Japan. The generation region of real-MLR events is most probably located in or very close to the geomagnetic equator at radial distances between 1.5 and 3 Earth radii.
The gaia -ESO survey : Calibration strategy

The Gaia -ESO survey (GES) is now in its fifth and last year of observations and has produced tens of thousands of high-quality spectra of stars in all Milky Way components. This paper presents the strategy behind the selection of astrophysical calibration targets, ensuring that all GES results on radial velocities, atmospheric parameters, and chemical abundance ratios will be both internally consistent and easily comparable with other literature results, especially from other large spectroscopic surveys and from Gaia . The calibration of GES is particularly delicate because of (i) the large space of parameters covered by its targets, ranging from dwarfs to giants, from O to M stars; these targets have a large wide of metallicities and also include fast rotators, emission line objects, and stars affected by veiling; (ii) the variety of observing setups, with different wavelength ranges and resolution; and (iii) the choice of analyzing the data with many different state-of-the-art methods, each stronger in a different region of the parameter space, which ensures a better understanding of systematic uncertainties. An overview of the GES calibration and homogenization strategy is also given, along with some examples of the usage and results of calibrators in GES iDR4, which is the fourth internal GES data release and will form the basis of the next GES public data release. The agreement between GES iDR4 recommended values and reference values for the calibrating objects are very satisfactory. The average offsets and spreads are generally compatible with the GES measurement errors, which in iDR4 data already meet the requirements set by the main GES scientific goals.
A Theory of the Emergence, Persistence, and Expression of Geographic Variation in Psychological Characteristics

Volumes of research show that people in different geographic regions differ psychologically. Most of that work converges on the conclusion that there are geographic differences in personality and values, but little attention has been paid to developing an integrative account of how those differences emerge, persist, and become expressed at the geographic level. Drawing from research in psychology and other social sciences, we present a theoretical account of the mechanisms through which geographic variation in psychological characteristics emerge and persist within regions, and we propose a model for conceptualizing the processes through which such characteristics become expressed in geographic social indicators. The proposed processes were examined in the context of theory and research on personality traits. Hypotheses derived from the model were tested using personality data from over half a million U.S. residents. Results provided preliminary support for the model, revealing clear patterns of regional variation across the U.S. and strong relationships between state-level personality and geographic indicators of crime, social capital, religiosity, political values, employment, and health. Overall, this work highlights the potential insights generated by including macrolevel perspectives within psychology and suggests new routes to bridging theory and research across several disciplines in the social sciences.
EARLY DIAGNOSIS OF PARKINSON'S DISEASE: LET THE PATIENT TELL YOU *

Parkinson’s disease (PD) is diagnosed primarily with a “low-tech” approach of listening (patient history) and observing (neurological examination), and in some cases watchful waiting over several years. Diagnosing idiopathic PD can be challenging due to its insidious onset, lack of pathognomonic signs or symptoms, and especially the lack of laboratory or imaging tests that confirm the diagnosis (a disease “marker”). Although historically considered to be a pure movement disorder, PD is now being recognized as a neuropsychiatric disorder with many non-motor symptoms that can predate motor symptoms and can be equally disabling. Depression is one of the most common non-motor PD symptoms. Early in the disease, there are many non-medical therapies that help to improve motor function, independence, and quality of life. Using extracts from an interview with a patient, who describes her early signs and symptoms and the diagnostic process from her point of view, this article discusses early diagnosis of PD, particularly with regard to patient history and non-motor features of PD. Currently available diagnostic tools, non-medical treatments of PD, and PD pathology are also discussed. Through their responses during a clinic visit, patients tell us what we need to know to diagnose PD and to decide what treatment will work best for them as individuals. (Adv Stud Med. 2008;8(12):413-418)
Virtual Batching: A New Scheduling Technique for Video-on-Demand Servers

In a video-on-demand (VOD) environment, batch-ing of requests is often applied to reduce the I/O demand and increase the availability of VOD services. This scheme, however, unfairly forces rst comers to wait for subscribers arriving late at the batch. Some of these victims may become impatient and decide to renege. To address this issue, we introduce a chaining technique which allows a client station being served to forward its video data to other client stations, which requested the same video, at a slightly later time. The forwarding of data is done using the same store-and-forward mechanism of the multicast facility used in batching. With this new feature, requests arriving at a chain can be served immediately; yet they are allowed to share a single video stream. Thus, chaining enjoys the beneet of batching without its side eeect of causing long access latencies. By combining batching and chaining , we also design a scheme called Virtual Batch-ing. It extends the standard chaining mechanism to allow a client station on a chain to multicast video data to other client stations which are admitted as a batch. Our simulation results indicate that this hybrid approach ooers signiicant performance improvement.
Internationalization of the Academic Profession: An Exploratory Study of Faculty Attitudes, Beliefs and Involvement at Public Universities in Pennsylvania

This study investigates the attitudes, beliefs, experiences and involvement related to internationalization by faculty members at a group of universities in the United States. Internationalization of higher education is defined as the process of integrating an international or intercultural dimension into the teaching, research and service functions of an institution (Knight, 2004). The definition is placed within a conceptual framework of rationales, stakeholders, and approaches to internationalization (Knight, 1999). Data collected from faculty at nine public universities in Pennsylvania (n = 829) were used to provide a descriptive and correlational analysis that: explores faculty attitudes, beliefs and experiences; reviews the extent to which faculty incorporate an international perspective into their teaching, research, and scholarship; determines what relationships exist between faculty characteristics, campus climate, and attitudes, beliefs and behaviors; and examines patterns that are used to describe or predict faculty members' orientation to internationalization (Morris 1996). Data were collected using a survey instrument accessed over the internet (Best & Krueger, 2004; Dillman, 2000). Data were analyzed by faculty characteristics and by research variables, including: international experiences at different educational stages, assessment of campus climate, faculty involvement in internationalization, and attitudes and beliefs about internationalization. The data show that important differences exist by gender, discipline, teaching responsibilities, tenure status, rank, and teaching/research preference. The research shows that faculty with higher levels of international experiences at different educational stages have higher levels of involvement in internationalization as faculty members, and that they also have more favorable attitudes and beliefs about internationalization. Furthermore, faculty with more favorable attitudes and beliefs about internationalization are likely to have higher levels of involvement in internationalization, although the strength of the relationship varies according to the three attitudes and beliefs factors identified in the factor analysis. A definition for the construct of an Orientation to Internationalization is provided. Several of the research findings replicate findings from the Carnegie Foundation for the Profession of Teaching's Study of the International Academic Profession (Altbach, 1996). Policy implications are provided for different sectors interested in internationalizing higher education. Recommendations on internationalizing the faculty are provided, as are suggestions for future research.