Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain

In this study we address the problem of interpreting a bootstrap tree. The main issue is choosing the threshold of clade selection in order to separate reliable clades from unreliable ones, depending on their bootstrap proportion. This threshold depends on the chosen error measure. We investigate error measures that stem from a generalization of Robinson and Foulds’ (1981) distance, used to quantify the divergence between the true phylogeny and the estimated trees. We propose two analytical approximations of the optimum threshold of clade selection to interpret (i.e., reduce) the bootstrap tree. We performed extensive simulations along the lines of Kuhner and Felsenstein (1994) using the neighbor-joining and the maximum-parsimony methods. These simulations show that our approximations cause only small losses in quality when compared to the optimum threshold resulting from empirical observation. Next, we measured the error reduction achieved when estimating the true phylogeny by the properly reduced bootstrap tree rather than by the complete original tree, obtained with a classical tree-building method. Our simulations on short sequences show that an error reduction of 39% is achieved with the parsimony method and an error reduction of 33% is achieved with the distance method when the error is measured with the standard Robinson and Foulds distance. The observed error reduction is shown to originate from an important decrease in Type I error (wrong inferences), while Type II error (omitted correct clades) is only slightly increased. Greater error reduction is achieved when shorter sequences are used, and when more importance is given to Type I error than to Type II error. To investigate the causes of error from another point of view, we propose a general decomposition of the error expectation in two terms of bias, and one of variance. Results for these terms show that no fundamental bias is introduced by the bootstrap process, the only source of bias being structural (lack of resolution). Moreover, the variance in the estimations is greatly reduced, providing another explanation for the better results of the reduced bootstrap tree compared with the original tree estimate.
Secretome‐based proteomics reveals sulindac‐modulated proteins released from colon cancer cells

Although experiments in rodents and human population‐based studies have demonstrated the efficacy of nonsteroidal anti‐inflammatory drugs (NSAIDs) such as sulindac in colorectal cancer (CRC) prevention, a detailed knowledge of the underlying mechanism of action of this drug is limited. To better understand the chemopreventitive effects of sulindac, especially early sulindac‐induced apoptotic events, we used the CRC cell line LIM1215 as an experimental model, focusing on proteins secreted into the LIM1215 culture medium – i.e., the secretome. This subproteome comprises both soluble‐secreted proteins and exosomes (30–100 nm diameter membrane vesicles released by several cell types). Selected secretome proteins whose expression levels were dysregulated by 1 mM sulindac treatment over 16 h were analyzed using 2‐D DIGE, cytokine array, Western blotting, and MS. Overall, 150 secreted proteins were identified, many of which are implicated in molecular and cellular functions such as cell proliferation, differentiation, adhesion, invasion, angiogenesis, metastasis, and apoptosis. Our secretome‐based proteomic studies have identified several secreted modulators of sulindac‐induced apoptosis action (e.g., Mac‐2 binding protein, Alix, 14‐3‐3 isoforms, profilin‐1, calumenin/Cab45 precursors, and the angiogenic/tumor growth factors interleukin 8 (IL‐8) and growth related oncogene (GRO‐α)) that are likely to improve our understanding of the chemopreventitive action of this NSAID in CRC.
Identification by 16S ribosomal RNA gene sequencing of Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis

Aims: To identify a strain of Gram negative facultative anaerobic curved bacillus, concomitantly isolated with Escherichia coli and Streptococcus milleri, from the blood culture of a 69 year old woman with acute gangrenous appendicitis. The literature on arcobacter bacteraemia and arcobacter infections associated with appendicitis was reviewed. Methods: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR product was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence alignment. Literature review was performed by MEDLINE search (1966–2000). Results: The bacterium grew on blood agar, chocolate agar, and MacConkey agar to sizes of 1 mm in diameter after 24 hours of incubation at 37°C in 5% CO2. It grew at 15°C, 25°C, and 37°C; it also grew in a microaerophilic environment, and was cytochrome oxidase positive and motile, typically a member of the genus arcobacter. Furthermore, phenotypic testing showed that the biochemical profile of the isolate did not fit into the pattern of any of the known arcobacter species. 16S rRNA gene sequencing showed one to two base differences between the isolate and A butzleri, but 35 to 39 base differences between the isolate and A cryaerophilus, indicating that the isolate was a strain of A butzleri. Only three cases of arcobacter bacteraemia with detailed clinical characteristics were found in the English literature. The sources of the arcobacter species in the three cases were largely unknown, although the gastrointestinal tract is probably the portal of entry of the A butzleri isolated from the present case because the two concomitant isolates (E coli and S milleri) in the blood culture were common flora of the gastrointestinal tract. In addition, A butzleri has previously been isolated from the abdominal contents or peritoneal fluid of three patients with acute appendicitis. Conclusions: 16S rRNA gene sequencing was useful in the identification of the strain of A butzleri isolated from the blood culture of a patient with acute gangrenous appendicitis. Arcobacter bacteraemia is rare. Further studies using selective medium for the delineation of the association between A butzleri and acute appendicitis are warranted.
Effects of Silica and Titanium Oxide Particles on a Human Neural Stem Cell Line: Morphology, Mitochondrial Activity, and Gene Expression of Differentiation Markers

Several in vivo studies suggest that nanoparticles (smaller than 100 nm) have the ability to reach the brain tissue. Moreover, some nanoparticles can penetrate into the brains of murine fetuses through the placenta by intravenous administration to pregnant mice. However, it is not clear whether the penetrated nanoparticles affect neurogenesis or brain function. To evaluate its effects on neural stem cells, we assayed a human neural stem cell (hNSCs) line exposed in vitro to three types of silica particles (30 nm, 70 nm, and <44 μm) and two types of titanium oxide particles (80 nm and < 44 μm). Our results show that hNSCs aggregated and exhibited abnormal morphology when exposed to the particles at concentrations ≥ 0.1 mg/mL for 7 days. Moreover, all the particles affected the gene expression of Nestin (stem cell marker) and neurofilament heavy polypeptide (NF-H, neuron marker) at 0.1 mg/mL. In contrast, only 30-nm silica particles at 1.0 mg/mL significantly reduced mitochondrial activity. Notably, 30-nm silica particles exhibited acute membrane permeability at concentrations ≥62.5 μg/mL in 24 h. Although these concentrations are higher than the expected concentrations of nanoparticles in the brain from in vivo experiments in a short period, these thresholds may indicate the potential toxicity of accumulated particles for long-term usage or continuous exposure.
Wessex Head Injury Matrix and Glasgow/Glasgow-Liege Coma Scale: A Validation and Comparison Study

The Wessex Head Injury Matrix (WHIM) is an assessment tool designed for use during and immediately after coma. The aim of this study was (1) to test a French adaptation of the WHIM, (2) to compare the WHIM to the Glasgow Coma Scale (GCS) and its extension, the Glasgow-Liège Coma Scale (GLS), and (3) to confirm the sequence of emergence of behaviours. The three scales were used to assess 23 patients admitted to an intensive care unit with a GCS score equal to or less than 8 for at least 1 hour, longitudinally. Results indicated that the WHIM had good concurrent validity with the GCS and GLS, good inter-rater agreement, and excellent test-retest reliability. The WHIM is more appropriate and sensitive than the GCS and the GLS for the period of emerging from coma and immediately afterwards, whereas the GLS is more appropriate than the WHIM for the deepest phase of coma, as it also assesses brainstem reflexes. Furthermore, analysis of our data confirmed the ordering of the 66 items of the WHIM as a function of sequence of recovery from coma, as suggested by its authors.
In Vitro and in Vivo Prevention of Human CD8+ CTL‐Mediated Xenocytotoxicity by Pig c‐FLIP Expression in Porcine Endothelial Cells

Overcoming cell‐mediated immunity, especially of human CD8+ CTLs, is important for the success of xenotransplantation. Our group has previously reported that the cytotoxicity of human CD8+ CTLs against pig endothelial cells (PEC) is highly detrimental and mediated in major part by the Fas/FasL apoptotic pathway. Cellular FLICE inhibitory protein (c‐FLIP) was originally identified as an inhibitor of death‐receptor signaling through binding competition with caspase‐8 for recruitment to Fas‐associated via death domain (FADD). Two major c‐FLIP variants result from alternative mRNA splicing: a short, 26‐KDa protein (c‐FLIPS) and a long, 55‐KDa form (c‐FLIPL). The cytoprotective effects of c‐FLIPS/L in xenograft cells remain controversial. This study demonstrates that the overexpression of c‐FLIPS/L genes markedly suppress human CD8+ CTL‐mediated xenocytotoxicity and, in addition, the cytoprotective effects of c‐FLIPL appear to be significantly stronger than those of c‐FLIPS. Furthermore, to prove the prolonged effects of xenograft survival, PEC transfectants with c‐FLIPS/L genes were transplanted under rat kidney capsules. Prolonged survival was elicited from FLIPS/L transfectants, whereas parental PEC was completely rejected through day 5, posttransplant. Thus, intracellular remodeling with the overexpression of c‐FLIPS/L in xenograft cells may avoid innate cellular attacks against xenografts and facilitate long‐term xenograft survival.
Hard X-Ray Emission from Elliptical Galaxies and Its Contribution to the X-Ray Background

We explore the implications of the discovery of hard, power-law X-ray sources in the spectra of nearby elliptical galaxies for the origin of the X-ray background (XRB). The spectra of these sources are consistent with models of thermal bremsstrahlung emission from low radiative efficiency accretion flows around central supermassive black holes and are unique in that they approximately match the spectrum of the hard XRB. If such sources, with luminosities consistent with those observed in nearby elliptical galaxies, are present in most early-type galaxies, then their integrated emission may contribute significantly to the XRB. These sources may also contribute to the hard source counts detected in deep X-ray surveys.
Design of UWB Radar Receiver Based on Intersection of Frequency Spectrum

In this paper, the influence of intersection of frequency spectrum on ultra wide band (UWB) radar receiver is analyzed, corresponding to which a novel method of designing filterbank based on the minimum variance criterion in frequency domain is presented. And a specific filterbank with flat passband, narrow transient band and deep stopband attenuation is designed. When utilized in UWB radar receiver, the spectrum aliasing of the input signal can be reduced without increasing the sampling rate of A/D. Moreover, the input signal can be reconstructed perfectly in real time
Stratified Programming: Towards a New Paradigm for Software Development

This paper introduces stratified programming, a novel approach for program construction. In essence, stratified programming allows the developer to build and execute software at various levels of abstraction, each level corresponding to a program stratum that provides a specific degree of functionality. Although there is a significant amount of work reported in the scientific literature on program refinement none of this work, to the best of our knowledge, has proposed mechanisms for switching the level of software details at the execution stage or suggested the use of program strata in a larger software engineering context. This not only makes the approach described in this paper highly innovative but also opens new related research and development directions across the entire software life-cycle. To illustrate the approach we present an example focused on the coding phase of the software process. Several avenues of further investigation are also indicated and the practical benefits of stratified programming are discussed in the context of modern software construction methodologies.
Flipping in a Technological Rich Classroom

The purpose of this study was to explore eighth grade students’ perception of a flipped classroom environment. It is difficult to engage and motivate eighth grade students. This study was created in order to determine if a flipped classroom would spark more interest and therefore eventually lead to an increased ability. More specifically, this study investigated how students perceive their learning is progressing in a flipped math classroom, and how engaged are they using the technology compared to the traditional classroom setting. The classroom environment was switched to a flipped classroom at the start of a new unit in October. At the conclusion of the unit, three weeks later, a survey was administered to gauge students’ perceptions. The survey evaluated students’ perception of their learning, the time spent, use of videos and a few questions specific to the flipped classroom approach. Individual interviews were also conducted at the conclusion of the study. This approach provided students an opportunity to share their thoughts and opinions in their own words to gain a deeper understanding of their experiences. The findings of this study support the research regarding the benefits of a flipped classroom. Students in the eighth grade class felt that they were engaged and communicated more with the teacher than in the previous unit which was not flipped. Students responses to the surveys indicated that they enjoyed learning at their own pace and found the at home video learning beneficial. FLIPPING IN A TECHNOLOGICAL RICH CLASSROOM 2
Relevance and action research in leisure

Abstract In this article, I argue that action research has a critical role to play in leisure studies. Its strength lies in its ability to foster change and rejuvenate community in postindustrial society. The interdependence between people that is so vital to the welfare of the collective can be more fully realized through action research in leisure and recreation. However, there is a need for researchers to be well trained and subsequently encouraged to engage in action research so as to further the social relevance of leisure studies in both research and practice.
Assessing biodiversity loss due to land use with Life Cycle Assessment: are we there yet?

Ecosystems are under increasing pressure from human activities, with land use and land‐use change at the forefront of the drivers that provoke global and regional biodiversity loss. The first step in addressing the challenge of how to reverse the negative outlook for the coming years starts with measuring environmental loss rates and assigning responsibilities. Pinpointing the global pressures on biodiversity is a task best addressed using holistic models such as Life Cycle Assessment (LCA). LCA is the leading method for calculating cradle‐to‐grave environmental impacts of products and services; it is actively promoted by many public policies, and integrated as part of environmental information systems within private companies. LCA already deals with the potential biodiversity impacts of land use, but there are significant obstacles to overcome before its models grasp the full reach of the phenomena involved. In this review, we discuss some pressing issues that need to be addressed. LCA mainly introduces biodiversity as an endpoint category modeled as a loss in species richness due to the conversion and use of land over time and space. The functional and population effects on biodiversity are mostly absent due to the emphasis on species accumulation with limited geographic and taxonomical reach. Current land‐use modeling activities that use biodiversity indicators tend to oversimplify the real dynamics and complexity of the interactions of species among each other and with their habitats. To identify the main areas for improvement, we systematically reviewed LCA studies on land use that had findings related to global change and conservation ecology. We provide suggestion as to how to address some of the issues raised. Our overall objective was to encourage companies to monitor and take concrete steps to address the impacts of land use on biodiversity on a broader geographical scale and along increasingly globalized supply chains.
Analysis of Pattern Reversal Visual Evoked

In this study, the pattern-reversal visual evoked potentials (PRVEP's) collected from normal and demented sub- jects are investigated by applying the quadratic spline wavelet analysis. The data are decomposed into six octave frequency bands. For quantitative purposes, the wavelet coefficients in the residual waveform representing the delta-theta band activity (0-8 Hz) are explored to characterize the (N70-P100-N130) complex. Specifically, the coefficients corresponding to the location of N70, P100, and N130 peaks are investigated for their sign in order to test whether they represent a consistent (N70-P100-N130) complex in the averaged waveform. Waveforms with normal latency (N70-P100-N130) complex are observed to have positive second, negative third, and positive fourth coefficients in ampli- tude in their residual scale standing for the delta-theta (0-8 Hz) band activity. The method allows for the analysis of oscillatory- phase behavior of the normal and pathological PRVEP's in their delta-theta band based on a few quantitative measures consistent with the time-frequency occurrence of the major components of the evoked potential. (47) have used an adaptive approach to spectral analysis of pattern-reversal visual evoked potentials (PRVEP's). This was achieved with the use of "tunable" spectral windows prior to transformation. The Ia-sinh (Kaiser) window was found to be most effective when compared with the Gaussian and the cosine-taper windows. Studies on EEG and visual evoked potential (VEP) analysis are also important in the clinical diagnosis of dementia since these tests are noninvasive and inexpensive. Alzheimer's dis- ease, the most common cause of dementia, is a degenerative disease of the cerebral cortex and subcortical structures. The relative severity of the pathological changes in the associative cortex accounts for the clinical finding of diminished visual interpretation skills with normal visual acuity. Impairment of visuo-cognitive skills is commonly found in this disease, i.e., the patients may have difficulties with a variety of complex visual tasks, such as tracing a target figure embedded in a more complex figure, or identifying single letters that are presented briefly and followed by a patterned masking stimulus. EEG abnormalities are very common in Alzheimer's disease and take the form of a decrease in alpha activity with replacement by theta, and eventually delta activity (10)-(14). A more specific indicator of dementia may be the VEP. Several different studies have found that flash VEP's are abnormal while pattern VEP's are normal in patients with Alzheimer's disease. The most consistent abnormality in the flash VEP
On-line MPSoC Scheduling Considering Power Gating Induced Power/Ground Noise

Power gating induced power/ground(P/G) noise is a major reliability problem facing by low power MPSoCs using power gating techniques. Powering on and off a process unit in MPSoCs will induce large P/G noise and can cause timing divergence and even functional errors in surrounding processing units. P/G noise is different from thermal or energy which is an accumulative effect. The noise level should be predicted and victim circuits should be protected before the noise is induced. hence, the power gating-aware scheduling problem with the consideration of P/G noise should be solved using an on-line method considering the run-time variation of tasks' execution time. In this paper, we formulate an on-line task scheduling problem with the consideration of P/G noise based on our detailed P/G noise analysis platform for MPSoC. An efficient on-line Greedy Heuristic (GH) algorithm that adapts well to real-time variation is proposed to reduce noise protection penalty and improve MPSoC performance. Our experiments show that the algorithm can achieve an average 26% performance improvement together with an average 73% noise protection penalty saving compared with the conservative stop-go method. We also compare our technique with a two-step solution that computes a static schedule at compile time and make adjustment on the schedule according to runtime variations. For benchmark with larger task number, GH method achieves impressive performance improvement comparing with the two-step solution.
Genome-wide identification of Chlamydia trachomatis antigens associated with trachomatous trichiasis.

PURPOSE Chlamydia trachomatis is the leading infectious cause of blindness. The goal of the current study was to search for biomarkers associated with C. trachomatis-induced ocular pathologies. METHODS We used a whole genome scale proteome array to systematically profile antigen specificities of antibody responses to C. trachomatis infection in individuals from trachoma-endemic communities with or without end-stage trachoma (trichiasis) in The Gambia. RESULTS When 61 trichiasis patients were compared with their control counterparts for overall antibody reactivity with organisms of different chlamydial species, no statistically significant difference was found. Both groups developed significantly higher titers of antibodies against C. trachomatis ocular serovars A and B than ocular serovar C, genital serovar D, or Chlamydia psittaci, whereas the titers of anti-Chlamydia pneumoniae antibodies were the highest. When antisera from 33 trichiasis and 26 control patients (with relatively high titers of antibodies to C. trachomatis ocular serovars) were reacted with 908 C. trachomatis proteins, 447 antigens were recognized by at least 1 of the 59 antisera, and 10 antigens by 50% or more antisera, the latter being designated as immunodominant antigens. More importantly, four antigens were preferentially recognized by the trichiasis group, with antigens CT414, CT667, and CT706 collectively reacting with 30% of trichiasis antisera but none from the normal group, and antigen CT695 reacting with 61% of trichiasis but only 31% of normal antisera. On the other hand, eight antigens were preferentially recognized by the control group, with antigens CT019, CT117, CT301, CT553, CT556, CT571, and CT709 together reacting with 46% of normal antisera and none from the trichiasis group, whereas antigen CT442 reacted with 35% of normal and 19% of trichiasis antisera respectively. CONCLUSIONS The current study, by mapping immunodominant C. trachomatis antigens and identifying antigens associated with both ocular pathology and protection, has provided important information for further understanding chlamydial pathogenesis and the development of subunit vaccines.