Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphogenesis in the yeast cell cycle: regulation by Cdc28 and cyclins

Analysis of cell cycle regulation in the budding yeast Saccharomyces cerevisiae has shown that a central regulatory protein kinase, Cdc28, undergoes changes in activity through the cell cycle by associating with distinct groups of cyclins that accumulate at different times. The various cyclin/Cdc28 complexes control different aspects of cell cycle progression, including the commitment step known as START and mitosis. We found that altering the activity of Cdc28 had profound effects on morphogenesis during the yeast cell cycle. Our results suggest that activation of Cdc28 by G1 cyclins (Cln1, Cln2, or Cln3) in unbudded G1 cells triggers polarization of the cortical actin cytoskeleton to a specialized pre-bud site at one end of the cell, while activation of Cdc28 by mitotic cyclins (Clb1 or Clb2) in budded G2 cells causes depolarization of the cortical actin cytoskeleton and secretory apparatus. Inactivation of Cdc28 following cyclin destruction in mitosis triggers redistribution of cortical actin structures to the neck region for cytokinesis. In the case of pre-bud site assembly following START, we found that the actin rearrangement could be triggered by Cln/Cdc28 activation in the absence of de novo protein synthesis, suggesting that the kinase may directly phosphorylate substrates (such as actin-binding proteins) that regulate actin distribution in cells.
Action and Traction: Cytoskeletal Control of Receptor Triggering at the Immunological Synapse

It is well known that F-actin dynamics drive the micron-scale cell shape changes required for migration and immunological synapse (IS) formation. In addition, recent evidence points to a more intimate role for the actin cytoskeleton in promoting T cell activation. Mechanotransduction, the conversion of mechanical input into intracellular biochemical changes, is thought to play a critical role in several aspects of immunoreceptor triggering and downstream signal transduction. Multiple molecules associated with signaling events at the IS have been shown to respond to physical force, including the TCR, costimulatory molecules, adhesion molecules, and several downstream adapters. In at least some cases, it is clear that the relevant forces are exerted by dynamics of the T cell actomyosin cytoskeleton. Interestingly, there is evidence that the cytoskeleton of the antigen-presenting cell also plays an active role in T cell activation, by countering the molecular forces exerted by the T cell at the IS. Since actin polymerization is itself driven by TCR and costimulatory signaling pathways, a complex relationship exists between actin dynamics and receptor activation. This review will focus on recent advances in our understanding of the mechanosensitive aspects of T cell activation, paying specific attention to how F-actin-directed forces applied from both sides of the IS fit into current models of receptor triggering and activation.
Echocardiographic evaluation during weaning from mechanical ventilation

INTRODUCTION: Echocardiographic, electrocardiographic and other cardiorespiratory variables can change during weaning from mechanical ventilation. OBJECTIVES: To analyze changes in cardiac function, using Doppler echocardiogram, in critical patients during weaning from mechanical ventilation, using two different weaning methods: pressure support ventilation and T‐tube; and comparing patient subgroups: success vs. failure in weaning. METHODS: Randomized crossover clinical trial including patients under mechanical ventilation for more than 48 h and considered ready for weaning. Cardiorespiratory variables, oxygenation, electrocardiogram and Doppler echocardiogram findings were analyzed at baseline and after 30 min in pressure support ventilation and T‐tube. Pressure support ventilation vs. T‐tube and weaning success vs. failure were compared using ANOVA and Student's t‐test. The level of significance was p<0.05. RESULTS: Twenty‐four adult patients were evaluated. Seven patients failed at the first weaning attempt. No echocardiographic or electrocardiographic differences were observed between pressure support ventilation and T‐tube. Weaning failure patients presented increases in left atrium, intraventricular septum thickness, posterior wall thickness and diameter of left ventricle and shorter isovolumetric relaxation time. Successfully weaned patients had higher levels of oxygenation. CONCLUSION: No differences were observed between Doppler echocardiographic variables and electrocardiographic and other cardiorespiratory variables during pressure support ventilation and T‐tube. However cardiac structures were smaller, isovolumetric relaxation time was larger, and oxygenation level was greater in successfully weaned patients.
Tycoon: A Market-Based Resource Allocation System

P2P clusters like the Grid and PlanetLab enable in principle the same statistical multiplexing efficiency gains for computing as the Internet provides for networking. The key unsolved problem is resource allocation. Existing solutions are not economically efficient and require high latency to acquire resources. We designed and implemented Tycoon, a market based distributed resource allocation system based on an Auction Share scheduling algorithm. Preliminary results show that Tycoon achieves low latency and high fairness while providing incentives for truth-telling on the part of strategic users .
High Levels of IL-10 and CD4+CD25hi+ Treg Cells in Endemic Burkitt’s Lymphoma Patients

Background: The interplay between Epstein-Barr virus infection, malaria, and endemic Burkitt’s Lymphoma is not well understood. Reports show diminished EBV-specific Th1 responses in children living in malaria endemic areas and deficiency of EBNA1-specific IFN-γ T cell responses in children with endemic Burkitt’s Lymphoma (eBL). This study, therefore, examined some factors involved in the loss of EBNA-1-specific T cell responses in eBL. Methods: T-cell subset frequencies, activation, and IFN-γ- or IL-4-specific responses were analyzed by flow-cytometry. Plasma cytokine levels were measured by ELISA. Results: CD4+ and CD8+ cells in age- and sex-matched healthy controls (n = 3) expressed more IFN-γ in response to all immunostimulants than in pediatric endemic BL (eBL) patients (n = 4). In healthy controls, IFN-γ expression was higher than IL-4 expression, whereas in eBL patients the expression of IL-4 by CD4+ cells to EBNA-1 was slightly higher than IFN-γ. Moreover, the blood levels of TNF-α was significantly lower (p = 0.004) while IL-10 was significantly higher (p = 0.038), in eBL patients (n = 21) compared to controls (n = 16). Additionally, the frequency of CD4+CD25hi+ T cells was higher in both age-matched acute uncomplicated malaria (n = 26) and eBL (n = 14) patients compared to healthy controls (n = 19; p = 0.000 and p = 0.027, respectively). Conclusion: The data suggest that reduced Th1 response in eBL might be due to increased levels of IL-10 and T reg cells.
Adaptive latitudinal variation in Common Blackbird Turdus merula nest characteristics

Nest construction is taxonomically widespread, yet our understanding of adaptive intraspecific variation in nest design remains poor. Nest characteristics are expected to vary adaptively in response to predictable variation in spring temperatures over large spatial scales, yet such variation in nest design remains largely overlooked, particularly amongst open-cup-nesting birds. Here, we systematically examined the effects of latitudinal variation in spring temperatures and precipitation on the morphology, volume, composition, and insulatory properties of open-cup-nesting Common Blackbirds’ Turdus merula nests to test the hypothesis that birds living in cooler environments at more northerly latitudes would build better insulated nests than conspecifics living in warmer environments at more southerly latitudes. As spring temperatures increased with decreasing latitude, the external diameter of nests decreased. However, as nest wall thickness also decreased, there was no variation in the diameter of the internal nest cups. Only the mass of dry grasses within nests decreased with warmer temperatures at lower latitudes. The insulatory properties of nests declined with warmer temperatures at lower latitudes and nests containing greater amounts of dry grasses had higher insulatory properties. The insulatory properties of nests decreased with warmer temperatures at lower latitudes, via changes in morphology (wall thickness) and composition (dry grasses). Meanwhile, spring precipitation did not vary with latitude, and none of the nest characteristics varied with spring precipitation. This suggests that Common Blackbirds nesting at higher latitudes were building nests with thicker walls in order to counteract the cooler temperatures. We have provided evidence that the nest construction behavior of open-cup-nesting birds systematically varies in response to large-scale spatial variation in spring temperatures.
Urinary Kallikrein Excretion in Hypertension

The urinary excretion of kallikrein, an enzyme which cleaves a vasodilator kinin from kininogen substrate, was examined in hypertensive rats and hypertensive patients. Excretion of kallikrein was found to increase with age in spontaneously hypertensive (SH) rats, while levels were lower and stable in normotensive Wistar control animals. Desoxycorticosterone (DOCA)-salt hypertensive rats excreted markedly more, while renal hypertensive rats excreted significantly less kallikrein than control animals. Measurements of urinary kallikrein in patients revealed lower levels in essential hypertension than in a control population, elevated levels in pheochromocytoma and primary aldosteronism, and normal levels in cases of renal artery stenosis. These results suggest a role for the kallikrein-kinin system in abnormal elevations of blood pressure.
Prostate cancer: prediction of extracapsular extension with endorectal MR imaging and three-dimensional proton MR spectroscopic imaging.

PURPOSE To determine if the addition of three-dimensional (3D) proton magnetic resonance (MR) spectroscopic imaging to endorectal MR imaging helps diagnose extracapsular extension (ECE) of prostate cancer. MATERIALS AND METHODS Endorectal MR imaging and 3D MR spectroscopic imaging were performed in 53 patients with prostate cancer before radical prostatectomy. MR imaging studies were evaluated by two independent readers unaware of histopathologic findings. The presence of ECE was graded on a five-point scale. At 3D MR spectroscopic imaging, cancer was diagnosed if the ratio of choline plus creatine to citrate was 2 or more SDs above normal. The accuracy of MR imaging alone was compared with that of combined MR imaging and 3D MR spectroscopic imaging, with use of the step-section histopathologic results as the standard of reference. RESULTS For the less experienced reader, the addition of 3D MR spectroscopic imaging to MR imaging significantly improved accuracy (area under the receiver operating characteristic curve [Az] = 0.75 vs Az = 0.62, P < .05). For the more experienced reader, the addition improved accuracy but not significantly (Az = 0.86 vs Az = 0.78). The addition also reduced interobserver variability (Az = 0.86 vs Az = 0.75). CONCLUSION The addition of 3D MR spectroscopic imaging to MR imaging improves accuracy for less experienced readers and reduces interobserver variability in the diagnosis of ECE of prostate cancer.
Edited film alignment via selective Hough transform and accurate template matching

Edited film alignment is the post-production process of finding small parts of unedited footage that temporally and spatially match an edited film. The huge amount of data to be processed makes significant downsampling of the videos essential in real-life applications. Simultaneously, professional users demand that the task be achieved with frame and pixel-level accuracy. We propose a novel selective Hough transform (SHT) and an accurate template matching method to address the difficult trade-off between accuracy and scalability. For robust temporal alignment, SHT investigates the selectivity of frame-level similarities and advantageously reduces the weights of mismatches. The template matching method encompasses spatial Hough transform and sum of squared differences (SSD) minimization. SSD is efficiently approximated by exploiting the second-order derivative of image intensity. Experiments conducted on real-world data show the superiority of our methods.
Critical challenges for requirement implementation in context of global software development: A systematic literature review

Context: Success of any software depends on the successful implementation of all of its Requirements. There exist a lot of challenges in successful implementation of requirement engineering (RE) process especially when we talk about global software development (GSD). Objective: The objective is to find challenges and barriers in path of RE in context of GSD and analyze the factors which influence the RE in GSD. Method: We have used systematic literature review (SLR) approach for our study. SLR is based on a planned protocol and is more thorough and systematic than ordinary literature survey Result: We have identified critical challenges like `Lack of effective communication', `Organizational change', `Lack of coordination and collaboration', `Lack of knowledge-sharing and awareness'. We have identified critical challenges like `Lack of effective communication', `Organizational change', `Lack of coordination and collaboration' which are common in both periods from 2000 to 2006 and 2007 to 2014.
Adding Aspect-Oriented Concepts to the High-Performance Component Model of SBASCO

SBASCO provides a new programming model for parallel and distributed numerical applications which exploits the combination of software components and skeletons. This paper presents an extension to both the model and implementation of SBASCO, so that the notion of aspect is applied in conjunction with the original paradigms. The objective is to achieve a higher level of modularity and reuse in parallel scientific codes and applications. Our aspects are managed as components which implement the (sequential or parallel) cross-cutting functionality. Aspects interact with the base code by means of connectors that express the cross-cutting nature of the target concerns. The way in which both aspect weaving and advice code execution are managed is critical for preserving the performance of applications. An implementation of the abstractions for distributed memory parallel systems based on MPI is discussed.
Development and Qualification of a Pharmacodynamic Model for the Pronounced Inoculum Effect of Ceftazidime against Pseudomonas aeruginosa

ABSTRACT Evidence is mounting in support of the inoculum effect (i.e., slow killing at large initial inocula [CFUo]) for numerous antimicrobials against a variety of pathogens. Our objectives were to (i) determine the impact of the CFUo of Pseudomonas aeruginosa on ceftazidime activity and (ii) to develop and validate a pharmacokinetic/pharmacodynamic (PKPD) mathematical model accommodating a range of CFUo. Time-kill experiments using ceftazidime at seven concentrations up to 128 mg/liter (MIC, 2 mg/liter) were performed in duplicate against P. aeruginosa PAO1 at five CFUo from 105 to 109 CFU/ml. Samples were collected over 24 h and fit by candidate models in NONMEM VI and S-ADAPT 1.55 (all data were comodeled). External model qualification integrated data from eight previously published studies. Ceftazidime displayed approximately 3 to 4 log10 CFU/ml net killing at 106.2 CFUo and concentrations of 4 mg/liter (or higher), less than 1.6 log10 CFU/ml killing at 107.3 CFUo, and no killing at 108.0 CFUo for concentrations up to 128 mg/liter. The proposed mechanism-based model successfully described the inoculum effect and the concentration-independent lag time of killing. The mean generation time was 28.3 min. The effect of an autolysin was assumed to inhibit successful replication. Ceftazidime concentrations of 0.294 mg/liter stimulated the autolysin effect by 50%. The model was predictive in the internal cross-validation and had excellent in silico predictive performance for published studies of P. aeruginosa ATCC 27853 for various CFUo. The proposed PKPD model successfully described and predicted the pronounced inoculum effect of ceftazidime in vitro and integrated data from eight literature studies to support translation from time-kill experiments to in vitro infection models.
Locally Learning Biomedical Data Using Diffusion Frames

Diffusion geometry techniques are useful to classify patterns and visualize high-dimensional datasets. Building upon ideas from diffusion geometry, we outline our mathematical foundations for learning a function on high-dimension biomedical data in a local fashion from training data. Our approach is based on a localized summation kernel, and we verify the computational performance by means of exact approximation rates. After these theoretical results, we apply our scheme to learn early disease stages in standard and new biomedical datasets.
25 years of Bayesian methods in the pharmaceutical industry: a personal, statistical bummel

Twenty‐five years ago the use of Bayesian methods in Pharmaceutical R&D was non‐existent. Today that is no longer true. In this paper I describe my own personal journey along the road of discovery of Bayesian methods to routine use in the pharmaceutical industry. Copyright © 2007 John Wiley & Sons, Ltd.
Iterative channel estimation and turbo equalization for time-varying channels in a coded OFDM-LTE system for 16-QAM and 64-QAM

The main targets for the next generation of mobile communication systems, with LTE as a main candidate, are increased data rates and improved spectrum efficiency. The transmission scheme for the LTE downlink is OFDM which enables the design of low complexity and high performance receivers, if the channel is time-invariant. However in high-mobility scenarios, where the channel is time-variant, the receiver design is more challenging. Therefore in this paper the turbo equalizer presented in [1] is extended to 16-QAM and 64-QAM to compensate the effect of the time-varying channel. Furthermore an iterative pilot-assisted channel estimator based on DPS-BEM is presented. BER performance of the LTE downlink for the ITU Vehicular A channel shows that the improvement due to iterative processing is substantial.
The expression and impact of antifungal grooming in ants

Parasites can cause extensive damage to animal societies in which many related individuals frequently interact. In response, social animals have evolved diverse individual and collective defences. Here, we measured the expression and efficiency of self‐grooming and allo‐grooming when workers of the ant Formica selysi were contaminated with spores of the fungal entomopathogen Metarhizium anisopliae. The amount of self‐grooming increased in the presence of fungal spores, which shows that the ants are able to detect the risk of infection. In contrast, the amount of allo‐grooming did not depend on fungal contamination. Workers groomed all nestmate workers that were re‐introduced into their groups. The amount of allo‐grooming towards noncontaminated individuals was higher when the group had been previously exposed to the pathogen. Allo‐grooming decreased the number of fungal spores on the surface of contaminated workers, but did not prevent infection in the conditions tested (high dose of spores and late allo‐grooming). The rate of disease transmission to groomers and other nestmates was extremely low. The systematic allo‐grooming of all individuals returning to the colony, be they contaminated or not, is probably a simple but robust prophylactic defence preventing the spread of fungal diseases in insect societies.
Performance Evaluation of Smoothing Algorithms for Transmitting Prerecorded Variable-Bit-Rate Video

The transfer of prerecorded, compressed variable-bit-rate video requires multimedia services to support large fluctuations in bandwidth requirements on multiple time scales. Bandwidth smoothing techniques can reduce the burstiness of a variable-bit-rate stream by transmitting data at a series of fixed rates, simplifying the allocation of resources in video servers and the communication network. This paper compares the transmission schedules generated by the various smoothing algorithms, based on a collection of metrics that relate directly to the server, network, and client resources necessary for the transmission, transport, and playback of prerecorded video. Using MPEG-1 and MJPEG video data and a range of client buffer sizes, we investigate the interplay between the performance metrics and the smoothing algorithms. The results highlight the unique strengths and weaknesses of each bandwidth smoothing algorithm, as well as the characteristics of a diverse set of video clips.
Maximal Data Piling in Discrimination

In a binary discrimination problem, a linear classifier finds a linear hyperplane that separates two classes by partitioning the data space. Especially in a High Dimension Low Sample Size (HDLSS) setting, there are linear separating hyperplanes such that the projections of the training data points onto their normal direction vectors are identically zero, or some non-zero constant. Of interest in this paper is a linear separating hyperplane such that the projections of the training data points from each class onto its normal direction vector have two distinct values, one for each class. This direction vector is uniquely defined in the subspace generated by the data. A simple formula is given to find this direction. In non-HDLSS settings, this direction vector is the same as the Fisher Linear Discrimination direction vector.
Amygdala damage eliminates monetary loss aversion

Losses are a possibility in many risky decisions, and organisms have evolved mechanisms to evaluate and avoid them. Laboratory and field evidence suggests that people often avoid risks with losses even when they might earn a substantially larger gain, a behavioral preference termed “loss aversion. ” The cautionary brake on behavior known to rely on the amygdala is a plausible candidate mechanism for loss aversion, yet evidence for this idea has so far not been found. We studied two rare individuals with focal bilateral amygdala lesions using a series of experimental economics tasks. To measure individual sensitivity to financial losses we asked participants to play a variety of monetary gambles with possible gains and losses. Although both participants retained a normal ability to respond to changes in the gambles’ expected value and risk, they showed a dramatic reduction in loss aversion compared to matched controls. The findings suggest that the amygdala plays a key role in generating loss aversion by inhibiting actions with potentially deleterious outcomes.