Miracle-dz/UniFAR-FTUs huggingface dataset:
An analysis of the role of the target membrane on the Gp64-induced fusion pore.

Influenza hemagglutinin (HA) and GP64 of the baculovirus Autographa californica multicapsid nuclear polyhedrosis virus induce strikingly different initial fusion pores when mediating fusion between host cells that express these fusion proteins and target cells (Plonsky and Zimmerberg, 1996; Spruce et al., 1989, 1991; Zimmerberg et al., 1994). However, in these experiments, variations in host and target membranes confounded the analysis of the role that major components of the fusion reaction play in determining initial pore characteristics. To determine the contribution of the target cell plasma membrane to the fusion pore phenotype, we studied GP64-induced fusion of stably transfected cells (Sf9(Op1D)) to either red blood cells (RBCs) or Sf9 cells. Initial fusion pores in Sf9(Op1D)/RBC and Sf9(Op1D)/Sf9 cell pairs exhibited the same conductance, and pore flickering was not observed in either combination of cells. This indicates that the target cell determines neither the size nor the reversibility of the initial pore. However, the target cell does influence the kinetics of pore formation. The waiting time between triggering and pore appearance was shorter for Sf9(Op1D)/RBC fusion than for Sf9(Op1D)/Sf9 pairs. No correlation between pore waiting time and conductance was found. This argues against a molecular model that assumes aggregation of the pore wall from a nonfixed number of components as the rate-limiting step in GP64 fusion pore formation.
Petrologic determination of ascent rates for the 1995–1997 Soufriere Hills Volcano andesitic magma

The recent eruption of the Soufriere Hills Volcano in Montserrat (July, 1995, to present; October, 1997) has produced a hornblende‐bearing, andesitic lava dome. It is possible to petrologically estimate changes in ascent rates of amphibole‐bearing magmas. For certain rates of decompression, a breakdown rim of fine‐grained, anhydrous reaction products forms where amphibole is in contact with melt. The thickness of the rim varies with ascent rate. Most of the amphibole phenocrysts in the magma storage region lack breakdown rims. About 10% have 200–400 µm‐thick, coarse‐grained breakdown rims that are interpreted to be relicts of a past heating event. Study of a time series of new dome andesites showed that ascent rate increased from December, 1995 (∼0.001 m/s), to July, 1996 (∼0.008 m/s), while eruptive style remained extrusive. Ascent rate increased to >0.012 m/s in August, 1996, and the first major explosive eruption occurred on 17–18 September, 1996.
Hybrid Deterministic/Monte Carlo Neutronics

In this paper we describe a hybrid deterministic/Monte Carlo algorithm for neutron transport simulation. The algorithm is based on nonlinear accelerators for source iteration, using Monte Carlo methods for the purely absorbing high-order problem and a Jacobian-free Newton--Krylov iteration for the low-order problem. We couple the Monte Carlo solution with the low-order problem using filtering to smooth the flux and current from the Monte Carlo solver and an analytic Jacobian-vector product to avoid numerical differentiation of the Monte Carlo results. We use a continuous energy deposition tally for the Monte Carlo simulation. We conclude the paper with numerical results which illustrate the effectiveness of the new algorithm.
Nonlinear filtering with signal dependent observation noise

The paper studies the filtering problem for a non-classical frame- work: we assume that the observation equation is driven by a signal dependent noise. We show that the support of the conditional distri- bution of the signal is on the corresponding level set of the derivative of the quadratic variation process. Depending on the intrinsic dimension of the noise, we distinguish two cases: In the first case, the conditional distribution has discrete support and we deduce an explicit represen- tation for the conditional distribution. In the second case, the filtering problem is equivalent to a classical one defined on a manifold and we deduce the evolution equation of the conditional distribution. The re- sults are applied to the filtering problem where the observation noise is an Ornstein-Uhlenbeck process.
Towards Scalable Representations of Object Categories: Learning a Hierarchy of Parts

This paper proposes a novel approach to constructing a hierarchical representation of visual input that aims to enable recognition and detection of a large number of object categories. Inspired by the principles of efficient indexing (bottom-up,), robust matching (top-down,), and ideas of compositionality, our approach learns a hierarchy of spatially flexible compositions, i.e. parts, in an unsupervised, statistics-driven manner. Starting with simple, frequent features, we learn the statistically most significant compositions (parts composed of parts), which consequently define the next layer. Parts are learned sequentially, layer after layer, optimally adjusting to the visual data. Lower layers are learned in a category-independent way to obtain complex, yet sharable visual building blocks, which is a crucial step towards a scalable representation. Higher layers of the hierarchy, on the other hand, are constructed by using specific categories, achieving a category representation with a small number of highly generalizable parts that gained their structural flexibility through composition within the hierarchy. Built in this way, new categories can be efficiently and continuously added to the system by adding a small number of parts only in the higher layers. The approach is demonstrated on a large collection of images and a variety of object categories. Detection results confirm the effectiveness and robustness of the learned parts.
Effect of Hyperoxia and Hypercapnia on Tissue Oxygen and Perfusion Response in the Normal Liver and Kidney

Objective Inhalation of air with altered levels of oxygen and carbon dioxide to manipulate tissue oxygenation and perfusion has both therapeutic and diagnostic value. These physiological responses can be measured non-invasively with magnetic resonance (MR) relaxation times. However, interpreting MR measurements is not straight-forward in extra-cranial organs where gas challenge studies have only begun to emerge. Inconsistent results have been reported on MR, likely because different organs respond differently. The objective of this study was to elucidate organ-specific physiological responses to gas challenge underlying MR measurements by investigating oxygenation and perfusion changes in the normal liver and kidney cortex. Materials and Methods Gas challenges (100% O2, 10% CO2, and carbogen [90% O2+10% CO2]) interleaved with room air was delivered to rabbits to investigate their effect on tissue oxygenation and perfusion. Real-time fiber-optic measurements of absolute oxygen and relative blood flow were made in the liver and kidney cortex. Results Only the liver demonstrated a vasodilatory response to CO2. Perfusion changes to other gases were minimal in both organs. Tissue oxygenation measurements showed the liver responding only when CO2 was present and the kidney only when O2 was present. Conclusion This study reveals distinct physiological response mechanisms to gas challenge in the liver and kidney. The detailed characterization of organ-specific responses is critical to improving our understanding and interpretation of MR measurements in various body organs, and will help broaden the application of MR for non-invasive studies of gas challenges.
Angular dependence of photoemission time delay in helium

Time delays of electrons emitted from an isotropic initial state with the absorption of a single photon and leaving behind an isotropic ion are angle independent. Using an interferometric method involving XUV attosecond pulse trains and an IR-probe field in combination with a detection scheme, which allows for full three-dimensional momentum resolution, we show that measured time delays between electrons liberated from the $1{s}^{2}$ spherically symmetric ground state of helium depend on the emission direction of the electrons relative to the common linear polarization axis of the ionizing XUV light and the IR-probing field. Such time delay anisotropy, for which we measure values as large as 60 as, is caused by the interplay between final quantum states with different symmetry and arises naturally whenever the photoionization process involves the exchange of more than one photon. With the support of accurate theoretical models, the angular dependence of the time delay is attributed to small phase differences that are induced in the laser-driven continuum transitions to the final states. Since most measurement techniques tracing attosecond electron dynamics involve the exchange of at least two photons, this is a general and significant effect that must be taken into account in all measurements of time delays involving photoionization processes.
The 〈 SPP 〉 Green Function and SU ( 3 ) Breaking in K l 3 Decays ∗

Using the 1/NC expansion scheme and truncating the hadronic spectrum to the lowestlying resonances, we match a meromorphic approximation to the 〈SPP 〉 Green function onto QCD by imposing the correct large-momentum falloff, both off-shell and on the relevant hadron mass shells. In this way we determine a number of chiral low-energy constants of O(p6), in particular the ones governing SU(3) breaking in the Kl3 vector form factor at zero momentum transfer. The main result of our matching procedure is that the known loop contributions largely dominate the corrections of O(p6) to f+(0). We discuss the implications of our final value fK π + (0) = 0.984±0.012 for the extraction of Vus from Kl3 decays. * Work supported in part by HPRN-CT2002-00311 (EURIDICE) and by Acciones Integradas, HU2002-0044 (MCYT, Spain), Project No. 19/2003 (Austria).
Recovery of Weak Common Factors by Maximum Likelihood and Ordinary Least Squares Estimation

This article examines the relative performance of two commonly used methods of parameter estimation in factor analysis, maximum likelihood (ML) and ordinary least squares (OLS). It is shown that ML will sometimes fail to recover a known population factor structure when OLS succeeds. A simulation study was conducted in which two types of error (model and sampling error) were introduced separately and in combination into correlation matrices generated from known population structures with at least one relatively weak major domain factor. Simulated correlation matrices were factor analyzed using both ML and OLS, and recovery of the relatively weak factor(s) was assessed. In situations with a moderate amount of error, ML often failed to recover the weak factor while OLS succeeded. It is suggested that the correspondence between the assumptions inherent in each method regarding error and the actual nature of error in the data may affect the success of recovery of weak common factors. An example using empirical data is also presented.
The promise of multi-band gravitational wave astronomy

We show that the black hole binary (BHB) coalescence rates inferred from the advanced LIGO (aLIGO) detection of GW150914 imply an unexpectedly loud GW sky at milli-Hz frequencies accessible to the evolving Laser Interferometer Space Antenna (eLISA), with several outstanding consequences. First, up to thousands of BHB will be individually resolvable by eLISA; second, millions of non resolvable BHBs will build a confusion noise detectable with signal-to-noise ratio of few to hundreds; third -- and perhaps most importantly -- up to hundreds of BHBs individually resolvable by eLISA will coalesce in the aLIGO band within ten years. eLISA observations will tell aLIGO and all electromagnetic probes weeks in advance when and where these BHB coalescences are going to occur, with uncertainties of<10s and<1deg^2. This will allow the pre-pointing of telescopes to realize coincident GW and multi-wavelength electromagnetic observations of BHB mergers. Time coincidence is critical because prompt emission associated to a BHB merger will likely have a duration comparable to the dynamical time-scale of the systems, and is only possible with low frequency GW alerts.
Power Control for Multi-antenna Gaussian Channels with Delayed Feedback

Channel feedback is delayed in all practical wireless systems. Adaptive transmission strategies need to account for this feedback delay in order to be effective. We consider multiple- input single-output systems that perform power control based on a delayed SNR estimate. For perfect channel state information at the receiver (CSIR) and delayed channel state information at the transmitter (CSIT), we derive an expression for the power control function that minimizes outage probability at a constant rate. For imperfect CSIR and delayed CSIT, we derive an upper- bound on outage probability, and an expression for the power control function that minimizes this upper-bound.
A knowledge-based development model: the research chair strategy

Purpose – The purpose of this paper is to introduce a model for the knowledge‐based development (KBD) of a region using a research chair strategy at Tecnologico de Monterrey, to describe its impact and to propose its use in organizations that generate scientific and technological knowledge, especially research groups, in a university environment.Design/methodology/approach – The approach employed in this research evolves around a strategy for setting up research chairs (research groups headed by a lead investigator) which is a type of action research methodology whose steps are: planning a research program which is clear, focused and with an impact on regional development, implementing it, observing the corresponding processes and results, and reflecting on them. The components of the KBD model include human and intellectual capital (research professors and research students), research products (journal articles, conference papers, books and patents), research funding, entrepreneurial spin‐offs emerging f.
Aiding program comprehension by static and dynamic feature analysis

Understanding a system's implementation without prior knowledge is a hard task for reengineers in general. However, some degree of automatic aid is possible. The authors present a technique for building a mapping between the system's externally visible behavior and the relevant parts of the source code. The technique combines dynamic and static analyses to rapidly focus on the system's parts urgently required for a goal-directed process of program understanding.
Effects of deficit irrigation on grain yield and some morphological traits of wheat cultivars in drought - prone conditions

This study was conducted to determine the influence of deficit irrigation on grain yield and some morphological traits of wheat cultivars. The experiment was a split plot randomized complete block design in four replications over two successive cropping seasons (2006-2008) at the Agricultural Research Station in Zahak, Iran. In the main plots were the different levels of deficit irrigation: T1= irrigation at all stages (full irrigation), T2= no irrigation before stem elongation, T3= no irrigation before flowering and T4= no irrigation before grain filling. Sampled in the sub plots were the four wheat cultivars: Hamoon, Kavir, Dez and Peethee nr2. The results of combined analysis of variance showed that the effect of irrigation in both seasons was significant on grain yield and morphological traits. The highest grain yield resulted from irrigation at all stages with a yield of 6275 kg/ha. Deficit irrigation was found to decrease grain yield by 5% at no irrigation before stem elongation, by 32% at no irrigation before flowering and by 52% at no irrigation before grain filling. Deficit irrigation affected the characteristics of; spikes/m 2 , biomass and harvest index. Grain yields were significantly different between the cultivars: Hamoon and Kavir cultivars produced the highest (5540kg/ha) and the least (4326kg/ha) grain yields, respectively. Hamoon had a higher drought tolerance therefore greater grain yield than the other cultivars in conditions of a drought-prone environment.
Performance-Based Vertical Memory Elasticity

Cloud computing offers the elasticity features by dynamically resizing the infrastructure in response to changes in workload demands to meet performance guarantees and minimize costs. In the last decade, a large body of work has been done in the area of horizontal elasticity, while only few research efforts addressed vertical elasticity. This paper develops a vertical elasticity controller for cloud-based applications using control theory principles to guarantee performance requirements by adjusting the memory allocation as a control knob. The novelty of our work lies on applying a controller synthesis technique by guaranteeing robustness and stability of the controlled system, using the application response time as a decision making criterion. The experimental results reveal that the controller is able to efficiently save at least 47% memory usage while keeping an acceptable user experience.
Evaluation of skin barrier function in allergic contact dermatitis and atopic dermatitis using method of the continuous TEWL measurement.

PURPOSE The aim of study was to determine usefulness of the method of continuous TEWL measurement in the evaluation of skin barrier function in physiological conditions and in allergic contact dermatitis (ACD) and atopic dermatitis (AD). MATERIAL AND METHODS Study was conducted on a group of 86 persons: 48 patients with allergic contact dermatitis, 18 with atopic dermatitis and 20 healthy individuals. Measurements of transepidermal water loss were made using custom-constructed device for continuous TEWL measurement. In each person the measurements of TEWL were made 4 times: measurement 0 (baseline)--before occlusion with 1% lauryl sulphate for 24 h, measurement 1-15 minutes after SLS patch removal, measurement 2-30 minutes after measurement 1 and measurement 3-30 minutes after measurement 2. Obtained data were statistically analyzed. RESULTS TEWL ratio values obtained in measurement 0 were as follows in individual groups of patients: 13.20 +/- 8.25 in the AD patients, 10.09 +/- 8.29 in ACD patients and 9.02 +/- 5.99 in control group. Analogous TEWL values in the subsequent measurements were: in measurement 1--16.08 +/- 11.17; 11.63 +/- 6.43; 17.39 +/- 12.41, in measurement 2--23.72 +/- 14.58; 14.71 +/- 6.46; 17.55 +/- 8.25, measurement 3--24.09 +/- 14.93; 16.34 +/- 6.32; 18.44 +/- 8.26. TEWL ratio values were higher in both groups of patients as compared to control group but not statistically significant (p = 0.1778). After 24 h exposition to SLS, TEWL ratio values increased in all examined groups as compared to baseline (0) measurement. All measurements, except for measurement No 1 in AD group of patients, showed statistically significant differences. The highest increase of TEWL values were observed in group of AD patients. CONCLUSIONS Delay in skin reaction to SLS in patients with atopic dermatitis provides evidence for different properties of water barrier of the skin in this group as compared to healthy individuals. Increasing tendency in TEWL values 1 hour after SLS removal might reflect persistent damage to water barrier of the skin by detergent. Method of continuous assessment of water barrier of epidermis, through the possibility of multiple measurement by TEWL in examined periods of time, decreased the risk of mistake and increased accuracy of measurement. Measurement of TEWL values allows for assessment of otherwise unnoticed damage to water barrier of the skin.
Expression and Post-Transcriptional Regulation of Maize Transposable Element MuDR and Its Derivatives

The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar. Here, we report previously unsuspected and ubiquitous MuDR homologs that produce both RNA and protein. MuDR transcript levels are proportional to MuDR copy number, and homolog transcript levels increase in active Mutator lines. A subset of homologs exhibits constitutive transcription in MuDR– and epigenetically silenced MuDR lines, suggesting independent transcriptional regulation. Surprisingly, immunodetection demonstrated nearly invariant levels of MuDR and homolog protein products in all tested Mutator and non-Mutator stocks. These results suggest a strict control over protein production, which might explain the uniform excision frequency of Mu elements. Moreover, the nonfunctional proteins encoded by homologs may negatively regulate Mutator activity and represent part of the host defense against this transposon family.
GSK3β Is Involved in the Relief of Mitochondria Pausing in a Tau-Dependent Manner

Mitochondrial trafficking deficits have been implicated in the pathogenesis of several neurological diseases, including Alzheimer's disease (AD). The Ser/Thre kinase GSK3β is believed to play a fundamental role in AD pathogenesis. Given that GSK3β substrates include Tau protein, here we studied the impact of GSK3β on mitochondrial trafficking and its dependence on Tau protein. Overexpression of GSK3β in neurons resulted in an increase in motile mitochondria, whereas a decrease in the activity of this kinase produced an increase in mitochondria pausing. These effects were dependent on Tau proteins, as Tau (-/-) neurons did not respond to distinct GSK3β levels. Furthermore, differences in GSK3β expression did not affect other parameters like mitochondria velocity or mitochondria run length. We conclude that GSK3B activity regulates mitochondrial axonal trafficking largely in a Tau-dependent manner.
GROWTH OF MAGNETIC FIELDS INDUCED BY TURBULENT MOTIONS

We present numerical simulations of driven magnetohydrodynamic (MHD) turbulence with weak/moderate imposed magnetic fields. The main goal is to clarify dynamics of magnetic field growth. We also investigate the effects of the imposed magnetic fields on the MHD turbulence, including, as a limit, the case of zero external field. Our findings are as follows. First, when we start off simulations with weak mean magnetic field only (or with small scale random field with zero imposed field), we observe that there is a stage at which magnetic energy density grows linearly with time. Runs with different numerical resolutions and/or different simulation parameters show consistent results for the growth rate at the linear stage. Second, we find that, when the strength of the external field increases, the equilibrium kinetic energy density drops by roughly the product of the rms velocity and the strength of the external field. The equilibrium magnetic energy density rises by roughly the same amount. Third, when the external magnetic field is not very strong (say, less than ∼0.2 times the rms velocity when measured in the units of Alfvén speed), the turbulence at large scales remains statistically isotropic, i.e., there is no apparent global anisotropy of order B0/v. We discuss implications of our results on astrophysical fluids.