Miracle-dz/UniFAR-FTUs huggingface dataset:
FusionFS: Toward supporting data-intensive scientific applications on extreme-scale high-performance computing systems

State-of-the-art, yet decades-old, architecture of high-performance computing systems has its compute and storage resources separated. It thus is limited for modern data-intensive scientific applications because every I/O needs to be transferred via the network between the compute and storage resources. In this paper we propose an architecture that hss a distributed storage layer local to the compute nodes. This layer is responsible for most of the I/O operations and saves extreme amounts of data movement between compute and storage resources. We have designed and implemented a system prototype of this architecture - which we call the FusionFS distributed file system - to support metadata-intensive and write-intensive operations, both of which are critical to the I/O performance of scientific applications. FusionFS has been deployed and evaluated on up to 16K compute nodes of an IBM Blue Gene/P supercomputer, showing more than an order of magnitude performance improvement over other popular file systems such as GPFS, PVFS, and HDFS.
Therapeutic Potentials of Silver Nanoparticle Complex of α-Lipoic Acid

Silver (SN) nanoparticles were re-dispersed in aqueous solution of Pluronic F127 and complexed with the antioxidant, alpha- Lipoic acid (LA). The nanoparticle - LA complex (SN-LA) was characterized using SEM. SN- LA exhibited DPPH radical scavenging activity in vitro and anti- inflammatory activity against acute and chronic paw models of edema in mice. SN-LA protected mice from whole body gamma radiation induced body weight losses and mortality revealing its radioprotecting capacity. Meanwhile, SN-LA administration to tumour- bearing mice prior to whole body gamma radiation exposure, aided in better tumour growth delay. The results suggest the feasibility in using SN-LA as a therapeutic adjuvant during cancer radiotherapy.
Comparison of three‐year clinical outcomes between sirolimus‐versus paclitaxel‐eluting stents in diabetic patients: Prospective randomized multicenter trial

Background: Three‐year follow‐up of major adverse cardiovascular event (MACE) (death, nonfatal myocardial infarction, target lesion revascularization) and the predictors of MACEs in diabetic patients after sirolimus‐eluting stent (SES) or paclitaxel‐eluting stent (PES) implantation have not been reported. Methods: Diabetic patients with de novo coronary lesions (169 patients with 190 lesions) were randomly assigned prospectively to either SES or PES. Results: Baseline characteristics were similar between the two groups. The rates of MACEs [5.9% (n = 5) in the SES vs. 9.5% (n = 8) in the PES Group, P = 0.374] and definite stent thrombosis [1.2% (n = 1) in the SES vs. 3.6% (n = 3) in the PES Group, P = 0.368] were similar in the two groups during the three‐year follow‐up. Multivariate logistic analysis showed that insulin treatment was the only independent predictor of MACE [odds ratio (OR) 8.60, 95% confidence interval (CI) 3.25–22.76, P < 0.001] and target vessel revascularization (TVR) (OR 9.50, 95% CI 3.07–29.44, P < 0.001) during the three‐year follow‐up. Conclusions: The rates of MACEs, TVR, and stent thrombosis during the three‐year follow‐up were similar in the SES and PES Groups. Insulin treatment was a main predictor of MACEs and TVR during the three‐year follow‐up after either SES or PES implantation. © 2009 Wiley‐Liss, Inc.
Surface approximation using weighted splines

The surface reconstruction problem is formulated as a two-stage reconstruction procedure. The first stage is a robust local fit to the data in a multiresolution scheme and the second is a regularized least squares fit, with the addition of an adaptive mechanism in the smoothness functional in order to make the solution well behaved. The authors present the details of the second stage in which they use the weighted bicubic spline as a surface representation in a regularization framework, with a Tikhonov stabilizer, as the smoothness norm. It is shown how the adaptive weights, in the stabilizer help the surface bend across discontinuities by varying the energy of the surface. <<ETX>>
Building carbon–carbon bonds using a biocatalytic methanol condensation cycle

Significance With the recent discoveries of large reserves of natural gas, the efficient utilization of one-carbon compounds for chemical synthesis would reduce the raw material cost for the petroleum-based chemical industry. Methanol is produced industrially from methane and is a feedstock chemical for the synthesis of higher carbon compounds. However, current chemical synthesis of higher carbon compounds from methanol requires high temperature and pressure. Natural biological pathways for methanol utilization are carbon and ATP inefficient. Here we constructed a synthetic biocatalytic pathway that allows the efficient conversion of methanol to higher-chain alcohols or other higher carbon compounds without carbon loss or ATP expenditure. The high carbon efficiency and favorable operating conditions are attractive for industrial applications. Methanol is an important intermediate in the utilization of natural gas for synthesizing other feedstock chemicals. Typically, chemical approaches for building C–C bonds from methanol require high temperature and pressure. Biological conversion of methanol to longer carbon chain compounds is feasible; however, the natural biological pathways for methanol utilization involve carbon dioxide loss or ATP expenditure. Here we demonstrated a biocatalytic pathway, termed the methanol condensation cycle (MCC), by combining the nonoxidative glycolysis with the ribulose monophosphate pathway to convert methanol to higher-chain alcohols or other acetyl-CoA derivatives using enzymatic reactions in a carbon-conserved and ATP-independent system. We investigated the robustness of MCC and identified operational regions. We confirmed that the pathway forms a catalytic cycle through 13C-carbon labeling. With a cell-free system, we demonstrated the conversion of methanol to ethanol or n-butanol. The high carbon efficiency and low operating temperature are attractive for transforming natural gas-derived methanol to longer-chain liquid fuels and other chemical derivatives.
Energy-consistent, Galerkin approach for the nonlinear dynamics of beams using intrinsic equations

The paper presents a Galerkin approach for the solution of nonlinear beam equations. The approach is energy consistent, that is, it is shown that the weighted residual integral describes energy flow. The Galerkin approach gives accurate results with fewer degrees of freedom as compared to low-order finite-element formulation. The Galerkin approach also leads to a nonlinear order-reduction technique that can be used to further decrease the order of the system. The reduced-order model is shown to capture the dominant nonlinearities in the system and is ideal for preliminary design and control synthesis.
Image‐based monitoring of one‐lung ventilation

Background and objectives: With the increasing demand for one‐lung ventilation in both thoracic surgery and other procedures, identifying the correct placement becomes increasingly important. Currently, endobronchial intubation is suspected based on a combination of auscultation and physiological findings. We investigated the ability of the visual display of airflow‐induced vibrations to detect single‐lung ventilation with a double‐lumen endotracheal tube. Methods: Double‐lumen tubes were placed prior to surgery. Tracheal and endobronchial lumens were alternately clamped to produce unilateral lung ventilation of right and left lung. Vibration response imaging, which detects vibrations transmitted to the surface of the thorax, was performed during both right‐ and left‐lung ventilation. Geographical area of vibration response image as well as amount and distribution of lung sounds were assessed. Results: During single‐lung ventilation, the image and video obtained from the vibration response imaging identifies the ventilated lung with a larger and darker image on the ventilated side. During single‐lung ventilation, 87.2 ± 5.7% of the measured vibrations was detected over the ventilated lung and 12.8 ± 5.7% over the non‐ventilated lung (P < 0.0001). It was also noted that during single‐lung ventilation, the vibration distribution in the non‐ventilated lung had a majority of vibration detected by the medial sensors closest to the midline (P < 0.05) as opposed to the midclavicular sensors when the lung is ventilated. Conclusions: During single‐lung ventilation, vibration response imaging clearly showed increased vibration in the lung that is being ventilated. Distribution of residual vibration differed in the non‐ventilated lung in a manner that suggests transmission of vibrations across the mediastinum from the ventilated lung. The lung image and video obtained from vibration response imaging may provide useful and immediate information to help one‐lung ventilation assessment.
Antisense-Based Progerin Downregulation in HGPS-Like Patients’ Cells

Progeroid laminopathies, including Hutchinson-Gilford Progeria Syndrome (HGPS, OMIM #176670), are premature and accelerated aging diseases caused by defects in nuclear A-type Lamins. Most HGPS patients carry a de novo point mutation within exon 11 of the LMNA gene encoding A-type Lamins. This mutation activates a cryptic splice site leading to the deletion of 50 amino acids at its carboxy-terminal domain, resulting in a truncated and permanently farnesylated Prelamin A called Prelamin A Δ50 or Progerin. Some patients carry other LMNA mutations affecting exon 11 splicing and are named “HGPS-like” patients. They also produce Progerin and/or other truncated Prelamin A isoforms (Δ35 and Δ90) at the transcriptional and/or protein level. The results we present show that morpholino antisense oligonucleotides (AON) prevent pathogenic LMNA splicing, markedly reducing the accumulation of Progerin and/or other truncated Prelamin A isoforms (Prelamin A Δ35, Prelamin A Δ90) in HGPS-like patients’ cells. Finally, a patient affected with Mandibuloacral Dysplasia type B (MAD-B, carrying a homozygous mutation in ZMPSTE24, encoding an enzyme involved in Prelamin A maturation, leading to accumulation of wild type farnesylated Prelamin A), was also included in this study. These results provide preclinical proof of principle for the use of a personalized antisense approach in HGPS-like and MAD-B patients, who may therefore be eligible for inclusion in a therapeutic trial based on this approach, together with classical HGPS patients.
Quantifying transcription factor kinetics: At work or at play?

Abstract Transcription factors (TFs) interact dynamically in vivo with chromatin binding sites. Here we summarize and compare the four different techniques that are currently used to measure these kinetics in live cells, namely fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single molecule tracking (SMT) and competition ChIP (CC). We highlight the principles underlying each of these approaches as well as their advantages and disadvantages. A comparison of data from each of these techniques raises an important question: do measured transcription kinetics reflect biologically functional interactions at specific sites (i.e. working TFs) or do they reflect non-specific interactions (i.e. playing TFs)? To help resolve this dilemma we discuss five key unresolved biological questions related to the functionality of transient and prolonged binding events at both specific promoter response elements as well as non-specific sites. In support of functionality, we review data suggesting that TF residence times are tightly regulated, and that this regulation modulates transcriptional output at single genes. We argue that in addition to this site-specific regulatory role, TF residence times also determine the fraction of promoter targets occupied within a cell thereby impacting the functional status of cellular gene networks. Thus, TF residence times are key parameters that could influence transcription in multiple ways.
The Allan Variance as an Estimator of the Long-Memory Parameter: Time-Domain and Wavelet Methods

Abstract : The Allan variance is a well-known estimator of frequency stability and is often used to classify a time series into one of the standard clock noise types. By identifying the power-law model for clock noise with its long-memory equivalent, the Allan variance can also serve as an estimate for the long-memory parameter. Although the Allan variance is not a maximum likelihood estimator, it can be used with regression techniques that employ minimum variance estimates. This work describes the analytic basis for using the Allan variance to estimate the memory parameter, and performance of several Allan-variance-based estimators is illustrated via simulation study. Maximum likelihood estimation is also discussed, and the performance of maximum-likelihood estimators is contrasted with that of the Allan-variance-based estimators.
Pathogenesis of vascular leak in dengue virus infection

Endothelial dysfunction leading to vascular leak is the hallmark of severe dengue. Vascular leak typically becomes clinically evident 3–6 days after the onset of illness, which is known as the critical phase. This critical phase follows the period of peak viraemia, and lasts for 24–48 hr and usually shows rapid and complete reversal, suggesting that it is likely to occur as a result of inflammatory mediators, rather than infection of the endothelium. Cytokines such as tumour necrosis factor‐α, which are known to be elevated in the critical phase of dengue, are likely to be contributing factors. Dengue NS1, a soluble viral protein, has also been shown to disrupt the endothelial glycocalyx and thus contribute to vascular leak, although there appears to be a discordance between the timing of NS1 antigenaemia and occurrence of vascular leak. In addition, many inflammatory lipid mediators are elevated in acute dengue viral infection such as platelet activating factor (PAF) and leukotrienes. Furthermore, many other inflammatory mediators such as vascular endothelial growth factor and angiopoietin‐2 have been shown to be elevated in patients with dengue haemorrhagic fever, exerting their action in part by inducing the activity of phospholipases, which have diverse inflammatory effects including generation of PAF. Platelets have also been shown to significantly contribute to endothelial dysfunction by production of interleukin‐1β through activation of the NLRP3 inflammasome and also by inducing production of inflammatory cytokines by monocytes. Drugs that block down‐stream immunological mediator pathways such as PAF may also be beneficial in the treatment of severe disease.
Leptospira interrogans Binds to Cadherins

Leptospirosis, caused by pathogenic species of Leptospira, is the most widespread zoonosis and has emerged as a major public health problem worldwide. The adhesion of pathogenic Leptospira to host cells, and to extracellular matrix (ECM) components, is likely to be necessary for the ability of leptospires to penetrate, disseminate and persist in mammalian host tissues. Previous work demonstrated that pathogenic L. interrogans binds to host cells more efficiently than to ECM. Using two independent screening methods, mass spectrometry and protein arrays, members of the cadherin family were identified as potential L. interrogans receptors on mammalian host surfaces. We focused our investigation on vascular endothelial (VE)-cadherin, which is widely expressed on endothelia and is primarily responsible for endothelial cell-cell adhesion. Monolayers of EA.hy926 and HMEC-1 endothelial cells produce VE-cadherin, bind L. interrogans in vitro, and are disrupted upon incubation with the bacteria, which may reflect the endothelial damage seen in vivo. Dose-dependent and saturable binding of L. interrogans to the purified VE-cadherin receptor was demonstrated and pretreatment of purified receptor or endothelial cells with function-blocking antibody against VE-cadherin significantly inhibited bacterial attachment. The contribution of VE-cadherin to leptospiral adherence to host endothelial cell surfaces is biologically significant because VE-cadherin plays an important role in maintaining the barrier properties of the vasculature. Attachment of L. interrogans to the vasculature via VE-cadherin may result in vascular damage, facilitating the escape of the pathogen from the bloodstream into different tissues during disseminated infection, and may contribute to the hemorrhagic manifestations of leptospirosis. This work is first to describe a mammalian cell surface protein as a receptor for L. interrogans.
Symbolic Dynamics Generated by a Combination of Graphs

In this paper we investigate the growth rate of the number of all possible paths in graphs with respect to their length in an exact analytical way. Apart from the typical rates of growth, i.e. exponential or polynomial, we identify conditions for a stretched exponential type of growth. This is made possible by combining two or more graphs over the same alphabet, in order to obtain a discrete dynamical system generated by a triangular map, which can also be interpreted as a discrete nonautonomous system. Since the vertices and the edges of a graph are usually used to depict the states and transitions between states of a discrete dynamical system, the combination of two (or more) graphs can be interpreted as the driving, or perturbation, of one system by another.
Causality and Primordial Tensor Modes

We introduce the real space correlation function of B-mode polarization of the cosmic microwave background (CMB) as a probe of superhorizon tensor perturbations created by inflation. By causality, any non-inflationary mechanism for gravitational wave production after reheating, like global phase transitions or cosmic strings, must have vanishing correlations for angular separations greater than the angle subtended by the particle horizon at recombination, i.e. θ 2°. Since ordinary B-modes are defined non-locally in terms of the Stokes parameters Q and U and therefore don't have to respect causality, special care is taken to define `causal -modes' for the analysis. We compute the real space -mode correlation function for inflation and discuss its detectability on superhorizon scales where it provides an unambiguous test of inflationary gravitational waves. The correct identification of inflationary tensor modes is crucial since it relates directly to the energy scale of inflation. Wrongly associating tensor modes from causal seeds with inflation would imply an incorrect inference of the energy scale of inflation. We find that the superhorizon -mode signal is above cosmic variance for the angular range 2° < θ < 4° and is therefore in principle detectable. In practice, the signal will be challenging to measure since it requires accurately resolving the recombination peak of the B-mode power spectrum. However, a future CMB satellite (CMBPol), with noise level ΔP 1μK-arcmin and sufficient resolution to efficiently correct for lensing-induced B-modes, should be able to detect the signal at more than 3σ if the tensor-to-scalar ratio isn't smaller than r 0.01.
Imaging Ultrasound imaging for the rheumatologist XXIV . Sonographic evaluation of wrist and hand joint and tendon involvement in systemic lupus erythematosus

1Cattedra di Reumatologia, Università di Pisa, Pisa, Italy; 2Cattedra di Reumatologia, IRCCS Policlinico S. Matteo, Università di Pavia, Pavia, Italy; 3Cattedra di Reumatologia, Università di Roma “La Sapienza”, Rome, Italy; 4Cattedra di Reumatologia, Università Politecnica delle Marche, Jesi, Italy; 5Department of Rheumatology, Antrim Hospital, Antrim, United Kingdom. Andrea Delle Sedie, MD Lucrezia Riente, MD Carlo Alberto Scirè, MD Annamaria Iagnocco, MD Emilio Filippucci, MD Gary Meenagh, MD Niccolò Possemato, MD Walter Grassi, MD, Professor Guido Valesini, MD, Professor Carlomaurizio Montecucco, MD, Professor Stefano Bombardieri, MD, Professor Please address correspondence and reprint requests to: Dr Andrea Delle Sedie, U.O. Reumatologia, Dipartimento di Medicina Interna, Università di Pisa, Via Roma 67, Pisa 56126, Italy. E-mail: adellese@lycos.com Received and accepted on December 11, 2009. Clin Exp Rheumatol 2009: 27: 897-901. © Copyright CLINICAL AND EXPERIMENTAL RHEUMATOLOGY 2009.
Learning to Generate Artificial Fovea Trajectories for Target Detection

This paper shows how ‘static’ neural approaches to adaptive target detection can be replaced by a more efficient and more sequential alternative. The latter is inspired by the observation that biological systems employ sequential eye movements for pattern recognition. A system is described, which builds an adaptive model of the time-varying inputs of an artificial fovea controlled by an adaptive neural controller. The controller uses the adaptive model for learning the sequential generation of fovea trajectories causing the fovea to move to a target in a visual scene. The system also learns to track moving targets. No teacher provides the desired activations of ‘eye muscles’ at various times. The only goal information is the shape of the target. Since the task is a ‘reward-only-at-goal’ task, it involves a complex temporal credit assignment problem. Some implications for adaptive attentive systems in general are discussed.
Cognitive deficits in children of alcoholics: At risk before the first sip!

Background: High family loading for alcoholism, early onset of alcohol use and childhood disinhibitory behaviors, persisting into adulthood, increase the susceptibility to alcoholism. At the psychophysiology level, reduced amplitude of the P300 component of the Evoked Response Potential is associated with externalizing psychopathology in children. Children of alcoholics have reduced P300 amplitudes. Preliminary data suggests a developmental lag phenomenon in the maturation of the P300. Aims: The study compares the amplitude and topography of the P300 generated in response to a visual task, between subjects at high risk (HR) and those at low risk (LR) for alcoholism and its relation to externalizing behaviors. Results: HR subjects have lower P300 amplitudes over frontal brain areas. Differences are greater in young, tending to converge with increasing age. There is a strong association between this reduced brain activation and an excess of externalizing behaviors in HR individuals. Conclusion: A maturational lag in brain development causing central nervous system disinhibition and externalizing behaviors may underlie the susceptibility to alcoholism.
Don't Believe the Hype: Local Media Slant, Local Advertising, and Firm Value

When local media report news about local companies, they use fewer negative words compared to the same media reporting about non-local companies. We document that one reason for this positive slant is due to the firms’ local media advertising expenditures. Abnormal positive local media slant strongly relates to firm equity values. The effect is stronger for small firms, firms held predominantly by individual investors, and firms with illiquid or highly volatile stock, low analyst following, or high dispersion of analyst forecasts. These findings show that news content varies systematically with the characteristics and conflicts of interest of the source.
CONCEPTS OF AUTISM: A REVIEW

INTRODUCTION Not all psychiatrists and paediatricians believe in the syndrome called infantile autism, although since Kanner’s now classical paper in 1943, generations of workers have been impressed by the uniqueness of the behaviour of certain handicapped children. There is some divergence of opinion as to the key diagnostic features of the syndrome: Kolvin, Ounsted et al. (1971a), suggest that gaze avoidance may be a key discriminative feature between psychoses of early, compared to late, onset. Rutter ( 1 968) feels that social withdrawal (used in his context to describe the symptom of autism), severe abnormalities of language development, and a variety of ritualistic compulsive phenomena, including stereotopies, are central or core diagnostic features of the autistic syndrome beginning in infancy.