Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Biexponential and Monoexponential Model of Diffusion Weighted Imaging in Evaluation of Renal Lesions: Preliminary Experience

Objectives:To obtain intravoxel incoherent motion (IVIM) parameters with biexponential analysis of multiple b-value diffusion-weighted imaging (DWI) and compare these parameters to apparent diffusion coefficient (ADC) obtained with monoexponential modeling in their ability to discriminate enhancing from nonenhancing renal lesions. Materials and Methods:Twenty-eight patients were imaged at 1.5 T utilizing contrast-enhanced (CE) magnetic resonance imaging (MRI) and breath-hold DWI using 8 b values (range: 0–800 s/mm2). Perfusion fraction (fp), tissue diffusivity (Dt), and pseudo-diffusion coefficient (Dp) were calculated using segmented biexponential analysis. ADCtotal and ADC0–400–800 were calculated with monoexponential fitting of the DWI data. fp, Dt, Dp, ADCtotal, and ADC0–400–800 were compared between enhancing and nonenhancing renal lesions. Receiver operating characteristic analysis was performed for all DWI parameters. fp was correlated with percent enhancement. Results:There were a total of 31 renal lesions (15 enhancing and 16 nonenhancing) in 28 patients on CE-MRI. fp of enhancing masses was significantly higher (27.9 vs. 6.1) and Dt was significantly lower (1.47 vs. 2.40 ×10−3 mm2/s). IVIM parameters fp and Dt demonstrated higher accuracy in differentiating enhancing from nonenhancing renal lesions compared with monoexponential parameters ADC0–400–800 and ADCtotal, with area under the curve of 0.946, 0.896, 0.854, and 0.675, respectively. There was a good correlation between fp and percent enhancement (r = 0.7; P < 0.001). Conclusion:IVIM parameters fp and Dt obtained with biexponential fitting of multi-b value DWI have higher accuracy compared with ADC (obtained with monoexponential fit) in discriminating enhancing from nonenhancing renal lesions. Furthermore, fp demonstrates good correlation with percent enhancement and can provide information regarding lesion vascularity without the use of exogenous contrast agent.
A novel approach to aortic intima-media thickness quantification from fetal ultrasound images

Intrauterine fetal growth restriction (IUGR) is linked to increased cardiovascular mortality during adulthood. IUGR induces an increase in aortic intima-media thickness (aIMT) which can be detected from fetal ultrasound images, potentially improving IUGR assessment and thus cardiovascular risk management. Unfortunately this measurement currently relies on tedious and error-prone manual tracing. The aims of this study were to develop and test a novel near-automated technique for aIMT quantification from ultrasound images. The proposed technique uses a level-set method (with a functional relying on a distance-based term) to identify blood-intima and media-adventitia interfaces as a basis for aIMT estimation. This approach was tested on images acquired from 10 subjects, and automatically extracted aIMT values were compared to reference values manually obtained by two interpreters. Results indicate that the accuracy of the proposed technique is close to that of manual tracing, suggesting that it could be adopted as a basis for fast and reliable near-automated aIMT estimation.
History-based Schemes and Implicit Path Enumeration

The Implicit Path Enumeration Technique is often used to compute the WCET of control-intensive programs. This method does not consider execution paths as ordered sequences of basic blocks but instead as lists of basic blocks with their respective execution counts. This way of describing an execution path is adequate to compute its execution time, provided that safe individual WCETs for the blocks are known. Recently, a model for branch prediction has been integrated into WCET computation with IPET. This model generates safe estimations of the branch misprediction counts. However, we show in this paper that these counts can be over-estimated because IPET does consider simplified flow information that do not completely reflect the program semantics. We show how additional information on nested loops can be specified so that the model provides tighter WCET estimations.
Multiple division cycles and long‐term survival of hepatocytes are distinctly regulated by extracellular signal‐regulated kinases ERK1 and ERK2

We investigated the specific role of the mitogen‐activated protein kinase (MAPK) extracellular signal‐regulated kinase 1 (ERK1)/ERK2 pathway in the regulation of multiple cell cycles and long‐term survival of normal hepatocytes. An early and sustained epidermal growth factor (EGF)‐dependent MAPK activation greatly improved the potential of cell proliferation. In this condition, almost 100% of the hepatocytes proliferated, and targeting ERK1 or ERK2 via RNA interference revealed the specific involvement of ERK2 in this regulation. However, once their first cell cycle was performed, hepatocytes failed to undergo a second round of replication and stayed blocked in G1 phase. We demonstrated that sustained EGF‐dependent activation of the MAPK/ERK kinase (MEK)/ERK pathway was involved in this blockage as specific transient inhibition of the cascade repotentiated hepatocytes to perform a new wave of replication and multiple cell cycles. We identified this mechanism by showing that this blockage was in part supported by ERK2‐dependent p21 expression. Moreover, continuous MEK inhibition was associated with a lower apoptotic engagement, leading to an improvement of survival up to 3 weeks. Using RNA interference and ERK1 knockout mice, we extended these results by showing that this improved survival was due to the specific inhibition of ERK1 expression/phosphorylation and did not involve ERK2. Conclusion: Our results emphasize that transient MAPK inhibition allows multiple cell cycles in primary cultures of hepatocytes and that ERK2 has a key role in the regulation of S phase entry. Moreover, we revealed a major and distinct role of ERK1 in the regulation of hepatocyte survival. Taken together, our results represent an important advance in understanding long‐term survival and cell cycle regulation of hepatocytes. (HEPATOLOGY 2009.)
Palmitoylation and Membrane Interactions of the Neuroprotective Chaperone Cysteine-string Protein*

Cysteine-string protein (CSP) is an extensively palmitoylated DnaJ-family chaperone, which exerts an important neuroprotective function. Palmitoylation is required for the intracellular sorting and function of CSP, and thus it is important to understand how this essential modification of CSP is regulated. Recent work identified 23 putative palmitoyl transferases containing a conserved DHHC domain in mammalian cells, and here we show that palmitoylation of CSP is enhanced specifically by co-expression of the Golgi-localized palmitoyl transferases DHHC3, DHHC7, DHHC15, or DHHC17. Indeed, these DHHC proteins promote stable membrane attachment of CSP, which is otherwise cytosolic. An inverse correlation was identified between membrane affinity of unpalmitoylated CSP mutants and subsequent palmitoylation: mutants with an increased membrane affinity localize to the endoplasmic reticulum (ER) and are physically separated from the Golgi-localized DHHC proteins. Palmitoylation of an ER-localized mutant could be rescued by brefeldin A treatment, which promotes the mixing of ER and Golgi membranes. Interestingly though, the palmitoylated mutant remained at the ER following brefeldin A washout and did not traffic to more distal membrane compartments. We propose that CSP has a weak membrane affinity that allows the protein to locate its partner Golgi-localized DHHC proteins directly by membrane “sampling. ” Mutations that enhance membrane association prevent sampling and lead to accumulation of CSP on cellular membranes such as the ER. The coupling of CSP palmitoylation to Golgi membranes may thus be an important requirement for subsequent sorting.
A case for an SC-preserving compiler

The most intuitive memory consistency model for shared-memory multi-threaded programming is sequential consistency (SC). However, current concurrent programming languages support a relaxed model, as such relaxations are deemed necessary for enabling important optimizations. This paper demonstrates that an SC-preserving compiler, one that ensures that every SC behavior of a compiler-generated binary is an SC behavior of the source program, retains most of the performance benefits of an optimizing compiler. The key observation is that a large class of optimizations crucial for performance are either already SC-preserving or can be modified to preserve SC while retaining much of their effectiveness. An SC-preserving compiler, obtained by restricting the optimization phases in LLVM, a state-of-the-art C/C++ compiler, incurs an average slowdown of 3.8% and a maximum slowdown of 34% on a set of 30 programs from the SPLASH-2, PARSEC, and SPEC CINT2006 benchmark suites. While the performance overhead of preserving SC in the compiler is much less than previously assumed, it might still be unacceptable for certain applications. We believe there are several avenues for improving performance without giving up SC-preservation. In this vein, we observe that the overhead of our SC-preserving compiler arises mainly from its inability to aggressively perform a class of optimizations we identify as eager-load optimizations. This class includes common-subexpression elimination, constant propagation, global value numbering, and common cases of loop-invariant code motion. We propose a notion of interference checks in order to enable eager-load optimizations while preserving SC. Interference checks expose to the compiler a commonly used hardware speculation mechanism that can efficiently detect whether a particular variable has changed its value since last read.
lNFLUENCE OF POROUS ELECTRODE STRUCTURE ON PEM FUEL CELLS DESIGN AND PERFORMANCE

Gas flow in fuel cell porous electrodes is usually modelled with Darcy’s law, which requires the definition of a resistance constant for the material. This can be done directly via experimentation or indirectly via numerical tuning to fit experimental data on cell behaviour. Both methods lack generality, as they do not take into account the particular porous structure of each electrode. In the present work, a numerical procedure for calculating the resistance constant for a given porous structure is presented. This procedure is based on Lattice Boltzmann models, which treat the problem from a microscopic point of view, reproducing collisions between fluid molecules and solid particles. It can be demonstrated that under certain hypotheses, these models yield Navier-Stokes equations on a macroscopic scale, hence obeying fluid mechanics laws. Here the flow in a set of thirty randomly generated porous structures was analyzed, thus obtaining a distribution of values for Darcy’s constant. The analysis was repeated for ten different pressure gradients applied to a portion of the electrode and for three different volume porosities. The results showed that, for a given volume porosity, the value of Darcy’s constant is strongly affected by the material porous structure. On the other hand, the mean value of resistance remained almost constant while varying the applied load, thus correctly reproducing the linear dependence between velocity and pressure gradient, as stated by Darcy’s law. As fuel cell models are a great help in designing and predicting component operation, a further analysis was carried out in order to study the influence of the electrode resistance constant on cell performance prediction. The Lattice Boltzmann model was used to obtain resistance data characteristic of fuel cell electrodes, and the results were implemented in a one dimensional fuel cell model. The simulations showed that the variation of Darcy’s constant does not significantly affect the prediction of the cell polarization curve, while a significant effect was found on the prediction of the exact operating point on the polarization curve. In conclusion, if accurate modelling of a fuel cell is required, great care must be taken in evaluating the electrodes resistance constant. The procedure presented here, coupled with a non destructive tomography scan of the electrode structure could greatly help in refining existent fuel cell models.
Gs&agr; deficiency in the dorsomedial hypothalamus underlies obesity associated with Gs&agr; mutations

Gs&agr;, encoded by Gnas, mediates hormone and neurotransmitter receptor–stimulated cAMP generation. Heterozygous Gs&agr;-inactivating mutations lead to obesity in Albright hereditary osteodystrophy (AHO) patients, but only when the mutations occur on the maternal allele. This parent-of-origin effect is due to Gs&agr; imprinting in the CNS, although the relevant CNS regions are unknown. We have now shown that mice with a Gnas gene deletion disrupting Gs&agr; expression on the maternal allele, but not the paternal allele, in the dorsomedial nucleus of the hypothalamus (DMH) developed obesity and reduced energy expenditure without hyperphagia. Although maternal Gnas deletion impaired activation of brown adipose tissue (BAT) in mice, their responses to cold environment remained intact. Similar findings were observed in mice with DMH-specific deficiency of melanocortin MC4R receptors, which are known to activate Gs&agr;. Our results show that Gs&agr; imprinting in the DMH underlies the parent-of-origin metabolic phenotype that results from Gs&agr; mutations and that DMH MC4R/Gs&agr; signaling is important for regulation of energy expenditure and BAT activation, but not the metabolic response to cold.
The Analysis of the Deformation and Contact Lubrication Problem of HPD Diesel Engine Connecting Rod Bearings Based on the FFT Method and Flexibility Matrix Method

Based on the fast fourier transform (FFT) and flexibility matrix method, the effects of the FFT and flexibility matrix method on the distribution of oil film pressure, elastic deformation in the steady load and the journal center orbit of the connecting rod big-end bearings in the dynamic load are investigated. The results are shown that when the eccentricity ratio is more than 1, the maximum oil film pressure obtained by FFT method is bigger on both ends of the journal bearing and on its intermediate position is smaller. To the connecting rod big-end bearing, under the dynamic load condition, there is the same trend of the journal center orbit with two methods. However, with FFT method, the journal is largely deviated from bearing center.
Serum albumin and self-reported prevalence of stroke: a population-based, cross-sectional study

Background Since information about the association between serum albumin and risk of stroke is limited the purpose of the present paper was to re-investigate this relationship. Design The study followed a cross-sectional design. Methods In the cross-sectional Norwegian Oslo Health Study the concentration of serum albumin and blood pressure was determined in a random sample of 5071 men and women, 30-75 years of age. Logistic regression was used to study the association between the serum albumin concentration and self-reported prevalence of stroke. In the sample there were 122 subjects with a history of stroke and 4949 subjects without. Results Low albumin (i.e. ≥ 47 versus >47 g/l) was associated with increased prevalence of self-reported stroke (odds ratio 1.83; 95% confidence interval, 1.20-2.78; P=0.005), after adjusting for age (≥ 45 versus ≥ 59 years) and sex. Including smoking, blood pressure and length of education into the model did not have any major influence on the result. Conclusion Low serum albumin is associated with increased prevalence of self-reported stroke.
Agents in bioinformatics, computational and systems biology

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.
Strong signatures of selection in the domestic pig genome

Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig—the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
Enhancing cross-language information retrieval by an automatic acquisition of bilingual terminology from comparable corpora

This paper presents an approach to bilingual lexicon extraction from comparable corpora and evaluations on Cross-Language Information Retrieval. We explore a bi-directional extraction of bilingual terminology primarily from comparable corpora. A combined statistics-based and linguistics-based model to select best translation candidates to phrasal translation is proposed. Evaluations using a large test collection for Japanese-English revealed the proposed combination of bi-directional comparable corpora, bilingual dictionaries and transliteration, augmented with linguistics-based pruning to be highly effective in Cross-Language Information Retrieval.
Fast Detection of Nutrient Limitation in Macroalgae and Seagrass with Nutrient-Induced Fluorescence

Background Rapid determination of which nutrients limit the primary production of macroalgae and seagrasses is vital for understanding the impacts of eutrophication on marine and freshwater ecosystems. However, current methods to assess nutrient limitation are often cumbersome and time consuming. For phytoplankton, a rapid method has been described based on short-term changes in chlorophyll fluorescence upon nutrient addition, also known as Nutrient-Induced Fluorescence Transients (NIFTs). Thus far, though, the NIFT technique was not well suited for macroalgae and seagrasses. Methodology & Principal Findings We developed a new experimental setup so that the NIFT technique can be used to assess nutrient limitation of benthic macroalgae and seagrasses. We first tested the applicability of the technique on sea lettuce (Ulva lactuca) cultured in the laboratory on nutrient-enriched medium without either nitrogen or phosphorus. Addition of the limiting nutrient resulted in a characteristic change in the fluorescence signal, whereas addition of non-limiting nutrients did not yield a response. Next, we applied the NIFT technique to field samples of the encrusting fan-leaf alga Lobophora variegata, one of the key algal species often involved in the degradation of coral reef ecosystems. The results pointed at co-limitation of L. variegata by phosphorus and nitrogen, although it responded more strongly to phosphate than to nitrate and ammonium addition. For turtle grass (Thalassia testudinum) we found the opposite result, with a stronger NIFT response to nitrate and ammonium than to phosphate. Conclusions & Significance Our extension of the NIFT technique offers an easy and fast method (30–60 min per sample) to determine nutrient limitation of macroalgae and seagrasses. We successfully applied this technique to macroalgae on coral reef ecosystems and to seagrass in a tropical inner bay, and foresee wider application to other aquatic plants, and to other marine and freshwater ecosystems.
Biomechanical Effects of the Weight of Side Loaded Carriage in Walking - Correlation between Body Center of Mass (COM) and Joint Moments

This study investigated biomechanical effects on the body center of mass(COM) and joint moments of lower extremity as the weight of sided load in walking. Also the present study showed correlation between body center of mass and joint moments. The motion data used as input data for inverse dynamic simulation were measured by the 3D motion analysis system. Eight healthy, college-aged subjects participated in the experiment, and they walked with side loaded carriage which weighs 0, 5, 10 and 15kg, respectively. Human skeletal models were generated and analyzed by using BRG. LifeMOD and SIMM. For inspection about inverse dynamic simulation results, MSC.ADAMS was used for forward dynamic simulation. As a result, the COM was more inclined to the opposite side of side loaded carriage as the weight increased. In stance phase, the magnitude of ankle plantar-flexion moment increased as the weight of side loaded carriage increased. In knee joint, the knee extension moment of unloading side was smaller than that of loading side when the weight increased. The hip extension moment of loading side was larger than that of unloading side. In the present study, the results showed that the human used the ankle and hip joint of loading side to support the body and the knee joint of unloading side to progress the walking with keeping the balance of the body. This study could be very useful to analyze the various biomechanical effects in other human working.
Nondeterministic Quantum Query and Quantum Communication Complexities

We study nondeterministic quantum algorithms for Boolean functions f. Such algorithms have positive acceptance probability on input x iff f(x)=1. In the setting of query complexity, we show that the nondeterministic quantum complexity of a Boolean function is equal to its ``nondeterministic polynomial'' degree. We also prove a quantum-vs-classical gap of 1 vs n for nondeterministic query complexity for a total function. In the setting of communication complexity, we show that the nondeterministic quantum complexity of a two-party function is equal to the logarithm of the rank of a nondeterministic version of the communication matrix. This implies that the quantum communication complexities of the equality and disjointness functions are n+1 if we do not allow any error probability. We also exhibit a total function in which the nondeterministic quantum communication complexity is exponentially smaller than its classical counterpart.