Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Nitrogen Uptake in Oilseed Rape cv Capitol during a Growth Cycle Using Influx Kinetics of Root Nitrate Transport Systems and Field Experimental Data

The use of kinetic equations of NO3- transport systems in oilseed rape (Brassica napus), determined by 15NO3- labeling under controlled conditions, combined with experimental field data from the INRA-Châlons rape database were used to model NO3- uptake during the plant growth cycle. The quantitative effects of different factors such as day/night cycle, ontogenetic stages, root temperature, photosynthetically active radiation, and soil nitrate availability on different components of the constitutive high-affinity transport systems, constitutive low-affinity transport systems, inducible low-affinity transport systems, and inducible high-affinity transport systems of nitrate were then determined to improve the model's predictions. Simulated uptake correlated well with measured values of nitrogen (N) uptake under field conditions for all N fertilization rates tested. Model outputs showed that the high-affinity transport system accounted for about 89% of total NO3- uptake (18% and 71% for constitutive high-affinity transport systems and inducible high-affinity transport systems, respectively) when no fertilizer was applied. The low-affinity transport system accounted for a minor proportion of total N uptake, and its activity was restricted to the early phase of the growth cycle. However, N fertilization in spring increased the duration of its contribution to total N uptake. Overall, data show that this mechanistic and environmentally regulated approach is a powerful means to simulate total N uptake in the field with the advantage of taking both physiologically regulated processes at the overall plant level and specific nitrate transport system characteristics into account.
Overview of the TREC 2008 Enterprise Track

Abstract : The goal of the enterprise track is to conduct experiments with enterprise data that reflect the experiences of users in real organizations. This year, we continued with the CERC collection introduced in TREC 2007 (Bailey et al., 2007). Topics were developed in conjunction with CSIRO Enquiries, who field email and telephone questions about CSIRO research from the public. The CERC corpus (CSIRO Enterprise Research Collection, http://es.csiro.au/cerc/) represents the public-facing web of the Australian Commonwealth Scientic and Industrial Research Organisation (CSIRO). Here, we summarize the main characteristics of this corpus; a complete description of the collection is given by Bailey et al. (2007).
Speaker Transformation Algorithm Using Segmental Codebooks (stasc) X

This paper presents a new voice conversion algorithm which modiies the utterance of a source speaker to sound like speech from a target speaker. We refer to the method as Speaker Transformation Algorithm using Segmental Codebooks (STASC). A novel method is proposed which nds accurate alignments between source and target speaker utterances. Using the alignments, source speaker acoustic characteristics are mapped to target speaker acoustic characteristics. The acoustic parameters included in the mapping are vocal tract, excitation, intonation, energy, and duration characteristics. Informal listening tests suggest that convincing voice conversion is achieved while maintaining high speech quality. The performance of the proposed system is also evaluated on a simple Gaussian mixture model based speaker identiication system, and the results show that the transformed speech is assigned higher likelihood by the target speaker model when compared to the source speaker model. z Permission is hereby granted to publish this abstract separately.
Synthesis of Melanin Pigment by Candida albicans In Vitro and during Infection

ABSTRACT Melanins are implicated in the pathogenesis of several important human diseases. This study confirmed the presence of melanin particles in Candida albicans in vitro and during infection. Dark particles were isolated from the digestion of C. albicans cultures and from infected tissue, as established by electron microscopy and immunofluorescence techniques.
Few Skewed Disks Found in First Closure-Phase Survey of Herbig Ae/Be Stars

Using the three-telescope IOTA interferometer on Mount Hopkins, we report results from the first near-infrared (λ = 1.65 μm) closure-phase survey of young stellar objects (YSOs). These closure phases allow us to unambiguously detect departures from centrosymmetry (i.e., skew) in the emission pattern from YSO disks on the scale of ~4 mas, expected from generic "flared disk" models. Six of 14 targets showed small, yet statistically significant nonzero closure phases, with largest values from the young binary system MWC 361-A and the (pre-main-sequence? ) Be star HD 45677. Our observations are quite sensitive to the vertical structure of the inner disk, and we confront the predictions of the "puffed-up inner wall" models of Dullemond, Dominik, & Natta (DDN). Our data support disk models with curved inner rims because the expected emission appears symmetrically distributed around the star over a wide range of inclination angles. In contrast, our results are incompatible with the models possessing vertical inner walls because they predict extreme skewness (i.e., large closure phases) from the near-IR disk emission that is not seen in our data. In addition, we also present the discovery of mysterious H-band "halos" (~5%-10% of light on scales 0.″01-0.″50) around a few objects, a preliminary "parametric imaging" study for HD 45677, and the first astrometric orbit for the young binary MWC 361-A.
Electroacupuncture protects against ischemic stroke by reducing autophagosome formation and inhibiting autophagy through the mTORC1-ULK1 complex-Beclin1 pathway

In a previous study by our group, we demonstrated that electroacupuncture (EA) activates the class I phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. There is considerable evidence that the downstream mammalian target of rapamycin complex 1 (mTORC1) plays an important role in autophagy following ischemic stroke. The aim of the present study was to determine whether EA exerts a neuroprotective effect through mTORC1-mediated autophagy following ischemia/reperfusion injury. Our results revealed that EA at the LI11 and ST36 acupoints attenuated motor dysfunction, improved neurological deficit outcomes and decreased the infarct volumes. The number of autophagosomes, autolysosomes and lysosomes was decreased following treatment with EA. Simultaneously, the levels of the autophagosome membrane maker, microtubule-associated protein 1 light chain 3 beta (LC3B)II/I, Unc-51-like kinase 1 (ULK1), autophagy related gene 13 Atg13) and Beclin1 (ser14) were decreased, whereas mTORC1 expression was increased in the peri-infarct cortex. These results suggest that EA protects against ischemic stroke through the inhibition of autophagosome formation and autophagy, which is mediated through the mTORC1-ULK complex-Beclin1 pathway.
Heritabilities of ocular biometrical traits in two croatian isolates with extended pedigrees.

PURPOSE To assess the effects of body stature and years of education, in addition to age and sex, on six oculometric traits and to estimate the heritabilities of these quantitative traits in two Croatian cross-population studies. METHODS Adult subjects living on the two Croatian islands of Vis and Korcula were recruited for a large epidemiologic and genetic study that included eye biometry, keratometry, and autorefraction. Effects and heritabilities were estimated by using general linear mixed models for axial length (AL), anterior chamber depth (ACD), corneal curvature (CC), corneal thickness (CT), lens thickness (LT), and spherical equivalent refraction (SER). Both cohorts were genotyped with dense SNP arrays, allowing the use of kinship coefficients derived from genotypic data (realized kinship) rather than from pedigree information (expected kinship). RESULTS Across cohorts, body mass index (BMI) did not consistently influence any of the ocular traits adjusted for age and/or sex, whereas height and years in education (YrEd) did, explaining up to an additional 5% of the variance (in CC). CT was the trait least influenced by covariates. Estimated heritabilities in Vis and Korcula, respectively, were 84% and 52% for CC, 75% and 71% for CT, 37% and 32% for LT, 59% and 45% for ACD, 37% and 74% for AL, and 0% and 17% for SER. CONCLUSIONS While heritabilities of CT and CC seemed uniformly high across studies of Caucasian datasets, estimates for SER varied widely and were at the lower end of the spectrum of published observations in our study.
Vascular extracellular superoxide dismutase activity in patients with coronary artery disease: relation to endothelium-dependent vasodilation.

BACKGROUND Increased inactivation of nitric oxide by oxygen free radicals contributes to endothelial dysfunction in patients with coronary artery disease (CAD). We therefore determined the activity of extracellular superoxide dismutase (EC-SOD), the major antioxidant enzyme system of the vessel wall, and its relation to flow-dependent, endothelium-mediated dilation (FDD) in patients with CAD. METHODS AND RESULTS SOD isoenzyme activity was determined in coronary arteries from 10 patients with CAD and 10 control subjects. In addition, endothelium-bound EC-SOD activity (eEC-SOD), released by heparin bolus injection, and FDD of the radial artery were measured in 35 patients with CAD and 15 control subjects. FDD, determined by high-resolution ultrasound, was assessed at baseline, after intra-arterial infusion of vitamin C, N-monomethyl-L-arginine, and combination of both. EC-SOD activity in coronary arteries (control subjects: 126+/-14; CAD: 63+/-11 U/mg protein; P<0.01) and eEC-SOD activity in vivo (control subjects: 14.5+/-1.1; CAD: 3.8+/-1.1 U. mL(-1). min(-1); P<0.01) were reduced in patients with CAD. Activity of eEC-SOD was positively correlated with FDD (r=0.47; P<0. 01) and negatively with the effect of the antioxidant vitamin C on FDD (r=-0.59; P<0.01). In young individuals with hypercholesterolemia, however, eEC-SOD activity was increased (21. 0+/-1.2 U. mL(-1). min(-1); n=10; P<0.05). CONCLUSIONS In patients with CAD, vascular EC-SOD activity is substantially reduced. The close relation between endothelium-bound EC-SOD activity and FDD suggests that reduced EC-SOD activity contributes to endothelial dysfunction in patients with CAD. In young hypercholesterolemic individuals, however, endothelium-bound EC-SOD activity is increased and may, in part, counteract impairment of endothelial function as the result of increased formation of oxygen free radicals.
On the Automated Synthesis of Enterprise Integration Patterns to Adapt Choreography-based Distributed Systems

The Future Internet is becoming a reality, providing a large-scale computing environments where a virtually infinite number of available services can be composed so to fit users' needs. Modern service-oriented applications will be more and more often built by reusing and assembling distributed services. A key enabler for this vision is then the ability to automatically compose and dynamically coordinate software services. Service choreographies are an emergent Service Engineering (SE) approach to compose together and coordinate services in a distributed way. When mismatching third-party services are to be composed, obtaining the distributed coordination and adaptation logic required to suitably realize a choreography is a non-trivial and error prone task. Automatic support is then needed. In this direction, this paper leverages previous work on the automatic synthesis of choreography-based systems, and describes our preliminary steps towards exploiting Enterprise Integration Patterns to deal with a form of choreography adaptation.
An Oscillation-Based On-Chip Temperature-Aware Dynamic Voltage and Frequency Scaling Scheme in System-on-a-Chip

SUMMARY The excessively high temperature in a chip may cause circuit malfunction and performance degradation, and thus should be avoided to improve system reliability. In this paper, a novel oscillation-based onchip thermal sensing architecture for dynamically adjusting supply voltage and clock frequency in System-on-a-Chip (SoC) is proposed. It is shown that the oscillation frequency of a ring oscillator reduces linearly as the temperature rises, and thus provides a good on-chip temperature sensing mechanism. An efficient Dynamic Voltage-to-Frequency Scaling (DF2VS) algorithm is proposed to dynamically adjust supply voltage according to the oscillation frequencies of the ring oscillators distributed in SoC so that thermal sensing can be carried at all potential hot spots. An on-chip Dynamic Voltage Scaling or Dynamic Voltage and Frequency Scaling (DVS or DVFS) monitor selects the supply voltage level and clock frequency according to the outputs of all thermal sensors. Experimental results on SoC benchmark circuits show the effectiveness of the algorithm that a 10% reduction in supply voltage alone can achieve about 20% power reduction (DVS scheme), and nearly 50% reduction in power is achievable if the clock frequency is also scaled down (DVFS scheme). The chip tempera
Demonstration of Two Different Processes of β-Cell Regeneration in a New Diabetic Mouse Model Induced by Selective Perfusion of Alloxan

To clarify the regeneration process of pancreatic β-cells, we established a new mouse model of diabetes induced by selective perfusion of alloxan after clamping the superior mesenteric artery. In this model, diabetes could be induced by the destruction of β-cells in alloxan-perfused segments, while β-cells in nonperfused segments were spared. Intraperitoneal glucose tolerance tests showed glucose intolerance, which gradually ameliorated and was completely normalized in 1 year with a concomitant increase of insulin content in the pancreas. Histological examination showed neoislet formation in the alloxan-perfused segment and the proliferation of spared β-cells in the nonperfused segment. In the alloxan-perfused segment, despite a marked reduction of islets in size and number at an early stage, both the number of islets, including islet-like cell clusters (ICCs), and the relative islet area significantly increased at a later stage. Increased single β-cells and ICCs were located in close contact with duct cell lining, suggesting that they differentiated from duct cells and that such extra-islet precursor cells may be important for β-cell regeneration in β-cell–depleted segment. In addition to β-cells, some nonhormone cells in ICCs were positive for nuclear insulin promoter factor 1, which indicated that most, if not all, nonhormone cells positive for this factor were β-cell precursors. In the nonperfused segment, the islet area increased significantly, and the highest 5-bromo-2-deoxyuridine–labeling index in β-cells was observed at day 5, while the number of islets did not increase significantly. This indicated that the regeneration of islet endocrine cells occurs mostly through the proliferation of preexisting intra-islet β-cells in the nonperfused segment. In conclusion, the regeneration process of β-cells varied by circumstance. Our mouse model is useful for studying the mechanism of regeneration, since differentiation and proliferation could be analyzed separately in one pancreas.
On a Catalogue of Metrics for Evaluating Commercial Cloud Services

Given the continually increasing amount of commercial Cloud services in the market, evaluation of different services plays a significant role in cost-benefit analysis or decision making for choosing Cloud Computing. In particular, employing suitable metrics is essential in evaluation implementations. However, to the best of our knowledge, there is not any systematic discussion about metrics for evaluating Cloud services. By using the method of Systematic Literature Review (SLR), we have collected the de facto metrics adopted in the existing Cloud services evaluation work. The collected metrics were arranged following different Cloud service features to be evaluated, which essentially constructed an evaluation metrics catalogue, as shown in this paper. This metrics catalogue can be used to facilitate the future practice and research in the area of Cloud services evaluation. Moreover, considering metrics selection is a prerequisite of benchmark selection in evaluation implementations, this work also supplements the existing research in benchmarking the commercial Cloud services.
High intracellular trehalase activity prevents the storage of trehalose in the yeast Dekkera bruxellensis

Dekkera bruxellensis hit the spotlight in the past decade mostly due to its rather high ability to adapt to several different fermentation processes. This yeast relies on different genetic and physiological aspects to achieve and preserve its high industrial fitness and some of these traits are shared with Saccharomyces cerevisiae. We have previously described that D. bruxellensis is unable to make use of accumulating trehalose as a strategy for cell adaptation and survival in the industrial scenario, as opposed to S. cerevisiae. Since trehalose is often involved in mechanisms related to cell protection, we aimed to investigate both cause and effect of the absence of this metabolite in the cell adaptive capacity in the industrial environment. Our results indicate that the major cause for the nonaccumulation of trehalose is the high constitutive activity of neutral trehalase. Therefore, the rate of trehalose degradation could be higher than its rate of synthesis, preventing accumulation. Altogether, our data elucidate the mechanisms involved in the lack of trehalose accumulation in D. bruxellensis as well as evaluates the implications of this feature.
A noise robust method for pattern discovery in quantized time series: the concept matrix approach

An efficient method for pattern discovery from discrete time series is introduced in this paper. The method utilizes two parallel streams of data, a discrete unit time-series and a set of labeled events, From these inputs it builds associative models between systematically co-occurring structures existing in both streams. The models are based on transitional probabilities of events at several different time scales. Learning and recognition processes are incremental, making the approach suitable for online learning tasks. The capabilities of the algorithm are demonstrated in a continuous speech recognition task operating in varying noise levels.
Structural manipulations of software architecture using Tarski relational algebra

A software architecture is typically drawn as a nested set of box and arrow diagrams. The boxes represent components of the software system and the edges represent interactions These diagrams correspond to typed graphs, in which there are a number of "types" or "colors" of edges, and in which there is a distinguished "contain" relation that represents the system hierarchy (the nesting of boxes). During reverse engineering, one often transforms such diagrams in various ways to make them easier to understand. These transformations include edge aggregation, box abstraction (closing a box to hide its contents), and box separation (separating a box from its surrounding system). Such transformations are essential in helping make software architecture diagrams useful in practice. Paper shows how structural manipulations such as these can be specified and automatically carried out in a notation based on Tarski's relational algebra. The operators in this algebra include relational composition, union, subtraction, etc. These operators are supported in a language called Grok. Grok scripts have been used in manipulating the graphs for large scale software systems, such as Linux, to help in program visualization and understanding.
The Emergence of Animal Social Complexity: theoretical and biobehavioral evidence

This paper will introduce a theory of emergent animal social complexity using various results from computational models and empirical results. These results will be organized into a vertical model of social complexity. This will support the perspective that social complexity is in essence an emergent phenomenon while helping to answer two interrelated questions. The first of these involves how behavior is integrated at units of analysis larger than the individual organism. The second involves placing aggregate social events into the context of processes occurring within individual organisms over time (e.g. genomic and physiological processes). By using a complex systems perspective, five principles of social complexity can be identified. These principles suggest that lower-level mechanisms give rise to high-level mechanisms, ultimately resulting in metastable networks of social relations. These network structures then constrain lower-level phenomena ranging from transient, collective social groups to physiological regulatory mechanisms within individual organisms. In conclusion, the broader implications and drawbacks of applying the theory to a diversity of natural populations will be discussed.
Finding the best shortcut in a geometric network

Given a Euclidean graph G in Rd with n vertices and m edges we consider the problem of adding a shortcut such that the stretch factor of the resulting graph is minimized. Currently, the fastest algorithm for computing the stretch factor of a Euclidean graph runs in O(mn+n2 log n) time, resulting in a trivial O(mn3+n4 log n) time algorithm for computing the optimal shortcut. First, we show that a simple modification yields the optimal solution in O(n4) time using O(n2) space. To reduce the running times we consider several approximation algorithms. Our main result is a (2+ε)-approximation algorithm with running time O(nm+n2(log n+1/ε3d)) using O(n2) space.
The MS 2 Coat Protein Shell is Likely Assembled Under Tension : A Novel Role for the MS 2 Bacteriophage A Protein as Revealed by Small-angle Neutron Scattering

0022-2836/$ see front matter Published Present addresses: D. A. Kuzman Inc., Gunpowder Branch, P.O. Box 6 Ground, MD 21010, USA; I. Elashvi Technology Transition Division, De Reduction Agency, 8725 John. J. Kin VA 22060, USA; C. O’Connell, Tetra Rd., Suite C, Gaithersburg, MD 208 Abbreviations used: SANS, small scattering; SAXS, small-angle X-ray scattering length density; cryo-EM, microscopy. E-mail address of the correspond susan.krueger@nist.gov Recombinant forms of the bacteriophage MS2 and its RNA-free (empty) MS2 capsid were analyzed in solution to determine if RNA content and/or the A (or maturation) protein play a role in the global arrangement of the virus protein shell. Analysis of the (coat) protein shell of recombinant versions of MS2 that lack the A protein revealed dramatic differences compared to wild-type MS2 in solution. Specifically, A protein-deficient virus particles form a protein shell of between 31(G1) Å and 37(G1) Å. This is considerably thicker than the protein shell formed by either the wild-type MS2 or the RNA-free MS2 capsid, whose protein shells have a thickness of 21(G1) Å and 25(G1) Å, respectively. Since the A protein is known to separate from the intact MS2 protein shell after infection, the thin shell form of MS2 represents the pre-infection state, while the postinfection state is thick. Interestingly, these A protein-dependent differences in the virus protein shell are not seen using crystallography, as the crystallization process seems to artificially compact the wild-type MS2 virion. Furthermore, when the A protein is absent from the virus shell (post-infection), the process of crystallization exerts sufficient force to convert the protein shell from the post-infection (thick) state to the preinfection (thin) conformation. In summary, the data are consistent with the idea that RNA content or amount does not affect the structure of the MS2 virus shell. Rather, the A protein influences the global arrangement of the virus coat dramatically, possibly by mediating the storage of energy or tension within the protein shell during virus assembly. This tension may later be used to eject the MS2 genomic RNA and A protein fragments into the host during infection. Published by Elsevier Ltd.