Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidating the Mechanisms of Assembly and Subunit Interaction of the Cellulose Synthase Complex of Arabidopsis Secondary Cell Walls*

Cellulose is the most abundant biopolymer in nature; however, questions relating to the biochemistry of its synthesis including the structure of the cellulose synthase complex (CSC) can only be answered by the purification of a fully functional complex. Despite its importance, this goal remains elusive. The work described here utilizes epitope tagging of cellulose synthase A (CESA) proteins that are known components of the CSC. To avoid problems associated with preferential purification of CESA monomers, we developed a strategy based on dual epitope tagging of the CESA7 protein to select for CESA multimers. With this approach, we used a two-step purification that preferentially selected for larger CESA oligomers. These preparations consisted solely of the three known secondary cell wall CESA proteins CESA4, CESA7, and CESA8. No additional CESA isoforms or other proteins were identified. The data are consistent with a model in which CESA protein homodimerization occurs prior to formation of larger CESA oligomers. This suggests that the three different CESA proteins undergo dimerization independently, but the presence of all three subunits is required for higher order oligomerization. Analysis of purified CESA complex and crude extracts suggests that disulfide bonds and noncovalent interactions contribute to the stability of the CESA subunit interactions. These results demonstrate that this approach will provide an excellent framework for future detailed analysis of the CSC.
Modelling Diverse Soil Attributes with Visible to Longwave Infrared Spectroscopy Using PLSR Employed by an Automatic Modelling Engine

The study tested a data mining engine (PARACUDA®) to predict various soil attributes (BC, CEC, BS, pH, Corg, Pb, Hg, As, Zn and Cu) using reflectance data acquired for both optical and thermal infrared regions. The engine was designed to utilize large data in parallel and automatic processing to build and process hundreds of diverse models in a unified manner while avoiding bias and deviations caused by the operator(s). The system is able to systematically assess the effect of diverse preprocessing techniques; additionally, it analyses other parameters, such as different spectral resolutions and spectral coverages that affect soil properties. Accordingly, the system was used to extract models across both optical and thermal infrared spectral regions, which holds significant chromophores. In total, 2880 models were evaluated where each model was generated with a different preprocessing scheme of the input spectral data. The models were assessed using statistical parameters such as coefficient of determination (R2), square error of prediction (SEP), relative percentage difference (RPD) and by physical explanation (spectral assignments). It was found that the smoothing procedure is the most beneficial preprocessing stage, especially when combined with spectral derivation (1st or 2nd derivatives). Automatically and without the need of an operator, the data mining engine enabled the best prediction models to be found from all the combinations tested. Furthermore, the data mining approach used in this study and its processing scheme proved to be efficient tools for getting a better understanding of the geochemical properties of the samples studied (e.g., mineral associations).
Glial swelling and astrogliosis produce diffusion barriers in the rat spinal cord

Cell swelling and astrogliosis (manifested as an increase in GFAP) were evoked in isolated rat spinal cords of 4–21‐day‐old rats by incubation in either 50 mM K+ or hypotonic solution (235 mosmol kg‐1). Application of K+ and hypotonic solution resulted at first in a decrease of extracellular space (ECS) volume fraction α (ECS volume/total tissue volume) and an increase in tortuosity λ (λ2 = free/apparent diffusion coefficient) in spinal gray (GM) and white matter (WM). These changes resulted from cell swelling, since the total water content (TW) in spinal cord was unchanged and the changes were blocked in Cl−‐free solution and slowed down by furosemide and bumetanide. Diffusion in WM was anisotropic, i.e., more facilitated along fibers (x‐axis) than across them (y‐ or z‐axis). The increase of λy,z was greater than that of λx, reaching unusually high values above 2.4. In GM only, during continuous 45 min application, α and λ started to return towards control values, apparently due to cell shrinkage of previously swollen cells since TW remained unchanged. This return was blocked by fluoroacetate, suggesting that most of the changes were due to the swelling of glia. A 45 min application of 50 mM K+ and, to a lesser degree, of hypotonic solution evoked astrogliosis, which persisted after washing out these solutions with physiological saline. During astrogliosis λ increased again to values as high as 2.0, while α either returned to or increased above control values. This persistent increase in λ after washout was also found in WM, and, in addition, the typical diffusion anisotropy was diminished. Our data show that glial swelling and astrogliosis are associated with a persistent increase in ECS diffusion barriers. This could lead to the impairment of the diffusion of neuroactive substances, extrasynaptic transmission, “crosstalk” between synapses and neuron‐glia communication. GLIA 25:56–70, 1999. © 1999 Wiley‐Liss, Inc.
Unobtrusiveness and efficiency in idle cycle stealing for PC grids

Summary form only given. Studies have shown that for a significant fraction of the time desktop PCs and workstations are under-utilized. To exploit these idle resources, various desktop/workstation grid systems have been developed. The ultimate goal of such systems is to maximize efficiency of resource usage while maintaining low obtrusiveness to machine owners. To this end, we created a new fine-grain cycle stealing approach and conducted a performance comparison study against the traditional coarse-grain cycle stealing. We developed a prototype of fine-grain cycle stealing, the Linger-Longer system, on a Linux cluster. The experiments on a cluster of desktop Linux PCs with benchmark applications show that, overall, fine-grain cycle stealing can improve efficiency of idle cycle usage by increasing the guest job throughput by 50% to 70%, while limiting obtrusiveness with no more than 3% of host job slowdown.
Role of Aortic Root Motion in the Pathogenesis of Aortic Dissection

Background—The downward movement of the aortic root during the cardiac cycle may be responsible for producing the circumferential tear observed in aortic dissections. Methods and Results—Contrast injections were investigated in 40 cardiac patients, and a finite element model of the aortic root, arch, and branches of the arch was built to assess the influence of aortic root displacement and pressure on the aortic wall stress. The axial displacement of the aortic root ranged from 0 to 14 mm. It was increased in patients with aortic insufficiency (22±13% of the sino-tubular junction diameter versus 12±9%) and reduced in patients with hypokinesis of the left ventricle (10±9% of sino-tubular junction versus 17±12%). The largest stress increase due to aortic root displacement was found approximately 2 cm above the sino-tubular junction, where the longitudinal stress increased by 50% to 0.32 Nmm−2 when 8.9-mm axial displacement was applied in addition to 120-mm Hg luminal pressure. A similar result was observed when the pressure load was increased to 180 mm Hg without axial displacement. Conclusions—Both aortic root displacement and hypertension significantly increase the longitudinal stress in the ascending aorta. For patients with hypertension who are at risk of dissection, aortic root movement may be monitored as an important risk factor.
Improved effect of the combination naltrexone/D-penicillamine in the prevention of alcohol relapse-like drinking in rats

Opioid antagonists are licensed drugs for treating alcohol use disorders; nonetheless, clinical studies have evidenced their limited effectiveness. Preclinical findings indicate that opioid receptor (OR) antagonists, such as naltrexone (NTX), reduce the alcohol deprivation effect (ADE). However, a detailed analysis of published data shows the existence of a delayed increase in ethanol consumption after continuous OR blockade, a phenomenon originally called as ‘delayed ADE’. We have recently reported that D-penicillamine (DP) is able to prevent ADE through a mechanism dependent on the inactivation of acetaldehyde, the main metabolite of ethanol. Hypothetically, OR activation would be triggered by acetaldehyde after ethanol consumption. Hence, we conjecture that the combination of NTX and DP, due to their distinct but complementary mechanisms to impede OR activation, may be more efficacious in the prevention of the ADE and, specifically, the ‘delayed ADE’. Herein, we compare the effects of the combination NTX/DP (NTX: 2×5 mg/kg SC injection daily/DP: SC infusion (0.25 mg/h)) versus NTX on the ADE in long-term ethanol-experienced rats. As expected, NTX-treated animals displayed a delayed ADE. However, NTX/DP treatment prevented this delayed effect. Our present data indicate that this combination therapy shows an adequate anti-relapse preclinical efficacy being able to overcome the preclinical limitations of NTX alone.
Improving Accessibility and Usability of Geo-referenced Statistical Data

We demonstrate three versions of YMap, a dynamic choropleth map tool for geo-referenced statistical data explorations. More details can be found in (Zhao et al. 2003)First we present the Visual Basic desktop version. Users can quickly visualize the distribution of a data attribute on the choropleth map by shading the map using that attribute, brush the tightly coupled scatterplot, map, and detail window, formulate conjunctive queries and view the query results immediately on the map and scatterplot by adjusting the double-thumb sliders, or zoom and pan to observe data patterns in smaller or denser regions. (Screenshots can be found in (Zhao et al. 2003)). Second we present the Java applet version for Web access. Web YMap uses special color-coded raster images to ship geographic shapes to the browser, which allows varieties of sub-second fine-grained interface controls as those in the desktop version, and has the features of short initial download time, near-constant performance scalability for larger numbers of geographic objects, and download-map-segment-only-when-necessary, which potentially reduces the overall data transfer over the network. As a result, Web YMap accommodates users with slow network connections and low-end machines. It also incorporates some new features such as the histogram bars coupled with the map within the sliders, and different slider and shader scales to allow more uniform filtering effect.Third we present auditory YMap that aims at supporting blind and vision-impaired users. It presents information using synthesized spatial sound instead of via visual perceptions. Sounds of different timbres, pitches, and spatial positions are tied to the map regions, the sliders, the histograms, and the sweeping lines. The spatial sounds create the effect of a virtual US state map hung in front of the user. Users can navigate the interface using only keyboard, and explore the data set though audio perceptions.
An improved model for tidally modulated grounding-line migration

Understanding grounding-line dynamics is necessary for predictions of long-term ice-sheet stability. However, despite growing observations of the tidal influence on grounding-line migration, this short-timescale migration is poorly understood, with most modeling attempts assuming beam theory to calculate displacements. Here we present an improved model of tidal grounding-line migration that treats migration as an elastic fracture problem, forced by the additional ocean water pressure from the tide. This new model predicts that the grounding line cannot be assumed to be in hydrostatic equilibrium and, furthermore, that migration is inherently asymmetric and nonlinear, with migration distances that are not proportional to the tidal load. Specifically, for constant surface slope, the grounding line migrates upstream approximately ten times further as the tide rises from mean sea level to high tide than it migrates downstream as the tide falls from mean sea level to low tide, and migration distances are substantially larger than simple flotation arguments suggest. Numerical tests also show that the dependence of migration distance on elastic moduli and ice-sheet thickness are inconsistent with predictions of beam theory for a range of realistic values. Finally, applying the new model to observations in Antarctica results in new estimates of bed slopes, though these estimates remain uncertain due to imperfect knowledge of the relevant rheological parameters.
Achievable Outage Rates with Improved Decoding of BICM Multiband OFDM under Channel Estimation Errors

We consider the decoding of bit interleaved coded modulation (BICM) applied to multiband OFDM for practical scenarios where only a noisy (possibly very bad) estimate of the channel is available at the receiver. First, a decoding metric based on the channel a posteriori probability density, conditioned on the channel estimate is derived and used for decoding BICM multiband OFDM. Then, we characterize the limits of reliable information rates in terms of the maximal achievable outage rates associated to the proposed metric. We also compare our results with the outage rates of a system using a theoretical decoder. Our results are useful for designing a communication system where a prescribed quality of service (QoS), in terms of achievable target rates with small error probability, must be satisfied even in the presence of imperfect channel estimation. Numerical results over both realistic UWB and theoretical Rayleigh fading channels show that the proposed method provides significant gain in terms of BER and outage rates compared to the classical mismatched detector, without introducing any additional complexity.
Genetic Effects on Cerebellar Structure Across Mouse Models of Autism Using a Magnetic Resonance Imaging Atlas

Magnetic resonance imaging (MRI) of autism populations is confounded by the inherent heterogeneity in the individuals' genetics and environment, two factors difficult to control for. Imaging genetic animal models that recapitulate a mutation associated with autism quantify the impact of genetics on brain morphology and mitigate the confounding factors in human studies. Here, we used MRI to image three genetic mouse models with single mutations implicated in autism: Neuroligin‐3 R451C knock‐in, Methyl‐CpG binding protein‐2 (MECP2) 308‐truncation and integrin β3 homozygous knockout. This study identified the morphological differences specific to the cerebellum, a structure repeatedly linked to autism in human neuroimaging and postmortem studies. To accomplish a comparative analysis, a segmented cerebellum template was created and used to segment each study image. This template delineated 39 different cerebellar structures. For Neuroligin‐3 R451C male mutants, the gray (effect size (ES) = 1.94, FDR q = 0.03) and white (ES = 1.84, q = 0.037) matter of crus II lobule and the gray matter of the paraflocculus (ES = 1.45, q = 0.045) were larger in volume. The MECP2 mutant mice had cerebellar volume changes that increased in scope depending on the genotype: hemizygous males to homozygous females. The integrin β3 mutant mouse had a drastically smaller cerebellum than controls with 28 out of 39 cerebellar structures smaller. These imaging results are discussed in relation to repetitive behaviors, sociability, and learning in the context of autism. This work further illuminates the cerebellum's role in autism. Autism Res 2014, 7: 124–137. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.
Intervention for lateral /s/ using electropalatography (EPG) biofeedback and an intensive motor learning approach: a case report.

BACKGROUND Visual biofeedback using electropalatography (EPG) has been beneficial in the treatment of some cases of lateral /s/ misarticulation. While EPG intervention is motorically based, studies have not commonly employed a motor learning approach to treatment. Furthermore, treatment success is measured primarily by change to EPG tongue-palate contact patterns and listener ratings conducted by speech-language therapists. Studies have not commonly measured articulatory change without the palate in-situ using acoustic analysis and non-professional listeners. AIMS To determine if an intensive treatment programme including both visual biofeedback (EPG) and traditional articulation techniques within a motor learning paradigm would result in functional improvement to /s/ articulation in an 11-year-old girl with persistent lateral misarticulation. METHODS & PROCEDURES Treatment involved 12 sessions of therapist-delivered treatment over 4 weeks followed by a 6-week home programme. Outcomes of the treatment programme were measured primarily using naive listener ratings and acoustic analysis of /s/ spectra. OUTCOMES & RESULTS Improvements to both the perceptual and spectral characteristics of /s/ articulation occurred following the treatment programme. CONCLUSIONS The study highlighted the benefit of an intensive approach to intervention incorporating both visual biofeedback and traditional articulation approaches. The inclusion of a 6-week structured home-programme was beneficial and resulted in consolidation of treatment gains.
Simulation of Flow Inside Heat Pipe: Sensitivity Study, Conditions and Configuration

Heat pipes are widely used as a heat transporting device in a variety of applications. From space satellites, large industrial appliances to a heat sink for cooling electronic components and packages. Heat pipes are extremely efficient because of their high effective thermal conductivity, compactness, low cost and reliability. Therefore, the designers of heat sinks are often required to optimize the performance of the heat pipe itself in order to improve the overall thermal management system of any particular equipment. However, the detailed internal modeling of a heat pipe presents a challenging problem for an engineer. It is a multi physics problem including two phase flow within porous media and with conjugate heat transfer adding the solicited high capillary and surface tension effect. In this present study, detailed modeling of the heat pipe considering the mentioned effects is pursued. A basic review of the governing equations describing the complete heat pipe operation is given. The commercially available simulation tool Fluent 6.3 is used to describe and solve these equations in a coupled conjugate heat transfer set up. The geometry of heat pipe is divided in two different regions which solve simultaneously. The first region is core region where only vapor flow is assumed. The second region consists of wall and wick structure through which the mass transfer due to wettability and heat dissipates through conduction. Water was used as flowing fluids through wick porous structure. Previous experimental as well as numerical models regarding the heat pipes have been studied and used for the verification of the present model along with a standard grid convergence study. The effects of different heat pipe length, heat fluxes, wall thickness, wall material and porosity are investigated. The pressure drop and wall temperature increase with the value of heat flux. Similarly, porosity and wall material affect the wall temperature distribution. The effect of wall thickness and heat pipe length was not significant. In addition, a theoretical model is developed for the pressure drop across the heat pipe in vapor region and the respective output was used for the simulation. Finally, the temperature distribution in wall and wick is shown and discussed.
Embedding Approaches to Combining Rules and Ontologies into Autoepistemic Logic

The combination of rules and ontologies has a central role in the ongoing development of the Semantic Web. In previous work, autoepistemic logic (AEL) was advocated as a uniform host formalism to study different such combinations, enabling comparisons on a common basis. In this paper, we continue this line of research and investigate different embeddings of major proposals to combine rules and ontologies into first-order autoepistemic logic (FO-AEL). In particular, we present embeddings for dl-programs, r-hybrid knowledge bases, and hybrid MKNF knowledge bases, which are representatives of different combination types. We study the embeddings in the context of FO-AEL under the standard-names assumption, but we also discuss variants using the any- and all-names semantics. Our results provide interesting insights into the properties of the discussed combination formalisms.
Transcranial Ultrasound Brain Perfusion Assessment With a Contrast Agent-Specific Imaging Mode: Results of a Two-Center Trial

Background and Purpose— The purpose of this study was to assess brain perfusion with an ultrasound contrast-specific imaging mode and to prove if the results are comparable between 2 centers using a standardized study protocol. Methods— A total of 32 individuals without known cerebrovascular disease were included in the study. Perfusion studies were performed ipsilaterally in an axial diencephalic plane after intravenous administration of 0.75 mL of Optison. Offline time intensity curves (TIC) were generated in different anatomic regions. Both centers used identical study protocols, ultrasound machines, and contrast agent. Results— In both centers, the comparison of the parameter time to peak intensity (TPI) revealed significantly shorter TPIs in the main vessel structures compared with any parenchymal region of interest (ROI), whereas no significant differences were seen between the parenchymal ROIs. The parameter peak intensity (PI) varied widely interindividually in both centers, whereas the inter-ROI comparison revealed statistical significance (P<0.05) in most of the cases according to the following pattern: (1) lentiforme nucleus > thalamus and white matter region, (2) thalamus > white matter region, and (3) main vessel > any parenchymal structure. Similar results were achieved in both centers independently. Conclusion— The study demonstrates that brain perfusion assessment with an ultrasound contrast-specific imaging mode is comparable between different centers using the same study protocol.
Static and Dynamic Characterization of the Temperature and Humidity Influence on IPMC Actuators

Several models that describe the behavior of ionic polymer-metal composite (IPMC)-based actuators can be found in the literature. The response of IPMC transducers as a function of modifying quantities is a matter of interest; however, it has not been investigated. It is reasonable to argue that environmental humidity and temperature represent the main modifying parameters. In fact, humidity changes the behavior of IPMC transducers, working as both sensors and actuators, because it changes the Young modulus of the devices and, hence, their mechanical response. The influence of temperature is suspected, because polymer characteristics are often influenced by this quantity. In a previous paper, the authors proposed a dynamic model and investigated the scaling effect of geometrical parameters, giving evidence of the excellent agreement between estimations that were obtained using the proposed model and corresponding observations. In this paper, the response of IPMC actuators to both temperature and relative humidity is analyzed, giving interesting information that both integrates IPMC models and allows for a better exploitation of IPMCs.