Miracle-dz/UniFAR-FTUs huggingface dataset:
Synergic interaction between amyloid precursor protein and neural cell adhesion molecule promotes neurite outgrowth

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases worldwide. The main features of AD are the pathological changes of density and distribution of intracellular neurofibrillary tangles (NFT) and extracellular amyloid plaques. The processing of amyloid beta precursor protein (APP) to β-amyloid peptide (Aβ) is one of the critical events in the pathogenesis of AD. In this study, we evaluated the role of the interaction of neural cell adhesion molecule (NCAM) and APP in neurite outgrowth using two different experimental systems: PC12E2 cells and hippocampal neurons that were isolated from wild type, APP knock-in and APP knock-out mice. PC12E2 cells or hippocampal neurons were co-cultured with NCAM-negative or NCAM-positive fibroblasts L929 cells. We found that APP promoted neurite outgrowth of PC12E2 cells and hippocampal neurons in either the presence or absence of NCAM. Secreted APP can rescue the neurite outgrowth in hippocampal neurons from APP knock-out mice. The interaction of APP and NCAM had synergic effect in promoting neurite outgrowth in both PC12E2 cells and hippocampal neurons. Our results suggested that the interaction of APP with NCAM played an important role in AD development and therefore could be a potential therapeutic target for AD treatment.
User-Friendly Methodology for Automatic Exploration of Compiler Options: A Case Study on the Intel XScale Microarchitecture

Finding an optimized combination of compiler options that benefits the most a given embedded application is a challenge for most application developers. It is only with a deep understanding of the application at hand and a fairly good knowledge of the compiler features that a programmer can achieve the desired results in terms of performance, power consumption and code size out of an application. We have developed a practical methodology for automatic exploring compiler options (UMECO) to solve the problem mentioned above. This paper reports a case study of this methodology on the Intel XScale microarchitecture. Based on practical experimentation, we enhance KCC, our research compiler infrastructure, with an extended user interface that the users can provide advice to. All are controlled by a reduced set of compiler flags. We also demonstrate a compiler trade-off strategy based on experimental results for a set of well known embedded benchmarks.
Vascular occlusion sites determine differences in lesion growth from early apparent diffusion coefficient lesion to final infarct.

BACKGROUND AND PURPOSE Occlusion of major cerebral arteries is the primary source of tissue damage in ischemic stroke and the target of thrombolytic therapy. We hypothesized that large infarcts in more proximal vascular occlusions correspond with substantially increased ischemic lesions shown on initial apparent diffusion coefficient (ADC) maps. METHODS Initial ADC lesions in 120 patients with acute ischemic stroke were analyzed within 6 hours of stroke onset. Patients were categorized on the basis of vascular occlusion, as shown on MR angiography. Lesion volumes were determined by using manual delineation (ADC(man)) and a threshold method for ADC values (<550 x 10(-9) mm(2)/s(-1), ADC(<550)). Infarct volumes were analyzed by using T2-weighted (n = 109) or CT (n = 11) images obtained on days 5-8. RESULTS Median lesion volumes for ADC(<550), ADC(man), and infarcts, respectively, were as follows: proximal internal carotid artery (ICA)/middle cerebral artery (MCA) occlusions, 10, 23, and 32 cm(3); carotid-T occlusions, 11, 37, and 138 cm(3); MCA trunk occlusions, 11, 27, and 44 cm(3)); and MCA branch occlusions 8, 27, and 21 cm(3). Initial ADC lesion volumes were different only between the carotid T and the MCA branch (P < .05). On days 5-8, infarct volumes decreased from proximal to distal sites (P < .05), with the exception of MCA trunk versus proximal ICA/MCA occlusions. Recanalization rate in carotid-T occlusion was significantly lower than those of all other occlusion types. CONCLUSION Initial ADC lesions can be small, even in patients with proximal vascular occlusions. These patients develop considerably large infarctions, suggesting a high potential for infarct growth. This growth might be averted with improved early recanalization of proximal vascular occlusions.
A Peroxygenase Pathway Involved in the Biosynthesis of Epoxy Fatty Acids in Oat[W][OA]

While oat (Avena sativa) has long been known to produce epoxy fatty acids in seeds, synthesized by a peroxygenase pathway, the gene encoding the peroxygenase remains to be determined. Here we report identification of a peroxygenase cDNA AsPXG1 from developing seeds of oat. AsPXG1 is a small protein with 249 amino acids in length and contains conserved heme-binding residues and a calcium-binding motif. When expressed in Pichia pastoris and Escherichia coli, AsPXG1 catalyzes the strictly hydroperoxide-dependent epoxidation of unsaturated fatty acids. It prefers hydroperoxy-trienoic acids over hydroperoxy-dienoic acids as oxygen donors to oxidize a wide range of unsaturated fatty acids with cis double bonds. Oleic acid is the most preferred substrate. The acyl carrier substrate specificity assay showed phospholipid and acyl-CoA were not effective substrate forms for AsPXG1 and it could only use free fatty acid or fatty acid methyl esters as substrates. A second gene, AsLOX2, cloned from oat codes for a 9-lipoxygenase catalyzing the synthesis of 9-hydroperoxy-dienoic and 9-hydroperoxy-trienoic acids, respectively, when linoleic (18:2-9c,12c) and linolenic (18:3-9c,12c,15c) acids were used as substrates. The peroxygenase pathway was reconstituted in vitro using a mixture of AsPXG1 and AsLOX2 extracts from E. coli. Incubation of methyl oleate and linoleic acid or linolenic acid with the enzyme mixture produced methyl 9,10-epoxy stearate. Incubation of linoleic acid alone with a mixture of AsPXG1 and AsLOX2 produced two major epoxy fatty acids, 9,10-epoxy-12-cis-octadecenoic acid and 12,13-epoxy-9-cis-octadecenoic acid, and a minor epoxy fatty acid, probably 12,13-epoxy-9-hydroxy-10-transoctadecenoic acid. AsPXG1 predominately catalyzes intermolecular peroxygenation.
Large Bets and Stock Market Crashes

Some market crashes occur because of significant imbalances in demand and supply. Conventional models fail to explain the large magnitudes of price declines. We propose a unified structural framework for explaining crashes, based on the insights of market microstructure invariance. A proper adjustment for differences in business time across markets leads to predictions which are different from conventional wisdom and consistent with observed price changes during the 1987 market crash and the 2008 sales by Société Générale. Somewhat larger-than-predicted price drops during 1987 and 2010 flash crashes may have been exacerbated by too rapid selling. Somewhat smaller-than-predicted price decline during the 1929 crash may be due to slower selling and perhaps better resiliency of less integrated markets.
The Effects of Intraabdominally Insufflated Carbon Dioxide on Hepatic Blood Flow During Laparoscopic Surgery Assessed by Transesophageal Echocardiography

Conflicting results have been published about the effects of carbon dioxide (CO2) pneumoperitoneum on splanchnic and liver perfusion. Several experimental studies described a pressure-related reduction in hepatic blood flow, whereas other investigators reported an increase as long as the intraabdominal pressure (IAP) remained less than 16 mm Hg. Our goal in the present study was to investigate the effects of insufflated CO2 on hepatic blood flow during laparoscopic surgery in healthy adults. Blood flow in the right and middle hepatic veins was assessed in 24 patients undergoing laparoscopic surgery by use of transesophageal Doppler echocardiography. Hepatic venous blood flow was recorded before and after 5, 10, 20, 30, and 40 min of pneumoperitoneum, as well as 1 and 5 min after deflation. Twelve patients undergoing conventional hernia repair served as the control group. The induction of pneumoperitoneum produced a significant increase in blood flow of the right and middle hepatic veins. Five minutes after insufflation of CO2 the median right hepatic blood flow index increased from 196 mL/min/m2 (95% confidence interval (CI), 140–261 mL/min/m2) to 392 mL/min/m2 (CI, 263–551 mL/min/m2) (P < 0.05) and persisted during maintenance of pneumoperitoneum. In the middle hepatic vein the blood flow index increased from 105 mL/min/m2 (CI, 71–136 mL/min/m2) to 159 mL/min/m2 (CI, 103–236 mL/min/m2) 20 min after insufflation of CO2. After deflation blood flow returned to baseline values in both hepatic veins. Conversely, in the control group hepatic blood flow remained unchanged over the entire study period. We conclude that induction of CO2 pneumoperitoneum with an IAP of 12 mm Hg is associated with an increase in hepatic perfusion in healthy adults.
Practical real-time hair rendering and shading

We present a real-time algorithm for hair rendering using a polygon model, which was used in the real-time animation Ruby: The Double Cross, appearing in this year’s SIGGRAPH animation festival. The hair shading model is based on the Kajiya-Kay model, and adds a real-time approximation of realistic specular highlights as observed by Marschner et al. We also describe a simple technique to render the semi-transparent hair model in approximate back-to-front order. Instead of executing a spatial sorting step on the CPU at run-time, we render the opaque and transparent hair regions in separate passes to resolve visibility.
Massively multi-query join processing in publish/subscribe systems

There has been much recent interest in XML publish/subscribe systems. Some systems scale to thousands of concurrent queries, but support a limited query language (usually a fragment of XPath 1.0). Other systems support more expressive languages, but do not scale well with the number of concurrent queries. In this paper, we propose a set of novel query processing techniques, referred to as Massively Multi-Query Join Processing techniques, for processing a large number of XML stream queries involving value joins over multiple XML streams and documents. These techniques enable the sharing of representations of inputs to multiple joins, and the sharing of join computation. Our techniques are also applicable to relational event processing systems and publish/subscribe systems that support join queries. We present experimental results to demonstrate the effectiveness of our techniques. We are able to process thousands of XML messages with hundreds of thousands of join queries on real RSS feed streams. Our techniques gain more than two orders of magnitude speedup compared to the naive approach of evaluating such join queries.
Pharmacokinetics and Pharmacodynamics of Imipenem during Continuous Renal Replacement Therapy in Critically Ill Patients

ABSTRACT The pharmacokinetics of imipenem were studied in adult intensive care unit (ICU) patients during continuous venovenous hemofiltration (CVVH; n = 6 patients) or hemodiafiltration (CVVHDF; n = 6 patients). Patients (mean ± standard deviation age, 50.9 ± 15.9 years; weight, 98.5 ± 15.9 kg) received imipenem at 0.5 g every 8 to 12 h (total daily doses of 1 to 1.5 g/day) by intravenous infusion over 30 min. Pre- and postmembrane blood (plasma) and corresponding ultrafiltrate or dialysate samples were collected 1, 2, 4, and 8 or 12 h (depending on dosing interval) after completion of the drug infusion. Drug concentrations were measured using validated high-performance liquid chromatography methods. Mean systemic clearance (CLS) and elimination half-life (t1/2) of imipenem were 145 ± 18 ml/min and 2.7 ± 1.3 h during CVVH versus 178 ± 18 ml/min and 2.6 ± 1.6 h during CVVHDF, respectively. Imipenem clearance was substantially increased during both CVVH and CVVHDF, with membrane clearance representing 25% and 32% of CLS, respectively. The results of this study indicate that CVVH and CVVHDF contribute to imipenem clearance to a greater degree than previously reported. Imipenem doses of 1.0 g/day appear to achieve concentrations adequate to treat most common gram-negative pathogens (MIC up to 2 μg/ml) during CVVH or CVVHDF, but doses of 2.0 g/day or more may be required to adequately treat and prevent resistance in pathogens with higher MICs (MIC = 4 to 8 μg/ml). Higher doses should only be used after consideration of potential central nervous system toxicities or other risks of therapy in these severely ill patients.
Video-based noncontact heart rate measurement using ear features

Heart rate measurement, especially out of clinical environments, has recently become a hot issue in the field of health monitoring. Video-based heart rate measurement is contactless and unobtrusive. However, most video-based heart rate measurements are sensitive to illumination changes. Inspired by a previous study which measures heart rate according to ballistocardiographic motion sensed by an ear-worn tri-axial accelerometer, we proposes to detect the ballistocardiographic motion of ear by tracking ear features in a video. Then we provide a video-based noncontact heart rate monitoring method. Scale-invariant features are employed to describe the structural characteristics of the ear, invariant to illumination changes and partial occlusion, which helps achieve movements of the ear. Relying on the signals of movements of ear features, underlying ballistocardiographic motion signal is separated and spectrum analyzed to estimate the heart rate. Experimental results demonstrate that by monitoring videos our method can obtain accurate heart rates close to the measurements gained by a contact sensor.
1 Prior Work on sequential incremental tree algorithms

Parallel tree contraction has been found to be a useful and quite powerful tool for the design of a wide class of efficient graph algorithms. We propose a corresponding technique for the parallel solution of problems with incremental changes in the data. In dynamic tree contraction problems, we are given an initial tree T , and then an on-line algorithm processes requests regarding T . Requests may be either incremental changes to T or requests for certain values computed using the tree. A simple example is maintaining the pre-order numbering on a tree. The on-line algorithm would then have to handle incremental changes to the tree, and would also have to quickly answer queries about the pre-order number of any tree node. Our dynamic algorithms are based on the prior parallel tree contraction algorithms, and hence we call such algorithms incremental tree contraction algorithms. By maintaining the connection between our incremental algorithms and the parallel tree contraction algorithm, we create incremental algorithms for tree contraction. We consider a dynamic binary tree T of ≤ n nodes and unbounded depth. We describe a procedure, which we call the dynamic parallel tree contraction algorithm, which incrementally processes various parallel modification requests and queries: (1) parallel requests to add or delete leaves of T , or modify labels of internal nodes or leaves of T , and also (2) parallel tree contraction queries which require recomputing values at specified nodes. Each modification or query is with respect to a set of nodes U in T . We make use of a random splitting tree as an aid ∗This paper is a revised version of the conference proceedings extended abstract: John H. Reif and Steve R. Tate, Dynamic Parallel Tree Contraction, 5th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA’94), Cape May, NJ, June 1994. pp. 114-121. †Department of Computer Science, Duke University, Durham, NC , USA and Adjunct, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi Arabia ‡Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC
Site‐2 protease regulated intramembrane proteolysis: Sequence homologs suggest an ancient signaling cascade

Site‐2 proteases (S2Ps) form a large family of membrane‐embedded metalloproteases that participate in cellular signaling pathways through sequential cleavage of membrane‐tethered substrates. Using sequence similarity searches, we extend the S2P family to include remote homologs that help define a conserved structural core consisting of three predicted transmembrane helices with traditional metalloprotease functional motifs and a previously unrecognized motif (GxxxN/S/G). S2P relatives were identified in genomes from Bacteria, Archaea, and Eukaryota including protists, plants, fungi, and animals. The diverse S2P homologs divide into several groups that differ in various inserted domains and transmembrane helices. Mammalian S2P proteases belong to the major ubiquitous group and contain a PDZ domain. Sequence and structural analysis of the PDZ domain support its mediating the sequential cleavage of membrane‐tethered substrates. Finally, conserved genomic neighborhoods of S2P homologs allow functional predictions for PDZ‐containing transmembrane proteases in extra‐cytoplasmic stress response and lipid metabolism.
Evolutionary rescue in populations of Pseudomonas fluorescens across an antibiotic gradient

Environmental change represents a major threat to species persistence. When change is rapid, a population's only means of persisting may be to evolve resistance. Understanding such ‘evolutionary rescues’ is important for conservation in the face of global change, but also in the agricultural and medical sciences, where the objective is rather population control or eradication. Theory predicts that evolutionary rescue is fostered by large populations and genetic variation, but this has yet to be tested. We replicated hundreds of populations of the bacterium Pseudomonas fluorescens SBW25 submitted to a range of doses of the antibiotic streptomycin. Consistent with theory, population size, and initial genetic diversity influenced population persistence and the evolution of antibiotic resistance. Although all treated populations suffered initial declines, those experiencing the smallest decreases were most likely to be evolutionarily rescued. Our results contribute to our understanding of how evolution may or may not save populations and species from extinction.
A Two-Level Temporal Fair Scheduler for Multi-Cell Wireless Networks

We propose a two-level scheduler for a frequency reuse-1 multi-cell wireless network satisfying inter-and intra-cell weighted temporal fairness constraints. As opposed to hard partitioning of the entire frequency band to different cell patterns in frequency reuse-M systems (M > 1), we propose sharing this band opportunistically in time by these patterns. Through numerical examples, we show notable gains in overall network throughput due to improved multi-user diversity in comparison with a conventional frequency reuse-3 system.
On the Effect of Counters in Guard Conditions When State-Based Multi-objective Testing

During test case generation from an extended finite state machine (EFSM), the counter problem is caused by the presence of guard conditions that refer to counter variables. Because such variables are initialized and updated by transitions in the EFSM, every traversal of the state machine graph is not necessarily feasible, i.e., executable. The problem manifests itself by the fact that a transition, a sequence of transitions, or a more complex behavior in the state machine, has to be repeatedly triggered to eventually trigger a specific behavior (another transition). In this paper we define different manifestations of the counter problem and experiment with a new search based solution for that problem. We also investigate how the counter problem affects a multi-objective genetic algorithm that generates test suites from an EFSM. We evaluate our solution and compare it with an existing one, using three different case studies.
Imaging the Impact of Chemically Inducible Proteins on Cellular Dynamics In Vivo

The analysis of dynamic events in the tumor microenvironment during cancer progression is limited by the complexity of current in vivo imaging models. This is coupled with an inability to rapidly modulate and visualize protein activity in real time and to understand the consequence of these perturbations in vivo. We developed an intravital imaging approach that allows the rapid induction and subsequent depletion of target protein levels within human cancer xenografts while assessing the impact on cell behavior and morphology in real time. A conditionally stabilized fluorescent E-cadherin chimera was expressed in metastatic breast cancer cells, and the impact of E-cadherin induction and depletion was visualized using real-time confocal microscopy in a xenograft avian embryo model. We demonstrate the assessment of protein localization, cell morphology and migration in cells undergoing epithelial-mesenchymal and mesenchymal-epithelial transitions in breast tumors. This technique allows for precise control over protein activity in vivo while permitting the temporal analysis of dynamic biophysical parameters.
Leveraging human factors to enhance query answering in crowdsourcing systems

In recent years, crowdsourcing has become essential in a wide range of Web applications. Human factors play a key role in achieving high quality answers in crowdsourcing-based solving tasks. The most major factor is pertained to the uncertainty of workers about the responses that they provide to resolve the task at hand. On the other hand, workers may have diverse levels of expertise and skill. It is then important to take into account both the degrees of uncertainty and expertise when aggregating the set of worker answers. In this paper, we investigate some advanced crowdsourcing aggregation methods to find the correct answers by leveraging both expertise and uncertainty of workers in a unified way. Workers' uncertainty is represented in a possibilistic way, while a fine-grained scale for interpreting the degrees of skill is introduced. Finally, we present some comprehensive experiments to validate the effectiveness of our proposal.
Une Double Hierarchie Infinie de Langages Verifiables

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