Miracle-dz/UniFAR-FTUs huggingface dataset:
Indicator dilution models for the quantification of microvascular blood flow with bolus administration of ultrasound contrast agents

Indicator dilution methods have a long history in the quantification of both macro- and microvascular blood flow in many clinical applications. Various models have been employed in the past to isolate the primary pass of an indicator after an intravenous bolus injection. The use of indicator dilution techniques allows for the estimation of hemodynamic parameters of a tumor or organ and thus may lead to useful diagnostic and therapy monitoring information. In this paper, we review and discuss the properties of the lognormal function, the gamma variate function, the diffusion with drift models, and the lagged normal function, which have been used to model indicator dilution curves in different fields of medicine. We fit these models to contrast-enhanced ultrasound time-intensity curves from liver metastases and the ovine corpora lutea. We evaluate the models' performance on the image data and compare their predictions for hemodynamic-related parameters such as the area under the curve, the mean transit time, the full-width at half-maximum, the time to the peak intensity, and wash-in time. The models that best fit the experimental data are the lognormal function and the diffusion with drift.
A new symbol-alphabet-aware multi-user detection scheme

In this letter, a new multi-user detection scheme is proposed. It employs a novel nonlinear minimum mean square error (MMSE) estimator that exploits the knowledge of symbol alphabet to estimate the interfering signals. After cancelling the estimated interference, a conventional linear multi-user detector such as the MMSE detector or, simply, the matched-filter receiver (MFR) is then used to detect the desired user signal. Simulation results demonstrate that the proposed detector significantly outperforms the conventional linear MMSE detector
Characterization of wound reepithelialization using a new human tissue-engineered corneal wound healing model.

PURPOSE The reepithelialization of the corneal surface is an important process for restoring the imaging properties of this tissue. The purpose of the present study was to characterize and validate a new human in vitro three-dimensional corneal wound healing model by studying the expression of basement membrane components and integrin subunits that play important roles during epithelial cell migration and to verify whether the presence of exogenous factors could accelerate the reepithelialization. METHODS Tissue-engineered human cornea was wounded with a 6-mm biopsy punch, and the reepithelialization from the surrounding margins was studied. Biopsy samples of the reepithelialized surface were harvested 3 days after wounding and were processed for histologic, electron microscopic, and immunofluorescence analyses. The effects of fibrin and epithelial growth factor (EGF) on wound reepithelialization were also studied. RESULTS Results demonstrated that this in vitro model allowed the migration of human corneal epithelial cells on a natural extracellular matrix. During reepithelialization, epithelial cell migration followed a consistent wavelike pattern similar to that reported for human corneal wound healing in vivo. This model showed a histologic appearance similar to that of native tissue as well as expression and modulation of basement membrane components and the integrin subunits known to be main actors during the wound healing process. It also allowed quantification of the reepithelialization rate, which was significantly accelerated in the presence of fibrin or EGF. The results indicated that alpha v beta6 integrin expression was increased in the migrating epithelial cells compared with the surrounding corneal tissue. CONCLUSIONS The similarity observed with the in vivo wound healing process supports the use of this tissue-engineered model for investigating the basic mechanisms involved in corneal reepithelialization. Moreover, this model may also be used as a tool to screen agents that affect reepithelialization or to evaluate the effect of growth factors before animal testing.
Sources of ozone over the North Atlantic and trans-Atlantic transport of pollution : a global model perspective

Contributed byQinbin Li (qli@io.harvard.edu), Daniel J. Jacob(djj@io.harvard.edu),Isabelle Bey (bey@io.harvard.edu), Robert M. Yantosca(bmy@io.harvard.edu), Brendan D. Field (bdf@io.harvard.edu), Hongyu Liu (hyl@io.harvard.edu), Jennifer A. Logan (jal@io.harvard.edu),Arlene M. Fiore (amf@io.harvard.edu), Randall V. Martin (rvm@io.harvard.edu), Bryan N. Duncan (bnd@io.harvard.edu), Harvard University, USA
A Novel Sequential Spectrum Sensing Method via Stochastic Resonance

As spectrum sensing detects the presence of primary user (PU) signal, an efficient and reliable spectrum sensing scheme plays a critical role in cognitive radio (CR). In this paper, a novel spectrum sensing method via stochastic resonance (SR) under low signal-to-noise ratio (SNR) is presented. It is shown that the introducing of suitable additional noise can enhance sequential energy detector (SED). Theoretical analysis and the optimal SR noise probability distribution function (PDF) are given. Simulation results show that in comparison with traditional sequential energy detection, our method delivers considerable reduction on the average sample number (ASN), while maintaining a comparable detection performance under low SNR.
Do mitochondrial properties explain intraspecific variation in thermal tolerance?

SUMMARY As global temperatures rise, there is a growing need to understand the physiological mechanisms that determine an organism's thermal niche. Here, we test the hypothesis that increases in mitochondrial capacity with cold acclimation and adaptation are associated with decreases in thermal tolerance using two subspecies of killifish (Fundulus heteroclitus) that differ in thermal niche. We assessed whole-organism metabolic rate, mitochondrial amount and mitochondrial function in killifish acclimated to several temperatures. Mitochondrial enzyme activities and mRNA levels were greater in fish from the northern subspecies, particularly in cold-acclimated fish, suggesting that the putatively cold-adapted northern subspecies has a greater capacity for increases in mitochondrial amount in response to cold acclimation. When tested at the fish's acclimation temperature, maximum ADP-stimulated (State III) rates of mitochondrial oxygen consumption in vitro were greater in cold-acclimated northern fish than in southern fish but did not differ between subspecies at higher acclimation temperatures. Whole-organism metabolic rate was greater in fish of the northern subspecies at all acclimation temperatures. Cold acclimation also changed the response of mitochondrial respiration to acute temperature challenge. Mitochondrial oxygen consumption was greater in cold-acclimated northern fish than in southern fish at low test temperatures, but the opposite was true at high test temperatures. These differences were reflected in whole-organism oxygen consumption. Our data indicate that the plasticity of mitochondrial function and amount differs between killifish subspecies, with the less high-temperature tolerant, and putatively cold adapted, northern subspecies having greater ability to increase mitochondrial capacity in the cold. However, there were few differences in mitochondrial properties between subspecies at warm acclimation temperatures, despite differences in both whole-organism oxygen consumption and thermal tolerance at these temperatures.
Genre and Layout in Multimodal Documents: Towards an Empirical Account

We argue for a model of document genre that encompasses both linguistic and graphical resources as a means of expression. Two bird books are analysed (1972 and 1996) and a simple framework presented for the description of graphical differentiation of communicative function. The analysis predicts that graphical differentiation in this genre is less in earlier publications. This suggestion is tested on a third bird book (1924) and found to be correct. However, the comparison shows that the genre itself has shifted over time, arguing for a 3-D model in which genre is represented as a shifting and interrelated set of parameters. Given this, analysis across genres and within genres across time is a very similar enterprise. A new project, GeM, has begun research into the appropriate model of genre for representing the generic differentiation of layout.
Stable isotopic compositions and fractionations of carbon monoxide at coastal and open ocean stations in the Pacific

[1] Included in this report are the results of the first isotopic studies of seawater-dissolved carbon monoxide (CO). Large variations in both carbon and oxygen isotopic compositions (δ13C: −44.7 ∼ −21.1‰PDB, and δ18O: +8.7 ∼ +32.9‰SMOW) were observed in seawater-dissolved CO due to the combination of isotopically light CO production in seawater and the enrichment of heavy isotopes during the microbial consumption of CO. Compared with the total δ13C value of dissolved organic matter (DOM), the isotopic compositions of the photochemically produced CO in seawater are depleted in 13C by more than 20‰, probably due to large fractionation processes during the photochemical production of CO from DOM. In addition, the isotopic fractionation factors resulting from the microbial oxidation of CO in seawater were estimated to be 1.005 ± 0.002 and 1.006 ± 0.002 for carbon (αc) and oxygen (αo) based on the incubation experiments. By calculating the weighted mean of the isotopic composition of CO according to the CO concentration observed in surface seawater, the mean δ13C and δ18O for CO emitted from the oceans were estimated to be −40‰ PDB and +15‰ SMOW, respectively. Oceanic CO is a unique source of 13C and 18O-depleted CO relative to that of fossil fuel combustion and biomass burning, which will help us create a better isotopic mass balance for both global and local CO budget.
Generative Goal-Driven User Simulation for Dialog Management

User simulation is frequently used to train statistical dialog managers for task-oriented domains. At present, goal-driven simulators (those that have a persistent notion of what they wish to achieve in the dialog) require some task-specific engineering, making them impossible to evaluate intrinsically. Instead, they have been evaluated extrinsically by means of the dialog managers they are intended to train, leading to circularity of argument. In this paper, we propose the first fully generative goal-driven simulator that is fully induced from data, without hand-crafting or goal annotation. Our goals are latent, and take the form of topics in a topic model, clustering together semantically equivalent and phonetically confusable strings, implicitly modelling synonymy and speech recognition noise. We evaluate on two standard dialog resources, the Communicator and Let's Go datasets, and demonstrate that our model has substantially better fit to held out data than competing approaches. We also show that features derived from our model allow significantly greater improvement over a baseline at distinguishing real from randomly permuted dialogs.
Book Reviews: WordNet: An Electronic Lexical Database

WordNet is perhaps the most important and widely used lexical resource for natural language processing systems up to now. WordNet: An Electronic Lexical Database, edited by Christiane Fellbaum, discusses the design of WordNet from both theoretical and historical perspectives, provides an up-to-date description of the lexical database, and presents a set of applications of WordNet. The book contains a foreword by George Miller, an introduction by Christiane Fellbaum, seven chapters from the Cognitive Sciences Laboratory of Princeton University, where WordNet was produced, and nine chapters contributed by scientists from elsewhere. Miller's foreword offers a fascinating account of the history of WordNet. He discusses the presuppositions of such a lexical database, how the top-level noun categories were determined, and the sources of the words in WordNet. He also writes about the evolution of WordNet from its original incarnation as a dictionary browser to a broad-coverage lexicon, and the involvement of different people during its various stages of development over a decade. It makes very interesting reading for casual and serious users of WordNet and anyone who is grateful for the existence of WordNet. The book is organized in three parts. Part I is about WordNet itself and consists of four chapters: "Nouns in WordNet" by George Miller, "Modifiers in WordNet" by Katherine Miller, "A semantic network of English verbs" by Christiane Fellbaum, and "Design and implementation of the WordNet lexical database and search software" by Randee Tengi. These chapters are essentially updated versions of four papers from Miller (1990). Compared with the earlier papers, the chapters in this book focus more on the underlying assumptions and rationales behind the design decisions. The description of the information contained in WordNet, however, is not as detailed as in Miller (1990). The main new additions in these chapters include an explanation of sense grouping in George Miller's chapter, a section about adverbs in Katherine Miller's chapter, observations about autohyponymy (one sense of a word being a hyponym of another sense of the same word) and autoantonymy (one sense of a word being an antonym of another sense of the same word) in Fellbaum's chapter, and Tengi's description of the Grinder, a program that converts the files the lexicographers work with to searchable lexical databases. The three papers in Part II are characterized as "extensions, enhancements and
A New Type of Composite Anchor Dated to the Fatimid‐Crusader Period from the Dead Sea, Israel

Two composite anchors of a kind not hitherto identified, each composed of a re‐used ashlar block, a wooden shank, two arms and a rope, were discovered recently on the Dead Sea shoreline. Two additional anchor weights of identical type were found in the same region. The two well‐preserved anchors were dated to the Fatimid‐Crusader period. The shank and the arms were made from local tree species: Christ thorn and tamarisk, and both ropes of date‐palm. © 2008 The Authors
Fast Dynamics of an Eel-Like Robot—Comparisons With Navier–Stokes Simulations

This paper proposes a dynamic model of the swim of elongated fish suited to the online control of biomimetic eel-like robots. The approach can be considered as an extension of the original reactive ldquolarge elongated body theoryrdquo of Lighthill to the 3-D self-propulsion to which a resistive empirical model has been added. While all the mathematical fundamentals have been detailed by Boyer . (http://www.irccyn.ec-nantes.fr/hebergement/Publications/2007/3721.pdf, 2007), this paper essentially focuses on the numerical validation and calibration of the model and the study of swimming gaits. The proposed model is coupled to an algorithm allowing us to compute the motion of the fish head and the field of internal control torque from the knowledge of the imposed internal strain fields. Based on the Newton-Euler formalism of robot dynamics, this algorithm works faster than real time. As far as precision is concerned, many tests obtained with several planar and 3-D gaits are reported and compared (in the planar case) with a Navier-Stokes solver, which, until today have been devoted to the planar swim. The comparisons obtained are very encouraging since in all the cases we tested, the differences between our simplified and reference simulations do not exceed 10%.
Human Rhinovirus Subviral A Particle Binds to Lipid Membranes over a Twofold Axis of Icosahedral Symmetry

ABSTRACT Minor group human rhinoviruses bind low-density lipoprotein (LDL) receptors for endocytosis. Once they are inside endosomes, the acidic pH triggers their dissociation from the receptors and conversion into hydrophobic subviral A particles; these attach to the membrane and transfer their single-strand, positive-sense RNA genome into the cytosol. Here, we allowed human rhinovirus 2 (HRV2) A particles, produced in vitro by incubation at pH 5.4, to attach to liposomes; cryo-electron microscopy 3-dimensional single-particle image reconstruction revealed that they bind to the membrane around a 2-fold icosahedral symmetry axis.
A distributed locality-aware neighbor selection algorithm for P2P video streaming over wireless mesh networks

Nowadays, deployment of peer-to-peer video streaming systems over wireless mesh networks has attained raising popularity among large number of users around the world. In this paper, we present an efficient peer-to-peer live video streaming architecture over multi-hop wireless mesh networks. In our proposed architecture, we take the physical topology of network into account and based on a distributed distributed locality-aware neighbor selection algorithm in the overlay construction phase, we generate an efficient mesh-based overlay on top of wireless mesh networks. In locality-aware neighbor selection algorithm, instead of choosing randomly, peers find their best neighbors based on their distance. It means that the overlay neighbors are either the direct physical neighbors or are located at a short distance. A prominent feature of our work is to simulate wireless mesh networks based on IEEE 802.11s standard, which makes our simulation more realistic. Our preliminary simulation result shows that our proposed neighbor selection algorithm reduces video distortion, which gives peers a chance to experience a better video quality.
Cross-correlogram between rat hippocampal and prefrontal neuronal activities

We recorded spontaneous multiple unit activities (MUAs) of the hippocampus and prefrontal cortex in urethane-anesthetized rats and analyzed cross-correlograms between these MUAs to investigate the functional connectivity of neuronal activities. Results of these analyses reveal a significant correlation between MUAs in these regions, in which the firing initiated from either hippocampus (type H-P) or prefrontal cortex (type P-H) according to the significant peak of cross-correlograms. Furthermore, the MUA bursts were counted: a significant correlation was found between the peak height of cross-correlograms and MUA burst counts in type H-P, but not type P-H. These results suggest that the correlation between the hippocampus and prefrontal cortex MUAs that are related to the burst firing might reflect functional connectivity.
"SINA: semantic interpretation of user queries for question answering on interlinked data" by Saeedeh Shekarpour with Prateek Jain as coordinator

The Data Web contains a wealth of knowledge on a large number of domains. Question answering over interlinked data sources is challenging due to two inherent characteristics. First, different datasets employ heterogeneous schemas and each one may only contain a part of the answer for a certain question. Second, constructing a federated formal query across different datasets requires exploiting links between the different datasets on both the schema and instance levels. In this dissertation, we present a question answering system, which transforms user supplied queries (i.e. either natural language sentences or keywords) into conjunctive SPARQL queries over a set of interlinked data sources. The contribution of this work is as follows: 1. A novel approach for determining the most suitable resources for a user-supplied query from different datasets (disambiguation). We employ a hidden Markov model, whose parameters were bootstrapped with different distribution functions. 2. A novel method for constructing a federated formal queries using the disambiguated resources and leveraging the linking structure of the underlying datasets. This approach essentially relies on a combination of domain and range inference as well as a link traversal method for constructing a connected graph which ultimately renders a corresponding SPARQL query. The results of our evaluation with three life-science datasets and 25 benchmark queries demonstrate the effectiveness of our approach by achieving 100% precision on QALD-1 and are able to perform as well as the best question answering system from the QALD-3 competition by answering 32 questions correctly.
Three-dimensional shear wave velocity imaging by ambient seismic noise tomography

SUMMARY 3-D shear wave velocity images are of particular interest for engineering seismology. To obtain information about the local subsoil structure, we present a one-step inversion procedure based on the computation of high-frequency correlation functions between stations of a small-scale array deployed for recording ambient seismic noise. The calculation of Rayleigh wave phase velocities is based on the frequency-domain SPatial AutoCorrelation technique. Constitutively, a tomographic inversion of the traveltimes estimated for each frequency is performed, allowing the laterally varying 3-D surface wave velocity structure below the array to be retrieved. We test our technique by using simulations of seismic noise for a simple realistic site and by using real-world recordings from a small-scale array performed at the Nauen test site (Germany). The results imply that the cross-sections from passive seismic interferometry provide a clear image of the local structural heterogeneities and the shear wave velocities are satisfactorily reproduced. The velocity structure is also found to be in good agreement with the results of geoelectrical measurements, indicating the potential of the method to be easily applied for deriving the shallow 3-D velocity structure in urban areas and for monitoring purposes.
Evaluating the ability of a hydrologic model to replicate hydro‐ecologically relevant indicators

It is a common practice to employ hydrologic models for assessing alterations to streamflow as a result of anthropogenically driven changes, such as riverine, land use, and climate change. However, the ability of the models to replicate different components of the hydrograph simultaneously is not clear. Hence, this study evaluates the ability of a standard hydrologic model set‐up: Variable Infiltration Capacity (VIC) hydrologic model for two headwater sub‐basins in the Fraser River (Salmon and Willow), British Columbia, Canada, with climate inputs derived from observations and statistically downscaled global climate models (GCMs); to simulate six general water resource indicators (WRIs) and 32 ecologically relevant indicators of hydrologic alterations (IHA). The results show a generally good skill of the observation‐driven VIC model in replicating most of the WRIs and IHAs. Although the WRIs, including annual volume, centre of timing, and seasonal flows, and the IHAs, including maximum and minimum flows, were reasonably well replicated, statistically significant differences in some of the monthly flows, number and duration of flow pulses, rise and fall rates, and reversals were noted. In the case of GCM‐driven results, additional monthly, maximum, and minimum flow indicators produced statistically significant differences. A number of issues with the model input/output data, hydrologic model parametrization and structure as well as downscaling methods were identified, which lead to such discrepancies. Therefore, there is a need to exercise caution in the use of model‐simulated indicators. Overall, the WRIs and IHAs can be useful tools for evaluating changes in an altered hydrologic system, provided the skill and limitations of the model in replicating these indicators are understood. © 2013 Her Majesty the Queen in Right of Canada. Hydrological Processes © 2013 John Wiley & Sons Ltd.