Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced transfer of terrestrially derived carbon to the atmosphere in a flooding event

Rising CO2 concentration in the atmosphere, global climate change, and the sustainability of the Earth's biosphere are great societal concerns for the 21st century. Global climate change has, in part, resulted in a higher frequency of flooding events, which allow for greater exchange between soil/plant litter and aquatic carbon pools. Here we demonstrate that the summer 2011 flood in the Mississippi River basin, caused by extreme precipitation events, resulted in a “flushing” of terrestrially derived dissolved organic carbon (TDOC) to the northern Gulf of Mexico. Data from the lower Atchafalaya and Mississippi rivers showed that the DOC flux to the northern Gulf of Mexico during this flood was significantly higher than in previous years. We also show that consumption of radiocarbon‐modern TDOC by bacteria in floodwaters in the lower Atchafalaya River and along the adjacent shelf contributed to northern Gulf shelf waters changing from a net sink to a net source of CO2 to the atmosphere in June and August 2011. This work shows that enhanced flooding, which may or may not be caused by climate change, can result in rapid losses of stored carbon in soils to the atmosphere via processes in aquatic ecosystems.
Glyph-Based Comparative Visualization for Diffusion Tensor Fields

Diffusion Tensor Imaging (DTI) is a magnetic resonance imaging modality that enables the in-vivo reconstruction and visualization of fibrous structures. To inspect the local and individual diffusion tensors, glyph-based visualizations are commonly used since they are able to effectively convey full aspects of the diffusion tensor. For several applications it is necessary to compare tensor fields, e.g., to study the effects of acquisition parameters, or to investigate the influence of pathologies on white matter structures. This comparison is commonly done by extracting scalar information out of the tensor fields and then comparing these scalar fields, which leads to a loss of information. If the glyph representation is kept, simple juxtaposition or superposition can be used. However, neither facilitates the identification and interpretation of the differences between the tensor fields. Inspired by the checkerboard style visualization and the superquadric tensor glyph, we design a new glyph to locally visualize differences between two diffusion tensors by combining juxtaposition and explicit encoding. Because tensor scale, anisotropy type, and orientation are related to anatomical information relevant for DTI applications, we focus on visualizing tensor differences in these three aspects. As demonstrated in a user study, our new glyph design allows users to efficiently and effectively identify the tensor differences. We also apply our new glyphs to investigate the differences between DTI datasets of the human brain in two different contexts using different b-values, and to compare datasets from a healthy and HIV-infected subject.
Phylogenetic Approach for Estimating Noh Archetypes

Noh is a classical Japanese stage art consisting of dance and music. It has been handed down since Kan'ami and his son, Zeami, perfected the art of Noh in the 14th and 15th centuries. Because of the nature of this stage art, the verses used in Noh have frequently been arranged by successors. Therefore, finding the original forms of earlier composers is complicated. In this paper, the author attempt to develop a new approach for estimating these originals on the basis of a phylogenetic analysis, which originated in the field of biology. Although phylogenetic analysis has been adapted in phylogenetic philology, it has not been applied to the study of Noh verses. Its application in this field would make it possible to trace the history of Noh manuscripts and establish archetypes of several Noh plays.
Biodistribution and clearance of quantum dots in small animals

CdSe-core, ZnS-capped semiconductor nanoparticles - quantum dots (QDs) - have been at the forefront of biomedical nanotechnology research thanks to their unique optical Η photophysical properties. In the present study the impact of the particle coating and size on their in vivo fate after intravenous (IV) injection into mice was studied by fluorescence methods. For this study, we compared organ-selective biodistribution and elimination routes of synthesized QDs coated with 3-mercaptopropionic acid (QD MPA) and commercially available Qtracker 705 nontargeted quantum dots with poly(ethylene glycol) coating (QD PEG). We observed primary accumulation of these QDs in lung. Experiments demonstrated that QD MPA and QD PEG have both remained fluorescent in lung after at least 24 hours postinjection. Moreover, QDs was seen to deposit mainly in liver, spleen, kidney and lymph nodes. We also concluded that QDs MPA and QDs 705 are both sequestered and not excreted with feces or urine.
Object stereo — Joint stereo matching and object segmentation

This paper presents a method for joint stereo matching and object segmentation. In our approach a 3D scene is represented as a collection of visually distinct and spatially coherent objects. Each object is characterized by three different aspects: a color model, a 3D plane that approximates the object's disparity distribution, and a novel 3D connectivity property. Inspired by Markov Random Field models of image segmentation, we employ object-level color models as a soft constraint, which can aid depth estimation in powerful ways. In particular, our method is able to recover the depth of regions that are fully occluded in one input view, which to our knowledge is new for stereo matching. Our model is formulated as an energy function that is optimized via fusion moves. We show high-quality disparity and object segmentation results on challenging image pairs as well as standard benchmarks. We believe our work not only demonstrates a novel synergy between the areas of image segmentation and stereo matching, but may also inspire new work in the domain of automatic and interactive object-level scene manipulation.
Can ProMED-mail Bootstrap Blogs? Automatic Labeling of Victim-reporting Sentences ?

Due to the proliferation of social media data and user-ge- nerated content available, monitoring trends or using this data in other scenarios becomes more interesting. Our research focuses on the extrac- tion of information on health events from user generated content with the objective to support Epidemic Intelligence. Speciflcally, we describe and evaluate a method for identifying sentences relevant for event extrac- tion. Labeled data is unavailable for this task and manual annotation is expensive. Therefore, in order to reduce the number of labeled examples, we apply a bootstrapping algorithm for this task. In more detail, we will study the suitability of a classifler trained on one text type (e-mails) for the classiflcation of texts of another text type (blogs).
A noise-aware click model for web search

Recent advances in click model have established it as an attractive approach to infer document relevance. Most of these advances consider the user click/skip behavior as binary events but neglect the context in which a click happens. We show that real click behavior in industrial search engines is often noisy and not always a good indication of relevance. For a considerable percentage of clicks, users select what turn out to be irrelevant documents and these clicks should not be directly used as evidence for relevance inference. Thus in this paper, we put forward an observation that the relevance indication degree of a click is not a constant, but can be differentiated by user preferences and the context in which the user makes her click decision. In particular, to interpret the click behavior discriminatingly, we propose a Noise-aware Click Model (NCM) by characterizing the noise degree of a click, which indicates the quality of the click for inferring relevance. Specifically, the lower the click noise is, the more important the click is in its role for relevance inference. To verify the necessity of explicitly accounting for the uninformative noise in a user click, we conducted experiments on a billion-scale dataset. Extensive experimental results demonstrate that as compared with two state-of-the-art click models in Web Search, NCM can better interpret user click behavior and achieve significant improvements in terms of both perplexity and NDCG.
On the Geometric Ergodicity of Metropolis-Hastings Algorithms for Lattice Gaussian Sampling

Sampling from the lattice Gaussian distribution has emerged as an important problem in coding, decoding, and cryptography. In this paper, the classic Metropolis-Hastings (MH) algorithm in Markov chain Monte Carlo methods is adopted for lattice Gaussian sampling. Two MH-based algorithms are proposed, which overcome the limitation of Klein’s algorithm. The first one, referred to as the independent Metropolis-Hastings-Klein (MHK) algorithm, establishes a Markov chain via an independent proposal distribution. We show that the Markov chain arising from this independent MHK algorithm is uniformly ergodic, namely, it converges to the stationary distribution exponentially fast regardless of the initial state. Moreover, the rate of convergence is analyzed in terms of the theta series, leading to predictable mixing time. A symmetric Metropolis-Klein algorithm is also proposed, which is proven to be geometrically ergodic.
Interaction between the SifA Virulence Factor and Its Host Target SKIP Is Essential for Salmonella Pathogenesis*

SifA is a Salmonella effector that is translocated into infected cells by the pathogenicity island 2-encoded type 3 secretion system. SifA is a critical virulence factor. Previous studies demonstrated that, upon translocation, SifA binds the pleckstrin homology motif of the eukaryotic host protein SKIP. In turn, the SifA-SKIP complex regulates the mobilization of the molecular motor kinesin-1 on the bacterial vacuole. SifA exhibits multiple domains containing functional motifs. Here we performed a molecular dissection and a mutational study of SifA to evaluate the relative contribution of the different domains to SifA functions. Biochemical and crystallographic analysis confirmed that the N-terminal domain of SifA is sufficient to interact with the pleckstrin homology domain of SKIP, forming a 1:1 complex with a micromolar dissociation constant. Mutation of the tryptophan residue in the WXXXE motif, which has been proposed to mimic active form of GTPase, deeply affected the stability and the translocation of SifA while mutations of the glutamic residue had no functional impact. A SifA L130D mutant that does not bind SKIP showed a ΔsifA-like phenotype both in infected cells and in the mouse model of infection. We concluded that the WXXXE motif is essential for maintaining the tertiary structure of SifA, the functions of which require the interaction with the eukaryotic protein SKIP.
Joint compression and restoration of images using wavelets and non-linear interpolative vector quantization

We present a wavelet based non-linear interpolative vector quantization scheme for joint compression and restoration of images; two tasks which are traditionally regarded as having conflicting goals. Vector quantizer codebook training is done using a training set consisting of pairs of the original image and its diffraction-limited counterpart. The designed VQ is then used to compress and simultaneously restore diffraction-limited images. Results from simulations indicate that the image produced at the output of the decoder is quantitatively and visually superior to the diffraction-limited image at the input to the encoder. We also compare the performance of several wavelet filters in our algorithm.
Theoretical Analysis and Tuning of Decentralized Probabilistic Auto-Scaling

A major impediment towards the industrial adoption of decentralized distributed systems comes from the di culty to theoretically prove that these systems exhibit the required behavior. In this paper, we use probability theory to analyze a decentralized auto-scaling algorithm in which each node probabilistically decides to scale in or out. We prove that, in the context of dynamic workloads, the average load of the system is maintained within a variation interval with a given probability, provided that the number of nodes and the variation interval length are higher than certain bounds. The paper also proposes numerical algorithms for approximating these minimum bounds.
A double dipoles per cell structure for solving common-mode resonance in tightly coupled dipole array

A key challenge in designing tightly coupled dipole arrays (TCDAs) and connected arrays is common-mode resonance, which could dramatically influence the bandwidth. In this article, a double dipoles per cell structure is applied in TCDA unit design in order to solve the resonance by moving the resonance frequency above the operation band. The simulation results show that the double dipoles per cell structure reduces the common-mode resonance effectively and the array achieves 3:1 bandwidth (from 3GHz to 9GHz). When scanning in H-plane and E-plane, respectively, the array achieves 3GHz to 9GHz and 3.5GHz to 9.2GHz bandwidth with the scan angle up to 45°.
Snap-to-fit, a haptic 6 DOF alignment tool for virtual assembly

Virtual assembly of complex objects has application in domains ranging from surgery planning to archaeology. In these domains the objective is to plan the restoration of skeletal anatomy or archaeological artifacts to achieve an optimal reconstruction without causing further damage. While graphical modeling plays a central role in virtual assembly, visual feedback alone is often insufficient since object contact and penetration is difficult to discern due to occlusion. Haptics can improve an assembly task by giving feedback when objects collide, but precise fitting of fractured objects guided by delicate haptic cues similar to those present in the physical world requires haptic display transparency beyond the performance of today's systems. We propose a haptic alignment tool that combines a 6 Degrees of Freedom (DOF) attraction force with traditional 6 DOF contact forces to pull a virtual object towards a local stable fit with a fixed object. The object forces are integrated into a virtual coupling framework yielding a stable haptic tool. We demonstrate the use of our system on applications from both cranio-maxillofacial surgery and archaeology, and show that we can achieve haptic rates for fractured surfaces with over 5000 points.
A Survey on Congestion Control Routing for Wireless Network

Wireless networks have long suffered from congestion. It occurs when source node transmits the data at a rate greater than that of a network device can accommodate. It causes the buffer on such devices to fill up and possibly overflow. It results in loss of packets. Most of the Routing protocols which are currently in use are not congestion Adaptive. Existing congestion control schemes treat congestion as an individual problem and propose ad hoc solution that is dissatisfied. Routing should not be aware of, but also be adaptive to network congestion. Adaptation to the congestion helps to increase both the effectiveness and efficiency of routing. These problems are solved by the congestion-aware routing protocols in certain degree. These protocols which are adaptive to congestion status of mobile ad-hoc network can greatly improve the network performance. Further it allows a network to operate in the region of low delay and high throughput. This survey paper concentrates on congestion detection and congestion avoidance.
Resident microglia, rather than blood‐derived macrophages, contribute to the earlier and more pronounced inflammatory reaction in the immature compared with the adult hippocampus after hypoxia‐ischemia

The mechanisms of neuronal injury after hypoxia–ischemia (HI) are different in the immature and the adult brain, but microglia activation has not been compared. The purpose of this study was to phenotype resident microglia and blood‐derived macrophages in the hippocampus after HI in neonatal (postnatal day 9, P9) or adult (3 months of age, 3mo) mice. Unilateral brain injury after HI was induced in Cx3cr1GFP/+Ccr2RFP/+ male mice on P9 (n = 34) or at 3mo (n = 53) using the Vannucci model. Resident microglia (Cx3cr1‐GFP+) proliferated and were activated earlier after HI in the P9 (1–3 days) than that in the 3mo hippocampus, but remained longer in the adult brain (3–7 days). Blood‐derived macrophages (Ccr2‐RFP+) peaked 3 days after HI in both immature (P9) and adult (3mo) hippocampi but were twice as frequent in adult brains, 41% vs. 21% of all microglia/macrophages. CCL2 expression was three times higher in the P9 hippocampi, indicating that the proinflammatory response was more pronounced in the immature brain after HI. This corresponded well with the higher numbers of galectin‐3‐positive resident microglia in the P9 hippocampi, but did not correlate with CD16/32‐ or CD206‐positive resident microglia or blood‐derived macrophages. In conclusion, resident microglia, rather than infiltrating blood‐derived macrophages, proliferate and are activated earlier in the immature than in the adult brain, but remain increased longer in the adult brain. The inflammatory response is more pronounced in the immature brain, and this correlate well with galectin‐3 expression in resident microglia. GLIA 2015;63:2220–2230
A grapheme-based method for automatic alignment of speech and text data

This paper introduces a method for automatic alignment of speech data with unsynchronised, imperfect transcripts, for a domain where no initial acoustic models are available. Using grapheme-based acoustic models, word skip networks and orthographic speech transcripts, we are able to harvest 55% of the speech with a 93% utterance-level accuracy and 99% word accuracy for the produced transcriptions. The work is based on the assumption that there is a high degree of correspondence between the speech and text, and that a full transcription of all of the speech is not required. The method is language independent and the only prior knowledge and resources required are the speech and text transcripts, and a few minor user interventions.
Visualisation de graphes avec Tulip : exploration interactive de grandes masses de données en appui à la fouille de données et à l'extraction de connaissances

Cet article decrit une etude de cas exhibant les qualites de la plateforme de visualisation de graphes Tulip, demontrant l'apport de la visualisation a la fouille de donnees interactive et a l'extraction de connaissances. Le calcul dSun graphe a partir d'indices de similarite est un exemple typique ou l'exploration visuelle et interactive de graphes vient en appui au travail de fouille de donnees. Nous penchons sur le cas ou l'on souhaite etudier une collection de documents afin d'avoir une idee des thematiques abordees dans la collection.
Recovery of postural control after cerebral concussion: new insights using approximate entropy.

CONTEXT The return-to-play decision after sport-related cerebral concussion depends in part on knowing when an athlete has fully recovered postural control after injury. OBJECTIVE To describe the postconcussion recovery of postural control using approximate entropy (ApEn), a regularity statistic from nonlinear dynamics. DESIGN Retrospective case series analysis. SETTING Sports medicine research laboratory. PATIENTS OR OTHER PARTICIPANTS Collegiate athletes from whom center-of-pressure and symptom data were collected at preseason, less than 48 hours after injury, and 48 to 96 hours after injury. MAIN OUTCOME MEASURE(S) Approximate entropy values reflecting the amount of randomness contained in center-of-pressure oscillations were calculated for anterior-posterior (AP) and medial-lateral (ML) time series. Equilibrium scores reflecting the amplitude of center-of-pressure AP oscillations were used to indicate postural stability. The number and severity of symptoms were described. RESULTS Compared with the healthy preseason state, ApEn values for the AP and ML time series generally declined immediately after injury in both steady and unsteady injured athletes. At 48 to 96 hours after injury, ApEn values for the ML time series remained significantly depressed (mean difference compared with preseason = -0.268, standard error = 0.072), even among athletes whose initial postural instability had resolved. We found few significant relationships between changes in ApEn values and changes in symptoms before and after injury. CONCLUSIONS The effects of cerebral concussion on postural control appear to persist for longer than 3 to 4 days, even among athletes with no signs of unsteadiness. Our results may reflect changes in neurophysiologic or mechanical constraints on postural control. Approximate entropy provides a theoretically distinct, valuable measurement alternative that may prove useful for reducing uncertainty in the return-to-play decision.
Mental non-motor imagery tasks classifications of brain computer interface for wheelchair commands using genetic algorithm-based neural network

A genetic algorithm (GA)-based neural network classification in the application of brain computer interface (BCI) for controlling a wheelchair is presented in this paper. This study uses an electroencephalography (EEG) as a non-invasive BCI approach to discriminate three non-motor imagery mental tasks for disabled individuals who may have difficulty in using BCI based motor imagery tasks. The three tasks classification is mapped into three wheelchair movements: left, right and forward and the relevant combination mental tasks used in this study are mental arithmetic, letter composing, Rubik's cube rolling, visual counting, ringtone imagery and spatial navigation. The results show the proposed system provides good classification performance after selecting the most effective of three discriminative tasks across combination of the different non-motor imagery mental tasks for the five subjects tested. The average classification accuracy is between 76% and 85 %, with information transfer rates varies from 0.5 to 0.8 bits per trial.
Reflectance and texture of real-world surfaces

In this work, we investigate the visual appearance of real-world surfaces and the dependence of appearance on the geometry of imaging conditions. We discuss a new texture representation called the BTF (bidirectional texture function) which captures the variation in texture with illumination and viewing direction. We present a BTF database with image textures from over 60 different samples, each observed with over 200 different combinations of viewing and illumination directions. We describe the methods involved in collecting the database as well as the importqance and uniqueness of this database for computer graphics. A related quantity to the BTF is the familiar BRDF (bidirectional reflectance distribution function). The measurement methods involved in the BTF database are conducive to simultaneous measurement of the BRDF. Accordingly, we also present a BRDF database with reflectance measurements for over 60 different samples, each observed with over 200 different combinations of viewing and illumination directions. Both of these unique databases are publicly available and have important implications for computer graphics.