Miracle-dz/UniFAR-FTUs huggingface dataset:
Stream morphological analysis by airborne laser altimetry and fractal dimension

The stream morphology may present different stages of fluvial processes by characteristics and sediments of various stream flow conditions; it played an important role for the stream cumulative stress. The stream morphology is being adjusted by the incoming stream flows as well as the sediments been carried. In Taiwan, streams are showing a very complicate topography due to the high eroding capability caused by secondary disasters such as landslides and debris flows after heavy rain or typhoon. Nevertheless, to understand the balancing characteristics between incoming flow and sediment regime is an important task for disaster prevention. Quantifying the morphology along a river channel has been proven difficult; till the airborne laser altimetry technology was implemented in the survey. In this study, the remote sensing techniques are employed to assist the studies on stream roughness distribution and morphological investigation. The results are proven to be valuable for hydrological and engineering applications. The stream roughness was derived from Light Detection and Ranging (LiDAR) records of Airborne Laser Altimeter. Data of the pre-disaster and the post-disaster were compared to determine the variability of stream morphology. Even the stream sediment grain size cannot be determined by high accuracy and high resolution LiDAR, topographic data can still be described as self-affined random fractals; namely, allowing fractal dimension to be implemented to understand the topographic roughness. In general, the greater the fractal dimension of the surface has, the rougher the surface is. In this study, fractal dimension are employed to evaluate the stream morphology. The results showed that the upperreaches demonstrate higher roughness values than the lower-reaches; the materials from debris flow and landslides also influence the incoming flow and sediment carrying capacities.
Standard filtration practices may significantly distort planktonic microbial diversity estimates

Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05–0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
A Comparison of Robust and Stochastic Receding Horizon Control of Discrete-Time Systems

In this thesis we study receding horizon control strategies for stochastic discrete-time linear systems with additive noise. This study is divided into two parts: First, we compare the performance of different receding horizon control techniques under constrained and unconstrained control input settings for some representative systems. It appears from our simulations that while in an unconstrained setting the robust method performs worst and the infinite horizon LQ controller performs best, no concrete conclusions can be drawn in the constrained setting. Second, we provide new results on stochastic stability (in the sense of the system being mean-square bounded,) of some of the receding horizon controllers under mild assumptions. This is effected by appending “negative drift conditions” to the the optimization routines and establishing the overall feasibility. In addition, with the aid of numerical examples we substantiate our theoretical results by showing mean-square boundedness of typical systems for different controllers under our conditions.
Quantifying Statistical Interdependence by Message Passing on Graphs—Part I: One-Dimensional Point Processes

Abstract We present a novel approach to quantify the statistical interdependence of two time series, referred to as stochastic event synchrony (SES). The first step is to extract “events” from the two given time series. The next step is to try to align events from one time series with events from the other. The better the alignment, the more similar the two time series are considered to be. More precisely, the similarity is quantified by the following parameters: time delay, variance of the timing jitter, fraction of noncoincident events, and average similarity of the aligned events. The pairwise alignment and SES parameters are determined by statistical inference. In particular, the SES parameters are computed by maximum a posteriori (MAP) estimation, and the pairwise alignment is obtained by applying the max-product algorithm. This letter deals with one-dimensional point processes; the extension to multidimensional point processes is considered in a companion letter in this issue. By analyzing surrogate data, we demonstrate that SES is able to quantify both timing precision and event reliability more robustly than classical measures can. As an illustration, neuronal spike data generated by the Morris-Lecar neuron model are considered.
Faster Spectral Sparsification of Laplacian and SDDM Matrix Polynomials

We propose a simple, faster and unified algorithm that computes in nearly linear time a spectral sparsifier D − M̂N ≈ε D − D ∑N i=0 γi(D M) of matrix-polynomials, where B = D −M ∈ R is either Laplacian or SDDM matrix with mB non-zero entries, the coefficients γi are induced by a mixture of discrete Binomial distributions (MDBD), and N = 2 k for k ∈ N. Our sparsification algorithm runs in time Õ(ε−2mB log 3 n · log N+ε ·nN · log n · log N) and exhibits a significant improvement over the previous best result of Cheng et al. [3] whose run time is Õ(ε ·mBN · poly(logn)). Although their algorithm handles general probability distributions, we demonstrate that MDBD approximate large class of continuous probability distributions. Moreover, we propose a nearly linear time algorithm that recovers exactly the coefficients of any convex combination of N +1 distinct Binomial distributions (MDBD), given as input the target probability distribution γ that is induced by a MDBD. In addition, we show that a simple preprocessing step speeds up the run time of Spielman and Peng’s [16] SDDM Solver from Õ(mB log 3 n · log κB) to Õ(mB log n+ n log n · log κB), where κB is the condition number of the input SDDM matrix B. The heart of our algorithm is a simple and efficient sparsification method that outputs a sparsifierD−M̂p for any Laplacian or SDDM matrix polynomialD−D ∑N i=0 BN,i(p)·(DM), whose coefficients follow Binomial distribution B(N, p). Then, based on preprocessed sparsifiers, we efficiently compute a convex combination of sparsifiers D − M̂pi , each of which corresponds to a different Binomial distribution B(N, pi), to obtain a sparsifier that is induced by a MDBD. Our analysis of the representational power of MDBD relies on Hald’s [10] result on mixture of Binomial distributions in the continuous setting, Cruz-Uribe and Neugebauer’s [6, 7] sharp guarantees for approximating integrals using the Trapezoid method, and Doha et al.’s [8] closed formula for higher order derivatives of Bernstein basis. When B is a dense Laplacian matrix, our result leads to the first nearly linear time algorithm for analyzing the long term behaviour of random walks induced by transition matrices of the form ∑N i=0 γi(D M), where γ is induced by MDBD and the random walk length N = Θ(n). We hope that our sparsification algorithm for SDDM matrices can be useful in the context of Machine Learning.
Pregnancy-related discontinuation of antidepressants and depression care visits among Medicaid recipients.

OBJECTIVE This study examined whether pregnancy is associated with discontinuation of care for depression among low-income women. METHODS Medicaid claims data from all 50 states were used in a matched cohort study design. The study included 3,237 women who gave birth between 1999 and 2000 and received depression treatment (antidepressant medications or a depression care visit) before initiating prenatal care. A control cohort of nonpregnant women receiving gynecologic care in the same period was matched by demographic and depression treatment characteristics. RESULTS Prepregnancy, the antidepressant use rate was 66%. During pregnancy, antidepressant use dropped to 27% in the pregnant cohort compared with 62% in the control group (rate ratio [RR] =.44, 95% confidence interval [CI]=.41-.46) and remained low postpartum compared with the control group (35% versus 48%, RR=.74, CI=.70-.78). Similarly, depression care visits during the pregnancy period were reduced to 31% among the pregnant cohort compared with 49% for the control group (RR=.65, CI=.61-.69) and remained lower postpartum relative to the control group (24% versus 31%, RR=.78, CI=.73-.85). Interactions with pregnancy status were found for race-ethnicity and receipt of cash assistance from Medicaid. White women in the pregnancy cohort had a greater reduction in depression care visits than nonwhite women during the pregnancy period but less reduction in antidepressant use postpartum relative to the control group. Cash assistance was associated with less discontinuation in depression care visits postpartum compared with the control group (p<.05). CONCLUSIONS Pregnancy was associated with discontinuation of any depression care among women receiving Medicaid; care did not resume postpartum. Race-ethnicity and Medicaid cash benefit status moderated this finding. Efforts are needed to mitigate these reductions.
DBETH: A Database of Bacterial Exotoxins for Human

Pathogenic bacteria produce protein toxins to survive in the hostile environments defined by the host's defense systems and immune response. Recent progresses in high-throughput genome sequencing and structure determination techniques have contributed to a better understanding of mechanisms of action of the bacterial toxins at the cellular and molecular levels leading to pathogenicity. It is fair to assume that with time more and more unknown toxins will emerge not only by the discovery of newer species but also due to the genetic rearrangement of existing bacterial genomes. Hence, it is crucial to organize a systematic compilation and subsequent analyses of the inherent features of known bacterial toxins. We developed a Database for Bacterial ExoToxins (DBETH, http://www.hpppi.iicb.res.in/btox/), which contains sequence, structure, interaction network and analytical results for 229 toxins categorized within 24 mechanistic and activity types from 26 bacterial genuses. The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based analyses are provided. Further, we have developed a prediction server attached to this database which aims to identify bacterial toxin like sequences either by establishing homology with known toxin sequences/domains or by classifying bacterial toxin specific features using a support vector based machine learning techniques.
Kinetics of Tempol for Prevention of Xerostomia Following Head and Neck Irradiation in a Mouse Model

Purpose: Radiotherapy is commonly used to treat the majority of patients with head and neck cancers. Salivary glands in the radiation field are dramatically affected by this procedure. The purpose of this study was to examine pharmacokinetic characteristics of the stable nitroxide 4-hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl (tempol) with respect to radioprotection of the salivary glands. Experimental Design: To evaluate the effect of different doses and times of administration, the heads of C3H mice were exposed to a single irradiation dose of 15 Gy, with i.p. tempol injection. To analyze other routes of administration, we injected 275 mg/kg tempol by an i.m. , i.v. , or s.c. route, 10 minutes before irradiation. We also tested whether oral administration of tempol in a topical form (either in a mouthwash or gel) provided any salivary gland protection. Results: Tempol treatment (137.5 or 275 mg/kg, i.p., 10 minutes before irradiation) significantly reduced irradiation-induced salivary hypofunction (∼50-60%). I.v. or s.c. administration of tempol also showed significant radioprotection, whereas i.m. administration proved to be ineffective. Topical use of tempol, either as a mouthwash or gel, also was radioprotective. Conclusions: Our results strongly suggest that tempol is a promising candidate for clinical application to protect salivary glands in patients undergoing radiotherapy for head and neck cancers.
Measuring Propagation in Online Social Networks: The Case of YouTube

We conducted a propagation analysis on an open social network, i.e., YouTube, by crawling one of its friendship networks and one of its subscribers (followers) networks. Our study is unique because it investigates the two main types of connections (i.e., friends and followers) within the same environment and interaction features. We observed that the effect on propagation of people who are not either in a friendship network or a subscription network is higher than that of friends or subscribers. Meanwhile, we found that even though the network of subscribers was denser than the network of friends, the magnitude of propagation in the subscription network was less than in the friendship network. We also noticed a low correlation between the popularity of content and its propagation in general, with a greater correlation in subscription networks than that in friendship networks.
Travel Broadens the Mind.

The onset of locomotion heralds one of the major life transitions in early development and involves a pervasive set of changes in perception, spatial cognition, and social and emotional development. Through a synthesis of published and hitherto unpublished findings, gathered from a number of converging research designs and methods, this article provides a comprehensive review and reanalysis of the consequences of self-produced locomotor experience. Specifically, we focus on the role of locomotor experience in changes in social and emotional development, referential gestural communication, wariness of heights, the perception of self-motion, distance perception, spatial search, and spatial coding strategies. Our analysis reveals new insights into the specific processes by which locomotor experience brings about psychological changes. We elaborate these processes and provide new predictions about previously unsuspected links between locomotor experience and psychological function. The research we describe is relevant to our broad understanding of the developmental process, particularly as it pertains to developmental transitions. Although acknowledging the role of genetically mediated developmental changes, our viewpoint is a transactional one in which a single acquisition, in this case the onset of locomotion, sets in motion a family of experiences and processes that in turn mobilize both broad-based and context-specific psychological reorganizations. We conclude that, in infancy, the onset of locomotor experience brings about widespread consequences, and after infancy, can be responsible for an enduring role in development by maintaining and updating existing skills.
ESPN: A case for energy-star photonic on-chip network

Photonic Network-on-Chips (NoCs) have recently been proposed due to their inherent low latency and high bandwidth. However, the high static power of the photonic components (e.g. laser source, resonators and waveguides) often results in energy-inefficient architectures. In this paper, we advocate the Energy-Star Photonic Network (ESPN) architecture that optimizes energy utilization via a two-pronged approach: (1) by enabling dynamic resource provisioning, ESPN adapts photonic network resources based on runtime traffic characteristics and (2) by utilizing all-optical adaptive routing, ESPN improves energy efficiency by intelligently exploiting existing network resources without introducing high latency and power hungry auxiliary routing mechanisms. Our evaluation results show that compared to the baseline design, ESPN reduces power and energy consumption under synthetic traffic patterns by 50% and 58% respectively.
Representative feature descriptor sets for robust handheld camera localization

We present a method to automatically determine a set of feature descriptors that describes an object such that it can be localized under a variety of viewpoints. Based on a set of synthetically generated views, local image features are detected, described and aggregated in a database. Our proposed method evaluates matches between these database features to eventually find a set of the most representative descriptors from the database. Using this scalable offline process, the localization success rate is significantly increased without adding computational load to the runtime method. Moreover, if camera localization is performed with respect to objects at a known gravity orientation, we propose to create multiple reference descriptor sets for different angles between the camera's principal axis and the gravity vector. This approach is particularly suited for handheld devices with built-in inertial sensors and enables matching against a reference dataset only containing the information relevant for camera poses that are consistent with the measured gravity. Comprehensive evaluations of the proposed methods using a large quantity of real camera images, a variety of objects, different cameras and different kinds of feature descriptors confirm that our approaches outperform standard feature descriptor-based methods.
Neural higher-order factors in conditional random fields for phoneme classification

We explore neural higher-order input-dependent factors inlinear-chain conditional random fields (LC-CRFs) for sequencelabeling. It is a fusion of two powerful models as higher-orderLC-CRFs with linear factors are well-established for sequencelabeling tasks, but they lack to model non-linear dependencies.Therefore, we present neural higher-order input-dependent fac-tors which map sub-sequences of inputs to sub-sequences ofoutputs using distinct multilayer perceptron sub-networks. Thisis important in many tasks, in particular, for phoneme classifi-cation where the phone representation strongly depends on thecontext phonemes. Experimental results for phoneme classifi-cation with LC-CRFs and neural higher-order factors confirmthis fact and we achieve the best ever reported phoneme clas-sification performance on TIMIT, i.e. a phoneme error rate of15:8%. Furthermore, we show that the success is not obviousas linear high-order factors degrade phoneme classification per-formance on TIMIT.
Role of interferon-stimulated responsive element-like element in interleukin-8 promoter in Helicobacter pylori infection.

BACKGROUND & AIMS Gastric mucosal interleukin (IL)-8 levels are related to the presence of both the cag pathogenicity island (PAI) and OipA. We investigated the regions of the IL-8 promoter and the upstream signaling involved in IL-8 gene transcription. METHODS We cocultured parental Helicobacter pylori and isogenic oipA, hopZ, or cagE gene knockout mutants with gastric cancer cells. The regulatory sites in the IL-8 promoter were examined by luciferase reporter gene assay, electrophoretic mobility shift assays, and immunoblot analyses. Phosphorylated signal transducers and activators of transcription 1 (STAT1) levels in the antral gastric mucosa were measured by enzyme-linked immunosorbent assay. RESULTS Maximal H. pylori -induced IL-8 gene transcription required the presence of the interferon-stimulated responsive element (ISRE)-like element, nuclear factor (NF)-kappa B and activator protein (AP)-1 binding sites. In vitro studies showed that OipA and the cag PAI were involved in inducing interferon regulatory factor (IRF)-1 to bind and activate the ISRE-like element and that the cag PAI, but not OipA, was involved in activating AP-1 and NF-kappa B. Both in vitro and in vivo studies showed that OipA, but not the cag PAI, was involved in STAT1 phosphorylation, as upstream signaling of IRF-1. CONCLUSIONS OipA and the cag PAI are both necessary for full activation of the IL-8 promoter but act via different pathways that diverge upstream of IRF-1 where only OipA is involved in the STAT1-IRF1-ISRE pathway. The mucosal inflammatory response to H. pylori infection is complex and involves different pathways converging on the IL-8 promoter.
Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design

Dengue is one of the most globally serious vector-borne infectious diseases in tropical and subtropical areas for which there are currently no effective vaccines. The most highly conserved flavivirus protein, NS5, is an indispensable target of CD8+ T-cells, making it an ideal vaccine design target. Using the Immune Epitope Database (IEDB), CD8+ T-cell epitopes of the dengue virus (DENV) NS5 protein were predicted by genotypic frequency of the HLA-A,-B, and-C alleles in Chinese population. Antigenicity scores of all predicted epitopes were analyzed using VaxiJen v2.0. The IEDB analysis revealed that 116 antigenic epitopes for HLA-A (21),-B (53), and-C (42) had high affinity for HLA molecules. Of them, 14 had 90.97–99.35% conversancy among the four serotypes. Moreover, five candidate epitopes, including 200NS5210 (94.84%, A*11:01), 515NS5525 (98.71%, A*24:02), 225NS5232 (99.35%, A*33:03), 516NS5523 (98.71%, A*33:03), and 284NS5291 (98.06%, A*33:03), were presented by HLA-A. Four candidate epitopes, including 234NS5241 (96.77%, B*13:01), 92NS599 (98.06%, B*15:01, B*15:02, and B*46:01), 262NS5269 (92.90%, B*38:02), and 538NS5547 (90.97%, B*51:01), were presented by HLA-B. Another 9 candidate epitopes, including 514NS5522 (98.71%, C*01:02), 514NS5524 (98.71%, C*01:02 and C*14:02), 92NS599 (98.06%, C*03:02 and C*15:02), 362NS5369 (44.84%, C*03:04 and C*08:01), 225NS5232 (99.35%, C*04:01), 234NS5241(96.77%, C*04:01), 361NS5369 (94.84%, C*04:01), 515NS5522 (98.71%, C*14:02), 515NS5524 (98.71%, C*14:02), were presented by HLA-C. Further data showed that the four-epitope combination of 92NS599 (B*15:01, B*15:02, B*46:01, C*03:02 and C*15:02), 200NS5210 (A*11:01), 362NS5369 (C*03:04, C*08:01), and 514NS5524 (C*01:02, C*14:02) could vaccinate >90% of individuals in China. Further in vivo study of our inferred novel epitopes will be needed for a T-cell epitope-based universal vaccine development that may prevent all four China-endemic DENV serotypes.