Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense)

The gut microbial community is one of the richest and most complex ecosystems on earth, and the intestinal microbes play an important role in host development and health. Next generation sequencing approaches, which rapidly produce millions of short reads that enable the investigation on a culture independent basis, are now popular for exploring microbial community. Currently, the gut microbiome in fresh water shrimp is unexplored. To explore gut microbiomes of the oriental river prawn (Macrobrachium nipponense) and investigate the effects of host genetics and habitats on the microbial composition, 454 pyrosequencing based on the 16S rRNA gene were performed. We collected six groups of samples, including M. nipponense shrimp from two populations, rivers and lakes, and one sister species (M. asperulum) as an out group. We found that Proteobacteria is the major phylum in oriental river prawn, followed by Firmicutes and Actinobacteria. Compositional analysis showed microbial divergence between the two shrimp species is higher than that between the two populations of one shrimp species collected from river and lake. Hierarchical clustering also showed that host genetics had a greater impact on the divergence of gut microbiome than host habitats. This finding was also congruent with the functional prediction from the metagenomic data implying that the two shrimp species still shared the same type of biological functions, reflecting a similar metabolic profile in their gut environments. In conclusion, this study provides the first investigation of the gut microbiome of fresh water shrimp, and supports the hypothesis of host species-specific signatures of bacterial community composition.
Consumer Willingness to Pay for Breads Marketed as "Low-Carbohydrate"

Bread producers are taking advantage of healthy feeding habits by developing new "low carbohydrate" products to entice customers. These low carbohydrate breads are generally more expensive than conventional types. This study tests the hypothesis that consumers are willing to pay higher premium for "low carbohydrate" breads at various locations and markets. We use retail data in a hedonic pricing framework to estimate the premium paid for the "low carbohydrate" attribute of bread. Results show that the implicit price of the "low carbohydrate" attribute of bread ranges from about 0.06¢ to 1.1¢ per gram, reflecting the amount consumers are willing to pay above the price of conventional bread.
A Review on Image Segmentation Clustering Algorithms

Clustering attempts to discover the set of consequential groups where those within each group are more closely related to one another than the others assigned to different groups. Image segmentation is one of the most important precursors for image processing–based applications and has a crucial impact on the overall performance of the developed systems. Robust segmentation has been the subject of research for many years, but till now published work indicates that most of the developed image segmentation algorithms have been designed in conjunction with particular applications. The aim of the segmentation process consists of dividing the input image into several disjoint regions with similar characteristics such as colour and texture. Keywords— Clustering, K-means, Fuzzy C-means, Expectation Maximization, Self organizing map, Hierarchical, Graph Theoretic approach.
Long-Term Effects of School Quality on Health and Lifestyle: Evidence from Comprehensive Schooling Reforms in England

Members of the National Child Development Study cohort attended very different types of secondary schools, as their schooling lay within the transition period of the comprehensive education reform in England and Wales. This provides a natural setting to explore the impact of educational attainment and of school quality on health and health-related behavior later in life. We use a combination of matching methods and parametric regressions to deal with selection effects and to evaluate differences in adult health outcomes and health-related behavior for cohort members exposed to the old selective and to the new comprehensive educational systems.
Lower-bound Estimate for Cost-sensitive Decision Trees

Abstract While an extensive body of literature investigates problems of decision trees growing, just a few study lower-bound estimates for the expected classification cost of decision trees, especially for varying costs of tests. In this paper the new lower-bound estimate is proposed. Computation of the estimate is reduced to solving a series of set-covering problems. Computational complexity and other properties of the lower-bound estimate are investigated. The top-down algorithm of tree construction based on the proposed estimate is tested against several popular greedy cost-sensitive heuristics on a range of standard data sets from UCI Machine Learning Repository.
Geometric Origin of CP Violation in an Extra-Dimensional Brane World

The fermion mass hierarchy and finding a predictive mechanism of the flavor mixing parameters remain two of the least understood puzzles facing particle physics today. In this work, we demonstrate how the realization of the Dirac algebra in the presence of two extra spatial dimensions leads to complex fermion field profiles in the extra dimensions. Dimensionally reducing to four dimensions leads to complex quark mass matrices in such a fashion that CP violation necessarily follows. We also present the generalization of the Randall-Sundrum scenario to the case of a multi-brane, six-dimensional brane-world and discuss how multi-brane worlds may shed light on the generation index of the SM matter content.
Policy optimization by marginal-map probabilistic inference in generative models

While most current work in POMDP planning focus on the development of scalable approximate algorithms, existing techniques often neglect performance guarantees and sacrifice solution quality to improve efficiency. In contrast, our approach to optimizing POMDP controllers by probabilistic inference and obtaining bounded on solution quality can be summarized as follows: (1) re-formulate POMDP planning as a task of marginal-MAP “mix” (max-sum) inference with respect to a new single-DBN generative model, (2) define a dual representation of the MMAP problem and derive a Bayesian variational approximation framework with an upper bound, (3) and design hybrid message-passing algorithms to optimize a POMDP policy by approximate variational MMAP inference in the DBN generative model.
Comparison and Evaluation of Routing Protocols Based on a Collaborative Simulation Using SUMO and NS3 with TraCI

Vehicle Ad hoc Network (VANET) is an emerging technology and a new application of mobile Ad Hoc technology in the field of traffic. As the simulation experiments cost less manpower and material resources and they are easy to reproduce the same scenario, VANET simulation technology has become a focus of scholars. But node mobility is strictly limited in the realistic traffic environment and fast moving speed leads to more frequent changes in network topology. So in VANET simulation, it is not appropriate to use traffic simulation tools or network simulation tools alone. In this paper, we integrated SUMO, middleware tool TraCI with NS3 to compare and evaluate the performance of four different topology based routing protocols. They are AODV, DSR, TORA and DSDV. We changed the node mobility and density to observe the experiment results. The main performance metrics for protocols are Packet Drop Ratio, Average Delay and Normalized Routing Load. We concluded that there are many differences and advantages under the proactive and reactive routing protocols from the values of metrics.
Comparing projected in-situ feedback at the manual assembly workplace with impaired workers

With projectors and depth cameras getting cheaper, assistive systems in industrial manufacturing are becoming increasingly ubiquitous. As these systems are able to continuously provide feedback using in-situ projection, they are perfectly suited for supporting impaired workers in assembling products. However, so far little research has been conducted to understand the effects of projected instructions on impaired workers. In this paper, we identify common visualizations used by assistive systems for impaired workers and introduce a simple contour visualization. Through a user study with 64 impaired participants we compare the different visualizations to a control group using no visual feedback in a real world assembly scenario, i.e. assembling a clamp. Furthermore, we introduce a simplified version of the NASA-TLX questionnaire designed for impaired participants. The results reveal that the contour visualization is significantly better in perceived mental load and perceived performance of the participants. Further, participants made fewer errors and were able to assemble the clamp faster using the contour visualization compared to a video visualization, a pictorial visualization and a control group using no visual feedback.
LITHIUM MINERAL WATERS EFFECT ON WNT PATHWAY SIGNALLING OF GLIAL CELLS

Lithium adjusts signalling activities regulating second messengers, transcription factors, and gene expression. The neurotrophic intermediary molecule GSK-3 was identified in 1996 as the target of lithium responsible for the developmental effects in Xenopus embryos. GSK-3 plays a broad role in cellular metabolism, including contributions to signalling activities, growth, and including several transcription factors such as c-jun, c-myc, heat shock factor 1, cytoskeletal proteins such as the microtubule-associated protein tau, and the antiapoptotic effects strongly implicates this enzyme as mediator of lithium's neuroprotective effects. Mixed glial cultures were prepared from neonatal Wistar rat cortex. Cultures derived from neonatal rat forebrain develop with a monolayer or large flat astrocytes attached to the culture dish, with many smaller cells of the oligodendrocytes lineage on their surface. Treatment of these cultures with lithium mineral waters from Mary Source compared to treatment with lithium chloride 2mM showed significant differences in cell morphology. Immunohistochemical studies for
Availability and End-to-end Reliability in Low Duty Cycle Multihop Wireless Sensor Networks

A wireless sensor network (WSN) is an ad-hoc technology that may even consist of thousands of nodes, which necessitates autonomic, self-organizing and multihop operations. A typical WSN node is battery powered, which makes the network lifetime the primary concern. The highest energy efficiency is achieved with low duty cycle operation, however, this alone is not enough. WSNs are deployed for different uses, each requiring acceptable Quality of Service (QoS). Due to the unique characteristics of WSNs, such as dynamic wireless multihop routing and resource constraints, the legacy QoS metrics are not feasible as such. We give a new definition to measure and implement QoS in low duty cycle WSNs, namely availability and reliability. Then, we analyze the effect of duty cycling for reaching the availability and reliability. The results are obtained by simulations with ZigBee and proprietary TUTWSN protocols. Based on the results, we also propose a data forwarding algorithm suitable for resource constrained WSNs that guarantees end-to-end reliability while adding a small overhead that is relative to the packet error rate (PER). The forwarding algorithm guarantees reliability up to 30% PER.
A simplified and robust protocol for immunoglobulin expression in E scherichia coli cell‐free protein synthesis systems

Cell‐free protein synthesis (CFPS) systems allow for robust protein expression with easy manipulation of conditions to improve protein yield and folding. Recent technological developments have significantly increased the productivity and reduced the operating costs of CFPS systems, such that they can compete with conventional in vivo protein production platforms, while also offering new routes for the discovery and production of biotherapeutics. As cell‐free systems have evolved, productivity increases have commonly been obtained by addition of components to previously designed reaction mixtures without careful re‐examination of the essentiality of reagents from previous generations. Here we present a systematic sensitivity analysis of the components in a conventional Escherichia coli CFPS reaction mixture to evaluate their optimal concentrations for production of the immunoglobulin G trastuzumab. We identify eight changes to the system, which result in optimal expression of trastuzumab. We find that doubling the potassium glutamate concentration, while entirely eliminating pyruvate, coenzyme A, NAD, total tRNA, folinic acid, putrescine and ammonium glutamate, results in a highly productive cell‐free system with a 95% reduction in reagent costs (excluding cell‐extract, plasmid, and T7 RNA polymerase made in‐house). A larger panel of other proteins was also tested and all show equivalent or improved yields with our simplified system. Furthermore, we demonstrate that all of the reagents for CFPS can be combined in a single freeze‐thaw stable master mix to improve reliability and ease of use. These improvements are important for the application of the CFPS system in fields such as protein engineering, high‐throughput screening, and biotherapeutics. © 2015 American Institute of Chemical Engineers Biotechnol. Prog. , 31:823–831, 2015
Shelling the Voronoi interface of protein–protein complexes reveals patterns of residue conservation, dynamics, and composition

The accurate description and analysis of protein–protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over‐ or underpredict the interface itself and cannot discriminate active from less relevant parts. We here extend a fast, parameter‐free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom's depth inside the interface. Our analysis of 54 protein–protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Orders coincide with residues that were found shielded from bulk water fluctuations in a recent molecular dynamics study. Yet, VSO predicts such “dry” residues without consideration of forcefields or dynamics at a dramatically reduced cost. The interface center is enriched in hydrophobic residues. Yet, this hydrophobic centering is not universal and does not mirror the far stronger geometric bias of water fluxes. The seemingly complex water dynamics at protein interfaces appears thus largely controlled by geometry. Sequence analysis supports the functional relevance of dry residues and residues with high VSO, both of which tend to be more conserved. On closer inspection, the spatial distribution of conservation argues against the arbitrary dissection into core or rim and thus refines previous results. Voronoi Shelling Order reveals clear geometric patterns in protein interface composition, function and dynamics and facilitates the comparative analysis of protein–protein interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Perceptions of money: Relationships between remembered parental rejection, extrinsic life aspirations and maladaptive attitudes toward money

Perceptions of Money: Relationships between Remembered Parental Rejection, Extrinsic Life Aspirations and Maladaptive Attitudes toward Money by Rebecca Jo Smith Advisor: Paul Wachtel, Ph.D. This study examined the extent to which maternal rejection, paternal rejection, maternal care, and maternal overprotection predict extrinsic life aspirations as well as maladaptive money attitudes in young adults. Additionally, this study sought to determine if the Adult Parental Acceptance-Rejection Questionnaire correlates with the Parental Bonding Instrument. The variable, extrinsic life aspirations, was examined to determine if it mediates between parental rejection and maladaptive money attitudes. Finally, the present study examined gender differences with regard to parental rejection, extrinsic life aspirations, and maladaptive money attitudes. A multiple regression analysis was conducted in a college sample of 366 participants using self-report measures. Results: Maternal rejection and paternal rejection were not found to be significant when predicting to extrinsic life aspirations, but greater maternal care and greater maternal overprotection were both found to be significantly associated with extrinsic life aspirations. Maternal rejection was found to predict higher endorsement of maladaptive money attitudes in respondents, but paternal rejection was not significant. Maternal care was not significantly associated with maladaptive money attitudes, but maternal overprotection was significantly and positively associated with the maladaptive money attitude composite score. There was a strong and significant negative correlation between the Parental Acceptance-Rejection total score for
GERMINATION ECOLOGY OF NEOTROPICAL PIONEERS: INTERACTING EFFECTS OF ENVIRONMENTAL CONDITIONS AND SEED SIZE

Germination provides many potentially unrecognized sources of variation in the regeneration niche. In this study we relate germination requirements and seed size for 16 species of pioneer trees to microclimatic conditions present in gaps in semi-deciduous rain forest in Panama. We found that, whereas increased duration of direct irradiance can be an effective indicator of the presence of a canopy gap across all scales of canopy openness, diel fluctuations in soil temperature effectively discriminate both understory sites and small gaps (25 m2) from larger gaps. Germination response was significantly related to seed size. Small-seeded species (seed mass 2 mg) germinated equally in light and darkness (wit.
Detecting partial discharge of polluted insulators based on ultraviolet imaging

Insulator is one of the most commonly used devices in transmission lines, so that the reliability of insulators is of great importance to the stable and safe operation of the electric grid. This paper analyzed the filthy discharge of polluted insulators based on ultraviolet (UV) imaging detection technology. By establishing an equivalent circuit model of polluted insulators, this paper analyzed and processed the causes and influencing factors of filthy discharge. Insulators were polluted artificially and discharged in the artificial climate chamber. The images and videos of this process were recorded and processed, based on which a characteristic of these images has been extracted and defined as “facula area percentage”. By analyzing and comparing the images' characteristics of discharges under different pollution level and different relative humidity, this paper acquired the patterns of how insulator discharges are influenced by pollution and humidity. By analyzing the influencing factors, such as gains, shot angles and distances, to the characteristics of those UV images, this paper also worked out the conversion formula under different gains, shot angles and distances, and proposed a standard for UV imaging.
Impact of star formation inhomogeneities on merger rates and interpretation of LIGO results

Within the next decade, ground based gravitational-wave detectors are in principle capable of determining the compact object merger rate per unit volume of the local universe to better than 20% with more than 30 detections. These measurements will constrain our models of stellar, binary and star cluster evolution in the nearby present-day and ancient universe. We argue that the stellar models are sensitive to heterogeneities (in age and metallicity at least) in such a way that the predicted merger rates are subject to an additional 30–50% systematic errors unless these heterogeneities are taken into account. Without adding new electromagnetic constraints on massive binary evolution or relying on more information from each merger (e.g., binary masses and spins), as few as the ≃ 5 merger detections could exhaust the information available in a naive comparison to merger rate predictions. As a concrete example immediately relevant to analysis of initial and enhanced LIGO results, we use a nearby-universe catalog to demonstrate that no one tracer of stellar content can be consistently used to constrain merger rates without introducing a systematic error of order O(30%) at 90% confidence (depending on the type of binary involved). For example, though binary black holes typically take many Gyr to merge, binary neutron stars often merge rapidly; different tracers of stellar content are required for these two types. More generally, we argue that theoretical binary evolution can depend sufficiently sensitively on star-forming conditions—even assuming no uncertainty in binary evolution model—that the distribution of star-forming conditions must be incorporated to reduce the systematic error in merger rate predictions below roughly 40%. We emphasize that the degree of sensitivity to star-forming conditions depends on the binary evolution model and on the amount of relevant variation in star-forming conditions. For example, if after further comparison with electromagnetic and gravitational-wave observations future population synthesis models suggest all BH-BH binary mergers occur promptly and therefore are associated with well-studied present-day star formation, the associated composition-related systematic uncertainty could be lower than the pessimistic value quoted above. Further, as gravitational-wave detectors will make available many properties of each merger—binary component masses, spins and even short GRB associations and host galaxies could be available—many detections can still be exploited to create high-precision constraints on binary compact object formation models.
Bounds for target tracking accuracy with probability of detection smaller than one

Recently several new results for Cramer-Rao lower bounds (CRLB's) in dynamical systems have been obtained. Several different approaches and approximations have been presented. For the general case of target tracking with a detection probability smaller than one and possibly in the presence of false measurements, two main approaches have been presented. One is the so called information reduction factor (IRF) approach and the other the enumeration (ENUM) approach, also referred to as conditioning approach. It has been shown that the ENUM approach leads to a strictly larger covariance matrix than the IRF approach, still being a lower bound of on the performance however. Thus, the ENUM approach provides a strictly tighter bound on the attainable performance. It has been conjectured that these bounds converge to one another in the limit or equivalently after an initial transition stage. In this paper we show, using some recent results on the so called modified Riccati (MR) equation and by means of counter examples, that this conjecture does not hold true in general. We also prove that it does hold true in the special case of deterministic target motion. Furthermore, we show that the detection probability has an influence on the limiting behaviors of the bounds. The various results are illustrated by means of representative examples.