Miracle-dz/UniFAR-FTUs huggingface dataset:
Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non‐host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non‐host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non‐host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro‐ and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host‐specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non‐host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally demonstrated that for two common forestry tree species, foliar fungal pathogen richness and infestation depend on local biodiversity. Thus, local tree diversity can have positive impacts on ecosystem functioning in managed forests by decreasing the level of fungal pathogen infestation.
Short-term synaptic plasticity in the deterministic Tsodyks–Markram model leads to unpredictable network dynamics

Significance Short-term synaptic plasticity contributes to the balance and regulation of brain networks from milliseconds to several minutes. In this paper we report the existence of a route to chaos in the Tsodyks and Markram model of short-term synaptic plasticity. The chaotic region corresponds to what in mathematics is called Shilnikov chaos, an unstable manifold that strongly modifies the shape of trajectories and induces highly irregular transient dynamics, even in the absence of noise. The interplay between the Shilnikov chaos and stochastic effects may give rise to some of the complex dynamics observed in neural systems such as transitions between up and down states. Short-term synaptic plasticity strongly affects the neural dynamics of cortical networks. The Tsodyks and Markram (TM) model for short-term synaptic plasticity accurately accounts for a wide range of physiological responses at different types of cortical synapses. Here, we report a route to chaotic behavior via a Shilnikov homoclinic bifurcation that dynamically organizes some of the responses in the TM model. In particular, the presence of such a homoclinic bifurcation strongly affects the shape of the trajectories in the phase space and induces highly irregular transient dynamics; indeed, in the vicinity of the Shilnikov homoclinic bifurcation, the number of population spikes and their precise timing are unpredictable and highly sensitive to the initial conditions. Such an irregular deterministic dynamics has its counterpart in stochastic/network versions of the TM model: The existence of the Shilnikov homoclinic bifurcation generates complex and irregular spiking patterns and—acting as a sort of springboard—facilitates transitions between the down-state and unstable periodic orbits. The interplay between the (deterministic) homoclinic bifurcation and stochastic effects may give rise to some of the complex dynamics observed in neural systems.
High Frequency Power Optimized Ring Voltage Controlled Oscillator for 65nm CMOS Technology

Voltage Controlled Oscillator (VCO) is key building block of Phase Locked Loop (PLL) and Radio Frequency (RF) communication system. The design of high performance VCOs has been increasingly more important and still is an active research area. Research on VCOs for the past decade has been concentrated in the areas of higher frequency, lower phase noise, low power, low operating voltage, and increased tuning range. Among the architectures of VCO, Ring Oscillator shows better performance so it is selected for the research. The VCO exhibit at high frequency tuning range from 1.06-1.17GHz; its power consumption is only 8.63mW. The circuit is simulated in Tanner Tool version-13environment. The optimization design and layout are done using S-EDIT software to make the oscillator as small as possible. In addition, T-spice and W-EDIT tools are used in the analysis and simulation to verify the predicted performance.
Degrees of Freedom Region of Wireless X Networks Based on Real Interference Alignment

We first consider a single hop wireless X network with K transmitters and J receivers, all with a single antenna. Each transmitter conveys an independent message for each receiver. The channel is assumed to have constant coefficients. We develop an interference alignment scheme for this setup and derive an achievable degrees of freedom (DoF) region. We show that in some cases, the derived region meets a previous outer bound, and hence, is the (exact) DoF region. For our achievability schemes, we divide each message into streams and use real interference alignment on the streams. Several previous results on the DoF region and total DoF for several special cases can be recovered from our result. Next, we consider a network model, such that each transmitter emits an arbitrary number of messages and each receiver can request an arbitrary subset of all emitted messages. We term this network the X network with multicast. We derive an achievability result for the DoF region of such networks, as well as an outer bound. Our achievability scheme is based on a novel extension of real interference alignment that enables us to achieve more points of the DoF region. This approach allows multiple messages from a single user to be aligned with other users' messages. Finally, we discuss some points on the outer bounds that are not achievable with any of the alignment schemes that we present.
User preferences for task-specific vs. generic application software

We conducted an ethnographic study to investigate the use of generic vs. task-specific application software by people who create and maintain presentation slides. Sixteen people were interviewed to determine how they prepare slides; what software they use; and how well the software supports various aspects of the task. The informants varied in how central slide preparation was to their jobs. The study was motivated by our beliefs that: 1) some software programs are task-generic, intended for use in a wide variety of tasks, while others are task-specific, intended to support very specific tasks; 2) taskspecific software is preferable, but is often not used because of cost, learning effort, or lack of availability; and 3) people who infrequently perform a task tend to use generic tools, while people who frequently perform a task tend to use task-specific tools. Our findings suggest that the truth is more complex: 1) task-specificity/genericness is not a simple continuum; 2) a task cannot be looked at in isolation without reference to a higher level goal; and 3) an alternative to task-specific programs is a modular collection of independent interoperable services supporting small subtasks.
Implementing reusable object-oriented components

Object oriented (OO) classes are generally not reusable because they are not meaningful in isolation; most classes only have meaning as members of cooperating suites of classes (e.g., design patterns). These suites usually arise in designs, but rarely exist as encapsulated entities in OO implementations. We present a method for directly mapping cooperating suites of classes into encapsulated C++ implementations. Our method is an improvement over the VanHilst and Notkin approach (M. VanHilst and D. Notkin, 1996) for implementing collaboration based designs and constitutes a step towards more reusable (object oriented) components.
Differential Roles of Individual Domains in Selection of Secretion Route of a Streptococcus parasanguinis Serine-Rich Adhesin, Fap1

ABSTRACT Fimbria-associated protein 1 (Fap1) is a high-molecular-mass glycosylated surface adhesin required for fimbria biogenesis and biofilm formation in Streptococcus parasanguinis. The secretion of mature Fap1 is dependent on the presence of SecA2, a protein with some homology to, but with a different role from, SecA. The signals that direct the secretion of Fap1 to the SecA2-dependent secretion pathway rather than the SecA-dependent secretion pathway have not yet been identified. In this study, Fap1 variants containing different domains were expressed in both secA2 wild-type and mutant backgrounds and were tested for their ability to be secreted by the SecA- or SecA2-dependent pathway. The presence or absence of the cell wall anchor domain (residues 2531 to 2570) at the C terminus did not alter the selection of the Fap1 secretion route. The Fap1 signal peptide (residues 1 to 68) was sufficient to support the secretion of a heterologous protein via the SecA-dependent pathway, suggesting that the signal peptide was sufficient for recognition by the SecA-dependent pathway. The minimal sequences of Fap1 required for the SecA2-dependent pathway included the N-terminal signal peptide, nonrepetitive region I (residues 69 to 102), and part of nonrepetitive region II (residues 169 to 342). The two serine-rich repeat regions (residues 103 to 168 and 505 to 2530) were not required for Fap1 secretion. However, they were both involved in the specific inhibition of Fap1 secretion via the SecA-dependent pathway.
Kinesin Light Chains Are Essential for Axonal Transport in Drosophila

Kinesin is a heterotetramer composed of two 115-kD heavy chains and two 58-kD light chains. The microtubule motor activity of kinesin is performed by the heavy chains, but the functions of the light chains are poorly understood. Mutations were generated in the Drosophila gene Kinesin light chain (Klc), and the phenotypic consequences of loss of Klc function were analyzed at the behavioral and cellular levels. Loss of Klc function results in progressive lethargy, crawling defects, and paralysis followed by death at the end of the second larval instar. Klc mutant axons contain large aggregates of membranous organelles in segmental nerve axons. These aggregates, or organelle jams (Hurd, D.D., and W.M. Saxton. 1996. Genetics. 144: 1075–1085), contain synaptic vesicle precursors as well as organelles that may be transported by kinesin, kinesin-like protein 68D, and cytoplasmic dynein, thus providing evidence that the loss of Klc function blocks multiple pathways of axonal transport. The similarity of the Klc and Khc (Saxton et al. 1991. Cell 64:1093–1102; Hurd, D.D., and W.M. Saxton. 1996. Genetics 144: 1075–1085) mutant phenotypes indicates that KLC is essential for kinesin function, perhaps by tethering KHC to intracellular cargos or by activating the kinesin motor.
A Nucleosome-Free dG-dC-Rich Sequence Element Promotes Constitutive Transcription of the Essential Yeast RIO1 Gene

Abstract RIO1 is an essential gene that encodes a protein serine kinase and is transcribed constitutively at a very low level. Transcriptional activation of RIO1 dispenses with a canonical TATA box as well as with classical transactivators or specific DNA-binding factors. Instead, a dG-dC-rich sequence element, that is located 40 to 48 bp upstream the single site of mRNA initiation, is essential and presumably constitutes the basal promoter. In addition, we demonstrate here that this promoter element comprises a nucleosomefree gap which is centered at the dG-dC tract and flanked by two positioned nucleosomes. This element is both, necessary and sufficient, for basal transcription initiation at the RIO1 promoter and, thus, constitutes a novel type of core promoter element.
Linear regression-based delay-bounded routing protocols for VANETs

Routing protocols for vehicular ad hoc networks (VANETs) have attracted a lot of attention recently. Most of the researches emphasize on minimizing the end-to-end delay without paying attention to reducing the usage of radio. This paper focuses on delay-bounded routing, whose goal is to deliver messages to the destination within user-defined delay and to minimize the usage of radio because radio spectrum is a limited resource. The messages can be delivered to the destination by the hybrid of data muling (carried by the vehicle) and forwarding (transmitted through radio). In the existing protocol, a vehicle may only switch the delivery strategy (muling or forwarding) at an intersection according to the available time of the next road segment, which is between the current intersection and the next intersection. To improve previous works, our protocol uses linear regression to predict the available time and the traveling distance, and thus, the vehicle can switch to a proper delivery strategy at a proper moment and can reduce the number of relays by radio. Our protocol contains two schemes: the greedy and centralized schemes. The greedy scheme uses only the current sampling data to predict the available time and decide when to switch the delivery strategy, whereas the centralized scheme uses the global statistical information to choose a minimum-cost path. Simulation results justify the efficiency of the proposed protocol. Copyright © 2011 John Wiley & Sons, Ltd.
Mechanism of branchial apical silver uptake by rainbow trout is via the proton-coupled Na+channel.

The branchial uptake mechanism of the nonessential heavy metal silver from very dilute media by the gills of freshwater rainbow trout was investigated. At concentrations >36 nM AgNO3, silver rapidly entered the gills, reaching a peak at 1 h, after which time there was a steady decline in gill silver concentration and a resulting increase in body silver accumulation. Below 36 nM AgNO3, there was only a very gradual increase in gill and body silver concentration over the 48-h exposure period. Increasing water sodium concentration ([Na+]; 0.05 to 21 mM) significantly reduced silver uptake, although, in contrast, increasing ambient [Ca2+] or [K+] up to 10 mM did not reduce silver uptake. Kinetic analysis of silver uptake at varying [Na+] showed a significant decrease in maximal silver transport capacity (173 ± 34 pmol ⋅ g-1 ⋅ h-1 at 0.1 mM [Na+] compared with 35 ± 9 at 13 mM [Na+]) and only a slight decrease in the affinity for silver transport ( K m; 55 ± 27 nM at 0.1 mM [Na+] compared with 91 ± 47 nM at 13 mM [Na+]). Phenamil (a specific blocker of Na+ channels), at a concentration of 100 μM, blocked Na+ uptake by 78% of control values (58% after washout), and bafilomycin A1 (a specific blocker of V-type ATPase), at a concentration of 2 μM, inhibited Na+ uptake by 57% of control values, demonstrating the presence of a proton-coupled Na+ channel in the apical membrane of the gills. Phenamil (after washout) and bafilomycin A1 also blocked silver uptake by 62 and 79% of control values, respectively, indicating that Ag+ is able to enter the apical membrane via the proton-coupled Na+ channel.
Bacterial colonization immediately after installation on oral titanium implants.

BACKGROUND Information on bacterial colonization immediately after dental implant insertion is limited. AIMS (1) To assess the early colonization on titanium implants immediately after placement and throughout the first 12 post-surgical weeks, (2) to compare the microbiota at interproximal subgingival implant and adjacent tooth sites. MATERIAL AND METHODS Subgingival plaque samples from implant and neighbouring teeth were studied by checkerboard DNA-DNA hybridization before surgery, 30 min after implant placement, and 1, 2, 4, 8, and 12 weeks after surgery. RESULTS Comparing bacterial loads at implant sites between 30 min after placement with 1-week data showed that only the levels of Veillonella parvula (P<0.05) differed with higher loads at week 1 post-surgically. Week 12 data demonstrated significantly higher bacterial loads for 15/40 species at tooth sites compared with pre-surgery (P-values varying between 0.05 and 0.01). Between the period immediately after surgery and 12 weeks at implant sites, 29/40 species was more commonly found at 12 weeks. Included among these bacteria at implant sites were Porphyromonas gingivalis (P<0.05), Tannerella forsythia, (P<0.01), and Treponema denticola (P<0.001). Immediately post-surgery 5.9% of implants, and 26.2% of teeth, and at week 12, 15% of implants, and 39.1% of teeth harbored Staphylococcus aureus. Comparing tooth and implant sites, significantly higher bacterial loads were found at tooth sites for 27/40 species after 30 min following implant placement. This difference increased to 35/40 species at 12 weeks post-surgically. CONCLUSIONS Bacterial colonization occurred within 30 min after implant placement. Early colonization patterns differed between implant and tooth surfaces.
Not Call Me Cellular Any More: The Emergence of Scaling Law, Fractal Patterns and Small-World in Wireless Networks

In conventional cellular networks, for base stations (BSs) that are deployed far away from each other, it is general to assume them to be mutually independent. Nevertheless, after long-term evolution of cellular networks in various generations, this assumption no longer holds. Instead, the BSs, which seem to be gradually deployed by operators in a service-oriented manner, have embedded many fundamentally distinctive features in their locations, coverage and traffic loading. These features can be leveraged to analyze the intrinsic pattern in BSs and even human community. In this paper, according to large-scale measurement datasets, we build up a correlation model of BSs by utilizing one of the most important features, ie. , spatial traffic. Coupling with the theory of complex networks, we make further analysis on the structure and characteristics of this traffic load correlation model. Numerical results show that the degree distribution follows scale-free property. Also the datasets unveil the characteristics of fractality and small-world. Furthermore, we apply collective influence (CI) algorithm to localize the influential base stations and demonstrate that some low-degree BSs may outrank BSs with larger degree.
CMA-ES with restarts for solving CEC 2013 benchmark problems

This paper investigates the performance of 6 versions of Covariance Matrix Adaptation Evolution Strategy (CMAES) with restarts on a set of 28 noiseless optimization problems (including 23 multi-modal ones) designed for the special session on real-parameter optimization of CEC 2013. The experimental validation of the restart strategies shows that: i). the versions of CMA-ES with weighted active covariance matrix update outperform the original versions of CMA-ES, especially on ill-conditioned problems; ii). the original restart strategies with increasing population size (IPOP) are usually outperformed by the bi-population restart strategies where the initial mutation stepsize is also varied; iii). the recently proposed alternative restart strategies for CMA-ES demonstrate a competitive performance and are ranked first w.r. t. the proportion of function-target pairs solved after the full run on all 10-, 30- and 50-dimensional problems.
FlyBase: improvements to the bibliography

An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the current content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.
Comparative evaluation of the antiplaque effectiveness of green tea catechin mouthwash with chlorhexidine gluconate

Aim: The aim of this study is to compare the antiplaque efficacy of green tea catechin mouthwash with chlorhexidine gluconate mouthwash. Materials and Methods: A single blinded cross-over study was conducted among 30 participants in the age group of 18-25 years. The mouthwash samples for the study were previously labeled assigning the letters: A (0.25% of green tea catechin mouthwash) and B (0.12% of chlorhexidine mouthwash). The study subjects were randomly divided into two groups of 15 each and the study was divided into two phases. In phase I, the mouthwash A was given to one group and other group was given mouthwash B. After a 15 day washout period, in phase II, both groups were given other mouthwash. At the end of each phase of 1 week, plaque score was recorded by using Turesky modification of the Quigley-Hein plaque index. Results: The plaque scores were compared and the difference between the green tea catechin and chlorhexidine mouthwash was determined by t-test. The difference between plaque scores were not statistically significant (P > 0.05). The results showed that both the groups that is green tea catechin mouthwash (0.25%) and chlorhexidine mouthwash (0.12%) have comparable results in plaque reduction. Conclusion: This study supports the effectiveness of green tea catechin mouthwash as an antiplaque agent. It should be explored as a cost-effective, long-term antiplaque rinse with prophylactic benefits.