Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating individual animal movement from observation networks

Observation network data comprise animal presences detected by observer stations at fixed spatial locations. Statistical analysis of these data is complicated by spatial bias in sampling and temporal variability in detection conditions. Advanced methods for analysis of these data are required but are currently underdeveloped. We propose a state‐space model (SSM) for observation network data to estimate detailed movements of individual animals. The underlying movement model is an Ornstein–Uhlenbeck (OU) process, which is stationary, and therefore has an inherent mechanism that models home range behaviour. An integral part of the approach is the detection function, which models the probability of logging animal presences. The detection function is also used to provide absence information when animals are undetected. Since the ability to detect an animal often depends on time‐varying external factors such as environmental conditions, we use covariate information about detection efficiency as control variables. Via simulation, we found that movement estimation error scales log‐linearly with network sparsity. This result can be used to indicate the number of stations necessary to achieve a desired upper bound on estimation error. Furthermore, we found that the SSM outperforms existing techniques in terms of estimating detailed movements and that estimates are robust towards mis‐specification of the detection function. We also tested the importance of accounting for time‐varying detection conditions and found that the probability of making wrong conclusions decreases substantially when covariate information is exploited. The model is used to estimate movements and home range of a humphead wrasse (Cheilinus undulatus) at Palmyra Atoll in the central Pacific Ocean. Here, detection conditions have a strong diel component, which is controlled for using detection efficiency information from a reference device. The presented approach enhances the toolbox for analysis of observation network data as collected by acoustic telemetry or potentially other aspiring methods such as camera trapping and mobile phone tagging. By explicitly modelling movement and observation processes, the model integrates all sources of uncertainty and provides a sound statistical basis for making well‐informed management decisions from imperfect information.
Legionella pneumophila Exploits PI(4)P to Anchor Secreted Effector Proteins to the Replicative Vacuole

The causative agent of Legionnaires' disease, Legionella pneumophila, employs the intracellular multiplication (Icm)/defective organelle trafficking (Dot) type IV secretion system (T4SS) to upregulate phagocytosis and to establish a replicative vacuole in amoebae and macrophages. Legionella-containing vacuoles (LCVs) do not fuse with endosomes but recruit early secretory vesicles. Here we analyze the role of host cell phosphoinositide (PI) metabolism during uptake and intracellular replication of L. pneumophila. Genetic and pharmacological evidence suggests that class I phosphatidylinositol(3) kinases (PI3Ks) are dispensable for phagocytosis of wild-type L. pneumophila but inhibit intracellular replication of the bacteria and participate in the modulation of the LCV. Uptake and degradation of an icmT mutant strain lacking a functional Icm/Dot transporter was promoted by PI3Ks. We identified Icm/Dot–secreted proteins which specifically bind to phosphatidylinositol(4) phosphate (PI(4)P) in vitro and preferentially localize to LCVs in the absence of functional PI3Ks. PI(4)P was found to be present on LCVs using as a probe either an antibody against PI(4)P or the PH domain of the PI(4)P-binding protein FAPP1 (phosphatidylinositol(4) phosphate adaptor protein-1). Moreover, the presence of PI(4)P on LCVs required a functional Icm/Dot T4SS. Our results indicate that L. pneumophila modulates host cell PI metabolism and exploits the Golgi lipid second messenger PI(4)P to anchor secreted effector proteins to the LCV.
Intradiscal Thermal Therapy Does Not Stimulate Biologic Remodeling in an In Vivo Sheep Model

Study Design. Thermal energy was delivered in vivo to ovine cervical discs and the postheating response was monitored over time. Objectives. To determine the effects of two distinctly different thermal exposures on biologic remodeling: a “high-dose” regimen intended to produce both cellular necrosis and collagen denaturation and a “low-dose” regimen intended only to kill cells. Summary of Background Data. Thermal therapy is a minimally invasive technique that may ameliorate discogenic back pain. Potential therapeutic mechanisms include shrinkage of collagenous tissues, stimulation of biologic remodeling, and ablation of cytokine-producing cells and nociceptive fibers. Methods. Intradiscal heating was performed using directional interstitial ultrasound applicators. Temperature and thermal dose distributions were characterized. The effects of high (>70 C, 10 minutes) and low (52 C–54 C, 10 minutes) temperature treatments on chronic biomechanical and architectural changes were compared with sham-treated and control discs at 7, 45, and 180 days. Results. The high-dose treatment caused both an acute and chronic loss of proteoglycan staining and a degradation of biomechanical properties compared with low-dose and sham groups. Similar amounts of degradation were observed in the low-dose and sham-treated discs relative to the control discs at 180 days after treatment. Conclusions. While a high temperature thermal protocol had a detrimental effect on the disc, the effects of low temperature treatment were relatively minor. Thermal therapy did not stimulate significant biologic remodeling. Future studies should focus on the effects of low-dose therapy on tissue innervation and pro-inflammatory factor production.
Excitonic condensation in a double-layer graphene system

The possibility of excitonic condensation in a recently proposed electrically biased double-layer graphene system is studied theoretically. The main emphasis is put on obtaining a reliable analytical estimate for the transition temperature into the excitonic state. As in a double-layer graphene system the total number of fermionic ‘flavors’ is equal to N = 8 due to two projections of spin, two valleys and two layers, the large-N approximation appears to be especially suitable for theoretical investigation of the system. On the other hand, the large number of flavors makes screening of the bare Coulomb interactions very efficient, which, together with the suppression of backscattering in graphene, leads to an extremely low energy of the excitonic condensation. It is shown that the effect of screening on the excitonic pairing is just as strong in the excitonic state as it is in the normal state. As a result, the value of the excitonic gap Δ is found to be in full agreement with the previously obtained estimate for the mean-field transition temperature Tc, the maximum possible value Δmax, Tmaxc ∼ 10−7ϵF (ϵF is the Fermi energy) of both being in a 1mK range for a perfectly clean system. This proves that the energy scale ∼10−7ϵF really sets the upper bound for the transition temperature and invalidates the recently expressed conjecture about the high-temperature first-order transition into the excitonic state. These findings suggest that, unfortunately, the excitonic condensation in graphene double-layers can hardly be realized experimentally.
Attacking the Pollard Generator

Let p be a prime and let c be an integer modulo p. The Pollard generator is a sequence (u<sub>n</sub>) of pseudorandom numbers defined by the relation u<sub>n+1</sub>equivu<sub>n</sub> <sup>2</sup>+c mod p. It is shown that if c and 9/14 of the most significant bits of two consecutive values u<sub>n</sub>,u<sub>n+1</sub> of the Pollard generator are given, one can recover in polynomial time the initial value u<sub>0</sub> with a probabilistic algorithm. This result is an improvement of a theorem in a recent paper which requires that 2/3 of the most significant bits be known
Three essays on health, aging and the family in contemporary China

While an inverse relationship between socioeconomic status (SES) and mortality has been well documented for many populations throughout the world, it remains unclear whether this relationship holds true for the oldest old. Most notably, some scholars have suggested that the relationship may disappear at the oldest ages. Using data from the 1998, 2000, and 2002 waves of “The Chinese Longitudinal Healthy Longevity Survey,” this paper examines the relationship between socioeconomic status and mortality among the oldest old (80 years and older) population in China. Our results show the continuing prevalence of SES differentials in mortality--higher SES is significantly associated with lower mortality risks--among the oldest old in China. We further show that the relationship holds regardless of how the oldest old are operationalized as 80+, 90+, or
Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora.
Influence of the Novelty-Seeking Endophenotype on the Rewarding Effects of Psychostimulant Drugs in Animal Models

Novelty seeking (NS), defined as a tendency to pursue novel and intense emotional sensations and experiences, is one of the most relevant individual factors predicting drug use among humans. High novelty seeking (HNS) individuals present an increased risk of drug use compared to low novelty seekers. The NS endophenotype may explain some of the differences observed among individuals exposed to drugs of abuse in adolescence. However, there is little research about the particular response of adolescents to drugs of abuse in function of this endophenotype, and the data that do exist are inconclusive. The present work reviews the literature regarding the influence of NS on psychostimulant reward, with particular focus on adolescent subjects. First, the different animal models of NS and the importance of this endophenotype in adolescence are discussed. Later, studies that have used the most common animal models of reward (self-administration, conditioned place preference paradigms) to evaluate how the NS trait influences the rewarding effects of psychostimulants are reviewed. Finally, possible explanations for the enhanced risk of developing substance dependence among HNS individuals are discussed. In conclusion, the studies referred to in this review show that the HNS trait is associated with: (1) increased initial sensitivity to the rewarding effects of psychostimulants, (2) a higher level of drug craving when the subject is exposed to the environmental cues associated with the drug, and (3) enhanced long-term vulnerability to relapse to drug consumption after prolonged abstinence.
Using the functional grammar to understand children’s written texts

This paper reports on an analysis of the assessment principles used in marking students’ written texts in the UK. It considers the assessment advice offered markers with respect to two stories written by 14 year old students in the Key Stage 3 English test in England. The observations offered on the written texts are shown to be general and lacking in much understanding of the ways the texts work linguistically. Using the functional grammar, an attempt is made to explore aspects of the grammatical organization of the two texts, and hence to reveal why one text was deemed superior to the other.
Fast and Scalable Pattern Mining for Media-Type Focused Crawling

Search engines targeting content other than hypertext documents require a crawler that discovers resources identifying files of certain media types. Naive crawling approaches do not guarantee a sufficient supply of new URIs (Uniform Resource Identifiers) to visit; effective and scalable mechanisms for discovering and crawling targeted resources are needed. One promising approach is to use data mining techniques to identify the media type of a resource without the need for downloading the content of the resource. The idea is to use a learning approach on features derived from patterns occuring in the resource identifier. We present a focused crawler as a use case for fast and scalable data mining and discuss classification and pattern mining techniques suited for selecting resources satisfying specified media types. We show that we can process an average of 17,000 URIs/second and still detect the media type of resources with a precision of more than 80% and a recall of over 65% for all media types.
'AIE-studio' - a pragmatist aesthetic approach for procedural sound design

This paper introduces the AIE-Studio (Audio Interfaces for Exploration), a modular dataflow patching library implemented with Pure Data. The AIE-Studio introduces new tools for procedural sound design through generative sonic and musical structures. Particular focus is on aesthetic experience. The designed modules allow versatile dataflow mapping through matrix routing system while also enabling the sound designer to influence generative processes of music creation. In particular, The AIE-Studio was used to create generative sonic and musical material in an embodied game-like application. In this paper we present key questions driving the research, theoretical background, research approach and the main development activities.
Efficient Lane Detection and Tracking in Urban Environments

Lane detection in urban environments is a challenging task. That is mainly due to the non existence of unique models, poor quality of lane markings due to wear, occlusions due to the presence of traffic and complex road geometry. In this work we present a novel lane detection and tracking algorithm for urban road scenarios based on weak models, which is implemented by a particle filter. The algorithm is implemented and experiments were carried out on Sydney urban roads. The results show the robustness of the algorithm to the problems inherent in urban road environments.
On Static and Dynamic Partitioning Behavior of Large-Scale P2P Networks

In this paper, we analyze the problem of network disconnection in the context of large-scale P2P networks and understand how both static and dynamic patterns of node failure affect the resilience of such graphs. We start by applying classical results from random graph theory to show that a large variety of deterministic and random P2P graphs almost surely (i.e., with probability 1-o(1)) remain connected under random failure if and only if they have no isolated nodes. This simple, yet powerful, result subsequently allows us to derive in closed-form the probability that a P2P network develops isolated nodes, and therefore partitions, under both types of node failure. We finish the paper by demonstrating that our models match simulations very well and that dynamic P2P systems are extremely resilient under node churn as long as the neighbor replacement delay is much smaller than the average user lifetime.
Oligometastases and Oligo-recurrence: The New Era of Cancer Therapy

Recurrence or metastasis of cancer has been considered to occur in the last stage of the patient's life. However, the new notions of oligometastases and oligo-recurrence have been proposed and the paradigm shift in the conceptualization of cancer metastasis or cancer recurrence. Oligometastases is the state in which the patient shows distant relapse in only a limited number of regions. Local therapy such as surgery, radiotherapy and radiofrequency ablation for the relapsed sites could thus improve patient's survival. On the other hand, oligo-recurrence is a notion similar to oligometastases. However, the conditions of oligo-recurrence has a primary site of the cancer controlled, meaning that all gross recurrent or metastatic sites could be treated using local therapy.
The Differential Interaction of Brucella and Ochrobactrum with Innate Immunity Reveals Traits Related to the Evolution of Stealthy Pathogens

Background During evolution, innate immunity has been tuned to recognize pathogen-associated molecular patterns. However, some α-Proteobacteria are stealthy intracellular pathogens not readily detected by this system. Brucella members follow this strategy and are highly virulent, but other Brucellaceae like Ochrobactrum are rhizosphere inhabitants and only opportunistic pathogens. To gain insight into the emergence of the stealthy strategy, we compared these two phylogenetically close but biologically divergent bacteria. Methodology/Principal Findings In contrast to Brucella abortus, Ochrobactrum anthropi did not replicate within professional and non-professional phagocytes and, whereas neutrophils had a limited action on B. abortus, they were essential to control O. anthropi infections. O. anthropi triggered proinflammatory responses markedly lower than Salmonella enterica but higher than B. abortus. In macrophages and dendritic cells, the corresponding lipopolysaccharides reproduced these grades of activation, and binding of O. anthropi lipopolysaccharide to the TLR4 co-receptor MD-2 and NF-κB induction laid between those of B. abortus and enteric bacteria lipopolysaccharides. These differences correlate with reported variations in lipopolysaccharide core sugars, sensitivity to bactericidal peptides and outer membrane permeability. Conclusions/Significance The results suggest that Brucellaceae ancestors carried molecules not readily recognized by innate immunity, so that non-drastic variations led to the emergence of stealthy intracellular parasites. They also suggest that some critical envelope properties, like selective permeability, are profoundly altered upon modification of pathogen-associated molecular patterns, and that this represents a further adaptation to the host. It is proposed that this adaptive trend is relevant in other intracellular α-Proteobacteria like Bartonella, Rickettsia, Anaplasma, Ehrlichia and Wolbachia.
Comparison of different DC-link voltage balancing methods for cascade H-bridge multilevel converter

Cascade H-bridge multilevel converter can be directly connected to the medium voltage grid, which can effectively improve the voltage stability of the power system. However, the imbalance of the DC-link voltage of each H-bridge module due to the power loss difference is a challenging issue, which would seriously affect the output performance of the cascade multilevel converter. Software based scheme is preferable to solve such problem because it requires no more hardware and is easy to implement. This paper compares the performance of two software based schemes, namely the negative-sequence voltage injection and zero-sequence voltage injection methods, employed in balancing the DC-link voltage of the cascade converter. It is concluded that the negative-sequence voltage injection scheme can provide stronger ability to balance the DC-link voltage with negative-sequence current injection to the grid, while the zero-sequence voltage injection scheme can balance the DC-link voltage without zero-sequence current injection. The simulation results verify the comparative analyses in this paper.
New continuous-flow mixed-radix (CFMR) FFT Processor using novel in-place strategy

The paper proposes a new continuous-flow mixed-radix (CFMR) fast Fourier transform (FFT) processor that uses the MR (radix-4/2) algorithm and a novel in-place strategy. The existing in-place strategy supports only a fixed-radix FFT algorithm. In contrast, the proposed in-place strategy can support the MR algorithm, which allows CF FFT computations regardless of the length of FFT. The novel in-place strategy is made by interchanging storage locations of butterfly outputs. The CFMR FFT processor provides the MR algorithm, the in-place strategy, and the CF FFT computations at the same time. The CFMR FFT processor requires only two N-word memories due to the proposed in-place strategy. In addition, it uses one butterfly unit that can perform either one radix-4 butterfly or two radix-2 butterflies. The CFMR FFT processor using the 0.18 /spl mu/m SEC cell library consists of 37,000 gates excluding memories, requires only 640 clock cycles for a 512-point FFT and runs at 100 MHz. Therefore, the CFMR FFT processor can reduce hardware complexity and computation cycles compared with existing FFT processors.
VTPin: practical VTable hijacking protection for binaries

VTable hijacking has lately been promoted to the de facto technique for exploiting C++ applications, and in particular web browsers. VTables, however, can be manipulated without necessarily corrupting memory, simply by leveraging use-after-free bugs. In fact, in the recent Pwn2Own competitions all major web browsers were compromised with exploits that employed (among others) use-after-free vulnerabilities and VTable hijacking. In this paper, we propose VTPin: a system to protect against VTable hijacking, via use-after-free vulnerabilities, in large C++ binaries that cannot be re-compiled or re-written. The main idea behind VTPin is to pin all the freed VTable pointers on a safe VTable under VTPin's control. Specifically, for every object deallocation, VTPin deallocates all space allocated, but preserves and updates the VTable pointer with the address of the safe VTable. Hence, any dereferenced dangling pointer can only invoke a method provided by VTPin's safe object. Subsequently, all virtual-method calls due to dangling pointers are not simply neutralized, but they can be logged, tracked, and patched. Compared to other solutions that defend against VTable hijacking, VTPin exhibits certain characteristics that make it suitable for practical and instant deployment in production software. First, VTPin protects binaries, directly and transparently, without requiring source compilation or binary rewriting. Second, VTPin is not an allocator replacement, and thus it does not interfere with the allocation strategies and policies of the protected program; it intervenes in the deallocation process only when a virtual object is to be freed for preserving the VTable pointer. Third, VTPin is fast; Mozilla Firefox, protected with VTPin, experiences an average overhead of 1%-4.1% when running popular browser benchmarks.