Miracle-dz/UniFAR-FTUs huggingface dataset:
FAILURE OF TRANSMISSION OF LOW-PATHOGENIC AVIAN INFLUENZA VIRUS BETWEEN MALLARDS AND FRESHWATER SNAILS: AN EXPERIMENTAL EVALUATION

Abstract In aquatic bird populations, the ability of avian influenza (AI) viruses to remain infectious in water for extended periods provides a mechanism that allows viral transmission to occur long after shedding birds have left the area. However, this also exposes other aquatic organisms, including freshwater invertebrates, to AI viruses. Previous researchers found that AI viral RNA can be sequestered in snail tissues. Using an experimental approach, we determined whether freshwater snails (Physa acuta and Physa gyrina) can infect waterfowl with AI viruses by serving as a means of transmission between infected and naïve waterfowl via ingestion. In our first experiment, we exposed 20 Physa spp. snails to an AI virus (H3N8) and inoculated embryonated specific pathogen–free (SPF) chicken eggs with the homogenized snail tissues. Sequestered AI viruses remain infectious in snail tissues; 10% of the exposed snail tissues infected SPF eggs. In a second experiment, we exposed snails to water contaminated with feces of AI virus–inoculated Mallards (Anas platyrhynchos) to evaluate whether ingestion of exposed freshwater snails was an alternate route of AI virus transmission to waterfowl. None of the immunologically naïve Mallards developed an infection, indicating that transmission via ingestion likely did not occur. Our results suggest that this particular trophic interaction may not play an important role in the transmission of AI viruses in aquatic habitats.
Tradition, Dynamics and Sustainability of Plant Species Composition and Management in Homegardens on Organic and Non-Organic Small Scale Farms in Alpine Eastern Tyrol, Austria

ABSTRACT In Eastern Tyrol (Austria), homegardens are an integral part of the farming system. The aim of this paper is to present evidence for the development of gardening in the study area and to identify differences/similarities between gardens at organic and non-organic farms. In 1997 and 1998, in homegardens on 91 organic and 105 non-organic farms from 12 communities, occurrence and abundance of cultivated plant species were surveyed and interviews were carried out about garden history, management and plant use. For the factor organic/non-organic, differences between gardens were statistically tested. Garden management is similar in organic/non-organic gardens, except mixed cropping and the use of alternative remedies to combat diseases, both with significantly higher occurrence on organic farms. Popular innovations from organic farming did not have a strong and clearly visible impact on management of homegardens. The population of cultivated plant species, until the 1960s approx. 51; nowadays approx. 587 species in all gardens, and main use of garden produce has been in a process of change with an increase in importance of species used as food and for decoration, but with no significant differences concerning organic/non-organic. Women farmers gardening in Eastern Tyrol are highly sympathetic to the principles of organic farming, even on non-organic farms. Sustainability can be increased when methods from organic gardening are promoted and tested locally more effectively. Science and policy should recognize the work of women farmers who maintain homegardens with high agrobiodiversity as part of their culture.
Principal Component Analysis and Automatic Relevance Determination in Damage Identification

This paper compares two neural network input selection schemes, the Principal Component Analysis (PCA) and the Automatic Relevance Determination (ARD) based on Mac-Kay's evidence framework. The PCA takes all the input data and projects it onto a lower dimension space, thereby reduc-ing the dimension of the input space. This input reduction method often results with parameters that have significant influence on the dynamics of the data being diluted by those that do not influence the dynamics of the data. The ARD selects the most relevant input parameters and discards those that do not contribute significantly to the dynamics of the data being modelled. The ARD sometimes results with important input parameters being discarded thereby compromising the dynamics of the data. The PCA and ARD methods are implemented together with a Multi-Layer-Perceptron (MLP) network for fault identification in structures and the performance of the two methods is as-sessed. It is observed that ARD and PCA give similar accu-racy levels when used as input-selection schemes. There-fore, the choice of input-selection scheme is dependent on the nature of the data being processed.
A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny

A phylogeny is a tree graph representation of genealogical relationships between biological objects. It is of general interest to estimate the phylogeny of whole organisms (species trees) using bio-molecular sequences. When multiple sequences are available for each organism such as with whole genome data, individual phylogenies estimated by each molecule (gene trees) may not be concordant. The lack of concordance may be due to actual biological mechanisms such as horizontal transfer of the molecules. Here, we present a new phylogeny estimation method designed to estimate the species tree despite such horizontal transfer. It uses the idea that horizontal transfer distorts distance relationships between pairs of species but a median estimate of the distances is robust to such distortions. We demonstrate the utility of our method using a simulation study.
Spontaneous hair cell regeneration in the neonatal mouse cochlea in vivo

Loss of cochlear hair cells in mammals is currently believed to be permanent, resulting in hearing impairment that affects more than 10% of the population. Here, we developed two genetic strategies to ablate neonatal mouse cochlear hair cells in vivo. Both Pou4f3DTR/+ and Atoh1-CreER™; ROSA26DTA/+ alleles allowed selective and inducible hair cell ablation. After hair cell loss was induced at birth, we observed spontaneous regeneration of hair cells. Fate-mapping experiments demonstrated that neighboring supporting cells acquired a hair cell fate, which increased in a basal to apical gradient, averaging over 120 regenerated hair cells per cochlea. The normally mitotically quiescent supporting cells proliferated after hair cell ablation. Concurrent fate mapping and labeling with mitotic tracers showed that regenerated hair cells were derived by both mitotic regeneration and direct transdifferentiation. Over time, regenerated hair cells followed a similar pattern of maturation to normal hair cell development, including the expression of prestin, a terminal differentiation marker of outer hair cells, although many new hair cells eventually died. Hair cell regeneration did not occur when ablation was induced at one week of age. Our findings demonstrate that the neonatal mouse cochlea is capable of spontaneous hair cell regeneration after damage in vivo. Thus, future studies on the neonatal cochlea might shed light on the competence of supporting cells to regenerate hair cells and on the factors that promote the survival of newly regenerated hair cells.
JPEG compression anti-forensics based on first significant digit distribution

Traces left by lossy compression processes have been widely studied in digital image forensics. In particular, the artifacts produced by JPEG compression have been characterized and exploited both in forensic methods and counter-forensic attacks. In this paper, we propose a novel anti-forensic procedure, aimed at concealing the traces of single JPEG compression by recovering the original distribution of first significant digits (FSD) of the DCT coefficients. We analyze the performance of our method and compare it with anti-forensic attacks reported in the literature in terms of quality of the resulting image. In addition, we prove the effectiveness of our approach as counter-forensic processing by measuring its impact on the performance of two different forensic tools, applied after the anti-forensic action.
Two-photon multilayer bit data storage by use of continuous-wave illumination

A continuous wave laser beam of an infrared wavelength at 800 nm is used for two-photon excitation in a photobleaching polymer for 3D bits data storage. We successfully demonstrate the recording and reading of multiple layers of data bits up to a depth of 100 micrometers within a thick photobleaching polymer. The achievable 3D bit density may be up to 3.5 Tbits/cm3 if a variable tube length can be implemented into the recording and reading processes.
Quantum phase transition of nonlinear light in the finite size Dicke Hamiltonian

We study the quantum phase transition of an N two-level system ensemble interacting with an optical degenerate parametric process, which can be described by the finite size Dicke Hamiltonian plus counter-rotating and quadratic field terms. Analytical closed forms of the critical coupling value and their corresponding separable ground states are derived in the weak and strong coupling regimes. The existence of bipartite entanglement between the two-level system ensemble and photon field as well as between ensemble components for moderate coupling is shown through numerical analysis. Given a finite size, our results also indicate the co-existence of squeezed fields and squeezed atomic ensembles.
Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients

The opportunistic pathogen Pseudomonas aeruginosa undergoes genetic change during chronic airway infection of cystic fibrosis (CF) patients. One common change is a mutation inactivating lasR, which encodes a transcriptional regulator that responds to a homoserine lactone signal to activate expression of acute virulence factors. Colonies of lasR mutants visibly accumulated the iridescent intercellular signal 4‐hydroxy‐2‐heptylquinoline. Using this colony phenotype, we identified P. aeruginosa lasR mutants that emerged in the airway of a CF patient early during chronic infection, and during growth in the laboratory on a rich medium. The lasR loss‐of‐function mutations in these strains conferred a growth advantage with particular carbon and nitrogen sources, including amino acids, in part due to increased expression of the catabolic pathway regulator CbrB. This growth phenotype could contribute to selection of lasR mutants both on rich medium and within the CF airway, supporting a key role for bacterial metabolic adaptation during chronic infection. Inactivation of lasR also resulted in increased β‐lactamase activity that increased tolerance to ceftazidime, a widely used β‐lactam antibiotic. Loss of LasR function may represent a marker of an early stage in chronic infection of the CF airway with clinical implications for antibiotic resistance and disease progression.
Isolated dysarthria due to extracerebellar lacunar stroke: a central monoparesis of the tongue

OBJECTIVES The pathophysiology of dysarthria can preferentially be studied in patients with the rare lacunar stroke syndrome of “isolated dysarthria”. METHODS A single study was carried out on seven consecutive patients with sudden onset of isolated dysarthria due to single ischaemic lesion. The localisation of the lesion was identified using MRI. The corticolingual, cortico-orofacial, and corticospinal tract functions were investigated using transcranial magnetic stimulation. Corticopontocerebellar tract function was assessed using 99mTc hexamethylpropylene amine oxime-single photon emission computerised tomography (HMPAO-SPECT) in six patients. Sensory functions were evaluated clinically and by somatosensory evoked potentials. RESULTS Brain MRI showed the lesions to be located in the corona radiata (n=4) and the internal capsule (n=2). No morphological lesion was identified in one patient. Corticolingual tract function was impaired in all patients. In four patients with additional cortico-orofacial tract dysfunction, dysarthria did not differ from that in patients with isolated corticolingual tract dysfunction. Corticospinal tract functions were normal in all patients. HMPAO-SPECT showed no cerebellar diaschisis, suggesting unimpaired corticopontocerebellar tract function. Sensory functions were not affected. CONCLUSION Interruption of the corticolingual pathways to the tongue is crucial in the pathogenesis of isolated dysarthria after extracerebellar lacunar stroke.
Exploiting Symmetry in Lifted CSPs

When search problems have large-scale symmetric structure, detecting and exploiting that structure can greatly reduce the size of the search space. Previous work has shown how to find and exploit symmetries in propositional encodings of constraint satisfaction problems (CSPs). Here we consider problems that have more compact "lifted" (quantified) descriptions from which propositional encodings can be generated. We describe an algorithm for finding symmetries in lifted representations of CSPs, and show sufficient conditions under which these symmetries can be mapped to symmetries in the propositional encoding. Using two domains (pigeonhole problems, and a CSP encoding of planning problems), we demonstrate experimentally that the approach of finding symmetries in lifted problem representations is a significant improvement over previous approaches that find symmetnes in propositional encodings.
The interplay of cognition and cooperation

Cooperation often involves behaviours that reduce immediate payoffs for actors. Delayed benefits have often been argued to pose problems for the evolution of cooperation because learning such contingencies may be difficult as partners may cheat in return. Therefore, the ability to achieve stable cooperation has often been linked to a species' cognitive abilities, which is in turn linked to the evolution of increasingly complex central nervous systems. However, in their famous 1981 paper, Axelrod and Hamilton stated that in principle even bacteria could play a tit-for-tat strategy in an iterated Prisoner's Dilemma. While to our knowledge this has not been documented, interspecific mutualisms are present in bacteria, plants and fungi. Moreover, many species which have evolved large brains in complex social environments lack convincing evidence in favour of reciprocity. What conditions must be fulfilled so that organisms with little to no brainpower, including plants and single-celled organisms, can, on average, gain benefits from interactions with partner species? On the other hand, what conditions favour the evolution of large brains and flexible behaviour, which includes the use of misinformation and so on? These questions are critical, as they begin to address why cognitive complexity would emerge when ‘simple’ cooperation is clearly sufficient in some cases. This paper spans the literature from bacteria to humans in our search for the key variables that link cooperation and deception to cognition.
Static Detection of User-specified Security Vulnerabilities in Client-side JavaScript

Program defects tend to surface late in the development of programs, and they are hard to detect. Security vulnerabilities are particularly important defects to detect. They may cause sensitive information to be leaked or the system on which the program is executed to be compromised. Existing approaches that use static analysis to detect security vulnerabilities in source code are often limited to a predetermined set of encoded security vulnerabilities. Although these approaches support a decent number of vulnerabilities by default, they cannot be configured for detecting vulnerabilities that are specific to the application domain of the analyzed program. In this paper we present JS-QL, a framework for detecting user-specified security vulnerabilities in JavaScript applications statically. The framework makes use of an internal domain-specific query language hosted by JavaScript. JS-QL queries are based on regular path expressions, enabling users to express queries over a flow graph in a declarative way. The flow graph represents the run-time behavior of a program and is computed by a static analysis. We evaluate JS-QL by expressing 9 security vulnerabilities supported by existing work and comparing the resulting specifications. We conclude that the combination of static analysis and regular path expressions lends itself well to the detection of user-specified security vulnerabilities.
Applying multiple time series data mining to large-scale network traffic analysis

Minimize false positive and false negative is one of the difficult problems of network traffic analysis. This paper propose a large-scale communications network traffic feature analysis method using multiple time series data mining, analyze multiple traffic feature time series as a whole, produce valid association rules of abnormal network traffic feature, characterize the entire communication network security situation accurately. Experiment with Abilene network data verify this method.
Cerebral Vasoconstriction in Vasovagal Syncope: Any Link With Symptoms?: A Transcranial Doppler Study

Background—Cerebral vasoconstriction has been described previously in vasovagal syncope (VVS). This phenomenon appears paradoxical in view of the well-known decrease of systemic vascular resistances taking places during VVS. We aimed to assess (1) whether cerebral vasoconstriction in VVS is an independent paradoxical phenomenon and (2) whether cerebral vasoconstriction has any link with symptoms and/or VVS onsets. Methods and Results—Seven young patients with recurrent VVS participated in the study. Each patient underwent monitoring of heart rate, blood pressure, cerebral blood flow velocity (by means of transcranial Doppler), end-tidal Pco2, peripheral oximetry, respiratory rate, and tidal volumes both at rest and during head-up tilt. All the subjects experienced tilt-induced VVS. A significant increase of respiratory tidal volumes was observed in each subject ≥160 seconds before VVS. This deep breathing induced a Pco2 decrease and, consequently, also a decrease in cerebral blood flow velocity and increase in cerebrovascular resistance (expressed by the increase of the pulsatility index). Within 40 seconds, 5 subjects started complaining of discomfort, in the absence of any significant blood pressure drop. Conclusions—Cerebral vasoconstriction is not a paradoxical phenomenon when it occurs before tilt-induced VVS but rather is only the physiological consequence of the hyperventilation-induced hypocapnia that occurs in habitual fainters. The large lag between the onset of syncope and cerebral vasoconstriction excludes the hypothesis that VVS is dependent on abnormal behavior of cerebral hemodynamics.
Low Complexity QPP Interleavers of Turbo Coding

Interleaver is an important component of turbo code and has a strong impact on its error correcting performance. Quadratic permutation polynomial (QPP) interleaver is a contention-free interleaver which is suitable for parallel turbo decoder implementation. To improve the performance of LTE QPP interleaver, largest-spread and maximum-spread QPP interleavers are analyzed for Long Term Evolution (LTE) turbo codes in this paper. Compared with LTE QPP interleaver, those algorithms have low computing complexity and better performances from simulation results.
Nearly Coherent Oscillations in Type I X-Ray Bursts from KS 1731–260

We present an analysis of the full set of Rossi X-Ray Timing Explorer (RXTE) observations of KS 1731-260 made between 1996 August and 1999 February, concentrating on the nine type I X-ray bursts that were observed. We find that the bursts divide naturally into two populations: "fast bursts" occur on the Banana Branch when the accretion rate is high and exhibit short decay times, high peak fluxes, and radius expansion episodes. "Slow bursts" occur in the Island State at lower accretion rates, have lower peak fluxes, higher fluences, longer decay times, and show no evidence of radius expansion. All five of the fast bursts, and none of the four slow bursts, show coherent oscillations near 524 Hz. Thus, the mechanism that produces the burst pulsations may well be related to the helium-rich burning process indicated by the other properties of the fast bursts. We perform in-burst phase connection of the burst pulsations, which allows us to unambiguously characterize their frequency evolution. That evolution exhibits a variety of behaviors, including a sharp spin-down during one burst. The frequency evolution exhibited by two bursts that occurred 2.6 yr apart is consistent with nearly the same exponential-relaxation model; in particular, the asymptotic frequencies of the two bursts differ by only 0.13 ± 0.09 Hz. The evolution during another burst, not modeled as exponential, shows a maximum frequency which is 0.6 ± 0.2 Hz greater than the smaller of these asymptotic frequencies. Applying our phase models, we find that the pulsations are spectrally harder than the burst emission, with the strength of the pulsations increasing monotonically with photon energy. Coherently summing all of the burst signals, we find upper limits of ~5% relative to the power of the main pulse on any modulation at 1/2 or 3/2 the main pulse frequency. We discuss our results in the context of models in which the burst pulsations are produced by a hot spot on the surface of a spinning neutron star.
An analysis of the feasibility of short read sequencing

Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20–30 nt, and that reads of 50 nt can provide reconstructed contigs (a contiguous fragment of sequence data) of 1000 nt and greater that cover 80% of human chromosome 1.
A Monolithically Integrated Large-Scale Optical Phased Array in Silicon-on-Insulator CMOS

A large-scale monolithic silicon nanophotonic phased array on a chip creates and dynamically steers a high-resolution optical beam in free space, enabling emerging applications in sensing, imaging, and communication. The scalable architecture leverages sub-array structure, mitigating the impact of process variation on the phased array performance. In addition, sharing control electronics among multiple optical modulators in the scalable architecture reduces the number of digital-to-analog converters (DACs) required for an <inline-formula> <tex-math notation="LaTeX">$N^{2}$ </tex-math></inline-formula> array from <inline-formula> <tex-math notation="LaTeX">$\mathcal {O}(N^{2})$ </tex-math></inline-formula> to <inline-formula> <tex-math notation="LaTeX">$\mathcal {O}(N)$ </tex-math></inline-formula>, allowing a small silicon footprint. An optical phased array for 1550-nm wavelength with 1024 uniformly spaced optical grating antennas, 1192 optical variable phase shifters, and 168 optical variable attenuators is integrated into a 5.7 mm <inline-formula> <tex-math notation="LaTeX">$\times$ </tex-math></inline-formula> 6.4 mm chip in a commercial 180-nm silicon-on-insulator RF CMOS technology. The control signals for the optical variable phase shifters and attenuators are provided by 136 DACs with 14-bit nonuniform resolution using 2.5-V input-output transistors. The implemented phased array can create 0.03° narrow optical beams that can be steered unambiguously within ±22.5°.