Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

Bacterial endophytes are ubiquitous to virtually all terrestrial plants. With the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. However, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. Here, we used cultivation-dependent and -independent approaches to assess the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations. We isolated members of nine bacterial genera. In particular, organisms affiliated with Stenotrophomonas maltophilia and Ochrobactrum spp. were isolated from both seed generations. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) of seed-extracted DNA revealed that approximately 45% of the bacterial community from the first seed generation was found in the second generation as well. In addition, we set up a greenhouse experiment to investigate abiotic and biotic factors influencing the endophytic bacterial community structure. PCR-DGGE profiles performed with DNA extracted from different plant parts showed that soil type is a major effector of the bacterial endophytes. Rice plants cultivated in neutral-pH soil favoured the growth of seed-borne Pseudomonas oryzihabitans and Rhizobium radiobacter, whereas Enterobacter-like and Dyella ginsengisoli were dominant in plants cultivated in low-pH soil. The seed-borne Stenotrophomonas maltophilia was the only conspicuous bacterial endophyte found in plants cultivated in both soils. Several members of the endophytic community originating from seeds were observed in the rhizosphere and surrounding soils. Their impact on the soil community is further discussed.
A Hierarchical Scale-and-Stretch Approach for Image Retargeting

Automated image retargeting techniques are becoming important with the proliferation of different display units, such as cell phones, notebooks, televisions etc. Scale-and-stretch techniques have been successfully used for resizing images into different aspect ratios, while also preserving the most prominent visual features. The main idea of scale-and-stretch techniques is to utilize a single grid with predefined resolution, and map onto it the single significance map. The problem of image resizing is subsequently formulated as an optimization problem, which determines the optimal deformation for every local region of the image based on their underling significance. The use, however, of a single grid with specific distribution is not robust with respect to the size of the significant regions that exist in the image. In this respect, this paper extents the scale-and-stretch techniques with the use of a hierarchical grid that incorporates the significance maps of different grid resolutions in a single grid. The proposed hierarchical approach surpasses current methods and manages to efficiently identify significant regions and achieve better results.
Maternal Feeding Controls Fetal Biological Clock

Background It is widely accepted that circadian physiological rhythms of the fetus are affected by oscillators in the maternal brain that are coupled to the environmental light-dark (LD) cycle. Methodology/Principal Findings To study the link between fetal and maternal biological clocks, we investigated the effects of cycles of maternal food availability on the rhythms of Per1 gene expression in the fetal suprachiasmatic nucleus (SCN) and liver using a transgenic rat model whose tissues express luciferase in vitro. Although the maternal SCN remained phase-locked to the LD cycle, maternal restricted feeding phase-advanced the fetal SCN and liver by 5 and 7 hours respectively within the 22-day pregnancy. Conclusions/Significance Our results demonstrate that maternal feeding entrains the fetal SCN and liver independently of both the maternal SCN and the LD cycle. This indicates that maternal-feeding signals can be more influential for the fetal SCN and particular organ oscillators than hormonal signals controlled by the maternal SCN, suggesting the importance of a regular maternal feeding schedule for appropriate fetal molecular clockwork during pregnancy.
Relative Comparison and Category Membership: The Case of Equity Analysts

Although audience perception is critical to the theory that classification affects rewards, such as ratings or sales, tests of the classification-rewards link occur without directly measuring audience perception. As a result, although a great deal is known about the mean level of rewards as a function of classification, little is known about the individual evaluations that underlie them and that contribute to the variance. I advance a process-based explanation for evaluative outcomes. Individuals make evaluations as a result of relative judgments on a subset of objects, comparing each object under consideration against a small set of others. Categorical boundaries matter to individuals perhaps because of personal preferences but also, importantly, because fit within boundaries determines how strictly to apply performance results. Simply by different individuals examining different subsets of objects, evaluative outcomes can vary dramatically, such that the same object may have different evaluations by audience members. Using recommendations by analysts at U.S. brokerages, I find support for the hypothesis that lower performance of a stock relative to other stocks already rated by a given analyst is associated with a lower likelihood of a high rating by an analyst, but this effect applies only to those stocks that fit clearly into industry boundaries. In general, the results suggest that the positive effect of category membership on evaluative outcomes, well established in prior literature, is contingent on the evaluative processes of individual audience members.
Predicting tunnelling-induced ground movements and interpreting field measurements using numerical analysis: Crossrail case study at Hyde Park

Ground response to the construction of the Crossrail tunnels in London Clay beneath Hyde Park has been modelled numerically using advanced finite-element analyses. The soil model used for modelling the London Clay was a kinematic hardening soil model (named M2-SKH). This model, when used for the St James's Park greenfield site, provided excellent predictions of tunnelling-induced ground movements. Comparison of the results from the analysis of the Hyde Park greenfield site with associated field monitoring data also suggests excellent predictions, even though in this case the tunnels were: of larger diameter; deeper in the London Clay; and constructed with earth-pressure-balance machines. The influence of lining permeability was found to influence significantly short- and longer-term predictions. Interpretation of the predicted surface and subsurface vertical and horizontal displacements due to the construction of the Crossrail tunnels exemplifies how numerical analysis can assist in explaining and identif.
DeepDive: Web-scale Knowledge-base Construction using Statistical Learning and Inference

We present an end-to-end (live) demonstration system called DeepDive that performs knowledge-base construction (KBC) from hundreds of millions of web pages. DeepDive employs statistical learning and inference to combine diverse data resources and best-of-breed algorithms. A key challenge of this approach is scalability, i.e., how to deal with terabytes of imperfect data eciently. We describe how we address the scalability challenges to achieve web-scale KBC and the lessons we have learned from building DeepDive.
Antimicrobial Susceptibility of Bordetella bronchiseptica Isolates from Swine and Companion Animals and Detection of Resistance Genes

Bordetella bronchiseptica causes infections of the respiratory tract in swine and other mammals and is a precursor for secondary infections with Pasteurella multocida. Treatment of B. bronchiseptica infections is conducted primarily with antimicrobial agents. Therefore it is essential to get an overview of the susceptibility status of these bacteria. The aim of this study was to comparatively analyse broth microdilution susceptibility testing according to CLSI recommendations with an incubation time of 16 to 20 hours and a longer incubation time of 24 hours, as recently proposed to obtain more homogenous MICs. Susceptibility testing against a panel of 22 antimicrobial agents and two fixed combinations was performed with 107 porcine isolates from different farms and regions in Germany and 43 isolates obtained from companion animals in Germany and other European countries. Isolates with increased MICs were investigated by PCR assays for the presence of resistance genes. For ampicillin, all 107 porcine isolates were classified as resistant, whereas only a single isolate was resistant to florfenicol. All isolates obtained from companion animals showed elevated MICs for β-lactam antibiotics and demonstrated an overall low susceptibility to cephalosporines. Extension of the incubation time resulted in 1–2 dilution steps higher MIC50 values of porcine isolates for seven antimicrobial agents tested, while isolates from companion animals exhibited twofold higher MIC50/90 values only for tetracycline and cefotaxime. For three antimicrobial agents, lower MIC50 and MIC90 values were detected for both, porcine and companion animal isolates. Among the 150 isolates tested, the resistance genes bla BOR-1 (n = 147), bla OXA-2, (n = 4), strA and strB (n = 17), sul1 (n = 10), sul2 (n = 73), dfrA7 (n = 3) and tet(A) (n = 8) were detected and a plasmid localisation was identified for several of the resistance genes.
Tunable CMOS delay gate with reduced impact of fabrication mismatch on timing parameters

This paper presents the analysis and design of a simple one-stage tunable delay gate with improved matching properties as compared with the commonly used “current starved inverter”. The operation of two delay lines employing these structures in a standard 90 nm CMOS technology was verified based on the post layout mismatch Monte Carlo simulations. Accounting for the fabrication mismatch, the delay generated by the proposed “output-split inverter” (OSI) circuit is about 10-30% more accurate as compared to the conventional current starved inverter occupying the same chip area.
Clozapine and concomitant medications: Assessing the completeness and accuracy of medication records for people prescribed clozapine under shared care arrangements

RATIONALE, AIM, AND OBJECTIVE The objective of the study is to assess the completeness and accuracy of medication records held by stakeholders (secondary care, general practice, and community pharmacy) for clozapine consumers managed in a shared care programme. METHODS This was an exploratory, descriptive study examining secondary and primary care medication records in a large, urban, public mental health service setting in Queensland, Australia. Consumers (18-65 years old) prescribed clozapine under shared care management with capacity to consent were eligible (n = 55) to participate. Information from medication and dispensing records was used by a pharmacist to compile a best possible medication history for each consumer. Discrepancies were identified through reconciliation of stakeholder records with the history. Discrepancies were defined as an omission, addition, or administration discrepancy (difference in dose, frequency, or clozapine brand). RESULTS Thirty-five (63.6%) consumers consented for records to be reviewed. Overall, 32 (91.4%) consumers had at least 1 discrepancy in their records with a mean of 4.9 discrepancies per consumer. Of 172 discrepancies, 127 (73.8%) were omissions. Primarily, concomitant medicines were omitted in 19/35 (54%) of secondary care records while clozapine was omitted in 13/32 (40.6%) of community pharmacies records. CONCLUSIONS Discrepancies were highly prevalent in the shared care medication records of clozapine consumers of this service. Where there is incomplete and inaccurate medication information, there is a risk of suboptimal clinical decision making, increasing the likelihood of adverse drug events. This study demonstrates a need for improved documentation and timely access to accurate and complete medication records for shared care stakeholders. Expanding the pharmacist's role in this setting could improve medication accuracy in documentation and related communication.
The Influence of Sociotechnological Mechanisms on Individual Motivation toward Knowledge Contribution in Problem-Solving Virtual Communities

Knowledge contribution in virtual communities is an important issue in the field of knowledge management. Based on Ames's theoretical framework on motivation, we propose a model for knowledge contribution in problem-solving virtual communities (PSVCs). The model includes two second-order individual motivations, with four major mechanisms in PSVCs that are associated with these motivations. Results confirm that only egoistic motives affect members' knowledge contribution in PSVCs. Further, knowledge repository and social identity are found to be important mechanisms for promoting knowledge contribution through egoistic motives. This paper concludes with theoretical and practical implications and provides insights for future research.
A Distributed Defense Framework for Flooding-Based DDoS Attacks

A flooding-based distributed denial of service (DDoS) attack sends a large amount of unwanted traffic to a victim machine. Existing network-level congestion control mechanisms are inadequate in preventing service quality from deteriorating because of these attacks. We propose a distributed framework to defend against DDoS attacks. It has three major components: detection, traceback, and traffic control. We present the traffic control component in detail in this paper. A distance-based rate limit mechanism is proposed to allow the traffic control component at the victim end request the defense systems at the source end to set up rate limits on the edge routers of the attack source ends. This rate limit mechanism efficiently reduces attack traffic from being forwarded to the victim. We evaluate the DDoS defense framework using the NS2 platform. The results demonstrate that the framework can effectively control attack traffic to sustain quality of service for legitimate traffic compared to the pushback technique.
Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.
Intrinsic Structural Disorder in Adenovirus E1A: a Viral Molecular Hub Linking Multiple Diverse Processes

Viruses are obligate intracellular parasites. Their genomes are not large enough to encode all the functions required to independently produce progeny; hence, viruses are absolutely dependent on host cell functions. Mechanistically, these host cell processes in eukaryotes are founded on an exquisitely complex series of molecular interactions. In particular, the execution of complex biological processes requires the precise interaction and regulation of thousands of proteins. The definition of cellular interactomes by systematic analysis of protein-protein interactions has revealed complex molecular networks (39, 82, 111, 122). Most cellular proteins interact with only one or two other proteins, making only one or two connections. However, the minority of proteins interact with tens, or even hundreds, of other proteins to form network hubs. Hub proteins play key roles in regulating and orchestrating the activity of the proteins they interact with, effectively creating functional modules within the cellular interactome (35, 48, 62). The central role served by cellular hub proteins in regulating cell functions makes them ideal targets during a viral infection. By targeting a single cellular hub, a viral regulatory protein can effectively gain control over an entire module, potentially comprised of hundreds of proteins. By targeting multiple cellular hubs, a virally encoded hub can transform the architecture of the cellular protein interaction network, reprogramming virtually all aspects of cell function and behavior. The viral oncogenes of the small DNA tumor viruses encode some of the most versatile and potent viral hub proteins. Among these, adenovirus E1A is one of the best characterized and is the subject of this review.
Digital Control Networks for Continuous Passive Plants Which Maintain Stability Using Cooperative Schedulers

This paper provides a sufficient framework to synthesize l 2 -stable networks in which the controller and plant can be subject to delays and data dropouts. This framework can be applied to control systems which use "soft-real-time" cooperative schedulers as well as those which use wired and wireless network feedback. The framework applies to plants and controllers which are passive, therefore these passive systems can be either linear, nonlinear, and (or) time-varying. This framework arises from fundamental results related to passive control, and scattering theory which are used to design passive force-feedback telemanipulation systems, in which we provide a short review. Theorem 3 states how a (non)linear (strictly input or strictly output) passive plant can be transformed to a discrete (strictly input) passive plant using a particular digital sampling and hold scheme. Furthermore, Theorem 4(5) provide new sufficient conditions for l 2 (and L 2 )-stability in which a strictly-output passive controller and plant are interconnected with only wave-variables. Lemma 2 shows it is sufficient to use discrete wave-variables when data is subject to fixed time delays and dropouts in order to maintain passivity. Lemma 3 shows how to safely handle time varying discrete wave-variable data in order to maintain passivity. Based on these new theories, we provide an extensive set of new results as they relate to LTI systems. For example, Proposition 2 shows how a LTI strictly-output passiveobserver can be implemented. We then present a new cooperative scheduler algorithm to implement an l 2 -stable control network. We also provide an illustrative simulated example which uses a passive observer followed with a discussion for future research.
In Vivo Assessment of Bone Ingrowth Potential of Three-Dimensional E-Beam Produced Implant Surfaces and the Effect of Additional Treatment by Acid Etching and Hydroxyapatite Coating

The bone ingrowth potential of three-dimensional E-beam-produced implant surfaces was examined by histology and compared to a porous plasma-sprayed control. The effects of acid etching and a hydroxyapatite (HA) coating were also evaluated by histology. Specimens were implanted in the distal femur of 10 goats. Histological analysis of bone ingrowth was performed 6 weeks after implantation. The E-beam-produced surfaces showed significantly better bone ingrowth compared to the plasma-sprayed control. Additional treatment of the E-beam surface structures with a HA coating, further improved bone ingrowth potential of these structures significantly. Acid etching of the E-beam structures did not influence bone ingrowth significantly. In conclusion, the HA-coated, E-beam-produced structures are promising potential implant surfaces.
Immunoquantitative Measurement of Soybean Aeroallergen Emissions

Environmental allergen exposure plays an important role in the development and expression of asthma and allergy. To study allergen exposure, it is necessary to actually measure allergen levels. Direct measurement is also needed to assess what levels lead to sensitisation or provoke symptoms in already sensitised subjects, and evaluate the efficacy of allergy reduction strategies (1). The measurement of aeroallergens plays a key role in asthma prevention. Both the epidemiological studies and the studies on specific IgE to soybean carried out following the asthma epidemics in Barcelona attributed their cause to the unloading of soybean in the harbour (2-3). The environmental intervention in September 1987 with the installation of bag filters in a silo led to a decrease in airborne soybean concentrations and the subsequent disappearance of the epidemics (4). The 1,555 U/m3 level of soybean allergen detected during a determined asthma epidemic day (5-6) was substantially higher than the highest value (165 U/m3) recorded in 22 unloading days after the interventions (4). These data show that the measurement of soybean aeroallergen levels in harbours loading and unloading soybean is of increasing importance in controlling the efficiency of the environmental interventions in order to prevent new asthma outbreaks in these areas. In the evaluation of occupational asthma, measurement of the causal agent in the air at worksites is a necessary additional link in the chain of evidence that a suspected allergen is the cause of the pathology. Such measurements are particularly useful when the allergen is unknown, the environment of interest has never before been assessed, and control measures have to be considered. Knowledge of the concentration at work also allows correlation between exposure of workers and an inhalation challenge test in the laboratory, which is performed in individual patients to confirm that the suspected allergenic material that evoked the IgE antibody can actually cause an asthmatic response (7). Thus, it is of great interest to monitor soybean dust levels indoors.