Miracle-dz/UniFAR-FTUs huggingface dataset:
T‐DNA insertion, plasmid rescue and integration analysis in the model mycorrhizal fungus Laccaria bicolor

Ectomycorrhiza is a mutualistic symbiosis formed between fine roots of trees and the mycelium of soil fungi. This symbiosis plays a key role in forest ecosystems for the mineral nutrition of trees and the biology of the fungal communities associated. The characterization of genes involved in developmental and metabolic processes is important to understand the complex interactions that control the ectomycorrhizal symbiosis. Agrobacterium‐mediated gene transfer (AMT) in fungi is currently opening a new era for fungal research. As whole genome sequences of several fungi are being released studies about T‐DNA integration patterns are needed in order to understand the integration mechanisms involved and to evaluate the AMT as an insertional mutagenesis tool for different fungal species. The first genome sequence of a mycorrhizal fungus, the basidiomycete Laccaria bicolor, became public in July 2006. Release of Laccaria genome sequence and the availability of AMT makes this fungus an excellent model for functional genomic studies in ectomycorrhizal research. No data on the integration pattern in Laccaria genome were available, thus we optimized a plasmid rescue approach for this fungus. To this end the transformation vector (pHg/pBSk) was constructed allowing the rescue of the T‐DNA right border (RB)–genomic DNA junctions in Escherichia coli. Fifty‐one Agrobacterium‐transformed fungal strains, picked up at random from a larger collection of T‐DNA tagged strains (about 500), were analysed. Sixty‐nine per cent were successfully rescued for the RB of which 87% were resolved for genomic integration sequences. Our results demonstrate that the plasmid rescue approach can be used for resolving T‐DNA integration sites in Laccaria. The RB was well conserved during transformation of this fungus and the integration analysis showed no clear sequence homology between different genomic sites. Neither obvious sequence similarities were found between these sites and the T‐DNA borders indicating non‐homologous integration of the transgenes. Majority (75%) of the integrations were located in predicted genes. Agrobacterium‐mediated gene transfer is a powerful tool that can be used for functional gene studies in Laccaria and will be helpful along with plasmid rescue in searching for relevant fungal genes involved in the symbiotic process.
Defining the Boundaries of Child Neglect

Child maltreatment does not exist in isolation from other forms of family violence. Notably, research supports the connection between wife abuse and child maltreatment, and research on the possible consequences to children exposed to domestic violence has influenced a redefinition of child maltreatment legislation and policy. Recently, some states have considered and passed legislation making witnessing of domestic violence, per se, a form of criminal child abuse. This article explores conceptual discontinuities in official definitions of child maltreatment in relation to domestic violence failure to protect matters by drawing on data from legislative reviews, child protective services, and individual-level definitions. Implications for policy, practice, and research are addressed.
Climate change and salinity in drinking water as a global problem: using remote-sensing methods to monitor surface water salinity

A still neglected consequence of climate change is increasing salinity levels in coastal areas. This is due to a combination of factors including sea-level rise and tropical cyclones transporting saltwater upstream. The salination of drinking water is a problem that could affect millions of people living in coastal areas globally. Excess dietary intake of salt is strongly associated with high blood pressure and gastric cancer. Saltwater intrusion can also have a detrimental effect on crops and agriculture. Measurements of salinity in coastal areas are urgently needed to estimate the extent of the problem and the correlation of saline waters with health outcomes. In situ measurements of salinity cannot capture the complicated spatial and temporal changes that take place in surface water bodies. In this article, we will discuss an effective alternative approach to mapping the salinity distribution of surface water using satellites.
A logical characterization of bisimulation for labeled Markov processes

This paper gives a logical characterization of probabilistic bisimulation for Markov processes. Bisimulation can be characterized by a very weak modal logic. The most striking feature is that one has no negation or any kind of negative proposition. Bisimulation can be characterized by several inequivalent logics; we report five in this paper and there are surely many more. We do not need any finite branching assumption yet there is no need of infinitely conjunction. We give an algorithm for deciding bisimilarity of finite state systems which constructs a formula that witnesses the failure of bisimulation.
Fully comprehensive mathematical approach to the expression of uncertainty in measurement

This paper analyzes the result of a measurement in the mathematical model of incomplete knowledge and shows how it can be treated in the framework of the theory of evidence. The random fuzzy variables are considered in order to express the result of a measurement together with its uncertainty, and a significant application is considered to prove the practical utility of the proposed approach
Robust spatiotemporal stereo for dynamic scenes

Stereo matching is a challenging problem, especially in the presence of noise or of weakly textured objects. Using temporal information in a binocular video sequence to increase the discriminability for matching has been introduced in the recent past, but all the proposed methods assume either constant disparity over time, or small object motions, which is not always true. We introduce a novel stereo algorithm that exploits temporal information by robustly aggregating a similarity statistic over time, in order to improve the matching accuracy for weak data, while preserving regions undergoing large motions without introducing artifacts.
The impact of smart fractions, cognitive ability of politicians and average competence of peoples on social development

Smart fraction theory supposes that gifted and talented persons are especially relevant for societal development. Using results for the 95 th percentile from TIMSS 1995- 2007, PISA 2000-2006 and PIRLS 2001-2006 we calculated an ability sum value (N=90 countries) for the upper level group (equivalent to a within country IQ-threshold of 125 or a student assessment score of 667) and compared its influence with the mean ability and the 5 th percentile ability on wealth (GDP), patent rates, Nobel Prizes, numbers of scientists, political variables (government effectiveness, democracy, rule of law, political liberty), HIV, AIDS and homicide. Additionally, using information on school and professional education, we estimated the cognitive competence of political leaders in N=90 countries. Results of correlations, regression and path analyses generally show a larger impact of the smart fractions' ability on positively valued outcomes than of the mean result or the 5 th percentile fraction. The influence of the 5 th percentile fraction on HIV, AIDS and homicide, however, was stronger. The intelligence of politicians was less important, a longitudinal cross- lagged analysis could show a positive influence on the cognitive development of nations.
Improving Cloud Availability with On-the-fly Schema Updates

Database applications undergo frequent schema changes. To change the schema, the application has to be shut down and migrated to the new version, or run in a mixed mode that supports old and new clients, e.g., via schema versioning. Shutdowns are problematic for applications that cannot tolerate downtime such as embedded, real-time or mission-critical systems; in the Cloud, shutdowns can lead to Service Level Agreement violations or worse, to service interruptions for critical platforms such as healthcare. Mixed-mode operation raises programmability, consistency and performance degradation issues. In this paper we present a system that exploits the march-forward nature of many database applications (no need to support old schema versions after the schema update) to provide on-the-y updates while ensuring consistency, and being transparent to clients. We first study schema evolution and database usage based on longitudinal studies of four popular open source applications. Next, we implement support for safe on-the-y schema updates on top of the popular SQLite database engine. Finally, we evaluate our approach using real-world schema changes and database usage scenarios for applications running in the Cloud on the Amazon Web Services platform, and on server systems. We show how on-the-y schema updates can increase Cloud applications' availability from less than two nines (99%) to more than six nines (99.9999%). More generally, our experiments indicate that SQLite-based applications can enjoy fully automatic on-the-y schema updates at a low, transient overhead.
Role of genes linked to sporadic Alzheimer’s disease risk in the production of β-amyloid peptides

Alzheimer’s disease (AD) is characterized by the presence of toxic protein aggregates or plaques composed of the amyloid β (Aβ) peptide. Various lengths of Aβ peptide are generated by proteolytic cleavages of the amyloid precursor protein (APP). Mutations in many familial AD-associated genes affect the production of the longer Aβ42 variant that preferentially accumulates in plaques. In the case of sporadic or late-onset AD, which accounts for greater than 95% of cases, several genes are implicated in increasing the risk, but whether they also cause the disease by altering amyloid levels is currently unknown. Through loss of function studies in a model cell line, here RNAi-mediated silencing of several late onset AD genes affected Aβ levels is shown. However, unlike the genes underlying familial AD, late onset AD-susceptibility genes do not specifically alter the Aβ42/40 ratios and suggest that these genes probably contribute to AD through distinct mechanisms.
Are we living in a string-dominated universe?

The holographic solution is a new exact solution to the Einstein field equations. It describes a compact self-gravitating object with properties similar to a black hole. Its entropy and temperature at infinity are proportional to the Hawking result. Instead of an event horizon, the holographic solution has a real spherical boundary membrane, situated roughly two Planck distances outside of the object's gravitational radius. The interior matter-state is singularity free. It consists out of string type matter, which is densely packed. Each string has a transverse extension of exactly one Planck area. This dense package of strings might be the reason, why the solution does not collapse to a singularity. The local string tension is inverse proportional to the average string length. This purely classical result has its almost exact correspondence in a recent result in string theory. The holographic solution suggest, that string theory is relevant also on cosmological scales. The large scale phenomena in the universe can be explained naturally in a string context. Due to the zero active gravitational mass-density of the strings the Hubble constant in a string dominated universe is related to its age by H t = 1. The WMAP measurements have determined H t \approx 1.02 \pm 0.02 experimentally. The nearly unaccelerated expansion in a string dominated universe is compatible with the recent supernova measurements. Under the assumption, that the cold dark matter (CDM) consists out of strings, the ratio of CDM to baryonic matter is estimated as \Omega_CDM / \Omega_b \approx 6.45. Some arguments are given, which suggest that the universe might be constructed hierarchically out of its most basic building blocks: strings and membranes.
template for two-page abstracts in Word 97 (PC)

TRENDS IN APOLLO SAMPLES COLLECTED AND IN SAMPLE USAGE: The 6 Apollo missions that landed on the lunar surface returned 2196 samples comprised of 382 kg. The 58 samples weighing 21.5 kg collected on Apollo 11 expanded to 741 samples weighing 110.5 kg by the time of Apollo 17. The main goal on Apollo 11 was to obtain some material and return it safely to Earth. As we gained experience, the sampling tools and a more specific sampling strategy evolved [1]. This trend is shown graphically in Figs. 1 & 2.
Micro‐geomorphology determines community structure of biological soil crusts at small scales

Biological soil crusts (BSCs) are ubiquitous communities of diminutive organisms such as cyanobacteria, green algae, lichens, mosses and others associated closely with particles of surface soil, forming a cohesive thin horizontal layer. The ecological roles of BSCs affecting soil nutrient cycling, stability and hydrological processes, influencing the germination and establishment of vascular plants, and serving as habitats for numerous arthropods and microorganism have been well documented. We tested the hypothesis that micro‐geomorphological features determine the spatial distribution of BSCs by reallocating related abiotic resources at small‐ and medium‐scales in the Tengger Desert. Our results showed that higher soil pH and higher total potassium content in topsoil positively correlated with the colonization of cyanobacteria and algae in the earliest successional stages of BSCs, while increasing dust deposition onto the topsoil enhanced the development of lichen and mosses in the later stages of BSCs. Increasing soil moisture raised the proportion of mosses and lichen in BSCs, this will possibly change the ecological functions of BSCs, such as nitrogen‐fixation by cyanobacteria, due to the conversion from a complex to relative simple type of BSC. Micro‐geomorphology has created various habitats at a small‐scale affecting colonization and development of cryptogams. This paper considers the contribution of micro‐geomorphology to biodiversity in the extreme arid desert systems. Copyright © 2010 John Wiley & Sons, Ltd.
Prospective Study of Visual Outcomes and Endothelial Survival With Descemet Membrane Automated Endothelial Keratoplasty

Purpose: To evaluate vision and endothelial cell survival in an initial Descemet membrane automated endothelial keratoplasty (DMAEK) series. Methods: This was a prospective nonrandomized study of an initial consecutive series of 40 DMAEK cases, performed with or without concomitant phacoemulsification and intraocular lens implantation. The graft was dissected with a microkeratome. A central 6- to 7-mm big bubble was created to separate endothelium from stroma, and the overlying stroma was excised. The graft was cut to 8.5- to 9.5-mm diameter and inserted with a pull through technique. Eyes were treated for Fuchs endothelial dystrophy, secondary corneal decompensation, or previous failed endothelial transplant. Best spectacle-corrected visual acuity, manifest refraction, pachymetry, and endothelial cell density were assessed. Results: Median best spectacle-corrected visual acuity was 20/30 at 1 month (range: 20/15-20/50), improved from 20/40 (range: 20/25-20/400) preoperatively, excluding 7 eyes (18%) with significant retinal pathology. Rates of 20/20, 20/25, 20/30, and 20/40 vision were 25%, 71%, 89%, and 100%, respectively, at 3 months and 48%, 74%, 93%, and 100%, respectively, at 6 months. Median endothelial cell loss relative to baseline donor cell density was 31% at 6 months. Air was reinjected in 10 eyes (25%) to promote graft attachment, and 2 grafts (5%) failed to clear. Conclusions: DMAEK provided significant improvement in visual acuity and marked reduction in central corneal thickness. DMAEK had a higher rate of postoperative air reinjection than Descemet stripping endothelial keratoplasty and comparable 6-month endothelial cell loss.
POUR PDF - copie

HOL-TestGen/CirTA is a theorem-prover based environment for test generation from specifications written in Circus. Circus is a formal specification language which combines the notions of states and complex data types in a Z-like style with a process-algebra in the tradition of CSP. The originality of HOL-TestGen/CirTA is that it is based on a machine-checked embedding in Isabelle/HOL of the semantics of this language. This provides the foundation of the test-generation rules and for their execution in form of symbolic computation. The result is an integrated tool chain that transforms, via rules derived from the semantic definition, the Circus specification of a system into a set of symbolic test cases, instantiates, compiles and submits them. This report presents a first case study performed on a component of a real-world medical monitoring system written in Java. In this case study, the generated test cases are compiled into a set of JUnit-testers and run against the implementation of the system under test. Various experiments were performed in order to analyze the performances and the efficiency of the test generation process. We show that a specific test generation tactic is more efficient than the generic procedure. A basic mutation analysis was experimented to give some assessment of our generated test cases.
Soil science: methods and applications.

1. Acknowledgements 2. Prologue 3. Soils in the Field Mineral Particles - the Soil Framework 4. Organic Materials - Alive and Dead 5. The Arrangement of Particles and Pores - Soil Structure 6. Water in Soils 7. Air in Soils - Supply and Demand 8. Particle Surfaces and Soil Solutions 9. Soil Acidity and Alkalinity 10. The Availability of Plant Nutrients - Potassium, Calcium and Magnesium 11. Phosphorous and Sulphur 12. Nitrogen in Soils 13. The Availability of Water in Soils 14. Soil Fertility 15. Salinity and Sodicity 16. Pesticides and Metals 17. Epilogue 18. Appendices 19. References
Partially Occluded Object-Specific Segmentation in View-Based Recognition

We present a novel object-specific segmentation method which can be used in view-based object recognition systems. Previous object segmentation approaches generate inexact results especially in partially occluded and cluttered environment because their top-down strategies fail to explain the details of various specific objects. On the contrary, our segmentation method efficiently exploits the information of the matched model views in view-based recognition because the aligned model view to the input image can serve as the best top-down cue for object segmentation. In this paper, we cast the problem of partially occluded object segmentation as that of labelling displacement and foreground status simultaneously for each pixel between the aligned model view and an input image. The problem is formulated by a maximum a posteriori Markov random field (MAP-MRF) model which minimizes a particular energy function. Our method overcomes complex occlusion and clutter and provides accurate segmentation boundaries by combining a bottom-up segmentation cue together. We demonstrate the efficiency and robustness of it by experimental results on various objects under occluded and cluttered environments.
MeTA

Physicians and health care organizations always collect large amounts of data during patient care. These large and high-dimensional datasets are usually characterized by an inherent sparseness. Hence, analyzing these datasets to figure out interesting and hidden knowledge is a challenging task. This article proposes a new data mining framework based on generalized association rules to discover multiple-level correlations among patient data. Specifically, correlations among prescribed examinations, drugs, and patient profiles are discovered and analyzed at different abstraction levels. The rule extraction process is driven by a taxonomy to generalize examinations and drugs into their corresponding categories. To ease the manual inspection of the result, a worthwhile subset of rules (i.e., nonredundant generalized rules) is considered. Furthermore, rules are classified according to the involved data features (medical treatments or patient profiles) and then explored in a top-down fashion: from the small subset of high-level rules, a drill-down is performed to target more specific rules. The experiments, performed on a real diabetic patient dataset, demonstrate the effectiveness of the proposed approach in discovering interesting rule groups at different abstraction levels.
REPLY Is That What Bayesians Believe ?

Griffiths, Chater, Norris, and Pouget (2012) argue that we have misunderstood the Bayesian approach. In their view, it is rarely the case that researchers are making claims that performance in a given task is near optimal, and few, if any, researchers adopt the theoretical Bayesian perspective according to which the mind or brain is actually performing (or approximating) Bayesian computations. Rather, researchers are said to adopt something more akin to what we called the methodological Bayesian approach, according to which Bayesian models are statistical tools that allow researchers to provide teleological explanations of behavior. In our reply we argue that many Bayesian researchers often appear to be make claims regarding optimality, and often appear to be making claims regarding how the mind computes at algorithmic and implementational levels of descriptions. We agree that some Bayesian theorists adopt the methodological approach, but we question the value of this approach. If Bayesian theories in psychology and neuroscience are only designed to provide insights into teleological questions, we expect that many readers have misunderstood, and hence there is a pressing need to clarify what Bayesian theories of cognition are all about.
Transplantation of viable meniscal allograft. Surgical technique.

BACKGROUND Few medium-term or long-term reports on meniscal allograft transplantations are available. In this study, we present the results of a survival analysis of the clinical outcomes of our first 100 procedures involving transplantation of viable medial and lateral meniscal allografts performed in ninety-six patients. METHODS Thirty-nine medial and sixty-one lateral meniscal allografts were evaluated after a mean of 7.2 years. Survival analysis was based on specific clinical end points, with failure of the allograft defined as moderate occasional or persistent pain or as poor function. An additional survival analysis was performed to assess the results of the sixty-nine procedures that involved isolated use of a viable allograft (twenty of the thirty-nine medial allograft procedures and forty-nine of the sixty-one lateral allograft procedures) and of the thirteen viable medial meniscal allografts that were implanted in combination with a high tibial osteotomy in patients with initial varus malalignment of the lower limb. RESULTS Overall, eleven (28%) of the thirty-nine medial allografts and ten (16%) of the sixty-one lateral allografts failed. The mean cumulative survival time (11.6 years) was identical for the medial and lateral allografts. The cumulative survival rates for the medial and lateral allografts at ten years were 74.2% and 69.8%, respectively. The mean cumulative survival time and the cumulative survival rate for the medial allografts used in combination with a high tibial osteotomy were 13.0 years and 83.3% at ten years, respectively. CONCLUSIONS Transplantation of a viable meniscal allograft can significantly relieve pain and improve function of the knee joint. Survival analysis showed that this beneficial effect remained in approximately 70% of the patients at ten years. This study identified the need for a prospective study comparing patients with similar symptoms and clinical findings treated with and without a meniscal allograft and followed for a longer period with use of clinical evaluation as well as more objective documentation tools regarding the actual fate of the allograft itself and the articular cartilage.