Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning spatial relations between objects from 3D scenes

In this work, we learn a limited number of abstractions which can then be used to form preconditions for motor actions. These abstractions take the form of spatial relations amongst objects. We consider three “classes” of spatial relation: The objects either are separated from, on-top of, or inside each other. We have tackled this same problem in previous work (Fichtl et al., 2013). Here we report on recent improved results using a novel application of histograms to visually recognise a spatial relation between objects in the environment. Using this histogram based approach we are able to report a very high rate of success when the system is asked to recognise a spatial relation.
A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny

The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.
A randomised placebo-controlled trial to explore the effect of suppressive therapy with acyclovir on genital shedding of HIV-1 and herpes simplex virus type 2 among Zimbabwean sex workers

Objectives: To determine the effect of daily acyclovir on genital shedding of HIV-1 and herpes simplex virus type 2 (HSV-2) in a randomised placebo-controlled trial among rural Zimbabwean sex workers. Methods: 214 women were recruited and tested for HIV-1 and HSV-2 antibodies, HIV plasma viral load, CD4 lymphocyte count and genital swabs for qualitative detection of HIV-1 and HSV-2 genital shedding. Women were randomly assigned to acyclovir 400 mg twice a day for 12 weeks or matching placebo and were followed weekly to detect HIV-1 or HSV-2 genital shedding. Shedding analyses were only undertaken on 125 women co-infected with HSV-2 and HIV-1. Data were analysed using logistic regression, with random effects modelling used to account for repeated measurements on the same women. Results: All women were randomly assigned to acyclovir or placebo; 125 of whom were co-infected with HIV-1 and HSV-2. 69 women were randomly assigned to acyclovir and 56 to placebo. Although twice daily acyclovir reduced rates of HSV-2 genital shedding, (adjusted odds ratio (AOR) 0.24; 95% CI 0.12 to 0.48; less than p<0.001), it had no effect on the proportion of visits at which HIV-1 shedding was detected (AOR 1.08; 95% CI 0.48 to 2.42; p = 0.9). Adherence varied between participants but even when adherence was high (as determined by pill count and extent of HSV-2 suppression) HIV-1 shedding was not reduced. Conclusion: Among these HIV-1 and HSV-2-seropositive women, suppressive acyclovir therapy had no effect on the rate of HIV genital shedding despite a reduction in genital HSV-2. Treatment adherence and its measurement clearly affect the interpretation of these results.
Plantation monitoring and yield estimation using autonomous quadcopter for precision agriculture

Recently, quadcopters with their advance sensors and imaging capabilities have become an imperative part of the precision agriculture. In this work, we have described a framework which performs plantation monitoring and yield estimation using the supervised learning approach, while autonomously navigating through an inter-row path of the plantation. The proposed navigation framework assists the quadcopter to follow a sequence of collision-free GPS way points and has been integrated with ROS (Robot Operating System). The trajectory planning and control module of the navigation framework employ convex programming techniques to generate minimum time trajectory between way-points and produces appropriate control inputs for the quadcopter. A new `pomegranate dataset' comprising of plantation surveillance video and annotated frames capturing the varied stages of pomegranate growth along with the navigation framework are being delivered as a part of this work.
R&D of micron sized nanoionic supercapacitors for self-powered MEMS in deep-sub-voltage regime

The development of impulse micron-sized sub-voltage supercapacitors (SCs) was initiated within the framework of a new direction, «nanoionics of advanced superionic conductors». A search for applications of nanoionic SCs was made with regard to the development of deep-sub-voltage nanoelectronics, self-powered nanosystems and related high-tech directions. New nanoionic fundamentals are introduced and the ways for the creation of advanced carbon-based nanostructures suited for different types of SCs are proposed.
Genetic recombination in avian retroviruses

The avian retroviruses—and probably other retroviruses as well—undergo a variety of recombinational events with relatively high efficiency. An understanding of the molecular basis of these events should provide insight into the important biological properties these agents exhibit when they become integrated into somatic or germ‐line host cells, when they exchange genetic information among themselves, or when they transduce host cell genes. In this article we review molecular models for homologous recombination, against a background of the other types of recombination events that arc typical of these viruses. It seems probable that the retroviruses will provide useful models for analysis of a variety of DNA rearrangements known to occur in eukaryotic cells.
A third order in-line pseudo-elliptic filter with a transmission zero extracted at its center

The paper presents a new approach to implement a real transmission zero in a third order in-line pseudo-elliptic filter. The transmission zero is extracted at an internal node in the in-line structure and not at the input or the output as in the well-known extracted pole technique. It is shown that the coupling coefficient that is directly responsible for the real transmission zero becomes too large and physically unrealizable if the extraction is performed at the input or the output as in the extracted pole technique. On the other hand, all coupling coefficient remain realizable if the extraction is performed at internal nodes. Furthermore, internal "impedance zones" can be independently scaled without affecting the overall response of the filter. Example filters are designed to demonstrate the validity of the approach.
Heat shock-regulated production of Escherichia coli beta-galactosidase in Saccharomyces cerevisiae

The HSP90 gene of the yeast Saccharomyces cerevisiae encodes a heat shock-inducible protein with an Mr of 90,000 (hsp90) and unknown function. We fused DNA fragments of a known sequence (namely, either end of a 1.4-kilobase EcoRI fragment which contains the S. cerevisiae TRP1 gene) to an EcoRI site within the coding sequence of the HSP90 gene. When these fusions are introduced into S. cerevisiae they direct the synthesis of unique truncated hsp90 proteins. By determining the size and charge of these proteins we were able to deduce the translational reading frame at the (EcoRI) fusion site. This information allowed us to design and construct a well-defined in-frame fusion between the S. cerevisiae HSP90 gene and the Escherichia coli lacZ gene. When this fused gene is introduced into S. cerevisiae on a multicopy plasmid vector, it directs the heat shock-inducible synthesis of a fused protein, which is an enzymatically active beta-galactosidase. Thus, for the first time, it is possible to quantitate the heat shock response in a eucaryotic organism with a simple enzyme assay.
Survival Association Rule Mining Towards Type 2 Diabetes Risk Assessment

Type-2 Diabetes Mellitus is a growing epidemic that often leads to severe complications. Effective preventive measures exist and identifying patients at high risk of diabetes is a major health-care need. The use of association rule mining (ARM) is advantageous, as it was specifically developed to identify associations between risk factors in an interpretable form. Unfortunately, traditional ARM is not directly applicable to survival outcomes and it lacks the ability to compensate for confounders and to incorporate dosage effects. In this work, we propose Survival Association Rule (SAR) Mining, which addresses these shortcomings. We demonstrate on a real diabetes data set that SARs are naturally more interpretable than the traditional association rules, and predictive models built on top of these rules are very competitive relative to state of the art survival models and substantially outperform the most widely used diabetes index, the Framingham score.
Predicting Adolescents' Disclosure of Personal Information in Exchange for Commercial Incentives: An Application of an Extended Theory of Planned Behavior

This study adopts a global theoretical framework to predict adolescents' disclosure of personal information in exchange for incentives offered by commercial Websites. The study postulates and tests the validity of a model based on the theory of planned behavior (TPB), including antecedent factors of attitude and perceived behavioral control (PBC). A survey was conducted among 1,042 respondents. Results from SEM analyses show that the hypothesized model fits the empirical data well. The model accounts for 61.9 percent of the variance in adolescents' intention to disclose and 43.7 percent of the variance in self-reported disclosure. Perceived social pressure exerted by significant others (subjective norm) is the most important TPB factor in predicting intention to disclose personal information in exchange for incentives. This finding suggests that in discussions of adolescents' information privacy, the importance of social factors outweighs the individually oriented TPB factors of attitude and PBC. Moreover, privacy concern and trust propensity are significant predictors of respondents' attitudes toward online disclosure in exchange for commercial incentives, whereas the frequency of Internet use significantly affects their level of PBC.
A fully-instrumented variable-frequency solid-state microwave generator for laboratory applications

Precise knowledge of the output power and frequency delivered by a microwave generator as well as the power reflected off connected loads are pre-requisites for studying microwave processes effectively. A fully-instrumented, variable power and variable-frequency microwave generator is designed and constructed using off-the-shelf components. The design is based on a solid-state 100 W GaN power amplifier and incorporates frequency control (0.7-2.7 GHz) and microwave power level control (0-100 W) as well as forward and reflected power monitoring. The whole system is designed to be compact and low cost. At 2.45 GHz, the generator displays a spectral purity of 4 MHz and low harmonic content.
Beyond simulations: serious games for training interpersonal skills in law enforcement

Serious games can be used to improve people’s social awareness by letting them experience difficult social situations and learn from these experiences. However, we assert that, when moving beyond the strict realism that social simulations offer, techniques from role play may be used that offer more possibilities for feedback and reflection. We discuss the design of two such serious games for interpersonal skills training in the domain of law enforcement. These games feature intelligent virtual agents with which trainees have to interact across different scenarios to improve their social awareness. By interacting with the virtual agents, trainees experience how their behaviour influences the course of the intervention and its outcomes. We discuss how we intend to improve the learning experience in these serious games by including meta-techniques from role play. We close by describing the current and future implementations of our serious games.
Epstein–Barr virus lymphoproliferative disease after hematopoietic stem cell transplant

Purpose of reviewEpstein–Barr virus (EBV) reactivation can cause significant morbidity and mortality after allogeneic hematopoietic stem cell transplant. Delays in reconstitution of EBV-specific T lymphocyte activity can lead to life-threatening EBV lymphoproliferative disease (EBV-PTLD). This review highlights recent advances in the understanding of pathophysiology, risk factors, diagnosis, and management of EBV viremia and PTLD. Recent findingsDuring the past decade, early detection strategies, such as serial measurement of EBV-DNA load, have helped identify high-risk patients and diagnose early lymphoproliferation. The most significant advances have come in the form of innovative treatment options, including manipulation of the balance between outgrowing EBV-infected B cells and the EBV cytotoxic T lymphocyte response, and targeting infected B cells with monoclonal antibodies, chemotherapy, unmanipulated donor lymphocytes, and donor or more recently third-party EBV cytotoxic T lymphocytes. Defining criteria for preemptive therapy remains a challenge. SummaryEBV reactivation is a significant complication after stem cell transplant. Continued improvements in risk stratification and treatment options are required to improve the morbidity and mortality caused by EBV-associated diseases. Current approaches use rituximab to deplete B cells or adoptive transfer of EBV cytotoxic T lymphocyte to reconstitute immunity. The availability of rapid EBV-specific T cell products offers the possibility of improved outcomes.
Formal Software Development : From Foundations to Tools

This exposé gives an overview of the author’s contributions to the area of formal software development. These range from foundational issues dealing with abstract models of computation to practical engineering issues concerned with tool integration and user interface design. We can distinguish three lines of work: Firstly, there is foundational work, centred around categorical models of rewriting. A new semantics for rewriting is developed, which abstracts over the concrete term structure while still being able to express key concepts such as variable, layer and substitution. It is based on the concept of a monad, which is well-known in category theory to model algebraic theories. We generalise this treatment to term rewriting systems, infinitary terms, term graphs, and other forms of rewriting. The semantics finds applications in functional programming, where monads are used to model computational features such as state, exceptions and I/O, and modularity proofs, where the layer structure becomes central. Secondly, we are concerned with formal proof and development, where we understand ‘formal’ as in formal logic (i.e. modelled inside a theorem prover.) The main contribution here are techniques for systematic generalisation of developments and proofs, called abstraction for reuse. We develop abstraction procedures for any logical framework, and implement them in Isabelle, combining proof term transformation known from type theory with tactical theorem proving. We further show how to model transformational development in-the-small in the TAS system by modelling window inferencing in Isabelle, and model development in-the-large by theory morphisms implemented via proof term transformation. Thirdly, we turn to tool development. We discuss suitable system architectures to implement formal methods tools, or integrate existing tools into a common framework. We consider user interfaces, introducing the design of a graphical user interface for the transformational development system TAS based on principles of direct manipulation, and showing how to combine the graphical user interface with a textual one based on the popular Emacs editor.
CS 4 ( CyberSecurity 4 ) . Graph-Centric Metrics , Monitoring , and Composite Analysis of Adversarial Activities on Networks

Reliable and proper functioning of information systems and communication networks is crucial to national security and defense. The highly complex, interconnected systems are often undergoing malicious intrusions and adversary attacks on a scale and complexity that have never been seen before. Metrics and band-aid solutions are available to amend security problems in individual devices. Unfortunately, these approaches could easily miss the big picture of the attacks on the entire network, thus increasing the risk of systematic defense failure and leakage of sensitive information. Such situation could expose our vulnerability and eventually lead to security failure of the entire network. The lack of metrics and models to assess attacks and defenses in the network level impaired our ability to better characterize, quantify, and understand their behaviors.
Simple method to analyze SNP‐based association studies using DNA pools

Association studies using DNA pools are in principle powerful and efficient to detect association between a marker allele and disease status, e.g., in a case‐control design. A common observation with the use of DNA pools is that the two alleles at a polymorphic SNP locus are not amplified in equal amounts in heterozygous individuals. In addition, there are pool‐specific experimental errors so that there is variation in the estimates of allele frequencies from different pools that are from the same individuals. As a result of these additional sources of variation, the outcome of an experiment is an estimated count of alleles rather than the usual outcome in terms of observed counts. In this study, we show analytically and by computer simulation that unequal amplification should be taken into account when testing for differences in allele frequencies between pools, and suggest a simple modification of the standard χ2 test to control the type I error rate in the presence of experimental error variation. The impact of experimental errors on the power of association studies is shown. Genet Epidemiol 24:291–296, 2003. © 2003 Wiley‐Liss, Inc.
Sex Differences in Consequences of Musculoskeletal Pain

Study Design. Cross-sectional population-based study. Objective. To study sex differences in consequences of musculoskeletal pain (MP): limited functioning, work leave or disability, and healthcare use. Summary of Background Data. MP is a major public health problem in developed countries due to high prevalence rates and considerable consequences. There are indications that consequences of MP differ for men and women. Methods. Data of a Dutch population-based study were used, limited to persons 25 to 64 years of age (n = 2517). Data were collected by a postal questionnaire. Results. Women with any MP report more healthcare use for MP, i.e., contact with a medical caregiver and use of medicines than men, while men report more work disability (ever in life) due to low back pain only, irrespective of work status. None of the sex differences can be explained by age, household composition, educational level, smoking status, overweight, physical activity, and pain catastrophizing. Older age was related to more limited functioning due to MP (women), work disability due to MP (men), and healthcare use due to MP (men and women). A one-person household was associated with work disability (women) and use of medicines (men). Low educational level was associated with limited functioning (men), work leave (men), contact with a medical caregiver (men), and work disability (men and women). Smoking was associated with limited functioning (men), work leave (women), and healthcare use (women). Physical inactivity was associated with limited functioning due to MP in women. Pain catastrophizing was associated with limited functioning, work leave, and healthcare use (men and women) and work disability (men). Conclusions. Consequences of MP show a slightly different pattern for men and women. Women with any MPreport more healthcare use for MP, while men report more work disability due to low back pain only. These sex differences can not be explained by general risk factors, but associations between these factors and consequences of MP show some sex differences.
Comparing continuous milking with sixty-day dry periods in successive lactations.

Abstract Five pairs of identical-twin dairy cows were used in a continuous comparison of dry period effects through four lactations. Prior to the second and third parturition one of each pair was milked continuously but the mates were given 60-day dry periods. All twins were given dry periods of 60 days or more before the fourth lactation. Average milk yield of the continuously milked cows in the first lactation was 2.6% above the controls, because they lactated an average of 21 days longer. In the second and third lactation the continuously milked twins produced only 75 and 62% respectively, as much as the controls; and in the fourth lactation they yielded slightly more than the controls. Twins of each pair were fed alike, except that extra grain was fed prepartum only to those milked continuously. This feeding difference resulted in heavier body weights of the continuously milked cows during the second and third lactations, so nutrient reserve difference should have favored the cows milked continuously. The inhibiting effect of continuous milking on the next lactation is more likely due to effects on the mammary gland and its regulating factors than to nutritional factors.
Using machine learning for content-based image retrieving

While there are simple and fast techniques for querying conventional databases and collections of texts, content-based retrieval of images still remains a problem to be solved. To eliminate the need for a trained user and refining queries, needed by some recent systems, we propose the use of machine learning to induct decision trees as a substitute for conventional queries.
Room reconstruction from a single spherical image by higher-order energy minimization

We propose a method for understanding a room from a single spherical image, i.e., reconstructing and identifying structural planes forming the ceiling, the floor, and the walls in a room. A spherical image records the light that falls onto a single viewpoint from all directions and does not require correlating geometrical information from multiple images, which facilitates robust and precise reconstruction of the room structure. In our method, we detect line segments from a given image, and classify them into two groups: segments that form the boundaries of the structural planes and those that do not. We formulate this problem as a higher-order energy minimization problem that combines the various measures of likelihood that one, two, or three line segments are part of the boundary. We minimize the energy with graph cuts to identify segments forming boundaries, from which we estimate structural the planes in 3D. Experimental results on synthetic and real images confirm the effectiveness of the proposed method.