Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine Mapping of a GWAS-Derived Obesity Candidate Region on Chromosome 16p11.2

Introduction Large-scale genome-wide association studies (GWASs) have identified 97 chromosomal loci associated with increased body mass index in population-based studies on adults. One of these SNPs, rs7359397, tags a large region (approx. 1MB) with high linkage disequilibrium (r²>0.7), which comprises five genes (SH2B1, APOBR, sulfotransferases: SULT1A1 and SULT1A2, TUFM). We had previously described a rare mutation in SH2B1 solely identified in extremely obese individuals but not in lean controls. Methods The coding regions of the genes APOBR, SULT1A1, SULT1A2, and TUFM were screened for mutations (dHPLC, SSCP, Sanger re-sequencing) in 95 extremely obese children and adolescents. Detected non-synonymous variants were genotyped (TaqMan SNP Genotyping, MALDI TOF, PCR-RFLP) in independent large study groups (up to 3,210 extremely obese/overweight cases, 485 lean controls and 615 obesity trios). In silico tools were used for the prediction of potential functional effects of detected variants. Results Except for TUFM we detected non-synonymous variants in all screened genes. Two polymorphisms rs180743 (APOBR p.Pro428Ala) and rs3833080 (APOBR p.Gly369_Asp370del9) showed nominal association to (extreme) obesity (uncorrected p = 0.003 and p = 0.002, respectively). In silico analyses predicted a functional implication for rs180743 (APOBR p.Pro428Ala). Both APOBR variants are located in the repetitive region with unknown function. Conclusion Variants in APOBR contributed as strongly as variants in SH2B1 to the association with extreme obesity in the chromosomal region chr16p11.2. In silico analyses implied no functional effect of several of the detected variants. Further in vitro or in vivo analyses on the functional implications of the obesity associated variants are warranted.
Effects of Food Deprivation and Olfactory and Visual Cues on Movement Patterns of Two Eleodes Species (Coleoptera: Tenebrionidae) in a Wind Tunnel

Terrestrial arthropods are challenged with locating food in a heterogeneous environment, and this activity may be mediated by the hunger level the animal is experiencing. We performed wind tunnel experiments to determine whether food deprivation in the terrestrial darkling beetles Eleodes extricata Say and Eleodes hispilabris Say affects their movement patterns and whether they orient to food by means of vision, olfaction, or both. Hunger affected foraging behavior with respect to whether beetles actually contacted food. However, the velocity and number of turns of both food-deprived and fed individuals did not significantly differ, indicating that food deprivation affects the ethological consequences but not the velocity and turning mechanics of foraging in these species. Both olfaction and vision were used to find food over short distances (<80 cm). Olfaction elicited a stronger navigational response than did vision, particularly within 25 cm of food.
Enabling SMEs to Use Cloud Computing Services – An Exploratory Study on Enterprises Strategy Alterations

Modern commercial enterprises, irrespective of their relative size and the scale of operations, have been enormously benefited from the ever increasing services related with the Information and Communication Technologies (ICT). While the theories and models associated with developments and expansions of modern enterprises and their activities are in multi-disciplinary nature, the technology facilitations for such activities are converging into the domain of ICT infrastructure. In effect, virtual enterprises, operating globally without a physical presence, often supersede most of the hurdles that govern traditional businesses, while challenging our present understanding of business strategies. The recent development towards the provision of scalable utility computing services, known as cloud computing, has introduced a further paradigm to the norms of virtual enterprise operations by successfully eliminating the computing infrastructure barriers that many business enterprises have been experiencing to date. In this work, we have investigated the benefits of cloud computing to business enterprises, with a particular interest on small and medium scale enterprises (SMEs). While presenting the specific benefits and challenges for SMEs from cloud computing, this exploratory study proposes a new paradigm to fit cloud technology into the present enterprise practices at the strategic level. The findings from a recently published global survey on cloud computing usage in enterprises by Computer Science Corporation (CSC) support our arguments with empirical evidence and rationalise our approach of value chain modification to overcome this challenge.
Widespread Pyrethroid and DDT Resistance in the Major Malaria Vector Anopheles funestus in East Africa Is Driven by Metabolic Resistance Mechanisms

Background Establishing the extent, geographical distribution and mechanisms of insecticide resistance in malaria vectors is a prerequisite for resistance management. Here, we report a widespread distribution of insecticide resistance in the major malaria vector An. funestus across Uganda and western Kenya under the control of metabolic resistance mechanisms. Methodology/Principal Findings Female An. funestus collected throughout Uganda and western Kenya exhibited a Plasmodium infection rate between 4.2 to 10.4%. Widespread resistance against both type I (permethrin) and II (deltamethrin) pyrethroids and DDT was observed across Uganda and western Kenya. All populations remain highly susceptible to carbamate, organophosphate and dieldrin insecticides. Knockdown resistance plays no role in the pyrethroid and DDT resistance as no kdr mutation associated with resistance was detected despite the presence of a F1021C replacement. Additionally, no signature of selection was observed on the sodium channel gene. Synergist assays and qRT-PCR indicated that metabolic resistance plays a major role notably through elevated expression of cytochrome P450s. DDT resistance mechanisms differ from West Africa as the L119F-GSTe2 mutation only explains a small proportion of the genetic variance to DDT resistance. Conclusion The extensive distribution of pyrethroid and DDT resistance in East African An. funestus populations represents a challenge to the control of this vector. However, the observed carbamate and organophosphate susceptibility offers alternative solutions for resistance management.
MIRACLE at ImageCLEFannot 2008: Classification of Image Features for Medical Image Annotation

This paper describes the participation of MIRACLE research consortium at the ImageCLEF Medical Image Annotation task of ImageCLEF 2008. A lot of effort was invested this year to develop our own image analysis system, based on MATLAB, to be used in our experiments. This system extracts a variety of global and local featu res including histogram, image statistics, Gabor features, fractal dimension, DCT and DWT coefficients, Tamura features and coocurrency matrix statistics. Then a k-Nearest Neighbour algorithm an alyzes the extracted image feature vectors to determine the IRMA code associated to a given image. The focus of our experiments is mainly to test and evaluate this system in-depth and to make a comparison among diverse configuration parameters such as number of images for the relevan ce feedback to use in the classification module.
Exploiting Graph Structure for Accelerating the Calculation of Shortest Paths in Wordnets

This paper presents an approach for substantially reducing the time needed to calculate the shortest paths between all concepts in a wordnet. The algorithm exploits the unique "star-like" topology of wordnets to cut down on time-expensive calculations performed by algorithms to solve the all-pairs shortest path problem in general graphs. The algorithm was applied to two wordnets of two different languages: Princeton WordNet (Fellbaum, 1998) for English, and GermaNet (Kunze and Lemnitzer, 2002), the German language wordnet. For both wordnets, the time needed for finding all shortest paths was brought down from several days to a matter of minutes.
Mathematisches Forschungsinstitut Oberwolfach Report No . 50 / 2007 Reassessing the Paradigms of Statistical Model-Building Organised

Statistical model-building is the science of constructing models from data and from information about the data-generation process, with the aim of analysing those data and drawing inference from that analysis. Many statistical tasks are undertaken during this analysis; they include classification , forecasting, prediction and testing. Model-building has assumed substantial importance, as new technologies enable data on highly complex phenomena to be gathered in very large quantities. This creates a demand for more complex models, and requires the model-building process itself to be adaptive. The word " paradigm " refers to philosophies, frameworks and methodolo-gies for developing and interpreting statistical models, in the context of data, and applying them for inference. In order to solve contemporary statistical problems it is often necessary to combine techniques from previously separate paradigms. The workshop addressed model-building paradigms that are at the frontiers of modern statistical research. It tried to create synergies, by delineating the connections and collisions among different paradigms. It also endeavoured to shape the future evolution of paradigms.
Evaluating the number of active flows in a scheduler realizing fair statistical bandwidth sharing

Despite its well-known advantages, per-flow fair queueing has not been deployed in the Internet mainly because of the common belief that such scheduling is not scalable. The objective of the present paper is to demonstrate using trace simulations and analytical evaluations that this belief is misguided. We show that although the number of flows in progress increases with link speed, the number that needs scheduling at any moment is largely independent of this rate. The number of such active flows is a random process typically measured in hundreds even though there may be tens of thousands of flows in progress. The simulations are performed using traces from commercial and research networks with quite different traffic characteristics. Analysis is based on models for balanced fair statistical bandwidth sharing and applies properties of queue busy periods to explain the observed behaviour.
MIMO-OFDM Crystallized Rate Regions

In this paper, we introduce the generalization of the concept of crystallized rate regions for MIMO-OFDM transmission. The extension from the OFDM and MIMO case to MIMO-OFDM scenario of the time-sharing convex hull of achievable rates is discussed and a new definition of the cost function for the rate region game is derived. Based on the new game definition, the simulation results for the MIMO-OFDM case are presented.
3D landmark model discovery from a registered set of organic shapes

We present a machine learning framework that automatically generates a model set of landmarks for some class of registered 3D objects: here we use human faces. The aim is to replace heuristically-designed landmark models by something that is learned from training data. The value of this automatically generated model is an expected improvement in robustness and precision of learning-based 3D landmarking systems. Simultaneously, our framework outputs optimal detectors, derived from a prescribed pool of surface descriptors, for each landmark in the model. The model and detectors can then be used as key components of a landmark-localization system for the set of meshes belonging to that object class. Automatic models have some intrinsic advantages; for example, the fact that repetitive shapes are automatically detected and that local surface shapes are ordered by their degree of saliency in a quantitative way. We compare our automatically generated face landmark model with a manually designed model, employed in existing literature.
Discovery of a variable lead-rich hot subdwarf: UVO 0825+15

UVO0825+15 is a hot bright helium-rich subdwarf which lies in {\it K2} Field 5 and in a sample of intermediate helium-rich subdwarfs observed with {\it Subaru/HDS}. The {\it K2} light curve shows low-amplitude variations, whilst the {\it Subaru} spectrum shows Pb{\sc iv} absorption lines, indicative of a very high lead overabundance. UVO0825+15 also has a high proper motion with kinematics typical for a thick disk star. Analyses of ultraviolet and intermediate dispersion optical spectra rule out a short-period binary companion, and provide fundamental atmospheric parameters of $T_{\rm off}=38\,900\pm270$\,K, $\log g/{\rm cm\,s^{-2}}=5.97\pm0.11$, $\log n_{\rm He}/n_{\rm H}=-0.57\pm0.01$, $E_{B-V}\approx0.03$, and angular radius $\theta = 1.062\pm0.006\times10^{-11}$ radians (formal errors). The high-resolution spectrum shows that carbon is $>2$ dex subsolar, iron is approximately solar and all other elements heavier than argon are at least 2 -- 4 dex overabundant, including germanium, yttrium and lead. Approximately 150 lines in the blue-optical spectrum remain unidentified. The chemical structure of the photosphere is presumed to be determined by radiatively-dominated diffusion. The {\it K2} light curve shows a dominant period around 10.8\,h, with a variable amplitude, its first harmonic, and another period at 13.3\,h. The preferred explanation is multi-periodic non-radial oscillation due to g-modes with very high radial order, although this presents difficulties for pulsation theory. Alternative explanations fail for lack of radial-velocity evidence. UVO0825+15 represents the fourth member of a group of hot subdwarfs having helium-enriched photospheres and 3--4 dex overabundances of trans-iron elements, and is the first lead-rich subdwarf to show evidence of pulsations.
Augmentation of nonsense mediated decay by rapamycin

RNA surveillance by the Nonsense Mediated Decay (NMD) pathway eliminates potentially deleterious transcripts containing Premature Termination Codons (PTCs). The transition from a pioneering round of translation to steady state translation is hypothesized to be a major checkpoint in this process. One hallmark of mRNAs licensed for translation is the exchange of 7-methylguanosine cap binding proteins. However, mRNAs undergoing steady state translation are also NMD substrates, raising mechanistic questions about the NMD checkpoint. To test the role of cap binding proteins in NMD, we modulated the protein composition of cytoplasmic messenger ribonucleoprotein particles (mRNPs) with the naturally occurring macrolide rapamycin. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD. Rapamycin-treatment significantly reduces the levels of endogenous and exogenous PTC-containing mRNA isoforms in a dose- and UPF1- dependent manner. PTC-containing transcripts exhibit a shorter half-life upon rapamacyin-treatment as compared to non-PTC isoforms. Rapamycin also causes depletion of PTC-containing mRNA isoforms from polyribosomes, suggesting that actively translating ribosomes can transition between low and high NMD states. Importantly, mRNPs show depletion of eIF4E and retention of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin potentiates pioneer-like mRNP context thereby decreasing NMD evasion.
Parallel sampling of GMRFs and geostatistical GMRF models

In this report the main focuses are geostatistical Gaussian Markov random field (GMRF) models and parallel exact sampling of GMRFs. There are also brief overviews of parallel computing and Markov chain Monte Carlo (MCMC) methods, and a literature review of parallel MCMC. The geostatistical GMRF models are constructed by discretising the domain region using a lattice. Instead of giving this lattice a Gaussian random field prior, that corresponds to a Gaussian process, a GMRF that is an approximation to the GRF is chosen. More computational benefits are achieved through the nice parallelisation possibilities of GMRF sampling end evaluation. The computationally expensive part of GMRF sampling is Choleskey decomposition of the precision matrix. Parallelisation is done with parallel algorithms from linear algebra for sparse symmetric positive definite matrices. The parallel GMRF sampler is tested for graphs and lattices, and gives both good speed-up and good scalability. A parallel one-block updating scheme Metropolis-Hastings sampler for latent GMRF models is constructed using a GMRF approximation to π(x|y, θ) as proposal for the latent field. It is used for a geostatistical GMRF model with binomial likelihood, and shows good mixing for both the latent field and the hyper-parameters, as well as good speed-up from the parallelisation.
Hand-guiding robots along predefined geometric paths under hard joint constraints

In this paper a method is presented that allows an operator to hand-guide a robot along a predefined geometric path. This is a common use case in robot assisted surgery, which often has high demands on precision. In order to ensure the path accuracy of the robot, joint velocity and joint acceleration constraints are enforced to prevent undesired saturation effects of the actuators. Furthermore, necessary optimization steps are calculated in an offline phase and utilized during runtime to ensure realtime capabilities. The functionality of the method is evaluated using simulated sensor readings, controlling a kinematic model of the robot. While the focus is on surgical applications, the method can be useful in other domains as well, e.g. rehabilitation robotics or industrial applications.
Regulation of DNA replication during the yeast cell cycle.

One central event that must occur exactly once per cell division cycle is the replication of the genomic DNA. One defining observation of the eukaryotic cell cycle is that the nuclear DNA replicates during a short period (the S phase) and that during that period each part of every chromosome is entirely replicated. Although there are many origins of DNA replication per chromosome, and it is known that not all of them are required to act in every cycle, nevertheless reinitiation in the same cycle at any one of them is never observed. For these reasons, it has long been assumed that the initiation of DNA replication is under very stringent control. When Hartwell et al. (1970) began systematic isolation of cell-division-cycle (cdc) mutants more than 20 years ago, it was expected that mutants specifically defective in DNA replication, especially those involved in initiation of DNA replication, would be prominent among the mutants that exhibit cdc phenotypes. Growing yeast cells show a morphology characteristic for the position they have reached in the cell cycle: The bud emerges just about the time that S phase begins and has reached its full size at the time that mitosis begins. Thus conditional-lethal mutants defective in DNA elongation were expected to arrest, under nonpermissive conditions, with a large bud. Indeed, temperature-sensitive mutations in genes specifying DNA polymerases (cdc2,
A power-aware wireless sensor network based bridge monitoring system

Recent proliferation of sensor networks in diverse applications has made the low-power wireless sensor network an important design issue. Structural health monitoring is one of the important applications of the wireless sensor network. A robust wireless structural monitoring strategy requires appropriate choice of the wireless network topology as well as some suitable protocols. This paper presents a power-aware sensor network, which can be used for the monitoring of bridges. Event-driven data communication protocols have been used to minimize energy drawn from the battery. All the sensor nodes remain in low-power sleep mode unless triggered either by a base station or by another sensor node in the neighborhood. Two ways of collecting data have been proposed and their performances in terms of the number of motes versus network lifetime have been compared.
Passive infrared localization with a Probability Hypothesis Density filter

In passive infrared localization (PIL) humans are located based on their thermal radiation. Thus, an active tag is not required and privacy is guaranteed due to non-identifying sensors. However, in case of multi-target tracking, the non-identifying sensors result in missing associations between targets and measurements. As additionally the number of humans in the surveillance region is unknown and varying, conventional localization approaches like the JPDA or MHT filter cannot be applied since they require a fixed number of targets or are not tractable.
Welfare reform and child well-being

In this paper we sort through conflicting theory and evidence regarding the impacts of welfare reform on children’s well-being and development. Our conclusions regarding likely child impacts depend crucially on the ages of the children studied. In the case of elementary-school children, the picture is fairly positive. We find strong evidence that welfare reform can be a potent force for enhancing achievement and positive behavior. When welfare reform packages do not appear to help younger children, there is little evidence of harm, even in the one experiment with time limits. If anything, the beneficial impacts are strongest for children in families with longer histories of welfare receipt. On the other hand, in the case of adolescents, more limited evidence suggests that welfare reforms may cause detrimental increases in school problems and risky behavior. The jury is still out on impacts on infants and toddlers. Our list of policy recommendations includes ways of better supporting work, providing after-school and community programs for older children, addressing safety-net issues for families with barriers to stable, full-time employment, and encouraging fathers to become more involved with their children. More generally, we hope that the debate over the future of welfare reform will pay more attention to children’s well-being, to the diverse situations in which children in low-income families find themselves, and to the very different developmental needs of children of different ages.
On improving the approximation ratio of the r-shortest common superstring problem

The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,. ,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently been published, the general objective is now to break the conceptual lower bound barrier of 2. This paper is a step ahead in this direction. Here we focus on a particular instance of the SCS problem, meaning the r-SCS problem, which requires all input strings to be of the same length, r. Golonev et al. proved an approximation ratio which is better than the general one for r<= 6. Here we extend their approach and improve their approximation ratio, which is now better than the general one for r<= 7, and less than or equal to 2 up to r = 6.
Software Development Effort Estimation Using Fuzzy Logic : A Review

Accurate effort prediction is an ongoing challenge to software engineers. It is an important task in the management of software projects. Effort estimation is the challenging and is an important area in the software project management research field. The development of software has always been characterized by the parameters that contain certain level of fuzziness. This requires some degree of uncertainty be introduced in the models, to make the model reliable. Fuzzy Logic techniques are used to tackle the uncertainty issues. Fuzzy Logics could produce better estimates provided that various parameters and factors pertaining to fuzzy logic are carefully set. The primary purpose of this paper is to estimate the software development effort using Fuzzy Logic Techniques in order to improve accuracies.