Miracle-dz/UniFAR-FTUs huggingface dataset:
A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

Background DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. Methodology/Principal Findings We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. Conclusions/Significance: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.
Simvastatin with or without ezetimibe in familial hypercholesterolemia.

BACKGROUND Ezetimibe, a cholesterol-absorption inhibitor, reduces levels of low-density lipoprotein (LDL) cholesterol when added to statin treatment. However, the effect of ezetimibe on the progression of atherosclerosis remains unknown. METHODS We conducted a double-blind, randomized, 24-month trial comparing the effects of daily therapy with 80 mg of simvastatin either with placebo or with 10 mg of ezetimibe in 720 patients with familial hypercholesterolemia. Patients underwent B-mode ultrasonography to assess the intima-media thickness of the walls of the carotid and femoral arteries. The primary outcome measure was the change in the mean carotid-artery intima-media thickness, which was defined as the average of the means of the far-wall intima-media thickness of the right and left common carotid arteries, carotid bulbs, and internal carotid arteries. RESULTS The primary outcome, the mean (+/-SE) change in the carotid-artery intima-media thickness, was 0.0058+/-0.0037 mm in the simvastatin-only group and 0.0111+/-0.0038 mm in the simvastatin-plus-ezetimibe (combined-therapy) group (P=0.29). Secondary outcomes (consisting of other variables regarding the intima-media thickness of the carotid and femoral arteries) did not differ significantly between the two groups. At the end of the study, the mean (+/-SD) LDL cholesterol level was 192.7+/-60.3 mg per deciliter (4.98+/-1.56 mmol per liter) in the simvastatin group and 141.3+/-52.6 mg per deciliter (3.65+/-1.36 mmol per liter) in the combined-therapy group (a between-group difference of 16.5%, P<0.01). The differences between the two groups in reductions in levels of triglycerides and C-reactive protein were 6.6% and 25.7%, respectively, with greater reductions in the combined-therapy group (P<0.01 for both comparisons). Side-effect and safety profiles were similar in the two groups. CONCLUSIONS In patients with familial hypercholesterolemia, combined therapy with ezetimibe and simvastatin did not result in a significant difference in changes in intima-media thickness, as compared with simvastatin alone, despite decreases in levels of LDL cholesterol and C-reactive protein. (ClinicalTrials.gov number, NCT00552097 [ClinicalTrials.gov].).
Network aware resource allocation in distributed clouds

We consider resource allocation algorithms for distributed cloud systems, which deploy cloud-computing resources that are geographically distributed over a large number of locations in a wide-area network. This distribution of cloud-computing resources over many locations in the network may be done for several reasons, such as to locate resources closer to users, to reduce bandwidth costs, to increase availability, etc. To get the maximum benefit from a distributed cloud system, we need efficient algorithms for resource allocation which minimize communication costs and latency. In this paper, we develop efficient resource allocation algorithms for use in distributed clouds. Our contributions are as follows: Assuming that users specify their resource needs, such as the number of virtual machines needed for a large computational task, we develop an efficient 2-approximation algorithm for the optimal selection of data centers in the distributed cloud. Our objective is to minimize the maximum distance, or latency, between the selected data centers. Next, we consider use of a similar algorithm to select, within each data center, the racks and servers where the requested virtual machines for the task will be located. Since the network inside a data center is structured and typically a tree, we make use of this structure to develop an optimal algorithm for rack and server selection. Finally, we develop a heuristic for partitioning the requested resources for the task amongst the chosen data centers and racks. We use simulations to evaluate the performance of our algorithms over example distributed cloud systems and find that our algorithms provide significant gains over other simpler allocation algorithms.
Technologies for value creation: an exploration of remote diagnostics systems in the manufacturing industry

Abstract. With firms increasingly relying on ubiquitous computing to implement major business initiatives, it is becoming ever more necessary to understand the technological aspects of business developments. This paper analyzes the use of remote diagnostics systems in the manufacturing industry and discusses the opportunities and challenges for the early adopters. It pays specific attention to the impact on business aspects such as the value creation process consisting of relationships, roles, and architecture and the value proposal consisting of a business offer and customer value. The study shows how ubiquitous computing allows manufacturers to become remote service providers while customers can either become co‐creators of value or passive receivers of created value. Ubiquitous computing also creates possibilities for the manufacturing industry to design new kinds of business offers based on remote presence. Studying remote diagnostics systems shows that ubiquitous computing creates value when deployed in products, and not just in relation to individuals. Moreover, the design of the value‐creation process should not be limited to the single supplier or customer organization, as ubiquitous computing applications take no notice of organizational boundaries.
Nominal-Yield-Area Tradeoff in Automatic Synthesis of Analog Circuits: A Genetic Programming Approach Using Immune-Inspired Operators

The synthesis of analog circuits is a complex and expensive task; whilst there are various approaches for the synthesis of digital circuits, analog design is intrinsically more difficult since analog circuits process voltages in a continuous range. In the field of analog circuit design, the genetic programming approach has received great attention, affording the possibility to design and optimize a circuit at the same time. However, these algorithms have limited industrial relevance, since they work with ideal components. Starting from the well known results of Koza and co-authors, we introduce a new evolutionary algorithm, called elitist Immune Programming (EIP), that is able to synthesize an analog circuit using industrial components series in order to produce reliable and low cost circuits. The algorithm has been used for the synthesis of low-pass filters; the results were compared with the genetic programming, and the analysis shows that EIP is able to design better circuits in terms of frequency response and number of components. In addition we conduct a complete yield analysis of the discovered circuits, and discover that EIP circuits attain a higher yield than the circuits generated via a genetic programming approach, and, in particular, the algorithm discovers a Pareto Front which respects nominal performance (sizing), number of components (area) and yield (robustness).
Mating system variation and assortative mating of sympatric bromeliads (Pitcairnia spp.) endemic to neotropical inselbergs.

PREMISE OF THE STUDY The mating system is an important component of the complex set of reproductive isolation barriers causing plant speciation. However, empirical evidence showing that the mating system may promote reproductive isolation in co-occurring species is limited. The mechanisms by which the mating system can act as a reproductive isolation barrier are also largely unknown. METHODS Here we studied progeny arrays genotyped with microsatellites and patterns of stigma-anther separation (herkogamy) to understand the role of mating system shifts in promoting reproductive isolation between two hybridizing taxa with porous genomes, Pitcairnia albiflos and P. staminea (Bromeliaceae). KEY RESULTS In P. staminea, we detected increased selfing and reduced herkogamy in one sympatric relative to two allopatric populations, consistent with mating system shifts in sympatry acting to maintain the species integrity of P. staminea when in contact with P. albiflos. CONCLUSIONS Mating system variation is a result of several factors acting simultaneously in these populations. We report mating system shifts as one possible reproductive barrier between these species, acting in addition to numerous other prezygotic (i.e., flower phenology and pollination syndromes) and postzygotic barriers (Bateson-Dobzhansky-Muller genetic incompatibilities).
Service provisioning in virtualization-based Cloud computing: Modeling and optimization

Cloud computing is an emerging computing paradigm that may change the way how information services are provisioned. Network virtualization plays a crucial role in a Cloud environment for abstracting and virtualizing various network infrastructures as services. Therefore virtual network services should be integrated with Cloud service to form the composite Cloud service. However, little research has focused on modeling and optimization of network virtualization in Cloud service provisioning to end users. In this paper, we model the Cloud service provisioning feature in virtualization-based Cloud computing, and propose an exact algorithm for QoS-aware service composition to optimize user's experiences for Cloud service access. Our theoretical analysis indicates that the proposed algorithm is light-weighted and cost-effective. We also compare the proposed algorithm against a variant of the best-known QoS routing algorithm experimentally. The results show that the proposed algorithm has better performance both in execution time and finding solution. We believe that the modeling technique and the algorithm presented in this paper are general and effective, thus are applicable to practical Cloud computing systems.
Fuzzy Adaptive Fault-Tolerant Output Feedback Attitude-Tracking Control of Rigid Spacecraft

This paper proposes a stable adaptive fuzzy fault-tolerant attitude-tracking controller for a rigid spacecraft in the presence of unavailable velocities, external disturbance, actuator faults, and actuator saturation. Fuzzy logic systems are applied to approximate the unknown nonlinear function vector, and a fuzzy adaptive observer is designed to estimate the unmeasured velocity of the rigid body. By using the backstepping technique, a novel adaptive fuzzy attitude-tracking fault-tolerant control scheme is developed. It has been testified that this control approach guarantees that all signals of the rigid spacecraft are bounded and the tracking error between the system output and the reference signal converges to a small neighborhood of zero. Simulation examples with constant faults and time-variant faults are provided to show the fault-tolerant effectiveness of the control method.
Prevención de los comportamientos sexuales de riesgo en los adolescentes: SIDA, otras enfermedades de transmisión sexual y embarazos no deseados Preventing sexual risk behaviours in adolescents: AIDS, other sexually transmitted disease, and unwanted pregnancies

At present, adolescents are a group which due to their behavioural, cognitive, and social characteristics, run the greatest risk of possible contagion. This threat to the health and well-being of adolescents is added to other problems already facing them, such as unwanted pregnacies and sexually transmitted diseases (STD), which are due to the non-use of preventive methods in sexual relations. The paper deals with biological, psychological (behavioural and cognitive), and social factors that may facilitate, interfere with or impede preventive sexual behaviours in adolescents. Some preventive intervention programmes are also reviewed and assessed. The discussion supports the advisability of unifying programmes aimed at the simultaneous prevention of all three risk areas to optimize available resources.
A DUAL-PROCESSING APPROACH TO ASSESSING AND CHANGING SMOKING ATTITUDES

Author(s): EMORY, JASON | Advisor(s): Song, Anna V | Abstract: Despite widespread knowledge as to the dangers associated with smoking behavior, 20% of the United States population continues to smoke (Center for disease control, 2011). Novel intervention techniques need to be developed for those who continue to smoke despite awareness of the associated health risks. This dissertation explores the possibility that implicit cognitions that occur automatically and outside of conscious awareness might be specifically targeted for the purpose of behavior change. Two research questions (RQ) have guided the theory and methodology used in these two studies: RQ 1) can smoking related implicit attitudes be delineated into subdomains that mirror domains of explicit smoking attitudes? , a RQ 2) can interventions that tap into smoking related implicit associations produce changes in implicit and explicit attitudes? Study 1 assessed multiple implicit measures of cognition, each designed to tap into a unique domain of implicit smoking attitudes. The results of a factor analysis conducted on the Implicit Association Test (IAT; Greenwald a Banaji, 1995) in study 1 suggest that all four IATs tap into the same basic construct. Thus the answer to RQ 1 appears to be negative: smoking related implicit attitudes cannot be delineated into distinct domains. Study 2 assesses a novel interactive intervention that utilizes implicit methods of message delivery in hopes of impacting implicit and explicit smoking attitudes. The results of this study suggest that explicit, but not implicit, attitude change occurred, providing partial support for RQ 2. Additional research in the area of implicit cognition of smoking behavior is necessary to build upon these findings and explore the plausibility of an implicit intervention as a means to help reduce smoking behavior. Future directions and implications for policy are discussed.
Canadian Study of Determinants of Endometabolic Health in ChIlDrEn (CanDECIDE study): a cohort study protocol examining the mechanisms of obesity in survivors of childhood brain tumours

Background Childhood obesity has reached epidemic proportions and is impacting children's health globally. In adults, obesity is associated with chronic low-grade inflammation that leads to insulin resistance, which is one of the important mechanisms through which dysregulation of metabolism occurs. There is limited information available about the contribution of inflammation to metabolic health in obese children, and how individual and lifestyle factors impact this risk. One of the paediatric groups at risk of higher rates of obesity includes the survivors of childhood brain tumours. The aim of this study was to evaluate the mechanisms that contribute to inflammation in obese survivors of childhood brain tumours. Methods and analysis This is a prospective cohort study. We will recruit lean and obese survivors of childhood brain tumours, and a control group composed of lean and obese children with no history of tumours. We will measure circulating and urinary cytokine levels and cytokine gene expression in monocytes. In addition, the methylation patterns of cytokine genes and that of toll-like receptor genes will be evaluated. These will be correlated with individual and lifestyle factors including age, sex, ethnicity, puberty, body mass index, fasting lipid levels, insulin sensitivity, diet, exercise, sleep, stress and built environment. The sample size calculation showed that we need 25 participants per arm Ethics and dissemination This study has received ethics approval from the institutional review board. Once completed, we will publish this work in peer-reviewed journals and share the findings in presentations and posters in meetings. Discussion This study will permit the interrogation of inflammation as a contributor to obesity and its complications in obese survivors of childhood brain tumours and compare them with lean survivors and lean and obese controls with no history of tumours, which may help identify therapeutic and preventative interventions to combat the rising tide of obesity.
Measurement of noise in the Monte Carlo point sampling method

This paper gives a concise overview of the techniques we have used to find out the degree of measuring the quality of rendered images and a level of noise in particular. First part of the paper presents designed and conducted psychophysical experiment involving human subjective judgment. Then, two of the existing numerical image comparison methods are considered in the context of assessing the level of noise produced by global illuminations algorithms. The results of the participants’ subjective responses are correlated with the data obtained from objective mathematical metrics. The main goal of research was to determine the objective and perceptual measure of quality for images with fixed sampling strategy. The results will help to establish the measures of identifying the human perception in the assessment of images generated with global illumination algorithms.
Post-ivermectin encephalopathy in Senegal: a case report

Ivermectin is an ant parasitic drug used for combating onchocerciasis and lymphatic filariasis. It works by inhibiting the function of neurons and muscles, thus causing paralysis of microfilariae. Side effects of this drug have been reported including post-ivermectin encephalopathy requiring emergency care in hospital. We report the case of a 35 years old patient living in rural areas of Senegal who presented two days after a mistake in administration of a second dose of ivermectin, headaches, altered consciousness and bilateral blindness. The workup revealed brain white matter lesions, abnormal liver function tests and biological inflammation without evidence of Loa loa microfilariae in blood and cerebrospinal fluid. Corticosteroid treatment was administered in emergency and patient recovered despite the persistence of bilateral blindness. Inflammatory process seems to have an important role in the pathophysiology of this encephalopathy. We should therefore carefully control the administration of this drugs.
Ensembles: understanding the instantiation of activities

Purpose – An ensemble is an intermediate unit of work between action and activity in the hierarchical framework proposed by classical activity theory. Ensembles are the mid‐level of activity, offering more flexibility than objects, but more purposeful structure than actions. The paper aims to introduce the notion of ensembles to understand the way object‐related activities are instantiated in practice.Design/methodology/approach – The paper presents an analysis of the practices of professional information workers in two different companies using direct and systematic observation of human behavior. It also provides an analysis and discussion of the activity theory literature and how it has been applied in areas such as human‐computer interaction and computer‐supported collaborative work.Findings – The authors illustrate the relevance of the notion of ensembles for activity theory and suggest some benefits of this conceptualization for analyzing human work in areas such as human‐computer interaction and com.
Spatial‐Temporal progress of peripheral nerve regeneration within a silicone chamber: Parameters for a bioassay

The spatial‐temporal progress of peripheral nerve regeneration across a 10‐mmgap within a silicone chamber was examined with the light and electron microscope at 2‐mm intervals. A coaxial, fibrin matrix was observed at 1 week with a proximal‐distal narrowing that extended beyond the midpoint of the chamber. At 2 weeks, Schwann cells, fibroblasts, and endothelial cells had migrated into the matrix from both nerve stumps. There was a delay of 7–14 days after nerve transection and chamber implantation before regenerating axons appeared in the chamber. At 2 weeks, nonmyelinated axons were seen only in the proximal 1–5 mm of the chamber in association with Schwann cells. Axons reached the distal stump by 3 weeks and a proximal‐distal gradient of myelination was observed. These observations define the parameters of a morphologic assay for regeneration in this chamber model which can be used to investigate cellular and molecular mechanisms underlying the success of peripheral nerve regeneration.
Stable Gene Regulatory Network Modeling From Steady-State Data †

Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites. In most applications, the regulatory network structure is unknown, and has to be reverse engineered from experimental data consisting of expression levels of the genes usually measured as messenger RNA concentrations in microarray experiments. Steady-state gene expression data are obtained from measurements of the variations in expression activity following the application of small perturbations to equilibrium states in genetic perturbation experiments. In this paper, the least absolute shrinkage and selection operator-vector autoregressive (LASSO-VAR) originally proposed for the analysis of economic time series data is adapted to include a stability constraint for the recovery of a sparse and stable regulatory network that describes data obtained from noisy perturbation experiments. The approach is applied to real experimental data obtained for the SOS pathway in Escherichia coli and the cell cycle pathway for yeast Saccharomyces cerevisiae. Significant features of this method are the ability to recover networks without inputting prior knowledge of the network topology, and the ability to be efficiently applied to large scale networks due to the convex nature of the method.
Minding the Gaps for Block Frank-Wolfe Optimization of Structured SVMs

In this paper, we propose several improvements on the block-coordinate Frank-Wolfe (BCFW) algorithm from Lacoste-Julien et al. (2013) recently used to optimize the structured support vector machine (SSVM) objective in the context of structured prediction, though it has wider applications. The key intuition behind our improvements is that the estimates of block gaps maintained by BCFW reveal the block suboptimality that can be used as an adaptive criterion. First, we sample objects at each iteration of BCFW in an adaptive non-uniform way via gapbased sampling. Second, we incorporate pairwise and away-step variants of Frank-Wolfe into the block-coordinate setting. Third, we cache oracle calls with a cache-hit criterion based on the block gaps. Fourth, we provide the first method to compute an approximate regularization path for SSVM. Finally, we provide an exhaustive empirical evaluation of all our methods on four structured prediction datasets.