Miracle-dz/UniFAR-FTUs huggingface dataset:
Food-frequency questionnaires: a review of their design, validation and utilisation

A review of the literature concerning the design, utilisation and validation of food-frequency questionnaires (FFQ) has been carried out using a semi-systematic approach to obtaining, reviewing and extracting data from articles. Databases were searched from 1980 to 1999. The present review identified 227 validation (from 1980 to September 1999) and 164 utilisation (for 1998 only) studies. A number of design issues have been evaluated through the present review. These include: the need to consider how portion sizes have been described, self-defined giving higher mean correlations; how an FFQ was administered, interviewer-administered giving higher mean correlations for some nutrients; how many items to include on an FFQ, those with the largest number of items having higher correlations. Validation techniques were described. Most validation studies involved comparing an FFQ against another dietary assessment method; only 19 % compared an FFQ to a biomarker. Measurement differences were most commonly assessed by correlation coefficients as opposed to other more appropriate methods. Mean correlation coefficients were highest for Ca and fat, and lowest for vitamin A and vegetables. The utilisation studies showed that FFQ were most commonly used in cross-sectional surveys, with ninety-three of the FFQ being designed to be disease-specific. The present review results were presented to a group of experts and a consensus arrived at concerning the development, validation and use of FFQ. Recommendations derived from the consensus arising from the literature review are presented as an appendix to the present paper.
Decadal Comparisons of Particulate Matter in Repeat Transects in the Atlantic, Pacific, and Indian Ocean Basins

Basin‐wide sections of beam cp (proxy for particle concentration) in ocean basins collected during numerous oceanographic programs over the last four decades record variable concentrations in euphotic surface waters, very low concentrations through most of the water column, and very low to very high concentrations near the seafloor. Sections resampled at decadal intervals show that intense benthic nepheloid layers (BNLs) recur in the same general locations in these repeat sections, most often where eddy kinetic energy (EKE: cm2 s−2) is high in overlying waters. Areas beneath regions of low surface EKE consistently have weak to no BNLs. The decadal persistence of the close connection between surface and benthic EKE and presence or absence of BNLs is clear. Understanding the location and causes of intense versus weak BNLs helps in assessing scavenging of adsorption‐prone elements in the deep sea and quantifying the impact of deep ocean sediment dynamics on sediment redistribution.
Goal-Oriented Knowledge Collection

Games with A Purpose (GWAP) has been demonstrated to be efficient in collecting large amount of knowledge from online users, e.g. Verbosity and Virtual Pet game. However, its effectiveness in knowledge base (KB) construction has not been explored in previous research. This paper examines the knowledge collected in the Virtual Pet game and presents an approach to collect more knowledge driven by the existing relations in KB. In this paper, goal-oriented knowledge collection successfully draws 10572 answers for the “food” domain. The answers are verified by online voting to show that 92.07% of them are good sentences and 95.89% of them are new sentences. This result is a significant improvement over the original Virtual Pet game, with 80.58% good sentences and 67.56% weekly new information.
Authorization of Animal Experiments Is Based on Confidence Rather than Evidence of Scientific Rigor

Accumulating evidence indicates high risk of bias in preclinical animal research, questioning the scientific validity and reproducibility of published research findings. Systematic reviews found low rates of reporting of measures against risks of bias in the published literature (e.g., randomization, blinding, sample size calculation) and a correlation between low reporting rates and inflated treatment effects. That most animal research undergoes peer review or ethical review would offer the possibility to detect risks of bias at an earlier stage, before the research has been conducted. For example, in Switzerland, animal experiments are licensed based on a detailed description of the study protocol and a harm–benefit analysis. We therefore screened applications for animal experiments submitted to Swiss authorities (n = 1,277) for the rates at which the use of seven basic measures against bias (allocation concealment, blinding, randomization, sample size calculation, inclusion/exclusion criteria, primary outcome variable, and statistical analysis plan) were described and compared them with the reporting rates of the same measures in a representative sub-sample of publications (n = 50) resulting from studies described in these applications. Measures against bias were described at very low rates, ranging on average from 2.4% for statistical analysis plan to 19% for primary outcome variable in applications for animal experiments, and from 0.0% for sample size calculation to 34% for statistical analysis plan in publications from these experiments. Calculating an internal validity score (IVS) based on the proportion of the seven measures against bias, we found a weak positive correlation between the IVS of applications and that of publications (Spearman’s rho = 0.34, p = 0.014), indicating that the rates of description of these measures in applications partly predict their rates of reporting in publications. These results indicate that the authorities licensing animal experiments are lacking important information about experimental conduct that determines the scientific validity of the findings, which may be critical for the weight attributed to the benefit of the research in the harm–benefit analysis. Similar to manuscripts getting accepted for publication despite poor reporting of measures against bias, applications for animal experiments may often be approved based on implicit confidence rather than explicit evidence of scientific rigor. Our findings shed serious doubt on the current authorization procedure for animal experiments, as well as the peer-review process for scientific publications, which in the long run may undermine the credibility of research. Developing existing authorization procedures that are already in place in many countries towards a preregistration system for animal research is one promising way to reform the system. This would not only benefit the scientific validity of findings from animal experiments but also help to avoid unnecessary harm to animals for inconclusive research.
Twinkle: A fast resource provisioning mechanism for internet services

A key benefit of Amazon EC2-style cloud computing service is the ability to instantiate a large number of virtual machines (VMs) on the fly during flash crowd events. Most existing research focuses on the policy decision such as when and where to start a VM for an application. In this paper, we study a different problem: how can the VMs and the applications inside be brought up as quickly as possible? This problem has not been solved satisfactorily in existing cloud services. We develop a fast start technique for cloud applications by restoring previously created VM snapshots of fully initialized application. We propose a set of optimizations, including working set estimation, demand prediction, and free page avoidance, that allow an application to start running with only partially loaded memory, yet without noticeable performance penalty during its subsequent execution. We implement our system, called Twinkle, in the Xen hypervisor and employ the two-dimensional page walks supported by the latest virtualization technology. We use the RUBiS and TPC-W benchmarks to evaluate its performance under flash crowd and failure over scenarios. The results indicate that Twinkle can provision VMs and restore the QoS significantly faster than the current approaches.
On the Chances of Completing the Game of "Perpetual Motion"

This brief paper describes the single-player card game called "Perpetual Motion" and reports on a computational analysis of the game's outcome. The analysis follows a Monte Carlo methodology based on a sample of 10,000 randomly generated games. The key result is that 54.55% +/- 0.89% of games can be completed (by a patient player! ) but that the remaining 45.45% result in non-terminating cycles. The lengths of these non-terminating cycles leave some outstanding questions.
Parameter Optimization in Waveform Relaxation for Fractional-Order $RC$ Circuits

The longitudinal waveform relaxation (WR) proposed by Gander and Ruehli converges faster than the classical WR method. For the former, a free parameter <inline-formula> <tex-math notation="LaTeX">$\alpha$ </tex-math></inline-formula> is contained, which has a significant effect on the convergence rate. The optimization of this parameter is thus an important issue in practice. Here, we apply this new WR method to the fractional-order <italic>RC</italic> circuits, and optimize such a parameter at the continuous and discrete levels (this gives two parameters <inline-formula> <tex-math notation="LaTeX">$\alpha ^{c}_{\mathrm{ opt}}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\alpha ^{d}_{\mathrm{ opt}}$ </tex-math></inline-formula>). We consider three simple but widely used convolution quadrature for discretization, based on the implicit-Euler method, the two-step backward difference formula, and the trapezoidal rule, and we derive the parameter <inline-formula> <tex-math notation="LaTeX">$\alpha ^{d}_{\mathrm{ opt}}$ </tex-math></inline-formula> for each quadrature. Interestingly, it is found that for the former two quadratures, the optimized parameter <inline-formula> <tex-math notation="LaTeX">$\alpha ^{d}_{\mathrm{ opt}}$ </tex-math></inline-formula> results in a much better convergence rate than <inline-formula> <tex-math notation="LaTeX">$\alpha ^{c}_{\mathrm{ opt}}$ </tex-math></inline-formula>, while for the quadrature based on the trapezoidal rule, <inline-formula> <tex-math notation="LaTeX">$\alpha ^{d}_{\mathrm{ opt}}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\alpha ^{c}_{\mathrm{ opt}}$ </tex-math></inline-formula> result in the same convergence rate.
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation

Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques have motivated the development of a large number of bioinformatics methods for the detection of regulatory motifs. The regulatory process is extremely complex and individual computational algorithms typically have very limited success in genome-scale studies. Here, we argue the importance of integrating multiple computational algorithms and present an infrastructure that integrates eight web services covering key areas of transcriptional regulation. We have adopted the client-side integration technology and built a consistent input and output environment with a versatile visualization tool named SeqVISTA. The infrastructure will allow for easy integration of gene regulation analysis software that is scattered over the Internet. It will also enable bench biologists to perform an arsenal of analysis using cutting-edge methods in a familiar environment and bioinformatics researchers to focus on developing new algorithms without the need to invest substantial effort on complex pre- or post-processors. SeqVISTA is freely available to academic users and can be launched online at http://zlab.bu. edu/SeqVISTA/web.jnlp, provided that Java Web Start has been installed. In addition, a stand-alone version of the program can be downloaded and run locally. It can be obtained at http://zlab.bu. edu/SeqVISTA.
A Sequential Approach to Sparse Component Analysis

A sequential approach to sparse component analysis (SeqTIF) is proposed in this paper. Although SeqTIF employs the estimation process of the simultaneous TIFROM algorithm, a source cancellation and deflation technique are also incorporated to sequentially estimate speech signals in the mixture. Results indicate that SeqTIF's separation performance shows a clear improvement upon the simultaneous TIFROM approach, due to the less restrictive assumptions it places upon the signals in the mixture. In particular, the analysis indicates SeqTIF's data efficiency is high, enabling the sequential approach to track a time-varying mixture with much greater accuracy than the simultaneous algorithm. Furthermore, SeqTIF is a more flexible approach, free from the constraints that a simultaneous approach places upon the mixing system
A Random-Surfer Web-Graph Model

In this paper we provide theoretical and experimental results on a random-surfer model for construction of a random graph. In this model, a new node connects to the existing graph by choosing a start node uniformly at random and then performing a short random walk. We show that in certain formulations, this results in the same distribution as the preferential-attachment random-graph model, and in others we give a direct analysis of power-law distribution of degrees or "virtual degrees" of the resulting graphs. We also present experimental results for a number of settings of parameters that we are not able to analyze mathematically.
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization

MOTIVATION Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization. RESULTS Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points. AVAILABILITY The method and the dataset are available at the Web page http://www.biocomp. unibo.it/savojard/Dislocate.html. GRHCRF code is available at http://www.biocomp. unibo.it/savojard/biocrf.html. CONTACT piero.fariselli@unibo.it.
A bi-objective location area planning for wireless phone network

In this paper, we propose an extension of the classical location area planning (LAP) problem in the wireless telephony system including additional objectives and constraints. The bi-objective location area planning (BOLAP) problem considers the minimisation of both distance costs between base transceiver stations and the base station controllers. A vector evaluated particle swarm optimisation (VEPSO) is then implemented to solve the bi-objective model. This heuristic operates in term of two swarms, each corresponding to one of the two objectives, and exchanging their best experience. A comparison of the proposed algorithm is performed with the statistical method being used by a major wireless telephone company. The empirical results show that the proposed approach dominates the operator’s method on one hand, and that the BOLAP is an effective generalisation of the classical LAP model on the other hand.
Sequestration and Inhibition of Daxx-Mediated Transcriptional Repression by PML

ABSTRACT PML fuses with retinoic acid receptor α (RARα) in the t(15;17) translocation that causes acute promyelocytic leukemia (APL). In addition to localizing diffusely throughout the nucleoplasm, PML mainly resides in discrete nuclear structures known as PML oncogenic domains (PODs), which are disrupted in APL and spinocellular ataxia cells. We isolated the Fas-binding protein Daxx as a PML-interacting protein in a yeast two-hybrid screen. Biochemical and immunofluorescence analyses reveal that Daxx is a nuclear protein that interacts and colocalizes with PML in the PODs. Reporter gene assay shows that Daxx drastically represses basal transcription, likely by recruiting histone deacetylases. PML, but not its oncogenic fusion PML-RARα, inhibits the repressor function of Daxx. In addition, SUMO-1 modification of PML is required for sequestration of Daxx to the PODs and for efficient inhibition of Daxx-mediated transcriptional repression. Consistently, Daxx is found at condensed chromatin in cells that lack PML. These data suggest that Daxx is a novel nuclear protein bearing transcriptional repressor activity that may be regulated by interaction with PML.
Living with Loss in the Anthropocene

Heatedly contested at various points in its development, climate change discourse is at once a political and social issue, an environmental and ecological issue, and a physical and mental health issue. Less attention has been paid to the latter. During her work with the terminally ill, Kübler-Ross (2005) outlined 5 stages of grief: anger, denial, bargaining, depression, and acceptance. That outline is now seen as analogous to the feelings that we may have towards issues of climate change, e.g., the real and perceived loss of ecosystem services, as well as uncertainty in regard to the future of humanity. With that in mind, I created The Anthropocene Adventurer magazine. Conceptualized as a visual and emotional response to climate change, The Anthropocene Adventurer magazine was developed to stimulate climate change communication. The Anthropocene Adventurer magazine grapples with the question, “What does one do when climate change hits home? ”
The Automatic Translation of Discourse Structures

We empirically show that there are significant differences between the discourse structure of Japanese texts and the discourse structure of their corresponding English translations. To improve translation quality, we propose a computational model for rewriting discourse structures. When we train our model on a parallel corpus of manually built Japanese and English discourse structure trees, we learn to rewrite Japanese trees as trees that are closer to the natural English rendering than the original ones.
Analysis of a Symmetric Rank-One Trust Region Method

Several recent computational studies have shown that the symmetric rank-one (SR1) update is a very competitive quasi-Newton update in optimization algorithms. This paper gives a new analysis of a trust region SR1 method for unconstrained optimization and shows that the method has an $n+1$ step $q$-superlinear rate of convergence. The analysis makes neither of the assumptions of uniform linear independence of the iterates nor positive definiteness of the Hessian approximations that have been made in other recent analyses of SR1 methods. The trust region method that is analyzed is fairly standard, except that it includes the feature that the Hessian approximation is updated after all steps, including rejected steps. We also present computational results that show that this feature, safeguarded in a way that is consistent with the convergence analysis, does not harm the efficiency of the SR1 trust region method.
Stabilization of Automotive Vehicles Using Active Steering and Adaptive Brake Control Allocation

In this work a dynamic control allocation approach is presented for an automotive vehicle yaw stabilization scheme. The stabilization strategy consists of a high level module that deals with the vehicle motion control objective (yaw rate reference generation and tracking), a low level module that handles the braking control for each wheel (longitudinal slip control and maximal tire-road friction parameter estimation), and an intermediate level dynamic control allocation module that generates the longitudinal slip reference for the low level brake control module and commands front wheel steering angle corrections. The control allocation design is such that the actual torque about the yaw axis tends to the desired torque calculated form the high level module, with desirable distribution of control forces satisfying actuator constraints and minimal control effort objectives. Conditions for uniform asymptotic stability are given for the case when the control allocation includes adaptation of the tire-road maximal friction coefficients, and the scheme has been implemented in a realistic non linear multi body vehicle simulation environment. The simulation cases show that the yaw control allocation strategy stabilizes the vehicle in extreme maneuvers where the non linear vehicle yaw dynamics otherwise (without active braking or active steering) becomes unstable in the sense of over- or under steering. The control allocation implementation is efficient and suitable for low cost automotive electronic control units.
Socio-economic factors responsible for poor utilisation of the primary health care services in a rural community in Nigeria.

A cross-sectional study was designed to gather information from 360 mothers of children under 5 years of age in order to find out the factors that affected utilisation of primary health care (PHC) services available in Barkin Ladi, a rural Local Government Area (L.G.A) in Plateau State, Nigeria. Of the 360 mothers interviewed using a structured questionnaire 357 (99.2%) were analysed. The major factors that cause non-attendance of the available services in the LGA included the high costs of drugs (29%) and service charges (19%), easy access to traditional healers (39%) and difficulty in getting transport to a health facility (30%). The unfriendly attitude of the health workers (3.6%) and the wasting of patients' time at the facility (7.8%) did not constitute serious constraints at attendance of facilities for use of services. Recommendations suggested for corrective measures included raising the standard of health workers through training, provision of integrated services at all Primary health Care (PHC) facilities, the introduction and sustenance of facility level through the Revolving Drug Fund Scheme.
SpiderVision: extending the human field of view for augmented awareness

We present SpiderVision, a wearable device that extends the human field of view to augment a user's awareness of things happening behind one's back. SpiderVision leverages a front and back camera to enable users to focus on the front view while employing intelligent interface techniques to cue the user about activity in the back view. The extended back view is only blended in when the scene captured by the back camera is analyzed to be dynamically changing, e.g. due to object movement. We explore factors that affect the blended extension, such as view abstraction and blending area. We contribute results of a user study that explore 1) whether users can perceive the extended field of view effectively, and 2) whether the extended field of view is considered a distraction. Quantitative analysis of the users' performance and qualitative observations of how users perceive the visual augmentation are described.
Planning with Abstraction Hierarchies can be Exponentially Less Efficient

It is well-known that state abstraction can speed up planning exponentially, under ideal condi tions. We add to the knowledge--showing that state abstraction may likewise slow down planning exponentially, and even result in generat ing an exponentially longer solution than necessary. This phenomenon can occur for abstraction hierarchies which are generated automatically by the ALPINE and HIGHPOINT algorithms. We further show that there is little hope of any drastic improvement upon these algorithms--it is computationally difficult to generate abstraction hierarchies which allow finding good approximations of optimal plans.