Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate EnOI-based data assimilation in the high resolution ocean model

The ensemble Optimal Interpolation (EnOI) method is considered for assimilation of observational data in the INMIO ocean model of high spatial resolution. Its parallel implementation is described in the form of the Data Assimilation Service (DAS) based on the Compact Modeling Framework (CMF3.0). The on EnOI based parallel algorithm is designed to assimilate data from various sources (drifters, satellites, etc) with the ability to construct cross-covariance matrices (between different model values) for adjusting all model fields and the model forecast as a whole, including those functions, for which there is no measurements. This method based on EnOI is planned to be used for all observational data available to date for the World Ocean.
ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm. ki.si/ligands.
THE COX RING OF M0,6

We prove that the Cox ring of the moduli space M0,6, of stable rational curves with 6 marked points, is finitely generated by sections corresponding to the boundary divisors and divisors which are pull-backs of the hyperelliptic locus in M3 via morphisms ρ : M0,6 → M3 that send a 6-pointed rational curve to a curve with 3 nodes by identifying 3 pairs of points. In particular this gives a self-contained proof of Hassett and Tschinkel’s result about the effective cone of M0,6 being generated by the above mentioned divisors.
Tracking loop for IR-UWB communications in IEEE 802.15 multi-path channels

In impulse-radio ultra-wide band (IR-UWB) communications, even a small timing error would lead to a serious degradation in system performance in the multi-path circumstance. To deal with the challenge, a novel hybrid synchronous sampling timing locked loop is proposed in this paper. Timing error detector, the crucial unit of TLL, is realized based on a maximum-likelihood estimation method. Both mathematical analysis and simulations on S-Curve and timing error variance indicate a high performance of the proposed TLL at low signal to noise rate. It is also demonstrated that in the environment of IEEE 802.15. 3a Multi-path channels, the proposed TLL improves system bit error rate (BER) performance by two orders of magnitude when the timing jitters are around half a pulse duration. Furthermore, it is observed through simulations that five figures selective Rake receiver is advisable for a satisfactory system BER performance.
High-accuracy positioning for indoor wireless sensor networks

In this paper, a new scheme to reduce the positioning error is investigated for wireless sensor networks (WSN). To be specific, conventional Distance Vector-Hop (Dv-Hop) algorithm fail to calculate the average distance per-hop with high precision that caused by the random distribution of the irregular network topology, greatly leading to the positioning error in the Dv-Hop algorithm. To enhance the positioning accuracy, we combine the Quantum Bacterial Foraging Optimization (QBFO) algorithm with the Dv-Hop algorithm, designing a new QBFO-Dv-Hop (Quantum Bacterial Foraging Optimization Dv-Hop) algorithm. In the QBFO-Dv-Hop algorithm, the average distance per-hop is calculated by the QBFO by using the minimum hops of nodes and the position information of anchor nodes are broadcast. Simulation results illustrate that the positioning error of 30% anchors can be effectively reduced without adding computation complexity, and computer simulation also shows that increasing the number of the unknown nodes or decreasing the communication radius can get better performance compared with other typical Dv-Hop algorithms.
Cranial base in craniofacial development: Developmental features, influence on facial growth, anomaly, and molecular basis

The cranial base is of crucial importance in integrated craniofacial development. As distinct from facial bones, it is formed through endochondral ossification. The posterior and anterior cranial bases are derived from distinct embryologic origins and grow independently — the anterior cranial base solely from the neural crest, the posterior cranial base from the paraxial mesoderm. The anterior cranial base has more prolonged and active growth and exerts more influence on facial growth than does the posterior cranial base. Cranial base angulation is a unique feature in modern human beings. Cranial base anomalies have been identified in many genetic and developmental disorders. The molecular basis of cranial base development and growth is being clarified. In this review, these aspects of cranial base are discussed in detail, with a focus on developmental features, roles in craniofacial growth, anomalies, and the genetic basis of development.
A Structured Review of Productivity Factors in Software Development

Analysing and improving productivity has been one of the main goals of software engineering research since its beginnings. A plethora of studies have been conducted on various factors that resulted in several models for analysis and prediction of productivity. However, productivity is still an issue in current software development and not all factors and their relationships are known. This paper reviews the large body of available literature in order to distill a list of the main factors influencing productivity investigated so far. The measure for importance here is the number of articles a factor is used in. Special consideration is given to soft or human-related factors in software engineering that are often not analysed with equal detail as more technical factors. The resulting list can be used to guide further analysis and as basis for building productivity models.
CEASAR: a smooth, accurate and robust centerline extraction algorithm

We present CEASAR, a centerline extraction algorithm that delivers smooth, accurate and robust results. Centerlines are needed for accurate measurements of length along winding tubular structures. Centerlines are also required in automatic virtual navigation through human organs, such as the colon or the aorta, as they are used to control movement and orientation of the virtual camera. We introduce a concise but general definition of a centerline, and provide an algorithm that finds the centerline accurately and rapidly. Our algorithm is provably correct for general geometries. Our solution is fully automatic, which frees the user from having to engage in data preprocessing. For a number of test datasets, we show the smooth and accurate centerlines computed by our CEASAR algorithm on a single 194 MHz MIPS R10000 CPU within five minutes.
Utilizing Hoare Logic to Strengthen Testing for Error Detection in Programs

Hoare logic (also known as Floyd-Hoare logic) can be used to formally verify the correctness of programs while testing provides a practical way to detect errors in programs. Unfortunately, the former is rarely applied in practice and the later is difficult to detect all existing errors. In this paper, we propose a novel technique that makes good use of Hoare logic to strengthen testing. The essential idea is first to use specification-based testing to discover all traversed program paths and then to use Hoare logic to prove their correctness. During the proof process, all errors on the paths can be detected. A case study is conducted to show its feasibility; an example taken from the case study is used to illustrate how the proposed method is applied; and discussion on the potential challenges to the method is presented.
Towards Affordable Disclosure of Spoken Word Archives

This paper presents and discusses ongoing work aiming at affordable disclosure of real-world spoken word archives in general, and in particular of a collection of recorded interviews with Dutch survivors of World War II concentration camp Buchenwald. Given such collections, the least we want to be able to provide is search at different levels and a flexible way of presenting results. Strategies for automatic annotation based on speech recognition – supporting e.g., within-document search– are outlined and discussed with respect to the Buchenwald interview collection. In addition, usability aspects of the spoken word search are discussed on the basis of our experiences with the online Buchenwald web portal. It is concluded that, although user feedback is generally fairly positive, automatic annotation performance is still far from satisfactory, and requires additional research.
Local recovery solutions from multi-link failures in MPLS-TE networks with probable failure patterns

MPLS-TE (traffic engineering) fast reroute proposes a local protection mechanism to reroute protected TE LSPs (label switched paths) quickly onto precomputed and signaled bypass tunnels. The paper explores the case of multiple network element failure scenarios. The undesired complexity inherent in the multiple failure scenario originates from the fact that those failure scenarios are more disruptive, and may require multiple bypass tunnels to cope with them. The paper adapts the MPLS local recovery schemes to multi-failure scenarios, while controlling the number of bypass tunnels that are required. This is achieved by mapping multi-failure scenarios onto probable failure patterns (PFPs). PFPs are characterized by their probability (or frequency) of occurrence during the network lifetime. A number of bypass tunnels is then computed to cope effectively with the PFPs according to their frequency or probability of occurrence. It is shown that by properly choosing how the PFPs are grouped, and how the corresponding bypass tunnels are computed, it is possible to trade the required number of bypass tunnels for their average length and outage probability, i.e., the probability that the local recovery scheme cannot cope with the occurrence of a multi-failure pattern.
Comparison of abstraction scenarios simulated by SWAT and SWAT-MODFLOW

ABSTRACT In hydrological modelling of catchments, wherein streams are groundwater-fed, an accurate representation of groundwater processes and their interaction with surface water is crucial. With this purpose, a coupled model was recently developed linking SWAT (Soil and Water Assessment Tool) with the fully-distributed groundwater model MODFLOW (Modular Groundwater Flow). In this study, SWAT and SWAT-MODFLOW were applied to a Danish groundwater-dominant catchment, simulating groundwater abstraction scenarios and assessing the benefits and drawbacks of SWAT-MODFLOW. Both models demonstrated good performance. However, SWAT-MODFLOW provided more realistic outputs when simulating abstraction: the decrease in streamflow was similar to the volume of water abstracted, while in SWAT the impact was negligible. SWAT also showed impacts on streamflow only when abstractions were taken from the shallow aquifer, not from the deep aquifer. Overall, SWAT-MODFLOW demonstrated wider possibilities for groundwater analysis, providing more insights than SWAT in supporting decision making in relation to environmental assessment.
Efficient motion planning for humanoid robots using lazy collision checking and enlarged robot models

Motion planning for humanoid robotic systems with many degrees of freedom is an important and still generally unsolved problem. To give the robot the ability of acting and navigating in complex environments, the motion planner has to find collision-free paths in a robust manner. The runtime of a planning algorithm is critical, since complex tasks require several planning steps where the collision detection and avoidance should be accomplished in reasonable time. In this paper we present an extension of standard sampling-based techniques using Rapidly Exploring Random Trees (RRT). We extend the free-bubble path validation algorithm from Quinlan, which can be used to guarantee the collision-free status of a C-space path between two samples. By using enlarged robot models it is possible to avoid costly distance calculations and therefore to speed up the planning process. We also present a combined approach based on lazy collision checking that brings together the advantages of fast sampling-based and exact path-validated algorithms. The proposed algorithms have been evaluated by experiments on a humanoid robot in a kitchen environment and by a comparison to a validation based on Quinlan's free bubbles approach.
Fault-Tolerant Techniques to Minimize the Impact of Crosstalk on Phase Encoded Communication Channels

An on-chip intermodule self-timed communication system is considered in which symbols are encoded by means of phase difference between transitions of signals on parallel wires. The reliability of such a channel is governed and significantly lowered by capacitive crosstalk effects between adjacent wires. A more robust high-speed phase-encoded channel can be designed by minimizing its vulnerability to crosstalk noise. This paper investigates the impact of crosstalk on phase-encoded transmission channels. A functional fault model is presented to characterize the problem. Two fault-tolerant schemes are introduced which are based on information redundancy techniques and a partial-order coding concept. The area overheads, performance, and fault-tolerant capability of those methods are compared. It is shown that a substantial improvement in the performance can be obtained for four-wire channels when using the fault-tolerant design approach, at the expense of 25 percent of information capacity per symbol.
Proposing regions from histopathological whole slide image for retrieval using Selective Search

In the field of pathological image analysis based on machine learning, the generation of appropriate training data set is significant but difficult. As a solution, this paper addresses a novel unsupervised region proposal method for histopathological whole slide image based on Selective Search. Specifically, the method utilizes multiple magnifications, modifies the similarity measure for grouping regions and proposes a new Nucleus-Cytoplasm color space to gain more region proposals. Additionally, a new retrieval acceleration method based on Latent Dirichlet Allocation and Supervised Hashing is raised. The experiments on a large-scale multi-class database of breast histopathological images demonstrate the effectiveness and efficiency of our methods.
Dietary Magnesium and C-reactive Protein Levels

Objective: Current dietary guidelines recommend adequate intake of magnesium (310–420mg daily) in order to maintain health and lower the risk of cardiovascular disease. Recent evidence from animal and clinical studies suggests that magnesium may be associated with inflammatory processes. The objective of this study was to determine whether dietary magnesium consumption is associated with C-reactive protein (CRP), a marker of inflammation, in a nationally representative sample. Methods: Analysis of adult (≥17 years) participants in a cross-sectional nationally representative survey (National Health and Nutrition Examination Survey 1999–2000 [NHANES]) who were not taking magnesium or magnesium-containing supplements. The primary outcome measure was high sensitivity CRP (elevated ≥3.0mg/L). Results: Among US adults, 68% consumed less than the recommended daily allowance (RDA) of magnesium, and 19% consumed less than 50% of the RDA. After controlling for demographic and cardiovascular risk factors, adults who consumed <RDA of magnesium were 1.48–1.75 times more likely to have elevated CRP than adults who consumed ≥RDA (Odds Ratio [OR] for intake <50% RDA = 1.75, 95% Confidence Interval [CI] 1.08–2.87). Adults who were over age 40 with a BMI >25 and who consumed <50% RDA for magnesium were 2.24 times more likely to have elevated CRP (95% CI 1.13–4.46) than adults ≥RDA. Conclusions: Most Americans consume magnesium at levels below the RDA. Individuals with intakes below the RDA are more likely to have elevated CRP, which may contribute to cardiovascular disease risk.
Multimedia over high speed networks: reducing network requirements with fast buffer fillup

The cost effective ABR service is suitable for transmitting bursty compressed video over ATM network. Here, we propose a fast buffer fillup (FBF) scheme to run VoD over ATM network with ABR service. We develop models to determine buffer size at the client and the server for our scheme. We also develop relationships between the startup delay, the ABR service parameters, and the network congestion status. Our results indicate that the new scheme minimizes the startup delay and has simple network resource requirements.
Multicues Face Detection in Complex Background for Frontal Faces

Face recognition (FR) systems are increasingly gaining more importance. Face detection and tracking in a complex scene forms the first step in building a practical FR system. In this paper a hybrid algorithm to detect face(s) in color images is introduced. The algorithm uses color histogram for skin (in the HSV color space) in conjunction with shape information and facial feature detection to quickly locate faces in a given image.
Hot, dry and different: Australian lizard richness is unlike that of mammals, amphibians and birds

Aims (1) To map the species richness of Australian lizards and describe patterns of range size and species turnover that underlie them. (2) To assess the congruence in the species richness of lizards and other vertebrate groups. (3) To search for commonalities in the drivers of species richness in Australian vertebrates.
Sketch Interpretation and Refinement Using Statistical Models

We present a system for generating 2D illustrations from hand drawn outlines consisting of only curve strokes. A user can draw a coarse sketch and the system would automatically augment the shape, thickness, color and surrounding texture of the curves making up the sketch. The styles for these refinements are learned from examples whose semantics have been pre-classified. There can be several styles applicable on a curve and the system automatically identifies which one to use and how to use it based on a curve's shape and its context in the illustration. Our approach is based on a Hierarchical Hidden Markov Model. We present a two level hierarchy in which the refinement process is applied at: the curve level and the scene level.
Human peripheral blood eosinophils produce and release interleukin‐8 on stimulation with calcium ionophore

We present evidence that human blood eosinophils produce interleukin (IL)‐8 when stimulated with calcium ionophore. Following in vitro culture of 99 % pure eosinophils with calcium ionophore, released IL‐8 was detectable by enzymelinked immunosorbent assay in supernatants. Eosinophil IL‐8 production was considerably greater than that of IL‐3 or granulocyte macrophage colony‐stimulating factor. Furthermore, eosinophil production of IL‐8 in the presence of calcium ionophore could be inhibited with the immunomodulating agent cyclosporin A and the protein synthesis inhibitor cycloheximide. In addition, following stimulation of highly purified blood eosinophils with calcium ionophore, IL‐8 mRNA was detectable after polymerase chain reaction amplification. In comparison with other cells on stimulation with calcium ionophore, eosinophils produce about half as much IL‐8 as neutrophils but significantly more than purified T cells. In contrast to monocytes and neutrophils, IL‐8 production was not inducible with IL‐1 or tumor necrosis factor. Finally, following calcium ionophore stimulation blood eosinophils were shown to contain cytoplasmic IL‐8 by employing a monoclonal antibody against IL‐8 in conjunction with immuno‐histochemistry. These observations demonstrate that eosinophils are capable of IL‐8 production and release, which may contribute to defense against parasites and to the pathophysiology of allergic and asthmatic disease.
Cohort studies in sexual health

J M Stephenson, A Babiker Examples of cohort studies in the sexual health literature are now increasingly common. The purpose of this article is to provide an overview of the design and analysis of cohort studies, along with a discussion of some of the potential problems with these studies which may be particularly relevant for cohorts which study factors related to sexual health. A comprehensive guide to the design and analysis of cohort studies can be found in the book by Breslow and Day.1 A cohort study is a type of study in which a group of individuals is followed through time. Although cohort studies are frequently referred to in the literature, one of the distinguishing features of an epidemiological cohort study (as opposed to the literal meaning of the word “cohort” as a “group or gathering” of individuals), is that it is longitudinal —that is, there is some follow up of the individuals recruited to the study. Thus, many so called cohort studies are simply cross sectional studies, where a group of individuals is recruited for a one-off assessment, and are not followed any further. We will not consider these studies in this article. The usual aim of a cohort study is to assess the relation between a specific event or disease outcome and exposure to one or more potential “risk” factors. The information on whether each individual has been exposed to these risk factors is usually collected at entry to the cohort, and the individuals recruited to the study are then monitored over time to see whether or not the event occurs. We may be interested in either the incidence of the event (that is, the rate of new events over a given time period), the average time until the event occurs, or the cumulative probability of …
Optimal Testing of Structured Knowledge

Adopting a decision-theoretic perspective, we investigate the problem of optimal testing of structured knowledge - the canonical example being a qualifying examination of a graduate student. The setting is characterized by several factors: examinee's knowledge structured around several inter-dependent topics, a limited "budget" of questions available to the examiner, a decision to be made (pass/fail), and an utility for good and bad decisions. The existence of multiple professors brings up additional issues such as committee formation, and the existence of multiple students brings up issues such as fairness.
The Iterative Bayesian Model Averaging Algorithm: an improved method for gene selection and classication using microarray data

is a supervised learning technique that in the context of microarray analysis is most frequently used to identify genes whose expression is correlated with specic phenotypes of the samples. Typically, the interest is in identifying genes that are predictive of disease. In such cases, both the accuracy of the prediction and the number of genes necessary to obtain a given accuracy is important. In particular, methods that select a small number of relevant genes and provide accurate classication of microarray samples aid in the development of simpler diagnostic tests. In addition, methods that adopt a weighted average approach over multiple models have the potential to provide more accurate predictions than methods that do not take model uncertainty into consideration. Hence, we developed the Bayesian Model Averaging (BMA) method for gene selection and classication