Miracle-dz/UniFAR-FTUs huggingface dataset:
PENSE: A Penalized Elastic Net S-Estimator

Penalized regression estimators have been widely used in recent years to improve the prediction properties of linear models, particularly when the number of explanatory variables is large. It is well-known that different penalties result in regularized estimators with varying statistical properties. Motivated by the analysis of plasma proteomic biomarkers that tend to form groups of correlated predictors, we focus here on estimators with an Elastic Net penalty, in order to keep these groups of variables together as they enter or leave the model. Given the presence of potential outliers in our data, we propose a class of penalized S-estimators which have very good robustness properties. Furthermore, these penalized S-estimators can be used as initial values to compute more efficient penalized M-estimators. In this paper we derive an algorithm to compute our proposed estimators, and also a data-driven method to select the penalty term, which is a critical part of any application with real data. Our robust penalized estimators have very good robustness properties and are also consistent under relatively weak assumptions. Our numerical experiments show that our proposals compare favourably to other robust penalized estimators. When applied to our motivating example, the robust estimators identify new potentially relevant biomarkers that are not found with non-robust alternatives. Moreover, the robust estimators identify two patients with a suspected low obstruction in the artery examined. Further measurements by a more accurate technique validated our predictions. 1
Comparison of two modern vaccines and previous influenza infection against challenge with an equine influenza virus from the Australian 2007 outbreak

During 2007, large outbreaks of equine influenza (EI) caused by Florida sublineage Clade 1 viruses affected horse populations in Japan and Australia. The likely protection that would be provided by two modern vaccines commercially available in the European Union (an ISCOM-based and a canarypox-based vaccine) at the time of the outbreaks was determined. Vaccinated ponies were challenged with a representative outbreak isolate (A/eq/Sydney/2888-8/07) and levels of protection were compared. A group of ponies infected 18 months previously with a phylogenetically-related isolate from 2003 (A/eq/South Africa/4/03) was also challenged with the 2007 outbreak virus. After experimental infection with A/eq/Sydney/2888-8/07, unvaccinated control ponies all showed clinical signs of infection together with virus shedding. Protection achieved by both vaccination or long-term immunity induced by previous exposure to equine influenza virus (EIV) was characterised by minor signs of disease and reduced virus shedding when compared with unvaccinated control ponies. The three different methods of virus titration in embryonated hens’ eggs, EIV NP-ELISA and quantitative RT-PCR were used to monitor EIV shedding and results were compared. Though the majority of previously infected ponies had low antibody levels at the time of challenge, they demonstrated good clinical protection and limited virus shedding. In summary, we demonstrate that vaccination with current EIV vaccines would partially protect against infection with A/eq/Sydney/2888-8/07-like strains and would help to limit the spread of disease in our vaccinated horse population.
Automatic Value Identification of Pointer-Type Pressure Gauge Based on Machine Vision

This paper presents a new method of value identification of pointer-type pressure gauges based on machine vision, by which an automatic calibration system can be designed. Hough Transformation, image subtraction and image thinning technique are employed to obtain the coordinate of the pointer rotating center. Through removing the pixels data outside of the circumference of the pointer in the single panel image, the linear equation of the pointer is achieved after the processing of image thinning and Hough transformation. Experiments are carried out on a pressure calibration device. The results show that the accuracy and speed of the automatic identification of the pressure gauge is improved.
Flow rate variation and biological agents that obstruct drippers of swine effluent

Emitter clogging is the major problem of drip irrigation systems operating with wastewater. The objective of this study was to evaluate the alteration of the flow rate variation coefficient (FVC) and to identify the biological agents that cause obstruction in drip units operating with swine effluent and public water supply. The experiment was set up in a split-plot scheme, with the times of application of swine effluent and public water supply in the main plots and dripper types in the secondary parcels, evaluating times of FVC in the tertiary parcels, using a completely randomized design (CRD) with three repetitions. The FVC of the drip subunits was calculated on every 40 hours as well as the microscopic analysis of the biological agents of clogging, until 160 h. At the end of the tests, biofilm samples were collected in each drip unit to identify the groups of predominant bacteria. The results indicated that the FVC was effective in detecting the clogging of the emitters, evidencing that the construction characteristics and the times of application of swine effluent and of the public water supply interfere in this process. Microscopic analyzes of the biofilm indicated that the main biological agents that caused obstruction were algae, bacteria, fungi and protozoa.
A systematic review of whole class, subject based, pedagogies with reported outcomes for the academic and social inclusion of pupils with special educational needs in mainstream classrooms

Schools across the world have responded to international and national initiatives designed to further the development of inclusive education. In England, there is a statutory requirement for all schools to provide effective learning opportunities for all pupils (QCA, 2000) and children with special educational needs (SEN) are positioned as having a right to be within mainstream classrooms accessing an appropriate curriculum (SENDA, 2001). Previous reviews which have sought to identify classroom practices that support the inclusion of children with SEN have been technically non-systematic and hence a need for a systematic review within this area has been identified (Nind et al., 2004; Rix et al., 2006). This systematic literature review is the last in a series of three.
Restrict Encoding for Mixed-Mode BIST

Programmable mixed-mode BIST schemes combine pseudo-random pattern testing and deterministic test. This paper presents a synthesis technique for a mixed-mode BIST scheme which is able to exploit the regularities of a deterministic test pattern set for minimizing the hardware overhead and memory requirements. The scheme saves more than 50% hardware costs compared with the best schemes known so far while complete programmability is still preserved.
Intravenous transplantation of allogeneic bone marrow mesenchymal stem cells and its directional migration to the necrotic femoral head

In this study, we investigated the feasibility and safety of intravenous transplantation of allogeneic bone marrow mesenchymal stem cells (MSCs) for femoral head repair, and observed the migration and distribution of MSCs in hosts. MSCs were labeled with green fluorescent protein (GFP) in vitro and injected into nude mice via vena caudalis, and the distribution of MSCs was dynamically monitored at 0, 6, 24, 48, 72 and 96 h after transplantation. Two weeks after the establishment of a rabbit model of femoral head necrosis, GFP labeled MSCs were injected into these rabbits via ear vein, immunological rejection and graft versus host disease were observed and necrotic and normal femoral heads, bone marrows, lungs, and livers were harvested at 2, 4 and 6 w after transplantation. The sections of these tissues were observed under fluorescent microscope. More than 70 % MSCs were successfully labeled with GFP at 72 h after labeling. MSCs were uniformly distributed in multiple organs and tissues including brain, lungs, heart, kidneys, intestine and bilateral hip joints of nude mice. In rabbits, at 6 w after intravenous transplantation, GFP labeled MSCs were noted in the lungs, liver, bone marrow and normal and necrotic femoral heads of rabbits, and the number of MSCs in bone marrow was higher than that in the, femoral head, liver and lungs. Furthermore, the number of MSCs peaked at 6 w after transplantation. Moreover, no immunological rejection and graft versus host disease were found after transplantation in rabbits. Our results revealed intravenously implanted MSCs could migrate into the femoral head of hosts, and especially migrate directionally and survive in the necrotic femoral heads. Thus, it is feasible and safe to treat femoral head necrosis by intravenous transplantation of allogeneic MSCs.
Cloud Adiabaticity and Its Relationship to Marine Stratocumulus Characteristics Over the Northeast Pacific Ocean

Cloud adiabaticity (α) is defined as the ratio of the actual liquid water path (LWPmeasured) in a cloud to its corresponding adiabatic value (LWPad). Processes such as drizzle and entrainment can lead to subadiabatic LWPmeasured. This study examines α and its relationship to microphysical properties for 86 cloud events over the Northeast Pacific Ocean based on data collected during four separate summertime airborne campaigns. For the study region, α was found to be 0.766 ± 0.134. For most cases, clouds with a low value of α were found to have lower droplet number concentration (Nd), higher droplet effective radius (re), higher relative dispersion (d), and higher rain rate (R). The subcloud aerosol concentration (Na) was often less for the low‐α cases. The relationship between α and the vertical profiles and cloud‐top characteristics for both the cloud droplet‐only spectrum and full spectrum (cloud and rain droplets) is also examined. Inclusion of rain droplets produced a larger change in d for the low‐α clouds as compared to the high‐α clouds. On average, R increased at cloud top for high‐α clouds but decreased at cloud top for low‐α clouds. Accounting for α when estimating Nd from Moderate Resolution Imaging Spectroradiometer retrievals results in better agreement with in situ Nd values. Results of this work motivate the need for additional focus on the factors governing α, such as cloud type, and implications of its value, especially for remote‐sensing retrievals.
Quantitative Chemical Mapping of InGaN Quantum Wells from Calibrated High-Angle Annular Dark Field Micrographs

Abstract We present a simple and robust method to acquire quantitative maps of compositional fluctuations in nanostructures from low magnification high-angle annular dark field (HAADF) micrographs calibrated by energy-dispersive X-ray (EDX) spectroscopy in scanning transmission electron microscopy (STEM) mode. We show that a nonuniform background in HAADF-STEM micrographs can be eliminated, to a first approximation, by use of a suitable analytic function. The uncertainty in probe position when collecting an EDX spectrum renders the calibration of HAADF-STEM micrographs indirect, and a statistical approach has been developed to determine the position with confidence. Our analysis procedure, presented in a flowchart to facilitate the successful implementation of the method by users, was applied to discontinuous InGaN/GaN quantum wells in order to obtain quantitative determinations of compositional fluctuations on the nanoscale.
A unified approach to the design of PWM-based sliding-mode voltage controllers for basic DC-DC converters in continuous conduction mode

This paper presents a simple unified approach to the design of fixed-frequency pulsewidth-modulation-based sliding-mode controllers for dc-dc converters operating in the continuous conduction mode. The design methodology is illustrated on the three primary dc-dc converters: buck, boost, and buck-boost converters. To illustrate the feasibility of the scheme, an experimental prototype of the derived boost controller/converter system is developed. Several tests are performed to validate the functionalities of the system
Abstract object state and version recovery in N-version programming

The paper deals with the use of software diversity, specifically, N-version programming (NVP) in object oriented (OO) systems. We formulate the problem of faulty version recovery and show how our NVP scheme, developed recently, can be extended to solve it. Our approach relies on using the abstract version state, which represents a common general description of the states of all correct version objects. The recovery consists in mapping the state of a correct version onto the state of the faulty version via the abstract state. We introduce a formal description of our model and show that many ideas related to object state abstraction can be found in the existing research on OO programming. We discuss extensions of LAYOM and PSL as promising practical approaches for developing recovery features in OO programming. As an alternative solution, we propose a meta-object architecture and a related protocol which can facilitate the solution of the object version recovery problem. The paper finishes with a brief discussion of engineering steps which have to be done for developing recoverable version objects and of some approaches which can improve the reusability of the scheme proposed.
Identifying Facts for TCBR

This paper explores a method to algorithmically distinguish case-specific facts from potentially reusable or adaptable elements of cases in a textual case-based reasoning (TCBR) system. In the legal domain, documents often contain casespecific facts mixed with case-neutral details of law, precedent, conclusions the attorneys reach by applying their interpretation of the law to the case facts, and other aspects of argumentation that attorneys could potentially apply to similar situations. The automated distinction of these two categories, namely facts and other elements, has the potential to improve quality of automated textual case acquisition. The goal is ultimately to distinguish case problem from solution. To separate fact from other elements, we use an information gain (IG) algorithm to identify words that serve as efficient markers of one or the other. We demonstrate that this technique can successfully distinguish case-specific fact paragraphs from others, and propose future work to overcome some of the limitations of this pilot project.
Comparative phylogeography of two sympatric beeches in subtropical China: Species-specific geographic mosaic of lineages

In subtropical China, large-scale phylogeographic comparisons among multiple sympatric plants with similar ecological preferences are scarce, making generalizations about common response to historical events necessarily tentative. A phylogeographic comparison of two sympatric Chinese beeches (Fagus lucida and F. longipetiolata, 21 and 28 populations, respectively) was conducted to test whether they have responded to historical events in a concerted fashion and to determine whether their phylogeographic structure is exclusively due to Quaternary events or it is also associated with pre-Quaternary events. Twenty-three haplotypes were recovered for F. lucida and F. longipetiolata (14 each one and five shared). Both species exhibited a species-specific mosaic distribution of haplotypes, with many of them being range-restricted and even private to populations. The two beeches had comparable total haplotype diversity but F. lucida had much higher within-population diversity than F. longipetiolata. Molecular dating showed that the time to most recent common ancestor of all haplotypes was 6.36 Ma, with most haplotypes differentiating during the Quaternary. [Correction added on 14 October 2013, after first online publication: the timeunit has been corrected to ‘6.36’. ] Our results support a late Miocene origin and southwards colonization of Chinese beeches when the aridity in Central Asia intensified and the monsoon climate began to dominate the East Asia. During the Quaternary, long-term isolation in subtropical mountains of China coupled with limited gene flow would have lead to the current species-specific mosaic distribution of lineages.
Stereo vision-based driver head pose estimation

In conjunction with the advancing development of driver assistance systems, driver observation becomes increasingly important. This paper proposes a new approach for driver's head pose estimation. With a stereo camera mounted in a realistic position on top of the center stack the system continuously tracks the orientation of the driver's head in realtime (25fps) using solely 3-D information. The systems processing chain comprises separate modules for head separation, pose estimation and pose tracking. Head separation employes a Bayesian modeling approach for robust head-torso separation. The pose estimation module uses Synchronized Submanifold Embedding (SSE), a nonlinear regression method, which includes a dimensionality reduction, a k-nearest neighbor search and a barycentric coordinate estimation. The tracking module estimates angular velocity of the head, using an Extended Kalman Filter (EKF) in quaternion space. Comprehensive experiments show, that the proposed system achieves high accuracy from a non-central camera position. Since the approach does not rely on facial feature points the system handles large pose variations and is not disturbed by (sun)glasses.
O.D.D.: A Promising but Incomplete Formalism for Individual-Based Model Specification

In this paper we introduce the ODD protocol, proposed in ecology for easing the communication and replication of Individual Based Models (IBM). First, we use it to describe a realistic model in epidemiology, which deals with the local determinants of the propagation of the H5N1 virus. From this description we first point out the advantages of ODD. Then we focus on its weaknesses, the major ones being its ambiguity and its inability to attain replication. Finally, we propose several improvements for this protocol in terms of re-organization, better specifications (adapted from existing software engineering methodologies) and the addition of a section dedicated to experimentations.
Maritime anomaly detection and threat assessment

Ships involved in commercial activities tend to follow set patterns of behaviour depending on the business in which they are engaged. If a ship exhibits anomalous behaviour, this could indicate it is being used for illicit activities. With the wide availability of automatic identification system (AIS) data it is now possible to detect some of these patterns of behaviour. Monitoring the possible threat posed by the worldwide movement of ships, however, requires efficient and robust automatic data processing to create a priority list for further investigation. This paper outlines five anomalous ship behaviours: deviation from standard routes, unexpected AIS activity, unexpected port arrival, close approach, and zone entry. For each behaviour, a process is described for determining the probability that it is anomalous. Individual probabilities are combined using a Bayesian network to calculate the overall probability that a specific threat is present. Examples of how the algorithms work are given using simulated and real data.
Emerging therapy for the treatment of acute lymphoblastic leukemia

Importance of the field: Over the last few decades, advances in acute lymphoblastic leukemia (ALL) therapy have led to long-term survival rates of > 80% in children; however, comparable rates have yet to be achieved in adults, and a large majority of patients relapse from their disease. Areas covered in this review: The review describes historical therapy and advancements in ALL treatment over the past few decades, while providing a concise review of the future direction of ALL therapy. Literature was collected through peer reviewed journals and the Pharmaprojects drug profile for ALL. What the reader will gain: Current information regarding prognostic factors for relapse, salvage therapy options and emerging drugs are provided in the review. Take home message: Development of new drugs with novel mechanisms, unique formulations of existing medications, as well as manipulation of current combinations of drugs remain vital to the success in adult ALL.
Fabrication and characterization of recombinant silk-elastinlike protein fibers for tissue engineering applications

The integration of functional and structural properties makes genetically engineered proteins appealing in tissue engineering. Silk-elastinlike proteins (SELPs), containing tandemly repeated polypeptide sequence derived from natural silk and elastin, are recently under active study due to the interesting structure. The biological, chemical, physical properties of SELPs have been extensively investigated for their possible applications in drug/gene delivery, surgical tissue sealing and spine repair surgery. However, the mechanical aspect has rarely been looked into. Moreover, many other biomaterials have been fabricated into fibers in micrometer and nanometer scale to build extracellular matrix-mimic scaffolds for tissue regeneration, but many have one or mixed defects such as: poor strength, mild toxicity or immune repulsion etc. The SELP fibers, with the intrinsic primary structures, have novel mechanical properties that can make them defects-minimized scaffolds in tissue engineering. In this study, one SELP (SELP-47K) was fabricated into microfibers and nanofibers by the techniques of wet-spinning and electrospinning. Microfibers of meters long were formed and collected from a methanol coagulation bath, and later were crosslinked by glutaraldehyde (GTA) vapor. The resultant microfibers displayed higher tensile strength up to 20 MPa and higher deformability as high as 700% when tested in hydrated state. Electrospinnig of SELP-47K in formic acid and water
Data utility modelling for mismatch reduction

In the "missing data" (MD) approach to noise robust automatic speech recognition (ASR), speech models are trained on clean data, and during recognition sections of spectral data dominated by noise are detected and treated as "missing". However, this all-or-nothing hard decision about which data is missing does not accurately reflect the probabilistic nature of missing data detection. Recent work has shown greatly improved performance by the "soft missing data" (SMD) approach, in which the "missing" status of each data value is represented by a continuous probability rather than a 0/1 value. This probability is then used to weight between the different likelihood contributions which the MD model normally assigns to each spectral observation according to its "missing" status. This article presents an analysis which shows that the SMD approach effectively implements a Maximum A-Posteriori (MAP) decoding strategy with missing or uncertain data, subject to the interpretation that the missing/not-missing probabilities are weights for a mixture pdf which models the pdf for each hidden clean data input, after conditioning by the noisy data input, a local noise estimate, and any information which may be available. An important feature of this "soft data" model is that control over the "evidence pdf" can provide a principled framework not only for ignoring unreliable data, but also for focusing attention on more discriminative features, and for data enhancement.
Design of a control limiter to improve the dynamic response of energy storage systems

This paper proposes an effective control scheme to improve the transient behavior of VSC-based energy storage systems facing energy saturations. This control is aimed to reduce abrupt transients following energy saturations of the storage device. The WSCC 9-bus test system is used for validating and discussing the proposed controller. In particular, the dynamic response of a battery energy storage undergoing energy saturations is tested considering deterministic as well as stochastic load variations. Simulation results shows that the proposed control scheme allows reducing installation costs while ensuring an adequate dynamic reponse of energy storage systems.