Miracle-dz/UniFAR-FTUs huggingface dataset:
A fully automated framework for lung tumour detection, segmentation and analysis

Early and correct diagnosis is a very important aspect of cancer treatment. Detection of tumour in Computed Tomography scan is a tedious and tricky task which requires expert knowledge and a lot of human working hours. As small human error is present in any work he does, it is possible that a CT scan could be misdiagnosed causing the patient to become terminal. This paper introduces a novel fully automated framework which helps to detect and segment tumour, if present in a lung CT scan series. It also provides useful analysis of the detected tumour such as its approximate volume, centre location and more. The framework provides a single click solution which analyses all CT images of a single patient series in one go. It helps to reduce the work of manually going through each CT slice and provides quicker and more accurate tumour diagnosis. It makes use of customized image processing and image segmentation methods, to detect and segment the prospective tumour region from the CT scan. It then uses a trained ensemble classifier to correctly classify the segmented region as being tumour or not. Tumour analysis further computed can then be used to determine malignity of the tumour. With an accuracy of 98.14%, the implemented framework can be used in various practical scenarios, capable of eliminating need of any expert pathologist intervention.
Subjective Cognitive Impairment Is a Predominantly Benign Condition in Memory Clinic Patients Followed for 6 Years: The Gothenburg-Oslo MCI Study

Background/Aims: In the quest for prevention or treatment, there is a need to find early markers for preclinical dementia. This study observed memory clinic patients with subjective cognitive impairment (SCI) and normal cognitive function at baseline. The primary aim was to address SCI as a potential risk factor for cognitive decline. The secondary aim was to address a potential relation between (1) baseline cerebrospinal fluid biomarkers and (2) a decline in memory performance over the first 2 years of follow-up, with a possible cognitive decline after 6 years. Methods: Eighty-one patients (mean age 61 years) were recruited from university memory clinics and followed up for 6 years. Results: Eighty-six percent of the cohort remained cognitively stable or improved, 9% developed mild cognitive impairment, and only 5% (n = 4) developed dementia. Regression analysis revealed that low levels of Aβ42 at baseline and memory decline during the first 2 years predicted dementia. When combined, these variables were associated with a 50% risk of developing dementia. Conclusions: Cognitive stability for 86% of the cohort suggests that SCI is predominantly a benign condition with regard to neuropathology. The low number of individuals who developed dementia limits the generalizability of the results and discussion of progression factors.
A Relativistic Jet in the Radio-quiet Quasar PG 1407+263

We present the results of a multiepoch radio monitoring campaign measuring the milliarcsecond structure of the jet in the radio-quiet quasar PG 1407+263. This is the highest sensitivity, highest resolution multiyear study of a distant active galaxy. The observations are naturally explained in terms of a beamed relativistic jet, some of whose fluctuations in flux density can be ascribed to interaction with the narrow-line region of the quasar. The optical properties of PG 1407+263, in particular the low equivalent widths of the emission lines, may be related to the fact that we are viewing this quasar almost pole-on, giving us a direct view into its broad-line region.
Survival of infants with spina bifida: a population study, 1979-94.

This study aimed to investigate the survival of infants born with spina bifida between 1979 and 1994 from the population-based Metropolitan Atlanta Congenital Defects Program (MACDP) and to identify clinical and demographic factors associated with survival. Survival status was obtained from MACDP records and the National Death Index. Survival rates were calculated using the Kaplan-Meier method. Risk factors potentially associated with survival were examined by the log-rank test. We assessed the independent effect of risk factors using the Cox proportional hazards model. Overall, 78.4% of children with spina bifida survived during the study period. Of the 235 infants born with spina bifida, 87.2% survived the first year of life. Survival to age 1 for the 1979-83, 1984-88 and 1989-94 birth cohorts was 82.7%, 88.5% and 91.0% respectively. In multivariable analysis, factors associated with increased mortality were low birthweight (<2500 g) (vs. > or =2500g, relative risk (RR) 2.3 [95% CI 1.1, 4.9]) and high lesions (vs. low lesions, RR 3.4 [95% CI 1.6, 7.1]). This study suggests a continuous improvement in survival among children born with spina bifida in Atlanta. Demographic and clinical factors are associated with length of survival. This information is useful for both clinicians and families who need to plan for the long-term care of these children.
Modelling farm production risk with copulae instead of correlations

The optimisation of production plans is an important topic in agriculture, often related to diversification and specialisation as the classical instruments of coping with production risk. Although the measurement of embedded risk is often inaccurate, it is nevertheless necessary for decision making to describe the common behaviour of different variables in a model. Imprecisely defined relationships influence the “right” choice, why it is important to find a good approximation of the real circumstances. In financial science, copula functions are frequently used instead of correlation coefficients to model joint price behaviour, because of the possibility to link the marginal distributions on multifarious ways. By now, agricultural science makes less use of this method. This research uses the concept of “partly nested Archimedean copula” to model the relationship between different crop yields and compares it with a correlation based approach. The analysis focuses the differences of the approaches in the context of production planning and the use of weather derivatives.
A Computationally Efficient and Robust Implementation of the Continuous-Discrete Extended Kalman Filter

We present a novel numerically robust and computationally efficient extended Kalman filter for state estimation in nonlinear continuous-discrete stochastic systems. The resulting differential equations for the mean-covariance evolution of the nonlinear stochastic continuous-discrete time systems are solved efficiently using an ESDIRK integrator with sensitivity analysis capabilities. This ESDIRK integrator for the mean- covariance evolution is implemented as part of an extended Kalman filter and tested on a PDE system. For moderate to large sized systems, the ESDIRK based extended Kalman filter for nonlinear stochastic continuous-discrete time systems is more than two orders of magnitude faster than a conventional implementation. This is of significance in nonlinear model predictive control applications, statistical process monitoring as well as grey-box modelling of systems described by stochastic differential equations.
Fast Learning Algorithm for Fuzzy Inference Systems using Vector Quantization

It is known that learning methods of fuzzy inference systems using vector quantization (VQ) and steepest descend method (SDM) are superior in terms of the number of rules. However, they need a great deal of learning time. The cause could be that both of VQ and SDM perform only local searches. On the other hand, it has been shown that a learning method of radial basis function (RBF) networks using VQ and generalized inverse method (GIM) is much fast. In this paper, we propose a new learning method using VQ, GIM and SDM. The method iterates three stages in the outer loop of the algorithm. The first stage adjust the fuzzy rule arrangement by using VQ, the second one determines the weights of fuzzy rules by using GIM, and the third one updates both of the rule arrangement and the weights. In order to demonstrate the validity of the proposed method, numerical simulations for function approximation and pattern classification problems are performed. Specifically, it is shown that the proposed method reduces the learning time to about one-tenth compared to conventional methods in function approximation problem.
Analysis of Energy Consumption of Deduplication in Storage Systems

Energy efficiency of storage system is an important research topic as it largely affects the energy consumption of data centers. Although the technology of deduplication can save resources in storage systems, it cannot always achieve good energy efficiency. In this paper, we propose an energy consumption model for storage systems. In addition, an energy-aware backup strategy has been designed for backup tasks to achieve the balance of the process in terms of energy consumption and deduplication efficiency. To validate the model and the strategy, we introduce an energy-aware disk simulation framework and implement it by extending Disk Sim that is widely used for storage research.
Selection of Reference Genes for Quantitative Real-Time PCR in Bamboo (Phyllostachys edulis)

Background The Moso bamboo (Phyllostachys edulis) is one of the most important forestry resources and plays essential ecological roles in southern China. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression data related to the unique traits of Moso bamboo will undoubtedly follow. Reverse transcription quantitative real-time PCR ((RT-)qPCR) is a widely used method for gene expression analysis. A necessary prerequisite of exact and reliable data is the accurate choice of reference genes. Result In this study, 14 candidate reference genes were chosen, and their expression levels were assessed by (RT-)qPCR in a set of six tissue samples (root, stem, mature stem, leaf, flower, and leaf sheath) and at two developmental stages (before and after flowering) in bamboo specimens obtained in three locations. The stability and suitability of the candidate reference genes were validated using the geNorm, NormFinder and BestKeeper programs. The results showed that TIP41 and NTB were suitable reference genes across all the tissues and at the different developmental stages examined in this study. While the expression of the NTB, TIP41 and UBQ were the mostly stable in different plant tissues samples, the expression of the TIP41, NTB and CAC were ranked the most stable in bamboo plants at various developmental stages. AP2-like gene was further assessed by using the reference genes TIP41 and NTB in comparison to ACT. Significant difference of the expression profile of AP2-like demonstrated the importance of choosing adequate reference genes in bamboo. Conclusion TIP41 and NTB were found to be homogeneously expressed and were adequate for normalization purposes, showing equivalent transcript levels in different samples. They are therefore the recommended reference genes for measuring gene expression in P. edulis.
Cytoplasmic foci are sites of mRNA decay in human cells

Understanding gene expression control requires defining the molecular and cellular basis of mRNA turnover. We have previously shown that the human decapping factors hDcp2 and hDcp1a are concentrated in specific cytoplasmic structures. Here, we show that hCcr4, hDcp1b, hLsm, and rck/p54 proteins related to 5′–3′ mRNA decay also localize to these structures, whereas DcpS, which is involved in cap nucleotide catabolism, is nuclear. Functional analysis using fluorescence resonance energy transfer revealed that hDcp1a and hDcp2 interact in vivo in these structures that were shown to differ from the previously described stress granules. Our data indicate that these new structures are dynamic, as they disappear when mRNA breakdown is abolished by treatment with inhibitors. Accumulation of poly(A)+ RNA in these structures, after RNAi-mediated inactivation of the Xrn1 exonuclease, demonstrates that they represent active mRNA decay sites. The occurrence of 5′–3′ mRNA decay in specific subcellular locations in human cells suggests that the cytoplasm of eukaryotic cells may be more organized than previously anticipated.
Soy, Soy Foods and Their Role in Vegetarian Diets

Soy is a basic food ingredient of traditional Asian cuisine used for thousands of years. In Western countries, soybeans have been introduced about a hundred years ago and recently they are mainly used for surrogate foods production. Soy and soy foods are common nutritional solutions for vegetarians, due to their high protein content and versatility in the production of meat analogues and milk substitutes. However, there are some doubts about the potential effects on health, such as the effectiveness on cardiovascular risk reduction or, conversely, on the possible disruption of thyroid function and sexual hormones. The soy components that have stimulated the most research interest are isoflavones, which are polyphenols with estrogenic properties highly contained in soybeans. In this review, we discuss the characteristics of soy and soy foods, focusing on their nutrient content, including phytoestrogens and other bioactive substances that are noteworthy for vegetarians, the largest soy consumers in the Western countries. The safety of use will also be discussed, given the growing trend in adoption of vegetarian styles and the new soy-based foods availability.
Free immunoglobulin light‐chain serum levels in the follow‐up of patients with monoclonal gammopathies: Correlation with 24‐hr urinary light‐chain excretion

In patients with light‐chain myeloma or primary AL‐amyloidosis, 24‐hr light‐chain excretion in the urine is considered an essential marker of the tumor mass. However, 24‐hr urine collection and analysis may be cumbersome and prone to inaccuracy. Recently, a sensitive immunonephelometric assay for immunoglobulin free light chains (FLC) in the serum was developed. We sought to determine whether the serum level of monoclonal FLC could be used as an indicator of urinary excretion and disease evolution. Seven patients with light‐chain myeloma and AL‐amyloidosis were studied, all of which had a monoclonal FLC that could be detected in the urine using standard methods. In four of these patients, follow‐up revealed a remarkable correlation between FLC serum levels and daily urinary excretions. The ratio of serum level to urinary light‐chain excretion, although stable in a given patient, was extremely variable between patients. In the three remaining cases featuring hardly measurable amounts of light chain in the urine, the serum FLC assay proved sensitive enough for correlation with clinical events. Thus, immunonephelometric measurement of serum FLCs is a reliable method for the follow‐up of patients with light‐chain secreting monoclonal gammopathies. Am. J. Hematol. 75:246–248, 2004. © 2004 Wiley‐Liss, Inc.
Low Confinement Loss Photonic Crystal Fiber (PCF) With Flat Dispersion over C-Band

A new structure of low confinement loss with flat dispersion PCF over C-band is proposed and analysed by full vector finite element method. A solid core PCF has been designed with circular air-holes of different diameters and the background index are calculated from Sellmeier equation. From the results it is confirmed that the proposed design finds application in communication with its extremely low confinement loss and flat dispersion over the Cband. Within the wavelength band 1. 5 μm to 1. 6 μm the fast axis mode vanishes leaving single polarization.
Venture from the Interior—Herpesvirus pUL31 Escorts Capsids from Nucleoplasmic Replication Compartments to Sites of Primary Envelopment at the Inner Nuclear Membrane

Herpesviral capsid assembly is initiated in the nucleoplasm of the infected cell. Size constraints require that newly formed viral nucleocapsids leave the nucleus by an evolutionarily conserved vescular transport mechanism called nuclear egress. Mature capsids released from the nucleoplasm are engaged in a membrane-mediated budding process, composed of primary envelopment at the inner nuclear membrane and de-envelopment at the outer nuclear membrane. Once in the cytoplasm, the capsids receive their secondary envelope for maturation into infectious virions. Two viral proteins conserved throughout the herpesvirus family, the integral membrane protein pUL34 and the phosphoprotein pUL31, form the nuclear egress complex required for capsid transport from the infected nucleus to the cytoplasm. Formation of the nuclear egress complex results in budding of membrane vesicles revealing its function as minimal virus-encoded membrane budding and scission machinery. The recent structural analysis unraveled details of the heterodimeric nuclear egress complex and the hexagonal coat it forms at the inside of budding vesicles to drive primary envelopment. With this review, I would like to present the capsid-escort-model where pUL31 associates with capsids in nucleoplasmic replication compartments for escort to sites of primary envelopment thereby coupling capsid maturation and nuclear egress.
Concrete syntax for objects: domain-specific language embedding and assimilation without restrictions

Application programmer's interfaces give access to domain knowledge encapsulated in class libraries without providing the appropriate notation for expressing domain composition. Since object-oriented languages are designed for extensibility and reuse, the language constructs are often sufficient for expressing domain abstractions at the semantic level. However, they do not provide the right abstractions at the syntactic level. In this paper we describe MetaBorg, a method for providing concrete syntax for domain abstractions to application programmers. The method consists of embedding domain-specific languages in a general purpose host language and assimilating the embedded domain code into the surrounding host code. Instead of extending the implementation of the host language, the assimilation phase implements domain abstractions in terms of existing APIs leaving the host language undisturbed. Indeed, MetaBorg can be considered a method for promoting APIs to the language level. The method is supported by proven and available technology, i.e. the syntax definition formalism SDF and the program transformation language and toolset Stratego/XT. We illustrate the method with applications in three domains: code generation, XML generation, and user-interface construction.
Software Security Through Open Source

The last few years have shown a worldwide rise in the attention for, and ac-tual use of, open source software (OSS), most notably of the operating systemLinuxandvariousapplicationsrunningontopofit. Variousmajorcompaniesand governments are adopting OSS. As a result, there are many publicationsconcerningitsadvantagesanddisadvantages. Theongoingdiscussionscoverawiderangeoftopics, suchasWindowsversusLinux, costissues, intellectualpropertyrights, developmentmethods, etc. Herewewishtofocusonsecurity
Luzzu -- A Framework for Linked Data Quality Assessment

The increasing variety of Linked Data on the Web makes it challenging to determine the quality of this data, and subsequently to make this information explicit to data consumers. Despite the availability of a number of tools and frameworks to assess Linked Data Quality, the output of such tools is not suitable for machine consumption, and thus consumers can hardly compare and rank datasets in the order of fitness for use. This paper describes Luzzu, a framework for Linked Data Quality Assessment. Luzzu is based on four major components: (1) an extensible interface for defining new quality metrics, (2) an interoperable, ontology-driven back-end for representing quality metadata and quality problems that can be reused within different semantic frameworks, (3) a scalable stream processor for data dumps and SPARQL endpoints, and (4) a customisable ranking algorithm taking into account user-defined weights. We show that Luzzu scales linearly against the number of triples in a dataset. We also demonstrate the applicability of the Luzzu framework by evaluating and analysing a number of statistical datasets with regard to relevant metrics.
13 Game Lenses for Designing Diverse Interactive Jogging Systems

HCI is increasingly interested in designing technology for being physically active, and in many cases focuses on jogging. We find that many current approaches seem to view jogging only through a lens of athletic performance. However, jogging is multifaceted, yet there is so far no collated list of alternative lenses through which jogging could be viewed at by designers. In this paper, we draw on game design thinking to articulate 13 lenses through which designers can examine jogging. These 13 lenses are derived from related work and our combined experience of having designed and studied three different jogging systems. The lenses enable a structured articulation of key opportunities that interactive technology offers for jogging designers. With our work, we aim to support designers who want to create diverse interactive jogging systems so that more people can profit from the many benefits of jogging.
Patterns of Congestion Collapse

In this paper we consider the potential for congestion collapse in a range of network scenarios. In particular, we are interested in the effect of the topology, the scheduling discipline (FIFO or FQ scheduling), the level of statistical multiplexing, the traffic characteristics, and other factors. We consider topologies more complex than a single congested link, or a single string of congested links. This paper first shows that it is possible to have high equilibrium loss rates with rational greedy senders sharing a FIFO link or with greedy senders sharing an FQ link with bursty cross-traffic. We then consider specific topologies with a range of senders to calculate steady-state packet loss rates and derive the goodput of the congested links. In particular, we find some scenarios where goodput is higher with FQ scheduling, and other scenarios where goodput is higher with FIFO scheduling.
Fiber Optic Projection-Imaging System for Shape Measurement in Confined Space

A fiber-based projection-imaging system is proposed for shape measurement in confined space. Owing to the flexibility of imaging fibers, the system can be used in special scenarios that are difficult for conventional experimental setups. Three experiments: open space, closed space, and underwater are designed to demonstrate the strength and weakness of the system. It is shown that when proper alignment is possible, relatively high accuracy can be achieved; the error is less than 2% of the overall height of a specimen. In situations where alignment is difficult, significantly increased error is observed. The error is in the form of gross-scale geometrical distortion; for example, flat surface is reconstructed with curvature. In addition, the imaging fibers may introduce fine-scale noise into phase measurement, which has to be suppressed by smoothing filters. Based on results and analysis, it is found that although a fiber-based system has its unique strength, existing calibration and processing methods for fringe patterns have to be modified to overcome its drawbacks so as to accommodate wider applications.
A visual odometer without 3 D reconstruction for aerial vehicles . Applications to building inspection *

This paper presents a vision-based method to estimate the *real motion of a single camera from views of a planar patch. Projective techniques allow to estimate camera motion from pixel space apparent motion without explicit 3-D reconstruction. In addition, the paper will present the HELINSPEC project, the framework where the proposed method has been tested, and will detail some applications in external building inspection that make use of the proposed techniques. Index Terms – feature matching, homography, visual odometer, UAV, building inspection.