Miracle-dz/UniFAR-FTUs huggingface dataset:
Software tools for breast cancer detection in positron emission mammography images

: Positron Emission Mammography (PEM) is a novel imaging technology utilizing a dedicated Positron Emission Breast scanner. Two detectors in a configuration that resembles a conventional mammography (MG) machine cover a 250x120x200 mm 3 volume, yielding 3D images of the breast, which is fixated be-tween the detectors, but not compressed. The procedure depends on the administration of a radioactive contrast agent, 18 F FDG, as used in common whole body PET scans. Clinical studies showed the equivalent sensitivity and superior specificity of PEM regardless of hormonal status, breast density, and other factors hampering MG and MRI. Yet, due to the novelty of the imaging modality, no software support besides basic viewing and measurement capabilities exists, and common PET software is not tailored to the specific tasks in PEM image analysis. We propose algorithms and prototypical implementations for the tasks of automatic background estimation, lesion detection, lesion volumetry, and lesion measurements.
Patient outcomes following surgical management of multinodular goiter

Background: the difference in the risk of thyroid malignancy for patients with multinodular goiter (MNG) and solitary nodular goiter (SNG) remains controversial. Although total thyroidectomy (TT) is the current preferred surgical option for MNG, permanent hypothyroidism in these patients may be a concern. Therefore, we discuss whether nontotal thyroidectomy is a reasonable alternative surgical option. Methods: A retrospective cohort study was performed for 1598 consecutive patients who underwent thyroid surgery for nodular goiter between January 2007 and December 2012. Numerous clinical parameters were collected and analyzed. Results: We reviewed 795 patients with MNG and 803 patients with SNG. The prevalence of malignancy on final pathology was significantly higher in the patients with MNG than in the patients with SNG (15.6% vs 10.1%, P = 0.001). However, a multivariate analysis revealed that this difference was insignificant (P = 0.50). Papillary carcinoma was the predominant type in both groups, but papillary microcarcinoma was more frequently found (41.1%) in the patients with MNG. The only multifocal cancers were of the papillary carcinoma histologic type, and the incidence of multifocal papillary carcinoma was significantly higher in the patients with MNG (23.4% vs 7.4%, P = 0.005). Reoperation was not required for the patients who underwent TT for goiter recurrence or incidental carcinoma. The overall rate of recurrence following nontotal thyroidectomy was 12.2%. Among the patients who underwent reoperation for goiter recurrence, 2 (20.0%) were complicated with permanent hypoparathyroidism. Among the patients who underwent a nontotal bilateral thyroidectomy, an average of 56.5% had permanent hypothyroidism. Conclusions: Multinodularity does not increase the risk of thyroid malignancy. However, patients with MNG who develop papillary carcinoma are at an increased risk of cancer multifocality. If a patient can tolerate lifelong thyroid hormone replacement, TT is the preferred surgical option because it helps avoid reoperation and the associated complications. Nontotal bilateral thyroidectomy does not ensure the preservation of thyroid hormone function.
Performance Analysis of routing protocol in Mobile Ad Hoc Network using NS-2

The MANET routing protocols DSDV, DSR and AODV are the most promising routing protocols. They can be used in MANET to route packets between mobile nodes. The main objective of this paper comparing the performance of DSDV, DSR and AODV routing protocols under different performance metrics like Throughput, Packet delivery ratio, Path optimality, Packets Delay (Jitter), Packets lost, etc. This paper also shows the performance results of simulation done under different network conditions.
Integrating the Physical and Link Layers in Modeling the Wireless Ad Hoc Networking MAC Protocol , Synchronous Collision Resolution

Providing a set of protocols that will support the demands of mobile wireless ad hoc networking is fraught with many challenges. Despite over 30 years of research and effort, ad hoc networking still remains a field of research rather than a field of practice. Many of these challenges, however, are created by the use of an inappropriate paradigm to define the network’s behavior. To date, the bulk of the research in this area has used a wired paradigm. We propose a new wireless paradigm that we believe is more suitable. The significance of the paradigm is that the wired paradigm tends to promote research in routing and higher layer protocols as a result of over simplifying the behavior of the link and physical layers. The wireless paradigm reveals that most of the networking functionality needs to be implemented at the link and physical layers. In this paper, we contrast the different paradigms and explain how the protocol, Synchronous Collision Resolution (SCR), provides a framework for implementing algorithms that will solve the challenges of ad hoc networking according to the wireless paradigm. To do research in this area and to ultimately answer critics’ concerns about the impact of the unreliable physical layer on the performance of SCR, has required us to make a sophisticated model of the physical layer. We describe how we implemented such a model using OPNET’s Modeler environment.
Nonstandard Hybrid and Crossover Design With Branch-Line Structures

In this paper, we tried to use a symbolic math function of Matlab to derive theoretical S-parameters of a general branch-line structure; and we then managed to obtain design equations for 90°, 180° hybrids, and crossovers with the derived S-parameter expressions. We found that we can obtain several types of useful configurations for hybrid and crossover design by varying branch-line lengths of the structure. Besides standard designs, more interesting nonstandard 90°, 180° hybrids, and crossovers can be designed with suggested configurations of the design equations. Several example designs were built and tested; what is more, a nonstandard combiner/divider working on 5.8-7.2 GHz was designed to provide compact size and lower insertion loss for high-power very small aperture terminal amplifiers.
Caspase-8-mediated PAR-4 cleavage is required for TNFα-induced apoptosis

The tumor suppressor protein prostate apoptosis response-4 (PAR-4) is silenced in a subset of human cancers and its down-regulation serves as a mechanism for cancer cell survival following chemotherapy. PAR-4 re-expression selectively causes apoptosis in cancer cells but how its pro-apoptotic functions are controlled and executed precisely is currently unknown. We demonstrate here that UV-induced apoptosis results in a rapid caspase-dependent PAR-4 cleavage at EEPD131G, a sequence that was preferentially recognized by caspase-8. To investigate the effect on cell growth for this cleavage event we established stable cell lines that express wild-type-PAR-4 or the caspase cleavage resistant mutant PAR-4 D131G under the control of a doxycycline-inducible promoter. Induction of the wild-type protein but not the mutant interfered with cell proliferation, predominantly through induction of apoptosis. We further demonstrate that TNFα-induced apoptosis leads to caspase-8-dependent PAR-4-cleavage followed by nuclear accumulation of the C-terminal PAR-4 (132-340) fragment, which then induces apoptosis. Taken together, our results indicate that the mechanism by which PAR-4 orchestrates the apoptotic process requires cleavage by caspase-8.
The classification of hydrologically homogeneous regions

Abstract With the operation and maintenance of streamgauging networks in many developing countries coming under increasing pressure through lack of funds and suitably trained personnel, greater reliance must be placed on procedures for transferring information from gauged to ungauged catchment areas. These approaches to generalizing hydrological variables, such as the quantiles of the frequency distributions of floods and low flows, are collectively referred to as regionalization methods. An important feature of these methods is the demarcation of hydrologically homogeneous regions. The latter may be regarded as an example of the wider problem of classification of data sets, for which a variety of modern informatic tools, such as artificial neural networks and fuzzy sets, may be invoked. Application of examples of these techniques to flood data for the southwest of England and Wales has demonstrated that classes may be defined by Representative Regional Catchments (RRCs), whose characteristics are hydrolo.
Multiple Alignment with Hidden Markov Models

Multiple alignment of sequences is an important problem in bioinformatics. For example, multiple alignment of proteins belonging to the same family can provide valuable information for the common protein structure. Looking at a multiple alignment one can identify patterns which are not obvious if one looks at just pairwise alignments between members of the family. Traditional alignment schemes first choose a scoring matrix and gap penalties and then use dynamic programming which gives exact result in O(N) operations for two sequences of length N. For multiple alignment of K sequences dynamic programming requires O(N) operations, which is exponential in K. Therefore the algorithm is not feasible for multiple alignment of more than a few sequences. On the other hand, protein families often contain hundreds of sequences. To avoid the problem various heuristic algorithms were introduced. However, it is often the case that the solution to a multiple alignment problem depends strongly on the scoring scheme. This poses the question of how to choose the most biologically relevant one. Another very important issue is that the scoring matrices and gap penalties are assumed to be independent of position along the sequence, while gene families often exhibit regions which are highly conserved and regions which are highly variable. In order to obtain the most biologically relevant multiple alignment these differences should be taken into account. If we want to construct multiple alignments based only on primary structure information, the variations of scoring matrices and gap penalties should be deduced from the sequences themselves. Hidden Markov Models (HMMs) are an implementation of the idea that the scoring parameters should guide the multiple alignment as much as the alignment should determine the scoring parameters. A Hidden Markov Model (HMM), λ, is a stochastic machine for generating (amino acid) sequences. Different sequences are generated with different probability. A sequence S is generated with probability P (S|λ). The goal is: Given an universe, Λ, of HMMs to chose the member, λ∗, which maximizes ∏ k=1.K P (Sk|λ), where S1, . , Sk are the sequences we try to align. The procedure of choosing λ∗ can be thought of as training a HMM using training set {S1, . , SK}. This is analogous to neural networks. The hope is that, after the training, the model have captured the essence of “what it means to be a member of this particular protein family”. If so, λ∗ will preferably generate amino acid sequences which belong to the family, i.e. sequences that exhibit the same
Influences of Frame Incongruence on Information Security Policy Outcomes: An Interpretive Case Study

Despite the significant resources organizations devote to information security policies, the policies rarely produce intended outcome. Prior research has sought to explain motivations for non-compliance and suggested approaches for motivating employees for compliance using theories largely derived from psychology. However, the socio-cognitive structures that shape employees' perceptions of the policies and how they influence policy outcomes have received only modest attention. In this study, the authors draw on the socio-cognitive theory of frames and on literature on information security policies in order to suggest a theoretical and analytical concept of Information Security Policy Frames of Reference (ISPFOR). The concept is applied as a sensitizing device, in order to systematically analyze and interpret how the perceptions of policies are shaped by the frames and how they influence policy outcomes. The authors apply the sensitizing device in an interpretive case study conducted at a large multinational internet service provider. The authorsâ€™ findings suggest the frames shape the perceptions and can provide a socio-cognitive explanation for unanticipated policy outcomes. Implications for research and practice are discussed.
Structure of the Madden-Julian Oscillation in the Superparameterized CAM

Abstract The detailed dynamic and thermodynamic space–time structures of the Madden–Julian oscillation (MJO) as simulated by the superparameterized Community Atmosphere Model version 3.0 (SP-CAM) are analyzed. Superparameterization involves substituting conventional boundary layer, moist convection, and cloud parameterizations with a configuration of cloud-resolving models (CRMs) embedded in each general circulation model (GCM) grid cell. Unlike most GCMs that implement conventional parameterizations, the SP-CAM displays robust atmospheric variability on intraseasonal space and time (30–60 days) scales. The authors examine a 19-yr SP-CAM simulation based on the Atmospheric Model Intercomparison Project protocol, forced by prescribed sea surface temperatures. Overall, the space–time structures of MJO convective disturbances are very well represented in the SP-CAM. Compared to observations, the model produces a similar vertical progression of increased moisture, warmth, and heating from the boundary layer t.
Overtreatment in couples with unexplained infertility.

STUDY QUESTION What is the percentage of overtreatment, i.e. fertility treatment started too early, in couples with unexplained infertility who were eligible for tailored expectant management? SUMMARY ANSWER Overtreatment occurred in 36% of couples with unexplained infertility who were eligible for an expectant management of at least 6 months. WHAT IS KNOWN ALREADY Prognostic models in reproductive medicine can help to identify infertile couples that would benefit from fertility treatment. In couples with unexplained infertility with a good chance of natural conception within 1 year, based on the Hunault prediction model, an expectant management of 6-12 months, as recommended in international fertility guidelines, prevents unnecessary treatment. STUDY DESIGN, SIZE, DURATION A retrospective cohort study in 25 participating clinics, with follow-up of all couples who were seen for infertility in 2011-2012. PARTICIPANTS/MATERIALS, SETTING, METHODS In all, 9818 couples were seen for infertility in the participating clinics. Couples were eligible to participate if they were diagnosed with unexplained infertility and had a good prognosis of natural conception (>30%) within 1 year based on the Hunault prediction model. Data to assess overtreatment were collected from medical records. Multilevel regression analyses were performed to investigate associations of overtreatment with patient and clinic characteristics. MAIN RESULTS AND THE ROLE OF CHANCE Five hundred and forty-four couples eligible for expectant management were included in this study. Among these, overtreatment, i.e. starting medically assisted reproduction within 6 months, occurred in 36%. The underlying quality indicators showed that in 34% no prognosis was calculated and that in 42% expectant management was not recommended. Finally, 16% of the couples for whom a correct recommendation of expectant management for at least 6 months was made, started treatment within 6 months anyway. Overtreatment was associated with childlessness, higher female age and a longer duration of infertility. No associations between overtreatment and clinic characteristics were found. LIMITATIONS, REASONS FOR CAUTION The response rate was low compared with other fertility studies. Evaluation of possible selection bias showed that responders had a higher socio-economic status than non-responders. WIDER IMPLICATIONS OF THE FINDINGS Our findings show that developing and publishing guideline recommendations on tailored expectant management (TEM) is not enough and that overtreatment still occurs frequently. Future research should focus on tailored efforts to implement guideline recommendations on TEM. STUDY FUNDING/COMPETING INTERESTS Supported by Netherlands Organisation for Health Research and Development (ZonMW). ZonMW had no role in designing the study, data collection, analysis and interpretation of data or writing of the report. Competing interests: none. TRIAL REGISTRATION NUMBER www.trialregister. nl NTR3405.
Plant Leaf Segmentation Using Non Linear K means Clustering

This paper presents a new approach for plant leaf image segmentation by applying non linear k means algorithm. The segmentation process presents a clustering mechanism for high resolution images in order to improve the precision and processing time. Plant image, however, always contain complicated background objects that interfere with the examination process and must be removed from the image prior to species classification. K means clustering is applied at the first level of segmentation to detect the structure of the plant leaf. At the second level Sobel edge detector is used to remove the unwanted segments to extract the exact part of the leaf shape. The performance of the proposed method is compared with other traditional methods to analyze the efficiency of the system. Experimental result shows that this new approach simplifies the process to extract shape related features and measurements of the leaf for higher accuracy.
Towards common European health policies: what are the implications for the Nordic countries?

Health care is an area that remains formally outside the competence of the EU. Despite this, the union’s influence on national health care policies has increased substantially over the past decade. In a series of rulings, the European Court of Justice (ECJ) established a de facto system of patient rights, which, under certain conditions, entitle European citizens to receive health care in other member states at the expense of the social insurance system of their home country. This undermines the autonomy of the member states in the area of health, a key sector in national welfare systems. In 2008, the Commission proposed a new directive on patients’ rights which builds directly on the ECJ rulings, thus consolidating politically the legal precedent set by the Court. The ECJ Court rulings have also spurred the initiation of a so-called OMC process in the area of health care, whereby the member states commit themselves to policy harmonization on a voluntary basis. In this paper, we review the contents of emerging EU policies in the area of health and discuss their implications for the Nordic health care systems. A central question is whether any coherent, common European policy may be discerned and, if so, how it will affect health care systems of the Nordic type, which are tax-based and universalistic in orientation?
An Efficient MCMC Method for Uncertainty Quantification in Inverse Problems

The connection between Bayesian statistics and the technique of regularization for inverse problems has been given significant attention in recent years. For example, Bayes’ law is frequently used as motivation for variational regularization methods of Tikhonov type. In this setting, the regularization function corresponds to the negative-log of the prior probability density; the fit-to-data function corresponds to the negative-log of the likelihood; and the regularized solution corresponds to the maximizer of the posterior density, known as the maximum a posteriori (MAP) estimator. While a great deal of attention has been focused on the development of techniques for efficient computation of MAP estimators (regularized solutions), less explored is the problem of uncertainty quantification, which corresponds to the problem of determining the shape, at least to some degree, of the posterior density in high probability regions. One way to do this is to sample from the posterior density using a Markov chain Monte Carlo (MCMC) method. In this paper, we present an MCMC method for use on linear inverse problems with independent and identically distributed Gaussian noise and Gaussian priors (quadratic regularization functions). From the MCMC samples, an estimator (regularized solution), and measures of variability in the estimator, are computed. Additionally, samples of the noise and prior precision parameters are computed, making regularization parameter selection unnecessary.
Interference models for heterogenous sources

Interference modeling is central to the analysis of many interference limited systems. The aggregate interference due to many individual interferers is often very difficult to characterize exactly, especially when lognormal shadowing and path loss is considered. Some results are available for homogeneous sources where the individual components have the same distribution, but many more detailed studies involve heterogeneous sources. Hence, in this paper we build upon previous models for homogeneous sources to develop three general purpose approaches to modeling the aggregate interference from heterogeneous sources which include both shadowing and path-loss. These models are the inverse gamma, inverse generalized gamma and extreme value distributions. These models are motivated by prior work as well as by three distinct interference scenarios relating to cognitive radio systems, digital television and femtocells. The models are fitted to these wide ranging examples and numerical results show good agreement, both for interference and SINR distributions.
Correcting Flicker in Color Motion Pictures

Despite active research work in the field of flicker correction, all the published work to date only deals with black and white motion pictures. In this paper, we will take flicker correction into the color space and propose a method to solve the flicker correction problem in color motion pictures. The method is based on a simplified flicker parameter model developed by us in [5] which was originally used for flicker correction in black and white motion pictures. Test results show that the proposed method is very effective in correcting flicker-damaged color films.