LLukas22/scidocs huggingface dataset:
Ovarian cancer prediction in adnexal masses using ultrasound-based logistic regression models: a temporal and external validation study by the IOTA group.

OBJECTIVES
The aims of the study were to temporally and externally validate the diagnostic performance of two logistic regression models containing clinical and ultrasound variables in order to estimate the risk of malignancy in adnexal masses, and to compare the results with the subjective interpretation of ultrasound findings carried out by an experienced ultrasound examiner ('subjective assessment').


METHODS
Patients with adnexal masses, who were put forward by the 19 centers participating in the study, underwent a standardized transvaginal ultrasound examination by a gynecologist or a radiologist specialized in ultrasonography. The examiner prospectively collected information on clinical and ultrasound variables, and classified each mass as benign or malignant on the basis of subjective evaluation of ultrasound findings. The gold standard was the histology of the mass with local clinicians deciding whether to operate on the basis of ultrasound results and the clinical picture. The models' ability to discriminate between malignant and benign masses was assessed, together with the accuracy of the risk estimates.


RESULTS
Of the 1938 patients included in the study, 1396 had benign, 373 had primary invasive, 111 had borderline malignant and 58 had metastatic tumors. On external validation (997 patients from 12 centers), the area under the receiver-operating characteristics curve (AUC) for a model containing 12 predictors (LR1) was 0.956, for a reduced model with six predictors (LR2) was 0.949 and for subjective assessment was 0.949. Subjective assessment gave a positive likelihood ratio of 11.0 and a negative likelihood ratio of 0.14. The corresponding likelihood ratios for a previously derived probability threshold (0.1) were 6.84 and 0.09 for LR1, and 6.36 and 0.10 for LR2. On temporal validation (941 patients from seven centers), the AUCs were 0.945 (LR1), 0.918 (LR2) and 0.959 (subjective assessment).


CONCLUSIONS
Both models provide excellent discrimination between benign and malignant masses. Because the models provide an objective and reasonably accurate risk estimation, they may improve the management of women with suspected ovarian pathology.
An Empirical Investigation of Systematic Reviews in Software Engineering

BACKGROUND: Systematic Literature Reviews (SLRs) have gained significant popularity among software engineering (SE) researchers since 2004. Several researchers have also been working on improving the scientific and technological support for SLRs in SE. We argue that there is also an essential need for evidence-based body of knowledge about different aspects of the adoption of SLRs in SE. OBJECTIVE: The main objective of this research is to empirically investigate the adoption and use of SLRs in SE research from various perspectives. METHOD: We used multi-method approach as it is based on a combination of complementary research methods which are expected to compensate each others' limitations. RESULTS: A large majority of the participants are convinced of the value of using a rigorous and systematic methodology for literature reviews. However, there are concerns about the required time and resources for SLRs. One of the most important motivators for performing SLRs is new findings and inception of innovative ideas for further research. The reported SLRs are more influential compared to the traditional literature reviews in terms of number of citations. One of the main challenges of conducting SLRs is drawing a balance between rigor and required effort. CONCLUSIONS: SLR has become a popular research methodology for conducting literature review and evidence aggregation in SE. There is an overall positive perception about this methodology. The findings provide interesting insights into different aspects of SLRs. We expect that the findings can provide valuable information to readers on what can be expected from conducting SLRs and the potential impact of such reviews.
Enterprise Risk Management Integrated framework for Cloud Computing

Enterprise Risk Management Integrated framework for Cloud Computing Dr. M. Suresh Babu Professor & Head, Department of Computer Applications, Madanapalle Institute of Technology & Science, Madanapalle, AP, India – 517325. A. Mahesh babu Research Scholar, Department of Computer Science & Technology, Sri Krishnadevaraya University, Anantapur – 515003, AP, India. M.Chandra Sekhar Research Scholar, Department of Computer Science & Technology, Sri Krishnadevaraya University, Anantapur – 515003, AP, India. -----------------------------------------------------------------------------ABSTRACT---------------------------------------------------The emergence of cloud computing is a fundamental shift towards new on-demand business models together with new implementation models for the applications portfolio, the infrastructure, and the data, as they are provisioned as virtual services using the cloud. These technological and commercial changes have an impact on current working practices. Businesses need to understand the impact of the new combinations of technology layers, and how they work together. A crucial part of this is analyzing and assessing the risks involved. In the evolution of computing technology, information processing has moved from mainframes to personal computers to server-centric computing to the Web. Today, many organizations are seriously considering adopting cloud computing, the next major milestone in technology and business collaboration. A supercharged version of delivering hosted services over the Internet, cloud computing potentially enables organizations to increase their business model capabilities and their ability to meet computing resource demands while avoiding significant investments in infrastructure, training, personnel, and software. In fall 2010, a Google executive testified before a U.S. congressional subcommittee that more than three million businesses worldwide were customers of its cloud service offerings. As with any new opportunity, cloud computing entails commensurate risks. It brings to organizations a different dimension of collaboration and human interaction, new organizational dependencies, faster resource fulfilment, and new business models.
Quantum Mechanical Metastability

We present a detailed discussion of some features of quantum mechanical metastability. We analyze the nature of decaying (quasistationary) states and the regime of validity of the exponencial law, as well as decays at finite temperature. We resort to very simple systems and elementary techniques to emphasize subtleties sometimes overlooked.
Analytical Solution to One-dimensional Advection-diffusion Equation with Several Point Sources through Arbitrary Time-dependent Emission Rate Patterns

Advection-diffusion equation and its related analytical solutions have gained wide applications in different areas. Compared with numerical solutions, the analytical solutions benefit from some advantages. As such, many analytical solutions have been presented for the advection-diffusion equation. The difference between these solutions is mainly in the type of boundary conditions, e.g. time patterns of the sources. Almost all the existing analytical solutions to this equation involve simple boundary conditions. Most practical problems, however, involve complex boundary conditions where it is very difficult and sometimes impossible to find the corresponding analytical solutions. In this research, first, an analytical solution of advection-diffusion equation was initially derived for a point source with a linear pulse time pattern involving constant-parameters condition (constant velocity and diffusion coefficient). Hence, using the superposition principle, the derived solution can be extended for an arbitrary time pattern involving several point sources. The given analytical solution was verified using four hypothetical test problems for a stream. Three of these test problems have analytical solutions given by previous researchers while the last one involves a complicated case of several point sources, which can only be numerically solved. The results show that the proposed analytical solution can provide an accurate estimation of the concentration; hence it is suitable for other such applications, as verifying the transport codes. Moreover, it can be applied in applications that involve optimization process where estimation of the solution in a finite number of points (e.g. as an objective function) is required. The limitations of the proposed solution are that it is valid only for constant-parameters condition, and is not computationally efficient for problems involving either a high temporal or a high spatial resolution.
CAD: an algorithm for citation-anchors detection in research papers

Citations are very important parameters and are used to take many important decisions like ranking of researchers, institutions, countries, and to measure the relationship between research papers. All of these require accurate counting of citations and their occurrence (in-text citation counts) within the citing papers. Citation anchors refer to the citation made within the full text of the citing paper for example: ‘[1]’, ‘(Afzal et al, 2015)’, ‘[Afzal, 2015]’ etc. Identification of citation-anchors from the plain-text is a very challenging task due to the various styles and formats of citations. Recently, Shahid et al. highlighted some of the problems such as commonality in content, wrong allotment, mathematical ambiguities, and string variations etc in automatically identifying the in-text citation frequencies. The paper proposes an algorithm, CAD, for identification of citation-anchors and its in-text citation frequency based on different rules. For a comprehensive analysis, the dataset of research papers is prepared: on both Journal of Universal Computer Science (J.UCS) and (2) CiteSeer digital libraries. In experimental study, we conducted two experiments. In the first experiment, the proposed approach is compared with state-of-the-art technique over both datasets. The J.UCS dataset consists of 1200 research papers with 16,000 citation strings or references while the CiteSeer dataset consists of 52 research papers with 1850 references. The total dataset size becomes 1252 citing documents and 17,850 references. The experiments showed that CAD algorithm improved F-score by 44% and 37% respectively on both J.UCS and CiteSeer dataset over the contemporary technique (Shahid et al. in Int J Arab Inf Technol 12:481–488, 2014). The average score is 41% on both datasets. In the second experiment, the proposed approach is further analyzed against the existing state-of-the-art tools: CERMINE and GROBID. According to our results, the proposed approach is best performing with F1 of 0.99, followed by GROBID (F1 0.89) and CERMINE (F1 0.82).
Randomized controlled trial of mindfulness-based stress reduction (MBSR) for survivors of breast cancer.

OBJECTIVES
Considerable morbidity persists among survivors of breast cancer (BC) including high levels of psychological stress, anxiety, depression, fear of recurrence, and physical symptoms including pain, fatigue, and sleep disturbances, and impaired quality of life. Effective interventions are needed during this difficult transitional period.


METHODS
We conducted a randomized controlled trial of 84 female BC survivors (Stages 0-III) recruited from the H. Lee Moffitt Cancer and Research Institute. All subjects were within 18 months of treatment completion with surgery and adjuvant radiation and/or chemotherapy. Subjects were randomly assigned to a 6-week Mindfulness-Based Stress Reduction (MBSR) program designed to self-regulate arousal to stressful circumstances or symptoms (n=41) or to usual care (n=43). Outcome measures compared at 6 weeks by random assignment included validated measures of psychological status (depression, anxiety, perceived stress, fear of recurrence, optimism, social support) and psychological and physical subscales of quality of life (SF-36).


RESULTS
Compared with usual care, subjects assigned to MBSR(BC) had significantly lower (two-sided p<0.05) adjusted mean levels of depression (6.3 vs 9.6), anxiety (28.3 vs 33.0), and fear of recurrence (9.3 vs 11.6) at 6 weeks, along with higher energy (53.5 vs 49.2), physical functioning (50.1 vs 47.0), and physical role functioning (49.1 vs 42.8). In stratified analyses, subjects more compliant with MBSR tended to experience greater improvements in measures of energy and physical functioning.


CONCLUSIONS
Among BC survivors within 18 months of treatment completion, a 6-week MBSR(BC) program resulted in significant improvements in psychological status and quality of life compared with usual care.
Reconstruction of Phase Space of Dynamical Systems Using Method of Time Delay

Selected elements of dynamical system (DS) theory approach to nonlinear time series analysis are introduced. Key role in this concept plays a method of time delay. The method enables us reconstruct phase space trajectory of DS without knowledge of its governing equations. Our variant is tested and compared with wellknown TISEAN package for Lorenz and Hénon systems. Introduction There are number of methods of nonlinear time series analysis (e.g. nonlinear prediction or noise reduction) that work in a phase space (PS) of dynamical systems. We assume that a given time series of some variable is generated by a dynamical system. A specific state of the system can be represented by a point in the phase space and time evolution of the system creates a trajectory in the phase space. From this point of view we consider our time series to be a projection of trajectory of DS to one (or more – when we have more simultaneously measured variables) coordinates of phase space. This view was enabled due to formulation of embedding theorem [1], [2] at the beginning of the 1980s. It says that it is possible to reconstruct the phase space from the time series. One of the most frequently used methods of phase space reconstruction is the method of time delay. The main task while using this method is to determine values of time delay τ and embedding dimension m. We tested individual steps of this method on simulated data generated by Lorenz and Hénon systems. We compared results computed by our own programs with outputs of program package TISEAN created by R. Hegger, H. Kantz, and T. Schreiber [3]. Method of time delay The most frequently used method of PS reconstruction is the method of time delay. If we have a time series of a scalar variable we construct a vector ( ) , ,..., 1 , N i t x i = in phase space in time ti as following: ( ) ( ) ( ) ( ) ( ) ( ) [ ], 1 ,..., 2 , , τ τ τ − + + + = m t x t x t x t x t i i i i i X where i goes from 1 to N – (m – 1)τ, τ is time delay, m is a dimension of reconstructed space (embedding dimension) and M = N – (m – 1)τ is number of points (states) in the phase space. According to embedding theorem, when this is done in a proper way, dynamics reconstructed using this formula is equivalent to the dynamics on an attractor in the origin phase space in the sense that characteristic invariants of the system are conserved. The time delay method and related aspects are described in literature, e.g. [4]. We estimated the two parameters—time delay and embedding dimension—using algorithms below. Choosing a time delay To determine a suitable time delay we used average mutual information (AMI), a certain generalization of autocorrelation function. Average mutual information between sets of measurements A and B is defined [5]:
Atorvastatin and fenofibrate have comparable effects on VLDL-apolipoprotein C-III kinetics in men with the metabolic syndrome.

OBJECTIVE
The metabolic syndrome (MetS) is characterized by insulin resistance and dyslipidemia that may accelerate atherosclerosis. Disturbed apolipoprotein (apo) C-III metabolism may account for dyslipidemia in these subjects. Atorvastatin and fenofibrate decrease plasma apoC-III, but the underlying mechanisms are not fully understood.


METHODS AND RESULTS
The effects of atorvastatin (40 mg/d) and fenofibrate (200 mg/d) on the kinetics of very-low density lipoprotein (VLDL)-apoC-III were investigated in a crossover trial of 11 MetS men. VLDL-apoC-III kinetics were studied, after intravenous d(3)-leucine administration using gas chromatography-mass spectrometry and compartmental modeling. Compared with placebo, both atorvastatin and fenofibrate significantly decreased (P<0.001) plasma concentrations of triglyceride, apoB, apoB-48, and total apoC-III. Atorvastatin, not fenofibrate, significantly decreased plasma apoA-V concentrations (P<0.05). Both agents significantly increased the fractional catabolic rate (+32% and +30%, respectively) and reduced the production rate of VLDL-apoC-III (-20% and -24%, respectively), accounting for a significant reduction in VLDL-apoC-III concentrations (-41% and -39%, respectively). Total plasma apoC-III production rates were not significantly altered by the 2 agents. Neither treatment altered insulin resistance and body weight.


CONCLUSIONS
Both atorvastatin and fenofibrate have dual regulatory effects on VLDL-apoC-III kinetics in MetS; reduced production and increased fractional catabolism of VLDL-apoC-III may explain the triglyceride-lowering effect of these agents.
Association between sleep apnea severity and blood coagulability: treatment effects of nasal continuous positive airway pressure

A prothrombotic state may contribute to the elevated cardiovascular risk in patients with obstructive sleep apnea (OSA). We investigated the relationship between apnea severity and hemostasis factors and effect of continuous positive airway pressure (CPAP) treatment on hemostatic activity. We performed full overnight polysomnography in 44 OSA patients (mean age 47±10 years), yielding apnea–hypopnea index (AHI) and mean nighttime oxyhemoglobin saturation (SpO2) as indices of apnea severity. For treatment, subjects were double-blind randomized to 2 weeks of either therapeutic CPAP (n=18), 3 l/min supplemental nocturnal oxygen (n=16) or placebo–CPAP (<1 cm H2O) (n=10). Levels of von Willebrand factor antigen (VWF:Ag), soluble tissue factor (sTF), D-dimer, and plasminogen activator inhibitor (PAI)-1 antigen were measured in plasma pre- and posttreatment. Before treatment, PAI-1 was significantly correlated with AHI (r=0.47, p=0.001) and mean nighttime SpO2 (r=−0.32, p=0.035), but these OSA measures were not significantly related with VWF:Ag, sTF, and D-dimer. AHI was a significant predictor of PAI-1 (R 2=0.219, standardized β=0.47, p=0.001), independent of mean nighttime SpO2, body mass index (BMI), and age. A weak time-by-treatment interaction for PAI-1 was observed (p=0.041), even after adjusting for age, BMI, pre-treatment AHI, and mean SpO2 (p=0.046). Post hoc analyses suggested that only CPAP treatment was associated with a decrease in PAI-1 (p=0.039); there were no changes in VWF:Ag, sTF, and D-dimer associated with treatment with placebo–CPAP or with nocturnal oxygen. Apnea severity may be associated with impairment in the fibrinolytic capacity. To the extent that our sample size was limited, the observation that CPAP treatment led to a decrease in PAI-1 in OSA must be regarded as tentative.
Diagnostic and prognostic value of serum antibodies against Pseudomonas aeruginosa in cystic fibrosis.

BACKGROUND
Eradication of Pseudomonas aeruginosa in patients with cystic fibrosis (CF) is possible if initiated early in the course of colonisation. To detect P aeruginosa as early as possible is therefore a major goal. This study was undertaken to validate a commercialised test for the detection of serum Pseudomonas antibodies in patients with CF.


METHODS
A representative cross sectional analysis of serum antibodies against three Pseudomonas antigens (alkaline protease, elastase, and exotoxin A) was performed in 183 patients with CF of mean age 16.7 years and FEV1 85.9% predicted. The results were correlated with microbiological results from the previous 2 years to calculate sensitivity, specificity, positive and negative predictive values. The following 2 years were assessed to determine prognostic predictive values.


RESULTS
A combination of all three tested antibodies yielded the best results with a sensitivity of 86%, specificity of 96%, and a positive predictive value of 97%. These values were higher if only patients in whom sputum cultures were available were considered (n = 76, sensitivity 95%, specificity 100%, positive predictive value 100%). The prognostic positive predictive value was high in intermittently infected patients (83%) but low in patients free of infection (33%), whereas the prognostic negative predictive value was high in patients free of infection (78%) and low in intermittently infected patients (58%).


CONCLUSIONS
Regular determination of serum antibodies may be useful in CF patients with negative or intermittent but not with positive P aeruginosa status. A rise in antibody titres indicates probable infection and eradication treatment may be initiated even in the absence of microbiological detection of P aeruginosa.
An approach for detecting, quantifying, and visualizing the evolution of a research field: A practical application to the Fuzzy Sets Theory field

This paper presents an approach to analyze the thematic evolution of a given research field. This approach combines performance analysis and science mapping for detecting and visualizing conceptual subdomains (particular themes or general thematic areas). It allows us to quantify and visualize the thematic evolution of a given research field. To do this, coword analysis is used in a longitudinal framework in order to detect the different themes treated by the research field across the given time period. The performance analysis uses different bibliometric measures, including the h-index, with the purpose of measuring the impact of both the detected themes and thematic areas. The presented approach includes a visualization method for showing the thematic evolution of the studied field. Then, as an example, the thematic evolution of the Fuzzy Sets Theory field is analyzed using the two most important journals in the topic: Fuzzy Sets and Systems and IEEE Transactions on Fuzzy Systems. © 2010 Elsevier Ltd. All rights reserved.
Max-margin Learning for Lower Linear Envelope Potentials in Binary Markov Random Fields

The standard approach to max-margin parameter learning for Markov random fields (MRFs) involves incrementally adding the most violated constraints during each iteration of the algorithm. This requires exact MAP inference, which is intractable for many classes of MRF. In this paper, we propose an exact MAP inference algorithm for binary MRFs containing a class of higher-order models, known as lower linear envelope potentials. Our algorithm is polynomial in the number of variables and number of linear envelope functions. With tractable inference in hand, we show how the parameters and corresponding feature vectors can be represented in a max-margin framework for efficiently learning lower linear envelope potentials.
Generative and incremental implementation for a scripting interface

Many systems may benefit from scripting support, but the implementation of it is seldom trivial, especially if the system has not originally been developed with scripting support in mind. In this paper we describe a generative, incremental process for creating an intuitive Python interface to a large, hierarchic COM library. The approach is illuminated with the original, real-life case study.