Miracle-dz/UniFAR-FTUs huggingface dataset:
CanPredict: a computational tool for predicting cancer-associated missense mutations

Various cancer genome projects are underway to identify novel mutations that drive tumorigenesis. While these screens will generate large data sets, the majority of identified missense changes are likely to be innocuous passenger mutations or polymorphisms. As a result, it has become increasingly important to develop computational methods for distinguishing functionally relevant mutations from other variations. We previously developed an algorithm, and now present the web application, CanPredict (http://www.canpredict.org/ or http://www.cgl.ucsf.edu/Research/genentech/canpredict/), to allow users to determine if particular changes are likely to be cancer-associated. The impact of each change is measured using two known methods: Sorting Intolerant From Tolerant (SIFT) and the Pfam-based LogR.E-value metric. A third method, the Gene Ontology Similarity Score (GOSS), provides an indication of how closely the gene in which the variant resides resembles other known cancer-causing genes. Scores from these three algorithms are analyzed by a random forest classifier which then predicts whether a change is likely to be cancer-associated. CanPredict fills an important need in cancer biology and will enable a large audience of biologists to determine which mutations are the most relevant for further study.
Dementia in Parkinson's Disease: A Clinical Review

Problem statement: Idiopathic Parkinson's Disease (PD) has being increasingly seen as a neuropsychiatric entity and no longer purely neurological, given the frequency and exuberance with which the psychiatric manifestations occurs. Approach: This review will focus on the epidemiology, clinical aspects, differential diagnosis with Alzheimer's Disease (AD) associated with parkinsonism, Dementia with Lewy Bodies (LBD), Progressive Supranuclear Palsy (PSP), Corticobasal Degeneration (CBD), Multiple System Atrophy (MSA), Vascular Parkinsonism and Normal Pressure Hydrocephalus (NPN), underlying mechanisms and treatment of dementia in PD. A literature review of the studies that investigated the dementia in PD was performed. Results: The dementia in PD has being increasingly recognized as a distinct nosological entity. Although specific etiologies for cognitive impairment remain unknown, a symptomatic treatment has been approved and strategies for early intervention are envisioned. Conclusion: Larger scale, placebo controlled clinical trials are needed to be explored in future studies to provide an evidence base to guide the management in dementia associated with PD.
One Political Economy, One Competitive Strategy?: Comparing Pharmaceutical Firms in Germany, Italy, and the UK

This book examines how firms adapt to the pressures of increasing international competition by testing the arguments on 'strategy specialization' proposed in the competitiveness literature in general, and by contributors to the 'varieties of capitalism' debate in particular. If different economies are characterized by distinct institutional arrangements, successful firms would be those that exploit the related comparative advantages and specialize in the competitive strategies facilitated by national institutions. One Political Economy, One Competitive Strategy? begins with an assessment of how many pharmaceutical firms in Germany, Italy, and the UK pursue strategies facilitated by national institutions governing the financial markets, antitrust activities, and the labour market. Quantitative analyses reveal that deviant firms, competing through institutionally unsupported strategies, outnumber conforming firms by far. Not only does this finding run counter to the expectations of the competitiveness literature, it brings up a whole new line of inquiry. How can firms compete through strategies that are not supported by national institutions? The book addresses this question and illustrates that firms do not necessarily exploit comparative institutional advantages, but that they can also circumvent institutional constraints. International markets and individual collaboration on a contractual basis allow firms to compete despite comparative institutional disadvantages. These findings suggest that trade liberalization does not lead to strategy specialization but to strategy diversification, depending on the inventiveness of entrepreneurs to develop individual approaches to compete.
Role models and trust in socio-political institutions : a case study in Eastern Germany, 1992 - 96

This paper discusses the development of trust in socio-political institutions on the part of youth in eastern Germany during the period 1992-96, with special emphasis on the effect of having parents as role model. The analysis is based on surveys of middle and high school students that were conducted by the authors in a county in Thuringia. A factor analysis of trust in a number of social and political institutions yielded a factor comprising five socio-political institutions that belong to the state sector and, for the most part, have a strong hierarchical structure: the military, police, legal system, public administration (but not the government proper), and parliament. Our multiple regression models (including parental role model, various political attitudes, evaluation of the economic situation, and stratification) showed that favorable attitudes towards unification and having parents as role model were the two most important determinants of having trust in socio-political institutions. The positive effects of these two variables on trust became stronger with growing temporal distance from unification during the early years of the transformation; the strength of the effects dropped slightly after 1994 but remained well above the 1992 level. These findings show that socialization variables are an important addition to situational and stratification factors in understanding the development of trust in socio-political institutions among eastern German youth.
Nutrient Sources and Transport in the Missouri River Basin, with Emphasis on the Effects of Irrigation and Reservoirs

Brown, Juliane B. , Lori A. Sprague, and Jean A. Dupree, 2011. Nutrient Sources and Transport in the Missouri River Basin, With Emphasis on the Effects of Irrigation and Reservoirs. Journal of the American Water Resources Association (JAWRA) 47(5):1034‐1060. DOI: 10.1111/j.1752‐1688.2011. 00584.x
Output-feedback stochastic nonlinear stabilization

We present the first result on global output-feedback stabilization (in probability) for stochastic nonlinear continuous-time systems. The class of systems that we consider is a stochastic counterpart of the broadest class of deterministic systems for which globally stabilizing controllers are currently available. Our controllers are "inverse optimal" and possess an infinite gain margin. The reader of the paper needs no prior familiarity with techniques of stochastic control.
Bayesian variable selection using cost-adjusted BIC, with application to cost-effective measurement of quality of health care

Summary of the RJMCMC cost-beneﬁt search results in the p=14 case. (B) Comparison of the utility and RJMCMC methods in how their best models trade oﬀ costand predictive accuracy AModel Cost Posterior probability PO 1k X 1 +X 2 +X 3 +X 4 +X 5 +X 6 +X 7 +X 12 9.0 0.453 1.00X 1 +X 2 +X 3 +X 4 +X 5 +X 7 +X 12 7.5 0.415 1.09X 1 +X 2 +X 3 +X 4 +X 5 +X 6 +X 12 8.0 0.054 8.40X 1 +X 2 +X 3 +X 4 +X 5 +X 6 +X 7 8.5 0.031 14.72Bp Method Model Cost Median devianceLS CV 14RJMCMCX 1 +X 2 +X 3 +X 4 +X 5 +X 6 +X 7 +X 12 9.0 1654 −0.329X 1 +X 2 +X 3 +X 4 +X 5 +X 7 +X 12 7.5 1676 −0.333Utility X 1 +X 3 +X 4 +X 5 5.5 1726 −0.34283RJMCMCX 1 +X 2 +X 3 +X 5 +X 12 +X 46 +X 49 +X 51 +X 70 +X 78 7.5 1645 −0.327UtilityX 1 +X 3 +X 4 +X 12 +X 46 +X 49 +X 57 6.5 ∗ 1693 −0.336 ∗ This model had a higher cost than the best model with p=14 because the utility approachwas not optimizing on cost but on a utility-based cost-beneﬁt tradeoﬀ. in Table 1 that all of these variables had marginal posterior probability 0in the RJMCMC method); four more variables had identical star patterns;and the other four variables were chosen by both methods as important,diﬀering only in how many stars they received. Table 5 uses a similar starsystem: two stars in columns 4 and 5 in this table signify membership in theglobally best model found by the utility and RJMCMC methods, respec-tively; one star in column 4 means that the variable appeared frequently inthe 100 best utility models [see Fouskakis and Draper (2008) for details],with one star in column 5 signifying that a variable often occurred in thehighest-posterior-probability RJMCMC models of Table 3. With p=83, theagreement between the two methods is also strong (although not as strongas with p=14): 60 variables were ignored by both methods, eight variableshad identical star patterns, three variables were chosen as important byboth methods but with diﬀerent star patterns, 10 variables were marked asimportant by the utility approach and not by RJMCMC, and two variableswere singled out by RJMCMC and not by utility (this represents substantialagreement on the importance of 85% of the variables). Table 6 gives a summary of the RJMCMC search results with p=14 andexamines the cost-beneﬁt tradeoﬀs of the utility and RJMCMC methods in
The client-side project manager: A practitioner of Design

SYNOPSISOur research adds to the client-side project management body of literature by demonstrating that these professionals display all the characteristics of Design Thinking Mentalities, Thinking Styles and Practices as identified by Hassi and Laakso (2011a) and that they utilize a broad range of the Design Thinking tools identified by Liedtka (2015) and Johansson-Sköldberg et al. (2013) when they deliver construction projects.RELEVANCE FOR PRACTICE/EDUCATIONOur findings indicate that client-side project managers should view their role differently to what has been traditionally accepted. The use of Design Thinking within the project management construct highlights that practitioners need to develop skills and tools that address, not just the compliance and control elements of project management, but also information gathering and problem solving techniques. This change of perspective creates opportunities for project managers to broaden their skill set in order to be able create further value in the Construction process.RESEARCH DESIGNOur research uses a Grounded Theory methodology to explore the ‘lived experience’ of client-side project managers to determine if they utilize Design Thinking when managing Construction projects. This is achieved by creating a framework from the work of Hassi and Laakso (2011a), Johansson-Sköldberg et al. (2013) and Liedtka (2015) to guide semi-structured interviews with a cohort of ten client-side project managers.MAIN FINDINGSOur research provides evidence of Design Thinking Mentalities, Thinking Styles, Practices and Tools being utilized by client-side project managers when delivering Construction projects. Our findings also identifies 15 project management tools used by client-side project managers when delivering Construction projects and highlight that the practice of client-side project management should not be viewed exclusively as part of the ‘Implementation’ process. RESEARCH IMPLICATIONSOur results support existing research on client-side project management and expand the Project Management body of literature by demonstrating how client-side project managers employ Design Thinking to handle poorly-defined projects.
CFS Working Paper No . 2004 / 10 Weather Forecasting for Weather Derivatives

We take a simple time-series approach to modeling and forecasting daily average temperature in U.S. cities, and we inquire systematically as to whether it may prove useful from the vantage point of participants in the weather derivatives market. The answer is, perhaps surprisingly, yes. Time-series modeling reveals conditional mean dynamics, and crucially, strong conditional variance dynamics, in daily average temperature, and it reveals sharp differences between the distribution of temperature and the distribution of temperature surprises. As we argue, it also holds promise for producing the long-horizon predictive densities crucial for pricing weather derivatives, so that additional inquiry into time-series weather forecasting methods will likely prove useful in weather derivatives contexts.
Customer Loyalty in e-Commerce Settings: An Empirical Study

The aim of this paper is to investigate the impact of individual dimensions of perceived service quality on customer satisfaction, trust and loyalty in e-commerce settings. Empirical results indicate that the perceived service quality has positive direct effects on both customer satisfaction and trust. The results also show that customer satisfaction appears to have a positive direct effect on trust, while both customer satisfaction and trust have direct positive effects on loyalty through word-of-mouth and intention. Thus, both satisfaction and trust play an imperative role in creating customer loyalty as suggested by many authors. Some theoretical and managerial implications and suggestions for future research are also provided.
The effect of a social group work based on hope therapy on social isolation among women with cancer

Cancer is one of the hardly curable diseases from which a large number of people suffer. In addition to having physical painful effects on patients, this disease has a lot of psychological and social effects on patients. One of the social consequences of this diseases is social isolation. The Hope Therapy intervention is one of the interventions affecting patients’ psychological and social aspects. The aim of the present study is to investigate the effect of Hope Therapy on social isolation of patients suffering from cancer. The present study was conducted via the clinical trial method and using the experimental pretest-posttest design. Research instruments were the Social Isolation Scale with 38 items and the Social Isolation Scale with five items. Their validity was confirmed via formal and content validity techniques, and their reliability was confirmed via Cronbach’s alpha. The study was conducted by random selection of 49 female patients suffering from cancer selected from charity centers of Behnam Daheshpour and Mahyar (in two 28-participant experimental and 21-participant control groups). The experimental group received 8-session Hope Therapy intervention with the Growth and Development Social Work Model consisting of three components of Goal, Will and Progress. The results of the present study were analyzed via the independent t-test and paired t-test. The results of the study indicated that the Hope Therapy intervention can be effective on the subjective aspect in Hawthorne’ scale and the objective aspect of social isolation (in the scale of Kalantari. In addition, this intervention results in reducing social isolation in the experimental groups. However, the intervention has no significant effect of other subscales. The Hope Therapy intervention and teamwork have been effective on reducing social isolation of patients suffering from cancer. Since cancer affects humans’ physical, mental, and social dimensions, therapeutic interventions on patients should consider social aspects as well.
Serum Vitamin A and Inflammatory Markers in Individuals with and without Chronic Obstructive Pulmonary Disease

Background. Vitamin A is essential for the preservation and integrity of the lung epithelium and exerts anti-inflammatory effects. Objective. Evaluating vitamin A in the serum and sputum and testing its correlation with inflammatory markers in individuals with or without COPD. Methods. We evaluated dietary intake, serum and sputum vitamin A, tumor necrosis factor alpha, interleukin- (IL-) 6, IL-8, and C-reactive protein in 50 COPD patients (age = 64.0 ± 8.8 y; FEV1 (forced expiratory volume in the first second) (%) = 49.8 ± 16.8) and 50 controls (age = 48.5 ± 7.4 y; FEV1 (%) = 110.0 ± 15.7). Results. COPD exhibited lower serum vitamin A (1.8 (1.2–2.1) versus 2.1 (1.8–2.4) μmol/L, P < 0.001) and lower vitamin A intake (636.9 (339.6–1349.6) versus 918.0 (592.1–1654.6) RAE, P = 0.05) when compared with controls. Sputum concentration of vitamin A was not different between groups. Sputum vitamin A and neutrophils were negatively correlated (R 2 = −0.26; P = 0.03). Smoking (0.197, P = 0.042) exhibited positive association with serum vitamin A. COPD was associated with lower serum concentrations of vitamin A without relationship with the systemic inflammation. Conclusions. Serum concentration of vitamin A is negatively associated with the presence of COPD and positively associated with smoking status. Sputum retinol is quantifiable and is negatively influenced by neutrophils. Although COPD patients exhibited increased inflammation it was not associated with serum retinol.
Web-Based Traffic Sentiment Analysis: Methods and Applications

With the booming of social media, sentiment analysis has developed rapidly in recent years. However, only a few studies focused on the field of transportation, which failed to meet the stringent requirements of safety, efficiency, and information exchange of intelligent transportation systems (ITSs). We propose the traffic sentiment analysis (TSA) as a new tool to tackle this problem, which provides a new prospective for modern ITSs. Methods and models in TSA are proposed in this paper, and the advantages and disadvantages of rule- and learning-based approaches are analyzed based on web data. Practically, we applied the rule-based approach to deal with real problems, presented an architectural design, constructed related bases, demonstrated the process, and discussed the online data collection. Two cases were studied to demonstrate the efficiency of our method: the “yellow light rule” and “fuel price” in China. Our work will help the development of TSA and its applications.
Economic Performance Competitor Benchmarking using Data-Mining Techniques

In this paper we analyze comparatively the macroeconomic performance of different Central and Eastern European countries by the means of Data Mining (DM) techniques. We analyze the economic situations of three EU countries (Poland, Slovenia and Latvia), a newlyaccepted one (Romania), and other two non-EU countries (Russia and Ukraine). We have depicted economic performance of countries using a number of macroeconomic variables for the time period from 1993 till 2000. The economic variables that we used were: Currency Value (CV) (the inverse of the Exchange Rate - ER), Domestic Prime Rate (Refinancing Rate – RR), Industrial Output (IO) compared to previous periods in percentages, Unemployment Rate (UR), Foreign Trade (FT) in millions of USA dollars. The dataset consists of monthly/annual data during the period 1993-2000, in total 225 cases with five variables each. As DM techniques we firstly applied Self-Organizing Map (SOM) to group the countries according to their economic performance. We applied a so-called “two-step” SOM clustering: firstly, we built larger maps that contained “raw” clusters and then, we re-grouped the “raw” clusters to form a smaller number of “real” clusters. We characterize each “real” cluster, using for each variable the following linguistic terms: VL – very low, L – low, A – average, H – high, VH – very high. Secondly, we go one step further and use the clustering results (of SOM) to build hybrid classification models to help position new countries’ performance within the existent economic performance clusters. This type of analysis can benefit the countries involved, EU in its monitoring process, business players such as international companies that want to expand their business and individual investors.
Nonparametric cooperative tracking in mobile Ad-Hoc networks

This paper presents a new nonparametric approach for cooperative localisation and tracking by fusing relative range measurements between mobile network equipped nodes. Standard approaches based on parametric methods are known to be limited to problems that contain Gaussian properties. This paper overcomes this limitation by proposing a novel particle filter based cooperative tracking approach that is suitable for mobile ad-hoc networks (MANETs). The filter maintains the marginal state of every node instead of a joint state of the group, and updates the estimates using a Gibbs sampler, which is known as a Markov chain Monte Carlo (MCMC) method. The performance of the proposed algorithm is demonstrated by examining 16 mobile nodes moving randomly while sharing information with neighbouring nodes in a MANET. The results show that the proposed approach facilitates the tracking of mobile nodes that do not have egocentric position information available. It also outperforms the EKF in systems with non-Gaussian properties.
Beliefs and Values among Rural Citizens: Shared Expectations for Educational Attainment?.

Discussions at the local, state, and national level have been focused on the importance of providing access and opportunity for college attendance. While these discussions are important to raising public interest in higher education attainment, they often negate how community values influence the college attendance decision process. This study sought to examine the beliefs and values of citizens in a rural mid-South county in order to understand how those beliefs and values might affect the decision to attend college. Data were collected from community members in a rural county with assistance from the chamber of commerce. A total of N = 220 citizens completed the instrument, which measured their beliefs and values associated with having a high regard for educational attainment. Exploratory factor analysis (EFA) was utilized to analyze the responses to the items contained in the instrument. Six factors emerged through the analysis of data, including value for education and quality of life, community identity and loyalty, social consciousness, value for religion and health, entertainment and leisure activities, and information access.
The constant objective value property for combinatorial optimization problems

Given a combinatorial optimization problem, we aim at characterizing the set of all instances for which every feasible solution has the same objective value. Our central result deals with multi-dimensional assignment problems. We show that for the axial and for the planar $d$-dimensional assignment problem instances with constant objective value property are characterized by sum-decomposable arrays. We provide a counterexample to show that the result does not carry over to general $d$-dimensional assignment problems. Our result for the axial $d$-dimensional assignment problem can be shown to carry over to the axial $d$-dimensional transportation problem. Moreover, we obtain characterizations when the constant objective value property holds for the minimum spanning tree problem, the shortest path problem and the minimum weight maximum cardinality matching problem.
A design approach for networks of Self-Sampled All-Digital Phase-Locked Loops

This paper addresses the problem of the stability and the performance analysis of N-nodes cartesian networks of self-sampled all digital phase-locked loops. It can be demonstrated that under certain conditions (such as proper filter coefficient values), a global and a local synchronization can be obtained. Our approach to find the optimal conditions consists of analyzing a corresponding linear average system of the cartesian network rather than constructing a piecewise-linear system which is extremely difficult to analyse. The constructed corresponding system takes into account the non-linearity of the network and especially the self-sampling property. It is then analyzed by linear performance criteria such as modulus margin to guarantee a robust stability of the cartesian network. The reliability of our approach is proved by transient simulations in networks of different sizes.