Miracle-dz/UniFAR-FTUs huggingface dataset:
Decomposing variation in population growth into contributions from environment and phenotypes in an age-structured population

Evaluating the relative importance of ecological drivers responsible for natural population fluctuations in size is challenging. Longitudinal studies where most individuals are monitored from birth to death and where environmental conditions are known provide a valuable resource to characterize complex ecological interactions. We used a recently developed approach to decompose the observed fluctuation in population growth of the red deer population on the Isle of Rum into contributions from climate, density and their interaction and to quantify their relative importance. We also quantified the contribution of individual covariates, including phenotypic and life-history traits, to population growth. Fluctuations in composition in age and sex classes ((st)age structure) of the population contributed substantially to the population dynamics. Density, climate, birth weight and reproductive status contributed less and approximately equally to the population growth. Our results support the contention that fluctuations in the population's (st)age structure have important consequences for population dynamics and underline the importance of including information on population composition to understand the effect of human-driven changes on population performance of long-lived species.
QuasR: quantification and annotation of short reads in R

Summary: QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization. Availability and implementation: QuasR is implemented in R and C/C++. Source code and binaries for major platforms (Linux, OS X and MS Windows) are available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/QuasR.html). The package includes a ‘vignette’ with step-by-step examples for typical work ﬂows. Contact: michael.stadler@fmi.ch Supplementary information: Supplementary data are available at Bioinformatics online.
ATVB in Focus Redox Mechanisms in Blood Vessels

Myeloperoxidase (MPO) is a leukocyte-derived enzyme that catalyzes the formation of a number of reactive oxidant species. In addition to being an integral component of the innate immune response, evidence has emerged that MPO-derived oxidants contribute to tissue damage during inflammation. MPO-catalyzed reactions have been attributed to potentially proatherogenic biological activities throughout the evolution of cardiovascular disease, including during initiation, propagation, and acute complication phases of the atherosclerotic process. As a result, MPO and its downstream inflammatory pathways represent attractive targets for both prognostication and therapeutic intervention in the prophylaxis of atherosclerotic cardiovascular disease. (Arterioscler Thromb Vasc Biol. 2005;25:1102-1111.)
Prostate Cancer Incidence and Prostate-Specific Antigen Testing Among HIV-Positive and HIV-Negative Men

Background:We investigated whether the reported lower incidence of prostate cancer in HIV-positive men is a result of confounding factors or reduced screening. Methods:We conducted a cohort study of 17,424 HIV-positive and 182,799 HIV-negative men enrolled in Kaiser Permanente (KP). Subjects were followed from the first KP enrollment after January 01, 1996 for KP Northern California (KPNC) and January 01, 2000 for KP Southern California until the earliest of prostate cancer diagnosis, loss to follow-up, or December 31, 2007. Poisson regression was used to compare cancer rates by HIV status adjusting for age, race, smoking, alcohol/drug abuse, overweight/obesity, and diabetes. For the KPNC subset, we analyzed additional available data by HIV status on testosterone deficiency, and on prostate-specific antigen (PSA) tests as a proxy for cancer screening. Results:The prostate cancer incidence rate was 102/100,000 person-years in HIV-positive men (n = 74 cases) and 131/100,000 person-years in HIV-negative men (n = 1195 cases), with an adjusted rate ratio of 0.73 (95% confidence interval: 0.57 to 0.92; P = 0.008). The reduced risk among HIV-positive men was greater for higher-stage cancers, which are less likely to be biased by screening differences than lower-stage cancers. In the KPNC subset, more HIV-positive (90.8%) than HIV-negative men (86.2%) received a PSA test by age 55 (P < 0.001). Decreased risk for HIV-positive men remained when examined only among those with a previous PSA test, and with adjustment for testosterone deficiency (rate ratio = 0.55; 95% confidence interval: 0.39 to 0.80; P = 0.001). Conclusions:Prostate cancer incidence rates are lower in HIV-positive compared with HIV-negative men, which is not explained by screening differences or the risk factors evaluated.
Summary of the National Demonstration Project and Recommendations for the Patient-Centered Medical Home

This article summarizes findings from the National Demonstration Project (NDP) and makes recommendations for policy makers and those implementing patient-centered medical homes (PCMHs) based on these findings and an understanding of diverse efforts to transform primary care. The NDP was launched in June 2006 as the first national test of a particular PCMH model in a diverse sample of 36 family practices, randomized to facilitated or self-directed groups. An independent evaluation team used a multimethod evaluation strategy, analyzing data from direct observation, depth interviews, e-mail streams, medical record audits, and patient and clinical staff surveys. Peer-reviewed manuscripts from the NDP provide answers to 4 key questions: (1) Can the NDP model be built? (2) What does it take to build the NDP model? (3) Does the NDP model make a difference in quality of care? and (4) Can the NDP model be widely disseminated? We find that although it is feasible to transform independent practices into the NDP conceptualization of a PCMH, this transformation requires tremendous effort and motivation, and benefits from external support. Most practices will need additional resources for this magnitude of transformation. Recommendations focus on the need for the PCMH model to continue to evolve, for delivery system reform, and for sufficient resources for implementing personal and practice development plans. In the meantime, we find that much can be done before larger health system reform.
Revisiting Frequency and Spatial Distribution: Innovation Collaboration for Biotech Firms

On-going debates rage over the to what extent spatial proximity, on the one hand, versus global interactions on the other hand, affect economic development. Spatial proximity of networks and firms with their partners are claimed as important for a number of phenomena, including firm survival, innovativeness and regional economic development. However, while some theories stress the importance of the spatial dimension, whereas other argues that the world is getting more and more globalized. Rather than assuming spatial proximity and collaboration affect innovation, this paper starts by questioning the extent to which collaboration and regions matter in relation to innovation. This paper addresses the frequency of different types and different forms of colocated partners for collaboration – based on an assumption that the firm places strategic value on choice of partners for innovation.
Perspectives From Before and After the Pediatric to Adult Care Transition: A Mixed-Methods Study in Type 1 Diabetes

OBJECTIVE Among the many milestones of adolescence and young adulthood, transferring from pediatric to adult care is a significant transition for those with type 1 diabetes. The aim of this study was to understand the concerns, expectations, preferences, and experiences of pretransition adolescents and parents and posttransition young adults. RESEARCH DESIGN AND METHODS Participants completed questionnaires and responded to open-ended qualitative questions regarding self-management, self-efficacy, and their expectations and experiences with pediatric and adult care providers across the transition process. RESULTS At a mean age of 16.1 years, most pretransition adolescents had not yet discussed transferring care with their parents or doctors. Although many posttransition young adults reported positive, supportive interactions, several described challenges locating or establishing a relationship with an adult diabetes care provider. Qualitative themes emerged related to the anticipated timing of transfer, early preparation for transition, the desire for developmentally appropriate interactions with providers, the maintenance of family and social support, and strategies for coordinating care between pediatric and adult care providers. CONCLUSIONS Standardizing transition preparation programs in pediatric care and introducing transition-oriented clinics for late adolescents and young adults prior to adult care may help address patients’ preferences and common transfer-related challenges.
Navigating the topical structure of academic search results via the Wikipedia category network

Searching for scientific publications on the Web is a tedious task, especially when exploring an unfamiliar domain. Typical scholarly search engines produce lengthy unstructured result lists that are difficult to comprehend, interpret and browse. We propose a novel method of organizing the search results into concise and informative topic hierarchies. The method consists of two steps: extracting interrelated topics from the result set, and summarizing the topic graph. In the first step we map the search results to articles and categories of Wikipedia, constructing a graph of relevant topics with hierarchical relations. In the second step we sequentially build nested summaries of the produced topic graph using a structured output prediction approach. Trained on a small number of examples, our method learns to construct informative summaries for unseen topic graphs, and outperforms unsupervised state-of-the-art Wikipedia-based clustering.
Effectiveness of Group Training Based on Acceptance and Commitment Therapy on Anxiety and Depression of Women with Breast Cancer

Background Breast cancer is the most common cancer in women that as a sudden event has profound effects on all aspects of patients’ lives. Psychosocial interventions may play important roles in reducing anxiety and depression among breast-cancer survivors. Therefore, group training based on acceptance and commitment therapy may help women to cope better with their condition, and decrease their anxiety and depression. Methods In a quasi-experimental study, 30 patients with breast cancer were selected by convenience sampling method and randomly assigned to 2 experimental and control groups. The experimental group attended acceptance and commitment training classes for 8 weeks continuously (each class lasting 90 minutes). Participants in both the experimental and control groups completed Beck Anxiety Inventory (BAI) and Beck Depression Inventory (BHI-II) as a pretest and posttest. Analysis of Covariance was used as the statistical method. Results In acceptance and commitment group training, anxiety and depression significantly decreased (p<0/05). These changes were not observed in the control group. Conclusion The results showed that group training based on acceptance and commitment therapy is an effective method in reducing anxiety and depression. Hence psychological interventions can be used to reduce psychological difficulties of women with breast cancer.
Advances in real-time database systems research

Abstract A Real-Time DataBase System (RTDBS) can be viewed as an amalgamation of a conventional DataBase Management System (DBMS) and a real-time system. Like a DBMS, it has to process transactions and guarantee ACID database properties. Furthermore, it has to operate in real-time, satisfying time constraints imposed on transaction commitments. A RTDBS may exist as a stand-alone system or as an embedded component in a larger multidatabase system. The publication in 1988 of a special issue of ACM SIGMOD Record on Real-Time DataBases signaled the birth of the RTDBS research area---an area that brings together researchers from both the database and real-time systems communities. Today, almost eight years later, I am pleased to present in this special section of ACM SIGMOD Record a review of recent advances in RTDBS research. There were 18 submissions to this special section, of which eight papers were selected for inclusion to provide the readers of ACM SIGMOD Record with an overview of current and future research directions within the RTDBS community. In this paper, I will summarize these directions and provide the reader with pointers to other publications for further information.
Ad hoc grid security infrastructure

This paper describes an ad hoc grid security infrastructure developed as a part of the Java CoG Kit project. It supports several requirements specific to the sporadic nature of ad hoc grids. It focuses on identity management, identity verification, and authorization control in spontaneous grid collaborations without pre-established policies or environments. It adopts established community standards, with modifications where needed. This paper also discusses the integration of the ad hoc grid security infrastructure in an ad hoc grid implementation. The implementation supports secure collaboration in ad hoc grids using commodity technologies such as the Java CoG Kit, JXTA, GSI, and XACML.
Computational modelling of the piglet brain to simulate near-infrared spectroscopy and magnetic resonance spectroscopy data collected during oxygen deprivation

We describe a computational model to simulate measurements from near-infrared spectroscopy (NIRS) and magnetic resonance spectroscopy (MRS) in the piglet brain. Piglets are often subjected to anoxic, hypoxic and ischaemic insults, as experimental models for human neonates. The model aims to help interpret measurements and increase understanding of physiological processes occurring during such insults. It is an extension of a previous model of circulation and mitochondrial metabolism. This was developed to predict NIRS measurements in the brains of healthy adults i.e. concentration changes of oxyhaemoglobin and deoxyhaemoglobin and redox state changes of cytochrome c oxidase (CCO). We altered and enhanced the model to apply to the anaesthetized piglet brain. It now includes metabolites measured by 31P-MRS, namely phosphocreatine, inorganic phosphate and adenosine triphosphate (ATP). It also includes simple descriptions of glycolysis, lactate dynamics and the tricarboxylic acid (TCA) cycle. The model is described, and its simulations compared with existing measurements from piglets during anoxia. The NIRS and MRS measurements are predicted well, although this requires a reduction in blood pressure autoregulation. Predictions of the cerebral metabolic rate of oxygen consumption (CMRO2) and lactate concentration, which were not measured, are given. Finally, the model is used to investigate hypotheses regarding changes in CCO redox state during anoxia.
Unsupervised Spectral Dual Assignment Clustering of Human Actions in Context

A recent trend of research has shown how contextual information related to an action, such as a scene or object, can enhance the accuracy of human action recognition systems. However, using context to improve unsupervised human action clustering has never been considered before, and cannot be achieved using existing clustering methods. To solve this problem, we introduce a novel, general purpose algorithm, Dual Assignment k-Means (DAKM), which is uniquely capable of performing two co-occurring clustering tasks simultaneously, while exploiting the correlation information to enhance both clusterings. Furthermore, we describe a spectral extension of DAKM (SDAKM) for better performance on realistic data. Extensive experiments on synthetic data and on three realistic human action datasets with scene context show that DAKM/SDAKM can significantly outperform the state-of-the-art clustering methods by taking into account the contextual relationship between actions and scenes.
Burst erasure correcting LDPC codes

In this paper low-density parity-check (LDPC) codes are designed for burst erasure channels. Firstly, lower bounds for the maximum length erasure burst that can always be corrected with message-passing decoding are derived as a function of the parity-check matrix properties. We then show how parity-check matrices for burst erasure correcting LDPC codes can be constructed using superposition, where the burst erasure correcting performance of the resulting codes is derived as a property of the stopping set size of the base matrices and the choice of permutation matrices for the superposition. This result is then used to design both single burst erasure correcting LDPC codes which are also resilient to the presence of random erasures in the received bits and LDPC codes which can correct multiple erasure bursts in the same codeword.
DOK3 Negatively Regulates LPS Responses and Endotoxin Tolerance

Innate immune activation via Toll-like receptors (TLRs), although critical for host defense against infection, must be regulated to prevent sustained cell activation that can lead to cell death. Cells repeatedly stimulated with lipopolysaccharide (LPS) develop endotoxin tolerance making the cells hypo-responsive to additional TLR stimulation. We show here that DOK3 is a negative regulator of TLR signaling by limiting LPS-induced ERK activation and cytokine responses in macrophages. LPS induces ubiquitin-mediated degradation of DOK3 leading to SOS1 degradation and inhibition of ERK activation. DOK3 mice are hypersensitive to sublethal doses of LPS and have altered cytokine responses in vivo. During endotoxin tolerance, DOK3 expression remains stable, and it negatively regulates the expression of SHIP1, IRAK-M, SOCS1, and SOS1. As such, DOK3-deficient macrophages are more sensitive to LPS-induced tolerance becoming tolerant at lower levels of LPS than wild type cells. Taken together, the absence of DOK3 increases LPS signaling, contributing to LPS-induced tolerance. Thus, DOK3 plays a role in TLR signaling during both naïve and endotoxin-induced tolerant conditions.
A low latency, loss tolerant architecture and protocol for wide area group communication

Group communication systems are proven tools upon which to build fault-tolerant systems. As the demands for fault-tolerance increase and more applications require reliable distributed computing over wide area networks, wide area group communication systems are becoming very useful. However, building a wide area group communication system is a challenge. This paper presents the design of the transport protocols of the spread wide area group communication system. We focus on two aspects of the system. First, the value of using overlay networks for application level group communication services. Second, the requirements and design of effective low latency link protocols used to construct wide area group communication. We support our claims with the results of live experiments conducted over the Internet.
At-Speed BIST for Board-Level Interconnect

This article describes a novel Boundary Scan-like Built-In Self-Test (BIST) conception for autonomous at-speed testing and diagnosis of interconnect. It is based on recently proposed very efficient design of test pattern generation and response analysis hardware, which allows detection and diagnosis of both static and dynamic faults upon interconnects between chips in a multi-chip environment. The paper presents a system-level overview of the new testing paradigm and demonstrates its advantages over other known methods. It is shown that this paradigm brings a never achieved before high level of universality, scalability, and configuration independence into the at-speed interconnect testing and diagnosis of interconnect.
Audience Evolution: New Technologies and the Transformation of Media Audiences

Audience Evolution: New Technologies and the Transformation of Media Audiences. Philip M. Napoli. New York, NY: Columbia University Press, 2010. 272 pp. $27.50 pbk. Philip Napoli's new book, Audience Evolution: New Technologies and the Transformation of Media Audiences, is a good combination of a critical approach to audience measurement as well as a thorough review of the development of audience information systems. His key argument is that technologies foster the collection and compilation of audience information beyond the traditional exposure model, and allow new dimensions of audience information be incorporated into business use. Napoli, a professor in the Graduate School of Business at Fordham University and director of the Donald McGannon Communication Research Center, focuses on the institutionalized audience, in which the audience is understood and used as currencies in the formal procedures and practices of institutions such as media organizations and advertisers. "The concept of audience is constructed and defined to reflect the economic and strategic imperatives of media organizations," he says. The book consists of six parts: (1) introduction, (2) contextualizing audience evolution, (3) the transformation of media consumption, (4) the transformation of audience information systems, (5) contesting audiences, and (6) the implications of audience revolution. Throughout, Napoli reminds readers that new and alternative dimensions of audience, such as engagement and appreciation of content, should be considered for a more complete picture of the audience's interaction with the content beyond the traditional exposure model. He also suggests that the new dimensions may increase acceptance of audience research results by content producers. The book builds on his previous Audience Economics: Media Institutions and the Audience Marketplace (2003). In this work, Napoli recognizes two key phenomena causing the change in media industries' conceptualization of audience related to technologies: audience fragmentation and audience autonomy. The proliferation of media platforms and outlets has resulted in diverting audience attention to more media channels. Various interactive technologies empower audiences to make choices and create user-generated content. The process of rationalization of audience understanding in the media industries highlighted in Audience Evolution is of high relevance to practitioners and researchers. By using "scientific methods" to collect audience information and then base business decisions upon them, media industries have moved from an intuitive model based on executive judgment to a more rational and objective model. There are, of course, negative consequences of such a model, such as stifling creativity and encouragement of homogenization. I like Napoli's discussion of the political economy of the audience measurement industry, in which various established media and stakeholders resist changes for their own interests and do not Support new measurement initiatives. …
A CCG-based System for Valence Shifting for Sentiment Analysis

The automatic classification of sentiment in text is becoming an im- portant area of research. In this work, we present a linguistic system for sen- tence-level valence annotation. Our system uses the formalism of Combinatory Categorial Grammar to represent words as functions acting on their syntactic arguments, which provides a unified way of implementing various classes of valence shifters. We propose two simple semi-automatic methods for estimat- ing the valence of individual terms based on the lexical relations of WordNet. We evaluate the system on the data generated for the Affective Text task of SemEval 2007 and show that it compares favourably with the systems partici- pating in the task.