Miracle-dz/UniFAR-FTUs huggingface dataset:
What factors potentially influence the ability of phylogenetic distance to predict trait dispersion in a temperate forest?

Abstract Although phylogenetic‐based approaches have been frequently used to infer ecological processes, they have been increasingly criticized in recent years. To date, the factors that affect phylogenetic signals and further the ability of phylogenetic distance to predict trait dispersion have been assumed but not empirically tested. Therefore, we investigate which factors potentially influence the ability of phylogenetic distance to predict trait dispersion. We quantified the phylogenetic and trait dispersions across size classes and spatial scales in a 9‐ha old‐growth temperate forest dynamics plot in northeastern China. Phylogenetic signals at the community level were generally lower than those at the species pool level, and phylogenetically clustered communities showed lower phylogenetic signals than did overdispersed communities. This pattern might explain the other three findings of our study. First, phylogenetically overdispersed communities performed better at predicting trait dispersion than did clustered communities. Second, the mean pairwise distance (MPD)‐based metric exhibited a stronger correlation with trait dispersion than did the mean nearest taxon distance (MNTD)‐based metric. Finally, the MNTD‐based metric showed that the prediction accuracy for trait dispersion decreased with increasing spatial scales, whereas its effects were weak on the MPD‐based metric. In addition, phylogeny could not determine the dispersions of all functional axes but was able to predict certain traits depending on whether they were evolutionarily conserved. These results were conserved when we removed the effects of space and environment. Our findings highlighted that using phylogenetic distance as a proxy of trait similarity might work in a temperate forest depending on the species in local communities sampled from total pool as well as the traits measured. Utilizing these rules, we should rethink the conclusions of previous studies that were based on phylogenetic‐based approaches.
Dental Optical Coherence Tomography

This review paper describes the applications of dental optical coherence tomography (OCT) in oral tissue images, caries, periodontal disease and oral cancer. The background of OCT, including basic theory, system setup, light sources, spatial resolution and system limitations, is provided. The comparisons between OCT and other clinical oral diagnostic methods are also discussed.
Trust in online social networks: A multifaceted perspective

In recent years, online social networks (OSNs) have gained great popularity and are now among the most frequently visited sites on the Web. Although security standards and practices are an increasing focus of attention, participants still reveal great amounts of sensitive information in the Web 2.0 environment. Obviously, online social networking takes place in a context of trust. However, trust is a concept with many facets and dimensions. To facilitate trust research in OSNs this article aims at clarifying the role of trust and the relevance of facets of trust, social capital and embeddedness in OSNs. First, the focus is on the individual's decision to trust and on processes through which trust actually emerges. Subsequently, trust is viewed as a structurally embedded asset or a property of relationships and networks that helps to shape interaction patterns within OSNs. A conceptual framework is developed that integrates theoretical concepts from the trust literature, social network and social capital theory, and helps to map different trust-related issues in OSNs.
A Fluid-Cell Interaction and Adhesion Algorithm for Tissue Coating of Cardiovascular Implants

In this manuscript we develop a fluid-cell interaction and adhesion algorithm applied to modeling the cell coating of artificial surfaces of cardiovascular implants for improved biocompatibility. The fluid-cell interaction and adhesion algorithm proposed in this manuscript is a multiscale model that captures the process of cell adhesion which occurs at a scale of a few nanometers and couples it with fluid-cell interaction which occurs at a scale of a few hundred microns. Cells are assumed rigid and neutrally buoyant. Cell adhesion is modeled using a kinetics-based dynamic adhesion algorithm. Fluid-cell interaction is modeled using the fictitious domain method with distributed Lagrange multipliers. The coupling between the two is achieved through a time-splitting scheme. Novel results regarding the influence of certain fluid dynamic parameters and adhesion parameters on the generation of a stable and strong tissue coating of artificial surfaces are presented. The modular nature of this algorithm makes it e.
The Economic Impacts of Altruism, Trust and Reciprocity: An Experimental Approach to Social Capital

This paper experimentally measures the ‘social capital’ of altruism, trust and reciprocity and empirically explores the impact of these norms on economic well-being. Using an experimental economic design that distinguishes trust and reciprocity from altruism, data were collected from individuals in a random sample of South African communities. Analyzed at the community level, these data suggest that while related, trust and reci
Evaluating the state of the art in disorder recognition and normalization of the clinical narrative

Objective The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System (UMLS) definition (Task 1a) and (ii) disorder mention normalization to an ontology (Task 1b). Such a community evaluation has not been previously executed. Task 1a included a total of 22 system submissions, and Task 1b included 17. Most of the systems employed a combination of rules and machine learners. Materials and methods We used a subset of the Shared Annotated Resources (ShARe) corpus of annotated clinical text—199 clinical notes for training and 99 for testing (roughly 180 K words in total). We provided the community with the annotated gold standard training documents to build systems to identify and normalize disorder mentions. The systems were tested on a held-out gold standard test set to measure their performance. Results For Task 1a, the best-performing system achieved an F1 score of 0.75 (0.80 precision; 0.71 recall). For Task 1b, another system performed best with an accuracy of 0.59. Discussion Most of the participating systems used a hybrid approach by supplementing machine-learning algorithms with features generated by rules and gazetteers created from the training data and from external resources. Conclusions The task of disorder normalization is more challenging than that of identification. The ShARe corpus is available to the community as a reference standard for future studies.
Examination of the Brain Processes Underlying Emotion Regulation within a Stress Resilient Population

Title of dissertation: EXAMINATION OF THE BRAIN PROCESSES UNDERLYING EMOTION REGULATION WITHIN A STRESS RESILIENT POPULATION Michelle E. Costanzo, Doctor of Philosophy, 2011 Dissertation directed by: Dr. Bradley D. Hatfield, Ph.D., FACSM, FAAKPE Neuroscience and Cognitive Sciences Program Emotion robustly affects the quality of cognitive-motor performance under conditions of mental stress. As such, the regulation of emotion is critical to successful execution of motor skills during emotional challenge. Previous investigations of the stressperformance relationship have typically focused on behavioral outcomes, however, few have adopted a cognitive neuroscience approach to examine the involved mechanisms underlying this relationship. Furthermore, it is unclear if individuals who have a history of superior performance under stress (stress resilient population) exhibit brain responses characterized by an efficiency of neural processing and an adaptive emotion regulatory strategy. Using functional magnetic resonance imaging (fMRI), the present study examined activation in critical brain regions during affective challenge (i.e., presentation of International Affective Picture System negative images and Sport-Specific negative images) in 13 elite athletes (intercollegiate football players who have demonstrated successful execution of cognitive-motor skills under mental stress) relative to an age-matched control group (n=12). The present dissertation is organized into three main sections. The first report, entitled Brain Processes during Motor Performance under Psychological Stress, an Independent Component Analysis of EEG, is an examination of brain processes during competitive stress. This study revealed non-essential neuromotor cerebral cortical noise with a quantified increase in complexity during a cognitivemotor task. The second report is entitled Efficiency of Affective Brain Processes in Expert Cognitive-Motor Performers during Emotional Challenge. This fMRI examination of elite athletes revealed processing economy in brain regions critical to self regulation, management of emotional impulses and social cognition. The third report, entitled The Specificity of Neural Regulatory Processes during Emotional Challenge in a Stress Resilient Population, examined with fMRI if elite athletes spontaneously engage in cognitive reappraisal during the presentation of arousing sport-specific images. Results suggest that elite athletes process sports-relevant affective information in an automatic manner, congruent with a cognitive reappraisal strategy, which neutralized the negative impact of the scenes. In conclusion, the results suggest that elite performers are important models of stress resilience and respond not only in an efficient manner to stressful events, but demonstrate an adaptive regulatory response when challenged within their domain of experience. EXAMINATION OF THE BRAIN PROCESSES UNDERLYING EMOTION REGULATION WITHIN A STRESS RESILIENT POPULATION
Deciphering the temporal link between pain and sleep in a heterogeneous chronic pain patient sample: a multilevel daily process study.

OBJECTIVES Because insomnia is a common comorbidity of chronic pain, scientific and clinical interest in the relationship of pain and sleep has surged in recent years. Although experimental studies suggest a sleep-interfering property of pain and a pain-enhancing effect of sleep deprivation/fragmentation, the temporal association between pain and sleep as experienced by patients is less understood. The current study was conducted to examine the influence of presleep pain on subsequent sleep and sleep on pain reports the next day, taking into consideration other related psychophysiologic variables such as mood and arousal. DESIGN A daily process study, involving participants to monitor their pain, sleep, mood, and presleep arousal for 1 wk. Multilevel modeling was used to analyze the data. SETTING In the patients' natural living and sleeping environment. PATIENTS One hundred nineteen patients (73.9% female, mean age = 46 years) with chronic pain and concomitant insomnia. MEASUREMENT An electronic diary was used to record patients' self-reported sleep quality/efficiency and ratings of pain, mood, and arousal at different times of the day; actigraphy was also used to provide estimates of sleep efficiency. RESULTS Results indicated that presleep pain was not a reliable predictor of subsequent sleep. Instead, sleep was better predicted by presleep cognitive arousal. Although sleep quality was a consistent predictor of pain the next day, the pain-relieving effect of sleep was only evident during the first half of the day. CONCLUSIONS These findings challenge the often-assumed reciprocal relationship between pain and sleep and call for a diversification in thinking of the daily interaction of these 2 processes.
A learning organization : machine or human?

– Aloin viime vuosikymmenen alussa ihmetella sita, miksi koulutus ei muuta tyoyhteisoja. Toisaalta ihmettelin vuonna 1993 Englannissa kongressissa sita, kuinka vahan oppivasta organisaatiosta tiedetaan, vaikka siita puhutaankin paljon, Raili Moilanen kertoo tutkimuksensa taustoista. Han kiinnostui aiheesta niin paljon etta toteutti tyossaan Jyvaskylan yliopiston johtamiskoulutuksessa Oppiva Yritys -koulutusohjelman vuonna 1993–94 ja innostui sen jalkeen tutkimaan oppivaa organisaatiota yha perusteellisemmin. Tuloksia ovat lisensiaattityo vuonna 1996, vaitoskirja ja ensi talvena ilmestyva oppikirja.
Molecular Abnormalities Underlying Bone Fragility in Chronic Kidney Disease

Prevention of bone fractures is one goal of therapy for patients with chronic kidney disease-mineral and bone disorder (CKD-MBD), as indicated by the Kidney Disease: Improving Global Outcomes guidelines. CKD patients, including those on hemodialysis, are at higher risk for fractures and fracture-related death compared to people with normal kidney function. However, few clinicians focus on this issue as it is very difficult to estimate bone fragility. Additionally, uremia-related bone fragility has a more complicated pathological process compared to osteoporosis. There are many uremia-associated factors that contribute to bone fragility, including severe secondary hyperparathyroidism, skeletal resistance to parathyroid hormone, and bone mineralization disorders. Uremia also aggravates bone volume loss, disarranges microarchitecture, and increases the deterioration of material properties of bone through abnormal bone cells or excess oxidative stress. In this review, we outline the prevalence of fractures, the interaction of CKD-MBD with osteoporosis in CKD patients, and discuss possible factors that exacerbate the mechanical properties of bone.
Understanding the Press Imaging of `Terrorist' A Pragmatic Visit to the Frankfurt School

/ Media is at the heart of many public debates in the same way as terrorism and Islam are part of a global discourse since the events of 9/11 in the United States. This article attempts to use the social construction of social problems approach to understand the media's imaging of `terrorists' in the context of Singapore. Combining media research with social critical reflection provides the tools to identify the social rationale dimension. The application of such a procedure reveals the complex relationships between the media and their role in the process of `nationbuilding'. The city-state fits the order model of society, where social integration, order and stability are fundamental. The Singaporean population is predominantly non-Islamic Chinese; however, geographically Singapore is located between Malaysia, a Muslim country, and Indonesia, where 89 percent of the population are Muslims. The article looks at Singapore's mainstream English-language newspaper, The Straits Times , and its representation of.
‘Are you by chance on the spectrum?’ Adolescents with autism spectrum disorder making sense of their diagnoses

The current phenomenological study aimed to provide a better understanding of how adolescents with autism spectrum disorder (ASD) identify with and make meaning of their diagnosis through exploration of their disability narratives. In order to gain a more comprehensive understanding of how adolescents with ASD negotiate the positive and negative aspects of their diagnoses, social discourse surrounding ASD, as well as their own meaning-making process, the current study explored adolescents’ descriptions of ASD and identification with labels of disability. Participants included 10 adolescents with ASD ranging in age from 13 to 20. Three main themes emerged from the qualitative interviews: formation of an ASD narrative; social construction of the label; and confusion regarding whether ASD is a disability. Results of this study indicate the need for reducing social stigma associated with ASD and disability labels.
Bandera: extracting finite-state models from Java source code

Finite-state verification techniques, such as model checking, have shown promise as a cost-effective means for finding defects in hardware designs. To date, the application of these techniques to software has been hindered by several obstacles. Chief among these is the problem of constructing a finite-state model that approximates the executable behavior of the software system of interest. Current best-practice involves hand construction of models which is expensive (prohibitive for all but the smallest systems), prone to errors (which can result in misleading verification results), and difficult to optimize (which is necessary to combat the exponential complexity of verification algorithms). The authors describe an integrated collection of program analysis and transformation components, called Bandera, that enables the automatic extraction of safe, compact finite-state models from program source code. Bandera takes as input Java source code and generates a program model in the input language of one of several existing verification tools; Bandera also maps verifier outputs back to the original source code. We discuss the major components of Bandera and give an overview of how it can be used to model check correctness properties of Java programs.
FDG-PET/CT based response-adapted treatment

Abstract It has been shown that [18F]fluorodeoxyglucose (FDG)-positron emission tomography (PET) provides robust and reproducible data for early metabolic response assessment in various malignancies. This led to the initiation of several prospective multicenter trials in malignant lymphoma and adenocarcinoma of the esophagogastric junction, in order to investigate whether the use of PET-guided treatment individualization results in a survival benefit. In Hodgkin lymphoma and aggressive non-Hodgkin lymphoma, several trials are ongoing. Some studies aim to investigate the use of PET in early identification of metabolic non-responders in order to intensify treatment to improve survival. Other studies aim at reducing toxicity without adversely affecting cure rates by safely de-escalating therapy in metabolic responders. In solid tumors the first PET response-adjusted treatment trials have been realized in adenocarcinoma of the esophagogastric junction. These trials showed that patients with an early metabolic response to neoadjuvant chemotherapy benefit from this treatment, whereas metabolic non-responders should switch early to surgery, thus reducing the risk of tumor progression during chemotherapy and the risk of toxic death. The trials provide a model for designing response-guided treatment algorithms in other malignancies. PET-guided treatment algorithms are the promise of the near future; the choice of therapy, its intensity, and its duration will become better adjusted to the biology of the individual patient. Today’s major challenge is to investigate the impact on patient outcome of personalized response-adapted treatment concepts.
Regression Testing Process Improvement for Specification Evolution of Real-World Protocol Software

Model-based testing helps test engineers automate their testing tasks so that they can be more cost-effective. When the model is changed due to the evolution of the specification, it is important to maintain the test suites up to date for regression testing. A complete regeneration of the whole test suite from the new model, although inefficient, is still frequently used in prac¬tice. To handle specification evolution effectively, we propose a test case reusability analysis technique to identify reusable test cases of the original test suite based on graph analysis, so that we can generate new test cases to cover only the change-related parts of the new model. Our experiment on four large protocol docu¬ment testing projects shows that the technique can significantly reduce regression testing time when compared with complete re¬generation of the test suites.
Interdisciplinary Medical Social Work: A Working Taxonomy

Findings from a year-long exploratory study aimed at describing universal functions of medical social work with interdisciplinary teams in acute care settings are reported here. A universal taxonomy of interdisciplinary social work skills and competencies was empirically identified through a participatory action research framework. Findings support previous conceptual descriptions of medical social work’s overarching and historical role to help interdisciplinary teams in acute care to consider patients’ home environment, knowledge, beliefs, culture, and resources during assessment, treatment, and discharge planning. The empirically determined taxonomy reported is intended to provide social workers a framework with which to articulate and evaluate their core competencies on interdisciplinary medical teams.
Identification of Gains on 1q and Epidermal Growth Factor Receptor Overexpression as Independent Prognostic Markers in Intracranial Ependymoma

Purpose: Pathogenesis of ependymomas is still poorly understood and molecular markers for risk-adapted patient stratification are not available. Our aim was to screen for novel genomic imbalances and prognostic markers in ependymal tumors. Experimental Design: We analyzed 68 sporadic tumors by matrix-based comparative genomic hybridization using DNA microarrays containing >6,400 genomic DNA fragments. Novel recurrent genomic gains were validated by fluorescence in situ hybridization using a tissue microarray consisting of 170 intracranial ependymomas. Candidate genes were also tested for mRNA expression by quantitative real-time PCR, and protein expression was determined by immunohistochemistry on the tissue microarray. Results: Chromosomal gain of 1q correlated with pediatric patients (P = 0.004), intracranial ependymomas (P = 0.05), and tumors of grade III (P = 0.002). Gain of 1q21.1-32.1 was associated with tumor recurrence in intracranial ependymomas (P < 0.001). Furthermore, gain of 1q25 as determined by fluorescence in situ hybridization represented an independent prognostic marker for either recurrence-free survival (P < 0.001) or overall survival (P = 0.003). Recurrent gains at 5p15.33 covering hTERT were validated by immunohistochemistry, and elevated protein levels correlated with adverse prognosis (P = 0.01). In addition to frequent gains and high-level amplification of epidermal growth factor receptor (EGFR) at 7p11.2, immunohistochemistry revealed protein overexpression to be correlated with poor prognosis (P = 0.002). EGFR protein status subdivides intracranial grade II ependymomas into two different risk groups (P = 0.03) as shown by multivariate analysis. Conclusions: Thus, the states of 1q25 and EGFR represent independent prognostic markers for intracranial ependymomas to identify patient subgroups with different risk profiles in further clinical investigations. Moreover, EGFR might serve as therapeutic target for more specific chemotherapy applications.
GENERATION 1.5 IN HAWAI'I: GAINING CRITICAL TOOLS FOR READING THE WORLD

A silver controller comprising a container, a core member fitted within the container, a filler material around the core member, and a fluid deflector extending around the filler material. The container has an inlet and an outlet and a base. The inlet is located at a higher level than the outlet. The core member has an aperture that is distal the base. The core member has a flange that extends outwardly above the aperture of the core member. The filler material is a metal above silver in the electromotive force series. The fluid deflector is connected to the flange and extends downwardly therefrom so as to be below the aperture in the core member. A plating shield is placed exterior of the fluid deflector. The plating shield is connected to the flange member at one end and generally abuts the bottom of the container at the other end. The plating shield is of a perforated metal suitable for allowing the passage of fluids therethrough. A conductive member is in electrical contact between the filler material and the plating shield.