Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Statistics and Data Analysis Simulation-based Bayesian Inference for Epidemic Models

Keywords: Bayesian inference Epidemic models Markov chain Monte Carlo Pseudo-marginal methods Smallpox a b s t r a c t A powerful and flexible method for fitting dynamic models to missing and censored data is to use the Bayesian paradigm via data-augmented Markov chain Monte Carlo (DA-MCMC). This samples from the joint posterior for the parameters and missing data, but requires high memory overheads for large-scale systems. In addition, designing efficient proposal distributions for the missing data is typically challenging. Pseudo-marginal methods instead integrate across the missing data using a Monte Carlo estimate for the likelihood, generated from multiple independent simulations from the model. These techniques can avoid the high memory requirements of DA-MCMC, and under certain conditions produce the exact marginal posterior distribution for parameters. A novel method is presented for implementing importance sampling for dynamic epidemic models, by conditioning the simulations on sets of validity criteria (based on the model structure) as well as the observed data. The flexibility of these techniques is illustrated using both removal time and final size data from an outbreak of smallpox. It is shown that these approaches can circumvent the need for reversible-jump MCMC, and can allow inference in situations where DA-MCMC is impossible due to computationally infeasible likelihoods. Mathematical models of infectious disease dynamics are useful tools to help explore the biological mechanisms of disease spread and to provide predictive information to guide the implementation of control policies and interventions (see e.g. Bailey, 1975; Keeling and Rohani, 2008). A common way to model epidemic systems is to consider that individuals progress through different epidemiological states over time. A simple example for a single epidemic of a disease such as influenza is an SIR model, in which individuals are classified as either susceptible to infection (S), infected and infectious (I), or removed (R; corresponding to recovered and immune, or dead). A functional form is then chosen to describe the movements of individuals between states, governed by a set of epidemiological parameters. Due to the inherently stochastic nature of infectious disease outbreaks, we eschew deterministic approximations in favor of fully stochastic models, in which state transitions are governed by sets of probability equations. Hence, multiple realizations of the system will result in a distribution of outcomes, even for a fixed set of parameter values (i.e. with no parameter uncertainty). Therefore the observed data are one realization of a stochastic process, the dynamics of …
Cognitive Side Effects of Brief Pulse Electroconvulsive Therapy: A Review

Cognitive impairment remains a common side effect of brief pulse electroconvulsive therapy (ECT), and its minimization has been the motivation for many different treatment modifications over the decades. The level of impairment has been shown to vary according to different technical parameters of ECT including, but not limited to, electrode placement, dosage, and waveform, as well as patient factors, such as age and premorbid intellect. Most past research has focused the assessment on memory impairments associated with ECT. Specifically, ECT can result in both anterograde and retrograde memory impairments. However, the study of non-memory cognitive functions after ECT has been relatively neglected. Furthermore, although considerable recovery has been observed within weeks of treatment completion, data are lacking in the longer term. The following article presents an overview of what is currently known about the pattern and recovery of cognitive side effects of ECT. Controversies within the literature and areas requiring further research are highlighted.
A View on Beta Cell Transplantation in Diabetes

Abstract: Organ donors also offer a source of insulin‐producing tissue that might be used for the treatment of diabetes. Clinical protocols for transplantation of this tissue aim for the prevention of chronic diabetes complications without introducing new serious side effects. Pancreas and islet cell transplantation are discussed in this perspective. The future of islet cell implants looks favorable but depends on finding ways to induce immune tolerance to the donor beta cells. Clinical trials can take advantage of relevant progress in animal models. In a limited study, recipient treatment with antilymphocyte antibodies and culture of donor cell preparations appeared useful to induce a state of operational immune tolerance in type 1 diabetic patients, as indirectly judged by graft survival and by analysis of auto‐ and alloreactivities in recipients. Use of cultured beta cell preparations also allows donor cell recruitment from suboptimal donor organs and increases the degree of standardization and quality control of islet cell grafts. The future of these grafts will depend on the development of techniques for the neogenesis of beta cells.
Improved outcome after relapse in children with acute myeloid leukaemia

In the Nordic Society for Paediatric Haematology and Oncology paediatric study acute myeloid leukaemia (AML) 93, event‐free survival was 50% and overall survival was 66%, indicating that many patients were cured following relapse. Factors influencing outcome in children with relapsed AML were investigated. The study included all 146 children in the Nordic countries diagnosed with AML between 1988 and 2003, who relapsed. Data on disease characteristics and relapse treatment were related to outcome. Sixty‐six percentage achieved remission with survival after relapse (5 years) 34 ± 4%. Of 122 patients who received re‐induction therapy, 77% entered remission with 40 ± 5% survival. Remission rates were similar for different re‐induction regimens but fludarabine, cytarabine, granulocyte colony‐stimulating factor‐based therapy had low treatment‐related mortality. Prognostic factors for survival were duration of first complete remission (CR1) and stem cell transplantation (SCT) in CR1. In early relapse (<1 year in CR1), survival was 21 ± 5% compared with 48 ± 6% in late relapse. For children receiving re‐induction therapy, survival in early relapse was 29 ± 6% and 51 ± 6% in late. Patients treated in CR1 with SCT, autologous SCT or chemotherapy had a survival of 18 ± 9, 5 ± 5 and 41 ± 5%, respectively. Survival was 62 ± 6% in 64 children given SCT as part of their relapse therapy. A significant proportion of children with relapsed AML can be cured, even those with early relapse. Children who receive re‐induction therapy, enter remission and proceed to SCT can achieve a cure rate of 60%.
Dual Abruptly Focus of Modulated Circular Airy Beams

In this paper, we propose a new kind of circular Airy beam whose spectrum is imposed an initial quadratic phase modulation (QPM). Unlike common abruptly autofocusing beams, we find that such modulated circular Airy beams (MCAB) at image plane, i.e., initial plane, may be morphed into conventional Airy patterns or Bessel-like patterns in spatial regime, depending on the magnitude of QPM. We further investigate the propagation characteristics of the MCAB both analytically and numerically. It is found that the focal intensity, as well as the size of focal spot, do not change with the QPM, but the latter greatly affects the focal trajectory and the focal position of MCAB. In particular, we show that, for the case of Airy pattern, MCAB will exhibit a dual abruptly focusing behaviors having the same focal intensity as well as size of focal spot, where there is one focus behind the image plane, and the another one is in front of it. On the other hand, for the case of Bessel-like pattern, the dual abruptly foci are simultaneously observed behind the image plane for positive QPM but in front of it for negative QPM, thus leading to the formation of an elegant optical bottle with paraboloidal shape. Such novel dual focusing behaviors are expected to be applied in the field of optical trapping and particle acceleration.
Newly synthesized acetylcholine receptors are located in the Golgi apparatus

Chick skeletal muscle cells in tissue culture were fixed and treated with saponin to allow [125I]alpha-bungarotoxin access into the cells while preserving ultrastructure. The kinetics of binding of iodinated alpha-bungarotoxin to intracellular acetylcholine (ACh) receptors and to surface A Ch receptors were comparable. About half of the intracellular ACh receptors are newly synthesized and in the pathway leading to incorporation into the plasma membrane. Correlated electron microscope autoradiographic and kinetic studies of this receptor population suggest that a substantial fraction of the newly synthesized ACh receptors are located in the Golgi apparatus, where they reside for approx. 2 h.
The smell of fear: innate threat of 2,5-dihydro-2,4,5-trimethylthiazoline, a single molecule component of a predator odor

In the last several years, the importance of understanding what innate threat and fear is, in addition to learning of threat and fear, has become evident. Odors from predators are ecologically relevant stimuli used by prey animals as warnings for the presence of danger. Of importance, these odors are not necessarily noxious or painful, but they have innate threat-like properties. This review summarizes the progress made on the behavioral and neuroanatomical fundamentals of innate fear of the predator odor, 2,5-dihydro-2,4,5-trimethylthiazoline (TMT), a component of fox feces. TMT is one of several single molecule components of predator odors that have been isolated in the last several years. Isolation of these single molecules has allowed for rapid advances in delineating the behavioral constraints and selective neuroanatomical pathways of predator odor induced fear. In naïve mice and rats, TMT induces a number of fear and defensive behaviors, including robust freezing, indicating it is an innate threat stimulus. However, there are a number of behavioral constraints that we do not yet understand. Similarly, while some of the early olfactory sensory pathways for TMT-induced fear are being delineated, the pathways from olfactory systems to emotional and motor output regions are less well understood. This review will focus on what we know and what we still need to learn about the behavior and neuroanatomy of TMT-induced fear.
“Like” Me: Shopping, Self-Display, Body Image, and Social Networking Sites

Ideals of beauty and product information are transmitted via sociocultural channels, including social media. Through the framework of objectification theory, we examined the relation of involvement on Facebook to women’s internalization of appearance ideals, psychological well-being, and their intentions to make online purchases. Participants were 796 female college students who completed online measures regarding internalization, sources of beauty information, social comparisons, body satisfaction, self-esteem, purchases referrals, and purchase intentions. Using structural equation modeling, we found that passive Facebook usage influenced the women’s internalization of societal beauty ideals, which was related inversely to the women’s satisfaction with their bodies and self-esteem. Active Facebook usage had direct effects on attention to friends’ referrals and purchase behaviors. Purchase intentions also were influenced by referrals, the importance they placed on social media outlets as sources of information about fashion and appearance, and a more positive self-image. Findings suggest that women’s intentions to make online purchases are determined through their involvement in social media, their friendship connections, and the extent to which their self-perceptions have been affected by sociocultural processes.
Assessment of benefits obtainable in a Hybrid Solar Vehicle using lookahead capabilities for incoming solar energy

In order to maximize the benefits of Hybrid Solar Vehicles, battery management should account for two conflicting requirements: at the end of driving the final state of charge (SOC) should be low enough to allow full storage of solar energy captured in the next parking phase, whereas the adoption of an unnecessary constantly-low value of final SOC would give additional energy losses and compromise battery lifetime. The adoption of on-board solar energy prediction can be therefore beneficial to select the best solution in terms of energy management. In order to assess the benefits achievable by using weather forecast, the effects of different strategies of selection of final SOC are studied by simulation over hourly solar data at different months, and the effects of forecast accuracy on fuel economy is analyzed. Finally, the forecast precision achievable by use of available on-line forecast tools is analyzed by comparison with sun power measured data.
Radioactive 26 Al and 60 Fe in the Milky Way : Implications of the RHESSI detection of 60 Fe

The recent detection of gamma-ray lines from radioactive 26 Al and 60 Fe in the Milky Way by the RHESSI satellite calls for a reassessment of the production sites of those nuclides. The observed gamma-ray line flux ratio is in agreement with calculations of nucleosynthesis in massive stars, exploding as SNII (Woosley and Weaver 1995); in the light of those results, this observation would suggest then that SNII are the major sources of 26 Al in the Milky Way, since no other conceivable source produces substantial amounts of 60 Fe. However, more recent theoretical studies find that SNII produce much higher 60 Fe/ 26 Al ratios than previously thought and, therefore, they cannot be the major 26 Al sources in the Galaxy (otherwise 60 Fe would be detected long ago, with a line flux similar to the one of 26 Al). Wolf-Rayet stars, ejecting 26 Al (but not 60 Fe) in their stellar winds, appear then as a most natural candidate. We point out, however, that this scenario faces also an important difficulty. Forthcoming results of ESA's INTEGRAL satellite, as well as consistent calculations of nucleosynthesis in massive stars (including stars of initial masses as high as 100 M⊙ and metallicities up to 3 Z⊙), are required to settle the issue.
Fibroblast growth factor–2 regulates the stability of nuclear bodies

Nuclear bodies are distinct subnuclear structures. The survival of motoneuron (SMN) gene is mutated or deleted in patients with the neurodegenerative disease spinal muscular atrophy (SMA). The gene product SMN is a marker protein for one class of nuclear bodies denoted as nuclear gems. SMN has also been found in Cajal bodies, which co-localize with gems in many cell types. Interestingly, SMA patients display a reduced number of gems. Little is known about the regulation of nuclear body formation and stabilization. We have previously shown that a nuclear isoform of the fibroblast growth factor–2 (FGF-223) binds directly to SMN. In this study, we analyzed the consequences of FGF-223 binding to SMN with regard to nuclear body formation. On a molecular level, we showed that FGF-223 competed with Gemin2 (a component of the SMN complex that is necessary for gem stabilization) for binding to SMN. Down-regulation of Gemin2 by siRNA caused destabilization of SMN-positive nuclear bodies. This process is reflected in both cellular and in vivo systems by a negative regulatory function of FGF-2 in nuclear body formation: in HEK293 cells, FGF-223 decreased the number of SMN-positive nuclear bodies. The same effect could be observed in motoneurons of FGF-2 transgenic mice. This study demonstrates the functional role of a growth factor in the regulation of structural entities of the nucleus.
Innovation society today: the reflexive creation of novelty

»Innovationsgesellschaft heute: Die reflexive Herstellung des Neuen«. While innovation has shaped modern society from its very inception, it is currently gaining new dimensions: Innovation is becoming increasingly reflexive, heterogeneously distributed, and ubiquitous. Reflexivity implies more than the intentional transformation of routine actions; it also refers to the transformation of social practices based on continuously (re-)produced knowledge about innovation. Thus, innovation itself becomes the aim and purpose of social activities: as the meaning and motif of (what we will refer to as the “semantics” of novelty), as a component of practical routines (the “pragmatics” of creative action), and, finally, as part of systematically (re-)produced social structures of generating novelty (the “grammar” of innovation regimes). Heterogeneous distribution refers to the observed shift from the individual entrepreneur to networks of innovation involving divergent actors. Ubiquity indicates the current expansion of innovation beyond the traditional spheres of science and economy and its generalization into an imperative for social action. This article presents a research framework that addresses the following key questions: How is novelty created reflexively, where can this process be observed, and which actors are driving it? By pursuing an extended notion of innovation, the framework promotes a sophisticated, sociological lens which is more encompassing than conventional economic perspectives. Our goal is to develop a more in-depth and empirically founded understanding of the meaning of innovation in contemporary society and the social processes it involves.
Tool use ability depends on understanding of functional dynamics and not specific joint contribution profiles

Researchers in cognitive neuroscience have become increasingly interested in how different aspects of tool use are integrated and represented by the brain. Comparatively less attention has been directed toward tool use actions themselves and how effective tool use behaviors are coordinated. In response, we take this opportunity to consider the mechanical principles of tool use actions and their relationship to motor learning. Using kinematic analysis, we examine both functional dynamics and joint contribution profiles of subjects with different levels of experience in a primordial percussive task. Our results show that the ability to successfully produce stone flakes using the Oldowan method did not correspond with any particular joint contribution profile. Rather, expertise in this tool use action was principally associated with the subject's ability to regulate the functional parameters that define the task itself.
Protein Fold Recognition using Residue-Based Alignments of Sequence and Secondary Structure

Protein structure prediction aims to determine the three-dimensional structure of proteins form their amino acid sequences. When a protein does not have similarity (homology) to any known fold, threading or fold recognition methods are used to predict structure. Fold recognition methods frequently employ secondary structure, solvent accessibility, and evolutionary information to enhance the accuracy and the quality of the predictions. In this paper, we present a residue based alignment method as an alternative to the state-of-the-art SSEA method, originally introduced by Przytycka et al., and further modified by McGuffin et al. We introduce a residue-based score function, which can incorporate amino acid similarity matrices such as BLOSUM into secondary structure similarity scoring and compute joint alignments. We show that the power of the SSEA method comes from the length normalization instead of the element alignment technique and similar performance can be achieved using residue-based alignments of secondary structures by optimizing gap costs. In simulations with the two benchmark datasets, our method performs slightly better than the SSEA in terms of the fold recognition accuracy. When the secondary structure similarity matrix is combined with the amino acid based BLOSUM30 matrix, the accuracy of our method improves further (4% for the McGuffin set and 10% for the Ding and Dubchak set). The availability of aligning the amino acid and secondary structure sequences in a joint manner offers a better starting point for more elaborate techniques that employ profile-profile alignments and machine learning methods.
Borna Disease Virus Persistence Causes Inhibition of Glutamate Uptake by Feline Primary Cortical Astrocytes

ABSTRACT Borna disease virus (BDV), a nonsegmented, negative-stranded (NNS) RNA virus, causes central nervous system (CNS) disease in a broad range of vertebrate species, including felines. Both viral and host factors contribute to very diverse clinical and pathological manifestations associated with BDV infection. BDV persistence in the CNS can cause neurobehavioral and neurodevelopmental abnormalities in the absence of encephalitis. These BDV-induced CNS disturbances are associated with altered cytokine and neurotrophin expression, as well as cell damage that is very restricted to specific brain regions and neuronal subpopulations. BDV also targets astrocytes, resulting in the development of prominent astrocytosis. Astrocytes play essential roles in maintaining CNS homeostasis, and disruption of their normal activities can contribute to altered brain function. Therefore, we have examined the effect of BDV infection on the astrocyte's physiology. We present here evidence that BDV can establish a nonlytic chronic infection in primary cortical feline astrocytes that is associated with a severe impairment in the astrocytes' ability to uptake glutamate. In contrast, the astrocytes' ability to uptake glucose, as well as their protein synthesis, viability, and rate of proliferation, was not affected by BDV infection. These findings suggest that, in vivo, BDV could also affect an important astrocyte function required to prevent neuronal excitotoxicity. This, in turn, might contribute to the neuropathogenesis of BDV.
Psychiatric Literacy and the Personality Disorders

Background: This study was concerned with investigating the mental health literacy of lay people in regard to the personality disorders. Method: 223 participants responded to a questionnaire entitled ‘eccentric people’ which contained vignettes of 10 personality disorders which they rated as well as labelled. Results: Lay people recognize people with personality disorders as being unhappy, unsuccessful at work and as having poor personal relationships, but do not associate these problems with psychological causes. Rates of correct labelling were under 7% for 7/10 personality disorders. Cluster A (apart from paranoid) was commonly labelled as depression or as an autism spectrum disorder. Clusters B and C (apart from obsessive-compulsive) were commonly labelled as ‘low self-esteem’. History of psychological education and illness were positively correlated with correct recognition of 70 and 60% of the personality disorders, respectively. Conclusion: The mental health literacy of lay people in regard to the personality disorders is low. This raises concerns for health-seeking behaviour and diagnosis, as well as stigma and social neglect of people living with personality disorders. The question of cultural influences on the manifestation, diagnosis and recognition of mental illnesses, and the personality disorders in particular, is discussed.