preVIEW: from a fast prototype towards a sustainable semantic search system for central access to COVID-19 preprints

The current COVID-19 pandemic emphasizes the use of so-called preprints - a type of publication that is not subject to peer review. Due to its global relevance, there is an immense number of COVID-19-related preprints every day. To help researchers find relevant information, we have developed the semantic search engine preVIEW, it integrates preprints from currently seven different preprint servers. For semantic indexing, we implemented various text mining components to tag, for example, diseases or SARS-CoV-2 specific proteins. While the service initially served as a prototype developed together with users, we present a re-engineering towards a sustainable semantic search system, which was inevitable due to the continuously growing number of preprint publications. This enables easy reuse of the components and allows rapid adaptation of the service to further user needs

Stochastic analysis of exit fluid temperature records from the active TAG hydrothermal mound (Mid-Atlantic Ridge, 26°N) : 2. Hidden Markov models of flow episodes

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): B09102, doi:10.1029/2007JB004961.I develop a stochastic signal model for episodic modes of variability in hydrothermal flow records using probabilistic functions of Markov processes (i.e., hidden Markov models, HMMs) and fit the model to exit fluid temperature time series data from diffuse flow sites on the active TAG hydrothermal mound. The flow states are modeled using Gamma densities to provide flexibility for application to a range of signal types. Between three and five flow states are needed to fit the diffuse flow temperature records from TAG, which correspond to models with between 10 and 28 degrees of freedom. The number of flow states required to fit a given record is related to the signal variance, with more variable records requiring a larger state space. HMMs thus provide an efficient signal model for episodic variability in hydrothermal flow records, suggesting that Markov processes may provide a means to generate stochastic subsurface flow models for deep-sea hydrothermal fields if the spatial flow correlations can be incorporated into a statistical framework. I also use the Viterbi algorithm to “decode” the time series data into best fitting state sequences, which can be used to classify the records into discrete flow episodes. This may provide an objective means to identify discrete events in a flow record if misclassification issues arising from nonepisodic variability (e.g., tidal forcing) can be addressed.This work was supported by the National Science Foundation (OCE-0137329)

Health-related quality of life among patients with treated alcohol use disorders, schizophreniform disorders or affective disorders and the influence of flexible and integrative psychiatric care models in Germany (PsychCare)

IntroductionFlexible and integrated treatment options (FIT) have been established in German psychiatric hospitals to enhance continuous and patient-centered treatment for patients with mental disorders. We hypothesized that patients with experience in FIT treatment showed higher health-related quality of life (HRQoL) and comparable symptom severity compared with patients treated as usual (TAU). Further, we expected that some sub-dimensions of HRQoL determined HRQoL results clearer than others, while certain factors influenced HRQoL and symptom severity stronger in the FIT compared to the TAU group. In addition, we hypothesized that HRQoL is correlated with symptom severity.MethodsWe undertook a controlled, prospective, multicenter cohort study (PsychCare) conducted in 18 psychiatric hospitals in Germany, using the questionnaires Quality of Well Being Self-Administered (QWB-SA) (HRQoL) and Symptom-Checklist-K-9 (SCL-K-9) (symptom severity) at recruitment (measurement I) and 15 months later (measurement II). We assessed overall HRQoL (measured in health utility weights (HUW) and symptom severity score for patients from FIT and TAU treatment. We investigated the QWB-SA dimensions and separated the results by diagnosis. We used beta regressions to estimate the effect of multiple co-variates on both outcomes. To investigate the correlation between HRQoL and symptom severity, we used Pearson correlation.ResultsDuring measurement I, 1,150 patients were recruited; while 359 patients participated during measurement II. FIT patients reported higher HUWs at measurement I compared to TAU patients (0.530 vs. 0.481, p = 0.003) and comparable HUWs at measurement II (0.581 vs. 0.586, p = 0.584). Symptom severity was comparable between both groups (I: 21.4 vs. 21.1, p = 0.936; II: 18.8 vs. 19.8, p = 0.122). We found lowest HRQoL and highest symptom severity in participants with affective disorders. HRQoL increased and symptom severity decreased over time in both groups. The QWB-SA dimension acute and chronic symptoms was associated with highest detriments in HRQoL. We identified risk/protective factors that were associated with lower quality of life and higher symptom severity in both groups. We confirmed that HRQoL was negatively associated with symptom severity.DiscussionHealth-related quality of life (during hospital treatment) was higher among patients treated in FIT hospitals compared to patients in routine care, while symptom severity was comparable between both groups

Long-Term Trajectories of Human Civilization

Purpose This paper aims to formalize long-term trajectories of human civilization as a scientific and ethical field of study. The long-term trajectory of human civilization can be defined as the path that human civilization takes during the entire future time period in which human civilization could continue to exist. Design/methodology/approach This paper focuses on four types of trajectories: status quo trajectories, in which human civilization persists in a state broadly similar to its current state into the distant future; catastrophe trajectories, in which one or more events cause significant harm to human civilization; technological transformation trajectories, in which radical technological breakthroughs put human civilization on a fundamentally different course; and astronomical trajectories, in which human civilization expands beyond its home planet and into the accessible portions of the cosmos. Findings Status quo trajectories appear unlikely to persist into the distant future, especially in light of long-term astronomical processes. Several catastrophe, technological transformation and astronomical trajectories appear possible. Originality/value Some current actions may be able to affect the long-term trajectory. Whether these actions should be pursued depends on a mix of empirical and ethical factors. For some ethical frameworks, these actions may be especially important to pursue

Psychological risk and protective factors for disability in chronic low back pain - a longitudinal analysis in primary care

Background: Utilizing psychological resources when dealing with chronic low back pain might aid the prevention of disability. The observational study at hand examined the longitudinal impact of resilience and coping resources on disability in addition to established risk factors. Methods: Four hundred eighty four patients with chronic low back pain (>3 months) were recruited in primary care practices and followed up for one year. Resilience, coping, depression, somatization, pain and demographic variables were measured at baseline. At follow-up (participation rate 89%), data on disability was collected. We first calculated bivariate correlations of all the predictors with each other and with follow-up disability. We then used a multiple regression to evaluate the impact of all the predictors on disability together. Results: More than half of the followed up sample showed a high degree of disability at baseline (53.7%) and had suffered for more than 10 years from pain (50.4%). Besides gender all of the predictors were bivariately associated with follow-up disability. However in the main analysis (multiple regression), disability at follow up was only predicted by baseline disability, age and somatization. There was no relationship between resilience and disability, nor between coping resources and disability. Conclusions: Although it is known that there are cross-sectional relationships between resilience/coping resources and disability we were not able to replicate it in the multiple regression. This can have several reasons: a) the majority of patients in our sample were much more disabled and suffered for a longer time than in other studies. Therefore our results might be limited to this specific population and resilience and coping resources might still have a protective influence in acute or subacute populations. b) We used a rather broad operationalization of resilience. There is emerging evidence that focusing on more concrete sub facets like (pain) self-efficacy and acceptance might be more beneficial

Implementation, effectiveness and political context of comprehensive primary health care: preliminary findings of a global literature review

Primary health care (PHC) is again high on the international agenda. It was the theme of The World Health Report in 2008, thirty years after the Alma-Ata Declaration, and has been the topic of a series of significant conferences around the world throughout 2008. What have we learnt about its impact in improving population health and health equity? What more do we still need to know? These two questions framed a four-year international research/capacity-building project, “Revitalizing Health for All” (RHFA), funded by the Canadian Global Health Research Initiative, which began in 2007. The findings of a global literature review conducted by this Initiative, and focusing on comprehensive primary health care - and how it has been implemented since Alma Ata are presented. The way in which the political context has affected the comprehensiveness of PHC is considered - along with a series of proposed future PHC research areas.Web of Scienc

Lack of Protection following Passive Transfer of Polyclonal Highly Functional Low-Dose Non-Neutralizing Antibodies

Recent immune correlates analysis from the RV144 vaccine trial has renewed interest in the role of non-neutralizing antibodies in mediating protection from infection. While neutralizing antibodies have proven difficult to induce through vaccination, extra-neutralizing antibodies, such as those that mediate antibody-dependent cellular cytotoxicity (ADCC), are associated with long-term control of infection. However, while several non-neutralizing monoclonal antibodies have been tested for their protective efficacy in vivo, no studies to date have tested the protective activity of naturally produced polyclonal antibodies from individuals harboring potent ADCC activity. Because ADCC-inducing antibodies are highly enriched in elite controllers (EC), we passively transferred highly functional non-neutralizing polyclonal antibodies, purified from an EC, to assess the potential impact of polyclonal non-neutralizing antibodies on a stringent SHIV-SF162P3 challenge in rhesus monkeys. Passive transfer of a low-dose of ADCC inducing antibodies did not protect from infection following SHIV-SF162P3 challenge. Passively administered antibody titers and gp120-specific, but not gp41-specific, ADCC and antibody induced phagocytosis (ADCP) were detected in the majority of the monkeys, but did not correlate with post infection viral control. Thus these data raise the possibility that gp120-specific ADCC activity alone may not be sufficient to control viremia post infection but that other specificities or Fc-effector profiles, alone or in combination, may have an impact on viral control and should be tested in future passive transfer experiments

Polyfunctional Hiv-Specific Antibody Responses Are Associated with Spontaneous Hiv Control

Elite controllers (ECs) represent a unique model of a functional cure for HIV-1 infection as these individuals develop HIV-specific immunity able to persistently suppress viremia. Because accumulating evidence suggests that HIV controllers generate antibodies with enhanced capacity to drive antibody-dependent cellular cytotoxicity (ADCC) that may contribute to viral containment, we profiled an array of extra-neutralizing antibody effector functions across HIV-infected populations with varying degrees of viral control to define the characteristics of antibodies associated with spontaneous control. While neither the overall magnitude of antibody titer nor individual effector functions were increased in ECs, a more functionally coordinated innate immune–recruiting response was observed. Specifically, ECs demonstrated polyfunctional humoral immune responses able to coordinately recruit ADCC, other NK functions, monocyte and neutrophil phagocytosis, and complement. This functionally coordinated response was associated with qualitatively superior IgG3/IgG1 responses, whereas HIV-specific IgG2/IgG4 responses, prevalent among viremic subjects, were associated with poorer overall antibody activity. Rather than linking viral control to any single activity, this study highlights the critical nature of functionally coordinated antibodies in HIV control and associates this polyfunctionality with preferential induction of potent antibody subclasses, supporting coordinated antibody activity as a goal in strategies directed at an HIV-1 functional cure

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical ‘phase transition’, whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have ‘memory’ of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects

A randomized controlled trial to prevent glycemic relapse in longitudinal diabetes care: Study protocol (NCT00362193)

BACKGROUND: Diabetes is a common disease with self-management a key aspect of care. Large prospective trials have shown that maintaining glycated hemoglobin less than 7% greatly reduces complications but translating this level of control into everyday clinical practice can be difficult. Intensive improvement programs are successful in attaining control in patients with type 2 diabetes, however, many patients experience glycemic relapse once returned to routine care. This early relapse is, in part, due to decreased adherence in self-management behaviors. OBJECTIVE: This paper describes the design of the Glycemic Relapse Prevention study. The purpose of this study is to determine the optimal frequency of maintenance intervention needed to prevent glycemic relapse. The primary endpoint is glycemic relapse, which is defined as glycated hemoglobin greater than 8% and an increase of 1% from baseline. METHODS: The intervention consists of telephonic contact by a nurse practitioner with a referral to a dietitian if indicated. This intervention was designed to provide early identification of self-care problems, understanding the rationale behind the self-care lapse and problem solve to find a negotiated solution. A total of 164 patients were randomized to routine care (least intensive), routine care with phone contact every three months (moderate intensity) or routine care with phone contact every month (most intensive). CONCLUSION: The baseline patient characteristics are similar across the treatment arms. Intervention fidelity analysis showed excellent reproducibility. This study will provide insight into the important but poorly understood area of glycemic relapse prevention