julilili42/papers huggingface dataset:
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
2022-08-27

Abstract Motivation Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a ‘theater of activity’ (ToA). An important question is, to what degree does the taxonomic and functional content of the former depend on the (details of the) latter? Here, we investigate a related technical question: Given a taxonomic and/or functional profile estimated from metagenomic sequencing data, how to predict the associated ToA? We present a deep-learning approach to this question. We use both taxonomic and functional profiles as input. We apply node2vec to embed hierarchical taxonomic profiles into numerical vectors. We then perform dimension reduction using clustering, to address the sparseness of the taxonomic data and thus make the problem more amenable to deep-learning algorithms. Functional features are combined with textual descriptions of protein families or domains. We present an ensemble deep-learning framework DeepToA for predicting the ToA of amicrobial community, based on taxonomic and functional profiles. We use SHAP (SHapley Additive exPlanations) values to determine which taxonomic and functional features are important for the prediction. Results Based on 7560 metagenomic profiles downloaded from MGnify, classified into 10 different theaters of activity, we demonstrate that DeepToA has an accuracy of 98.30%. We show that adding textual information to functional features increases the accuracy. Availability and implementation Our approach is available at http://ab.inf.uni-tuebingen.de/software/deeptoa. Supplementary information Supplementary data are available at Bioinformatics online.
S11-4 Participatory physical activity promotion in senior residencies
2022-08-27

Abstract Background During their final life decade, people in Germany tend to live in senior residences or nursing homes. Re-location to such institutionalized homes is associated with declining levels of physical activity. Beside intrapersonal factors, like dealing with illness, social and physical environments might be decisive in shaping residents' physical activity levels. At the same time, it remains largely underresearched what residents themselves perceive as barriers and promoters of physical activity. This presentation aims to introduce first results of BaSAlt (BMG, 2019-2022), a participatory research project on physical activity promotion in senior residences in Germany. Methods We draw upon data from the BaSAlt study (2019-2022) in eight German senior residences, generated using Photovoice with 48 residents, staff, and visitors, as well as semi-structured interviews (n = 24), group discussions (n = 8), cooperative planning in future workshops (n = 16) and document analysis. Recorded and transcribed interviews, photos, discussions, as well as documents are subject to thematic analysis (Braun &amp; Clarke 2016). All participating actors become part of data collection, and analysis, as well as in developing and implementing change projects to promote physical activity informed by findings. Results The presentation will highlight similarities and differences in participants' perceptions of physical activity-related promoters and barriers. We will present a preliminary comparative assessment of the organizational readiness in participating senior residences and potential consequences for cooperative planning in future workshops. Our aim is to initiate concrete action to improve physical activity promotion. Conclusions The BaSAlt design recognizes residents, staff, and visitors as experts of their own lives, which allows for greater awareness of people's unique experiences and perceptions. The participatory approach used both for data collection and intervention planning might help uncover physical activity-related promoters and barriers that might otherwise have remained hidden and thus support the development of individualized and targeted action for physical activity promotion.
S11 Improving knowledge co-creation and participation in physical activity promotion: The cooperative planning approach
2022-08-27

Abstract A central problem of current efforts to promote health and physical activity (PA) is that many successful projects remain stuck in the demonstration phase and are not implemented successfully at scale. The use of participatory and/or co-creation approaches has been suggested to avoid this ?pilot project trap? and better adapt interventions to target group needs and setting specificities. This symposium intends to introduce to an international audience a particular participatory concept that has become increasingly popular in PA promotion in Germany in recent years: The Cooperative Planning approach has been successfully used in sport facility planning, local and regional PA policy development, and various settings of PA promotion (incl. kindergartens, schools, vocational training, and communities). The workshop will shed light on the theoretical background and methodology of Cooperative Planning as well as its specific application in select settings. The first presentation will introduce the concept of Cooperative Planning, outline potential areas of application, and compare it with other popular participatory and co-creation approaches in PA promotion. Following this, we will provide evidence from ongoing projects employing the approach to promote PA in kindergartens (Presentation 2) and in the community setting (Presentation 3). Presentation 4 will introduce an example from the retirement home setting and also highlight ways of combining Cooperative Planning with other approaches such as photovoice and participatory evaluation. The final presentation will provide an outlook on the future extension of the concept by introducing the idea of the Practice Dive, which may be used to further optimize knowledge co-creation between researchers and practitioners. A closer look at the Cooperative Planning approach is both timely and relevant for an international audience for a number of reasons: Conceptually, Cooperative Planning is a theory-based framework that combines ideas of participation and co-creation for PA into an innovative whole-of-system approach. From a practical PA promotion perspective, it transcends many existing techniques by focusing both on engaging multipliers and members of the target group, and by involving all of them in the decisive intervention development process (e.g. rather than only via opinion polls or focus groups). This symposium will allow us to combine evidence from four different projects, highlighting both the specificities of working in different settings as well as different aspects and possible extensions of the Cooperative Planning approach.
Disentangling the effects of biomass and productivity in plant competition
2022-08-28

Abstract The relationship between competition and productivity in plant communities is unclear, and this is likely to be due to (1) a confusion in the literature between productivity and biomass, (2) the lack of studies assessing variation in competition in all combinations of biomass and productivity. We assessed the outcome of plant–plant interactions by removing the neighbors around five focal species in 14 herbaceous communities with contrasting biomasses and productivities: meadows with high biomass and productivity, heathlands with high biomass and low productivity, understory communities of deciduous forests with low biomass and high productivity and calcareous grasslands with low biomass and low productivity. Competition intensity was quantified with the relative interaction index (RII) calculated for both survival and growth of the transplanted targets assessed with the increase in leaf number. To examine which traits better explain variation in competition and what drives variation in diversity, we also quantified litter decomposition rate, species composition and diversity and six morphological traits related to plant size and growth rate for eight dominant species of each community. Our main questions were: (1) Is competition mostly related to biomass or productivity? (2) Which traits of the community dominants better explain variation in competition? (3) Is variation in competition and related traits correlated with variation in diversity? Competition for survival significantly increased with increasing community biomass (but not productivity). In addition, competition for survival increased with the size traits and competitive effects of the dominant species of the communities, whereas diversity decreased. Competition for growth also increased with increasing productivity, but only for high‐biomass communities. Additionally, the increase in competition for growth with increasing soil fertility, as measured with litter decomposition rate, was only due to an increase in target growth in plots without neighbors and was unrelated to community competitive effects and species diversity. The results of our study illustrate how the confusion between productivity and biomass could have contributed to the long‐standing debate on variation in competition along productivity gradients and its consequence for diversity.
Georg Simmel Goes Virtual: From ‘Philosophy of Landscape’ to the Possibilities of Virtual Reality in Landscape Research
2022-08-28

With his text “Philosophy of Landscape” (German original: “Philosophie der Landschaft”), the German sociologist and philosopher Georg Simmel laid a foundation for landscape research that is still significant today. In the text, he equates the creation and perception of landscape with the creation of a painting. In doing so, he provided an essential foundation for landscape research with a constructivist orientation. In order to be able to grasp the differentiated nature of landscape analytically and to apply it to Simmel’s understanding of landscape, we resort to the approach of the three landscapes, which was developed from Karl Popper’s theory of the three worlds. The pictorial metaphor of Simmel’s understanding of landscapes, however, had the effect of limiting landscape to the visual, and often to what he described as ‘natural’. It did not address the power-bound nature of landscape. These aspects, however, are of great importance in current discussions about landscape. Aspects of power, multisensuality, and the incorporation of non-natural elements gain additional currency through the creation of augmented and virtual landscapes. This concerns, on the one hand, the creation of these landscapes, on the other hand, their individual internal consciousness, as well as their social construction. These show, not least, the contingency of landscape construction. They offer possibilities for the investigation of landscape stereotypes, and how innovations can be fed into the social construction of landscape to engage other senses beyond the sense of sight. The aim of our paper is to use conceptual critique to reflect on the conceptual development of social and cultural studies in landscape research since Simmel and to present its potential for framing research on AR and VR landscapes.
Using Multiparametric Cardiac Magnetic Resonance to Phenotype and Differentiate Biopsy-Proven Chronic from Healed Myocarditis and Dilated Cardiomyopathy
2022-08-28

(1) Objectives: To discriminate biopsy-proven myocarditis (chronic vs. healed myocarditis) and to differentiate from dilated cardiomyopathy (DCM) using cardiac magnetic resonance (CMR). (2) Methods: A total of 259 consecutive patients (age 51 ± 15 years; 28% female) who underwent both endomyocardial biopsy (EMB) and CMR in the years 2008–2021 were evaluated. According to right-ventricular EMB results, patients were divided into either chronic (n = 130, 50%) or healed lymphocytic myocarditis (n = 60, 23%) or DCM (n = 69, 27%). The CMR protocol included functional, strain, and late gadolinium enhancement (LGE) imaging, T2w imaging, and T2 mapping. (3) Results: Left-ventricular ejection fraction (LV-EF) was higher, and the indexed end-diastolic volume (EDV) was lower in myocarditis patients (chronic: 42%, median 96 mL/m2; healed: 49%, 86 mL/m2) compared to the DCM patients (31%, 120 mL/m2), p &lt; 0.0001. Strain analysis demonstrated lower contractility in DCM patients vs. myocarditis patients, p &lt; 0.0001. Myocarditis patients demonstrated a higher LGE prevalence (68% chronic; 59% healed) than the DCM patients (45%), p = 0.01. Chronic myocarditis patients showed a higher myocardial edema prevalence and ratio (59%, median 1.3) than healed myocarditis (23%, 1.3) and DCM patients (13%, 1.0), p &lt; 0.0001. T2 mapping revealed elevated values more frequently in chronic (90%) than in healed (21%) myocarditis and DCM (23%), p &lt; 0.0001. T2 mapping yielded an AUC of 0.89 (sensitivity 90%, specificity 76%) in the discrimination of chronic from healed myocarditis and an AUC of 0.92 (sensitivity 86%, specificity 91%) in the discrimination of chronic myocarditis from DCM, both p &lt; 0.0001. (4) Conclusions: Multiparametric CMR imaging, including functional parameters, LGE and T2 mapping, may allow differentiation of chronic from healed myocarditis and DCM and therefore help to optimize patient management in this clinical setting.
Linking neuronal and hemodynamic network signatures in the resting human brain
2022-08-28

Abstract Despite several studies investigating the relationship between blood-oxygen-level-dependent functional MRI (BOLD-fMRI) and neuroelectric activity, our understanding is rather incomplete. For instance, the canonical hemodynamic response function (HRF) is commonly used, regardless of brain region, frequency of electric activity and functional networks. We studied this relationship between BOLD-fMRI and electroencephalography (EEG) signal of the human brain in detail using simultaneous fMRI and EEG in healthy awake human subjects at rest. Signals from EEG sensors were filtered into different frequency bands and reconstructed it in the three-dimensional source space. The correlation of the time courses of the two modalities were quantified on a voxel-by-voxel basis on full-brain level as well as separately for each resting state network, with different temporal shifts and EEG frequency bands. We found highly significant correlations between the BOLD-fMRI signal and simultaneously measured EEG, yet with varying time-lags for different frequency bands and different resting state networks. Additionally, we found significant negative correlations with a much longer delay in the fMRI BOLD signal. The positive correlations were mostly around 6-8 seconds delayed in the BOLD time course while the negative correlations were noticed with a BOLD delay of around 20 to 26 seconds. These positive and negative correlation patterns included the commonly reported alpha and gamma bands but also extend in other frequency bands giving characteristic profiles for different resting state networks. Our results confirm recent works that suggest that the relationship between the two modalities is rather brain region / network-specific than a global function and suggest that applying a global canonical HRF for electrophysiological data is probably insufficient to account for the different spatial and temporal dynamics of different brain networks. Moreover, our results suggest that the HRF also varies in different frequency bands giving way to further studies investigating cross-frequency coupling and its interplay with resting state networks.
Speciesist bias in AI: how AI applications perpetuate discrimination and unfair outcomes against animals
2022-08-29

Abstract Massive efforts are made to reduce biases in both data and algorithms to render AI applications fair. These efforts are propelled by various high-profile cases where biased algorithmic decision-making caused harm to women, people of color, minorities, etc. However, the AI fairness field still succumbs to a blind spot, namely its insensitivity to discrimination against animals. This paper is a critical comment on current fairness research in AI. It is the first to describe the ‘speciesist bias’ and investigate it in several different AI systems by reflecting on the problem via a normative analysis and by probing, in several case studies, image recognition, word embedding, and language models with established methods for bias detection. We claim that animals matter morally and that discriminating against them is unethical. Furthermore, we provide evidence for speciesist biases in all the mentioned areas of AI. We find that speciesist biases are solidified by many mainstream AI applications, especially in the fields of computer vision as well as natural language processing. In both cases, this occurs because the models are trained on datasets in which speciesist patterns prevail. Therefore, AI technologies currently play a significant role in perpetuating and normalizing violence against animals. To change this, AI fairness frameworks must widen their scope and include mitigation measures for speciesist biases. This paper addresses the AI community in this regard and stresses the influence AI systems can have on either increasing or reducing the violence that is inflicted on animals, especially on farmed animals.
Specific Gait Changes in Prodromal Hereditary Spastic Paraplegia Type 4: preSPG4 Study
2022-08-29

ABSTRACT Background In hereditary spastic paraplegia type 4 (SPG4), subclinical gait changes might occur years before patients realize gait disturbances. The prodromal phase of neurodegenerative disease is of particular interest to halt disease progression by future interventions before impairment has manifested. Objective The objective of this study was to identify specific movement abnormalities before the manifestation of gait impairment and quantify disease progression in the prodromal phase. Methods Seventy subjects participated in gait assessment, including 30 prodromal SPAST pathogenic variant carriers, 17 patients with mild‐to‐moderate manifest SPG4, and 23 healthy control subjects. An infrared‐camera‐based motion capture system assessed gait to analyze features such as range of motion and continuous angle trajectories. Those features were correlated with disease severity as assessed by the Spastic Paraplegia Rating Scale, neurofilament light chain as a fluid biomarker indicating neurodegeneration, and motor‐evoked potentials. Results Compared with healthy control subjects, we found an altered gait pattern in prodromal pathogenic variant carriers during the swing phase in the segmental angle of the foot (Dunn's post hoc test, q = 3.1) and heel ground clearance (q = 2.8). Furthermore, range of motion of segmental angle was reduced for the foot (q = 3.3). These changes occurred in prodromal pathogenic variant carriers without quantified leg spasticity in clinical examination. Gait features correlated with neurofilament light chain levels, central motor conduction times of motor‐evoked potentials, and Spastic Paraplegia Rating Scale score. Conclusions Gait analysis can quantify changes in prodromal and mild‐to‐moderate manifest SPG4 patients. Thus, gait features constitute promising motor biomarkers characterizing the subclinical progression of spastic gait and might help to evaluate interventions in early disease stages. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
Hydrotherapeutic Heat Application as Support in Febrile Patients: A Scoping Review
2022-08-29

<b><i>Background:</i></b> Most often, fever is still treated by lowering body temperature with medication. In complementary and integrative health care, patients are supported during illness to use the positive effects of fever. Accompanying applications from the field of hydrotherapy are often used for gentle cooling, but there are references that warming in fever can also be used as a support. The aim of this scoping review was to identify available evidence on how, when, and why patients with fever are treated with heat application. <b><i>Methods:</i></b> The MEDLINE, CINAHL, EMBASE, COCHRANE, Google, and Google Scholar databases as well as references of identified literature were searched. As sources of evidence, publications studying patients who received heat application or were kept warm in febrile condition, regardless of medical situation, type of health care setting, and geographical background, were taken into consideration. <b><i>Results:</i></b> The literature search identified 1698 publications, of which only 7 were included. Methods of applying heat were the use of electric warming blankets, hot packs, hot-water bottles, or hot water footbaths. Most of the studies on heat application used temperatures of about 40°C and reported significantly <i>lower</i> body temperature after heat application. <b><i>Conclusions:</i></b> The literature suggests that hydrotherapeutic heat application is a common and well-appreciated method in Middle Eastern and Asian regions to support febrile patients. Using heat to support the energy-intensive and uncomfortable phase of rising fever may improve comfort, prevent unnecessarily high fever, and save biological energy. Therefore, high-quality studies on the role of heat application in fever are expected to be of high relevance for future fever management guidelines and integrative health care in general.
Introduction and elimination, left and right
2022-08-29

Functional programming language design has been shaped by the framework of natural deduction, in which language constructs are divided into introduction and elimination rules for producers of values. In sequent calculus-based languages, left introduction rules replace (right) elimination rules and provide a dedicated sublanguage for consumers of values. In this paper, we present and analyze a wider design space of programming languages which encompasses four kinds of rules: Introduction and elimination, both left and right. We analyze the influence of rule choice on program structure and argue that having all kinds of rules enriches a programmer’s modularity arsenal. In particular, we identify four ways of adhering to the principle that ”the structure of the program follows the structure of the data“ and show that they correspond to the four possible choices of rules. We also propose the principle of bi-expressibility to guide and validate the design of rules for a connective. Finally, we deepen the well-known dualities between different connectives by means of the proof/refutation duality.
Robustness of exponential attractors for infinite dimensional dynamical systems with small delay and application to 2D nonlocal diffusion delay lattice systems
2022-08-29

We first present some sufficient conditions for the construction of a robust family of exponential attractors for infinite dimensional dynamical systems with small time delay perturbation. In particular, we prove that this family of exponential attractors is stable in the sense of the symmetric Hausdorff distance as the delay effects vanish. The abstract result is then applied to two-dimensional nonlocal diffusion lattice systems with small delay.
Tuning Aerogel Properties for Aerospace Applications
2022-08-29

Aerogels are lightweight nanoporous material that offers various advantageous applications owing to their unique mechanical and thermal insulation property. Several unique attributes like the high porosity, large surface area, low thermal conductivity, low density, and high thermal insulation have proven them to be suitable materials to be used in aerospace applications. However, the lack of mechanical strength limits their use, and thus tailoring the properties through reinforcement, or simply modifying the synthesis method is crucial. The tuned aerogels with excellent mechanical properties can serve as a promising material to be used in numerous aerospace applications. Moreover, the chapter addresses the various methods to tune the aerogel properties for increasing their usability in aerospace applications.