Miracle-dz/UniFAR-FTUs huggingface dataset:
Vicarious Rewards Modulate the Drift Rate of Evidence Accumulation From the Drift Diffusion Model

Taking other people’s interests into account is a fundamental ability allowing humans to maintain relationships. Yet, the mechanisms by which monetary incentives for close others influence perceptual decision-making processes remain elusive. Here, we compared perceptual decisions motivated by payoffs for oneself or a close relative. According to drift diffusion models (DDMs), perceptual decisions are made when sensory evidence accumulated over time – with a given drift rate – reaches one of the decision boundaries. We used these computational models to identify whether the drift rate of evidence accumulation or the decision boundary is affected by these two sources of motivation. Reaction times and sensitivity were modulated by three factors: the Difficulty (motion coherence of the moving dots), the Payoff associated with, and the Beneficiary of the decision. Reaction times (RTs) were faster for easy compared to difficult trials and faster for high payoffs as compared to low payoffs. More interestingly, RTs were also faster for self than for other-affecting decisions. Finally, using DDM, we found that these faster RTs were linked to a higher drift rate of the decision variable. This study offers a mechanistic understanding of how incentives for others and motion coherence influence decision-making processes.
Subjective Cognitive Decline and Nighttime Sleep Alterations, a Longitudinal Analysis

Objective: The aim of this study was to analyze quantitative sleep changes and their implication on subjective cognitive decline (SCD). Objective sleep patterns were investigated by an actigraph and recorded at the baseline and 2-year after in order to examine specific sleep alterations in SCD. Background: Sleep disorders are very common among average elderly adults and an altered sleep pattern is known to be a risk factor for future development of mild cognitive impairment (MCI) and dementia. Recent studies have shown how sleep is objectively altered in average senior adults with SCD, without any other significant change in cognition and behavior or brain structure. Considering that both SCD and disrupted sleep are risk factors for future MCI and dementia, with sleep only as a modifiable risk factor, further research is required to deeply investigate the interaction between sleep and SCD. Methods: Among 70 community-dwelling elderly individuals who had been enrolled at baseline, 35 (64.6 ± 5.6 years, 15 M/20 F) underwent a complete neuropsychological battery and 1-week wrist actigraphy recording 2 years later during the follow-up stage. Individuals were divided into two groups according to their SCD Questionnaire (SCD-Q) score. Sleep hours, sleep efficiency and onset latency, napping and time awake after sleep onset (WASO) were collected. All individuals underwent structural magnetic resonance imaging (MRI) examination to exclude brain disorders. Data collection was performed at baseline and after 2 years at the follow-up phase. Results: A significantly different night sleep time between the two groups was observed: SCD showed a lower total sleep time (TST) than non-SCD subjects. Moreover, a total time spent in bed (TIB) was significantly lower in SCD subjects over 2 years of observation. Conclusions: Objective changes over time of the sleep pattern, specifically TIB and TST, are present in SCD individuals. The results of the study show that sleep alterations are common in SCD and underline the clinical importance of screening in order to assess sleep alterations as well as improve sleep in average adults with SCD complaints.
Allelopathic Effects of Native Versus Invasive Plants on One Major Invader

Allelopathy is defined as the effects (stimulatory and inhibitory) of a plant on the development of neighboring plants through the release of secondary compounds. Autoallelophaty is the beneficial or harmful effect of a plant species on itself. The allelopathic potential belonging to a native species could induce a biotic resistance against invasive plants, whereas allelochemicals released by exotic species could favor the establishment of invasive species (invasional meltdown). The aim of our study was to examine the potential allelopathic effect of four plant species on the target species Ludwigia hexapetala using two experiments. In the first experiment, we tested the allelopathic effect of root and leaf leachates of the two congeneric exotic species Ludwigia hexapetala and Ludwigia peploides on L. hexapetala, while in the second experiment, we studied the allelopathic effect of root and leaf leachates of a sympatric exotic species Myriophyllum aquaticum and of one native species Mentha aquatica on L. hexapetala. We measured the stem length to calculate the relative growth rate and four physiological traits (nitrogen balance index and flavonol, chorophyll, anthocyanin indices) of the target plants on a weekly basis. At the end of the experiment, we determined the aboveground and belowground biomass. We also counted the number of lateral branches and measured their lengths. We found that the root leachates of L. peploides and of Myriophyllum aquaticum had stimulated the synthesis of flavonols of L. hexapetala. Leaf leachate of L. hexapetala also stimulated its own flavonol synthesis. Also, the root leachate of L. peploides had stimulated the total biomass and length of lateral branches of L. hexapetala, whereas the production of lateral branches had been stimulated by root leachates of both Ludwigia species and by leaf leachate of Myriophyllum aquaticum. The autoallelopathy of L. hexapetala could explain its invasiveness. Both leachates produced by Mentha aquatica had no effect on the physiological and morphological traits of the invasive L. hexapetala and indicated no biotic resistance in the recipient community. The two invasive plant species Myriophyllum aquaticum and L. peploides could favor the establishment of L. hexapetala. These results suggested an “invasional meltdown. ”
Variation of the BrO/SO2 Molar Ratio in the Plume of Tungurahua Volcano Between 2007 and 2017 and Its Relationship to Volcanic Activity

Recent long-term observations of the bromine monoxide (BrO) to sulphur dioxide (SO2) molar ratio in volcanic plumes have suggested a link between changes in the BrO/SO2 ratio and the volcanic activity. Nevertheless, understanding of the mechanisms determining this link is still limited due to the lack of studies on volcanic bromine release from the melt into the atmosphere. We present the results of 10 years (2007–2017) of observations of the BrO/SO2 molar ratio in the volcanic plume of Tungurahua volcano, Ecuador. Following the nearly continuous eruptive activity from 1999 to 2008, Tungurahua showed alternating phases of eruptive activity separated by periods of quiescence between late 2008 and March 2016, after which degassing intensity decreased below detection. By comparing the BrO/SO2 molar ratios collected from 13 eruptive phases to volcanic activity, this study aims to broaden the global observational database investigating their link. For this purpose, we combine three different methods to retrieve the BrO/SO2 molar ratio to analyse variations over different timescales. We identify a cyclic pattern in BrO/SO2 molar ratios for 11 of the 13 eruptive phases. The phases are initialised by low BrO/SO2 molar ratios between 2 and 6 × 10−5 coinciding with vulcanian-type activity followed by a strong increase to ratios ranging between 4 and 17 × 10−5 when eruptive dynamism shifts to strombolian. For five phases, we additionally observe a progressive decrease to the initial values of 2 to 5 × 10−5 toward the end of the phase. This clear pattern indicates a connection between the BrO/SO2 molar ratio and eruptive dynamics. Based on our new data, we propose a conceptual model of the volcanic processes taking place at Tungurahua during the eruptive phases. Our data furthermore indicate that maximal BrO/SO2 molar ratios observed during each phase could be related to the input of volatile-rich magma into the active part of the volcanic system of Tungurahua. This study shows that long-term BrO/SO2 molar ratios can be used as a proxy for the volatile status as well as temporal evolution of the volcanic system. © 2019 Warnach, Bobrowski, Hidalgo, Arellano, Sihler, Dinger, Lubcke, Battaglia, Steele, Galle, Platt and Wagner.
Identification of a Novel Plasmid Lineage Associated With the Dissemination of Metallo-β-Lactamase Genes Among Pseudomonads

Acquisition of metallo-β-lactamases (MBLs) represents one of most relevant resistance mechanisms to all β-lactams, including carbapenems, ceftolozane and available β-lactamase inhibitors, in Pseudomonas spp. VIM-type enzymes are the most common acquired MBLs in Pseudomonas aeruginosa and, to a lesser extent, in other Pseudomonas species. Little is known about the acquisition dynamics of these determinants, that are usually carried on integrons embedded into chromosomal mobile genetic elements. To date, few MBL-encoding plasmids have been described in Pseudomonas spp. , and their diversity and role in the dissemination of these MBLs remains largely unknown. Here we report on the genetic features of the VIM-1-encoding plasmid pMOS94 from P. mosselii AM/94, the earliest known VIM-1-producing strain, and of related elements involved in dissemination of MBL. Results of plasmid DNA sequencing showed that pMOS94 had a modular organization, consisting of backbone modules associated with replication, transfer and antibiotic resistance. Plasmid pMOS94, although not typable according to the PBRT scheme, was classifiable either in MOBF11 or MPFT plasmid families. The resistance region included the class I integron In70, carrying blaV IM-1, in turn embedded in a defective Tn402-like transposon. Comparison with pMOS94-like elements led to the identification of a defined plasmid lineage circulating in different Pseudomonas spp. of clinical and environmental origin and spreading different MBL-encoding genes, including blaIMP-63, blaBIM, and blaV IM-type determinants. Genetic analysis revealed that this plasmid lineage likely shared a common ancestor and had evolved through the acquisition and recombination of different mobile elements, including the MBL-encoding transposons. Our findings provide new insights about the genetic diversity of MBL-encoding plasmids circulating among Pseudomonas spp. , potentially useful for molecular epidemiology purposes, and revealed the existence and persistence of a successful plasmid lineage over a wide spatio-temporal interval, spanning over five different countries among two continents and over 20-years.
Wildfires Influence Abundance, Diversity, and Intraspecific and Interspecific Trait Variation of Native Bees and Flowering Plants Across Burned and Unburned Landscapes

Wildfire regimes are changing in the western United States, yet we have little basic understanding of how wildfires influence native bees, the resources they depend on for food and nesting, or the traits that influence their interactions with plants. In burned and unburned areas in Montana, USA, we investigated the abundance and diversity of native bees, floral and nesting resources, nesting success, and traits of flowers and bees. In two of the three localities studied, burned areas, including areas that burned with high-severity wildfires, supported higher density and diversity of native bees and the flowers they depend on for food and larval provisioning. Burned areas also had more bare ground for ground-nesting bees and more available coarse woody debris for cavity-nesting bees than unburned areas. Moreover, cavity-nesting bees were completely unsuccessful at nesting in artificial nesting boxes in unburned areas, while nesting success was 40% in burned areas. Mean bee intertegular distance (a trait strongly correlated with tongue length, foraging distance, and body size) was similar between burned and unburned areas. However, wildfires influenced both interspecific and intraspecific trait variation of bees and plants. Intraspecific variation in bee intertegular distance was higher in unburned than burned areas. Both interspecific and intraspecific variation in floral traits important for interactions with pollinators were generally higher in burned than unburned areas. Thus, wildfires generally increased the density and species diversity of bees and flowers as well as trait variation at both trophic levels. We conclude that wildfires – even large, high-severity wildfires – create conditions that support native bees and the resources they need to flourish, but that unburned areas maintain trait variation in landscape mosaics with heterogeneous fire conditions.
Feasability of Introducing a Thioether Ring in Vasopressin by nisBTC Co-expression in Lactococcus lactis

Introducing one or more intramolecular thioether bridges in a peptide provides a promising approach to create more stable molecules with improved pharmacodynamic properties and especially to protect peptides against proteolytic degradation. Lanthipeptides are compounds that naturally possess thioether bonds in their structure. The model lanthipeptide, nisin, is produced by Lactococcus lactis as a core peptide fused to a leader peptide. The modification machinery responsible for nisin production, including the Ser/Thr-dehydratase NisB and the cyclase NisC, can be applied for introducing a thioether bridge into peptides fused to the nisin leader peptide, e.g., to replace a disulfide bond. Vasopressin plays a key role in water homeostasis in the human body and helps to constrict blood vessels. There are two cysteine residues in the structure of wild type vasopressin, which form a disulfide bridge in the mature peptide. Here, we show it is possible to direct the biosynthesis of vasopressin variants in such a way that the disulfide bridge is replaced by a thioether bridge using the nisin modification machinery NisBTC, albeit at low efficiency. Vasopressin mutants were fused either to the nisin leader peptide directly (Type A), after the first three rings of nisin (Type B/C), or after full nisin (Type D). The type B strategy was optimal for expression. LC-MS/MS data verified the formation of a thioether bridge, which provides proof of principle for this modification in vasopressin. This is a first step prior to the necessary increase of the production yield and further purification of these peptides to finally test their biological activity in tissue and animal models.
Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia

Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes.
CRTAM Protects Against Intestinal Dysbiosis During Pathogenic Parasitic Infection by Enabling Th17 Maturation

The gastrointestinal tract hosts the largest collection of commensal microbes in the body. Infections at this site can cause significant perturbations in the microbiota, known as dysbiosis, that facilitate the expansion of pathobionts, and can elicit inappropriate immune responses that impair the intestinal barrier function. Dysbiosis typically occurs during intestinal infection with Toxoplasma gondii. Host resistance to T. gondii depends on a potent Th1 response. In addition, a Th17 response is also elicited. How Th17 cells contribute to the host response to T. gondii remains unclear. Here we show that class I-restricted T cell-associated molecule (CRTAM) expression on T cells is required for an optimal IL-17 production during T. gondii infection. Moreover, that the lack of IL-17, results in increased immunopathology caused by an impaired antimicrobial peptide production and bacterial translocation from the intestinal lumen to the mesenteric lymph nodes and spleen.
Conexp-Clj - A Research Tool for FCA

There is a plenitude of software programs to analyze data sets using notions from formal concept analysis (FCA). For example, there are 64 FCA related projects listed on GitHub. Those are developed in ten different programming languages and provide tools and libraries for computing formal concepts and alike. The research tool conexp-clj sticks out in this list. It is the only application in the FCA realm developed using the programming language Clojure, which is a modern, dynamic, and functional dialect of the Lisp programming language running on the Java platform. We summarize in this work the extensive set of notions from FCA that are covered by conexp-clj, show recent developments, present simple examples on a real world data set and depict a timeline for our next goals.
pymcmcstat: A Python Package for Bayesian Inference Using Delayed Rejection Adaptive Metropolis

Many scientific problems require calibrating a set of model parameters to fit a set of data. Various approaches exist for performing this calibration, but not all of them account for underlying uncertainty within the problem. Examples of this uncertainty include random noise within experimental measurements as well as errors due to model discrepancy; i.e., missing physics in the model. A Bayesian framework provides a natural perspective from which to perform model calibration to accommodate this uncertainty. To utilize this approach, we make several assumptions regarding the problem.
A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful tool for investigation the genome-wide distribution of DNA binding protein and their modifications. Yet, the computational analysis of Next-Generation Sequencing datasets is still a bottleneck for most of the experimental researchers. Most often, this type of analysis require multiple steps i.e. read quality control, mapping to a reference genome, peak calling, annotation and functional enrichment analysis that are performed by various tools e.g. fastp (S. Chen, Zhou, Chen, & Gu, 2018), bowtie2 (Langmead & Salzberg, 2012) or samtools (Li et al., 2009) only to name a few. These various tools require different software dependencies and can have different software versions and/or incompatibilities which might impair the analysis reproducibility. Here we provide a complete, user-friendly and highly customized ChIP-seq analysis pipeline for paired-end (Illumina) data based on the Snakemake workflow manager (Koster & Rahmann, 2012).
A High-Level Survey of Video Annotation and Retrieval Systems

Videos are an integral part of current information technologies and the web. The demand for efficient retrieval rises with the increasing number of videos, which is equally true for video annotation techniques as matadata is the primary source of most retrieval systems. Existing surveys about video annotation and retrieval cover specific approaches and the underlying analysis technologies. In contrast to these surveys, we focus on the big picture that is common for all of today’s systems, their distinguishing features, and we try to point out research trends and access points for further reading. This high-level survey addresses researchers that are new to the field and require a proper overview as well as individuals and enterprises that want to make up their minds about the annotation and retrieval possibilities they have. In this work, we start with a general definition of video documents before different aspects of annotation and retrieval systems are discussed in combination with user intentions and interaction processes. KeywordsContent-Based Video Analysis; Video Search and Retrieval; Metadata; Automatic and Interactive Annotation
More than just friends: in-home use and design recommendations for sensing socially assistive robots (SARs) by older adults with depression

Abstract As healthcare turns its focus to preventative community-based interventions, there is increasing interest in using in-home technology to support this goal. This study evaluates the design and use of socially assistive robots (SARs) and sensors as in-home therapeutic support for older adults with depression. The seal-like SAR Paro, along with onboard and wearable sensors, was placed in the homes of 10 older adults diagnosed with clinical depression for one month. Design workshops were conducted before and after the in-home implementation with participating older adults and clinical care staff members. Workshops showed older adults and clinicians sawseveral potential uses for robots and sensors to support in-home depression care. Long-term in-home use of the robot allowed researchers and participants to situate desired robot features in specific practices and experiences of daily life, and some user requests for functionality changed due to extended use. Sensor data showed that participants’ attitudes toward and intention to use the robot were strongly correlated with particular Circadian patterns (afternoon and evening) of robot use. Sensor data also showed that those without pets interacted with Paro significantly more than those with pets, and survey data showed they had more positive attitudes toward the SAR. Companionship, while a desired capability, emerged as insufficient to engage many older adults in long-term use of SARs in their home.
SCONE: Open Source Software for Predictive Simulation of Biological Motion

Mobility impairments pose an increasing burden on our ageing society, urging researchers and clinicians to invent new assistive technologies and improve medical treatment. However, their efforts are impeded by a gap in our understanding of biological motion. Even though individual branches of neuroscience and biomechanics have produced a wealth of knowledge of the components comprising biological motion, the fundamental question of how the neural, muscular and skeletal systems operate together to produce efficient and purposeful motion remains largely unanswered.