Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Spotted Knapweed on Diversity and Abundance of Small Mammals in Grand Sable Dunes, Michigan, USA

ABSTRACT: Spotted knapweed (Centaurea stoebe L. ssp. micranthos [Gugler] Hayek) is an exotic plant that displaces native vegetation leading to altered plant and animal communities. We compared small mammal abundance and diversity in areas with, and without, spotted knapweed in Grand Sable Dunes, Michigan, to determine whether presence of this plant affected the small mammal community. We live trapped small mammals in June and August 2003 in six plots in native dune vegetation and in six plots in areas with spotted knapweed and native dune vegetation. Mean number of captures per trap of mice in spotted knapweed plots ( = 0.50 ± 0.31) was nearly double that in native plot ( = 0.27 ± 0.19; F1,20 = 18.251, P < 0.001). Amount of total vegetative cover in spotted knapweed plots ( = 71 ± 12% SD) was almost twice that in native plots ( = 37 ± 11%). Mean number of captures per trap was positively related to percent cover (F1,20 = 5.239, P = 0.033). Mice are seed and insect predators, seed and spore dispersers, and serve as prey for numerous species. Thus, the positive response by mice to the spotted knapweed invasion may have caused additional changes to this community.
An Improved Method on U-net Near Coastal Areas

ABSTRACT Xu, S. ; He, X. , and Li, X. , 2020. An improved method on U-net near coastal areas. In: Zheng, C.W. ; Wang, Q. ; Zhan, C. , and Yang, S.B. (eds.), Air-Sea Interaction and Coastal Environments of the Maritime and Polar Silk Roads. Journal of Coastal Research, Special Issue No. 99, pp. 48-53. Coconut Creek (Florida), ISSN 0749-0208. Object recognition near coastal area is the hotspot in recent years. However, the problems such as lack of precision, low efficiency and low fault tolerance of these traditional methods are an obstacle of hyperspectral image. This paper proposes an improved method on U-net deep learning model to identify these categories. Firstly, data enhancement processing is implemented on mini-batch×mini-batch×3 patches of cropped randomly images to improve the generalization ability of training network. Secondly, an improved U-net deep learning model is developed to extract the feature information automatically. Next, the improved model can be trained repeatedly by the cross-entropy loss function and INadam optimization algorithm to seek better results. Finally, obtained optimal model is used to extract the object information accurately. Simulation and experimental results show that the proposed method has better detection performance, higher training accuracy with lower loss fluctuation than state-of-the-art methods.
A general inverse problem approach to neural function modeling in Drosophila melanogaster

The development of models of brain function remains a complex problem given the difficulty of extracting organizational principles from observations on a variety of morphologically and physiologically different neurons. State of the art results in this modeling research have been obtained by a different route, by leveraging the power of deep learning. However, this approach takes advantage of neuroscientific knowledge only to a limited extent. Here, I adopt a perspective that aims at combining experimental data and optimization algorithms by framing this modeling research as an inverse problem. To illustrate the method, I collected calcium imaging data from the first two regions of the olfactory processing pathway of the fruit fly Drosophila melanogaster, the antennal lobe and the calix of the mushroom bodies. In each case, our method gives accurate predictions for large fractions of recorded glomeruli and neurons, and the inferred networks recover known features of the biological counterpart.
Effects of environmental stress on species rich assemblages

Selye's widely used model of responses of individual organisms to a stressor (1973, American Science, 61: 692 699) is not appropriate for describing effects at the population or community level. At the ecosystem level a number of functional responses have been suggested by Rapport, Regier & Hutchinson (1985, American Naturalist, 125: 617–640) but detailed analysis shows that, in general, functional responses are not sensitive to the early detection of impending ecosystem damage. Three clear changes in community structure occur in response to stressors. These are reduction in diversity, retrogression to dominance by opportunist species and reduction in mean size of the dominating species. Statistically significant reductions in diversity occur rather late in the sequence of increased stressor impact. The first stages of impact are clearly shown by moderately common species yet most attention has concentrated on the common species. Species which dominate in heavily stressed habitats are often species complexes and the possible genetic mechanisms causing this are considered. Whilst changes in the mean size of the dominant organisms can be shown in experiments there is no clear evidence that recorded reductions in the size of North Atlantic and North Sea plankton are induced by man-made stressors.
An Extension of Stock Composition Analysis to include Marking Data

Population characteristics and man-made marks have been applied separately to gather information on the stock composition of mixed-stock fisheries. This paper develops an extension of the finite mixture problem with learning samples model of Fournier et al. (1984. Can. J. Fish. Aquat. Sci. 41: 400–408) to include marking data as well as morphometric, meristic, or biochemical genetic data for stock composition analyses. Simulation studies are used to test the model on a previously described "problem cluster" that consists of stocks that exhibit high levels of genetic affinity. The test results show that the inclusion of marking data can improve the accuracy of stock composition estimates.
Electrophysiology and Structural Connectivity of the Posterior Hypothalamic Region: Much to Learn From a Rare Indication of Deep Brain Stimulation

Cluster headache (CH) is among the most common and debilitating autonomic cephalalgias. We characterize clinical outcomes of deep brain stimulation (DBS) to the posterior hypothalamic region through a novel analysis of the electrophysiological topography and tractography-based structural connectivity. The left posterior hypothalamus was targeted ipsilateral to the refractory CH symptoms. Intraoperatively, field potentials were captured in 1 mm depth increments. Whole-brain probabilistic tractography was conducted to assess the structural connectivity of the estimated volume of activated tissue (VAT) associated with therapeutic response. Stimulation of the posterior hypothalamic region led to the resolution of CH symptoms, and this benefit has persisted for 1.5-years post-surgically. Active contacts were within the posterior hypothalamus and dorsoposterior border of the ventral anterior thalamus (VAp). Delta- (3 Hz) and alpha-band (8 Hz) powers increased and peaked with proximity to the posterior hypothalamus. In the posterior hypothalamus, the delta-band phase was coupled to beta-band amplitude, the latter of which has been shown to increase during CH attacks. Finally, we identified that the VAT encompassing these regions had a high proportion of streamlines of pain processing regions, including the insula, anterior cingulate gyrus, inferior parietal lobe, precentral gyrus, and the brainstem. Our unique case study of posterior hypothalamic region DBS supports durable efficacy and provides a platform using electrophysiological topography and structural connectivity, to improve mechanistic understanding of CH and this promising therapy.
Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis

Leaf senescence is a developmental process designed for nutrient recycling and relocation to maximize growth competence and reproductive capacity of plants. Thus, plants integrate developmental and environmental signals to precisely control senescence. To genetically dissect the complex regulatory mechanism underlying leaf senescence, we identified an early leaf senescence mutant, rse1. RSE1 encodes a putative glycosyltransferase. Loss-of-function mutations in RSE1 resulted in precocious leaf yellowing and up-regulation of senescence marker genes, indicating enhanced leaf senescence. Transcriptome analysis revealed that salicylic acid (SA) and defense signaling cascades were up-regulated in rse1 prior to the onset of leaf senescence. We found that SA accumulation was significantly increased in rse1. The rse1 phenotypes are dependent on SA-INDUCTION DEFICIENT 2 (SID2), supporting a role of SA in accelerated leaf senescence in rse1. Furthermore, RSE1 protein was localized to the cell wall, implying a possible link between the cell wall and RSE1 function. Together, we show that RSE1 negatively modulates leaf senescence through an SID2-dependent SA signaling pathway.
Epidemiology of Pneumocystis jirovecii Pneumonia and (Non-)use of Prophylaxis

Objectives: Pneumocystis jirovecii pneumonia (PCP) is an AIDS-defining illness. In patients with HIV, the benefit of PCP prophylaxis is well-defined when the CD4 T-cell count decreases below 200 cells/μL. In other immunocompromised patients, the value of PCP prophylaxis is not always as well-established. This study aimed to describe the epidemiology of PCP in recent years and assess how many patients with PCP did or did not receive prophylaxis in the month preceding the infection. Material and Methods: A multicenter retrospective study was performed in 3 tertiary care hospital. A list of patients that underwent broncho-alveolar lavage sampling and Pneumocystis jirovecii (PJ) PCR testing was retrieved from the microbiology laboratories. An in-house PJ quantitative PCR (qPCR) was used in each center. A cycle threshold (Ct) value of ≤ 28.5–30 was considered a probable PCP. For patients with a positive PJ qPCR but above this threshold, a predefined case definition of possible PCP was defined as a qPCR Ct value ≤ 34–35 and both of the following criteria: 1. Clinical and radiological features compatible with PCP and 2. The patient died or received PCP therapy and survived. Patient files from those with a qPCR Ct value ≤ 35 were reviewed to determine whether the patient fulfilled the case definition and if PCP prophylaxis had been used in the weeks preceding the PCP. Disease-specific guidelines, as well as hospital-wide guidelines, were used to evaluate if prophylaxis could be considered indicated. Results: From 2012 to 2018, 482 BAL samples were tested. Two hundred and four had a qPCR Ct value ≤ 35 and were further evaluated: 90 fulfilled the definition of probable and 63 of possible PCP while the remaining 51 were considered colonized. Seventy-four percentages of the patients with PCP were HIV-negative. Only 11 (7%) of the 153 patients had received prophylaxis, despite that in 133 (87%) cases prophylaxis was indicated according to guidelines. Conclusion: In regions where HIV testing and treatment is available without restrictions, PCP is mainly diagnosed in non-HIV immunocompromised patients. More than four out of five patients with PCP had not received prophylaxis. Strategies to improve awareness of antimicrobial prophylaxis guidelines in immunocompromised patients are urgently needed.
The Addition of EGFR Inhibitors in Neoadjuvant Therapy for KRAS-Wild Type Locally Advanced Rectal Cancer Patients: A Systematic Review and Meta-Analysis

Background Patients with locally advanced rectal cancer (LARC) are at higher risk of local and distant recurrence and are thus more vulnerable to metastatic diseases. Neoadjuvant chemoradiotherapy (nCRT) and subsequent curative resection with total mesorectal excision (TME) followed by adjuvant chemotherapy have been recommended by the National Comprehensive Cancer Network (NCCN) guidelines as standard of care for LARC patients. However, the efficacy of the addition of epidermal growth factor receptor (EGFR) inhibitors in kirsten rat sarcoma viral oncogene (KRAS)-wild type LARC patients remains uncertain. Materials PubMed, Embase, and Web of Science were searched to retrieve records on the application of EGFR inhibitors in a neoadjuvant setting for LARC patients. pCR was used as surrogate endpoint to perform data synthesis in a single-arm setting. Results Ten cohorts covering 540 subjects were eligible in this systematic review. The pooled pCR rate for EGFR inhibitors was 15% (95% confidence interval (95% CI), 11–20%; I2 = 55.2%); the pooled estimates of Grade 3/4 diarrhea, Grade 3/4 hand–foot syndrome, Grade 3/4 acneiform rash were 17% (95% CI, 4–34%; I2 = 93.3%), 2% (95% CI, 0–5%; I2 = 13.7%), and 15% (95% CI, 9–22%; I2 = 65.4%), respectively. Conclusion The addition of EGFR inhibitors in the nCRT for KRAS-wild type LARC patients provides comparable efficacy and acceptable safety. However, the results should be interpreted cautiously due to the small amount of relevant data and need further confirmation by more future studies.
From Near-Optimal Bayesian Integration to Neuromorphic Hardware: A Neural Network Model of Multisensory Integration

While interacting with the world our senses and nervous system are constantly challenged to identify the origin and coherence of sensory input signals of various intensities. This problem becomes apparent when stimuli from different modalities need to be combined, e.g., to find out whether an auditory stimulus and a visual stimulus belong to the same object. To cope with this problem, humans and most other animal species are equipped with complex neural circuits to enable fast and reliable combination of signals from various sensory organs. This multisensory integration starts in the brain stem to facilitate unconscious reflexes and continues on ascending pathways to cortical areas for further processing. To investigate the underlying mechanisms in detail, we developed a canonical neural network model for multisensory integration that resembles neurophysiological findings. For example, the model comprises multisensory integration neurons that receive excitatory and inhibitory inputs from unimodal auditory and visual neurons, respectively, as well as feedback from cortex. Such feedback projections facilitate multisensory response enhancement and lead to the commonly observed inverse effectiveness of neural activity in multisensory neurons. Two versions of the model are implemented, a rate-based neural network model for qualitative analysis and a variant that employs spiking neurons for deployment on a neuromorphic processing. This dual approach allows to create an evaluation environment with the ability to test model performances with real world inputs. As a platform for deployment we chose IBM's neurosynaptic chip TrueNorth. Behavioral studies in humans indicate that temporal and spatial offsets as well as reliability of stimuli are critical parameters for integrating signals from different modalities. The model reproduces such behavior in experiments with different sets of stimuli. In particular, model performance for stimuli with varying spatial offset is tested. In addition, we demonstrate that due to the emergent properties of network dynamics model performance is close to optimal Bayesian inference for integration of multimodal sensory signals. Furthermore, the implementation of the model on a neuromorphic processing chip enables a complete neuromorphic processing cascade from sensory perception to multisensory integration and the evaluation of model performance for real world inputs.
Multiple origins of insular woodiness on the Canary Islands are consistent with palaeoclimatic aridification

Aim Insular woodiness, referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen at least 38 times on the Canary Islands. Distribution patterns and physiological experiments have suggested a link between insular woodiness and increased drought stress resistance in current-day species, but we do not know in which palaeoclimatic conditions these insular woody lineages originated. Therefore, we estimated the timing of colonisation events and origin of woodiness of multiple Canary Island lineages and reviewed the palaeoclimate based on literature. Location Canary Islands (Spain). Taxon 37 lineages, including 24 insular woody and 13 non-insular woody (i.e. herbaceous, ancestrally woody, and derived woody). Methods To enable a simultaneous dating analysis for all 37 lineages, two chloroplast markers (matK and rbcL) for 135 Canary Island species and 103 closely related continental relatives were sequenced and aligned to an existing matK-rbcL dataset including ca 24,000 species that was calibrated with 42 fossils from outside the Canaries. After constraining the species to the family level, 200 RAxML runs were performed and dated with TreePL. Results Woodiness in 80-90% of the insular woody lineages originated within the last 7 Myr, coinciding with the onset of major aridification events nearby the Canaries (start of north African desertification, followed by Messinian salinity crisis); in ca 55-65% of the insular woody lineages studied, woodiness developed within the last 3.2 Myr during which Mediterranean seasonality (yearly summer droughts) became established on the Canaries, followed by dry Pleistocene glacial fluctuations. Main conclusions Although details of the initial colonisation and settlement of many island plant lineages remain elusive, our results are consistent with palaeodrought as a potential driver for woodiness in most of the insular woody Canary Island lineages studied.
Reversing Lipopolysaccharide Toxicity by Ligating the Macrophage Fcγ Receptors1

Our laboratory has previously demonstrated that the ligation of phagocytic receptors on macrophages can influence cytokine production. In this study, we examine the cytokine responses to multiple inflammatory stimuli following FcγR ligation. Macrophages were stimulated in vitro with LPS, lipoteichoic acid, CD40 ligand, or low molecular mass hyaluronic acid. All of these stimuli were proinflammatory in character, inducing the production of high levels of IL-12, but only modest amounts of IL-10. The coligation of FcγR along with these stimuli resulted in an anti-inflammatory profile, abrogating IL-12 production and inducing high levels of IL-10. The modulation of these two cytokines occurred by two independent mechanisms. Whereas the abrogation of IL-12 biosynthesis was a property shared by several macrophage receptors, the induction of IL-10 was specific to the FcγR. The biological relevance of these observations was examined in murine models of endotoxemia, in which FcγR ligation induced the rapid production of IL-10 and prevented IL-12 synthesis. Mice could be passively immunized with Abs to LPS to reverse inflammatory cytokine production, and the transfer of macrophages whose FcγR had been ligated could rescue mice from lethal endotoxemia. Thus, the ligation of the macrophage FcγR can be exploited to prevent inappropriate inflammatory cytokine responses.
Microbial helpers allow cyanobacteria to thrive in ferruginous waters

The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O2 on the planet’s surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe2+ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe2+-rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe2+ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with ROS defense mechanisms increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe2+ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations, and may expand the upper bound for tolerable Fe2+ concentrations for cyanobacteria.
Optimal forgetting: Semantic compression of episodic memories

It has extensively been documented that human memory exhibits a wide range of systematic distortions, which have been associated with resource constraints. Resource constraints on memory can be formalised in the normative framework of lossy compression, however traditional lossy compression algorithms result in qualitatively different distortions to those found in experiments with humans. We argue that the form of distortions is characteristic of relying on a generative model adapted to the environment for compression. We show that this semantic compression framework can provide a unifying explanation of a wide variety of memory phenomena. We harness recent advances in learning deep generative models, that yield powerful tools to approximate generative models of complex data. We use three datasets, chess games, natural text, and hand-drawn sketches, to demonstrate the effects of semantic compression on memory performance. Our model accounts for memory distortions related to domain expertise, gist-based distortions, contextual effects, and delayed recall. Author summary Human memory performs surprisingly poorly in many everyday tasks, which have been richly documented in laboratory experiments. While constraints on memory resources necessarily imply a loss of information, it is possible to do well or badly in relation to available memory resources. In this paper we recruit information theory, which establishes how to optimally lose information based on prior and complete knowledge of environmental statistics. For this, we address two challenges. 1, The environmental statistics is not known for the brain, rather these have to be learned over time from limited observations. 2, Information theory does not specify how different distortions of original experiences should be penalised. In this paper we tackle these challenges by assuming that a latent variable generative model of the environment is maintained in semantic memory. We show that compression of experiences through a generative model gives rise to systematic distortions that qualitatively correspond to a diverse range of observations in the experimental literature.
Ray tracing models for estimating light collection properties of microstructured tapered optical fibers for optical neural interfaces

Tapered optical fibers (TFs) were recently employed for depth-resolved monitoring of functional fluorescence in sub-cortical brain structures, enabling light collection from groups of a few cells through small optical windows located on the taper edge [1]. Here we present a numerical model to estimate light collection properties of microstructured TFs implanted in scattering brain tissue. Ray tracing coupled with Henyey-Greenstein scattering model enables the estimation of both light collection and fluorescence excitation fields in three dimensions, whose combination is employed to retrieve the volume of tissue probed by the device.