Miracle-dz/UniFAR-FTUs huggingface dataset:
Further Development of Small Hydropower Facilities Will Significantly Reduce Sediment Transport to the Pantanal Wetland of Brazil

Small hydropower (SHP) facilities, which are defined by installed capacities <10–50 MW, are increasingly being built around the world. SHPs are viewed as less environmentally harmful than larger dams, although there has been little research to support that assertion. Numerous SHPs have been built, and many more are in development or proposed, in rivers that drain into the Pantanal, a world-renowned floodplain wetland. Three river systems with the largest contributions of sediments to the Pantanal—the Cuiabá, upper Taquari, and Coxim rivers—remain largely undammed. The upland tributaries transport sediments into the Pantanal, thereby affecting geomorphological dynamics and biological productivity of downstream floodplains. This study presents measurements from upstream and downstream of current hydropower facilities, most of which are SHPs, throughout the upland watersheds of the Upper Paraguay River basin to reveal how these facilities may affect the transport of suspended sediments and of bedload sediments. In addition, a predictive model using artificial neural networks (ANNs) estimates the impact of building 80 future SHPs on sediment transport based on observations at current facilities as well as the spatial distribution of future facilities. More than half of current facilities retained suspended sediments: 14 of the 29 facilities showed >20% net retention of suspended sediments, two others retained between 10 and 20%, seven were within 10%, and six showed >10% net release. Bedload sediment transport was a small component of total sediment transport in rivers with high total sediment loads. Multiyear series of satellite images confirm sediment accumulation in several cases. Model predictions of the impacts of future hydropower facilities on suspended sediment concentrations and transport show retention of a large fraction (often much >20%) of sediment inputs. Summing riverine transport rates for inflows into the Pantanal indicates that currently envisioned future hydropower development would reduce the suspended sediment transport by ∼62% from the current rate. This study shows that if SHPs are built on sediment-rich rivers, this may prove problematic for the facilities as well as for downstream ecosystems. These results support recommendations that several river systems presently lacking dams in their lower reaches should be excluded from future hydropower development to maintain the sediment supply to the Pantanal.
The Soil Nutrient Environment Determines the Strategy by Which Bacillus velezensis HN03 Suppresses Fusarium wilt in Banana Plants

Biological control agents (BCAs) are considered as one of the most important strategies for controlling Fusarium wilt, and bioorganic fertilizer, in particular, has been extensively investigated. However, little is known regarding how a biocontrol microorganism affects the suppression mechanisms when combined with different amendments. In this study, a pot experiment was performed using banana plants to investigate the different mechanisms by which the biocontrol bacterium Bacillus velezensis HN03 (isolated from our laboratory) and amendments suppress Fusarium wilt. The incidence of banana wilt was decreased under HN03 and was reduced further when HN03 was combined with compost, particularly wormcast. In the suppression of Fusarium wilt, HN03 was found to influence the soil environment in various ways. HN03 increased the peroxidase level, which improves plant defense, and was highest when combined with wormcast, being 69 times higher than when combined with cow dung compost. The high accumulation of Mg and P in the “HN03 + wormcast” and Zn and Mn in the “HN03 + cow dung” treatments was negatively correlated with disease incidence. Furthermore, HN03 re-established the microbial community destroyed by the pathogen and further increased the level of suppression in the wormcast. HN03 also enhanced the functional traits of the soil, including defensive mechanism-related traits, and these traits were further enhanced by the combination of HN03 + wormcast.
Habitat Shape Affects Polyploid Establishment in a Spatial, Stochastic Model

Polyploidy contributes massively to the taxonomic and genomic diversity of angiosperms, but certain aspects of polyploid evolution are still enigmatic. The establishment of a new polyploid lineage following whole-genome duplication (WGD) is a critical step for all polyploid species, but this process is difficult to identify and observe in nature. Mathematical models offer an opportunity to study this process by varying parameters related to the populations, habitats, and organisms involved in the polyploid establishment process. While several models of polyploid establishment have been published previously, very few incorporate spatial factors, including spatial relationships between organisms, habitat shape, or population density. This study presents a stochastic, spatial model of polyploid establishment that shows how factors such as habitat shape and dispersal type can influence the fixation and persistence of nascent polyploids and modulate the effects of other factors. This model predicts that narrow, constrained habitats such as roadsides and coastlines may enhance polyploid establishment, particularly in combination with frequent clonal reproduction, limited dispersal, and high population density. The similarity between this scenario and the growth of many invasive or colonizing species along disturbed, narrow habitats such as roadsides may offer a partial explanation of the prevalence of polyploidy among invasive species.
Synchronous Biodegradability and Production of Dissolved Organic Matter in Two Streams of Varying Land Use

In aquatic ecosystems, dissolved organic matter (DOM) composition is driven by land use, microbial activity, and seasonal variation in hydrology and water temperature, and, in turn, its microbial bioavailability is expected to vary due to differences in its composition. It is commonly assumed that DOM of terrestrial origin is resistant to microbial activity because it is composed of more complex aromatic compounds. However, the effect of DOM sources on the microbial reworking and degradation of the DOM pool remains debated. We performed laboratory incubation experiments to examine how temporal changes in DOM composition influence its microbial biodegradability in two contrasting streams (agricultural and forested) in southern Ontario, Canada. Despite a more allochthonous-like DOM signature in the forest stream and a more autochthonous-like DOM signature in the agriculture stream, we found that biodegradation and production of DOC were the same in both streams and synchronous throughout the sampling period. However, the initial DOM composition impacted how the DOM pool changed upon degradation. During the incubations, both autochthonous-like and allochthonous-like fractions of the DOM pool increased. We also found that a greater change in DOM composition during the incubations induced higher degradation of carbon. Finally, temporal variation in DOC biodegradation and production over time or across streams was not related to DOM composition, although there was a significant relationship between BDOC and nutrient concentrations in the agriculture stream. This observation potentially challenges the notion that DOM origin predicts its bioavailability and suggests that broad environmental factors shape DOC consumption and production in aquatic ecosystems. More research is needed to better understand the drivers of microbial biodegradability in streams, as this ultimately determines the fate of DOM in aquatic ecosystems.
A Comparative Meta-Analysis and in silico Analysis of Differentially Expressed Genes and Proteins in Canine and Human Bladder Cancer

Canine and human bladder cancer present similar anatomical, morphological, and molecular characteristics, and dogs can be considered a model for human bladder cancer. However, the veterinary literature lacks information regarding cross-validation analysis between human and canine large-scale data. Therefore, this research aimed to perform a meta-analysis of the canine literature on bladder cancer, identifying genes and proteins previously evaluated in these studies. In addition, we also performed a cross-validation of the canine transcriptome data and the human data from The Cancer Genome Atlas (TCGA) to identify potential markers for both species. The meta-analysis was performed using the following indexing terms: “bladder” AND “carcinoma” AND “dog” in different international databases, and 385 manuscripts were identified in our initial search. Then, several inclusion criteria were applied, and only 25 studies met these criteria. Among these studies, five presented transcriptome data, and 20 evaluated only isolated genes or proteins. Regarding the studies involving isolated protein analysis, the HER-2 protein was the most studied (3/20), followed by TAG-72 (2/20), COX-2 (2/20), survivin (2/20), and CK7 (2/20), and the remaining nine studies evaluated one isolated protein each. Regarding the cross-validation analysis of human and canine transcriptome data, we identified 35 dysregulated genes, including ERBB2, TP53, EGFR, and E2F2. Our results demonstrate that the canine literature on bladder cancer previously focused on the evaluation of isolated markers with no association with patient survival. This limitation may be related to the lack of a homogenous protocol for treating patients and the lack of follow-up during treatment. In addition, the lack of information regarding tumor muscle invasion can be considered an important limitation when comparing human and canine bladder tumors. Our in silico analysis involving canine and human transcriptome data provided several genes with the potential to be markers for both human and canine bladder tumors, and these genes should be considered for future studies on canine bladder cancer.
IL-1β Induced Cytokine Expression by Spinal Astrocytes Can Play a Role in the Maintenance of Chronic Inflammatory Pain

It is now widely accepted that the glial cells of the central nervous system (CNS) are key players in many processes, especially when they are activated via neuron-glia or glia-glia interactions. In turn, many of the glia-derived pro-inflammatory cytokines contribute to central sensitization during inflammation or nerve injury-evoked pathological pain conditions. The prototype of pro-inflammatory cytokines is interleukin-1beta (IL-1β) which has widespread functions in inflammatory processes. Our earlier findings showed that in the spinal cord (besides neurons) astrocytes express the ligand binding interleukin-1 receptor type 1 (IL-1R1) subunit of the IL-1 receptor in the spinal dorsal horn in the chronic phase of inflammatory pain. Interestingly, spinal astrocytes are also the main source of the IL-1β itself which in turn acts on its neuronal and astrocytic IL-1R1 leading to cell-type specific responses. In the initial experiments we measured the IL-1β concentration in the spinal cord of C57BL/6 mice during the course of complete Freund adjuvant (CFA)-induced inflammatory pain and observed a peak of IL-1β level at the time of highest mechanical sensitivity. In order to further study astrocytic activation, primary astrocyte cultures from spinal cords of C57BL/6 wild type and IL-1R1 deficient mice were exposed to IL-1β in concentrations corresponding to the spinal levels in the CFA-induced pain model. By using cytokine array method we observed significant increase in the expressional level of three cytokines: interleukin-6 (IL-6), granulocyte-macrophage colony stimulating factor (GM-CSF) and chemokine (C-C motif) ligand 5 (CCL5 or RANTES). We also observed that the secretion of the three cytokines is mediated by the NFkB signaling pathway. Our data completes the picture of the IL-1β-triggered cytokine cascade in spinal astrocytes, which may lead to enhanced activation of the local cells (neurons and glia as well) and can lead to the prolonged maintenance of chronic pain. All these cytokines and the NFkB pathway can be possible targets of pain therapy.
Effectiveness of an Innovative Cognitive Treatment and Telerehabilitation on Subjects With Mild Cognitive Impairment: A Multicenter, Randomized, Active-Controlled Study

Background In recent years, the potential usefulness of cognitive training procedures in normal aging and mild cognitive impairment (MCI) have received increased attention. Objective The main aim of this study was to evaluate the efficacy of the face-to-face cognitive virtual reality rehabilitation system (VRRS) and to compare it to that of face-to-face cognitive treatment as usual for individuals with MCI. Moreover, we assessed the possibility of prolonging the effects of treatment with a telerehabilitation system. Methods A total of 49 subjects with MCI were assigned to 1 of 3 study groups in a randomized controlled trial design: (a) those who received face-to-face cognitive VRRS (12 sessions of individualized cognitive rehabilitation over 4 weeks) followed by telerehabilitation (36 sessions of home-based cognitive VRRS training, three sessions for week); (b) those who received face-to-face cognitive VRRS followed by at-home unstructured cognitive stimulation (36 sessions of home-based unstructured cognitive stimulation, three sessions for week); and (c) those who received face-to-face cognitive treatment as usual (12 sessions of face-to-face cognitive treatment as usual). Results An improvement in memory, language and visuo-constructional abilities was observed after the end of face-to-face VRRS treatment compared to face-to-face treatment as usual. The application of home-based cognitive VRRS telerehabilitation seems to induce more maintenance of the obtained gains than home-based unstructured stimulation. Discussion The present study provides preliminary evidence in support of individualized VRRS treatment and telerehabilitation delivery for cognitive rehabilitation and should pave the way for future studies aiming at identifying optimal cognitive treatment protocols in subjects with MCI. Clinical Trial Registration www.ClinicalTrials. gov, identifier NCT03486704.
Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics

Predictive models that map double-stranded regulatory DNA to molecular signals of regulatory activity should, in principle, produce identical predictions regardless of whether the sequence of the forward strand or its reverse complement (RC) is supplied as input. Unfortunately, standard convolutional neural network architectures can produce highly divergent predictions across strands, even when the training set is augmented with RC sequences. Two strategies have emerged in the literature to enforce this symmetry: conjoined a.k. a. “siamese” architectures where the model is run in parallel on both strands & predictions are combined, and RC parameter sharing or RCPS where weight sharing ensures that the response of the model is equivariant across strands. However, systematic benchmarks are lacking, and neither architecture has been adapted to base-resolution signal profile prediction tasks. In this work, we extend conjoined and RCPS models to signal profile prediction, and introduce a strong baseline: a standard model (trained on RC augmented data) that is converted to a conjoined model only after it has been trained, which we call a “post-hoc” conjoined model. We then conduct benchmarks on both binary and signal profile prediction. We find post-hoc conjoined models consistently perform as well as or better than models that were conjoined during training, and present a mathematical intuition for why. We also find that - despite its theoretical appeal - RCPS performs surprisingly poorly on certain tasks, in particular, signal profile prediction. In fact, RCPS can sometimes do worse than even standard models trained with RC data augmentation. We prove that the RCPS models can represent the solution learned by the conjoined models, implying that the poor performance of RCPS may be due to optimization difficulties. We therefore suggest that users interested in RC symmetry should default to post-hoc conjoined models as a reliable baseline before exploring RCPS. Code: https://github.com/hannahgz/BenchmarkRCStrategies
Essential histone chaperones collaborate to regulate transcription and chromatin integrity

Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. We have discovered that the physical interaction between two essential histone chaperones, Spt6 and Spn1/Iws1, is required for transcriptional accuracy and nucleosome organization. To understand this requirement, we have isolated suppressors of an spt6 mutation that disrupts the Spt6-Spn1 interaction. Several suppressors are in a third essential histone chaperone, FACT, while another suppressor is in the transcription elongation factor Spt5/DSIF. The FACT suppressors weaken FACT-nucleosome interactions and bypass the requirement for Spn1, possibly by restoring a necessary balance between Spt6 and FACT on chromatin. In contrast, the Spt5 suppressor modulates Spt6 function in a Spn1-dependent manner. Despite these distinct mechanisms, both suppressors alleviate the nucleosome organization defects caused by disruption of the Spt6-Spn1 interaction. Taken together, we have uncovered a network in which histone chaperones and other elongation factors coordinate transcriptional integrity and chromatin structure.
Sustained Pupil Responses Are Modulated by Predictability of Auditory Sequences

The brain is highly sensitive to auditory regularities and exploits the predictable order of sounds in many situations, from parsing complex auditory scenes, to the acquisition of language. To understand the impact of stimulus predictability on perception, it is important to determine how the detection of predictable structure influences processing and attention. Here, we use pupillometry to gain insight into the effect of sensory regularity on arousal. Pupillometry is a commonly used measure of salience and processing effort, with more perceptually salient or perceptually demanding stimuli consistently associated with larger pupil diameters. In two experiments we tracked human listeners' pupil dynamics while they listened to sequences of 50-ms tone pips of different frequencies. The order of the tone pips was either random, contained deterministic (fully predictable) regularities (experiment 1, n = 18, 11 female) or had a probabilistic regularity structure (experiment 2, n = 20, 17 female). The sequences were rapid, preventing conscious tracking of sequence structure thus allowing us to focus on the automatic extraction of different types of regularities. We hypothesized that if regularity facilitates processing by reducing processing demands, a smaller pupil diameter would be seen in response to regular relative to random patterns. Conversely, if regularity is associated with heightened arousal and attention (i.e., engages processing resources) the opposite pattern would be expected. In both experiments we observed a smaller sustained (tonic) pupil diameter for regular compared with random sequences, consistent with the former hypothesis and confirming that predictability facilitates sequence processing. SIGNIFICANCE STATEMENT The brain is highly sensitive to auditory regularities. To appreciate the impact that the presence of predictability has on perception, we need to better understand how a predictable structure influences processing and attention. We recorded listeners' pupil responses to sequences of tones that followed either a predictable or unpredictable pattern, as the pupil can be used to implicitly tap into these different cognitive processes. We found that the pupil showed a smaller sustained diameter to predictable sequences, indicating that predictability eased processing rather than boosted attention. The findings suggest that the pupil response can be used to study the automatic extraction of regularities, and that the effects are most consistent with predictability helping the listener to efficiently process upcoming sounds.
Genetic evidence for bidirectional causal effects between resilience and well-being

Resilience and well-being are strongly related. People with higher levels of well-being are more resilient after stressful life events or trauma and vice versa. Less is known about the underlying sources of overlap and causality between the constructs. In a sample of 11.304 twins and 2.572 siblings from the Netherlands Twin Register, we investigated the overlap and possible direction of causation between resilience (i.e. the absence of psychiatric symptoms despite negative life events) and well-being (i.e. satisfaction with life) using polygenic scores (PGS), twin-sibling models, and the Mendelian Randomization Direction of Causality (MR-DoC) model. The longitudinal twin-sibling models showed significant phenotypic correlations between resilience and well-being (.41/.51 at time 1 and 2). PGS analyses suggested that genetic factors influencing one trait, also predict the other. Twin-sibling modeling confirmed this genetic correlation (.71) and showed a strong environmental correlation (.93). In line with causality, both genetic (51%) and environmental (49%) factors contributed significantly to the covariance between resilience and well-being. Further causality analyses consistently showed bidirectional causality and the MR-DoC model confirmed these causal effects. Well-being explained 34% (T1) and 46% (T2) of the variance in resilience and resilience explained 44% (T1) and 51% (T2) of the variance in resilience. To conclude, we find evidence for bidirectional causality between well-being and resilience that survives correction for genetic confounding. As resilience and well-being are both negatively related to psychopathology, the mutual effects can have implications for interventions to lower psychopathology vulnerability.