Miracle-dz/UniFAR-FTUs huggingface dataset:
The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.
Lightweight concrete masonry units based on processed granulate of corn cob as aggregate

A research work was performed in order to assess the potential application of processed granulate of corn cob (PCC) as an alternative lightweight aggregate for the manufacturing process of lightweight concrete masonry units (CMU). Therefore, CMU-PCC were prepared in a factory using a typical lightweight concrete mixture for non-structural purposes. Additionally, lightweight concrete masonry units based on a currently applied lightweight aggregate such as expanded clay (CMU-EC) were also manufactured. An experimental work allowed achieving a set of results that suggest that the proposed building product presents interesting material properties within the masonry wall context. Therefore, this unit is promising for both interior and exterior applications. This conclusion is even more relevant considering that corn cob is an agricultural waste product.
Structural and Mutational Analysis of Functional Differentiation between Synaptotagmins-1 and -7

Synaptotagmins are known to mediate diverse forms of Ca2+-triggered exocytosis through their C2 domains, but the principles underlying functional differentiation among them are unclear. Synaptotagmin-1 functions as a Ca2+ sensor in neurotransmitter release at central nervous system synapses, but synaptotagmin-7 does not, and yet both isoforms act as Ca2+ sensors in chromaffin cells. To shed light into this apparent paradox, we have performed rescue experiments in neurons from synaptotagmin-1 knockout mice using a chimera that contains the synaptotagmin-1 sequence with its C2B domain replaced by the synaptotagmin-7 C2B domain (Syt1/7). Rescue was not achieved either with the WT Syt1/7 chimera or with nine mutants where residues that are distinct in synaptotagmin-7 were restored to those present in synaptotagmin-1. To investigate whether these results arise because of unique conformational features of the synaptotagmin-7 C2B domain, we determined its crystal structure at 1.44 Å resolution. The synaptotagmin-7 C2B domain structure is very similar to that of the synaptotagmin-1 C2B domain and contains three Ca2+-binding sites. Two of the Ca2+-binding sites of the synaptotagmin-7 C2B domain are also present in the synaptotagmin-1 C2B domain and have analogous ligands to those determined for the latter by NMR spectroscopy, suggesting that a discrepancy observed in a crystal structure of the synaptotagmin-1 C2B domain arose from crystal contacts. Overall, our results suggest that functional differentiation in synaptotagmins arises in part from subtle sequence changes that yield dramatic functional differences.
Hepatitis C Virus NS4B Can Suppress STING Accumulation To Evade Innate Immune Responses

ABSTRACT The cyclic dinucleotide 2′,3′-cGAMP can bind the adaptor protein STING (stimulator of interferon [IFN] genes) to activate the production of type I IFNs and proinflammatory cytokines. We found that cGAMP added to the culture medium could suppress the replication of the hepatitis C virus (HCV) genotype 1b strain Con1 subgenomic replicon in human hepatoma cells. Knockdown of STING expression diminished the inhibitory effect on replicon replication, while overexpression of STING enhanced the inhibitory effects of cGAMP. The addition of cGAMP into 1b/Con1 replicon cells significantly increased the expression of type I IFNs and antiviral interferon-stimulated genes. Unexpectedly, replication of the genotype 2a JFH1 replicon and infectious JFH1 virus was less sensitive to the inhibitory effect of cGAMP than was that of 1b/Con1 replicon. Using chimeric replicons, 2a NS4B was identified to confer resistance to cGAMP. Transient expression of 2a NS4B resulted in a pronounced inhibitory effect on STING-mediated beta IFN (IFN-β) reporter activation compared to that of 1b NS4B. 2a NS4B was found to suppress STING accumulation in a dose-dependent manner. The predicted transmembrane domain of 2a NS4B was required to inhibit STING accumulation. These results demonstrate a novel genotype-specific inhibition of the STING-mediated host antiviral immune response. IMPORTANCE The cyclic dinucleotide cGAMP was found to potently inhibit the replication of HCV genotype 1b Con1 replicon but was less effective for the 2a/JFH1 replicon and infectious JFH1 virus. The predicted transmembrane domain in 2a NS4B was shown to be responsible for the decreased sensitivity to cGAMP. The N terminus of NS4B has been reported to suppress STING-mediated signaling by disrupting the interaction of STING and TBK1 and/or MAVS. We show that 2a/JFH1 NS4B has an additional mechanism to evade STING signaling through suppressing STING accumulation.
Controlling the Temporal Structure of Brain Oscillations by Focused Attention Meditation

Our focus of attention naturally fluctuates between different sources of information even when we desire to focus on a single object. Focused attention (FA) meditation is associated with greater control over this process, yet the neuronal mechanisms underlying this ability are not entirely understood. Here, we hypothesize that the capacity of attention to transiently focus and swiftly change relates to the critical dynamics emerging when neuronal systems balance at a point of instability between order and disorder. In FA meditation, however, the ability to stay focused is trained, which may be associated with a more homogeneous brain state. To test this hypothesis, we applied analytical tools from criticality theory to EEG in meditation practitioners and meditation‐naïve participants from two independent labs. We show that in practitioners—but not in controls—FA meditation strongly suppressed long‐range temporal correlations (LRTC) of neuronal oscillations relative to eyes‐closed rest with remarkable consistency across frequency bands and scalp locations. The ability to reduce LRTC during meditation increased after one year of additional training and was associated with the subjective experience of fully engaging one's attentional resources, also known as absorption. Sustained practice also affected normal waking brain dynamics as reflected in increased LRTC during an eyes‐closed rest state, indicating that brain dynamics are altered beyond the meditative state. Taken together, our findings suggest that the framework of critical brain dynamics is promising for understanding neuronal mechanisms of meditative states and, specifically, we have identified a clear electrophysiological correlate of the FA meditation state.
Rotation-Sensitive Regression for Oriented Scene Text Detection

Text in natural images is of arbitrary orientations, requiring detection in terms of oriented bounding boxes. Normally, a multi-oriented text detector often involves two key tasks: 1) text presence detection, which is a classification problem disregarding text orientation; 2) oriented bounding box regression, which concerns about text orientation. Previous methods rely on shared features for both tasks, resulting in degraded performance due to the incompatibility of the two tasks. To address this issue, we propose to perform classification and regression on features of different characteristics, extracted by two network branches of different designs. Concretely, the regression branch extracts rotation-sensitive features by actively rotating the convolutional filters, while the classification branch extracts rotation-invariant features by pooling the rotation-sensitive features. The proposed method named Rotation-sensitive Regression Detector (RRD) achieves state-of-the-art performance on several oriented scene text benchmark datasets, including ICDAR 2015, MSRA-TD500, RCTW-17, and COCO-Text. Furthermore, RRD achieves a significant improvement on a ship collection dataset, demonstrating its generality on oriented object detection.
Convolutional Neural Networks and Language Embeddings for End-to-End Dialect Recognition

Dialect identification (DID) is a special case of general language identification (LID), but a more challenging problem due to the linguistic similarity between dialects. In this paper, we propose an end-to-end DID system and a Siamese neural network to extract language embeddings. We use both acoustic and linguistic features for the DID task on the Arabic dialectal speech dataset: Multi-Genre Broadcast 3 (MGB-3). The end-to-end DID system was trained using three kinds of acoustic features: Mel-Frequency Cepstral Coefficients (MFCCs), log Mel-scale Filter Bank energies (FBANK) and spectrogram energies. We also investigated a dataset augmentation approach to achieve robust performance with limited data resources. Our linguistic feature research focused on learning similarities and dissimilarities between dialects using the Siamese network, so that we can reduce feature dimensionality as well as improve DID performance. The best system using a single feature set achieves 73% accuracy, while a fusion system using multiple features yields 78% on the MGB-3 dialect test set consisting of 5 dialects. The experimental results indicate that FBANK features achieve slightly better results than MFCCs. Dataset augmentation via speed perturbation appears to add significant robustness to the system. Although the Siamese network with language embeddings did not achieve as good a result as the end-to-end DID system, the two approaches had good synergy when combined together in a fused system.
Using Stable Isotope Analysis to Understand the Migration and Trophic Ecology of Northeastern Pacific White Sharks (Carcharodon carcharias)

The white shark (Carcharodon carcharias) is a wide-ranging apex predator in the northeastern Pacific (NEP). Electronic tagging has demonstrated that white sharks exhibit a regular migratory pattern, occurring at coastal sites during the late summer, autumn and early winter and moving offshore to oceanic habitats during the remainder of the year, although the purpose of these migrations remains unclear. The purpose of this study was to use stable isotope analysis (SIA) to provide insight into the trophic ecology and migratory behaviors of white sharks in the NEP. Between 2006 and 2009, 53 white sharks were biopsied in central California to obtain dermal and muscle tissues, which were analyzed for stable isotope values of carbon (δ13C) and nitrogen (δ15N). We developed a mixing model that directly incorporates movement data and tissue incorporation (turnover) rates to better estimate the relative importance of different focal areas to white shark diet and elucidate their migratory behavior. Mixing model results for muscle showed a relatively equal dietary contribution from coastal and offshore regions, indicating that white sharks forage in both areas. However, model results indicated that sharks foraged at a higher relative rate in coastal habitats. There was a negative relationship between shark length and muscle δ13C and δ15N values, which may indicate ontogenetic changes in habitat use related to onset of maturity. The isotopic composition of dermal tissue was consistent with a more rapid incorporation rate than muscle and may represent more recent foraging. Low offshore consumption rates suggest that it is unlikely that foraging is the primary purpose of the offshore migrations. These results demonstrate how SIA can provide insight into the trophic ecology and migratory behavior of marine predators, especially when coupled with electronic tagging data.
Assessment of spinal somatosensory systems with diffusion tensor imaging in syringomyelia

Objective: The use of diffusion tensor imaging with three-dimensional fibre tracking (DTI-FT) was tested for the assessment of spinal sensory tract lesions. The relationships between tract lesions quantified with DTI-FT were systematically examined, and somatosensory dysfunction was assessed with quantitative sensory testing (QST) and laser-evoked potentials (LEP), in patients with syringomyelia. Methods: 28 patients with cervical syringomyelia and thermosensory impairment of the hands, and 19 healthy volunteers, were studied. A DTI-FT of the spinal cord was performed, focusing on the upper segment (C3–C4) of the syrinx. Three-dimensional DTI-FT parameters (fractional anisotropy (FA) and apparent diffusion coefficient (ADC)) of the full, anterior and posterior spinal cord were individually compared with QST (thermal detection thresholds) and LEP (amplitude, latency and spinothalamic tract (STT) conduction time) of the hands. Results: Patients had a significantly lower FA, but not ADC, than healthy subjects. The mean FA of the full section of the spinal cord was correlated both to sensory deficits (ie, increase in warm (rho = −0.63, p<0.010) and cold thresholds (rho = −0.72; p<0.001 of the hands)) and to changes in LEP parameters, in particular STT conduction time (rho = −0.75; p<0.010). Correlations between FA and the clinical and electrophysiological measures were higher in the anterior area (where the spinothalamic tracts are located) than in the posterior area of the spinal cord. Conclusions: The data indicate that diffusion tensor imaging with 3D-fibre tracking is a new imaging method suitable for the objective and quantitative anatomical assessment of spinal somatosensory system dysfunction.
Ecophysiological Traits May Explain the Abundance of Climbing Plant Species across the Light Gradient in a Temperate Rainforest

Climbing plants are a key component of rainforests, but mechanistic approaches to their distribution and abundance are scarce. In a southern temperate rainforest, we addressed whether the dominance of climbing plants across light environments is associated with the expression of ecophysiological traits. In mature forest and canopy gaps, we measured leaf size, specific leaf area, photosynthetic rate, and dark respiration in six of the most abundant woody vines. Mean values of traits and their phenotypic change (%) between mature forest and canopy gaps were predictor variables. Leaf size and specific leaf area were not significantly associated with climbing plant dominance. Variation in gas-exchange traits between mature forest and canopy gaps explained, at least partly, the dominance of climbers in this forest. A greater increase in photosynthetic rate and a lower increase in dark respiration rate when canopy openings occur were related to the success of climbing plant species. Dominant climbers showed a strategy of maximizing exploitation of resource availability but minimizing metabolic costs. Results may reflect phenotypic plasticity or genetic differentiation in ecophysiological traits between light environments. It is suggested that the dominant climbers in this temperate rainforest would be able to cope with forest clearings due to human activities.
Comparison of biofilm formation and motility processes in arsenic‐resistant Thiomonas spp. strains revealed divergent response to arsenite

Bacteria of the genus Thiomonas are found ubiquitously in arsenic contaminated waters such as acid mine drainage (AMD), where they contribute to the precipitation and the natural bioremediation of arsenic. In these environments, these bacteria have developed a large range of resistance strategies among which the capacity to form particular biofilm structures. The biofilm formation is one of the most ubiquitous adaptive response observed in prokaryotes to various stresses, such as those induced in the presence of toxic compounds. This study focused on the process of biofilm formation in three Thiomonas strains (CB1, CB2 and CB3) isolated from the same AMD. The results obtained here show that these bacteria are all capable of forming biofilms, but the architecture and the kinetics of formation of these biofilms differ depending on whether arsenite is present in the environment and from one strain to another. Indeed, two strains favoured biofilm formation, whereas one favoured motility in the presence of arsenite. To identify the underlying mechanisms, the patterns of expression of some genes possibly involved in the process of biofilm formation were investigated in Thiomonas sp. CB2 in the presence and absence of arsenite, using a transcriptomic approach (RNA‐seq). The findings obtained here shed interesting light on how the formation of biofilms, and the motility processes contribute to the adaptation of Thiomonas strains to extreme environments.
Predictors and Prognostic Value of Worsening Renal Function During Admission in HFpEF Versus HFrEF: Data From the KorAHF (Korean Acute Heart Failure) Registry

Background Worsening renal function (WRF) is associated with adverse outcomes in patients with heart failure. We investigated the predictors and prognostic value of WRF during admission, in patients with preserved ejection fraction (HFpEF) versus those with reduced ejection fraction (HFrEF). Methods and Results A total of 5625 patients were enrolled in the KorAHF (Korean Acute Heart Failure) registry. WRF was defined as an absolute increase in creatinine of ≥0.3 mg/dL. Transient WRF was defined as recovery of creatinine at discharge, whereas persistent WRF was indicated by a nonrecovered creatinine level. HFpEF and HFrEF were defined as a left ventricle ejection fraction ≥50% and ≤40%, respectively. Among the total population, WRF occurred in 3101 patients (55.1%). By heart failure subgroup, WRF occurred more frequently in HFrEF (57.0% versus 51.3%; P<0.001 in HFrEF and HFpEF). Prevalence of WRF increased as creatinine clearance decreased in both heart failure subgroups. Among various predictors of WRF, chronic renal failure was the strongest predictor. WRF was an independent predictor of adverse in‐hospital outcomes (HFrEF: odds ratio; 2.75; 95% confidence interval, 1.50–5.02; P=0.001; HFpEF: odds ratio, 9.48; 95% confidence interval, 1.19–75.89; P=0.034) and 1‐year mortality (HFrEF: hazard ratio, 1.41; 95% confidence interval, 1.12–1.78; P=0.004 versus HFpEF: hazard ratio, 1.72; 95% confidence interval, 1.23–2.42; P=0.002). Transient WRF was a risk factor for 1‐year mortality, whereas persistent WRF had no additive risk compared to transient WRF. Conclusions In patients with acute heart failure patients, WRF is an independent predictor of adverse in‐hospital and follow‐up outcomes in both HFrEF and HFpEF, though with a different effect size. Clinical Trial Registration URL: https://www.clinicaltrials. gov. Unique identifier: NCT01389843.
An Experimental Study on the Effect of Temperature on Piezoelectric Sensors for Impedance-Based Structural Health Monitoring

The electromechanical impedance (EMI) technique is considered to be one of the most promising methods for developing structural health monitoring (SHM) systems. This technique is simple to implement and uses small and inexpensive piezoelectric sensors. However, practical problems have hindered its application to real-world structures, and temperature effects have been cited in the literature as critical problems. In this paper, we present an experimental study of the effect of temperature on the electrical impedance of the piezoelectric sensors used in the EMI technique. We used 5H PZT (lead zirconate titanate) ceramic sensors, which are commonly used in the EMI technique. The experimental results showed that the temperature effects were strongly frequency-dependent, which may motivate future research in the SHM field.
Growth and Demography of the Solitary Scleractinian Coral Leptopsammia pruvoti along a Sea Surface Temperature Gradient in the Mediterranean Sea

The demographic traits of the solitary azooxanthellate scleractinian Leptopsammia pruvoti were determined in six populations on a sea surface temperature (SST) gradient along the western Italian coasts. This is the first investigation of the growth and demography characteristics of an azooxanthellate scleractinian along a natural SST gradient. Growth rate was homogeneous across all populations, which spanned 7 degrees of latitude. Population age structures differed between populations, but none of the considered demographic parameters correlated with SST, indicating possible effects of local environmental conditions. Compared to another Mediterranean solitary scleractinian, Balanophyllia europaea, zooxanthellate and whose growth, demography and calcification have been studied in the same sites, L. pruvoti seems more tolerant to temperature increase. The higher tolerance of L. pruvoti, relative to B. europaea, may rely on the absence of symbionts, and thus the lack of an inhibition of host physiological processes by the heat-stressed zooxanthellae. However, the comparison between the two species must be taken cautiously, due to the likely temperature differences between the two sampling depths. Increasing research effort on determining the effects of temperature on the poorly studied azooxanthellate scleractinians may shed light on the possible species assemblage shifts that are likely to occur during the current century as a consequence of global climatic change.