Miracle-dz/UniFAR-FTUs huggingface dataset:
Glass Half-Full or Half-Empty? A Fire-Resistant Species Triggers Divergent Regeneration in Low-Resilience Pastures

Fire may divert or arrest natural regeneration in abandoned pastures throughout the tropics, transforming them to low-resilience systems that do not recover even in the absence of disturbances. Understanding regeneration in degraded landscapes is crucial to decision-making and predicting the outcome of passive or active restoration actions. We aimed to understand the effects of intensifying fire regimes on post-fire natural regeneration in sites degraded by logging and fire in the Brazilian Atlantic Forest. We studied five areas with different fire regimes (i.e., different fire frequencies and post-fire regeneration time), dominated by Moquiniastrum polymorphum (Asteraceae), a widely-distributed species with fire resistance traits. We analyzed differences in structure, diversity, the amplitude of the species' geographic distribution, and floristic composition. We recorded Leaf Area Index and grass cover to understand the effect of canopy closure on fire exclusion and analyzed functional traits related to succession and response to fire (specific leaf area, height, wood density, bark thickness, seed mass). Post-fire regeneration was slow and fire-prone and dominance by M. polymorphum decreased with less disturbance, as other species entered the communities. Structure, diversity, and functional composition recovered along the gradient but did not reach old-growth values. The taxonomic composition was strikingly different in burned areas and forests, irrespective of fire history. Natural regeneration followed a divergent trajectory, marked by the establishment of other widely-distributed species, which suggests a long-term floristic impoverishment. The establishment of M. polymorphum allows these pastures to exit grass-fire cycles. Longer post-fire recovery and fewer fire events allow for canopy closure, grass exclusion, and eventually fire suppression. This two-step dynamic breaks a crucial barrier for restoration from degraded pastures and represents a more desirable state than pastures. However, relying only upon natural regeneration results in impoverished secondary forests. Given the pervasive effects of deforestation and fire, natural regeneration observed in tropical landscapes may correspond to impoverished new secondary forests that fail to attain conservation targets for the biome. Preventing future fires and controlling grass cover in the understory is crucial to avoid their retrogression to pastures and to treat them as regeneration templates for active restoration.
Psychological Biomarkers and Fibrosis: An Innovative Approach to Non-alcoholic Fatty Liver Disease

Background: It is unknown how perceived social support and the progression of liver damage influence the psychosocial profile of patients with non-alcoholic fatty liver disease (NAFLD). In the present study, we therefore investigated which biomarkers influence the quality of life, mental health, and coping strategies of NAFLD patients. Methods: Quality of life (SF-12 and CLDQ-NAFLD), mental health (HADS and BDI-II), and coping strategies (COPE-28) were evaluated by high or low perceived social support (MSPSS) and the presence of non-alcoholic steatohepatitis (NASH) and significant fibrosis in 492 biopsy-proven NAFLD patients. The results were compared with quality of life normality tables for the general Spanish population. We also determined whether liver histology and biopsychosocial variables predicted participants' quality of life. Results: Interactive effects were found in vitality (p = 0.05), activity (p = 0.005), anxiety (p = 0.04), and denial (p = 0.04), with NASH patients showing a higher-risk biopsychosocial profile when they perceived less social support. Furthermore, patients with low perceived social support showed lower quality of life, worse mental health, and more maladaptive coping than those with high perceived social support, regardless of NASH presence. Patients with significant fibrosis showed lower quality of life compared to those without or the general Spanish population. Patients with significant fibrosis also reported worse mental health and more maladaptive coping. Lastly, significant fibrosis, female sex, greater anxiety and depressive symptoms, and worse physical and mental health-related quality of life were found to be independent determinants of worse disease-specific quality of life in these patients. Conclusions: Low perceived social support, significant fibrosis, and female sex were independently associated with a higher-risk psychosocial profile in NAFLD. These findings support the role of psychological biomarkers based on quality of life, mental health, and coping strategies in the management of these patients and suggest the potential benefits of a psychological intervention.
GenOrigin: A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their own network in the genomes, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific gene, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically dated the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using protein-family-based pipeline with Wagner parsimony algorithm. We also collected gene age estimate data from other studies and uniformed the gene age estimates to time ranges in million years for comparison across studies. All the data were cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a userfriendly new database of gene age estimates, where users can browse gene age estimates by species, age and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, was provided to researchers for exploring gene functions.
Hypoxia Drives Dihydropyrimidine Dehydrogenase Expression in Macrophages and Confers Chemoresistance in Colorectal Cancer

Hypoxia induces HIF2α-mediated overexpression of dihydropyrimidine dehydrogenase in TAMs, leading to chemoresistance to 5-FU in colon cancers. Colorectal adenocarcinoma is a leading cause of death worldwide, and immune infiltration in colorectal tumors has been recognized recently as an important pathophysiologic event. In this context, tumor-associated macrophages (TAM) have been related to chemoresistance to 5-fluorouracil (5-FU), the first-line chemotherapeutic agent used in treating colorectal cancers. Nevertheless, the details of this chemoresistance mechanism are still poorly elucidated. In the current study, we report that macrophages specifically overexpress dihydropyrimidine dehydrogenase (DPD) in hypoxia, leading to macrophage-induced chemoresistance to 5-FU via inactivation of the drug. Hypoxia-induced macrophage DPD expression was controlled by HIF2α. TAMs constituted the main contributors to DPD activity in human colorectal primary or secondary tumors, while cancer cells did not express significant levels of DPD. In addition, contrary to humans, macrophages in mice do not express DPD. Together, these findings shed light on the role of TAMs in promoting chemoresistance in colorectal cancers and identify potential new therapeutic targets. Significance: Hypoxia induces HIF2α-mediated overexpression of dihydropyrimidine dehydrogenase in TAMs, leading to chemoresistance to 5-FU in colon cancers.
Applications of Human Skin Microbiota in the Cutaneous Disorders for Ecology-Based Therapy

The skin represents the exterior interface between the human body with the environment while providing a home to trillions of the commensal microorganisms—collectively referred to as the skin microbiota. These microbes that coexist in an established balance play a pivotal role in the protection of cutaneous health and the orchestration of skin homeostasis. However, the well-controlled but delicate balance can be perturbed by alterations in the skin microbial communities, namely, dysbiosis, often due to commensals defeated by pathogens competing for space and nutrients, which leads to the occurrence of multiple cutaneous disorders. In view of this, the analysis of skin microbiota constituents in skin diseases is crucial for defining the role of commensal microbes and treatment of skin diseases. Emerging evidence shows that the ecology-based therapy of microbial transplantation has been proven as a valid therapeutic strategy for cutaneous disorders caused by skin microbial dysbiosis. Although its mechanism is not well-understood, there are already some applications for ecology-based therapy with the aim of correcting the imbalances on the cutaneous ecosystem. In this review, we summarize the interactions between dysbiosis and the cutaneous disorders, including homeostasis and dysbiosis of skin microbiota, microbial composition in skin diseases, and the mechanisms and applications of reversing or ameliorating the dysbiosis by the targeted manipulation of the skin microbiota, which may contribute to aid development of therapeutic modality for ecology-based therapy.
Rv2577 of Mycobacterium tuberculosis Is a Virulence Factor With Dual Phosphatase and Phosphodiesterase Functions

Tuberculosis, a lung disease caused by Mycobacterium tuberculosis (Mtb), is one of the ten leading causes of death worldwide affecting mainly developing countries. Mtb can persist and survive inside infected cells through modulation of host antibacterial attack, i.e., by avoiding the maturation of phagosome containing mycobacteria to more acidic endosomal compartment. In addition, bacterial phosphatases play a central role in the interplay between host cells and Mtb. In this study, we characterized the Rv2577 of Mtb as a potential alkaline phosphatase/phosphodiesterase enzyme. By an in vitro kinetic assay, we demonstrated that purified Rv2577 expressed in Mycobacterium smegmatis displays both enzyme activities, as evidenced by using the artificial substrates p-NPP and bis-(p-NPP). In addition, a three-dimensional model of Rv2577 allowed us to define the catalytic amino acid residues of the active site, which were confirmed by site-directed mutagenesis and enzyme activity analysis, being characteristic of a member of the metallophosphatase superfamily. Finally, a mutation introduced in Rv2577 reduced the replication of Mtb in mouse organs and impaired the arrest of phagosomes containing mycobacteria in early endosomes; which indicates Rv2577 plays a role in Mtb virulence.
Touch Recognition with Attentive End-to-End Model

Touch is the earliest sense to develop and the first mean of contact with the external world. Touch also plays a key role in our socio-emotional communication: we use it to communicate our feelings, elicit strong emotions in others and modulate behavior (e.g compliance). Although its relevance, touch is an understudied modality in Human-Machine-Interaction compared to audition and vision. Most of the social touch recognition systems require a feature engineering step making them difficult to compare and to generalize to other databases. In this paper, we propose an end-to-end approach. We present an attention-based end-to-end model for touch gesture recognition evaluated on two public datasets (CoST and HAART) in the context of the ICMI 15 Social Touch Challenge. Our model gave a similar level of accuracy: 61% for CoST and 68% for HAART and uses self-attention as an alternative to feature engineering and Recurrent Neural Networks.
Visible Emission Line Coronagraph on Aditya-L1

B. Raghavendra Prasad*, Dipankar Banerjee, Jagdev Singh, S. Nagabhushana, Amit Kumar, P. U. Kamath, S. Kathiravan, Suresh Venkata, N. Rajkumar, V. Natarajan, Madhur Juneja, Pawan Somu, Vaibhav Pant, Nigar Shaji, K. Sankarsubramanian, Asit Patra, R. Venkateswaran, Abhijit Avinash Adoni, S. Narendra, T. R. Haridas, Shibu K. Mathew, R. Mohan Krishna, K. Amareswari and Bhavesh Jaiswal Indian Institute of Astrophysics, 2nd Block, Koramangala, Bengaluru 560 034, India ISRO Satellite Centre, Old Airport Road, Vimanapura Post, Bengaluru 560 017, India Space Applications Centre, Jodhpur Tekra, Ambawadi Vistar, P.O. , Ahmedabad 380 015, India Laboratory for Electro-Optics Systems, First Phase, Peenya Industrial Estate, Bengaluru 560 058, India ISRO Inertial Systems Unit, Vattiyoorkavu PO, Thiruvananthapuram 695 013, India Udaipur Solar Observatory, Near Fatehpur Lake, Shilpgram, Udaipur 313 004, India
Towards Engagement Recognition of People with Dementia in Care Settings

Roughly 50 million people worldwide are currently suffering from dementia. This number is expected to triple by 2050. Dementia is characterized by a loss of cognitive function and changes in behaviour. This includes memory, language skills, and the ability to focus and pay attention. However, it has been shown that secondary therapy such as the physical, social and cognitive activation of People with Dementia (PwD) has significant positive effects. Activation impacts cognitive functioning and can help prevent the magnification of apathy, boredom, depression, and loneliness associated with dementia. Furthermore, activation can lead to higher perceived quality of life. We follow Cohen's argument that activation stimuli have to produce engagement to take effect and adopt his definition of engagement as "the act of being occupied or involved with an external stimulus".
Detecting Aggressiveness in Mexican Spanish Tweets with LSTM + GRU and LSTM + CNN Architectures

This paper presents a description of our participation in MEX-A3T 2020 aggressiveness detection on the Spanish Mexican tweets track. The goal of this task is to analyze a corpus comprised of Spanish Mexican tweets and identify its aggressiveness level (aggressive or not). For this task, we proposed two architectures; the first one is a BiLSTM + GRU based, and the second is a BiLSTM + CNN based architecture. After experimenting and evaluating, our BiLSTM + CNN model achieves 63.88% on aggressive class F1-Score, and our BiLSTM + CNN model achieves 63.87% on aggressive class F1-Score.
Increasing the Range of Modulation Indices with the Polarities of Cells and Switching Constraint Reliefs for the Selective Harmonic Elimination Pulse Width Modulation Technique

In this paper an improved low frequency selective harmonic elimination-PWM (SHE-PWM) technique for Cascaded H-bridge (CHB) converters is proposed. The proposed method is able to eliminate low order harmonics from the output voltage of the converter for a wide range of modulation indices. To solve SHE-PWM equations, especially for low modulation indices, a modified method is used which employs either the positive or negative voltage polarities of H-bridge cells to increase the freedom degrees of each cell. Freedom degrees of the switching angles are also used to increase the range of available solutions for non-linear SHE equations. The proposed SHE methods can successfully eliminate up to 25 harmonic from a 7-level output voltage by using just nine switching transitions or a 150 Hz switching frequency. To confirm the validity of the proposed method, simulation and experimental results have been presented.
Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance

Background Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination in endemic regions. Methods Five ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae. Results Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with blaCTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term adaptation of resistance plasmids such as IncX3 or IncN. Conclusion Since the bacterial acquisition of smaller resistance plasmids such as IncX3 or IncN from other Enterobacteriaceae can be much faster than the larger IncY plasmids, the rapid expansion of these genotypically novel XDR S. Typhi could potentially cause large outbreaks. Therefore, continuous monitoring of S. Typhi lineages carrying cephalosporin resistance on IncX3 or IncN plasmids is vital not just for India but globally. Importance Genomic analysis of cephalosporin resistant S. Typhi isolated from India indicates the potential of S. Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae. We identified the occurrence of independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58/4.3. 1.2 lineage. A short term adaptation of drug-resistant plasmids in H58/4.3. 1.2 lineage can be the reason for the sporadic cases cephalosporin resistant S. Typhi in India. However, the IncY plasmid acquired by isolates that belong to H58/4.3. 1.1 lineage appeared to be well adapted as observed in XDR S. Typhi outbreak in Pakistan. Plasmid acquisition and maintenance of cephalosporin resistant S. Typhi appears to be specific to the phylogenetic lineage as lineages differ in compensating the initial cost imposed by the plasmid. The stable maintenance of these resistance plasmids without a fitness cost, are determinant in understanding the future spread of cephalosporin resistance in S. Typhi. Therefore, critical strategies in monitoring and control of cephalosporin resistant S. Typhi is needed to tackle further public health crisis.
A Cross-Session Dataset for Collaborative Brain-Computer Interfaces Based on Rapid Serial Visual Presentation

Brain-computer interfaces (BCIs) based on rapid serial visual presentation (RSVP) have been widely used to categorize target and non-target images. However, it is still a challenge to detect single-trial event related potentials (ERPs) from electroencephalography (EEG) signals. Besides, the variability of EEG signal over time may cause difficulties of calibration in long-term system use. Recently, collaborative BCIs have been proposed to improve the overall BCI performance by fusing brain activities acquired from multiple subjects. For both individual and collaborative BCIs, feature extraction and classification algorithms that can be transferred across sessions can significantly facilitate system calibration. Although open datasets are highly efficient for developing algorithms, currently there is still a lack of datasets for a collaborative RSVP-based BCI. This paper presents a cross-session EEG dataset of a collaborative RSVP-based BCI system from 14 subjects, who were divided into seven groups. In collaborative BCI experiments, two subjects did the same target image detection tasks synchronously. All subjects participated in the same experiment twice with an average interval of ∼23 days. The results in data evaluation indicate that adequate signal processing algorithms can greatly enhance the cross-session BCI performance in both individual and collaborative conditions. Besides, compared with individual BCIs, the collaborative methods that fuse information from multiple subjects obtain significantly improved BCI performance. This dataset can be used for developing more efficient algorithms to enhance performance and practicality of a collaborative RSVP-based BCI system.
Dual Colorimetric Sensor for Hg2+/Pb2+ and an Efficient Catalyst Based on Silver Nanoparticles Mediating by the Root Extract of Bistorta amplexicaulis

Environmental pollution derivated from toxic metals and organic toxins is becoming a serious issue worldwide because of their harmful effects on the ecosystem and human health. Here we are reporting an extremely selective and cost-effective colorimetric sensor for simultaneous recognition of Hg2+ and Pb2+ by using green synthesized silver nanoparticles (AgNPs) mediated from the environmental friendly roots extract of Bistorta amplexicaulis. Biogenic synthesized AgNPs were well-characterized by various spectroscopic techniques e.g., UV-vis, FT-IR, XRD, AFM, and Zetasizer. The photophysical potential of synthesized AgNPs toward common metal cations was explored via absorption spectroscopy and colorimetric assay. The hypsochromic shift in the SPR band of AgNPs can easily be detected through naked eyes vision from dark brown to light yellow in the case of Hg2+. A substantial reduction in the absorbance of AgNPs was recorded upon mixing with Pb2+. AgNPs based colorimetric sensor is highly sensitive toward Hg2+ and Pb2+ with a limit of detection (LOD) of 8.0 × 10−7 M and 2.0 × 10−7 M for Hg2+ and Pb2+, respectively. Furthermore, AgNPs showed promising catalytic activity for the degradation of methyl orange dye. These results demonstrate that Bistorta amplexicaulis stabilized silver nanoparticles have potential applications as a colorimetric sensor and an effective catalyst for the degradation of methyl orange.
Effect of Novel Remodeled Bicycle Pedal Training on Balance Performance in Athletes With Functional Ankle Instability

Context Appropriate training without risk of injury is a critical concern for athletes. Remodeled bicycle pedal training with multi-directional challenges may be effective in improving the balance performance of athletes with functional ankle instability (FAI). Objective To evaluate the effects of 6-week modified bicycle pedal training on the balance ability and proprioception of athletes with FAI. Design Randomized controlled trial. Setting University motion analysis laboratory. Participants Fourteen healthy athletes (healthy group) and twenty-six athletes with FAI and an age of 18 to 30 years old. The participants with FAI were randomly distributed to two groups, designated as the training group (AI-T group) and non-training group (AI-NT group), respectively. The athletes in the AI-T group received 6-week remodeled bicycle pedal training, while those in the AI-NT group received no intervention at all. Intervention A 6-week training using modified bicycle pedal capable of moving freely during loading cycle vs no intervention. Main Outcome Measures The passive ankle joint position sense (JPS) in four angles and the center of pressure (COP) parameters were analyzed during single-leg standing with and without vision, respectively. Results A 6-week remodeled pedal training: (1) significantly improved the passive JPS of ankle in all directions (P < 0.05); (2) reduced the excursion of the COP in the medial-lateral (ML) direction (p < 0.05), the velocity of the COP in the ML direction (p < 0.05), and the RMS of the COP in the ML direction (P < 0.05) during single-leg standing both with and without vision. Conclusion The remodeled bicycle pedal training improved the passive JPS and reduced the postural sway in single-leg standing both with and without vision. Therefore, remodeled bicycle pedal training can be considered for inclusion in rehabilitation programs for athletes with FAI to restore the proprioception and balance ability.