Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti

Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.
Differences in Gut Microbial and Serum Biochemical Indices Between Sows With Different Productive Capacities During Perinatal Period

Maternal gut microflora changes dramatically during perinatal period and plays a vital role in animal health and reproductive performance. However, little is known about the microbial differences between sows with different productive capacities during perinatal period. Hence, this study explored fecal microbial diversity, composition, metabolic functions, and phenotypes differences between high productive capacity (HPC, litter size ≥ 15) and low productive capacity (LPC, litter size ≤ 7) sows during late pregnancy (LP, the third day before due date) and early stage after parturition (EAP, the third day after parturition) as well as serum biochemical indices differences after parturition. Results showed that HPC sows had lower microbial richness at LP stage and higher microbial diversity at EAP stage than LPC sows. Several genera belonging to the Prevotellaceae family exhibited higher abundance, while some genera belonging to the Ruminococcaceae family exhibited lower abundance in HPC sows compared to LPC sows at LP stage. Moreover, the relative abundance of Eubacterium_coprostanoligenes_group and Ruminococcaceae_UCG-014 in HPC sows was significantly higher than that in LPC sows at EAP stage. The predicted metabolic functions related to Lipopolysaccharide biosynthesis were significantly higher in HPC sows at LP stage. Further, HPC sows had significantly higher blood urea nitrogen (BUN) and high-density lipoprotein cholesterol (HDL-C) levels after parturition, and there were strong correlations between BUN level and the relative abundance of genera belonging to the Ruminococcaceae families. These results indicated that the HPC sows may experience greater inflammation than LPC sows at LP stage. Inflammation environment might impact health but promote parturition. The microbial differences at EAP stage might be beneficial to hemostasis and anti-inflammation, which might contribute to postpartum recovery in HPC sow.
Deep Learning Techniques to Improve the Performance of Olive Oil Classification

The olive oil assessment involves the use of a standardized sensory analysis according to the “panel test” method. However, there is an important interest to design novel strategies based on the use of Gas Chromatography (GC) coupled to mass spectrometry (MS), or ion mobility spectrometry (IMS) together with a chemometric data treatment for olive oil classification. It is an essential task in an attempt to get the most robust model over time and, both to avoid fraud in the price and to know whether it is suitable for consumption or not. The aim of this paper is to combine chemical techniques and Deep Learning approaches to automatically classify olive oil samples from two different harvests in their three corresponding classes: extra virgin olive oil (EVOO), virgin olive oil (VOO), and lampante olive oil (LOO). Our Deep Learning model is built with 701 samples, which were obtained from two olive oil campaigns (2014–2015 and 2015–2016). The data from the two harvests are built from the selection of specific olive oil markers from the whole spectral fingerprint obtained with GC-IMS method. In order to obtain the best results we have configured the parameters of our model according to the nature of the data. The results obtained show that a deep learning approach applied to data obtained from chemical instrumental techniques is a good method when classifying oil samples in their corresponding categories, with higher success rates than those obtained in previous works.
Major Depressive Disorder Associated With Reduced Cortical Thickness in Women With Temporal Lobe Epilepsy

Background: Major Depressive Disorder (MDD) is highly prevalent in patients with mesial temporal lobe epilepsy (MTLE), especially in women, carrying significant morbidity. This study aimed to investigate the cortical thickness (CT) abnormalities associated with MDD in women with MTLE and hippocampal atrophy (HA). Also, we investigated the impact of MDD upon the volumes of the hippocampus and amygdala in these patients. Methods: We included 50 women with MTLE and HA (20 left, LMTLE; 30 right, RMTLE), 41 healthy women in the control group, and 15 women with MDD without epilepsy. MTLE patients were subdivided into three groups: MTLE-without-MDD (23 MTLE patients without MDD), MTLE-mild-MDD (nine MTLE patients with mild symptoms of MDD), and MTLE-severe-MDD (18 MTLE patients with moderate to severe symptoms of MDD). The five groups were balanced for age (p = 0.56). All participants had high-resolution 3D T1-weighted images in a 3T scanner. We used FreeSurfer 6.0 for volumetry and CT parcellation. All participants were submitted to a clinical psychological evaluation through the Structured Clinical Interview for DSM-IV (SCID-IV) and completed the Beck Depression Inventory (BDI-II). Results: We identified a smaller ipsilateral amygdala volume (p = 0.04) in the MTLE-severe-MDD group when compared to the control group. Our results presented a reduced ipsilateral lateral orbitofrontal cortex (p = 0.02) in the MTLE-severe-MDD in comparison to the MTLE-mild-MDD group. We also identified a thinner ipsilateral fusiform gyrus (p < 0.01) in the MTLE-severe-MDD compared to both MTLE-without-MDD and control groups. A reduced CT of the contralateral superior frontal gyrus (p = 0.02) was observed in the MTLE-severe-MDD in comparison to the MTLE-mild-MDD group. Conclusions: The identification of areas with reduced CT and atrophy of the ipsilateral amygdala in women with MTLE and MDD suggest that the cortical thinning in the network of the paralimbic system is related to the co-occurrence and intensity of depressive symptoms in this group.
Navigating Complexities: Agent-Based Modeling to Support Research, Governance, and Management in Small-Scale Fisheries

The sustainable governance and management of small-scale fisheries (SSF) is challenging, largely due to their dynamic and complex nature. Agent-based modeling (ABM) is a computational modeling approach that can account for the dynamism and complexity in SSF by modeling entities as individual agents with different characteristics and behavior, and simulate how their interactions can give rise to emergent phenomena, such as over-fishing and social inequalities. The structurally realistic design of agent-based models allow stakeholders, experts, and scientists across disciplines and sectors to reconcile different knowledge bases, assumptions, and goals. ABMs can also be designed using any combination of theory, quantitative data, or qualitative data. In this publication we elaborate on the untapped potential of ABM to tackle governance and management challenges in SSF, discuss the limitations of ABM, and review its application in published SSF models. Our review shows that, although few models exist to date, ABM has been used for diverse purposes, including as a research tool for understanding cooperation and over-harvesting, and as a decision-support tool, or participatory tool, in case-specific fisheries. Even though the development of ABMs is often time- and resource intensive, it is the only dynamic modeling approach that can represent entities of different types, their heterogeneity, actions, and interactions, thus doing justice to the complex and dynamic nature of SSF which, if ignored can lead to unintended policy outcomes and less sustainable SSF.
Rhythm-Motor Dual Task Intervention for Fall Prevention in Healthy Older Adults

This study aimed to investigate the effects of a rhythm-motor dual task intervention on cognitive and gait control for older adults in relation to fall prevention. Ten healthy older adults participated in a rhythm-motor dual task intervention and 10 participated in the control group. The intervention group received 16 30-min intervention sessions for 8 weeks. During the intervention sessions, participants engaged in walking or bimanual tapping as a primary motor task with concurrent rhythm tasks including playing instruments and rhythmic chanting or singing. At pretest and post-test, measures of cognition, balance/mobility, and gait were administered. A significant difference between groups was found for part B of the Trail Making Test (TMT-B) measure that involved executive control of attention. Also, changes in the gait ratio in the dual task condition of walking while playing an instrument were significantly different between groups. The findings in this study support the use of the rhythm-motor dual task intervention for increasing available cognitive resources and improving gait control, which are critical factors in fall prevention.
The Effectiveness of Crisis Line Services: A Systematic Review

Background: Crisis lines are a standard component of a public health approach to suicide prevention. Clinical aims include reducing individuals' crisis states, psychological distress, and risk of suicide. Efforts may also include enhancing access and facilitating connections to behavioral health care. This review examines models of crisis line services for demonstrated effectiveness. Methods: Literature searches of Medline, EMBASE, PsycINFO, Web of Science, CINAHL, Cochrane Library, and Google Scholar were conducted from January 1, 1990, to May 7, 2018. Experts were contacted, and references were mined for additional studies. Eligible studies provided health- or utilization-related effectiveness outcome(s). Results were graded according to the Oxford Centre for Evidence-Based Medicine and evaluated for risk of bias using the Effective Public Health Practice Project quality assessment tool for quantitative studies. Results: Thirty-three studies yielded effectiveness outcomes. In most cases findings regarding crisis calls vs. other modalities were presented. Evaluation approaches included user- and helper-reported data, silent monitoring, and analyses of administrative records. About half of studies reported immediate proximal outcomes (during the crisis service), and the remaining reported distal outcomes (up to four years post-contact). Most studies were rated at Oxford level four evidence and 80% were assessed at high risk of bias. Conclusions: High quality evidence demonstrating crisis line effectiveness is lacking. Moreover, most approaches to demonstrating impact only measured proximal outcomes. Research should focus on innovative strategies to assess proximal and distal outcomes, with a specific focus on behavioral health treatment engagement and future self-directed violence.
Molecular Basis for Mucolytic Therapy

Airway mucus is a complex, viscoelastic gel that has a three-dimensional structure. It is composed of water, mucous glycoproteins, low molecular weight ions, proteins and lipids. The three-dimensional structure of the mucous gel depends on a number of forms of bonding, such as ionic bonds and disulphide bridges. Airway obstruction in cystic fibrosis (CF) lung disease is accompanied by the accumulation of thick and viscous secretions resulting from chronic infection and inflammation, promoting recurrent exacerbations. The normal, free-flow ing airway mucus becomes thick and purulent in patients suffering from CF lung disease. Therefore, current approaches to the treatment of CF include strategics for changing the physical properties of pulmonary secretions with the goal of improving airway clearance. Some of the same strategies may be applicable in the larger group of patients with chronic obstructive airway diseases, including bronchiectasis and chronic obstructive pulmonary disease. This paper reviews various approaches to mucolysis based on the molecular nature of crosslinking and bonding in mucin gels. A brief review of the structure and biochemistry of airway mucus is followed by a discussion of the various physical and biochemical approaches to mucolysis. Seven representative mucotropic modalities are presented: N-acetylcysteine; urea; hypertonic saline; recombinant human DNase; gelsolin; oscillation; and surfactants. Each of these mucotropic modalities acts on a different component within the mucous gel. Finally, the possibilities of mucolytic synergism among these various agents are conside red.
Metacognitive Therapy for Individuals at High Risk of Developing Psychosis: A Pilot Study

Developing effective interventions for preventing first episode psychosis have been an important research focus in the last decade. Cognitive behavioral therapy is a currently indicated treatment for people at ultra-high risk of psychosis, however, access and resource issues limit its delivery within the NHS. Treatments which partial out potential active ingredients and are aimed at a range of psychological difficulties seen within this population have the potential to be more efficacious and efficient. We conducted a single-arm exploratory pilot trial, designed to investigate the feasibility and acceptability of Metacognitive therapy for individuals at ultra-high risk (UHR) of developing psychosis. Trial uptake was good, with 11 out of 12 referred individuals meeting for an eligibility assessment (one individual was excluded prior to the assessment). Of these, 10 individuals were eligible and included in the trial. Retention to treatment was high with 80% treatment adherence gained and an overall average of 8 sessions completed. All participants were offered follow-up assessments immediately post-treatment and at 6 months, which comprised measures of psychotic like experiences, anxiety and depression, and metacognitive processes implicated in the model. Retention to the post-treatment (12-week) follow-up was good, with 80% completion; however retention to the 6-month follow-up was lower at 60%. Clinically significant results were observed in psychotic like experiences, anxiety, depression and functioning with medium to large effect sizes. Measures related to beliefs and processes targeted within MCT showed clinically significant change with medium to large effect sizes. Our results suggest that MCT based upon a specific metacognitive model for individuals meeting ARMS criteria may be an important treatment target and warrants further attention. Limitations and possible focuses for future research are discussed. Registration: ISRCTN53190465 http://www.isrctn. com/ISRCTN53190465.
Novel Action Targets of Natural Product Gliotoxin in Photosynthetic Apparatus

Gliotoxin (GT) is a fungal secondary metabolite that has attracted great interest due to its high biological activity since it was discovered by the 1930s. It exhibits a unique structure that contains a N-C = O group as the characteristics of the classical PSII inhibitor. However, GT’s phytotoxicity, herbicidal activity and primary action targets in plants remain hidden. Here, it is found that GT can cause brown or white leaf spot of various monocotyledonous and dicotyledonous plants, being regarded as a potential herbicidal agent. The multiple sites of GT action are located in two photosystems. GT decreases the rate of oxygen evolution of PSII with an I 50 value of 60 µM. Chlorophyll fluorescence data from Chlamydomonas reinhardtii cells and spinach thylakoids implicate that GT affects both PSII electron transport at the acceptor side and the reduction rate of PSI end electron acceptors’ pool. The major direct action target of GT is the plastoquinone QB-site of the D1 protein in PSII, where GT inserts in the QB binding niche by replacing native plastoquinone (PQ) and then interrupts electron flow beyond plastoquinone QA. This leads to severe inactivation of PSII RCs and a significant decrease of PSII overall photosynthetic activity. Based on the simulated modeling of GT docking to the D1 protein of spinach, it is proposed that GT binds to the-QB-site through two hydrogen bonds between GT and D1-Ser264 and D1-His252. A hydrogen bond is formed between the aromatic hydroxyl oxygen of GT and the residue Ser264 in the D1 protein. The 4-carbonyl group of GT provides another hydrogen bond to the residue D1-His252. So, it is concluded that GT is a novel natural PSII inhibitor. In the future, GT may have the potential for development into a bioherbicide or being utilized as a lead compound to design more new derivatives.
Developing Diagnostic Frameworks in Veterinary Behavioral Medicine: Disambiguating Separation Related Problems in Dogs

Diagnoses are widely used in both human and veterinary medicine to describe the nature of a condition; by contrast, syndromes are collections of signs that consistently occur together to form a characteristic presentation. Treatment of syndromes, due to either their lack of a clear biological cause or multiple causes, necessarily remains non-specific. However, the discovery of interventions may help refine the definition of a syndrome into a diagnosis. Within the field of veterinary behavioral medicine, separation related problems (SRPs) provide a good example of a syndrome. We describe here a comprehensive process to develop a diagnostic framework (including quality control assessments), for disambiguating the signs of SRPs as an example of a heterogeneous behavioral syndrome in non-human animals requiring greater diagnostic and treatment precision. To do this we developed an online questionnaire (243 items) that covered the full spectrum of theoretical bases to the syndrome and undertook a large-scale survey of the presenting signs of dogs with one or more of the signs of SRPs (n = 2,757). Principal components analysis (n1 = 345), replicated in a second sample (n2 = 417; total n = 762), was used to define the structure of variation in behavioral presentation, while hierarchical agglomerative cluster analysis cross checked with the partitioned around medoids method was used to determine sub-populations. A total of 54 signs were of value in defining a latent structure consisting of seven principal components (termed “exit frustration,” “social panic,” “elimination,” “redirected frustration,” “reactive communication,” “immediate frustration,” “noise sensitivity”), which divided the population in four clusters (termed “exit frustration,” “redirected reactive,” “reactive inhibited” and “boredom” related SRPs) with 11 sub-clusters (3, 3, 3, and 2, respectively). We used a bottom-up data-driven approach with numerous quality checks for the definition of robust clusters to provide a robust methodology for nosological studies in veterinary behavioral medicine, that can extend our understanding of the nature of problems beyond SRPs. This provides a solid foundation for future work examining aetiological, and differential treatment outcomes, that will allow both more effective treatment and prevention programmes, based on a fully appreciation of the nature of the problem of concern.
Long Noncoding RNA RAET1K Enhances CCNE1 Expression and Cell Cycle Arrest of Lung Adenocarcinoma Cell by Sponging miRNA-135a-5p

Molecular dysregulation is believed to participate in the onset and progression of lung adenocarcinoma (LUAD). This study aimed to identify and evaluate the potential key long noncoding RNAs (lncRNAs) involved in the significant dysfunctional process of LUAD. We found that lncRNA retinoic acid early transcript 1K (RAET1K) was upregulated in tumor tissues and were correlated with a poor prognosis of patients with LUAD; further, for the first time, we detected the biological roles of RAET1K. Weighted gene correlation network and gene set enrichment analysis revealed that high RAET1K expression is related to cell cycle dysfunction through upregulated cyclin E1 (CCNE1) by targeting miR-135. The dual-luciferase reporter gene assay was performed to clarify the binding relationship between RAET1K and miR-135a-5p in transgenic A549 and H1299 cells. Real-time PCR and Western blot analyses showed that RAET1K overexpression and miR-135a-5p inhibition exerted a strong synergistic effect on CCNE1 expression, and cell cycle flow cytometry analysis was used to confirm the arrest of A549 and H1299 cells at the G1/S phase. The lncRNA RAET1K/miR-135a-5p axis might participate in the regulation of LUAD progression by influencing CCNE1 expression and the accumulation of cells arrested at the G1/S phase boundary.
Memristor-Based Edge Detection for Spike Encoded Pixels

Memristors have many uses in machine learning and neuromorphic hardware. From memory elements in dot product engines to replicating both synapse and neuron wall behaviors, the memristor has proved a versatile component. Here we demonstrate an analog mode of operation observed in our silicon oxide memristors and apply this to the problem of edge detection. We demonstrate how a potential divider exploiting this analog behavior can prove a scalable solution to edge detection. We confirm its behavior experimentally and simulate its performance on a standard testbench. We show good performance comparable to existing memristor based work with a benchmark score of 0.465 on the BSDS500 dataset, while simultaneously maintaining a lower component count.