Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.
Aberration of miRNAs Expression in Leukocytes from Sporadic Amyotrophic Lateral Sclerosis

Background: Accumulating evidence indicates that miRNAs play an important role in the development of amyotrophic lateral sclerosis (ALS). Most of previous studies on miRNA dysregulation in ALS focused on the alterative expression in ALS animal model or in limited samples from European patients with ALS. In the present study, the miRNA expression profiles were investigated in Chinese ALS patients to explore leukocytes miRNAs as a potential biomarker for the diagnosis of ALS. Methods: We analyzed the expression profiles of 1733 human mature miRNAs using microarray technology in leukocytes obtained from 5 patients with sporadic ALS (SALS) and 5 healthy controls. An independent group of 83 SALS patients, 24 Parkinson's disease (PD) patients and 61 controls was used for validation by real-time polymerase chain reaction assay. Area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. In addition, target genes and signaling information of validated differential expression miRNAs were predicted using Bioinformatics. Results: Eleven miRNAs, including four over-expressed and seven under-expressed miRNAs detected in SALS patients compared to healthy controls were selected for validation. Four under-expressed microRNAs, including hsa-miR-183, hsa-miR-193b, hsa-miR-451, and hsa-miR-3935, were confirmed in validation stage by comparison of 83 SALS patients and 61 HCs. Moreover, we identified a miRNA panel (hsa-miR-183, hsa-miR-193b, hsa-miR-451, and hsa-miR-3935) having a high diagnostic accuracy of SALS (AUC 0.857 for the validation group). However, only hsa-miR-183 was significantly lower in SALS patients than that in PD patients and in HCs, while no differences were found between PD patients and HCs. By bioinformatics analysis, we obtained a large number of target genes and signaling information that are linked to neurodegeneration. Conclusion: This study provided evidence of abnormal miRNA expression patterns in the peripheral blood leukocytes of SALS patients. Leukocytes miRNAs provide a promising opportunity for detection of SALS. The specificity of under-expression of hsa-miR-183 in SALS needs to be confirmed by further miRNA studies on other neurodegenerative diseases.
Deep Spatiality: Unsupervised Learning of Spatially-Enhanced Global and Local 3D Features by Deep Neural Network With Coupled Softmax

The discriminability of the bag-of-words representations can be increased via encoding the spatial relationship among virtual words on 3D shapes. However, this encoding task involves several issues, including <italic>arbitrary mesh resolutions</italic>, <italic>irregular vertex topology</italic>, <italic>orientation ambiguity on 3D surface</italic>, <italic>invariance to rigid</italic>, and <italic>non-rigid shape transformations</italic>. To address these issues, a novel unsupervised spatial learning framework based on deep neural network, <italic>deep spatiality</italic> (DS), is proposed. Specifically, DS employs two novel components: <italic>spatial context extractor</italic> and <italic>deep context learner</italic>. Spatial context extractor extracts the spatial relationship among virtual words in a local region into a <italic>raw spatial representation</italic>. Along a <italic>consistent circular direction</italic>, a <italic>directed circular graph</italic> is constructed to encode relative positions between pairwise virtual words in each face ring into a <italic>relative spatial matrix</italic>. By decomposing each relative spatial matrix using singular value decomposition, the raw spatial representation is formed, from which deep context learner conducts unsupervised learning of the global and local features. Deep context learner is a deep neural network with a novel model structure to adapt the proposed <italic>coupled softmax layer</italic>, which encodes not only the discriminative information among local regions but also the one among global shapes. Experimental results show that DS outperforms state-of-the-art methods.
Benford’s Law and Dunbar’s Number: Does Facebook Have a Power to Change Natural and Anthropological Laws?

This paper presents the SmartSocial Dataset which describes 1,826 Facebook users with lots of details, including their connections and their interactions (e.g., posts, likes, and comments). We first present a detailed analysis of descriptive and network characteristics of the SmartSocial Dataset to provide evidence for its representativeness. Afterward, we analyze the relationship between social and behavioral characteristics of SmartSocial Dataset users and Benford’s Law as well as Dunbar’s Number, to test whether Facebook has the power to change natural (Benford) and anthropological (Dunbar) laws. We find that Facebook’s features are aligned with the Benford’s Law but redefine the way how Dunbar’s Number is calculated. Finally, we demonstrate how those findings could help researchers and business practitioners who collect Facebook data sets in a way to indicate whether there is serious sampling problem with the data set they collected.
Dose perturbations from implanted helical gold markers in proton therapy of prostate cancer

Implanted gold fiducial markers are widely used in radiation therapy to improve targeting accuracy. Recent investigations have revealed that metallic fiducial markers can cause severe perturbations in dose distributions for proton therapy, suggesting smaller markers should be considered. The objective of this study was to estimate the dosimetric impact of small gold markers in patients receiving proton therapy for prostate cancer. Small, medium, and large helical wire markers with lengths of 10 mm and helix diameters of 0.35 mm, 0.75 mm, and 1.15 mm, respectively, were implanted in an anthropomorphic phantom. Radiographic visibility was confirmed using a kilovoltage x‐ray imaging system, and dose perturbations were predicted from Monte Carlo simulations and confirmed by measurements. Monte Carlo simulations indicated that size of dose perturbation depended on marker size, orientation, and distance from the beam's end of range. Specifically, the perturbation of proton dose for the lateral‐opposed‐pair treatment technique was 31% for large markers and 23% for medium markers in a typical oblique orientation. Results for perpendicular and parallel orientations were respectively lower and higher. Consequently, these markers are not well suited for use in patients receiving proton therapy for prostate cancer. Dose perturbation was not observed for the small markers, but these markers were deemed too fragile for transrectal implantation in the prostate. PACS number: 87.53. Pb
Impact of Different Tidal Volume Levels at Low Mechanical Power on Ventilator-Induced Lung Injury in Rats

Tidal volume (VT) has been considered the main determinant of ventilator-induced lung injury (VILI). Recently, experimental studies have suggested that mechanical power transferred from the ventilator to the lungs is the promoter of VILI. We hypothesized that, as long as mechanical power is kept below a safe threshold, high VT should not be injurious. The present study aimed to investigate the impact of different VT levels and respiratory rates (RR) on lung function, diffuse alveolar damage (DAD), alveolar ultrastructure, and expression of genes related to inflammation [interleukin (IL)-6], alveolar stretch (amphiregulin), epithelial [club cell secretory protein (CC)16] and endothelial [intercellular adhesion molecule (ICAM)-1] cell injury, and extracellular matrix damage [syndecan-1, decorin, and metalloproteinase (MMP)-9] in experimental acute respiratory distress syndrome (ARDS) under low-power mechanical ventilation. Twenty-eight Wistar rats received Escherichia coli lipopolysaccharide intratracheally. After 24 h, 21 animals were randomly assigned to ventilation (2 h) with low mechanical power at three different VT levels (n = 7/group): (1) VT = 6 mL/kg and RR adjusted to normocapnia; (2) VT = 13 mL/kg; and 3) VT = 22 mL/kg. In the second and third groups, RR was adjusted to yield low mechanical power comparable to that of the first group. Mechanical power was calculated as [(ΔP,L2/Est,L)/2]× RR (ΔP,L = transpulmonary driving pressure, Est,L = static lung elastance). Seven rats were not mechanically ventilated (NV) and were used for molecular biology analysis. Mechanical power was comparable among groups, while VT gradually increased. ΔP,L and mechanical energy were higher in VT = 22 mL/kg than VT = 6 mL/kg and VT = 13 mL/kg (p < 0.001 for both). Accordingly, DAD score increased in VT = 22 mL/kg compared to VT = 6 mL/kg and VT = 13 mL/kg [23(18.5–24.75) vs. 16(12–17.75) and 16(13.25–18), p < 0.05, respectively]. VT = 22 mL/kg was associated with higher IL-6, amphiregulin, CC16, MMP-9, and syndecan-1 mRNA expression and lower decorin expression than VT = 6 mL/kg. Multiple linear regression analyses indicated that VT was able to predict changes in IL-6 and CC16, whereas ΔP,L predicted pHa, oxygenation, amphiregulin, and syndecan-1 expression. In the model of ARDS used herein, even at low mechanical power, high VT resulted in VILI. VT control seems to be more important than RR control to mitigate VILI.
Organic Phototransistors With Chemically Doped Conjugated Polymer Interlayers for Visible and Near Infrared Light Detection

Organic phototransistors were fabricated by inserting the patterned layers of a chemically doped conjugated polymer, poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS), between the gate electrodes and the gate-insulating layers in order to enable detection of both visible and near infrared (NIR) light. The transistor performance in the dark was slightly improved by the presence of the PEDOT:PSS interlayers. The present organic phototransistors exhibited a gradual increase in drain current (both output and transfer modes) and a noticeable shift in threshold voltage (transfer mode) upon illumination with both visible (550 nm) and NIR (800 and 1000 nm) light. In addition, the net photocurrent could be amplified by increasing either gate voltage or drain voltage. The corrected responsivity was initially improved by increasing the gate voltage but strongly dependent on the combination of gate and drain voltages. Finally, the present organic phototransistors with the PEDOT:PSS interlayers delivered comparable responsivity in both visible and NIR ranges.
Determinants of corporate cash holdings: Evidence from Portuguese publicly traded firms

This paper investigates the determinants of cash holdings of publicly traded Portuguese firms. We find that such firms hold less cash than similar companies operating in countries where both shareholders and creditors’ rights are more tightly protected by the law. In addition, our regression results suggest that leverage, other liquid assets, and firm growth are negatively correlated with our sample firms’ cash holdings whereas long-term debt and financial distress are positively correlated. Our findings cannot be reconciled with just one of the existent theories (trade-off, pecking order and free cash-flow theory), and emphasize the importance of a country’s legal, institutional, and economic environment for explaining firms’ cash holdings decisions.
Participation of children and youth with neurodevelopmental disorders in after-school activities

Abstract Aim: The aim of this study was to compare the level of participation in social, leisure and recreational activities in a group with intellectual disability, a group with autistic spectrum disorders, and a typically developing group. Method: The sample included 157 children of both genders, between 7 and 16 years of age (M = 11.03, SD =2.59). The Activities Questionnaire, which consists of: social, leisure, recreational activities, and friendship, was used in the research. Results: Participants with intellectual disability participated in a significantly larger number of all assessed activities than their peers with autistic spectrum disorders. There were no statistically significant differences in the frequency of participation in observed activities among the three groups of participants. Participants with intellectual disability were more independent than participants with autistic spectrum disorders in social and leisure activities, and needed less parental support in leisure activities. Participants with intellectual disability and autistic spectrum disorders had friendly relationships mainly with peers with disabilities. The influence of gender was detected in certain activities in all three groups of participants. Conclusions: Participants with disability participate in social, leisure and recreational activities less than their typically developing peers. The activities in which they participate are mainly stereotypical, highly structured, and take place in the presence of parents. IMPLICATIONS FOR REHABILITATION Forming a richer network of support services which would be oriented towards organizing social, leisure and recreational activities of persons with disabilities in the community. It is necessary to improve support programs which would focus on strengthening the competencies and resources of parents. The improvement of formal and informal support should provide a wider network, and better and more frequent social relationships between persons with and without disabilities.
Neurosteroid Biosynthesis Upregulation: A Novel Promising Therapy for Anxiety Disorders and PTSD

Generalized anxiety, panic, and posttraumatic stress disorder (PTSD) are debilitating conditions, which have an incidence of one in ten persons in the general population and epidemiological studies also report that these disorders often occur with depression (1-3). Anxiolytic benzodiazepines, including diazepam and alprazolam, remain the best and most used treatments for these conditions (4-7). However, their therapeutic use is associated with side effects, which include sedation and rapid development of tolerance as well as dependence. This results in severe discontinuation symptoms and often to drug abuse (4-6, 8; 9). In many patients, including patients with PTSD, the pharmacological effects of these drugs are very weak and there is a large number of non-responders (10-12). This has stimulated drug design that for many decades has focused in the development of new more effective therapies for anxiety disorders (13-15). Novel neuronal biomarkers for the pharmacological targets of the next generation of anxiolytic drugs have been discovered. The downregulation of neurosteroid biosynthesis has been implicated in the pathophysiology of anxiety and depressive disorders (reviewed in 16). Decreases in cerebrospinal fluid (clinical studies) and brain content (preclinical studies) of the GABAA receptor-active progesterone derivative, allopregnanolone, have been associated with affective and mood disorders, which includes depression, anxiety spectrum disorders, PTSD, premenstrual dysphoric disorder, schizophrenia, and impulsivity (17-27). Thus, elevating or normalizing the downregulation of brain allopregnanolone levels could be a promising therapeutic strategy for these psychiatric disorders. This prompted investigations to develop new neurosteroidogenic agents to contrast allopregnanolone biosynthesis deficits in anxiety and depression (28-31). We measured allopregnanolone levels in the cerebrospinal fluid (CSF) of PTSD patients assuming that allopregnanolone levels in the CSF reflect the levels of this neurosteroid in the brain (17). Also, in depressed patients, the concentration of allopregnanolone in the CSF was decreased by about 50-60% of the levels measured in non-psychiatric patients (26). The CSF allopregnanolone level decrease is likely induced by a downregulation of the expression of 5┙-reductase type I mRNA in the prefrontal-cortex (area BA9) that we measured in
SAFTE-VAT Functionality Effects on Flight Instructors' Situation Awareness and Instrument Student Pilots' Performance during FTD Training

Researcher: Rafael E. Abreu Vega Title: SAFTE-VAT Functionality Effects on Flight Instructors' Situation Awareness and Instrument Student Pilots' Performance During FTD Training Institution: Embry-Riddle Aeronautical University Degree: Master of Science in Aeronautics Year: 2016 SAFTE-VAT is a virtual air traffic control systems that adds the capability to integrate automated air traffic control functionality and generate semiautonomous and autonomous air traffic to the Frasca 172S level 6 plus FTD to improve behavioral fidelity and to facilitate flight instructors the capacity to focus more on instructing student pilots instead of role-playing ATC duties. While SAFTE-VAT may offer a more realistic ATC interaction experience onboard the FTD that may result in a positive transfer of training increase, the effects on flight instructors’ situation awareness and overall student pilot performance are uncertain. In this small study, flight instructors and instrument student pilots were observed completing while lesson 32 of the FA221 instrument course was onboard a Frasca 172S level 6 plus FTD with and without the used of SAFTE-VAT. During each FTD lesson 32 flight instructors were queried to test for situation awareness. Student performance data was collected upon completion of each FTD lesson and analyzed. The results revealed the possibility of situation awareness decrease during periods of low FTD activity levels when SAFTE-VAT was used. Student performance data favored the lessons conducted without the SAFTE-VAT.
Sustained Expression of Negative Regulators of Myelination Protects Schwann Cells from Dysmyelination in a Charcot–Marie–Tooth 1B Mouse Model

Schwann cell differentiation and myelination in the PNS are the result of fine-tuning of positive and negative transcriptional regulators. As myelination starts, negative regulators are downregulated, whereas positive ones are upregulated. Fully differentiated Schwann cells maintain an extraordinary plasticity and can transdifferentiate into “repair” Schwann cells after nerve injury. Reactivation of negative regulators of myelination is essential to generate repair Schwann cells. Negative regulators have also been implicated in demyelinating neuropathies, although their role in disease remains elusive. Here, we used a mouse model of Charcot–Marie–Tooth neuropathy type 1B (CMT1B), the P0S63del mouse characterized by ER stress and the activation of the unfolded protein response, to show that adult Schwann cells are in a partial differentiation state because they overexpress transcription factors that are normally expressed only before myelination. We provide evidence that two of these factors, Sox2 and Id2, act as negative regulators of myelination in vivo. However, their sustained expression in neuropathy is protective because ablation of Sox2 or/and Id2 from S63del mice of both sexes results in worsening of the dysmyelinating phenotype. This is accompanied by increased levels of mutant P0 expression and exacerbation of ER stress, suggesting that limited differentiation may represent a novel adaptive mechanism through which Schwann cells counter the toxic effect of a mutant terminal differentiation protein. SIGNIFICANCE STATEMENT In many neuropathies, Schwann cells express high levels of early differentiation genes, but the significance of these altered expression remained unclear. Because many of these factors may act as negative regulators of myelination, it was suggested that their misexpression could contribute to dysmyelination. Here, we show that the transcription factors Sox2 and Id2 act as negative regulators of myelination in vivo, but that their sustained expression in Charcot–Marie–Tooth type 1B (CMT1B) represents an adaptive response activated by the Schwann cells to reduce mutant protein toxicity and prevent demyelination.
The effect of gantry spacing resolution on plan quality in a single modulated arc optimization

Volumetric‐modulated arc technique (VMAT) is an efficient form of IMRT delivery. It is advantageous over conventional IMRT in terms of treatment delivery time. This study investigates the relation between the number of segments and plan quality in VMAT optimization for a single modulated arc. Five prostate, five lung, and five head‐and‐neck (HN) patient plans were studied retrospectively. For each case, four VMAT plans were generated. The plans differed only in the number of control points used in the optimization process. The control points were spaced 2°, 3°, 4°, and 6° apart, respectively. All of the optimization parameters were the same among the four schemes. The 2° spacing plan was used as a reference to which the other three plans were compared. The plan quality was assessed by comparison of dose indices (DIs) and generalized equivalent uniform doses (gEUDs) for targets and critical structures. All optimization schemes generated clinically acceptable plans. The differences between the majority of reference and compared DIs and gEUDs were within 3%. DIs and gEUDs which differed in excess of 3% corresponded to dose levels well below the organ tolerances. The DI and the gEUD differences increased with an increase in plan complexity from prostates to HNs. Optimization with gantry spacing resolution of 4° seems to be a very balanced alternative between plan quality and plan complexity. PACS number: 87.55. de