Miracle-dz/UniFAR-FTUs huggingface dataset:
Type IV Pili-Independent Photocurrent Production by the Cyanobacterium Synechocystis sp. PCC 6803

Biophotovoltaic devices utilize photosynthetic organisms such as the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) to generate current for power or hydrogen production from light. These devices have been improved by both architecture engineering and genetic engineering of the phototrophic organism. However, genetic approaches are limited by lack of understanding of cellular mechanisms of electron transfer from internal metabolism to the cell exterior. Type IV pili have been implicated in extracellular electron transfer (EET) in some species of heterotrophic bacteria. Furthermore, conductive cell surface filaments have been reported for cyanobacteria, including Synechocystis. However, it remains unclear whether these filaments are type IV pili and whether they are involved in EET. Herein, a mediatorless electrochemical setup is used to compare the electrogenic output of wild-type Synechocystis to that of a ΔpilD mutant that cannot produce type IV pili. No differences in photocurrent, i.e., current in response to illumination, are detectable. Furthermore, measurements of individual pili using conductive atomic force microscopy indicate these structures are not conductive. These results suggest that pili are not required for EET by Synechocystis, supporting a role for shuttling of electrons via soluble redox mediators or direct interactions between the cell surface and extracellular substrates.
Matrix and habitat quality in a montane cloud-forest landscape: amphibians in coffee plantations in central Veracruz, Mexico

Abstract Context. The processes of fragmentation, habitat loss, degradation and their combined effects are formidable threats to amphibian populations. Aims. We evaluate the effect of three land use-type variables and nine landscape matrix quality factors on amphibian presence in four coffee agro-ecosystems and two cloud-forest fragments in central Veracruz, Mexico. Methods. Each site was thoroughly searched using the visual-encounter survey technique along different trails in the most feasible microhabitats for detecting amphibians during four rainy seasons (2005, 2006, 2008 and 2009). Centred on the location where each amphibian species was first recorded, we established what we refer to as a buffer area within a radius of 1.5 km. A Co-Inertia mathematical model was used to determine which of the explanatory variables contributed to maintaining amphibian diversity. The landscape variables were landscape-quality index, open areas, canopy cover (low, intermediate, dense) at the matrix level, river, road and human population density and site size. Local variables were elevation, plant-structure and biological-impact indices. Key results. During the study we recorded 1078 amphibians belonging to 26 species, 17 genera and 10 families. The variables explaining the composition of amphibian diversity were river and human population density, low canopy cover at the matrix level, elevation, site size and plant-structure index. Amphibian diversity increased as the structural complexity of the habitat increased, and the former was positively correlated with fragment size. Conclusion. The present study indicated that coffee agro-ecosystems and the cloud-forest fragments in the region form a gradient in habitat quality and landscape variables that exert a differential influence on amphibian assemblages, and that each species responds uniquely to different variables. Implications. Coffee agro-ecosystems and forest fragments cannot be seen as homogenous patches with a certain habitat quality, separate from the landscape matrix in which they are immersed. Stakeholders are not advised to rely on a single strategy to conserve the amphibian community, but rather should aim to maintain a heterogeneous landscape with forest fragments and coffee agro-ecosystems that have a complex vertical plant structure at the habitat level, especially in highly river-dense landscapes.
Laminar Flow Protects Vascular Endothelial Tight Junctions and Barrier Function via Maintaining the Expression of Long Non-coding RNA MALAT1

Atherosclerotic plaque preferentially develops in arterial curvatures and branching regions, where endothelial cells constantly experience disturbed blood flow. By contrast, the straight arteries are generally protected from plaque formation due to exposure of endothelial cells to vaso-protective laminar blood flow. However, the role of flow patterns on endothelial barrier function remains largely unclear. This study aimed to investigate new mechanisms underlying the blood flow pattern-regulated endothelial integrity. Exposure of human endothelial cells to pulsatile shear (PS, mimicking the laminar flow) compared to oscillatory shear (OS, mimicking the disturbed flow) increased the expressions of long non-coding RNA MALAT1 and tight junction proteins ZO1 and Occludin. This increase was abolished by knocking down MALAT1 or Nesprin1 and 2. PS promoted the association between Nesprin1 and SUN2 at the nuclear envelopes, and induced a nuclear translocation of β-catenin, likely through enhancing the interaction between β-catenin and Nesprin1. In the in vivo study, mice were treated via intraperitoneal injection with β-catenin agonist SKL2001 or its inhibitor XAV939, and they were then subjected to Evans blue injection to assess aortic endothelial permeability. The aortas exhibited a reduced wall permeability to Evans blue in SKL2001-treated mice whereas an enhanced permeability in XAV939-treated mice. We concluded that laminar flow promotes nuclear localization of Nesprins, which facilitates the nuclear access of β-catenin to stimulate MALAT1 transcription, resulting in increased expressions of ZO1 and Occludin to protect endothelial barrier function.
An Ethnobotanical Study on Qīng-Căo-Chá Tea in Taiwan

Herbal tea, a beverage prepared from a variety of plant materials excluding the leaves of the tea plant Camellia sinensis (L.) Kuntze of the family Theaceae, for a long time, has been consumed by most Chinese people for preventive and/or therapeutic health care. Usually, it is brewed or prepared as a decoction of local plants in water. The qīng-căo-chá tea, a commercial herbal tea, is the most common among many differently formulated herbal teas in Taiwan. For hundreds of years, qīng-căo-chá tea has played an important role in the prevention and treatment of diseases associated with the environmental conditions in Taiwan. However, research studies in this field have been insufficient. The raw material formulas of qīng-căo-chá tea have always been passed down from “masters” to “apprentices. ” Hence, there is no systematic collation or record, and, therefore, there is a need to assess and confirm the composition, safety, and effectiveness of the raw materials. This study aimed to document the uses of Taiwan's qīng-căo-chá tea through a semi-structured interview survey and investigate the background of traditional practitioners, tea compositions, and plant origins and uses. This will improve our understanding of the knowledge inherited by the practitioners and the theoretical basis of the medicinal uses of these teas. In our field investigation, we visited 86 shops and assessed 71 raw ingredients of qīng-căo-chá tea. A semi-structured questionnaire was used to conduct the interviews. During the interviews, in addition to written records, audio and video recordings were made, and photographs were taken with the permission of the interviewees. The qīng-căo-chá raw materials have long been used as herbal teas, although more research should clarify their efficacy and safety. Traditional sellers of qīng-căo-chá tea were mainly males, and most shops have been in operation for more than 71 years. Some of the raw materials were derived from multiple sources, including different plants, and were often mixed without any safety concerns. To our knowledge, this is the first systematic ethnobotanical study on qīng-căo-chá tea that assesses and confirms its herbal ingredients. Our study represents a reference for herbal teas in Taiwan that can be used by the public and regulatory agencies.
Occurrence of a RAGE-Mediated Inflammatory Response in Human Fetal Membranes

Context: Sterile inflammation has been shown to play a key role in the rupture of the fetal membranes (FMs). Moreover, an early and exacerbated runaway inflammation can evolve into a preterm premature rupture of membranes and lead to potential preterm birth. In this context, we investigated the receptor for advanced glycation end products (RAGE), an axis implied in physiological sterile inflammation, in conjunction with two major ligands: AGEs and High-Mobility Group Box 1 (HMGB1). Our first objective was to determine the spatiotemporal expression profiles of the different actors of the RAGE-signaling axis in human FMs, including its intracellular adaptors Diaphanous-1 and Myd88. Our second goal was to evaluate the functionality of RAGE signaling in terms of FMs inflammation. Methods The presence of the actors (RAGE, HMGB1, Myd88, and Diaphanous-1) at the mRNA level was investigated by reverse transcription quantitative polymerase chain reaction (RT-qPCR) in the human amnion and choriodecidua at the three trimesters and at term. Measurements were conducted at two distinct zones: the zone of intact morphology (ZIM) and the zone of altered morphology (ZAM). Then, proteins were quantified using Western blot analysis, and their localization was evaluated by immunofluorescence in term tissues. In addition, pro-inflammatory cytokine secretion was quantified using a Multiplex assay after the treatment of amnion and choriodecidua explants with two RAGE ligands (AGEs and HMGB1) in the absence or presence of a RAGE inhibitor (SAGEs). Results The FMs expressed the RAGE-signaling actors throughout pregnancy. At term, RNA and protein overexpression of the RAGE, HMGB1, and Diaphanous-1 were found in the amnion when compared to the choriodecidua, and the RAGE was overexpressed in the ZAM when compared to the ZIM. The two RAGE ligands (AGEs and HMGB1) induced differential cytokine production (IL1β and TNFα) in the amnion and choriodecidua. Conclusion Considered together, these results indicate that RAGE signaling is present and functional in human FMs. Our work opens the way to a better understanding of FMs weakening dependent on a RAGE-based sterile inflammation.
Macroevolution of Flower Color Patterning: Biased Transition Rates and Correlated Evolution with Flower Size

Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date, there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible floral patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias toward non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.
A Revision of Philander (Marsupialia: Didelphidae), Part 2: Phylogenetic Relationships and Morphological Diagnosis of P. nigratus Thomas, 1923

ABSTRACT Newly available molecular sequences and morphological data suggest that Philander nigratus Thomas, 1923, is a valid species. Currently known from just eight specimens collected in the Peruvian departments of Junín and Ayacucho, P. nigratus does not appear to be closely related to either of the congeneric taxa with which it was previously synonymized.
Liberte, Egalite, Fraternite... Contamine? Estimating the impact of French municipal elections on COVID-19 spread in France

On March 15, about 20,000,000 voters cast their vote for the first round of the 2020 French municipal elections. We investigate the extent to which this event contributed to the COVID-19 epidemics in France. To this end, we first predict each departement's own dynamics using information up to the election to calibrate a standard logistic model. We then take advantage of electoral turnout differences between departements to distinguish the impact of the election on prediction errors in hospitalizations from that of simultaneously implemented anti-contagion policies. We report a detrimental effect of the election in locations that were at relatively advanced stages of the epidemics by the time of the election. In contrast, we show that the election did not contribute to the epidemics in departements with lower infection levels by March 15. All in all, our estimates suggest that elections accounted for about 4,000 excess hospitalizations by the end of March, which represents 15% of all hospitalizations by this time. They also suggest that holding elections in June may not be as detrimental.
Interpersonal Neural Synchronization During Cooperative Behavior of Basketball Players: A fNIRS-Based Hyperscanning Study

Accumulating evidence has consistently shown that team-based sports (such as basketball) are beneficial to interpersonal cooperation. However, its neural correlate remains to be discovered, especially in the perspective of two-person neuroscience. In this study, 12 dyads of basketball players and 12 dyads of college students who had no experience of team-based sports training were asked to perform joint-drawing task and control task. During task performance, neural activities were recorded in frontal area by the functional near-infrared spectroscopy (fNIRS)-based hyperscanning approach. The results demonstrated that dyads of basketball players were faster to finish joint-drawing task and showed higher subjective cooperativeness than dyads of college students. Meanwhile, significant interpersonal neural synchronization (INS) was observed in the dorsolateral prefrontal area only when pairs of basketball players performed joint-drawing task, but not control task. Therefore, we provide the first piece of inter-brain evidence for enhanced cooperative behavior in the individuals with team-based sports training, which could make us deeply understand exact neural correlate for experience-dependent changes of cognitions in humans.
Molekulare Funktionsanalyse von Microcystin in Microcystis aeruginosa PCC 7806

Microcystins are the most common cyanobacterial toxins found in freshwater lakes and reservoirs throughout the world. They are frequently produced by the unicellular, colonial cyanobacterium Microcystis; however, the role of the peptide for the producing organismen is poorly understood. In this study we describe the first global approach to investigate this topic on a molecular level. Proteomic studies with M. aeruginosa PCC 7806 wild-type and several microcystin-deficient mutants indicated a physiological function for microcystin. Microcystin was shown to influence the abundance of several proteins which have an intraor extracellular function. A prominent candidate is RubisCO, the key enzyme of the calvin cycle. RubisCO and other proteins, initially selected by 2D analysis, are putative cellular binding partners of microcystin. A potentially interaction mechanismen is the kovalent binding of microcystin to cysteine residues of the protein. Moreover, several knockouts of microcystin biosynthesis genes result in an overexpression of a putative morpho-type specific factor, named MrpC. This protein possibly mediates cell-cell interactions in Microcystis.
Autologous Stem Cell Transplantation in Common Variable Immunodeficiency: A Case of Successful Treatment of Severe Refractory Autoimmune Encephalitis

Common variable immunodeficiency (CVID) is the most common primary immunodeficiency in adults. It is associated with hypogammaglobulinemia, recurring infections and autoimmune phenomena. Treatment includes immunoglobulin substitution and immunosuppressants. Autoimmune neurological manifestations of CVID are rare and occur predominantly as granulomatous disease. We report the case of a 35-year-old woman with CVID who developed autoimmune encephalitis as demonstrated by double cerebral biopsy. Infectious or malignant causes could be excluded. Despite intensive immunosuppressive therapy with common regimens no significant improvement could be achieved. Ultimately, an autologous hematopoietic stem cell transplantation (HSCT) was performed, resulting in lasting complete remission of the encephalitis. To our knowledge, this is the first report of refractory autoimmune phenomena in CVID treated by autologous HSCT.
An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models

Protein-ligand binding affinity is a key pharmacodynamic endpoint in drug discovery. Sole reliance on experimental design, make, and test cycles is costly and time consuming, providing an opportunity for computational methods to assist. Herein, we present results comparing random forest and feed-forward neural network proteochemometric models for their ability to predict pIC50 measurements for held out generic Bemis-Murcko scaffolds. In addition, we assess the ability of conformal prediction to provide calibrated prediction intervals in both a retrospective and semi-prospective test using the recently released Grand Challenge 4 data set as an external test set. In total, random forest and deep neural network proteochemometric models show quality retrospective performance but suffer in the semi-prospective setting. However, the conformal predictor prediction intervals prove to be well-calibrated both retrospectively and semi-prospectively showing that they can be used to guide hit discovery and lead optimization campaigns.
A Review of Default Mode Network Connectivity and Its Association With Social Cognition in Adolescents With Autism Spectrum Disorder and Early-Onset Psychosis

Recent studies have demonstrated substantial phenotypic overlap, notably social impairment, between autism spectrum disorder (ASD) and schizophrenia. However, the neural mechanisms underlying the pathogenesis of social impairments across these distinct neuropsychiatric disorders has not yet been fully examined. Most neuroimaging studies to date have focused on adults with these disorders, with little known about the neural underpinnings of social impairments in younger populations. Here, we present a narrative review of the literature available through April 2020 on imaging studies of adolescents with either ASD or early-onset psychosis (EOP), to better understand the shared and unique neural mechanisms of social difficulties across diagnosis from a developmental framework. We specifically focus on functional connectivity studies of the default mode network (DMN), as the most extensively studied brain network relevant to social cognition across both groups. Our review included 29 studies of DMN connectivity in adolescents with ASD (Mean age range = 11.2–21.6 years), and 14 studies in adolescents with EOP (Mean age range = 14.2–24.3 years). Of these, 15 of 29 studies in ASD adolescents found predominant underconnectivity when examining DMN connectivity. In contrast, findings were mixed in adolescents with EOP, with five of 14 studies reporting DMN underconnectivity, and an additional six of 14 studies reporting both under- and over-connectivity of the DMN. Specifically, intra-DMN networks were more frequently underconnected in ASD, but overconnected in EOP. On the other hand, inter-DMN connectivity patterns were mixed (both under- and over-connected) for each group, especially DMN connectivity with frontal, sensorimotor, and temporoparietal regions in ASD, and with frontal, temporal, subcortical, and cerebellar regions in EOP. Finally, disrupted DMN connectivity appeared to be associated with social impairments in both groups, less so with other features distinct to each condition, such as repetitive behaviors/restricted interests in ASD and hallucinations/delusions in EOP. Further studies on demographically well-matched groups of adolescents with each of these conditions are needed to systematically explore additional contributing factors in DMN connectivity patterns such as clinical heterogeneity, pubertal development, and medication effects that would better inform treatment targets and facilitate prediction of outcomes in the context of these developmental neuropsychiatric conditions.
Screening Depressive Disorders With Tree-Drawing Test

Objective: Diagnosis of psychiatric disease is still a major issue. Two key reasons are- there are variations in the opinions of the medical doctors and the presentation of a disease among the patients. Here we introduce a kind of mental projective test, tree-drawing test, trying to extract and analyze objective indexes in tree-drawing test in patients with depression. Methods: The tree-drawing test was administered to 43 patients with major depressive disorders, 48 sub-threshold subjects, and 59 healthy subjects. Features of the drawing trees were analyzed using a kind of computer image recognition and data acquisition software. Quantitative indexes collected from pictures drawn by patients with major depression, patients with sub-threshold depression, and control subjects were compared using the ANOVA test. Results: Five quantitative features (canopy area, canopy height, canopy width, trunk width, and total area of trees) were found to be statistically significant among the groups, while seven other features (trunk area, trunk height, root width, root height, root area, ratio of crown to trunk height, and ratio of crown to trunk area) showed no statistical significance. Further analysis with LSD-t test revealed that six quantitative indexes were significantly related to the depression symptoms, and six others were not statistically significant. Eleven quantitative indexes were not statistically significant when the depressive symptoms were compared with the subthreshold depression group, and the only index with statistical significance was canopy width. Conclusion: Five quantitative indexes in the drawing tree are statistically significant in the depression patients were compared with those of the control subjects. Quantitative indexes of the tree-drawing test are of great value in assisting with the diagnosis of psychiatric disorders.