Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.
β-carotene Rescues Busulfan Disrupted Spermatogenesis Through Elevation in Testicular Antioxidant Capability

β-carotene, precursor of vitamin A, is an excellent antioxidant with many beneficial properties. It is a lipid-soluble antioxidant and a very effective quencher of reactive oxygen species (ROS) to reduce the oxidative stress. In contrast to vitamin A, β-carotene is not toxic even consumed in higher amount when it is delivered from natural plant products. Recently, we found that β-carotene acts as a potential antioxidant in the oocyte to improve its quality. Even though many studies have been reported that β-carotene has the beneficial contribution to the ovarian development and steroidogenesis, it is unknown the effects of β-carotene on the spermatogenesis. This investigation aimed to explore the hypothesis that β-carotene could improve spermatogenesis and the underlying mechanism. And we found that β-carotene rescued busulfan disrupted spermatogenesis in mouse with the increase in the sperm concentration and motility. β-carotene improved the expression of genes/proteins important for spermatogenesis, such as VASA, DAZL, SYCP3, PGK2. Moreover, β-carotene elevated the testicular antioxidant capability by the elevation of the antioxidant glutathione and antioxidant enzymes SOD, GPX1, catalase levels. In conclusion, β-carotene may be applied for the infertile couples by the improvement of spermatogenesis, since, worldly many couples are infertile due to the idiopathic failed gametogenesis (spermatogenesis).
Ecological Specialization Within a Carnivorous Fish Family Is Supported by a Herbivorous Microbiome Shaped by a Combination of Gut Traits and Specific Diet

Animals have been developing key associations with micro-organisms through evolutionary processes and ecological diversification. Hence, in some host clades, phylogenetic distance between hosts is correlated to dissimilarity in microbiomes, a pattern called phylosymbiosis. Teleost fishes, despite being the most diverse and ancient group of vertebrates, have received little attention from the microbiome perspective and our understanding of its determinants is currently limited. In this study, we assessed the gut microbiome of 12 co-occurring species of teleost representing a large breadth of ecological diversity and originating from a single family (i.e., the Sparidae). We tested how host evolutionary history, diet composition and morphological traits are related to fish gut microbiome. Despite fish species having different microbiomes, there is no phylosymbiosis signal in this fish family, but gut length and diet had a strong influence on the microbiome. We revealed that the only species with a specialized herbivorous diet, Sarpa salpa had a 3.3 times longer gut than carnivorous species and such a long gut favor the presence of anaerobic bacteria typical of herbivorous gut microbiomes. Hence, dietary uniqueness is paired with both unique gut anatomy and unique microbiome.
PREPARATION, CHEMICAL CHARACTERIZATION, AND ELECTRONIC SPECTRA OF 6-(2-PYRIDYLAZO)-3-ACETAMIDOPHENOL AND ITS METAL COMPLEXES

The stereochemistry of new iron(III), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of 6-(2-pyridylazo)-3-acetamidophenol (H2L) is studied on the basis of their analytical, spectroscopic, magnetic, thermal and conductance data. The dissociation constant of the ligand as well as the stability constants of its metal complexes have been determined spectrophotometrically. On the basis of the infrared spectra the coordination behaviour of the ligand to the metal ions is investigated. Magnetic susceptibility and solid reflectance spectral measurements are used to infer the structure. The prepared complexes are found to have the general formulae [M(HL)(H2O)x](A) · yH2O (M = Cu(II), Zn(II), Cd(II) and Fe(III); HL = 6-(2-pyridylazo)-3-acetamidophenolate; A = acetate in case of Cu(II) and Zn(II) or chloride in case of Cd(II) and Fe(III), x = 1–3 and y = 0–5) or [M(H2L)(H2O) x ]Cl2 · yH2O (M = Ni(II) and Co(II); H2L = 6-(2-pyridylazo)-3-acetamidophenol, x = 3 and y = 5–6).
Retraction: Epigenetic silenced miR‐125a‐5p could be self‐activated through targeting Suv39H1 in gastric cancer

Epigenetic silenced miR-125a-5p could be self-activated through targeting Suv39H1 in gastric cancer. Mingzhi Cai, Qiuxian Chen, Juntao Shen, Chenbing Lv and Lisheng Cai. J Cell Mol Med. 2018; 22: 4721-4731. The above article from Journal of Cellular and Molecular Medicine, published online on 17 August 2018 on Wiley Online Library (wileyonlinelibrary.com) and in Volume 22, pp. 4721-4731, has been retracted by agreement between the authors, the journal Editor-in-Chief and John Wiley & Sons Ltd. The retraction has been agreed because parts of the data and figures that the authors presented in the paper are flawed. The conclusions drawn from the data and figures presented could not be considered as reliable.
Zoledronic Acid-Loaded Hybrid Hyaluronic Acid/Polyethylene Glycol/Nano-Hydroxyapatite Nanoparticle: Novel Fabrication and Safety Verification

Osteosarcoma is a malignant tumor that often occurs in adolescents and children. Zoledronic acid, a new-generation bisphosphonate, has been widely used as an antitumor drug to inhibit bone metastasis. However, the rapid renal elimination results in low effective concentrations. Meanwhile, high-dose intravenous zoledronic acid administration leads to severe side effects. The present study fabricated an organic–inorganic hybrid nanoparticle as the carrier of zoledronic acid. The rod-like nanoparticle, which had 150-nm length and 40-nm cross-sectional diameter, consisted of a hyaluronic acid/polyethylene glycol (HA-PEG) polymer shell and a nano-hydroxyapatite (nHA) core, with zoledronic acid molecules loading on the surface of nHA and clearance of HA-PEG shell. The nanoparticle was characterized by microscopic analysis, in vitro release study, cytotoxicity analysis, and in vivo immune response examination. Results showed that the compact and stable structure could achieve high drug loading efficiency, sustained drug release, and great biocompatibility. In vitro and in vivo experiments revealed the low cytotoxicity and acceptable immune response under low-dose nanoparticle treatment, indicating its potential application for future osteosarcoma therapeutic strategies.
Prophylactic Modulation of Methane and Nitrous Oxide Emitted from Ruminants Livestock for Sustainable Animal Agriculture

Major greenhouse gases (GHG) attributed to animal agriculture sector are methane (CH 4 ) and nitrous oxide (N 2 O), either generated from enteric fermentation or manure. The abatement mechanism of rumen CH 4 emission may be divided to direct and indirect suppression to methanogens in the rumen.The most significant strategy to mitigate ruminal CH 4 emission in indirect manner is to promote alternative metabolic pathway to dispose of the reducing power, competing with methanogenesis for H 2 uptake. This includes prebiotics and probiotics (mostly propionate enhancers) which consume metabolic hydrogen (H 2 ) compete with methanogens and abate rumen methanogenesis in indirect manner. With regard to mitigate GHG emissions from manure, such waste has been proposed as a renewable energy and nitrogen sources through biogas plant. Furthermore, in advanced new biogas system, the ammonia stripping from digested slurry of livestock manure in biogas plant has been examined to apply to nitrogen recycling-options mitigating N 2 O emission. These options are: (1) ammonolysis on fiber-rich feedstuffs, (2) saccharification of the NH 3 treated cellulose biomass to produce bio-ethanol, and (3) reformed hydrogen into NH 3 fuel cell to generate electricity with proton exchange membrane fuel cell (PEM). Key words: rumen methane, nitrous oxide, probiotics, prebiotics, ammonia stripping
Endovascular Therapy for Basilar Arterial Trunk Aneurysms

Background: Although aneurysms rarely occur in the basilar artery (BA) trunk, the majority of those that do are dissection aneurysms. Currently, the mainstream therapy for BA trunk aneurysms is endovascular therapy (EVT), which mainly includes single coiling or conventional low-metal-coverage stent-assisted EVT, but the efficacy remains to be evaluated. Methods: A retrospective study was performed for the patients who were admitted to our institution for BA trunk aneurysms and underwent EVT. A total of 28 patients were collected in this study. Results: The patients were aged 23–71 years (53.7 ± 11.5 years on average); nine were female (32.1%, 9/28), and 19 were male (67.9%, 19/28). The patients were given single coiling or conventional low-metal-coverage stent-assisted EVT. Among the 28 patients, 10 (35.7%, 10/28) developed complications, 90% (9/10) of which were ischemic and 10% (1/10) were hemorrhagic. Among the 28 patients, 5 (17.9%, 5/28) died. The surviving 23 patients (82.1%, 23/28) recovered well. Conclusions: This study found that for BA trunk aneurysms, single coiling or conventional low-metal-coverage stent-assisted EVT still had some risks. The risks are mainly from brainstem ischemia. Therefore, the perforators of the BA trunk must be carefully evaluated and prevented from receiving damage from the EVT procedure. This study also shows that 82.1% of patients recovered well. Therefore, EVT can result in an acceptable prognosis.
Development and Application of Endothelial Cells Derived From Pluripotent Stem Cells in Microphysiological Systems Models

The vascular endothelium is present in all organs and blood vessels, facilitates the exchange of nutrients and waste throughout different organ systems in the body, and sets the tone for healthy vessel function. Mechanosensitive in nature, the endothelium responds to the magnitude and temporal waveform of shear stress in the vessels. Endothelial dysfunction can lead to atherosclerosis and other diseases. Modeling endothelial function and dysfunction in organ systems in vitro, such as the blood–brain barrier and tissue-engineered blood vessels, requires sourcing endothelial cells (ECs) for these biomedical engineering applications. It can be difficult to source primary, easily renewable ECs that possess the function or dysfunction in question. In contrast, human pluripotent stem cells (hPSCs) can be sourced from donors of interest and renewed almost indefinitely. In this review, we highlight how knowledge of vascular EC development in vivo is used to differentiate induced pluripotent stem cells (iPSC) into ECs. We then describe how iPSC-derived ECs are being used currently in in vitro models of organ function and disease and in vivo applications.
An Integrative Pharmacology-Based Pattern to Uncover the Pharmacological Mechanism of Ginsenoside H Dripping Pills in the Treatment of Depression

Objectives: To evaluate the pharmacodynamical effects and pharmacological mechanism of Ginsenoside H dripping pills (GH) in chronic unpredictable mild stress (CUMS) model rats. Methods: First, the CUMS-induced rat model was established to assess the anti-depressant effects of GH (28, 56, and 112 mg/kg) by the changes of the behavioral indexes (sucrose preference, crossing score, rearing score) and biochemical indexes (serotonin, dopamine, norepinephrine) in Hippocampus. Then, the components of GH were identified by ultra-performance liquid chromatography-iron trap-time of flight-mass spectrometry (UPLC/IT-TOF MS). After network pharmacology analysis, the active ingredients of GH were further screened out based on OB and DL, and the PPI network of putative targets of active ingredients of GH and depression candidate targets was established based on STRING database. The PPI network was analyzed topologically to obtain key targets, so as to predict the potential pharmacological mechanism of GH acting on depression. Finally, some major target proteins involved in the predictive signaling pathway were validated experimentally. Results: The establishment of CUMS depression model was successful and GH has antidepressant effects, and the middle dose of GH (56 mg/kg) showed the best inhibitory effects on rats with depressant-like behavior induced by CUMS. Twenty-eight chemical components of GH were identified by UPLC/IT-TOF MS. Subsequently, 20(S)-ginsenoside Rh2 was selected as active ingredient and the PPI network of the 43 putative targets of 20(S)-ginsenoside Rh2 containing in GH and the 230 depression candidate targets, was established based on STRING database, and 47 major targets were extracted. Further network pharmacological analysis indicated that the cAMP signaling pathway may be potential pharmacological mechanism regulated by GH acting on depression. Among the cAMP signaling pathway, the major target proteins, namely, cAMP, PKA, CREB, p-CREB, BDNF, were used to verify in the CUMS model rats. The results showed that GH could activate the cAMP-PKA-CREB-BDNF signaling pathway to exert antidepressant effects. Conclusions: An integrative pharmacology-based pattern was used to uncover that GH could increase the contents of DA, NE and 5-HT, activate cAMP-PKA-CREB-BDNF signaling pathway exert antidepressant effects.
A survey on the soundscape perception before and during the COVID-19 pandemic in Italy

Abstract At the time of the COVID-19 pandemic, the impact of lockdown measures highlights changes in terms of sounds and noises present in the everyday life. The present paper deals with this peculiar and unexpected scenario as studied by means of an online survey consisting of 18 questions and distributed to residents in the Italian territory. For studying the unprecedented effect of the pandemic, participants were asked to fill the questionnaire, providing personal data, describing context and characteristics of the house in which they live and making a comparison of the lockdown soundscape with the pre-lockdown one. About four hundred questionnaires have been collected and analysed in order to define correlations between personal and perception variables. Using logistic regression models, changes have been studied during the two abovementioned periods. It has been observed that the perception of traffic noise has increased for people over 35 years old and the noise produced by the neighbourhood has been more statistically significant for employed respondents. Future outlook might provide the spread of the questionnaire in other countries for a global evaluation of the data, to be also acquired with reference to the after-lockdown period.
Genótipos de feijoeiro comum sob deficiência hídrica

The objective of the work was to study the adaptation of common bean genotypes to water deficit. Fortynine genotypes were evaluated in a randomized block design, with three replications, in experiments with and without water deficit, conducted at the Experimental Station of SEAGRO, in Porangatu-GO during 2006 and 2007. Multivariable analysis was applied using de Ward’s method and the genotypes were divided in four groups based on the average grain yield of each water treatment, during the two years of the experimentation. The genotypes BRA 130583 CIAT G 6490 and FT 84 - 292 were classified as the most productive in the absence or under water deficit, while the genotypes BRA 283983 CIAT G 6492, BRA 129721 CIAT G 6896, and G 983 were classified as productive in the absence of water deficit, but they were more sensitive to this stress. It was also verified that the number of pods per plant was the most sensitive agronomic component to water deficit in common bean.
The Aryl Hydrocarbon Receptor Attenuates Acute Cigarette Smoke-Induced Airway Neutrophilia Independent of the Dioxin Response Element

Cigarette smoke is a prevalent respiratory toxicant that remains a leading cause of death worldwide. Cigarette smoke induces inflammation in the lungs and airways that contributes to the development of diseases such as lung cancer and chronic obstructive pulmonary disease (COPD). Due to the presence of aryl hydrocarbon receptor (AhR) ligands in cigarette smoke, activation of the AhR has been implicated in driving this inflammatory response. However, we have previously shown that the AhR suppresses cigarette smoke-induced pulmonary inflammation, but the mechanism by which the AhR achieves its anti-inflammatory function is unknown. In this study, we use the AhR antagonist CH-223191 to inhibit AhR activity in mice. After an acute (3-day) cigarette smoke exposure, AhR inhibition was associated with significantly enhanced neutrophilia in the airways in response to cigarette smoke, mimicking the phenotype of AhR-deficient mice. We then used genetically-modified mouse strains which express an AhR that can bind ligand but either cannot translocate to the nucleus or bind its cognate response element, to show that these features of the AhR pathway are not required for the AhR to suppress pulmonary neutrophilia. Finally, using the non-toxic endogenous AhR ligand FICZ, we provide proof-of-concept that activation of pulmonary AhR attenuates smoke-induced inflammation. Collectively, these results support the importance of AhR activity in mediating its anti-inflammatory function in response to cigarette smoke. Further investigation of the precise mechanisms by which the AhR exerts is protective functions may lead to the development of therapeutic agents to treat people with chronic lung diseases that have an inflammatory etiology, but for which few therapeutic options exist.
Reading Fictional Narratives to Improve Social and Moral Cognition: The Influence of Narrative Perspective, Transportation, and Identification

There is a long tradition in philosophy and literary criticism of belief in the social and moral benefits of exposure to fiction, and recent empirical work has examined some of these claims. However, little of this research has addressed the textual features responsible for the hypothesized cognitive effects. We present two experiments examining whether readers’ social and moral cognition are influenced by the perspective from which a narrative is told (voice and focalization), and whether potential effects of perspective are mediated by transportation into the story or by identification with the protagonist. Both experiments employed a between-subjects design in which participants read a short story, either in the first-person voice using internal focalization, third-person voice using internal focalization, or third-person voice using external focalization. Social and moral cognition was assessed using a battery of tasks. Experiment 1 (N = 258) failed to detect any effects of perspective or any mediating roles of transportation or identification. Implementing a more rigorous adaptation of the third-person story using external focalization, Experiment 2 (N = 262) largely replicated this pattern. Taken together, the evidence reported here suggests that perspective does not have a significant impact on the extent to which narratives modulate social and moral cognition, either directly or indirectly via transportation and identification.
Clostridioides difficile Phage Biology and Application.

Clostridium difficile, now reclassified as Clostridioides difficile, is the causative agent of C. difficile infections (CDI). CDI is particularly challenging in healthcare settings because highly resistant spores of the bacterium can persist in the environment, making it difficult to curb outbreaks. Dysbiosis of the microbiota caused by the use of antibiotics is the primary factor that allows C. difficile to colonize the gut and cause diarrhea and colitis. For this reason, antibiotics targeting C. difficile can be ineffective at preventing recurrent episodes because they exacerbate and prolong dysbiosis. The emergence of antibiotic resistance in C. difficile also presents a significant threat. The diverse array of bacteriophages (phages) that infect C. difficile could offer new treatment strategies and greater insight into the biology of the pathogen. In this review, we summarize the current knowledge regarding C. difficile phages and discuss what is understood about their lifestyles and genomics. Then, we examine how phage infection modifies bacterial gene expression and pathogenicity. Finally, we discuss the potential clinical applications of C. difficile phages such as whole phage therapy and phage-derived products, and we highlight the most promising strategies for further development.