Miracle-dz/UniFAR-FTUs huggingface dataset:
CsrA-controlled proteins important for Acinetobacter baumannii desiccation tolerance

Hospital environments serve as excellent reservoirs for the opportunistic pathogen Acinetobacter baumannii in part because it is exceptionally tolerant to desiccation. To understand the functional basis this trait, we used transposon sequencing (Tn-seq) to identify genes contributing to desiccation tolerance in A. baumannii strain AB5075. We identified 142 candidate desiccation tolerance genes, one of which encoded the global post-transcriptional regulator CsrA. We characterized CsrA in more detail by using proteomics to identify proteins that were differentially present in wild type and csrA mutant cells. Among these were a predicted universal stress protein A, an iron-containing redox protein, a KGG-domain containing protein, and catalase. Subsequent mutant analysis showed that each of these proteins was required for A. baumannii desiccation tolerance. The amino acid sequence of the KGG-domain containing protein predicts that it is an intrinsically disordered protein. Such proteins are critical for desiccation tolerance of the small animals called tardigrades. This protein also has a repeat nucleic acid binding amino acid motif, suggesting that it may protect A. baumannii DNA from desiccation-induced damage.
Rampant transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of a human fungal pathogen

Microorganisms survive and compete by stochastically acquiring mutations that enhance fitness. Although increased mutation rates are often deleterious in multicellular organisms, hypermutation can be beneficial for microbes experiencing strong selective pressures. Infections caused by Cryptococcus neoformans are responsible for ∼15% of AIDS-related deaths and associated with high mortality rates, attributable to a dearth of antifungal drugs and drug resistance. We identified two hypermutator C. neoformans clinical isolates in which Cnl1 transposon insertions were responsible for drug resistance. Whole-genome sequencing revealed both hypermutator genomes harbor a nonsense mutation in the RNAi component ZNF3 and hundreds of Cnl1 elements organized into massive subtelomeric arrays on every chromosome. QTL mapping identified a significant locus associated with hypermutation that included znf3. CRISPR-mediated editing of the znf3 nonsense mutation abolished hypermutation and restored siRNA production. In sum, hypermutation and drug resistance in these isolates results from RNAi loss and a significant burden of Cnl1 elements.
The Role of Low Molecular Weight Fungal Metabolites in Grapevine Trunk Disease Pathogenesis: Eutypa Dieback and Esca

Eutypa dieback and Esca are serious grapevine trunk diseases (GTDs) caused by fungal consortia causing large economic losses in vineyards. Depending on the disease the species involved include Eutypa lata, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. There is a need to understand the complex pathogenesis mechanisms used by these causative fungi to develop treatments for the diseases they cause. Low molecular weight metabolites (LMW) are known to be involved in non-enzymatic oxygen radical generation in fungal degradation of wood by some Basidiomycota species, and as part of our work to explore the basis for fungal consortia pathogenesis, LMW metabolite involvement by the causal GTD fungi was explored. The GTD fungal pathogens examined, Eutypa lata, Phaeoacremonium minimum and Phaeomoniella chlamydospora, were found to produce low molecular weight iron binding metabolites that preferentially reduced iron or redox cycled to produce hydrogen peroxide. Uniquely, different LMW metabolites isolated from the GTD fungi promoted distinct chemistries that are important in a type of non-enzymatic catalysis known as chelator-mediated Fenton (CMF) reactions. CMF chemistry promoted by LMW metabolites from these fungi allowed for the generation of highly reactive hydroxyl radicals under conditions promoted by the fungi. We hypothesize that this new reported mechanism may help to explain the necrosis of woody grapevine tissue as a causal mechanism important in pathogenesis in these two grapevine trunk diseases. IMPORTANCE Understanding the pathogenesis of grape trunk diseases (GTDs) is the key to the development of disease control and treatment. While fungal extracellular enzyme systems are typically cited relative to their fungal mechanisms in pathogenesis, non-enzymatic mechanisms have been less studied in this regard and the role of low molecular weight (LMW) fungal metabolites in GTD development is quite limited. In this article, we demonstrate that GTD-causative fungal pathogens Eutypa lata, Phaeoacremonium minimum and Phaeomoniella chlamydospore produce LMW phenolic metabolites under iron-restricted conditions. These metabolites undergo a series of redox reactions, with different fungi producing metabolites that preferentially either reduce iron, or generate hydrogen peroxide, under conditions simulating grapevine woody tissue. These conditions have the potential to promote generation of highly damaging hydroxyl radicals through a mechanism that appears to be similar to non-enzymatic chelator-mediated Fenton (CMF) chemistry which is involved in fungal degradation of wood by non-related fungal orders. This is the first report of CMF chemistry promoted by GTD-causative fungi under laboratory conditions and the research suggests an alternate pathway that may contribute to pathogenesis in GTDs, and a potential target for vine protection.
Évaluation de la structure épidermique des substituts cutanés produits par la méthode d'auto-assemblage

Une adaptation de la methode d’auto-assemblage developpee au LOEX permet de produire des substituts cutanes bicouches ayant un phenotype psoriasique. Le premier objectif de ce travail etait d’evaluer si une conservation par la congelation des substituts cutanes etait envisageable afin d’avoir acces a ces derniers en tout temps pour effectuer des analyses physiochimiques sans delais. Les etudes realisees sur des substituts sains montrent qu’elle ne l’est pas dans sa methodologie actuelle puisqu’elle affecte la fonction barriere des substituts. Par ailleurs, en raison du role des lipides epidermiques dans la fonction barriere et de leur implication dans le psoriasis, une caracterisation de ces lipides a ete effectuee par chromatographie en phase gazeuse. Les resultats obtenus montrent principalement une diminution de la proportion d’acide linoleique dans les substituts par rapport a la peau normale humaine. Ces resultats sont prometteurs en raison du role de cet acide et de ses metabolites dans l’inflammation. %%%%Adaptation of the self-assembly method developed at LOEX allows us to produce bilayered skin substitutes with psoriatic phenotype. The first aim of this study was to evaluate if freezing of the skin substitutes is possible without affecting its integrity, in order to access the skin substitutes in anytime to perform physicochemical analysis without delay. Results, obtained with control skin substitutes produced via the standard described self-assembly method, showed that freezing clearly affected the skin barrier function of the skin substitutes. Moreover, because of their implication in skin barrier and in psoriasis pathology, epidermal skin lipids of control and psoriatic skin substitutes were characterized by gas chromatography. Results showed mainly a significant reduction of the linoleic acid proportion in skin substitutes compared to normal human skin. These results are promising because of the implication of linoleic acid and its metabolites in inflammation.
Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd

Flux balance analysis (FBA) is a crucial method to analyze large-scale constraint-based metabolic networks and computing design strategies for strain production in metabolic engineering. However, as it is often non-straightforward to obtain such design strategies to produce valuable metabolites, many tools have been proposed based on FBA. Among them, GridProd, which divides the solution space into small squares by focusing on the cell growth rate and the target metabolite production rate to efficiently find the reaction deletion strategies, was extended to CubeProd, which divides the solution space into small cubes. However, as GridProd and CubeProd naively divide the solution space into equal sizes, even places where solutions are unlikely to exist are examined. To address this issue, we introduce dynamic solution space division methods based on CubeProd for faster computing by avoiding searching in places where the solutions do not exist. We applied the proposed method DynCubeProd to iJO1366, which is a genome-scale constraint-based model of Escherichia coli. Compared with CubeProd, DynCubeProd significantly accelerated the calculation of the reaction deletion strategy for each target metabolite production. In addition, under the anaerobic condition of iJO1366, DynCubeProd could obtain the reaction deletion strategies for almost 40% of the target metabolites that the elementary flux vector-based method, which is one of the most effective methods in existence, could not. The developed software is available on https://github.com/Ma-Yier/DynCubeProd.
Transcriptome Analysis Reveals Impaired Fertility and Immunity Under Salinity Exposure in Juvenile Grass Carp

Grass carp (Ctenopharyngodon idellus) is one of the most economically important aquaculture species and is widely cultured in China. However, its wild populations in many rivers are increasingly declining, and seawater intrusion is one of the most important threats to their survival. However, the mechanisms underlying the decline due to salinity pressure are still unknown. Here, we performed a comparative transcriptome analysis of C. idellus larvae in response to salinity exposures; a total of 481 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in eight Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, among which steroid biosynthesis was the most important one, with the highest enrichment score. The pathway plays an important role in the development of the testes and ovary. Interestingly, all DEGs in steroid biosynthesis showed a down regulation, indicating that salinity exposure may pose damage to the fertility of C. idellus. Furthermore, three immunity-associated pathways (cytokine–cytokine receptor interaction, Toll-like receptor signaling pathway, and NOD-like receptor signaling pathway) were also significantly enriched, suggesting impaired immunity and a high risk of disease infection under salinity exposure. Overall, damage to both fertility and immunity would decrease the number of offspring and increase the risk of death due to disease infection. Our results provide a potential molecular mechanism underlying the decline of wild C. idellus populations in the Pearl River.
Production of Four 15N-Labelled Cobalamins via Biosynthesis Using Propionibacterium freudenreichii

Cobalamins (vitamin B12) are required by humans for their essential roles as enzyme cofactors in diverse metabolic processes. The four most common cobalamin vitamers are hydroxocobalamin (OHCbl), adenosylcobalamin (AdoCbl), methylcobalamin (MeCbl), and cyanocobalamin (CNCbl). Humans are not able to synthesise cobalamins de novo and thus must acquire them from external sources. Therefore, a reliable and robust analytical method to determine the cobalamins in dietary sources is highly required. For such a purpose, stable isotope dilution assays (SIDAs) with LC-MS/MS are most suited due to their superior sensitivity, specificity, and ability to compensate for matrix effects and analyte loss during sample work-up. However, a critical bottleneck for developing a SIDA method for cobalamins is the availability of stable isotope-labelled internal standards. In the present study, we harnessed the potential of Propionibacterium (P.) freudenreichii for the biosynthesis of 15N-labelled cobalamins. First, we developed a chemically defined medium (CDM) containing ammonium sulphate as a single nitrogen source except three essential vitamins that supported long-term stable growth of P. freudenreichii throughout continuous transfers. The CDM was further optimised for cobalamin production under different incubation schemes. With the optimised CDM and incubation scheme, fully 15N-labelled cobalamins were obtained in P. freudenreichii with a final yield of 312 ± 29 μg/L and 635 ± 102 μg/L, respectively, for [15N]-OHCbl and [15N]-AdoCbl. Additionally, an optimised incubation process under anaerobic conditions was successfully employed to produce specifically labelled [15N, 14N2]-cobalamins, with a yield of 96 ± 18 μg/L and 990 ± 210 μg/L, respectively, for [15N, 14N2]-OHCbl and [15N, 14N2]-AdoCbl. The labelled substances were isolated and purified by solid phase extraction and semi-preparative HPLC. Chemical modifications were carried out to produce [15N]-CNCbl and [15N]-MeCbl. Eventually, 15N-labelled compounds were obtained for the four cobalamin vitamers in high chromatographic and isotopic purity with desired 15N-enrichment and labelling patterns, which are perfectly suited for future use in SIDAs or other applications that require isotopologues.
Can We Commit Future Managers to Honesty?

In a competitive business environment, dishonesty can pay. Self-interested executives and managers can have incentive to shade the truth for personal gain. In response, the business community has considered how to commit these executives and managers to a higher ethical standard. The MBA Oath and the Dutch Bankers Oath are examples of such a commitment device. The question we test herein is whether the oath can be used as an effective form of ethics management for future executives/managers—who for our experiment we recruited from a leading French business school—by actually improving their honesty. Using a classic Sender-Receiver strategic game experiment, we reinforce professional identity by pre-selecting the group to which Receivers belong. This allows us to determine whether taking the oath deters lying among future managers. Our results suggest “yes and no.” We observe that these future executives/managers who took a solemn honesty oath as a Sender were (a) significantly more likely to tell the truth when the lie was detrimental to the Receiver, but (b) were not more likely to tell the truth when the lie was mutually beneficial to both the Sender and Receiver. A joint product of our design is our ability to measure in-group bias in lying behavior in our population of subjects (comparing behavior of subjects in the same and different business schools). The experiment provides clear evidence of a lack of such bias.
Perceived Risk of Infection Linked to Changes in Comfort in Social Situations From Before to During the COVID-19 Pandemic

Background: Social lives have significantly changed since social distancing measures have been implemented to prevent the spread of the coronavirus disease 2019 (COVID-19). This study aimed to investigate how our appraisal of social situations changed during the pandemic. Methods: In two online surveys, conducted in October 2019 and April 2020, 58 participants rated their personal level of comfort for sketches depicting social situations. Situations were separately categorized according to the risk of a possible COVID-19 infection and changes in ratings were analyzed by using a repeated measures ANOVA. Moreover, potential influencing factors on the change in ratings such as perceived infection risk and social factors like regular frequency and liking of social interactions were examined. Results: There was a significant interaction (p < 0.001) between time of measurement and risk category. Comfort ratings of depicted situations with low and medium infection risk were higher during the second compared to the first survey period. Ratings of high-risk situations did not change significantly, although there was a tendency toward lower ratings during the pandemic. Multiple regression analyses showed that perceived probability of short-term infection could explain variance in the change of ratings of social situations with low- and medium risk, but not perceived probability of long-term infection or social factors. Conclusion: The results suggest that the change of participant's appraisal of the social situations during the COVID-19 pandemic relates to perceived infection risk. Both, the risk associated with the specific scenario as well as the general belief of short-term infection risk were associated with change. This change predominantly manifested in greater thought of comfort during low and medium risk situations, which might give a sense of safety during the pandemic. The finding that high-risk social situations were not rated as uncomfortable as expected must be considered with regard to the young sample and may not be generalizable to other individuals. Further research is necessary to evaluate long-term effects on social interactions caused by global pandemics such as the COVID-19 pandemic.
A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage

The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.
The Use of Micro Retractor in Endoscopic Endonasal Posterior Pseudocapsule Resection of Pituitary Macroadenoma. Technical Note

Background The endoscopic endonasal approach and extra-pseudocapsule resection may be the main progress in modern pituitary surgery. However, for pituitary macroadenomas, discerning the pseudocapsule in the posterior plane of the tumor may be difficult. When the anterior-inferior debulking is performed, the early subsidence of the thinning normal pituitary gland and enlarged diaphragm may obstruct the surgical dissection view. Method We describe the technique of using a micro retractor for the endoscopic endonasal posterior pseudocapsule resection of pituitary macroadenomas. This micro retractor that was 2 mm in width was placed at the 12 o’clock position on the nostrils, and the end was fixed in the flexible arms of the self-retaining retractor system. The head of the micro retractor elevated the herniated diaphragm sellae in order to continue the posterior pseudocapsule resection of the pituitary macroadenoma. Result The technique was performed very easily and no complication was observed. Conclusion The use of this micro retractor can increase the view of the posterior margin of the adenomas to facilitate the pseudocapsule dissection.
Eyewitness Memory for Person Identification: Predicting Mugbook Recognition Accuracy According to Person Description Abilities and Subjective Confidence of Witnesses

Mugbook searches are conducted in case a suspect is not known and to assess if a previously convicted person might be recognized as a potential culprit. The goal of the two experiments reported here was to analyze if prior statements and information about the suspect can aid in the evaluation if such a mugbook search is subsequently advised or not. In experiment 1, memory accuracy for person descriptors was tested in order to analyze, which attributes could be chosen to down-scale the mugbook prior to testing. Results showed that age was the most accurate descriptor, followed by ethnicity and height. At the same time self-assessed low subjective accuracy of culprit descriptions by the witness seemed to be divergent to the objective actual performance accuracy. In experiment 2, a mugbook search was conducted after participants viewed a video of a staged crime and gave a description of the culprit. Results showed that accuracy in mugbook searches correlated positively with the total number of person descriptors given by the witness as well as with witness’ description of external facial features. Predictive confidence (i.e., subjective rating of own performance in the subsequent mugbook search), however did not show any relation to the identification accuracy in the actual mugbook search. These results highlight the notion that mugbooks should not be conducted according to the subjective estimation of the witness’ performance but more according to the actual statements and descriptions that the witness can give about the culprit.
Graph-Based Visual Manipulation Relationship Reasoning Network for Robotic Grasping

To grasp the target object stably and orderly in the object-stacking scenes, it is important for the robot to reason the relationships between objects and obtain intelligent manipulation order for more advanced interaction between the robot and the environment. This paper proposes a novel graph-based visual manipulation relationship reasoning network (GVMRN) that directly outputs object relationships and manipulation order. The GVMRN model first extracts features and detects objects from RGB images, and then adopts graph convolutional network (GCN) to collect contextual information between objects. To improve the efficiency of relation reasoning, a relationship filtering network is built to reduce object pairs before reasoning. The experiments on the Visual Manipulation Relationship Dataset (VMRD) show that our model significantly outperforms previous methods on reasoning object relationships in object-stacking scenes. The GVMRN model is also tested on the images we collected and applied on the robot grasping platform. The results demonstrated the generalization and applicability of our method in real environment.
Correction: Aqueous extract of Cordyceps sinensis potentiates the antitumor effect of DDP and attenuates therapy-associated toxicity in non-small cell lung cancer via IκBα/NFκB and AKT/MMP2/MMP9 pathways

Correction for ‘Aqueous extract of Cordyceps sinensis potentiates the antitumor effect of DDP and attenuates therapy-associated toxicity in non-small cell lung cancer via IκBα/NFκB and AKT/MMP2/MMP9 pathways’ by Xiaowei Huo et al., RSC Adv. , 2017, 7, 37743–37754.
Efficient one-pot three-component method for the synthesis of highly fluorescent coumarin-containing 3,5-disubstituted-2,6-dicyanoaniline derivatives under microwave irradiation

ABSTRACT A simple and concise approach to the synthesis of coumarin-containing highly fluorescent asymmetric/symmetric 3,5-diaryl/heteroaryl-2,6-dicyanoaniline derivatives are reported. The compounds were synthesized through base catalyzed three-component one-pot synthesis reaction of 2-(1-(7-(diethylamino)-2-oxo-2H-chromen-3-yl)ethylidene)malononitrile, aliphatic, aromatic/heteroaromatic aldehydes, and malononitrile in solvent-free reaction medium, catalyzed by piperidine under microwave irradiation method. The reaction gave the novel, highly fluorescent coumarin-containing 3,5-disubstituted-2,6-dicyanoaniline derivatives in good yields at 300 W, 80 °C in 2 min. This method provides several advantages; such as shorter reaction time, environmental friendliness, simple workup procedure, lower energy consumption and, generally, good yields with high purity. In addition, the synthesized compounds are fluorescently active dyes even in day light, except for compounds including nitro substituent, and show maximum absorption wavelengths (λabs.max) in the visible region in DMSO at room temperature. Thermal properties of all the synthesized compounds were also evaluated with thermal gravimetric analysis for usability as optic dye. Optical and thermal screening studies of the compounds showed that the dyes have excellent photophysical and thermal stability properties. GRAPHICAL ABSTRACT