Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation

Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function. Legionella pneumophila is the causative agent of Legionnaires' disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival of L. pneumophila in the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence that L. pneumophila can bind mucins on its surface, but this is not dependent on ChiA. This demonstrates that additional peripheral mucin binding proteins are also expressed in L. pneumophila. We also show that the ChiA C-terminal chitinase domain has novel Zn2+-dependent peptidase activity against mammalian mucin-like proteins, namely MUC5AC and the C1-esterase inhibitor, and that ChiA promotes bacterial penetration of mucin gels. Our findings suggest that ChiA can facilitate passage of L. pneumophila through the alveolar mucosa, can modulate the host complement system and that ChiA may be a promising target for vaccine development.
Energy Analysis of the Tillage Systems in Second Crop Corn Production

ABSTRACT The aim of this experiment, to examine the energy input and output in the second crop corn production using four different tillage systems for soil preparation: (1) minimum tillage with stubble (MTS), (2) minimum tillage without stubble (MT), (3) conventional tillage with stubble (CTS), and (4) conventional tillage without stubble (CT). Corn was sown as a second crop just after harvest of wheat. Direct and indirect energy inputs consisting of machinery, fertilizers, seeds, irrigations and chemicals were converted into energy units according to their amounts being consumed. The machinery and fuel energy inputs for the tillage operation were reduced 53.7% with MT compared to CTS. The total energy input for producing corn utilizing CTS was 20,608 MJ/ha, compared to 19,102 MJ/ha for producing corn with MT. When the grain yield was taken into account, the energy output/input ratios for MTS, MT, CTS and CT were estimated to be 6.3, 7.6, 6.6 and 7.0, respectively. The tillage systems did not statistically affect uniformity of plant spacing, but statistically affected the yield. The grain yield was the greatest (8,719 kg/ha) in CT compared to the other tillage treatments.
Deep Learning-Based Human Activity Real-Time Recognition for Pedestrian Navigation

Several pedestrian navigation solutions have been proposed to date, and most of them are based on smartphones. Real-time recognition of pedestrian mode and smartphone posture is a key issue in navigation. Traditional ML (Machine Learning) classification methods have drawbacks, such as insufficient recognition accuracy and poor timing. This paper presents a real-time recognition scheme for comprehensive human activities, and this scheme combines deep learning algorithms and MEMS (Micro-Electro-Mechanical System) sensors’ measurements. In this study, we performed four main experiments, namely pedestrian motion mode recognition, smartphone posture recognition, real-time comprehensive pedestrian activity recognition, and pedestrian navigation. In the procedure of recognition, we designed and trained deep learning models using LSTM (Long Short-Term Memory) and CNN (Convolutional Neural Network) networks based on Tensorflow framework. The accuracy of traditional ML classification methods was also used for comparison. Test results show that the accuracy of motion mode recognition was improved from 89.9%, which was the highest accuracy and obtained by SVM (Support Vector Machine), to 90.74% (LSTM) and 91.92% (CNN); the accuracy of smartphone posture recognition was improved from 81.60%, which is the highest accuracy and obtained by NN (Neural Network), to 93.69% (LSTM) and 95.55% (CNN). We give a model transformation procedure based on the trained CNN network model, and then obtain the converted . tflite model, which can be run in Android devices for real-time recognition. Real-time recognition experiments were performed in multiple scenes, a recognition model trained by the CNN network was deployed in a Huawei Mate20 smartphone, and the five most used pedestrian activities were designed and verified. The overall accuracy was up to 89.39%. Overall, the improvement of recognition capability based on deep learning algorithms was significant. Therefore, the solution was helpful to recognize comprehensive pedestrian activities during navigation. On the basis of the trained model, a navigation test was performed; mean bias was reduced by more than 1.1 m. Accordingly, the positioning accuracy was improved obviously, which is meaningful to apply DL in the area of pedestrian navigation to make improvements.
A quicker way to clone.

We present BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences. By filtering out redundancy and putative paralogs, sequence comparisons to orthologous groups, instead of to single sequences in the database, can improve both functional prediction and phylogenetic inference. BLASTO computes the significance score of each orthologous group based on the individual BLAST hits in the orthologous group, using the number of taxa in the group as an optional weight. This allows users to control the species diversity of the orthologous groups. BLASTO incorporates the best-known multispecies ortholog databases, including NCBI Clusters of Orthologous Group, NCBI euKaryotic Orthologous Group database, OrthoMCL, MultiParanoid and TIGR Eukaryotic Gene Orthologues database, and offers a useful platform to integrate orthology information into functional inference and evolutionary studies of individual sequences. BLASTO is accessible online at http://oxytricha.princeton. edu/
Lowering Extracellular pH Raises Intracellular Calcium in Cultured Rat Astrocytes

The relationship between extracellular pH and intracellular calcium concentration ([Ca2+] 1) in primary culture of neonatal rat astrocytes with Ca2+-indicator dye indo-1/acetoxymethyl ester and a confocal microscope was investigated. In 65 of 86 astrocytes studied, lowering extracellular pH by changing the perfusate solution from pH 7.4 to 6.4 was followed by increases in [Ca2+] 1 in cytoplasm. The increases in [Ca2+] 1 were seen on stimulation and/or during reperfusion. Of all the cells, 45.4% showed a transient pattern and 30.2% manifested a sustained pattern. The results suggest that a short interval but excessive acidic stimulation may be one of the signals that raises [Ca2+] 1 in a certain population of cerebral astrocytes.
Process intensification for cytochrome P450 BM3‐catalyzed oxy‐functionalization of dodecanoic acid

Selective oxy‐functionalization of nonactivated C‐H bonds is a long‐standing “dream reaction” of organic synthesis for which chemical methodology is not well developed. Mono‐oxygenase enzymes are promising catalysts for such oxy‐functionalization to establish. Limitation on their applicability arises from low reaction output. Here, we showed an integrated approach of process engineering to the intensification of the cytochrome P450 BM3‐catalyzed hydroxylation of dodecanoic acid (C12:0). Using P450 BM3 together with glucose dehydrogenase for regeneration of nicotinamide adenine dinucleotide phosphate (NADPH), we compared soluble and co‐immobilized enzymes in O2‐gassed and pH‐controlled conversions at high final substrate concentrations (≥40mM). We identified the main engineering parameters of process output (i.e., O2 supply; mixing correlated with immobilized enzyme stability; foam control correlated with product isolation; substrate solubilization) and succeeded in disentangling their complex interrelationship for systematic process optimization. Running the reaction at O2‐limited conditions at up to 500‐ml scale (10% dimethyl sulfoxide; silicone antifoam), we developed a substrate feeding strategy based on O2 feedback control. Thus, we achieved high reaction rates of 1.86g·L−1·hr−1 and near complete conversion (≥90%) of 80mM (16g/L) C12:0 with good selectivity (≤5% overoxidation). We showed that “uncoupled reaction” of the P450 BM3 (~95% utilization of NADPH and O2 not leading to hydroxylation) with the C12:0 hydroxylated product limited the process efficiency at high product concentration. Hydroxylated product (~7g; ≥92% purity) was recovered from 500ml reaction in 82% yield using ethyl‐acetate extraction. Collectively, these results demonstrate key engineering parameters for the biocatalytic oxy‐functionalization and show their integration into a coherent strategy for process intensification.
Surgical and Immunohistochemical Outcomes of Scleral Reconstruction with Autogenic, Allogenic and Xenogenic Grafts: An Experimental Rabbit Model

ABSTRACT Purpose: Choukroun’s platelet-rich fibrin (PRF), a second-generation platelet concentrate, has unique morphological and chemical features and may be considered as a scaffold for scleral reinforcement and regeneration. The purpose of this study was to compare the use of xenogenic human-derived amniotic membrane (HAM), allogenic sclera, and autogenic PRF in rabbit lamellar scleral defect model with respect to both anatomical and immunohistochemical improvement. Methods: A total of 45 adult New Zealand rabbits were randomized into five groups: normal control; without surgical procedure, negative control; scleral defect model (SDM), xenogenic HAM; SDM+HAM graft, allogenic sclera; SDM+allogenic sclera graft, autogenic PRF; SDM+autogenic PRF graft. Clinical findings, Hematoxylin&Eozin (HE), Masson Trichrome, Verhoeff Acid Fuchsin, Transforming Growth Factor β Receptor 1, Fibroblast Growth Factor, Bone Morphogenetic Protein 2, collagen type 1, aggrecan, and Matrix Metalloproteinase 2 were evaluated. Results: Ocular surface inflammation was significantly lower in normal control and autogenic PRF groups (p < .001). Graft was avascular and not integrated to scleral wound area in 25% rabbits of allogenic sclera group (p = .02), was out of the scleral wound in 33.3% rabbits of xenogenic HAM group (p > .05), all the grafts were at the normal location and viable in autogenic PRF group. The inflammation and vascularization in autogenic PRF group was significantly lower than negative control and xenogenic HAM groups in HE (p < .001). The collagen score of negative control and xenogenic HAM groups were significantly lower than normal control (p < .001) and autogenic PRF (p < .001) groups. There were insignificant differences between allogenic sclera and autogenic PRF groups (p > .05). For immunohistochemistry, the closest values to normal control group were detected in autogenic PRF group for all immunomarkers. Conclusion: Autogenic PRF showed superior features via its excellent anatomical and chemical composition for scleral regeneration when compared to single-layered xenogenic HAM and allogenic sclera grafts.
mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow

Abstract Gene flow between species may cause variations in branch length and topology of gene tree, which are beyond the expected variations from ancestral processes. These additional variations make it difficult to estimate parameters during speciation with gene flow, as the pattern of these additional variations differs with the relationship between isolation and migration. As far as we know, most methods rely on the assumption about the relationship between isolation and migration by a given model, such as the isolation-with-migration model, when estimating parameters during speciation with gene flow. In this article, we develop a multispecies coalescent approach which does not rely on any assumption about the relationship between isolation and migration when estimating parameters and is called mstree. mstree is available at https://github.com/liujunfengtop/MStree/ and uses some mathematical inequalities among several factors, which include the species divergence time, the ancestral population size, and the number of gene trees, to estimate parameters during speciation with gene flow. Using simulations, we show that the estimated values of ancestral population sizes and species divergence times are close to the true values when analyzing the simulation data sets, which are generated based on the isolation-with-initial-migration model, secondary contact model, and isolation-with-migration model. Therefore, our method is able to estimate ancestral population sizes and speciation times in the presence of different modes of gene flow and may be helpful to test different theories of speciation.
Nanocellulose-Based Inks for 3D Bioprinting: Key Aspects in Research Development and Challenging Perspectives in Applications—A Mini Review

Nanocelluloses have emerged as a catalogue of renewable nanomaterials for bioink formulation in service of 3D bioprinting, thanks to their structural similarity to extracellular matrices and excellent biocompatibility of supporting crucial cellular activities. From a material scientist’s viewpoint, this mini-review presents the key research aspects of the development of the nanocellulose-based bioinks in 3D (bio)printing. The nanomaterial properties of various types of nanocelluloses, including bacterial nanocellulose, cellulose nanofibers, and cellulose nanocrystals, are reviewed with respect to their origins and preparation methods. Different cross-linking strategies to integrate into multicomponent nanocellulose-based bioinks are discussed in terms of regulating ink fidelity in direct ink writing as well as tuning the mechanical stiffness as a bioactive cue in the printed hydrogel construct. Furthermore, the impact of surface charge and functional groups on nanocellulose surface on the crucial cellular activities (e.g., cell survival, attachment, and proliferation) is discussed with the cell–matrix interactions in focus. Aiming at a sustainable and cost-effective alternative for end-users in biomedical and pharmaceutical fields, challenging aspects such as biodegradability and potential nanotoxicity of nanocelluloses call for more fundamental comprehension of the cell–matrix interactions and further validation in in vivo models.
Molecular characterization, expression pattern and RNAi‐mediated silencing of vitellogenin receptor gene in almond moth, Cadra cautella

The almond moth is an important pest of date fruits worldwide. The females produce several eggs; however, role of vitellogenin receptor (VgR) in oocyte development by mediating endocytosis of major yolk protein precursor Vg remains yet unexplored. To investigate the role of vitellogenin receptor (VgR) in reproduction, Cadra cautella vitellogenin receptor (CcVgR) transcript was obtained using rapid amplification of cDNA ends‐polymerase chain reaction. Expression analysis of CcVgR was performed using reverse transcriptase and quantitative polymerase chain reaction (qPCR) in different developmental stages. RNA interference was performed by injecting CcVgR‐based double‐stranded (ds)RNA at different exposure times. The results revealed that CcVgR is 5421 bp long, encoded 1807 amino acid, belongs to low‐density lipoprotein receptor superfamily and contains all conserved domains. Expression analysis confirmed that CcVgR is sex‐specific and starts to express in female larvae on day 19. Additionally, RNA interference (RNAi) of CcVgR‐based dsRNA inhibited CcVgR expression up to 83% after 72 h, reduced fecundity and hatchability, and confirmed involvement of CcVgR in C. cautella reproduction. This report provides a basis for gene silencing in this species, and proposes RNAi technology potential for pest management.
Physiological and cytological response of salt-tolerant and non-tolerant barley to salinity during germination and early growth

Seven barley cultivars (Franklin, Gairdner, YU6472, Numar, CM72, ZND3 and YUQS) were evaluated for NaCl tolerance in relation to physiological and cytological responses during germination. Standard germination techniques were employed using blotting paper saturated with different NaCl solutions (0, –0.3, –0.6, –0.9, –1.2, –1.5 or –1.8 MPa) at 20°C. The results showed significant differences among varieties for germination percentage, frequency of abnormal seedlings, and Na+, K+ uptake. Of the 7 barley cultivars, CM72 was similar in salt tolerance to Numar, while YUQS and ZND3 were the most sensitive to high salinity. The tolerant cultivars showed much higher germination percentage under salinity stress than susceptible varieties. Both CM72 and Numar maintained more than 90% germination at –1.2 MPa osmotic potential while YUQS and ZND3 had only 57% germination at the same level of salinity. The tolerant varieties also showed shorter mean germination time at low osmotic potential. The start of the first mitosis was delayed, while both the frequencies of aberrant anaphases at the first cell divisions, and the numbers of abnormal seedlings were increased in higher salt concentrations. During the seedling stage, tolerant varieties showed significantly higher K+ concentrations, lower Na+ concentrations, lower Na+/K+ ratio and higher photosynthetic rate than susceptible varieties under salinity stress. Screening of barley cultivars or breeding lines could be best achieved by a combination of germination testing and measurement of photosynthetic rate and/or Na/K balance in young seedlings.
Psychosocial implications of living with familial risk of a psychiatric disorder and attitudes to psychiatric genetic testing: A systematic review of the literature

The aim of this systematic review was to synthesize the existing evidence documenting the psychosocial implications of living with a familial risk of an adult‐onset psychiatric disorder. Six databases were searched systematically to identify qualitative and quantitative studies, which explored perspectives of those at increased risk for psychiatric disorders, as well as the general public. Thematic analysis was used to identify major themes. Thirty‐five articles met the eligibility criteria and reported on the views of 4,896 participants. The literature demonstrates strong interest in psychiatric genetic testing of adults as well as children, whereas attitudes toward prenatal testing were much less positive. Predictors of interest in testing, as well as perceived advantages and disadvantages were identified. Very few studies are available on anticipated and actual reactions to receiving results. Studies show that the majority of participants feel that having a genetic explanation would alleviate some of the stigma associated with mental illness. This review shows that interest in, and predictors of attitudes toward, psychiatric genetic testing are well researched, but the extent to which attitudes will translate into actual testing uptake is unknown. Future research also needs to assess the actual behavioral and psychological impact of genetic testing.
Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans

Gene expression regulation is achieved through an intricate network of molecular interactions, in which trans-acting transcription factors (TFs) and small noncoding RNAs (sncRNAs), including microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), play a key role. Recent observations allowed postulating an interplay between TFs and sncRNAs, in that they may possibly share DNA-binding sites. The aim of this study was to analyze the complete subset of miRNA and piRNA sequences stored in the main databases in order to identify the occurrence of conserved motifs and subsequently predict a possible innovative interplay with TFs at a transcriptional level. To this aim, we adopted an original in silico workflow to search motifs and predict interactions within genome-scale regulatory networks. Our results allowed categorizing miRNA and piRNA motifs, with corresponding TFs sharing complementary DNA-binding motifs. The biological interpretation of the gene ontologies of the TFs permitted observing a selective enrichment in developmental pathways, allowing the distribution of miRNA motifs along a topological and chronological frame. In addition, piRNA motifs were categorized for the first time and revealed specific functional implications in somatic tissues. These data might pose experimental hypotheses to be tested in biological models, towards clarifying novel in gene regulatory routes.
Leptomonas lactosovorans n. sp., a Lactose-Utilizing Trypanosomatid: Description and Nutritional Requirements1

Leptomonas lactosovorans n. sp. is described from the gut of the reduviid hemipteran Zelurus martinsi. It can be grown in a defined medium. The requirements for amino acids, vitamins, purine, and heme were similar to those established for Crithida fasciculata. Growth is stimulated by aeration. Generation time is longer than for any other insect trypanosomatid described; its utilization of lactose as a carbon source is a unique feature among trypanosomatids.
Epidemiology of nonalcoholic fatty liver disease in non‐obese populations: Meta‐analytic assessment of its prevalence, genetic, metabolic, and histological profiles

As a subgroup of nonalcoholic fatty liver disease (NAFLD), patients with non‐obese NAFLD may also have an increased risk of adverse hepatic and metabolic outcomes. We aimed to estimate the prevalence and incidence of non‐obese NAFLD and to describe its clinical characteristics in this systematic review and meta‐analysis.