Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
Changes in ground-foraging ant assemblages along a disturbance gradient in a tropical agricultural landscape

Changes in ground-foraging ant assemblages occurring along an agricultural intensification gradient were analysed in Nicaragua (Central America). Five habitat types were compared: secondary forest fragments, organic shade coffee and cocoa plantations, corn fields and active pastures. Ants were captured by tuna baiting following standardised protocols. Species richness and diversity decreased along the gradient from forest to the pasture, and each of the agricultural systems (cocoa, coffee and corn plantations) significantly differed in diversity. Species composition also differed along the disturbance gradient, as shown by multivariate analysis. Forest and pasture were at the extremes of the gradient and shared no common species. The ant assemblages associated with coffee plots, although poorer in species, were more similar to those of the forest than to those of the cocoa plantations. The observed trends confirm that shaded agro-forestry plantations can help to maintain high biodiversity levels in tropical landscapes.
A novel nonsense mutation in TNNT2 in a Chinese pedigree with hypertrophic cardiomyopathy

Supplemental Digital Content is available in the text Abstract Rationale: Hypertrophic cardiomyopathy (HCM) is an inherited myocardial disease and a common cause of sudden cardiac death, heart failure, atrial fibrillation and stroke. In families affected by HCM, genotyping is useful for identifying susceptible relatives. In the present study, we investigated the disease-causing mutations in a three-generation Chinese family with HCM using whole exome sequencing (WES). Patient concerns: The proband, a 50-year-old man, was diagnosed with HCM at the age of 41 years. He presented with an asymmetric hypertrophic interventricular septum and a maximum interventricular septum thickness of 18.04 mm. His third elder sister, niece and daughter were also clinically affected by HCM. Diagnosis: Autosomal dominant HCM. Interventions: Seven family members, including 4 affected members, accepted WES. The genetic variants were subsequently called using Genome Analysis Toolkit and annotated using the InterVar program. Following frequency filtration by the Genome Aggregation Database, the variants were evaluated using an in-house bioinformatics analysis pipeline. Outcomes: HCM was transmitted as an autosomal dominant trait in the family. An extremely rare stop gained mutation, rs796925245 (g.1:201359630G>A, c.835C>T, p.Gln279Ter) in the troponin T2 (TNNT2) gene was identified as the disease-causing mutation. The stop gained mutation was predicted to result in a truncated troponin T protein in cardiac sarcomere. An adolescent family member who had normal echocardiographic measurements was found to carry the same disease-causing mutation. Lessons: A novel nonsense TNNT2 mutation was identified as the HCM-causing mutation in this Chinese pedigree. Since HCM shows a low penetrance by clinical criteria in adolescents, the adolescent mutation carrier, who is still clinically unaffected, should be offered routine follow-ups and sport activity recommendations to prevent adverse events including sudden cardiac death in the future.
Study on the differentially expressed genes and signaling pathways in dermatomyositis using integrated bioinformatics method

Abstract Dermatomyositis is a common connective tissue disease. The occurrence and development of dermatomyositis is a result of multiple factors, but its exact pathogenesis has not been fully elucidated. Here, we used biological information method to explore and predict the major disease related genes of dermatomyositis and to find the underlying pathogenic molecular mechanism. The gene expression data of GDS1956, GDS2153, GDS2855, and GDS3417 including 94 specimens, 66 cases of dermatomyositis specimens and 28 cases of normal specimens, were obtained from the Gene Expression Omnibus database. The 4 microarray gene data groups were combined to get differentially expressed genes (DEGs). The gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of DEGs were operated by the database for annotation, visualization and integrated discovery and KEGG orthology based annotation system databases, separately. The protein–protein interaction networks of the DEGs were built from the STRING website. A total of 4097 DEGs were extracted from the 4 Gene Expression Omnibus datasets, of which 2213 genes were upregulated, and 1884 genes were downregulated. Gene ontology analysis indicated that the biological functions of DEGs focused primarily on response to virus, type I interferon signaling pathway and negative regulation of viral genome replication. The main cellular components include extracellular space, cytoplasm, and blood microparticle. The molecular functions include protein binding, double-stranded RNA binding and MHC class I protein binding. KEGG pathway analysis showed that these DEGs were mainly involved in the toll-like receptor signaling pathway, cytosolic DNA-sensing pathway, RIG-I-like receptor signaling pathway, complement and coagulation cascades, arginine and proline metabolism, phagosome signaling pathway. The following 13 closely related genes, XAF1, NT5E, UGCG, GBP2, TLR3, DDX58, STAT1, GBP1, PLSCR1, OAS3, SP100, IGK, and RSAD2, were key nodes from the protein–protein interaction network. This research suggests that exploring for DEGs and pathways in dermatomyositis using integrated bioinformatics methods could help us realize the molecular mechanism underlying the development of dermatomyositis, be of actual implication for the early detection and prophylaxis of dermatomyositis and afford reliable goals for the curing of dermatomyositis.
Triton X‐114 Fractionated Subcellular Proteome of Leptospira interrogans Shows Selective Enrichment of Pathogenic and Outer Membrane Proteins in the Detergent Fraction

The Triton X‐114‐based solubilization and temperature‐dependent phase separation of proteins is used for subcellular fractionation where, aqueous, detergent, and pellet fractions represents cytoplasmic, outer membrane (OM), and inner membrane proteins, respectively. Mass spectrometry‐based proteomic analysis of Triton X‐114 fractions of proteomic analysis of Leptospira interrogans identified 2957 unique proteins distributed across the fractions. The results are compared with bioinformatics predictions on their subcellular localization and pathogenic nature. Analysis of the distribution of proteins across the Triton X‐114 fractions with the predicted characteristics is performed based on “number” of unique type of proteins, and “quantity” which represents the amount of unique protein. The highest number of predicted outer membrane proteins (OMPs) and pathogenic proteins are found in aqueous and pellet fractions, whereas detergent fraction representing the OM has the highest quantity of OMPs and pathogenic proteins though lower in number than the aqueous and pellet fractions. This leaves the possibility of an upsurge in pathogenic proteins and OMPs on the OM under pathogenic conditions suggesting their potential use to combat leptospirosis. Further, the Triton X‐114 subcellular fractions are more correlated to enrichment of pathogenic proteins predicted by MP3 software than predicted localization.
Where are we moving in the classification of idiopathic inflammatory myopathies?

Purpose of review Discoveries of myositis-specific antibodies, transcriptomic signatures, and clinicoseropathological correlation support classification of idiopathic inflammatory myopathies (IIM) into four major subgroups: dermatomyositis, immune-mediated necrotizing myopathy (IMNM), antisynthetase syndrome (ASS), and inclusion body myositis (IBM) whereas leaving polymyositis as a historical nonspecific diagnosis of exclusion. This review summarizes and comments on recent knowledge regarding the major subgroup of IIM. Recent findings Type 1 interferon (IFN1) pathway activation is the most prominent in dermatomyositis whereas type 2 interferon (IFN2) pathway activation is high in IBM and ASS; neither pathway is distinct in IMNM. Myxovirus-resistant protein A, IFN1 surrogate marker, is now one of definite dermatomyositis muscle biopsy criteria in the new 2018 European Neuromuscular Centre classification of dermatomyositis; the classification emphasizes on different categorization with and without dermatomyositis-specific antibody result. Novel HLA loci associated with anti-TIF1-γ, anti-Mi-2, and anti-Jo-1 antibodies in Caucasian population are identified. Associations of chaperon-assisted selective autophagy (CASA) and complement-mediated autoimmunity in IMNM as well as highly differentiated T cells in IBM are discovered. Summary Current IIM classification requires integrated clinicoseropathological approaches. Additional information, such as transcriptomics, HLA haplotyping, and potential biomarkers help tailoring categorization that may have future diagnostic and therapeutic implications.
Chronic obstructive pulmonary disease caused by inhalation of dust

Abstract Background: A meta-analysis was performed to evaluate the relationship between chronic obstructive pulmonary disease (COPD) and occupational dust exposure, and to provide a scientific basis for the prevention and treatment of COPD caused by occupational factors. Methods: PubMed and Embase databases were used to search for original epidemiological literature related to theme. Both random and fixed effects models were used to calculate pooled odds ratios and their corresponding 95% confidence intervals. Review Manager was used to perform data analysis. Results: Nine studies were included in the meta-analysis in accordance with the inclusion criteria. There was a significantly obvious correlation between occupational dust exposure and COPD of the population-based studies assessed in this article. The risk of developing COPD for workers exposed to dust was 1.51 times higher than for controls (I2 = 40%, 95% confidence interval: 1.27-1.79). The presence of publication bias was not found. Conclusion: The study provided evidence supporting the association between occupational dust exposure and the risk of developing COPD.
Rethinking sense of coherence: Perceptions of comprehensibility, manageability, and meaningfulness in a group of Palestinian health care providers operating in the West Bank and Israel

Drawing on a salutogenic perspective, we explored sense of coherence (SOC) in a group of Palestinian mental health care providers living and working in Israel and the occupied Palestinian territories (West Bank). Specifically, we conducted a qualitative exploration of the cultural characteristics of SOC and its components (comprehensibility, manageability, and meaningfulness) in two groups of Palestinian Muslim helpers. We found that context-specific features of SOC can mobilize generalized resistance resources for coping with traumatic and stressful experiences, even in an environment characterized by political instability, military violence, and social trauma. Ten main themes emerged from the thematic content analysis: acceptance, reacting to adversity, acknowledging human insecurity (comprehensibility), self-control, talking to family, education as a resource for survival, connecting to the severity of the event, responsibility as a source of control (manageability), religiosity, and sense of belonging (meaningfulness). The Islamic faith, as expressed through the concepts of Sumud and Taslim, seemed to permeate individuals’ ability to attribute meaning to historical and transgenerational trauma, as well as to their ongoing traumatic conditions, thus acting as their ultimate source of health and wellbeing. A holistic, spiritual, and collectivist outlook helped respondents to approach their lives with optimism. We discuss the implications for mental health care providers and future research directions.
The phase of the BAO on observable scales

The baryon acoustic oscillations (BAO) provide an important bridge between the early universe and the expansion history at late times. While the BAO has primarily been used as a standard ruler, it also encodes recombination era physics, as demonstrated by a recent measurement of the neutrino-induced phase shift in the BAO feature. In principle, these measurements offer a novel window into physics at the time of baryon decoupling. However, our analytic understanding of the BAO feature is limited, particularly for the range of Fourier modes measured in surveys. As a result, it is unclear what the BAO phase teaches us about the early universe beyond what is already known from the cosmic microwave background (CMB). In this paper, we provide a more complete (semi-)analytic treatment of the BAO on observationally relevant scales. In particular, we compute corrections to the frequency and phase of the BAO feature that arise from higher order effects which occur in the tight coupling regime and during baryon decoupling. The total phase shift we find is comparable to a few percent shift in the BAO scale (frequency) and thus relevant in current data. Our results include an improved analytic calculation of the neutrino induced phase shift template that is in close agreement with the numerically determined template used in measurements of the CMB and BAO.
In vitro biocompatibility evaluation of radiolytically synthesized silver/polyvinyl hydrogel nanocomposites for wound dressing applications

Nano silver/polyvinyl alcohol hydrogel nanocomposites have been prepared using gamma irradiation technique. Gamma irradiation serves as a crosslinking agent for the polyvinyl alcohol hydrogels and also acts as a reducing agent for reduction of Ag+ ions to zero valent Ag0 within the polyvinyl alcohol crosslinked network. The microstructural characteristics of the prepared composites were studied using powder X-ray diffraction, ultraviolet–visible spectroscopy, Fourier-transform infrared spectroscopy and field emission scanning electron microscopy analysis. The data obtained by these characterizations indicate the homogeneous distribution of silver nanoparticles on the polyvinyl alcohol network. The swelling properties and mechanical parameters of the silver/polyvinyl alcohol hydrogel nanocomposites tend to show improvements, making them a better material for wound care applications. The silver/polyvinyl alcohol hydrogel nanocomposites have shown good antibacterial potential against both Gram-positive and Gram-negative bacteria and shown nil or minimal cytotoxic effect on human melanoma (SK-MEL-2) and mouse melanoma (B16-F1) cell lines. Overall, it was concluded that under optimized condition, silver/polyvinyl alcohol hydrogel nanocomposites synthesized using gamma irradiation technique are excellent candidates for wound dressing application.
Methodological Uncertainty and Multi-Strategy Analysis: Case Study of the Long-Term Effects of Government Sponsored Youth Training on Occupational Mobility

Sociological practitioners often face considerable methodological uncertainty when undertaking a quantitative analysis. This methodological uncertainty encompasses both data construction (e.g. defining variables) and analysis (e.g. selecting and specifying a modelling procedure). Methodological uncertainty can lead to results that are fragile and arbitrary. Yet, many practitioners may be unaware of the potential scale of methodological uncertainty in quantitative analysis, and the recent emergence of techniques for addressing it. Recent proposals for ‘multi-strategy’ approaches seek to identify and manage methodological uncertainty in quantitative analysis. We present a case-study of a multi-strategy analysis, applied to the problem of estimating the long-term impact of 1980s UK government-sponsored youth training. We use this case study to further highlight the problem of cumulative methodological fragilities in applied quantitative sociology and to discuss and help develop multi-strategy analysis as a tool to address them.
Analysis of Ionospheric TEC Anomalies during Super Typhoons Megi and Meranti

ABSTRACT Sun, J.L. ; Zhang, Z.Y. ; Liu, X. ; Zhang, C. , Mou, Z.H. , 2020. Analysis of ionospheric TEC anomalies during super typhoons Megi and Meranti. In: Bai, X. and Zhou, H. (eds.), Advances in Water Resources, Environmental Protection, and Sustainable Development. Journal of Coastal Research, Special Issue No. 115, pp. 692-695. Coconut Creek (Florida), ISSN 0749-0208. In this paper, we detected and analyzed ionospheric anomalies during the 2016 super typhoons Megi and Meranti using the sliding interquartile range method applied to the ionospheric total electron content (TEC) grid data from the Global Ionospheric Model (GIM) provided by the Center for Orbit Determination in Europe (CODE). We found that ionospheric TEC anomalies occurred 2 days before the origination of super typhoon Megi. The anomalies occurred from 02:00 to 12:00 local time over a period of 10 h, with a maximum outlier of 12 TEC units over the typhoon center. Anomalies occurred in the ionosphere over both the area near the typhoon center and the corresponding equatorial magnetic conjugate region. The anomalies in both areas showed approximately the same trends. It is very likely that the disturbances from the ionospheric anomalies over the typhoon center were one of the precursors for the typhoon event. Similar ionospheric anomalies also occurred in the ionosphere 2 days before the formation and development of super typhoon Meranti. The global ionospheric TEC distribution was even more complex on that day. The existence of multiple peaks and valleys in the maximum outlier near the typhoon center was possibly associated with the position of the typhoon center and the GIM grid points or the wind speeds over the typhoon center.
Phylogenetics of Hawaiian Diplazium (Athyriaceae: Polypodiales)

Abstract. Hawaii is home to four species in the fern genus Diplazium: Diplazium arnottii, D. esculentum, D. molokaiense, and D. sandwichianum. Three are endemic to the Hawaiian Islands, and one is introduced and naturalized (D. esculentum). They vary in frequency, from very abundant (D. sandwichianum) to rare and critically endangered (D. molokaiense). Prior to this work, the phylogenetic relationships of only D. esculentum had been estimated due to lack of information available about these species. In this study, we inferred phylogenetic relationships of the Hawaiian Diplazium based on six chloroplast regions – atpA, atpB, matK, rbcL, rps4+rps4–trnS IGS, and trnL intron+trnL–trnF IGS. We downloaded these plastid markers from GenBank for an additional 83 Diplazium species and two Athyrium species, and used the latter as outgroups. The resulting phylogeny inferred from combined data indicated that D. arnottii and D. sandwichianum are sister taxa, likely with origins in the Paleotropics. Morphologically, the two species can be distinguished by leaf dissection and lengths of sori. Diplazium molokaiense is sister to the Asian D. heterocarpum (among our sampled taxa). Diplazium molokaiense is distinguished from other species in the clade by its large sori and longer fronds. Our results reveal the phylogenetic placements of three Diplazium species and corroborate the placement of a fourth species.
Design and Implementation of Marine Automatic Target Recognition System Based on Visible Remote Sensing Images

ABSTRACT Gao, X.B. , 2020. Design and implementation of marine automatic target recognition system based on visible remote sensing images. In: Bai, X. and Zhou, H. (eds.), Advances in Water Resources, Environmental Protection, and Sustainable Development. Journal of Coastal Research, Special Issue No. 115, pp. 277-279. Coconut Creek (Florida), ISSN 0749-0208. In the process of visible light remote sensing imaging, different sea surface wave conditions have different reflection ability to illumination, which makes the brightness, contrast and other information of visible light remote sensing images have great changes. Marine ship target recognition is an important application of image processing in remote sensing field. Based on pixel-level fusion of visible and infrared bispectral images, this paper extracts features from fusion results, and recognizes targets in images according to the matching of target image features and template image features. Comprehensive utilization of image preprocessing, image smoothing and anti-cloud interference algorithms can quickly and accurately realize ship target detection under the complex background of land and sea. The experimental results show that the algorithm is effective both in physical mechanism and in actual image effect.
Development and Characterization of Microsatellite Markers for the Endemic Frog Nyctibatrachus kempholeyensis and Cross Amplification with Other Nyctibatrachus Species from the Western Ghats, India

Abstract: The genus Nyctibatrachus is endemic to the Western Ghats, India, and includes a number of species that are highly restricted in their distribution. Nyctibatrachus kempholeyensis is an endemic species distributed in the Central Western Ghats. In this paper we describe the development of eight polymorphic microsatellite markers for N. kempholeyensis. These markers were tested for cross-amplification in other Nyctibatrachus species. In addition, we confirmed the cross-amplification of three microsatellite markers from another species, N. major. The 11 microsatellites were screened with 76 individuals of N. kempholeyensis and were found to have 3–8 alleles per locus, with observed heterozygosity ranging from 0.15 to 0.95. These microsatellite markers could be used to study population diversity across fragmented habitats, to quantify genetic structure, and to assess gene flow across the populations in this endemic genus.