Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and Quantitation of Polyphenolic Compounds in Senna macranthera var pudibunda From the Northeast of Brazil

Until recently, there was a lack of information on the phytochemical composition of the taxon Senna. Recent reports show that Senna splendida, Senna gardneri, and Senna georcica are characterized by profiles dominated by flavonoids, naphthapyrones, and stilbenes. Here, we studied the phytochemical composition of Senna macranthera var pudibunda (Benth) Irwin & Barneby for comparison. A total of 26 polyphenolic compounds were identified in methanol extracts of various botanical parts of Senna macranthera var pudibunda (Benth.) Irwin & Barneby. The higher concentration (on a dry weight basis) of polyphenolic compounds was detected in the leaves (48.55 g/kg), bark (21.26 g/kg), and roots (17.08 g/kg), whereas a lower concentration of polyphenolic compounds was detected in the fruits (6.67 g/kg). The polyphenolic profiles of the various botanical parts were dominated by flavan-3-ols and flavan-3-ol dimers. The bark and roots contained only these components (100%), whereas flavonoids were also identified as minor components in the leaves (15.7%) and the fruits (5.6%), respectively. The flavan-3-ol conjugates comprised the well-known procyanidins, along with the rarely reported afzelechin, giobourtinidol and procassinidin dimers.
Fences reduce habitat for a partially migratory ungulate in the Northern Sagebrush Steppe

Few studies have examined differential responses of partially migratory ungulates to human development or activity, where some individuals in a population migrate and others do not. Yet understanding how animals with different movement tactics respond to anthropogenic disturbance is key to sustaining global ungulate migrations. We examined seasonal resource selection of a partially migratory population of pronghorn (Antilocapra americana) in the Northern Sagebrush Steppe of Alberta, Saskatchewan, and Montana from 2003 to 2011. We developed step‐selection functions (SSF) for migrant and resident pronghorn during the summer and winter at two spatial scales (second order and third order) and then integrated SSFs across scales to estimate pronghorn responses to fences and subsequent habitat loss from these features while accounting for responses to other resource use. Both migrant and resident pronghorn showed the strongest responses to natural and anthropogenic features at the second order and weaker responses at the third order. Selection responses of migrant and residents differed the most in response to normalized difference vegetation index, topography, and anthropogenic features. Seasonally, selection for intermediate greenness was strongest in summer, whereas avoidance of roads strongly influenced winter resource selection of both tactics. Both migrant and resident pronghorn showed strong avoidance of fencing at both spatial scales during summer and winter. Model predictions with complete removal of fences from the landscape (i.e., natural conditions) predicted an increase in the area of high‐quality habitat of 16–38%. In contrast, doubling fence density on the landscape decreased the amount of high‐quality habitat by 1–11% and increased low‐quality habitat by 13–21%. Our results suggest that pronghorn winter and summer ranges can be improved by reducing the density of fences on the landscape, or mitigation measures to enhance fence crossings, to alleviate the indirect loss of habitat for this important endemic prairie species.
The complete mitochondrial genome of pygmy red-toothed shrew (Chodsigoa parva)

Abstract The study of pygmy red-toothed shrew (Chodsigoa parva), which is the smallest species of geuns Chodsigoa, is extremely lacking. Also, it is classified as data deficient (DD) on The IUCN Red List. Here, we obtained a complete mitochondrial genome of Chodsigoa parva. The mitochondrial genome of C. parva is totally 17,216 bp in length and it is composed of 13 protein-coding genes, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions. We restructured Bayesian phylogenetic tree by using 19 species those belong to family Soricidae. The mitochondrial genome can provide basic data for further study about the phylogenetic relationship of family Soricidae.
In-silico Structural Annotation of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays L.)

Aims: The aim of this study was In-Silico structural annotation of an amino acid sequence of Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in Maize (Zea mays) retrieved from NCBI with the accession number PWZ58979. Study Design: The use of In-Silico studies for the structural annotation of Methylthioadenosine Nucleosidase protein. Place and Duration of Study: The research was conducted at the Bioinformatics Laboratory, Chevron Biotechnology Centre, Modibbo Adama University of Yola, Nigeria. Between June 2018 to July 2018. Methodology: The Methylthioadenosine Nucleosidase protein was retrieved from NCBI, physical and chemical parameters were calculated using ExPASy - ProtParam tool, the server SOPMA was used for secondary structure analysis (helix, sheets, and coils) and I-TASSER was used to obtain the 3D structure. Results: ExPASy - Prot Param tool computated the various physical and chemical parameters such as molecular weight (MW) 30117.97, total number of positively (+R) 27, negatively charged residues (-R) 30, theoretical isoelectric point (pI) 5.96, aliphatic index (AI) 103.67 and grand average hydropathy (GRAVY) 0.293. The SOPMA server was used for calculating the secondary structural features of protein sequences as Alpha helix 39.16%, Extended strand 14.69%, Beta turn 6.64% and Random coil 39.51%. I-Tasser was used for predicting the 3D structure where 2qttA from PDB was used as the template. Conclusion: This study helped in understanding the structural analysis of the Methylthioadenosine Nucleosidase Protein Zm00014a_031618 in maize (Z. mays).
Survey of the Native and Nonnative Vascular Plant Species of Three Islands in Lake Winnipesaukee, New Hampshire

ii ACKNOWLEDGEMENTS. iii LIST OF TABLES. v LIST OF FIGURES. viii I. LITERATURE REVIEW. 1 II. OBJECTIVES AND HYPOTHESES. 17 III. SITE DESCRIPTION. 19 IV. METHODS. 22 V. RESULTS Overstory Composition. 31 Understory Composition. 37 Sørensen’s Index of Similarity. 41 Plants of Concern and Disturbance Rubrics. 46 VI. DISCUSSION 2011 Sampling. 52 Plants of Concern. 53 Four Zones and the Ecological Land Use Plan. 55 Future Studies. 55 VII. CONCLUSIONS AND SIGNIFICANCE OF STUDY. 57 BIBLIOGRPAHY. 59 APPENDIX. 65 VITA. 118
Of Microbes and Mange: Consistent changes in the skin microbiome of three canid species infected with sarcoptic mange

Sarcoptic mange is a highly contagious skin disease caused by the ectoparasitic mite, Sarcoptes scabiei. Although it afflicts over 100 mammal species worldwide, sarcoptic mange remains a disease obscured by variability at the individual, population, and species levels. Amid this variability, it is critical to identify consistent drivers of morbidity, particularly at the skin barrier. We characterized the skin microbiome of three species of North American canids: coyotes (Canis latrans), red foxes (Vulpes vulpes), and gray foxes (Urocyon cinereoargenteus). Comparing mange-infected and uninfected individuals, we found remarkably consistent signatures of microbial dysbiosis associated with mange infection. Across genera, mange-infected canids exhibited reduced microbial diversity, altered community composition, and increased abundance of opportunistic pathogens. The primary bacteria comprising these secondary infections were Staphylococcus pseudintermedius, previously associated with canid ear and skin infections, and Corynebacterium spp, previously found among the gut flora of S. scabiei mites and hematophagous arthropods. Considered together, this evidence suggests that mange infection consistently alters the canid skin microbiome and facilitates secondary bacterial infection. These results provide valuable insights into the pathogenesis of mange at the skin barrier of North American canids and can inspire novel treatment strategies. By further adopting a “One Health” framework that considers mites, microbes, and the potential for interspecies transmission, we can better elucidate the patterns and processes underlying this ubiquitous and enigmatic disease.
Infection of Borrelia burgdorferi sensu lato of small mammals in Yunnan Province, China

Background Lyme disease is caused by Borrelia burgdorferisensulato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases of B. burgdorferi infections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Yunnan Province, Southwestern China. Yunnan Province is a tropical area with a diverse topographic range and sustains a high biodiversity of small mammals that could potentially play an important role in the transmission of a variety of B. burgdorferigenospecies. Methods 3659 small mammals were captured in 159 sample siteslocated 23 countries inYunnan Province and screened for BBSL infection by nested PCR based on 5S-23S rRNA intergenic spacer gene of BBSL.Univariate and multivariate forward stepwise logistic regression analysis was used to access the association between infections and related risk factors. Results Infection with BBSL was confirmed in 3.99%(146/3659) of small mammals. Significant differences in prevalence rates of BBSL were observed at varying landscape types and altitudes.Small mammals in forested areas had higher prevalence rates than other landscape types as did small mammals found at altitudes greater than 2500 meters. The 5S-23S rRNA intergenic spacergene revealed that there were 5 genotype of BBSL, including B. afzelii, B. burgdorferisensustricto, B.japonica, B.gariniiand B.valaisiana, which demonstrate the genetic diversity and regional distribution. Conclusions There exists a wide distribution and genetic diversity of endemic BBSL in Southwestern China, warranting further investigations and monitoring of clinical disease in individuals presenting with symptoms of Lyme disease in these areas. Author summary Lyme disease is caused by Borrelia burgdorferi sensu lato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases of Borrelia burgdorferi sensu lato infections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Southwestern China. This study documents potential small mammal reservoir hosts collected from a large of sample sites from different landscape types and altitudes, with PCR and sequencing identifying the wide distribution and genetic diversity of endemic Borrelia burgdorferi sensu lato in Southwestern China. This was the first report that B. japonica was detected in Apodemus draco and Niviventer excelsior in China. This study adds to body of literature on Borrelia burgdorferi sensu lato in China. This work will provide insight regarding small mammals to target for surveillance and we access the association between gender, developmental stage of rodents, environmental landscape and altitude to better prevent human exposure.
Development and Evaluation of Multiplex PCR for the Detection of Carbapenemase-Producing Enterobacteriaceae

Background: The isolation of carbapenemase-produc-ing Enterobacteriaceae (CPE) has become increas-ingly common. Continuous surveillance for these or-ganisms is essential because their infections are closely related to outbreaks of illness and are asso-ciated with high mortality rates. The aim of this study was to develop and evaluate multiplex PCR as a means of detecting several important CPE genes simultaneously. Methods: We aimed to develop a multiplex PCR that could detect seven CPE genes simultaneously. The multiplex PCR was composed of seven primer sets for the detection of KPC, IMP, VIM, NDM-1, GES, OXA-23, and OXA-48. We designed different PCR product sizes of at least 100 bp. We evaluated the performance of this new test using 69 CPE-positive clinical isolates. Also, we confirmed the specificity to rule out false-positive reactions by using 71 carbape-nem-susceptible clinical strains. Results: A total of 69 CPE clinical isolates showed positive results and were correctly identified as KPC (N=14), IMP (N=13), OXA-23 (N=12), OXA-48 (N=11), VIM (N=9), GES (N=5), and NDM (N=5) by the multiplex PCR. All 71 carbapenem-susceptible clinical isolates, including Enterococcus faecalis , Escherichia coli , Klebsiella pneumoniae , Acinetobacter baumannii , and Pseudomonas aeruginosa , showed negative results. Conclusion: This multiplex PCR can detect seven CPE genes at a time and will be useful in clinical laboratories. (Ann Clin Microbiol 2019;22:9-13)
The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana

Transposable elements (TEs) are DNA repeats that must remain silenced to ensure cell integrity. Several epigenetic pathways including DNA methylation and histone modifications are involved in the silencing of TEs, and in the regulation of gene expression. In Arabidopsis thaliana, the TE-derived plant mobile domain (PMD) proteins have been involved in TE silencing, genome stability, and control of developmental processes. Using a forward genetic screen, we found that the PMD protein MAINTENANCE OF MERISTEMS (MAIN) acts synergistically and redundantly with DNA methylation to silence TEs. We found that MAIN and its close homolog MAIN-LIKE 1 (MAIL1) interact together, as well as with the phosphoprotein phosphatase (PPP) PP7-like (PP7L). Remarkably, main, mail1 and pp7l mutants display similar developmental phenotypes, and share common subsets of upregulated TEs and misregulated genes. Finally, phylogenetic analyses of PMD and PP7-type PPP domains among the Eudicot lineage suggest neo-association processes between the two protein domains to potentially generate new protein function. We propose that, through this interaction, the PMD and PPP domains may constitute a functional protein module required for the proper expression of genes and silencing of TEs. AUTHOR SUMMARY The plant mobile domain (PMD) is a protein domain of unknown function that is widely spread in the angiosperm plants. Although most PMDs are associated with repeated DNA sequences called transposable elements (TEs), plants have domesticated the PMD to produce genic versions that play important roles within the cell. In Arabidopsis thaliana, MAINTENANCE OF MERISTEMS (MAIN) and MAIN-LIKE 1 (MAIL1) are genic PMDs that are involved in genome stability, developmental processes, and silencing of TEs. The mechanisms involving MAIN and MAIL1 in these cellular processes remain elusive. Here, we show that MAIN, MAIL1 and the phosphoprotein phosphatase (PPP) named PP7-like (PP7L) interact to form a protein complex that is required for the proper expression of genes, and the silencing of TEs. Phylogenetic analyses revealed that PMD and PP7-type PPP domains are evolutionary connected, and several plant species express proteins carrying both PMD and PPP domains. We propose that interaction of PMD and PPP domains would create a functional protein module involved in mechanisms regulating gene expression and repressing TEs.
BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows

Automated image analysis has become key to extract quantitative information from biological microscopy images, however the methods involved are now often so complex that they can no longer be unambiguously described using written protocols. We introduce BIAFLOWS, a web based framework to encapsulate, deploy, and benchmark automated bioimage analysis workflows (the software implementation of an image analysis method). BIAFLOWS helps fairly comparing image analysis workflows and reproducibly disseminating them, hence safeguarding research based on their results and promoting the highest quality standards in bioimage analysis.
Hypolipidemic Effect of Trixis angustifolia Aqueous Extract on Triton WR-1339- and High-Fat Diet-Induced Hyperlipidemic Mice

The aim of the present study was to evaluate the hypolipidemic effect of Trixis angustifolia aqueous extract (TxAE) on Triton WR-1339- and high-fat diet-induced hyperlipidemic mice. In the Triton model, treatment with TxAE at 100 and 200 mg/kg body weight produced a significant decrease in triglycerides and very low-density lipoprotein levels and a significant increase in high-density lipoprotein (HDL). Similarly, administration of TxAE along with the high-fat diet induced a significant decrease in serum total cholesterol, low-density lipoproteins, and increase in HDL. In addition, a phytochemical study of TxAE led to the isolation of 2 previously described compounds: pebrellin and xanthomicrol. This is the first time that these compounds have been identified in a plant extract with hypolipidemic effect. The results suggest the possible therapeutic potential of TxAE as a hypolipidemic agent supporting the usage of T. angustifolia as a traditional medicine.
Parameterization of the Durations of Phases of Foot-And-Mouth Disease in Cattle

The objective of the current study was to update parameterization of mathematical simulation models for foot-and-mouth disease (FMD) spread in cattle utilizing recent knowledge of FMD virus (FMDV) pathogenesis and infection dynamics to estimate the duration of distinct phases of FMD. Specifically, the durations of incubation, latent, and infectious periods were estimated for 3 serotypes (O, Asia1, and A) of FMDV, individually and collectively (pan-serotypic). Animal-level data were used in Accelerated Failure Time (AFT) models to estimate the duration of the defined phases of infection, while also investigating the influence of factors related to the experimental design (exposure methods) and virus serotype on disease progression. Substantial influences upon the estimated duration of distinct phases of FMD included the quantity of viral shedding used as a proxy for the onset of infectiousness, virus serotypes, and experimental exposure methods. The use of detection of any viral RNA in nasal secretions as a proxy of infectiousness lengthened the total infectious period compared to use of threshold-based detection. Additionally, the experimental system used to infect the animals also had significant effects on the duration of distinct phases of disease. Overall, the mean [95% Confidence Interval (CI)] durations of pan-serotype disease phases in cattle were estimated to be: incubation phase = 3.6 days (2.7–4.8), latent phase = 1.5 days (1.1–2.1), subclinical infectious phase = 2.2 days (1.5–3.5), clinical infectious phase = 8.5 days (6.2–11.6), and total infectious phase = 10.8 days (8.2–14.2). This study highlights the importance of identifying appropriate proxy measures to define the onset and duration of infectiousness in FMDV-infected cattle in the absence of actual transmission data. Additionally, it is demonstrated herein that factors associated with experimental design, such as virus exposure methods, may significantly affect disease progression in individual animals and should be considered when data is extrapolated from experimental studies. Given limitations in experimental data availability, pan-serotypic parameters which include all routes of exposure and a threshold-defined onset of infectiousness may be the most robust parameters for exploratory disease spread modeling approaches, when information on the specific virus of interest is not available.
Periodical cicada emergence resource pulse tracks forest expansion in a tallgrass prairie landscape

Understanding factors that influence resource pulses is an important aspect of ecosystem ecology. We quantified below‐ to aboveground energy and nutrient fluxes during the 2015 periodical cicada emergence from forest habitats in a tallgrass prairie matrix and compared results to our prior studies of the 1998 emergence in the same watershed. We estimated 35.2 million cicadas emerged across 159 ha in 2015, almost 2× more than the 19.6 million across 98 ha in 1998. The 2015 emergence resulted in below‐ to aboveground fluxes of 9.4 metric tons of ash‐free dry mass and 1.12 metric tons of N, both ~2× greater than 1998. This corresponds to 59 kg C/ha and 7 kg N/ha in and adjacent to forested areas in 2015. Increased emergence in 2015 was a result of spatial expansion of cicadas, not higher densities. Periodical cicadas are expanding with forest habitats in this region. Cicadas expand into and oviposit in ~40% of available forest habitat during each emergence. Accordingly, we predict the 2032 emergence will span ~245 ha. Our study demonstrates how human alterations to a landscape, in this case forest expansion linked to fire suppression and reduced grazing, can alter the magnitude and extent of a resource pulse.
Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins

Dengue virus (DENV) and other mosquito-borne flaviviruses are highly dependent on the ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), for efficient infection. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We used ribosome profiling to evaluate viral and cellular translation in RPLP1/2-depleted cells. This revealed that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). RPLP1/2 function to enhance ribosome elongation at this position and increase viral protein stability, possibly by improving co-translational folding of DENV proteins. We also analyzed the effects of RPLP1/2 depletion on cellular translation. We find that RPLP1/2 affects ribosome density for a small subset of cellular mRNAs. However, meta-analysis of ribosome positions on all cellular mRNAs revealed slightly increased accumulation of ribosomes downstream of start codons in RPLP1/2-depleted cells, suggesting that RPLP1/2 enhance elongation efficiency. Importantly, we found that ribosome density on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, implying a role for RPLP1/2 in transmembrane protein biogenesis. Together, our findings reveal insights into the function of RPLP1/2 in DENV and cellular translation.
On the discovery of subpopulation-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) has quickly become an empowering technology to profile the transcriptomes of individual cells on a large scale. Many early analyses of differential expression have aimed at identifying differences between subpopulations, and thus are focused on finding subpopulation markers either in a single sample or across multiple samples. More generally, such methods can compare expression levels in multiple sets of cells, thus leading to cross-condition analyses. However, given the emergence of replicated multi-condition scRNA-seq datasets, an area of increasing focus is making sample-level inferences, termed here as differential state analysis. For example, one could investigate the condition-specific responses of cell subpopulations measured from patients from each condition; however, it is not clear which statistical framework best handles this situation. In this work, we surveyed the methods available to perform cross-condition differential state analyses, including cell-level mixed models and methods based on aggregated “pseudobulk” data. We developed a flexible simulation platform that mimics both single and multi-sample scRNA-seq data and provide robust tools for multi-condition analysis within the muscat R package.