Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and characterization of microsatellite markers from the yellow passion fruit (Passiflora edulis f. flavicarpa)

Here we described the development of the first set of Passiflora microsatellite loci isolated from an enriched genomic library. A sample of 43 individuals from 12 accessions of the yellow passion fruit was used to characterize those loci, which revealed up to 20 alleles per locus. Two loci were monomorphic. The observed (HO) and expected (HE) heterozygosities were very similar, as expected for a self-incompatible species. Allelic diversity (HT) was 0.444. This set of markers will permit genetic structure analyses of cultivated and wild populations of Passiflora, and contribute for integrating genetic maps based on dominant markers, as they can provide bridge alleles.
Estimation of Multi-Species Leaf Area Index Based on Chinese GF-1 Satellite Data Using Look-Up Table and Gaussian Process Regression Methods

Leaf area index (LAI) is an important biophysical parameter, which can be effectively applied in the estimation of vegetation growth status. At present, amounts of studies just focused on the LAI estimation of a single plant type, while plant types are usually mixed rather than single distribution. In this study, the suitability of GF-1 data for multi-species LAI estimation was evaluated by using Gaussian process regression (GPR), and a look-up table (LUT) combined with a PROSAIL radiative transfer model. Then, the performance of the LUT and GPR for multi-species LAI estimation was analyzed in term of 15 different band combinations and 10 published vegetation indices (VIs). Lastly, the effect of the different band combinations and published VIs on the accuracy of LAI estimation was discussed. The results indicated that GF-1 data exhibited a good potential for multi-species LAI retrieval. Then, GPR exhibited better performance than that of LUT for multi-species LAI estimation. What is more, modified soil adjusted vegetation index (MSAVI) was selected based on the GPR algorithm for multi-species LAI estimation with a lower root mean squared error (RMSE = 0.6448 m2/m2) compared to other band combinations and VIs. Then, this study can provide guidance for multi-species LAI estimation.
Key for northwest european rosaceae pollen

Abstract All main types of pollen grains in Rosaceae seem to be variations of the same theme: a tricolporate pollen, with or without operculum. In most cases the exine sculpture is the best feature for classification; and combined with other characteristics, it is possible to separate some species earlier considered undistinguishable.
Sex pheromone for monitoring flight periods and population densities of the pine sawfly, Diprion jingyuanensis Xiao et Zhang (Hym., Diprionidae)

Abstract: The pine sawfly, Diprion jingyuanensis Xiao et Zhang, is a serious pest of Chinese pine (Pinus tabulaeformis Carr.) in the northern parts of China. The general biology of this recently described sawfly species is little known and in the present study we used a synthetic pheromone to monitor its flight period and to evaluate the possibility to use pheromone traps as a tool for estimating and predicting population densities. The attractant pheromone of D. jingyuanensis is (1S,2R,6R)‐1,2,6‐trimethyldodecyl propionate and in this study we used a four‐isomer threo‐mixture containing the active attractant. Both doses tested, 1 and 2 mg/trap, revealed the same seasonal flight pattern, the higher dosage demonstrating more clear flight peaks. The first flight peak of D. jingyuanensis occurred in mid‐June during all 3 years, 1997–1999, and in 1997 and 1998 a second flight peak was also recorded in mid‐July. The flight period was similar in time for populations located at higher (1400 m) and lower altitude (1100 m), from early June to late July or early August. Temperature was the main weather factor‐affecting trap catches. Diurnal flight activity began at 9.00, peaked at 13.00 and lasted until 20.00. A series of tests with traps in different positions within stands and trees were conducted and the results demonstrated the importance of standardizing the trapping protocol in population monitoring studies. By using traps with 2 mg baits it is possible to detect sawfly occurrence at very low population densities, not detectable by other means. Strong positive correlations between trap catch and relative population density were found in 2000 and 2001, but not in 1998, when only few sites were monitored and the population was in a decreasing phase. The results are promising for future large‐scale use of pheromone‐based monitoring of D. jingyuanensis.
Size, acetylation and concentration of chitooligosaccharide elicitors determine the switch from defence involving PAL activation to cell death and water peroxide production in Arabidopsis cell suspensions

Chitosan oligomers are known elicitors of plant defence mechanisms. In this work, chitooligosaccharides of different degrees of polymerization and degrees of acetylation were prepared and characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The effect of the degree of polymerization (DP), degree of acetylation and concentration of these chitooligosaccharides on defence activation in Arabidopsis thaliana suspension-cultured cells was studied. Our study results show that fully deacetylated chitooligosaccharides (chitosan oligomers) induce, depending on their DP and concentration, phenylalanine ammonia-lyase (PAL) activation, H2O2 synthesis and cell death in A. thaliana cell suspensions. The progressive reacetylation of the chitosan oligomer elicitors progressively impaired their ability to enhance H2O2 accumulation and cell death, but did not affect the activation of PAL.
Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes

Background Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent. Methodology/Principal findings Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the Wuchereria bancrofti and Plasmodium falciparum genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of P. falciparum, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the W. bancrofti genome predicted a ribosomal sequence to be the genome’s most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the W. bancrofti genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. Conclusions/Significance Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study’s objectives.
Uncovering Factors Influencing Instructors’ Decision Process when Considering Implementation of a Course-Based Research Experience

Course-based undergraduate research experiences (CUREs) are an effective way to expose large numbers of students to authentic research, yet most laboratory courses still use traditional “cookbook” methods. While barriers to using CUREs have been captured postimplementation, little is known about the decision mindset before implementation or what features of CURE design may mitigate perceived barriers. Perception of an innovation (such as a CURE) influences the likelihood of its adoption, and diffusion of innovations theory posits that the decision to adopt is largely influenced by five perceived features of an innovation: relative advantage, compatibility, complexity, observability, and trialability. We conducted interviews with instructors considering using the Prevalence of Antibiotic Resistance in the Environment (PARE) project to assess their perceptions of CUREs and motivations for using PARE. Instructors viewed CUREs as having relative advantages over traditional methods; however, CUREs were also viewed as complex, with instructors citing multiple barriers. Instructors were motivated to use PARE because of its potential scientific impact and compatibility with their courses’ structures and resources. Instructors perceived PARE to have few barriers to implementation compared with other CUREs. Designing CUREs that address common instructor barriers and drivers could increase the rate of diffusion of CUREs.
KEGG-expressed genes and pathways in triple negative breast cancer

Abstract Background: The incidence of triple negative breast cancer (TNBC) is at a relatively high level, and our study aimed to identify differentially expressed genes (DEGs) in TNBC and explore the key pathways and genes of TNBC. Methods: The gene expression profiling (GSE86945, GSE86946 and GSE102088) data were obtained from Gene Expression Omnibus Datasets, DEGs were identified by using R software, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were performed by the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools, and the protein-protein interaction (PPI) network of the DEGs was constructed by the STRING database and visualized by Cytoscape software. Finally, the survival value of hub DEGs in breast cancer patients were performed by the Kaplan–Meier plotter online tool. Results: A total of 2998 DEGs were identified between TNBC and health breast tissue, including 411 up-regulated DEGs and 2587 down-regulated DEGs. GO analysis results showed that down-regulated DEGs were enriched in gene expression (BP), extracellular exosome (CC), and nucleic acid binding, and up-regulated were enriched in chromatin assembly (BP), nucleosome (CC), and DNA binding (MF). KEGG pathway results showed that DEGs were mainly enriched in Pathways in cancer and Systemic lupus erythematosus and so on. Top 10 hub genes were picked out from PPI network by connective degree, and 7 of top 10 hub genes were significantly related with adverse overall survival in breast cancer patients (P < .05). Further analysis found that only EGFR had a significant association with the prognosis of triple-negative breast cancer (P < .05). Conclusions: Our study showed that DEGs were enriched in pathways in cancer, top 10 DEGs belong to up-regulated DEGs, and 7 gene connected with poor prognosis in breast cancer, including HSP90AA1, SRC, HSPA8, ESR1, ACTB, PPP2CA, and RPL4. These can provide some guidance for our research on the diagnosis and prognosis of TNBC, and further research is needed to evaluate their value in the targeted therapy of TNBC.
Dramatic improvement after tocilizumab of severe COVID‐19 in a child with sickle cell disease and acute chest syndrome

REFERENCES 1. Thomas-Ruddel D, Winning J, Dickmann P, et al. Coronavirus disease 2019 (COVID-19): update for anesthesiologists and intensivists March 2020. Anaesthesist. 2020;69(4):225-235. 2. Bhatraju PK, Ghassemieh BJ, Nichols M, et al. Covid-19 in critically ill patients in the Seattle region case series. N Engl J Med. 2020;382: 2012-2022. 3. Levi MT, Thachil J, Iba T, Levy JH. Coagulation abnormalities and thrombosis in patients with COVID-19. Lancet Haematol. 2020;7(6):e438-e440. 4. Azkur AK, Akdis M, Azkur D, et al. Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in COVID-19. Allergy. 2020. https://doi.org/10.1111/all.14364. Online ahead of print. 5. Goeijenbier M, van Wissen M, van de Weg C, et al. Review: viral infections and mechanisms of thrombosis and bleeding. J Med Virol. 2012; 84(10):1680-1696. 6. Lazarian G, Quinquenel A, Bellal M, et al. Autoimmune hemolytic anemia associated with Covid-19 infection. Br J Haematol. 2020. https:// doi.org/10.1111/bjh.16794. Online ahead of print. 7. Zulfiqar AA, Lorenzo-Villalba N, Hassler P, Andres E. Immune thrombocytopenic purpura in a patient with Covid-19. N Engl J Med. 2020;382(18):e43.
An elevational shift in butterfly species richness and composition accompanying recent climate change

The geographic ranges of many species have shifted polewards and uphill in elevation associated with climate warming, leading to increases in species richness at high latitudes and elevations. However, few studies have addressed community‐level responses to climate change across the entire elevational gradients of mountain ranges, or at warm lower latitudes where ecological diversity is expected to decline. Here, we show uphill shifts in butterfly species richness and composition in the Sierra de Guadarrama (central Spain) between 1967–1973 and 2004–2005. Butterfly communities with comparable species compositions shifted uphill by 293 m (± SE 26), consistent with an upward shift of approximately 225 m in mean annual isotherms. Species richness had a humped relationship with elevation, but declined between surveys, particularly at low elevations. Changes to species richness and composition primarily reflect the loss from lower elevations of species whose regional distributions are restricted to the mountains. The few colonizations by specialist low‐elevation species failed to compensate for the loss of high‐elevation species, because there are few low‐elevation species in the region and the habitat requirements of some of these prevent them from colonizing the mountain range. As a result, we estimated a net decline in species richness in approximately 90% of the region, and increasing community domination by widespread species. The results suggest that climate warming, combined with habitat loss and other drivers of biological change, could lead to significant losses in ecological diversity in mountains and other regions where species encounter their lower latitudinal‐range margins.
Exploring factors improving support for vaccinations among Polish primary care physicians

In Poland, primary care physicians are the most used and most trusted source of information on immunisation. We aimed to explore factors influencing support for vaccinations among physicians employed in the childhood immunisation programme, in order to inform education of healthcare workers and programme organization. In June-July 2017, we carried out a national cross-sectional survey of physicians working in randomly selected primary healthcare practices, and interviewed them by telephone. We assessed support for vaccinations using an ordinal scale (0–6) comprised of three equally weighted questions on the respondent support of the programme and vaccination of self and family. We also created a scale (0–3) based on correct answers to vaccination myths. We used ordered logistic regression to investigate factors independently influencing support for vaccinations, reporting the proportional odds ratios and 95% confidence intervals for one unit increase in the support score. Of 2,609 respondents contacted, we interviewed 500 (19%). The median vaccination support score (0–6) was 5 (IQR 2). After adjusting for other variables, we did not find significant effects of sex, medical specialty, adhering to recommendations, attending a conference in previous year, using non-scientific sources of information and self-assessed knowledge on vaccination support score. Age over 60 years, correctly addressing vaccination myths and use of one or more than one scientific sources of knowledge, significantly improved support for vaccinations (aOR = 1.97, 1.57, 3.09 and 2.68, respectively). We recommend to increase the amount, quality and accessibility of evidence-based educational materials for primary care physicians working with childhood immunisations.
Clarification and concentration of sugar cane juice through ultra, nano and reverse osmosis membranes

The performance of ultrafiltration (UF) membranes with molecular weight cut off (MWCO) of 1000 and 3500 Da in clarifying sugar cane juice was investigated, as well as the performance of a nanofiltration (NF) membrane with MWCO of 200 Da and a reverse osmosis (RO) membrane in concentrating sugar cane juice. For both cases the sugar cane juice had been limed and partially clarified. The UF membranes were found to be effective at clarifying the sugar cane juice in terms of purity rise and reduction in turbidity, colour, starch and protein. A purity rise of approximately 6 was achieved by both UF membranes at trans-membrane pressures (TMP) from 15 to 25 bar. However, Brix reduction in the permeate was between 14.5 and 41.85% and 12.11 and 26.52% for 1000 Da and 3500 Da membranes respectively. For the 200 Da and RO membranes the Brix in the concentrate was increased from 7.65 to 12.3 after 3 hours of operation for the 200 Da membrane at a TMP of 10 bar, whilst the Brix in the concentrate was increased from 15.65 to 27.6 after 3 hours of operation for the RO membrane at a TMP of 35 bar. Overall, UF membranes were found to be unsuitable for clarification of sugar cane juice since significant amount of Brix is reduced in the permeate, whilst RO membranes were found to be effective for concentration of sugar cane juice.
Oncostatin M upregulates Livin to promote keratinocyte proliferation and survival via ERK and STAT3 signalling pathways

What is the central question of this study? What controls the proliferation and apoptosis in the pathogenesis of psoriasis? What is the main finding and its importance? The pathogenesis psoriasis involves abnormal homeostasis of keratinocytes, with hyperproliferation and decreasing apoptosis. An inhibitor of apoptosis protein family molecule, Livin, is highly expressed in psoriasis vulgaris lesional skin tissue. Expression of Livin was upregulated at transcription and protein levels after stimulation with oncostatin M (OSM). OSM promoted the survival of HaCaT cells in oxidative stress conditions. Expression of Livin and proliferation of HaCaT cells stimulated by OSM was regulated through ERK and STAT3 signalling pathways. This study might provide new insights into targeted therapy for psoriasis.
A Comparative Analysis of Breast Cancer Detection and Diagnosis Using Data Visualization and Machine Learning Applications

In the developing world, cancer death is one of the major problems for humankind. Even though there are many ways to prevent it before happening, some cancer types still do not have any treatment. One of the most common cancer types is breast cancer, and early diagnosis is the most important thing in its treatment. Accurate diagnosis is one of the most important processes in breast cancer treatment. In the literature, there are many studies about predicting the type of breast tumors. In this research paper, data about breast cancer tumors from Dr. William H. Walberg of the University of Wisconsin Hospital were used for making predictions on breast tumor types. Data visualization and machine learning techniques including logistic regression, k-nearest neighbors, support vector machine, naïve Bayes, decision tree, random forest, and rotation forest were applied to this dataset. R, Minitab, and Python were chosen to be applied to these machine learning techniques and visualization. The paper aimed to make a comparative analysis using data visualization and machine learning applications for breast cancer detection and diagnosis. Diagnostic performances of applications were comparable for detecting breast cancers. Data visualization and machine learning techniques can provide significant benefits and impact cancer detection in the decision-making process. In this paper, different machine learning and data mining techniques for the detection of breast cancer were proposed. Results obtained with the logistic regression model with all features included showed the highest classification accuracy (98.1%), and the proposed approach revealed the enhancement in accuracy performances. These results indicated the potential to open new opportunities in the detection of breast cancer.
Influence of montane isolation and refugia on population structure of Sorex palustris in western North America

Abstract The contemporary geographic distribution and interrelation of populations result from landscape structure, habitat specificity, and historical climate fluctuations. We examined the impact of Pleistocene environmental history on mitochondrial genealogies of the water shrew (Sorex palustris) in montane systems of western North America to test hypotheses concerning historical recolonization. Our main focus lies on the regional scale of the Pacific Northwest and the extent to which disjunct populations are associated with discrete, isolated mountains. We analyzed 87 specimens from the entire western portion of the species range to assess broadscale genealogical relationships. We then examined 61 individuals selected from 21 specific high-elevation sites in the Pacific Northwest to test whether these populations are structured in accord with distinct montane regions. Across western North America in general the relationship among S. palustris lineages is unresolved, suggesting a recent and rapid radiation from a common ancestral population. In the Pacific Northwest we found evidence of clades that are uniquely associated with individually isolated montane regions, clades that are distributed across several montane regions, and distinct clades that co-occur within the same montane region. We conclude that populations of S. palustris in western North America are derived from a single, southern, late-Pleistocene refugium. We also suggest that lineages shifted geographically by following the most northerly postglacial expansion of the boreal forest system.