Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening and Bioassay of Entomopathogenic Fungi for the Control of Silverleaf Whitefly, Bemisia argentifolli

Isolates of Beauveria bassiana (Balsamo) Vuillemin, Paecilomyces farinosus (Holm ex SF Gray) Brown and Smith and Verticillium lecanii (Zimmermann) Viegas were evaluated for their pathogenicity to adults, eggs, first and third instars of silverleaf whitefly, Bemisia argentifolli (Bellows and Perring) (Homoptera: Aleyrodidae). Conidial dilutions were prepared in 0.05% Tween® and leaves treated by immersion in these suspensions. Assessments of nymphal infection were made 2, 3, 5, 7, and 10 days post-treatment. Infection rates in adults and eggs were made 14 days post-treatment. All isolates were pathogenic to nymphs and adults. None of the isolates were pathogenic to eggs. Isolates L3444 (P. farinosus) and L3009 (B. bassiana) were the most pathogenic to first instars and adults with LC50 and LC90 values of 7.3 × 104 and 3.1 × 106 conidia/ml, and 1.3 × 106 and 1.0 × 107 conidia/ml, respectively. Isolate FR20 (V. lecanii) was the most pathogenic to third instars with LC50 and LC90 values of 4.8 × 103 and 7.4 × 105 conidia/ml, respectively. Results imply that L3444 and L3009 are the most efficient isolates, based on their pathogenicity to first instars and adults. Results are discussed in relation to using fungi for management of silverleaf whitefly in greenhouses. RésuméDes isolats de Beauveria bassiana ( Balsamo) Vuillemin, Paecillomyces farinosus (Holm ex SF) Brown et Smith, et Verticillium lecanii (Zimmerman) Viegas ont été évalués quant à leur pathogénicité pour les adultes, les oeufs et les larves du premier et troisième stades de développement de l’aleurode du peuplier, Bemisia argentifolli (Bellows et Perring) (Homoptera: Aleyrodidae). Les dilutions de conidies étaient préparées dans une solution du Tween 0,05%® et les feuilles traitées par immersion dans ces suspensions. La recherche des nymphes infectées fut effectuée 2,3,5, 7 et 10 jours après le traitement. Le taux d’infection chez les adultes et les oeufs était évalué 14 jours après le traitement. Tous les isolats ont montré un pouvoir pathogène vis-à-vis des nymphes et les adultes mais aucun d’entre eux n’a manifesté de pathogénicité à l’égard des oeufs. Les isolats L3444 (P. farinosus) et L3009 (B. bassiana) étaient les plus pathogènes vis-à-vis des premiers stades de développement et des adultes. A la CL50 et CL90, les concentrations respectives étaient de 7,3 × 104 et de 3,1 × 106 conidies / ml pour les premiers stades, et de 1,3 × 106 et de 1,0 × 107 conidies / ml pour les adultes. L’isolat FR20 (V. lecanii) fut le plus effectif pour nymphes du 3ème stade de développement avec des valeurs respectives de la CL50 et CL90 équivalentes à 4,8 × 103 et 7,4 × 105 conidies / ml. Les résultats suggèrent que, compte tenu de leur pathogénicité vis-à-vis des premiers stades et des adultes, les isolats L3444 et L3009 sont les plus efficaces. Les résultats discutent aussi de l’utilisation des produits fongiques pour le contrôle de l’aleurode du peuplier argenté dans les serres.
Evaluating Human Autosomal Loci for Sexually Antagonistic Viability Selection in Two Large Biobanks

Sex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very extreme in order to produce and maintain reported levels of between-sex allelic differentiation. We address this paradox between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n=438,427) along with a second large, independent cohort (BioVU, n=93,864). We performed association tests between genetically ascertained sex and genotypes. Although we found dozens of genome-wide significant associations, none replicated across samples. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well-powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.
Tumor to normal single cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Neuroblastoma is a childhood cancer that resembles developmental stages of the neural crest. It is not established what developmental processes neuroblastoma cancer cells represent. Here, we sought to reveal the phenotype of neuroblastoma cancer cells by comparing cancer (n=19,723) with normal fetal adrenal single cell transcriptomes (n=57,972). Our principal finding was that the neuroblastoma cancer cell resembled fetal sympathoblasts, but no other fetal adrenal cell type. The sympathoblastic state was a universal feature of neuroblastoma cells, transcending cell cluster diversity, individual patients and clinical phenotypes. We substantiated our findings in 650 neuroblastoma bulk transcriptomes and by integrating canonical features of the neuroblastoma genome with transcriptional signals. Overall, our observations indicate that there exists a pan-neuroblastoma cancer cell state which may be an attractive target for novel therapeutic avenues. One Sentence Summary Comparisons of neuroblastoma cells and relevant normal adrenal cells reveal a uniform cell state that characterizes neuroblastoma across patients and disease phenotypes.
Proteomics of Galápagos Marine Iguanas Links Function of Femoral Gland Proteins to the Immune System

Femoral glands secrete a wax-like substance on the inner side of lizard hind legs, which is thought to function as a mode of chemical communication. Though the minor volatile fraction is well studied, the major protein fraction remains enigmatic. Here, we use proteomics to analyze proteins in femoral gland secretions of the Galápagos marine iguana. Although we found no evidence for proteins and peptides involved in chemical communication, we found several immune-regulatory proteins which also demonstrate anti-microbial functions. Accordingly, we show that femoral gland proteins and peptides function as a barrier against microbial infection and may prevent the rapid degradation of volatile substances. Graphical Abstract Highlights Comprehensive transcriptome and proteome of the Galápagos Marine Iguana. Analysis of femoral gland proteome. Identification of antimicrobial activity in femoral gland secretions. Communication between individuals via molecules, termed chemosignaling, is widespread among animal and plant species. However, we lack knowledge on the specific functions of the substances involved for most systems. The femoral gland is an organ that secretes a waxy substance involved in chemical communication in lizards. Although the lipids and volatile substances secreted by the femoral glands have been investigated in several biochemical studies, the protein composition and functions of secretions remain completely unknown. Applying a proteomic approach, we provide the first attempt to comprehensively characterize the protein composition of femoral gland secretions from the Galápagos marine iguana. Using samples from several organs, the marine iguana proteome was assembled by next-generation sequencing and MS, resulting in 7513 proteins. Of these, 4305 proteins were present in the femoral gland, including keratins, small serum proteins, and fatty acid-binding proteins. Surprisingly, no proteins with discernible roles in partner recognition or inter-species communication could be identified. However, we did find several proteins with direct associations to the innate immune system, including lysozyme C, antileukoproteinase (ALP), pulmonary surfactant protein (SFTPD), and galectin (LGALS1) suggesting that the femoral glands function as an important barrier to infection. Furthermore, we report several novel anti-microbial peptides from the femoral glands that show similar action against Escherichia coli and Bacillus subtilis such as oncocin, a peptide known for its effectiveness against Gram-negative pathogens. This proteomics data set is a valuable resource for future functional protein analysis and demonstrates that femoral gland secretions also perform functions of the innate immune system.
Long-term regeneration trends from a silvicultural systems trial in lowland cool temperate rainforest in Tasmania

A trial was established at Sumac, north-western Tasmania, in 1976 to compare five alternative treatments for logging and regeneration of lowland cool temperate rainforest dominated by Nothofagus cunninghamii. Harvesting treatments included selective sawlogging, stripfelling, shelterwood, clearfelling with cull retention, and clearfelling. Clearfelled and some stripfelled areas were burnt after harvesting. All areas were allowed to regenerate naturally. Eight mast N. cunninghamii seedfalls were recorded at the site from 1975 to 1996. Dense regeneration occurred after logging treatments that retained mature trees within 40 m of the treatment (i.e. the selective sawlog, stripfell and shelterwood treatments). Some regeneration also occurred after clearfelling with cull retention but not after clearfelling. Although regeneration was dominated by Nothofagus, other rainforest canopy species were also present and are likely to be maintained in logged stands. Seedlings established on both burnt and mechanically disturbed seedbeds. Growth of N. cunninghamii seedlings was fastest in open conditions, where mean annual height increments, measured over 18 years, were 40 cm/yr. In the same period, height increments under a closed canopy averaged only 14 cm/yr. Growth of regeneration after the selective sawlogging treatment was slow due to heavy shading. Potential yields on retained strips after stripfelling will be reduced by myrtle wilt and windthrow. Of the partial-harvesting treatments, the shelterwood treatment is likely to achieve the highest yields over a rotation.
Effects of Higher Serum Lipid Levels on the Risk of Parkinson's Disease: A Systematic Review and Meta-Analysis

Background: The causal relationship between serum lipid levels and the risk of Parkinson's disease (PD) remains largely uncertain. We summarized the existing controversial evidence on this topic. Methods: We searched the electronic databases for observational studies from January 1988 to March 2020. We applied random-effects models to calculate pooled relative risk (RR) with their 95% confidence intervals (CI). Random-effects dose-response meta-analyses were further conducted to explore the dose-risk relationship. Results: Twelve cohort studies and three case-control studies were included in this meta-analysis. Higher levels of serum low-density lipoprotein cholesterol (LDL-C) were inversely associated with the subsequent risk of PD (RR 0.73, 95% CI 0.57–0.93), whereas, there were no associations between serum levels of total cholesterol (TC) (RR 0.91, 95% CI 0.73–1.13), high-density lipoprotein cholesterol (HDL-C) (RR 0.97, 95% CI 0.73–1.27), or triglycerides (TG) (RR 0.85, 95% CI 0.55–1.29) and the risk of PD. Further dose-response meta-analysis revealed that every 38.6 mg/dL (1mmol/L) increase in serum LDL-C correlates with a 7% decreased risk of PD. Conclusions: Our paper supports the protective effect of higher serum LDL-C on the subsequent risk of PD. More prospective cohort studies are warranted to confirm the conclusion, and further fundamental researches are needed to elucidate the underlying biological mechanisms.
From local resynchronization to global pattern recovery in the zebrafish segmentation clock

Rhythmic spatial gene expression patterns termed the segmentation clock regulate vertebrate body axis segmentation during embryogenesis. The integrity of these patterns requires local synchronization between neighboring cells by Delta-Notch signaling and its inhibition results in defective segment boundaries. The oscillating tissue deforms substantially throughout development, but whether such tissue-scale morphogenesis complements local synchronization during pattern generation and segment formation is not understood. Here, we investigate pattern recovery in the zebrafish segmentation clock by washing out a Notch inhibitor, allowing resynchronization at different developmental stages, and analyzing the recovery of normal segments. Although from previous work no defects are expected after recovery, we find that washing out at early stages causes a distinctive intermingling of normal and defective segments, suggesting unexpectedly large fluctuations of synchrony before complete recovery. To investigate this recovery behavior, we develop a new model of the segmentation clock combining key ingredients motivated by prior experimental observations: coupling between neighboring oscillators, a frequency profile, a gradient of cell mixing, tissue length change, and cell advection pattern. This model captures the experimental observation of intermingled normal and defective segments through the formation of persistent phase vortices of the genetic oscillators. Experimentally observed recovery patterns at different developmental stages are predicted by temporal changes of tissue-level properties, such as tissue length and cell advection pattern in the model. These results suggest that segmental pattern recovery occurs at two scales: local pattern formation and transport of these patterns through tissue morphogenesis, highlighting a generic mechanism of pattern dynamics within developing tissues. SIGNIFICANCE Interacting genetic oscillators can generate a coherent rhythm and a tissue-level pattern from an initially desynchronized state. Using experiment and theory we study resynchronization and pattern recovery of the zebrafish segmentation clock, which makes the embryonic body segments. Experimental perturbation of intercellular signaling with an inhibitor results in intermingled normal and defective segments. According to theory, this behavior may be caused by persistent local vortices scattered in the tissue during pattern recovery. Full pattern recovery follows dynamic global properties, such as tissue length and advection pattern, in contrast to other genetic oscillators in a static tissue such as circadian clocks. Our work highlights how dynamics of tissue level properties may couple to biochemical pattern formation in tissues and developing embryos.
Recombinant Ganoderma lucidum Immunomodulatory Protein Improves the Treatment for Chemotherapy-Induced Neutropenia

Ganoderma lucidum, also known as LINGZHI, has a long tradition of use in folk medicine of the Far East, which is documented in the oldest Chinese pharmacopoeia, declaring it a superior medicine. LINGZHI-8 (LZ-8) is an immunoregulatory fungal protein isolated from the fruiting body of Ganoderma lucidum. Neutropenia is a condition with an abnormally low levels of neutrophils in the blood, which is caused by numerous medical conditions or medications, such as chemotherapy. The current study demonstrated that recombinant LZ-8 (rLZ-8) from Pichia promoted the differentiation of bone marrow hematopoietic stem cells (HSCs) into granulocytes in a neutropenia mouse model induced by cyclophosphamide. Also, it regulated the CXCR4-SDF1 axis to promote the mobilization of HSCs and the release of neutrophils from the bone marrow to peripheral blood. Binding of rLZ-8 to the colony stimulating factor 1 receptor (CSF1R) promotes the differentiation of HSCs into primitive CFU colonies. These results suggested that rLZ-8 has a potential effect in the treatment of chemotherapy-induced neutropenia.
Effectiveness of short-term progestogen primings for the induction of fertile oestrus with eCG in ewes during late seasonal anoestrus

Two hundred and seventy-seven ewes were used in three experiments during late seasonal anoestrus to evaluate short-term progestogen primings for equine chorionic gonadotropin (eCG)-induced oestrus. In experiment 1, medroxy-progesterone acetate (MAP) sponges were inserted for 6, 9 or 13 days in nulliparous ewes. Percentage of ewes in oestrus (92.3, 85.7 and 96.4%, respectively) and conception rates (66.7, 75.0 and 63.0%, respectively) did not differ among groups (T > 0·05). In experiment 2, MAP sponges were inserted for 1, 2, 3, 6 or 12 days in multiparous ewes. Percentages of ewes in oestrus were higher with 3, 6 or 12 days than with 1 or 2 days of priming (72.2, 93.8 and 87.5% v . 25.0 and 33.3% respectively, P v . 27.8%, P
Epidemiological model with anomalous kinetics - The Covid-19 pandemics

We generalize the phenomenological, law of mass action-like, SIR and SEIR epidemiological models to situations with anomalous kinetics. Specifically, the contagion and removal terms, normally linear in the fraction $I$ of infecteds, are taken to depend on $I^{,q_{up}}$ and $I^{,q_{down}}$, respectively. These dependencies can be understood as highly reduced effective descriptions of contagion via anomalous diffusion of susceptibles and infecteds in fractal geometries, and removal (i.e., recovery or death) via complex mechanisms leading to slowly decaying removal-time distributions. We obtain rather convincing fits to time series for both active cases and mortality with the same values of $(q_{up},q_{down})$ for a given country, suggesting that such aspects may in fact be present in the evolution of the Covid-19 pandemic. We also obtain approximate values for the effective population $N_{eff}$, which turns out to be a small percentage of the entire population $N$ for each country.
Quantitative Near-Infrared Imaging of Platelets in Platelet-Rich Fibrin (PRF) Matrices: Comparative Analysis of Bio-PRF, Leukocyte-Rich PRF, Advanced-PRF and Concentrated Growth Factors

Platelet-rich fibrin (PRF) is a fibrin matrix enriched with platelets. The PRF matrix is thought to form a steep gradient of platelet density around the region corresponding to the buffy coat in anticoagulated blood samples. However, this phenomenon has not yet been proven. To visualize platelet distribution in PRF in a non-invasive manner, we utilized near-infrared (NIR) imaging technology. In this study, four types of PRF matrices, bio-PRF, advanced-PRF (A-PRF), leukocyte-rich PRF (L-PRF), and concentrated growth factors (CGF) were compared. Blood samples collected from healthy, non-smoking volunteers were immediately centrifuged using four different protocols in glass tubes. The fixed PRF matrices were sagittally divided into two equal parts, and subjected to modified immunohistochemical examination. After probing with NIR dye-conjugated secondary antibody, the CD41+ platelets were visualized using an NIR imager. In L-PRF and CGF, platelets were distributed mainly on and below the distal surface, while in bio-PRF and A-PRF, platelet distribution was widespread and homogenous. Among three regions of the PRF matrices (upper, middle, and lower), no significant differences were observed. These findings suggest that platelets aggregate on polymerizing fibrin fibers and float up as a PRF matrix into the plasma fraction, amending the current “gradient” theory of platelet distribution.
Genetic variation in phytosterol content of winter rapeseed (Brassica napus L.) and development of NIRS calibration equations

Rapeseed oil is one of the richest natural sources of phytosterols, known to reduce the LDL-cholesterol levels, one of the major cardiovascular disease risk factors. Increasing the phytosterol content in rapeseed could give an added value to the oil and derived products. Our objective was to analyse the genetic variation of phytosterol content in modern winter rapeseed cultivars and resynthesized lines following field experiments and to develop a near-infrared reflectance spectroscopic (NIRS) calibration for high throughput estimation of phytosterol content. Phytosterol content as analysed by gas-liquid chromatography ranged from 3565 to 4800 mg/kg seed for modern cultivars and from 2079 to 4329 mg/kg seed for resynthesized lines. The NIRS calibration showed a high fraction of explained variance in cross-validation of 0.81 for total phytosterol content and the standard error of cross-validation was 241 mg/kg. The results show that the cultivars contain already high phytosterol contents. The NIRS calibrations developed for total phytosterol content should be useful for germplasm screening and in breeding programmes aimed at increasing the phytosterol content in rapeseed.
Long-range neural coherence encodes stimulus information in primate visual cortex

In the primary visual cortex, neurons with similar receptive field properties are bound together through widespread networks of horizontal connections that span orientation columns. How connectivity across the cortical surface relates to stimulus information is not fully understood. We recorded spiking activity and the local field potential (LFP) from the primary visual cortex of marmoset monkeys and examined how connectivity between distant orientation columns affect the encoding of visual orientation. Regardless of their spatial separation, recording sites with similar orientation preferences have higher coherence between spiking activity and the local field potential than sites with different preferred orientation. Using information theoretic methods, we measured the amount of stimulus information that is shared between pairs of sites. More stimulus information can be decoded from pairs with the same preferred stimulus orientation than the pairs with a different preferred orientation, and the amount of information is significantly correlated with the magnitude of beta-band spike-LFP coherence. These effects remained after controlling for firing rate differences. Our results thus show that spike-LFP synchronization in the beta-band is associated with the encoding of stimulus information within the primary visual cortex of marmoset monkeys. Significance Statement A fundamental step in processing images in the visual cortex is coordinating the neural activity across distributed populations of neurons. Here, we demonstrate that populations of neurons in the primary visual cortex of marmoset monkeys with the same stimulus orientation preference temporally coordinate their activity patterns when presented with a visual stimulus. We find maximum synchronization in the beta range depends on the similarity of orientation preference at each pair of the neural population.