Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism

Environmental conditions influence specialized plant metabolism. However, many studies aiming to understand these modulations have been conducted with model plants and/or under controlled conditions, thus not reflecting the complex interaction between plants and environment. To fully grasp these interactions, we investigated the specialized metabolism and genetic diversity of a native plant in its natural environment. We chose Myrcia bella due to its medicinal interest and occurrence in Brazilian savanna regions with diverse climate and soil conditions. An LC-HRMS-based metabolomics approach was applied to analyze 271 samples harvested across seven regions during the dry and rainy season. Genetic diversity was assessed in a subset of 40 samples using amplified fragment length polymorphism. Meteorological factors including rainfall, temperature, radiation, humidity, and soil nutrient and mineral composition were recorded in each region and correlated with chemical variation through multivariate analysis (MVDA). Marker compounds were selected using a statistically informed molecular network and annotated by dereplication against an in silico database of natural products. The integrated results evidenced different chemotypes, with variation in flavonoid and tannin content mainly linked to soil conditions. Different levels of genetic diversity and distance of populations were found to be correlated with the identified chemotypes. These observations and the proposed analytical workflow contribute to the global understanding of the impact of abiotic factors and genotype on the accumulation of given metabolites and, therefore, could be valuable to guide further medicinal exploration of native species.
A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy

The secondary structure prediction of proteins is a classic topic of computational structural biology with a variety of applications. During the past decade, the accuracy of prediction achieved by state-of-the-art algorithms has been >80%; meanwhile, the time cost of prediction increased rapidly because of the exponential growth of fundamental protein sequence data. Based on literature studies and preliminary observations on the relationships between the size/homology of the fundamental protein dataset and the speed/accuracy of predictions, we raised two hypotheses that might be helpful to determine the main influence factors of the efficiency of secondary structure prediction. Experimental results of size and homology reductions of the fundamental protein dataset supported those hypotheses. They revealed that shrinking the size of the dataset could substantially cut down the time cost of prediction with a slight decrease of accuracy, which could be increased on the contrary by homology reduction of the dataset. Moreover, the Shannon information entropy could be applied to explain how accuracy was influenced by the size and homology of the dataset. Based on these findings, we proposed that a proper combination of size and homology reductions of the protein dataset could speed up the secondary structure prediction while preserving the high accuracy of state-of-the-art algorithms. Testing the proposed strategy with the fundamental protein dataset of the year 2018 provided by the Universal Protein Resource, the speed of prediction was enhanced over 20 folds while all accuracy measures remained equivalently high. These findings are supposed helpful for improving the efficiency of researches and applications depending on the secondary structure prediction of proteins. To make future implementations of the proposed strategy easy, we have established a database of size and homology reduced protein datasets at http://10.life. nctu.edu. tw/UniRefNR.
Culture of Unfertilized Embryo Sacs of Pearl Millet - Pennisetum glaucum (L.) R. Br.

The morphology and structure of isolated unfertilized embryo sacs of pearl millet, Pennisetum glaucum (L.) R.Br. is similar to those in situ. In all cultivars a minimum of five intact embryo sacs could be isolated from 30 ovaries per hr. Isolated embryo sacs (30-50%) were viable for four days on MS medium. An increase in the number of polar nuclei was osberved in 15% of the embryo sacs cultured for two - four days on MS + 3.0 mg/l BAP. These results hold promise in generating gynogenetic haploids from some pearl millet cultivars.
Automated anti-Mullerian hormone measurement: data review to provide insights and interpretation

Abstract Objective and Methods: All women seen at the Homerton Fertility Center, London (Site 1, n = 1787) and Hewitt Fertility Center, Liverpool (Site 2, n = 1258) in 15 months had serum AMH measured using the Access 2 fully automated benchtop immunoassay analyzer(Beckman Coulter Inc,) and a subset (n = 2031) were followed up to determine eggs collected and clinical pregnancy rates (CPR). Results AMH results were pooled and a table with 2.5 and 97.5 percentiles for each age group constructed. Based on Youden index, the optimal cut off for low responders (0–3 eggs), was 5.5 pmol/l (87% sensitivity, 55% specificity) and for high responders (>15 eggs) 15.6 pmol/l (78% sensitivity, 57% specificity). AMH correlated with number of eggs collected (r = 0.48) and clinical pregnancies (r = 0.14), (p < .0001). Conclusions The table of AMH levels measured using the Access 2 fully automated immunoassay system according to age may be used as a reference and cutoff levels for high and poor responders are clearly defined to help tailor controlled ovarian stimulation, maximizing efficiency and ensuring patient safety. The use of a random access automated immunoassay system means that blood sampled on arrival can produce an AMH result in 40 mins by the time the subject enters the doctor’s clinic together with other relevant endocrine markers.
Early response of the platypus to climate warming

Combining a climatic envelope modelling technique with more than two centuries (1800–2009) of distribution records has revealed the effects of a changing climate on the egg‐laying monotreme, the platypus, Ornithorhynchus anatinus. We show that the main factor associated with platypus occurrence switched from aquatic habitat availability (estimated by rainfall) to thermal tolerances (estimated by annual maximum temperature) in the 1960s. This correlates directly with the change in the annual maximum temperature anomaly from cooler to warmer conditions in southeastern Australia. Modelling of platypus habitat under emission scenarios (A1B, A2, B1 and B2) revealed large decreases (>30%) in thermally suitable habitat by 2070. This reduction, compounded by increasing demands for water for agriculture and potable use, suggests that there is real cause for concern over the future status of this species, and highlights the need for restoration of thermal refugia within the platypus’ modelled range.
On taxonomic membership

Abstract Taxonomic membership frequencies exhibit distributions in which groups with few numbers of subtaxa are much more common in a clade than those with more subtaxa. Here, a “broken plate” model is developed to describe such taxonomic memberships; some higher taxonomic group (the plate) is randomly subdivided into intermediate taxonomic units (plate fragments), whose sizes are dependent on the number of taxonomic subunits that they each contain. Theoretical distributions of membership frequencies produced by this model yield a superior fit to data from both modern and fossil groups, as illustrated by classifications for primarily fossil brachiopods and entirely modern mammals. The nature of these distributions is consistent with the contention that Linnaean membership frequencies result from the random partitioning of taxonomic/morphologic space. Moreover, numbers of taxa contained within hierarchically equivalent groups are unrelated, as are membership numbers at taxonomically higher and lower levels of consideration. Agreement between observed taxonomic memberships and those anticipated from the random partitioning of diversity as described by the “broken plate” model bears directly on a number of fundamental questions including the significance of extreme polytypy and inferred causes of adaptive radiation within many taxonomic groups.
Screening of an Epigenetic Drug Library Identifies 4-((hydroxyamino)carbonyl)-N-(2-hydroxyethyl)-N-Phenyl-Benzeneacetamide that Reduces Melanin Synthesis by Inhibiting Tyrosinase Activity Independently of Epigenetic Mechanisms

The aim of this study was to identify novel antimelanogenic drugs from an epigenetic screening library containing various modulators targeting DNA methyltransferases, histone deacetylases, and other related enzymes/proteins. Of 141 drugs tested, K8 (4-((hydroxyamino)carbonyl)-N-(2-hydroxyethyl)-N-phenyl-benzeneacetamide; HPOB) was found to effectively inhibit the α-melanocyte-stimulating hormone (α-MSH)-induced melanin synthesis in B16-F10 murine melanoma cells without accompanying cytotoxicity. Additional experiments showed that K8 did not significantly reduce the mRNA and protein level of tyrosinase (TYR) or microphthalmia-associated transcription factor (MITF) in cells, but it potently inhibited the catalytic activity TYR in vitro (IC50, 1.1–1.5 µM) as compared to β-arbutin (IC50, 500–700 µM) or kojic acid (IC50, 63 µM). K8 showed copper chelating activity similar to kojic acid. Therefore, these data suggest that K8 inhibits cellular melanin synthesis not by downregulation of TYR protein expression through an epigenetic mechanism, but by direct inhibition of TYR catalytic activity through copper chelation. Metal chelating activity of K8 is not surprising because it is known to inhibit histone deacetylase (HDAC) 6 through zinc chelation. This study identified K8 as a potent inhibitor of cellular melanin synthesis, which may be useful for the treatment of hyperpigmentation disorders
Joint SVBRDF Recovery and Synthesis From a Single Image using an Unsupervised Generative Adversarial Network

We want to recreate spatially-varying bi-directional reﬂectance distribution functions (SVBRDFs) from a single image. Pro-ducing these SVBRDFs from single images will allow designers to incorporate many new materials in their virtual scenes, increasing their realism. A single image contains incomplete information about the SVBRDF, making reconstruction difﬁcult. Existing algorithms can produce high-quality SVBRDFs with single or few input photographs using supervised deep learning. The learning step relies on a huge dataset with both input photographs and the ground truth SVBRDF maps. This is a weakness as ground truth maps are not easy to acquire. For practical use, it is also important to produce large SVBRDF maps. Existing algorithms rely on a separate texture synthesis step to generate these large maps, which leads to the loss of consistency be-tween generated SVBRDF maps. In this paper, we address both issues simultaneously. We present an unsupervised generative adversarial neural network that addresses both SVBRDF capture from a single image and synthesis at the same time. From a low-resolution input image, we generate a large resolution SVBRDF, much larger than the input images. We train a generative adversarial network (GAN) to get SVBRDF maps, which have both a large spatial extent and detailed texels. We employ a two-stream generator that divides the training of maps into two groups (normal and roughness as one, diffuse and specular as the other) to better optimize those four maps. In the end, our method is able to generate high-quality large scale SVBRDF maps from a single input photograph with repetitive structures and provides higher quality rendering results with more details compared to the previous works. Each input for our method requires individual training, which costs about 3 hours
Molecular Mechanisms of Merkel Cell Polyomavirus Transformation and Replication.

Viral infection underlies a significant share of the global cancer burden. Merkel cell polyomavirus (MCPyV) is the newest member of the human oncogenic virus family. Its discovery over a decade ago marked the beginning of an exciting era in human tumor virology. Since then, significant evidences have emerged to support the etiologic role of MCPyV in Merkel cell carcinoma (MCC), an extremely lethal form of skin cancer. MCPyV infection is widespread in the general population. MCC diagnoses have tripled over the past 20 years, but effective treatments are currently lacking. In this review, we highlight recent discoveries that have shaped our understanding of MCPyV oncogenic mechanism and host cellular tropism, as well as the molecular events occurring in the viral infectious life cycle. These insights will guide future efforts in developing novel virus-targeted therapeutic strategies for treating the devastating human cancers associated with this new tumorigenic virus. Expected final online publication date for the Annual Review of Virology, Volume 7 is September 29, 2020. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Larvicidal, Ovicidal, and Repellent Activities of Marine Sponge Cliona celata (Grant) Extracts against Culex quinquefasciatus Say and Aedes aegypti L. (Diptera: Culicidae)

Solvent extracts of marine sponge Cliona celata (Grant) were screened for larvicidal, ovicidal, and repellent properties against the filarial vector Culex quinquefasciatus Say and dengue vector Aedes aegypti L. Larvicidal and ovicidal activities of hexane, ethyl acetate, and methanol extracts were tested in four different concentrations ranging as 62.5, 125, 250, and 500 ppm. Among the three solvent extracts of C. celata, methanol extract showed the highest larvicidal activity at 500 ppm against both mosquito species. The LC50 and LC90 values of C. celata methanol extract were recorded as 95.63 and 242.16 ppm against C. quinquefasciatus larvae and 158.40 and 780.16 ppm against A. aegypti larvae, respectively. Ovicidal activity was high in methanol extract, in which 100% ovicidal activity was recorded in C. quinquefasciatus, and 72% ovicidal activity was recorded in A. aegypti at 500 ppm. The hexane extract was found to be the most effective protectant against the adult mosquitoes of both species. The mean protection time recorded in hexane extract was up to 273 and 165 min at 5 mg/cm2 dosage against C. quinquefasciatus and A. aegypti, respectively. Considering these bioactivities, C. celata could be used to obtain some novel pesticidal molecules.
Treatment of Panic Disorder and/or Generalized Anxiety Disorder With A Guided Self-Help Manual

The aim of this pilot study was to test the effectiveness and feasibility of a new, guided self-help program in five selected primary care patients with panic disorder (PD) or generalized anxiety disorder (GAD). Most patients achieved a clinically relevant improvement after 12 weeks of treatment with large effect sizes (Cohen's d) on all measures. Two patients could be considered as recovered according to the criteria of Jacobson and Truax (1991). Although all of the patients appeared to improve on all outcome measures, PD was easier to treat than GAD. These results suggest that a guided self-help manual treatment is an effective treatment possibility for PD and GAD in primary care. When these results can be replicated in a controlled trial in a larger sample, guided self-help treatment may be a first-line treatment in general practice in a step-by-step care approach of PD and GAD.
The Effects of UV-A Light Provided in Addition to Standard Lighting on Plumage Condition in Laying Hens

Simple Summary Laying hens, like other poultry species, can perceive ultraviolet radiation; nevertheless, standard lighting in poultry houses does not contain UV-A light (UV). However, little is known about the impact of light quality (daylight spectrum by UV-A light illumination) on plumage loss, skin injuries and the production parameters of laying hens. Presuming that offering a daylight spectrum to hens could help to prevent the loss of feathers and skin damage caused by pecking, about 92,000 Lohmann Brown hens with untrimmed beaks were kept on a farm in different barns. In order to measure effects of a daylight spectrum, half of them were kept in poultry housing illuminated with UV-A light provided in addition to standard lighting. The other half was exposed to standard lighting for poultry houses. The results indicate that separately offered UV-A light alone cannot prevent damage to the hens’ integument caused by pecking. In general, complex interactions in conjunction with UV supplementation influenced the birds’ behavior. In order to promote animal health and welfare, further research is necessary to find out more about the appropriate level of UV supplementation and suitable light sources besides optimum light spectrum. Abstract Natural light with ultraviolet spectrum (UV) influences the birds´ perception, the reflectivity of their plumage and affects bird behavior. Therefore, in Germany, laying hens kept in barns should be provided with daylight inlets. Nevertheless, lighting in laying hen houses with a UV proportion is not common practice and little is known about the detailed effects of UV-A lighting during the entire rearing and production period. The present on-farm study examines the impact of light quality on plumage loss, skin injuries and production parameters of laying hens. Therefore, about 92,000 Lohmann Brown hens with untrimmed beaks were kept on a farm in two different groups. Half of them were housed in a barn containing 10 pens illuminated by additional UV-A light (simulate “daylight spectrum”). The other half in the second barn were equally grouped, but exposed to standard lighting for poultry houses. Health, production parameters and plumage condition were monitored during rearing and production. The study results reveal that additional UV-A light is associated with the occurrence of plumage damage and cannibalistic injuries during production. In all groups, the plumage condition of the hens was intact when the hens started laying and declined with age. Therefore, complex interactions alongside UV illumination, environmental enrichment, feed and feeding strategies as well as other management factors that possibly affected both feather damage and skin injuries must also be taken into account.
Identical Hik-Rre Systems Are Involved in Perception and Transduction of Salt Signals and Hyperosmotic Signals but Regulate the Expression of Individual Genes to Different Extents in Synechocystis*

In previous studies, we characterized five histidine kinases (Hiks) and the cognate response regulators (Rres) that control the expression of ∼70% of the hyperosmotic stress-inducible genes in the cyanobacterium Synechocystis sp. PCC 6803. In the present study, we screened a gene knock-out library of Rres by RNA slot-blot hybridization and with a genome-wide DNA microarray and identified three Hik-Rre systems, namely, Hik33-Rre31, Hik10-Rre3, and Hik16-Hik41-Rre17, as well as another system that included Rre1, that were involved in perception of salt stress and transduction of the signal. We found that these Hik-Rre systems were identical to those that were involved in perception and transduction of the hyperosmotic stress signal. We compared the induction factors of the salt stress- and hyperosmotic stress-inducible genes that are located downstream of each system and found that these genes responded to the two kinds of stress to different respective extents. In addition, the Hik33-Rre31 system regulated the expression of genes that were specifically induced by hyperosmotic stress, whereas the system that included Rre1 regulated the expression of one or two genes that were specifically induced either by salt stress or by hyperosmotic stress. Our observations suggest that the perception of salt and hyperosmotic stress by the Hik-Rre systems is complex and that salt stress and hyperosmotic stress are perceived as distinct signals by the Hik-Rre systems.
Spatial analyses of bottlenose dolphin–fisheries interactions reveal human avoidance off a productive lagoon in the western Gulf of Mexico

Studying interactions between cetaceans and humans is fundamental to assess their ecological significance and the impact of human activities on marine wildlife. Delphinids have historically been associated with human maritime activities, and while evidence suggests that such interactions are becoming more frequent worldwide, these remain poorly studied. Areas of potential interaction and differences in dolphin affinity to interact with humans were used to test hypotheses about the spatial distribution and temporal variation in dolphin–fisheries interactions off the highly productive Alvarado lagoon, in the western Gulf of Mexico. Line-transect surveys yielded 928 dolphin, 980 vessel, and 320 fishing gear target records, the latter involving mostly the shrimp fishery. No temporal differences were found in daily relative abundance of dolphins ( = 8.1 h−1, SD = 9.7), vessels ( = 7.8 h−1, SD = 5.9) or fishing gear ( = 2.4 h−1, SD = 2.6) between two consecutive years. Non-random spatial distributions indicated higher target concentrations at the lagoon entrance; however, dolphins and fishers were found to evade each other, possibly to prevent competition; dolphins only interacted with gillnets (28.6% of vessels and 22.6% of fishing gear). We observed small areas of potentially intentional and random encounters outside the entrance of the lagoon and low or null potential for interactions elsewhere. Only 18.9% of dolphin schools (44.8% of the 172 photo-identified animals) interacted with fisheries mostly by chance. Resident individuals (N = 23) tended to avoid humans, likely in response to negative reinforcement caused by aggressions from fishers. Hence, the potential intentionality of a few individuals to interact with fisheries, show they bare higher risks while attempting to benefit from gillnetted prey. This research unveils the chronic and acute exposure of the dolphin community to artisanal fisheries within the area, having important reciprocal consequences on their distributions and activities.
CLUZH at SIGMORPHON 2020 Shared Task on Multilingual Grapheme-to-Phoneme Conversion

This paper describes the submission by the team from the Institute of Computational Linguistics, Zurich University, to the Multilingual Grapheme-to-Phoneme Conversion (G2P) Task of the SIGMORPHON 2020 challenge. The submission adapts our system from the 2018 edition of the SIGMORPHON shared task. Our system is a neural transducer that operates over explicit edit actions and is trained with imitation learning. It is well-suited for morphological string transduction partly because it exploits the fact that the input and output character alphabets overlap. The challenge posed by G2P has been to adapt the model and the training procedure to work with disjoint alphabets. We adapt the model to use substitution edits and train it with a weighted finite-state transducer acting as the expert policy. An ensemble of such models produces competitive results on G2P. Our submission ranks second out of 23 submissions by a total of nine teams.