Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning optimal decisions with confidence

Significance Popular models for the trade-off between speed and accuracy of everyday decisions usually assume fixed, low-dimensional sensory inputs. In contrast, in the brain, these inputs are distributed across larger populations of neurons, and their interpretation needs to be learned from feedback. We ask how such learning could occur and demonstrate that efficient learning is significantly modulated by decision confidence. This modulation predicts a particular dependency pattern between consecutive choices and provides insight into how a priori biases for particular choices modulate the mechanisms leading to efficient decisions in these models. Diffusion decision models (DDMs) are immensely successful models for decision making under uncertainty and time pressure. In the context of perceptual decision making, these models typically start with two input units, organized in a neuron–antineuron pair. In contrast, in the brain, sensory inputs are encoded through the activity of large neuronal populations. Moreover, while DDMs are wired by hand, the nervous system must learn the weights of the network through trial and error. There is currently no normative theory of learning in DDMs and therefore no theory of how decision makers could learn to make optimal decisions in this context. Here, we derive such a rule for learning a near-optimal linear combination of DDM inputs based on trial-by-trial feedback. The rule is Bayesian in the sense that it learns not only the mean of the weights but also the uncertainty around this mean in the form of a covariance matrix. In this rule, the rate of learning is proportional (respectively, inversely proportional) to confidence for incorrect (respectively, correct) decisions. Furthermore, we show that, in volatile environments, the rule predicts a bias toward repeating the same choice after correct decisions, with a bias strength that is modulated by the previous choice’s difficulty. Finally, we extend our learning rule to cases for which one of the choices is more likely a priori, which provides insights into how such biases modulate the mechanisms leading to optimal decisions in diffusion models.
Identifying Streptococcus pneumoniae genes associated with invasive disease using pangenome-based whole genome sequence typing

Streptococcus pneumoniae is a normal commensal of the upper respiratory tract but can also invade the bloodstream or CSF (cerebrospinal fluid), causing invasive pneumococcal disease (IPD). In this study, we attempt to identify genes associated with IPD by applying a random forest machine-learning algorithm to whole genome sequence (WGS) data. We find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of these genes, 23 genes have previously shown to be directly relevant to IPD, while the other 18 are uncharacterized.
Yield of forage, grain and biomass in eight hybrids of maize with different sowing dates and environmental conditions

The aim was to evaluate yield of forage, grain and biomass and fibre content of eight hybrids of maize (Rio-Grande, Arrayan, Genex 778, Narro 2010, Advance 2203, DAS 2358, P4082W and HT9150W) during two sowing seasons (spring/summer) for two consecutive years at La Laguna in Torreon, Mexico. Once the grain progression of the kernel milk line was ⅓, green forage yield (GFY), dry matter (DM), neutral detergent fiber (NDF) and acid detergent fiber (ADF) were determined. When the corncobs were fully mature, grain yield (GY) and biomass production (TBP) were determined. Weather conditions were recorded during the experiment. The results indicated that maximum temperature was higher and rainfall lower in the summer sowing and second year. Spring sowing had significantly higher yields of GFY, DM, GY and TBP compared to summer sowing. The first year of study showed significantly higher yields regarding GFY, GY and TBP, but FDN, FDA, DM content compared to the second year. The best hybrid for GFY and DM was Rio-Grande; for FDN and FDA was Advance 2203; for GY was HT9150W and finally for TBP was Arrayan. Regardless of the hybrid used and the sowing season, production of maize depended on external factors such as maximum temperature and rainfall; therefore, producers need to consider sowing in spring to avoid the negative effect of high temperatures on plant development.
Ecological tipping points for an invasive kelp in rocky reef algal communities

: Invasive species are affecting coastal ecosystems worldwide and there are many potential mechanisms that allow their spread into native communities. To investigate this phenomenon, we used an experiment in which the canopy of the southern bull kelp Durvillaea ant arctica was removed in 2 seasons and community development was followed over 3 yr. The invasive kelp Undaria pinnatifida recruited almost exclusively into plots from which the natural canopy had been removed. We examined, through a series of regression tree models and change point analyses, the gradients of community responses that allowed the successful recruitment of this invasive species. Analyses revealed a range of coinciding conditions, especially a decline in fucoid cover below 20% and an increase in turf cover above 80%, that facilitated Undaria recruitment. The abundance of molluscan grazers and cover of subcanopy algae had lesser effects on Undaria recruitment. In an ecological sense, there was a clear tipping point in the interaction between canopy loss and the subsequent expansion of coralline turf that allowed communities to switch from dominance by native species to seasonal dominance of Undaria . This study illustrates the complex nature of disturbance thresholds and inter actions within the native communities that can facilitate the spread and recruitment success of Undaria .
Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain

Pain sensing neurons, nociceptors, are key drivers of neuropathic pain. We used translating ribosome affinity purification (TRAP) to comprehensively characterize up-and down-regulated mRNA translation in Scn10a-positive nociceptors in chemotherapy-induced neuropathic pain. We provide evidence that an underlying mechanism driving these changes in gene expression is a sustained mTORC1 activation driven by MNK1-eIF4E signaling. RagA, a GTPase controlling mTORC1 activity, is identified as a novel target of MNK1-eIF4E signaling, demonstrating a new link between these distinct signaling pathways. Neuropathic pain and RagA translation are strongly attenuated by genetic ablation of eIF4E phosphorylation, MNK1 elimination or treatment with the MNK inhibitor eFT508. We reveal a novel translational circuit for the genesis of neuropathic pain with important implications for next generation neuropathic pain therapeutics. One Sentence Summary Cell-specific sequencing of translating mRNAs elucidates signaling pathology that can be targeted to reverse neuropathic pain
Improved prediction of chronological age from DNA methylation limits it as a biomarker of ageing

DNA methylation is associated with age. The deviation of age predicted from DNA methylation from actual age has been proposed as a biomarker for ageing. However, a better prediction of chronological age implies less opportunity for biological age. Here we used 13,661 samples (from blood and saliva) in the age range of 2 to 104 years from 14 cohorts measured on Illumina HumanMethylation450/EPIC arrays to perform prediction analyses. We show that increasing the sample size achieves a smaller prediction error and higher correlations in test datasets. We demonstrate that smaller prediction errors provide a limit to how much variation in biological ageing can be captured by methylation and provide evidence that age predictors from small samples are prone to confounding by cell composition. Our predictor shows a similar or better performance in non-blood tissues including saliva, endometrium, breast, liver, adipose and muscle, compared with Horvath’s across-tissue age predictor.
Plankton Abundance and Physico-chemical Water Quality of Effluent Impacted Waterbodies in Ile-Ife, Nigeria

An effluent receiving stream and Opa River to which it drains within Obafemi Awolowo University, South-Western Nigeria, were studied to ascertain the level of physico-chemical and biological pollution. Water samples were collected and analysed using various standard methods for planktonic abundance and selected physico-chemical parameters over a period of seven months. Most of the water quality parameters investigated showed statistically insignificant differences between the stream and Opa River, except of conductivity, nitrate and turbidity. Notable parameters were nutrient level indicator parameters (conductivity, nitrate, organic matter, COD and planktonic abundance) whose mean concentrations were higher in the effluent receiving stream than in Opa River. Even more, the seasonal variations of some of the investigated parameters (sulphate, organic matter and conductivity) at both sampled stations revealed the effect of anthropogenic run-off as additional source of dissolved nutrient and chemical enrichment rather than the effluent only. Highest occurrence of Chlorophyceae and abundance of Bacillariophyceae in the studied water bodies revealed a level of organic pollution, while the low occurrence species diversity of copepod, cladocera, diptera and protozoa further connotes the unfavourable physico-chemical condition of the water bodies. However, this effect was observed to be reduced at the point where the stream emptied into Opa River. Hence, the effect of the effluent discharge may not pose a health risk to several rural communities downstream which rely on the receiving water body primarily as their source of domestic water. Nevertheless, due to the level of organic pollution recorded, it could be suggested that the oxidation pond effluent discharge should be treated and/or recycled before discharge into this natural body of water.
Development of novel probes for enterovirus B group to study uncoating and infection

Martikainen, Mari Development of novel probes for enterovirus B group to study uncoating and infection Jyväskylä: University of Jyväskylä, 2012, p. (Jyväskylä Studies in Biological and Environmental Science ISSN 1456-9701; 325) ISBN 978-951-39-6867-0 (nid.) ISBN 978-951-39-6868-7 (PDF) Yhteenveto: Uudenlaisten markkereiden kehittäminen enterovirus B ryhmän virusten kapsidin aukeamisen ja infektion tutkimiseen Diss. Enterovirus B group (EV-B) viruses are important human pathogens which cause a variety of diseases from mild respiratory illnesses to more severe acute infections such as myocarditis and meningitis. EV-Bs have also been associated with chronic infections and autoimmune diseases such as type I diabetes. Because of their significance, better and more accurate methods are necessary to track and visualize viruses in vitro and in vivo. This thesis focus on the development of novel probes to label viruses site-specifically and track infection in vitro. First, we established a covalent conjugation between gold nanocluster markers and EV-B viruses. We were able to visualize through electron microscopy site-specific labelling of cysteines on the viral capsid surface. Second, we developed probes targeted to the hydrophobic pocket of the enterovirus capsid. The probes were synthesized based on a hydrophobic pocket binding drug pleconaril. Successful binding of the probe was confirmed with nuclear magnetic resonance measurements. The probe was conjugated to a fluorescent KU Orange 2 dye or Au102 gold nanocluster, and further studied by confocal and electron microscopy. The third section of this thesis studied the infectious entry pathway of three different coxsackievirus B1 (CVB1) strains. All of the studied strains appeared to use the previously suggested EV-B group entry pathway: macropinocytic entry dependent on Na+/H+ and Rac1 and independent of acidification. However, strain specific kinetic differences in the infection of nonpolarized cells were revealed. Importantly, one of the CVB1 strains infected cells independently from endosomal sorting complexes required for transport (ESCRT) driven multivesicular bodies (MVBs), and initiated the virus uncoating with slower kinetics. The results indicate that the ESCRT driven biogenesis of MVBs is required for efficient uncoating and infection. Thus, the viruses show remarkable similarities to other well studied EV-B viruses.
In vitro somatic embryogenesis of high yielding varieties of rice ( Oryza sativa L.)

Rice ( Oryza sativa L.) belongs to the family Gramineae and is the staple food for half of the world’s population and occupies almost one-fifth of the total land area covered under cereals. Now-a-days, the production of rice is hampered due to climatic changes. Therefore, it is essential to develop variety which is tolerant to abiotic and biotic stresses. The present investigation was conducted to establish an efficient and simple protocol for regeneration of four agronomically important indica rice varieties (Khandagiri, Udayagiri, Swarna and Pratikhya). Somatic embryogenesis were achieved from immature zygotic embryos on Murashige and Skoog (MS) medium supplemented with 3 mg/l 2,4-D (2,4-dichlorophenoxyacetic acid), 1.0 mg/l kinetin and 3% (w/v) sucrose within 4 weeks of culture. The secondary somatic embryogenesis was also achieved in subsequent subculture on MS medium supplemented with 2 mg/l 2,4-D and 2.0 mg/l kinetin and 200 mg/l L-proline. The percentage of embryogenic calli proliferation were 82.4, 83.7, 88.4 and 84.4 in variety Khandagiri, Udayagiri, Swarna and Pratikhya respectively on MS basal medium supplemented with 3.0 mg/l 2,4-D, 2.0 mg/l Kinetin and 200 mg/l L-proline. Inclusion of higher concentration of L-proline (400 mg/l) in the induction medium, the growth of calli was reduced. The maximum percentage of somatic embryo germination took place in medium supplemented with 2.0 mg/l kinetin, 0.25 mg/l NAA and 50 mg/l adenine sulfate within 4 weeks of culture. The regenerated plantlets were transferred to pots for acclimatization. About 80% of plants were survived in the greenhouse condition. Keywords: Somatic embryogenesis, immature zygotic embryos, Indica rice, plant regeneration African Journal of Biotechnology Vol. 12(42), pp. 6113-6118
Spatial scale dependence of factors driving climate regulation services in the Americas

Aim: A key hypothesis in macroecology is that the relative importance of factors driving ecological phenomena changes with spatial scale. However, studies on ecosystem services usually ignore this. Here, we test how the importance of factors related to climate regulation services varies with spatial extent (i.e., area of assessment) and how covariation among factors affects scale dependencies. Location: The Americas. Time period: Present. Major taxa studied: Plants. Methods: We combined a multi‐model inference framework with variance partitioning to quantify the importance of factors that could potentially influence climate regulation services (i.e., albedo, evapotranspiration and primary productivity). We quantified abiotic (climate, soil, heterogeneity in soils/topography), biotic (open vegetation, forest area and biomass, plant functional traits) and anthropogenic (forest fragmentation, managed vegetation, non‐vegetated surfaces) conditions and tested their importance in relation to climate regulation services at spatial extents ranging from 9 × 103 to 1 × 106 km2. Results: We found that the importance of abiotic factors in relation to climate regulation services increases with spatial extent. However, we found no evidence for a change from primarily biotically to abiotically driven climate regulation services with increasing spatial extent. All spatial extent dependencies were heavily influenced by covariation between abiotic, biotic and anthropogenic factors. After accounting for covariation, we found a primacy of abiotic factors as drivers of climate regulation services across spatial extents. Biotic and anthropogenic factors were less important than abiotic factors, and their independent effects were conserved across spatial extents. Main conclusions: Our results show that the relative importance of abiotic factors related to climate regulation services depends on spatial extent. Biotic and anthropogenic factors are less important for climate regulation services than abiotic factors, and this hierarchy is scale invariant. Our findings suggest that spatial extent dependence needs to be quantified and assessed in climate‐change mitigation projects that focus on ecosystem services.
Neuropeptidergic regulation of mosquito host-seeking behaviour

Mosquitoes are vectors of numerous pathogens that cause human diseases, putting more than half of the world’s population at risk. These diseases are transmitted when a mosquito takes a blood meal following the successful seeking of a human host. Hostseeking is highly state dependent and predominantly mediated by olfactory cues. The goal of this thesis is to describe the neuropeptidergic regulation of the state dependent odour-mediated host-seeking behaviour. In order to identify and characterize the neuropeptides that are modulated by feeding and are involved in host-seeking, I analysed the antennal lobes, the primary olfactory centre, of Aedes aegypti, using semi-quantitative MALDI-TOF mass spectrometry. Functional evidence for the involvement of the identified neuropeptides in the regulation of host-seeking was provided using neuropeptide injections. I demonstrated that short neuropeptide F-2 (sNPF-2) and allatostatin-A-5 (AstA-5) are regulated upon blood feeding and that the injection of a binary mix of sNPF-2 and AstA-5 inhibited host-seeking in non-blood fed mosquitoes, mimicking the effect of a blood meal. I next characterized the sNPF and AstA receptors (sNPFR and AstAR) from Ae. aegypti and two other important disease vectors, Culex quinquefasciatus and Anopheles coluzzii assessing the receptor conservation and function as well as the regulation of the receptors in response to blood feeding. Within the AstA signalling system, I described a dipteran-specific duplication of the AstARs (R1 and R2) in mosquitoes. Functional characterization revealed that the AstAR2s show a higher sensitivity to AstAs compared to AstAR1s in the culicine mosquitoes Ae.aegypti and Cx. quinquefasciatus. In contrast, both AstARs in An. coluzzii showed a similar sensitivity to the AstA ligands, which suggests a divergence in the AstA signalling in mosquitoes. This is in contrast to the sNPFRs in the three species, which showed a high conservation in structure and receptor sensitivity. Blood feeding results in a selective regulation of transcript abundance of the more sensitive AstAR2 and the sNPFR in Cx. quinquefasciatus, but not in Ae. aegypti or An. coluzzii. This is indicative of differences in the regulatory mechanisms for AstA and sNPF in Cx. quinquefasciatus compared with the other species. In this thesis, I provide strong evidence that host-seeking is regulated by complex mechanisms involving at least two neuropeptidergic systems. These findings may shed new light on previous results and should encourage further investigation of other neuropeptide families. The functional characterization of the AstA and sNPF receptors leads to a better understanding of the conservation and regulation of neuropeptide signalling system and provides new targets for future research.
Genetic analysis and meiotic role of the Saccharomyces cerevisiae RecQ helicase SGS1

SGS1, a Saccharomyces cerevisiae 3 '-5 ' DNA helicase, is a homologue of the Escherichia coli RecQ gene. It is essential for genomic stability both during mitosis and meiosis. The purpose of this thesis is to provide a better understanding of the role of this helicase during meiotic recombination. In meiosis, SGS1 mutant cells display a decrease in sporulation efficiency and spore viability. In addition, the unusual spore viability pattern observed in SGS1 mutants cannot be explained solely by meiosis I or meiosis II missegregations. These problems could be partially explained by defects in mitotic chromosome segregation or problems with meiotic S-phase. Cytological experiments demonstrating an increase in synapsis initiation complexes and axial associations in sgslA could be explained by an early function of Sgslp in meiosis, such as the unwinding of inappropriate strand invasion events. Consistent with this, we observed increased gene conversion, increased homeologous recombination and increased interaction between sister chromatids. Recent observations have suggested that, Sgslp and Top3p in S. cerevisiae, and the human orthologue protein BLM, in conjunction with the Top3a protein, can dissolve double Holliday junctions. Physical analyses of double-strand break repair in meiosis, combined with the genetic analysis of this work, indicate a late function of the Sgsl protein in the dissolution of double Holliday junctions. We have shown an unusual class of tetrads in which non-sister spores and recombinant spores are dead. We interpret this as a consequence of the failure to untangle intertwined chromatids. This defect in SGS1 mutant strains could be explained by either the presence of pre-meiotic S-phase catenates, a defect in crossover resolution and/or a defect in the dissolution of closely spaced double Holliday junctions.
Toxicity studies and body weights changes in Wistar rats following oral administration of methanol extract from indigenous ganoderma sp.in Nigeria

Submit Manuscript | http://medcraveonline.com Health Organization reporting that over 80 % of the world’s population still relies on herbal medicine as their primary source of healthcare, and with millions of Africans of all ages relying on herbal medicines for primary healthcare [1]. Which underscores the importance of herbal medicine in healthcare delivery system. Despite these, little effort is being made to apply traditional medicine into Veterinary practice [2] beyond its use by herdsmen. Although, traditional medicine can be a source of medication to widen the therapeutic arsenal against range of diseases, [3,4], it is important to know that plants produce diverse array of chemical substances that may form the basis for their use in traditional medicine to treat variety of disease conditions, and can therefore, be an enormous potential source of raw material for new chemotherapeutic agents [5]. However, these chemicals produced by plants can have other unwanted pharmacological effects on some tissues, haematological parameters and other indices of production. Among a range of plants that are currently being investigated for there medicinal properties is the mushroom, Ganoderma lucidum. The evaluation of toxic activities of this mushroom is important in order to consider safe preparations that can enable the definition of the intrinsic toxicity and the effects the acute and sub acute dose of the mushroom has on its consumers [6]. Although, extracts of this mushroom is reported to possess a number of pharmacologically active phytochemicals and elements [7] with evidence of a lot of medicinal properties [8-14], it was also reported to have unwanted toxicological effects on internal organs such as liver, kidneys, lungs, spleen and the heart [15]. Preparations of this mushroom are used as tea or components of immune boosters (immunoboostR) and as other antioxidant supplement. This study is therefore important, to evaluate the acute and sub acute toxic effects of extracts of this mushroom.