Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating the temporal autocorrelation of demographic rates into structured population models

Population dynamics are typically temporally autocorrelated: population sizes are positively or negatively correlated with past population sizes. Previous studies have found that positive temporal autocorrelation increases the risk of extinction due to ‘inertia’ that prolongs downward fluctuations in population size. However, temporal autocorrelation has not yet been analyzed at the level of life cycle transitions. We developed an R package, colorednoise, which creates stochastic matrix population projections with distinct temporal autocorrelation values for each matrix element. We used it to analyze long‐term demographic data on 25 populations from the COMADRE and COMPADRE databases and simulate their stochastic dynamics. We found a broad range of temporal autocorrelation across species, populations and life cycle stages. The number of stage‐classes in the matrix strongly affected the temporal autocorrelation of the growth rate. In the plant populations, reproduction transitions had more negative temporal autocorrelation than survival transitions, and matrices dominated by positive temporal autocorrelation had higher extinction risk, while in animal populations transition type was not associated with noise color. Our results indicate that temporal autocorrelation varies across life cycle transitions, even among populations of the same species. We present the colorednoise package for researchers to analyze the temporal autocorrelation of structured demographic rates.
Imitation as a model-free process in human reinforcement learning

While there is not doubt that social signals affect human reinforcement learning, there is still no consensus about their exact computational implementation. To address this issue, we compared three hypotheses about the algorithmic implementation of imitation in human reinforcement learning. A first hypothesis, decision biasing, postulates that imitation consists in transiently biasing the learner’s action selection without affecting her value function. According to the second hypothesis, model-based imitation, the learner infers the demonstrator’s value function through inverse reinforcement learning and uses it for action selection. Finally, according to the third hypothesis, value shaping, demonstrator’s actions directly affect the learner’s value function. We tested these three psychologically plausible hypotheses in two separate experiments (N = 24 and N = 44) featuring a new variant of a social reinforcement learning task, where we manipulated the quantity and the quality of the demonstrator’s choices. We show through model comparison that value shaping is favored, which provides a new perspective on how imitation is integrated into human reinforcement learning.
Impact of early childhood malnutrition on the adult brain function: an ERP study

According to the World Health Organization, 45% of deaths among children under 5 years of age are caused by childhood malnutrition, which affects 224 million children worldwide. The Barbados Nutrition Study (BNS) is a 50+year longitudinal study on a Barbadian cohort (N=258) with histories of moderate to severe protein-energy malnutrition (PEM) in the first year of life and healthy controls. Interestingly, a recent BNS publication used quantitative electroencephalography (EEG) to show differences in brain function (lower alpha1 activity and higher theta, alpha2 and beta activity) in children who suffered from early PEM compared to healthy controls. However, the adult brain function following early childhood PEM has not been reported in this cohort. In the current study, EEG recordings were undertaken during a Go-No-Go task on a subsample of the BNS cohort (n=55) at ages 45-51 years. Evoked-related potentials (ERP) analyses show that, compared to the control group (n=29), participants with histories of early PEM (n=24) presented with lower N2 amplitudes and a higher omission error rates, associated with conflict monitoring and attention deficits, respectively. These results may be linked to the attention and executive impairments that have been previously reported in this cohort.
Malaria parasite immune evasion and adaptation to its mosquito host is influenced by the acquisition of multiple blood meals

A minimum of two blood meals are required for a mosquito to acquire and transmit malaria, yet Anopheles mosquitoes frequently obtain additional blood meals during their adult lifespan. To determine the impact of subsequent blood-feeding on parasite development in Anopheles gambiae, we examined rodent and human Plasmodium parasite infection with or without an additional non-infected blood meal. We find that an additional blood meal significantly reduces P. berghei immature oocyst numbers, yet does not influence mature oocysts that have already begun sporogony. This is in contrast to experiments performed with the human parasite, P. falciparum, where an additional blood meal does not affect oocyst numbers. These observations are reproduced when mosquitoes were similarly challenged with an artificial protein meal, suggesting that parasite losses are due to the physical distension of the mosquito midgut. We provide evidence that feeding compromises the integrity of the midgut basal lamina, enabling the recognition and lysis of immature P. berghei oocysts by the mosquito complement system. Moreover, we demonstrate that additional feeding promotes P. falciparum oocyst growth, suggesting that human malaria parasites exploit host resources provided with blood-feeding to accelerate their growth. This contrasts experiments with P. berghei, where the size of surviving oocysts is independent of an additional blood meal. Together, these data demonstrate differences in the ability of Plasmodium species to evade immune detection and adapt to utilize host resources at the oocyst stage, representing an additional, yet unexplored component of vectorial capacity that has important implications for transmission of malaria.
The Effect of Hat on Phototherapy-Induced Hypocalcemia in Icteric Newborns

Background & Aim: Phototherapy plays a significant role in the treatment and prevention of hyperbilirubinemia in neonates. However, this treatment modality may itself result in the development of some complications. A lesser-known complication of the phototherapy is hypocalcemia. Some studies reported hypocalcemia accompanied by a decrease in serum melatonin concentration, yet this effect can be prevented by shielding the occiput. The aim of the present study was determining the prevalence of phototherapy-induced hypocalcemia and comparing its incidence between a group of neonates whose heads were covered during phototherapy and a group of neonates who received phototherapy without hat. Patients and Method: In a randomized clinical trial, 120 icteric neonates were evaluated in two groups of 60. All of the subjects were full term and weighed more than 2500 grams. For group A routine phototherapy was done without shielding the head and the second group(B) used hats that covered occipital area. All neonates were completely normal on physical examination. Serum bilirubin and calcium was checked on arrival, 48 hours after starting phototherapy, and 24 hours after discontinuation of the treatment. Group A was considered as the control group. A comparative study was made between these groups to determine the efficacy of hat for prevention of hypocalcemia. Results: 18 neonates(15%) developed hypocalcemia after starting phototherapy. There was a statistically significant difference between the prevalence of hypocalcemia in group A(77.77%) and group B(22.22%)(p=0.000). None of the hypocalcemic neonates was clinically symptomatic. Serum level of calcium returned to normal 24 hours after discontinuation of phototherapy in almost all hypocalcemic neonates. Conclusion: The study showed that covering neonate's head and occipital area during phototherapy decreases phototherapy-induced hypocalcemia.
Genome-wide Analysis In Response to N and C Identifies New Regulators for root AtNRT2 Transporters

In Arabidopsis thaliana, the High-Affinity Transport System (HATS) for root NO3- uptake depends mainly on four NRT2 transporters, namely NRT2.1, NRT2.2, NRT2.4 and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways have been shown to control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 genes expression to the interaction of these signals has never been specifically investigated and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4 and NRT2.5 in response to N/C signals. Our systems analysis of the data highlighted the potential role of three putative transcription factors, TGA3, MYC1 and bHLH093. Functional analysis of mutants combined with yeast one hybrid experiments confirmed that all 3 transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. One sentence summary Identification of three transcription factors involved in the regulation of NRT2s transporters using a systems biology approach and NRT2.1 as target gene in response to combinations of N/C treatments
The biological control of the grapevine downy mildew disease using Ochrobactrum sp.

Grape downy mildew, caused by Plasmopara viticola (Berk. & M.A. Curtis) Berl. & De Toni 1888, is a widespread fungal disease that causes serious harm to the grape production. The long-term continuous use of chemical pesticides has caused issues with the resistance, residues and resurgence, as well as creating environmental pollution and the declining quality of the products. A biological control offers a safe and effective method to control diseases. We determined the in vitro antagonistic activity of 303 bacterial strains from infected grapevine leaves, and 12 isolates showed some level of antagonism in a detached leaf assay. Isolate SY286 reduced the disease severity in the detached leaves by 93.18%, and showed good control effects in a field assay. The scanning electron microscopy showed the damaged P. viticola cell walls when the mycelia and sporangia were treated with the fermentation liquor of isolate SY286. Furthermore, it showed an antagonistic activity against Phytophthora capsici, Phytophthora infestans, Botrytis cinerea, Fusarium oxysporum, Colletotrichum orbiculare, Trichothecium roseum, and Botryosphaeria berengeriana. The isolate was identified as Ochrobactrum sp. combined with its morphological characteristics, physiological and biochemical reactions and 16S rDNA sequence analysis, and it has the potential to control the grapevine downy mildew.
Evaluation of red rice genotypes against brown planthopper, BPH (Nilaparvata lugens Stal.) by phenotypic analysis and study of mechanism of resistance involved

Red rice genotypes are characterized by their huge nutritional values. Apart from this property, they also possess valuable sources of resistance to many biotic and abiotic stresses. In the present investigation, a total of 215 red rice accessions collected from north east and other parts of India were screened for their resistance against brown plant hopper (BPH) at National Rice Research Institute (NRRI), Cuttack by following modified screening technique. The results showed, among 215 genotypes, 4 were highly resistant, 11 were resistant and 13 were moderately resistant against BPH. The rest 187 genotypes were either susceptible or highly susceptible. The mechanism of resistance in these identified lines was studied. The nymphal survivility and development was lower in resistant genotypes (Mata Meher 43.33%) after 5day of release as compared to susceptible check TN-1 (100% survivility). Similarly the nymphal developmental period was less in resistant lines than TN-1 (100% nymphs were developed in to adult) after 15 days of release. The highly resistant genotype Matameher has shown lowest FPLI index (6.75) as compared to resistant(R), moderately resistant (MR) and susceptible (S) reactions.
Quantitative properties of a feedback circuit predict frequency-dependent pattern separation

Feedback inhibitory motifs are important for pattern separation in several species. How feedback circuits implement pattern separation of biologically plausible, temporally structured input in mammals is poorly understood, partly because the spatiotemporal organization of the net output of these circuits has not been characterized. We have quantitatively determined key properties of net feedback inhibition in the mouse dentate gyrus, a region critically involved in pattern separation. Feedback inhibition is recruited steeply with a low dynamic range (0 to 4% of active GCs), and with a non-uniform spatial profile. Additionally, net feedback inhibition shows frequency-dependent facilitation, driven by strongly facilitating mossy fiber inputs. Computational analyses show a significant contribution of the feedback circuit to pattern separation of theta modulated inputs, even within individual theta cycles. Moreover, pattern separation was selectively boosted at gamma frequencies, in particular for highly similar inputs. This effect was highly robust, suggesting that frequency dependent pattern separation is a key feature of the feedback inhibitory microcircuit.
Screening for susceptibility and tolerance to Meloidogyne incognita and M. javanica in okra cultivars in Iraq

Kandouh, B.H. , A.E. Hasan, A.M. Abd-Al-Rasoul and B.S. Sipes. 2019. Screening for susceptibility and tolerance to Meloidogyne incognita and M. javanica in okra cultivars in Iraq. Arab Journal of Plant Protection, 37(3): 279-285. Ten okra cultivars were screened for their susceptibility and resistance/tolerance to the root-knot nematodes Meloidogyne incognita and M. javanicain in a two-trial experiment under ambient conditions. 14 days old okra seedlings were inoculated with 3000 egg/J2 of M. incognita or M. javanica. The nematode reproduction factor (Rf) was used to determine susceptibility or resistance among tested cultivars, and cultivars were considered highly susceptibleif Rf ≥ 2, susceptible if 2 >Rf ≥ 1 and resistant if Rf< 1. Whereas, magnitude of reduction in plant shoot weight (ShW) over the control indicated tolerance and the categories tolerant, moderately tolerant and intolerant were established, when ShW reduction was <10%, 10-20% and >20%, respectively. Most of the cultivars tested were susceptible at various levels. Although Rf of M. javanica was always higher than that of M. incognita, but the plant growth (Shoot weight) was rather more highly affected by M. incognita than by M. javanica. Lahluba was the only resistant cv. to both nematode species, tolerant to M. javanica but intolerant to M. incognita (>30% ShW reduction). Taiwan Hybrid F1 was resistant/intolerant (shoot and root weight were decreased) to M. javanica and susceptible/moderately tolerant to M. incognita. Although M. incognita infected Musoliya, it showed high rates of egg masses (EMR) and galling (GR), thus it was moderately resistant and highly tolerant. Betraa was the most susceptible to both nematode species with moderate tolerance to M. javanica and intolerant to M. incognita. Clemson Spineless was susceptible/tolerant to M. incognita despite of EMR, GR and Rf high values. All the other cultivars failed in the category of susceptible/intolerant. The galling index did not always reflect the reproduction index or the rate of shoot weight reduction. Nematode reproduction Rf was reliable as susceptibility-resistance indicator as well as the extent of ShW reduction for tolerance assessment. The severe root weight reduction due to nematode infection may also indicate plant intolerance. Different levels of resistance and tolerance to nematode infection can be found among okra varieties. Selecting okra cultivars resistant and tolerant to Meloidogyne spp. is an effective approach to maintain high yield, mitigate yield costs and manage the nematode population.
Studies on the chemical constituents of Opuntia vulgaris

The seven compounds of Opuntia vulgaris were obtained and identified as: beta-sitosterol (I); stigmasterol (II); opuntiol (III); stearic acid (IV); stigmast-3, 6-dione (V); daucosterol (VI); beta-D-glucuse (VII). Seven compounds were isolated from this plant for the first time.
Role of the central junction in folding topology of the protein-free human U2–U6 snRNA complex

Intron removal during splicing of precursor pre-mRNA requires assembly of spliceosomal small nuclear (sn)RNAs into catalytically competent conformations to promote two transesterification reactions. U2 and U6 snRNA are the only snRNAs directly implicated in pre-mRNA splicing catalysis, but rearrangement and remodeling steps prior to catalysis require numerous proteins. Previous studies have shown that the protein-free U2-U6 snRNA complex adopts two conformations characterized by four and three helices surrounding a central junction in equilibrium. To analyze the role of the central junction in positioning the two helices critical for formation of the active site, we used ensemble time-resolved fluorescence resonance energy transfer to measure distances between fluorophores at selected locations in constructs representing the protein-free human U2-U6 snRNA complex. Data describing four angles in the four-helix conformer suggest the complex adopts a tetrahedral geometry; addition of Mg2+ results in shortening of the distances between neighboring helices, indicating compaction of the complex around the junction. In contrast, the three-helix conformer shows a closer approach between the two helices bearing critical elements, but addition of Mg2+ widens the distance between these stems. Presence of Mg2+ also enhances the steady state fraction of the three-helix conformer found to be active in spliceosomes. Although the central junction assumes a significant role in orienting helices, in neither conformer, with or without Mg2+, are the critical helices positioned sufficiently close to favor interaction, implying that a major role of spliceosomal remodeling proteins is to overcome such distances to create and stabilize a catalytically active fold.
An Angiosperm Species Dataset Reveals Relationships between Seed Size and Two-Dimensional Shape

Datasets containing information on seed size have been published and are currently available. Nevertheless, there is a lack in the literature of a dataset dedicated to seed shape. We present a preliminary version for a dataset on seed morphology based on a comparison of seed shape with geometric figures. Similarity of the outline of seed images with geometric models is considered as a basis to classify seeds according to the geometric figures they resemble (e.g., ellipse, oval, cardioid). This allows, first, the classification of plant species according to their geometric type of seed, and second, seed shape quantification. For each seed image, the percent of similarity of their outline with a geometric figure can be calculated as a J index. Similarity in absolute terms is considered only when the J index >90. This criterion is important to avoid ambiguity and increase discrimination. The dataset opens the possibility of studying the relationship between seed shape and other variables such as seed size, genome complexity, life form or adaptive responses.
TRPA1 expression provides new insights into thermal perception by the sea urchin Strongylocentrotus intermedius

Abstract Thermal perception is crucial for the fitness of marine invertebrates in intertidal and shallow waters. TRPA1 is a non-selective cation channel that belongs to the TRP family with pivotal roles in initiating signal transduction of thermal perception. We investigated expression patterns of SiTRPA1 in different tissues (tube feet, coelomocytes, gonads and gut) of the sea urchin Strongylocentrotus intermedius. SiTRPA1 expression patterns under acute and long-term temperature stimuli were investigated in tube feet of sea urchins. In the present study, the highest expression of SiTRPA1 was detected in tube feet of S. intermedius. The SiTRPA1 expression level in tube feet were significantly 235.7-fold, 450.0-fold and 3299.7-fold higher than those in the coelomocytes, gonads and gut (df = 3, F = 47.382, P < 0.001). Expression levels of SiTRPA1 in the other tissues (coelomocytes, gonads and gut) were not significantly different (df = 3, F = 47.382, P = 0.972). There was no significant difference of SiTRPA1 expression among all groups in the acute temperature increase experiment (df = 4, F = 0.25, P = 0.902). In the acute temperature decrease experiment, the expression of SiTRPA1 showed no significant difference among all groups (df = 4, F = 1.802, P = 0.205). With long-term exposure (6 weeks) to different temperatures, SiTRPA1 expression in the low temperature group (10°C) was significantly higher than those in the high temperature (20°C) and the control groups (15°C) (df = 2, F = 9.57, P = 0.014). There was no significant difference of SiTRPA1 expression between the high temperature (20°C) and the control temperature (15°C) groups (df = 2, F = 9.57, P = 0.808). These results indicate that SiTRPA1 expression significantly responds to long-term low temperature but not to acute temperature decrease. The present study provides new insights on the distribution and temporal expression of TRPA1 in marine invertebrates after acute and long-term temperature stimuli.
Identifying density-dependent interactions in collective cell behaviour

Scratch assays are routinely used to study collective cell behaviour in vitro. Typical experimental protocols do not vary the initial density of cells, and typical mathematical modelling approaches describe cell motility and proliferation based on assumptions of linear diffusion and logistic growth. Jin et al. (2016) find that the behaviour of cells in scratch assays is density dependent, and showed that standard modelling approaches cannot simultaneously describe data initiated across a range of initial densities. To address this limitation, we calibrate an individual based model to scratch assay data across a large range of initial densities. Our model allows proliferation, motility and a direction bias to depend on interactions between neighbouring cells. By considering a hierarchy of models where we sequentially remove interactions, we perform model selection analysis to identify the minimum interactions required for the model to simultaneously describe data across all initial densities. The calibrated model is able to match the experimental data across all densities and captures details about the spatial structure of cells. Our primary findings provide strong evidence to suggest that motility is density-dependent in these experiments. On the other hand, we do not see the effect of crowding on proliferation in these experiments. These results are significant as they are precisely the opposite of the assumptions in standard continuum models, such as the Fisher-Kolmogorov equation and generalisations of the Fisher-Kolmogorov equation.