Miracle-dz/UniFAR-FTUs huggingface dataset:
ULF waves at comets Halley and Giacobini-Zinner: Comparison with simulations

This paper compares observations and numerical simulations of magnetic fluctuations near the proton and water group ion cyclotron frequencies as a function of distance from the comets Giacobini-Zinner and Halley. Because the Doppler shift of the ion cyclotron resonance is equal and opposite to that associated with the flow of the solar wind plasma past the observer, one can monitor the amplitude of waves due to different cyclotron resonant instabilities by examining the amplitude of waves near the gyrofrequency of the respective ions as measured in the spacecraft frame. This expectation has been checked by comparison of the data to results of a one-dimensional electromagnetic hybrid simulation of two-ion pickup. Distant from both comets the wave amplitudes are very weak. But as the comet is approached, the wave amplitude grows. These observations are consistent with computer simulations which predict amplitudes that depend on the properties of the injected beams and the local injection rate. {copyright} American Geophysical Union 1989
A life-history perspective on the evolutionary interplay of sex ratios and parental sex roles

Parental care is one of the most diverse social behaviours, and caring by the male, female or both parents is essential for successful reproduction of many organisms. Theoretical and empirical studies suggest that parental sex roles are associated with biased sex ratios. However, there is considerable debate on the causal relationship between parental sex roles and sex ratio biases and on the relative importance of the operational sex ratio (OSR), the adult sex ratio (ASR), and the maturation sex ratio (MSR). Here we use individual-based evolutionary simulations to investigate the joint evolution of sex-specific parental behaviour and the various sex ratios in several life history scenarios. We show that sex differences in maturation time or mortality rates at various life-history stages predict the evolution of parental sex roles relatively well: typically, but not always, parental care is biased toward the sex with the lower mortality or the faster maturation. The association of parental sex roles with the various sex ratios is more intricate. In our simulations, the operational sex ratio at evolutionary equilibrium was typically biased toward the less-caring sex. However, the direction and strength of OSR biases often changed drastically in the course of evolution, implying that, rather than being a driver of parental sex roles, OSR biases emerge as a consequence of sex-biases in parental care. When the MSR or the ASR is biased, this bias is generally associated with a bias in parental care: the overrepresented sex does most of the caring. However, the opposite pattern (that the underrepresented sex did most of the caring) also occurs in some scenarios. Moreover, pronounced parental sex roles may also evolve in the absence of an MSR or ASR bias. Taken together, we conclude that none of the sex ratios can be viewed as drivers of a parental care bias; they rather co-evolve with parental care bias in a subtle manner.
Long-range inhibitory axons from medial entorhinal cortex target lateral entorhinal neurons projecting to the hippocampus

Functionally distinct information encoded by the two main divisions of the entorhinal cortex (EC), the lateral EC (LEC) and the medial EC (MEC), is thought to be first integrated at the level of the hippocampus. Here we examine a circuit connecting MEC to LEC that supports functional interplay at the level of the two entorhinal domains. Using a combination of anatomical, in vitro electrophysiological and behavioral experiments in the mouse, we report that axons from MEC somatostatin-expressing GABAergic neurons densely distribute in layer I of LEC, where they drive strong and near selective inhibition of principal neurons in layer IIa. This inhibitory pathway is accompanied by MEC glutamatergic axons that innervate multiple layers of LEC and preferentially synapse onto principal neurons in layers IIb and III. Our findings indicate that excitatory and inhibitory projections from MEC may separately regulate the activity of different populations of hippocampal-projecting principal neurons in LEC.
NetworkExtinction: an R package to simulate extinction’s propagation and rewiring potential in ecological networks

Earth’s biosphere is currently undergoing drastic reorganisation as a consequence of the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, subsequently leading to secondary extinctions, exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for direct simulation and quantification of extinction cascades and the creation of novel interactions (i.e. rewiring) remains absent. Here, we present NetworkExtinction - a novel R package which we have developed to explore the propagation of species extinctions sequences through ecological networks as well as quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction we have integrated ecological theory and computational simulations to develop functionality with which users may analyze and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions while allowing for user-specified secondary extinction thresholds and realisation of rewiring potential. With the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In-built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can define the degree distribution of the network by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analyzing a Chilean coastal marine food web. NetworkExtinction is a compact and easy-to-use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds, and rewiring potential. Therefore, this package is particularly useful to evaluate ecosystem responses to anthropogenic and environmental perturbations that produce non-random species extinctions.
Public perceptions, knowledge and factors associated with the acceptability of genetically modified foods in Kampala city, Uganda

Food is a basic human need important for the survival of all human beings. The rapidly growing world population puts pressure on food sources, inviting the need to devise mechanisms to sustain it. Biotechnology has developed important measures for improving plants and livestock as a remedy for food security with aim to achieve the Sustainable Development goal two (2). Globally, the adoption and use of genetically modified foods (GMFs) has been controversial as it is in Uganda today due to concerns related to the risk uncertainties. This study was therefore conducted to assess the public perceptions, knowledge and factors that influence the acceptability of genetically modified foods in Kampala City. This was a cross sectional quantitative study that involved one hundred and ninety-eight participants. The data were collected using a survey tool and summarized using descriptive and linear regression analysis. The findings of this study showed that almost two-thirds of participants (129/198, 65%) had some basic knowledge on genetically modified foods. About 45.3% (90/198) of the participants perceived genetically modified foods as being unsafe for human consumption. Eighty-eight participants (44.3%) perceived them as being associated with major human health and environmental safety concerns. The acceptability of these foods was significantly associated with gender, education level, nutritional value and health effects. Female participants were more likely to accept genetically modified foods (OR.4.84 95% CI: 1.37 - 7.68). Those who perceived genetically modified foods as being of high nutrition value were more likely to accept them (OR. 3.07, 95% CI: 1.27 - 7.37). The public is predominantly aware of genetical modified foods since a big proportion had basic knowledge about them although with a lot of misinformation. People with a higher education level had positive perceptions on the use of these foods hence a need to educate the public to dispel misinformation that influences their acceptability
The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells

The Myc proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by Myc transcriptionally upregulates the core pre-mRNA splicing machinery and causes mis-regulation of alternative splicing. However, our understanding of how splicing changes are directed by Myc is limited. We performed a signaling pathway-guided splicing analysis to identify Myc dependent splicing events. These included an HRAS cassette exon repressed by Myc across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of hnRNP H gene expression with Myc hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, hnRNP F expression showed a positive correlation with Myc hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal new mechanisms for Myc-dependent regulation of splicing, and point to new possible therapeutic targets in prostate cancers. SIGNIFICANCE STATMENT Myc Transformation by the proto-oncogene c-Myc causes dysregulation of the pre-mRNA splicing reaction in cancer, but it is not known how mRNA isoform changes are directed by Myc. Here, we use bioinformatics to identify a splicing event in another proto-oncogene, HRAS, that is regulated by Myc across multiple tumor types. We identify new splicing regulators, hnRNP’s H and F, that control this HRAS exon by binding to enhancer elements within its downstream intron. Additional pan-cancer bioinformatic analyses show hnRNP H expression to be anti- correlated with Myc hallmarks, consistent with the reduced splicing of the HRAS exon in Myc driven cancer. These findings uncover new mechanisms by which Myc can alter splicing in cancer cells and provide new molecular targets for potential therapeutics.
Wikipedia as a tool for contemporary history of science: A case study on CRISPR

Rapid developments and methodological divides hinder the study of how scientific knowledge accumulates, consolidates and transfers to the public sphere. Our work proposes using Wikipedia, the online encyclopedia, as a historiographical source for contemporary science. We chose the high-profile field of gene editing as our test case, performing a historical analysis of the English-language Wikipedia articles on CRISPR. Using a mixed method approach, we qualitatively and quantitatively analyzed its text, sections and references, alongside 50 affiliated articles. These, we found, documented CRISPR’s maturation from a fundamental scientific discovery to a biotechnological revolution with vast social and cultural implications. We developed automated tools to support such research generically and demonstrated its applicability on two other scientific fields we have previously studied - COVID-19 and Circadian clocks. This method makes use of Wikipedia as a digital and free archive, documenting the incremental growth of knowledge and the manner scientific research accumulates and translates into public discourse. Using Wikipedia in this manner compliments and overcomes some issues with contemporary histories and can also augment existing bibliometric research.
Claspin-Dependent and -Independent Chk1 Activation by a Panel of Biological Stresses

Replication stress has been suggested to be an ultimate trigger of carcinogenesis. Oncogenic signal, such as overexpression of CyclinE, has been shown to induce replication stress. Here, we show that various biological stresses, including heat, oxidative stress, osmotic stress, LPS, hypoxia, and arsenate induce activation of Chk1, a key effector kinase for replication checkpoint. Some of these stresses indeed reduce the fork rate, inhibiting DNA replication. Analyses of Chk1 activation in the cell population with western analyses showed that Chk1 activation by these stresses is largely dependent on Claspin. On the other hand, single cell analyses with Fucci cells indicated that while Chk1 activation during S phase is dependent on Claspin, that in G1 is mostly independent of Claspin. We propose that various biological stresses activate Chk1 either directly by stalling DNA replication fork or by some other mechanism that does not involve replication inhibition. The former pathway predominantly occurs in S phase and depends on Claspin, while the latter pathway, which may occur throughout the cell cycle, is largely independent of Claspin. Our findings provide evidence for novel links between replication stress checkpoint and other biological stresses and points to the presence of unknown mechanisms of Chk1 activation in mammalian cells.
T-cell receptor specific protein language model for prediction and interpretation of epitope binding (ProtLM.TCR)

The cellular adaptive immune response relies on epitope recognition by T-cell receptors (TCRs). We used a language model for TCRs (ProtLM.TCR) to predict TCR-epitope binding. This model was pre-trained on a large set of TCR sequences (~62.106) before being fine-tuned to predict TCR-epitope bindings across multiple human leukocyte antigen (HLA) of class-I types. We then tested ProtLM.TCR on a balanced set of binders and non-binders for each epitope, avoiding model shortcuts like HLA categories. We compared pan-HLA versus HLA-specific models, and our results show that while computational prediction of novel TCR-epitope binding probability is feasible, more epitopes and diverse training datasets are required to achieve a better generalized performances in de novo epitope binding prediction tasks. We also show that ProtLM.TCR embeddings outperform BLOSUM scores and hand-crafted embeddings. Finally, we have used the LIME framework to examine the interpretability of these predictions.
Proopiomelanocortin (POMC) is a negative regulator of tadpole aggression through opioid receptor signaling

Aggression is a common behavioral response to limited environmental resources. Most research on the neural basis of aggression in vertebrates focuses on adult males, where sex steroid hormones and the ventromedial hypothalamus are important regulators of aggressive behavior. However, the young of many species also display aggression, although the neural basis of juvenile aggression is not well understood. Here we examine juvenile aggression in Mimic poison frog (Ranitomeya imitator) tadpoles, who live in small isolated pools with limited resources and display aggressive behaviors towards intruder tadpoles. We first conducted a longitudinal study of dyadic behavior and found aggressive behavior increases with tadpole age. We next evaluated which brain regions may be important for tadpole aggression by quantifying pS6-positive cells as a proxy for neural activity. We found more pS6-positive cells in the ventral hypothalamus of aggressive tadpoles compared to controls, similar to findings in adult mammals. We then quantified colocalization of pS6 with vasopressin and oxytocin cells and found no difference across behavior groups. Based on this information, we hypothesized that similar brain regions, but different neuromodulators, may promote aggression in juvenile tadpoles compared to the literature in adult animals. We then used an untargeted approach to molecularly profile pS6-positive neurons and found enrichment of the proopiomelanocortin (POMC) gene in aggressive tadpoles. As POMC is cleaved into several signaling peptides, we used pharmacology to target each pathway and discovered that blocking opioid receptors increases aggressive behavior. Together, this work suggests that POMC-derived B-endorphin is a negative regulator of juvenile aggression through the opioid receptor signaling. More broadly, this work suggests that similar brain regions, but different signaling molecules may be used to regulate aggression in adult and juvenile animals.
Signatures of Electrical Stimulation Driven Network Interactions in the Human Limbic System

Stimulation-evoked signals are starting to be used as biomarkers to indicate the state and health of brain networks. The human limbic network, often targeted for brain stimulation therapy, is involved in emotion and memory processing. Previous anatomic, neurophysiological, and functional studies suggest distinct subsystems within the limbic network (Rolls, 2015). Studies using intracranial electrical stimulation, however, have emphasized the similarities of the evoked waveforms across the limbic network. We test whether these subsystems have distinct stimulation-driven signatures. In eight patients (four male, four female) with drug-resistant epilepsy, we stimulated the limbic system with single-pulse electrical stimulation. Reliable corticocortical evoked potentials (CCEPs) were measured between hippocampus and the posterior cingulate cortex (PCC) and between the amygdala and the anterior cingulate cortex (ACC). However, the CCEP waveform in the PCC after hippocampal stimulation showed a unique and reliable morphology, which we term the “limbic Hippocampus-Anterior nucleus of the thalamus-Posterior cingulate, HAP-wave. ” This limbic HAP-wave was visually distinct and separately decoded from the CCEP waveform in ACC after amygdala stimulation. Diffusion MRI data show that the measured end points in the PCC overlap with the end points of the parolfactory cingulum bundle rather than the parahippocampal cingulum, suggesting that the limbic HAP-wave may travel through fornix, mammillary bodies, and the anterior nucleus of the thalamus (ANT). This was further confirmed by stimulating the ANT, which evoked the same limbic HAP-wave but with an earlier latency. Limbic subsystems have unique stimulation-evoked signatures that may be used in the future to help network pathology diagnosis. SIGNIFICANCE STATEMENT The limbic system is often compromised in diverse clinical conditions, such as epilepsy or Alzheimer’s disease, and characterizing its typical circuit responses may provide diagnostic insight. Stimulation-evoked waveforms have been used in the motor system to diagnose circuit pathology. We translate this framework to limbic subsystems using human intracranial stereo EEG (sEEG) recordings that measure deeper brain areas. Our sEEG recordings describe a stimulation-evoked waveform characteristic to the memory and spatial subsystem of the limbic network that we term the “limbic HAP-wave. ” The limbic HAP-wave follows anatomic white matter pathways from hippocampus to thalamus to the posterior cingulum and shows promise as a distinct biomarker of signaling in the human brain memory and spatial limbic network.
Magellanic Cloud Cepheids: Abundances

We have determined parameters and abundances for three SMC and nine LMC Cepheids that have not been previously studied spectroscopically for metallicity, as well as three SMC and one LMC Cepheids observed previously by Luck & Lambert. This work nearly doubles the number of Cepheids with spectroscopic metallicities in the SMC and triples the number in the LMC. For Galactic reference stars we have determined the abundances of 11 supergiants of spectral type F0 to K1. These abundances are used herein to examine the dispersion in cosmic [Fe/H] values found in LMC Cepheids by Luck & Lambert, and in later papers will be used to correct the distance moduli obtained by us for these Cepheids using the visual surface brightness technique. The Magellanic Cloud Cepheids tend to be longer-period Cepheids (the period range examined was from 37 to 133 days), and thus have physical gravities (derived from the period-luminosity relation and an inferred mass) that are 1.0 dex and lower. Spectroscopic gravities (derived by forcing the total Fe content, as determined from Fe I and Fe II, to be equal) are even lower. Fortunately, the [Fe/H] content as determined from Fe I is not strongly dependent on gravity and is thus well determined. We combine our abundances with other published high-resolution spectroscopic results, deriving a mean [Fe/H] for the SMC of -0.68 (σ = 0.13, n = 25). The total range seen in the [Fe/H] ratios derived herein is -0.84 to -0.65. This result is in agreement with previous studies showing a small intrinsic range in the metallicities in the SMC. For the LMC, from the Cepheids studied here we obtain -0.30 (σ = 0.12, n = 10), with a range of -0.55 to -0.19. Combining all available data, we obtain a mean [Fe/H] of -0.34 (σ = 0.15, n = 32). From this analysis, there is little evidence for a significant metallicity dispersion in the LMC.
A Constraint Programming Library for Preemptive and Non-Preemptive Scheduling

This paper presents an overview of C LAIRE SCHEDULE, a constraint programming library for preemptive and non-preemptive scheduling. The l ack of an efficient tool to handle particular scheduling situations involving interruptible act ivities, time-versus-capacity tradeoffs, and activities for which capacity can vary over time, led us to develop this library, based on CLAIRE, a high-level functional and object-oriented language wit h advanced rule processing capabilities. The paper provides a short description of th e constraint propagation techniques introduced in CLAIRE SCHEDULE and an overview of its functional interface. It also reports some benchmarks on two academic problems (the ship loadi ng problem, and the preemptive job-shop scheduling problem) and an outline of our first operational application.