Miracle-dz/UniFAR-FTUs huggingface dataset:
SvFUL2, an A-class MADS-box transcription factor, is necessary for inflorescence determinacy in model panicoid cereal, Setaria viridis

Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture, yet little is known about the intersecting pathways and how they are rewired during development. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Previous reports of A-class genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and CRISPR/Cas9-based gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersect of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.
Is the perception of their own odour effective in orienting the exploratory activity of cave fishes

Spatial knowledge of the surrounding environment is extremely important for animals to locate and efficiently exploit available resources (e.g., food, shelters, mates). Fishes usually acquire spatial information about their home range through vision, but vision fails in the dark and other sensory pathways have to be exploited. Fishes possess a remarkable olfactory system and have evolved a refined ability of chemical detection and recognition. Nevertheless, while the role of chemical cues in spatial orientation is well known in long-distance salmonid migrations, it has never been investigated in orientation within local, familiar areas. Here we report the first evidence that fish swimming can be topographically polarized by self-odour perception. When an unfamiliar area was experimentally scented with fish self-odour, the cave cyprinid Phreatichthys andruzzii Vinciguerra, 1924 behaved as if the area was previously explored. The fish preferred an odour-free area to a self-odour-scented one, and when offere.
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion

The disruption of mitochondrial dynamics has detrimental consequences for mitochondrial and cellular homeostasis and leads to the activation of the mitochondrial unfolded protein response (UPRmt), a quality control mechanism that adjusts cellular metabolism and restores homeostasis. To identify genes involved in the induction of UPRmt in response to a block in mitochondrial fusion, we performed a genome-wide RNAi screen in Caenorhabditis elegans mutants lacking the gene fzo-1, which encodes the ortholog of mammalian Mitofusin. We find that approximately 90% of the 299 suppressors and 86 enhancers identified are conserved in humans and that one third of the conserved genes have been implicated in human disease. Furthermore, many of the 385 genes have roles in developmental processes, which suggests that mitochondrial function and the response to stress are defined during development and maintained throughout life. In addition, we find that enhancers are predominantly ‘mitochondrial’ genes and suppressors ‘non-mitochondrial’ genes, which indicates that the maintenance of mitochondrial homeostasis has evolved as a critical cellular function that when disrupted can be compensated for by a variety of cellular processes. Our analysis of ‘non-mitochondrial’ enhancers and ‘mitochondrial’ suppressors suggests that organellar contact sites, especially between ER and mitochondria, are of importance for mitochondrial homeostasis. Finally, we uncovered several genes involved in IP3 signaling that modulate UPRmt in fzo-1 mutants, found a potential link between pre-mRNA splicing and UPRmt activation and identified the Miga-1/2 ortholog K01D12.6 as required for mitochondrial dynamics in C. elegans.
A dynamic and spatially periodic micro-pattern of HES5 expression underlies the probability of neuronal differentiation in the mouse spinal cord

Some regulatory transcription factors (TFs), such as the Helix-loop-Helix TF, HES5, show dynamic expression including ultradian oscillations, when imaged in real time at the single cell level. Such dynamic expression is key for enabling cell state transitions in a tissue environment. In somitogenesis, such expression is highly synchronised in blocks of tissue (somites), however, in neurogenesis it is not known how single cell dynamics are coordinated, the multiscale pattern that emerges and the significance for differentiation. In this study, we monitor the expression of HES5 protein ex-vivo in the developing spinal cord and identify the existence of microclusters of HES5 expressing progenitors that are spatially periodic along the dorso-ventral (D-V) axis and that in addition are temporally dynamic. We use multiscale computational modelling to show that such microclusters arise at least in part from local synchronisation in HES5 levels between single cells mediated by Notch-Delta interactions. We find that the HES5 microclusters are less dynamic in the presence of a Notch inhibitor showing that Notch mediated cell-cell communication is required for temporal characteristics. Moreover, predictions from the computational modelling and experimental data show that the strength of interaction between neighbouring cells is a key factor controlling the rate of differentiation in a domain specific manner. Our work provides evidence of co-ordination between single cells in the tissue environment during the progenitor to neural transition and shows the functional role of complexity arising from simple interactions between cells. Key findings HES5 is expressed in microclusters that are spatially periodic along the dorsal-ventral axis in mouse spinal cord and are also dynamic in the temporal domain. Notch signalling maintains the temporal characteristics of the pattern. Based on dynamic data and computational modelling, microclusters can arise from single cell oscillators that are weakly coupled via Notch. Computational modelling predicts that the spatial pattern and the probability for progenitor differentiation is regulated by the coupling strength between cells. Motorneuron progenitor domain has higher rate of differentiation than interneuron progenitor domain and a spatial pattern of HES5 more similar to a checker-board type salt-and-pepper pattern, corresponding to a higher coupling strength. Overall Periodic HES5 micro-patterns can be generated by local synchronisation of low coherence single cell oscillators present in spinal cord tissue and these patterns are maintained in a dynamic way through Notch mediated cell-cell interactions. A computational model predicts that coupling strength changes spatial patterns of expression and in turn, the probability of progenitor differentiation. We confirm that between adjacent progenitor domains in the spinal cord, the rate of differentiation correlates with spatial patterns of HES5.
Responses to Heartbeats in Ventromedial Prefrontal Cortex Contribute to Subjective Preference-Based Decisions

Forrest Gump or The Matrix? Preference-based decisions are subjective and entail self-reflection. However, these self-related features are unaccounted for by known neural mechanisms of valuation and choice. Self-related processes have been linked to a basic interoceptive biological mechanism, the neural monitoring of heartbeats, in particular in ventromedial prefrontal cortex (vmPFC), a region also involved in value encoding. We thus hypothesized a functional coupling between the neural monitoring of heartbeats and the precision of value encoding in vmPFC. Human participants of both sexes were presented with pairs of movie titles. They indicated either which movie they preferred or performed a control objective visual discrimination that did not require self-reflection. Using magnetoencephalography, we measured heartbeat-evoked responses (HERs) before option presentation and confirmed that HERs in vmPFC were larger when preparing for the subjective, self-related task. We retrieved the expected cortical value network during choice with time-resolved statistical modeling. Crucially, we show that larger HERs before option presentation are followed by stronger value encoding during choice in vmPFC. This effect is independent of overall vmPFC baseline activity. The neural interaction between HERs and value encoding predicted preference-based choice consistency over time, accounting for both interindividual differences and trial-to-trial fluctuations within individuals. Neither cardiac activity nor arousal fluctuations could account for any of the effects. HERs did not interact with the encoding of perceptual evidence in the discrimination task. Our results show that the self-reflection underlying preference-based decisions involves HERs, and that HER integration to subjective value encoding in vmPFC contributes to preference stability. SIGNIFICANCE STATEMENT Deciding whether you prefer Forrest Gump or The Matrix is based on subjective values, which only you, the decision-maker, can estimate and compare, by asking yourself. Yet, how self-reflection is biologically implemented and its contribution to subjective valuation are not known. We show that in ventromedial prefrontal cortex, the neural response to heartbeats, an interoceptive self-related process, influences the cortical representation of subjective value. The neural interaction between the cortical monitoring of heartbeats and value encoding predicts choice consistency (i.e., whether you consistently prefer Forrest Gump over Matrix over time. Our results pave the way for the quantification of self-related processes in decision-making and may shed new light on the relationship between maladaptive decisions and impaired interoception.
An unexpected bifurcation in the Pointed transcriptional effector network contributes specificity and robustness to retinal cell fate acquisition

Spatiotemporally specific and robust cell fate transitions are fundamental to the development of appropriately patterned tissues. In the Drosophila retina, receptor tyrosine kinase / mitogen activated protein kinase (MAPK) signaling acts through the transcriptional effector Pointed (Pnt) to direct two distinct rounds of photoreceptor specification. A relay mechanism between two Pnt isoforms, a MAPK responsive form PntP2 and a constitutively active form PntP1, initiates and sustains the transcriptional response. Here, we report an unexpected bifurcation in the Pnt effector network. We show that PntP2 works redundantly with a closely related but previously uncharacterized isoform, PntP3, to activate pntP1 during specification of first round photoreceptors. Intrinsic activity differences between PntP2 and PntP3, combined with positive and negative transcriptional auto- and cross-regulation, buffer first-round fates against conditions of low signaling. In contrast, in a mechanism that may be adaptive to the stronger signaling environment used to specify second round fates, PntP2 uniquely activates pntP1. We propose that differences in expression patterns, transcriptional activities and regulatory interactions between Pnt isoforms together facilitate context-appropriate cell fate specification in different signaling environments.
Evaluating Management Risks using Landscape Trajectory Analysis: A Case Study of California Fisher

ABSTRACT Ecosystem management requires an understanding of how landscapes vary in space and time, how this variation can be affected by management decisions or stochastic events, and the potential consequences for species. Landscape trajectory analysis, coupled with a basic knowledge of species habitat selection, offers a straightforward approach to ecological risk analysis and can be used to project the effects of management decisions on species of concern. The fisher (Martes pennanti) occurs primarily in late-successional forests which, in the Sierra Nevada mountains, are susceptible to high-intensity wildfire. Understanding the effects of fuels treatments and fire on the distribution of fisher habitat is a critical conservation concern. We assumed that the more a treated landscape resembled occupied female fisher home ranges, the more likely it was to be occupied by a female and therefore the lower the risk to the population. Thus, we characterized important vegetation attributes within the home ranges of 16 female fishers and used the distribution of these attributes as a baseline against which the effects of forest management options could be compared. We used principal components analysis to identify the major axes defining occupied female fisher home ranges and these, in addition to select univariate metrics, became our reference for evaluating the effects of landscape change. We demonstrated the approach at two management units on the Sierra National Forest by simulating the effects of both no action and forest thinning, with and without an unplanned fire, on vegetation characteristics over a 45-yr period. Under the no action scenario, landscapes remained similar to reference conditions for approximately 30-yr until forest succession resulted in a loss of landscape heterogeneity. Comparatively, fuel treatment resulted in the reduction of certain forest elements below those found in female fisher home ranges yet little overall change in habitat suitability. Adding a wildfire to both scenarios resulted in divergence from reference conditions, though in the no action scenario the divergence was 4 × greater and the landscape did not recover within the 45-yr timeframe. These examples demonstrate that combining the results of forest growth and disturbance modeling with habitat selection data may be used to quantify the potential effects of vegetation management activities on wildlife habitat.
HDFS Pipeline Reconstruction to Avoid Data Loss

Hadoop is a popular framework designed to deal with very large sets of data, ranging from gigabytes to terabytes, and large Hadoop clusters store millions of these files. Hadoop Distributed File System (HDFS) uses a pipeline process to write the data into blocks. Namenode then sends the available blocks list so that a pipeline is created based on datanodes having empty blocks. In this paper we customize the datanode replacement policy using configuration parameters in case there is datanode failure in the pipeline process. In this approach the write process resumes even though there are less number of datanodes, i.e. even having single datanode. In the single datanode case, the data is lost since we have only one copy of the data. This paper addresses the issue of having a single datanode in the write operation to take action on clearing up unwanted data like tmp, trash folders and snapshots to have enough space to proceed further in the write operation and avoid the data loss.
Modular Enzymatic Cascade Synthesis of Nucleotides Using a (d)ATP Regeneration System

Nucleoside-5’-triphosphates (NTPs) and their analogs are building blocks of DNA and are important compounds in both pharmaceutical and molecular biology applications. Currently, commercially available base or sugar modified NTPs are mainly synthesized chemically. Since the chemical production of NTPs is time-consuming and generally inefficient, alternative approaches are under development. Here we present a simple, efficient and generalizable enzymatic synthesis method for the conversion of nucleosides to NTPs. Our one-pot method is modular, applicable to a wide range of natural and modified nucleotide products and accesses NTPs directly from cheap nucleoside precursors. Nucleoside kinases, nucleoside monophosphate (NMP) kinases and a nucleoside diphosphate (NDP) kinase were applied as biocatalysts. Enzymes with different substrate specificities were combined to produce derivatives of adenosine and cytidine triphosphate with conversions of 4 to 26%. The implementation of a (deoxy)ATP recycling system resulted in a significant increase in the conversion to all NTP products, furnishing 4 different NTPs in quantitative conversion. Natural (deoxy)NTPs were synthesized with 60 to >99% conversion and sugar- and base-modified NTPs were produced with 69 to >99% and 27 to 75% conversion, respectively. The presented method is suitable for the efficient synthesis of a wide range of natural and modified NTPs in a sustainable one-pot process.
Editorial: Modeling Play in Early Infant Development

1 Intelligent Robotics, Department of Computer Science, Aberystwyth University, Aberystwyth, United Kingdom, 2 Psychology, Temple University, Philadelphia, PA, United States, 3 Infant Action Lab, Psychology Department, New York University, New York, NY, United States, 4 Institut National de Recherche en Informatique et en Automatique (INRIA), Rocquencourt, France, 5 The Lego Foundation, Billund, Denmark
Emergence of Stable Synaptic Clusters on Dendrites Through Synaptic Rewiring

The connectivity structure of neuronal networks in cortex is highly dynamic. This ongoing cortical rewiring is assumed to serve important functions for learning and memory. We analyze in this article a model for the self-organization of synaptic inputs onto dendritic branches of pyramidal cells. The model combines a generic stochastic rewiring principle with a simple synaptic plasticity rule that depends on local dendritic activity. In computer simulations, we find that this synaptic rewiring model leads to synaptic clustering, that is, temporally correlated inputs become locally clustered on dendritic branches. This empirical finding is backed up by a theoretical analysis which shows that rewiring in our model favors network configurations with synaptic clustering. We propose that synaptic clustering plays an important role in the organization of computation and memory in cortical circuits: we find that synaptic clustering through the proposed rewiring mechanism can serve as a mechanism to protect memories from subsequent modifications on a medium time scale. Rewiring of synaptic connections onto specific dendritic branches may thus counteract the general problem of catastrophic forgetting in neural networks.
Are firms ready to use big data analytics to create value? The role of structural and psychological readiness

ABSTRACT In this study, we leverage Information Technology (IT) readiness literature and resource-based view (RBV) to investigate the impact of firm structural and psychological readiness on firm value creation, as mediated by big data analytics usage. The proposed research model is empirically validated using survey data from 179 senior IT managers. The findings demonstrate the importance of both structural (i.e. IT infrastructure capability, tools functionality, employee analytical capability, and bigness of data) and psychological readiness (i.e. IT proactive climate) in enhancing firm value creation through big data analytics usage. These results provide interesting theoretical and practical insights.
The effect of cattle manure and chemical fertilizer on yield and yield component of barley (Hordeum vulgare )

In order to study the effect of the interaction of manure and chemical fertilizer on yield and yield component of barley, an experiment was conducted as split plot design on randomized complete block design with three replications in research field of Zabol University, 2008. Different proportions of manure and chemical fertilizer treatments were composed of 100% manure (F1), 100% chemical fertilizer (F2), 50% manure + 50% chemical fertilizer (F3) and control (F4) as the main plot. Use of micro nutrient elements were composed of Iron Sulfate (N1), Zinc Sulfate (N2), Manganese Sulfate (N3) and control (N4) as sub plot in this experiment. Results showed that the effect of different proportions of manure and chemical fertilizer treatment on grain yield and yield components properties with the exception of grain number/ear, were significant. Nutrient treatments had a significant effect on grain yield and yield components in barley and among this nutrient use of Fe (N1) had maximum effect on grain component of barley. Key words: Barley (Hordeum vulgare), chemical fertilizer, manure, yield.
Multiple mechanisms regulate the human replication factors : replication protein A and DNA polymerase A-during DNA replication and DNA repair

Replikationsprotein A (RPA) und DNA-Polymerase a-Primase sind zwei Proteine, die bei der DNA-Replikation, -Reparatur und -Rekombination von zentraler Bedeutung sind. Ihre verschiedenen Funktionen werden durch direkte Interaktion mit DNA oder durch Wechselwirkungen mit anderen Proteinen ausgeubt. Mithilfe zweier monoklonaler Antikorper, die den N-Terminus bzw. den C-Terminus der p70-Untereinheit von RPA erkennen, konnte die Existenz von mindestens zwei immunologisch distinkten Subpopulationen von RPA nachgewiesen werden und ihre biochemischen und zellbiologischen Eigenschaften untersucht werden. Desweiteren konnte mittels eines phosphospezifischen Antikorpers fur die p68-Untereinheit ein neuer regulatorischer Mechanismus fur die Phosphorylierung der DNA-Polymerase a-Primase beschrieben werden.
Natural Killer cell activation, reduced ACE2, TMPRSS2, cytokines G-CSF, M-CSF and SARS-CoV-2-S pseudovirus infectivity by MEK inhibitor treatment of human cells

COVID-19 affects vulnerable populations including elderly individuals and patients with cancer. Natural Killer (NK) cells and innate-immune TRAIL suppress transformed and virally-infected cells. ACE2, and TMPRSS2 protease promote SARS-CoV-2 infectivity, while inflammatory cytokines IL-6, or G-CSF worsen COVID-19 severity. We show MEK inhibitors (MEKi) VS-6766, trametinib and selumetinib reduce ACE2 expression in human cells. In some human cells, remdesivir increases ACE2-promoter luciferase-reporter expression, ACE2 mRNA and protein, and ACE2 expression is attenuated by MEKi. In serum-deprived and stimulated cells treated with remdesivir and MEKi we observed correlations between pRB, pERK, and ACE2 expression further supporting role of proliferative state and MAPK pathway in ACE2 regulation. We show elevated cytokines in COVID-19-(+) patient plasma (N=9) versus control (N=11). TMPRSS2, inflammatory cytokines G-CSF, M-CSF, IL-1α, IL-6 and MCP-1 are suppressed by MEKi alone or with remdesivir. We observed MEKi stimulation of NK-cell killing of target-cells, without suppressing TRAIL-mediated cytotoxicity. Pseudotyped SARS-CoV-2 virus with a lentiviral core and SARS-CoV-2 D614 or G614 SPIKE (S) protein on its envelope infected human bronchial epithelial cells, small airway epithelial cells, or lung cancer cells and MEKi suppressed infectivity of the pseudovirus. We show a drug class-effect with MEKi to stimulate NK cells, inhibit inflammatory cytokines and block host-factors for SARS-CoV-2 infection leading also to suppression of SARS-CoV-2-S pseudovirus infection of human cells. MEKi may attenuate SARS-CoV-2 infection to allow immune responses and antiviral agents to control disease progression.