Miracle-dz/UniFAR-FTUs huggingface dataset:
Maize ZmbZIP33 Is Involved in Drought Resistance and Recovery Ability Through an Abscisic Acid-Dependent Signaling Pathway

Analyzing the transcriptome of maize leaves under drought stress and rewatering conditions revealed that transcription factors were involved in this process, among which ZmbZIP33 of the ABSCISIC ACID-INSENSITIVE 5-like protein 5 family was induced to significantly up-regulated. The functional mechanism of ZmbZIP33 in Abscisic acd (ABA) signaling pathway and its response to drought stress and rewatering has not been studied yet. The present study found that ZmbZIP33 contains a DNA-binding and dimerization domain, has transcriptional activation activity, and is highly homologous to SbABI1,SitbZIP68 and OsABA1. The expression of ZmbZIP33 is strongly up-regulated by drought, high salt, high temperature, and ABA treatments. Overexpression of ZmbZIP33 remarkably increased chlorophyll content and root length after drought stress and rewatering, and, moreover, cause an accumulation of ABA content, thereby improving drought resistance and recovery ability in Arabidopsis. However, silencing the expression of ZmbZIP33 (BMV-ZmbZIP33) remarkably decreased chlorophyll content, ABA content, superoxide dismutase and peroxidase activities, and increased stomatal opening and water loss rate compared with BMV (control). It showed that silencing ZmbZIP33 lead to reduced drought resistance and recovery ability of maize. ABA sensitivity analysis found that 0.5 and 1 μmol/L treatments severely inhibited the root development of overexpression ZmbZIP33 transgenic Arabidopsis. However, the root growth of BMV was greatly inhibited for 1 and 5μmol/L ABA treatments, but not for BMV-ZmbZIP33. Subcellular localization, yeast two-hybrid and BIFC further confirmed that the core components of ABA signaling pathways ZmPYL10 and ZmPP2C7 interacted in nucleus, ZmPP2C7 and ZmSRK2E as well as ZmSRK2E and ZmbZIP33 interacted in the plasma membrane. We also found that expression levels of ZmPYL10 and ZmSRK2E in the BMV-ZmbZIP33 mutant were lower than those of BMV, while ZmPP2C7 was the opposite under drought stress and rewatering. However, expression of ZmPYL10 and ZmSRK2E in normal maize leaves were significantly up-regulated by 3–4 folds after drought and ABA treatments for 24 h, while ZmPP2C7 was down-regulated. The NCED and ZEP encoding key enzymes in ABA biosynthesis are up-regulated in overexpression ZmbZIP33 transgenic line under drought stress and rewatering conditions, but down-regulated in BMV-ZmbZIP33 mutants. Together, these findings demonstrate that ZmbZIP33 played roles in ABA biosynthesis and regulation of drought response and rewatering in Arabidopsis and maize thought an ABA-dependent signaling pathway.
Clinical and Imaging Profile of Patients with Palatal Tremor

Palatal tremor (PT) is an uncommon movement disorder that may be classified into symptomatic (SPT) or essential (EPT). The etiology of SPT is varied, with involvement of the Guillain‐Mollaret triangle (GMT) and inferior olivary hypertrophy. EPT is associated with ear clicks and normal imaging and may have a functional basis.
Surface enhanced spatially offset Raman spectroscopic (SESORS) imaging – the next dimension

SESORS - Surface enhanced spatially offset Raman spectroscopy–imaging is explored for the first time in this study. Multiplexed surface enhanced Raman scattering (SERS) signals have been recovered non-invasively from a depth of 20 mm in tissues for the first time and reconstructed to produce a false colour image. Four unique ‘flavours’ of SERS nanoparticles (NPs) were injected into a 20 × 50 × 50 mm porcine tissue block at the corners of a 10 mm square. A transmission Raman data cube was acquired over an 11 × 11 pixel grid made up of 2 mm steps. The signals were reconstructed using the unique peak intensities of each of the nanoparticles. A false colour image of the relative signal levels was produced, demonstrating the capability of multiplexed imaging of SERS nanoparticles using deep Raman spectroscopy. A secondary but no less significant achievement was to demonstrate that Raman signals from SERS nanoparticles can be recovered non-invasively from samples of the order of 45–50 mm thick. This is a significant step forward in the ability to detect and identify vibrational fingerprints within tissue and offers the opportunity to adapt these particles and this approach into a clinical setting for disease diagnosis.
Hydrothermal dissolution of mixed southern hardwoods

Abstract A hydrothermal dissolution profile of wood components cellulose, hemicelluloses, and lignin of hardwood during autohydrolysis for 100 min at temperatures from 130 to 170°C in a modified accelerated solid extraction system (Dionex ASE-100) is described. The content of cellulose, hemicelluloses, lignin, acetyl, and uronic acid groups remaining in the extracted wood were determined. The extract was analyzed for oligosaccharides and monosaccharides, lignin, acetic acid, uronic acid, furfural, and hydroxymethylfurfural. Xylo-oligomers are the predominant component in the extract at temperatures higher than 150°C. At temperatures higher than 160°C, small amounts of furfural and hydroxymethylfurfural are generated. Most of the arabinan and galactan are removed from the wood at 160°C. The xylan remaining in the wood is acetylated at the same degree as in the original wood. In the extract, the ratio of acetyl groups bound to xylo-oligosaccharides decreases with increasing temperature. The content of uronic acid groups found in the extract obtained after autohydrolysis at T≥150°C is significantly smaller than that calculated from the decrease in uronic content of the wood.
Social network sites and requirements engineering: A systematic literature review

A large volume of highly diverse and real‐time data provided by social network sites has revolutionized several data analytical sciences such as stock exchange fluctuation prediction, sentiment analysis, and political affiliations prediction. From a software engineering viewpoint, social network sites have produced an unprecedented opportunity for software development organizations to monitor the opinion of the large population of users of their systems. The extracted data from social network sites can be used to extract information about newly launched systems, and it enable software development organizations to obtain rapid technical and social feedback about their systems. This paper presents on a systematic literature review of the published research articles on how requirements engineering (RE) activities are conducted using social network sites, elaborated in studies published between 2011 and 2019. From the resulting studies, we extracted data to answer our four questions related to social network site (SNS)‐based RE approaches focusing on requirements elicitation, prioritization, and negotiation activities. Thirty‐one relevant studies were identified and analyzed to answer our research questions. Among 31 studies, 62% of the studies reportedly support requirements elicitation activity, and 14% of the studies reportedly support requirements elicitation, prioritization, and negotiation activities. Ten percent studies were about requirements elicitation and prioritization activities, 7% of the studies support both requirements elicitation and negotiation activities, and prioritization activity was supported by 7% of the studies. It was also observed that 58% of the selected studies adopted semi‐automatic approaches to conduct RE activities while 21% of the selected studies proposed automatic tools, and 21% of the selected studies adopted manual approaches to conduct RE activities. The outcomes of this systematic literature review indicate that social network sites can be a major source that can be used successfully to extract and identify user requirements. Moreover, this systematic literature review also presents implications of this study for practitioners and researchers including challenges, unresolved issues, and future research directions.
Perceiving and remembering speech depend on multifractal nonlinearity in movements producing and exploring speech

Speech perception and memory for speech require active engagement. Gestural theories have emphasized mainly the effect of speaker’s movements on speech perception. They fail to address the effects of listener movement, focusing on communication as a boundary condition constraining movement among interlocutors. The present work attempts to break new ground by using multifractal geometry of physical movement as a common currency for supporting both sides of the speaker-listener dyads. Participants self-paced their listening to a narrative, after which they completed a test of memory querying their narrative comprehension and their ability to recognize words from the story. The multifractal evidence of nonlinear interactions across timescales predicted the fluency of speech perception. Self-pacing movements that enabled listeners to control the presentation of speech sounds constituted a rich exploratory process. The multifractal nonlinearity of this exploration supported several aspects of memory for the perceived spoken language. These findings extend the role of multifractal geometry in the speaker’s movements to the narrative case of speech perception. In addition to posing novel basic research questions, these findings make a compelling case for calibrating multifractal structure in text-to-speech synthesizers for better perception and memory of speech.
Distinct “driving” versus “modulatory” influences of different visual corticothalamic pathways

Higher-order (HO) thalamic nuclei interact extensively with the cerebral cortex and are innervated by excitatory corticothalamic (CT) populations in layers 5 and 6. While these distinct CT projections have long been thought to have different functional influences on the HO thalamus, this has never been directly tested. By optogenetically inactivating different CT populations in the primary visual cortex (V1) of awake mice, we demonstrate that layer 5, but not layer 6, CT projections drive visual responses in the HO visual pulvinar, even while both pathways provide retinotopic, baseline excitation to their thalamic targets. Inactivating the superior colliculus also suppressed visual responses in the pulvinar, demonstrating that cortical layer 5 and subcortical inputs both contribute to HO visual thalamic activity - even at the level of putative single neurons. Altogether, these results indicate a functional division of driver and modulator CT pathways from V1 to the visual thalamus in vivo.
Biasing RNA coarse-grained folding simulations with Small–Angle X–ray Scattering (SAXS) data

RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecule’s energy landscape is rough and can exhibits a multitude of deep basins. In the absence of a high-resolution structure, Small Angle X-ray Scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low-resolution of this data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations “on-the-fly” leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structures predictions based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.
CNAHap: a germline haplotyping method using tumor allele-specific copy number alteration

Haplotype phasing is indispensable to study human genetics. The pervasiveness of large copy number variant segments in solid tumors brings possibilities to resolve long germline phasing blocks utilizing allele imbalance in tumor data. Although there exist such studies, none of them provide easy-use software based on availability and usability. Herein, we present a novel tool, CNAHap, to determine the allele-specific copy number in tumor and then phase germline variants according to the imbalanced alleles in tumor genomes. We also provide interactive web interfaces to visualize the copy number and phase landscape from CNAHap. On in silico datasets, CNAHap demonstrates higher allele-specific copy number calling accuracy than the benchmark tool and generates long phasing blocks. As a case study on Hepatocellular carcinoma, CNAHap successfully generates huge phase blocks with the averages of N50 and N90 as 25M and 7M, respectively, and finds the Olfactory receptor family is recurrent amplified. Our results illustrate the efficacy of CNAHap in determining tumor allele-specific copy numbers and their long germline haplotypes. CNAHap is available at https://github.com/bowentan/CNAHap and the CNAHap visualization web interfaces are hosted at bio.oviz. org.
Identifying key federal, state and private lands strategies for achieving 30x30 in the US

Achieving ambitious conservation goals to conserve at least 30% of US lands and waters by 2030 (“30x30”) will require a multi-scale baseline understanding of current protections, key decision makers, and policy tools for moving forward. To help conservationists and decision makers support the science-based call to address the biodiversity and climate crises, we analyze the current spatial patterns of imperiled species biodiversity and carbon stores in the U.S. relative to protected areas. Analyses demonstrate that 30x30 is numerically achievable nationally, but high spatial heterogeneity highlights the need for tailored approaches from a mix of authorities at federal, regional, and state scales. Critically, current land protections rarely overlap with areas essential for conserving imperiled species biodiversity and mitigating climate change. Nearly one-fifth of unprotected biodiversity hotspots and carbon-rich areas are also at risk of either land conversion or climate exposure by 2050. We discuss this baseline relative to key policy considerations for making practical, substantive progress toward the goal.
SYNTHESIS, CHARACTERIZATION, ANTI BACTERIAL ACTIVITY AND ECOTOXICITY OF SILVER NANOPARTICLES FROM CALLUS EXTRACT OF JUSTICIA JENDARACIA (BURM.F)

Objective. Synthesis of silver nanoparticles from callus extract of Justicia jendaracia ( Burm.f) and the anti bacterial activity ,ecotoxicity of the synthesized particles has been studied in the present study. Methods . The callus was induced in Murashige and Skoog (MS) medium supplemented with growth regulators and evaluated for nanoparticles synthesis. Anti bacterial activity was studied against human pathogenic bacteria Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 29213) was done by well diffusion assay.Ecotoxicity study was studied against Vigna mungo under pot assay. Results. The extract from the callus showed ability of synthesis of nanoparticles with plasmon absorption maxima at 430 nm, spherical particles with the size range of 50–65 nm. The antibacterial activity with these synthesized nanoparticles showed distinct effect on the all the tested strains. Ecotoxicity study reveals that nanoparticles did not cause any distinct effect on soil macronutrients, soil enzyme activity, soil microbial population and plant growth parameters of Vigna mungo . Conclusion. Present study would suggest possible utilization of biogenic silver nanoparticles from the callus extract of Justicia jendaracia as the therapeutic agent without causing any undesirable effects to the environment. KEY WORDS. Callus, Justicia Jendaracia , Silver Nanoparticles,Anti Bacterial Activity,Eco Toxicity
Genetic Architecture of Kernel Compositional Variation in a Maize Diversity Panel

Maize (Zea mays L.) is a multi-purpose row crop grown worldwide, which overtime has often been bred for increased yield at the detriment of lower composition grain quality. Some knowledge of the genetic factors that affect quality traits has been discovered through the study of classical maize mutants. However, much of the underlying genetic architecture controlling these traits and the interaction between these traits remains unknown. To better understand variation that exists for grain compositional traits in maize, we evaluated 501 diverse temperate maize inbred lines in five unique environments and predicted 16 compositional traits (e.g. carbohydrates, protein, starch) based on the output of near-infrared (NIR) spectroscopy. Phenotypic analysis found substantial variation for compositional traits and the majority of variation was explained by genetic and environmental factors. Correlations and trade-offs among traits in different maize types (e.g. dent, sweetcorn, popcorn) were explored and significant differences and correlations were detected. In total, 22.9-71.1% of the phenotypic variation across these traits could be explained using 2,386,666 single nucleotide polymorphism (SNP) markers generated from whole genome resequencing data. A genome-wide association study (GWAS) was conducted using these same markers and found 70 statistically significant loci for 12 compositional traits. This study provides valuable insights in the phenotypic variation and genetic architecture underlying compositional traits that can be used in breeding programs for improving maize grain quality. Core Ideas Understanding kernel compositional variation is important for food grade corn improvement. Genetic and environmental factors account for most of the variation in compositional traits. A broad range in trait heritabilities was observed across compositional traits. Compositional trade-offs will be important to consider when conducting multitrait breeding. Compositional traits are mostly controlled by a large number of small effect loci.
Up and to the light: intra- and interspecific variability of photo- and geo-tactic oviposition preferences in genus Trichogramma

Trichogramma are parasitic microwasps much used as biological control agents. The genus is known to harbor tremendous diversity, at both inter- and intra-specific levels. The successful selection of Trichogramma strains for biocontrol depends on characterizing the existing diversity in this group, especially regarding oviposition performance and behavior. Oviposition preferences in relation to environmental cues such as light and gravity have received little attention so far, although they are suspected to play an important role in microhabitat selection and parasitism patterns. The extent of their variability, and their potential correlated variations, is virtually unknown. Here we use a novel experimental approach relying on automatic image analysis to characterize the oviposition preferences in relation to light and gravity, as well as their interaction, in 25 populations of Trichogramma from five species. We show that most Trichogramma populations and species harbour preferences for light and preferences for elevated parts. However, the two traits harbor significant inter and intraspecific variation. The effects of light and gravity on oviposition patterns were found to be almost perfectly additive overall, with two exceptions. Oviposition preference patterns were not static but very plastic in time: preferences tended to relax over consecutive days, and the strongest preferences relaxed the fastest, presumably because of the density-dependent effect of resource depletion. A correlation of oviposition patterns with the vegetation stratum at which populations were sampled suggests that different species/populations may be associated with different strata with corresponding differentiation in light- and gravity-related oviposition preferences. This article has been peer-reviewed and recommended by Peer Community in Zoology doi: https://doi.org/10.24072/pci.zool. 100008
Effects on brain activity after creative mathematical reasoning when considering individual differences in cognitive ability

Many learning opportunities of mathematical reasoning in school encourage imitative learning procedures (algorithmic reasoning, AR) instead of engaging in more constructive reasoning processes (e.g., creative mathematical reasoning, CMR). Here, we employed a within-subject intervention in the classroom with pupils in upper secondary schools followed by a test situation during brain imaging with fMRI one week later. We hypothesized that learning with CMR compared to AR should lead to a CMR-effect, characterized by better performance and differential brain activity during test. We observed higher brain activity in key regions for mathematical cognition such as left angular gyrus and left inferior frontal gyrus on tasks previously learnt with CMR compared to AR. The effects remained when controlling for individual differences in cognitive abilities, as well as performance and response time differences between the two conditions. Encouraging pupils to engage in constructive processes when learning mathematical reasoning might thus have lasting beneficial effects.
Astrocytes are implicated in BDNF-mediated enhancement of hippocampal long-term potentiation

It is known that astrocytes, by the Ca2+-dependent release of gliotransmitters, which then act in pre- and post-synaptic receptors, modulate neuronal transmission and plasticity. Thus, hippocampal θ-burst long-term potentiation (LTP), which is a form of synaptic plasticity, can be modulated by astrocytes, since these cells release gliotransmitters that are crucial for the maintenance of LTP. Therefore, in this study, we hypothesized that the facilitatory action of BDNF upon LTP would involve astrocytes. To address that possibility, fEPSP recordings were performed in CA3-CA1 area of hippocampal slices from three different experimental models: Wistar rats where astrocytic metabolism was selectively reduced by a gliotoxin, the DL-fluoricitric acid (FC), IP3R2−/− mice, which lack IP3R2-mediated Ca2+-signaling in astrocytes and dn-SNARE transgenic mice, in which the SNARE-dependent release of gliotransmittersis impaired. For the three models we observed that the astrocytic impairment abolished the excitatory BDNF effect upon hippocampal LTP, only while inducing LTP with a mild θ-burst stimulation paradigm. The present data shows for the first time that astrocytes play an active role in the facilitatory action of BDNF upon LTP, depending on stimulation paradigm.