Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined Pressure Sensor With Enhanced Dynamic Range Based on Thin Films of Nanotubes and Graphite Nanobelts

Herein, we demonstrate the prototype of a combined flexible pressure sensor based on ultrathin multiwall carbon nanotubes (MWCNTs) and graphite nanobelts (GNBs) films embedded in polydimethylsiloxane (PDMS). A simple and scalable modified Langmuir–Blodgett method was used for deposition of both MWCNT and GNB films. The use of two types of carbon nanostructures (nanotubes and GNBs) with distinctly different mechanical properties allowed obtaining enhanced dynamic range for pressure sensing. Short response time, good sensibility and flexibility, and low power consumption for enhanced pressure range make possible applications of the sensor for healthcare monitoring and as a component in the human–machine interfaces application.
ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the entire set of biochemical reactions occurring in a cell. Constraint-based modeling tools like flux balance analysis (FBA) developed for the purposes of predicting metabolic flux distribution using GEMs face considerable difficulties in estimating metabolic flux alterations between experimental conditions. Particularly, the most appropriate metabolic objective for FBA is not always obvious, likely context-specific, and not necessarily the same between conditions. Here, we propose a new method, called ΔFBA (deltaFBA), that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions. Notably, ΔFBA does not require specifying the cellular objective to produce the flux change predictions. We showcased the performance of ΔFBA through several case studies involving the prediction of metabolic alterations caused by genetic and environmental perturbations in Escherichia coli and caused by Type-2 diabetes in human muscle.
Tonsil Mycobiome in PFAPA (Periodic Fever, Aphthous Stomatitis, Pharyngitis, Adenitis) Syndrome: A Case-Control Study

Periodic fever, aphthous stomatitis, pharyngitis and adenitis syndrome (PFAPA) is the most common periodic fever syndrome in children with unknown etiology, effectively treated with tonsillectomy. Earlier we have shown that tonsil microbiome is different in patients with PFAPA as compared to that in controls. Recently, fungal microbiome, mycobiome, has been linked to the pathogenesis of inflammatory diseases. We now investigated the role of mycobiome of tonsils in PFAPA. Random forest classification, a machine learning approach, was used for the analysis of mycobiome data. We examined tonsils from 30 children with PFAPA and 22 control children undergoing tonsillectomy for non-infectious reasons. We identified 103 amplicon sequence variants, mainly from two fungal phyla, Ascomycota and Basidiomycota. The mean relative abundance of Candida albicans in the tonsil mycobiome was 11% (95% CI: 19 to 27%) in cases and 3.4 % (95% CI: -0.8% to 8%) in controls, p =0.104. Mycobiome data showed no statistical difference in differentiating between PFAPA cases and controls compared to a random chance classifier (area under the curve (AUC) = 0.47, SD = 0.05, p = 0.809). In conclusion, in this controlled study, tonsillar mycobiome in children with PFAPA syndrome did not differ from that of the controls.
ANTIOXIDANT AND ANTICANCER ACTIVITIES OF NYCTANTHES ARBOR-TRISTIS

Traditional medicine with a long history has played a prominent role in treating diseases throughout the world. India became a herbal hub. In India, several medicinal plants were found to possess anticancer agents since plants contain significant amount of phytochemicals that are antioxidant which can be used for the prevention and treatment of cancer. In the present study, the antioxidant activity by DPPH free radical scavenging assay and anticancer activity by MTT reduction cytotoxicity assay was investigated on MDA-MB 231 Breast Cancer Cell Lines. The dried leaf (DLM), fruit (DFM) and stem (DSM) of Nyctanthes arbor-tristis extracted in methanol were used for this assay and the results revealed that DFM at 15 μg/ml conc. exhibited strong inhibition of cancerous cell growth with 46%, whereas 71% inhibition was observed with DLM at 30 μg/ml conc. and DSM at 30 μg/ml conc. showed 82% inhibition. The maximum anti-oxidant activity obtained with DFM at 1000mg/ml conc. is 93.8% whereas the least activity observed is 27.8% at 1.0 mg/ml concentration with DSM.
Hearing loss is associated with delayed neural responses to continuous speech

We investigated the impact of hearing loss on the neural processing of speech. Using a forward modeling approach, we compared the neural responses to continuous speech of 14 adults with sensorineural hearing loss with those of age-matched normal-hearing peers. Compared to their normal-hearing peers, hearing-impaired listeners had increased neural tracking and delayed neural responses to continuous speech in quiet. The latency also increased with the degree of hearing loss. As speech understanding decreased, neural tracking decreased in both populations; however, a significantly different trend was observed for the latency of the neural responses. For normal-hearing listeners, the latency increased with increasing background noise level. However, for hearing-impaired listeners, this increase was not observed. Our results support the idea that the neural response latency indicates the efficiency of neural speech processing. Hearing-impaired listeners process speech in silence less efficiently than normal-hearing listeners. Our results suggest that this reduction in neural speech processing efficiency is a gradual effect which occurs as hearing deteriorates. Moreover, the efficiency of neural speech processing in hearing-impaired listeners is already at its lowest level when listening to speech in quiet, while normal-hearing listeners show a further decrease in efficiency when the noise level increases. From our results, it is apparent that sound amplification does not solve hearing loss. Even when listing to speech in silence at a comfortable loudness, hearing-impaired listeners process speech less efficiently.
Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 × 10−8. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.
CometChip Enables Parallel Analysis of Multiple DNA Repair Activities

DNA damage can be cytotoxic and mutagenic and is directly linked to aging, cancer, and heritable diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these advanced applications of the CometChip platform, we expand the efficacy of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.
Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11–14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.
Transcriptomic analysis reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes

Various forms of fasting, including time-restricted feeding, alternate day fasting, and periodic fasting have shown promise in clinical and pre-clinical studies to normalize body weight, improve metabolic health, and protect against disease. Recent studies suggest that β-hydroxybutyrate (βOHB), a characteristic ketone body of the fasted metabolic state, acts as a potential signaling molecule mediating the beneficial effects of the various forms of fasting, potentially by acting as a histone deacetylase inhibitor. In the first part we investigated whether βOHB, in comparison to the well-established histone deacetylase inhibitor butyrate, influences cellular differentiation in vitro. In C2C12 myotubes, 3T3-L1 adipocytes, and THP-1 monocytes, millimolar concentrations of βOHB did not alter differentiation, as determined by gene expression and histological assessment, whereas equimolar concentrations of butyrate potently impaired differentiation in all cell types. RNA-sequencing revealed that unlike butyrate, βOHB minimally impacted gene expression in adipocytes, macrophages, and hepatocytes. However, in myocytes, βOHB upregulated genes involved in the TCA cycle and oxidative phosphorylation, while downregulating genes belonging to cytokine and chemokine signal transduction. Overall, our data do not support the notion that βOHB serves as a powerful signaling molecule regulating gene expression in adipocytes, macrophages and hepatocytes, but suggest that βOHB may act as a niche signaling molecule in muscle.
Long-term changes in the breeding biology of a New Zealand bellbird population suggest plasticity in life-history responses to ecological restoration

Ecological restoration projects provide excellent opportunities to study how animals adapt their life-history strategies in response to changeable environments. A fundamental way animals can optimise reproductive success in changing conditions is trading-off aspects of their breeding system. The New Zealand bellbird (Anthornis melanura) has had a long-term presence on the small restoration island, Tiritiri Matangi Island (Tiri), spanning the island’s degraded agricultural past to its current extensively restored state. We studied the breeding biology of this bellbird population to assess how their reproductive life-history strategies have responded over time to the restoration on Tiri. We compared the current breeding data (2012–2016) of the bellbirds with data from between 2001–2010 (including Baillie, 2011, Cope, 2007), and from 1977–1978 (Anderson and Craig, 2003), prior to the island’s restoration. We also explored associations between abiotic/biotic factors and bellbird reproductive success for the most recent period (2012–2016). Our main finding was that clutch size significantly declined over time from a mean of 3.6 to 2.4 eggs per nest and this decline correlated with increasing population density. This is consistent with a density dependent effect, although further data are required to empirically test this conclusion. Overall, the earliest spring laying dates were in late August and the latest extended to January, with all chicks fledged by the end of February. Nest success was 47% (range 40 – 54%) across 2012–2016, falling within a similar range as previous studies. We found little effect of year, weather, parental age or morphometrics on reproductive success. We observed directional change in patterns of parental investment between 1977–1978 and 2012–2016; in 2012–2016, parents persisted with raising single broods rather than abandoning and re-nesting to raise larger broods. These results suggest that the bellbirds’ life-history traits are plastic in response to local conditions which provides an advantage when repopulating a regenerating or changing habitat.
Regeneration of spinal motor axons: Negative regulation by Celsr2 implicating Cdc42/Rac1 and JNK/c-Jun signaling

During development, cadherins Celsr2 and Celsr3 control axon navigation. Unlike Celsr3, Celsr2 remains expressed in the adult, suggesting unexplored roles in maintenance and repair. Here we show that Celsr2 knockdown promotes motor axon regeneration in mouse and human spinal cord explants and cultured motor neurons. Celsr2 downregulation is accompanied by increased levels of GTP-bound Rac1 and Cdc42, and of JNK and c-Jun proteins. Using a branchial plexus injury model, we show that forelimb functional recovery is improved in Celsr2 mutant versus control mice. Compared to controls, in mutant mice, reinnervated biceps muscles are less atrophic, contain more newly formed neuromuscular junctions, and generate larger electromyographic potentials, while motor neuron survival and axon regeneration are improved. GTP-bound Rac1 and Cdc42, JNK and c-Jun are upregulated in injured mutant versus control spinal cord. In conclusion, Celsr2 negatively regulates motor axon regeneration via Cdc42/Rac1/JNK/c-Jun signaling and is a target for neural repair.
The Locus Coeruleus- Norepinephrine System in Stress and Arousal: Unraveling Historical, Current, and Future Perspectives

Arousal may be understood on a spectrum, with excessive sleepiness, cognitive dysfunction, and inattention on one side, a wakeful state in the middle, and hypervigilance, panic, and psychosis on the other side. However, historically, the concepts of arousal and stress have been challenging to define as measurable experimental variables. Divergent efforts to study these subjects have given rise to several disciplines, including neurobiology, neuroendocrinology, and cognitive neuroscience. We discuss technological advancements that chronologically led to our current understanding of the arousal system, focusing on the multifaceted nucleus locus coeruleus. We share our contemporary perspective and the hypotheses of others in the context of our current technological capabilities and future developments that will be required to move forward in this area of research.
Activity and Stability of Oxides During Oxygen Evolution Reaction‐‐‐From Mechanistic Controversies Toward Relevant Electrocatalytic Descriptors

Plotting the roadmap of future “renewable energy highway” requires drastic technological advancement of devices like electrolyzers and fuel cells. Technological breakthrough is practically impossible without advanced fundamental understanding of interfacial energy conversion processes, including electrocatalytic water splitting. Particularly challenging is the oxygen evolution reaction which imposes high demands on the long-term activity of electrocatalysts and electrode support materials. To cross the “Rubicon” and in a deterministic manner claim that we developed principles of rational catalyst design, we need first to comprehend the determinants of electrocatalytic activity as well as character of their time evolution. How reliable are reported activity and stability trends, could we interrelate activity and stability, and how meaningful that relation really is are some of the important questions that have to be tackled in building of a more comprehensive view on critically important anodic oxygen evolution.
Diel transcriptional pattern contributes to functional and taxonomic diversity in supraglacial microbial communities

Despite the harsh environmental conditions, glacier surfaces host metabolically active bacterial communities, especially in cryoconite holes, small ponds filled with melting water and with a fine-grained sediment at the bottom. We investigated the daily changes in transcript profiles of the microbial community of a cryoconite hole on an Alpine glacier. Using a metatranscriptomic shotgun sequencing, we observed different level of expression of the main carbon and energy metabolisms along the day. Oxygenic and anoxygenic photosynthesis peaked their activity at the sunrise and sunset, respectively, and showed an inhibition at midday, in response to high solar radiation. Carbon fixation genes were expressed all day long with the lowest coverage at night. Different microbial populations were responsible for this metabolic function along the day. Cyanobacteria and Algae were the most active primary producers at the sunrise and the sunset, whereas at night and at noon chemosynthetic proteobacteria, likely hydrogen oxidisers, were most active. Furthermore, the observed temporal cascade of transcript peaks of photosynthesis and respiration recalls those occurring in both coastal and open waters in ocean, thus supporting the hypothesis that conserved temporally phased biotic interactions are ubiquitous among aquatic communities worldwide.
Cooperative and aggressive behaviours vary between ranks in anemonefish social hierarchies

Many animal groups consist of individuals organised in dominance hierarchies, based on age, size or fighting ability. Lower ranked individuals often do not reproduce themselves but perform cooperative behaviours to help the reproductive output of dominant individuals or the group as a whole. Theoretical models suggest that individuals of higher rank should show increased amounts of aggressive behaviours, such as aggressions towards other group members, but should decrease the amount of cooperative behaviours, such as brood care or territory maintenance. Most empirical tests of these models focus on insect or mammalian systems where kin selection plays a large role, rather than animals that live in groups of unrelated individuals. Here we use two anemonefish species to test hypotheses of variation in cooperation and aggression with respect to social rank and species, for social systems where group members are unrelated. We assessed the behaviours of each rank in 20 groups of Amphiprion percula and 12 groups of A. perideraion in Kimbe Bay, Papua New Guinea. We also performed a removal experiment to test if cooperative and aggressive behaviours are likely adaptive, i.e., if they change as an individual ascends in rank. Our results show differences between the two species, with A. percula showing more cooperative behaviours and A. perideraion showing more aggressive behaviours, despite them being closely related and sharing a very similar ecology. With respect to both cooperation and aggression we found consistent differences between ranks in both species, with higher ranks performing more aggressive as well as more cooperative behaviours. When we experimentally provided lower ranked individuals (rank 4) an opportunity to ascend in the hierarchy, they showed more aggression and more cooperation in line with our observations for rank 3 individuals. Thus, we show that rank specific behavioural patterns are likely adaptive in anemonefishes and that some model predictions do not hold in systems where kin selection benefits are absent. Rather, future fitness benefits through territory inheritance and group augmentation likely motivate cooperative and aggressive behaviours by subordinates in groups of unrelated vertebrates.
Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

Plant small RNAs (sRNAs) play important roles in plant growth and development by modulating expression of genes and transposons. In many flowering plant species, male reproductive organs, the anthers, produce abundant phased small interfering RNAs (phasiRNAs). Two classes of reproductive phasiRNAs are generally known, mostly from monocots: pre-meiotic 21-nt phasiRNAs triggered by miR2118, and meiotic 24-nt phasiRNAs triggered by miR2275. Here, we describe conserved and non-conserved triggers of 24-nt phasiRNAs in several eudicots. We found that the abundant 24-nt phasiRNAs in the basal eudicot columbine are produced by the canonical trigger, miR2275, as well as by other non-conserved triggers, miR482/2118 and aco_cand81. These triggering miRNAs are localized in microspore mother cells (MMC) and tapetal cells of meiotic and post-meiotic stage anthers. Furthermore, we identified a new trigger (miR11308) of 24-nt phasiRNAs and an expanded number of 24-PHAS loci in wild strawberry. We validated the presence of miR2275-derived 24-nt phasiRNAs pathway in rose. Finally, we evaluated all the eudicots that have been validated for the presence of 24-nt phasiRNAs as models to study biogenesis and function of 24-nt phasiRNAs and conclude that columbine would be an excellent model because of its extensive number of 24-PHAS loci and its diversity of trigger miRNAs.