Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-Tuning of Gene Expression by tRNA-Derived Fragments during Abiotic Stress Signal Transduction

When plants are subjected to unfavorable environmental conditions, overall gene expression in stressed cells is altered from a programmed pattern for normal development to an adaptive pattern for survival. Rapid changes in plant gene expression include production of stress responsive proteins for protection as well as reduction of irrelevant proteins to minimize energy consumption during growth. In addition to the many established mechanisms known to modulate gene expression in eukaryotes, a novel strategy involving tRNA-derived fragments (tRFs) was recently reported to control gene expression. In animals, tRFs are shown to play a certain role in infected or cancer cells. However, tRFs are expected to function in the regulation of gene expression against abiotic stress conditions in plants. Moreover, the underlying mechanism linking up-regulation of tRFs under stress conditions with the stress tolerant response remains unknown. In this review, the biogenesis and putative function of diverse tRFs in abiotic stress signaling are discussed with a focus on tRFs as a transcriptional/post-transcriptional/translational regulator.
The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes

Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.
NTRK Fusions Define a Novel Uterine Sarcoma Subtype With Features of Fibrosarcoma

Tropomyosin receptor kinase (Trk) inhibitors have shown high response rates in patients with tumors harboring NTRK fusions. We identified 4 NTRK fusion-positive uterine sarcomas that should be distinguished from leiomyosarcoma and undifferentiated uterine sarcoma. NTRK rearrangements were detected by fluorescence in situ hybridization (FISH) and/or targeted RNA or DNA sequencing in 4 undifferentiated uterine sarcomas with spindle cell morphology. Because of histologic overlap with leiomyosarcoma, TrkA and pan-Trk immunohistochemistry was performed in 97 uterine leiomyosarcomas. NTRK1 and NTRK3 FISH was performed on tumors with TrkA or pan-Trk staining. We also performed whole transcriptome RNA sequencing of a leiomyosarcoma with TrkA expression and targeted RNA sequencing of 2 additional undifferentiated uterine sarcomas. FISH and/or targeted RNA or DNA sequencing in the study group showed TPM3-NTRK1, LMNA-NTRK1, RBPMS-NTRK3, and TPR-NTRK1 fusions. All tumors were composed of fascicles of spindle cells. Mitotic index was 7 to 30 mitotic figures per 10 high power fields; tumor necrosis was seen in 2 tumors. Desmin, estrogen receptor, and progesterone receptor were negative in all tumors, while pan-Trk was expressed in all tumors with concurrent TrkA staining in 3 of them. TrkA and/or pan-Trk staining was also seen in 6 leiomyosarcomas, but these tumors lacked NTRK fusions or alternative isoforms by FISH or whole transcriptome sequencing. No fusions were detected in 2 undifferentiated uterine sarcomas. NTRK fusion-positive uterine spindle cell sarcomas constitute a novel tumor type with features of fibrosarcoma; patients with these tumors may benefit from Trk inhibition. TrkA and pan-Trk expression in leiomyosarcomas is rare and does not correlate with NTRK rearrangement.
Supporting dynamic bandwidth adjustment based on virtual transport link in software-defined IP over optical networks

Packet and optical networks are managed independently in both current carrier networks and datacenter interconnection networks, which results in a lack of service agility and is a significant source of capital expenditure and operating expense overhead for the network operator. In our previous works, we have proposed and experimentally demonstrated a software-defined networking- based architecture (service-aware architecture) for converged control of packet and optical networks. In this paper, we first propose a concept called virtual transport link (VTL) to support dynamic link aggregation in software- defined IP over optical networks. Then, the VTL-based dynamic bandwidth adjustment (VTL-DBA) method is proposed for improving the resource utilization and for simplifying service provisioning. The feasibility of our proposals is experimentally verified on our software-defined IP over optical networks testbed. The performance of the VTL-DBA method is also evaluated based on our simulation platform in terms of resource usage, resource utilization, and blocking probability. For carrying quality guaranteed services, VTL-DBA saves 25% of transport resources on average compared with static bandwidth allocation methods, and it shows an increase of 15% in the average resource utilization. For carrying both quality guaranteed services and quality tolerant services, VTL-DBA reduces the service blocking probability to only 10% on average with higher resource utilization than static bandwidth allocation methods.
Filling in the gaps: using testing and restudy to promote associative learning

ABSTRACT Although testing has been shown to potentiate subsequent learning [Izawa, C. (1966). Reinforcement-test sequences in paired-associate learning. Psychological Reports, 18, 879–919. ], the mechanisms that influence this effect are not entirely understood. The present research examined the relationship between associative binding and test-potentiation effects. We hypothesised that test-potentiation effects would be most pronounced when participants could easily extract the relationship among word groupings. Towards that end, we compared three-word groupings, or triads, that were either semantically related or unrelated. Participants engaged in repeated study, repeated testing, or engaged in interpolated study and test prior to a final test. Final test performance was greatest for participants who engaged in interpolated study and test on related triads. The results support three primary conclusions: (1) testing aids in associative binding; (2) associative binding is facilitated by retrieval practice and restudy pairings; and (3) pre-existing associations facilitate test-potentiation effects.
Multifunctional Three-Dimensional Nanoelectronic Networks for Smart Materials and Cyborg Tissues

Nanomaterials provide unique opportunities at the interface betweennanoelectronics and biology. “Bottom-up” synthesized nanowire(NW) with defined functionality can be assembled and enabled into three-dimensional(3D) flexible nanoelectronic networks. The microto nanoscale electronic units blur the distinction between electronics and cells/tissue in terms of length scale and mechanical stiffness. These unconventional 3D nanoelectronic networks can thus provide a path towards truly seamless integration of non-living electronics and living systems. In this thesis, I will introduce a general method for fabricating 3Dmacroporous NW nanoelectronic networks and their integration with hydrogel, elastomer and living tissues, with an emphasis on the realization of two-way communication between active nanoelectronics and the passive or living systems in which they are embedded. First, fabrication of 3D macroporous NW nanoelectronic networks will be described. Examples showing hundreds of individually addressable, multifunctional nanodevices fully distributed and interconnected throughout 3D networks will be illustrated. Proof-of-concept studies ofmacroporousnanoelectronic networks embedded throughhydrogels andpolymers demonstrate the ability for dynamically mapping pH gradients and strain fields. Second, a universal method to improve the long-term stability of semiconductor NWs in physiological environments using atomic layer deposition(ALD) of dielectric metal oxides
Gesture-Based Process Modeling Using Multi-Touch Devices

Contemporary business process modeling tools provide menu-based user interfaces for defining and visualizing process models. Such menu-based interactions have been optimized for applications running on desktop computers, but are limited regarding their use on multi-touch devices. At the same time, the widespread use of mobile devices in daily business life as well as their multi-touch capabilities offer promising perspectives for intuitively defining and changing business process models. Additionally, multi-touch tables will foster collaborative business process modeling based on natural as well as intuitive gestures and interactions. This paper presents the results of an experiment that investigated the way users define and change business process models using multi-touch devices. Based on experiment results, a core gesture set is designed enabling the easy definition and change of business process models with multi-touch devices. Finally, a proof-of-concept implementation of this core gesture set is presented. Overall, gesture-based process modeling and multi-touch devices will foster new ways of collaborative business process modeling.
Sexual Conflict over the Maintenance of Sex: Effects of Sexually Antagonistic Coevolution for Reproductive Isolation of Parthenogenesis

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.
Differences in Mismatch Responses to Vowels and Musical Intervals: MEG Evidence

We investigated the electrophysiological response to matched two-formant vowels and two-note musical intervals, with the goal of examining whether music is processed differently from language in early cortical responses. Using magnetoencephalography (MEG), we compared the mismatch-response (MMN/MMF, an early, pre-attentive difference-detector occurring approximately 200 ms post-onset) to musical intervals and vowels composed of matched frequencies. Participants heard blocks of two stimuli in a passive oddball paradigm in one of three conditions: sine waves, piano tones and vowels. In each condition, participants heard two-formant vowels or musical intervals whose frequencies were 11, 12, or 24 semitones apart. In music, 12 semitones and 24 semitones are perceived as highly similar intervals (one and two octaves, respectively), while in speech 12 semitones and 11 semitones formant separations are perceived as highly similar (both variants of the vowel in ‘cut’). Our results indicate that the MMN response mirrors the perceptual one: larger MMNs were elicited for the 12–11 pairing in the music conditions than in the language condition; conversely, larger MMNs were elicited to the 12–24 pairing in the language condition that in the music conditions, suggesting that within 250 ms of hearing complex auditory stimuli, the neural computation of similarity, just as the behavioral one, differs significantly depending on whether the context is music or speech.
Effects of Linguistic Labels on Visual Attention in Children and Young Adults

Effects of linguistic labels on learning outcomes are well-established; however, developmental research examining possible mechanisms underlying these effects have provided mixed results. We used a novel paradigm where 8-year-olds and adults were simultaneously trained on three sparse categories (categories with many irrelevant or unique features and a single rule defining feature). Category members were either associated with the same label, different labels, or no labels (silent baseline). Similar to infant paradigms, participants passively viewed individual exemplars and we examined fixations to category relevant features across training. While it is well established that adults can optimize their attention in forced-choice categorization tasks without linguistic input, the present findings provide support for label induced attention optimization: simply hearing the same label associated with different exemplars was associated with increased attention to category relevant features over time, and participants continued to focus on these features on a subsequent recognition task. Participants also viewed images longer and made more fixations when images were paired with unique labels. These findings provide support for the claim that labels may facilitate categorization by directing attention to category relevant features.
Packaging and Delivery of Chemical Weapons: A Defensive Trojan Horse Stratagem in Chromodorid Nudibranchs

Background Storage of secondary metabolites with a putative defensive role occurs in the so-called mantle dermal formations (MDFs) that are located in the more exposed parts of the body of most and very likely all members of an entire family of marine mollusks, the chromodorid nudibranchs (Gastropoda: Opisthobranchia). Given that these structures usually lack a duct system, the mechanism for exudation of their contents remains unclear, as does their adaptive significance. One possible explanation could be that they are adapted so as to be preferentially attacked by predators. The nudibranchs might offer packages containing highly repugnant chemicals along with parts of their bodies to the predators, as a defensive variant of the strategic theme of the Trojan horse. Methodology and Principal Findings We detected, by quantitative 1H-NMR, extremely high local concentrations of secondary metabolites in the MDFs of six species belonging to five chromodorid genera. The compounds were purified by chromatographic methods and subsequently evaluated for their feeding deterrent properties, obtaining dose-response curves. We found that only distasteful compounds are accumulated in the reservoirs at concentrations that far exceed the values corresponding to maximum deterrent activity in the feeding assays. Other basic evidence, both field and experimental, has been acquired to elucidate the kind of damage that the predators can produce on both the nudibranchs' mantles and the MDFs. Significance As a result of a long evolutionary process that has progressively led to the accumulation of defensive chemical weapons in localized anatomical structures, the extant chromodorid nudibranchs remain in place when molested, retracting respiratory and chemosensory organs, but offering readily accessible parts of their body to predators. When these parts are masticated or wounded by predators, breakage of the MDFs results in the release of distasteful compounds at extremely high concentration in a way that maximizes their repugnant impact.
Cognitive Styles and Psychotic Experiences in a Community Sample

Introduction In clinical populations paranoid delusions are associated with making global, stable and external attributions for negative events. Paranoia is common in community samples but it is not known whether it is associated with a similar cognitive style. This study investigates the association between cognitive style and paranoia in a large community sample of young adults. Methods 2694 young adults (mean age 17.8, SD 4.6) from the ALSPAC cohort provided data on psychotic experiences and cognitive style. Psychotic experiences were assessed using a semi-structured interview and cognitive style was assessed using the Cognitive Styles Questionnaire-Short Form (CSQ-SF) on the same occasion. Logistic regression was used to investigate associations between paranoia and CSQ-SF scores, both total and domain-related (global, stable, self, external). The role of concurrent self-reported depressive symptoms in the association was explored. Results Paranoia was associated with Total CSQ-SF scores (adjusted OR 1.69 95% CI 1.29, 2.22), as well as global (OR 1.56 95% CI 1.17, 2.08), stable (OR 1.56 95% CI 1.17, 2.08) and self (OR 1.37 95% CI 1.05, 1.79) domains, only Total score and global domain associations remained after additional adjustment for self-reported depression. There was no association between paranoia and external cognitive style (OR 1.10 95% CI 0.83, 1.47). Conclusion Paranoid ideation in a community sample is associated with a global rather than an external cognitive style. An external cognitive style may be a characteristic of more severe paranoid beliefs. Further work is required to determine the role of depression in the association between cognitive style and paranoia.
Spatial and Temporal Variations in Stable Carbon (δ13C) and Nitrogen (δ15N) Isotopic Composition of Symbiotic Scleractinian Corals

Tropical scleractinian corals are considered autotrophic as they rely mainly on photosynthesis-derived nutrients transferred from their photosymbionts. Corals are also able to capture and ingest suspended particulate organic matter, so heterotrophy can be an important supplementary trophic pathway to optimize coral fitness. The aim of this in situ study was to elucidate the trophic status of 10 coral species under contrasted environmental conditions in a French Polynesian lagoon. Carbon (δ13C) and nitrogen (δ15N) isotopic compositions of coral host tissues and photosymbionts were determined at 3 different fringing reefs during wet and dry seasons. Our results highlighted spatial variability in stable isotopic compositions of both coral host tissues and photosymbionts. Samples from the site with higher level of suspended particulate matter were 13C-depleted and 15N-enriched relative to corals and photosymbionts from less turbid sites. However, differences in both δ13C and δ15N between coral host tissues and their photosymbionts (Δhost-photosymbionts 13C and Δhost-photosymbionts 15N) were small (0.27 ± 0.76‰ and 1.40 ± 0.90‰, respectively) and similar at all sites, thus indicating no general increases in the heterotrophic pathway. Depleted δ13C and enriched δ15N values of coral host tissues measured at the most turbid site were explained by changes in isotopic composition of the inorganic nutrients taken up by photosymbionts and also by changes in rate of isotopic fractionation with environmental conditions. Our results also highlighted a lack of significant temporal variations in δ13C and δ15N values of coral host and photosymbiont tissues and in Δhost-photosymbionts 13C and Δhost-photosymbionts 15N values. This temporal stability indicated that corals remained principally autotrophic even during the wet season when photosymbiont densities were lower and the concentrations of phytoplankton were higher. Increased coral heterotrophy with higher food availability thus appears to be species-specific.
The Effect of Antitumor Glycosides on Glioma Cells and Tissues as Studied by Proton HR-MAS NMR Spectroscopy

The effect of the treatment with glycolipid derivatives on the metabolic profile of intact glioma cells and tumor tissues, investigated using proton high resolution magic angle spinning (1H HR-MAS) nuclear magnetic resonance (NMR) spectroscopy, is reported here. Two compounds were used, a glycoside and its thioglycoside analogue, both showing anti-proliferative activity on glioma C6 cell cultures; however, only the thioglycoside exhibited antitumor activity in vivo. At the drug concentrations showing anti-proliferative activity in cell culture (20 and 40 µM), significant increases in choline containing metabolites were observed in the 1H NMR spectra of the same intact cells. In vivo experiments in nude mice bearing tumors derived from implanted C6 glioma cells, showed that reduction of tumor volume was associated with significant changes in the metabolic profile of the same intact tumor tissues; and were similar to those observed in cell culture. Specifically, the activity of the compounds is mainly associated with an increase in choline and phosphocholine, in both the cell cultures and tumoral tissues. Taurine, a metabolite that has been considered a biomarker of apoptosis, correlated with the reduction of tumor volume. Thus, the results indicate that the mode of action of the glycoside involves, at least in part, alteration of phospholipid metabolism, resulting in cell death.
Current Challenges and Opportunities in the Prevention and Management of Diabetic Foot Ulcers

Diabetic foot ulcers remain a major health care problem. They are common, result in considerable suffering, frequently recur, and are associated with high mortality, as well as considerable health care costs. While national and international guidance exists, the evidence base for much of routine clinical care is thin. It follows that many aspects of the structure and delivery of care are susceptible to the beliefs and opinion of individuals. It is probable that this contributes to the geographic variation in outcome that has been documented in a number of countries. This article considers these issues in depth and emphasizes the urgent need to improve the design and conduct of clinical trials in this field, as well as to undertake systematic comparison of the results of routine care in different health economies. There is strong suggestive evidence to indicate that appropriate changes in the relevant care pathways can result in a prompt improvement in clinical outcomes.