Miracle-dz/UniFAR-FTUs huggingface dataset:
Micropetrosis – Occlusion of Osteocyte Lacunae

Abstract This article summarizes the current knowledge on micropetrosis – osteocyte lacunar occlusion, while focusing on the latest data on osteocyte viability and diabetic bone disease. The lacunae are fluid-filled ellipsoid spaces where osteocytes reside within the mineralized matrix. During osteocyte lifetime, the lacunar space is kept in a non-mineralized state. However, a dying osteocyte appears to enable the initiation of lacunar mineralization – creating a fossil within the living tissue. Elevated frequencies of micropetrosis are observed with advanced age, but also type 1 diabetes mellitus. The latter is a common health threat to our society with rising numbers of patients suffering from the disease associated symptoms including a secondary type of osteoporosis with an elevated risk of fragility fractures. While the underlying mechanism of diabetic bone disease is not entirely understood, more evidence is pointing towards a combinatory effect of loss of bone mass and an impaired overall bone quality. The high number of micropetrotic osteocyte lacunae leads to a more brittle bone tissue prone to microcracking. Further investigations are required to determine the implications of elevated micropetrosis as a reliable target of bone fragility.
Direct detection of time-resolved Rabi oscillations in a single quantum dot via resonance fluorescence

Abstract : OpticalRabi oscillations are coherent population oscillations of a two - level system coupled by an electric dipole transition when driven by a strong nearly resonant optical field. In quantum dot structures, these measurements have typically been performed as a function of the total pulse area function of ohm(0)(t)(dt) where the pulse area varies as a function of Rabi frequency. Here, we report direct detection of the time - resolved coherent transient response of the resonance fluorescence to measure the time evolution of the optical Rabi oscillations in a single charged InAs quantum dot. We extract a decoherence rate consistent with the limit from the excited.
Singular value decomposition for texture analysis

Texture is an important characteristic of analyzing images. A variety of texture features have been proposed for texture discrimination, whereas a best set of texture features never exists. This paper considers statistical textures which can be viewed as realizations of some stochastic processes, or viewed as images containing no apparent objects. We propose using singular value decomposition (SVD) strategy for texture analysis including (a) using the proportion of dominant singular values of an image matrix as texture features for texture discrimination, (b) the singular value decomposition automatically provides a compression technique for textures due to the dependency of neighboring pixels, and (c) an algorithm based on SVD is proposed to synthesize textures. The texture features derived from SVD are stable according to the stability of SVD. Experiments for discriminating synthesized textures and natural textures, for compressing texture data and for synthesizing textures are also given to demonstrate the proposed strategy.
A separation theorem for totally-sewn 4-polytopes

The Separation Problem, originally posed by K. Bezdek in [1], asks for the minimum number s(O, K) of hyperplanes needed to strictly separate an interior point O in a convex body K from all faces of K. It is conjectured that s(O, K) ≦ 2d in d-dimensional Euclidean space. We prove this conjecture for the class of all totally-sewn neighbourly 4-dimensional polytopes.
A-BDF: A Generalization of the Backward Differentiation Formulae

A one parameter family of generalized BDF, the so-called A-BDF, is proposed and analyzed. Formulae of this new family are A0-stable up to order 7, especially A-stable in orders 1 and 2 and $A(\alpha)$-stable in orders 3 to 7, respectively. The nonexistence result of A0-stable formulae of order larger than 7, given by [C. W. Cryer, BIT, 12 (1972), pp. 17--25], [D. M. Creedon and J. J. H. Miller, BIT, 15 (1975), pp. 244--249], is extended to the A-BDF. After implementing these formulae in LSODE, a considerably larger set of stiff problems with oscillatory modes can be solved efficiently and accurately.
Foster caring as ‘professional parenting’: A grounded theory of the relationships between parent and professional in long-term foster care

Whilst it has been suggested that fostering involves being both a parent and a professional, little is known about how foster carers manage these roles. This study aimed to develop an explanatory theory and model of the processes involved in fostering looked after children and the relationship between the roles of parent and professional. Ten foster carers offering intended long-term placements to looked after children and five social care professionals who provide support to foster carers were interviewed. Data were analysed using grounded theory. A preliminary model was developed which suggested that the relationship between the two roles changed over time. Many described initially identifying with the parental role before experiencing challenges that necessitated also taking a professional one. Over time, these separate roles appeared to blend and become interconnected, such that foster carers became ‘professional–parents’. These findings extend our understanding of the complexity of the foster carer role and may link to existing role theories. They may also have important clinical implications for the support and training of foster carers, particularly in the early stages of the fostering journey. Further research, including the use of more diverse samples, is needed to extend these findings.
Synthesis and characterization of a novel silver nanoparticles decorated functionalized single-walled carbon nanotubes nanohybrids embedded polyaniline ternary nanocomposites: thermal, dielectric, and sensing properties

ABSTRACT The recent research paper describes the synthesis of the silver nanoparticles (AgNPs) coated functionalized single-walled carbon nanotubes (f-SWNTs) hybrid nanofillers reinforced polyaniline (PANI) (PANI/Ag@f-SWNTs) nanocomposites, which was carried out through in situ polymerization process to analyze its thermal, dielectric, and sensing properties. The Fourier transform infrared (FTIR) spectroscopy showed the occurrence of interphase interactions within the Ag@f-SWNTs hybrid nanofillers and PANI matrix. The Raman spectroscopy indicated the blue shift with increase in intensity of the band that confirms the decoration of AgNPs on the surface of the f-SWNTs. The structural behavior of the PANI/Ag@f-SWNTs nanocomposites was investigated via X-ray diffraction (XRD) spectroscopy, which revealed the presence of the face centered cubic (FCC) crystal structure of the AgNPs. X-ray photoelectron spectroscopy (XPS) evaluated the chemical composition and bond structure of the nanocomposites. The morphology of the nanocomposites is studied from scanning electron microscopy (SEM) and transmission electron microscopy (TEM), which displayed the well decoration of the AgNPs on the surface of the f-SWNTs. The thermal and dielectric properties of the PANI/Ag@f-SWNTs nanocomposites were examined by using thermogravimetry-differential scanning calorimetry (TG-DSC) and dielectric relaxation spectroscopy (DRS), respectively. The thermal and dielectric properties of the PANI/Ag@f-SWNTs nanocomposites were significantly enhanced owing to the development of robust interphase interactions between the Ag@f-SWNTs hybrid nanofillers and PANI matrix that arises due to the homogeneous dispersion of the Ag@f-SWNTs nanohybrids within the PANI matrix through in situ polymerization process. The Cr(VI) metal ion sensing behavior of the PANI and PANI ternary nanocomposites was studied through UV-Vis spectroscopy, which indicates significant improvement in sensing behavior of the PANI/Ag@f-SWNTs ternary nanocomposites as compared to the pure PANI matrix. GRAPHICAL ABSTRACT
Advanced modeling of electron avalanche process in polymeric dielectric voids: Simulations and experimental validation

This paper deals with aging phenomena in polymers under electric stress. In particular, we focus our efforts on the development of a novel theoretical method accounting for the discharge process (partial discharge) in well known defects present in polymers, which are essentially tiny air gaps embedded in a polymeric matrix. Such defects are believed to act as trigger points for the partial discharges and their induced aging process. The model accounts for the amplitude as well as the energy distribution of the electrons during their motion, particularly at the time in which they impact on the polymer surface. The knowledge of the number of generated electrons and of their energy distributions is fundamental to evaluate the amount of damage caused by an avalanche on the polymer-void interface and get novel insights of the basic phenomena underlying the relevant aging processes. The calculation of such quantities would require generally the combined solution of the Boltzmann equation in the energy and space.
R-loops and Topoisomerase 1 facilitate formation of transcriptional DSBs at gene bodies of hypertranscribed genes

DNA double-stranded breaks (DSBs) are considered the most deleterious type of DNA damage. Although cytotoxic levels of DSBs occur mainly due to external factors, such as ionizing irradiation and UV radiation, DSBs can occur naturally under physiological conditions through cell’s natural processes such as transcription and replication. However, how physiological DSBs are generated during transcription is still poorly understood. Here, we mapped DSBs using in-suspension break labeling in situ and sequencing (sBLISS) and re-analysis of ChIP-seq and DRIP-seq data, along with immunofluorescence staining for DNA damage markers in MCF-7 cells. Mapping of DSBs revealed their occurrence at highly expressed genes that are enriched with Topoisomerase 1 (TOP1), the main enzyme responsible for resolving positive and negative supercoiling, and with R-loops. Depleting R-loops and TOP1 decreased DSBs specifically at highly expressed and TOP1/R-loops-enriched genes implying that TOP1 and R-loops are the main causes of transcriptional DSBs. These findings propose a model in which DSBs in highly expressed genes, mainly oncogenes, are caused by resolving of R-loops and the catalytic activity of TOP1. Our data also reveal that these genes, despite being highly fragile, are covered by γ-H2AX suggesting efficient repair signaling. Our findings underscore the critical roles of TOP1 and R-loops in regulating DSBs in hypertranscribed oncogenes implicated in carcinogenesis.
Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere

Summary The point centromere of budding yeast specifies assembly of the large multi-subunit kinetochore complex. By direct attachment to the mitotic spindle, kinetochores couple the forces of microtubule dynamics to power chromatid segregation at mitosis. Kinetochores share a conserved architecture comprising the centromere-associated inner kinetochore CCAN (constitutive centromere-associated network) complex and the microtubule-binding outer kinetochore KMN network. The budding yeast inner kinetochore additionally includes the centromere-binding CBF1 and CBF3 complexes. Here, we reconstituted the complete yeast inner kinetochore complex assembled onto the centromere-specific CENP-A nucleosome (CENP-ANuc) and determined its structure using cryo-EM. This revealed a central CENP-ANuc, wrapped by only one turn of DNA, and harboring extensively unwrapped DNA ends. These free DNA duplexes function as binding sites for two CCAN protomers, one of which entraps DNA topologically and is positioned precisely on the centromere by the sequence-specific DNA-binding complex CBF1. The CCAN protomers are connected through CBF3 to form an arch-like configuration, binding 150 bp of DNA. We also define a structural model for a CENP-ANuc-pathway to the outer kinetochore involving only CENP-QU. This study presents a framework for understanding the basis of complete inner kinetochore assembly onto a point centromere, and how it organizes the outer kinetochore for robust chromosome attachment to the mitotic spindle.
Interactive auditory task reveals complex sensory-action integration in mouse primary auditory cortex

Predictive coding theory postulates that the brain achieves perception by actively making predictions about the incoming sensory information and correcting them if errors signals arise. These signals are likely the most relevant when the individual is actively interacting with the environment and where the sensory outcome determines the ongoing action. In addition, the cerebral cortex is thought to play a key role in generating these signals. Thus, to study the representation of error signals in the primary sensory cortex, we trained mice to perform an interactive auditory task that coupled their actions to the generated sound and perturbed this coupling to evoke putative error responses. We imaged Layer 2/3 (L2/3) and Layer 4 (L4) neurons in the mouse primary auditory cortex, and we identified not only neurons that mainly encoded action related information but also neurons encoding the mismatch between the action and the sound. These results show that a subset of A1 neurons encode the nonlinear interactions between the sound and the action. Furthermore, more L2/3 neurons encoded action related information than L4, indicating that action-sound integration emerges hierarchically in A1 circuits. Together, our results show that complex interactions between action and sound happen in A1 and that some A1 neurons responses reflect the violation of the learnt relationship between the action and sound feedback. Thus, primary sensory cortices not only encode sensory driven activity but also represent the complex interplay between sensory inputs, expectations, and errors.
PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-extinct mega-fauna have enabled unprecedented insights into their evolutionary history. In contrast to the field of ancient DNA - where several computational methods exist to process and analyze sequencing data - few tools exist for handling ancient protein sequence data. Instead, most studies rely on loosely combined custom scripts, which makes it difficult to reproduce results or share methodologies across research groups. Here, we present PaleoProPhyler: a new fully reproducible pipeline for aligning ancient peptide data and subsequently performing phylogenetic analyses. The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. We describe the various steps of the pipeline and its many functionalities, and provide some examples of how to use it. PaleoProPhyler allows researchers with little bioinformatics experience to efficiently analyze palaeoproteomic sequences, so as to derive insights from this valuable source of evolutionary data.
Amodal population clock in the primate medial premotor system for rhythmic tapping

The neural substrate for beat extraction and response entrainment to auditory and visual rhythms is still unknown. Here we analyzed the population activity of hundreds of medial premotor neurons of monkeys performing an isochronous tapping guided by brief flashing stimuli or auditory tones. The animals showed a strong bias towards visual than auditory metronomes, with rhythmic tapping that was more precise and accurate on the former. The population dynamics shared the following properties across modalities: the circular dynamics of the neural trajectories formed a regenerating loop for every produced interval; the trajectories converged in similar state space at tapping times resetting the clock; the tempo of the synchronized tapping was encoded in the trajectories by a combination of amplitude modulation and temporal scaling. In addition, the modality induced a displacement in the neural trajectories in auditory and visual subspaces without greatly altering time keeping mechanism. These results suggest that the interaction between the MPC amodal internal representation of pulse and a modality specific external input generates a neural rhythmic clock whose dynamics governs rhythmic tapping execution across senses.
A unifying theory explains seemingly contradicting biases in perceptual estimation

Perceptual biases are widely regarded as a window into the computational principles underlying human perception. To understand these biases, previous work has proposed a number of conceptually different and even seemingly contradicting ingredients, including attraction to a Bayesian prior, repulsion from the prior due to efficient coding, and central tendency effects on a bounded range. We present a unifying Bayesian theory of biases in perceptual estimation. We theoretically demonstrate an additive decomposition of perceptual biases into attraction to a prior, repulsion away from regions with high encoding precision, and regression away from the boundary. The results reveal a simple and universal rule for predicting the direction of perceptual biases. Our theory accounts for, and leads to new understandings of biases in the perception of a variety of stimulus attributes, including orientation, color, and magnitude.
marmite defines a novel conserved neuropeptide family mediating nutritional homeostasis

Neuropeptides play a key role in regulating physiology and behavior, including feeding. While animals modify their food choices to respond to the lack of specific nutrients, the mechanisms mediating nutrient-specific appetites remain unclear. Here, we identified marmite (mmt), a previously uncharacterized Drosophila melanogaster gene encoding a secreted peptide that controls feeding decisions. We show that both mmt mutants and neuronal knockdown of mmt specifically increased the intake of proteinaceous food, whereas neuronal mmt overexpression reduced protein appetite. mmt expression is also higher in animals maintained on amino acid rich food, suggesting that mmt encodes a protein-specific satiety signal. Mmt is expressed in a small number of neurons in the adult nervous system, with a single pair of neurons modulating protein appetite. Finally, sequence and phylogenetic analysis showed that mmt is part of an ancient and conserved family of neuropeptides, including the poorly understood vertebrate neuropeptides B and W genes. Functional experiments showed that mmt and vertebrate NPB and NPW modulate food intake in both flies and mice. Therefore, we discovered an ancient family of neuropeptides involved in controlling feeding across phyla.
Identification of the rice Rc gene as a main regulator of seed survival under dry storage conditions.

Seed deterioration during storage results in poor germination, reduced vigor, and non-uniform seedling emergence. The aging rate depends on storage conditions and genetic factors. This study aims to identify these genetic factors determining the longevity of rice (Oryza sativa L.) seeds stored under experimental aging conditions mimicking long-term dry storage. Genetic variation for tolerance to aging was studied in 300 Indica rice accessions by storing dry seeds under an elevated partial pressure of oxygen (EPPO) condition. A genome-wide association analysis identified eleven unique genomic regions for all measured germination parameters after aging, differing from those previously identified in rice under humid experimental aging conditions. The significant single nucleotide polymorphism in the most prominent region was located within the Rc gene, encoding a bHLH transcription factor. Storage experiments using near-isogenic rice lines (SD7-1D (Rc) and SD7-1d (rc)) with the same allelic variation confirmed the role of the wildtype Rc gene, providing stronger tolerance to dry EPPO aging. In the seed pericarp, a functional Rc gene results in accumulation of proanthocyanidins, an important sub-class of flavonoids having strong antioxidant activity, which may explain the variation in tolerance to dry EPPO aging. This article is protected by copyright. All rights reserved.
Social tolerance as strategy to resolve group conflicts: an experimental study on tug-of-war competition of burying beetles

In animal groups with dominance hierarchies, there often occurs a tug-of-war competition over resources and reproduction between dominants and subordinates, because neither is able to fully control the other. Consequently, individuals may mitigate within-group conflict, either by fighting others or by signalling their willingness to tolerate others. Nevertheless, how such a tolerance interaction evolves remains unclear. Here, we addressed this knowledge gap and tested the tug-of-war competition hypothesis, by investigating whether subordinates pay to stay in the group by helping dominants (pay-to-stay), and whether dominants pay costs by living with subordinates in the group (pay-from-staying). We used the burying beetles, Nicrophorus vespilloides, which compete with intra- and inter-specifics for valuable carcasses that are needed for reproduction. Multiple conspecifics can reproduce together through communal breeding, thereby enhancing benefits in terms of reproduction and resource defence against competitors. In communal associations, larger individuals are often dominant in carcass use and reproduction, whereas subordinates have restricted access to the carcass. Our findings show that cooperative subordinates paid costs by helping dominant breeders in carcass preparation in order to be tolerated (i.e. increased access towards the carcass) by dominant breeders, but subordinates did not increase their reproductive success by helping. Such tolerance was eliminated by a high interspecific competition with blowfly maggots. Our results also show that dominant males, but not dominant females, benefitted more from the presence of subordinates, partly due to a sex difference in the compensation strategy of dominants. Overall, our study demonstrates that a social tolerance occurring in situations with a tug-of-war competition could be a common strategy to resolve conflicts in animal societies.