Miracle-dz/UniFAR-FTUs huggingface dataset:
Electrically modified lyophilic silver hydrosol inhibits bacterial growth in a dose-dependent manner in vitro and in vivo

Abstract Silver has been known for many medicinal uses in the forms of colloidal silver and silver nanoparticles, both of which pose possible health risks when improperly applied. Silver in the form of an electrically modified hydrosol bypasses the adverse effects of prior forms, yet still maintains potent antimicrobial properties. This study focuses on the efficacy of this electrically modified silver hydrosol against Alcaligenes faecalis, Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, and Staphylococcus epidermidis in an in vitro concentration-dependent manner and an in vivo dose-dependent manner. The in vitro concentration-dependent test is a modified Kirby-Bauer disk diffusion method to measure the zone of inhibition (ZOI). The in vivo dose-dependent test measures percent decrease on live epithelial tissue. The concentration-dependent test results found statistically significant ZOI (all p < 0.01), yet all but S. epidermidis treatments failed post-hoc test significance. The dose-dependent test yielded a near-total eradication of cultured bacteria, up to a 100% decrease in bacterial growth (p ≤ 0.0463), with no change between treated and untreated epithelial cells. These results suggest safe usage of the silver hydrosol in vivo and support the hypothesis of high-efficacy dose-dependent treatment on multiple nosocomial gram negative and gram positive bacterial strains. Future research could focus on silver hydrosol's interaction within a living system with exhaustive testing on the effects on endogenous microflora and hepatocytes for presence of silver oxide.
Incipient fault diagnosis for T–S fuzzy systems with application to high-speed railway traction devices

This study addresses the problem of incipient fault detection and diagnosis for Takagi–Sugeno (T–S) fuzzy systems and explores further results of total measurable fault information residual (ToMFIR). First, T–S fuzzy model is used to describe the global dynamics of a non-linear system and the model of incipient actuator faults is formalised. Second, based on the ToMFIR, a novel incipient fault detection method is proposed, which removes the assumptions on system structure in some existing work. Further, sliding-mode observers combined with ToMFIR-based thresholds are designed for incipient fault isolation. Finally, application results conducted on a high-speed railway traction device are given to illustrate the effectiveness of the proposed approach.
Norwegian Data on Prevalence, Sexual Risk Behaviors, Sexual Problems, and Sexual Satisfaction in Women Who Have Sex Exclusively with Women, Women Who Have Sex Exclusively with Men, and Women Who Have Sex with Men and Women

Abstract Objective The study explores the difference between Women Who Have Sex Exclusively with Men (WSEM), Women Who Have Sex Exclusively with Women (WSEW), and Women Who Have Sex with Women and Men (WSWM). Method The data were obtained from a survey of a probability-based web sample of 1967 Norwegian women. Results Most WSWM identified themselves as heterosexuals (76.3%), and three out of 10 used a condom when having sex with a new partner. The highest number of sex partners during the last year was reported by WSWM. More WSEW than the other categories reported premature orgasm. Conclusions WSWM should be targeted in health campaigns.
The degree of T cell stemness differentially impacts the potency of adoptive cancer immunotherapy in a Lef-1 and Tcf-1 dependent manner

Generating stem memory T cells (TSCM) is a key goal for improving cancer immunotherapy. Yet, the optimal way to modulate signaling pathways that enrich TSCM properties remains elusive. Here, we discovered that the degree to which the PI3Kδ pathway is blocked pharmaceutically can generate T cells with differential levels of stemness properties. This observation was based on the progressive enrichment of transcriptional factors of stemness (Tcf-1 and Lef-1). Additional investigation revealed that T cells with high stemness features had enhanced metabolic plasticity, marked by heightened mitochondrial function and glucose uptake. Conversely, T cells with low or medium features of stemness expressed more inhibitory checkpoint receptors (Tim-3, CD39) and were vulnerable to antigen-induced cell death. Only TCR-antigen specific T cells with high stemness persisted following adoptive transfer in vivo and mounted protective immunity to melanoma tumors. Likewise, the strongest level of PI3Kδ blockade in vitro generated human tumor infiltrating lymphocytes (TILs) and CAR T cells with heightened stemness properties, in turn bolstering their capacity to regress human mesothelioma tumors. We find that the level of stemness T cells possess in vitro differentially impacts their potency upon transfer in three tumor models. Mechanistically, both Lef-1 and Tcf-1 sustain anti-tumor protection by high TSCM, as deletion of either one compromised cellular therapy. Collectively, these findings highlight the therapeutic potential of carefully modulating PI3Kδ signaling in T cells to confer high stemness and mediate protective responses to solid tumors.
Uptake of environmental DNA in Bacillus subtilis occurs all over the cell surface through a dynamic pilus structure

At the transition to stationary phase, a subpopulation of Bacillus subtilis cells can enter the developmental state of competence, where DNA is taken up through the cell envelope, is processed to single stranded DNA, which is incorporated into the genome if sufficient homology between sequences exists. We show here that the initial step of transport across the cell wall occurs via a true pilus structure, with an average length of about 500 nm, which assembles at various places on the cell surface. Once assembled, the pilus remains at one position and can be retracted in a time frame of seconds. The major pilin, ComGC, was studied at a single molecule level in live cells. ComGC was found in two distinct populations, one that would correspond to ComGC freely diffusing throughout the cell membrane, and one that is relatively stationary, likely reflecting pilus-incorporated molecules. The ratio of 65% diffusing and 35% stationary ComGC changed towards more stationary molecules upon addition of external DNA, while the number of pili in the population did not strongly increase. These findings suggest that the pilus assembles stochastically, but engages more pilin monomers from the membrane fraction in the presence of transport substrate. Our data reveal that localized transport of DNA into the cytosol at a single cell pole is preceded by localization throughout the periplasm and efficient uptake through the entire cell surface by a dynamic pilus. Importance Horizontal gene transfer (HGT) is important for bacterial evolution and the adaption to new environments. Through HGT, genes can be transferred between bacteria, which can lead to antibiotic resistance development, especially critical with regards to pathogenic bacterial species. One mechanism of HGT is natural competence, through which bacteria can take up DNA under natural conditions and incorporate it into their chromosomes. For DNA uptake, a complex will be formed that is conserved among Gram-positive and Gram-negative bacteria, in spite of different envelope architectures. We show that in Bacillus subtilis, where the part of the uptake complex spanning the cell membrane localizes to a single cell pole, transport through the cell wall is mediated by a visible pilus structure that can extend and retract to pull DNA into the periplasm. Thus, DNA uptake from the environment is not limited to polar sites, but is channelled into the cytosol at the pole. Single molecule dynamics of ComGC revealed a static, likely pilus-bound, and a mobile fraction of ComGC within the cell membrane. Addition of environmental DNA increased the static fraction of molecules, showing that pilus dynamics respond to DNA binding.
The CGG triplet repeat binding protein 1 counteracts DNA secondary structure-induced transcription-replication conflicts

Short tracts of trinucleotide repeats with less than 10 repeats are found frequently throughout the genome without any apparent negative impact on DNA replication fork progression or transcription elongation. CGG binding protein 1 (CGGBP1) binds to CGG triplet repeats and has been implicated in multiple cellular processes such as transcription, replication and DNA damage. Here, we show that CGGBP1 binds to human gene promoter sites prone to G-quadruplex and R-loop secondary structure formation. Altering CGGBP1 levels results in the accumulation of R-loops and causes a defect in transcriptional elongation by RNA polymerase II, which subsequently leads to replication fork stalling and transcription-replication conflicts. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures and cells rely on specific DNA-binding factors to maintain proper transcription and replication progression at short trinucleotide repeats.
Topology in general relativity

A number of theorems and definitions which are useful in the global analysis of relativistic world models are presented. It is shown in particular that, under certain conditions, changes in the topology of spacelike sections can occur if and only if the model is acausal. Two new covering manifolds, embodying certain properties of the universal covering manifold, are defined, and their application to general relativity is discussed.
A temporal hierarchy of object processing in human visual cortex

Our brain constructs increasingly sophisticated representations along the ventral visual pathway to support object recognition. To understand how these representations unfold over time, we recorded human intracranial electroencephalography responses to 120 object images at five consecutive stages of the ventral pathway from V1 to occipitotemporal areas. Using representational similarity analysis, we confirmed that response patterns were more strongly driven by low-order stimulus properties at early stages and high-order category information at late stages, respectively. Interestingly, response patterns also became less stimulus-driven and more categorical at all stages over time, from ∼100 to 200 ms post-stimulus. During this period, we found significant noise correlation between single-trial response patterns across stages, indicating tight inter-areal coupling. Thus, multi-areal recurrent processes may be essential in building high-order object representations.
LeishMANIAdb: a comparative resource for Leishmania proteins

Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host-pathogen Protein-Protein Interactions (PPIs). Here we present LeishMANIAdb, a database specifically designed to investigate how Leishmania virulence factors may interfere with host proteins. Since the secretomes of different Leishmania species are only partially characterized, we collected various experimental evidence and used computational predictions to identify Leishmania secreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host-pathogen interactions of 211 proteins, and the localization/function of 3764 transmembrane (TM) proteins of different Leishmania species. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database, available at https://leishmaniadb.ttk. hu may provide novel insights into Leishmania host-pathogen interactions and help to identify new therapeutic targets for this neglected disease.
CEP76 is a critical regulator of male germ cell transition zone function and tail composition

The transition zone is a specialised gate at the base of cilia/flagella, which segregates the ciliary compartment from the cytoplasm and strictly regulates protein entry. In this study, we have identified CEP76 as an essential germ cell transition zone protein, involved in the selective entry and incorporation of key proteins required for sperm function and fertility into the ciliary compartment and ultimately the sperm tail. In its absence sperm tails are shorter and immotile as a consequence of deficits in essential sperm motility proteins including DNAH2 and AKAP4, which accumulate at the sperm neck in the mutant. We demonstrate CEP76 is required for sperm tail fibrous sheath formation, outer dense fibre loading and axoneme stability in the principal piece and ultimately sperm motility. Finally, we identify that CEP76 dictates annulus positioning and composition, adding further evidence that the spermatid transition zone and annulus are part of the same functional structure.
MicroCT-based imaging of microvasculature within the bone tissue

Angiogenesis is essential for skeletal development, bone healing and regeneration. Various research areas, especially implantology and tissue engineering, would benefit from improved three-dimensional (3D) imaging of the vasculature within bone tissue. X-ray microtomography (microCT) is a well-suited non-destructive 3D imaging technique for bone morphology. For the detection of vessels, a contrast-enhanced microCT-imaging must be used. Limited contrast between perfusion agents and mineralized bone has been the major drawback of this approach, making their distinct segmentation problematic. A decalcification step resolves this issue but inhibits simultaneous assessment of intracortical bone microstructure and vascular morphology. Moreover, the problem of contrasting becomes further compounded in samples with metal implants. This study describes μAngiofil-enhanced microCT-based visualization of vasculature within bone tissue in various small and large animal models, with and without decalcification. We present simultaneous microvascular and bone imaging in murine tibia, murine bone metastatic model, pulp chamber, gingiva and periodontal ligaments. In a large animal model (minipig) we perform visualization and segmentation of different tissue types and vessels in the hemimandible containing metal implants. Our manuscript introduces the first non-destructive approach for 3D imaging of the vasculature within soft and hard tissues in the vicinity of metal implants in a large animal model.
Comment on “Cleaved surface of i -AlPdMn quasicrystals: Influence of the local temperature elevation at the crack tip on the fracture surface roughness”

Quasicrystals are intermetallic compounds with long-range quasiperiodic translational order, composed of atomic clusters, which can be interpreted as basic geometric building blocks. It is a persistent discussion whether these clusters also represent physical entities. Cleavage planes of fractured icosahedral AlPdMn as well as sputtered surfaces annealed up to about 900 K are rough with clusterlike protrusions. Fivefold surfaces annealed at higher temperatures exhibit flat terraces. Thus, obviously, the clusters cannot be termed supermolecules. However, experiments and numerical simulations indicate that fracture is influenced by the clusters. Thus, they determine physical properties. In a recent paper, Ponson et al. [Phys. Rev. B 74, 184205 (2006)] investigated experimental fracture surfaces of AlPdMn and questioned the signature of the clusters. In this comment, we study the self-affinity of cleavage planes obtained by molecular-dynamics simulations. We conclude that the findings of Ponson et al. are not excluding a physical role of the clusters in quasicrystals.
Bayesian Comparison of ARIMA and Stationary ARMA Models

Time series analysts have long been concerned with distinguishing stationary “generating processes” from processes for which differencing is required to induce stationarity. In practical applications, this issue is addressed almost invariably through formal hypothesis testing. In this paper, we explore some aspects of the Bayesian approach to the problem, leading to the calculation of posterior odds ratios. Interesting features arise in the simplest possible variant of the problem, where a choice has to be made between a random walk and a stationary first order autoregressive model. We discuss in detail the analysis of this case, and also indicate how our approach extends to the more general comparison of an ARIMA model with a stationary competitor.
Repeats Mimic Pathogen-Associated Patterns Across a Vast Evolutionary Landscape

An emerging hallmark across human diseases – such as cancer, autoimmune and neurodegenerative disorders – is the aberrant transcription of typically silenced repetitive elements. Once active, a subset of repeats may be capable of “viral mimicry”: the display of pathogen-associated molecular patterns (PAMPs) that can, in principle, bind pattern recognition receptors (PRRs) of the innate immune system and trigger inflammation. Yet how to quantify the landscape of viral mimicry and how it is shaped by natural selection remains a critical gap in our understanding of both genome evolution and the immunological basis of disease. We propose a theoretical framework to quantify selective forces on virus-like features as the entropic cost a sequence pays to hold a non-self PAMP and show our approach can predict classes of viral-mimicry within the human genome and across eukaryotes. We quantify the breadth and conservation of viral mimicry across multiple species for the first time and integrate selective forces into predictive evolutionary models. We show HSATII and intact LINE-1 (L1) are under selection to maintain CpG motifs, and specific Alu families likewise maintain the proximal presence of inverted copies to form double-stranded RNA (dsRNA). We validate our approach by predicting high CpG L1 ligands of L1 proteins and the innate receptor ZCCHC3, and dsRNA present both intracellularly and as MDA5 ligands. We conclude viral mimicry is a general evolutionary mechanism whereby genomes co-opt pathogen-associated features generated by prone repetitive sequences, likely offering an advantage as a quality control system against transcriptional dysregulation.
MonTM: Monitoring-Based Thermal Management for Mixed-Criticality Systems

With a rapidly growing functionality of embedded real-time applications, it becomes inevitable to integrate tasks of different safety integrity levels on one many-core processor leading to a large-scale mixed-criticality system. In this process, it is not sufficient to only isolate shared architectural resources, as different tasks executing on different cores also possibly interfere via the many-core processor’s thermal management. This can possibly lead to best-effort tasks causing deadline violations for safety-critical tasks. In order to prevent such a scenario, we propose a monitoring-based hardware extension that communicates imminent thermal violations between cores via a lightweight interconnect. Building on this infrastructure, we propose a thermal strategy such that best-effort tasks can be throttled in favor of safety-critical tasks. Furthermore, assigning static voltage/frequency (V/f) levels to each safety-critical task based on their worst-case execution time may result in unnecessary high V/f levels when the actual execution finishes faster. To free the otherwise wasted thermal resources, our solution monitors the progress of safety-critical tasks to detect slack and safely reduce their V/f levels. This increases the thermal headroom for best-effort tasks, boosting their performance. In our evaluation, we demonstrate our approach on an 80-core processor to show that it satisfies the thermal and deadline requirements, and simultaneously reduces the run-time of best-effort tasks by up to 45% compared to the state of the art.
Root distribution characteristics of three typical plantations in a Loess Hills region

: The root is the main organ through which plants absorb water and nutrients. The development and distribution of roots have an extremely important impact on plant growth. In order to understand the root distribution characteristics of typical artificial forests in Loess Hills areas and provide a scientific basis for vegetation restoration in the future, a case study was carried out on three artificial forests ( Populus tomentosa , Pinus tabuliformis and Armeniaca sibirica ), located in Longtan watershed, Anding District, Dingxi City, Gansu Province. The study analyzed root length density, root area density and root biomass density in different soil depths and diameter degrees, and the results showed that: (1) Fine roots of different diameter classes were dominant in all three artificial forests. The root length and root area densities of fine roots and total roots were the following: Populus tomentosa>Pinus tabulaeformis>Armeniaca sibirica , while the root biomass density was the following: Pinus tabulaeformis>Populus tomentosa>Armeniaca sibirica . The Pinus tabulaeformis forest had the highest root length and root area densities of middle roots and coarse roots. (2) In the vertical soil profile, the root length, root area, and root biomass densities of total and fine roots decreased with increasing soil depth. However, the vertical distribution feature of middle and coarse roots was not clear. (3) The root length density, root area density and root biomass density of fine and total roots were significantly and positively correlated with soil total carbon, total nitrogen, organic carbon, and water content. The root length and root area densities of middle roots were significantly correlated with soil total carbon, total nitrogen, total phosphorus, and organic carbon. The root length and root area densities of coarse roots were significantly correlated with soil total carbon. The increase in soil carbon, nitrogen and water contents had a synergistic effect on the growth of the root system to a certain extent.
Soil organic carbon spatial distribution and reserve estimation of different soil types in Yanqi Basin oasis area

: We investigated the density and spatial distribution of Yanqi basin oasis farmland soil organic carbon (SOC) among different soil types. Using long-term monitoring data from the Yanqi basin of the Xinjiang oasis area, we applied the DeNitrification- DeComposition (DNDC) model to conduct a simulated experiment. The results of the experiment showed that the DNDC model accurately simulated the SOC and its dynamic changes in this region, producing a correlation coefficient ( r ) higher than 92.75%. The relative error (E) was between 2.98% and 4.12%, indicating that the model has high reliability. In 2018, the SOC density in the 0-20 cm layer in the oasis area of Yanqi Basin was 12000 - 28000 kg · hm -2 , and the total soil organic carbon reserves were 2414 Mg, with obvious differences among regions. Additionally, significant differences in SOC density and reserves were detected among soil types. The SOC density was highest in marsh soil at 25136 kg · hm -2 and lowest in stony soil at 13335 kg · hm -2 . The implementation of specific field management measures for different regions and soil types is essential to restore the SOC cycle balance and facilitate the sustainable development of farmland in China.