Miracle-dz/UniFAR-FTUs huggingface dataset:
Electrical Manipulation of Donor Spin Qubits in Silicon and Germanium

Many proposals for quantum information devices rely on electronic or nuclear spins in semiconductors because of their long coherence times and compatibility with industrial fabrication processes. One of the most notable qubits is the electron spin bound to phosphorus donors in silicon, which offers coherence times exceeding seconds at low temperatures. These donors are naturally isolated from their environments to the extent that silicon has been coined a “semiconductor vacuum”. While this makes for ultra-coherent qubits, it is difficult to couple two remote donors so quantum information proposals rely on high density arrays of qubits. Here, single qubit addressability becomes an issue. Ideally one would address individual qubits using electric fields — which can be easily confined. Typically these schemes rely on tuning a donor spin qubit onto and off of resonance with a magnetic driving field. In this thesis, we measure the electrical tunability of phosphorus donors in silicon and use the extracted parameters to estimate the effects of electric-field noise on qubit coherence times. Our measurements show that donor ionization may set in before electron spins can be sufficiently tuned. We therefore explore two alternative options for qubit addressability. First, we demonstrate that nuclear spin qubits can be directly driven using electric fields instead of magnetic fields and show that this approach offers several advantages over magnetically driven spin resonance. In particular, spin transitions can occur at half the spin resonance frequency and double quantum transitions (magnetic-dipole forbidden) can occur. In a second approach to realizing tunable qubits in semiconductors, we explore the option of replacing silicon with germanium. We first measure the coherence and relaxation times for shallow donor spin qubits in natural and isotopically enriched germanium. We find that in isotopically enriched material, coherence times can exceed 1 ms and is limited by a single-phonon T1 process. At lower frequencies or lower temperatures the qubit coherence times should substantially increase. iii Finally, we measure the electric field tunability of donors in germanium and find a four order-of-magnitude enhancement in the spin-orbit Stark shift and confirm that the donors should be tunable by at least 4 times the electron spin ensemble linewidth (in isotopically enriched material). Germanium should therefore also be more sensitive to electrically driven nuclear magnetic resonance. Based on these results germanium is a promising alternative to silicon for spin qubits.
Reversed Sexual Size Dimorphism in the Ryukyu Scops Owl Otus elegans on Minami-Daito Island

Abstract One of the consequences of selections acting on body size is the difference in body size between the sexes or sexual size dimorphism. Although many hypotheses have been proposed for reversed sexual size dimorphism (RSD) in raptors, ornithologists have rarely paid attention to temporal aspects of RSD when testing their hypotheses. Because selection pressures may vary temporally, describing temporal variation in RSD is a first step towards understanding evolutionary mechanism which shape and maintain the dimorphism. Here, we describe RSD in the population of Ryukyu Scops Owls Otus elegans on Minami-daito Island using a dataset of the external measurements of 770 individuals obtained during a 17-year long-term population monitoring project. Females were larger than males in body mass, culmen length, bill depth, bill width, tail length and flattened wing length, whereas males were larger than females in tarsus and head lengths. Among these traits, the degree and direction of RSD of body mass, tarsus length, bill depth and flattened wing length varied across years. There were neither increasing nor decreasing trends in RSD. This is a rare study which addressed temporal variation in RSD in a raptor species.
New Principles of Non-Linear Integral Inequalities on Time Scales

Abstract The concept of inequalities in time scales has attracted the attention of mathematicians for a quarter century. And these studies have inspired the solution of many problems in the branches of physics, biology, mechanics and economics etc. In this article, new principles of non-linear integral inequalities are presented in time scales via diamond-α dynamic integral and the nabla integral.
Knockdown of lncRNA TapSAKI alleviates LPS-induced injury in HK-2 cells through the miR-205/IRF3 pathway

Abstract Sepsis is a common and lethal syndrome. Long non-coding RNA (lncRNA) transcript predicting survival in AKI (TapSAKI) has recently been found to serve as an important regulator in sepsis. However, the underlying mechanism of TapSAKI in sepsis pathogenesis remains largely unknown. Our data demonstrated that lipopolysaccharide (LPS)-induced HK-2 cell injury by weakening cell viability and enhancing cell apoptosis and inflammation. TapSAKI was upregulated and miR-205 was downregulated in LPS-induced HK-2 cells. TapSAKI knockdown or miR-205 overexpression alleviated LPS-induced cytotoxicity in HK-2 cells. TapSAKI sequestered miR-205 via acting as a miR-205 sponge. Moreover, the mitigating effect of TapSAKI silencing on LPS-induced HK-2 cell injury was mediated by miR-205. Additionally, the interferon regulatory factor 3 (IRF3) signaling was involved in the regulation of the TapSAKI/miR-205 axis on LPS-induced HK-2 cell damage. Our current study suggested that TapSAKI silencing relieved LPS-induced injury in HK-2 cells at least in part by sponging miR-205 and regulating the IRF3 signaling pathway, highlighting a novel understanding for sepsis pathogenesis and a promising target for this disease treatment.
Struggling to Fix Teams in Real Work Settings: A Challenge Assessment and an Intervention Toolbox

Abstract After more than 80 years in predicting organizational performance, empirical evidence reveals a science of teams that seems unable to consistently implement solutions for teams performing in real work settings –outside and away from the isolated teams breeding in research laboratories in the academic context. To bridge this growing practitioners-researchers divide, we first identify five main challenges involved in working with teams today (purposeful team staffing; proper task design and allocation; task and interaction process functionality; appropriate affective tone; and suitable team assessment). And second, we offer a toolbox of interventions (empowering and restorative) to help practitioners to transform the potential threats inherent in these challenges into opportunities for team effectiveness. Our five-challenge diagnosis and proposed intervention toolbox contribute to better address research questions and theoretical falsifiability using teams performing in real work settings, and to assess and intervene in teams by adjusting their internal functioning to contextual conditions and constraints.
Chilean Version of the Empathy Quotient (EQ) Scale: Adaptation and Psychometric Properties

Abstract We evaluated the psychometric properties of the empathy quotient (EQ) scale translated to Spanish in Chile. We estimated its structural validity, and its construct validity with other convergent measures of empathy and attachment, as well an inversely associated construct such as aggression. We used a general sample of students and community individuals (n = 336). Participants completed the EQ, Interpersonal Reactivity Index (IRI), and Buss-Perry Aggression Questionnaire (BPAQ). Another exclusively community group (n = 102) completed Collins Adult Attachment scale and the EQ. CFA and ESEM analyses confirmed the structural model fit of the data to three previously reported dimensions of the EQ: cognitive empathy (CE), emotional reactivity (ER) and social skills (SS). Sex-differences in emotional reactivity, and the predicted relationships with the convergent measures were observed. The current Chilean version of the EQ resulted in an appropriate multidimensional measurement of empathy. Finally, providing a specific social skills dimension extends the traditional conception of cognitive and affective empathy to the social realm in the Chilean context.
Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites

New SARS-CoV-2 variants are continuously emerging with critical implications for therapies or vaccinations. All 22 N-glycan sites of SARS-CoV-2 Spike remain highly conserved among the variants B.1. 1.7, 501Y.V2 and P.1, opening an avenue for robust therapeutic intervention. Here we used a comprehensive library of mammalian carbohydrate-binding proteins (lectins) to probe critical sugar residues on the full-length trimeric Spike and the receptor binding domain (RBD) of SARS-CoV-2. Two lectins, Clec4g and CD209c, were identified to strongly bind to Spike. Clec4g and CD209c binding to Spike was dissected and visualized in real time and at single molecule resolution using atomic force microscopy. 3D modelling showed that both lectins can bind to a glycan within the RBD-ACE2 interface and thus interferes with Spike binding to cell surfaces. Importantly, Clec4g and CD209c significantly reduced SARS-CoV-2 infections. These data report the first extensive map and 3D structural modelling of lectin-Spike interactions and uncovers candidate receptors involved in Spike binding and SARS-CoV-2 infections. The capacity of CLEC4G and mCD209c lectins to block SARS-CoV-2 viral entry holds promise for pan-variant therapeutic interventions.
A mechanism with severing near barbed ends and annealing explains structure and dynamics of dendritic actin networks

Single molecule imaging has shown that part of actin disassembles within a few seconds after incorporation into the dendritic filament network in lamellipodia, suggestive of frequent destabilization near barbed ends. To investigate the mechanisms behind network remodeling, we created a stochastic model with polymerization, depolymerization, branching, capping, uncapping, severing, oligomer diffusion, annealing, and debranching. We find that filament severing, enhanced near barbed ends, can explain the single molecule actin lifetime distribution, if oligomer fragments reanneal to free ends with rate constants comparable to in vitro measurements. The same mechanism leads to actin networks consistent with measured filament, end, and branch concentrations. These networks undergo structural remodeling, leading to longer filaments away from the leading edge, at the +/- 35° orientation pattern. Imaging of actin speckle lifetimes at sub-second resolution verifies frequent disassembly of newly-assembled actin. We thus propose a unified mechanism that fits a diverse set of basic lamellipodia phenomenology.
Establishment of a Patient-Derived, Magnetic Levitation-Based, 3D Spheroid Granuloma Model for Human Tuberculosis

Tuberculous granulomas that develop in response to Mycobacterium tuberculosis (M.tb) infection are highly dynamic entities shaped by the host immune response and disease kinetics. Within this microenvironment, immune cell recruitment, polarization and activation is driven not only by co-existing cell types and multi-cellular interactions, but also by M.tb-mediated changes involving metabolic heterogeneity, epigenetic reprogramming and rewiring of the transcriptional landscape of host cells. There is an increased appreciation of the in vivo complexity, versatility and heterogeneity of the cellular compartment that constitutes the tuberculosis (TB) granuloma, and the difficulty in translating findings from animal models to human disease. Here we describe a novel biomimetic in vitro 3-dimentional (3D) human lung granuloma model, resembling early “innate” and “adaptive” stages of the TB granuloma spectrum, and present results of histological architecture, host transcriptional characterization, mycobacteriological features, cytokine profiles and spatial distribution of key immune cells. A range of manipulations of immune cell populations in these granulomas will allow the study of host/pathogen pathways involved in the outcome of infection, as well as pharmacological interventions. IMPORTANCE Tuberculosis is a highly infectious disease, with granulomas as its hallmark. Granulomas play an important role in the control of M.tb infection and as such are crucial indicators for our understanding of host resistance to TB. Correlates of risk and protection to M.tb are still elusive, and the granuloma provides the perfect environment in which to study the immune response to infection and broaden our understanding thereof; however, human granulomas are difficult to obtain, and animal models are costly and do not always faithfully mimic human immunity. In fact, most TB research is conducted in vitro on immortalized or primary immune cells and cultured in 2D on flat, rigid plastic, which does not reflect in vivo characteristics. We have therefore conceived a 3D, human in vitro granuloma model which allows researchers to study features of granuloma-forming diseases, in an 3D structural environment resembling in vivo granuloma architecture and cellular orientation.
Constrained evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through sequence duplication

Neisseria commensals are an indisputable source of resistance for their pathogenic relatives; however, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≤ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n=7/16), we find mutations encoding resistance converge on the gene encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through duplication events. Importantly, one of the laboratory evolved mutations in rpmH is identical, and two nearly identical, to those recently reported to confer high-level resistance to azithromycin in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Finally, we assessed the potential of horizontal transfer of derived resistance mutations into multiple strains of N. gonorrhoeae. Though we were unable to transform N. gonorrhoeae in this case, studies like this will be critical for predicting commensal alleles that are at risk of rapid dissemination into pathogen populations. Importance Commensal bacterial populations have been increasingly recognized for their importance as sources of resistance for pathogens, however the collection of antimicrobial resistance (AMR) mechanisms within these communities are often understudied. The risk of reduced antibiotic susceptibility as a result of horizontal gene transfer (HGT) is amplified in highly recombinogenic genera, such as the Neisseria. Indeed, there have been multiple documented cases of macrolide and beta-lactam resistance acquisition in the pathogen N. gonorrhoeae from close commensal relatives. This work uncovers multiple novel azithromycin resistance-conferring mutations in a Neisseria commensal through experimental evolution, investigates their fitness impacts, and explores the possibility of transfer to N. gonorrhoeae. Ultimately these types of studies will illuminate those resistance mutations that may rapidly be acquired across species boundaries.
Characterisation of nanofibrils from soy protein and their potential applications for food thickener and building blocks of microcapsules

ABSTRACT Soy protein isolate (SPI) was isolated from Indonesian soybean var. Grobogan and converted into protein nanofibrils. Their functionalities as a food thickener and building blocks for microcapsules were investigated and compared with those of commercial whey protein isolate (WPI). The isolation yield was about 58% with SPI’s protein content of about 90% on dry basis. Long, curved, and branched SPI fibrils with a few nanometers of diameter were obtained by heating SPI suspension at pH 2.0. The solution of SPI fibrils was shear thinning with much higher viscosity than the unheated SPI which was Newtonian. The fibrils showed a good potential as building blocks of microcapsules prepared by layer-by-layer adsorption method, which were similar to WPI fibrils.
Early life Western diet-induced memory impairments and gut microbiome changes in female rats are long-lasting despite healthy dietary intervention

Objective Consumption of a Western diet during adolescence results in hippocampus (HPC)-dependent memory impairments and gut microbiome dysbiosis. Whether these adverse outcomes are reversible in adulthood following intervention with a healthy diet is unknown. Here we assessed the short- and long-term effects of adolescent consumption of a Western diet enriched with either sugar alone, or sugar and fat on metabolic outcomes, HPC-dependent memory, and gut microbiota. Methods Adolescent female rats (PN 26) were fed a standard chow diet (CTL), a chow diet with access to 11% sugar solution (SUG), or a junk food cafeteria-style diet (CAF) containing a variety of fat- and/or sugar-enriched foods. During adulthood (PN 65+), metabolic outcomes, HPC-dependent memory, and gut microbial populations were evaluated both before and after a 5-week dietary intervention period where all groups were fed a diet of water standard chow. Results Prior to the dietary intervention both the CAF and SUG groups demonstrated impaired HPC-dependent memory, increased adiposity, and altered gut microbial populations relative to controls. However, impaired peripheral glucose regulation was only observed in the SUG group. The dietary intervention reversed the metabolic dysfunction in both the CAF and SUG groups, whereas HPC-dependent memory impairments were reversed in the SUG, but not the CAF group. The composition of the gut microbiota remained distinct from controls in both groups after dietary intervention. Conclusions While the metabolic impairments associated with adolescent cafeteria diet consumption are reversible in adulthood with dietary intervention, the HPC-dependent memory impairments and the gut microbiome dysbiosis persist.
Codependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks

The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity they also affect each other. The nature of such “codependency” is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalises synaptic codependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity, while neighbouring excitatory-excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, codependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighbourly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena.
γδT Cells Are Required for CD8+ T Cell Response to Vaccinia Viral Infection

Vaccinia virus (VV) is the most studied member of the poxvirus family, is responsible for the successful elimination of smallpox worldwide, and has been developed as a vaccine vehicle for infectious diseases and cancer immunotherapy. We have previously shown that the unique potency of VV in the activation of CD8+ T cell response is dependent on efficient activation of the innate immune system through Toll-like receptor (TLR)-dependent and -independent pathways. However, it remains incompletely defined what regulate CD8+ T cell response to VV infection. In this study, we showed that γδT cells play an important role in promoting CD8+ T cell response to VV infection. We found that γδT cells can directly present viral antigens in the context MHC-I for CD8+ T cell activation to VV in vivo, and we further demonstrated that cell-intrinsic MyD88 signaling in γδT cells is required for activation of γδT cells and CD8+ T cells. These results illustrate a critical role for γδT cells in the regulation of adaptive T cell response to viral infection and may shed light on the design of more effective vaccine strategies based on manipulation of γδT cells. Importance Targeting the immune systems has powerful potentials to treat many disorders, such as some cancers and viral infections. By understanding how the immune system responds to model infections, we can better determine strategies to manipulate our immune systems. Vaccinia virus is responsible for the worldwide elimination of smallpox and produces one of the longest immune responses known in humans. We know from previous findings that NK cells are required for initial immune response and CD8+ T cells are required for the elimination of the virus. How CD8+ T cells are activated in response to Vaccinia virus is not fully understood. This manuscript found that γδT cells activate CD8+ T cells in response to Vaccinia virus infection through MyD88 pathway
Are narrow-ranging species doomed to extinction? Projected dramatic decline in future climate suitability of two highly threatened species

Narrow-ranging species are usually omitted from Species distribution models (SDMs) due to statistical constraints, while they are predicted to be particularly vulnerable to climate change. The recently available high-resolution environmental predictors, along with recently developed methods enable to increase the eligibility of narrow-ranging species for SDMs, provided their distribution is well known. We fill a gap of knowledge on the effect of predicted climate change on narrow-ranging species. We modelled the distribution of the golden mantella frog Mantella aurantiaca and the Manapany day gecko Phelsuma inexpectata, for which the distribution of their occurrence records is well documented. Our modelling scheme included a range of processes susceptible to address statistical issues related to narrow-ranging species. We predict an alarming decline in climate suitability in the whole current distribution area of both species by 2070, potentially leading to a complete extinction in most scenarios. We identified the areas with the best climate suitability in the future, but these remain largely suboptimal regarding species climatic niche. The high level of habitat fragmentation suggests that both species likely need to be at least partly translocated. Climate change may not only drive range contractions or distribution shifts in narrow-ranging species, but may lead to the complete extirpation of suitable environments across their entire region. This study suggests that the level of threats of narrow-ranging species already identified as threatened may be underestimated, especially in heterogeneous tropical areas. We stress the need to develop sampling campaigns and implement proactive actions for narrow-ranging species in the tropics.