Miracle-dz/UniFAR-FTUs huggingface dataset:
Candida auris evades innate immunity by using metabolic strategies to escape and kill macrophages while avoiding antimicrobial inflammation

Candida auris causes life-threatening, drug-resistant infections. In addition to drug resistance, therapeutic innovation is hindered by our limited knowledge of the mechanisms used by C. auris to evade immunity and establish infection. Here we show that C. auris escapes phagocytic containment and kills macrophages, and demonstrate that the mechanisms rely on metabolic regulation. We found that C. auris-infected macrophages undergo immunometabolic reprogramming and increase glycolysis but this does not lead to the expected antimicrobial responses, as macrophages fail to activate IL-1β cytokine and curb C. auris growth. Further analysis showed that C. auris relies on its own metabolic capacity to egress from macrophages, cause macrophage metabolic stress and cell death, and establish infection in vivo. We identified a transcriptional regulator of C. auris metabolism and macrophage evasion, and further show that, contrary to several other pathogens, C. auris-induced macrophage metabolic dysfunction and death fail to activate the NLRP3 inflammasome. Consequently, inflammasome-dependent antimicrobial responses remain inhibited throughout infection. Our findings establish a pivotal role for metabolic regulation in enabling C. auris to eliminate macrophages while remaining immunologically silent to ensure its own survival.
Using surfactants to control the formation and size of wakes behind moving bubbles at order-one Reynolds numbers

A bubble translating through a continuous liquid (i.e. Newtonian) phase moves as a sphere when inertial and viscous forces are small relative to capillary forces. Spherical bubbles with stress-free interfaces do not retain wakes at their trailing ends as inertial forces become important (increasing Reynolds number). This is in contrast to translating spheres with immobile interfaces in which flow separation and wake formation occurs at order-one Reynolds number. Surfactants present in the continuous phase adsorb onto a bubble surface as it translates, and affect the interfacial mobility by creating tension gradient forces. Adsorbed surfactant is convected to the trailing end of the bubble, lowers the tension there relative to the front, and creates a tension gradient which reduces the surface flow. For low bulk concentrations of surfactant (or if kinetic exchange between bulk and surface is slow relative to convection), diffusion towards the surface is much slower than convection, and surfactant is swept into an immobile cap at the trailing end. As with solid spheres, these caps entrain wakes at order-one Reynolds number. In adsorptive bubble technologies where solutes transfer between the bubble and the continuous phase, usually through thin boundary layers around the bubble surface (high Péclet number), these wakes generally form owing to the presence of surfactant impurities. The wake presence retards the interphase transfer displacing the thin boundary layer towards the front end of the bubble; as mass transfer through the wake is much slower than through the boundary layer, the mass transfer is reduced. Our recent theoretical research has demonstrated that at low Reynolds numbers, the mobility of a surfactant-retarded bubble interface can be increased by raising the bulk concentration of a surfactant which kinetically rapidly exchanges between the surface and the bulk. At high bulk concentrations the interface saturates with surfactant, effectively removing the tension gradient. In this paper, we demonstrate theoretically that this interfacial control is still realized at order-one Reynolds numbers, and, more importantly, we show that the control can be used to manipulate the formation, size and ultimately the disappearance of a wake. This wake removal mechanism has the potential to dramatically increase the interphase transfer in adsorptive bubble technologies.
Wald-Type Testing and Estimation Methods for Asymmetric Comparisons of Poisson Rates

This article considers the problem of asymmetric comparisons, that is, instances where one treatment serves as the compelling standard treatment for a certain disease or health condition, where the asymmetric comparisons are performed in terms of the Poisson rates. We propose asymptotic Wald-type tests and confidence intervals suitable for demonstrating superiority and noninferiority for a given margin. The testing methods for the difference and ratio are based on the unconstrained (MLE) and constrained (CMLE) maximum likelihood estimator. The resulting CMLE-based tests for asymmetric comparisons are equivalent to the standard (i.e., those for symmetric comparisons) CMLE-based tests. The asymmetric tests as well as the standard MLE-based tests are evaluated via simulations. The CMLE-based asymmetric tests are shown to adequately control the Type I error in most settings, while the MLE-based asymmetric tests are shown to have this property only in settings with relatively large sample sizes and means. In all settings, the MLE-based asymmetric tests are more powerful than both the asymmetric CMLE-based and the standard MLE-based tests. We also propose asymptotic confidence intervals that can be used to estimate the difference or ratio of the two rates (the presentation of this content includes supplementary material that is available online), and discuss how power and sample size estimation can be done to aid in study planning. Supplementary materials for this article are available online.
Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia

Deoxygenation can be fatal for many marine animals; however, some sponge species are tolerant of hypoxia and anoxia. Indeed, two sponge species, Eurypon sp. 2 and Hymeraphia stellifera, survive seasonal anoxia for months at a time. To understand their tolerance mechanisms, we performed differential gene expression analyses on the sponges, their mitochondria and their microbial symbionts under in situ conditions of normoxia, hypoxia and anoxia. Each species possessed a unique microbiome, but the microbiomes of each species were dominated by a species-specific Thaumarchaeon and a Gammaproteobacterium. Holobiont gene expression was species-and oxygen-level dependent, though there were some shared interspecific responses to deoxygenation. In general, few changes occurred in the expression of sponge metabolic genes as a function of oxygenation level, indicating that they may remain metabolically active under anoxia. However, ATP synthesis genes were significantly upregulated under hypoxia when compared to normoxia, and genes for DNA replication were downregulated. Mitochondrial gene expression was effectively unchanged under both hypoxia and anoxia. Nevertheless, both anoxia and hypoxia caused upregulation of heat shock proteins (HSPs), indicating cellular level adaptations to deoxygenation stress. A meta-analysis demonstrated that sponge transcriptional responses to anoxia were distinct from those displayed by other invertebrates while dormant, and the hypothesis of sponge dormancy under anoxia was not supported. Thaumarchaeota symbionts also upregulated stress response genes in hypoxia, while maintaining expression of oxygen-dependent metabolic pathways under hypoxia and anoxia. Gammaproteobacteria symbionts showed relatively few noteworthy changes in gene expression in response to anoxia but decreased metabolic gene expression in hypoxia. There was no clear evidence of upregulated anaerobic respiration in the transcriptomes of the sponge holobionts under anoxia or hypoxia. The tolerance of some sponges to prolonged anoxia warrants further investigation and could give them an advantage in future oceans following climate change as well as in ancient oceans when oxygen concentrations were lower than at present.
Leadership Support in a Pandemic: Middle School Teacher Perceptions of Emergency Remote Teaching

Abstract The authors examined middle level teachers’ perceptions and experiences of leadership support during the sudden transition to emergency remote teaching (ERT) during the COVID-19 pandemic. For this qualitative case study, the research questions were: How did middle school teachers perceive their leaders’ support for teaching online? What were teacher beliefs about student attendance and virtual education? Survey data were collected from teachers at a middle school (Grades 6–8) in rural Virginia, and six respondents participated in one-on-one interviews. The responses yielded six findings illuminating perceptions of support for teaching virtually from principals and other administrators: (a) leaders listened to teachers’ issues, concerns, and suggestions; (b) administration was supportive, helpful, and positive; (c) administrators assisted with parental communication; (d) attendance in online classes was poor; (e) absent students failed to learn; and (f) additional professional development for online teaching was desired. Leadership supports are revealed for assisting with faculty adaptation to and effectiveness with remote instruction. Because case studies have yet to examine educational leadership relative to faculty roles and functions during an emergency, this study contributes vital understandings from the middle level teacher standpoint.
This paper is included in the Proceedings of the 21st USENIX Conference on File and Storage Technologies.

Despite the progress of cloud-native technologies, existing distributed file systems are ill-suited for multi-tenant cloud-native applications for two reasons, First, their clients are typically heavyweight, resulting in a low level of resource multiplexing among containers. Second, their architecture is based on network gateway and falls short in providing efficient, highly-available and scalable I/O services for cloud-native applications. In this paper, we propose Fisc, a large-scale, cloud-native-oriented distributed file system. Fisc introduces three key designs: (1) a lightweight file system client to improve the multiplexing of resources with a two-layer resource aggregation, (2) a storage-aware distributed gateway to improve the performance, availability and scalability of I/O services, and (3) a DPU-based virtio-Fisc device offloading key functions to hardware. Fisc has been deployed in production for over three years and now serves cloud applications running over 3 million cores. Results show that Fisc client only consumes 69% CPU resources compared to the traditional file system client. The production environment shows that the average latency of online searching tasks is less than 500 µ s when they access their files in Fisc.
Modeling the marmoset brain using embryonic stem cell-derived cerebral assembloids

Studying the non-human primate (NHP) brain is required for the translation of rodent research to humans, but remains a challenge for molecular, cellular, and circuit-level analyses in the NHP brain due to the lack of in vitro NHP brain system. Here, we report an in vitro NHP cerebral model using marmoset (Callithrix jacchus) embryonic stem cell-derived cerebral assembloids (CAs) that recapitulate inhibitory neuron migration and cortical network activity. Cortical organoids (COs) and ganglionic eminence organoids (GEOs) were induced from cjESCs and fused to generate CAs. GEO cells expressing the inhibitory neuron marker LHX6 migrated toward the cortical side of CAs. COs developed their neural activity from a synchronized pattern to an unsynchronized pattern as COs matured. CAs showed mature neural activity with an unsynchronized pattern. The marmoset assembloid system will provide an in vitro platform for the NHP neurobiology and facilitate translation into humans in neuroscience research, regenerative medicine, and drug discovery.
Aging phenomena in ferrofluids suitable for magnetic biosensor applications

Aging phenomena were investigated in three different ferrofluids containing submicron sized magnetic beads consisting of a cluster of iron oxide nanoparticles embedded in a dextrane matrix with primary amine groups on the surface (one fresh sample and one sample aged during three months) and with a plain surface (only dextrane on the surface, aged for three months), suitable for magnetic biosensor applications. The main characterization technique used was measurement of the frequency dependent complex magnetization using a superconducting quantum interference device. The experimental factors considered were the effect of ultrasonication, temperature, dc bias magnetic field, and addition of sodium dodecyl sulphate surfactant. The stability against aging was found to depend strongly on the bead surface, and the reproducibility of a refreshing procedure involving addition of surfactant in combination with ultrasonication was shown to be low. Aggregation was shown to be strongly affected by the presence of ev.
Lamb's Hydrostatic Adjustment for Heating of Finite Duration

Abstract Lamb’s hydrostatic adjustment problem for the linear response of an infinite, isothermal atmosphere to an instantaneous heating of infinite horizontal extent is generalized to include the effects of heating of finite duration. Three different time sequences of the heating are considered: a top hat, a sine, and a sine-squared heating. The transient solution indicates that heating of finite duration generates broader but weaker acoustic wave fronts. However, it is shown that the final equilibrium is the same regardless of the heating sequence provided the net heating is the same. A Lagrangian formulation provides a simple interpretation of the adjustment. The heating generates an entropy anomaly that is initially realized completely as a pressure excess with no density perturbation. In the final state the entropy anomaly is realized as a density deficit with no pressure perturbation. Energetically the heating generates both available potential energy and available elastic energy. The former remains.
The Big (Genetic) Sort? Reassessing Migration Patterns and Their Genetic Imprint in the UK

This study reassesses Abdel Abdellaoui et al.’s findings that genetically selective migration may lead to persistent and accumulating socioeconomic and health inequalities between “types” (rich or poor) of places in the UK. Their work categorized migrants who moved to the same “type” of place (rich-to-rich or poor-to-poor) as non-migrants. We re-investigate the question of genetically selective migration by examining migration patterns between places rather than “place-types” and find genetic selectively in whether people migrate rather than where. For example, we find evidence of positive selection of people with genetic variants correlated better education moving from rich to poor places with our measure of migration that was obscured in the earlier work that used a non-standard measure of migration.
Cautionary note on ribonuclease activity of recombinant PR-10 proteins

We studied the biochemical properties of three splicing isoforms of PR-10 from rubber tree (Hevea brasiliensis) and found that purified recombinant HbPR10 can cause RNA degradation in vitro, a well-known activity described for many PR-10 proteins. This ribonuclease activity was observed for all three HbPR10 splicing isoforms and is abolished by boiling. However, inclusion of a negative control proteins revealed that ribonuclease activity rather originates from RNases that are copurified from E. coli, which are overlooked by traditionally used controls such as heat inactivation, RNase inhibitors and negative control proteins obtained with different procedures. The crucial control proteins are missing for at least nine reports on ribonuclease activity in PR-10 proteins published by different laboratories worldwide, indicating that proper controls are frequently overlooked in ribonuclease assays. The raised cautionary note applies to several PR-10 proteins with proclaimed ribonuclease activities and call for the use of different assays and mutant PR-10 proteins as control.
Climatic factors and host species composition at hibernation sites drive the incidence of bat fungal disease

Emerging infectious diseases pose a remarkable threat to wildlife, and their incidence will likely be further exacerbated due to climate change. Therefore, developing new, preferably minimally invasive yet effective monitoring systems is crucial for conservation. We investigated whether the occurrence of white-nose disease (WND), a fungal disease of hibernating bats, can be predicted using local climatic conditions and host community composition at hibernation sites. In addition, we used our model to predict the current worldwide potential global distribution of white-nose disease, revealing areas that may be under risk if the pathogen is introduced, and further applied our model to a climate change scenario to illuminate how the potential global distribution of the disease may shift in the future. To achieve this, we fitted a logistic regression model using open-source climate data (mean annual surface temperature (MAST), annual precipitation) and hibernation site census data from 441 hibernacula across Europe. We then applied our model to the current global climatic conditions, as well as a climate change scenario for years 2061–2080, to illuminate the current and future potential global distribution of the disease. We discovered a positive association between the occurrence of WND and Myotis emarginatus, M. myotis/blythii, and M. mystacinus/brandtii, whereas Rhinolophus ferrumequinum and R. hipposideros were negatively associated with the disease. In addition, we were able to detect several areas in the southern hemisphere, that are likely to be at risk if the pathogen is introduced, and demonstrate that climate change may cause a remarkable shift in the distribution range of the disease. We further show that MAST can be used to predict the occurrence of WND, with the highest probability in areas where MAST was 8.3 °C. Our results highlight the importance of environmental factors in controlling the manifestation of disease in localities where both the pathogen and suitable hosts are present, and the massive impact climate change could have in reshaping and expanding the geographic range where WND can occur.
GL-Cache: Group-level learning for efficient and high-performance caching

Web applications rely heavily on software caches to achieve low-latency, high-throughput services. To adapt to changing workloads, three types of learned caches (learned evictions) have been designed in recent years: object-level learning, learning-from-distribution, and learning-from-simple-experts. However, we argue that the learning granularity in existing approaches is either too fine (object-level), incurring significant computation and storage overheads, or too coarse (workload or expert-level) to capture the differences between objects and leaves a considerable efficiency gap. In this work, we propose a new approach for learning in caches (“group-level learning”), which clusters similar objects into groups and performs learning and eviction at the group level. Learning at the group level accumulates more signals for learning, leverages more features with adaptive weights, and amortizes overheads over objects, thereby achieving both high efficiency and high throughput. We designed and implemented GL-Cache on an opensource production cache to demonstrate group-level learning. Evaluations on 118 production block I/O and CDN cache traces show that GL-Cache has a higher hit ratio and higher throughput than state-of-the-art designs. Compared to LRB (object-level learning), GL-Cache improves throughput by 228× and hit ratio by 7% on average across cache sizes. For 10% of the traces (P90), GL-Cache provides a 25% hit ratio increase from LRB. Compared to the best of all learned caches, GL-Cache achieves a 64% higher throughput, a 3% higher hit ratio on average, and a 13% hit ratio increase at the P90.
Impact of Indoor Environmental Quality on Hotel Guests’ Behaviors

ABSTRACT This study explores the impact of indoor environmental quality (IEQ) (i.e., indoor air quality, thermal comfort, acoustic quality, and interior space and furnishings) on overall service quality (OSQ), customer satisfaction, and customer loyalty. Hotel guests were selected to examine the proposed IEQ model developed grounded on the Mehrabian-Russell model and Bitner’s conceptual model. To analyze the data, the PLS-SEM was utilized. Results indicate the following significant relationships: between interior space and furnishings and OSQ, between interior space and furnishings and customer satisfaction. Results also show that two significant factors influencing customer satisfaction are thermal comfort and IAQ. In turn, they influence customer loyalty. Implications for researchers and managers are discussed.
Vibration and Buckling of Deep Beam-Columns on Two-Parameter Elastic Foundations

Natural frequencies and buckling stresses of a deep beam-column on two-parameter elastic foundations are analyzed by taking into account the effect of shear deformation, depth change (the transverse displacement w can vary in the depth direction of beam-columns) and rotatory inertia. By using the method of power series expansion of displacement components, a set of fundamental dynamic equations of a one-dimensional higher order theory for thin rectangular beam-columns subjected to axial stress is derived through Hamilton's principle. Several sets of truncated approximate theories are applied to solve the eigenvalue problems of a simply supported deep elastic beam-column. In order to assure the accuracy of the present theory, convergence properties of the minimum natural frequency and the buckling stress are examined in detail. It is noted that the present approximate theories can predict the natural frequencies and buckling stress of deep beam-columns on elastic foundations accurately compared with the Timoshenko beam theory and the classical beam theory.
Theoretical analysis of the shield tunnel face stability in dry sandy strata

Abstract Predicting reasonable tunnel face support pressure is crucial for maintain the tunnel face stability. The silo-wedge model is widely used in calculating face support pressure in dry sandy strata. As one of the key assumptions in the silo-wedge model, the influence of area equivalent method on the calculations of limit face support pressure is investigated in this study. To better describe the geometry of failure zone in three-dimensional (3 D) perspective, an improved limit equilibrium model which consist of the semi-cylindrical silo, the semi-circular truncated cone, and the local sphere model is proposed based on the experimental results of previous research. The formula of limit face support pressure can be derived without the assumption of area equivalent, which is assessed via a series of existing theoretical models and experimental results.