Miracle-dz/UniFAR-FTUs huggingface dataset:
Macrophage Cell Lines and Murine Infection by Salmonella enterica Serovar Typhi L-Form Bacteria

Antibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic resistance genes is well established, much less is known about the temporary and reversible resistance induced by antibiotic treatment, such as that due to treatment with bacterial cell wall-inhibiting antibiotics such as ampicillin. ABSTRACT Antibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic resistance genes is well established, much less is known about the temporary and reversible resistance induced by antibiotic treatment, such as that due to treatment with bacterial cell wall-inhibiting antibiotics such as ampicillin. Typically, ampicillin concentration in the blood and other tissues gradually increases over time after initiation of the treatment. As a result, the bacterial population is exposed to a concentration gradient of ampicillin during the treatment of infectious diseases. This is different from in vitro drug testing, where the organism is exposed to fixed drug concentrations from the beginning until the end. To mimic the mode of antibiotic exposure of microorganisms within host tissues, we cultured the wild-type, ampicillin-sensitive Salmonella enterica serovar Typhi Ty2 strain (S. Typhi Ty2) in the presence of increasing concentrations of ampicillin over a period of 14 days. This resulted in the development of a strain that displayed several features of the so-called L-form of bacteria, including the absence of the cell wall, altered shape, and lower growth rate compared with the parental form. Studies of the pathogenesis of S. Typhi L-form showed efficient infection of the murine and human macrophage cell lines. More importantly, S. Typhi L-form was also able to establish infection in a mouse model to the extent comparable to its parental form. These results suggested that L-form generation following the initiation of treatment with antibiotics could lead to drug escape of S. Typhi and cell to cell (macrophages) spread of the bacteria, which sustain the infection. Oral infection by the L-form bacteria underscores the potential of rapid disease transmission through the fecal-oral route, highlighting the need for new approaches to decrease the reservoir of infection.
Engineered Cas9 extracellular vesicles as a novel gene editing tool

Abstract Extracellular vesicles (EVs) have shown promise as biological delivery vehicles, but therapeutic applications require efficient cargo loading. Here, we developed new methods for CRISPR/Cas9 loading into EVs through reversible heterodimerization of Cas9‐fusions with EV sorting partners. Cas9‐loaded EVs were collected from engineered Expi293F cells using standard methodology, characterized using nanoparticle tracking analysis, western blotting, and transmission electron microscopy and analysed for CRISPR/Cas9‐mediated functional gene editing in a Cre‐reporter cellular assay. Light‐induced dimerization using Cryptochrome 2 combined with CD9 or a Myristoylation‐Palmitoylation‐Palmitoylation lipid modification resulted in efficient loading with approximately 25 Cas9 molecules per EV and high functional delivery with 51% gene editing of the Cre reporter cassette in HEK293 and 25% in HepG2 cells, respectively. This approach was also effective for targeting knock‐down of the therapeutically relevant PCSK9 gene with 6% indel efficiency in HEK293. Cas9 transfer was detergent‐sensitive and associated with the EV fractions after size exclusion chromatography, indicative of EV‐mediated transfer. Considering the advantages of EVs over other delivery vectors we envision that this study will prove useful for a range of therapeutic applications, including CRISPR/Cas9 mediated genome editing.
Prolymphangiogenic Effects of 9-cis Retinoic Acid Are Enhanced at Sites of Lymphatic Injury and Dependent on Treatment Duration in Experimental Postsurgical Lymphedema.

Background: Patients undergoing surgical treatment for solid tumors are at risk for development of secondary lymphedema due to intraoperative lymphatic vessel injury. The damaged lymphatic vessels fail to adequately regenerate and lymphatic obstruction leads to fluid and protein accumulation in the interstitial space and chronic lymphedema develops as a result. There are currently no effective pharmacological agents that reduce the risk of developing lymphedema or treat pre-existing lymphedema, and management is largely palliative. The present study investigated the efficacy of various 9-cis retinoic acid (9-cis RA) dosing strategies in reducing postsurgical lymphedema by utilizing a well-established mouse tail lymphedema model. Methods and Results: Short-duration treatment with 9-cis RA did not demonstrate a significant reduction in postoperative tail volume, nor an improvement in lymphatic clearance. However, long-term treatment with 9-cis RA resulted in decreased overall tail volume, dermal thickness, and epidermal thickness, with an associated increase in functional lymphatic clearance and lymphatic vessel density, assessed by LYVE-1 immunostaining, compared with control. These effects were seen at the site of lymphatic injury, with no significant changes observed in uninjured sites such as ear skin and the diaphragm. Conclusions: Given the reported results indicating that 9-cis RA is a potent promoter of lymphangiogenesis and improved lymphatic clearance at sites of lymphatic injury, investigation of postoperative 9-cis RA administration to patients at high risk of developing lymphedema may demonstrate positive efficacy and reduced rates of postsurgical lymphedema.
Accelerated sea-level rise is suppressing CO2 stimulation of tidal marsh productivity: A 33-year study

Accelerating relative sea-level rise (RSLR) is threatening coastal wetlands. However, rising CO2 concentrations may also stimulate carbon sequestration and vertical accretion, counterbalancing RSLR. A coastal wetland dominated by a C3 plant species was exposed to ambient and elevated levels of CO2 in situ from 1987 to 2019 during which time ambient CO2 concentration increased 18% and sea level rose 23 cm. Plant production did not increase in response to gradually rising ambient CO2 concentration during this period. Elevated CO2 increased shoot production relative to ambient CO2 for the first two decades, but from 2005 to 2019, elevated CO2 stimulation of production was diminished. The decline coincided with increases in relative sea level above a threshold that hindered root productivity. While elevated CO2 stimulation of elevation gain has the potential to moderate the negative impacts of RSLR on tidal wetland productivity, benefits for coastal wetland resilience will diminish in the long term as rates of RSLR accelerate.
Multi-omics approaches for comprehensive analysis and understanding of the immune response in the miniature pig breed

The porcine immune system has an important role in pre-clinical studies together with understanding the biological response mechanisms before entering into clinical trials. The size distribution of the Korean minipig is an important feature that make this breed ideal for biomedical research and safe practice in post clinical studies. The extremely tiny (ET) minipig serves as an excellent model for various biomedical research studies, but the comparatively frail and vulnerable immune response to the environment over its Large (L) size minipig breed leads to additional after born care. To overcome this pitfall, comparative analysis of the genomic regions under selection in the L type breed could provide a better understanding at the molecular level and lead to the development of an enhanced variety of ET type minipig. In this study, we utilized whole genome sequencing (WGS) to identify traces of artificial selection and integrated them with transcriptome data generated from blood samples to find strongly selected and differentially expressed genes of interest. We identified a total of 35 common genes among which 7 were differentially expressed and showed selective sweep in the L type over the ET type minipig breed. The stabilization of these genes were further confirmed using nucleotide diversity analysis, and these genes could serve as potential biomarkers for the development of a better variety of ET type pig breed.
Feature-based Control of Physics-based Character Animation

Creating controllers for physics-based characters is a long-standing open problem in animation and robotics. Such controllers would have numerous applications while potentially yielding insight into human motion. Creating controllers remains difficult: current approaches are either constrained to track motion capture data, are not robust, or provide limited control over style. This thesis presents an approach to control of physics-based characters based on high-level features of human movement, such as center-of-mass, angular momentum, and end-effector motion. Objective terms are used to control each feature, and are combined via optimization. We show how locomotion can be expressed in terms of a small number of features that control balance and end-effectors. This approach is used to build controllers for biped balancing, jumping, walking, and jogging. These controllers provide numerous benefits: human-like qualities such as arm-swing, heel-off, and hip-shoulder counter-rotation emerge automatically during walking; controllers are robust to changes in body parameters; control parameters apply to intuitive properties; and controller may be mapped onto entirely new bipeds with different topology and mass distribution, without controller modifications. Transitions between multiple types of gaits, including walking, jumping, and jogging, emerge automatically. Controllers can traverse challenging terrain while following high-level user commands at interactive rates. This approach uses no motion capture or off-line optimization process. Although we focus on the challenging case of bipedal locomotion, many other types of controllers stand to benefit from our approach.
Robust finite-time line-of-sight angular rate estimation in missile guidance

This paper documents a robust finite-time line-of-sight angular rate estimation in missile guidance. Through geometric homogeneity and Lyapunov theories, it is shown that the observer estimation errors can converge into a bounded nonzero residual set in finite time and the upper bound can be lowered by parameter tunings. For estimation performance improvement, the sliding mode gains are also determined theoretically. With the help of these gains, it is proved that the observer estimation errors can converge to zero in finite time. Detailed simulation results with some comparisons are performed to validate the proposed formulation.
Energy Adaptive Infrastructure for Sustainable Cloud Data Centres

With the raising concerns about the environment, the ICT equipments have been pointed out as a major and ever rising source of energy consumption and pollution. Among those ICT equipments, data centres play obviously a major role with the rise of the Cloud computing paradigm. In the recent years, researchers have focused on reducing the energy consumption of data centres. Furthermore, future environmentally friendly data centres are also expected to prioritize the usage of renewable energies over brown energies. However, managing the energy consumption within a data centre is challenging because data centres are complex facilities which supports a huge variety of hardware, computing styles and SLAs. Those may evolve through time as user requirements can change rapidly. Furthermore, differently from non-renewable energy sources, the availability of renewable energies is very volatile and time dependent: e.g. solar power is obtainable only during the day, and is subject to variations due to the meteorological conditions. The goal in this case is to shift the workload of running applications, according to the forecasted availability of the renewable energy. In this thesis we propose a flexible framework called Plug4Green able to reduce the energy consumption of a Cloud data centre. Plug4Green is based on the Constraint Programming paradigm, allowing it to take into account a great number of constraints regarding energy, hardware and SLAs in data centres. We also propose the concept of an energy adaptive software controller (EASC), able to augment the usage of renewable energies in data centres. The EASC supports two kind of applications: service-oriented and task-oriented applications; and two kind of computing environments: Infrastructure as a Service and Platform as a Service. We evaluated our solutions in several trials executed in the testbeds of Milan and Trento, Italy. Results show that Plug4Green was able to reduce the power consumption by 27% in the Milan trial, while the EASC was able to augment the renewable energy percentage by 7.07pp in the Trento trial.
Using Social Indicators to Evaluate the Effectiveness of Outreach in Two Indiana Watersheds

Nonpoint source pollution is recognized as one of the greatest threats to water quality in the United States. Outreach is one tool that can be used to help increase public awareness and motivate action towards addressing water issues. In order to create effective outreach, we must understand public perceptions of water quality, perceived barriers to implementing environmental solutions, and what types of outreach best connect with target audiences. In 2010, social indicator surveys were distributed in two watersheds in Indiana to gather baseline data on urban and agricultural residents' attitudes towards and usage of water quality conservation practices. Local watershed organizations then used various outreach methods to encourage residents to implement specific practices. In 2014, post-project surveys were conducted in both watersheds to assess whether the outreach efforts had been effective. Even with outreach efforts, many residents still were unaware that specific water pollutants were problems in their watershed. There were, however, positive changes in overall water quality attitudes. Changes in awareness and adoption of conservation practices varied by watershed and resident type, yet generally moved in a positive direction or were unchanged. The primary barrier to practice adoption for all respondents was cost. Outreach events were generally not well attended and did little to change attendee behavior. Some outreach activities seem to be more useful than others in terms of self-reported effectiveness while others are clearly visible to the community and may be a helpful way to raise awareness.
The fruB Gene of Streptococcus mutans Encodes an Endo-Levanase That Enhances Growth on Levan and Influences Global Gene Expression

Carbohydrate metabolism and acid production are essential for the development of dental caries. As a by-product of sucrose metabolism, formation, and degradation of fructans enhances the severity of caries by S. mutans in animal models. ABSTRACT Streptococcus mutans, the primary etiologic agent of human dental caries, and a variety of oral Streptococcus and Actinomyces spp. synthesize high molecular mass homopolymers of fructose (fructans) with predominantly β2,1- (inulins) or β2,6-linkages (levans). The ability of S. mutans to degrade fructans contributes to the severity of dental caries. The extracellular product of fruA of S. mutans is an exo- β-d-fructofuranosidase that releases fructose from levan and inulin. Located 70 bp downstream of fruA, fruB encodes a member of the glycoside hydrolase family 32, but the function of FruB has not been established. Growth assays performed using wild-type UA159 and fruB-deficient derivatives, with fructans as the sole carbohydrate source, showed a significant reduction in the growth rate of a fruB mutant on levan, but not on inulin. A purified, recombinant FruB protein degraded levan to release mainly fructooligosaccharides. Driven by the fruA promoter and a secondary promoter located in the 3′ region of the fruA sequence, the fruB gene is inducible by fructose and especially by levan, but a stable stem-loop structure in the intergenic region likely modulates transcriptional read-through from fruA. Transcriptomic analysis of UA159 and a fruB mutant grown on 0.2% levan revealed differential expression of genes encoding ABC transporters, transcriptional regulators and genes involved in growth and stress tolerance. The ability of FruB to enhance levan metabolism and the high degree of conservation of FruB across S. mutans isolates imply a significant contribution of FruB to the fitness and virulence of this pathogen in human dental biofilms. IMPORTANCE Carbohydrate metabolism and acid production are essential for the development of dental caries. As a by-product of sucrose metabolism, formation, and degradation of fructans enhances the severity of caries by S. mutans in animal models. This study highlights a significant breakthrough in identifying FruB in S. mutans as an endolevanase that contributes to efficient utilization of levan, a specific type of fructan produced by certain commensals but not S. mutans. Transcriptomic analysis revealed that FruB-dependent levan metabolism impacted global gene regulation, including a large number of novel genes. Considering the preference for levan by both FruA and FruB, the conservation of fruAB in S. mutans might represent a competitive advantage in access to the energy storage produced by dental microbiome. This is the first report demonstrating the presence of an endolevanase in S. mutans, therefore should be of broad interest to the fields of dental caries and complex carbohydrate metabolism.
Advance of T regulatory cells in tumor microenvironment remodeling and immunotherapy in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is highly aggressive, deadly, and is rarely diagnosed early. Regulatory T cells (Treg) are a multifunctional class of immunosuppressive T cells that help maintain immunologic homeostasis and participate in autoimmune diseases, transplants, and tumors. This cell type mediates immune homeostasis, tolerance, and surveillance and is associated with poor outcomes in PDAC. Tregs remodel the tumor immune microenvironment, mediate tumor immune escape, and promote tumor invasion and metastasis. A promising area of research involves regulating Tregs to reduce their infiltration into tumor tissues. However, the complexity of the immune microenvironment has limited the efficacy of immunotherapy in PDAC. Treg modulation combined with other treatments is emerging. This review summarizes the mechanisms of Tregs activity in tumor immune microenvironments in PDAC and the latest developments in immunotherapy and clinical trials.
Hierarchical Bayesian modeling of multi-country mortality rates

As world populations age along with speedy internationalization, forecasting mortality for multiple countries or populations with similar socio-economic conditions or close cultural connections has become essential. We apply the hierarchical Bayesian theory to the random walk with drift model governing the dynamics of the logarithm of central death rates for each age and population. Using the mortality data for both genders of three developed countries for an age span 25–84 and a series of fitting age-year windows, and further extending the data set to include both genders of twenty countries, we conclude that the proposed hierarchical Bayesian framework can more accurately capture the mortality trends and overall outperforms the Lee–Carter model and its three extensions in mortality forecasting. Grouping both genders of the twenty countries in three ways, we find that the expected improvement rates per year in the logarithm of central death rate for all twenty countries converge to about 2% except for the US.
Luminescence imaging and toxicity assessment of graphene quantum dots using in vitro models

Abstract Graphene quantum dots (GQDs) have been of high interest due to their size and optical characteristics, which improves when functional groups are added to their borders and defects. In this work, the in vitro toxicity of aqueous dispersion of GQDs (w/wo amino-functionalization) was investigated in two different cellular models (S. cerevisiae and H9c2 cell line). Results in yeast suggest that when at up to 25 % volume concentration, the effect of all tested GQDs was only inhibitory, and, in both cellular models, the toxic effect is rigorously dose-dependent. The comparison of IC50 values of all the tested GQDs reveals no significant variations among them, pointing to non-carbonized citric acid as the more toxic precursor. The obtained data suggest that functionalization makes GQDs less toxic, being the one functionalized with thioacetamide slightly more toxic, followed by the ones functionalized with thiourea and glutathione, respectively. Results confirm that their toxicity is characteristics as a whole, and not as the sum of the toxicity of the precursors. In both models, concentrations up to 2 % showed no significant toxicity. Finally, fluorescence microscopy images suggest that GQDs interact with the cellular membrane and enter in the cell, manifesting fluorescent properties.
Deep Learning for Time Series Forecasting: Tutorial and Literature Survey

Deep learning based forecasting methods have become the methods of choice in many applications of time series prediction or forecasting often outperforming other approaches. Consequently, over the last years, these methods are now ubiquitous in large-scale industrial forecasting applications and have consistently ranked among the best entries in forecasting competitions (e.g., M4 and M5). This practical success has further increased the academic interest to understand and improve deep forecasting methods. In this article we provide an introduction and overview of the field: We present important building blocks for deep forecasting in some depth; using these building blocks, we then survey the breadth of the recent deep forecasting literature.
Participatory Design, Development, and Testing of Assistive Health Robots with Older Adults: An International Four-year Project

Participatory design includes stakeholders in the development of products intended to solve real-life challenges. Involving end users in the design of robots is vital for developing effective, useful, acceptable and user-friendly products that meet expectations, needs, and preferences. This four-year international project developed and evaluated a home-based robot for mood stabilization and cognitive improvement in older adults with mild cognitive impairment and age-related health needs. The daily-care robot was developed in collaboration with experts, carers, relatives, and older adults, through six phases. Two phases were dedicated to cognitive stimulation games. This paper provides a summary of the participatory design and mixed-methods evaluation processes undertaken to develop, refine, and test the robot. The final robot and games were acceptable to older adults, and useful for delivering stimulating activities and providing reminders for medication, health and wellbeing checks. Personalization is required to optimize human-robot interaction, and imagery and speech should be consistent with local users. Functions should be personalizable to accommodate individual health needs and preferences. This project highlights the importance of participatory design and testing robotics in end-user environments, as technical issues associated with long-term use were uncovered. Recommendations for future development and the design of assistive health robots are made.