Miracle-dz/UniFAR-FTUs huggingface dataset:
Hydrogels for 3D Neural Tissue Models: Understanding Cell-Material Interactions at a Molecular Level

The development of 3D neural tissue analogs is of great interest to a range of biomedical engineering applications including tissue engineering of neural interfaces, treatment of neurodegenerative diseases and in vitro assessment of cell-material interactions. Despite continued efforts to develop synthetic or biosynthetic hydrogels which promote the development of complex neural networks in 3D, successful long-term 3D approaches have been restricted to the use of biologically derived constructs. In this study a poly (vinyl alcohol) biosynthetic hydrogel functionalized with gelatin and sericin (PVA-SG), was used to understand the interplay between cell-cell communication and cell-material interaction. This was used to probe critical short-term interactions that determine the success or failure of neural network growth and ultimately the development of a useful model. Complex primary ventral mesencephalic (VM) neural cells were encapsulated in PVA-SG hydrogels and critical molecular cues that demonstrate mechanosensory interaction were examined. Neuronal presence was constant over the 10 day culture, but the astrocyte population decreased in number. The lack of astrocytic support led to a reduction in neural process outgrowth from 24.0 ± 1.3 μm on Day 7 to 7.0 ± 0.1 μm on Day 10. Subsequently, purified astrocytes were studied in isolation to understand the reasons behind PVA-SG hydrogel inability to support neural network development. It was proposed that the spatially restrictive nature (or tight mesh size) of PVA-SG hydrogels limited the astrocytic actin polymerization together with a cytoplasmic-nuclear translocation of YAP over time, causing an alteration in their cell cycle. This was confirmed by the evaluation of p27/Kip1 gene that was found to be upregulated by a twofold increase in expression at both Days 7 and 10 compared to Day 3, indicating the quiescent stage of the astrocytes in PVA-SG hydrogel. Cell migration was further studied by the quantification of MMP-2 production that was negligible compared to 2D controls, ranging from 2.7 ± 2.3% on Day 3 to 5.3 ± 2.9% on Day 10. This study demonstrates the importance of understanding astrocyte-material interactions at the molecular level, with the need to address spatial constraints in the 3D hydrogel environment. These findings will inform the design of future hydrogel constructs with greater capacity for remodeling by the cell population to create space for cell migration and neural process extension.
Cyclin G2 Inhibits Oral Squamous Cell Carcinoma Growth and Metastasis by Binding to IGFBP3 and Regulating the FAK-SRC-STAT Signaling Pathway

The cell cycle protein cyclin G2 is considered a tumor suppressor. However, its regulatory effects and potential mechanisms in oral cancers are not well understood. This study aimed to investigate the effect of cyclin G2 on oral squamous cell carcinoma (OSCC). The data from 80 patients with OSCC were utilized to predict the abnormal expression of cyclin G2. The proliferation and metastasis were determined by a cell counting Kit-8 assay, flow cytometry, a wound-healing assay and a cell invasion assay. The expression of key proteins and genes associated with the cyclin G2 signaling pathways was determined by western blotting and real-time PCR, respectively. The orthotopic nude mice model was established by a mouth injection of SCC9 cells overexpressing cyclin G2. We showed that the low level of cyclin G2 in OSCC, which is negatively correlated with clinical staging, was a negative prognostic factor for the disease. We also found that cyclin G2 inhibited the proliferation, metastasis and blocked the cell cycle at G1/S of OSCC cells, suggesting that cyclin G2 has an inhibitory effect in OSCC. Mechanistically, cyclin G2 inhibited the growth and metastasis of OSCC by binding to insulin-like growth factor binding protein 3 (IGFBP3) and regulating the focal adhesion kinase (FAK) -SRC-STAT signal transduction pathway. Cyclin G2 competed with integrin to bind to IGFBP3; the binding between integrin and IGFBP3 was reduced after cyclin G2 overexpression, thereby inhibiting the phosphorylation of FAK and SRC. These results showed that cyclin G2 inhibited the progression of OSCC by interacting with IGFBP3 and that it may be a new target for OSCC treatment.
Depauperation and divergence of plant‐specialist herbivore assemblages in a fragmented tropical landscape

1. Our understanding of the structure and spatial organisation of biological assemblages in human‐modified tropical landscapes has critical importance to improve conservation actions. Investigations on this topic have focused on local (α) diversity patterns, overlooking the changes in species turnover (β diversity) between sites, and its consequences on total (γ) diversity.
Talent, Career Choice and Competition: The Gender Wage Gap at the Top

We propose a management career model where females face a gender-specific career hurdle. We show that female managers will, on average, be more skilled than male managers, since females from the low end of the talent distribution will abstain from investing in a career as a manager. The average female manager will then be better at mitigating more intense product market competition. When the intensity of product market competition increases, hirings and wages for female managers will therefore increase relative to those of male managers. Using Swedish matched employer-employee data, we find strong empirical evidence for all these predictions.
Parental perceptions of COVID-19–like illness in their children

Objectives The objective of the study is to explore parents' perceptions of COVID-19–like symptoms in their child and attitudes towards isolating from others in the household when unwell. Study design The study used qualitative, semistructured interviews. Methods The study involved thirty semistructured telephone interviews with parents of children between 4 and 18 years. Thirty semistructured telephone interviews with parents of children between 4 and 18 years. Results We found four themes relating to symptom attribution (‘normalising symptoms’, ‘err on the side of caution’, ‘experience of temperature’, ‘symptoms not normal for us’). In general, parents were more likely to attribute symptoms to COVID-19 if a temperature was present or the symptoms were perceived as ‘unusual’ for their family. Four themes relating to self-isolation (‘difficult to prevent contact with children’, ‘isolation would be no different to lockdown life’, ‘ability to get food and supplies’, ‘limited space’). Parents believed they would find isolation within the household difficult or impossible if they had dependent children, had limited space or could not shop for groceries. Conclusions The findings highlight complexities in symptom perception, attribution and household isolation. We suggest that they can be overcome by (a) providing better guidance on what symptoms require action, (b) providing guidance as to how to prevent infection within the household and (c) by supporting families with grocery shopping through a potential second or third wave.
Induction of Progenitor Exhausted Tissue-Resident Memory CD8+ T Cells Upon Salmonella Typhi Porins Adjuvant Immunization Correlates With Melanoma Control and Anti-PD-1 Immunotherapy Cooperation

Immunotherapy has improved the clinical response in melanoma patients, although a relevant percentage of patients still cannot be salvaged. The search for the immune populations that provide the best tumor control and that can be coaxed by immunotherapy strategies is a hot topic in cancer research nowadays. Tumor-infiltrating TCF-1+ progenitor exhausted CD8+ T cells seem to grant the best melanoma prognosis and also efficiently respond to anti-PD-1 immunotherapy, giving rise to a TIM-3+ terminally exhausted population with heightened effector activity. We tested Porins from Salmonella Typhi as a pathogen associated molecular pattern adjuvant of natural or model antigen in prophylactic and therapeutic immunization approaches against murine melanoma. Porins induced protection against melanomas, even upon re-challenging of tumor-free mice. Porins efficiently expanded IFN-γ-producing CD8+ T cells and induced central and effector memory in lymph nodes and tissue-resident (Trm) T cells in the skin and tumors. Porins induced TCF-1+ PD-1+ CD8+ Trm T cells in the tumor stroma and the presence of this population correlated with melanoma growth protection in mice. Porins immunization also cooperated with anti-PD-1 immunotherapy to hamper melanoma growth. Importantly, the potentially protective Trm populations induced by Porins in the murine model were also observed in melanoma patients in which their presence also correlated with disease control. Our data support the use of cancer vaccination to sculpt the tumor stroma with efficient and lasting Trm T cells with effector activities, highlighting the use of Porins as an adjuvant. Furthermore, our data place CD8+ Trm T cells with a progenitor exhausted phenotype as an important population for melanoma control, either independently or in cooperation with anti-PD-1 immunotherapy.
Associations of Platelet Count with Inflammation and Response to Anti-TNF-α Therapy in Patients with Ankylosing Spondylitis

Background: Increased platelet count has been reported in ankylosing spondylitis (AS) patients, but its clinical significance is still largely elusive. The objective of this study was to evaluate the clinical role of platelet count in AS patients, especially its impact on treatment outcomes. Methods: A case-control study containing 35 AS patients receiving anti-tumor necrosis factor-α (anti-TNF-α) therapy and 45 healthy controls was performed, and AS patients were followed at least 6 months after anti-TNF-α therapy. A systematic review and meta-analysis of studies containing relevant data on outcomes of interest was also performed. Results: AS patients had significantly higher platelet count than controls (p = 0.0001), and the significantly increased platelet count in AS patients was confirmed in a meta-analysis of 14 studies involving 1,223 AS patients and 913 controls (mean difference = 39.61, 95% CI 27.89–51.34, p < 0.001). Besides, platelet count was significantly correlated with ESR (p < 0.001) and was moderately correlated with ASDAS-CRP score (p = 0.002). Moreover, anti-TNF-α therapy could reduce platelet count in AS patients at the first month and the effect was maintained through the treatment duration. In the prospective follow-up study of those 35 AS patients, those responders to anti-TNF-α therapy had significantly lower platelet count than nonresponders (p = 0.015). Logistic regression analysis suggested that lower platelet count was associated with higher possibility of achieving good response to anti-TNF-α therapy in AS patients (odds ratio = 2.26; 95% CI = 1.06–4.82; p = 0.035). Conclusion: This study suggested that platelet count was associated with inflammation severity and treatment outcomes in AS patients, and elevated platelet count was a promising biomarker of poorer response to anti-TNF-α therapy. The findings above need to be validated in more future studies.
Coordination of Morpho-Physiological and Metabolic Traits of Cistus incanus L. to Overcome Heatwave-Associated Summer Drought: A Two-Year On-Site Field Study

The shrub Cistus incanus L. is well-adapted to Mediterranean conditions thanks to its morpho-anatomical, physiological and biochemical traits. However, its distribution and survival in coastal dunes will be likely threatened by ongoing runaway climate change. We investigated how the harsh climatic conditions generated by the 2015 summer heat wave triggered specific anatomical, physiological, and biochemical responses of this species in its natural environment. These adjustments were compared to those measured in summer 2014. The drier and hotter conditions of summer 2015 determined an increment in leaf lamina thickness, due to a greater palisade parenchyma, thus leading to an increase in the whole leaf mass per area. These morphoanatomical adjustments enhanced leaf resistance against dehydration, optimized carbon assimilation, and delayed leaf senescence. In addition, the higher amount of secondary metabolites detected for 2015, in particular tannins and monoterpenes, contributed to the maintenance of physiological performances even under hotter and drier conditions, preventing oxidative stress through the consumption of excess reducing power. In conclusion, our study offers new evidence on the integration of morphophysiological and metabolic adjustments of this species growing in its natural habitat to cope with ongoing climate change.
Comparison of Humoral Immune Responses to Different Forms of Salmonella enterica Serovar Gallinarum Biovar Gallinarum

Fowl typhoid is caused by Salmonella enterica serovar Gallinarum biovar Gallinarum (SG), and live attenuated, rough vaccine strains have been used. Both humoral and cellular immune responses are involved in protection, but the humoral responses to different forms of SG antigens are unclear. In this study, we compared humoral responses to a killed oil-emulsion (OE) smooth vaccine (SG002) and its rough mutant vaccine (SR2-N6) strains using proteomics techniques. We identified two immunogenic outer membrane proteins (OmpA and OmpX), and the selected linear epitopes were successfully applied in peptide-ELISA. Our peptide- and total OMP-ELISAs were used to compare the temporal humoral responses to various SG antigens: OE SG002 and SR2-N6; live, killed [PBS-suspension (PS) and OE)] and mixed (live and PS) formulations of another rough vaccine strain (SG 9R); and orally challenge with a field strain. Serum antibodies to the linear epitopes of OmpA and OmpX lasted only for the first 2 weeks, but serum antibodies against OMPs increased over time. The rough strain (SR2-N6) and mixed SG 9R induced higher serum antibody titers than the smooth strain (SG002) and single SG 9R (OE, live and PS SG 9R), respectively. Infection with the field strain delayed the serum antibody response by ~2 weeks. Mucosal immunity was not induced by any formulation, except for infection with the field strain after SG 9R vaccination. Thus, our results may be useful to understand humoral immunity against various SG antigens and to improve vaccine programs and serological diagnosis in the field.
Comparative whole-genome analysis reveals genetic adaptation of the invasive pinewood nematode

Genetic adaptation to new environments is essential for invasive species. To explore the genetic underpinnings of invasiveness of a dangerous invasive species, the pinewood nematode (PWN) Bursaphelenchus xylophilus, we analysed the genome-wide variations of a large cohort of 55 strains isolated from both the native and introduced regions. Comparative analysis showed abundant genetic diversity existing in the nematode, especially in the native populations. Phylogenetic relationships and principal component analysis indicate a dominant invasive population/group (DIG) existing in China and expansion beyond, with few genomic variations. Putative origin and migration paths at a global scale were traced by targeted analysis of rDNA sequences. A progressive loss of genetic diversity was observed along spread routes. We focused on variations with a low frequency allele (<50%) in the native USA population but fixation in DIG, and a total of 25,992 single nuclear polymorphisms (SNPs) were screened out. We found that a clear majority of these fixation alleles originated from standing variation. Functional annotation of these SNP-harboured genes showed that adaptation-related genes are abundant, such as genes that encode for chemoreceptors, proteases, detoxification enzymes, and proteins involved in signal transduction and in response to stresses and stimuli. Some genes under positive selection were predicted. Our results suggest that adaptability to new environments plays essentially roles in PWN invasiveness. Genetic drift, mutation and strong selection drive the nematode to rapidly evolve in adaptation to new environments, which including local pine hosts, vector beetles, commensal microflora and other new environmental factors, during invasion process.
Dynamic Variation Characteristics of the Riparian Zone Temperature Distribution under Fluctuating Water Levels: Field Experiments and Numerical Modeling

ABSTRACT Ren, J.; Chen, B. ; Li, Y. ; Dai, J., and Men, L. , 2020. Dynamic variation characteristics of the riparian zone temperature distribution under fluctuating water levels: Field experiments and numerical modeling. Journal of Coastal Research, 36(6), 1178–1196. Coconut Creek (Florida), ISSN 0749-0208. Understanding the variations in water and heat transfer along the riparian zone under water-level fluctuations is essential for river water management, groundwater extraction, and ecosystem sustainability. The main purpose of this study is to describe the dynamics of the temperature field of the Dongting Lake beach under the fluctuation in the water level and to quantify its main influencing factors. Taking the section of Dongting Lake beach as the research object, an in situ monitoring device was used to monitor the water level, water temperature, and temperature at different depths of the beach in real time for 55 days, and the hydrothermal coupling model of the Dongting Lake beach was calibrated and verified. The main factors affecting the temperature field of the beach were determined by the global sensitivity analysis method. The results show that the fluctuation in the continental beach temperature field is small in the horizontal direction, the stratification phenomenon is obvious in the vertical direction, the temperature gradually rises with increasing depth, and the daily changes are weakened. During the high water level, the deep temperature of the beach has no obvious gradient change in the vertical direction, and as the water level of the river decreases, the external environmental temperature has a greater influence on the internal temperature field of the beach, resulting in a relatively pronounced gradient change in the deep temperature at the low water level. The results of the Morris one at a time global sensitivity analysis show that the permeability coefficient (Ks) has the greatest influence on the sensitivity of the model, followed by the porosity (n) and soil thermal conductivity (λs). The saturated moisture content (θs), residual moisture content (θr), and soil-specific heat capacity (Cs) have no significant effect on the model.
Exploring Effect of Residual Electric Charges on Cryptographic Circuits

Building leakage models is important in designing countermeasures against side-channel attacks (SCAs), and Hamming-weight/distance (HW/HD) models are traditional leakage models. Electromagnetic analysis (EMA) attacks using a tiny EM probe are the most powerful SCAs. Recent studies have reported that EMA attacks can measure SCA leaks not included in the HW/HD models [16,19]. A current-path leak is one such leak, and a mirror circuit was introduced as a countermeasure against it. We experimentally found that a mirror circuit insufficiently hides (decreases) EMA leaks, resulting in residual electric charges (RECs) between stacked transistors leaking secret information. REC leaks are not included in the current-path leakage model as well as the HW/HD leakage models. RECs can carry the history of the gate's state over multiple clock cycles. Therefore, we propose a countermeasure against REC leaks and designed advanced encryption standard-128 (AES-128) circuits using IO-masked dual-rail read-only memory (MDR-ROM) with a 180-nm complementary metal-oxide-semiconductor (CMOS) process. We compared the resilience of our AES-128 circuits against EMA attacks with and without our countermeasure. We also discuss RECs' effect on physically unclonable functions (PUFs). RECs do not make PUFs vulnerable but affect PUF performance. We demonstrate that RECs affect the performance of arbiter PUFs (APUFs) we fabricated with 180- and 40-nm CMOS processes.
Complete Genome Sequences of the Escherichia coli Donor Strains ST18 and MFDpir

Escherichia coli ST18 and MFDpir are donors commonly used to transfer oriTRP4-containing plasmids to diverse bacteria via conjugation. ST18 and MFDpir were constructed via multiple genetic manipulations involving several E. coli strains. Here, we used Illumina and Nanopore sequencing to determine the complete genomes of these widely used strains. ABSTRACT Escherichia coli ST18 and MFDpir are donors commonly used to transfer oriTRP4-containing plasmids to diverse bacteria via conjugation. ST18 and MFDpir were constructed via multiple genetic manipulations involving several E. coli strains. Here, we used Illumina and Nanopore sequencing to determine the complete genomes of these widely used strains.
Data-Driven Supervised Learning for Life Science Data

Life science data are often encoded in a non-standard way by means of alpha-numeric sequences, graph representations, numerical vectors of variable length, or other formats. Domain-specific or data-driven similarity measures like alignment functions have been employed with great success. The vast majority of more complex data analysis algorithms require fixed-length vectorial input data, asking for substantial preprocessing of life science data. Data-driven measures are widely ignored in favor of simple encodings. These preprocessing steps are not always easy to perform nor particularly effective, with a potential loss of information and interpretability. We present some strategies and concepts of how to employ data-driven similarity measures in the life science context and other complex biological systems. In particular, we show how to use data-driven similarity measures effectively in standard learning algorithms.
Cell-length heterogeneity: a population-level solution to growth/virulence trade-offs in the plant pathogen Dickeya dadantii

Necrotrophic plant pathogens acquire nutrients from dead plant cells, which requires the disintegration of the plant cell wall and tissue structures by the pathogen. Infected plants lose tissue integrity and functional immunity as a result, exposing the nutrient rich, decayed tissues to the environment. One challenge for the necrotrophs to successfully cause secondary infection (infection spread from an initially infected plant to the nearby uninfected plants) is to effectively utilize nutrients released from hosts towards building up a large population before other saprophytes come. In this study, we observed that the necrotrophic pathogen Dickeya dadantii exhibited heterogeneity in bacterial cell length in an isogenic population during infection of potato tuber. While some cells were regular rod-shape (<10μm), the rest elongated into filamentous cells (>10μm). Short cells tended to occur at the interface of healthy and diseased tissues, during the early stage of infection when active attacking and killing is occurring, while filamentous cells tended to form at a later stage of infection. Short cells expressed all necessary virulence factors and motility, whereas filamentous cells did not engage in virulence, were non-mobile and more sensitive to environmental stress. However, compared to the short cells, the filamentous cells displayed upregulated metabolic genes and increased growth, which may benefit the pathogens to build up a large population necessary for the secondary infection. The segregation of the two subpopulations was dependent on differential production of the alarmone guanosine tetraphosphate (ppGpp). When exposed to fresh tuber tissues or freestanding water, filamentous cells quickly transformed to short virulent cells. The pathogen adaptation of cell length heterogeneity identified in this study presents a model for how some necrotrophs balance virulence and vegetative growth to maximize fitness during infection.