Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-instructional roles for Notch signaling in T cell development

Mammalian immunity requires the presence of a broad and diverse repertoire of antigen receptors that can recognize the virtually infinite number of pathogenic epitopes encountered over a lifetime of a host, along with the ability to flexibly mount organized and pathogen-specific immune responses, as orchestrated by cytokines and CD4+ helper T (Th) cells. The Notch signaling pathway plays a critical role both in the generation of the T cell repertoire and in Th cell differentiation. However, while Notch is well understood to instruct early T lineage development at the expense of alternate lineages, it is unclear how Notch regulates the differentiation of a common naÃ ̄ve progenitor into one of the many Th cell subsets. To clarify the molecular mechanism used by Notch to influence Th cell differentiation, the dynamics of Notch target binding and gene regulation were analyzed at early time points after T cell activation. Rather than finding that Notch signaling acts via the canonical instructional paradigm, these studies find that Notch acts as an unbiased integrator of environmental differentiation cues, such that it simultaneously promotes the differentiation of multiple inflammatory Th cell populations. These findings are supported by in vivo gain-of-function studies in which Notch signaling is constitutively activated in peripheral T cells. Unlike previous work showing that hyperactivation of the Notch pathway in T lineage progenitors yields aggressive T cell acute lymphoblastic leukemia, these mice go on to develop a lethal autoinflammatory disorder, resulting from the Notch pathway promoting the differentiation of Th1, Th2, and Th17 cells. Additionally, these studies reveal that Notch signaling acts to destabilize regulatory T cell differentiation. Altogether, the work presented in this thesis evinces a novel non-instructional paradigm for Notch signaling, with broad implications for our understanding of Th cell differentiation, hematopoietic development, and cancer biology. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Immunology First Advisor Warren S. Pear
Bats as bioindicators – the need of a standardized method for acoustic bat activity surveys

1. The species‐rich group of bats fills a wide range of ecological niches and provides ecosystem services like pest control. Bats are known to be sensitive to environmental stressors and could, therefore, be used in assessing ecosystem quality. To use bats as bioindicators, a standardized bat survey method needs to be established as the existing approaches vary in their methodology, and results are, therefore, often not comparable.
The spectroscopic detection and bacterial colonisation of synthetic microplastics in coastal marine sediments

Synthetic microplastics (≤5-mm fragments) are anthropogenic contaminants that are rapidly accumulating in coastal environments worldwide. The distribution, abundance, ecological impacts and fate of these pollutants are poorly understood. In this study, a novel reflectance micro-FT-IR spectroscopy method was developed to detect microplastics in sediments from 17 sites (UK), using polyethylene (PE) as the model polymer. Additionally, a 14-day laboratory microcosm experiment was used to characterise bacterial succession on low-density polyethylene (LDPE) fragments over time and across three sediment types (ranging from sand to silt) from the Humber Estuary, UK. In contrast with ATR-FT-IR measurements, micro-FT-IR measurements in reflectance mode were susceptible to refractive error when analysing irregularly shaped PE fragments. However, molecular mapping by reflectance micro-FT-IR spectroscopy successfully detected PE within polymer-spiked sediments and in a non-spiked sediment retentate. Moreover, reflectance micro-FT-IR spectra of PE were consistent across all 17 sampling sites. Bacteria were found to rapidly colonise LDPE fragments, with bacterial community structure and diversity differing significantly from those in bulk sediments, as demonstrated by scanning electron microscopy, T-RFLP analysis and 16S rRNA gene sequencing. The composition of LDPE-colonising assemblages within different sediment types increasingly converged over time, with 16S rRNA gene sequencing analysis identifying site-specific populations of the genera Arcobacter (Epsilonproteobacteria) and Colwellia (Gammaproteobacteria) as dominant members (up to 93% of sequences) of the plastic-associated communities after 14 days of exposure. Log-fold increases in the relative abundance of LDPE-associated bacteria occurred within 7 days of exposure with bacterial abundance differing significantly across sediment types, as shown by Q-PCR amplification of 16S rRNA genes. Attachment of bacterial cells and specifically of Colwellia spp. onto LDPE surfaces was demonstrated by CARD-FISH analysis. These results provide a foundation to both developing improved spectroscopy methods to detect microplastics, and characterising ecological interactions between microorganisms and microplastic debris within marine sediments.
The Venusian Atmospheric Oxygen Ion Escape: Extrapolation to the Early Solar System

The present atmosphere of Venus contains almost no water, but recent measurements indicate that in its early history, Venus had an Earth‐like ocean. Understanding how the Venusian atmosphere evolved is important not only for Venus itself but also for understanding the evolution of other planetary atmospheres. In this study, we quantify the escape rates of oxygen ions from the present Venus to infer the past of the Venusian atmosphere. We show that an extrapolation of the current escape rates back in time leads to the total escape of 0.02–0.6 m of a global equivalent layer of water. This implies that the loss of ions to space, inferred from the present state, cannot account for the loss of an historical Earth‐like ocean. We find that the O+ escape rate increases with solar wind energy flux, where more energy available leads to a higher escape rate. Oppositely, the escape rate decreases slightly with increased extreme ultraviolet radiation (EUV) flux, though the small variation of EUV flux over the measured solar cycle may explain the weak dependency. These results indicate that there is not enough energy transferred from the solar wind to Venus' upper atmosphere that can lead to the escape of the atmosphere over the past 3.9 billion years. This means that the Venusian atmosphere did not have as much water in its atmosphere as previously assumed or the present‐day escape rates do not represent the historical escape rates at Venus. Otherwise, some other mechanisms have acted to more effectively remove the water from the Venusian atmosphere.
An updated overview of the geographic and bathymetric distribution of Savalia savaglia

The distribution of gold coral Savalia savaglia is modified on the basis of bibliographic information and recent occurrence data, collected using a ROV (Remotely Operated Vehicle) and SCUBA divers. The species is long-lived, rare and has been exploited in the past by divers for collection purposes. S. savaglia is listed in Annex II of the SPA/BD Protocol of the Barcelona Convention and has a wider distribution than previously thought, including both the Mediterranean Sea and the Atlantic Ocean. Our results highlighted that specimens mainly live at a depth range of 15-90 m, but may reach as deep as 900 m in the Mediterranean Sea. This species can form monospecific facies of hundreds of colonies, as observed in Montenegro (Adriatic Sea), between 10 and 20 m, and in the Canary Islands, at a depth range of 27-70 m. Recent data highlighted numerous cases of specimens that were endangered by lost fishing gear, which exposed this species to further threats. Considering its longevity and structural role, it is urgent to develop an effective protection measure for S. savaglia , thereby increasing research efforts and implementing protection areas for this species.
Humility, differentiation of self, and clinical training in spiritual and religious competence

ABSTRACT Spiritual and religious (S/R) competence is an important yet under-studied area of clinical multicultural competence. In a sample of clinicians who attended seminars on a specific S/R group training model, we examined the roles of humility and differentiation of self (DoS) in predicting S/R attitudes and S/R self-efficacy, as well as perceived barriers to implementing this training model in clinical settings. DoS mediated the relationship between humility and S/R self-efficacy, but not between humility and S/R attitudes. Further, four barriers emerged to implementing the presented training model. A discussion of the findings and implications for training are included.
Germination and gene expression as affected by aminocyclopropane-1-carboxylic acid in deteriorated soybean seed

ABSTRACT Seed aging leads to reduced germination and vigor, especially in long-term storage, which can significantly reduce crop yields. Hence, identifying genetic mechanisms and providing physiological approaches to alleviate the deterioration process are needed. The current study was conducted in a series of laboratory experiments with soybean (Glycine max (L.) Merr. ) in 2015. Accelerated aging durations (0 d, 6 d, and 10 d), priming solutions [dry seed, water, and 50 µM aminocyclopropane-1-carboxylic acid (ACC)] and priming periods (6 h and 12 h) were considered experimental factors. Total RNA was extracted from whole dry and imbibed seeds using hexadecyltrimethylammonium method. Genes and associated accessions studied were: LIG4 (XM_003546387.3), CTR1 (BW653506.1), GAI1 (BW656807.1), NCED1 (AK244131.1), and NCED5 (AK245513.1). With increasing severity of seed deterioration, the expression of LIG4, CTR1, GAI1, and NCED1 significantly increased, whereas a decreasing trend was observed for NCED5 expression. ACC had an inhibitory effect on germination index in aged soybean seed, which was associated with expression level of LIG4. Priming with ACC considerably reduced the inhibitory effect of CTR1, GAI1, and NCED1 in 6-day aged seeds, resulting in a positive effect on germination. It seems that positive or negative effects of ethylene priming on soybean germination depend on severity of seed deterioration.
A New Sparse Dimension Reduction Method for Hyperspectral Images

Motivated by the development of sparse representation, many sparsity-based methods have been successfully applied in Hyperspectral images (HSI) domain. These methods are beneficial to find the intrinsic structure from the high dimension data. Sparse dimension reduction is becoming one of the research hotspots, more efforts are needed to be further. In this paper, we present a new unsupervised dimension reduction (DR) method, which is called unsupervised double sparse learning method (UDSDL). UDSDL inherits the merits of sparse representation, it can support the possibility of data compressing while preserving more discriminative features. Experiments on a real HSI data set collected by the Airborne visible/Infrared Imaging Spectrometer are performed to demonstrate the effectiveness of the proposed UDSDL method.
Early Mobilization in the ICU: A Multicenter Survey of Clinicians’ Knowledge, Attitude and Practices in Resource-Limited Hospital Settings

Background: Prolonged stay in the Intensive Care Unit (ICU) is associated with impaired physical function, low quality of life and increased cost of care. Evidence suggests early mobilization (EM) in the ICU is safe, feasible and results in physiological and functional improvement in critically ill patients. Despite its benefits, EM in the ICU is not a common practice. Factors relating to healthcare provider, such as level of knowledge, attitude and practices may contribute to this trend. As a first step towards adopting routine EM in our ICU, we investigated the current level of knowledge, attitude and practices of care professional about EM. Methods: We conducted a cross-sectional survey to assess level of knowledge, attitude and practices of clinician towards early mobilization in four teaching hospitals in southwestern Nigeria, using a 20-item questionnaire adapted from previous studies. Results: A total of 131 health care providers comprising of 58 (44%) physicians, 34 (26%) physiotherapist and 39 (30%) nurses participated in the study. Most (89%) clinician indicated knowledge about benefits of EM, but only 30% showed adequate knowledge about what constitute EM. 5% of the participants had knowledge about EM guidelines. 45 (80%) reported that the risk associated with early mobilization of patients on mechanical ventilator (MV) outweighs its benefits. While 75% of the respondents indicated they will not ambulate patient on mechanical ventilator or on vasopressor agents, 65% agreed that critically ill patient could be mobilized in the ICU. Most (83%) of the participants did not train or work at an institution where patients are mobilized in the ICU and consequently feel they are not competent to implement EM. More physiotherapist indicated willingness to ambulate patient on mechanical ventilator, while more physicians reported unwillingness to ambulate patients on vasopressor agents (p<0.05). Conclusion: There is good level of knowledge about early mobilization of intensive care patients among participants, but current level of practice are low as most perceive the risks associated with EM outweigh its benefits.
Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence

Ch. 1: Introduction Ch. 2: Occupancy in Ecological Investigations Ch. 3: Fundamental Principles of Statistical Inference Ch. 4: Single-species, Single-season Occupancy Models Ch. 5: Single-species, Single-season Models with Heterogeneous Detection Probabilities Ch. 6: Design Issues for Single-species, Single-season Occupancy Models Ch. 7: Single-species, Multiple-seasons Occupancy Models Ch. 8: Examining the Local Species Pool Ch. 9: Interspecific Relationships Between Species Ch.10: Extensions and Future Work
Hierarchical Energy Optimization With More Realistic Power Consumption and Interference Models for Ultra-Dense Networks

To fulfill the high capacity requirements of 5G and B5G, ultra-dense network (UDN) is a promising technology. As the network becomes denser, energy consumption becomes one of the primary concerns of the operators. To reduce the power consumption of UDN, in this paper, we propose a hierarchical energy optimization approach with two energy-efficient strategies: one is dynamic coverage for large time-scale scenario; the other is individual power adjustment based on weakly standard interference mapping for small time-scale scenario. Considering a more realistic power consumption model, the optimization problem is formulated as adapting network capacity to users’ demands, so as to improve energy consumption and other network performances e.g., load balancing. The proposed approach owns the following advantages: First, it can obtain the optimal solution with low computational complexity; second, they are distributed and thus the considered problem can be solved in a parallel manner; all of these make the proposed methods suitable for UDN. Simulation results verify that the proposed approach can obtain the optimal solution in few iterations and the complexity of computation is low.
Games for interactive spatial planning: SPLASH a prototype strategy game about water management

The research project Games for interactive spatial planning was carried out within the programme Virtual countryside. This programme aims at exploring new methodologies and technologies to deal with the increasing complexity of the countryside, An overview of games in general, characteristics and genres of games, differences between computerized and non-computerized games, research items and game design procedures are discussed. The interactive planning process and the role games can play in it are described. Finally a case description of the improvement of the prototype SPLASH is given.
Toxin-Antitoxin Battle in Bacteria

Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined "conditional cooperativity". Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxinlevel, and then again transcription at high toxin level ([1] and references therein). Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for wide a range of parameters [2]. We demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state. Conditional cooperativity also secures that the antitoxin dominated state has a substantial amount of toxins present, which helps the transition to the toxin dominated state under stress. These features may be relevant for understanding persister formation in E. coli. References: [1] I. Cataudella, A.Trusina, K. Sneppen, K. Gerdes, and N. Mitarai, Nucl. Acids Res. (2012) 40, 6424-6434. [2] I. Cataudella, K. Sneppen, K. Gerdes, and N. Mitarai, Plos. Comput. Biol. (2013) 8, e1003174.
Sustainable Banking: New Forms of Investing under the Umbrella of the 2030 Agenda

(1) Social Impact Bonds (SIBs) foster the relationships between public and private sectors while adding value to new forms of investment that are closely linked to Socially Responsible Investments (SRIs). In this context, Sustainable Developments Goals (SDGs) aim to strengthen global partnerships in order to achieve the 2030 Agenda. Sustainable banking should consider its role in both new responsible investment products and the 2030 Agenda. This study aims to: (i) estimate the ROI of SIBS, (ii) define a financial formulation and a measurement system, and (iii) explain the relationship between SIBs and SDGs. (2) This research analyzes SIBs from an SDG approach, and proposes a valuation model based on a financial options valuation methodology that clarifies the financial value of the world’s first SIB (Peterborough Prison, UK). (3) Findings suggest that investors expect to have a negative return of 16.48%, and that this expected loss may be compensated for by the short- and long-term positive impact of an intervention in society. (4) It is shown that SIBs provide an opportunity to reach SDG 17 and improve sustainable investment portfolios, while providing an opportunity to strengthen a company’s Corporate Social Responsibility policy and its corporate reputation.
Perceived Benefits and Challenges of Flipped Classroom: Voices From Teachers in Hong Kong’s Higher Education

Flipped classroom is increasingly being adopted in higher education institutions worldwide. Many studies on flipped classroom focused on evaluating its impact on students. Relatively little is known about the perceived benefits and challenges of flipped classroom from the teachers’ perspective. The present research conducted indepth interviews with 28 teachers from diverse academic disciplines in five different universities in Hong Kong. These teachers were recruited to share their experiences in adopting flipped classroom in their practice. Flipped classroom was found to be associated with many benefits to the teachers, such as gaining the flexibility in the use of class time, increased opportunity for the teachers’ professional development, and enhanced interaction with students. However, there are challenges in integrating flipped classroom in their teaching practice. Specifically, many found it challenging to motivate students to engage in the pre-class learning material. Their workload also increased when implementing and managing the flipped classroom. It was difficult for some of them to adopt the new teaching approach. The teachers also shared a variety of strategies to overcome these challenges. Possible measures of institutional support to help teachers to reap the benefits of this new learning approach while mitigating the challenges will be discussed.
Fast Scale Invariant Tracker and Re-identification for First-Person Social Videos

ABSTRACT We address the problem of pedestrian tracking in videos of crowded scene which are captured by first-person viewpoint. The constant motion of camera and pedestrian makes this task challenging. The prime challenges are natural head motion of wearer and target loss and reappearance in a later frame, due to frequent changes in field of view. We propose that the use of first-person vision specific optical flow information and also the modification in the update process along with search region of trackers are useful to identify a lost target in a later frame. This process is termed re-identification in this paper. The specific trackers modified are MEEM and STRUCK. In addition to re-identification we achieve scale invariant tracking (upto scale variation) and speed up by a factor of 2. We name our tracker as EgoTracker, since it utilizes the information which is specific to egocentric vision.
EFFECT OF ANTIOXIDATIVE TREATMENTS ON LIPID OXIDATION IN SKINLESS FILLET OF PACIFIC SAURY COLOLABIS SAIRA IN FROZEN STORAGE

Skinless fillets were prepared from Pacific saury Cololabis saira of varying degrees of freshness and then stored at −20 and −40C for 12 months to investigate the effects of lipid oxidation on quality deterioration. Peroxide value and 4-hydroxy-2-hexenal levels increased with storage temperature (−40 < −20C) and corresponded with freshness. Peroxide value and 4-hydroxy-2-hexenal levels increased remarkably in frozen-thawed Pacific saury skinless fillets in comparison with raw Pacific saury; vitamin E was reduced for only 3 months. Lipid oxidation was inhibited when antioxitant-treated skinless fillets were stored at −20C for 12 months, immersed in 0.8% vitamin E or packed with an oxygen absorber. The 4-hydroxy-2-hexenal content was strongly correlated with propanal, a decomposition product of lipid oxidation that yields a fishy odor. PRACTICAL APPLICATIONS This study introduces processing techniques for high quality of skinless fillets from Pacific saury and evaluates the lipid oxidation levels of skinless fillets stored in freezer for 12 months. Results of this study will contribute to prevent fish product such as skinless fillets from lipid oxidation and to improve the quality of skinless fillets from fatty fish such as the Pacific saury.