Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of complex life cycles

The majority of all animal species have a metamorphosis, even though fossil evidence suggests that this life-history strategy only evolved a few times. It is thought that ontogenetic niche shifts, where individuals change their diet, habitat, and/or behaviour during their life, have been the first steps towards complex life cycles where individuals undergo metamorphosis. Niche shifts and metamorphosis are life-history strategies that evolved millions of years ago. Little is known about the ecological conditions that promoted their evolution. The aim of the research in this thesis is to understand under which ecological conditions niche shifts and metamorphosis may have evolved. The evolution of these life-history strategies is investigated with mathematical models that study evolution in an ecological setting. The results in chapter 2 and 3 show that the evolution of ontogenetic niche shifts is limited by a trade-off between early and late foraging efficiencies. While it is beneficial for individuals to switch to another food source during their development, it is not possible to specialize on this food when this has negative consequences for their offspring. In chapter 4 it is shown that metamorphosis evolves to allow independent evolution of the different life stages. Metamorphosis is, however, very costly and can therefore only evolve under limited conditions. The results in chapter 5 show that metamorphosis does often not disappear when the ecological conditions change. The main result of this thesis is that metamorphosis is difficult to evolve, but, once evolved, it is a robust strategy that does not easily disappear.
Rapid Access of Antibodies to α5β1 Integrin Overexpressed on the Luminal Surface of Tumor Blood Vessels

Integrin α 5 β 1 is overexpressed on endothelial cells of tumor vessels and is uniformly and rapidly accessible to antibodies in the bloodstream. Here, we determined whether antibodies rapidly gain access to integrin overexpressed on the abluminal (basolateral) surface of endothelial cells through vascular leakiness or whether the rapid accessibility results instead because the integrin is overexpressed on the luminal (apical) surface of endothelial cells due to loss of cell polarity. Using tumors in RIP-Tag2 transgenic mice as a model, we first compared the binding pattern of intravascular anti-α 5 β 1 integrin antibody with the leakage pattern of nonspecific IgG. The distributions did not match: anti-α 5 β 1 integrin antibody uniformly labeled the tumor vasculature, but IgG was located in patchy sites of leakage. We next injected an antibody to fibrinogen/fibrin, which resulted in patchy labeling of tumors that matched the leakage of IgG and the overall distribution of fibrin in tumors. Similarly, injected antibodies to the basement membrane protein fibronectin, a ligand of α 5 β 1 integrin, or type IV collagen produced patchy sites of leakage instead of uniform labeling of vascular basement membrane. Differences in the kinetics of labeling, which for α 5 β 1 integrin antibody was near maximal by 10 minutes but for the other antibodies gradually increased over 6 hours, indicated differences in accessibility of their respective targets. Isosurface rendering of confocal microscopic images was consistent with antibody binding to α 5 β 1 integrin on the luminal surface of endothelial cells. Together, these findings indicate that the rapid accessibility of α 5 β 1 integrin in RIP-Tag2 tumors results from overexpression of the integrin on the luminal surface of tumor vessels.
Semi-Supervised Learning with Generative Adversarial Networks

As society continues to accumulate more and more data, demand for machine learning algorithms that can learn from data with limited human intervention only increases. Semisupervised learning (SSL) methods, which extend supervised learning algorithms by enabling them to use unlabeled data, play an important role in addressing this challenge. In this thesis, a framework unifying the traditional assumptions and approaches to SSL is defined. A synthesis of SSL literature then places a range of contemporary approaches into this common framework. Our focus is on methods which use generative adversarial networks (GANs) to perform SSL. We analyse in detail one particular GAN-based SSL approach [Dai et al. (2017)]. This is shown to be closely related to two preceding approaches. Through synthetic experiments we provide an intuitive understanding and motivate the formulation of our focus approach. We then theoretically analyse potential alternative formulations of its loss function. This analysis motivates a number of research questions that centre on possible improvements to, and experiments to better understand the focus model. While we find support for our hypotheses, our conclusion more broadly is that the focus method is not especially robust.
Technology transfers, foreign investment and productivity spillovers: evidence from Vietnam

This paper provides new evidence on the relationship between foreign direct investment (FDI) and the productivity of domestic firms. Using a specially designed survey on a sample of over 7,500 manufacturing firms in Vietnam we uncover some of the mechanisms that explain productivity spillovers from FDI through vertical linkages along the supply chain. Our results suggest that domestic firms experience more productivity spillovers through forward linkages from foreign-input suppliers to domestic input users than through backward linkages from foreign customers to domestic producers of inputs. Productivity externalities from upstream sectors are associated with joint venture foreign investors while downstream sectors experience direct technology transfers from upstream wholly foreign owned investors. Spillovers from FDI through backward linkages are also detected but only when competition from imported intermediates is controlled for and are associated with innovations and technology investments made by firms.
Bacillus subtilis biofilm induction by plant polysaccharides

Significance The plant growth-promoting bacterium Bacillus subtilis is frequently found associated with plant roots where it protects plants from infection. Here, we demonstrate that B. subtilis root attachment depends on production of an extracellular matrix that holds the cells together in multicellular communities termed biofilms. We found that plant polysaccharides (major components of the plant’s cell wall) act as an environmental cue that triggers biofilm formation by the bacterium. Furthermore, these plant polysaccharides can serve as a carbon source used to produce the extracellular matrix. This work sheds light on how plants stimulate their colonization by this plant growth-promoting rhizobacterium. Bacillus subtilis is a plant-beneficial Gram-positive bacterium widely used as a biofertilizer. However, relatively little is known regarding the molecular processes underlying this bacterium's ability to colonize roots. In contrast, much is known about how this bacterium forms matrix-enclosed multicellular communities (biofilms) in vitro. Here, we show that, when B. subtilis colonizes Arabidopsis thaliana roots it forms biofilms that depend on the same matrix genes required in vitro. B. subtilis biofilm formation was triggered by certain plant polysaccharides. These polysaccharides served as a signal for biofilm formation transduced via the kinases controlling the phosphorylation state of the master regulator Spo0A. In addition, plant polysaccharides are used as a source of sugars for the synthesis of the matrix exopolysaccharide. The bacterium's response to plant polysaccharides was observed across several different strains of the species, some of which are known to have beneficial effects on plants. These observations provide evidence that biofilm genes are crucial for Arabidopsis root colonization by B. subtilis and provide insights into how matrix synthesis may be triggered by this plant.
On the stability region of congestion control

It is well known that congestion control can be viewed as a distributed iterative algorithm solving a global optimization problem that maximizes the total system utility. In this paper, we study the stability region of a network employing congestion control algorithms derived from such an optimization framework. Previous work in the literature typically adopts a time-scale separation assumption, which assumes that, whenever the number of users in the system changes, the data rates of the users are adjusted instantaneously to the optimal rate allocation computed by the global optimization problem. Under this assumption, it has been shown that such rate allocation policies can achieve the largest possible stability region. However, this time-scale separation assumption, although technically convenient, rarely holds in practice. In this paper, we remove this time-scale separation assumption and show that the largest possible stability region can still be achieved by a large class of congestion control algorithms derived from the optimization framework. Our result provides new insights on the performance implication of congestion control and on the choices of the parameters of the congestion controller.
A longitudinal study of changes in learners' cognitive states during and following an information literacy teaching intervention

Purpose – This paper seeks to identify the changes in cognition associated with becoming information‐literate, specifically, in relation to the evaluation of information. Additionally, it puts forward a model for a teaching and learning intervention that engages the learner and leads to higher order information literacy (IL) thinking. From a theoretical perspective the research integrates ideas from the fields of IL, teaching and learning, e‐learning and information behaviour (IB). Design/methodology/approach – Three interventions were designed to develop the information literacies of first‐year undergraduates studying Sport and Exercise at Staffordshire University, to teach and test IL. Interventions took a blended approach and combined face‐to‐face and online social network learning (OSNL) – also referred to as social media learning (SML) – and focused on one aspect of information literacy: the ability to evaluate source material. Data were captured via interviews, focus groups and from the online discus.
Ultralong-haul transmission of 40-Gb/s RZ-DPSK in a 10/40 G hybrid system over 2500 km of NZ-DSF

We report on dense wavelength-division-multiplexing transmission of 40-Gb/s return-to-zero differential phase-shift keying at distances of 2500 km over conventional nonzero dispersion-shifted fibers with large system margins and small transmission penalties in a hybrid system comprising of interleaved 10and 40-Gb/s data rates. We use all-Raman amplifiers with 100-km amplifier spacing and compare the transmission performance of the hybrid system to that of a system carrying only 40-Gb/s traffic.
Improved tumour control probability with MRI-based prostate brachytherapy treatment planning

Abstract Backgroun. Due to improved visibility on MRI, contouring of the prostate is improved compared to CT. The aim of this study was to quantify the benefits of using MRI for treatment planning as compared to CT-based planning for temporary implant prostate brachytherapy. Material and methods. CT and MRI image data of 13 patients were used to delineate the prostate and organs at risk (OARs) and to reconstruct the implanted catheters (typically 12). An experienced treatment planner created plans on the CT-based structure sets (CT-plan) and on the MRI-based structure sets (MRI-plan). Then, active dwell-positions and weights of the CT-plans were transferred to the MRI-based structure sets (CT-planMRI-contours) and resulting dosimetric parameters and tumour control probabilities (TCPs) were studied. Results. For the CT-planMRI-contours a statistically significant lower target coverage was detected: mean V100 was 95.1% as opposed to 98.3% for the original plans (p < 0.01). Planning on CT caused cold-spots that influence the TCP. MRI-based planning improved the TCPs by 6–10%, depending on the parameters of the radiobiological model used for TCP calculation. Basing the treatment plan on either CT- or MRI-delineations does not influence plan quality. Conclusion. Evaluation of CT-based treatment planning by transferring the plan to MRI reveals underdosage of the prostate, especially at the base side. Planning on MRI can prevent cold-spots in the tumour and improves the TCP.
Validation and application of a novel integrated genetic screening method to a cohort of 1,112 men with idiopathic azoospermia or severe oligozoospermia

Microdeletions of the Y chromosome (YCMs), Klinefelter syndrome (47,XXY), and CFTR mutations are known genetic causes of severe male infertility, but the majority of cases remain idiopathic. Here, we describe a novel method using single molecule Molecular Inversion Probes (smMIPs), to screen infertile men for mutations and copy number variations affecting known disease genes. We designed a set of 4,525 smMIPs targeting the coding regions of causal (n = 6) and candidate (n = 101) male infertility genes. After extensive validation, we screened 1,112 idiopathic infertile men with non‐obstructive azoospermia or severe oligozoospermia. In addition to five chromosome YCMs and six other sex chromosomal anomalies, we identified five patients with rare recessive mutations in CFTR as well as a patient with a rare heterozygous frameshift mutation in SYCP3 that may be of clinical relevance. This results in a genetic diagnosis in 11–17 patients (1%–1.5%), a yield that may increase significantly when more genes are confidently linked to male infertility. In conclusion, we developed a flexible and scalable method to reliably detect genetic causes of male infertility. The assay consolidates the detection of different types of genetic variation while increasing the diagnostic yield and detection precision at the same or lower price compared with currently used methods.
Online Reverse Auctions and the Dynamics of Trust

This research explores the effect of the introduction of online reverse auctions (ORAs) on interorganizational trust between buyers and suppliers in the retail industry. Building upon the notion of the spirit of the technology and the organizing vision, we shed light on the "equivoque" nature of ORAs. In an integrative model, we show how the desocialization associated with the introduction to ORAs can lead to distrust. Our findings show specifically the importance of the role played by technical problems and rumors.
A Systematic Review of Biochar Research, with a Focus on Its Stability in situ and Its Promise as a Climate Mitigation Strategy

Background Claims about the environmental benefits of charring biomass and applying the resulting “biochar” to soil are impressive. If true, they could influence land management worldwide. Alleged benefits include increased crop yields, soil fertility, and water-holding capacity; the most widely discussed idea is that applying biochar to soil will mitigate climate change. This claim rests on the assumption that biochar persists for hundreds or thousands of years, thus storing carbon that would otherwise decompose. We conducted a systematic review to quantify research effort directed toward ten aspects of biochar and closely evaluated the literature concerning biochar's stability. Findings We identified 311 peer-reviewed research articles published through 2011. We found very few field studies that addressed biochar's influence on several ecosystem processes: one on soil nutrient loss, one on soil contaminants, six concerning non-CO2 greenhouse gas (GHG) fluxes (some of which fail to support claims that biochar decreases non-CO2 GHG fluxes), and 16–19 on plants and soil properties. Of 74 studies related to biochar stability, transport or fate in soil, only seven estimated biochar decomposition rates in situ, with mean residence times ranging from 8 to almost 4,000 years. Conclusions Our review shows there are not enough data to draw conclusions about how biochar production and application affect whole-system GHG budgets. Wide-ranging estimates of a key variable, biochar stability in situ, likely result from diverse environmental conditions, feedstocks, and study designs. There are even fewer data about the extent to which biochar stimulates decomposition of soil organic matter or affects non-CO2 GHG emissions. Identifying conditions where biochar amendments yield favorable GHG budgets requires a systematic field research program. Finally, evaluating biochar's suitability as a climate mitigation strategy requires comparing its effects with alternative uses of biomass and considering GHG budgets over both long and short time scales.
Impact of bifurcation lesions on clinical outcome and prognosis of primary angioplasty in acute myocardial infarction.

AIMS The aim of this study was to determine the impact of bifurcation lesions on outcomes after primary percutaneous intervention (PCI) for acute myocardial infarction. METHODS AND RESULTS We retrospectively reviewed a single-centre database of 646 patients admitted for primary angioplasty within 12 hours after AMI. We compared baseline characteristics and outcomes between bifurcation and non-bifurcation lesions. Bifurcation lesions were found in 23% of patients. They predominantly involved the left anterior descending artery. Provisional T-stenting was used in 89.3% of patients (with stenting of the main branch in 82% and of both branches in 7.3%), side-branch protection in 54.6%, and final kissing balloon inflation in 33%. The procedural success rate was 92% for the main branch of bifurcation lesions compared with 93% for non-bifurcation lesions (P=0.65). Major adverse cardiac event (MACE) rates were comparable in the two groups: in-hospital MACE was 13.3% in the bifurcation group versus 11.4% in the non-bifurcation group (P=0.72), and the 1-year total MACE rate was 22.6% in the bifurcation group versus 19.5% in the non-bifurcation group (P=0.56). CONCLUSIONS Bifurcation lesions are common in patients with AMI. In a population with AMI, immediate and mid-term outcomes of primary PCI were similar in patients with and without bifurcation lesions.
Immediate-Early Signaling Induced by E-cadherin Engagement and Adhesion*

Epithelial cell-cell interactions require localized adhesive interactions between E-cadherin on opposing membranes and the activation of downstream signaling pathways that affect membrane and actin dynamics. However, it is not known whether E-cadherin engagement and activation of these signaling pathways are locally coordinated or whether signaling is sustained or locally down-regulated like other receptor-mediated pathways. To obtain high spatiotemporal resolution of immediate-early signaling events upon E-cadherin engagement, we used laser tweezers to place beads coated with functional E-cadherin extracellular domain on cells. We show that cellular E-cadherin accumulated rapidly around beads, reaching a sustained plateau level in 1-3 min. Phosphoinositides and Rac1 co-accumulated with E-cadherin, reached peak levels with E-cadherin, but then rapidly dispersed. Both E-cadherin and Rac1 accumulated independently of Rac1 GTP binding/hydrolysis, but these activities were required for Rac1 dispersal. E-cadherin accumulation was dependent on membrane dynamics and actin polymerization, but actin did not stably co-accumulate with E-cadherin; mathematical modeling showed that diffusion-mediated trapping could account for the initial E-cadherin accumulation. We propose that initial E-cadherin accumulation requires active membrane dynamics and involves diffusion-mediated trapping at contact sites; to propagate further contacts, phosphatidylinositol 3-kinase and Rac1 are transiently activated by E-cadherin engagement and initiate a new round of membrane dynamics, but they are subsequently suppressed at that site to allow maintenance of weak E-cadherin mediated adhesion.
Human health risk assessment of heavy metals via dietary intake of vegetables grown in wastewater irrigated area of Rewa, India

In India, farmers are blindly using untreated industrial waste water for crops and vegetable production especially in peri-urban areas. Nowadays, increasing attention has focused on heavy metal concentrations of vegetables all over the world. Heavy metals have positive and negative roles in human life. Intake of vegetables is an important path of heavy metal toxicity to human being. The use of industrial waste water for irrigation exposes humans at various health risks. This is because heavy metals are not easily biodegradable and consequently can be accumulated in human vital organs. This situation cause varying degree of illness based on acute and chronic exposures. The present study was conducted to assess the risk to human health by heavy metals (Fe, Zn, Cu, Pb, Cd, Mn and Cr) through the intake of locally grown vegetables in Rewa city (M.P.) India, where, soils contaminated with heavy metals were mainly due to waste water irrigation from Cement Plants (Bela and Naubasta) and may be possible atmospheric deposition. The higher standard deviation reveals higher variation as in the heavy metal distributions from the point source of emission to the adjacent areas. In present study a value of intake of heavy metals in human diet was calculated to estimate the risk to human health. From the results the hazardous quotient (HQ) of all studied heavy metals indicated that all vegetables were safe with no risk to human health except for Pb (>1.0 to near 1.0) contamination in Spinach, Cauliflower and Radish had potential for human health risk due to consumption of these vegetables grown in the area having long term uses of untreated waste water for irrigation. Children are at somewhat higher risk than adults. However, DIR (<1.0) & HI (within1.0 to near 5.0) for all studied vegetables was found to be safe i.e. free of risks, it is therefore indicated that there is a relative absence of health risks associated with the ingestion of contaminated vegetables.
Host-seeking behavior and management of tsetse.

Economically important insect species often possess a specific sequence of behaviors susceptible to manipulation or interference by humans. This observation is particularly true of tsetse, Glossina spp. , whose behavior as adults has been successfully exploited with several control techniques. The effectiveness of ground and aerial spraying, for example, is based on knowl­ edge of tsetse resting behavior (1, 55, 68, 112), while the use of baits (animal mimics) exploits tsetse host-seeking behavior (62, 122). In this review, we highlight the most significant discoveries concerning the host-seeking be­ havior of tsetse, particularly in relation to their implementation in improving the efficacy of baits. Both male and female adult tsetse are obligate blood feeders. Behavior associated with this habit, in combination with a relatively low reproductive rate, even when conditions are ideal, make tsetse species vulnerable to management procedures involving baits (60, 74). The concept of using baits to attract and kill tsetse is almost 100 years old. The first record of their successful use was as part of a tsetse eradication campaign on the island of Principe (20). The first bait techniques usually involved traps designed to imitate visually the vertebrate host, or involved