Miracle-dz/UniFAR-FTUs huggingface dataset:
Creation of a Gilded Trap by the High Economic Value of the Maine Lobster Fishery

Abstract: Unsustainable fishing simplifies food chains and, as with aquaculture, can result in reliance on a few economically valuable species. This lack of diversity may increase risks of ecological and economic disruptions. Centuries of intense fishing have extirpated most apex predators in the Gulf of Maine (United States and Canada), effectively creating an American lobster (Homarus americanus) monoculture. Over the past 20 years, the economic diversity of marine resources harvested in Maine has declined by almost 70%. Today, over 80% of the value of Maine's fish and seafood landings is from highly abundant lobsters. Inflation‐corrected income from lobsters in Maine has steadily increased by nearly 400% since 1985. Fisheries managers, policy makers, and fishers view this as a success. However, such lucrative monocultures increase the social and ecological consequences of future declines in lobsters. In southern New England, disease and stresses related to increases in ocean temperature resulted in more than a 70% decline in lobster abundance, prompting managers to propose closing that fishery. A similar collapse in Maine could fundamentally disrupt the social and economic foundation of its coast. We suggest the current success of Maine's lobster fishery is a gilded trap. Gilded traps are a type of social trap in which collective actions resulting from economically attractive opportunities outweigh concerns over associated social and ecological risks or consequences. Large financial gain creates a strong reinforcing feedback that deepens the trap. Avoiding or escaping gilded traps requires managing for increased biological and economic diversity. This is difficult to do prior to a crisis while financial incentives for maintaining the status quo are large. The long‐term challenge is to shift fisheries management away from single species toward integrated social‐ecological approaches that diversify local ecosystems, societies, and economies.
Mapbuilding for dynamic environments using grid vectors

This paper addresses the problem of creating a geometric map with a mobile robot in a dynamic indoor environment. To form an accurate model of the environment, we present a novel map representation called the ‘grid vector’, which combines each vector that represents a directed line segment with a slender occupancy grid map. A modified expectation maximization (EM) based approach is proposed to evaluate the dynamic objects and simultaneously estimate the robot path and the map of the environment. The probability of each grid vector is evaluated in the expectation step and then used to distinguish the vector into static and dynamic ones. The robot path and map are estimated in the maximization step with a graph-based simultaneous localization and mapping (SLAM) method. The representation we introduce provides advantages on making the SLAM method strictly statistic, reducing memory cost, identifying the dynamic objects, and improving the accuracy of the data associations. The SLAM algorithm we present is efficient in computation and convergence. Experiments on three different kinds of data sets show that our representation and algorithm can generate an accurate static map in a dynamic indoor environment.
Epirubicin suppresses proliferative and metastatic potential by downregulating transforming growth factor‐β‐induced expression in urothelial carcinoma

Transforming growth factor‐β‐induced (TGFΒI) is considered to be a vital gene in several carcinomas. In this study we determined the effect of TGFBI on the proliferative and metastatic potential of human urothelial carcinoma (UC) cells as well as its mRNA and protein expression, which were detected by RT‐PCR and western blot, respectively. UC cell proliferation was analyzed by WST‐1 assay and Hoechst 33258 staining. The effect of TGFBI on UC cell metastasis was analyzed using adhesion, migration and invasion assays. We found that TGFBI increased the proliferation of UC cells. Moreover, TGFBI enhanced the adhesion, migration and invasion of UC cells by upregulating MMP‐2, MMP‐9 and calpain‐2 expression. We evaluated the effect of Epirubicin (EPI) on the regulation of TGFBI expression and found that TGFBI acts as a downstream target of EPI and is suppressed by EPI in UC cells. EPI is more effective in inhibiting the proliferation and metastasis of UC cells with high TGFBI expression. This study demonstrates that TGFBI might lead to tumorigenesis and progression of UC and those cells with high TGFBI expression may be vulnerable to relapse. EPI could prove to be a therapeutic option in patients with high TGFBI expressing UC cells.
Embedded ensemble encoding hypothesis: The role of the “Prepared” cell

We here reconsider current theories of neural ensembles in the context of recent discoveries about neuronal dendritic physiology. The key physiological observation is that the dendritic plateau potential produces sustained depolarization of the cell body (amplitude 10–20 mV, duration 200–500 ms). Our central hypothesis is that synaptically‐evoked dendritic plateau potentials lead to a prepared state of a neuron that favors spike generation. The plateau both depolarizes the cell toward spike threshold, and provides faster response to inputs through a shortened membrane time constant. As a result, the speed of synaptic‐to‐action potential (AP) transfer is faster during the plateau phase. Our hypothesis relates the changes from “resting” to “depolarized” neuronal state to changes in ensemble dynamics and in network information flow. The plateau provides the Prepared state (sustained depolarization of the cell body) with a time window of 200–500 ms. During this time, a neuron can tune into ongoing network activity and synchronize spiking with other neurons to provide a coordinated Active state (robust firing of somatic APs), which would permit “binding” of signals through coordination of neural activity across a population. The transient Active ensemble of neurons is embedded in the longer‐lasting Prepared ensemble of neurons. We hypothesize that “embedded ensemble encoding” may be an important organizing principle in networks of neurons.
Linear Hypothesis Testing in Dense High-Dimensional Linear Models

ABSTRACT We propose a methodology for testing linear hypothesis in high-dimensional linear models. The proposed test does not impose any restriction on the size of the model, that is, model sparsity or the loading vector representing the hypothesis. Providing asymptotically valid methods for testing general linear functions of the regression parameters in high-dimensions is extremely challenging—especially without making restrictive or unverifiable assumptions on the number of nonzero elements. We propose to test the moment conditions related to the newly designed restructured regression, where the inputs are transformed and augmented features. These new features incorporate the structure of the null hypothesis directly. The test statistics are constructed in such a way that lack of sparsity in the original model parameter does not present a problem for the theoretical justification of our procedures. We establish asymptotically exact control on Type I error without imposing any sparsity assumptions on model parameter or the vector representing the linear hypothesis. Our method is also shown to achieve certain optimality in detecting deviations from the null hypothesis. We demonstrate the favorable finite-sample performance of the proposed methods, via a number of numerical and a real data example. Supplementary materials for this article are available online.
Identification of Existing Information Technology Services and Their Potential to Support Patient Empowerment in Cancer Survivors

Background: Patient empowerment may be an effective approach to strengthen the role of cancer survivors and to reduce the burden on health care. However, it is not well conceptualized, notably in oncology. Furthermore, it is unclear to what extent information technology (IT) services can contribute to empowerment of cancer survivors. Objective: We aim to define the conceptual components of patient empowerment of chronic disease patients, especially cancer survivors, and to explore the contribution of existing and new IT services to promote empowerment. Methods: Electronic databases were searched to identify theoretical and empirical articles regarding empowerment. We extracted and synthesized conceptual components of patient empowerment (ie, attributes, antecedents, and consequences) according to the integrated review methodology. We identified recent IT services for cancer survivors by examining systematic reviews and a proposed inventory of new services, and we related their features and effects to the identified components of empowerment. Results: Based on 26 articles, we identified five main attributes of patient empowerment: (1) being autonomous and respected, (2) having knowledge, (3) having psychosocial and behavioral skills, (4) perceiving support from community, family, and friends, and (5) perceiving oneself to be useful. The latter two were specific for the cancer setting. Systematic reviews of IT services and our additional inventory helped us identify five main categories: (1) educational services, including electronic survivorship care plan services, (2) patient-to-patient services, (3) electronic patient-reported outcome (ePRO) services, (4) multicomponent services, and (5) portal services. Potential impact on empowerment included knowledge enhancement and, to a lesser extent, enhancing autonomy and skills. Newly developed services offer promising and exciting opportunities to empower cancer survivors, for instance, by providing tailored advice for supportive or follow-up care based on patients' input. Conclusions: We identified five main components of empowerment and showed that IT services may especially contribute to empowerment by providing knowledge. The components of empowerment could be used to develop IT services for cancer survivors. It is important to take into account patients’ needs, follow up on these needs, and create a service that is attractive and easy to use. (J Med Internet Res 2015;17(11):e270) doi:10.2196/jmir.4818
Optimization of Cultivation Conditions for Azotobacter vinelandii D-08, Producer of the Polysaccharide Levan, for Obtaining Biocomposite Materials

A prospective binder composed of a microbial polysaccharide levan present in the culture fluid was obtained. The synthesis of levan was carried out by an Azotobacter vinelandii bacteria strain using molasses, distillery stillage, and milk whey as the nutrient medium. The maximum amount of levan produced in these experiments was 14.5 g/L. Composite materials were obtained based on wood waste and biological binder. Depending on the pressing behaviour, materials were obtained within a density range of 1083 to 1443 kg/m3 and a tensile strength of 7.2 to 32.4 MPa. Water absorption and thickness swelling were 7.2% and 14.9%, respectively. During hot pressing, the resulting materials changed in their attenuated total reflection-frustrated total reflection (ATR-FTR) spectra at frequencies of 930, 1000, and 1750 cm-1, indicating the occurrence of chemical and structural changes in individual components of the lignocellulosic raw materials and changes in the composition of biological binding agent. Analysis of the physico-mechanical properties and other results of the composite materials using scanning electron microscopy (SEM) and X-ray microtomography suggested that composite materials based on the microbial polysaccharide levan-containing binder are advanced, new, and eco-friendly substances.
UvA-DARE ( Digital Academic Repository ) Biodiversity of the genus Cladophialophora

Cladophialophora is a genus of black yeast-like fungi comprising a number of clinically highly significant species in addition to environmental taxa. The genus has previously been characterized by branched chains of ellipsoidal to fusiform conidia. However, this character was shown to have evolved several times independently in the order Chaetothyriales. On the basis of a multigene phylogeny (nucLSU, nucSSU, RPB1), most of the species of Cladophialophora (including its generic type C. carrionii) belong to a monophyletic group comprising two main clades (carrioniiand bantiana-clades). The genus includes species causing chromoblastomycosis and other skin infections, as well as disseminated and cerebral infections, often in immunocompetent individuals. In the present study, multilocus phylogenetic analyses were combined to a morphological study to characterize phenetically similar Cladophialophora strains. Sequences of the ITS region, partial Translation Elongation Factor 1-α and β-Tubulin genes were analysed for a set of 48 strains. Four novel species were discovered, originating from soft drinks, alkylbenzene-polluted soil, and infected patients. Membership of the both carrionii and bantiana clades might be indicative of potential virulence to humans.
Interannual variation patterns of total ozone and lower stratospheric temperature in observations and model simulations

We report results from a multiple linear regression analysis of long-term total ozone observations (1979 to 2000, by TOMS/SBUV), of temperature reanalyses (1958 to 2000, NCEP), and of two chemistry-climate model simulations (1960 to 1999, by ECHAM4.L39(DLR)/CHEM (=E39/C), and MAECHAM4-CHEM). The model runs are transient experiments, where observed sea surface temperatures, increasing source gas concentrations (CO2, CFCs, CH4, N2O, NOx), 11-year solar cycle, volcanic aerosols and the quasi-biennial oscillation (QBO) are all accounted for. MAECHAM4-CHEM covers the atmosphere from the surface up to 0.01 hPa (? 80 km). For a proper representation of middle atmosphere (MA) dynamics, it includes a parametrization for momentum deposition by dissipating gravity wave spectra. E39/C, on the other hand, has its top layer centered at 10 hPa (? 30 km). It is targeted on processes near the tropopause, and has more levels in this region. Despite some problems, both models generally reproduce the observed amplitudes and much of the observed low-latitude patterns of the various modes of interannual variability in total ozone and lower stratospheric temperature. In most aspects MAECHAM4-CHEM performs slightly better than E39/C. MAECHAM4-CHEM overestimates the long-term decline of total ozone, whereas underestimates the decline over Antarctica and at northern mid-latitudes. The true long-term decline in winter and spring above the Arctic may be underestimated by a lack of TOMS/SBUV observations in winter, particularly in the cold 1990s. Main contributions to the observed interannual variations of total ozone and lower stratospheric temperature at 50 hPa come from a linear trend (up to -10 DU/decade at high northern latitudes, up to -40 DU/decade at high southern latitudes, and around -0.7 K/decade over much of the globe), from the intensity of the polar vortices (more than 40 DU, or 8 K peak to peak), the QBO (up to 20 DU, or 2 K peak to peak), and from tropospheric weather (up to 20 DU, or 2 K peak to peak). Smaller variations are related to the 11-year solar cycle (generally less than 15 DU, or 1 K), or to ENSO (up to 10 DU, or 1 K). These observed variations are replicated well in the simulations. Volcanic eruptions have resulted in sporadic changes (up to -30 DU, or +3 K). At low latitudes, patterns are zonally symmetric. At higher latitudes, however, strong, zonally non-symmetric signals are found close to the Aleutian Islands or south of Australia. Such asymmetric features appear in the model runs as well, but often at different longitudes than in the observations. The results point to a key role of the zonally asymmetric Aleutian (or Australian) stratospheric anti-cyclones for interannual variations at high-latitudes, and for coupling between polar vortex strength, QBO, 11-year solar cycle and ENSO.
1 The Evolution of Social Evolution

Why do animals live in cooperative groups? How do these societies function? These are the types of questions that motivated both of us in graduate school to study the evolutionary causes and consequences of sociality. We became part of a large and diverse group of scientists studying animal social behavior, a group that today spans the biological sciences, even extending into mathematics, engineering, and more. There are national and international societies, specialized journals, graduate programs, and institutes – each devoted in one way or another to studying animal social behavior. There is a vast body of knowledge about sociality in a diversity of animal species. As we come to know more about social diversity, synthesis has become more challenging. Ambitious, comprehensive narratives in the vein of Sociobiology (Wilson, 1975) are all but absent today (Sapp, 1994). But that was not always the case. Early naturalists once composed sweeping treatments of cooperation in nature (Cronin, 1991; Dugatkin, 2006; Dixon, 2008). If you have ever wondered how a wasp is like a bird, with notable exceptions (e.g. Brockmann, 1997; Korb & Heinze, 2008; Székely, et al., 2010), you would have to dig deep into the literature to even find them discussed on the same pages. Modern animal behaviorists have become more specialized when it comes to studies of animal societies. In editing this volume, the two of us were motivated to return to our original graduate school questions, to look beyond the organisms we are familiar with (birds, shrimps, aphids, ants), and begin to synthesize the features of social life that unite disparate animal taxa. In doing so, we take an admittedly optimistic view of animal sociality, arguing that there are convergent and common themes that span vertebrate and invertebrate societies. There is room for debate, and our goal with this book is to re-energize the conversation between scholars who think comparatively about the major animal lineages containing species that form societies. In this introductory chapter, we begin with a short description of what it means to study sociality and social evolution in animals, and then provide a brief retrospective of studies of animal social behavior from Darwin to the present. We are not historians, and
Fish and robot dancing together: bluefin killifish females respond differently to the courtship of a robot with varying color morphs

The experimental integration of bioinspired robots in groups of social animals has become a valuable tool to understand the basis of social behavior and uncover the fundamental determinants of animal communication. In this study, we measured the preference of fertile female bluefin killifish (Lucania goodei) for robotic replicas whose aspect ratio, body size, motion pattern, and color morph were inspired by adult male killifish. The motion of the fish replica was controlled via a robotic platform, which simulated the typical courtship behavior observed in killifish males. The positional preferences of females were measured for three different color morphs (red, yellow, and blue). While variation in preference was high among females, females tend to spend more time in the vicinity of the yellow painted robot replicas. This preference may have emerged because the yellow robot replicas were very bright, particularly in the longer wavelengths (550–700 nm) compared to the red and blue replicas. These findings are in agreement with previous observations in mosquitofish and zebrafish on fish preference for artificially enhanced yellow pigmentation.
Recent Diagnostic Techniques in Mycology

The frequency of fungal infections, especially of Invasive Fungal Infections (IFIs), has risen dramatically in recent years, and has high morbidity and mortality. Early and accurate diagnosis is important for timely implementation of antifungal therapy and decreasing the unnecessary use of toxic antifungal agents. Conventional microbiological, histological and radiological techniques remain the cornerstone of diagnosis but are insensitive and have a limited impact on clinical decision-making. There is always a need to characterize fungi quickly and accurately which can be done by rapid diagnostic techniques like antigen detection and molecular techniques. This is a brief review of all the microbiological techniques- conventional and recent alternative techniques especially elaborating antigen detection and molecular techniques which are available for diagnosis of fungal infections.
The Role of B Cell Targeting in Chronic Graft-Versus-Host Disease

Chronic graft-versus-host disease (cGVHD) is a leading cause of late morbidity and mortality following allogeneic stem cell transplantation. Current therapies, including corticosteroids and calcineurin inhibitors, are only effective in roughly 50% of cases; therefore, new treatment strategies are under investigation. What was previously felt to be a T cell disease has more recently been shown to involve activation of both T and B cells, as well as a number of cytokines. With a better understanding of its pathophysiology have come more expansive preclinical and clinical trials, many focused on B cell signaling. This report briefly reviews our current understanding of cGVHD pathophysiology and reviews clinical and preclinical trials with B cell-targeted agents.
Overview on zein protein: a promising pharmaceutical excipient in drug delivery systems and tissue engineering

ABSTRACT Introduction: Natural pharmaceutical excipients have been applied extensively in the past decades owing to their safety and biocompatibility. Zein, a natural protein of plant origin offers great benefit over other synthetic polymers used in controlled drug and biomedical delivery systems. It was used in a variety of medical fields including pharmaceutical and biomedical drug targeting, vaccine, tissue engineering, and gene delivery. Being biodegradable and biocompatible, the current review focuses on the history and the medical application of zein as an attractive still promising biopolymer. Areas covered: The current review gives a broadscope on zein as a still promising protein excipient in different fields. Zein- based drug and biomedical delivery systems are discussed with special focus on current and potential application in controlled drug delivery systems, and tissue engineering. Expert opinion: Zein as a protein of natural origin can still be considered a promising polymer in the field of drug delivery systems as well as in tissue engineering. Although different researchers spotted light on zein application in different industrial fields extensively, the feasibility of its use in the field of drug delivery replenished by investigators in recent years has not yet been fully approached.
Tracking the Continuous Evolutionary Processes of an Endogenous Retrovirus of the Domestic Cat: ERV-DC

An endogenous retrovirus (ERV) is a remnant of an ancient retroviral infection in the host genome. Although most ERVs have lost their viral productivity, a few ERVs retain their replication capacity. In addition, partially inactivated ERVs can present a potential risk to the host via their encoded virulence factors or the generation of novel viruses by viral recombination. ERVs can also eventually acquire a biological function, and this ability has been a driving force of host evolution. Therefore, the presence of an ERV can be harmful or beneficial to the host. Various reports about paleovirology have revealed each event in ERV evolution, but the continuous processes of ERV evolution over millions of years are mainly unknown. A unique ERV family, ERV-DC, is present in the domestic cat (Felis silvestris catus) genome. ERV-DC proviruses are phylogenetically classified into three genotypes, and the specific characteristics of each genotype have been clarified: their capacity to produce infectious viruses; their recombination with other retroviruses, such as feline leukemia virus or RD-114; and their biological functions as host antiviral factors. In this review, we describe ERV-DC-related phenomena and discuss the continuous changes in the evolution of this ERV in the domestic cat.