Miracle-dz/UniFAR-FTUs huggingface dataset:
Multispecies population modelling of the common dolphin ("Delphinus delphis"), the bottlenose dolphin ("Tursiops truncatus") and the southern stock of European hake ("Merluccius merluccius"), in Atlantic waters of the Iberian Peninsula

Construction of ecosystem models requires detailed information on trophic interactions which may not be readily available, especially for top predators such as cetaceans. Such information can also be useful to estimate natural mortality (M) for fish stock assessments and to evaluate the potential for competition between cetaceans and fisheries. In the present chapter consumption estimates and confidence limits are provided, taking into account sampling error, for consumption of fish by the four most common cetaceans along the Atlantic coast of the Iberian Peninsula, while highlighting the uncertainties and biases inherent in the information presently available on energy requirements, diet and population size. It was estimated that common dolphins (Delphinus delphis) consume around 6800 (95% CI, 4871 9476) tons of sardine (Sardina pilchardus), 8800 (6195 12647) tons of gadids, 1100 (721 1662) tons of European hake (Merluccius merluccius) and 1900 (1222 2752) tons of scads (Trachurus sp.) annually. For striped dolphins (Stenella coeruleoalba), prey consumed were 900 (196 2661) tons of sardine, 6200 (3448 11129) tons of gadids, 200 (11 504) tons of hake and 1600 (0 5318) tons of scads. Estimated amounts taken by harbour porpoises (Phocoena phocoena) and bottlenose dolphins (Tursiops truncatus) were much lower, reflecting their low abundance in the area. Cetacean predation on sardine represented 2 8% of the current M value, indicating that cetaceans probably have little influence on sardine population dynamics. For the southern hake stock, estimated average removal by cetaceans often exceeded M. While this may indicate that both M and the consumption estimates for hake require revision it also suggests that cetaceans could have a significant impact on hake populations. The lack of good estimates of field metabolic rate for most species probably represents the most serious barrier to reliably quantifying the role of cetaceans in the ecosystem. See the related publication in Annex 5. Chapter 1: Quantifying the predation on sardine and hake by cetaceans in the Atlantic waters of the Iberian Peninsula 32 4.
Maintaining Habitat Connectivity for Conservation

Maintaining Habitat Connectivity for Conservation Bronwyn Rayfield Doctor of Philosophy Department of Ecology and Evolutionary Biology University of Toronto 2009 Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species’ movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit of producing spatially aggregated reserves based on functional species requirements.
Modeling the Depletion and Recovery of the Outer Radiation Belt During a Geomagnetic Storm: Combined MHD and Test Particle Simulations

During geomagnetic storms the intensities of the outer radiation belt electron population can exhibit dramatic variability. Deep depletions in intensity during the main phase are followed by increases during the recovery phase, often to levels that significantly exceed their prestorm values. To study these processes, we simulate the evolution of the outer radiation belt during the 17 March 2013 geomagnetic storm using our newly developed radiation belt model (Conservative Hamiltonian Integrator for Magnetospheric Particles) based on test particle and coupled 3‐D ring current and global magnetohydrodynamic (MHD) simulations, and driven solely with solar wind and F10.7 flux data. Our approach differs from previous work in that we use MHD information to identify regions of strong, bursty, and azimuthally localized earthward convection in the magnetotail where test particles are then seeded. We validate our model using in situ Van Allen Probe electron intensities over a multiday period and show that our model is able to reproduce meaningful qualitative and quantitative agreement. Analysis of our model enables us to study the processes that govern the transition from the prestorm to poststorm outer belt. Our analysis demonstrates that during the early main phase of the storm the preexisting outer belt is largely wiped out via magnetopause losses, and subsequently, a new outer belt is created during a handful of discrete, mesoscale injections. Finally, we demonstrate the potential importance of magnetic gradient trapping in the transport and energization of outer belt electrons using a controlled numerical experiment.
Recent advances in targeting the autotaxin-lysophosphatidate-lipid phosphate phosphatase axis in vivo

Abstract Extracellular lysophosphatidate (LPA) is a potent bioactive lipid that signals through six G-protein-coupled receptors. This signaling is required for embryogenesis, tissue repair and remodeling processes. LPA is produced from circulating lysophosphatidylcholine by autotaxin (ATX), and is degraded outside cells by a family of three enzymes called the lipid phosphate phosphatases (LPPs). In many pathological conditions, particularly in cancers, LPA concentrations are increased due to high ATX expression and low LPP activity. In cancers, LPA signaling drives tumor growth, angiogenesis, metastasis, resistance to chemotherapy and decreased efficacy of radiotherapy. Hence, targeting the ATX-LPA-LPP axis is an attractive strategy for introducing novel adjuvant therapeutic options. In this review, we will summarize current progress in targeting the ATX-LPA-LPP axis with inhibitors of autotaxin activity, LPA receptor antagonists, LPA monoclonal antibodies, and increasing low LPP expression. Some of these agents are already in clinical trials and have applications beyond cancer, including chronic inflammatory diseases.
Alternative infectious entry pathways for dengue virus serotypes into mammalian cells

The entry of two dengue virus (DENV) serotypes into Vero cells was analysed using biochemical inhibitors, dominant negative mutants of cellular proteins involved in endocytic pathways, fluorescence microscopy and infectivity determinations. By treatment with dansylcadaverine and chlorpromazine and overexpression of a dominant negative form of the Eps15 protein, a clathrin‐mediated endocytosis for productive DENV‐1 internalization into Vero cells was demonstrated whereas the infectious entry of DENV‐2 in the same cell system was independent of clathrin. Treatment with the inhibitors nystatin and methyl‐β‐cyclodextrin, as well as transfection of Vero cells with dominant negative caveolin‐1, had no effect on DENV‐2 virus infection. It was also shown, by using the K44A mutant and the inhibitor dynasore, that dynamin was required for DENV‐2 entry. Consequently, the infectious entry of DENV‐2 into Vero cells occurs by a non‐classical endocytic pathway independent of clathrin, caveolae and lipid rafts, but dependent on dynamin. By contrast, DENV‐2 entry into A549 cells was clathrin‐dependent, as previously reported in HeLa, C6/36 and BS‐C‐1 cells. Our results conclusively show, for the first time, a differential mode of infective entry for DENV‐1 and DENV‐2 into a common host cell, Vero cells, as well as alternative entry pathways for a given serotype, DENV‐2, into different types of cells.
Atmospheric histories and emissions of chlorofluorocarbons CFC-13 (CClF 3 ), ΣCFC-114 (C 2 Cl 2 F 4 ), and CFC-115 (C 2 ClF 5 )

Abstract. Based on observations of the chlorofluorocarbons CFC-13 (chlorotrifluoromethane), ΣCFC-114 (combined measurement of both isomers of dichlorotetrafluoroethane), and CFC-115 (chloropentafluoroethane) in atmospheric and firn samples, we reconstruct records of their tropospheric histories spanning nearly 8 decades. These compounds were measured in polar firn air samples, in ambient air archived in canisters, and in situ at the AGAGE (Advanced Global Atmospheric Gases Experiment) network and affiliated sites. Global emissions to the atmosphere are derived from these observations using an inversion based on a 12-box atmospheric transport model. For CFC-13, we provide the first comprehensive global analysis. This compound increased monotonically from its first appearance in the atmosphere in the late 1950s to a mean global abundance of 3.18 ppt (dry-air mole fraction in parts per trillion, pmol mol−1) in 2016. Its growth rate has decreased since the mid-1980s but has remained at a surprisingly high mean level of 0.02 ppt yr−1 since 2000, resulting in a continuing growth of CFC-13 in the atmosphere. ΣCFC-114 increased from its appearance in the 1950s to a maximum of 16.6 ppt in the early 2000s and has since slightly declined to 16.3 ppt in 2016. CFC-115 increased monotonically from its first appearance in the 1960s and reached a global mean mole fraction of 8.49 ppt in 2016. Growth rates of all three compounds over the past years are significantly larger than would be expected from zero emissions. Under the assumption of unchanging lifetimes and atmospheric transport patterns, we derive global emissions from our measurements, which have remained unexpectedly high in recent years: mean yearly emissions for the last decade (2007–2016) of CFC-13 are at 0.48 ± 0.15 kt yr−1 (> 15 % of past peak emissions), of ΣCFC-114 at 1.90 ± 0.84 kt yr−1 (∼ 10 % of peak emissions), and of CFC-115 at 0.80 ± 0.50 kt yr−1 (> 5 % of peak emissions). Mean yearly emissions of CFC-115 for 2015–2016 are 1.14 ± 0.50 kt yr−1 and have doubled compared to the 2007–2010 minimum. We find CFC-13 emissions from aluminum smelters but if extrapolated to global emissions, they cannot account for the lingering global emissions determined from the atmospheric observations. We find impurities of CFC-115 in the refrigerant HFC-125 (CHF2CF3) but if extrapolated to global emissions, they can neither account for the lingering global CFC-115 emissions determined from the atmospheric observations nor for their recent increases. We also conduct regional inversions for the years 2012–2016 for the northeastern Asian area using observations from the Korean AGAGE site at Gosan and find significant emissions for ΣCFC-114 and CFC-115, suggesting that a large fraction of their global emissions currently occur in northeastern Asia and more specifically on the Chinese mainland.
Improvement in Spectral Properties of Quantization Noise of Harmonic Signal Using Multiresolution Quantization

Multiresolution quantization (MQ) is used in modern equipment designed for wideband spectrum measurements with high dynamic range. Such time-domain measurement systems significantly reduce measurement time. Only basic theoretical analyses of the possible influences of MQ on the fidelity of the measured spectrum have been performed until today. Therefore, the real contribution of the method to the quality of measurement should be clarified. In this paper, a new model of quantization noise is proposed for MQ. It was derived from a model of power spectral density previously used for uniform quantization. A system with two different quantization steps used for the quantization of harmonic input signal is considered. The model suitability for such conditions is proved by simulation and confronted with experimental results. Multiresolution measurements were acquired using a dual-channel data acquisition card and personal-computer postprocessing.
The Holographic Storage of Study Models

The storage and recall of dental study models pose major problems for orthodontists. This problem may be solved by taking holographic films of study models. A method is described for their fabrication and some preliminary measurements are reported. The image produced by this method has a measurable three-dimensionality which can be produced at a very reasonable cost.
Pancreatectomy Versus Conservative Management for Pancreatic Cancer: A Question of Lead-time Bias

Objectives:Pancreatectomy is regarded as the only curative treatment for cancer of the pancreas. A population-based study was conducted to examine its efficacy within the general community. Methods:Overall and cancer-specific survivals were compared between individuals treated with pancreatectomy and those managed nonsurgically. Kaplan-Meier analysis was used, based on both time from diagnosis and attained age (age at diagnosis plus time from diagnosis). Results:A total of 7830 Surveillance Epidemiology and End Results cases of localized cancer of the pancreatic head were retrieved, diagnosed from 2000 to 2008. Median follow-up was 12 months; the pancreatectomy cohort was 5 years younger and had 7-fold less stage III disease. Overall and cancer-specific survivals were 17% and 21% at 5 years from time of diagnosis in the pancreatectomy cohort versus 2% and 4% in the nonsurgical cohort, respectively (P<0.001). However, the overall and cancer-specific survival curves were nearly superimposed on each other when based on attained age. Moreover, the proportion of deaths attributable to pancreatic cancer exceeded 85% in both cohorts. Conclusions:A lead-time bias is hypothesized to explain the survival discrepancies seen between time from diagnosis and attained age analyses; the pancreatectomy cohort was diagnosed earlier, with less disease. If most of these individuals had occult metastases at diagnosis, which manifested later and caused death at similar ages as the nonsurgical cohort, their survival from time of diagnosis would appear speciously improved. A randomized controlled trial would be necessary to confirm whether or not the survival advantage ascribed to pancreatectomy should be attributed to lead-time bias.
Cholinergic plasticity in the hippocampus

Tests were made for use-dependent plasticity in the cholinergic projections to hippocampus. Transient infusion of the cholinergic agonist carbachol into hippocampal slices induced rhythmic activity that persisted for hours after washout. Comparable effects were obtained with physostigmine, a drug that blocks acetylcholine breakdown and thereby enhances cholinergic transmission. It thus seems that activation of cholinergic synapses induces lasting changes in hippocampal physiology. Two lines of evidence indicated that cholinergic synapses are also the sites at which the plasticity is expressed. First, the induction and expression of the rhythms were not blocked by the N-methyl-d-aspartate receptor antagonist d-2-amino-5-phosphonovaleric acid, indicating that a long-term potentiation effect between pyramidal cells was not involved. Second, a muscarinic antagonist (atropine) completely abolished stable rhythmic activity after agonist washout. This result indicates that endogenous cholinergic activity is responsible for the persistence of rhythmic oscillations. These experiments suggest that short periods of intense cholinergic activity induce lasting changes in cholinergic synapses and thus extend such forms of plasticity to beyond the glutamatergic system.
Graph Rigidity, Cyclic Belief Propagation, and Point Pattern Matching

A recent paper (Caetano et al., 2006) proposed a provably optimal, polynomial time method for performing near-isometric point pattern matching by means of exact probabilistic inference in a chordal graphical model. Its fundamental result is that the chordal graph in question is shown to be globally rigid, implying that exact inference provides the same matching solution as exact inference in a complete graphical model. This implies that the algorithm is optimal when there is no noise in the point patterns. In this paper, we present a new graph which is also globally rigid but has an advantage over the graph, its maximal clique size is smaller, rendering inference significantly more efficient. However, this graph is not chordal and thus standard junction tree algorithms cannot be directly applied. Nevertheless, we show that loopy belief propagation in such a graph converges to the optimal solution. This allows us to retain the optimality guarantee in the noiseless case, while substantially reducing both memory requirements and processing time. Our experimental results show that the accuracy of the proposed solution is indistinguishable when there is noise in the point patterns.
Investigation of False Positive Results with an Oral Fluid Rapid HIV-1/2 Antibody Test

Background In March 2004, the OraQuick® rapid HIV antibody test became the first rapid HIV test approved by the US Food and Drug Administration for use on oral fluid specimens. Test results are available in 20 minutes, and the oral fluid test is non-invasive. From August 2004–June 2005, we investigated a sudden increase in false-positive results occurring in a performance study of OraQuick® oral-fluid rapid HIV tests in Minnesota. Methodology/Principal Findings In a field investigation, we reviewed performance study data on oral-fluid and whole-blood OraQuick® rapid HIV test device lots and expiration dates and assessed test performance and interpretation with oral-fluid and whole-blood specimens by operators who reported false-positive results. We used multivariate logistic regression to evaluate client demographic and risk characteristics associated with false-positive results. Next, we conducted an incidence study of false-positive OraQuick rapid HIV tests in nine US cities and tested both oral-fluid and finger-stick whole-blood specimens from clients; reactive tests were confirmed with Western blot. Sixteen (4.1%) false-positive oral-fluid results occurred in the performance study from April 15, 2004 through August 31, 2004 with unexpired devices from six test lots among 388 HIV-uninfected clients (specificity, 95.9%; 95% CI: 93.4–97.6). Three test operators who had reported false-positive results performed and interpreted the test according to package-insert instructions. In multivariate analysis, only older age was significantly associated with false-positive results (adjusted odds ratio = 4.5, 95% CI: 1.2–25.7). In the incidence study, all valid oral-fluid and whole-blood results from 2,268 clients were concordant and no false-positive results occurred (100% specificity). Conclusions/Significance The field investigation did not identify a cause for the increase in false-positive oral-fluid results, and the incidence study detected no false-positive results. The findings suggest this was an isolated cluster; the test's overall performance was as specified by the manufacturer.
Hippocampal volume is reduced in schizophrenia and schizoaffective disorder but not in psychotic bipolar I disorder demonstrated by both manual tracing and automated parcellation (FreeSurfer).

This study examined hippocampal volume as a putative biomarker for psychotic illness in the Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) psychosis sample, contrasting manual tracing and semiautomated (FreeSurfer) region-of-interest outcomes. The study sample (n = 596) included probands with schizophrenia (SZ, n = 71), schizoaffective disorder (SAD, n = 70), and psychotic bipolar I disorder (BDP, n = 86); their first-degree relatives (SZ-Rel, n = 74; SAD-Rel, n = 62; BDP-Rel, n = 88); and healthy controls (HC, n = 145). Hippocampal volumes were derived from 3Tesla T1-weighted MPRAGE images using manual tracing/3DSlicer3.6. 3 and semiautomated parcellation/FreeSurfer5.1,64bit. Volumetric outcomes from both methodologies were contrasted in HC and probands and relatives across the 3 diagnoses, using mixed-effect regression models (SAS9.3 Proc MIXED); Pearson correlations between manual tracing and FreeSurfer outcomes were computed. SZ (P = .0007-.02) and SAD (P = .003-.14) had lower hippocampal volumes compared with HC, whereas BDP showed normal volumes bilaterally (P = .18-.55). All relative groups had hippocampal volumes not different from controls (P = .12-.97) and higher than those observed in probands (P = .003-.09), except for FreeSurfer measures in bipolar probands vs relatives (P = .64-.99). Outcomes from manual tracing and FreeSurfer showed direct, moderate to strong, correlations (r = .51-.73, P < .05). These findings from a large psychosis sample support decreased hippocampal volume as a putative biomarker for schizophrenia and schizoaffective disorder, but not for psychotic bipolar I disorder, and may reflect a cumulative effect of divergent primary disease processes and/or lifetime medication use. Manual tracing and semiautomated parcellation regional volumetric approaches may provide useful outcomes for defining measurable biomarkers underlying severe mental illness.
“I’m a Keep Rising. I’m a Keep Going Forward, Regardless”

A growing number of health and social science research findings document Black men’s adversities, but far less is known about their strengths. The purpose of this study was to explore resilience among low-income, urban, Black men. Semistructured interviews produced rich narratives, which uncovered numerous sociostructural stressors in men’s lives, such as racism, incarceration, and unemployment. Most men were resilient despite these challenges, however, and described five main forms of resilience: (a) perseverance; (b) a commitment to learning from hardship; (c) reflecting and refocusing to address difficulties; (d) creating a supportive environment; and (e) drawing support from religion/spirituality. Analysis of men’s challenge and resilience narratives revealed the need to understand and promote low-income, urban, Black men’s resilience via a broader ecosocial perspective which acknowledges the importance of social and community-level protective factors to support individual men’s efforts to survive and thrive amid their adversities.
Research Methods for Group Recommender System

In this article we argue that the research on group recommender systems must look more carefully at group dynamics in decision making in order to produce technologies that will be truly beneficial for users. Hence, we illustrate a user study method aimed at observing and measuring the evolution of user preferences and actions in a tourism decision making task: finding a destination to visit. We discuss the benefits and caveats of such an observational study method and we present the implications that the derived data and findings may have on the design of interactive group recommender systems.