Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Climate and Estuarine Habitat Characteristics on Coastal Fisheries - A Case Study for Queensland, Australia

Estuarine habitats such as seagrass beds, mangrove forests, salt marshes, mud and sandflats are considered important habitats supporting a diverse range of fish and crustaceans of ecological and economic importance. Many commercial fish species use estuarine habitats as nurseries or breeding grounds and have lifecycles correlated to rainfall and temperature variations. Despite the globally recognised ecological value of estuaries, there is little direct evidence to support the estuary–fisheries linkage paradigm. Traditionally, analyses of the importance of estuarine habitat characteristics to commercial fish catch have taken the single-habitat approach, i.e., assessing the value of individual habitat types. Different estuarine habitats offer different, and arguably, complementary functions and services to nekton during their life cycle. Connectivity of habitats is therefore likely to play a major role in fish movement and abundance. Little is known of movement patterns of estuary-dependent fish species within the estuarine landscape and few if any studies have applied the idea of spatial habitat metrics, in particular, connectivity, to estuarine environments. Elements of climate, such as temperature and rainfall, may impact on sustainable coastal fish production. How these factors, which are strongly related to global climate change, may influence future coastal fish production will have significant implications for sustainable fishery management. This thesis examines relationships between estuarine habitat characteristics, climate and commercial fish species in Queensland, Australia, with the objective of gaining clearer insight into how estuarine habitats may support commercial fisheries. The following specific questions were addressed: (1) What knowledge gaps exist in the literature regarding the role of climate and estuarine habitats in sustaining coastal fisheries? (2) What deficiencies exist in studies that addressed the relationship between estuarine habitats, climate (e.g., rainfall and temperature) and fisheries and how may existing data sets be refined to allow better analyses of this relationship? (3) What are the key structural features of estuarine habitats (e.g., connectivity) and the role of temperature and rainfall influencing coastal fishery production? (4) What are the implications of the relationships between fish catch, estuarine habitat and climate, for fisheries management?
Living in Heterogeneous Woodlands – Are Habitat Continuity or Quality Drivers of Genetic Variability in a Flightless Ground Beetle?

Although genetic diversity is one of the key components of biodiversity, its drivers are still not fully understood. While it is known that genetic diversity is affected both by environmental parameters as well as habitat history, these factors are not often tested together. Therefore, we analyzed 14 microsatellite loci in Abax parallelepipedus, a flightless, forest dwelling ground beetle, from 88 plots in two study regions in Germany. We modeled the effects of historical and environmental variables on allelic richness, and found for one of the regions, the Schorfheide-Chorin, a significant effect of the depth of the litter layer, which is a main component of habitat quality, and of the sampling effort, which serves as an inverse proxy for local population size. For the other region, the Schwäbische Alb, none of the potential drivers showed a significant effect on allelic richness. We conclude that the genetic diversity in our study species is being driven by current local population sizes via environmental variables and not by historical processes in the studied regions. This is also supported by lack of genetic differentiation between local populations sampled from ancient and from recent woodlands. We suggest that the potential effects of former fragmentation and recolonization processes have been mitigated by the large and stable local populations of Abax parallelepipedus in combination with the proximity of the ancient and recent woodlands in the studied landscapes.
A Semismooth Newton Method for Nonlinear Parameter Identification Problems with Impulsive Noise

This work is concerned with nonlinear parameter identification in partial differential equations subject to impulsive noise. To cope with the non-Gaussian nature of the noise, we consider a model with $\mbox{L}^1$ fitting. However, the nonsmoothness of the problem makes its efficient numerical solution challenging. By approximating this problem using a family of smoothed functionals, a semismooth Newton method becomes applicable. In particular, its superlinear convergence is proved under a second-order condition. The convergence of the solution to the approximating problem as the smoothing parameter goes to zero is shown. A strategy for adaptively selecting the regularization parameter based on a balancing principle is suggested. The efficiency of the method is illustrated on several benchmark inverse problems of recovering coefficients in elliptic differential equations, for which one- and two-dimensional numerical examples are presented.
Less Exposure to Daily Ambient Light in Winter Increases Sensitivity of Melatonin to Light Suppression

This study was carried out to examine the seasonal difference in the magnitude of the suppression of melatonin secretion induced by exposure to light in the late evening. The study was carried out in Akita (39° North, 140° East), in the northern part of Japan, where the duration of sunshine in winter is the shortest. Ten healthy male university students (mean age: 21.9±1.2 yrs) volunteered to participate twice in the study in winter (from January to February) and summer (from June to July) 2004. According to Japanese meteorological data, the duration of sunshine in Akita in the winter (50.5 h/month) is approximately one‐third of that in summer (159.7 h/month). Beginning one week prior to the start of the experiment, the level of daily ambient light to which each subject was exposed was recorded every minute using a small light sensor that was attached to the subject's wrist. In the first experiment, saliva samples were collected every hour over a period of 24 h in a dark experimental room (<15 lux) to determine peak salivary melatonin concentration. The second experiment was conducted after the first experiment to determine the percentage of melatonin suppression induced by exposure to light. The starting time of exposure to light was set 2 h before the time of peak salivary melatonin concentration detected in the first experiment. The subjects were exposed to light (1000 lux) for 2 h using white fluorescent lamps (4200 K). The percentage of suppression of melatonin by light was calculated on the basis of the melatonin concentration determined before the start of exposure to light. The percentage of suppression of melatonin 2 h after the start of exposure to light was significantly greater in winter (66.6±18.4%) than summer (37.2±33.2%), p<0.01). The integrated level of daily ambient light from rising time to bedtime in summer was approximately twice that in winter. The results suggest that the increase in suppression of melatonin by light in winter is caused by less exposure to daily ambient light.
Wideband Differential Bandpass Filters on Multimode Slotline Resonator With Intrinsic Common-Mode Rejection

In this paper, two kinds of wideband differential filters with intrinsic common-mode (CM) rejection are proposed. Both these filters are realized based on the multimode slotline resonators under the dual- and triple-mode resonance, respectively. For Filter 1, the microstrip lines with a pair of differential ports at the two sides are directly tapped on a slotline resonator. For Filter 2, the slotline resonator is connected with two pairs of microstrip open-ended stubs both at top and bottom layers at the beginning. In these two filters, the CM signals are effectively rejected during electromagnetic field conversion. Only the differential-mode performances are left to be focused on. A systematic design method is then presented with simplified circuit models in differential mode, and frequency responses of these models are synthesized and further mapped into physical dimensions. Transformers are used in the mapping procedure and their turn ratios are calculated to find the exact final dimensions or are properly used to realize desired performance with some unattainable impedance values in synthesized simplified models. Finally, two filters are designed, fabricated, and measured to support the design method.
MIMO Capacity with Per-Antenna Power Constraint

In this paper, we consider the single-user MIMO channel with per-antenna power constraint. We formulate the capacity optimization problem with per-antenna constraint in the SDP framework and analyze its optimality conditions. We establish in closed-form the optimal input covariance matrix as a function of the dual variable. We then propose a simple algorithm to find this optimal input covariance and the capacity. Results show that the capacity with per-antenna power can be significantly different from those with sum power or with independent multiple access constraint.
Metabolomic markers reveal novel pathways of ageing and early development in human populations

Background Human ageing is a complex, multifactorial process and early developmental factors affect health outcomes in old age. Methods Metabolomic profiling on fasting blood was carried out in 6055 individuals from the UK. Stepwise regression was performed to identify a panel of independent metabolites which could be used as a surrogate for age. We also investigated the association with birthweight overall and within identical discordant twins and with genome-wide methylation levels. Results We identified a panel of 22 metabolites which combined are strongly correlated with age (R2 = 59%) and with age-related clinical traits independently of age. One particular metabolite, C-glycosyl tryptophan (C-glyTrp), correlated strongly with age (beta = 0.03, SE = 0.001, P = 7.0 × 10−157) and lung function (FEV1 beta = −0.04, SE = 0.008, P = 1.8 × 10−8 adjusted for age and confounders) and was replicated in an independent population (n = 887). C-glyTrp was also associated with bone mineral density (beta = −0.01, SE = 0.002, P = 1.9 × 10−6) and birthweight (beta = −0.06, SE = 0.01, P = 2.5 × 10−9). The difference in C-glyTrp levels explained 9.4% of the variance in the difference in birthweight between monozygotic twins. An epigenome-wide association study in 172 individuals identified three CpG-sites, associated with levels of C-glyTrp (P < 2 × 10−6). We replicated one CpG site in the promoter of the WDR85 gene in an independent sample of 350 individuals (beta = −0.20, SE = 0.04, P = 2.9 × 10−8). WDR85 is a regulator of translation elongation factor 2, essential for protein synthesis in eukaryotes. Conclusions Our data illustrate how metabolomic profiling linked with epigenetic studies can identify some key molecular mechanisms potentially determined in early development that produce long-term physiological changes influencing human health and ageing.
NeuronCyto II: An automatic and quantitative solution for crossover neural cells in high throughput screening

Microscopy is a fundamental technology driving new biological discoveries. Today microscopy allows a large number of images to be acquired using, for example, High Throughput Screening (HTS) and 4D imaging. It is essential to be able to interrogate these images and extract quantitative information in an automated fashion. In the context of neurobiology, it is important to automatically quantify the morphology of neurons in terms of neurite number, length, branching and complexity, etc. One major issue in quantification of neuronal morphology is the “crossover” problem where neurites cross and it is difficult to assign which neurite belongs to which cell body. In the present study, we provide a solution to the “crossover” problem, the software package NeuronCyto II. NeuronCyto II is an interactive and user‐friendly software package for automatic neurite quantification. It has a well‐designed graphical user interface (GUI) with only a few free parameters allowing users to optimize the software by themselves and extract relevant quantitative information routinely. Users are able to interact with the images and the numerical features through the Result Inspector. The processing of neurites without crossover was presented in our previous work. Our solution for the “crossover” problem is developed based on our recently published work with directed graph theory. Both methods are implemented in NeuronCyto II. The results show that our solution is able to significantly improve the reliability and accuracy of the neurons displaying “crossover. ” NeuronCyto II is freely available at the website: https://sites.google. com/site/neuroncyto/, which includes user support and where software upgrades will also be placed in the future. © 2016 The Authors. Cytometry Part A Published by Wiley Periodicals, Inc. on behalf of ISAC.
Nonlinear Shape Registration without Correspondences

In this paper, we propose a novel framework to estimate the parameters of a diffeomorphism that aligns a known shape and its distorted observation. Classical registration methods first establish correspondences between the shapes and then compute the transformation parameters from these landmarks. Herein, we trace back the problem to the solution of a system of nonlinear equations which directly gives the parameters of the aligning transformation. The proposed method provides a generic framework to recover any diffeomorphic deformation without established correspondences. It is easy to implement, not sensitive to the strength of the deformation, and robust against segmentation errors. The method has been applied to several commonly used transformation models. The performance of the proposed framework has been demonstrated on large synthetic data sets as well as in the context of various applications.
Reduced Vancomycin Susceptibility in Staphylococcus aureus, Including Vancomycin-Intermediate and Heterogeneous Vancomycin-Intermediate Strains: Resistance Mechanisms, Laboratory Detection, and Clinical Implications

SUMMARY The emergence of vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) over the past decade has provided a challenge to diagnostic microbiologists to detect these strains, clinicians treating patients with infections due to these strains, and researchers attempting to understand the resistance mechanisms. Recent data show that these strains have been detected globally and in many cases are associated with glycopeptide treatment failure; however, more rigorous clinical studies are required to clearly define the contribution of hVISA to glycopeptide treatment outcomes. It is now becoming clear that sequential point mutations in key global regulatory genes contribute to the hVISA and VISA phenotypes, which are associated predominately with cell wall thickening and restricted vancomycin access to its site of activity in the division septum; however, the phenotypic features of these strains can vary because the mutations leading to resistance can vary. Interestingly, changes in the staphylococcal surface and expression of agr are likely to impact host-pathogen interactions in hVISA and VISA infections. Given the subtleties of vancomycin susceptibility testing against S. aureus, it is imperative that diagnostic laboratories use well-standardized methods and have a framework for detecting reduced vancomycin susceptibility in S. aureus.
A new control method of permanent magnet generator for maximum power tracking in wind turbine application

This paper discusses a new and simple control method for maximum power tracking in a variable speed wind turbine by using a step-up dc-dc converter. The output voltage of permanent magnet generator is connected to a fixed dc-link through a three-phase rectifier and the dc-dc converter. A maximum power-tracking algorithm calculates the speed command that corresponds to maximum power output of the turbine. The dc-dc converter uses this speed command to control the output power of the permanent magnet generator, such that the speed of generator tracks the command speed. A current regulated PWM voltage source inverter maintains the output voltage of dc-dc converter at a fixed value by balancing the input and output power to the dc-link. In addition, the inverter can improve power factor and inject a current with very low harmonic distortion into the utility grid. The generating system has potentials of high efficiency, good flexibility, and low cost.
Molecular Characterization of α–Lactalbumin Folding Variants That Induce Apoptosis in Tumor Cells*

This study characterized a protein complex in human milk that induces apoptosis in tumor cells but spares healthy cells. The active fraction was purified from casein by anion exchange chromatography. Unlike other casein components the active fraction was retained by the ion exchanger and eluted after a high salt gradient. The active fraction showed N-terminal amino acid sequence identity with human milk α-lactalbumin and mass spectrometry ruled out post-translational modifications. Size exclusion chromatography resolved monomers and oligomers of α-lactalbumin that were characterized using UV absorbance, fluorescence, and circular dichroism spectroscopy. The high molecular weight oligomers were kinetically stable against dissociation into monomers and were found to have an essentially retained secondary structure but a less well organized tertiary structure. Comparison with native monomeric and molten globule α-lactalbumin showed that the active fraction contains oligomers of α-lactalbumin that have undergone a conformational switch toward a molten globule-like state. Oligomerization appears to conserve α-lactalbumin in a state with molten globule-like properties at physiological conditions. The results suggest differences in biological properties between folding variants of α-lactalbumin.
Midterm local efficacy and survival after radiofrequency ablation of lung tumors with minimum follow-up of 1 year: prospective evaluation.

PURPOSE To prospectively evaluate the local efficacy of radiofrequency (RF) ablation of lung neoplasms, with a minimum follow-up period of 1 year. MATERIALS AND METHODS Sixty patients (34 men and 26 women; age range, 27-81 years; mean age, 66 years) with 100 lung tumors gave written informed consent to be enrolled in a prospective study that was approved by the local ethics committee. There were five or fewer tumors per patient, each with a diameter of less than 40 mm (mean +/- standard deviation, 17 mm +/- 10). RF ablation was performed in tumors by using computed tomographic (CT) guidance. Follow-up CT studies were obtained within 48 hours after treatment and at 2, 4, 6, 9, and 12 months thereafter to evaluate treatment outcome and complications. Lung spirometry measurements were obtained before and 4 weeks after RF ablation. RESULTS Ninety-seven of 100 targeted tumors were treated and required 163 RF ablations (1.68 per tumor), each lasting 14 minutes +/- 8, delivered during 74 procedures. The 18-month estimated rate of incomplete local treatment at CT was 7% (95% confidence interval: 3%, 14%) per tumor and 12% (95% confidence interval: 5%, 23%) per patient. An ablation area at least four times larger than the initial tumor was predictive of complete ablation treatment (P = .02). There was a trend toward better efficacy for tumors smaller than 2 cm in diameter (P = .066). Overall survival and lung disease-free survival at 18 months were 71% and 34%, respectively. The main adverse event was a pneumothorax, which occurred in 54% of procedures, but a chest tube was required in only 9% of the procedures. No modification of respiratory function was found when spirometry measurements obtained before and within 2 months after RF ablation were compared (P = .51). CONCLUSION RF ablation has a high local efficacy and is well tolerated.
Cell-cell contacts mediated by E-cadherin (uvomorulin) restrict invasive behavior of L-cells

L-cells were cotransfected with plasmids coding for mouse E-cadherin (uvomorulin) and the neophosphotransferase gene, and stable transfectants expressing E-cadherin at the cell surface were selected and cloned. Control transfection was done with the neophosphotransferase gene alone. The invasive migration of transfected and untransfected L-cells into three-dimensional collagen gels was then analyzed. L-cells not expressing E-cadherin migrated efficiently into the gels, whereas invasion of the E-cadherin-expressing L-cells was restricted in a cell density dependent manner. At sparse density, when the cells exhibited little cell-cell contacts, no difference was observed between the level of invasion of the cadherin-expressing cells and the control cells. However, with increasing cell density, decreasing amounts of the cadherin-expressing cells but increasing amounts of the control cells migrated into the gels. At confluent density hardly any cadherin-expressing cells were able to migrate into the gels. The inhibition of the invasion of the cadherin-expressing cells could be reverted if confluent cells were cultured in the presence of monoclonal antibodies against E-cadherin. Since the expression of E-cadherin did not influence the invasive mobility of single cells, these results indicate that E-cadherin-mediated cell-cell contacts inhibited invasive cellular migration. Time-lapse videoscopy and studies of cell migration from a monolayer into a cell-free area demonstrated that the restricted invasion could be explained by contact inhibition of cell movement of the cadherin-expressing cells.
Efficient Computation of Representative Families with Applications in Parameterized and Exact Algorithms

Let M=(E, I) be a matroid and let S={S1, ċ , St} be a family of subsets of E of size p. A subfamily Ŝ ⊆ S is q-representative for S if for every set Y⊆E of size at most q, if there is a set X ∈ S disjoint from Y with X∪ Y ∈ I, then there is a set Xˆ ∈ Ŝ disjoint from Y with Xˆ ∪ Y ∈ I. By the classic result of Bollobás, in a uniform matroid, every family of sets of size p has a q-representative family with at most (p+qp) sets. In his famous “two families theorem” from 1977, Lovász proved that the same bound also holds for any matroid representable over a field F. We give an efficient construction of a q-representative family of size at most (p+qp) in time bounded by a polynomial in (p+qp), t, and the time required for field operations. We demonstrate how the efficient construction of representative families can be a powerful tool for designing single-exponential parameterized and exact exponential time algorithms. The applications of our approach include the following: —In the Long Directed Cycle problem, the input is a directed n-vertex graph G and the positive integer k. The task is to find a directed cycle of length at least k in G, if such a cycle exists. As a consequence of our 6.75k+o(k)nO(1) time algorithm, we have that a directed cycle of length at least log n, if such a cycle exists, can be found in polynomial time. —In the Minimum Equivalent Graph (MEG) problem, we are seeking a spanning subdigraph D′ of a given n-vertex digraph D with as few arcs as possible in which the reachability relation is the same as in the original digraph D. —We provide an alternative proof of the recent results for algorithms on graphs of bounded treewidth showing that many “connectivity” problems such as Hamiltonian Cycle or Steiner Tree can be solved in time 2O(t)n on n-vertex graphs of treewidth at most t. For the special case of uniform matroids on n elements, we give a faster algorithm to compute a representative family. We use this algorithm to provide the fastest known deterministic parameterized algorithms for k-Path, k-Tree, and, more generally, k-Subgraph Isomorphism, where the k-vertex pattern graph is of constant treewidth.