Miracle-dz/UniFAR-FTUs huggingface dataset:
Global change in the functional diversity of marine fisheries exploitation over the past 65 years

Overexploitation is recognized as one of the main threats to global biodiversity. Here, we report a widespread change in the functional diversity of fisheries catches from the large marine ecosystems (LMEs) of the world over the past 65 years (1950 to 2014). The spatial and temporal trends of functional diversity exploited from the LMEs were calculated using global reconstructed marine fisheries catch data provided by the Sea Around Us initiative (including subsistence, artisanal, recreational, industrial fisheries, and discards) and functional trait data available in FishBase. Our analyses uncovered a substantial increase in the functional richness of both ray-finned fishes (80% of LMEs) and cartilaginous species (sharks and rays) (75% of LMESs), in line with an increase in the taxonomic richness, extracted from these ecosystems. The functional evenness and functional divergence of these catches have also altered substantially over the time span of this study, with considerable geographic variation in the patterns detected. These trends show that global fisheries are increasingly targeting species that play diverse roles within the marine ecosystem and underline the importance of incorporating functional diversity in ecosystem management.
American black bears and hair snares: a behavioral analysis

Abstract: Despite the widespread use of noninvasive hair-sampling for American black bear (Ursus americanus) population monitoring, there is no explicit analysis of black bear behavior at hair snare sites. During 2016, we deployed hair snares and camera traps at 40 sites across the northern Lower Peninsula of Michigan, USA, and collected 560 video recordings of black bear activity. Our objectives were to develop an ethogram of bear behaviors at snare sites and quantify their occurrence. We found that bears allocated their time consistently when they were physically inside or outside of the snare, but they divided their time among multiple behaviors when crossing the wire. The inconsistencies in wire crossing revealed unexpected behaviors with important implications for study design. Our findings explicitly describe how black bears interact with hair snares, provide recommendations for addressing the influence of behavior on sampling efficiency, and establish a foundation for further study of animal behavior at hair snares.
Cyclically producing the same average muscle-tendon force with a smaller duty increases metabolic rate

Ground contact duration and stride frequency each affect muscle metabolism and help scientists link walking and running biomechanics to metabolic energy expenditure. While these parameters are often used independently, the product of ground contact duration and stride frequency (i.e. duty factor) may affect muscle contractile mechanics. Here, we sought to separate the metabolic influence of the duration of active force production, cycle frequency and duty factor. Human participants produced cyclic contractions using their soleus (which has a relatively homogeneous fibre type composition) at prescribed cycle-average ankle moments on a fixed dynamometer. Participants produced these ankle moments over short, medium and long durations while maintaining a constant cycle frequency. Overall, decreased duty factor did not affect cycle-average fascicle force (p ≥ 0.252) but did increase net metabolic power (p ≤ 0.022). Mechanistically, smaller duty factors increased maximum muscle-tendon force (p < 0.001), further stretching in-series tendons and shifting soleus fascicles to shorter lengths and faster velocities, thereby increasing soleus total active muscle volume (p < 0.001). Participant soleus total active muscle volume well-explained net metabolic power (r = 0.845; p < 0.001). Therefore, cyclically producing the same cycle-average muscle-tendon force using a decreased duty factor increases metabolic energy expenditure by eliciting less economical muscle contractile mechanics.
Heuristics and optimal solutions to the breadth–depth dilemma

Significance From choosing among the many courses offered in graduate school to dividing budget into research programs, the breadth–depth is a commonplace dilemma that arises when finite resources (e.g., time, money, cognitive capabilities) need to be allocated among a large range of alternatives. For such problems, decision makers need to trade off breadth—allocating little capacity to each of many alternatives—and depth—focusing capacity on a few options. We found that little available capacity (less than 10 samples for search) promotes allocating resources broadly, and thus breadth search is favored. Increased capacity results in an abrupt transition toward favoring a balance between breadth and depth. We finally describe a rich casuistic and heuristics for metareasoning with finite resources. In multialternative risky choice, we are often faced with the opportunity to allocate our limited information-gathering capacity between several options before receiving feedback. In such cases, we face a natural trade-off between breadth—spreading our capacity across many options—and depth—gaining more information about a smaller number of options. Despite its broad relevance to daily life, including in many naturalistic foraging situations, the optimal strategy in the breadth–depth trade-off has not been delineated. Here, we formalize the breadth–depth dilemma through a finite-sample capacity model. We find that, if capacity is small (∼10 samples), it is optimal to draw one sample per alternative, favoring breadth. However, for larger capacities, a sharp transition is observed, and it becomes best to deeply sample a very small fraction of alternatives, which roughly decreases with the square root of capacity. Thus, ignoring most options, even when capacity is large enough to shallowly sample all of them, is a signature of optimal behavior. Our results also provide a rich casuistic for metareasoning in multialternative decisions with bounded capacity using close-to-optimal heuristics.
Simultaneous spectrum sensing, data transmission and Energy harvesting in multi‐channel cognitive sensor Networks with imperfect signal cancellation

In multichannel cognitive sensor networks, the sensor users which have limited energy budgets sense the spectrum to determine the activity of the primary user. If the spectrum is idle, the sensor user can access the licensed spectrum. However, during the spectrum sensing, no data transmits. For improving the network throughput and saving more energy consumption, we propose the simultaneous spectrum sensing and data transmission scheme where the sensor receiver decodes the received signal, and from the remaining signal, the status of the channel (idle/busy) is determined. We also consider that the sensor users are powered by a radio‐frequency (RF) energy harvester. In this case, energy harvesting, data transmission, and spectrum sensing are done simultaneously. On the other hand, we select the proper sensor users for spectrum sensing and energy harvesting. We also allocate the best channels for data transmission simultaneously so that the network throughput maximizes and the constraints on the energy consumption and the detection performance are satisfied for each band. We formulate the problem and model it as a coalition game in which sensors act as game players and decide to make coalitions. Each coalition selects one of the channels to sense and transmit data, while the necessary detection probability and false alarm probability and also the energy consumption constraints are satisfied. The utility function of a coalition is proposed based on the energy consumption, false alarm probability, detection probability, and the network throughput. This paper proposes an efficient algorithm to reach a Nash‐stable coalition structure. It is demonstrated that the proposed method maximizes the network throughput and reduces the energy consumption while it provides sufficient detection quality, in comparison to other existent methods.
Cellular and molecular mechanisms of salinity acclimation in an amphidromous teleost fish

Inanga (Galaxias maculatus) is an amphidromous fish species that is able to successfully inhabit a variety of salinities. Using an integrated approach this thesis has characterised for the first time the physiological characteristics that facilitate acclimation in inanga. Structural studies using scanning electron microscopy (SEM) and laser scanning confocal microscopy (LSCM) revealed freshwater-acclimated inanga have a high density of apical pits and freshwater-type mitochondria-rich cells (MRCs) that can facilitate ion absorption from the hypo-osmotic environment. In seawater, inanga remodel their gills by increased proliferation of seawater-type MRCs to facilitate ion secretion in the hyper-osmotic environment. Concentration-dependent sodium (Na + ) kinetic analysis revealed that at a whole body level, inanga regulate Na + using a saturable, high affinity, low capacity uptake system which makes them extremely adept at extracting Na + from very dilute freshwater environments. In fact inanga displayed an uptake affinity (Km) of 52 ± 29 μM, which is one of the lowest ever recorded in freshwater fish. The sodium/potassium ATPase transporter (NKA) is central to Na + regulation within the gill. In high salinties inanga displayed increased NKA activity (6.42 ± 0.51 μmol ADP mg protein -1 h -1 ) in an effort to excrete the excess Na + , diffusively gained from the hyperosmotic environment. This increase in NKA was most likely a reflection of the proliferation of NKA-containing MRCs. The NKA activities seen in freshwaterand 50% seawateracclimated inanga were similar (2.54 ± 0.19 and 2.07 ± 0.22 μmol ADP mg protein -1 h -1 respectively) to each other suggesting the inanga gill is capable of supporting ion regulation in brackish waters without a significant increase in NKA activities, and the energeticallyexpensive changes in gill structure and function that accompany such a change. Molecular investigation of NKA isoform expression using quantitative PCR (qPCR) showed that inanga displayed salinity-induced changes in the expression of the three α NKA isoform variants investigated. Isoform α1a exhibited a pattern consistent with an important role in freshwater, confirming results from other fish species. While it is generally accepted that α1b isoform is the predominant NKA isoform in seawater, inanga did not display this pattern with a freshwater dominance seen. None of the salinity-induced changes could quantitatively
Allozymic and Morphological Evidence for a Progenitor-Derivative Species Pair in Camassia (Liliaceae)

Analyses of morphological and isozymic variability were used to discriminate pop- ulations of Camassia angusta from those of C. scilloides. Camassia scilloides had a distinct, earlier flowering period than C. angusta. Populations identified on the basis of differences in relative flowering time showed little morphological and isozymic divergence but could be correctly clas- sified by taxon-specific patterns of variation for these characters. The allozymes of C. angusta were mostly a subset of those of C. scilloides; the latter had nine unique, rare alleles at 10 loci and the former had only two. Camassia angusta, therefore, may be a relatively recent derivative of C. scilloides. While the taxa have diverged little from each other for the characters examined, they appear reproductively isolated and should be maintained taxonomically as separate species. The genus Camassia Lindl. (Liliaceae) com- prises bulbous, scapose, diploid perennials. Ca- massia biflora (Ruiz & Pavon) Cocucci was de- scribed from South America and is distributed from Peru to Chile, east to Argentina (Cocucci 1969). In western North America, Camassia in- cludes four species (Gould 1942): the wide-
Endocrine and Metabolic Responses to Endurance Exercise Under Hot and Hypoxic Conditions

Purpose We explored the effect of heat stress during an acute endurance exercise session in hypoxia on endocrine and metabolic responses. Methods A total of 12 healthy males cycled at a constant workload (60% of the power output associated with their maximal oxygen uptake under each respective condition) for 60 min in three different environments: exercise under hot and hypoxia (H+H; fraction of inspiratory oxygen or FiO2: 14.5%, 32°C), exercise under hypoxia (HYP; FiO2: 14.5%, 23°C), and exercise under normoxia (NOR; FiO2: 20.9%, 23°C). After completing the exercise, participants remained in the chamber for 3 h to evaluate metabolic and endocrine responses under each environment. Changes in muscle oxygenation (only during exercise), blood variables, arterial oxygen saturation, and muscle temperature were determined up to 3 h after exercise. Results Serum erythropoietin (EPO) level was increased to similar levels in both H+H and HYP at 3 h after exercise compared with before exercise (P < 0.05), whereas no significant increase was found under NOR. No significant difference between H+H and HYP was observed in the serum EPO level, blood lactate level, or muscle oxygenation at any time (P > 0.05). Exercise-induced serum growth hormone (GH) elevation was significantly greater in H+H compared with HYP (P < 0.05) and HYP showed significantly lower value than NOR (P < 0.05). Arterial oxygen saturation during exercise was significantly lower in H+H and HYP compared with NOR (P < 0.05). Furthermore, H+H showed higher value compared with HYP (P < 0.05). Conclusion The serum EPO level increased significantly with endurance exercise in hypoxia. However, the addition of heat stress during endurance exercise in hypoxia did not augment the EPO response up to 3 h after completion of exercise. Exercise-induced GH elevation was significantly augmented when the hot exposure was combined during endurance exercise in hypoxia. Muscle oxygenation levels during endurance exercise did not differ significantly among the conditions. These findings suggest that combined hot and hypoxic stresses during endurance exercise caused some modifications of metabolic and endocrine regulations compared with the same exercise in hypoxia.
Towards chronomic medicine: Enrichment and linkage of chronotype markers with rare disease associated genes

The role of the circadian clock is becoming apparent in many aspects of human health and disease. Large scale GWAS studies have delivered high numbers of genetic markers for chronotype, which can be used to find links to Mendelian disorders. We used the variants in the 1,000 genomes study to estimate linkage disequilibrium for these chronotype markers. We analysed genes in high linkage disequilibrium with the chronotype markers for enrichment of disease-causing genes, and looked for enrichment of common HPO terms in the wider disease associated genes. We identified that two cardiovascular disorders, cardiomyopathy, and the inherited cardiac arrhythmia Long QT Syndrome, along with the immune system disorder complement component 2 deficiency were significantly enriched MIM diseases. In contrast the most common HPO terms were developmental and neurological terms. This analysis provides a starting point for identifying the circadian contribution to disease outside of the core circadian clock genes, by providing candidate conditions and loci for identifying circadian modifier variants.
Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis

Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.
Power System Stabilizers for Inverter Dominated Future Power Systems

This paper proposes implementation of power system stabilizer (PSS) function in inverters for stabilizing low frequency power oscillations in future inverter dominated power systems (PS). It considers several concepts and solutions for PSS taking into account the expected characteristics of the future power systems with high share of renewable energy sources. Implementation of inverters with PSS function is proposed for stabilizing low frequency power oscillations. Several classical PSS types are studied to outline the essence of the process and to examine the potential for their implementation in inverters. For design and conditioning purposes, small signal stability analysis model is first used. Nonlinear simulation using Matlab/Simulink is applied on a single machine infinite bus system (SMIB) to show the performance of different PSS types in enhancement of power system dynamics. A ΔP PSS Simulink model is constructed. A comparison between ΔP, Δω and multiband PSS under various disturbance conditions is performed to evaluate the effectiveness of the examined model and to validate the applicability of the approach. The functional requirements and characteristics of the inverter based PSS are evaluated and tested using literature analysis and laboratory experiments performed at the Power System Stability Laboratory of TU-Sofia.
Modeling the distribution of odonates: a review

Species distribution models (SDMs) can be used to answer a variety of questions about Odonata (dragonflies and damselflies) distributions because locality data for species are readily available. We provide an overview of SDMs and review 30 studies that have used SDMs to examine factors governing odonate distributions in current and projected future scenarios. These studies had objectives that included predicting the potential geographical distribution of a species based on scattered records, quantifying hotspots for biodiversity and identifying reserve gaps, assessing species’ environmental requirements and limitations, quantifying dispersal abilities of species with different life histories, studying niche conservatism among sympatric species, modeling the effect of forecasted climate change on species distributions, and examining the efficacy of different modeling approaches. We point out limitations in the use of SDMs for these purposes, including effects of limited taxonomic coverage and limited spatial resolution at fine scales. We also highlight potential future areas where use of SDMs can advance our knowledge of odonate–environment interactions.
The effects of resveratrol on cell cycle, apoptosis, and NF-kB activation

Purpose: To study the effect of resveratrol, a putative chemopreventive phytoalexin, on DNA synthesis, cell cycle, apoptosis, and the possible involvement of the transcription factor NF-κB. Methods: HL-60, a suspension human promyelocytic leukemia cell line, and HepG2, an epithelial human hepatoma-derived cell line were chosen as models. Incorporation of 3H-labelled thymidine and cell cycle distribution, assessed by binding of Propidium Iodine and flow cytometry, were used to evaluate the effect on cell proliferation. The effect on apoptosis was studied by the use of several assays. The nuclei were stained with DAPI and subsequently visualised with fluorescence microscopy. Bound Annexin-V and activity of Caspase-8 were evaluated by flow cytometry. Cleavage of Caspase-3 was assessed by Western blot. The effect of resveratrol on NF-κB transactivating activity was studied by a reporter gene assay. Phosphorylation of the RelA/p65 NF-κB subunit was evaluated by Western blot. Levels of resveratrol were evaluated by light-absorption, and size of isolated cell nuclei was assessed by flow cytometry. Results: Resveratrol induces a complex dose and time dependent reduction in incorporation of 3H-labelled thymidine. The IC50 value increased with increase in incubation time and short term treatment had an inhibitory effect on the incorporation of thymidine. These effects are previously unreported for the used cell lines. It was observed for the first time that when in FCS containing solution, levels of resveratrol decreased. It was found that resveratrol induced a dose dependent accumulation in the S and G1 phases of the cell cycle in both cell lines. In addition, an enlargement of the HL-60 but not HepG2 nuclei was observed. The nuclear enlarging effect is previously unreported. Resveratrol was found to stimulate apoptosis in a dose dependent manner in HL-60 cells. Caspase-3 and Caspase-8 were furthermore found to be activated. Basal and TNF-α stimulated NF-κB activity was found to be inhibited by resveratrol in a dose dependent manner. HL-60 cells were furthermore found not to be suitable for studying phosphorylation of RelA/p65. Conclusion: Resveratrol modulates the cell cycle in a complex fashion. Apoptosis is stimulated in a dose dependent manner, with activation of the extrinsic and the intrinsic pathways. The involvement of NF-κB in the observed cellular effects remains unclear.
Ideal Membership Problem and a Majority Polymorphism over the Ternary Domain

The Ideal Membership Problem (IMP) asks if an input polynomial f ∈ F [ x 1 , . , x n ] with coeﬃcients from a ﬁeld F belongs to an input ideal I ⊆ F [ x 1 , . , x n ]. It is a well-known fundamental problem with many important applications, though notoriously intractable in the general case. In this paper we consider the IMP for polynomial ideals encoding combinatorial problems and where the input polynomial f has degree at most d = O (1) (we call this problem IMP d ). Our main interest is in understanding when the inherent combinatorial structure of the ideals makes the IMP d “hard” (NP-hard) or “easy” (polynomial time) to solve. Such a dichotomy result between “hard” and “easy” IMPs was recently achieved for Constraint Satisfaction Problems over ﬁnite domains [5, 24] (this is equivalent to IMP 0 ) and IMP d for the Boolean domain [16], both based on the classiﬁcation of the IMP through functions called polymorphisms. For the latter result, each polymorphism determined the complexity of the computation of a suitable Gröbner basis. In this paper we consider a 3-element domain and a majority polymorphism (constraints under this polymorphism are a generalisation of the 2-SAT problem). By using properties of the majority polymorphism and assuming graded lexicographic ordering of monomials, we show that the reduced Gröbner basis of ideals whose varieties are closed under the majority polymorphism can be computed in polynomial time. This proves polynomial time solvability of the IMP d for these constrained problems. We conjecture that this result can be extended to a general ﬁnite domain of size k = O (1). This is a ﬁrst step towards the long term and challenging goal of generalizing the dichotomy results of solvability of the IMP d for a ﬁnite domain.