Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges of transferring models of fish abundance between coral reefs

Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we developed predictive models of total fish abundance and of abundance by fish family for ten representative taxonomic families for the Great Barrier Reef (GBR) using multiple temporal scenarios. We then tested if models developed for the GBR (reference system) could predict fish abundances at Ningaloo Reef (NR; target system), i.e., if these GBR models could be successfully transferred to NR. Models of abundance by fish family resulted in improved performance (e.g., 44.1% <R2 < 50.6% for Acanthuridae) compared to total fish abundance (9% <R2 < 18.6%). However, in contrast with previous transferability obtained for similar models for fish species richness from the GBR to NR, transferability for these fish abundance models was poor. When compared with observations of fish abundance collected in NR, our transferability results had low validation scores (R2 < 6%, p > 0.05). High spatio-temporal variability of patterns in fish abundance at the family and population levels in both reef systems likely affected the transferability of these models. Inclusion of additional predictors with potential direct effects on abundance, such as local fishing effort or topographic complexity, may improve transferability of fish abundance models. However, observations of these local-scale predictors are often not available, and might thereby hinder studies on model transferability and its usefulness for conservation planning and management.
Association between serotonin transporter polymorphisms (5-HTTLPR) and the MADRS Dysphoria, Retardation, and Vegetative Subscale scores in the treatment of depression

Objective We investigated the association between serotonin- or 5-hydroxytryptamine (5-HT)-related gene polymorphisms and response to antidepressant treatment in a specific symptom cluster of major depression by using the three-factor model of the Montgomery–Åsberg Depression Rating Scale (MADRS), ie, dysphoria (items of sadness, pessimistic thoughts, and suicidal thoughts), retardation (items of lassitude, inability to feel, apparent sadness, and concentration difficulties), and vegetative symptoms (items of reduced sleep, reduced appetite, and inner tension). Methods This study was an open-label and nonrandomized trial. A total of 160 patients with baseline MADRS scores of ≥21, who were treated with fluvoxamine or milnacipran for 6 weeks, were included in the statistical analysis. Polymorphisms within a 5-HT transporter (5-HTT) gene-linked polymorphic region (5-HTTLPR), a variable number of tandem repeats in the second intron of the 5-HTT gene (5-HTTVNTR), and 5HT2A receptor (1438G/A) were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results The 5-HTTLPR polymorphisms affected the MADRS score change in dysphoria, but not in retardation, vegetative, or total symptoms. Dysphoria scores significantly decreased in patients with the S/S genotype compared to those in patients with the short (S)/long (L) + L/L genotype. However, 5-HTTVNTR and 1438G/A polymorphisms were not significantly associated with the treatment response to any cluster of depressive symptoms. When a Bonferroni correction was made, however, our results did not reach the criteria for statistical significance. Conclusion The use of a single total depression rating scale may not be sufficient to accurately estimate the clinical response to antidepressants. Analyzing a subset of symptoms in psychological scales could be important when performing pharmacogenetic studies.
Detrimental Effects of Helium Ion Irradiation on Cognitive Performance and Cortical Levels of MAP-2 in B6D2F1 Mice

The space radiation environment includes helium (4He) ions that may impact brain function. As little is known about the effects of exposures to 4He ions on the brain, we assessed the behavioral and cognitive performance of C57BL/6J × DBA2/J F1 (B6D2F1) mice three months following irradiation with 4He ions (250 MeV/n; linear energy transfer (LET) = 1.6 keV/μm; 0, 21, 42 or 168 cGy). Sham-irradiated mice and mice irradiated with 21 or 168 cGy showed novel object recognition, but mice irradiated with 42 cGy did not. In the passive avoidance test, mice received a slight foot shock in a dark compartment, and latency to re-enter that compartment was assessed 24 h later. Sham-irradiated mice and mice irradiated with 21 or 42 cGy showed a higher latency on Day 2 than Day 1, but the latency to enter the dark compartment in mice irradiated with 168 cGy was comparable on both days. 4He ion irradiation, at 42 and 168 cGy, reduced the levels of the dendritic marker microtubule-associated protein-2 (MAP-2) in the cortex. There was an effect of radiation on apolipoprotein E (apoE) levels in the hippocampus and cortex, with higher apoE levels in mice irradiated at 42 cGy than 168 cGy and a trend towards higher apoE levels in mice irradiated at 21 than 168 cGy. In addition, in the hippocampus, there was a trend towards a negative correlation between MAP-2 and apoE levels. While reduced levels of MAP-2 in the cortex might have contributed to the altered performance in the passive avoidance test, it does not seem sufficient to do so. The higher hippocampal and cortical apoE levels in mice irradiated at 42 than 168 cGy might have served as a compensatory protective response preserving their passive avoidance memory. Thus, there were no alterations in behavioral performance in the open filed or depressive-like behavior in the forced swim test, while cognitive impairments were seen in the object recognition and passive avoidance tests, but not in the contextual or cued fear conditioning tests. Taken together, the results indicate that some aspects of cognitive performance are altered in male mice exposed to 4He ions, but that the response is task-dependent. Furthermore, the sensitive doses can vary within each task in a non-linear fashion. This highlights the importance of assessing the cognitive and behavioral effects of charged particle exposure with a variety of assays and at multiple doses, given the possibility that lower doses may be more damaging due to the absence of induced compensatory mechanisms at higher doses.
EFFECTS OF NOISE ON SLEEP IN SHIFT WORKERS

Introduction. This study focused on the effects of noise on sleep at night and day and on after-effects i.e. sleepiness and impaired performance during a following 8-h work shift. Methods. Forty-eight persons (23 male, 25 female; 19-30 yrs) slept in a balanced order four consecutive nights (23-7 h) and four consecutive days (14-22 h) in the laboratory and performed thereafter 8-h work shifts in the morning or in the night, respectively. Sleep was indicated by the Sleep Efficiency Index (SEI) and the Sleep Disturbance Index (SDI). Sleepiness was rated after awakening and hourly during work shifts, and during the latter followed by four performance tests. The first and another randomly chosen sleep period were noise-free. During the six other sleep periods the participants were exposed to railway and to road traffic noise with equivalent noise levels between 41 and 56 dBA. Results. SEI and SDI indicated worse sleep during days than during nights but were only moderately affected by noise. Sleepiness was the only variable where noise and shift type showed an interaction. Soon after awakening sleepiness was rated higher after night than after day sleep and higher after noise exposure during sleep. Sleepiness was after sleep in noise throughout the work shifts higher than after sleep in quiet and reaction times were then prolonged. Conclusion. The same noise had the same effect on day sleep and on night sleep. In the real life situation noise is about 8 to 15 dBA higher during the day than during the night suggesting stronger sleep disturbances of day sleep.
Spray Characterization and Herbicide Efficacy as Influenced by Pulse-Width Modulation Sprayers

Pulse-width modulation (PWM) sprayers can improve application accuracy through flow control, turn compensation, and high-resolution overlap control by pulsing an electronically-actuated solenoid valve and controlling the relative proportion of time each solenoid valve is open (duty cycle). The objective of this experiment was to identify the droplet size distribution and nozzle tip pressure when influenced by PWM duty cycle, nozzle technology, and gauge pressure to provide PWM guidelines. The experiment was conducted in a low-speed wind tunnel at the Pesticide Application Technology Laboratory using a SharpShooter® PWM system. In general, for non-venturi nozzles, as duty cycle decreased, droplet size slightly increased between 40% to 100% duty cycles. Conversely, venturi nozzles did not always follow this trend. The lowest duty cycle evaluated (20%) negatively impacted droplet size and caused inconsistencies for all nozzle by pressure combinations. The addition of a solenoid valve lowered nozzle tip pressure while gauge pressure remained constant indicating a restriction is present within the solenoid valve. Greater orifice sizes increased the pressure loss observed. Duty cycle minimally impacted nozzle tip pressure trends which were similar to the electrical square wave PWM signals. However, venturi nozzles deviated from this trend, specifically twin-fan, single pre-orifice venturi nozzles. In conclusion, venturi nozzles are not 26 recommended for PWM systems as they may lead to inconsistent applications, specifically in regards to droplet size generation and nozzle tip pressures. Spray pressures of 276 kPa or greater and PWM duty cycles of 40% or greater are recommended to ensure proper PWM operation.
Fluctuation relations for anomalous dynamics

We consider work fluctuation relations (FRs) for generic types of dynamics generating anomalous diffusion: Lévy flights, long-correlated Gaussian processes and time-fractional kinetics. By combining Langevin and kinetic approaches we calculate the probability distributions of mechanical and thermodynamical work in two paradigmatic nonequilibrium situations, respectively: a particle subject to a constant force and a particle in a harmonic potential dragged by a constant force. We check the transient FR for two models exhibiting superdiffusion, where a fluctuation-dissipation relation does not exist, and for two other models displaying subdiffusion, where there is a fluctuation-dissipation relation. In the two former cases the conventional transient FR is not recovered, whereas in the latter two it holds either exactly or in the long-time limit.
Plant salt tolerance: adaptations in halophytes.

BACKGROUND Most of the water on Earth is seawater, each kilogram of which contains about 35 g of salts, and yet most plants cannot grow in this solution; less than 0·2% of species can develop and reproduce with repeated exposure to seawater. These 'extremophiles' are called halophytes. SCOPE Improved knowledge of halophytes is of importance to understanding our natural world and to enable the use of some of these fascinating plants in land re-vegetation, as forages for livestock, and to develop salt-tolerant crops. In this Preface to a Special Issue on halophytes and saline adaptations, the evolution of salt tolerance in halophytes, their life-history traits and progress in understanding the molecular, biochemical and physiological mechanisms contributing to salt tolerance are summarized. In particular, cellular processes that underpin the ability of halophytes to tolerate high tissue concentrations of Na+ and Cl−, including regulation of membrane transport, their ability to synthesize compatible solutes and to deal with reactive oxygen species, are highlighted. Interacting stress factors in addition to salinity, such as heavy metals and flooding, are also topics gaining increased attention in the search to understand the biology of halophytes. CONCLUSIONS Halophytes will play increasingly important roles as models for understanding plant salt tolerance, as genetic resources contributing towards the goal of improvement of salt tolerance in some crops, for re-vegetation of saline lands, and as 'niche crops' in their own right for landscapes with saline soils.
Recent advances in the study of high-temperature behaviour of non-stoichiometric TaCx, HfCx and ZrCx carbides in the domain of their congruent melting point

The parameters of the solidus and liquidus phase transitions for TaCx, HfCx and ZrCx are studied using a laser heating technique. A special emphasis is given to the accurate measurement of temperature and determination of spectral emissivity in course of the laser heating using advanced multichannel pyrometry. The phase transitions corresponding to the solidus and the liquidus are determined by means of the laser-probe reflectometry and by the peculiarities in the behaviour of spectral emissivity in the vicinity of the phase transitions and by the high-speed video recording of the melt formation and freezing. New data on solidus and liquidus parameters for the Zr–C system in the homogeneity domain (solid solution) are presented. The temperatures of congruent melting of super-refractory carbides TaC and HfC are determined along with the data on their solidus and liquidus lines close to the composition of congruent melting.
Glycine betaine affects the antioxidant system and ion accumulation and reduces salinity-induced damage in safflower seedlings

Safflower ( Carthamus tinctorius L.) is an important oilseed crop, usually grown on a small scale and in salt-affected soils. Salinity stress can cause oxidative damage to plants. Upregulation of the antioxidant defense system induced by glycine betaine (GlyBet) alleviates the damaging effects of oxidative stress in plants. In the present investigation, seeds were treated with 0, 10, 30 and 60 mM of GlyBet solutions. Germination and the primary growth of the seedling were examined using sodium chloride salt (NaCl) at 0 (non-stress), 50, 100 and 150 mM concentrations. The obtained results indicate that at 50 and 100 mM NaCl, priming with 30 and 60 mM GlyBet increased root and shoot lengths compared to the control (0 mM). In addition, at all stress levels, priming with 60 mM GlyBet led to lower malondialdehyde, total soluble sugars and proline contents than in control seedlings. Priming with GlyBet increased catalase (CAT), superoxide dismutase (SOD) enzyme activities and protein content, while it reduced the activity of peroxidase (POD) under salinity stress. In addition, priming with GlyBet reduced the Na + /K + ratio of seedlings and increased K + under all salinity stress levels. Priming with 60 mM GlyBet also reduced the Na + content under 150 mM NaCl. Together, these results show that 60 mM GlyBet had the most pronounced effect on tolerance to salinity stress in safflower seedling. The GlyBet-increased tolerance to salt in safflower was mainly related to increased CAT and SOD activities, and the prevention of cell membrane damage as a result of reduced lipid peroxidation and improved ion homeostasis under salinity stress condition. DOI: 10.2298/ABS160216089A Received: February 16, 2016; Revised: April 25, 2016; Accepted: May 23, 2016; Published online: October 21, 2016 How to cite this article: Alasvandyari F, Mahdavi B, Hosseini Shahab M. Glycine betaine affects the antioxidant system and ion accumulation and reduces salinity-induced damage in safflower seedlings. Arch Biol Sci. 2017;69(1):139-47.
CD 4 : CD 8 Ratio and CD 8 Count as Prognostic Markers for Mortality in Human Immunodeficiency Virus-Infected Patients on Antiretroviral Therapy : The Antiretroviral Therapy Cohort Collaboration ( ARTCC )

Adam Trickey, Margaret T. May, Philipp Schommers, Jan Tate, Suzanne M. Ingle, Jodie L. Guest, M. John Gill, Robert Zangerle, Mike Saag, Peter Reiss, Antonella d’Arminio Monforte, Margaret Johnson, Viviane D. Lima, Tim R. Sterling, Matthias Cavassini, Linda Wittkop, Dominique Costagliola, and Jonathan A. C. Sterne; for the Antiretroviral Therapy Cohort Collaboration (ART-CC) School of Social and Community Medicine, University of Bristol, United Kingdom; Department I for Internal Medicine, University Hospital of Cologne, Germany; Yale University School of Medicine, West Haven, Connecticut; HIV Atlanta Veterans Affairs Cohort Study, Atlanta Veterans Affairs Medical Center, Decatur, Georgia; Division of Infectious Diseases, University of Calgary, Alberta, Canada; Innsbruck Medical University, Austria; Division of Infectious Disease, Department of Medicine, University of Alabama, Birmingham; Stichting HIV Monitoring, and Division of Infectious Diseases and Department of Global Health, Academic Medical Center, University of Amsterdam, and Amsterdam Institute for Global Health and Development, The Netherlands; Clinic of Infectious Diseases and Tropical Medicine, San Paolo Hospital, University of Milan, Italy; Department of HIV Medicine, Royal Free London NHS Foundation Trust, United Kingdom; British Columbia Centre for Excellence in HIV/AIDS, and Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Vanderbilt University School of Medicine, Nashville, Tennessee; Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Switzerland; and INSERM, Unit of Epidemiology and Biostatistics, Bordeaux, and Sorbonne Universités, INSERM, UPMC Université Paris 06, Institut Pierre Louis d’épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
Neuroscience and Biobehavioral Reviews Innovative solutions to novel drug development in mental health

There are many new advances in neuroscience and mental health which should lead to a greater under- standing of the neurobiological dysfunction in neuropsychiatric disorders and new developments for early, effective treatments. To do this, a biomarker approach combining genetic, neuroimaging, cogni- tive and other biological measures is needed. The aim of this article is to highlight novel approaches for pharmacological and non-pharmacological treatment development. This article suggests approaches that can be taken in the future including novel mechanisms with preliminary clinical validation to provide a toolbox for mechanistic studies and also examples of translation and back-translation. The review also emphasizes the need for clinician-scientists to be trained in a novel way in order to equip them with the conceptual and experimental techniques required, and emphasizes the need for private-public partnership and pre-competitive knowledge exchange. This should lead the way for important new holistic treatment developments to improve cognition, functional outcome and well-being of people with neuropsychiatric disorders.
Modelling ultrafast laser ablation

This review is devoted to the study of ultrafast laser ablation of solids and liquids. The ablation of condensed matter under exposure to subpicosecond laser pulses has a number of peculiar properties which distinguish this process from ablation induced by nanosecond and longer laser pulses. The process of ultrafast ablation includes light absorption by electrons in the skin layer, energy transfer from the skin layer to target interior by nonlinear electronic heat conduction, relaxation of the electron and ion temperatures, ultrafast melting, hydrodynamic expansion of heated matter accompanied by the formation of metastable states and subsequent formation of breaks in condensed matter. In case of ultrashort laser excitation, these processes are temporally separated and can thus be studied separately. As for energy absorption, we consider peculiarities of the case of metal irradiation in contrast to dielectrics and semiconductors. We discuss the energy dissipation processes of electronic thermal wave and lattice heating. Different types of phase transitions after ultrashort laser pulse irradiation as melting, vaporization or transitions to warm dense matter are discussed. Also nonthermal phase transitions, directly caused by the electronic excitation before considerable lattice heating, are considered. The final material removal occurs from the physical point of view as expansion of heated matter; here we discuss approaches of hydrodynamics, as well as molecular dynamic simulations directly following the atomic movements. Hybrid approaches tracing the dynamics of excited electrons, energy dissipation and structural dynamics in a combined simulation are reviewed as well.
Jasmonate‐regulated Arabidopsis stress signalling network

Plants respond to biotic and abiotic factors in the external environment. These include wounding, pathogen and pest attack, and changes in light and temperature. They also respond to internal signals produced during development, such as during the formation of flowers. These responses generally involve the re-programming of gene expression. Biotic and abiotic stress signal perception responses have commonly been represented as three pathways, which can be distinguished by the production of jasmonates, ethylene or salicylic acid. Each of these pathways therefore involves the perception of the stress, the synthesis of the signal molecule, the perception of the signal molecule and the ensuing response. An added complication is that these signalling pathways act both locally, at the point of the stress, and systemically. Much of what we know about these signalling pathways has come from studies of responses to the signal molecules, and of mutants altered in the production of, or sensitivity to, these signal molecules. This has provided clear indications that the pathways interact significantly. Because biotic and abiotic stresses induce the production of all three of these signal molecules, albeit in differing amounts, it is more appropriate to view the response output as the integration of a signalling network that involves the production of jasmonates, salicylic acid and ethylene. In this review, we provide an update on the regulation of jasmonic acid biosynthesis and the suggested roles for different biologically active intermediates in this pathway in Arabidopsis, and describe the jasmonate signalling mutants identified so far. We also examine how outputs from the jasmonate, salicylic acid and ethylene signalling pathways are integrated in the regulation of stress response and plant development. We use Boolean gates as a tool to represent the molecular networks and provide a qualitative description of the transmission of the signals. Finally, we illustrate how protein degradation, a common mechanism regulating many plant processes, may act as the ultimate level of integration between signalling pathways.