Miracle-dz/UniFAR-FTUs huggingface dataset:
Mortality and movement of Yellowtail Flounder (Limanda ferruginea) tagged off New England

From 2003 to 2006, 44,882 Yellowtail Flounder (Limanda ferruginea) were captured and released with conventional disc tags in the western North Atlantic as part of a cooperative Yellowtail Flounder tagging study. From these releases, 3767 of the tags were recovered. The primary objectives of this tagging program were to evaluate the mortality and large-scale movement of Yellowtail Flounder among 3 stock areas in New England. To explore mortality, survival and recovery rate were estimated from traditional Brownie tag-recovery models fitted to the data with Program MARK. Models were examined with time and sex-dependent parameters over several temporal scales. The models with a monthly scale for both survival and recovery rate had the best overall fit and returned parameter estimates that were biologically reasonable. Estimates of survival from the tag-recovery models confirm the general magnitude of total mortality derived from age-based stock assessments but indicate that survival was greater for females than for males. In addition to calculating mortality estimates, we examined the pattern of release and recapture locations and revealed frequent movements within stock areas and less frequent movement among stock areas. The collaboration of fishermen and scientists for this study successfully resulted in independent confirmation of previously documented patterns of movement and mortality rates from conventional age-based analyses.
LOW ENERGY SPECTRAL INDEX AND Ep EVOLUTION OF QUASI-THERMAL PHOTOSPHERE EMISSION OF GAMMA-RAY BURSTS

Recent observations by the Fermi satellite suggest that a photosphere emission component is contributing to the observed spectrum of many gamma-ray bursts (GRBs). One important question is whether the photosphere component can interpret the typical 'Band' function of GRBs with a typical low energy photon spectral index α ∼ –1. We perform a detailed study of the photosphere emission spectrum by progressively introducing several physical ingredients previously not fully incorporated, including the probability distribution of the location of a dynamically evolving photosphere, superposition of emission from an equal arrival time 'volume' in a continuous wind, the evolution of optical depth of a wind with finite but evolving outer boundary, as well as the effect of different top-hat wind luminosity (L{sub w} ) profiles. By assuming a comoving blackbody spectrum emerging from the photosphere, we find that for an outflow with a constant or increasing L{sub w} , the low-energy spectrum below the peak energy (E{sub p} ), can be modified to F {sub ν} ∼ ν{sup 1.5} (α ∼ +0.5). A softer (–1 < α < +0.5) or flat (α = –1) spectrum can be obtained during the L{sub w} decreasing phase or high-latitude-emission-dominated phase. We also study the evolutionmore » of E{sub p} as a function of wind and photosphere luminosity in this photosphere model. An E{sub p} – L tracking pattern can be reproduced if a certain positive dependence between the dimensionless entropy η and L{sub w} is introduced. However, the hard-to-soft evolution pattern cannot be reproduced unless a contrived condition is invoked. In order to interpret the Band spectrum, a more complicated photosphere model or a different energy dissipation and radiation mechanism is needed. « less
Understanding poverty dynamics in Kenya

Combining qualitative-quantitative approaches, we examined the reasons behind household movements into and out of poverty across Kenya, and how they differ by livelihood zones. Among the 4773 households studied, 42 per cent were poor 15 years ago and 50 per cent are poor at the present time. Over the same period, 12 per cent of the households escaped poverty, while another 20 per cent fell into poverty. While some national trends were evident - such as the role of health problems in driving people into poverty and the importance of off-farm income in getting them out - many reasons differ across livelihood zones, thus this paper provides an example of how regionally differentiated anti-poverty policies can be investigated and designed. Copyright © 2009 John Wiley & Sons, Ltd.
Freeway Roadside Management: The Urban Forest Beyond the White Line

A national survey was conducted in the United States to learn more about public preferences and perceptions regarding forest and vegetation planning and management in urban freeway roadsides. In response to images depicting a visual continuum of landscape management treatments, drivers most preferred settings having tree plantings that screen adjacent commercial land uses. Preference results suggest solutions for landscape practices that create visual quality for drivers and provide visibility for commercial properties adjacent to freeway roadsides. The research also investigated public attitudes about roadside functions, uses, and public willingness to support roadside management expenditures. Increasingly, transportation agencies are designing urban roadside landscapes to achieve multiple objectives and perform multiple functions. This research offers insights on how to incorporate urban forestry into the planning and management of high-speed urban transportation corridors.
Flexible free-standing graphene paper with interconnected porous structure for energy storage

A novel porous graphene paper is prepared via freeze drying a wet graphene oxide gel, followed by thermal and chemical reduction. The macroscopic structure of the formed graphene paper can be tuned by the water content in the gel precursor. With 92% water content, an interconnected macroporous network can be formed. This porous graphene (PG) paper exhibits excellent electrochemical properties. It can deliver a high discharge capacity of 420 mA h g−1 at a current density of 2000 mA g−1 when used as binder-free lithium ion battery anode. PG paper exhibits a specific capacitance of 137 F g−1 at 1 A g−1 in a flexible all-solid-state supercapacitor with PVA/H2SO4 electrolyte. It can maintain 94% of its capacitance under bending. This electrochemical performance and mechanical flexibility makes it an excellent material for flexible energy storage devices.
NIPA 1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis

Department of Neurology and Department of Neuroloscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands, Department of Neurology, University Hospital Leuven, University of Leuven, Leuven, Belgium, Vesalius Research Center, VIB, Leuven, Belgium, Department of Neurology, University of Ulm, Ulm, Germany, Department of Neurology, Charité University Hospital, Humboldt-University, Berlin, Germany, Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, and German Center for Neurodegenerative Diseases, Tübingen, Germany and Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Sciences and University Medical Center Utrecht, The Netherlands
What is Nominal Tense ? A Case Study of Paraguayan Guaranı́

Over the past ten years, several papers have described and analyzed a number of languages with nominal temporal affixes, i.e., grammatical items with temporal properties which attach to noun phrases and affect the temporal interpretation of the noun phrase (cf., e.g., Demirdache 1996, Burton 1997, Lecarme 1999, Nordlinger and Sadler 2000, Wiltschko 2003, Haude 2004, Nordlinger and Sadler 2004, Lecarme 2004). The nominal temporal suffixes of Paraguayan Guaranı́ are illustrated in (1). The noun phrase peteı̃ óga ‘a house’ in (1a) is not marked with a temporal suffix, and the sentence means that the entity that is identified by the demonstrative kova ‘this’ and the noun phrase peteı̃ óga ‘a house’ is a house at the utterance time. In (1b) and (1c), the noun phrase is marked with the nominal temporal suffix -kue and -rã, respectively, which has an effect on the temporal interpretation of the noun phrase. In (1b), the entity that is identified by the demonstrative kova ‘this’ is not a house anymore at the utterance time but was a house in the past. In (1c), the entity is not a house yet at the utterance time but is in the process of becoming a house.1
The Murky Waters of Medical Practice in India: Ethics, Economics and Politics of Healthcare

This is a brief essay discussing some key aspects of the current debates on medical corruption and malpractices in India. I highlight few illustrations from recent research and argue that the falling standards of medical practice in the country is a fallout of a combination of dwindling ethical principles and misplaced economic incentives arising out of the neoliberal manifestations of waning role of the State, even for a merit good such as healthcare.
Why do some oil exporters experience civil war but others do not?: investigating the conditional effects of oil

According to quantitative studies, oil seems the only natural resource that is robustly linked to civil war onset. However, recent debates on the nexus of oil and internal conflict have neglected the fact that there are a number of peaceful rentier oil states in existence. Few efforts have been made to explain why some oil-exporting countries have experienced civil war while others have not. We thus address this puzzle, by arguing that civil war risks depend on the specific conditions of oil production and how they come to structure state–society relations. Specifically, we expect that states that are either highly dependent on oil or who have problematic relations with oil regions are prone to civil war. However, these risks will be mitigated either when democratic institutions can manage conflicts peacefully or when abundant oil revenues can be spent in such a way as to buy peace. We test this conditional argument by comparing 39 net oil exporters, using a (crisp-set) Qualitative Comparative Analysis – a methodology particularly suited to test conditional relationships in medium-N samples. Our results largely confirm our conditional hypotheses. Conditions of oil production are ambiguous, and particular combinations thus explain the onset of civil war. Specifically, we find that high abundance is sufficient to ensure peace, while two distinct pathways lead to civil war: the combination of high dependence and low abundance, as well as the overlap of ethnic exclusion and oil reserves in non-abundant and non-democratic oil states.
Development of virulence to Meloidogyne incognita on resistant pepper rootstocks

The root-knot nematode (RKN) Meloidogyne incognita is a major soil parasite of pepper crops in greenhouses in Southeast Spain. Due to the limitations of the use of soil fumigants, grafting plants on resistant rootstocks (R-rootstocks) has become an important alternative to chemical nematicides. The repeated use of R-rootstocks can bring about the selection of virulent populations capable of overcoming resistance. We carried out a six-year investigation on resistant rootstocks in a naturally M. incognita infested greenhouse, and found that two successive years of growing plants grafted on R-rootstocks Atlante (ATL) were sufficient to overcome resistance (galling index 1.5 and 5.6 in the first and second years respectively). A large variability was observed between several R-rootstocks. Two R-rootstocks (C19 and Snooker) behaved like ATL while two others (Terrano and DRO 8801) were not infected by RKN. Laboratory studies with the same R-rootstocks, inoculated with two nematode isolates (avirulent and virulent against ATL) confirmed the greenhouse results, indicating that some rootstocks may be infested by virulent populations and others may not. It suggests that different R-genes, which are differentially overcome by RKN, have been introgressed into the rootstocks. This may have consequences for the management of resistant rootstocks in the field.
Harvesting Fertilized Rye Cover Crop: Simulated Revenue, Net Energy, and Drainage Nitrogen Loss

Fertilizing winter rye increased estimated revenue and harvestable biomass. Fertilizing winter rye increased net energy production. Harvesting fertilized winter rye reduced simulated drainage N loss. Rye revenue in response to fertilizer rate plateaued at approximately 120 kg N ha−1. Field studies are needed to evaluate fertilized/harvested rye cover crop.
Appendix to : Macroeconomic Effects of Banking Sector Losses across Structural Models

1 Matteo Iacoviello: An Estimated model of Banks with Financing Frictions . 2 1.1 The Dynamic Model . 3 1.1.1 Household Savers . 3 1.1.2 Household Borrowers . 3 1.1. 3 Bankers . 4 1.1. 4 Entrepreneurs . 5 1.1. 5 Equilibrium . 6 1.1. 6 Shocks . 7 1.2 Calibration . 8 2 Francisco Covas and John Driscoll: A Nonlinear Model of Borrowing Constraints . 10 2.
Parasitism in the social bee Apis mellifera: quantifying costs and benefits of behavioral resistance to Varroa destructor mites

The case of a host-parasite relationship may provide a good model to evaluate the costs and bene- fits of some behaviors, an area in which field data a currently lacking. European (EHB) and Africanized (AHB) honey bees are two Apis mellifera subspecies that coexist in Mexico, the former highly compatible with Varroa destructor, the latter less compatible. Here we examine two mechanisms that could explain the low compatibility between AHB and V. destructor in Mexico: (1) grooming behavior appeared significantly more intensive in AHB colonies, but was nevertheless ineffective; (2) EHB removed 8.03% of the infested brood, while AHB removed 32.46%, especially between 5 and 7 days post-capping. Though the cost of re- moving infested brood was not different between subspecies, the result, in terms of the amount of removed in- fested brood, was significantly higher for AHB. For both bees, there is thus a real cost, since removing a pupa results in a lower number of adult bees. We discuss the possibility that the removal of infested brood corre- sponds with a threshold above which the cost of removal becomes greater than the benefit. Apis mellifera / Varroa destructor / parasitology / costs and benefits / behavioral resistance
Quantifying Uncertainty in High Dimensional Inverse Problems by Convex Optimisation

Inverse problems play a key role in modern image/signal processing methods. However, since they are generally ill-conditioned or ill-posed due to lack of observations, their solutions may have significant intrinsic uncertainty. Analysing and quantifying this uncertainty is very challenging, particularly in high-dimensional problems and problems with non-smooth objective functionals (e.g. sparsity-promoting priors). In this article, a series of strategies to visualise this uncertainty are presented, e.g. highest posterior density credible regions, and local credible intervals (cf. error bars) for individual pixels and superpixels. Our methods support non-smooth priors for inverse problems and can be scaled to high-dimensional settings. Moreover, we present strategies to automatically set regularisation parameters so that the proposed uncertainty quantification (UQ) strategies become much easier to use. Also, different kinds of dictionaries (complete and over-complete) are used to represent the image/signal and their performance in the proposed UQ methodology is investigated.
Being on the same wavelength: Behavioral synchrony between partners and its influence on the experience of intimacy

Although coordination between partners has been considered in the clinical literature as an indication of intimate relationships, the influence of simple motor synchrony on the experience of intimacy has not been established yet. Four studies examined whether synchrony, temporal alignment of simple motor periodic behaviors between partners, instilled a sense of intimacy. In Study 1, same-sex strangers discussed positive or neutral events while their motion synchrony and experiences of intimacy were measured. In Study 2, same-sex strangers pedaled bicycles in either synchronous or asynchronous rhythms while discussing personal events and then rated how intimate they felt. Studies 3 and 4 examined whether the effect of synchronization would generalize to perceptions of intimacy and desire among romantically involved heterosexual participants. Results showed that key aspects of intimacy were associated with synchrony or were higher following synchronized versus unsynchronized interactions, suggesting that synchrony serves as a nonverbal mechanism that promotes closeness in intimate situations.
How Does Nitrogen and Perenniality Influence Belowground Biomass and Nitrogen Use Efficiency in Small Grain Cereals?

Perennial cropping systems typically exhibit extensive root systems that contribute to important ecosystem services. However, the root systems and the distribution of roots throughout the soil profile in novel perennial grains have yet to be reported. In addition, understanding the full impact of perennial grain cropping systems on belowground processes requires knowledge of how N regimes might influence biomass partitioning and N retention. Here, we quantified root biomass distribution, crop biomass allocation, and whole-crop fertilizer N use efficiency (NUE, defined as the ratio of plant N to total N fertilizer applied) in annual winter wheat (Triticum aestivum L. ‘Caledonia’) and perennial intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R. Dewey] across three N treatments over a 3-yr period. Nitrogen treatments included Low N (90 kg ha−1 of poultry manure), Mid N (90 kg ha−1 of urea), and High N (135 kg ha−1 of urea). As a perennial plant, IWG had significantly greater root biomass than annual wheat to the 40-cm depth (p < 0.05), but no differences were found between the crops at deeper depths. Nitrogen treatments did not affect root biomass, except for IWG in its fourth year (p < 0.05). Regardless of N level, IWG always had greater whole-crop NUE than annual wheat (p < 0.05). Results demonstrate that IWG roots represent a large pool of N that contributes to enhanced NUE and ultimately greater N retention than in annual wheat roots. C.D. Sprunger and S.W. Culman, School of Environment and Natural Resources, Ohio State Univ., Wooster, OH 44691; G.P. Robertson, W.K. Kellogg Biological Station, Michigan State Univ., Hickory Corners, MI 49060; G.P. Robertson and S.S. Snapp, Dep. of Plant, Soil, and Microbial Sciences, Michigan State Univ., East Lansing, MI 48824. Received 22 Feb. 2018. Accepted 31 May 2018. *Corresponding author (sprunger.29@osu.edu). Assigned to Associate Editor Florian Wichern. Abbreviations: IWG, perennial intermediate wheatgrass; KBS, W.K. Kellogg Biological Station; NUE, nitrogen use efficiency. Published in Crop Sci. 58:2110–2120 (2018). doi: 10.2135/cropsci2018.02. 0123 © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. Published August 10, 2018
EffEct of hypoxia on thE ExprEssion of nuclEar gEnEs Encoding mitochondrial protEins in u 87 glioma cElls

We have studied the effect of hypoxia on the expression of nuclear genes encoding mitochondrial proteins in u87 glioma cells under the inhibition of iRE1 (inositol requiring enzyme-1), which controls cell proliferation and tumor growth as a central mediator of endoplasmic reticulum stress. it was shown that hypoxia down-regulated gene expression of malate dehydrogenase 2 (mDh2), malic enzyme 2 (mE2), mitochondrial aspartate aminotransferase (GOT2), and subunit b of succinate dehydrogenase (sDhb) in control (transfected by empty vector) glioma cells in a gene specific manner. at the same time, the expression level of mitochondrial naDP+-dependent isocitrate dehydrogenase 2 (iDh2) and subunit D of succinate dehydrogenase (sDhD) genes in these cells does not significantly change in hypoxic conditions. it was also shown that the inhibition of ІRE1 signaling enzyme function in u87 glioma cells decreases the effect of hypoxia on the expression of mE2, GOT2, and sDhb genes and introduces the sensitivity of iDh2 gene to hypoxia. Furthermore, the expression of all studied genes depends on iRE1-mediated endoplasmic reticulum stress signaling in gene specific manner, because ІRE1 knockdown significantly decreases their expression in normoxic conditions, except for iDh2 gene, which expression level is strongly up-regulated. Therefore, changes in the expression level of nuclear genes encoding mE2, mDh2, iDh2, sDhb, sDhD, and GOT2 proteins possibly reflect metabolic reprogramming of mitochondria by hypoxia and iRE1-mediated endoplasmic reticulum stress signaling and correlate with suppression of glioma cell proliferation under inhibition of the iRE1 enzyme function.
Does long-term warming a ff ect C and N allocation in a Mediterranean shrubland ecosystem ? Evidence from a 13 C and 15 N labeling fi eld study

In the Mediterranean basin the effects of climate warming on ecosystem functioning will strongly depend on the warming intensity directly but also on its effects on evapotranspiration and nutrient cycling. Climate manipulation experiments under field conditions are a source of unique empirical evidence regarding climate-related modifications of biotic processes. A field night-time warming experiment, simulating the predicted near-future increase in ambient temperatures (+0.3 up to 1 °C), was established in a Mediterranean shrub community located in Porto Conte (Italy) in 2001. After 11 years of continuous treatment, we labeled the dominant shrub Cistus monspeliensis with CO2 and studied the dynamics of the label allocation between aboveground and belowground pools and fluxes in warmed and ambient plots within 2 weeks of the chasing period. The interactions between C and N metabolism were assessed by parallel labeling of soil with KNO3. Most of the assimilated C was respired by Cistus shoots (28–51%) within two weeks. Cistus under warming respired more C label and tended to allocate less C to leaves, branches and roots. The higher C and N content in microbial biomass in warming plots, combined with the higher N content in plant tissues and soil, evidenced a greater N mobilization in soil and a better nutrient status of the plants as compared to the ambient treatment. Acceleration of N cycling is probably responsible for higher respiratory C losses, but combined with the reduction in the number of frost days, should also positively affect plant photosynthetic performance. We conclude that, although Cistus plants are already growing in conditions close to their thermal optimum, long-term warming will positively affect the performance of this species, mainly by reducing the nutrient constraints. This positive effect will highly depend on the frequency and amount of rain events and their interactions with soil N content.
An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin‐biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half‐sibs in nature most probably reduce the opportunity and advantage of kin‐biased behaviour, in contrast to laboratory studies conducted in artificial, high‐density conditions.