Miracle-dz/UniFAR-FTUs huggingface dataset:
A temperature dependent trophic cascade modifies temperature dependence of ecosystem function

Ecological communities and their ecosystem functions are sensitive to temperature, and aquatic habitats worldwide continue to experience unprecedented warming. Understanding ecological effects of warming requires linking empirical evidence to theories that allow projection to unobserved conditions. Metabolic scaling theory and its tests suggest that warming accelerates ecosystem functions (e.g., oxygen flux), yet this prediction apparently contradicts community-level studies suggesting warming is a stressor that can reduce ecosystem function. We sought to reconcile these predictions with an experimental test of the hypothesis that cascading trophic interactions modify the temperature-dependence of community structure and ecosystem fluxes. In a series of independent freshwater ecosystems exposed to a thermal gradient, we found that warmer temperatures strengthened the trophic cascade increased and indirectly changed community structure by altering grazer species composition and phytoplankton biomass. Temperature-driven community shifts only modestly affected the temperature dependence of net ecosystem oxygen fluxes. Over the 10 °C thermal gradient, NPP and ER increased ∼2.7-fold among ecosystems, while standing phytoplankton biomass declined by 85-95%. The exponential increase in oxygen flux over the thermal gradient, as well as monotonic declines in phytoplankton standing stock, suggested no threshold effects of warming across systems. We also observed temperature variation over time, within ecosystems. For phytoplankton biomass, temporal variation had the opposite effect to spatial variation, suggesting that within-community temporal change in community structure was not predicted by space-for-time substitution. We conclude that food chain length can modify effects of temperature on ecosystem fluxes, but that temperature can still have continuous and positive effects on ecosystem fluxes, consistent with patterns based on large-scale, macroecological comparisons. Changes in community structure, including temperature dependent trophic cascades, may be compatible with prevailing and predictable effects of temperature on ecosystem functions related to fundamental effects of temperature on metabolism. Statement of authorship JG & MIO designed the study, MIO & US provided materials, JG & SJC performed research and collected data, JG performed zooplankton analysis, SJC performed phytoplankton analysis, JG & MIO performed modeling work, analyzed data output, and wrote the first draft, and all authors contributed substantially to reviews
Fourier methods and combinatorics in learning theory

In this thesis we study computational learning theory. Our main problem is the following: given an unknown function f : X → {0, 1} and some sort of oracle access to f, can we construct a function "close" to f? We are concerned primarily with two perspectives: making use of orthogonal decompositions and learning theory conjectures that naturally lead to combinatorics results. With relation to the former topic, we attempt to generalize beyond the most commonly studied PAC-learning model: learning from independent labeled random examples over the uniform distribution. We make two contributions in this way: (1) We study the problem of learning from random walks. Specifically, we give a quasi-polynomial for learning the class of "threshold-of-parities" under the uniform distribution from random walks. Further, we generalize known results about learning DNF expressions and agnostically learning juntas into more general random walk models. (2) We study learning from independent labeled random examples over arbitrary product distributions. We show that essentially every result about learning boolean functions over the uniform distribution on the boolean cube via Fourier methods can be transferred to any product distribution. The crux of the method is a very simple but powerful proof relating the noise sensitivity of a function under the uniform distribution to its noise sensitivity under any product distribution. Also, we make two contributions to combinatorics, both related to the Kruskal-Katona Theorem: (1) Using the Kruskal-Katona Theorem from extremal combinatorics, we show that any monotone boolean function "close" to the majority function has large total influence, and thus requires an exponential-size circuit to compute it for any constant depth. The motivation is a conjecture of Benjamini, Kalai, and Schramm, which we ultimately disprove with an explicit counterexample. (2) We extend the celebrated Kahn-Kalai-Linial Theorem to more general settings; we eliminate the seeming dependence on product distributions. Using this theorem in an appropriate scenario, we prove a stability version of the Kruskal-Katona Theorem. Finally, equipped with this theorem, we prove a conjecture of Blum, Burch, and Langford on learning monotone functions.
Chemical composition and physiological quality of wheat seeds with the application of trinexapac-ethyl, a plant growth regulator

This study evaluated the effect of the plant growth regulator trinexapac-ethyl on chemical composition and physiological quality of wheat seeds produced under fertilization for high yield potential. The experiment was performed under completely randomized design with five treatments (0; 200; 400; 600; 800 mL ha-1 of the commercial product Moddus ) and four repetitions. The plant growth regulator was applied at elongation via foliar spraying. Seeds were harvested at the end of crop cycle. Variables evaluated were 1000 seeds weight, germination and first count of germination, speed of germination index, seedling dry matter, electrical conductivity, accelerated ageing and the contents of total soluble sugars, starch, amino acids and proteins. The first count of germination increased until the higher dose. Electrical conductivity after three hours of imbibition reduced at the doses of 600 mL ha-1 and 800 mL ha-1, indicating greater seed physiological quality. Starch showed a trend of increase until the dose of 448 mL ha-1; amino acids until the dose of 243 mL ha-1 and protein until the dose of 417 mL ha-1. The content of total soluble sugars decreased with the increasing dose of the plant growth regulator. Therefore, wheat seeds produced from plants in which trinexapac-ethyl is applied present higher vigor and greater contents of starch, protein and amino acids, but lower content of total soluble sugars. Our results demonstrate that trinexapac-ethyl can be used for wheat management in seed production fields in the recommended dose (400 mL ha-1) with benefits in seed quality and composition.
RANbodies: reporter-nanobody fusions as versatile, small, sensitive immunohistochemical reagents

Sensitive and specific antibodies are essential for detecting molecules in cells and tissues. However, currently used polyclonal and monoclonal antibodies are often less sensitive than desired, difficult to produce, and available in limited quantities. A promising recent approach to circumvent these limitations is to employ chemically-defined antigen-combining sites called nanobodies, derived from single chain camelid antibodies. Here, we used nanobodies to prepare sensitive unimolecular detection reagents by genetically fusing cDNAs encoding nanobodies to enzymatic or antigenic reporters. We call these fusions between a reporter and a nanobody RANbodies. They can be used to localize epitopes and to amplify signals from fluorescent proteins. They be generated and purified simply and in unlimited amounts, and can be preserved safely and inexpensively in the form of DNA or digital sequence.
PERFORMANCE OF POLYMERIC MEMBRANES FOR PHOSPHOLIPID REMOVAL FROM RESIDUAL PALM FIBRE OIL/HEXANE MISCELLA

Palm pressed fibre, a by-product from the processing of crude palm oil contains about 5%-8% residual oil (on dry basis). The oil contains a high amount of minor components such as phospholipids, carotenes and vitamin E. This study investigates the ability of polymeric membranes to remove phospholipid from residual palm fibre oil/hexane miscella. The performance of 10 kDa polyethersulphone (PES), 20 kDa PES and 30 kDa polyvinylidene fluoride (PVDF) membranes were evaluated. A detailed evaluation on 30 kDa PVDF showed that permeate flux increases with the increase of operating pressure, temperature and agitation speed. Increasing operating pressure from 2 to 6 bar with a temperature of 40 degrees C and speed of 300 rpm resulted in the retention of phospholipids from 81% to 95%. The resistance of the membrane due to concentration polarisation ranged from 30.6 to 97.0 x 10(12) m(-2) which gave 79%-84% of total resistance values indicating significant influence on the permeate flux. A complete 23 experimental design indicated statistically that the increased pressure, temperature and agitation speed resulted in a higher permeate flux. An increase in pressure and agitation speed also increased the retention of phospholipid. However, the regression model obtained from this study showed that the temperature had a negative effect on the retention of phospholipid.
Canopy cover and structural complexity affect the phylogenetic composition of a pond-dwelling Neotropical anuran metacommunity

Phylogenetic information has been increasingly included into (meta)community assembly studies. However, recent studies have challenged the framework commonly used to infer processes from phylogenetic structure. Amphibians are good model organisms to study processes promoting structure in metacommunities, since they are subjected to different environmental and spatial processes throughout their biphasic life cycle. Pond canopy cover is one of these environmental factors that strongly influence the distribution of species and traits of several freshwater taxa, including larval amphibians (e.g., behavior, color, fin height, and length of intestine). Here, I tested the influence of pond canopy cover, floating vegetation, and pond morphology on the phylogenetic structure of an anuran metacommunity in the Atlantic Forest of Southeastern Brazil. I sampled tadpoles in 13 ponds and marshes from June 2008 and July 2009 in the Serra da Bocaina National Park, São Paulo. After building a metacommunity phylogeny, I used an eigenvector-based technique to describe the metacommunity phylogenetic composition (Principal Coordinates of Phylogenetic Structure, PCPS). I then run a db-RDA to evalute whether a subset of these eigenvectors can be explained by environmental variables. I found that pond canopy cover and floating vegetation were the main variables influencing lineage sorting in this metacommunity. Canopy cover separated hylid lineages from other families that were associated with open areas. Floating vegetation separated two hylid tribes (Cophomantini and Dendropsophini). Our results mainly suggest that the effect of canopy cover and floating vegetation on the structure of anuran metacommunity may affect not only species, but also entire lineages.
Biometric characterization of Campomanesia xanthocarpa (Mart.) O. Berg. in an araucaria forest

The present research aimed to analyze biometric characteristics of Campomanesia xanthocarpa and its fruits and its fruit yield. This study was developed in araucaria forest at Irati National Forest, Parana state. To perform this analysis, 31 individuals were selected and the total height and commercial height, diameter breast height (DBH), crown diameter, crown length, crown proportion, crown formal, salience index, range index and slenderness rate were measured. From the fruits, variables as length, width, weight and number of seeds per fruit were measured. The fruit yield was estimated by means of the fruit number per branch and the average fruit weight per tree. The species presented total height, DBH and crown diameter of 14.2 m, 32.09 cm and 9.5 m, respectively. The crown diameter is 30 times greater than DBH, and 49.71% from total height is occupied by its crown. The fruits presented 22.01 mm, 19.74 mm, 6.64 g and eight units for width, length, weight and seeds/fruit, respectively. The yield was 1.273 fruits, with 8.64 kg.tree-1. The species presents slow growth, with slender crown and resistance to weathering. Its fruits had great potential for selection for commercialization.
Brays and bits: information theory applied to acoustic communication sequences of bottlenose dolphins

Abstract Acoustic call sequences are important components of vocal repertoires for many animal species. Bottlenose dolphins (Tursiops truncatus) produce a wide variety of vocalizations, in different behavioural contexts, including some conspicuous vocal sequences – the ‘bray series’. The occurrence of brays is still insufficiently documented, contextually and geographically, and the specific functions of these multi-unit emissions are yet to be understood. Here, acoustic emissions produced by bottlenose dolphins in the Sado estuary, Portugal, were used to provide a structural characterization of the discrete elements that compose the bray series. Information theory techniques were applied to analyse bray sequences and explore the complexity of these calls. Log-frequency analysis, based on bout criterion interval, confirmed the bout structure of the bray series. A first-order Markov model revealed a distinct pattern of emission for the bray series’ elements, with uneven transitions between elements. The order in these sequential emissions was not random and consecutive decreases in higher order entropy values support the notion of a well-defined structure in the bray series. The key features of animal signal sequences here portrayed suggest the presence of relevant information content and highlight the complexity of the bottlenose dolphin’s acoustic repertoire.
Evaluating the establishment success of Microctonus aethiopoides (Hymenoptera: Braconidae), a parasitoid of the alfalfa weevil (Coleoptera: Curculionidae), across the northern Great Plains of North America

Abstract The alfalfa weevil (Hypera postica (Gyllenhal); Coleoptera: Curculionidae), is a destructive pest of alfalfa (Medicago sativa Linnaeus; Fabaceae) worldwide. The biological control parasitoid, Microctonus aethiopoides Loan (Hymenoptera: Braconidae), was successfully introduced, and considered highly effective, in the eastern and mid-western United States of America. Redistribution efforts carried out throughout the 1980s reported initial establishment in the northern Great Plains, however follow-up studies to assess long-term persistence and efficacy are lacking. We resurveyed the counties in which M. aethiopoides had been initially recovered following redistribution in Montana (Flathead and Petroleum counties), Wyoming (Platte County), and South Dakota (Brookings County), to gauge whether this species has become permanently established and, if so, assess levels of parasitism in the field. We collected adult weevils from five fields in each county, and reared them in the laboratory to assess parasitism. Despite rearing more than 1000 weevils, no parasitoids were recovered from any of the locations sampled in our study, suggesting a widespread failure of M. aethiopoides to persist in the region. Thus, M. aethiopoides does not currently appear to be an important biological control agent of alfalfa weevil in the northern Great Plains. More intensive surveys will be required to assess the extent of the distributional limits of this species throughout the region.
A new rhynchosaur maxillary tooth plate morphotype expands the disparity of the group in the Ischigualasto Formation (Late Triassic) of Northwestern Argentina

Abstract Rhynchosaurs are a clade of quadruped, herbivorous stem-archosaur diapsids restricted to the Triassic Period. The group became globally distributed and the numerically dominant tetrapods of several terrestrial ecosystems before their extinction. Derived rhynchosaurs are characterized by a specialized masticatory apparatus, composed of a blade-and-groove occlusion with multiple longitudinal maxillary tooth rows. The morphology of the maxillary tooth plate has shown to be taxonomically and phylogenetically informative. So far, two rhynchosaur maxillary tooth plate morphotypes are known in Argentina, one belonging to an unnamed stenaulorhynchine from the Chañares Formation and the other to the hyperodapedontine Hyperodapedon sanjuanensis, the single rhynchosaur species currently name for the Ischigualasto Formation. Here we describe a new rhynchosaur maxillary tooth plate morphotype based on an indeterminate hyperodapedontine specimen from the Ischigualasto Formation. This maxillary tooth plate (PVL 2728) possesses a single longitudinal groove that divides symmetric lateral and medial tooth-bearing areas with relatively large tooth crowns, which is an uncommon combination of features among hyperodapedontines. These qualitative observations in addition to quantitative analyses show that the morphology of PVL 2728 differs from that of, at least, other sampled South American rhynchosaurs. Therefore, this specimen expands the morphological disparity of rhynchosaurs in northwest Argentina and southwestern Pangaea.
Comparative mapping in common and silver-leaf sunflower

Several wild sunflower (Helianthus) species important sources of genetic diversity for enhancing the performance of cultivars and single-cross hybrids of common sunflower (H. annuus = ANN; 2n = 2x = 34). Silver-leaf sunflower (H. argophyllus = ARG; 2n = 2x = 34), which diverged 375,000 to 500,000 years before present from ANN, is a source of disease resistance alleles. We developed an ARG mapping population by crossing an outbred individual (ARG1805-1) to a nuclear male-sterile inbred line of ANN (NMS801), screened 1,417 previously mapped DNA markers, and mapped 299 polymorphic loci in the testcross hybrid mapping population (n = 94). Eighteen ARG linkage groups were aligned with ANN and chromosomal rearrangements were identified using 194 orthologous loci. We identified 11 colinear linkage groups, 2 syntenic chromosomes carrying segmental duplications and inversions, and 5 chromosomes carrying non-reciprocal translocations. The reduction in fertility and meiotic abnormalities observed in ANN x ARG hybrids are caused by 6 chromosomal rearrangements which could impede gene-flow. INDEX WORDS: Comparative mapping, Introgression, Inversion, Sunflower, Synteny, Translocation COMPARATIVE MAPPING IN COMMON AND SILVER-LEAF SUNFLOWER
The ballasting effect of Saharan dust deposition on aggregate dynamics and carbon export: Aggregation, settling, and scavenging potential of marine snow

Lithogenic material such as Saharan dust can be incorporated into organic aggregates and act as ballast, potentially enhancing the marine carbon export via increased sinking velocities of aggregates. We studied the ballasting effects of Saharan dust on the aggregate dynamics in the upwelling region off Cape Blanc (Mauritania). Aggregate formation from a natural plankton community exposed to Saharan dust deposition resulted in higher abundance of aggregates with higher sinking velocities compared to aggregate formation with low dust. This higher aggregate abundance and sinking velocities potentially increased the carbon export 10‐fold when the aggregates were ballasted by Saharan dust. After aggregate formation in the surface waters, subsequent sinking through suspended Saharan dust minerals had no influence on aggregate sizes, abundance, and sinking velocities. We found that aggregates formed in the surface ocean off Mauritania were already heavily ballasted with lithogenic material and could therefore not scavenge any additional minerals during their descent. This suggests that carbon export to the deep ocean in regions with high dust deposition is strongly controlled by dust input to the surface ocean while suspended dust particles in deeper water layers do not significantly interact with sinking aggregates.
Influence of water supply and fluctuations on yield and quality of lemon balm (Melissa offici-nalis L.)

The response of lemon balm (Melissa officinalis) on drought stress was investigated in a pot experiment in 2015-16. In treatment S1, plants grew in 40% saturation of soil water capacity (SWC) for six weeks. In treatment S2, the same level of water supply was used for three weeks, while the control plants received irrigation up to 70% SWC throughout the experimental period. In the second year, after the stress period, a 3 week re-hydration phase was also carried out. Growth, morphology, biomass, active components and antioxidant capacity of the plants were measured. Six weeks growth at reduced soil water content (40% soil water capacity) resulted in a significant decrease of all morphological features of lemon balm as well as the fresh mass of shoots, as compared to the control (70% SWC). The effect of the shorter drought treatment (3 weeks) was less characteristic. After the three week recovery period no significant difference concerning number of branches, leaf length and fresh shoot mass was detectable among the plants. Thus, the retarding effect of even the 6 week drought stress (S1) was reversible in lemon balm. The changes in active components (volatile compounds, phenolics, rosmarinic acid) and antioxidant capacity did not show meaningful changes due to the treatments. After a three-week re-hydration period a significant increase was found in each parameter. It was established that a six week period of water shortage (water content of 40% SWC) could threaten the yield of lemon balm, although re-hydration by regular irrigation may induce significant recovery. The impact of water shortage on the quality of the drug was less critical.
CD95 receptor activation by ligand-induced trimerization is independent of its partial pre-ligand assembly

CD95 (Fas, APO-1, TNFRSF6) is a widely expressed single-pass transmembrane protein that is implicated in cell death, inflammatory response, proliferation and cell migration. CD95 ligand (CD95L, FasL, TNFSF6), is a potent apoptotic inducer in the membrane form but not when cleaved into soluble CD95L (sCD95L). Here, we aimed at understanding the relation between ligand-receptor multimerization and receptor activation by correlating the kinetics of ligand binding, receptor oligomerization, FADD (FAS-Associated via Death Domain) recruitment and caspase-8 activation inside living cells. Using single molecule localization microscopy and Förster resonance energy transfer imaging we show that the majority of CD95 receptors on the plasma membrane are monomeric at rest. This was confirmed functionally as the wild-type receptor is not blocked by a receptor mutant that cannot bind ligand. Moreover, using time-resolved fluorescence imaging approaches we demonstrated that receptor multimerization follows instantaneously ligand binding, whereas FADD recruitment is delayed. This process can explain the typical delay time seen with caspase-8 activity reporters. Finally, the low activity of sCD95L, which was caused by inefficient FADD recruitment, was not explained by the low avidity for the receptor but by a receptor clustering mechanism that was different from the one induced by the strong apoptosis inducer IZ-sCD95L. Our results reveal that receptor activation is modulated by the capacity of its ligand to trimerize it. Highlights At a density of less than 10 receptors per µm2 CD95 exists as monomer (58%) and dimer (42%) Pre-formed dimers do not contribute to ligand-induced CD95 apoptotic signaling The PLAD of CD95 attenuates overexpression-induced, ligand-independent cell death soluble CD95L can rapidly multimerize CD95 after binding but it is still a poor inducer of apoptosis through inefficient FADD recruitment FADD recruitment kinetics but not ligand binding kinetics correlates with caspase-8 onset of activity