Miracle-dz/UniFAR-FTUs huggingface dataset:
ECOSYSTEM EFFECTS OF BIODIVERSITY: A CLASSIFICATION OF HYPOTHESES AND EXPLORATION OF EMPIRICAL RESULTS

The increasing evidence for effects of biodiversity on ecosystem properties and processes indicates that effects may vary strongly over the range of studied systems. In order to explore patterns and draw some preliminary conclusions on biodiversity effects in different ecological contexts, we have compiled empirical data from original studies and reviews on effects of biodiversity in natural, agricultural, and forestry systems. We classified hypotheses according to observed ecosystem variables and trophic contexts; trophic contexts were distinguished according to the trophic position of the observed ecosystem variable and the trophic position of the organismic group whose diversity is hypothesized to cause an effect. With four basic ecosystem variables and 14 trophic contexts we obtained 56 permutations or specific hypotheses. Of these, 20 have so far been experimentally tested. We review the results reported from experimental tests of each hypothesis and examine how the reported effects are associated wi.
THE ROLE OF UNDERSTORY VEGETATION IN THE NUTRIENT CYCLE OF FORESTED ECOSYSTEMS IN THE MOUNTAIN HEMLOCK BIOGEOCLIMATIC ZONE

The biogeochemical role of understory vegetation was investigated in three sites rep- resenting a typical topographic sequence of xeric, mesic, and hygric site types characteristic of the Mountain Hemlock Biogeoclimatic Zone. Overstory biomass on the three sites was estimated to be 60.9, 55.7, and 34.5 kg/M2 for the hygric, mesic, and xeric site types, respectively. Average values for understory biomass were: 44.1, 66.1, and 399 g/m2 for the hygric, mesic, and xeric site types. Understory aboveground production (UAP) values of 26.0, 14.2, and 63.1 g.m-2-yr- for the hygric, mesic, and xeric site types were equivalent to 11.3, 6.1, and 48.6% of the estimated overstory aboveground production. The understory was found to cycle a much greater proportion of its total nutrient (N, P, Ca, Mg, K, Zn, Cu) standing crop annually compared to overstory. Approximately 80%o of the macronutrients present in the understory standing crop are found in the understory annual production on the hygric site type. Estimates of 17.6, 8.3, and 20.6 g-m2.yr-t of total understory aboveground litterfall (ex- clusive of the moss layer) were obtained for the hygric, mesic, and xeric sites, respectively. Under- story was shown to return a significant proportion of the litterfall nutrients on a yearly basis, the bulk of which was returned as a single pulse during the first autumn snowfall. Understory vegetation above the moss layer was shown to have a significant effect on the quantity of nutrients present in throughfall precipitation. The effect was seasonal with P04-P, NO:-N, and NH4-N being removed in the spring and Ca, Mg, and K being added to overstory throughfall in the autumn. Modifications of water chemistry previously attributed to the forest floor may in some cases reflect unmeasured influences of understory vegetation.
Seasonal population dynamics and maturation of Neoechinorhynchus pungitius (Acanthocephala: Neoechinorhynchidae) infecting brook stickleback, Culaea inconstans, from Sioux Creek, Wisconsin, U.S.A

Seasonal population dynamics and maturation of the acanthocephalan Neoechinorhynchus pungitius from brook stickleback (Culaea inconstans) were investigated. Stickleback were collected monthly at Sioux Creek, Wisconsin from April 1981 to May 1982 (excluding December, January, and February). Forty-seven percent (292/620) were infected with N. pungitius, which exhibited seasonal periodicity in prevalence, mean intensity, and maturation. Prevalence and mean intensities were lowest in summer and increased through autumn owing to recruitment of juvenile and immature worms. Prevalence and mean intensity reached their peaks by April and May, and N. pungitius infrapopulations were composed primarily of mature worms. Egg production began in May and continued throughout early summer. Neoechinorhynchus pungitius males appeared shorter lived than females, as the June and July infrapopulations were comprised mostly of females. Prevalence and mean intensity of N. pungitius increased as brook stickleback length increased.
The timing of abscission affects dispersal distance in a wind‐dispersed tropical tree

Summary 1. Seed dispersal is a short-term phenomenon with long-term consequences for population survival and spread. Physiological mechanisms that target the release of seeds to particular sets of environmental conditions that maximize the probability of long-distance dispersal should evolve if long dispersal distance enhances fitness. 2. In this study, we use high-frequency censuses of seeds actually dispersed, high-frequency within-canopy meteorological observations and long-term measurements of above-canopy wind to investigate the environmental conditions that control the timing of seed abscission at different time-scales for a wind-dispersed tropical tree, Luehea seemannii. 3. We show that seed abscission follows a typical seasonal pattern, is rare at night and is most prevalent during periods of prolonged updrafts, higher temperature, with negative feedback when the heat canopy flux is relatively high. 4. We use phenomenological (super-WALD) and mechanistic (coupled Eulerian–Lagrangian closure) models to estimate the relative effects of the timing of seed release at different subannual temporal scales (seconds–hours) on the resulting long-term (season–decade) dispersal kernels. We find that periods of high wind speed increase the probability of long-distance dispersal between 100–1000 m, but decrease the probability at distances further than 1000 m relative to unbiased environmental conditions. We also find abscission during updrafts to increase the probability of long-distance dispersal at distances greater than 100 m. 5. Synthesis: We observe preferential abscission during updrafts in a tropical wind-dispersed tree. We use mechanistic models and long-term wind statistics to estimate the dispersal consequences of preferential seed release in specific environmental conditions. We find that the timing of the dispersal season may be influenced by wind conditions that maximize long-distance dispersal; however, there are likely other environmental factors essential for their determination. Our approach provides a method to bridge between small turbulence scales and large ecosystem scales to predict dispersal kernels. These findings shed light on the evolutionary processes that drive optimization of the timing of seed abscission and may be incorporated into plant population movement models to increase their accuracy and predictive power.
An alternative for antibiotic se in poultry: probiotics

Over the past 50 years, there has been increasing amounts of antibiotics used prophylactically and as growth promoters. Today, there is a consumer and governmental outcry to eliminate that practice from poultry and livestock production. Evidence has been accumulated to show that there is a link between risk of zoonotic disease and growth promoting antibiotic usage in livestock and poultry. Therefore, alternatives to the use of growth promoting antibiotics must be found to promote growth or production at or near the genetic potential of the modern day broiler, turkey, and egg producer. The use of probiotics has many potential benefits and include modified host metabolism, immuno-stimulation, anti-inflammatory reactions, exclusion and killing of pathogens in the intestinal tract, reduced bacterial contamination on processed broiler carcasses, enhanced nutrient absorption and performance, and ultimately decreased human health risk. The development of these factors generally can be ascribed to the ability of most probiotic products to balance and maintain the intestinal microflora in poultry species.
Isolation and characterization of a cDNA from Catharanthus roseus which is highly homologous with phosphate transporter

Abstract The PIT1 gene which is highly homologous with phosphate transporter was isolated from Catharanthus roseus and analyzed. The cBNA PIT1 contained an open reading frame of 542 amino acids and its sequence showed a 31, 30, and 34% identity with the phosphate transporter of Saccharomyces cerevisiae (PBO84), Neurospora crassa (PHO-5), and Glomus versiforme (GvPT), respectively. Furthermore, the cDNA PIT1 encoded a highly hydrophobic protein with 12 putative membrane-spanning regions and contained a conserved amino acid sequence reported in the human glucose transporter super-family* S. cerevisiae strain DpU (pho84 knockout strain) was unable to grow on low phosphate (55 μM) medium (LP medium). Expression of the PIT1 cDNA enabled DpU to grow on LP medium. Northern hybridization analysis revealed that the PIT1 gene was expressed in roots, stems, and young whole plant of C. roseus, but not in leaves.
Grammar Induction with Neural Language Models: An Unusual Replication

Grammar induction is the task of learning syntactic structure without the expert-labeled treebanks (Charniak and Carroll, 1992; Klein and Manning, 2002). Recent work on latent tree learning offers a new family of approaches to this problem by inducing syntactic structure using the supervision from a downstream NLP task (Yogatama et al., 2017; Maillard et al., 2017; Choi et al., 2018). In a recent paper published at ICLR, Shen et al. (2018) introduce such a model and report near state-of-the-art results on the target task of language modeling, and the first strong latent tree learning result on constituency parsing. During the analysis of this model, we discover issues that make the original results hard to trust, including tuning and even training on what is effectively the test set. Here, we analyze the model under different configurations to understand what it learns and to identify the conditions under which it succeeds. We find that this model represents the first empirical success for neural network latent tree learning, and that neural language modeling warrants further study as a setting for grammar induction.
Inbreeding depression in two field trials of young pinus sylvestris (L.)

Inbreeding depression after selfing was estimated in two field trials of Pinus sylvestris, age 11 and 14 years, respectively, by comparing stem volume and height after selfing and outcrossing. For the majority of trees, inbreeding caused a statistically significant reduction in stem volume. The average inbreeding depression for stem volume was 46% and 66% for the two trials, respectively, with a large variation among trees. For one of the trials, the inbreeding depression for height remained at a constant level between age 6 to 14 years, while the inbreeding depression increased between age 6 to 11 years for the other trial. Inbreeding depression was not found to be correlated with the GCA for stem volume of the individual trees. The relative phenotypic within‐family variance was found to be higher in progenies after selfing as compared to outcrossing.
PTH-027 Impact of changes in guidance on variceal prophylaxis on rate of variceal haemorrhage in gloucestershire

Introduction Oesophageal varices develop as a consequence of portal hypertension in patients with cirrhosis and account for around 10% of admissions with acute GI bleeding in the UK with a significant in-hospital mortality rate of 15%. 1 In 2015–2016 the BSG and NICE published new guidance recommending endoscopic variceal band ligation for primary prevention of bleeding.2 3 A subsequent change in local policy sees patients with grade 2 or 3 varices identified during elective upper GI (UGI) endoscopy offered endoscopic variceal band ligation routinely. We aimed was to assess the impact of this policy change on the rate of variceal haemorrhages. Methods Electronic endoscopy records at Gloucestershire Hospitals NHS Foundation Trust were interrogated to identify procedures performed for variceal surveillance (VS) or UGI bleeding and where the diagnosis was variceal bleeding over two periods: Jan-May 2015 and Oct 2017 to Mar 2018. Results Of the 92 VS procedures performed in the first period, 53 had varices, of which 9 (17%) underwent prophylactic banding. Of the 246 VS procedures performed in the second period, 166 had varices, of which 52 (31.3%) underwent prophylactic banding. The proportionate number of variceal bleeds in the first and second period was 8.8% (n=10) and 6% (n=17) respectively. Conclusions The increase in prophylactic banding since the policy change appears to have reduced the proportionate number of variceal bleeds by 2.6%. This is seen alongside a significantly increased number of patients attending for VS, for unclear reasons. This could simply reflect the increasing burden of chronic liver disease.4 However, given the short interval period it could reflect an improvement in identifying patients suitable for variceal screening. References Jairath V, et al. Acute variceal haemorrhage in the United Kingdom: patient characteristics, management and outcomes in a nationwide audit. Dig Liver Dis 2014;46:419–26. Tripathi D, et al. UK guidelines on the management of variceal haemorrhage in cirrhotic patients. Gut 2015;0:1–25. Cirrhosis in over 16s: assessment and management. NICE [NG50]. Pimpin L, et al. Burden of liver disease in Europe: Epidemiology and analysis of risk factors to identify prevention policies. J Hepatol 2018;69(3):718–35.
Parsing, Word Associations and Typical Predicate-Argument Relations

There are a number of coUocational constraints in natural languages that ought to play a more important role in natural language parsers. Thus, for example, it is hard for most parsers to take advantage of the fact that wine is typically drunk, produced, and sold, but (probably) not pruned. So too, it is hard for a parser to know which verbs go with which prepositions (e.g., set up) and which nouns fit together to form compound noun phrases (e.g., computer programmer). This paper will attempt to show that many of these types of concerns can be addressed with syntactic methods (symbol pushing), and need not require explicit semantic interpretation. We have found that it is possible to identify many of these interesting co-occurrence relations by computing simple summary statistics over millions of words of text. This paper will summarize a number of experiments carried out by various subsets of the authors over the last few years. The term collocation will be used quite broadly to include constraints on SVO (subject verb object) triples, phrasal verbs, compound noun phrases, and psycholinguistic notions of word association (e.g., doctor~nurse). 1. Mutual Information Church and Hanks (1989) discussed the use of the mutual information statistic in order to identify a variety of interesting linguistic phenomena, ranging from semantic relations of the doctor/nurse type (content word/content word) to lexico-syntacfic co-occurrence constraints between verbs and prepositions (content word/function word). Mutual information, l(x;y), compares the probability of observing word x and word y together (the joint probability) with the probabilities of observing x and y independently (chance). l(x;y) -= log 2 P(x,y) e(x) e(y) If there is a genuine association between x and y, then the joint probability P(x,y) will he much larger than chance P(x) P(y), and consequently l(x;y) >> 0, as illustrated in the table below. If there is no interesting relationship between x and y, then P(x,y) = P(x) P(y), and thus, I(x;y) = 0. If x and y are in complementary distribution, then P(x,y) will be much less than P(x) P(y), forcing l(x;y) << 0. Word probabilities, P(x) and P(y), are estimated by counting the number of observations of x and y in a corpus, f (x) and f(y), and normalizing by N, the size of the corpus. Joint probabilities, P(x,y), are estimated by counting the number of times that x is followed by y in a window of w words, fw(x,y), and normalizing by N (w 1). 2 1. The paper was previously presented at International Workshop on Parsing Technologies, CMU, 1989. 2. The window size parameter allows us to look at different scales. Smaller window sizes will identify fixed expressions (idioms), noun phrases, and other relations that hold over short ranges; larger window sizes will highlight semantic concepts and other relationships that hold over larger scales.
Distinct Weathering Ability and Populations of Culturable Mineral-Weathering Bacteria in the Rhizosphere and Bulk Soils of Morus Alba

In this study, we isolated and compared the weathering effectiveness and population of mineral-weathering bacteria from the rhizosphere and bulk soils of Morus alba grown in a mineral-rich soil. Eighty-four isolates could release Si, Al, K, and Fe from potash feldspar. Weathering effectiveness and pattern of the isolates differed between the rhizosphere and bulk soils. The proportion of the highly effective Si, Al, K, and Fe solubilizers was significantly higher in the rhizosphere soils than in the bulk soils. Notably, the proportion of the highly effective acid-producing isolates was also significantly higher in the rhizosphere soils. The 84 mineral-weathering isolates were affiliated with 15 bacterial genera. Distinct mineral-weathering genera were observed between the rhizosphere and bulk soils. The results suggested that the highly effective mineral-weathering bacteria were selected in the rhizosphere soils and the mineral-weathering bacteria from the rhizosphere and bulk soils might weather potash feldspar through different mechanisms.
The evolution of non-motif selectivity determinants in Monosiga brevicollis PDZ domains

The evolution of signaling pathways is complex and well-studied. In particular, the emergence of animal multicellularity had a major impact on protein-protein interactions and signaling systems in eukaryotic cells. However, choanoflagellates, our closest non-metazoan ancestor, contain a number of closely related signaling and trafficking proteins and domains. In addition, because choanoflagellates can adopt a rosette-/multicellular-like state, a lot can be gained by comparing proteins involved in choanoflagellate and human signaling pathways. Here, we look at how selectivity determinants evolved in the PDZ domain. There are over 250 PDZ domains in the human proteome, which are involved in critical protein-protein interactions that result in large multimolecular complexes, e.g., in the postsynaptic density of neuronal synapses. Binding of C-terminal sequences by PDZ domains is often transient and recognition typically involves 6 residues or less, with only 2 residues specifying the binding motif. We solved high resolution crystal structures of Monosiga brevicollis PDZ domains homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains to investigate if the non-motif preferences are conserved, despite hundreds of millions of years of evolution. We also calculated binding affinities for GIPC, SHANK1, and SNX27 PDZ domains from M. brevicollis. Overall, we found that peptide selectivity is conserved between these two disparate organisms, with one exception, mbDLG-3. In addition, we identify 178 PDZ domains in the M. brevicollis proteome, including 11 new sequences, which we verified using Rosetta and homology modeling. Overall, our results provide novel insight into signaling pathways in the choanoflagellate organism.
Risk assessment and management scenarios for ballast water mediated species introductions into the Baltic Sea.

This risk assessment study follows the environmental match of donor and recipient regions of ballast water and the voyage duration as risk quantifiers. The ports considered were Gothenburg (Sweden), Copenhagen (Denmark), Kiel (Germany), Klaipeda (Lithuania), Kemi, Tornio and Raahe as one port region (Finland), and Skoldvik/Kilpilahti (Finland). All selected Baltic ports have at least one donor port in the highest risk category, all extreme and high risk donor ports are located in Europe, but mostly outside the Baltic Sea. The most frequently reported high-risk donor ports are Rotterdam (6 times), Bremerhaven (5), Amsterdam (4) and Antwerp (3), and most high-risk donor ports are the major hub ports in Europe. The paper concludes with ballast water management scenarios for intra-Baltic shipping and for vessels engaged on voyages outside the Baltic.
The CS2 fimbrial antigen from escherichia coli, purification, characterization and partial covalent structure

The CS2 fimbrial antigen was isolated by salt and isoelectric precipitation and by column chromatography. The purified antigen was free of other fimbrial proteins present on the same bacterial strain. Analysis of the N-terminal amino acid sequence indicated extensive homology with the CFA1 fimbrial antigen, which was surprising since the two proteins do not show any immunological cross reactivity. It could therefore be concluded that the N-terminal parts of these fimbrial proteins are not located on the surfaces of the proteins and might be involved in conservation of the structural integrity of these proteins.
Relating changes in understorey diversity to environmental drivers in an ancient forest in northern Belgium

Background and aims - A renewed interest in the functional role and dynamics of forest understorey plant communities has lead to an increasing number of publications that present the results of understorey resurveys. However, studies looking at the possible causes of temporal changes in the understorey often lack data on soil and tree layer conditions for the old survey. We investigated how changes in the tree layer, soil, and understorey were related in two contrasting forest types. Methods - Full re-inventory of the tree layer (1997, 2010) and resurvey of the soil and understorey in 40 plots on a permanent grid (1993, 2011) in an ancient temperate deciduous forest. The 1.83 ha study area consisted of a part dominated by oak (Quercus robur) and beech (Fagus sylvatica) and a part dominated by ash (Fraxinus excelsior). Key results - Overall, the basal area and shade-casting ability of the tree layer had increased. In the oak-beech forest, the soil pH had decreased; below ash, the topsoil pH had increased. The understorey species richness had increased, and the change in species richness was correlated with the change in soil pH and basal area, the latter in the oak-beech forest only. The observed patterns in understorey dissimilarity were different for the dataset including or excluding the regeneration of woody species. Conclusions - The changes in soil and understorey differed between the two forest types, and there were some indications of recovery from soil acidification in the ash forest.
Occurrence of Oligosialic Acids on Integrin α5Subunit and Their Involvement in Cell Adhesion to Fibronectin*

Integrin α5β1, a major fibronectin receptor, functions in a wide variety of biological phenomena. We have found that α2–8-linked oligosialic acids with 5 ≤ degree of polymerization (DP) ≤ 7 occur on integrin α5 subunit of the human melanoma cell line G361. The integrin α5 subunit immunoprecipitated with anti-integrin α5 antibody reacted with the monoclonal antibody 12E3, which recognizes oligo/polysialic acid with DP ≥ 5 but not with the polyclonal antibody H.46 recognizing oligo/polysialic acid with DP ≥ 8. The occurrence of oligosialic acids was further demonstrated by fluorometric C7/C9analysis on the immunopurified integrin α5subunit. Oligosialic acids were also found in the α5 subunit of several other human cells such as foreskin fibroblast and chronic erythroleukemia K562 cells. These results suggest the ubiquitous modification with unique oligosialic acids occurs on the α5 subunit of integrin α5β1. The adhesion of human melanoma G361 cells to fibronectin was mainly mediated by integrin α5β1. Treatment of cells with sialidase from Arthrobacter ureafaciens cleaving α2–3-, α2–6-, and α2–8-linked sialic acids inhibited adhesion to fibronectin. On the other hand, N-acetylneuraminidase II, which cleaves α2–3 and α2–6 but not α2–8 linkages, showed no inhibitory activity. After the loss of oligosialic acids, integrin α5β1 failed to bind to fibronectin-conjugated Sepharose, indicating that the oligosialic acid on the α5 subunit of integrin α5β1 plays important roles in cell adhesion to fibronectin.