Miracle-dz/UniFAR-FTUs huggingface dataset:
X-ray Crystal Structure of the Liver X Receptor β Ligand Binding Domain

The x-ray crystal structures of the human liver X receptor β ligand binding domain complexed to sterol and nonsterol agonists revealed a perpendicular histidinetryptophan switch that holds the receptor in its active conformation. Hydrogen bonding interactions with the ligand act to position the His-435 imidazole ring against the Trp-457 indole ring, allowing an electrostatic interaction that holds the AF2 helix in the active position. The neutral oxysterol 24(S),25-epoxycholesterol accepts a hydrogen bond from His-435 that positions the imidazole ring of the histidine above the pyrrole ring of the tryptophan. In contrast, the acidic T0901317 hydroxyl group makes a shorter hydrogen bond with His-435 that pulls the imidazole over the electron-rich benzene ring of the tryptophan, possibly strengthening the electrostatic interaction. Point mutagenesis of Trp-457 supports the observation that the ligand-histidine-tryptophan coupling is different between the two ligands. The lipophilic liver X receptor ligand-binding pocket is larger than the corresponding steroid hormone receptors, which allows T0901317 to adopt two distinct conformations. These results provide a molecular basis for liver X receptor activation by a wide range of endogenous neutral and acidic ligands.
Timing of autumn migration and biometric characteristics of migrating populations of European Robin (Erithacus rubecula L., 1958) in North-Eastern Poland

We studied the autumn migration of the European robin (Erithacus rubecula) through north-eastern Poland. During the study period 2002–2004 we analysed a total of 2375 individuals: 1991 first-year birds and 349 adults. First-year birds had shorter wings than adults. Body condition was influenced by age, year of migration fat content and arrival time. Our results show that first-year birds arrived earlier, had low-fat levels and were in a comparatively poorer body condition to that of the adults and were less effective foragers. Stopover length decreased during the migration season for both age groups as a result of rush to their wintering areas because of winter approach. We found that adult females arrived later than adult males.
The Isolation of Pleiotropic Mutants of Pseudomonas aminovorans Deficient in the Ability to Grow on Methylamine and an Examination of their Enzymic Constitution

Summary: Mutants deficient in several enzymes of methylamine oxidation and assimilation have been obtained by treating Pseudomonas aminovorans with ultraviolet light. One of these mutants was studied in detail and was shown to lack the enzymes of trimethylamine and dimethylamine oxidation. In addition, activities of the following enzymes, all postulated as being involved in C1 metabolism, were lost: hydroxypyruvate reductase, serine-glyoxylate aminotransferase, isocitrate lyase, phosphoeno/pyruvate carboxylase, N-methylglutamate dehydrogenase, γ-glutamylmethylamide synthetase, formate dehydrogenase and dye-linked formaldehyde dehydrogenase. In contrast, three enzymes - NAD+,glutathione-linked formaldehyde dehydrogenase, N-methylalanine dehydrogenase and N-methylglutamate synthase - were retained. This phenotype suggests either a lesion in a regulatory gene, a deletion in an early structural gene of an operon or the loss of a plasmid. Results obtained indicated that P. aminovorans possesses an isocitrate lyase-serine pathway.
Colonization resistance of the digestive tract in conventional and antibiotic-treated mice.

SUMMARY The effect of oral administration of antibiotics on the intestinal flora of conventional mice and their resistance to colonization by orally introduced Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa was studied. Colonization resistance (CR) was expressed as the log of the oral bacterial dose followed by a persistent take in 50 % of the contaminated animals. The intestinal flora was virtually eliminated by the antibiotics and this elimination was accompanied by a precipitous fall of CR. CR gradually returned to normal values during the period of repopulation of the intestinal tract by the organisms surviving the treatment. Antibiotic treatment resulted in the disappearance of Enterobacteriaceae, enterococci, staphylococci and yeasts and, under appropriate housing conditions, the animals remained free of these organisms indefinitely. Germ-free mice contaminated with the intestinal flora of an antibiotic-treated animal and their offspring housed in a germ-free isolator showed high values of CR. Their intestinal flora consisted of anaerobic bacteria only. Apparently, these anaerobes are responsible for CR in these and in conventional mice.
Is There a Farm Size–Productivity Relationship in African Agriculture? Evidence from Rwanda

Whether the negative relationship between farm size and crop productivity that is confirmed in a large global literature holds in Africa is of considerable policy relevance. Plot-level data from Rwanda point toward constant returns to scale and a strong negative relationship between farm size and crop output per hectare that is robust across specifications and emerges also if profits with family labor valued at shadow wages are used but disappears if family labor is valued at market rates. In Rwanda, labor market imperfections, rather than other unobserved factors, seem to be a key reason for the inverse farm-size productivity relationship. (JEL O13, Q15)
Number of nitrate- and nitrite-reducing Selenomonas ruminantium in the rumen, and possible factors affecting its growth

The cell number of Selenomonas ruminantium (S. ruminantium) that reduces nitrate and nitrite in the rumen was usually 8–10% of the total number of S. ruminantium (an order of 106/mL). The percentage was not affected by the roughage/concentrate ratio or nitrate content of the diet in 2 weeks. However, feeding a high-nitrate diet for 12 weeks increased the percentage. The percentage of lactate-using S. ruminantium, such as the ssp. lactilytica, was less than 1% of the total number of S. ruminantium. No S. ruminantium was found that used formate as an electron donor for nitrate and nitrite reduction. Lactate and H2 appeared to be important for nitrate and nitrite reduction by S. ruminantium. Nitrate reduction by S. ruminantium was enhanced by the coexistence of amylolytic bacteria in a medium containing starch, and as a result, nitrite accumulation increased. Coexistence of cellulolytic bacteria facilitated the growth of S. ruminantium in a medium containing cellulose, and consequently increased nitrite reduction. In order to suppress nitrite accumulation in the rumen, it may be important to enhance fiber digestion.
Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota)

Phylogenetic relationships of the genera Cladia, Heterodea and Ramalinora were reconstructed using a combined dataset of ribosomal nuclear ITS and LSU and mitochondrial SSU, and protein-coding Mcm7 DNA sequences. Maximum likelihood and Bayesian analyses strongly supported a monophyletic group in which the species of the foliose genus Heterodea and the crustose genus Ramalinora were nested within the fruticose genus Cladia. Alternative hypothesis testing rejected an independent status of Ramalinora. We tested the hypothesis that an adaptive radiation led to the morphological disparity found in the Cladia clade. Gamma-statistics indicated a significantly disproportional clustering of origins of extant lineages at the base of the Cladia clade and lineage-through-time plots were also consistent with the hypothesis of an adaptive radiation at the base of the Cladia clade. Ancestral-range reconstructions supported an origin of Cladia and the three major lineages within Cladia in Australia. On the basis of these results, we propose an evolutionary hypothesis for the genus. The results suggest that processes of adaptive radiation of the ancestor of Cladia in Australia led to the morphological disparity in the extant taxa, and that the broad distribution of some extant species is due to subsequent long-distance dispersal.
History of an invader, Scaptomyza flava (Fallen, 1823) (Diptera: Drosophilidae)

Abstract In New Zealand, the European leaf mining fly, Scaptomyza (Scaptomyza) flava (Fallen, 1823) (Diptera: Drosophilidae), is a pest of gypsophila and brassicas. Scaptomyza flava was first found in Levin (March 1964) and in 1965 was found in Hastings (March), Lincoln (July), and Nelson (December). By January 1968 it was found in Auckland and Gisborne. Voucher specimens in New Zealand show the species was correctly identified by the Commonwealth Institute of Entomology in 1965. However, this information was lost, and parasitoids of Agromyzidae were released (1969–71) to control what was initially assumed to be an agromyzid leaf miner of brassicas. The identity of the fly as S. flava was confirmed by Bock in 1988. In this study, six New Zealand insect collections were examined and field collections were made to confirm host associations, parasitism, and colonisation. Two parasitoids have been reared from S. flava in New Zealand, and overseas at least two other parasitoid species are known from this species. This investigation emphasises the need for good communication about new pests and proper care for voucher specimens.
Abstract

Treatment of upper respiratory infections in cats, Dossin, O. , Gruet, P. & Thomas, E. (1998) Journal of Small Animal Practice 39, 286 Deltamethrin- and diazinon-impregnated collars for combating dog fleas, Franc, M. & Cadiergues, M-C. (1998) American Journal of Veterinary Research 59, 59 Effects of PRRSV on neonatal pigs, Mengeling, W. L. , Lager, K. M. & Vorwald, A. C. (1998) American Journal of Veterinary Research 59, 52
Does Unemployment Increase Crime?

OLS may understate the effect of unemployment on crime because of the endogeneity problem (Raphael and Winter-Ember 2001). In this paper, we use changes in the real exchange rate, state manufacturing sector percentages, and state union membership rates as novel instrumental variables to carry out 2SLS estimations. We find a one-percentage-point increase in unemployment would increase property crime by 1.8 percent under the OLS method, but that the elasticity goes up to 4 percent under 2SLS. The larger 2SLS effect has significant policy implications because it explains 30 percent of the property crime change during the 1990s.
The Neurotoxic Effect of Sickle Cell Hemoglobin

A growing body of experimental evidence suggests that the oxidative neurotoxicity of hemoglobin A may contribute to neuronal loss after CNS hemorrhage. Several hemoglobin variants, including hemoglobin S, are more potent oxidants in cell-free systems. However, despite the increased incidence of hemorrhagic stroke associated with sickle cell disease, little is known of the effect of hemoglobin S on cells of neural origin. In the present study, its toxicity was quantified and directly compared with that of hemoglobin A in murine cortical cell cultures. Reactive oxygen species production, as assessed by cellular fluorescence after treatment with dihydrorhodamine 123, was significantly increased by exposure to 10 μM hemoglobin S for 2–4 h. Neuronal death, as measured by propidium iodide staining and lactate dehydrogenase release, commenced at 4 h; for a 20-h exposure, the EC50 was approximately 0.71 μm. Glial cells were not injured. Cell death was completely blocked by iron chelation with deferoxamine or phenanthroline. Direct comparison of sister cultures exposed to either hemoglobin A or hemoglobin S revealed a similar amount of cell injury in both groups. A significant difference was consistently observed only after treatment with 1 μM hemoglobin for 20 h, which resulted in death of approximately one third more neurons with hemoglobin S than with hemoglobin A. The results of this study suggest that sickle cell hemoglobin is neurotoxic at physiologically relevant concentrations. This toxicity is iron-dependent, oxidative, and quantitatively similar to that produced by hemoglobin A.
Phylogeny and Biogeography of North American and Asian Pedicularis (Orobanchaceae)

Abstract Pedicularis is a genus of over 600 species distributed throughout tundra and alpine habitats of the Northern Hemisphere. Phylogenetic relationships of North American species to Asian species were reconstructed by sampling sequences from nuclear ribosomal internal transcribed spacer (ITS) regions and the plastid matK region of 28 North American species, collected in the field or sampled from herbarium specimens, and 134 accessions of 102 Asian and three European species, obtained from GenBank. Maximum parsimony (PAUP) and Bayesian (MrBayes) analyses of ITS and combined ITS and matK data reveal two robustly supported monophyletic North American clades derived from Asian ancestors. Biogeographic analysis (S-DIVA) suggests Asia plus Japan, the Cascade Range, or Rocky Mountains as highly probable ancestral areas without involving Beringia for one clade. In the other clade, Asia plus the Rocky Mountains is specified as the most probable ancestral area, but less probable alternatives also include Asia plus Europe, Japan, or Beringia. Once established in North America, dispersal/divergence throughout North America occurred out of Rocky Mountain and/or Cascade Range ancestral centers of distribution. Beringian and European species are derived from North American centers rather than being part of ancestral areas for North American species.
Response of antarctic terrestrial microarthropods to long-term climate manipulations

The terrestrial biota of the Antarctic Peninsula region are experiencing marked changes in climate, especially rising temperatures, precipitation, and UV-B radiation—a combination unique worldwide. These changes, combined with the inherent simplicity of terrestrial communities, have led to their use as “model systems” to predict the future climate change responses of biota at lower latitudes. However, studies integrating responses at different levels of the community trophic structure are lacking. We report here the consequences on the soil microarthropod community of a four-year, multivariate, climate-manipulation experiment carried out over vegetation near Palmer Station, Anvers Island, western Antarctic Peninsula. The experiment used a multifactorial randomized-block design, deploying filters to raise temperatures and reduce ultraviolet (UV)-B (280–320 nm) or both UV-B and UV-A (320–400 nm) radiation of existing vegetation, with further water and fertilizer amendment treatments. Seven microarthropod species recovered in sufficient numbers for statistical analyses showed considerable spatial aggregation independent of treatment, a feature typical of many soil invertebrates. Analyses using negative binomial generalized linear modeling identified further significant and consistent treatment impacts on both individual species and species groups. Relative to controls, manipulations increasing temperature decreased numbers of microarthropods (particularly Collembola), as did exposure to near-ambient levels of UV radiation (separate significant effects for both UV-A and UV-B), while water amendment increased numbers. The impacts of temperature and water are consistent with our understanding of the importance of these two environmental variables and their interaction in Antarctic terrestrial ecosystems. The negative impact of UV (-A or -B) on arthropod heterotroph and detritivore populations in the Antarctic terrestrial food web is likely to be a secondary consequence of UV impact on vegetation characteristics. This is, again, consistent with general predictions of the impact of changing UV climate on ecosystem function.
Comparative growth and photosynthetic responses of native and adventive iceplant taxa to salinity stress

An ability to tolerate salinity can be critical for plants growing in coastal environments. We hypothesised that differences in salinity tolerance might explain variations in vigour and distribution patterns among four iceplant taxa on the Wellington coast. Growth rates, biomass allocation and quantum efficiencies of photosystem II were compared under three salinity levels for Carpobrotus edulis, Carpobrotus chilensis, Disphyma australe and a hybrid presumed to be C. edulis × D. australe. Carpobrotus edulis was significantly less tolerant of seawater-strength salinity relative to the other taxa. The data did not support a correlation between salinity tolerance and competitiveness in these iceplants. Chlorophyll a fluorescence measurements revealed no permanent adverse impacts on photosynthetic efficiency resulting from long-term exposure to salinity. However, salt-induced growth differences observed among iceplant taxa are probably due to the changes in their photosynthetic capacities.
Landscape Features, Home-Range Size and Density of Northern Badgers (Meles meles)

Knowledge of badger density is important for their conservation especially in areas with low badger densities. Therefore, we aimed to build a simple model to estimate badger density in northern Europe on the basis of habitat characteristics. A radio-tracking study in southern Finland showed that habitat structure of the landscape affects home-range sizes of northern badgers. The data collected from the literature indicate that badger density and home-range size correlate negatively but the relationship was non-linear, with highest densities and smallest home ranges in England. Consequently, badger density can be estimated on the basis of habitat characteristics of the area: density is higher when the proportion of mixed forests is high and that of large spruce forests low and vice versa. Because other factors, such as hunting and predation may be involved, density values should be treated as rough estimates of the density in different landscapes in Finland.
Contrasting Conventional with Multi-Level Modeling Approaches to Meta-Analysis: Expectation Consistency in U.K. Woodland Recreation Values

The paper presents a variety of meta analysis models of woodland recreation benefit estimates, contrasting conventionally estimated models with those provided by novel, multi-level modeling (MLM) techniques (Goldstein 1995). Our conventional models suggest that studies carried out by certain authors are associated with unusually large residuals within our meta-analysis. However, the MLMapproach explicitly incorporates the hierarchical nature of meta-analysis data, with estimates nested within study sites and authors. These residuals are not a significant determinant upon values, suggesting that, at least in this aspect, estimates may be more robust than indicated by less sophisticated models. (JELQ26)
The Properties of Equally Weighted Risk Contribution Portfolios

Minimum-variance portfolios and equally weighted portfolios have recently prompted great interest from both academic researchers and market practitioners because their construction does not rely on expected average returns and, therefore, is assumed to be robust. In this article, the authors consider a related approach in which the risk contribution from each portfolio component is made equal, maximizing the diversification of risk, at least, on an ex ante basis. Roughly speaking, the resulting portfolio is similar to a minimum-variance portfolio subject to a diversification constraint on the weights of its components. The authors derive the theoretical properties of such a portfolio and show that its volatility is located between those of minimum-variance and equally weighted portfolios. Empirical applications confirm that ranking. Equally weighted risk contribution portfolios appear to be an attractive alternative to minimum-variance and equally weighted portfolios and, therefore, could be considered a good trade-off between the two approaches in terms of absolute risk level, risk budgeting, and diversification.
CORRECTION

NEUROSCIENCE. For the article ‘‘Changes in extracellular space size and geometry in APP23 transgenic mice: A model of Alzheimer’s disease,’’ by Eva Syková, Ivan Vořı́s̆ek, Tatiana Antonova, Tomás̆ Mazel, Melanie Meyer-Luehmann, Mathias Jucker, Milan Hájek, Michael Or, and Jan Bures̆, which appeared in issue 2, January 11, 2005, of Proc. Natl. Acad. Sci. USA (102, 479–484; first published January 3, 2005; 10.1073 pnas.0408235102), due to a printer’s error, the author name Michael Or should have appeared as Michael Ort. The online version has been corrected. The corrected author line appears below.
The expansion of maize root‐cap mucilage during hydration. 2. Observations on soil‐grown roots by cryo‐scanning electron microscopy

Expansion of root-cap mucilage during hydration was followed by cryo-scanning analytical microscopy of soil-grown roots of Zea diploperennis and Zea mays. Roots examined directly from the soil have no expanded mucilage. Their condensed, unexpanded mucilage is in three domains, periplasmic, intercellular and peripheral to the cap tissue. Carbon concentration is the same in the three domains. During hydration there is no change in carbon concentration as the condensed mucilage moves through these three domains; however there is a sharp drop at the periphery where a gel phase transition occurs. The rate of expansion of the mucilage blob around the root tip is limited by the rate of this gel phase transition.
Lipid Metabolism Responses in Rats Fed Docosahexaenoic Acid Given as Monoacylglycerol, Diacylglycerol, Triacylglycerol, and Ethyl Ester

We examined the effects of the dietary docosahexaenoic acid (DHA), given as monoacylglycerol (MG), diacylglycerol (DG), triacylglycerol (TG) and ethyl ester (EE), on plasma and liver lipid profiles in rats. Male Sprague-Dawley rats were fed semi purified diets containing 10% fat with a constant polyunsaturated/monounsaturated/saturated fatty acid ratio for 1 week. One% of DHA-MG, DG, TG and EE were added to the rat’s diets as a substitute for fat. Control rats were fed a fat containing linoleic acid as a sole polyunsaturated fatty acid. The apparent absorption rates of the total fat and DHA were almost quantitative (>95%) in all groups. The plasma concentrations of total and HDL cholesterol in the four DHA-supplemented groups were significantly lower than in the control group. DHA-DG and TG were more effective for lowering plasma total cholesterol concentration than DHA-MG. Also, DHA-DG was more effective than DHA-EE. The plasma TG concentration was significantly lower only in the DHA-DG and TG groups than in the control group, while this effect was more pronounced in DHA-TG than in DHA-DG. DHA feeding increased the proportion of n-3 fatty acids accompanying a complementary decrease of arachidonic acid in liver lipid fractions. The percentages of total n-3 fatty acids were significantly higher in the DHA-TG group than in other DHA groups in liver total lipids. These results suggest that the structural differences of DHA-containing lipids in dietary fats affected lipid metabolism differently in rats, and the DHA-DG and TG more effectively reduced plasma lipids than DHA-MG and EE.