bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining halo occupation distribution and cosmic growth rate using multipole power spectrum
Authors: Hikage Chiaki 
Published: March 2014

Abstract
We propose a new method of measuring halo occupation distribution (HOD) together with cosmic growth rate using multipole components of galaxy power spectrum Pl(k). The non-linear redshift-space distortion due to the random motion of satellite galaxies, i.e. Fingers-of-God, generates high-l multipole anisotropy in galaxy clustering, such as the hexadecapole (l = 4) and tetra-hexadecapole (l = 6), which are sensitive to the fraction and the velocity dispersion of satellite galaxies. Using simulated samples following the HOD of luminous red galaxies, we find that the input HOD parameters are successfully reproduced from Pl(k), and that high-l multipole information help to break the degeneracy among HOD parameters. We also show that the measurements of the cosmic growth rate as well as the satellite fraction and velocity dispersions are significantly improved by adding the small-scale information of high-l multipoles.
Preparation of next-generation DNA sequencing libraries from ultra-low amounts of input DNA: Application to single-molecule, real-time (SMRT) sequencing on the Pacific Biosciences RS II
Authors: Raley Castle , Munroe David , Jones Kristie , Tsai Yu-Chih , Guo Yan , Tran Bao , Gowda Sujatha , Troyer Jennifer L. , Soppet Daniel R , Stewart Claudia , Stephens Robert , Chen Jack , Skelly TF , Heiner Cheryl , Korlach Jonas , Nissley Dwight 
Published: March 2014

AbstractWe have developed and validated an amplification-free method for generating DNA sequencing libraries from very low amounts of input DNA (500 picograms – 20 nanograms) for singlemolecule sequencing on the Pacific Biosciences (PacBio) RS II sequencer. The common challenge of high input requirements for single-molecule sequencing is overcome by using a carrier DNA in conjunction with optimized sequencing preparation conditions and re-use of the MagBead-bound complex. Here we describe how this method can be used to produce sequencing yields comparable to those generated from standard input amounts, but by using 1000-fold less starting material.
Seedling resistance, tolerance and escape from herbivores: insights from co‐dominant canopy tree species in a resource‐poor African rain forest
Authors: Norghauer Julian M. , Glauser Gaëtan , Newbery David M. 
Published: March 2014

Summary

Although plants can reduce the impacts of herbivory in multiple ways, these defensive traits are often studied in isolation and an understanding of the resulting strategies is incomplete.

In the study reported here, empirical evidence was simultaneously evaluated for the three main sets of traits available to plants: (i) resistance through constitutive leaf traits, (ii) tolerance to defoliation and (iii) escape in space, for three caesalpiniaceous tree species Microberlinia bisulcata, Tetraberlinia bifoliolata and T. korupensis, which co‐dominate groves within the lowland primary rain forest of Korup National Park (Cameroon).

Mesh cages were placed around individual wild seedlings to exclude insect herbivores at 41 paired canopy gap and understorey locations. After following seedling growth and survival for c. 2 years, caged and control treatments were removed, leaves harvested to determine nutrient and phenolic concentrations, leaf mass per area estimated, and seedling performance in gaps followed for a further c. 2 years to quantify tolerance to the leaf harvesting.

The more nutrient‐rich leaves of the weakly shade‐tolerant M. bisulcata were damaged much more in gaps than the two strongly shade‐tolerant Tetraberlinia species, which had higher leaf mass per area and concentrations of total phenols. Conversely, the faster‐growing M. bisulcata was better able to tolerate defoliation in terms of height growth (reflushing capacity), but not at maintaining overall leaf numbers, than the other two species.

Across gaps, insect‐mediated Janzen–Connell effects were most pronounced for M. bisulcata, less so for T. korupensis, and not detectable for T. bifoliolata. The three species differed distinctly in their secondary metabolic profiles.

Taken together, the results suggested a conceptual framework linking the three sets of traits, one in which the three co‐dominant species adopt different strategies towards herbivore pressure depending on their different responses to light availability. This study is one of the first in a natural forest ecosystem to examine resistance to, tolerance of, and escape from herbivory among a group of co‐occurring tropical tree species.
Earlier leaf‐out rather than difference in freezing resistance puts juvenile trees at greater risk of damage than adult trees
Authors: Vitasse Yann , Lenz Armando , Hoch Günter , Körner Christian 
Published: March 2014

Summary

In temperate climates, seedlings and saplings have often been assumed to be more sensitive to late‐spring freezes than conspecific adult trees. Yet, no data are available to compare the freezing resistance of juvenile and adult trees at their phenologically most sensitive stage, that is, during leaf‐out.

Emerging leaves of seedlings, saplings and adult trees were collected in spring 2013 in seven temperate tree species in a mature mixed forest in the foothills of the Swiss Jura Mountains. Freezing resistance of these emerging leaves was assessed using different target temperatures (−13 to +4 °C) in seven computer‐controlled freezers. Additionally, we assessed the risk that species encounter freeze damages based on temperature data recorded since 1898.

The different study species showed contrasting freezing resistance, with the LT50 (median lethal freezing temperature) of emerging leaves ranging from −3.5 ± 0.2 °C (Fraxinus excelsior) to −8.3 ± 0.2 °C (Prunus avium). Within species, juvenile trees (seedlings or saplings) were found to be as sensitive to freezing temperatures as mature trees when the same developmental stage of foliage was compared. Based on phenological observations made during spring 2012, long time series of temperatures indicate a very low risk of freeze damage at the study site, especially for adult trees.

Synthesis. We conclude that seedlings and saplings are more prone to freeze damage than adult trees because of their earlier flushing rather than due to a higher sensitivity to freezing as such. Our study highlights that the timing of spring phenology has evolved in such a way that it minimizes the risk of freeze damage according to the species‐specific LT50. Early flushing species are among the most freezing‐resistant species during flushing, whereas late flushing species are among the least resistant. We conclude that for the examined species the species‐specific freezing resistance during leaf emergence could be extracted from either adult or juvenile trees, as long as it is estimated at a same phenological stage.
Extracellular matrix is modulated in advanced glycation end products milieu via a RAGE receptor dependent pathway boosted by transforming growth factor‐β1 在晚期糖基化终末产物环境中细胞外基质通过RAGE受体依赖性途径调节，转化生长因子‐β1可以促进这种调节
Authors: Serban Andreea Iren , Stanca Loredana , Geicu Ovidiu Ionut , Munteanu Maria Cristina , Costache Marieta , Dinischiotu Anca 
Published: March 2014

AbstractBackgroundInterstitial fibrosis is induced by imbalances in extracellular matrix homeostasis. Advanced glycation end products (AGEs) can bind and activate the receptor for AGEs (RAGE), which is involved in diabetic nephropathy. We set out to identify the role of AGEs in producing alterations leading to matrix hypertrophy and the pathway through which aminoguanidine, as well as anti‐RAGE and anti‐transforming growth factor (TGF)‐β1 antibody treatments could prevent these modifications.MethodsHuman embryonic kidney (HEK‐293) cells were exposed to glycated bovine serum albumin (AGE‐BSA) and co‐treated with neutralizing antibodies or aminoguanidine. The effects on the transcriptional and translational levels of RAGE, TGF‐β1 and collagen IV were evaluated, while metalloproteinase activity was assessed by gelatin zymography.ResultsAGE‐BSA (200 μg/mL) upregulated RAGE's expression, while TGF‐β1 synthesis and the formation of its bioactive form were increased in a dose‐dependent manner by AGEs. AGE‐BSA exposure increased both matrix metalloproteinase (MMP) activity and collagen IV synthesis, boosted by TGF‐β1 upregulation. Aminoguanidine's effects revealed that small concentrations (10 μmol/L) enhance AGE‐BSA effects, by increasing the expression of RAGE and TGF‐β1, while higher concentrations (100 μmol/L) contribute to their downregulation.ConclusionsAlthough AGEs regulate RAGE and TGF‐β1 by distinct pathways, RAGE activation leads to a further increase of TGF‐β1 levels. MMP‐2 activity seems to rely on TGF‐β1, while MMP‐9 was dependent on RAGE. These factors converge to control collagen IV turnover. Furthermore, although the antibody treatments might appear more efficient than AG in decreasing collagen IV levels, the cells compensate the RAGE and TGF‐β1 blockade by increasing the mRNA expression of these proteins.
Rheumatoid factor in idiotypic regulation of autoimmunity
Authors: Beduleva Liubov , Menshikov Igor , Stolyarova Elena , Fomina Kseniya , Lobanova Olga , Ivanov Pavel , Terentiev Alexey 
Published: March 2014

AbstractAimRheumatoid factor (RF) is known to be heterogeneous, and RFs detected by various methods exhibit different characteristics. In addition to interacting with the Fc region of immunoglobulin G (IgG), certain RFs are able to recognize idiotypes of antibodies. Given the important role of idiotypic interactions in regulating autoimmunity, we hypothesize that RF is involved in regulation of lymphocyte activity against autoimmune disease‐inducing antigens via idiotype–anti‐idiotype interactions with these lymphocytes.MethodRF level and the existence of idiotype–anti‐idiotype interactions between RF and antibodies to autoimmunity‐inducing antigens were studied in rats resistant and sensitive to collagen‐induced arthritis, encephalomyelitis and atherosclerosis. RF was assayed by agglutination of tanned IgG‐loaded erythrocytes.ResultsRat resistance to autoimmune disease is associated with high RF production during the initiation of the immune response, and a low RF level during this period may be a preclinical marker of experimental autoimmune disease manifestation. RF‐containing sera compete with an antigen if the RF‐containing sera were obtained from rats immunized with that antigen, and they non‐specifically inhibit binding of different antigen‐antibody pairs. This suggests that RFs are anti‐idiotypic antibodies that carry two kinds of paratopes: a particular paratope that recognizes the antigen‐binding sites of antibodies, and a shared paratope that serves to recognize the recurrent idiotype on antibodies. Antigenic epitopes for the shared RF paratope can be created in the hinge region of Fc fragments of homologous IgG.ConclusionRF detected by agglutination of tanned IgG‐loaded erythrocytes is involved in negative idiotypic regulation of lymphocytes specific to autoimmunity‐inducing antigens.
Rapid assessment of wildlife abundance: estimating animal density with track counts using body mass–day range scaling rules
Authors: Keeping D. 
Published: March 2014

AbstractLimited resources in conservation dictate the need for efficient means of assessing wildlife abundance. Body mass–day range scaling rules and empirical track counts were applied to an established formula to estimate a wide range of wildlife densities. Using the southern Kalahari ecosystem of Botswana as an example, I provide the first comprehensive density estimates for the mammalian wildlife community (>0.2 kg), including densities for several species previously unattainable by other methods. Among a subset of species, empirical day ranges from this area were consistently greater than those predicted using scaling rules modeled with species from diverse ecosystems. I applied a correction factor based on this discrepancy, which generated values congruent with independent density estimates from the area. Although accurate measures of day range are a practical constraint to estimating densities from track counts, the results suggest that modest efforts to obtain location‐specific day range estimates for a subset of species can improve density estimates for others derived from general allometric relationships. Given the strength of track surveys to accumulate unbiased observations quickly, in environments where animal tracks are readily visible, this approach shows potential for the rapid assessment of wildlife abundance.
Predictors of extinction risk of passerine birds in aCentralEuropean country
Authors: Koleček J. , Albrecht T. , Reif J. 
Published: March 2014

AbstractTo develop effective conservation measures, it is crucial that we understand how ecological and life‐history traits relate to risk of species extinction. Through the use of phylogenetic generalized least‐squares regression, this study assesses the relative importance of habitat specialization, life history, migration strategy and climatic niche as predictors of national threat level for 86 passerine bird species breeding in theCzechRepublic. We found that, after controlling for variation in breeding distribution, slow life history increases the extinction risk in habitat specialist species, but reduces such risk in habitat generalists. The higher threat of habitat specialists is consistent with their higher sensitivity to human‐induced environmental perturbations, most notably to the habitat loss. However, our results suggest that the negative effects of habitat specialization appear to be somewhat compensated for by fast life history. For example, species with fast life histories typically display higher fecundity than species with slow life histories. At the same time, slow life history can be beneficial for habitat generalists that are not as badly affected by habitat destruction as habitat specialists. Such species are able to allocate more energy to future reproduction and could wait for optimal environmental conditions before breeding, leading to more favourable population status in the long term. Finally, we also found that species breeding in warmer areas experience higher extinction risk than species breeding in colder areas. Although the effect of climatic niche is usually attributed to the impact of climate change, we suggest that the habitat destruction is more likely an explanation because the warmer lowland regions are heavily exploited by intensive agriculture and industrial and urban development. Based upon these results, we suggest that current conservation effort, especially in warmer zones, may not sufficiently address the requirements of the habitat specialists with slow histories.
Effects of inhalational anaesthetics in experimental allergic asthma
Authors: Burburan S. M. , Silva J. D. , Abreu S. C. , Samary C. S. , Guimarães I. H. L. , Xisto D. G. , Morales M. M. , Rocco P. R. M. 
Published: March 2014

SummaryWe evaluated whether isoflurane, halothane and sevoflurane attenuate the inflammatory response and improve lung morphofunction in experimental asthma. Fifty‐six BALB/c mice were sensitised and challenged with ovalbumin and anaesthetised with isoflurane, halothane, sevoflurane or pentobarbital sodium for one hour. Lung mechanics and histology were evaluated. Gene expression of pro‐inflammatory (tumour necrosis factor‐α), pro‐fibrogenic (transforming growth factor‐β) and pro‐angiogenic (vascular endothelial growth factor) mediators, as well as oxidative process modulators, were analysed. These modulators included nuclear factor erythroid‐2 related factor 2, sirtuin, catalase and glutathione peroxidase. Isoflurane, halothane and sevoflurane reduced airway resistance, static lung elastance and atelectasis when compared with pentobarbital sodium. Sevoflurane minimised bronchoconstriction and cell infiltration, and decreased tumour necrosis factor‐α, transforming growth factor‐β, vascular endothelial growth factor, sirtuin, catalase and glutathione peroxidase, while increasing nuclear factor erythroid‐2‐related factor 2 expression. Sevoflurane down‐regulated inflammatory, fibrogenic and angiogenic mediators, and modulated oxidant–antioxidant imbalance, improving lung function in this model of asthma.
How Finance Penetrates its Other: A Cautionary Tale on the Financialization of a Dutch University
Authors: Engelen Ewald , Fernandez Rodrigo , Hendrikse Reijer 
Published: March 2014

AbstractIf any organization ought to be immune to the forces of financialization, it is a publicly funded university in corporatist Europe. Shielded from the intrusion by financial metrics, values and professionals through a strong historically rooted tradition of self‐management by powerful professional guilds, continental universities should largely have avoided the marketization and managerialization of Anglophone universities. Not so, this case study of a Dutch public university suggests. From 1995 onwards, a shift in real estate management—devolving responsibilities from the Dutch state to universities—served as a Trojan horse for financialization, triggering changes in organizational culture and a power shift from teaching and research professionals to accountants, real‐estate developers, financiers and their ilk. This case suggests that the power of finance is such that no societal domain is immune. The paper ends with a call for more non‐metropolitan case studies of financialization and argues that the only hope for salvation is a more self‐conscious defense of traditional academic values by the guardians of higher learning themselves.
L‐typeCa2+channel current characteristics are preserved in rat tail artery myocytes after one‐day storage
Authors: Mugnai P. , Durante M. , Sgaragli G. , Saponara S. , Paliuri G. , Bova S. , Fusi F. 
Published: March 2014

AbstractAimTo develop a cheap and simple method of storing for 24‐h vascular tissue and single myocytes while preserving therein the biophysical and pharmacological characteristics ofL‐typeCa2+channels and contractile activity.MethodsRings or vascular smooth muscle cells obtained from the rat tail main artery were used either freshly (R0h andVSMC0h) or stored for 24 h (R24h andVSMC24h) at 4 °C, to record whole‐cell L‐type Ca2+currents (ICa(L)) or measure contractile responses.ResultsR0h/VSMC0h and R24h/VSMC24h comparably contracted when stimulated with phenylephrine, highKCl orATP. In bothVSMC0h andVSMC24h,ICa(L)was identified and characterized as a stable inward current for at least 35 min;ICa(L)was comparably inhibited by the Ca2+antagonists nifedipine, verapamil and diltiazem and increased by the Ca2+channel agonist (S)‐(‐)‐Bay K 8644; current density and current–voltage relationships were similar; at more hyperpolarized holding potentials,ICa(L)intensity increased comparably; nifedipine shifted the steady‐state inactivation curve towards more negative potentials, while verapamil blockedICa(L)in a frequency‐dependent manner and slowed down the rate of recovery from inactivation in a comparable way.ConclusionFindings show that smooth muscle contractile activity and the biophysical and pharmacological features of L‐type Ca2+channels are similar inVSMC24h andVSMC0h. The fact that reproducible results were obtained in vascular myocytes up to 24 h after dissociation may facilitate vascular smooth muscle cell investigation by increasing throughput and reducing the number of animals required.
The role of nitric oxide in the cardiovascular response to chronic and acute hypoxia in White Leghorn chicken (Gallus domesticus)
Authors: Iversen N. K. , Wang T. , Baatrup E. , Crossley D. A. 
Published: March 2014

AbstractAimPrenatal hypoxia due to placental insufficiency results in deleterious phenotypes and compensatory mechanisms including increased sympathetic tone. Utilizing the embryonic chicken model, we investigated (i) changes in nitric oxide (NO)‐mediated tone in response to chronic hypoxic development and (ii) the in vivo role of NO‐mediated tone during acute hypoxic exposure, which has not been previously studied. We hypothesized that NO tone on the cardiovascular system would be unaffected by chronic hypoxic incubation in White Leghorn chicken (Gallus domesticus) embryos.MethodsWe measured arterial pressure, heart rate and femoral blood flow (via a Doppler flow probe) in response to acute hypoxia (10% O2) and pharmacological manipulations in normoxic‐ and hypoxic (15% O2)‐incubated embryos. This was performed at 70 and 90% of total incubation time (21 days). At 70% of incubation (day 15), blood volume and chorioallantoic membrane development are maximal; 90% of incubation (day 19) is 1 day prior to lung ventilation.ResultsAcute hypoxic exposure decreased femoral flow in both 90% groups, but increased femoral artery resistance in the hypoxic group. NO tone increased during development, but was not affected by hypoxic incubation. Inhibition of NO production by L‐NAME (100 mg kg−1) revealed that NO plays a significant role in the flow response to hypoxia.ConclusionChronic hypoxic incubation has no effect on cardiovascular NO tone during White Leghorn chicken development. In the intact animal, NO function during acute hypoxic stress is suppressed by hypoxic incubation, indicating that chronic hypoxic stress dampens the NO contribution.
In vitro fermentation of feed ingredients by fresh or frozen pig fecal inocula
Authors: Pastorelli Grazia , Faustini Massimo , Attard Everaldo 
Published: March 2014

AbstractIn vitro techniques can offer a rapid, repeatable and cost‐effective alternative to in vivo experiments. We investigated the gas production (GP) of nine different feeds commonly used in Italian and Maltese pig farms in order to assess the use of the Ankom system in this species and to compare the in vitro microbial activity fresh or frozen inocula derived from piglet feces. Proximate and polyphenolic analyses were determined for all substrates. Fermentation profiles were measured according to the cumulative GP technique. Analysis of GP values revealed significant differences in the fermentation patterns mainly due to substrate and inoculum effects. Fermentation parameters varied significantly according to the substrate ingredients. The frozen inoculum generally led to more total GP than for fresh, with the exception of hard wheat bran pellets (HWBP), pelleted pulp and mature carob. Conversely the fresh fecal inoculum had an earlier maximum time to reach maximum GP than the frozen, showing a higher maximum rate of GP in all substrates excepting for HWBP. A significant difference in frozen and fresh inocula was found for the complete formulation. Further studies are required to confirm the variation between fresh and frozen fecal inocula to a wider range of feed, including those that could have negative biological effects.