bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: The vertical transition approximation
Authors: D’Alessandro Maira , Aschi Massimiliano , Mazzuca Claudia , Palleschi Antonio , Amadei Andrea
Published: September 2013

In this paper we describe in detail a general and efficient methodology, based on the perturbed matrix method and molecular dynamics simulations, to model UV-Vis absorption and emission spectra including vibrational and conformational effects. The basic approximation used is to consider all the chromophore atomic coordinates as semiclassical degrees of freedom, hence allowing the calculation of the complete spectral signal by using the electronic vertical transitions as obtained at each possible chromophore configuration, thus including the contributions of vibrations and conformational transitions into the spectrum. As shown for the model system utilized in this paper, solvated 1-phenyl-naphthalene, such an approximation can be rather accurate to reproduce the absorption and emission spectral line shape and properties when, as it often occurs, the vertical vibronic transition largely overlaps the other non-negligible vibronic transitions.
Direct numerical simulation of transitional mixed convection flows: Viscous and inviscid instability mechanisms
Authors: Sengupta T. K. , Bhaumik S. , Bose Rikhi
Published: September 2013

Receptivity studies using direct numerical simulation require computations of equilibrium flow and its response to deterministic excitation. Equivalent flow problem, without heat interaction for zero-pressure gradient boundary layer, has been studied with respect to wall-excitation by a finite difference high accuracy method based on the solution of Navier-Stokes equation in Sengupta and Bhaumik [Phys. Rev. Lett.107, 154501 (2011)] and Sengupta et al. [Phys. Rev. E85, 026308 (2012)]. One of the key features of this study has been that the same methodology is used for computing the equilibrium flow and the disturbance field. Computation of equilibrium flow was performed by solving Navier-Stokes equation to include the leading edge of the plate, so that the effects of leading edge singularity and the growth of the boundary layer is included in the nonlinear framework. When the same methodology is attempted for mixed convection flows past horizontal plate (with Boussinesq approximation to model heat transfer effects) some of the equilibrium flow features could not be explained with linear viscous instability theory results. For horizontal hot flat plate with adiabatic wall conditions, the equilibrium flow could be computed and its receptivity could be correlated with linear spatial theory for lower buoyancy parameter. Here, we focus on receptivity of mixed convection flows to wall excitation for the following cases which do not allow computing the equilibrium flows from the solution of Navier-Stokes equation: (i) Aadiabatic horizontal flat plate cooled significantly at the leading edge only and (ii) strongly heated isothermal wedge flow for a wedge angle of 60°. The cold plate case is particularly interesting as the linear spatial theory indicates enhanced stabilization for higher magnitude of the buoyancy parameter. Results presented for the cold plate case indicates disturbance growth outside the shear layer. This prompted us to re-investigate various mechanisms of instability present for mixed convection flows. There is no definitive study for inviscid mechanism in this respect and the present effort not only fills this void, but also explains the relative roles of viscous and inviscid mechanisms for strong heat transfer effects, within the Boussinesq approximation.
Design for enhanced thermo-electric pumping in light emitting diodes
Authors: Gray Dodd J. , Santhanam Parthiban , Ram Rajeev J.
Published: September 2013

We present a strategy for optimization of thermo-electric pumping in light emitting diodes (LEDs). We use a finite element model for charge transport in a GaInAsSb/GaSb double hetero-junction LED that is verified experimentally to consider optimal design and operation of low-bias LEDs. The wall-plug efficiency is shown to be enhanced by over 200× at nanowatt power levels and 20× at microwatt power levels. A design for room-temperature operation of a 2.2 μm LED with 100% efficiency is proposed—this represents a 110 °C reduction of the temperature required to observe unity efficiency.
Heterodyned toroidal microlaser sensor
Authors: Maker Ashley J. , Armani Andrea M.
Published: September 2013

Optical microcavity sensors have demonstrated success in detecting analytes with high sensitivity. Typically, the sensor output is monitored using oscilloscopes or optical spectrum analyzers; however, these instruments can significantly limit the sensing performance. In the present work, we address this limitation by developing a neodymium-doped toroid microlaser and heterodyning it with a reference laser. The resulting beat signal is analyzed on an electrical spectrum analyzer. By performing comparative temperature sensing experiments, we demonstrate that the heterodyning improves the detection limit over 60-fold while also improving the temporal resolution and the signal to noise ratio up to 50-fold.
Some advantages of intermediate band solar cells based on type II quantum dots
Authors: Luque Antonio , Linares Pablo G. , Mellor Alex , Andreev Viacheslav , Marti Antonio
Published: September 2013

Unlike Type I, Type II quantum dots do not have hole bound states. This precludes that they invade the host semiconductor bandgap and prevents the reduction of voltage in intermediate band solar cells. It is proven here that the optical transition between the hole extended states and the intermediate bound states within the host bandgap is much stronger than in Type I quantum dots, increasing the current and making this structure attractive for manufacturing these cells.
Human evolution and diet: a modern conundrum of health versus meat consumption, or is it?
Authors: Mann N.
Published: September 2013

Despite negative press reports on the effect of meat and other animal-source foods (ASFs) on human health and a vocal minority who contend that humans evolved as vegetarians, scientific evidence contradicts these views. For several million years before the development of agriculture, our ancestors were heavily reliant on ASFs as a source of energy and critical substrates such as protein and long-chain omega-3 fatty acids. Numerous lines of evidence in the anthropological literature have confirmed this scenario. Studies on ASF composition and clinical trials on ASF consumption have provided clear evidence of a requirement for meat in the diet to provide nutrients essential to health, such as Vitamin B12, long-chain omega-3 fatty acids and bioavailable forms of iron and zinc. Other studies have demonstrated that lean ASFs have a role in cholesterol-lowering diets and are important for mental function. Finally, it is possible and desirable to produce meat of a lean nature that mimics the many healthy attributes of wild-game meats and, by emphasising pasture feeding over grain feeding, this can be achieved to a large extent in Australia.
Duckweed (Landoltia punctata) in dog diets decreases digestibility but improves stool consistency
Authors: Brown W. Y. , Choct M. , Pluske J. R.
Published: September 2013

In the present experiment, duckweed is evaluated as a novel protein source for dogs by incorporating Landoltia punctata into dog diets at 10%, 20% and 30%. The inclusion of duckweed resulted in significant (P < 0.001) linear decreases in DM, gross energy and crude protein digestibility. The addition of the exogenous enzyme phytase significantly (P = 0.03) improved crude protein digestibility in the diet of 30% duckweed inclusion. The inclusion of duckweed in the diets had no significant effect on palatability, but resulted in firmer stools (P = 0.003).
Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity
Authors: Miura Tohru , Shibata Takehiko , Kusano Kohji
Published: September 2013

Significance

Human health is generally maintained even when important genes are mutated because the human genome is diploid, with two sets of genomic DNA. Thus, various genes are heterozygous, with one functional and one defective allele at their loci. Somatic cells often incur DNA double-strand breaks by the direct effects of DNA-damaging agents, including oxidative stress, and indirectly, such as through DNA replication-fork collapse at damaged sites. Double-strand breaks are repaired through recombination processes, including homologous recombination and nonhomologous end-joining. These processes include the risk of losing a functional allele, called loss of heterozygosity (LOH). This study revealed that a putative antirecombinase, Srs2 DNA helicase, is a key enzyme to promote LOH-less recombination repair of double-strand breaks.
Structural features of Argonaute–GW182 protein interactions
Authors: Pfaff Janina , Hennig Janosch , Herzog Franz , Aebersold Ruedi , Sattler Michael , Niessing Dierk , Meister Gunter
Published: September 2013

Significance

MicroRNAs (miRNAs) are short RNA molecules that negatively regulate the expression of protein-coding genes in many eukaryotes. In order to do so, miRNAs interact with a member of the Argonaute (Ago) protein family and guide it to partially complementary sequences on mRNAs. Ago proteins interact with a member of the GW182 protein family, which, in turn, recruits additional factors and coordinates all downstream steps. In our study, we have characterized Ago–GW182 protein interactions using biochemical and biophysical methods. We define the interaction surfaces on GW182 and Ago proteins and provide a model for the binding mechanism and specificity.
Early evolution of the T-box transcription factor family
Authors: Sebé-Pedrós Arnau , Ariza-Cosano Ana , Weirauch Matthew T. , Leininger Sven , Yang Ally , Torruella Guifré , Adamski Marcin , Adamska Maja , Hughes Timothy R. , Gómez-Skarmeta José Luis , Ruiz-Trillo Iñaki
Published: September 2013

Significance

The T-box transcription factors are key players in animal development and they were considered strictly animal-specific. We show that T-box genes have instead an important premetazoan evolutionary history, being present in several nonmetazoan unicellular taxa. Notably, we find thatCapsaspora owczarzaki, a unicellular relative of animals, has a Brachyury homolog functionally conserved with metazoans. Through experiments inXenopus, we demonstrate thatC. owczarzakiBrachyury lacks, however, the target specificity displayed by metazoan Brachyury homologs, including sponges. This suggests that the subfunctionalization of T-box classes was established at the onset of Metazoa through new interactions with cofactors, concomitantly with the diversification of the T-box family.
Fe–N
2
/CO complexes that model a possible role for the interstitial C atom of FeMo-cofactor (FeMoco)
Authors: Rittle Jonathan , Peters Jonas C.
Published: September 2013

Significance

Biological nitrogen reduction is a fascinating transformation whose mechanism remains uncertain. Recently, an interstitial carbon has been identified within the FeMo-cofactor (FeMoco) of nitrogenase whose role is unknown and warrants model studies. In this report we disclose a series of five-coordinate Fe complexes bound to an ancillary ligand featuring a central C atom. This model system coordinates N
2
trans to the C atom, and displays unusual Fe–C bonding motifs that may shed light on a possible role of the interstitial carbon in FeMoco.
Urocortin 2 autocrine/paracrine and pharmacologic effects to activate AMP-activated protein kinase in the heart
Authors: Li Ji , Qi Dake , Cheng Haiying , Hu Xiaoyue , Miller Edward J. , Wu Xiaohong , Russell Kerry S. , Mikush Nicole , Zhang Jiasheng , Xiao Lei , Sherwin Robert S. , Young Lawrence H.
Published: September 2013

Urocortin 2 (Ucn2), a peptide of the corticotropin-releasing factor (CRF) family, binds with high affinity to type 2 CRF receptors (CRFR2) on cardiomyocytes and confers protection against ischemia/reperfusion. The mechanisms by which the Ucn2-CRFR2 axis mitigates against ischemia/reperfusion injury remain incompletely delineated. Activation of AMP-activated protein kinase (AMPK) also limits cardiac damage during ischemia/reperfusion. AMPK is classically activated by alterations in cellular energetics; however, hormones, cytokines, and additional autocrine/paracrine factors also modulate its activity. We examined the effects of both the endogenous cardiac Ucn2 autocrine/paracrine pathway and Ucn2 treatment on AMPK regulation. Ucn2 treatment increased AMPK activation and downstream acetyl-CoA carboxylase phosphorylation and glucose uptake in isolated heart muscles. These actions were blocked by the CRFR2 antagonist anti–sauvagine-30 and by a PKCε translocation-inhibitor peptide (εV1-2). Hypoxia-induced AMPK activation was also blunted in heart muscles by preincubation with either anti–sauvagine-30, a neutralizing anti-Ucn2 antibody, or εV1-2. Treatment with Ucn2 in vivo augmented ischemic AMPK activation and reduced myocardial injury and cardiac contractile dysfunction after regional ischemia/reperfusion in mice. Ucn2 also directly activated AMPK in ex vivo
-
perfused mouse hearts and diminished injury and contractile dysfunction during ischemia/reperfusion. Thus, both Ucn2 treatment and the endogenous cardiac Ucn2 autocrine/paracrine pathway activate AMPK signaling pathway, via a PKCε-dependent mechanism, defining a Ucn2-CRFR2-PKCε-AMPK pathway that mitigates against ischemia/reperfusion injury.
Inhibition of the p110α isoform of PI 3-kinase stimulates nonfunctional tumor angiogenesis
Authors: Soler Adriana , Serra Helena , Pearce Wayne , Angulo Ana , Guillermet-Guibert Julie , Friedman Lori S. , Viñals Francesc , Gerhardt Holger , Casanovas Oriol , Graupera Mariona , Vanhaesebroeck Bart
Published: September 2013

Understanding the direct, tumor cell–intrinsic effects of PI 3-kinase (PI3K) has been a key focus of research to date. Here, we report that cancer cell–extrinsic PI3K activity, mediated by the p110α isoform of PI3K, contributes in an unexpected way to tumor angiogenesis. In syngeneic mouse models, inactivation of stromal p110α led to increased vascular density, reduced vessel size, and altered pericyte coverage. This increased vascularity lacked functionality, correlating with enhanced tumor hypoxia and necrosis, and reduced tumor growth. The role of p110α in tumor angiogenesis is multifactorial, and includes regulation of proliferation and DLL4 expression in endothelial cells. p110α in the tumor stroma is thus a regulator of vessel formation, with p110α inactivation giving rise to nonfunctional angiogenesis, which can stunt tumor growth. This type of vascular aberration differs from vascular endothelial growth factor–centered antiangiogenesis therapies, which mainly lead to vascular pruning. Inhibition of p110α may thus offer a new antiangiogenic therapeutic opportunity in cancer.
Direct interaction of eag domains and cyclic nucleotide–binding homology domains regulate deactivation gating in hERG channels
Authors: Gianulis Elena C. , Liu Qiangni , Trudeau Matthew C.
Published: September 2013

Human ether-á-go-go (eag)-related gene (hERG) potassium channels play a critical role in cardiac repolarization and are characterized by unusually slow closing (deactivation) kinetics. The N-terminal “eag” domain and a C-terminal C-linker/cyclic nucleotide–binding homology domain (CNBHD) are required for regulation of slow deactivation. The region between the S4 and S5 transmembrane domains (S4–S5 linker) is also implicated in this process, but the mechanism for regulation of slow deactivation is unclear. Here, using an eag domain–deleted channel (hERG Δeag) fused to Citrine fluorescent protein, we found that most channels bearing individual alanine mutations in the S4–S5 linker were directly regulated by recombinant eag domains fused to a cyan fluorescent protein (N-eag-CFP) and had robust Förster resonance energy transfer (FRET). Additionally, a channel bearing a group of eight alanine residues in the S4–S5 linker was not measurably regulated by N-eag-CFP domains, but robust FRET was measured. These findings demonstrate that the eag domain associated with all of the S4–S5 linker mutant channels. In contrast, channels that also lacked the CNBHD (hERG Δeag ΔCNBHD-Citrine) were not measurably regulated by N-eag-CFP nor was FRET detected, suggesting that the C-linker/CNBHD was required for eag domains to directly associate with the channel. In a FRET hybridization assay, N-eag-CFP had robust FRET with a C-linker/CNBHD-Citrine, suggesting a direct and specific interaction between the eag domain and the C-linker/CNBHD. Lastly, coexpression of a hERG subunit lacking the CNBHD and the distal C-terminal region (hERG ΔpCT-Citrine) with hERG Δeag-CFP subunits had FRET and partial restoration of slow deactivation. Collectively, these findings reveal that the C-linker/CNBHD, but not the S4–S5 linker, was necessary for the eag domain to associate with the channel, that the eag domain and the C-linker/CNBHD were sufficient for a direct interaction, and that an intersubunit interaction between the eag domain and the C-linker/CNBHD regulated slow deactivation in hERG channels at the plasma membrane.
Protein evolution along phylogenetic histories under structurally constrained substitution models
Authors: Arenas Miguel , Dos Santos Helena G. , Posada David , Bastolla Ugo
Published: September 2013

Motivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes.

Results: We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process.

Availability:  ProteinEvolver is written in C, can run in parallel and is freely available from http://code.google.com/p/proteinevolver/.

Contact:  marenas@cbm.uam.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database
Authors: Pedersen Brent S. , Yang Ivana V. , De Subhajyoti
Published: September 2013

Motivation: The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.

Results: We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions—exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant function, suggesting potential function of these regulatory RNAs in neuronal diseases. Third, lamina-associated genomic regions are highly enriched in olfaction-related genes, indicating a role of nuclear organization in their regulation.

Availability: CruzDB is available at https://github.com/brentp/cruzdb under the MIT open-source license.

Contact:  bpederse@gmail.com or subhajyoti.de@ucdenver.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Complement protein C3 exacerbates prion disease in a mouse model of chronic wasting disease
Authors: Michel Brady , Ferguson Adam , Johnson Theodore , Bender Heather , Meyerett-Reid Crystal , Wyckoff A. Christy , Pulford Bruce , Telling Glenn C. , Zabel Mark D.
Published: September 2013

Accumulating evidence shows a critical role of the complement system in facilitating attachment of prions to both B cells and follicular dendritic cells and assisting in prion replication. Complement activation intensifies disease in prion-infected animals, and elimination of complement components inhibits prion accumulation, replication and pathogenesis. Chronic wasting disease (CWD) is a highly infectious prion disease of captive and free-ranging cervid populations that utilizes the complement system for efficient peripheral prion replication and most likely efficient horizontal transmission. Here we show that complete genetic or transient pharmacological depletion of C3 prolongs incubation times and significantly delays splenic accumulation in a CWD transgenic mouse model. Using a semi-quantitative prion amplification scoring system we show that C3 impacts disease progression in the early stages of disease by slowing the rate of prion accumulation and/or replication. The delayed kinetics in prion replication correlate with delayed disease kinetics in mice deficient in C3. Taken together, these data support a critical role of C3 in peripheral CWD prion pathogenesis.
The AP-1 transcription factor JunD activates the leukocyte immunoglobulin-like receptor 1 distal promoter
Authors: Davidson Chelsea L. , Cameron Lisa E. , Burshtyn Deborah N.
Published: September 2013

Leukocyte immunoglobulin-like receptor 1 (LILRB1) is an inhibitory receptor that binds classical and non-classical MHC-I as well as UL18, a viral MHC-I homolog. LILRB1 is encoded within the leukocyte receptor complex and is widely expressed on immune cells. Two distinct promoters used differentially by lymphoid and myeloid cells were previously identified, but little is known regarding molecular regulation of each promoter or cell-type-specific usage. Here, we have investigated the transcriptional regulation of human LILRB1 focusing on elements that drive expression in NK cells. We found that while both the distal and proximal promoter regions are active in reporter plasmids in lymphoid and myeloid cells, the proximal promoter is used minimally to transcribe LILRB1 in NK cells compared with monocytes. We defined a 120-bp core region of transcriptional activity in the distal promoter that can bind several factors in NK cell nuclear extracts. Within this region, we investigated overlapping putative AP-1 sites. An inhibitor of JNK decreased LILRB1 transcript in a LILRB1+ NK cell line. Upon examining binding of specific AP-1 factors, we found JunD associated with the LILRB1 distal promoter. Finally, depletion of JunD led to a decrease in distal promoter transcript, indicating an activating role for JunD in regulation of LILRB1 transcription. This study presents the first description of regions/factors required for activity of the LILRB1 distal promoter, the first description of a role for JunD in NK cells and suggests a potential mechanism for dynamic regulation of LILRB1 by cytokines.
A synchrotron jet from a post-asymptotic giant branch star
Authors: Pérez-Sánchez A. F. , Vlemmings W. H. T. , Tafoya D. , Chapman J. M.
Published: September 2013

The evolution of low- and intermediate-initial-mass stars beyond the asymptotic giant branch (AGB) remains poorly understood. High-velocity outflows launched shortly after the AGB phase are thought to be the primary shaping mechanism of bipolar and multipolar planetary nebulae. However, little is known about the launching and driving mechanism for these jets, whose momentum and energy often far exceed the energy that can be provided by radiation pressure alone. Here, we report on the direct evidence of a magnetically collimated jet shaping the bipolar morphology of the circumstellar envelope of a post-AGB star. We present radio continuum observations of the post-AGB star IRAS 15445−5449 (OH 326.5−0.4) which has water masers tracing a fast bipolar outflow. Our observations confirm the earlier observed steep negative spectral index of the spectral energy distribution (SED) above ∼3 GHz, and resolve, for the first time, the emission to originate from a radio jet, proving the existence of such jets around a post-AGB star. The SED is consistent with a synchrotron jet embedded in a sheath of thermal electrons. We find a close correspondence between the extent and direction of the synchrotron jet and the bipolar shape of the object observed at other wavelengths, suggesting that the jet is responsible for the source morphology. The jet is collimated by a magnetic field of the order of mG at almost 7000 au from the central star. We recover observations from the Australia Telescope Compact Array archive that indicate that the emission measure of the thermal component has increased by a factor of 3 between 1998 and 2005 after which it has remained constant. The short time-scale evolution of the radio emission suggests a short lifetime for the jet. The observations of a synchrotron jet from a post-AGB star with characteristics similar to those from protostars and young stellar objects, for instance, suggest that magnetic launching and collimation is a common feature of astrophysical jets.
Critical Role of Interleukin-11 in Isoflurane-mediated Protection against Ischemic Acute Kidney Injury in Mice
Authors: Ham Ahrom , Kim Mihwa , Kim Joo Yun , Brown Kevin M. , Yeh James , D’Agati Vivette D. , Lee H. Thomas
Published: September 2013

Background:

Isoflurane releases renal tubular transforming growth factor-β1 (TGF-β1) and protects against ischemic acute kidney injury. Recent studies suggest that TGF-β1 can induce a cytoprotective cytokine interleukin (IL)-11. In this study, the authors tested the hypothesis that isoflurane protects against ischemic acute kidney injury by direct induction of renal tubular IL-11 synthesis.

Methods:

Human kidney proximal tubule cells were treated with 1.25–2.5% isoflurane or carrier gas (room air + 5% carbon dioxide) for 0–16 h. The authors also anesthetized C57BL/6 mice with 1.2% isoflurane or with equianesthetic dose of pentobarbital for 4 h. In addition, the authors subjected IL-11 receptor (IL-11R) wild-type, IL-11R–deficient, or IL-11 neutralized mice to 30-min renal ischemia followed by reperfusion under 4 h of anesthesia with pentobarbital or isoflurane (1.2%).

Results:

Isoflurane increased IL-11 synthesis in human (approximately 300–500% increase, N = 6) and mouse (23 ± 4 [mean ± SD] fold over carrier gas group, N = 4) proximal tubule cells that were attenuated by a TGF-β1–neutralizing antibody. Mice anesthetized with isoflurane showed significantly increased kidney IL-11 messenger RNA (13.8 ± 2 fold over carrier gas group, N = 4) and protein (31 ± 9 vs. 18 ± 2 pg/mg protein or approximately 80% increase, N = 4) expression compared with pentobarbital-anesthetized mice, and this increase was also attenuated by a TGF-β1–neutralizing antibody. Furthermore, isoflurane-mediated renal protection in IL-11R wild-type mice was absent in IL-11R–deficient mice or in IL-11R wild-type mice treated with IL-11–neutralizing antibody (N = 4–6).

Conclusion:

In this study, the authors suggest that isoflurane induces renal tubular IL-11 via TGF-β1 signaling to protect against ischemic acute kidney injury.
Human Milk Oligosaccharides Protect Against Enteropathogenic Escherichia coli Attachment In Vitro and EPEC Colonization in Suckling Mice
Authors: Manthey Carolin F. , Autran Chloe A. , Eckmann Lars , Bode Lars
Published: September 2013

Breast‐feeding reduces the risk of enteric bacterial infections in newborns in part because of human milk oligosaccharides (HMOs), complex glycans that are present in human milk, but not in infant formula. Enteropathogenic Escherichia coli (EPEC) are attaching/effacing pathogens that cause serious diarrheal illness with potentially high mortality in infants. We isolated HMOs from pooled human milk and found that they significantly reduce EPEC attachment to cultured epithelial cells. In suckling mice, administration of HMOs significantly reduced colonization with EPEC compared with untreated controls. These data suggest an essential role for HMOs in the prevention of EPEC infections in human infants.
Primary Spontaneous Cerebrospinal Fluid Leaks and Idiopathic Intracranial Hypertension
Authors: Pérez Mario A. , Bialer Omer Y. , Bruce Beau B. , Newman Nancy J. , Biousse Valérie
Published: September 2013

Introduction:

Idiopathic intracranial hypertension (IIH) is increasingly recognized as a cause of spontaneous cerebrospinal fluid (CSF) leak in the otolarnygological and neurosurgical literature. The diagnosis of IIH in patients with spontaneous CSF leaks typically is made a few weeks after surgical repair of the leak when symptoms and signs of elevated intracranial pressure (ICP) appear.

Methods:

Case reports and literature review. Two young obese women developed spontaneous CSF rhinorrhea related to an empty sella in one and a cribriform plate encephalocele in the other. Both patients underwent surgical repair of the CSF leak. A few weeks later, they developed chronic headaches and bilateral papilledema. Lumbar punctures showed elevated CSF opening pressures with normal CSF contents, with temporary improvement of headaches. A man with a 3-year history of untreated IIH developed spontaneous CSF rhinorrhea. He experienced improvement of his headaches and papilledema after a CSF shunting procedure, and the rhinorrhea resolved after endoscopic repair of the leak.

Results:

These cases and the literature review confirm a definite association between IIH and spontaneous CSF leak based on: 1) similar demographics; 2) increased ICP in some patients with spontaneous CSF leak after leak repair; 3) higher rate of leak recurrence in patients with raised ICP; 4) patients with intracranial hypertension secondary to tumors may develop CSF leak, confirming that raised ICP from other causes than IIH can cause CSF leak.

Conclusions:

CSF leak occasionally may keep IIH patients symptom-free; however, classic symptoms and signs of intracranial hypertension may develop after a CSF leak is repaired, exposing these patients to a high risk of recurrence of the leak unless an ICP-lowering intervention is performed.
High-resolution alkenone palaeobarometry indicates relatively stable
p
CO
2
during the Pliocene (3.3–2.8 Ma)
Authors: Badger Marcus P. S. , Schmidt Daniela N. , Mackensen Andreas , Pancost Richard D.
Published: September 2013

Temperature reconstructions indicate that the Pliocene was approximately 3
°
C warmer globally than today, and several recent reconstructions of Pliocene atmospheric CO
2
indicate that it was above pre-industrial levels and similar to those likely to be seen this century. However, many of these reconstructions have been of relatively low temporal resolution, meaning that these records may have failed to capture variations associated with the 41 kyr glacial–interglacial cycles thought to have operated in the Pliocene. Here we present a new, high temporal resolution alkenone carbon isotope-based record of
p
CO
2
spanning 3.3–2.8 Ma from Ocean Drilling Program Site 999. Our record is of high enough resolution (approx. 19 kyr) to resolve glacial–interglacial changes beyond the intrinsic uncertainty of the proxy method. The record suggests that Pliocene CO
2
levels were relatively stable, exhibiting variation less than 55 ppm. We perform sensitivity studies to investigate the possible effect of changing sea surface temperature (SST), which highlights the importance of accurate and precise SST reconstructions for alkenone palaeobarometry, but demonstrate that these uncertainties do not affect our conclusions of relatively stable
p
CO
2
levels during this interval.
A 40-million-year history of atmospheric CO2
Authors: Zhang Yi Ge , Pagani Mark , Liu Zhonghui , Bohaty Steven M. , DeConto Robert
Published: September 2013

The alkenone–pCO2methodology has been used to reconstruct the partial pressure of ancient atmospheric carbon dioxide (pCO2) for the past 45 million years of Earth's history (Middle Eocene to Pleistocene epochs). The present long-term CO2record is a composite of data from multiple ocean localities that express a wide range of oceanographic and algal growth conditions that potentially bias CO2results. In this study, we present apCO2record spanning the past 40 million years from a single marine locality, Ocean Drilling Program Site 925 located in the western equatorial Atlantic Ocean. The trends and absolute values of our new CO2record site are broadly consistent with previously published multi-site alkenone–CO2results. However, newpCO2estimates for the Middle Miocene are notably higher than published records, with averagepCO2concentrations in the range of 400–500 ppm. Our results are generally consistent with recentpCO2estimates based on boron isotope-pH data and stomatal index records, and suggest that CO2levels were highest during a period of global warmth associated with the Middle Miocene Climatic Optimum (17–14 million years ago, Ma), followed by a decline in CO2during the Middle Miocene Climate Transition (approx. 14 Ma). Several relationships remain contrary to expectations. For example, benthic foraminiferalδ18O records suggest a period of deglaciation and/or high-latitude warming during the latest Oligocene (27–23 Ma) that, based on our results, occurred concurrently with a long-term decrease in CO2levels. Additionally, a large positiveδ18O excursion near the Oligocene–Miocene boundary (the Mi-1 event, approx. 23 Ma), assumed to represent a period of glacial advance and retreat on Antarctica, is difficult to explain by our CO2record alone given what is known of Antarctic ice sheet history and the strong hysteresis of the East Antarctic Ice Sheet once it has grown to continental dimensions. We also demonstrate that in the Neogene with low CO2levels, algal carbon concentrating mechanisms and spontaneous biocarbonate–CO2conversions are likely to play a more important role in algal carbon fixation, which provides a potential bias to the alkenone–pCO2method.
The roles ofcis- andtrans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression
Authors: Meiklejohn Colin D. , Coolon Joseph D. , Hartl Daniel L. , Wittkopp Patricia J.
Published: September 2013

Evolutionary changes in gene expression underlie many aspects of phenotypic diversity within and among species. Understanding the genetic basis for evolved changes in gene expression is therefore an important component of a comprehensive understanding of the genetic basis of phenotypic evolution. Using interspecific introgression hybrids, we examined the genetic basis for divergence in genome-wide patterns of gene expression betweenDrosophila simulansandDrosophila mauritiana. We find thatcis-regulatory andtrans-regulatory divergences differ significantly in patterns of genetic architecture and evolution. The effects ofcis-regulatory divergence are approximately additive in heterozygotes, quantitatively different between males and females, and well predicted by expression differences between the two parental species. In contrast, the effects oftrans-regulatory divergence are associated with largely dominant introgressed alleles, have similar effects in the two sexes, and generate expression levels in hybrids outside the range of expression in both parental species. Although the effects of introgressedtrans-regulatory alleles are similar in males and females, expression levels of the genes they regulate are sexually dimorphic between the parentalD. simulansandD. mauritianastrains, suggesting that pure-species genotypes carry unlinked modifier alleles that increase sexual dimorphism in expression. Our results suggest that independent effects ofcis-regulatory substitutions in males and females may favor their role in the evolution of sexually dimorphic phenotypes, and thattrans-regulatory divergence is an important source of regulatory incompatibilities.
TED, an Autonomous and Rare Maize Transposon of theMutatorSuperfamily with a High Gametophytic Excision Frequency
Authors: Li Yubin , Harris Linda , Dooner Hugo K.
Published: September 2013

Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.
Residual stress analysis of diamond-coated WC–Co cutting tools: separation of film and substrate information by grazing X-ray diffraction
Authors: Meixner M. , Klaus M. , Genzel Ch. , Reimers W.
Published: September 2013

Chemical vapour deposition (CVD) of diamond surface layers is an effective way of improving the properties of cemented carbide cutting tools. Inadequate coating adhesion is one of the main issues and it may be affected by the residual stresses of the CVD diamond films. The most common methods for nondestructive residual stress analysis are based on X-ray diffraction. The present paper deals with the particular case of determining the residual stress state of thin CVD diamond layers deposited on cobalt cemented tungsten carbide (WC–Co) substrates. It will be shown that the application of the conventional sin2ψ method might lead to erroneous results, as a result of superimposing diffraction lines originating from cobalt and the diamond coating. An approach to separating information on the substrate and film, based on grazing conditions in the symmetrical Ψ mode of diffraction, is presented. The results, revealing large compressive stresses within the coating, are compared with those obtained by supplementary micro-Raman spectroscopy investigations.
Fourier crystal diffractometry based on refractive optics
Authors: Ershov Petr , Kuznetsov Sergey , Snigireva Irina , Yunkin Vyacheslav , Goikhman Alexander , Snigirev Anatoly
Published: September 2013

X-ray refractive lenses are proposed as a Fourier transformer for high-resolution X-ray crystal diffraction. By employing refractive lenses the wave transmitted through the object converts into a spatial intensity distribution at its back focal plane according to the Fourier-transform relations. A theoretical consideration of the Fourier-transform technique is presented. Two types of samples were studied in Bragg reflection geometry: a grating made of strips of a thin SiO2film on an Si substrate and a grating made by profiling an Si crystal. Fourier patterns recorded at different angles along the rocking curves of the Si 111 Bragg reflection were analysed.
Study of the internal structure of polymer micelles by anomalous small-angle X-ray scattering at two edges
Authors: Sakou Megumi , Takechi Atsuro , Murakami Shin-ichi , Sakurai Kazuo , Akiba Isamu
Published: September 2013

Anomalous small-angle X-ray scattering with two marker elements was applied to the structural analysis of poly(4-vinylphenol rubidium salt)-block-poly(4-bromostyrene) (RbPVPh-b-PBrS) micelles, where Br and Rb were the markers for the hydrophobic core and the hydrated corona, respectively. By using two different markers for the hydrophobic core and the hydrated corona, the form factors of the core and corona were extracted separately from the scattering profile of the whole RbPVPh-b-PBrS micelles. The form factor of the hydrophobic core (the spatial distribution of Br) revealed that the core was regarded as a solid sphere with a smooth surface and a radius of 47 nm. Conversely, the form factor of the spatial distribution of Rb+indicated that the shell of the RbPVPh-b-PBrS micelles was 15 nm thick.
Topsoil removal improves various restoration treatments of a Mediterranean steppe (La Crau, southeast France)
Authors: Jaunatre Renaud , Buisson Elise , Dutoit Thierry
Published: September 2013

Question

Can topsoil removal improve restoration efficiency of several ecological engineering techniques (nurse species seeding, hay transfer and soil transfer) for restoring a Mediterranean steppe, species‐rich plant community?

Location

La Crau area, southeast France (Provence).

Methods

After the rehabilitation of a 357‐ha herbaceous, sheep‐grazed rangeland suitable for threatened steppe birds in a formerly abandoned industrial orchard in the last French Mediterranean steppe (La Crau area), four experimental treatments were applied, with or without topsoil removal. Topsoil was removed on a 5000‐m² area and the four treatments (control, nurse species seeding, hay transfer and soil transfer) were applied within this area where topsoil was removed and within the area where topsoil was not removed. Three years later, soil chemistry, soil seed bank, vegetation cover and height, plant species richness, composition and diversity were compared.

Results

Removing topsoil partly restored soil conditions and significantly reduced the non‐target seed bank. Moreover, species richness and similarity to the reference steppe was significantly increased with topsoil removal. Topsoil removal, combined with soil transfer and hay transfer, created a community that most closely resembled the reference during the study period.

Conclusion

In order to restore plant community composition, topsoil removal is a relevant method to increase the efficiency of other ecological restoration techniques, especially those that strengthen dispersal processes.
Serious Hazards of Transfusion (SHOT) haemovigilance and progress is improving transfusion safety
Authors: Bolton‐Maggs Paula H. B. , Cohen Hannah
Published: September 2013

The Serious Hazards of Transfusion (SHOT) UK confidential haemovigilance reporting scheme began in 1996. Over the 16 years of reporting, the evidence gathered has prompted changes in transfusion practice from the selection and management of donors to changes in hospital practice, particularly better education and training. However, half or more reports relate to errors in the transfusion process despite the introduction of several measures to improve practice. Transfusion in the UK is very safe: 2·9 million components were issued in 2012, and very few deaths are related to transfusion. The risk of death from transfusion as estimated from SHOT data in 2012 is 1 in 322 580 components issued and for major morbidity, 1 in 21 413 components issued; the risk of transfusion‐transmitted infection is much lower. Acute transfusion reactions and transfusion‐associated circulatory overload carry the highest risk for morbidity and death. The high rate of participation in SHOT by National Health Service organizations, 99·5%, is encouraging. Despite the very useful information gained about transfusion reactions, the main risks remain human factors. The recommendations on reduction of errors through a ‘back to basics’ approach from the first annual SHOT report remain absolutely relevant today.
Non‐irradiated female survivors of childhood acute lymphoblastic leukaemia are at risk of long‐term increases in weight and body mass index
Authors: Harper Robert L. C. , Breene Richard A. L. , Gattens Michael , Williams Rachel M. , Murray Matthew J.
Published: September 2013

We report long‐term, including final height, auxological data from our retrospective study of non‐irradiated survivors of childhood acute lymphoblastic leukaemia (ALL). Body mass index (BMI) standard deviation score (SDS) increases in females, due to increased weight‐SDS, persisted to final height, with probable adverse long‐term health outcomes. In contrast, males demonstrated increased BMI‐SDS in follow‐up, due to reduced height‐SDS, not increased weight‐SDS, but such changes had resolved by final height. Childhood ALL survivors, particularly females, are therefore at potential increased risk of developing the metabolic syndrome during follow‐up. We recommend that strategies to minimize weight gain should be implemented during ALL treatment.
We Make the Road by Walking: Challenging Conceptualisations of Leisure Time for Children in Poverty
Authors: Roets Griet , Cardoen Dries , Bouverne‐De Bie Maria , Roose Rudi
Published: September 2013

In this article, we discuss a research project focusing on the ways in which children in poverty spend and experience their leisure time. We argue that the dominant conceptualisation of leisure time participation reduces poverty to a lack of social and cultural capital, marginalising poor children as passive objects of socialisation. Inspired by the interpretative paradigm of lifeworld orientation, three insights are identified throughout poor children's experiences, which include the following: (i) challenging taken‐for‐granted divisions of time; (ii) giving meaning to regimes of time as an ongoing learning process; and (iii) imagining a socially just future.
Temperatures and the growth and development of maize and rice: a review
Authors: Sánchez Berta , Rasmussen Anton , Porter John R
Published: September 2013

Because of global land surface warming, extreme temperature events are expected to occur more often and more intensely, affecting the growth and development of the major cereal crops in several ways, thus affecting the production component of food security. In this study, we have identified rice and maize crop responses to temperature in different, but consistent, phenological phases and development stages. A literature review and data compilation of around 140 scientific articles have determined the key temperature thresholds and response to extreme temperature effects for rice and maize, complementing an earlier study on wheat. Lethal temperatures and cardinal temperatures, together with error estimates, have been identified for phenological phases and development stages. Following the methodology of previous work, we have collected and statistically analysed temperature thresholds of the three crops for the key physiological processes such as leaf initiation, shoot growth and root growth and for the most susceptible phenological phases such as sowing to emergence, anthesis and grain filling. Our summary shows that cardinal temperatures are conservative between studies and are seemingly well defined in all three crops. Anthesis and ripening are the most sensitive temperature stages in rice as well as in wheat and maize. We call for further experimental studies of the effects of transgressing threshold temperatures so such responses can be included into crop impact and adaptation models.