bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum Theory on Genome Evolution
Authors: Luo LiaoFu
Published: December 2015

A model of genome evolution is proposed. Based on several general assumptions the evolutionary theory of a genome is formulated. Both the deterministic classical equation and the stochastic quantum equation are proposed. The classical equation is written in a form of of second-order differential equations on nucleotide frequencies varying in time. It is proved that the evolutionary equation can be put in a form of the least action principle and the latter can be used for obtaining the quantum generalization of the evolutionary law. The wave equation and uncertainty relation for the quantum evolution are deduced logically. Two fundamental constants of time dimension, the quantization constant and the evolutionary inertia, are introduced for characterizing the genome evolution. During speciation the large-scale rapid change of nucleotide frequency makes the evolutionary inertia of the dynamical variables of the genome largely decreasing or losing. That leads to the occurrence of quantum phase of the evolution. The observed smooth/sudden evolution is interpreted by the alternating occurrence of the classical and quantum phases. In this theory the probability of new-species formation is calculable from the first-principle. To deep the discussions we consider avian genome evolution as an example. More concrete forms on the assumed potential in fundamental equations, namely the diversity and the environmental potential, are introduced. Through the numerical calculations we found that the existing experimental data on avian macroevolution are consistent with our theory. Particularly, the law of the rapid post-Cretaceous radiation of neoavian birds can be understood in the quantum theory. Finally, the present work shows the quantum law may be more general than thought, since it plays key roles not only in atomic physics, but also in genome evolution.
Inferring protein-protein interaction networks from inter-protein sequence co-evolution
Authors: Feinauer Christoph , Szurmant Hendrik , Weigt Martin , Pagnani Andrea
Published: December 2015

Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on theDirect-Coupling Analysisof the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data.
SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
Authors: Chun Sang Y. , Rodriguez Caitlin M. , Todd Peter K. , Mills Ryan E.
Published: December 2015

Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Existing analytical approaches applied to this technology make use of sequence fragment length or frame occupancy to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy. Here, we present an analytical tool that models the overall tri-nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Our software, SPECtre, examines the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript against an idealized reference signal. A comparison of SPECtre against current methods on existing and new data shows a marked improvement in accuracy for detecting active translation and exhibits overall high sensitivity at a low false discovery rate.

Availability and Implementation:

SPECtre source code is available for download athttps://github.com/mills-lab/spectre.

Contact:remills@med.umich.edu
Worldwide patterns of genomic variation and admixture in gray wolves
Authors: Fan Zhenxin , Silva Pedro , Gronau Ilan , Wang Shuoguo , Armero Aitor Serres , Schweizer Rena M. , Ramirez Oscar , Pollinger John , Galaverni Marco , Ortega Del-Vecchyo Diego , Du Lianming , Zhang Wenping , Zhang Zhihe , Xing Jinchuan , Vilà Carles , Marques-Bonet Tomas , Godinho Raquel , Yue Bisong , Wayne Robert K.
Published: December 2015

The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter–gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.
The dangerous new synthetic drug α-PVP as the hydrated chloride salt α-pyrrolidinopentiophenone hydrochloride 0.786-hydrate
Authors: Wood Matthew R. , Bernal Ivan , Lalancette Roger A.
Published: December 2015

α-Pyrrolidinovalerophenone (α-PVP), a dangerous designer drug, is now being marketed around the world as a harmless `bath salt', when in reality it is a powerful β-ketone phenethylamine stimulant. A sample of the free base from a recent law-enforcement seizure was crystallized as the HCl salt [systematic name: 1-(1-oxo-1-phenylpentan-2-yl)pyrrolidin-1-ium chloride 0.786-hydrate], C15H22NO+·Cl−·0.786H2O. In the crystal structure, the propyl chain is nearly perpendicular to both the phenyl ring and the carbonyl group. The hydrogen-bonding scheme involves the quaternary N atom, the Cl−anion and the partially occupied (0.786) water molecule, forming centrosymmetric dimers.
Crystal structure of dichloridobis(dimethylN-cyanodithioiminocarbonate)cobalt(II)
Authors: Diop Mouhamadou Birame , Diop Libasse , Oliver Allen G.
Published: December 2015

The structure of the mononuclear title complex, [{(H3CS)2C=NC[triple-bond] N}2CoCl2], consists of a CoIIatom coordinated in a distorted tetrahedral manner by two Cl−ligands and the terminalNatoms of two dimethylN-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6)° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515(su?)Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.
Crystal structure of K0.75[FeII3.75FeIII1.25(HPO3)6]·0.5H2O, an open-framework iron phosphite with mixed-valent FeII/FeIIIions
Authors: Larrea Edurne S. , Mesa José Luis , Legarra Estibaliz , Aguayo Andrés Tomás , Arriortua Maria Isabel
Published: December 2015

Single crystals of the title compound, potassium hexaphosphitopentaferrate(II,III) hemihydrate, K0.75[FeII3.75FeIII1.25(HPO3)6]·0.5H2O, were grown under mild hydrothermal conditions. The crystal structure is isotypic with Li1.43[FeII4.43FeIII0.57(HPO3)6]·1.5H2O and (NH4)2[FeII5(HPO3)6] and exhibits a [FeII3.75FeIII1.25(HPO3)6]0.75−open framework with disordered K+(occupancy 3/4) as counter-cations. The anionic framework is based on (001) sheets of two [FeO6] octahedra (one with point group symmetry 3.. and one with point group symmetry .2.) linked along [001] through [HPO3]2−oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octahedra, giving rise to channels with a radius ofca3.1 Å where the K+cations and likewise disordered water molecules (occupancy 1/4) are located. O...O contacts between the water molecule and framework O atoms of 2.864 (5) Å indicate hydrogen-bonding interactions of medium strength. The infrared spectrum of the compound shows vibrational bands typical for phosphite and water groups. The Mössbauer spectrum is in accordance with the presence of FeIIand FeIIIions.
Crystal structure of 4,6-dichloro-5-methylpyrimidine
Authors: Medjani Meriem , Hamdouni Noudjoud , Brihi Ouarda , Boudjada Ali , Meinnel Jean
Published: December 2015

The title compound, C5H4Cl2N2, is essentially planar with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for an N atom. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers, enclosing anR22(6) ring motif.
Crystal structure of [bis(2-aminoethyl-κN)(2-{[4-(trifluoromethyl)benzylidene]amino}ethyl)amine-κN]dichloridocopper(II)
Authors: Bussey Katherine A. , Cavalier Annie R. , Mraz Margaret E. , Holderread Ashley S. , Oshin Kayode D. , Oliver Allen G. , Zeller Matthias
Published: December 2015

The CuIIatom in the title compound, [CuCl2(C14H21F3N4)], adopts a coordination geometry that is between distorted square-based pyramidal and very Jahn–Teller-elongated octahedral. It is coordinated by three N atoms from the bis(2-aminoethyl)(2-{[4-(trifluoromethyl)benzylidene]amino}ethyl)amine and two chloride ligands. The two crystallographically unique copper complexes present in the asymmetric unit exhibit noticeable differences in the coordination bond lengths. Considering the CuIIatoms as having square-pyramidal geometry, the basal Cu—Cl bond lengths are typical [2.2701 (12) and 2.2777 (12) Å], while the apical distances are considerably elongated [2.8505 (12) and 2.9415 (12) Å]. For each molecule, a CuIIatom from inversion-related molecules are in nearby proximity to the remaining axial CuIIsites, but the Cu...Cl distances are very long [3.4056 (12) and 3.1645 (12) Å], attributable to van der Waals contacts. Nonetheless, these contacts appear to have some structure-directing properties, leading to association into dimers. These dimers associateviastacking of the aromatic rings to form extended zigzag chains.
Bacillus licheniformistrehalose-6-phosphate hydrolase structures suggest keys to substrate specificity
Authors: Lin Min-Guan , Chi Meng-Chun , Naveen Vankadari , Li Yi-Ching , Lin Long-Liu , Hsiao Chwan-Deng
Published: December 2015

Trehalose-6-phosphate hydrolase (TreA) belongs to glycoside hydrolase family 13 (GH13) and catalyzes the hydrolysis of trehalose 6-phosphate (T6P) to yield glucose and glucose 6-phosphate. The products of this reaction can be further metabolized by the energy-generating glycolytic pathway. Here, crystal structures ofBacillus licheniformisTreA (BlTreA) and its R201Q mutant complexed withp-nitrophenyl-α-D-glucopyranoside (R201Q–pPNG) are presented at 2.0 and 2.05 Å resolution, respectively. The overall structure ofBlTreA is similar to those of other GH13 family enzymes. However, detailed structural comparisons revealed that the catalytic site ofBlTreA contains a long loop that adopts a different conformation from those of other GH13 family members. Unlike the homologous regions ofBacillus cereusoligo-1,6-glucosidase (BcOgl) andErwinia rhaponticiisomaltulose synthase (NX-5), the surface potential of theBlTreA active site exhibits a largely positive charge contributed by the four basic residues His281, His282, Lys284 and Lys292. Mutation of these residues resulted in significant decreases in the enzymatic activity ofBlTreA. Strikingly, the281HHLK284motif and Lys292 play critical roles in substrate discrimination byBlTreA.
In meso in situserial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Authors: Huang Chia-Ying , Olieric Vincent , Ma Pikyee , Howe Nicole , Vogeley Lutz , Liu Xiangyu , Warshamanage Rangana , Weinert Tobias , Panepucci Ezequiel , Kobilka Brian , Diederichs Kay , Wang Meitian , Caffrey Martin
Published: December 2015

Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase forin situdiffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase orin mesomethod of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introducedin meso in situserial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, α-helical and β-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.
Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study
Authors: Dippel Andrew B. , Olenginski Gregory M. , Maurici Nicole , Liskov Melanie T. , Brewer Scott H. , Phillips-Piro Christine M.
Published: December 2015

The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolution and permit a direct correlation between the structure and spectroscopic data to be made. The structural implications were quantified by comparing the root-mean-square deviation (r.m.s.d.) between the crystal structure of wild-type sfGFP and the protein constructs containing either pCNF or pCCF in the local environment around the UAAs and in the overall protein structure. The results suggest that the selective placement of these spectroscopic reporter UAAs permits local protein environments to be studied in a relatively nonperturbative fashion with site-specificity.
Exchange Rate Dynamics and the Skill Structure of Labor Demand in Tunisian Manufacturing Industries
Authors: Zmami Mourad , Ben‐Salha Ousama
Published: December 2015

This paper provides empirical evidence on the effects of exchange rates movements on the demand for labor by skill in Tunisia. Using a panel of manufacturing industries from 1990 to 2010, findings suggest that only the demand for skilled labor positively responds to effective exchange rates depreciation. When the focus is shifted to bilateral exchange rates, it is shown that contrary to the USD/TND exchange rate, the EUR/TND exchange rate significantly affects the demand for the skilled labor force. The disaggregation of industries according to the technological intensity reveals that the effects of exchange rates on the demand for skilled labor are more important in medium‐high technology industries than in low technology industries. On the contrary, the effects on the demand for unskilled labor remain not significant in the two categories of industries.
What Drives Foreign Direct Investment in Africa? An Empirical Investigation with Panel Data
Authors: Mijiyawa Abdoul’ Ganiou
Published: December 2015

This paper analyzes factors that drive foreign direct investment (FDI) in Africa. To do so, for the first time in the literature, the paper uses 5‐year panel data and the system‐GMM technique over the period 1970–2009. The main results are as follows: (a) larger countries attract more FDI; (b) regardless of their size, however, more open countries, politically stable countries, and countries offering higher return to investment also attract FDI; (c) FDI inflows are persistent in Africa. This suggests that countries that manage to attract FDI today are likely to attract more FDI in the future.
Private Capital Flows and Economic Growth of Sub‐Saharan African Countries
Authors: Alley Ibrahim
Published: December 2015

In theory, private capital flows (PCF) augment domestic capital for economic growth. In sub‐Saharan African (SSA) economies, foreign direct investment per capita (FDIC), portfolio investment per capita (PIC) and bank lending per capita (BLC) components of PCF grew inversely to gross domestic product per capita (GDPC). Previous studies have attributed this problem largely to recipient economies' structural features, with little attention paid to PCF shocks (sharp fluctuations from the equilibrium path). Employing annual data on 14 SSA countries from 1990 to 2013, this study estimated a neoclassical growth model to evaluate the effects of PCF shocks on the SSA countries' economic output and growth. The results showed that private capital flows positively affected economic output and growth, as hypothesized in theory. The effects of PCF shocks were negative, however, and are thus culpable for poor response of the region's economic performance to inflows of private capital.
Applying Statistical Causal Analyses to Agricultural Conservation: A Case Study Examining P Loss Impacts
Authors: Qian Song S. , Harmel R. Daren
Published: December 2015

Estimating the effect of agricultural conservation practices on reducing nutrient loss using observational data can be confounded by factors such as differing crop types and management practices. As we may not have the full knowledge of these confounding factors, conventional statistical meta‐analysis methods can be misleading. We discuss the use of two statistical causal analysis methods for quantifying the effects of water and soil conservation practices in reducing P loss from agricultural fields. With the propensity score method, a subset of data was used to form a treatment group and a control group with similar distributions of confounding factors. With the multilevel modeling method, data were stratified based on important confounding factors, and the conservation practice effect was evaluated for each stratum. Both methods resulted in similar estimates of the conservation practice effect (total P load reduction avg. ~70%). In addition, both methods show evidence of conservation practices reducing the incremental increase in total P export per unit increase in fertilizer application. These results are presented as examples of the types of outcomes provided by statistical causal analyses, not to provide definitive estimates of P loss reduction. The enhanced meta‐analysis methods presented within are applicable for improved assessment of agricultural practices and their effects and can be used for providing realistic parameter values for watershed‐scale modeling.
Noel Pearson's Role in the Northern Territory Intervention: Radical Centrist or Polarising Partisan?
Authors: Curchin Katherine
Published: December 2015

Noel Pearson is one of Australia's most prominent and influential Aboriginal intellectuals. This article examines a major idea in his writing: the “quest for a radical centre”. Through the concept of the radical centre, Pearson articulates both his desire to transcend existing policy paradigms and an ethics of partisanship which emphasizes the importance of listening to and negotiating with one's political adversaries. Pearson's development of this concept is explored in light of the role Pearson has played as leading advocate for Indigenous welfare reform, and especially his pivotal contribution to the public debate over the introduction of the Northern Territory Emergency Response Intervention by the Howard government in 2007.
Effect of the acute general surgical unit: a regional perspective
Authors: Pritchard Natasha , Newbold Ryan , Robinson Kerian , Ooi Wei Ming
Published: December 2015

Background

Acute surgical units have gained favour in Australia and New Zealand. However, there is a lack of evidence regarding their effectiveness in regional centres. We aim to investigate the effect of the introduction of the Acute General Surgical Unit (AGSU) on the outcomes for patients undergoing emergency appendicectomies or cholecystectomies in a regional hospital.

Methods

AGSU was introduced in March 2012. We conducted a retrospective comparison analysis of patients admitted 2 years prior to and 2 years after the introduction of AGSU. Primary outcomes included length of stay, time to theatre, after hours and overnight operating. Secondary outcomes included negative appendicectomy rate, conversion to open cholecystectomy and bile duct injuries.

Results

No difference was seen between pre and post‐AGSU introduction in median time to theatre in the appendicectomy group (8.00 h versus 9.24 h) or cholecystectomy group (17.63 h versus 17.75 h). Additionally, there was no difference between median length of stay in the appendicectomy group (47.52 h versus 48.00 h) or the cholecystectomy group (71.50 h versus 70.67 h). Night operating was significantly reduced in the positive appendicectomy group (4.4% versus 9.1%, P = 0.027) and the overall cholecystectomy group (0.43% versus 3.4%, P = 0.035), however overall after hours operating remained equivalent.

Conclusions

The introduction of the AGSU unit led to a significant reduction in overnight operating, which may improve patient outcomes and surgeon satisfaction. Length of stay and time to theatre did not change. Future directions include further research into the impact of theatre access on emergency surgery outcomes.
Meanings of Intimacy after Obergefell v. Hodges: Reflections on Policy Change and Reply to Commentary
Authors: Frost David M.
Published: December 2015

In this reply to the commentary on Frost and Gola (2015), I address three primary substantive themes raised across the authors’ responses, with particular attention to research on intimacy in same‐sex couples’ lives after the U.S. Supreme Court Decision in Obergefell v. Hodges: (a) the complexities inherent to between‐group comparisons of members of same‐sex and heterosexual couples; (b) the continued relevance of stigma in the relational experiences of same‐sex couples; and (c) the potential role of attachment in same‐sex couples’ experiences of stigma and intimacy.
Combined liver mobilization and retraction: A novel technique to obtain the optimal surgical field during laparoscopic total gastrectomy
Authors: Yoshikawa Kozo , Shimada Mitsuo , Higashijima Jun , Nakao Toshihiro , Nishi Masaaki , Takasu Chie , Kashihara Hideya , Eto Syohei
Published: December 2015

Introduction

During laparoscopic gastrectomy, it is important to establish a good operative field and ensure an adequate working space. The combined liver mobilization and retraction method is used to get a safe and optimal view.

Methods

We retrospectively analyzed 32 consecutive patients who underwent laparoscopic total gastrectomy for gastric cancer. The patients were divided into two groups: the mobilization (+) group (n = 12) and the mobilization (−) group (n = 20). Hepatic function tests were performed in all patients.

Results

Mobilization provided a satisfactory view of the working field, especially the gastroesophageal junction and the angle of His during laparoscopic total gastrectomy, and no complications were observed during liver retraction. On postoperative hepatic function testing, there was no significant difference between the two groups on any day.

Conclusions

Combined liver mobilization and retraction may be helpful in laparoscopic total gastrectomy.
Resveratrol preserves the function of human platelets stored for transfusion
Authors: Lannan Katie L. , Refaai Majed A. , Ture Sara K. , Morrell Craig N. , Blumberg Neil , Phipps Richard P. , Spinelli Sherry L.
Published: December 2015

Stored platelets undergo biochemical, structural and functional changes that lead to decreased efficacy and safety of platelet transfusions. Not only do platelets acquire markers of activation during storage, but they also fail to respond normally to agonists post‐storage. We hypothesized that resveratrol, a cardioprotective antioxidant, could act as a novel platelet storage additive to safely prevent unwanted platelet activation during storage, while simultaneously preserving normal haemostatic function. Human platelets treated with resveratrol and stored for 5 d released less thromboxane B2 and prostaglandin E2 compared to control platelets. Resveratrol preserved the ability of platelets to aggregate, spread and respond to thrombin, suggesting an improved ability to activate post‐storage. Utilizing an in vitro model of transfusion and thromboelastography, clot strength was improved with resveratrol treatment compared to conventionally stored platelets. The mechanism of resveratrol's beneficial actions on stored platelets was partly mediated through decreased platelet apoptosis in storage, resulting in a longer half‐life following transfusion. Lastly, an in vivo mouse model of transfusion demonstrated that stored platelets are prothrombotic and that resveratrol delayed vessel occlusion time to a level similar to transfusion with fresh platelets. We show resveratrol has a dual ability to reduce unwanted platelet activation during storage, while preserving critical haemostatic function.
Livelihoods Limitations: The Political Economy of Urban Poverty in Dhaka, Bangladesh
Authors: Banks Nicola
Published: December 2015

Research in Bangladesh reveals the limitations of actor‐oriented frameworks for understanding urban poverty that assess household livelihoods on the basis of a household's portfolio of assets or capitals. The narrow focus of these frameworks on households and their depoliticized definition of social capital overlook the political roots of urban poverty. The informal systems of governance that dominate resource distribution within low‐income settlements ensure that the social resources necessary for long‐term household improvement are confined to a small elite. Only through extending our analysis beyond the household level, to explore their position within this local political economy of employment and enterprise, can we recognize the limitations placed on household efforts to improve their livelihoods.
Quantifying the erosion effect on current carbon budget of European agricultural soils at high spatial resolution
Authors: Lugato Emanuele , Paustian Keith , Panagos Panos , Jones Arwyn , Borrelli Pasquale
Published: December 2015

The idea of offsetting anthropogenic CO2 emissions by increasing global soil organic carbon (SOC), as recently proposed by French authorities ahead of COP21 in the ‘four per mil’ initiative, is notable. However, a high uncertainty still exits on land C balance components. In particular, the role of erosion in the global C cycle is not totally disentangled, leading to disagreement whether this process induces lands to be a source or sink of CO2. To investigate this issue, we coupled soil erosion into a biogeochemistry model, running at 1 km2 resolution across the agricultural soils of the European Union (EU). Based on data‐driven assumptions, the simulation took into account also soil deposition within grid cells and the potential C export to riverine systems, in a way to be conservative in a mass balance. We estimated that 143 of 187 Mha have C erosion rates <0.05 Mg C ha−1 yr−1, although some hot‐spot areas showed eroded SOC >0.45 Mg C ha−1 yr−1. In comparison with a baseline without erosion, the model suggested an erosion‐induced sink of atmospheric C consistent with previous empirical‐based studies. Integrating all C fluxes for the EU agricultural soils, we estimated a net C loss or gain of −2.28 and +0.79 Tg yr−1 of CO2eq, respectively, depending on the value for the short‐term enhancement of soil C mineralization due to soil disruption and displacement/transport with erosion. We concluded that erosion fluxes were in the same order of current carbon gains from improved management. Even if erosion could potentially induce a sink for atmospheric CO2, strong agricultural policies are needed to prevent or reduce soil erosion, in order to maintain soil health and productivity.
N fertilizer and harvest impacts on bioenergy crop contributions to SOC
Authors: Stewart Catherine E. , Follett Ronald F. , Pruessner Elizabeth G. , Varvel Gary E. , Vogel Kenneth P. , Mitchell Robert B.
Published: December 2015

Belowground root biomass is infrequently measured and simply represented in models that predict landscape‐level changes to soil carbon stocks and greenhouse gas balances. Yet, crop‐specific responses to N fertilizer and harvest treatments are known to impact both plant allocation and tissue chemistry, potentially altering decomposition rates and the direction and magnitude of soil C stock changes and greenhouse gas fluxes. We examined switchgrass (Panicum virgatum L.) and corn (Zea mays L.,) yields, belowground root biomass, C, N and soil particulate organic matter‐C (POM‐C) in a 9‐year rainfed study of N fertilizer rate (0, 60, 120 and 180 kg N ha−1) and harvest management near Mead, NE, USA. Switchgrass was harvested with one pass in either August or postfrost, and for no‐till (NT) corn, either 50% or no stover was removed. Switchgrass had greater belowground root biomass C and N (6.39, 0.10 Mg ha−1) throughout the soil profile compared to NT‐corn (1.30, 0.06 Mg ha−1) and a higher belowground root biomass C:N ratio, indicating greater recalcitrant belowground root biomass C input beneath switchgrass. There was little difference between the two crops in soil POM‐C indicating substantially slower decomposition and incorporation into SOC under switchgrass, despite much greater root C. The highest N rate decreased POM‐C under both NT‐corn and switchgrass, indicating faster decomposition rates with added fertilizer. Residue removal reduced corn belowground root biomass C by 37% and N by 48% and subsequently reduced POM‐C by 22% compared to no‐residue removal. Developing productive bioenergy systems that also conserve the soil resource will require balancing fertilization that maximizes aboveground productivity but potentially reduces SOC sequestration by reducing belowground root biomass and increasing root and soil C decomposition.
Somatosensory temporal discrimination is prolonged during migraine attacks
Authors: Boran H. Evren , Cengiz Bülent , Bolay Hayrunnisa
Published: December 2015

Background and Objective

Symptoms and signs of sensorial disturbances are characteristic features of a migraine headache. Somatosensory temporal discrimination measures the temporal threshold to perceive two separate somaesthetic stimuli as clearly distinct. This study aimed to evaluate somaesthetic perception in migraine patients by measuring the somatosensory temporal discrimination thresholds.

Methods

The study included 12 migraine patients without aura and 12 volunteers without headache. Somatosensory temporal discrimination threshold (STDT) values were measured in the face (V3) and hands (C7) during a lateralized headache attack and the headache‐free interictal period. The disease duration, pain intensity, phonophobia, photophobia, nausea, vomiting, and brush allodynia were also recorded during the migraine attack.

Results

STDT values were within normal limits and not different between the control group and the interictal period in migraine patients. Compared to the headache‐free period, STDT values during the attack were significantly prolonged in the contralateral hand (C7) (155.7 ± 84.2 vs 40.6 ± 16.1 ms [P < .001]), ipsilateral hand (C7) (88.6 ± 51.3 vs 31.4 ± 14.2 ms [P < 0.001]), contralateral face (V3) (65.5 ± 35.4 vs 37.6 ± 22.2 ms [P = .006]) and ipsilateral face (V3) (104.1 ± 44.5 vs 37.5 ± 21.4 ms [P < 0.001]) according to the lateralization of the headache. Ictal STDT values of the contralateral hand and ipsilateral face were significantly increased compared to that of the ipsilateral hand and contralateral face (155.7 ± 84.2 ms vs 88.6 ± 5.1.3 ms [P = .001], 104.1 ± 44.5 ms vs 65.5 ± 35.4 ms [P = 0.001]). No allodynia was detected in the areas that were tested for somatosensory temporal discrimination. The visual analog scale scores were correlated with the somatosensory temporal discrimination thresholds of the contralateral hand (r = 0.602, P = .038), whereas no correlation was detected between the somatosensory temporal discrimination thresholds and disease duration, brush allodynia in the forehead, phonophobia, photophobia, nausea and vomiting.

Conclusion

The study demonstrates for the first time that somatosensory temporal discrimination thresholds are elevated during migraine attacks. A transient disruption of the central processing of somaesthetic stimuli during the lateralized migraine attack may provide additional information to understand the mechanisms of the cognitive and sensory perception impairment associated with migraine headache and may have diagnostic value.
Rituximab for subcutaneous delivery: Clinical management principles from a nursing perspective
Authors: Carlson Julia , Cox Keith , Bedwell Kylie , Ku Mathew
Published: December 2015

Nurses play an integral role in administering treatments to patients with non‐Hodgkin's lymphomas. Intravenous (IV) rituximab was approved by the Australian Therapeutic Goods Administration in 1998, and a novel subcutaneous (SC) formulation was approved in 2014. Fixed‐dose SC rituximab is highly concentrated; co‐formulation with a fully human recombinant vorhyaluronidase alfa enzyme helps overcome the physiological barriers of the SC space, facilitating drug dispersion. Despite a different pharmacokinetic profile to the IV preparation, SC rituximab demonstrates a comparable efficacy/safety profile. Most frequently occurring rituximab‐related adverse events include neutropenia, nausea and constipation, and administration‐related reactions are more frequent with the SC preparation. Compared with IV, SC delivery reduces treatment times and nurse workload, and patients report greater comfort and convenience.

This article sets out nursing considerations for optimal administration of SC rituximab, including premedication, drug handling/preparation, injection technique, after‐care and management of adverse events, particularly administration‐related reactions.
Melatonin: the dawning of a treatment for fibrosis?
Authors: Hu Wei , Ma Zhiqiang , Jiang Shuai , Fan Chongxi , Deng Chao , Yan Xiaolong , Di Shouyin , Lv Jianjun , Reiter Russel J. , Yang Yang
Published: December 2015

Fibrosis is a common occurrence following organ injury and failure. To date, there is no effective treatment for this condition. Melatonin targets numerous molecular pathways, a consequence of its antioxidant and anti‐inflammatory actions that reduce excessive fibrosis. Herein, we review the multiple protective effects of melatonin against fibrosis. There exist four major phases of the fibrogenic response including primary injury to the organ, activation of effector cells, the elaboration of extracellular matrix (ECM) and dynamic deposition. Melatonin regulates each of these phases. Additionally, melatonin reduces fibrosis levels in numerous organs. Melatonin exhibits its anti‐fibrosis effects in heart, liver, lung, kidney, and other organs. In addition, adhesions which occur following surgical procedures are also inhibited by melatonin. The information reviewed here should be significant to understanding the protective role of melatonin against fibrosis, contribute to the design of further experimental studies related to melatonin and the fibrotic response and shed light on a potential treatment for fibrosis.
Supply Chain Psychological Contract Breach: An Experimental Study across National Cultures
Authors: Eckerd Stephanie , Boyer Kenneth K. , Qi Yinan , Eckerd Adam , Hill James A.
Published: December 2015

Supply disruptions are commonplace in today's global supply chain environment. The sheer magnitude of daily transactions makes it inevitable that there will be disruptions, further exacerbated by differences in cultural norms and attitudes that add a layer of complexity to managerial response. In this research, we examine the impact of national culture on individuals' responses to supply disruptions due to psychological contract breach. Using data from controlled experiments conducted with 158 subjects in China and 125 subjects in the U.S., we evaluate changes in decision‐making behaviors and assessments of attitudinal outcomes regarding trust and repurchase intentions. Our results show post‐breach behavioral differences based on national culture, but find that these differences are short‐term in nature. Additionally, cultural differences show up in both of the attitudinal outcomes assessed in this research. Following a psychological contract breach, individuals from the U.S. express less trust in their supply chain partner and less willingness to work with that partner again in the future as compared to individuals from China. Our research suggests that managers and scholars interested in the cultural influences on the response to supply disruption will benefit from further research and understanding focusing on the intersection of psychological contract breach and cultural distance.
Mutation of p53 Gene and Its Correlation with the Clinical Outcome in Dogs with Lymphoma
Authors: Koshino A. , Goto‐Koshino Y. , Setoguchi A. , Ohno K. , Tsujimoto H.
Published: December 2015

Background

p53 plays a key role in the apoptotic event induced by chemotherapeutic agents. Mutation of p53 gene has been observed in various spontaneous tumors in humans and is associated with a poor prognosis. p53 abnormalities have been evaluated in several tumors in dogs; however, the association of p53 gene mutation with clinical outcome in dogs with lymphoma has not been documented.

Hypothesis/Objectives

The aim of this study was to examine p53 mutation in canine lymphoma cells and its association with the clinical outcome.

Animals

Forty‐three dogs with previously untreated high‐grade lymphoma referred to the University of Tokyo were included in this study.

Methods

Prospective cohort study. We examined p53 gene (exon 4–8) mutation in the tumor tissues from 43 dogs with lymphoma using PCR‐SSCP (polymerase chain reaction – single‐strand conformational polymorphism) analysis, followed by nucleotide sequencing of the abnormal bands.

Results

Of the 43 dogs, 7 dogs (16%) had p53 mutation, whereas 36 dogs (84%) were devoid of p53 mutation. Overall response rate after remission induction was significantly lower (33% versus 88%, P = .002) in dogs with lymphomas having p53 mutation than those with lymphomas devoid of p53 mutation. Overall survival time was significantly shorter (67 days versus 264 days, P = .004) in dogs with lymphoma with p53 mutation than those with lymphoma retaining wild‐type p53.

Conclusion and Clinical Importance

Mutations of p53 gene were detected in a proportion of canine lymphoma cells from untreated dogs and can be associated with a poor prognosis.
Chronic granulomatous disease: Clinical, molecular, and therapeutic aspects
Authors: Chiriaco Maria , Salfa Irene , Di Matteo Gigliola , Rossi Paolo , Finocchi Andrea
Published: December 2015

Chronic granulomatous disease (CGD) is a rare primary immunodeficiency caused by defects in the genes encoding any of the NADPH oxidase components responsible for the respiratory burst of phagocytic leukocytes. CGD is a genetically heterogeneous disease with an X‐linked recessive (XR‐CGD) form caused by mutations in the CYBB gene encoding the gp91phox protein, and an autosomal recessive (AR‐CGD) form caused by mutations in the CYBA, NCF1, NCF2, or NCF4 genes encoding p22phox, p47phox, p67phox, and p40phox, respectively. Patients suffering from this disease are susceptible to severe life‐threatening bacterial and fungal infections and excessive inflammation characterized by granuloma formation in any organ, for instance, the gastrointestinal and genitourinary tract. An early diagnosis of and the prompt treatment for these conditions are crucial for an optimal outcome of affected patients. To prevent infections, CGD patients should receive lifelong antibiotics and antifungal prophylaxis. These two measures, as well as newer more effective antimicrobials, have significantly modified the natural history of CGD, resulting in a remarkable change in overall survival, which is now around 90%, reaching well into adulthood. At present, hematopoietic stem cell transplantation (HSCT) is the only definitive treatment that can cure CGD and reverse organ dysfunction. Timing, donor selection, and conditioning regimens remain the key points of this therapy. In recent years, gene therapy (GT) for XR‐CGD has been proposed as an alternative to HSCT for CGD patients without a matched donor. After the failure of the first trials performed with retroviral vectors, some groups have proposed the use of regulated SIN‐lentiviral vectors targeting gp91phox expression in myeloid cells to increase the safety and efficacy of the GT protocols.
Clinical and immunological characteristics of a pediatric population with food protein‐induced enterocolitis syndrome (FPIES) to fish
Authors: González‐Delgado Purificación , Caparrós Esther , Moreno M Victoria , Clemente Fernando , Flores Emilio , Velásquez Laura , Rubio Gonzalo , Fernández Javier
Published: December 2015

Background

Food protein‐induced enterocolitis (FPIES) is an uncommon, non‐IgE‐mediated food allergy that usually debuts in infancy with profuse vomiting, lethargy, and pallor 2–4 h following ingestion of the offending food. Its immune mechanism is not known. We aimed to describe the clinical features and outcome of children with fish‐FPIES as well as to investigate on cellular immune response implicated.

Methods

Prospective and follow‐up clinical study of children with FPIES by fish over a period between 2004 and 2013 was conducted. Measurement in vitro of both cytokine production in peripheral blood mononuclear cells (PBMCs) and expression of HLA‐DR in monocyte‐derived dendritic cells stimulated with fish extracts.

Results

Sixteen children (seven male and nine female) were included, with a mean age of onset at 10 months. Diagnosis was established after a median of 4 reactions. Twelve patients were treated in emergency room, and two were admitted in intensive care. Patch tests were positive in six patients. Skin prick tests (SPTs) and specific IgE to all fish tested were negative. Only three children reached tolerance at a mean age of 4.5 years. Eight children avoided fish because of positive oral food challenge (OFC) after 6 years of age. Other patients have not been challenged because of parent refusal to OFC or a recent diagnosis. TNF‐α was increased in patients, and a significant elevation of the HLA‐DR marker was also observed in these patients vs. control donors.

Conclusions

FPIES caused by fish in many cases presents with severe clinical manifestations. Patch test has poor diagnostic value, and OFC is the gold standard to test tolerance. The cytokine TNF‐α may be implicated in the clinical symptoms. Higher expression of HLA‐DR in dendritic cells has also been detected in our patients.
Convergence in feeling, divergence in physiology: How culture influences the consequences of disgust suppression and amplification among European Americans and Asian Americans
Authors: Soto José A. , Lee Elizabeth A. , Roberts Nicole A.
Published: December 2015

Much empirical work documents the downsides of suppressing emotions. Emerging research points to the need for a more sophisticated and culturally informed approach to understanding the consequences of emotion regulation. To that end, we employed behavioral, self‐report, and psychophysiological measures to examine the consequences of two types of emotion regulation (suppression and amplification) in a sample of 28 Asian Americans and 31 European Americans. Participants were shown a neutral film and then a series of disgust‐eliciting films during which they were asked to regulate their response by suppressing or amplifying their emotional behavior (counterbalanced). Despite self‐reporting equal levels of disgust, European Americans showed greater skin conductance reactivity than Asian Americans in both regulation conditions, but not in response to a neutral film. These findings extend work on divergence in the consequences of emotion regulation across different cultural groups, which could help identify optimal emotion regulation strategies for health and well‐being.