bluuebunny/crossref_metadata_2025 huggingface dataset:
Spin-orbit couplings within the equation-of-motion coupled-cluster framework: Theory, implementation, and benchmark calculations
Authors: Epifanovsky Evgeny , Klein Kerstin , Stopkowicz Stella , Gauss Jürgen , Krylov Anna I.
Published: August 2015

We present a formalism and an implementation for calculating spin-orbit couplings (SOCs) within the EOM-CCSD (equation-of-motion coupled-cluster with single and double substitutions) approach. The following variants of EOM-CCSD are considered: EOM-CCSD for excitation energies (EOM-EE-CCSD), EOM-CCSD with spin-flip (EOM-SF-CCSD), EOM-CCSD for ionization potentials (EOM-IP-CCSD) and electron attachment (EOM-EA-CCSD). We employ a perturbative approach in which the SOCs are computed as matrix elements of the respective part of the Breit-Pauli Hamiltonian using zeroth-order non-relativistic wave functions. We follow the expectation-value approach rather than the response-theory formulation for property calculations. Both the full two-electron treatment and the mean-field approximation (a partial account of the two-electron contributions) have been implemented and benchmarked using several small molecules containing elements up to the fourth row of the periodic table. The benchmark results show the excellent performance of the perturbative treatment and the mean-field approximation. When used with an appropriate basis set, the errors with respect to experiment are below 5% for the considered examples. The findings regarding basis-set requirements are in agreement with previous studies. The impact of different correlation treatment in zeroth-order wave functions is analyzed. Overall, the EOM-IP-CCSD, EOM-EA-CCSD, EOM-EE-CCSD, and EOM-SF-CCSD wave functions yield SOCs that agree well with each other (and with the experimental values when available). Using an EOM-CCSD approach that provides a more balanced description of the target states yields more accurate results.
Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure
Authors: Hoy Erik P. , Mazziotti David A.
Published: August 2015

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.
Rapid, culture-independent, optical diagnostics of centrifugally captured bacteria from urine samples
Authors: Schröder Ulrich-Christian , Bokeloh Frank , O'Sullivan Mary , Glaser Uwe , Wolf Katharina , Pfister Wolfgang , Popp Jürgen , Ducrée Jens , Neugebauer Ute
Published: August 2015

This work presents a polymeric centrifugal microfluidic platform for the rapid and sensitive identification of bacteria directly from urine, thus eliminating time-consuming cultivation steps. This “Lab-on-a-Disc” platform utilizes the rotationally induced centrifugal field to efficiently capture bacteria directly from suspension within a glass-polymer hybrid chip. Once trapped in an array of small V-shaped structures, the bacteria are readily available for spectroscopic characterization, such as Raman spectroscopic fingerprinting, providing valuable information on the characteristics of the captured bacteria. Utilising fluorescence microscopy, quantification of the bacterial load has been achieved for concentrations above 2 × 10−7 cells ml−1 within a 4 μl sample. As a pilot application, we characterize urine samples from patients with urinary tract infections. Following minimal sample preparation, Raman spectra of the bacteria are recorded following centrifugal capture in stopped-flow sedimentation mode. Utilizing advanced analysis algorithms, including extended multiplicative scattering correction, high-quality Raman spectra of different pathogens, such as Escherichia coli or Enterococcus faecalis, are obtained from the analyzed patient samples. The whole procedure, including sample preparation, requires about 1 h to obtain a valuable result, marking a significant reduction in diagnosis time when compared to the 24 h and more typically required for standard microbiological methods. As this cost-efficient centrifugal cartridge can be operated using low-complexity, widely automated instrumentation, while providing valuable bacterial identification in urine samples in a greatly reduced time-period, our opto-microfluidic Lab-on-a-Disc device demonstrates great potential for next-generation patient diagnostics at the of point-of-care.
The influence of MoOx gap states on hole injection from aluminum doped zinc oxide with nanoscale MoOx surface layer anodes for organic light emitting diodes
Authors: Jha Jitendra Kumar , Santos-Ortiz Reinaldo , Du Jincheng , Shepherd Nigel D.
Published: August 2015

The effective workfunction of Al doped ZnO films (AZO) increased from 4.1 eV to 5.55 eV after surface modification with nanoscale molybdenum sub-oxides (MoOx). Hole only devices with anodes consisting of 3 nm of MoOx on AZO exhibited a lower turn-on voltage (1.5 vs 1.8 V), and larger charge injection (190 vs 118 mA/cm2) at the reference voltage, compared to indium tin oxide (ITO). AZO devices with 10 nm of MoOx exhibited the highest workfunction but performed poorly compared to devices with 3 nm of MoOx, or standard ITO. Ultraviolet photoelectron, X-ray photoelectron, and optical spectroscopies indicate that the 3 nm MoOx films are more reduced and farther away from MoO3 stoichiometry than their 10 nm equivalents. The vacancies associated with non-stoichiometry result in donor-like gap states which we assign to partially occupied Mo 4d levels. We propose that Fowler-Nordheim tunneling from these levels is responsible for the reduction in threshold voltage measured in devices with 3 nm of MoOx. A schematic band diagram is proposed. The thicker MoOx layers are more stoichiometric and resistive, and the voltage drop across these layers dominates their electrical performance, leading to an increase in threshold voltage. The results indicate that AZO with MoOx layers of optimal thickness may be potential candidates for anode use in organic light emitting diodes.
Trap states in enhancement-mode double heterostructures AlGaN/GaN high electron mobility transistors with different GaN channel layer thicknesses
Authors: He Yunlong , Li Peixian , Wang Chong , Li Xiangdong , Zhao Shenglei , Mi Minhan , Pei Jiuqing , Zhang Jincheng , Ma Xiaohua , Hao Yue
Published: August 2015

This is the report on trap states in enhancement-mode AlGaN/GaN/AlGaN double heterostructures high electron mobility transistors by fluorine plasma treatment with different GaN channel layer thicknesses. Compared with the thick GaN channel layer sample, the thin one has smaller 2DEG concentration, lower electron mobility, lower saturation current, and lower peak transconductance, but it has a higher threshold voltage of 1.2 V. Deep level transient spectroscopy measurements are used to obtain the accurate capture cross section of trap states. By frequency dependent capacitance and conductance measurements, the trap state density of (1.98–2.56) × 1012 cm−2 eV−1 is located at ET in a range of (0.37–0.44) eV in the thin sample, while the trap state density of (2.3–2.92) × 1012 cm−2 eV−1 is located at ET in a range of (0.33–0.38) eV in the thick one. It indicates that the trap states in the thin sample are deeper than those in the thick one.
Drift velocity versus electric field in ⟨110⟩ Si nanowires: Strong confinement effects
Authors: Li Jing , Mugny Gabriel , Niquet Yann-Michel , Delerue Christophe
Published: August 2015

We have performed atomistic simulations of the phonon-limited high field carrier transport in ⟨110⟩ Si nanowires with small diameter. The carrier drift velocities are obtained from a direct solution of the non-linear Boltzmann transport equation. The relationship between the drift velocity and the electric field considerably depends on the carrier, temperature, and diameter of the nanowires. In particular, the threshold between the linear and non-linear regimes exhibits important variations. The drift velocity reaches a maximum value and then drops. These trends can be related to the effects of quantum confinement on the band structure of the nanowires. We also discuss the impact of the different phonon modes and show that high-energy phonons can, unexpectedly, increase the drift velocity at a high electric field.
Template-free synthesis of Nd0.1Bi0.9FeO3 nanotubes with large inner diameter and wasp-waisted hysteresis loop
Authors: Li X. , Guo F. , Wang S. Y. , Wang X. , Xu X. L. , Gao J. , Liu W. F.
Published: August 2015

One-dimensional (1D) nanotubes of Nd0.1Bi0.9FeO3 (NBFO) with an inner diameter of ∼50 nm were synthesized via sol-gel based electrospinning without template assistant. The phases, morphologies, crystalline structures, and magnetic properties of these 1D nanostructures were characterized by means of X-ray diffraction, scanning electron microscopy, transmission electron microscopy and SQUID, respectively. It was found that the calcination condition plays a crucial role in determining the morphologies and the magnetic properties. Interestingly, these 1D NBFO nanotubes exhibit wasp-waisted magnetic hysteresis with a lower coercivity and larger saturation magnetization, which were prevalent in natural rocks and artificial composite materials. The origin of these wasp-waisted hysteresis loops was discussed.
Time within reproductive season, but not age or inbreeding coefficient, affects seminal and sperm quality in the whooping crane (Grus americana)
Authors: Brown M. E. , Converse S. J. , Chandler J. N. , Crosier A. L. , Lynch W. , Wildt D. E. , Keefer C. L. , Songsasen N.
Published: August 2015

All living whooping cranes (Grus americana) are descended from 16 or fewer birds that remained alive in the early 1940s, a bottleneck that puts the species at potential risk for inbreeding depression. Although AI is commonly used in the management of the captive population of this species, little is known about seminal traits or factors affecting sperm quality in the whooping crane. In the present study, semen samples were collected from 29 adult males (age 3–27 years) during the early (March), mid (April) and late (May) breeding season over 2 consecutive years. The effects of donor age, time within reproductive season and level of inbreeding on seminal characteristics were analysed using regression and information–theoretic model selection. Only time within reproductive season significantly affected seminal traits, with total numbers of spermatozoa and proportions of pleiomorphisms increasing across the season. We conclude that, even with a highly restricted number of founders, there is no discernible influence of inbreeding (at the levels described) on sperm output or quality. Furthermore, although there is variance in seminal quality, the whooping crane produces significant numbers of motile spermatozoa throughout the breeding season, similar to values reported for the greater sandhill crane (Grus canadensis tabida).
Evolution of Dissipative Anisotropic Expansion-Free Axial Fluids
Authors: Sharif M. , Nasir Zunaira
Published: August 2015

A general study of non-static restricted class of axial system with anisotropic dissipative expansion-free fluid under geodesic condition is carried out. It is found that expansion-free model must be dissipative under geodesic condition to preserve axial symmetry. We also investigate this system without geodesic condition. Finally, the role of dissipation is explored via transport equation.
New Agegraphic Pilgrim Dark Energy in f(T, TG
) Gravity
Authors: Jawad Abdul , Debnath Ujjal
Published: August 2015

In this work, we briefly discuss a novel class of modified gravity like f(T, TG) gravity. In this background, we assume the new agegraphic version of pilgrim dark energy and reconstruct f(T, TG) models for two specific values of s. We also discuss the equation of state parameter, squared speed of sound and wDE-w′DE plane for these reconstructed f(T, TG) models. The equation of state parameter provides phantom-like behavior of the universe. The wDE-w′DE plane also corresponds to ΛCDM limit, thawing and freezing regions for both models.
The Analytical Parametrization of Fusion Barrier by Using the Skyrme Energy-Density Function Model
Authors: Zanganeh V. , Mirzaei M. , Wang N.
Published: August 2015

Using the skyrme energy density formalism, a pocket formula is introduced for barrier heights and positions of 95 fusion reactions (48 ≤ ZP ZT ≤ 1520) with respect to the charge and mass numbers of the interacting nuclei. It is shown that the parameterized values of RB and VB are able to reproduce the corresponding experimental data with good accuracy. Moreover, the absolute errors of our formulas are less than those obtained using the analytical parametrization forms of the fusion barrier based on the proximity versions. The ability of the parameterized forms of the barrier heights and its positions to reproduce the experimental data of the fusion cross section have been analyzed using the Wong model.
Hopf Bifurcation in a New Four-Dimensional Hyperchaotic System*
Authors: Li Xin , Yan Zhen-Ya
Published: August 2015

In this paper, the Hopf bifurcation in a new hyperchaotic system is studied. Based on the first Lyapunov coefficient theory and symbolic computation, the conditions of supercritical and subcritical bifurcation in the new hyperchaotic system are obtained. Numerical simulations are used to illustrate some main results.
Structural, Elastic, and Electronic Properties of a New Phase of Carbon*
Authors: Xing Meng-Jiang , Li Bin-Hua , Yu Zheng-Tao , Chen Qi
Published: August 2015

Based on density function theory with the ultrasoft pseudopotential scheme in the frame of the local density approximation and the generalized gradient approximation, the structural, elastic, and electronic properties of carbon with P2221 phase have been systematically studied in this paper. The calculated results show that the P2221 phase of carbon is mechanically stable and dynamically stable at ambient pressure. The anisotropy studies of Young's modulus, Poisson's ratio, shear anisotropic factor, the percentage of elastic anisotropy for bulk modulus, the percentage of elastic anisotropy for shear modulus and the universal anisotropic index show that P2221 phase of carbon exhibits anisotropy. In addition, P2221 phase is an indirect semiconductor with bandgap of 3.423 eV. But, the band gap of P2221 phase for carbon increase with increasing pressure.
Structural and Optical Properties of Point Defects in α-SiO2 Cluster*
Authors: Liu Meng , Lu Peng-Fei , Yang Yang , Wu Li-Yuan , Su Rui , Chen Jun
Published: August 2015

First-principles methods based on the density functional theory (DFT) are used in order to calculate the structural and optical properties of α-SiO2 cluster with the non-bridging oxygen hole centers (NBOHC) and NBOHC-E' defects. We clarify the stable structure of the NBOHC-E' point defects for the first time using the functional B3LYP, which is also tested to investigate the influence of electronic properties. The calculation is carried out for cluster configurations extracted from supercell. The results of optical absorption peak for Si2O7H6 and Si5O16H12 with NBOHC-E' defects are found at 2.66 eV, which is higher than the often observed OA peak at 2.0 eV for the NBOHC defect in α-SiO2. The overall absorption spectra are in qualitative agreement with the experiment.
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments
Authors: Kosugi Shunichi , Hirakawa Hideki , Tabata Satoshi
Published: August 2015

Motivation: Genome assemblies generated with next-generation sequencing (NGS) reads usually contain a number of gaps. Several tools have recently been developed to close the gaps in these assemblies with NGS reads. Although these gap-closing tools efficiently close the gaps, they entail a high rate of misassembly at gap-closing sites.

Results: We have found that the assembly error rates caused by these tools are 20–500-fold higher than the rate of errors introduced into contigs by de novo assemblers. We here describe GMcloser, a tool that accurately closes these gaps with a preassembled contig set or a long read set (i.e. error-corrected PacBio reads). GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency.

Availability and implementation: GMcloser and an accompanying tool (GMvalue) for evaluating the assembly and correcting misassemblies except SNPs and short indels in the assembly are available at https://sourceforge.net/projects/gmcloser/.

Contact: shunichi.kosugi@riken.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
A global synthesis of survival estimates for microbats
Authors: Lentini Pia E. , Bird Tomas J. , Griffiths Stephen R. , Godinho Lisa N. , Wintle Brendan A.
Published: August 2015

Accurate survival estimates are needed to construct robust population models, which are a powerful tool for understanding and predicting the fates of species under scenarios of environmental change. Microbats make up 17% of the global mammalian fauna, yet the processes that drive differences in demographics between species are poorly understood. We collected survival estimates for 44 microbat species from the literature and constructed a model to determine the effects of reproductive, feeding and demographic traits on survival. Our trait-based model indicated that bat species which produce more young per year exhibit lower apparent annual survival, as do males and juveniles compared with females and adults, respectively. Using 8 years of monitoring data for two Australian species, we demonstrate how knowledge about the effect of traits on survival can be incorporated into Bayesian survival analyses. This approach can be applied to any group and is not restricted to bats or even mammals. The incorporation of informative priors based on traits can allow for more timely construction of population models to support management decisions and actions.
The extended evolutionary synthesis: its structure, assumptions and predictions
Authors: Laland Kevin N. , Uller Tobias , Feldman Marcus W. , Sterelny Kim , Müller Gerd B. , Moczek Armin , Jablonka Eva , Odling-Smee John
Published: August 2015

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
Constraining the role of early land plants in Palaeozoic weathering and global cooling
Authors: Quirk Joe , Leake Jonathan R. , Johnson David A. , Taylor Lyla L. , Saccone Loredana , Beerling David J.
Published: August 2015

How the colonization of terrestrial environments by early land plants over 400 Ma influenced rock weathering, the biogeochemical cycling of carbon and phosphorus, and climate in the Palaeozoic is uncertain. Here we show experimentally that mineral weathering by liverworts—an extant lineage of early land plants—partnering arbuscular mycorrhizal (AM) fungi, like those in 410 Ma-old early land plant fossils, amplified calcium weathering from basalt grains threefold to sevenfold, relative to plant-free controls. Phosphate weathering by mycorrhizal liverworts was amplified 9–13-fold over plant-free controls, compared with fivefold to sevenfold amplification by liverworts lacking fungal symbionts. Etching and trenching of phyllosilicate minerals increased with AM fungal network size and atmospheric CO
2
concentration. Integration of grain-scale weathering rates over the depths of liverwort rhizoids and mycelia (0.1 m), or tree roots and mycelia (0.75 m), indicate early land plants with shallow anchorage systems were probably at least 10-fold less effective at enhancing the total weathering flux than later-evolving trees. This work challenges the suggestion that early land plants significantly enhanced total weathering and land-to-ocean fluxes of calcium and phosphorus, which have been proposed as a trigger for transient dramatic atmospheric CO
2
sequestration and glaciations in the Ordovician.
The solid-state emmissive chalcone (2E)-1-(5-chlorothiophen-2-yl)-3-[4-(dimethylamino)phenyl]prop-2-en-1-one
Authors: Rodríguez-Lugo Rafael E. , Urdaneta Neudo , Pribanic Bruno , Landaeta Vanessa R.
Published: August 2015

Orange rectangular blocks suitable for X-ray diffraction analysis were obtained for the previously reported [Ahmad & Bano (2011).Int. J. ChemTech Res.3, 1470–1478] title chalcone, C15H14ClNOS. This solid-emissive chalcone exhibits a planar structure and the bond parameters are compared with related compounds already described in the literature. The determination of the structure of this chalcone is quite relevant because it will play an important role in theoretical calculations to investigate potential two-photon absorption processes and could also be useful for studying the interaction of such compounds with a biological target.
Crystal structure of dibromidobis(1,3-dibenzyl-1,3-diazinan-2-one-κO)cobalt(II)
Authors: Rais Eduard , Flörke Ulrich , Wilhelm René
Published: August 2015

The unit cell of the title complex, [CoBr2(C18H20N2O)2], contains 1.5 formula units per asymmetric unit with one molecule sitting on a general site and a second one halved by a crystallographic twofold rotation axis passing through the CoIIcation. Both CoIIatoms are coordinated in a distorted tetrahedral manner by two Br−ligands and two O atoms of the pyrimidinone (OPyr) groups. The Br—Co—Br coordination angles are similar [115.46 (4) and 115.20 (5)°], while the O—Co—O angles differ slightly more [102.26 (18) and 98.1 (2)°]. Similarly, the Co—Br bond lengths are almost identical [2.3721 (9), 2.3757 (10) and 2.3809 (10) Å], with a larger difference between the Co—O bond lengths [1.929 (4), 1.926 (4) and 1.955 (4) Å]. The three independent OPyr groups present envelope conformations, with three C and two N atoms lying in well defined planes with maximum deviations from the least-squares planes of 0.047, 0.031 and 0.036 Å, and the external-most C atoms protruding by 0.654 (6), 0.643 (7) and 0.656 (6) Å out of the planes. The dihedral angles between the planar fractions of the OPyr planes are 50.5 (1)° for the nonsymmetric molecule and 49.7 (1)° for the symmetric one. Non-covalent interactions are of the C—H...Br type and they are weak, hardly shorter than van der Waals radii, with an H...Br distance range of 3.00–3.04 Å. The intermolecular interactions define chains parallel to [101].
Exploring linkage disequilibrium
Authors: Baird Stuart J. E.
Published: August 2015

Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignoreLDat our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 ‘independent witnesses’ of the evolutionary process. If instead, we sample variation at 1000 loci, many areboundto be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that evenLDcreated far in the past will not have dissipated, so wecannottreat the 1000 loci as independent witnesses (Barton). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us aboutLDgenerating events far in the past, for example human/Neanderthal admixture (Fuet al.). With increased marker density, biologists must increase their awareness ofLDand, in this issue of Molecular Ecology Resources, Kemppainenet al. () make software available that can only help in this process:LDna allows patterns ofLDin a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understandingLD.
Guidelines for the Reporting of Treatment Trials for Alcohol Use Disorders
Authors: Witkiewitz Katie , Finney John W. , Harris Alex H. S. , Kivlahan Daniel R. , Kranzler Henry R.
Published: August 2015

Background

The primary goals in conducting clinical trials of treatments for alcohol use disorders (AUDs) are to identify efficacious treatments and determine which treatments are most efficacious for which patients. Accurate reporting of study design features and results is imperative to enable readers of research reports to evaluate to what extent a study has achieved these goals. Guidance on quality of clinical trial reporting has evolved substantially over the past 2 decades, primarily through the publication and widespread adoption of the Consolidated Standards of Reporting Trials statement. However, there is room to improve the adoption of those standards in reporting the design and findings of treatment trials for AUD.

Methods

This paper provides a narrative review of guidance on reporting quality in AUD treatment trials.

Results

Despite improvements in the reporting of results of treatment trials for AUD over the past 2 decades, many published reports provide insufficient information on design or methods.

Conclusions

The reporting of alcohol treatment trial design, analysis, and results requires improvement in 4 primary areas: (i) trial registration, (ii) procedures for recruitment and retention, (iii) procedures for randomization and intervention design considerations, and (iv) statistical methods used to assess treatment efficacy. Improvements in these areas and the adoption of reporting standards by authors, reviewers, and editors are critical to an accurate assessment of the reliability and validity of treatment effects. Continued developments in this area are needed to move AUD treatment research forward via systematic reviews and meta‐analyses that maximize the utility of completed studies.
Habitat‐specific population trajectories in boreal waterbirds: alarming trends and bioindicators for wetlands
Authors: Lehikoinen A. , Rintala J. , Lammi E. , Pöysä H.
Published: August 2015

Identification of conservation priorities is a fundamental issue for successful nature conservation. This can be done by looking at population trends of species in different habitats. Boreal zone is the key breeding area for manyEurasian waterbirds. Wetlands of the boreal zone can be roughly classified into two different groups: nutrient‐poor oligotrophic and nutrient‐rich eutrophic water ecosystems. Earlier work has shown that eutrophic lake‐specialist species have declined compared with generalists and species preferring oligotrophic lakes. However, it is not known if species that live in both habitats show habitat‐specific population trends. We used monitoring data of breeding waterbirds inFinland from 1986 to 2013 to evaluate habitat‐specific population trends in five generalist duck species, which mostly overwinter in the coastal waters of West Europe. Population trend of tufted duck was highly significantly more positive in oligotrophic wetlands compared with populations in eutrophic wetlands, and two other species had similar but weaker effects. In addition, we established bird population state indicators for oligotrophic and eutrophic water ecosystems inFinland. The indicators revealed that the populations in eutrophic wetlands have on average halved since early 1990s. The populations in oligotrophic wetlands have remained stable, except a moderate decline since the late 2000s. Our findings support the idea that the waterbird populations of the eutrophic wetlands are in serious trouble. This is likely due to over‐eutrophication of these ecosystems. Conservation and management actions should be urgently taken to halt the loss of biodiversity in these globally threatened freshwater ecosystems.
Hypothermic Machine Perfusion Decreases Renal Cell Apoptosis During Ischemia/Reperfusion Injury via the Ezrin/AKT Pathway
Authors: Zhang Yang , Fu Zhen , Zhong Zibiao , Wang Ren , Hu Long , Xiong Yan , Wang Yanfeng , Ye Qifa
Published: August 2015

This study aimed to explore the potential mechanisms of hypothermic machine perfusion (HMP)—a more efficient way to preserve kidneys from donors after cardiac death than static cold storage (CS), then to provide the basis for further improving donor quality. Twelve healthy male New Zealand rabbits (12 weeks old, weighing 3.0 ± 0.3 kg) were randomly divided into two groups: the HMP group and CS group (n = 6). Rabbits’ left kidney was subjected to 35 min of warm ischemic time by clamping the left renal pedicle and 1 h of reperfusion. The kidneys were then hypothermically (4–8°C) preserved in vivo for 4 h with HCA‐II solution using HMP or CS methods. Then rabbits underwent a right nephrectomy and the kidney tissues were collected after 24 h of reperfusion. TUNEL staining was performed on paraffin sections to detect apoptosis, and the expressions of cleaved caspase‐3, ezrin, AKT, and p‐AKT in frozen kidney tissues were detected by Western blotting. The ezrin expression was further confirmed by immunohistochemistry analysis. The apoptosis rate and expression of cleaved caspase‐3 in the HMP group were significantly lower than the CS group (P < 0.001 and P = 0.002), meanwhile the expression of cleaved caspase‐3 in the HMP and CS groups was significantly increased compared with the normal group (P = 0.035 and P < 0.001), and the expression of ezrin and p‐AKT in the HMP group was significantly higher than the CS group (P = 0.005, 0.014). HMP decreased the renal cell apoptosis rate during ischemia/reperfusion injury via the ezrin/AKT pathway.
PLAG1 and NCAPG‐LCORL in livestock
Authors: Takasuga Akiko
Published: August 2015

A recent progress on stature genetics has revealed simple genetic architecture in livestock animals in contrast to that in humans. PLAG1 and/or NCAPG‐LCORL, both of which are known as a locus for adult human height, have been detected for association with body weight/height in cattle and horses, and for selective sweep in dogs and pigs. The findings indicate a significant impact of these loci on mammalian growth or body size and usefulness of the natural variants for selective breeding. However, association with an unfavorable trait, such as late puberty or risk for a neuropathic disease, was also reported for the respective loci, indicating an importance to discriminate between causality and association. Here I review the recent findings on quantitative trait loci (QTL) for stature in livestock animals, mainly focusing on the PLAG1 and NCAPG‐LCORL loci. I also describe our recent efforts to identify the causative variation for the third major locus for carcass weight in Japanese Black cattle.
Relationships between immunoglobulin M and immunoglobulin G or A in colostrum of Japanese black multiparous cows
Authors: Taniguchi Saya , Wang Mengdong , Ikeda Shuntaro , Yoshioka Hidetugu , Nagase Hiroshi , Kitamura Shoko , Itoyama Erina , Murakami Hiroaki , Sugimoto Miki , Kume Shinichi
Published: August 2015

This study was conducted to clarify the relationships among immunoglobulin (Ig)M, IgG, IgA, β‐carotene, vitamin A and α‐tocopherol contents in colostrum of 24 Japanese Black multiparous cows in order to evaluate the role of IgM on colostral IgG and IgA production. Compared with colostral IgG, colostral IgM and IgA were very low but varied widely. There was positive correlation between colostral IgM and IgG, but colostral IgM was not related with colostral IgA. There was no relationship between colostral IgM and age of cows, although colostral IgG was increased with aging. There were positive correlations among colostral β‐carotene, vitamin A and α‐tocopherol and these vitamins were positively correlated with colostral IgM and IgG. These results indicate that fat‐soluble vitamins may affect colostral IgG and IgM in cows and colostral IgG increases with the increase of colostral IgM.
Association between thyroid‐stimulating hormone and blood pressure in adults: an 11‐year longitudinal study
Authors: Langén Ville L. , Niiranen Teemu J. , Puukka Pauli , Sundvall Jouko , Jula Antti M.
Published: August 2015

Background

The results of longitudinal studies on the association between thyroid function and blood pressure (BP) are divided. This study aimed to investigate this association in cross‐sectional and longitudinal settings in a nationwide, random sample representative of the Finnish adult population aged 30 and over.

Methods

The study sample was randomly drawn from the population register. A total of 5655 participants were included in the baseline analyses and 3453 in the 11‐year prospective analyses. The associations between baseline TSH and (i) BP and BP change over time; and (ii) prevalent and incident hypertension were assessed using linear and logistic models, adjusted for age, gender, smoking and body mass index.

Results

A positive association (β ± standard error) was observed between TSH and diastolic (0·36 ± 0·12, P = 0·003) but not systolic BP (0·16 ± 0·21, P = 0·45) at baseline. TSH was negatively associated with 11‐year BP change in men (systolic: −0·92 ± 0·41, P = 0·03; diastolic: −0·66 ± 0·26, P = 0·01) but not in women (P ≥ 0·09 for systolic and diastolic BP change). Participants in the highest TSH tertile within the TSH reference interval (0·4–3·4 mU/L), as compared with the lowest, had increased odds of prevalent (odds ratio 1·22, 95% confidence interval 1·05–1·43, P = 0·01) but not incident hypertension (odds ratio 0·93, 95% confidence interval 0·73–1·19, P = 0·58).

Conclusions

A modest association was found between increasing TSH and prevalent but not incident hypertension. TSH was inversely associated with BP change in men in our study. These findings contest an independent role of thyroid function at normal to near‐normal levels in the pathogenesis of hypertension.
Birth outcomes of patients with isolated anorectal malformations: A population‐based case‐control study
Authors: Vermes Gabor , László Daniel , Czeizel Andrew E. , Ács Nándor
Published: August 2015

In most patients affected by isolated anorectal malformation (IARM) the etiology is largely unknown. Thus, the aim of our project was to analyze possible risk factors forIARM. In the first step, birth outcomes of cases withIARMwere analyzed on the basis of maternal socio‐demographic variables, and these data are presented in this paper. Gestational age at delivery, birthweight, preterm birth, low birthweight and small for gestational age of cases withIARMwere evaluated in the function of maternal age, birth/pregnancy order, marital and employment status of mothers in the population‐based large dataset of theHungarianCase‐ControlSurveillance ofCongenitalAbnormalities, 1980–1996. The study samples included 231 live‐born cases withIARM, 361 matched and 38 151 population controls without any defect.IARMsare more frequent in males, twins and newborn infants with low birthweight and small‐for‐gestational‐age, the latter being the consequence of intrauterine growth restriction. In addition, mothers of cases were younger but with higher birth order, and had lower socio‐economic status. These maternal variables are characteristic for the gypsy population inHungary. The higher proportion of gypsy women among the mothers of cases withIARMwas confirmed during the home visits of the study. Male sex and intrauterine growth restriction of cases, in addition to low socioeconomic status and gypsy origin of mothers may have a role in the risk ofIARMs.
Bioavailability of insulin detemir and human insulin at the level of peripheral interstitial fluid in humans, assessed by open‐flow microperfusion
Authors: Bodenlenz M. , Ellmerer M. , Schaupp L. , Jacobsen L. V. , Plank J. , Brunner G. A. , Wutte A. , Aigner B. , Mautner S. I. , Pieber T. R.
Published: August 2015

Aims

To find an explanation for the lower potency of insulin detemir observed in humans compared with unmodified human insulin by investigating insulin detemir and human insulin concentrations directly at the level of peripheral insulin‐sensitive tissues in humans in vivo.

Methods

Euglycaemic‐hyperinsulinaemic clamp experiments were performed in healthy volunteers. Human insulin was administered i.v. at 6 pmol/kg/min and insulin detemir at 60 pmol/kg/min, achieving a comparable steady‐state pharmacodynamic action. In addition, insulin detemir was doubled to 120 pmol/kg/min. Minimally invasive open‐flow microperfusion (OFM) sampling methodology was combined with inulin calibration to quantify human insulin and insulin detemir in the interstitial fluid (ISF) of subcutaneous adipose and skeletal muscle tissue.

Results

The human insulin concentration in the ISF was ∼115 pmol/l or ∼30% of the serum concentration, whereas the insulin detemir concentration in the ISF was ∼680 pmol/l or ∼2% of the serum concentration. The molar insulin detemir interstitial concentration was five to six times higher than the human insulin interstitial concentration and metabolic clearance of insulin detemir from serum was substantially reduced compared with human insulin.

Conclusions

OFM proved useful for target tissue measurements of human insulin and the analogue insulin detemir. Our tissue data confirm a highly effective retention of insulin detemir in the vascular compartment. The higher insulin detemir relative to human insulin tissue concentrations at comparable pharmacodynamics, however, indicate that the lower potency of insulin detemir in humans is attributable to a reduced effect in peripheral insulin‐sensitive tissues and is consistent with the reduced in vitro receptor affinity.
Movement‐related activity during goal‐directed hand actions in the monkey ventrolateral prefrontal cortex
Authors: Simone Luciano , Rozzi Stefano , Bimbi Marco , Fogassi Leonardo
Published: August 2015

Grasping actions require the integration of two neural processes, one enabling the transformation of object properties into corresponding motor acts, and the other involved in planning and controlling action execution on the basis of contextual information. The first process relies on parieto‐premotor circuits, whereas the second is considered to be a prefrontal function. Up to now, the prefrontal cortex has been mainly investigated with conditional visuomotor tasks requiring a learned association between cues and behavioural output. To clarify the functional role of the prefrontal cortex in grasping actions, we recorded the activity of ventrolateral prefrontal (VLPF) neurons while monkeys (Macaca mulatta) performed tasks requiring reaching–grasping actions in different contextual conditions (in light and darkness, memory‐guided, and in the absence of abstract learned rules). The results showed that the VLPF cortex contains neurons that are active during action execution (movement‐related neurons). Some of them showed grip selectivity, and some also responded to object presentation. Most movement‐related neurons discharged during action execution both with and without visual feedback, and this discharge typically did not change when the action was performed with object mnemonic information and in the absence of abstract rules. The findings of this study indicate that a population of VLPF neurons play a role in controlling goal‐directed grasping actions in several contexts. This control is probably exerted within a wider network, involving parietal and premotor regions, where the role of VLPF movement‐related neurons would be that of activating, on the basis of contextual information, the representation of the motor goal of the intended action (taking possession of an object) during action planning and execution.
Evidence of post‐glacial secondary contact and subsequent anthropogenic influence on the genetic composition of Fennoscandian moose (Alces alces)
Authors: Kangas Veli‐Matti , Kvist Laura , Kholodova Marina , Nygrén Tuire , Danilov Pjotr , Panchenko Danila , Fraimout Antoine , Aspi Jouni
Published: August 2015

Aim

To determine whether a contemporary population of the moose (Alces alces), a large northern ungulate, retains genetic signatures of post‐glacial recolonization and/or the effects of anthropogenic factors. We focused on investigating spatial genetic structure and the distribution of genetic diversity of this species to clarify its still obscure history.

Location

Eastern Fennoscandia, Northern Europe.

Methods

In total, 574 Finnish and Russian Karelian moose were genotyped at 16 microsatellite loci, and the mitochondrial control region was sequenced from 224 individuals. Spatially explicit Bayesian clustering, multivariate and spatial autocorrelation methods were applied alongside traditional F‐statistics to study the effects of landscape on genetic structure. The demographic history of our study populations was explored with coalescent analysis and Bayesian skyline plots.

Results

A major mitochondrial divergence of moose was discovered between northern parts of Finland and the rest of the studied area. Landscape genetic analyses on the microsatellite data identified three genetic clusters connected by clines, with coalescent analysis indicating the division to be of ancient origin. Additionally, recent population bottlenecks were detected using Bayesian skyline plots.

Main conclusions

Our results indicate a post‐glacial secondary contact between two distinct moose mitochondrial lineages that diverged during the Pleistocene, whereas admixture of three diverged genetic subpopulations was detected using microsatellites. The emergence of these subpopulations was estimated to have occurred after the post‐glacial recolonization of Fennoscandia. The observed genetic bottlenecks coincide with recorded historical population declines in the 18th century. We conclude that the contemporary genetic composition of the moose population in eastern Fennoscandia has been affected by both ancient and recent factors.
Activation of matrix metalloproteinase in dorsal hippocampus drives improvement in spatial working memory after intra‐VTA nicotine infusion in rats
Authors: Shu Hui , Zheng Guo‐qing , Wang Xiaona , Sun Yanyun , Liu Yushan , Weaver John Michael , Shen Xianzhi , Liu Wenlan , Jin Xinchun
Published: August 2015

The hippocampus receives dopaminergic projections from the ventral tegmental area (VTA) and substantia nigra. These inputs appear to provide a modulatory signal that influences hippocampus‐dependent behaviors. Enhancements in working memory performance have been previously reported following acute smoking/nicotine exposure. However, the underlying mechanism remains unclear. This study investigated the effects of nicotine on spatial working memory (SWM) and the mechanisms involved. Delayed alternation T‐maze task was used to assess SWM. In situ and gel gelatin zymography were used to detect matrix metalloproteinase‐9 (MMP‐9) in SWM. Systemic or local (intra‐VTA) administration of nicotine significantly improves SWM, which was accompanied by increased MMP‐9 activity in dorsal hippocampus (dHPC). Intra‐dHPC administration of MMP inhibitor FN‐439 abolished the memory enhancement induced by intra‐VTA nicotine infusion. FN‐439 had no effect on locomotor behavior. Our data suggest that intra‐VTA nicotine infusion activates MMP‐9 in dHPC to improve SWM in rats.

image

Our study showed the brain region and mechanism underlying nicotine‐induced spatial working memory improvement. In response to nicotine treatment, VTA‐hippocampus circuit is activated and MMP‐9 activation in dorsal hippocampus mediates the memory improvement. Our data suggest nicotine increases spatial working memory by activating MMP‐9 in dorsal hippocampus. Nicotine improves spatial working memory by enhancing an ability to use Win‐shift strategy and increasing correct choice. This effect is mediated by the VTA‐hippocampus circuit and MMP‐9 in dHPC is activated with intra‐VTA nicotine infusion in rats.