bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple way to improve multivariate analyses of paleoecological data sets
Authors: Alroy John 
Published: February 2015

AbstractMultivariate methods such as cluster analysis and ordination are basic to paleoecology, but the messy nature of fossil occurrence data often makes it difficult to recover clear patterns. A recently described faunal similarity index based on the Forbes coefficient improves results when its complement is employed as a distance metric. This index involves adding terms to the Forbes equation and ignoring one of the counts it employs (that of species found in neither of the samples under consideration). Analyses of simulated data matrices demonstrate its advantages. These matrices include large and small samples from two partially overlapping species pools. In a cluster analysis, the widely used Dice coefficient and the Euclidean distance metric both create groupings that reflect sample size, the Simpson index suggests large differences that do not exist, and the corrected Forbes index creates groupings based strictly on true faunal overlap. In a principal coordinates analysis (PCoA) the Forbes index almost removes the sample-size signal but other approaches create a second axis strongly dominated by sample size. Meanwhile, species lists of late Pleistocene mammals from the United States capture biogeographic signals that standard ordination methods do recover, but the adjusted Forbes coefficient spaces the points out more sensibly. Finally, when biome-scale lists for living mammals are added to the data set and extinct species are removed, correspondence analysis misleadingly separates out the biome lists, and PCoA based on the Dice coefficient places them to the edge of the cloud of fossil assemblage data points. PCoA based on the Forbes index places them in more reasonable positions. Thus, only the adjusted Forbes index is able to recover true biological patterns. These results suggest that the index may be useful in analyzing not only paleontological data sets but any data set that includes species lists having highly variable lengths.
Mutation load under additive fitness effects
Authors: BERGEN ANDREW C. 
Published: February 2015

SummaryUnder the traditional mutation load model based on multiplicative fitness effects, the load in a population is 1−e−U, whereUis the genomic deleterious mutation rate. Because this load becomes high under largeU, synergistic epistasis has been proposed as one possible means of reducing the load. However, experiments on model organisms attempting to detect synergistic epistasis have often focused on a quadratic fitness model, with the resulting general conclusion being that epistasis is neither common nor strong. Here, I present a model of additive fitness effects and show that, unlike multiplicative effects, the equilibrium frequency of an allele under additivity is dependent on the average absolute fitness of the population. The additive model then results in a load ofU/(U +1), which is much lower than 1−e−Ufor largeU. Numerical iterations demonstrate that this analytic derivation holds as a good approximation under biologically relevant values of selection coefficients andU. Additionally, regressions ontoDrosophilamutation accumulation data suggest that the common method of inferring epistasis by detecting large quadratic terms from regressions is not always necessary, as the additive model fits the data well and results in synergistic epistasis. Furthermore, the additive model gives a much larger reduction in load than the quadratic model when predicted from the same data, indicating that it is important to consider this additive model in addition to the quadratic model when inferring epistasis from mutation accumulation data.
4-Nitrobenzaldehyde thiosemicarbazone: a new compound derived from S-(-)-limonene that induces mitochondrial alterations in epimastigotes and trypomastigotes of Trypanosoma cruzi
Authors: BRITTA ELIZANDRA APARECIDA , SCARIOT DÉBORA BOTURA , FALZIROLLI HUGO , DA SILVA CLEUZA CONCEIÇÃO , UEDA-NAKAMURA TÂNIA , DIAS FILHO BENEDITO PRADO , BORSALI REDOUANE , NAKAMURA CELSO VATARU 
Published: February 2015

SUMMARYTrypanosoma cruzi is the causative agent of Chagas’ disease, a parasitic disease that remains a serious health concern with unsatisfactory treatment. Drugs that are currently used to treat Chagas’ disease are partially effective in the acute phase but ineffective in the chronic phase of the disease. The aim of the present study was to evaluate the antitrypanosomal activity and morphological, ultrastructural and biochemical alterations induced by a new molecule, 4-nitrobenzaldehyde thiosemicarbazone (BZTS), derived from S-(-)-limonene against epimastigote, trypomastigote and intracellular amastigote forms of T. cruzi. BZTS inhibited the growth of epimastigotes (IC50 = 9·2 μm), intracellular amastigotes (IC50 = 3·23 μm) and inhibited the viability of trypomastigotes (EC50 = 1·43 μm). BZTS had a CC50 of 37·45 μm in LLCMK2 cells. BZTS induced rounding and distortion of the cell body and severely damaged parasite mitochondria, reflected by extensive swelling and disorganization in the inner mitochondrial membrane and the presence of concentric membrane structures inside the organelle. Cytoplasmic vacuolization, endoplasmic reticulum that surrounded organelles, the loss of mitochondrial membrane potential, and increased mitochondrial O2•ˉ production were also observed. Our results suggest that BZTS alters the ultrastructure and physiology of mitochondria, which could be closely related to parasite death.
Comparative evaluation of three surveillance systems for infectious equine diseases in France and implications for future synergies
Authors: AMAT J. P. , HENDRIKX P. , TAPPREST J. , LEBLOND A. , DUFOUR B. 
Published: February 2015

SUMMARYIt is necessary to assess surveillance systems for infectious animal diseases to ensure they meet their objectives and provide high-quality health information. Each system is generally dedicated to one disease and often comprises various components. In many animal industries, several surveillance systems are implemented separately even if they are based on similar components. This lack of synergy may prevent optimal surveillance. The purpose of this study was to assess several surveillance systems within the same industry using the semi-quantitative OASIS method and to compare the results of the assessments in order to propose improvements, including future synergies. We have focused on the surveillance of three major equine diseases in France. We have identified the mutual and specific strengths and weaknesses of each surveillance system. Furthermore, the comparative assessment has highlighted many possible synergies that could improve the effectiveness and efficiency of surveillance as a whole, including the implementation of new joint tools or the pooling of existing teams, tools or skills. Our approach is an original application of the OASIS method, which requires minimal financial resources and is not very time-consuming. Such a comparative evaluation could conceivably be applied to other surveillance systems, other industries and other countries. This approach would be especially relevant to enhance the efficiency of surveillance activities when resources are limited.
CHANCE, PROVIDENCE, AND IMPERIAL ENNUI IN ALFRED DOMETT’SRANOLF AND AMOHIA: A SOUTH-SEA DAY-DREAM
Authors: Roberts Hugh 
Published: February 2015

“I have read your poems– you can do anything” wrote Robert Browning to his close friend Alfred Domett on May 22, 1842, shortly after the latter had emigrated to New Zealand (Browning, Domett and Arnould 35). If this was in part friendly overpraise of Domett's verse, it was also a prognostication as to the effect of emigration. The idea (which also underlies Browning's poetic treatment of Domett's departure in the figure of Waring who “gave us all the slip”) was that “partial retirement and stopping the ears against the noise outside” would open up the possibility of something startlingly new: the little I, or anybody, can do as it is, comes of themgoing to New Zealand. . . . What I meant to say was – that only in your present condition of life, so far as I can see, is there any chance of your being able to find out . . . (sic) what is wanted, and how to supply the want when you precisely find it (35).
The psychiatrist’s duty to protect
Authors: Knoll James L. 
Published: February 2015

Responding to the California Supreme Court’s decision and its related legal obligations in Tarasoff v. Regents of Univ. of California over 30 years ago has become a standard part of mental health practice. This case influenced legal requirements governing therapists’ duty to protect third parties in nearly every state in the country. The final ruling in Tarasoff emphasized that therapists have a duty to protect individuals who are being threatened with bodily harm by their patients.This article will provide a brief overview and update on duty to protect legal requirements. Clinical guidelines for addressing threats and the duty to protect will be discussed, along with risk management approaches. The article will conclude with a sample vignette illustrating these principles.
Synthesis and characterization of ZnS with controlled amount of S vacancies for photocatalytic H2 production under visible light
Authors: Wang Gang , Huang Baibiao , Li Zhujie , Lou Zaizhu , Wang Zeyan , Dai Ying , Whangbo Myung-Hwan 
Published: February 2015

AbstractControlling amount of intrinsic S vacancies was achieved in ZnS spheres which were synthesized by a hydrothermal method using Zn and S powders in concentrated NaOH solution with NaBH4 added as reducing agent. These S vacancies efficiently extend absorption spectra of ZnS to visible region. Their photocatalytic activities for H2 production under visible light were evaluated by gas chromatograph and the midgap states of ZnS introduced by S vacancies were examined by density functional calculations. Our study reveals that the concentration of S vacancies in the ZnS samples can be controlled by varying the amount of the reducing agent NaBH4 in the synthesis and the prepared ZnS samples exhibit photocatalytic activity for H2 production under visible-light irradiation without loading noble metal. This photocatalytic activity of ZnS increases steadily with increasing the concentration of S vacancies until the latter reaches an optimum value. Our density functional calculations show that S vacancies generate midgap defect states in ZnS, which lead to visible-light absorption and responded.
A novel mechanism of post-translational modulation of HMGA functions by the histone chaperone nucleophosmin
Authors: Arnoldo Laura , Sgarra Riccardo , Chiefari Eusebio , Iiritano Stefania , Arcidiacono Biagio , Pegoraro Silvia , Pellarin Ilenia , Brunetti Antonio , Manfioletti Guidalberto 
Published: February 2015

AbstractHigh Mobility Group A are non-histone nuclear proteins that regulate chromatin plasticity and accessibility, playing an important role both in physiology and pathology. Their activity is controlled by transcriptional, post-transcriptional and post-translational mechanisms. In this study we provide evidence for a novel modulatory mechanism for HMGA functions. We show that HMGAs are complexed in vivo with the histone chaperone nucleophosmin (NPM1), that this interaction requires the histone-binding domain of NPM1 and that NPM1 modulates both DNA-binding affinity and specificity of HMGAs. By focusing on two human genes whose expression is directly regulated by HMGA1, the Insulin receptor (INSR) and the Insulin-like growth factor-binding protein 1 (IGFBP1) genes, we demonstrated that occupancy of their promoters by HMGA1 was NPM1-dependent, reflecting a mechanism in which the activity of these cis-regulatory elements is directly modulated by NPM1 leading to changes in gene expression. HMGAs need short stretches of AT-rich nucleosome-free regions to bind to DNA. Therefore, many putative HMGA binding sites are present within the genome. Our findings indicate that NPM1, by exerting a chaperoning activity towards HMGAs, may act as a master regulator in the control of DNA occupancy by these proteins and hence in HMGA-mediated gene expression.
Cross-talk between signaling pathways: The link between plant secondary metabolite production and wounding stress response
Authors: Jacobo-Velázquez Daniel A. , González-Agüero Mauricio , Cisneros-Zevallos Luis 
Published: February 2015

AbstractPlants subjected to wounding stress produce secondary metabolites. Several of these metabolites prevent chronic diseases and can be used as colorants, flavors and as antimicrobials. This wound-induced production of plant secondary metabolites is mediated by signaling-molecules such as reactive oxygen species (ROS), ethylene (ET) and jasmonic acid (JA). However, their specific role and interactions that modulate the wound-respond in plants is not fully understood. In the present study, a subtractive cDNA library was generated, to better understand the global response of plants to wounding stress. Carrot (Daucus carota) was used as a model system for this study. A total of 335 unique expressed sequence tags (ESTs) sequences were obtained. ESTs sequences with a putative identity showed involvement in stress-signaling pathways as well as on the primary and secondary metabolism. Inhibitors of ROS biosynthesis, ET action and JA biosynthesis alone and in combination were applied to wounded-carrots in order to determine, based on relative gene expression data, the regulatory role of ET, JA and ROS on the wound-response in plants. Our results demonstrate that ROS play a key role as signaling-molecules for the wound-induced activation of the primary and secondary metabolism whereas ET and JA are essential to modulate ROS levels.
ATP Exhibits Antimicrobial Action by Inhibiting Bacterial Utilization of Ferric Ions
Authors: Tatano Yutaka , Kanehiro Yuichi , Sano Chiaki , Shimizu Toshiaki , Tomioka Haruaki 
Published: February 2015

AbstractATP up-regulates macrophage antimycobacterial activity in a P2X7-dependent manner, but little is known about whether ATP directly exhibits antimicrobial effects against intracellular mycobacteria. In this study, we found that ATP inhibited the growth of various bacteria, including Staphylococcus, Pseudomonas and mycobacteria, without damaging bacterial surface structures. Using gene technology, we newly established an enterobactin-deficient (entB−) mutant from ATP-resistant Klebsiella pneumoniae and found the recovery of ATP susceptibility in the enterobactin-deleted mutant. Therefore, ATP's antibacterial activity is attributable to its iron-chelating ability. Since ATP distributed in the cytosol of macrophages at high concentrations, ATP appears to augment macrophage's antimicrobial activity by directly attacking intracytosolic and intra-autophagosomal pathogens. Furthermore, ATP exhibited combined effects with some antimicrobials against methicillin-resistant S. aureus (MRSA) and M. intracellulare, suggesting its usefulness as an adjunctive drug in the chemotherapy of certain intractable infections.
Analysis, design and experimental verification of a field‐modulated permanent‐magnet machine for direct‐drive wind turbines
Authors: Li Xianglin , Chau Kwok Tong , Cheng Ming 
Published: February 2015

This paper presents the design and experimental verification of a field‐modulated permanent‐magnet (FMPM) machine using spoke‐magnet outer rotor for direct‐drive wind turbines. The fundamental operation and optimised design process of the proposed machine are elaborated and discussed in detail. The electromagnetic analytical calculation is used for the initial determination of the prototype design, mainly concerning the special constraints of wind power generation, and the two‐dimensional finite element analysis is also applied to optimise and investigate the detailed characteristics. A 5 kW prototype is constructed, and the measured performances have verified the analysis and design, justifying that the proposed machine can offer significant advantages of high‐torque capability and low‐voltage regulation. Experience gained from this study has led to develop a general design guideline for the open‐slot FMPM machine using spoke‐magnet outer rotor for direct‐drive applications.
Design and analysis of double‐sided slotless axial‐flux permanent magnet machines with conventional and new stator core
Authors: Hekmati Parham , Yazdanpanah Reza , Mirsalim Mojtaba 
Published: February 2015

The objective of this paper is to present the design equations of the conventional double‐sided axial‐flux slotless brushless DC machine (BLDC) and the new one with the trapezoidal cross‐section core as well as performances comparison based on the proposed design algorithm. Direct search method is used to find the optimum designs, whereas machines with the rated power of 0.25–10 kW are compared. Efficiency and size of the optimum designed machines are presented to make a comprehensive study for choosing the best topology from the viewpoint of electrical and geometrical characteristics. Finite element analysis and experimental results are presented to show the validity of the derived equations and the design outcomes.
Asymmetric structure with high electric–thermal conversion efficiency for nanoscale phase change memory based on three‐dimensional simulation
Authors: Lan Tian , Sun Jinjie , Cheng Xiao Min , Zhou Jiao , Miao Xiangshui 
Published: February 2015

How to decrease the reset current is a key point for improving the performance of phase change memory (PCM). Therefore, an asymmetric structure of PCM is proposed to achieve this aim. Using ANSYS, three‐dimensional finite element models were established to simulate the efficiency of electric–thermal conversion in PCM cells with an asymmetric structure and a conventional symmetric structure. Simulation results show that the peak temperature in the asymmetric cell with a feature size (FS) of 16 nm is higher than that in the conventional symmetric cell with the same FS by 37.2% when the same current pulse is applied. In an asymmetric cell, the current path and heat dissipating conditions are quite different from those in a symmetric cell, which leads to the remarkable enhancement in electric–thermal conversion efficiency. Simulation results also suggest a proper offset value in asymmetric structures, with which the efficiency of electric–thermal conversion can be further improved. If this new structure is used in fabrication, no additional cost will be incurred because the only difference between symmetric and asymmetric structures is the position of the top opening of the electrodes, indicating that the new structure is highly compatible with modern fabrication processes of PCM.
Synthesis and characterisation of pore‐expanded mesoporous silica materials
Authors: Ma Juanjuan , Liu Qiming , Chen Dandan , Wen Sheng , Wang Tianhe 
Published: February 2015

Mesoporous silicas are synthesised using 1,3,5‐trimethylbenzene (TMB) and heptanes as pore expanders. Small‐angle X‐ray diffraction and N2 adsorption–desorption isotherms at 77 K were used to characterise the pore structure of the prepared materials. The porosity increased with the added TMB amount for samples using TMB as a pore expander and a total pore value of 2.48 cm3/g was obtained, representing an increase by a factor of 2.4 as compared with mesoporous silica without TMB addition. For samples with heptanes as a pore expander, the pore volume increased with synthesis temperature. The mesoporous silica synthesised at 52°C had a total pore volume of 2.38 cm3/g.
On convex relaxation of graph isomorphism
Authors: Aflalo Yonathan , Bronstein Alexander , Kimmel Ron 
Published: February 2015

Significance
Graphs are a ubiquitous mathematical abstraction used in numerous problems in science and engineering. Of particular importance is the need to find the best structure-preserving matching of graphs. Since graph matching (GM) is a computationally intractable problem, numerous heuristics exist to approximate its solution. An important class of GM heuristics is relaxation techniques based on replacing the original problem by a continuous convex program. Conditions for applicability or inapplicability of such convex relaxations are poorly understood. In this study, we propose easy to check spectral properties to characterize a wide family of graphs for which we prove equivalence of convex relaxation to the exact GM.
Mother’s voice and heartbeat sounds elicit auditory plasticity in the human brain before full gestation
Authors: Webb Alexandra R. , Heller Howard T. , Benson Carol B. , Lahav Amir 
Published: February 2015

Significance
Newborns can hear their mother’s voice and heartbeat sounds before birth. However, it is unknown whether, how early, and to what extent the newborn's brain is shaped by exposure to such maternal sounds. This study provides evidence for experience-dependent plasticity in the auditory cortex in preterm newborns exposed to authentic recordings of maternal sounds before full-term brain maturation. We demonstrate that the auditory cortex is more adaptive to womb-like maternal sounds than to environmental noise. Results are supported by the biological fact that maternal sounds would otherwise be present in utero had the baby not been born prematurely. We theorize that exposure to maternal sounds may provide newborns with the auditory fitness necessary to shape the brain for hearing and language development.
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs
Authors: Londin Eric , Loher Phillipe , Telonis Aristeidis G. , Quann Kevin , Clark Peter , Jing Yi , Hatzimichael Eleftheria , Kirino Yohei , Honda Shozo , Lally Michelle , Ramratnam Bharat , Comstock Clay E. S. , Knudsen Karen E. , Gomella Leonard , Spaeth George L. , Hark Lisa , Katz L. Jay , Witkiewicz Agnieszka , Rostami Abdolmohamad , Jimenez Sergio A. , Hollingsworth Michael A. , Yeh Jen Jen , Shaw Chad A. , McKenzie Steven E. , Bray Paul , Nelson Peter T. , Zupo Simona , Van Roosbroeck Katrien , Keating Michael J. , Calin George A. , Yeo Charles , Jimbo Masaya , Cozzitorto Joseph , Brody Jonathan R. , Delgrosso Kathleen , Mattick John S. , Fortina Paolo , Rigoutsos Isidore 
Published: February 2015

Significance
MicroRNAs (miRNAs) are small ∼22-nt RNAs that are important regulators of posttranscriptional gene expression. Since their initial discovery, they have been shown to be involved in many cellular processes, and their misexpression is associated with disease etiology. Currently, nearly 2,800 human miRNAs are annotated in public repositories. A key question in miRNA research is how many miRNAs are harbored by the human genome. To answer this question, we examined 1,323 short RNA sequence samples and identified 3,707 novel miRNAs, many of which are human-specific and tissue-specific. Our findings suggest that the human genome expresses a greater number of miRNAs than has previously been appreciated and that many more miRNA molecules may play key roles in disease etiology.
Selective molecular transport through the protein shell of a bacterial microcompartment organelle
Authors: Chowdhury Chiranjit , Chun Sunny , Pang Allan , Sawaya Michael R. , Sinha Sharmistha , Yeates Todd O. , Bobik Thomas A. 
Published: February 2015

SignificanceHere, we describe a type of selective channel formed by a nonmembrane protein that is used to control metabolite movement between cellular compartments. In this case, the channel controls the movement of metabolites between the bacterial cytoplasm and the lumen of a bacterial microcompartment, a primitive organelle that is bounded by a protein shell and lacks any lipid bilayer. These studies are the first to our knowledge to prove selective molecular transport through a protein-based barrier. These findings broaden our understanding of how cells control the movement of molecules between cellular compartments, which is fundamental to biological systems. It also solves a key question about the function of bacterial microcompartments, which themselves impact many diverse and important biological processes.