bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indirect Mixed Antiglobulin Reaction (MAR) as a Screening Procedure for Antisperm Antibodies. I. Methodological Studies
Authors: MEINERTZ HELLE 
Published: December 2015

ABSTRACT: Direct mixed antiglobulin reaction (MAR) cannot always be carried out because it requires motile spermatozoa in the patient's ejaculate. Therefore, the indirect MAR for IgG and IgA using donor spermatozoa sensitized with serum or seminal plasma from patients was investigated with the aim of developing a practical screening procedure for antisperm antibodies involving a characterization of the Ig‐class of the antibodies.Samples from 23 men, 13 men with and 10 men without agglutinating antisperm antibodies, were used for the methodological experiments with the indirect MAR. Among three procedures to diminish the amount of nonbound immunoglobulin after sensitizing the donor spermatozoa with serial dilutions of serum or seminal plasma, a swim‐up method was found to be optimal. The indirect MAR was carried out with glutaraldehyde‐fixed sheep erythrocytes coated with IgG or IgA and various dilutions of anti‐IgG and anti‐IgA, respectively.These experiments led to a standardization of the indirect MAR, making it sensitive, easy to read, and allowing the reactions for IgG and IgA to be compared on an approximately equimolecular basis.
Suicide: Bad Act or Good Intervention
Authors: Clements Collen D. , Sider Roger C. , Perlmutter Richard 
Published: December 2015

AbstractThis article develops a different perspective on the ethics of suicide, based on theoretical and clinical grounds. In terms of value theory, applying “good” or “bad” to the suicide act makes no sense. We need to shift our focus from a search for an ethical statement about suicide (e.g., “rational suicide”) to the ethical justification for intervention based on the needs and interests of an affirming therapeutic profession. We choose to intervene because of values we hold about well‐functioning, existence, potential for human life; and because as empathic, social beings, we feel for others and are motivated by that feeling. This justification leads us to suggest a situational case‐centered ethics for suicide intervention.
In situ marker‐based assessment of leaf trait evolutionary potential in a marginal European beech population
Authors: Bontemps A. , Lefèvre F. , Davi H. , Oddou‐Muratorio S. 
Published: December 2015

AbstractEvolutionary processes are expected to be crucial for the adaptation of natural populations to environmental changes. In particular, the capacity of rear edge populations to evolve in response to the species limiting conditions remains a major issue that requires to address their evolutionary potential. In situ quantitative genetic studies based on molecular markers offer the possibility to estimate evolutionary potentials manipulating neither the environment nor the individuals on which phenotypes are measured. The goal of this study was to estimate heritability and genetic correlations of a suite of leaf functional traits involved in climate adaptation for a natural population of the tree Fagus sylvatica, growing at the rear edge of the species range. Using two marker‐based quantitative genetics approaches, we obtained consistent and significant estimates of heritability for leaf phenological (phenology of leaf flush), morphological (mass, area, ratio mass/area) and physiological (δ13C, nitrogen content) traits. Moreover, we found only one significant positive genetic correlation between leaf area and leaf mass, which likely reflected mechanical constraints. We conclude first that the studied population has considerable genetic diversity for important ecophysiological traits regarding drought adaptation and, second, that genetic correlations are not likely to impose strong genetic constraints to future population evolution. Our results bring important insights into the question of the capacity of rear edge populations to evolve.
Association of interferon lambda‐1 with herpes simplex viruses‐1 and ‐2, Epstein–Barr virus, and human cytomegalovirus in chronic periodontitis
Authors: Muzammil  , Jayanthi D , Faizuddin Mohamed , Noor Ahamadi H.M. 
Published: December 2015

AbstractAimPeriodontal tissues facilitate the homing of herpes viruses that elicit the immune‐inflammatory response releasing the interferons (IFN). IFN lambda‐1 (λ1) can suppress the replication of viruses, and induces the antiviral mechanism. The aim of the present study was to evaluate the association between IFN‐λ1 and periodontal herpes viruses in the immunoregulation of chronic periodontal disease.MethodsThe cross‐sectional study design included 30 chronic periodontitis patients with a mean age of 42.30 ± 8.63 years. Gingival crevicular fluid collected was assessed for IFN‐λ1 using enzyme–linked immunosorbent assay and four herpes viruses were detected using multiplex polymerase chain reaction technique. IFN‐λ1 levels were compared between virus‐positive and ‐negative patients for individual and total viruses.ResultsFifty per cent (n = 15) of patients were positive for the four herpes viruses together; 50% (n = 15), 30% (n = 9), 26.7% (n = 8), and 40% (n = 12) were positive for herpes simplex virus (HSV)‐1, Epstein–Barr virus, HSV‐2, and human cytomegalovirus, respectively. The mean concentrations of IFN‐λ1 in virus‐positive patients (14.38 ± 13.95) were lower than those of virus‐negative patients (228.26 ± 215.35). INF‐λ1 levels in individual virus groups were also lower in virus‐positive patients compared to virus‐negative patients, with P < 0.001.ConclusionsThese results suggest that IFN‐λ1 could have antiviral and therapeutic value against the viruses in the pathogenesis of chronic periodontitis.
Phylogenetic utility of LEAFY gene in Cinnamomum (Lauraceae): Gene duplication and polymerase chain reaction‐mediated recombination
Authors: Huang Jian‐Feng , Li Lang , Conran John G. , Li Jie 
Published: December 2015

AbstractLow copy nuclear genes show great potential to provide phylogenetic information, but their use has been hampered by several inherent adverse factors. Polymerase chain reaction (PCR)‐mediated recombination ranks among these factors and occurs when high levels of similar paralogs for a low‐copy nuclear gene coexist within a single PCR amplification reaction. In this study, the LEAFY gene was cloned and sequenced for 63 Cinnamomum species and two copies of the second intron were found within species of the diploid sect. Cinnamomum. Although these two copies are very similar, they can be distinguished easily due to a specific ca. 47‐bp segment that is missing in the “short sequence” copy. The “long sequence” copy performed well in phylogenetic analysis of Cinnamomum and is largely consistent with phylogenetic relationships based on internal transcribed spacer region sequences. In contrast, the “short sequence” copy was problematic for phylogenetic reconstruction and PCR‐mediated recombination was detected in 20 of the 38 Cinnamomum species with two LEAFY copies. Thirty‐one recombinants were discriminated and the breakpoints suggested by the programs RDP3 and GARD were distributed randomly along the recombination sequences. This study shows that duplication in low‐copy nuclear genes and problems associated with PCR‐mediated recombination need to be given more attention in phylogenetic studies.
Happiness Vs Contentment? A Case for a Sociology of the Good Life
Authors: McKenzie Jordan 
Published: December 2015

AbstractDespite the enormous growth in happiness research in recent decades, there remains a lack of consistency in the use of the terms happiness, satisfaction, contentment and well‐being. In this article I argue for a sociologically grounded distinction between happiness and contentment that defines the former as positive affect and the latter as positive reflection. Contentment is therefore understood as a fulfilling relationship with the self and society (to borrow from G.H. Mead's terminology) and happiness involves pleasurable experiences. There is a history of similar distinctions in philosophy and psychoanalysis, but much of the contemporary discourse fails to distinguish between individual and collective definitions of happiness. This article will argue that happiness and contentment ought not to be treated as competing approaches to the good life, but as complimentary forms of emotional experience. Further, I argue that the current interest in happiness can be linked to larger culture shifts involving neoliberalism and individualism.
Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats
Authors: Senerchia Natacha , Felber François , North Béatrice , Sarr Anouk , Guadagnuolo Roberto , Parisod Christian 
Published: December 2015

AbstractThe maintenance of species integrity despite pervasive hybridization is ruled by the interplay between reproductive barriers. Endogenous postzygotic isolation will shape the patterns of introgression in hybrid zones, leading to variable outcomes depending on the genetic mechanism involved. Here, we analysed experimental and natural hybrid populations ofAegilops geniculataandAegilops triuncialisto examine the genetics of species boundaries in the face of gene flow. Because long‐terminal repeat retrotransposons (LTR‐RTs) showing differential evolutionary trajectories are probably to affect hybrid dysgenesis and reproductive isolation between these wild wheat species, we addressed the impact ofLTR‐RTs in shaping introgression between them. Experimental settings involving artificial sympatry and enforced crossings quantified strong, but incomplete reproductive isolation, and highlighted asymmetrical endogenous postzygotic isolation between the two species. Natural hybrid zones located in the northern Golan Heights were analysed using plastidDNA, amplified fragment length polymorphisms (AFLP) marking random sequences, and sequence‐specific amplified polymorphisms (SSAP) tracking insertions from sixLTR‐RTfamilies. This analysis demonstrated asymmetrical introgression and genome reorganization. In comparison with random sequences and quiescentLTR‐RTs, thoseLTR‐RTs predicted to be activated following conflicting interactions in hybrids revealed differential introgression across the hybrid zones. As also reported for synthetic F1 hybrids, suchLTR‐RTs were specifically reorganized in the genomes of viable hybrids, confirming that conflicts between selfishLTR‐RTs may represent key incompatibilities shaping species boundaries and fostering long‐term species integrity in the face of gene flow.
Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations
Authors: Cruz de Carvalho Maria Helena , Sun Hai‐Xi , Bowler Chris , Chua Nam‐Hai 
Published: December 2015

Summary

Phosphorus (P) is an essential element to all living cells, yet fluctuations in P concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton groups, adapting to and surviving periods of suboptimal conditions and resuming growth as soon as nutrient concentrations permit. A knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete.

By strand‐specific RNA sequencing, we analyzed the global transcriptome changes of the diatom Phaeodactylum tricornutum in response to P fluctuations over a course of 8 d, defining five distinct physiological states.

This study reports previously unidentified genes highly responsive to P stress in P. tricornutum. Our data also uncover the complexity of the P. tricornutum P‐responsive sensory and signaling system that combines bacterial two‐component systems with more complex pathways reminiscent of metazoans. Finally, we identify a multitude of novel long intergenic nonprotein coding RNAs (lincRNAs) specifically responsive to P depletion, suggesting putative regulatory roles in the regulation of P homeostasis.

Our work provides additional molecular insights into the resilience of diatoms and their ecological success, and opens up novel routes to address and explore the function and regulatory roles of P. tricornutum lincRNAs in the context of nutrient stress.
EffectorP: predicting fungal effector proteins from secretomes using machine learning
Authors: Sperschneider Jana , Gardiner Donald M. , Dodds Peter N. , Tini Francesco , Covarelli Lorenzo , Singh Karam B. , Manners John M. , Taylor Jennifer M. 
Published: December 2015

Summary

Eukaryotic filamentous plant pathogens secrete effector proteins that modulate the host cell to facilitate infection. Computational effector candidate identification and subsequent functional characterization delivers valuable insights into plant–pathogen interactions. However, effector prediction in fungi has been challenging due to a lack of unifying sequence features such as conserved N‐terminal sequence motifs. Fungal effectors are commonly predicted from secretomes based on criteria such as small size and cysteine‐rich, which suffers from poor accuracy.

We present EffectorP which pioneers the application of machine learning to fungal effector prediction.

EffectorP improves fungal effector prediction from secretomes based on a robust signal of sequence‐derived properties, achieving sensitivity and specificity of over 80%. Features that discriminate fungal effectors from secreted noneffectors are predominantly sequence length, molecular weight and protein net charge, as well as cysteine, serine and tryptophan content. We demonstrate that EffectorP is powerful when combined with in planta expression data for predicting high‐priority effector candidates.

EffectorP is the first prediction program for fungal effectors based on machine learning. Our findings will facilitate functional fungal effector studies and improve our understanding of effectors in plant–pathogen interactions. EffectorP is available at http://effectorp.csiro.au.
Composition and toxigenic potential of the Fusarium graminearum species complex from maize ears, stalks and stubble in Brazil
Authors: Kuhnem P. R. , Ward T. J. , Silva C. N. , Spolti P. , Ciliato M. L. , Tessmann D. J. , Del Ponte E. M. 
Published: December 2015

A large collection (n = 539) of Fusarium graminearum species complex (FGSC) isolates was obtained from Brazilian maize, and collections formed according to geography and maize part: (i) kernel (n = 110) from south and south‐central Brazil; (ii) stalk (n = 134) from Paraná state (south); and (iii) stubble (n = 295) from Rio Grande do Sul state (south). Species composition, identified using a multilocus genotype approach, was assessed separately in each collection due to differences in geographic sampling. Overall, three species were found: F. meridionale (Fmer; 67% prevalence) with the nivalenol (NIV) genotype, F. graminearum (Fgra; 19%) with the 15‐acetyl (A) deoxynivalenol (DON) genotype, and F. cortaderiae (Fcor; 14%) with the NIV (49/74) or the 3‐ADON (25/74) genotype. In kernels, Fmer was spread across all locations and Fgra and Fcor were found mostly at high elevation (>800 m a.s.l.). The majority (97·8%) of stalk isolates was assigned to Fmer; three were assigned to Fgra. In the stubble, Fmer was less dominant (53%), with a shift towards Fcor as the most frequent species at high elevation sites (>600 m a.s.l.). No differences in the mycelial growth rate were observed among isolates from each species grown at 15°C. Fgra grew faster at 25°C and Fmer showed the widest range of variation across the isolates at both temperatures. The survey data suggest that Fmer may outcompete other species on ears and stalks in comparison to stubble. Additional sampling that controls for other factors, as well as direct testing of aggressiveness on ears and stalk tissue, will be needed to fully evaluate this hypothesis.
Does More Balanced Survey Response Imply Less Non-Response Bias?
Authors: Schouten Barry , Cobben Fannie , Lundquist Peter , Wagner James 
Published: December 2015

SummaryRecently, various indicators have been proposed as indirect measures of non-response error in surveys. They employ auxiliary variables, external to the survey, to detect non-representative or unbalanced response. A class of designs known as adaptive survey designs maximizes these indicators by applying different treatments to different subgroups. The natural question is whether the decrease in non-response bias that is caused by adaptive survey designs could also be achieved by non-response adjustment methods. We discuss this question and provide theoretical and empirical considerations, supported by a range of household and business surveys. We find evidence that more balanced response coincides with less non-response bias, even after adjustment.
Heat‐acclimatization and pre‐cooling: a further boost for endurance performance?
Authors: Schmit C. , Le Meur Y. , Duffield R. , Robach P. , Oussedik N. , Coutts A. J. , Hausswirth C. 
Published: December 2015

To determine if pre‐cooling (PC) following heat‐acclimatization (HA) can further improve self‐paced endurance performance in the heat, 13 male triathletes performed two 20‐km cycling time‐trials (TT) at 35 °C, 50% relative humidity, before and after an 8‐day training camp, each time with (PC) or without (control) ice vest PC. Pacing strategies, physiological and perceptual responses were assessed during each TT. PC and HA induced moderate (+10 ± 18 W; effect size [ES] 4.4 ± 4.6%) and very large (+28 ± 19 W; ES 11.7 ± 4.1%) increases in power output (PO), respectively. The overall PC effect became unclear after HA (+4 ± 14 W; ES 1.4 ± 3.0%). However, pacing analysis revealed that PC remained transiently beneficial post‐HA, i.e., during the first half of the TT. Both HA and PC pre‐HA were characterized by an enhanced PO without increased cardio‐thermoregulatory or perceptual disturbances, while post‐HA PC only improved thermal comfort. PC improved 20‐km TT performance in unacclimatized athletes, but an 8‐day HA period attenuated the magnitude of this effect. The respective converging physiological responses to HA and PC may explain the blunting of PC effectiveness. However, perceptual benefits from PC can still account for the small alterations to pacing noted post‐HA.
Outlier or Model of Austerity in Europe? The Case ofIrish Social Protection Reform
Authors: Dukelow Fiona , Considine Mairéad 
Published: December 2015

AbstractThis article analyses the evolution of theIrish economic crisis and its implications for social protection policy, specifically for working age adults, in the context ofEuropean integration andIreland's status as a small state member of theEU. We look at how neither small state characteristics, nor the position of small states in theEU, both of which raise problematic issues in their own right, are alone responsible forIreland's crisis situation. Such factors need to be understood in conjunction with national policy models and preferences which, in theIrish case, leant it something of an outlier status in theEU. Substantiating this argument and considering its implications for social protection reform, the article first examines the evolution ofIreland's liberal and increasingly financialized growth model in the context of greaterEuropean economic integration and how its risks intensified, but were also obscured, under Economic and Monetary Union (EMU). Second, against this backdrop and despite the growingEUrole in social policy, it examines how national policy factors meant that focus on income transfers remained dominant in social protection developments during the growth period spanning the mid‐1990s to 2008. Third, it analyses the unprecedented degree of social protection retrenchment and reform occurring since the crisis, highlighting the congruence between national efforts and the impact of conditionalities associated with financial assistance. The article concludes by considering the question of to what extentIreland will remain an outlier post‐crisis given the direction theEUhas taken in dealing with the Eurozone crisis to date.
Spatial organization of cellulose microfibrils and matrix polysaccharides in primary plant cell walls as imaged by multichannel atomic force microscopy
Authors: Zhang Tian , Zheng Yunzhen , Cosgrove Daniel J. 
Published: December 2015

SummaryWe used atomic force microscopy (AFM), complemented with electron microscopy, to characterize the nanoscale and mesoscale structure of the outer (periclinal) cell wall of onion scale epidermis – a model system for relating wall structure to cell wall mechanics. The epidermal wall contains ~100 lamellae, each ~40 nm thick, containing 3.5‐nm wide cellulose microfibrils oriented in a common direction within a lamella but varying by ~30 to 90° between adjacent lamellae. The wall thus has a crossed polylamellate, not helicoidal, wall structure. Montages of high‐resolutionAFMimages of the newly deposited wall surface showed that single microfibrils merge into and out of short regions of microfibril bundles, thereby forming a reticulated network. Microfibril direction within a lamella did not change gradually or abruptly across the whole face of the cell, indicating continuity of the lamella across the outer wall. A layer of pectin at the wall surface obscured the underlying cellulose microfibrils when imaged byFESEM, but not byAFM. TheAFMthus preferentially detects cellulose microfibrils by probing through the soft matrix in these hydrated walls.AFM‐based nanomechanical maps revealed significant heterogeneity in cell wall stiffness and adhesiveness at the nm scale. By color coding and merging these maps, the spatial distribution of soft and rigid matrix polymers could be visualized in the context of the stiffer microfibrils. Without chemical extraction and dehydration, our results provide multiscale structural details of the primary cell wall in its near‐native state, with implications for microfibrils motions in different lamellae during uniaxial and biaxial extensions.
RhD negativity among pregnant women in multiethnic Suriname
Authors: Zonneveld Rens , Schmitz Peter , Eppink Jedda , Mac Donald M. Sigrid , Nahar‐van Venrooij Lenny M.W. , Kanhai Humphrey H.H. , Zijlmans Wilco C.W.R. 
Published: December 2015

BACKGROUNDRhD negativity is distributed unevenly among different ethnicities. In this study we explored the frequencies of RhD negativity in pregnant women in multiethnic Suriname, along with screening results for red blood cell (RBC) antibodies in these women and their offspring. Results may help identify women at risk for hemolytic disease of the fetus and newborn.STUDY DESIGN AND METHODSA retrospective study was performed in pregnant women who delivered at three major hospitals in Suriname between January 1, 2013, and December 31, 2014.RESULTSThe overall prevalences of RhD negativity among 8686 women was 4.3%. The percentages of RhD negativity in Maroons, Creoles, and Hindustani women were 7.2, 5.4, and 3.7%, respectively. Chinese and Javanese women had very low prevalences of 0.8 and 0.5%, respectively, and Amerindians showed no RhD negativity. Antibody screening was positive in six D– (five Maroons and one Creole) women and weakly positive in three women (two Creoles and one Maroon), making overall antibody prevalence 4.4%. In 15 (5.5%; 10 Maroons, four Creoles, one Chinese) newborns from D– mothers antibody screening was positive.CONCLUSIONIn the multiethnic Surinamese population RhD negativity among pregnant women varied between 0.0 and 7.2% between ethnic groups. RBC antibodies were detected during pregnancy and in newborns in 4.4 and 5.5%, respectively.