bluuebunny/crossref_metadata_2025_split huggingface dataset:
How old are quantitative trait loci and how widely do they segregate?
Authors: Kemper K.E. , Hayes B.J. , Daetwyler H.D. , Goddard M.E. 
Published: March 2015

SummaryThe mutations that cause genetic variation in quantitative traits could be old and segregate across many breeds or they could be young and segregate only within one breed. This has implications for our understanding of the evolution of quantitative traits and for genomic prediction to improve livestock. We investigated the age of quantitative trait loci (QTL) for milk production traits identified as segregating in Holstein dairy cattle. We use a multitrait method and found that six of 11 QTL also segregate in Jerseys. Variants identified as Holstein‐only QTL were fixed or rare [minor allele frequency (MAF) < 0.05] in Jersey. The age of the QTL mutations appears to vary from perhaps 2000 to 50 000 generations old. The older QTL tend to have high derived allele frequencies and often segregate across both breeds. Holstein‐only QTL were often embedded within longer haplotypes, supporting the conclusion that they are typically younger mutations that have occurred more recently than QTL that segregate in both breeds. A reference population for genomic prediction using both Holsteins and Jersey cattle incorrectly predicted a QTL in Jersey cattle when the QTL only segregates in Holsteins. Overcoming this error should help to make genomic prediction more accurate in smaller breeds.
Quantitative genetics of disease traits
Authors: Wray N.R. , Visscher P.M. 
Published: March 2015

SummaryJohn James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James’ most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case–control data and review recent applications in human genetics.
Managing the rate of increase in average co‐ancestry in a rolling front tree breeding strategy
Authors: Kerr R.J. , McRae T.A. , Dutkowski G.W. , Tier B. 
Published: March 2015

SummaryIn breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long‐ and short‐term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by the STBA (Pinus radiata and Eucalyptus globulus) is the long interval (up to 7 years) between when an individual is mated and when its progeny is first assessed in field trials and performance data included in the national performance database. Mate selection methods must therefore recognize the large pool of unmeasured progeny generated over recent years of crossing. In addition, the substantial delay between when an individual is selected in a field trial and when it is clonally copied into a mating facility (breeding arboretum) means that selection and mating must occur as a two‐step process. In this article, we describe modifications to preselection and mate selection algorithms that allow unmeasured progeny (juveniles) to be recognized. We also demonstrate that the addition of hypothetical new progeny to the juvenile pool is important for computing the increase in average co‐ancestry in the population. Methods outlined in this article may have relevance to animal breeding programmes where between mating and progeny measurement, new rounds of mating are initiated.
Relationship of Leptin with adiposity and inflammation and Resistin with disease severity in Psoriatic patients undergoing anti‐TNF‐alpha therapy
Authors: Pina T. , Genre F. , Lopez‐Mejias R. , Armesto S. , Ubilla B. , Mijares V. , Dierssen‐Sotos T. , Gonzalez‐Lopez M.A. , Gonzalez‐Vela M.C. , Blanco R. , Hernández J.L. , Llorca J. , Gonzalez‐Gay M.A. 
Published: March 2015

AbstractBackgroundAltered secretion patterns of proinflammatory adipokines may influence the increased risk of cardiovascular mortality observed in patients with chronic inflammatory diseases.ObjectiveTo determine whether two adipokines, leptin and resistin, correlate with metabolic syndrome features and disease severity in psoriatic patients who underwent anti‐TNF‐α therapy.MethodsProspective study of consecutive non‐diabetic patients with moderate‐to‐severe psoriasis who completed 6 months of therapy with anti‐TNF‐α‐ adalimumab. Patients with kidney disease, hypertension or body mass index ≥35 Kg/m2 were excluded. Metabolic and clinical evaluation was performed at the onset of anti‐TNF‐α treatment and at month 6.ResultsTwenty‐nine patients were assessed. A correlation between adiposity and leptin was observed (waist circumference and leptin levels after 6 months of therapy: r = 0.43; P = 0.030). Leptin concentration also correlated with blood pressure before adalimumab onset (systolic: r = 0.48; P = 0.013 and diastolic blood pressure: r = 0.50; P = 0.010 ). A marginally significant negative correlation between insulin sensitivity (QUICKI) and leptin levels was also observed. CRP levels correlated with leptin prior to the onset of adalimumab (r = 0.45; P = 0.020) and with resistin both before (r = 0.45; P = 0.020) and after 6 months of therapy (r = 0.55; P = 0.004). A positive association between parameters of disease activity such as BSA (r = 0.60; P = 0.001) and PASI (r = 0.63; P = 0.001) prior to the onset of adalimumab therapy and resistin concentrations was also disclosed. No significant changes in leptin and resistin concentrations following the 6‐month treatment with adalimumab were seen.ConclusionIn patients with moderate‐to‐severe psoriasis leptin correlates with metabolic syndrome features and inflammation whereas resistin correlate with inflammation and disease severity.
Native Amazonians’ Strategic Urbanization: Shaping Territorial Possibilities through Cities
Authors: McSweeney Kendra , Jokisch Brad 
Published: March 2015

ResumenEste artículo se basa en fuentes etnográficas dispares con la finalidad de examinar la relación entre la urbanización de la población de la Amazonía y su lucha por los derechos al territorio. En el argumento que ésta dinámica contraria a la intuición, merece una mayor atención, especialmente porque recientes políticas sobre la urbanización indígena ocultan dicha posibilidad. Específicamente muestro cómo en la Amazonía: (1) las cadenas migratorias que conectan remotas ciudades con las tierras indígenas, a menudo han sido forjadas por los líderes indígenas que viajan a los lugares donde reside el poder del estado, con el fin de demandar sus derechos sobre el territorio; (2) la vida en las ciudades puede servir para politizar a los citadinos indígenas, con consecuencias a largo plazo en sus luchas por el territorio; (3) el movimiento de la población indígena entre las ciudades y sus territorios de origen puede mantener y difundir estos efectos políticos a través del espacio y del tiempo. Presto atención a estas dinámicas con el objetivo de cuestionar la posible justificación de los textos políticos de la desposesión de las tierras indígenas enmarcando la urbanización indígena como genérica, inevitable y, en última instancia, desempoderando las posiciones indígenas sobre el territorio. [Amazonía, migración, pueblos indígenas, territorialización, territorio, urbanización]
Pueblos indígenas y usos contra‐hegemónicos de la ley en la disputa por la justicia: La Policía Comunitaria de Guerrero
Authors: Sierra María Teresa 
Published: March 2015

ResumenEn México y América Latina, en general, aumentan los casos en que los pueblos indígenas hacen un uso contra‐hegemónico de la ley para disputar la justicia y defender sus derechos. Esto sucede con la Policía Comunitaria de Guerrero, institución emblemática de los pueblos indígenas de México que desde 1998 garantiza de manera autónoma la seguridad y la justicia en un amplio territorio del sur occidente del país. A partir de un juicio público inédito en el que por primera vez actores no estatales juzgan a autoridades judiciales del Estado analizo el sentido en que consejeros y autoridades de la Comunitaria recurren a la ley oficial para exigir el respeto a su propio derecho y a sus instituciones. Desnudan de esta manera el carácter ambiguo y fragmentario de la ley, la impunidad de la justicia oficial así como la fragilidad del poder soberano que termina negociando con las autoridades indígenas. Esto sucede en contextos de aumento drástico de la inseguridad y la violencia en la región y en el país, al mismo tiempo que actores estatales, del crimen organizado y de compañías mineras transnacionales, presionan por acceder a los territorios indígenas.
“Fraudulent” Identities: The Politics of Defining Quilombo Descendants in Brazil
Authors: Farfán‐Santos Elizabeth 
Published: March 2015

AbstractThis article analyzes the role of historians and anthropologists in the conceptualization of “quilombo,” past and present, in Brazil. The validity of the new political identity, remanescente de quilombo (quilombo descendant), has been contested by the popular media as a “fraudulent” identity used by black communities to obtain land rights. While the term quilombo was used by the Portuguese Crown to refer to three or more fugitive slaves in hiding, quilombo descendants have been defined beyond the limits of simply the ancestors of fugitive slaves. I argue that when it comes to quilombo descendants obtaining actual rights they are often dismissed as frauds until proven authentic. Their authenticity depends not only on their ability to perform and describe the ancestral history of their community, but more importantly, in their ability to tell a specific history of their past as it has been written and incorporated into the Brazilian national imaginary.
The Legislative Lacuna on Assisted Reproduction: Reimagining the Modern Mexican State
Authors: Braff Lara 
Published: March 2015

ResumenBasado en el trabajo de campo en las clínicas de fertilidad de la Ciudad de México, este artículo examina cómo los pacientes y médicos que forman parte de tratamientos de fertilidad re‐imaginan su relación con el Estado. Ambos ven las tecnologías de reproducción asistida (TRAs) como algo problemático en México debido a la ausencia de una ley que regule sus usos. La pretensión de estos actores es que los oficiales del Estado aprueben una ley que proteja a los pacientes y los embriones y que legitime a los médicos de fertilidad en Mexico. La expectativa es que las clínicas de fertilidad locales se emparejen con aquellas del hemisferio norte. Al suplicar un mayor involucramiento del Estado con las TRAs, mis informantes se encuentran re‐conceptualizando el Estado en términos completamente modernos: responsivo a sus preocupaciones reproductivas y ya no exclusivamente dedicado a estrategias de control de la población propias de finales del siglo XX.
Tourism and the Transformation of Daily Life Along the Riviera Maya of Quintana Roo, Mexico
Authors: Pi‐Sunyer Oriol , Thomas R. Brooke 
Published: March 2015

ResumenEn el espacio de menos de dos décadas, los habitantes de Quintana Roo han tenido que enfrentar cambios radicales ocasionados por el turismo de masas. El turismo se ha convertido en la industria dominante y esto ha puesto en marcha un ciclo de desarrollo turístico y de migración masiva de otras partes de México y del exterior. Una región que no hace mucho tiempo se consideraba el territorio más marginal de la nación, hoy atrae millones de turistas de todo el mundo, la mayoría de los Estados Unidos y Europa. En un contexto de cambio acelerado y control empresarial, la vida de muchas personas, incluso la población maya, es altamente imprevisible y estresante. La expansión del turismo se ha desplazado recientemente a Tulum, una ciudad que está emergiendo como una localidad de pequeños, pero bien cómodos, hoteles.
The effect of CO2 laser treatment on skin tissue
Authors: Baleg Sana Mohammed Anayb , Bidin Noriah , Suan Lau Pik , Ahmad Muhammad Fakarruddin Sidi , Krishnan Ganesan , Johari Abd Rahman , Hamid Asma 
Published: March 2015

SummaryBackground/ObjectiveThe aim of this study was to evaluate the effects of multiple pulses on the depth of injury caused by CO2 laser in an in vivo rat model.MethodsA 10 600‐nm CO2 laser was applied to rat skin, with one side of the rat dorsal skin being exposed, leaving the other side as a control.ResultsAll of the various laser pulses tested led to gradual loss of epidermal thickness as well as a dramatic increase in thermal damage depth. Collagen coagulation was most effective with ten pulses of CO2 laser, while the strength of irradiated skin tissue increased as the influence of the laser increased.ConclusionFundamental laser–skin interaction effects were studied using a CO2 laser. The photodamaged areas obtained from laser interaction were recorded via couple charge device video camera and analyzed via ImageJ software. Photodamage induced by CO2 laser is due to photothermal effects, which involve burning and vaporizing mechanisms to ablate the epidermis layer. The burning area literally expands and penetrates deep into the dermis layer, subsequently causing collagen coagulation. This fundamental study shows in detail the effect of CO2 laser interaction with skin. The CO2 attributed severe burning, producing deep coagulation, and induced strength to treated skin.
H2O2 activates matrix metalloproteinases through the nuclear factor kappa B pathway and Ca2+ signals in human periodontal fibroblasts
Authors: Osorio C. , Cavalla F. , Paula‐Lima A. , Díaz‐Araya G. , Vernal R. , Ahumada P. , Gamonal J. , Hernández M. 
Published: March 2015

BackgroundThe mechanisms involved in reactive oxygen species and matrix metalloproteinase (MMP)‐mediated periodontal tissue breakdown are unknown.ObjectiveTo determine the effect of H2O2 in MMP‐2 and MMP‐9 activity, and the involvement of nuclear factor kappa B (NFκB) and Ca2+‐mediated signals in human periodontal ligament fibroblasts.Material and MethodsPrimary cultures were characterized for their phenotype and exposed for 24 h to sublethal doses (2.5–10 μm) of H2O2 or control media. NFκB involvement was evaluated through immunofluorescence of p65 subunit, using the NFκB blocking peptide SN50 and catalase. Ca2+ signals were analyzed by loading the cells with Fluo4‐AM and recording the fluorescence changes in a confocal microscope before and after the addition of H2O2. 1,2‐bis(o‐aminophenoxy) ethane‐N,N,N′,N′‐tetraacetic acid‐acetoxymethyl was used to chelate intracellular Ca2+. The activity and levels of MMP‐2 and MMP‐9 were analyzed by gelatin zymogram and densitometric scanning, and enzyme‐linked immunosorbent assay, respectively. Statistical analysis was performed with stata V11.1 software using the ANOVA test.ResultsH2O2 at concentrations of 2.5–5 μm induced Ca2+ signaling and NFκB subunit p65 nuclear translocation, whereas catalase, SN50 and BAPTA‐AM prevented p65 nuclear translocation. H2O2 at 2.5–5 μm significantly increased MMP‐9 and MMP‐2 activity, while SN50 resulted in lower MMP‐2 and MMP‐9 activity rates compared with controls.ConclusionSublethal H2O2 induces Ca2+‐dependent NFκB signaling with an increase in MMP gelatinolytic activity in human periodontal ligament.
Direct effect of streptozotocin on periodontal ligament cells through myeloid cell leukemia‐1
Authors: Shin J.‐A. , Hong I.‐S. , Oh S. , Cho S.‐D. , Lee K.‐E. 
Published: March 2015

ObjectiveWe hypothesized that streptozotocin (STZ) has a direct impact on periodontal ligament cell (PDL) damage as a potential direct inducer of periodontitis.BackgroundSince diabetes was accepted as one of the risk factors for the development of periodontal disease, various scientific studies have been undertaken in the STZ‐induced periodontal disease models. STZ induces β‐cell damage and subsequent diabetes development in vivo. Until now, assessment of the impacts of STZ‐induced experimental diabetes on periodontitis has generally been conducted on the fundamental assumption that STZ have no direct action on PDL and its function. However, several recent studies suggest that STZ also directly affect many different biological functions in various tissues or organs.Material and MethodsTo assess the apoptotic effects of STZ on PDLs, they were treated with or without STZ at different concentrations. Qualitative estimation of apoptotic cell death was obtained by live/dead assay. The expression levels of apoptosis‐related proteins were evaluated by western blot analysis.ResultsSTZ inhibits growth and induces apoptosis in PDLs in a dose‐dependent manner. Furthermore, STZ dramatically induced Mcl‐1 downregulation in a proteasome‐dependent manner and thereby induced apoptosis of PDLs through the Bak/Bax apoptotic signaling pathway.ConclusionOur results support the hypothesis that suppression of the cellular Mcl‐1 levels by STZ may be at least partly attributed to the development of periodontitis in STZ‐induced diabetic animal models.
T‐lymphocyte phenotype and function triggered by Aggregatibacter actinomycetemcomitans is serotype‐dependent
Authors: Díaz‐Zúñiga J. , Melgar‐Rodríguez S. , Alvarez C. , Monasterio G. , Benítez A. , Ciuchi P. , Díaz C. , Mardones J. , Escobar A. , Sanz M. , Vernal R. 
Published: March 2015

Background and ObjectiveBased on lipopolysaccharide (LPS) antigenicity, different Aggregatibacter actinomycetemcomitans serotypes have been described. Serotype b strains have demonstrated a stronger capacity to trigger cytokine production on dendritic cells (DCs). As DCs regulate the development of T‐lymphocyte lineages, the objective of this investigation was to study the response of T lymphocytes after being stimulated with autologous DCs primed with different bacterial strains belonging to the most prevalent serotypes of A. actinomycetemcomitans in humans: a–c.Material and MethodsHuman DCs were primed with increasing multiplicity of infection (10−1–102) or the purified LPS (10–50 ng/mL) of A. actinomycetemcomitans serotypes a–c and then used to stimulate autologous naïve CD4+ T lymphocytes. The T‐helper (Th) type 1, Th2, Th17 and T‐regulatory transcription factors T‐bet, GATA‐3, RORC2 and Foxp3, which are the master‐switch genes implied in their specific differentiation, as well as T‐cell phenotype‐specific cytokine patterns were quantified by real‐time reverse transcription–polymerase chain reaction and enzyme‐linked immunosorbent assay. In addition, the intracellular expression of T‐bet/interferon‐γ, GATA‐3/interleukin‐4, RORC2/interleukin‐17A and Foxp3/transforming growth factor‐β1 was analysed by double staining and flow cytometry.ResultsAll the A. actinomycetemcomitans serotypes led to T‐lymphocyte activation; however, when T lymphocytes were stimulated with DCs primed with the A. actinomycetemcomitans serotype b strain or their purified LPS, higher levels of Th1‐ and Th17‐associated transcription factors and cytokines were detected compared with similar experiments with the other serotypes.ConclusionThese results demonstrate that serotype b of A. actinomycetemcomitans has a higher capacity of trigger Th1 and Th17 phenotype and function and it was demonstrated that their LPS is a more potent immunogen compared with the other serotypes.
Bacteriophage predation promotes serovar diversification in Listeria monocytogenes
Authors: Eugster Marcel R. , Morax Laurent S. , Hüls Vanessa J. , Huwiler Simona G. , Leclercq Alexandre , Lecuit Marc , Loessner Martin J. 
Published: March 2015

SummaryListeria monocytogenes is a bacterial pathogen classified into distinct serovars (SVs) based on somatic and flagellar antigens. To correlate phenotype with genetic variation, we analyzed the wall teichoic acid (WTA) glycosylation genes of SV 1/2, 3 and 7 strains, which differ in decoration of the ribitol‐phosphate backbone with N‐acetylglucosamine (GlcNAc) and/or rhamnose. Inactivation of lmo1080 or the dTDP‐l‐rhamnose biosynthesis genes rmlACBD (lmo1081–1084) resulted in loss of rhamnose, whereas disruption of lmo1079 led to GlcNAc deficiency. We found that all SV 3 and 7 strains actually originate from a SV 1/2 background, as a result of small mutations in WTA rhamnosylation and/or GlcNAcylation genes. Genetic complementation of different SV 3 and 7 isolates using intact alleles fully restored a characteristic SV 1/2 WTA carbohydrate pattern, including antisera reactions and phage adsorption. Intriguingly, phage‐resistant L. monocytogenes EGDe (SV 1/2a) isolates featured the same glycosylation gene mutations and were serotyped as SV 3 or 7 respectively. Again, genetic complementation restored both carbohydrate antigens and phage susceptibility. Taken together, our data demonstrate that L. monocytogenes SV 3 and 7 originate from point mutations in glycosylation genes, and we show that phage predation represents a major driving force for serovar diversification and evolution of L. monocytogenes.
Factors associated with nutritional status in children aged 5–24 months in the Republic of Cameroon
Authors: Nagahori Chikako , Tchuani Jean Paul , Yamauchi Taro 
Published: March 2015

AbstractThis study was conducted to clarify nutritional status and associated factors in 5–24 month old children in the district of Batouri, Republic of Cameroon. Mothers were interviewed using a semistructured questionnaire, and the child's weight, length, head circumference, and mid‐upper arm circumference was collected. The data were compared with child growth standards proposed by the World Health Organization using Z‐scores; χ2‐test, Fisher's exact test, and Wilcoxon rank sum test were used to determine variables associated with malnutrition. A total of 100 mother–child pairs participated in this study; valid data from 100 pairs were subjected to analysis. The percentages of children with malnutrition indicators were wasting (6%), stunting (31%), underweight (14%), and low mid‐upper arm circumference (16%). Five factors were found to be statistically significant in their association with the children's malnutrition: mother's age, child's age, mother's educational level, mothers who had family planning information, and the source of tap water. A high percentage of stunting was positively associated with a high percentage of chronic malnutrition. We speculate that insufficient nutrition was more likely to begin after weaning.