bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudo‐value approach for comparing survival medians for dependent data
Authors: Ahn Kwang Woo , Mendolia Franco 
Published: December 2013

AbstractSurvival median is commonly used to compare treatment groups in cancer‐related research. The current literature focuses on developing tests for independent survival data. However, researchers often encounter dependent survival data such as matched pair data or clustered data. We propose a pseudo‐value approach to test the equality of survival medians for both independent and dependent survival data. We investigate the type I error and power of the proposed method by a simulation study, in which we examine independent and dependent data. The simulation study shows that the proposed method performs equivalently to the existing methods for independent survival data and performs better for dependent survival data. A study comparing survival median times for bone marrow transplants illustrates the proposed method. Copyright © 2013 John Wiley & Sons, Ltd.
Cesarean scar pregnancy and early placenta accreta share common histology
Authors: Timor‐Tritsch I. E. , Monteagudo A. , Cali G. , Palacios‐Jaraquemada J. M. , Maymon R. , Arslan A. A. , Patil N. , Popiolek D. , Mittal K. R. 
Published: December 2013

ABSTRACTObjectiveTo determine, by evaluation of histological slides, images and descriptions of early (second‐trimester) placenta accreta (EPA) and placental implantation in cases of Cesarean scar pregnancy (CSP), whether these are pathologically indistinguishable and whether they both represent different stages in the disease continuum leading to morbidly adherent placenta in the third trimester.MethodsThe database of a previously published review of CSP and EPA was used to identify articles with histopathological descriptions and electronic images for pathological review. When possible, microscopic slides and/or paraffin blocks were obtained from the original researchers. We also included from our own institutions cases of CSP and EPA for which pathology specimens were available. Two pathologists examined all the material independently and, blinded to each other's findings, provided a pathological diagnosis based on microscopic appearance. Interobserver agreement in diagnosis was determined.ResultsForty articles were identified, which included 31 cases of CSP and 13 cases of EPA containing histopathological descriptions and/or images of the pathology. We additionally included six cases of CSP and eight cases of EPA from our own institutions, giving a total of 58 cases available for histological evaluation (37 CSP and 21 EPA) containing clear definitions of morbidly adherent placenta. In the 29 cases for which images/slides were available for histopathological evaluation, both pathologists attested to the various degrees of myometrial and/or scar tissue invasion by placental villi with scant or no intervening decidua, consistent with the classic definition of morbidly adherent placenta. Based on the reviewed material, cases with a diagnosis of EPA and those with a diagnosis of CSP showed identical histopathological features. Interobserver correlation was high (kappa = 0.93).ConclusionsEPA and placental implantation in CSP are histopathologically indistinguishable and may represent different stages in the disease continuum leading to morbidly adherent placenta in the third trimester. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.
Genetic regulation of flowering time in annual and perennial plants
Authors: Khan Muhammad Rehman Gul , Ai Xiao‐Yan , Zhang Jin‐Zhi 
Published: December 2013

Flowering time plays a significant role in the reproductive success of plants. So far, five major pathways to flowering have been characterized in Arabidopsis, including environmental induction through photoperiod, vernalization, and gibberellins and autonomous floral iation, and aging by sequentially operating miRNAs (typically miR156 and miR172) responding to endogenous cues. The balance of signals from these pathways is integrated by a common set of genes (FLOWERING LOCUS C, FLOWERING LOCUS T, LEAFY, and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1) that determine the flowering time. Recent studies have indicated that epigenetic modification, alternative splicing, antisense RNA and chromatin silencing regulatory mechanisms play an important role in this process by regulating related flowering gene expression. In this review, we discuss the current understanding in genetic regulation of the phase transition from vegetative to reproductive growth by using Arabidopsis as a model. We also describe how this knowledge has been successfully applied for identifying homologous genes from perennial crops. Furthermore, detailed analysis of the similarities and differences between annual and perennial plants flowering will help elucidate the mechanisms of perennial plant maturation and regulation of floral initiation.This article is categorized under:

RNA in Disease and Development > RNA in Development
Neutral Pentacoordinate Silicon(IV) Complexes with a Tridentate Dianionic O,N,O or N,N,O Ligand, an Anionic PhX Ligand (X = O, S, Se), and a Phenyl Group: Synthesis and Structural Characterization in the Solid State and in Solution
Authors: Weiß Jörg , Theis Bastian , Baus Johannes A. , Burschka Christian , Bertermann Rüdiger , Tacke Reinhold 
Published: December 2013

Abstract A series of neutral pentacoordinate silicon(IV) complexes with a SiO3NC, SiO2SNC, SiO2SeNC, SiO2N2C, SiOSN2C, or SiOSeN2C skeleton was synthesized and structurally characterized by multinuclear NMR spectroscopy in the solid state and in solution and by single‐crystal X‐ray diffraction. The compounds studied contain a tridentate dianionic O,N,O or N,N,O ligand, an anionic PhX ligand (X = O, S, Se), and a phenyl group. The structures, NMR spectroscopic parameters, and chemical properties of these silicon(IV) complexes were compared with those of related compounds that contain a tridentate dianionic S,N,O ligand instead of the O,N,O or N,N,O ligand.
Trends in Incidentally Identified Thyroid Cancers Over a Decade: A Retrospective Analysis of 2,090 Surgical Patients
Authors: Bahl Manisha , Sosa Julie A. , Nelson Rendon C. , Esclamado Ramon M. , Choudhury Kingshuk Roy , Hoang Jenny K. 
Published: December 2013

AbstractBackgroundThe aim of this study was to describe trends in the incidence of incidental thyroid cancers and compare their characteristics with clinically presenting cancers.MethodsWe performed a retrospective review of patients with thyroid cancer who underwent thyroid surgery from 2003 to 2012. Patients’ initial presentation was categorized as incidental (on imaging or final surgical pathology) or clinical (palpable or symptomatic) cancer. Characteristics of incidental and clinical cancers were compared.ResultsOf the 2,090 patients who underwent thyroid surgery, 680 (33 %) were diagnosed with cancer. One hundred ninety (28 %) were incidental cancer, of which 101 were detected on imaging studies and 89 were detected on analysis of the surgical pathology specimens. The incidence of thyroid cancer increased by 7.6‐fold from 2003 to 2012. The proportion of incidental cancers on imaging did not increase, but incidental cancers found on pathology steadily increased from 6 % in 2003 to 20 % in 2012. 84 % of the cancers were papillary cancer, and the proportion of papillary cancer was similar for both clinical and incidental cancers. Clinical cancers were larger than incidental cancers on imaging (2.2 vs. 1.8 cm, p = 0.02). Incidental cancers on imaging were less likely to have lateral compartment nodal metastases (7 vs. 13 %, p < 0.001).ConclusionsThyroid cancer diagnoses have increased at our institution, but the proportion of incidental cancers identified on imaging relative to clinical cancers has been stable over a decade and is not the sole explanation for the observed increase in thyroid cancer diagnoses. Incidental cancers on imaging are smaller in size and less likely to have lateral compartment nodal metastases than clinical cancers.
Reciprocal Associations Between Depressive Symptoms and Disordered Eating Among Adolescent Girls and Boys: A Multiwave, Prospective Study
Authors: Ferreiro Fátima , Wichstrøm Lars , Seoane Gloria , Senra Carmen 
Published: December 2013

Abstract
Symptoms of depression and eating disorders increase during adolescence, particularly among girls, and they tend to co-occur. Despite this evidence, there is meager research on whether depression increases the risk of future eating pathology, or vice versa, and we do not know whether these processes are different for adolescent girls and boys. Accordingly, this study explored the prospective reciprocal associations between depressive symptoms and disordered eating at different time points from preadolescence to mid-adolescence and tested the moderator effect of gender on these associations. A community-based sample of Spanish youth (N = 942, 49 % female) was assessed at ages of approximately 10-11 (T1), 12-13 (T2), 14-15 (T3), and 16-17 (T4) years. The bidirectional relationships between depressive symptoms and disordered eating were estimated in an autoregressive cross-lagged model with latent variables. A unidirectional, age-specific association between depressive symptoms at T1 and disordered eating at T2 was found. No other significant cross-lagged effect emerged, but the stability of the constructs was considerable. Gender did not moderate any of the links examined. Regardless of gender, the transition from childhood to adolescence appears to be a key period when depressive symptoms foster the development of disordered eating. These findings suggest that early prevention and treatment of depression targeting both girls and boys may result in lower levels of depressive symptoms and disordered eating in adolescence.
Do patients with functional chest pain have neuroplastic reorganization of the pain matrix? A diffusion tensor imaging study
Authors: Frøkjær Jens Brøndum , Boldea Andra Sorina , Hoff Dag Arne Lihaug , Krarup Anne Lund , Hatlebakk Jan Gunnar , Dimcevski Georg , Drewes Asbjørn Mohr 
Published: December 2013

Abstract

Background and aims
In functional chest pain (FCP) of presumed esophageal origin central nervous system hyperexcitability is generally believed to play an important role in pain pathogenesis. However, this theory has recently been challenged. Using magnetic resonance diffusion tensor imaging, the aim was to characterize any microstructural reorganization of the pain neuromatrix in FCP patients.

Methods
13 FCP patients and 20 matched healthy controls were studied in a 3T MR scanner. Inclusion criteria were relevant chest pain, normal coronary angiogram and normal upper gastrointestinal evaluation. Apparent diffusion coefficient (ADC) (i.e. mean diffusivity of water) and fractional anisotropy (FA) (i.e. directionality of water diffusion as a measure of fiber organization) values were assessed in the secondary sensory cortex, cingulate cortex, insula, prefrontal cortex, and amygdala.

Results
Overall, including all regions, no difference in ADC and FA values was found between the patients and controls (P = 0.79 and P = 0.23, respectively). Post-hoc tests revealed no difference in ADC and FA values of the individual regions. However, a trend of patients having increased ADC in the mid insula grey matter and increased FA in the mid insula white matter was observed (both P = 0.065).

Conclusions
This explorative study suggests that microstructural reorganization of the central pain neuromatrix may not be present in well-characterized FCP patients.

Implications
This finding, together with recent neurophysiologal evidence, challenges the theory of visceral hypersensitivity due to changes in the central nervous system in FCP patients.
The Augmented Base Locus in Positive Characteristic
Authors: Cascini Paolo , McKernan James , Mustaţǎ Mircea 
Published: December 2013

AbstractLet L be a nef line bundle on a projective scheme X in positive characteristic. We prove that the augmented base locus of L is equal to the union of the irreducible closed subsets V of X such that L∣V is not big. For a smooth variety in characteristic 0, this was proved by Nakamaye using vanishing theorems.
Comparison of growth curves of two genotypes of dairy goats using nonlinear mixed models
Authors: REGADAS FILHO J. G. L. , TEDESCHI L. O. , RODRIGUES M. T. , BRITO L. F. , OLIVEIRA T. S. 
Published: December 2013

SUMMARYThe objective of the current study was to assess the use of nonlinear mixed model methodology to fit the growth curves (weightv.time) of two dairy goat genotypes (Alpine, +A and Saanen, +S). The nonlinear functions evaluated included Brody, Von Bertalanffy, Richards, Logistic and Gompertz. The growth curve adjustment was performed using two steps. First, random effectsu1,u2andu3were linked to the asymptotic body weight (β1), constant of integration (β2) and rate constant of growth (β3) parameters, respectively. In addition to a traditional fixed-effects model, four combinations of models were evaluated using random variables: all parameters associated with random effects (u1,u2andu3), onlyβ1andβ2(u1andu2), onlyβ1andβ3(u1andu3) and onlyβ1(u1). Second, the fit of the best adjusted model was refined by using the power variance and modelling the error structure. Residual variance ($\sigma _e^2 $) and the Akaike information criterion were used to evaluate the models. After the best fitting model was chosen, the genotype curve parameters were compared. The residual variance was reduced in all scenarios for which random effects were considered. The Richards (u1andu3) function had the best fit to the data. This model was reparameterized using two isotropic error structures for unequally spaced data, and the structure known in the literature as SP(MATERN) proved to be a better fit. The growth curve parameters differed between the two genotypes, with the exception of the constant that determines the proportion of the final size at which the inflection point occurs (β4). The nonlinear mixed model methodology is an efficient tool for evaluating growth curve features, and it is advisable to assign biologically significant parameters with random effects. Moreover, evaluating error structure modelling is recommended to account for possible correlated errors that may be present even when using random effects. Different Richard growth curve parameters should be used for the predominantly Alpine and Saanen genotypes because there are differences in their growth patterns.
Trophic niche differentiation and microhabitat utilization revealed by stable isotope analyses in a dry-forest bat assemblage at Ankarana, northern Madagascar
Authors: Dammhahn Melanie , Goodman Steven M. 
Published: December 2013

Abstract:Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measured stable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4‰ in δ15N and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3‰ enriched over plants) and different insectivorous bats as secondary consumers (c. 4‰ enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of δ13C–δ15N bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.
‘If labels for GM food were present, would consumers trust them?’ Insights from a consumer survey in Uganda
Authors: Kikulwe Enoch Mutebi , Falck-Zepeda José , Wesseler Justus 
Published: December 2013

AbstractFood labelling is costly. Food labelling is often demanded with the introduction of new food products such as genetically modified (GM) food. If consumers do not have trust in the label, scarce resources are wasted. This paper investigates factors affecting the trust in food labels among Ugandan consumers. The results suggest that older, less-educated individuals of smaller household sizes and with trust in government institutions have more trust in food labels. Other factors were also found to be important. The government has to consider those differences in consumer trust when designing a GM labelling policy.
Diversity and gaps in Pennisetum glaucum subsp. monodii (Maire) Br. germplasm conserved at the ICRISAT genebank
Authors: Upadhyaya H. D. , Reddy K. N. , Singh Sube , Gowda C. L. L. , Irshad Ahmed M. , Kumar Vinod 
Published: December 2013

The International Crops Research Institute for the Semi-Arid Tropics conserves 335 accessions of Pennisetum glaucum subsp. monodii originated in 13 countries. In the present study, the collection was evaluated and assessed for diversity and geographical gaps. A wide variation was observed in the collection for total tillers per plant (16 to 609), productive tillers per plant (12 to 368), leaf length (21.3 to 58.8 cm) and leaf width (8.1 to 33.1 mm), indicating high fodder yield potential of the collection. The accessions of cluster 3 flowered late, grew tall with thick stems and long and broad leaves, and differed significantly from those of cluster 1 and cluster 2. The accessions of cluster 2 were found to be promising for tillering. The highly significant positive correlation (r= 0.944) between total and productive tillers per plant suggests that the selection for total tillers will result in selection for productive tillers. A total of 354 districts located in 86 provinces of eight countries in the primary centre of origin for pearl millet were identified as geographical gaps. The probability map generated using FloraMap in the present study matched quite closely to the origin of pearl millet, supporting the prediction of P.glaucum subsp. monodii occurrence in the primary centre of diversity for pearl millet. The high fodder yield potential of P.glaucum subsp. monodii germplasm and low intensity of collection in countries under study suggest the need for launching germplasm collection missions, exclusively for pearl millet wild relatives to fill taxonomic and geographical gaps in the collection.
Symbiotic relationships between soil fungi and plants reduce N2O emissions from soil
Authors: Bender S Franz , Plantenga Faline , Neftel Albrecht , Jocher Markus , Oberholzer Hans-Rudolf , Köhl Luise , Giles Madeline , Daniell Tim J , van der Heijden Marcel G A 
Published: December 2013

Abstract
N2O is a potent greenhouse gas involved in the destruction of the protective ozone layer in the stratosphere and contributing to global warming. The ecological processes regulating its emissions from soil are still poorly understood. Here, we show that the presence of arbuscular mycorrhizal fungi (AMF), a dominant group of soil fungi, which form symbiotic associations with the majority of land plants and which influence a range of important ecosystem functions, can induce a reduction in N2O emissions from soil. To test for a functional relationship between AMF and N2O emissions, we manipulated the abundance of AMF in two independent greenhouse experiments using two different approaches (sterilized and re-inoculated soil and non-mycorrhizal tomato mutants) and two different soils. N2O emissions were increased by 42 and 33% in microcosms with reduced AMF abundance compared to microcosms with a well-established AMF community, suggesting that AMF regulate N2O emissions. This could partly be explained by increased N immobilization into microbial or plant biomass, reduced concentrations of mineral soil N as a substrate for N2O emission and altered water relations. Moreover, the abundance of key genes responsible for N2O production (nirK) was negatively and for N2O consumption (nosZ) positively correlated to AMF abundance, indicating that the regulation of N2O emissions is transmitted by AMF-induced changes in the soil microbial community. Our results suggest that the disruption of the AMF symbiosis through intensification of agricultural practices may further contribute to increased N2O emissions.
Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents
Authors: Müller Albert Leopold , de Rezende Júlia Rosa , Hubert Casey R J , Kjeldsen Kasper Urup , Lagkouvardos Ilias , Berry David , Jørgensen Bo Barker , Loy Alexander 
Published: December 2013

AbstractMicrobial biogeography is influenced by the combined effects of passive dispersal and environmental selection, but the contribution of either factor can be difficult to discern. As thermophilic bacteria cannot grow in the cold seabed, their inactive spores are not subject to environmental selection. We therefore conducted a global experimental survey using thermophilic endospores that are passively deposited by sedimentation to the cold seafloor as tracers to study the effect of dispersal by ocean currents on the biogeography of marine microorganisms. Our analysis of 81 different marine sediments from around the world identified 146 species-level 16S rRNA phylotypes of endospore-forming, thermophilic Firmicutes. Phylotypes showed various patterns of spatial distribution in the world oceans and were dispersal-limited to different degrees. Co-occurrence of several phylotypes in locations separated by great distances (west of Svalbard, the Baltic Sea and the Gulf of California) demonstrated a widespread but not ubiquitous distribution. In contrast, Arctic regions with water masses that are relatively isolated from global ocean circulation (Baffin Bay and east of Svalbard) were characterized by low phylotype richness and different compositions of phylotypes. The observed distribution pattern of thermophilic endospores in marine sediments suggests that the impact of passive dispersal on marine microbial biogeography is controlled by the connectivity of local water masses to ocean circulation.
Structural basis of AMPK regulation by small molecule activators
Authors: Xiao Bing , Sanders Matthew J. , Carmena David , Bright Nicola J. , Haire Lesley F. , Underwood Elizabeth , Patel Bhakti R. , Heath Richard B. , Walker Philip A. , Hallen Stefan , Giordanetto Fabrizio , Martin Stephen R. , Carling David , Gamblin Steven J. 
Published: December 2013

AbstractAMP-activated protein kinase (AMPK) plays a major role in regulating cellular energy balance by sensing and responding to increases in AMP/ADP concentration relative to ATP. Binding of AMP causes allosteric activation of the enzyme and binding of either AMP or ADP promotes and maintains the phosphorylation of threonine 172 within the activation loop of the kinase. AMPK has attracted widespread interest as a potential therapeutic target for metabolic diseases including type 2 diabetes and, more recently, cancer. A number of direct AMPK activators have been reported as having beneficial effects in treating metabolic diseases, but there has been no structural basis for activator binding to AMPK. Here we present the crystal structure of human AMPK in complex with a small molecule activator that binds at a site between the kinase domain and the carbohydrate-binding module, stabilising the interaction between these two components. The nature of the activator-binding pocket suggests the involvement of an additional, as yet unidentified, metabolite in the physiological regulation of AMPK. Importantly, the structure offers new opportunities for the design of small molecule activators of AMPK for treatment of metabolic disorders.