bluuebunny/crossref_metadata_2025_split huggingface dataset:
An annotated consensus genetic map forPinus taedaL. and extent of linkage disequilibrium in three genotype-phenotype discovery populations
Authors: Westbrook Jared W. , Chhatre Vikram E. , Wu Le-Shin , Chamala Srikar , Neves Leandro Gomide , Muñoz Patricio , Martínez-García Pedro J. , Neale David B. , Kirst Matias , Mockaitis Keithanne , Nelson C. Dana , Peter Gary F. , Davis John M. , Echt Craig S. 
Published: December 2014

ABSTRACTA consensus genetic map forPinus taeda(loblolly pine) was constructed by merging three previously published maps with a map from a pseudo-backcross betweenP. taedaandP. elliottii(slash pine). The consensus map positioned 4981 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.48 centiMorgans and total map length was 2372 centiMorgans. Functional predictions for 4762 markers for expressed sequence tags were improved by alignment to full-lengthP. taedatranscripts. Alignments to theP. taedagenome mapped 4225 scaffold sequences onto linkage groups. The consensus genetic map was used to compare the extent of genome-wide linkage disequilibrium in an association population of distantly relatedP. taedaindividuals (ADEPT2), a multiple-family pedigree used for genomic selection studies (CCLONES), and a full-sib quantitative trait locus mapping population (BC1). Weak linkage disequilibrium was observed in CCLONES and ADEPT2. Average squared correlations, R2, between genotypes at SNPs less than one centiMorgan apart was less than 0.05 in both populations and R2did not decay substantially with genetic distance. By contrast, strong and extended linkage disequilibrium was observed among BC1 full-sibs where average R2decayed from 0.8 to less than 0.1 over 53 centiMorgans. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association and quantitative trait locus mapping between genotype-phenotype discovery populations.
Model checking to assess T-helper cell plasticity
Authors: Abou-Jaoudé Wassim , Monteiro Pedro T. , Naldi Aurélien , Grandclaudon Maximilien , Soumelis Vassili , Chaouiya Claudine , Thieffry Denis 
Published: December 2014

AbstractComputational modeling constitutes a crucial step towards the functional understanding of complex cellular networks. In particular, logical modeling has proven suitable for the dynamical analysis of large signaling and transcriptional regulatory networks. In this context, signaling input components are generally meant to convey external stimuli, or environmental cues. In response to such external signals, cells acquire specific gene expression patterns modeled in terms of attractors (e.g.stable states). The capacity for cells to alter or reprogram their differentiated states upon changes in environmental conditions is referred to as cell plasticity.In this article, we present a multivalued logical framework along with computational methods recently developed to efficiently analyze large models. We mainly focus on a symbolic model checking approach to investigate switches between attractors subsequent to changes of input conditions.As a case study, we consider the cellular network regulating the differentiation of T-helper cells, which orchestrate many physiological and pathological immune responses. To account for novel cellular subtypes, we present an extended version of a published model of T-helper cell differentiation. We then use symbolic model checking to analyze reachability properties between T-helper subtypes upon changes of environmental cues. This allows for the construction of a synthetic view of T-helper cell plasticity in terms of a graph connecting subtypes with arcs labeled by input conditions. Finally, we explore novel strategies enabling specific T-helper cell polarizing or reprograming events.
Down-Regulation of Kelch Domain-Containing F-Box Protein in Arabidopsis Enhances the Production of (Poly)phenols and Tolerance to Ultraviolet Radiation
Authors: Zhang Xuebin , Gou Mingyue , Guo Chunrong , Yang Huijun , Liu Chang-Jun 
Published: December 2014

AbstractPhenylpropanoid biosynthesis in plants engenders myriad phenolics with diverse biological functions. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway, directing primary metabolic flux into a phenylpropanoid branch. Previously, we demonstrated that the Arabidopsis (Arabidopsis thaliana) Kelch domain-containing F-box proteins, AtKFB01, AtKFB20, and AtKFB50, function as the negative regulators controlling phenylpropanoid biosynthesis via mediating PAL’s ubiquitination and subsequent degradation. Here, we reveal that Arabidopsis KFB39, a close homolog of AtKFB50, also interacts physically with PAL isozymes and modulates PAL stability and activity. Disturbing the expression of KFB39 reciprocally affects the accumulation/deposition of a set of phenylpropanoid end products, suggesting that KFB39 is an additional posttranslational regulator responsible for the turnover of PAL and negatively controlling phenylpropanoid biosynthesis. Furthermore, we discover that exposure of Arabidopsis to ultraviolet (UV)-B radiation suppresses the expression of all four KFB genes while inducing the transcription of PAL isogenes; these data suggest that Arabidopsis consolidates both transcriptional and posttranslational regulation mechanisms to maximize its responses to UV light stress. Simultaneous down-regulation of all four identified KFBs significantly enhances the production of (poly)phenols and the plant’s tolerance to UV irradiation. This study offers a biotechnological approach for engineering the production of useful phenolic chemicals and for increasing a plant’s resistance to environmental stress.
Predicting climate warming effects on green turtle hatchling viability and dispersal performance
Authors: Cavallo Catherine , Dempster Tim , Kearney Michael R. , Kelly Ella , Booth David , Hadden Kate M. , Jessop Tim S. 
Published: December 2014

Summary

Ectotherms are taxa considered highly sensitive to rapid climate warming. This is because body temperature profoundly governs their performance, fitness and life history. Yet, while several modelling approaches currently predict thermal effects on some aspects of life history and demography, they do not consider how temperature simultaneously affects developmental success and offspring phenotypic performance, two additional key attributes that are needed to comprehensively understand species responses to climate warming.

Here, we developed a stepwise, individual‐level modelling approach linking biophysical and developmental models with empirically derived performance functions to predict the effects of temperature‐induced changes to offspring viability, phenotype and performance, using green sea turtle hatchlings as an ectotherm model. Climate warming is expected to particularly threaten sea turtles, as their life‐history traits may preclude them from rapid adaptation.

Under conservative and extreme warming, our model predicted large effects on performance attributes key to dispersal, as well as a reduction in offspring viability. Forecast sand temperatures produced smaller, weaker hatchlings, which were up to 40% slower than at present, albeit with increased energy stores. Conversely, increases in sea surface temperatures aided swimming performance.

Our exploratory study points to the need for further development of integrative individual‐based modelling frameworks to better understand the complex outcomes of climate change for ectotherm species. Such advances could better serve ecologists to highlight the most vulnerable species and populations, encouraging prioritization of conservation effort to the most threatened systems.
Heat‐induced mortality and expression of heat shock proteins in Colorado potato beetles treated with imidacloprid
Authors: Chen Jie , Kitazumi Ai , Alpuerto Jasper , Alyokhin Andrei , de los Reyes Benildo 
Published: December 2014

AbstractThe Colorado potato beetle is an important pest of solanaceous plants in the Northern Hemisphere. Better understanding of its physiological responses to temperature stress and their interactions with still‐prevalent chemical control has important implications for the management of this insect. We measured mortality and expression of the Hsp70 heat shock proteins in the Colorado potato beetle larvae exposed to sublethal concentration of the commonly used insecticide imidacloprid, and to supraoptimal temperatures. Both turned out to be significant stress factors, although induction of Hsp70 by imidacloprid observed in the present study was low compared to its induction by the heat. The two factors also interacted with each other. At an extreme temperature of 43 °C, exposure to a sublethal dose of imidacloprid resulted in a significant rise in larval mortality, which was not observed at an optimal temperature of 25 °C. Heat‐stressed larvae also failed to respond to imidacloprid by producing more Hsp70. These findings suggest that when field rates of insecticides become insufficient for killing the exposed beetles under optimal temperature conditions due to the evolution of resistance in beetle populations, they may still reduce the probability of resistant beetles surviving the heat shock created by using propane flamers as a rescue treatment.
Putative nicotinic acetylcholine receptor subunits express differentially through the life cycle of codling moth, Cydia pomonella (Lepidoptera: Tortricidae)
Authors: Martin Jessica A. , Garczynski Stephen F. 
Published: December 2014

AbstractNicotinic acetylcholine receptors (nAChRs) are the targets of neonicotinoids and spinosads, two insecticides used in orchards to effectively control codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae). Orchardists in Washington State are concerned about the possibility of codling moth field populations developing resistance to these two insecticides. In an effort to help mitigate this issue, we initiated a project to identify and characterize codling moth nAChR subunits expressed in heads. This study had two main goals; (i) identify transcripts from a codling moth head transcriptome that encode for nAChR subunits, and (ii) determine nAChR subunit expression profiles in various life stages of codling moth. From a codling moth head transcriptome, 24 transcripts encoding for 12 putative nAChR subunit classes were identified and verified by PCR amplification, cloning, and sequence determination. Characterization of the deduced protein sequences encoded by putative nAChR transcripts revealed that they share the distinguishing features of the cys‐loop ligand‐gated ion channel superfamily with 9 α‐type subunits and 3 β‐type subunits identified. Phylogenetic analysis comparing these protein sequences to those of other insect nAChR subunits supports the identification of these proteins as nAChR subunits. Stage expression studies determined that there is clear differential expression of many of these subunits throughout the codling moth life cycle. The information from this study will be used in the future to monitor for potential target‐site resistance mechanisms to neonicotinoids and spinosads in tolerant codling moth populations.
De novo assembly of the transcriptome of Acanthaster planci testes
Authors: Stewart Michael James , Stewart Praphaporn , Rivera‐Posada Jairo 
Published: December 2014

AbstractA key strategy to reduce coral loss is the development of effective control method for the corallivorous crown‐of‐thorns sea star (Acanthaster planci), an omnipresent scourge and threat to the biodiversity of reefs in the Indo‐Pacific region. Limited genetic resources are available for this highly fecund species. In this study, we explored one aspect at the heart of A. planci outbreaks, the male reproductive system. Using high‐throughput sequencing technology, we report for first time the production of a comprehensive transcriptomic data set for the testes of A. placni that can aid in understanding the molecular mechanisms involved in A. planci spermatogenesis and fertilization. Through de novo transcriptome sequencing, we produced 52 965 998 raw reads corresponding to 4.76 Gb clean read data. From this, 243 870 contigs were assembled with Trinity and used to construct 92 792 unigenes. Distinct genes were then annotated with blastx yielding 30 810 unigenes above the cut‐off E‐value set at 10−5, with ESTScan database query analyses yielding up to 5366 unigenes to known hits. The identification of genes directly involved in sperm development (DEAD‐box family proteins), motility, fertilization and signalling (Bindin/Speract receptor) are also discussed.
Estimates from non‐replicated population surveys rely on critical assumptions
Authors: Knape Jonas , Korner‐Nievergelt Fränzi 
Published: December 2014

Summary

N‐mixture and occupancy models are often used to account for non‐detections in population surveys. The consensus has been that the methods require data that are replicated in space, as well as within a short period of time while the population at each site remains closed, in order for parameters such as detection probabilities and expected abundances to be identifiable. The requirement of replication prohibits the use of N‐mixture and occupancy models for many surveys in practice. Recently, some studies have argued that N‐mixture and occupancy models for surveys with only one visit at each site are identifiable when covariates for both detection probabilities and expected abundances, with at least one distinct covariate for each, are available (Journal of Plant Ecology, 5, 2012, 22; Environmetrics, 23, 2012, 197).

We investigate the reasons for why detection probabilities have traditionally been considered unestimable from non‐replicated counts and how the new methods sidestep these issues. We further use simulations to investigate properties of the new estimators.

We show that detection probabilities of the single‐visit models with covariates are non‐identifiable and that absolute abundances cannot be estimated when particular link functions are employed (log links for both expected abundance and detection probability). Further, assumptions about the range within which detection probabilities vary are necessary to render estimability. The possibility of estimating abundance from single‐visit surveys therefore implicitly hinges on knowledge about the link functions. Simulations show that estimates of abundance can be highly variable and sensitive to the choice of link function. We further show how a reduced parameterization of an N‐mixture model for surveys repeated over time, without replication under closure but where detection probabilities are constant over time, corresponds to a Poisson model.

Non‐robust estimation can result in misleading conclusions about population abundance. When estimating abundance from count data that are not replicated, it is therefore important to be aware of how imprecise estimators may be and how sensitive they are to model assumptions.
The concurrence of subacute cutaneous lupus erythematosus and hand‐foot syndrome in a patient undergoing capecitabine chemotherapy
Authors: Li Zhiming , Jiang Nanyan , Xu Yunsheng 
Published: December 2014

AbstractWe describe an unusual case of subacute cutaneous lupus erythematosus concurrent with hand‐foot syndrome, apparently associated with capecitabine treatment. We hypothesise that subacute cutaneous lupus erythematosus and hand‐foot syndrome may occur in a novel overlap syndrome.
Successful treatment of Dowling‐Degos disease using intense pulsed light
Authors: Gupta Aakriti , Huilgol Shyamala C 
Published: December 2014

AbstractDowling‐Degos disease (DDD) is a rare inherited pigmentary disorder characterised by reticulate pigmentation at flexural sites. No treatment modality has yet been established as a definitive method for the effective elimination of lentigines in DDD. We present a case of a 24‐year old woman with DDD treated successfully using intense pulsed light as a novel management strategy.
Fractionated microneedle radiofrequency for treatment of primary axillary hyperhidrosis: A sham control study
Authors: Fatemi Naeini Farahnaz , Abtahi‐Naeini Bahareh , Pourazizi Mohsen , Nilforoushzadeh Mohammad Ali , Mirmohammadkhani Majid 
Published: December 2014

AbstractBackground/ ObjectivePrimary axillary hyperhidrosis (PAH) creates social stress in patients. Although there are several options for treating PAH, only surgical modalities have conferred a permanent solution. This study evaluated the clinical effectiveness of fractionated microneedle radiofrequency (FMR) treatment for PAH.MethodsThis study is based on a single‐blind, sham control comparative design. In all, 25 patients with severe PAH underwent three sessions of FMR at 3‐week intervals. One side was treated with FMR while the other was sham controlled. Efficacy was evaluated using the hyperhidrosis disease severity scale (HDSS), sweating intensity visual analogue scale (VAS) and patient satisfaction at baseline, 3 weeks after each session and at 3 months after the last. Skin biopsies were obtained from two enrolled patients.ResultsThe HDSS and VAS demonstrated significant improvement after treatment on the treated side in comparison with the control side. The mean ± SD of the HDSS after 21 weeks were 1.87 ± 0.61 and 3.38 ± 0.49 (P < 0.001) for the treated and the controlled side, respectively. The follow‐up evaluation revealed that 79% of the patients showed a 1 or 2‐score decrease in HDSS. In total, 80% of patients reported more than 50% satisfaction at the end of the study. Histopathological findings showed a decrease of the number of the sweat glands in the treated side, confirming the above findings.ConclusionsTreatment of PAH with FMR as a non‐invasive modality can be a safe option with positive therapeutic effects on HDSS without any long‐lasting side effects.
Cutaneous non‐tuberculous mycobacterial infection in patients with chronic graft‐versus‐host disease: A case series
Authors: Moreno‐Bonilla Gilberto , Choy Bonita , Fernandez‐Peñas Pablo 
Published: December 2014

AbstractWe report the first case series of allogeneic haematopoietic stem‐cell transplant patients with graft versus host disease who developed cutaneous non‐tuberculous mycobacteria infection. A multidisciplinary approach, reduction of immunosuppressive medications, combination of antibiotics, close skin surveillance and excision of suitable lesions are recommended in this specific subgroup.
Gemcitabine and vinorelbine treatment in cutaneous T‐cell lymphoma in four patients
Authors: Mohd Affandi Azura , Blumetti Tatiana Pinto , Wells Jillian , Hertzberg Mark , Fernandez‐Peñas Pablo 
Published: December 2014

AbstractTreatment options for advanced stage cutaneous T‐cell lymphoma (CTCL) are limited by the their efficacy and side‐effects profile. Gemcitabine, a pyrimidine analogue, has been reported to be efficacious in CTCL. Most of the studies published used gemcitabine as a single agent in treating advanced CTCL. Our small case series demonstrated that a combination of gemcitabine and vinorelbine induced partial remission in all four patients with refractory or advanced CTCL, although the effects were not sustained for a long duration (2–6 months). Two patients had neutropenia and one had acute hepatitis, requiring discontinuation of treatment.
Think UV, not heat!
Authors: Wong Celestine C , Liu Wenyuan , Gies Peter , Nixon Rosemary 
Published: December 2014

AbstractBackgroundAustralia has the highest incidence of skin cancer in the world, a preventable disease caused primarily by exposure to ultraviolet radiation (UVR) in sunlight. Health promotion strategies play a significant role in sun protection.ObjectivesTo assess the understanding of a population sample as to the time of year that the sun was ‘at its most burning’ in Melbourne, Australia.MethodsA cross‐sectional study was performed using questionnaires completed at corporate skin checks, conducted on 668 participants during 2011 to 2013.ResultsOnly a minority (n = 82, 12%) gave the correct theoretical answer; the summer solstice or 21–22 December, while another 38% (n = 254) correctly named December and January as the times when the UVR is actually highest. In all, 18% (n = 122) said February was the month when the temperature is hottest and 170 (25%) either mentioned the period May–August when UVR is negligible in Melbourne or had no idea, including saying ‘all year round’. There was no significant difference in this knowledge between different age groups.ConclusionOne‐quarter of participants did not understand that sunburn was related to high levels of UVR, which occur in summer. Almost one‐fifth associated the heat of February with the highest UVR. Understanding these concepts is important for Australians residing in cooler parts of southern Australia, as UVR levels may be high and yet the temperature may be relatively cool. There needs to be more emphasis on UVR in sun awareness campaigns to prompt sun‐protective behaviour.
Evaluation of insulin resistance in idiopathic hirsutism compared with polycystic ovary syndrome patients and healthy individuals
Authors: Bonakdaran Shokoufeh , Kiafar Bita , Barazandeh Ahmadabadi Fatemeh 
Published: December 2014

AbstractIntroductionHirsutism is defined as the excessive male‐pattern growth of hair in women. Hirsutism is often idiopathic or the consequence of polycystic ovary syndrome (PCOS). Insulin resistance is common in PCOS (especially in obese patients) but the association between insulin resistance and idiopathic hirsutism (IH) is not clear. The aim of this study was to investigate the rate of insulin resistance in IH, compared with healthy individuals and patients with PCOS.MethodsThe study included three groups, patients with idiopathic hirsutism, PCOS and healthy women. Each group included 30 non‐obese women. Fasting blood sugar (FBS), insulin level and insulin resistance (estimated by the homeostasis model assessment [HOMA‐IRIR]) were compared in the three groups.ResultsThere was a significant difference between the age of the women with IH compared with two other groups. There were no significant difference in levels of serum insulin (P = 0.49, HOMA‐IR (P = 0.47) and prevalence of insulin resistance (P = 0.07) in the three groups. The age‐adjusted prevalence of insulin resistance was similar in the three groups.ConclusionInsulin resistance was no more frequent in IH patients than in healthy control groups.
Nasal‐type extranodal natural killer/T‐cell lymphoma presenting as a solitary non‐healing lower leg ulcer
Authors: Liaw Tse‐Yuan , Hu Stephen Chu‐Sung 
Published: December 2014

AbstractNasal‐type extranodal natural killer/T‐cell lymphoma (ENTCL) is an aggressive form of non‐Hodgkin's lymphoma with a poor prognosis. Primary cutaneous lesions ofENTCLusually present as nodules or infiltrative plaques. The presentation ofENTCLas a solitary ulcer, in the absence of other cutaneous lesions and systemic symptoms and signs, is extremely rare and may be easily misdiagnosed. In this report, we describe an unusual case ofENTCLwith a diagnostically challenging clinical presentation as a solitary non‐healing leg ulcer in an elderly woman.