bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial DNA reveals high genetic divergence between populations of Chalcides mertensi Klausewitz, 1954 (Reptilia: Scincidae) from Tunisia
Authors: Giovannotti Massimo , Nisi Cerioni Paola , Splendiani Andrea , Kalboussi Mohsen , Ruggeri Paolo , Caputo Barucchi Vincenzo 
Published: September 2013

Genetic diversity of four populations of Chalcides mertensi (Klausewitz, 1954) from Tunisia was analyzed by means of the Restriction Fragment Length Polymorphism (RFLP) analysis of two fragments of mitochondrial DNA (mtDNA) encompassing NADH dehydrogenase subunits 1 and 2 (ND-1/2) and NADH dehydrogenase subunits 3, 4 and 4L (ND-3/4). Phylogenetic relationships between haplotypes were inferred by analysing the sequence of 396 base pairs at the 5′ end of the mitochondrial gene encoding cytochrome b and a segment of 12S rRNA gene (386 bp). The results of this study highlighted a pronounced genetic divergence between the populations from northern (Ain Soltane and Tabarka) and southern (Kasserine and Sidi Bouzid) Tunisia, that the phylogenetic analysis recovered as two distinct taxonomic entities. These two groups of populations can therefore be ascribed to two distinct taxa, with southern populations probably representing the typical C. mertensi, whereas northern individuals are likely to represent a new species of grass swimming Chalcides. The divergence between these two taxonomic entities can be referred to palaeogeographic and palaeoclimatic events that have affected northwestern Africa during the last 10 Million years. The analysed populations show a low genetic variability that can be related to the past climatic and geologic events and the colonization processes that took place with environmental amelioration, and to the peripheral position of these populations in the distributional range of the species. However, a more exhaustive study, including Algerian and Moroccan skink populations will be necessary in order to clarify these issues.
Taxonomic revision of Drymoluber Amaral, 1930 (Serpentes: Colubridae)
Authors: COSTA HENRIQUE CALDEIRA , MOURA MÁRIO RIBEIRO , FEIO RENATO NEVES 
Published: September 2013

The present study is a taxonomic revision of the genus Drymoluber Amaral, 1930, using meristic and morphometric characters, aspects of external hemipenial morphology and body coloration. Sexual dimorphism occurs in D. dichrous and D. brazili but was not detected in D. apurimacensis. Morphological variation within D. dichrous is related to geographic distance between populations. Furthermore, variation in the number of ventrals and subcaudals in D. dichrous and D. brazili follows latitudinal and longitudinal clinal patterns. Drymoluber dichrous is diagnosed by the presence of 15-15-15 smooth dorsal scale rows with two apical pits, and 157–180 ventrals and 86–110 subcaudals; it occurs along the eastern versant of the Andes, in the Amazon forest, on the Guiana Shield, in the Atlantic forest, and its transitional areas with the Caatinga and Cerrado. Drymoluber brazili has 17-17-15 smooth dorsal scale rows with two apical pits, 182–202 ventrals and 109–127 subcaudals, and ranges throughout the Caatinga, Cerrado, Atlantic forest and transitional areas between these last two domains. Drymoluber apurimacensis has 13-13-13 smooth dorsal scale rows without apical pits, 158–182 ventrals and 84–93 subcaudals, and occurs in the Apurímac Valley, south of the Apurímac and Pampas rivers in Peru.
Exploring the Mechanisms of Ice Nucleation on Kaolinite: From Deposition Nucleation to Condensation Freezing
Authors: Welti André , Kanji Zamin A. , Lüönd F. , Stetzer Olaf , Lohmann Ulrike 
Published: September 2013

AbstractTo identify the temperature and humidity conditions at which different ice nucleation mechanisms are active, the authors conducted experiments on 200-, 400-, and 800-nm size-selected kaolinite particles, exposing them to temperatures between 218 and 258 K and relative humidities with respect to ice (RHi) between 100% and 180%, including the typical conditions for cirrus and mixed-phase-cloud formation. Measurements of the ice active particle fraction as a function of temperature and relative humidity with respect to ice are reported. The authors find enhanced activated fractions when water saturation is reached at mixed-phase-cloud temperatures between 235 and 241 K and a distinct increase in the activated fraction below 235 K at conditions below water saturation. To provide a functional description of the observed ice nucleation mechanisms, the experimental results are analyzed by two different particle-surface models within the framework of classical nucleation theory. Describing the ice nucleation activity of kaolinite particles by assuming deposition nucleation to be the governing mechanism below water saturation was found to be inadequate to represent the experimental data in the whole temperature range investigated. The observed increase in the activated fraction below water saturation and temperatures below 235 K corroborate the assumption that an appreciable amount of adsorbed or capillary condensed water is present on kaolinite particles, which favors ice nucleation.
Interpolation of Missing Temperature Data at Meteorological Stations Using P-BSHADE*
Authors: Xu Cheng-Dong , Wang Jin-Feng , Hu Mao-Gui , Li Qing-Xiang 
Published: September 2013

Abstract
Some climate datasets are incomplete at certain places and times. A novel technique called the point estimation model of Biased Sentinel Hospitals-based Area Disease Estimation (P-BSHADE) is introduced to interpolate missing data in temperature datasets. Effectiveness of the technique was empirically evaluated in terms of an annual temperature dataset from 1950 to 2000 in China. The P-BSHADE technique uses a weighted summation of observed stations to derive unbiased and minimum error variance estimates of missing data. Both the ratio and covariance between stations were used in calculation of these weights. In this way, interpolation of missing data in the temperature dataset was improved, and best linear unbiased estimates (BLUE) were obtained. Using the same dataset, performance of P-BSHADE was compared against three estimators: kriging, inverse distance weighting (IDW), and spatial regression test (SRT). Kriging and IDW assume a homogeneous stochastic field, which may not be the case. SRT employs spatiotemporal data and has the potential to consider temperature nonhomogeneity caused by topographic differences, but has no objective function for the BLUE. Instead, P-BSHADE takes into account geographic spatial autocorrelation and nonhomogeneity, and maximizes an objective function for the BLUE of the target station. In addition to the theoretical advantages of P-BSHADE over the three other methods, case studies for an annual Chinese temperature dataset demonstrate its empirical superiority, except for the SRT from 1950 to 1970.
Mental health consumer and caregiver perceptions of stigma in Australian community pharmacies
Authors: Knox Kathy , Fejzic Jasmina , Mey Amary , Fowler Jane L , Kelly Fiona , McConnell Denise , Hattingh Laetitia , Wheeler Amanda J 
Published: September 2013

Background: The stigma of mental illness can be a barrier to effective medication management in the community pharmacy setting. This article explored mental health consumers’ or caregivers’ experiences of stigma in Australian community pharmacies. Materials: Semi-structured interviews and focus groups were conducted with a purposive sample of consumers or caregivers ( n = 74). Interview transcripts were analysed using a general inductive approach. Discussion: Stigma presented a barrier to effective mental health management. Self-stigma impeded consumers’ community pharmacy engagement. Positive relationships with knowledgeable staff are fundamental to reducing stigma. Conclusions: Findings provide insight into the stigma of mental illness in community pharmacies.
Emergency room decision-making for urgent cranial computed tomography: selection criteria for subsets of non-trauma patients
Authors: Tung Christer , Lindgren Arne , Siemund Roger , van Westen Danielle 
Published: September 2013

Background Computed tomography (CT) of the brain is used extensively in the urgent work-up of patients with a suspicion of intracranial pathology, but is often normal. Previously proposed selection criteria aim at limiting the ordering of urgent cranial CT in the non-trauma population, while maintaining high sensitivity for diagnoses demanding immediate attention. Purpose To retrospectively evaluate these selection criteria in a general non-trauma population from a Swedish tertiary hospital, as well as in a nested subgroup that lacks guidelines at present, namely where the chief complaint was not headache, symptoms clearly indicating stroke, seizures, or vertigo. Material and Methods Medical records of 346 patients (114 in the nested group) who had undergone urgent cranial CT were reviewed. Selection criteria as proposed by Rothrock (patient age ≥60 years, presence of new onset focal neurologic deficit, headache with vomiting, or altered mental status) were used. Acute cerebral infarction, intracranial hemorrhage, malignancy, infection, cerebral edema, or hydrocephalus were considered significant findings. Results The prevalence of significant findings was 10.1%. The Rothrock criteria had a sensitivity of 97.1% (identifying 34 of 35 significant findings) among all 346 patients and 100% (10/10) among the 114 patients in the subgroup and resulted in a potential scan reduction rate of 22.8% and 11.4%, respectively. In the patient with significant pathology, that was not selected for CT, focal neurological symptoms were not described as newly onset. Conclusion Although 100% sensitivity was not achieved, our results may contribute to the evidence that in the absence of focal neurologic deficit, headache with vomiting or altered mental status in patients aged <60 years cranial tomography can be refrained from, in the general population as well as in the subgroup defined above. Further research might validate patient history as a parameter.
The relationship between insulin sensitivity and maximal oxygen uptake is confounded by method of adjustment for body composition
Authors: Grice Brian A , Mason Clinton C , Weil E Jennifer , Knowler William C , Pomeroy Jeremy 
Published: September 2013

Background: The use of ratios for analyzing physiologic variables often creates spurious associations. Methods: Results of a euglycaemic clamp, a graded exercise test to measure maximal oxygen uptake (VO2max) and underwater weighing in 358 nondiabetic adults (166 women and 192 men) were used to compare the effects of weight standardization by division or by partial Spearman correlations on the association between VO2max and insulin sensitivity. Results: VO2max and insulin sensitivity were negatively correlated when VO2max was divided by weight. When partial Spearman correlations were used to adjust VO2max for body composition, the correlation between VO2max and insulin sensitivity was greatly diminished. Conclusions: Division of VO2max by weight does not adjust for weight, but it creates spurious associations between VO2max and insulin sensitivity.
Signaling the end of chronic lymphocytic leukemia: new frontline treatment strategies
Authors: Hallek Michael 
Published: September 2013

AbstractThe management of chronic lymphocytic leukemia (CLL) is undergoing profound changes. Several new drugs have been approved for CLL treatment (fludarabine, bendamustine, and the monoclonal antibodies alemtuzumab, rituximab, and ofatumumab) and many more drugs are in advanced clinical development to be approved for this disease. In addition, the extreme heterogeneity of the clinical course and our improved ability to foresee the prognosis of this leukemia by the use of clinical, biological, and genetic parameters now allow us to characterize patients with a very mild onset and course, an intermediate prognosis, or a very aggressive course with high-risk leukemia. Therefore, it becomes increasingly challenging to select the right treatment strategy for each condition. This article summarizes the currently available diagnostic and therapeutic tools and gives an integrated recommendation of how to manage CLL in 2013. Moreover, I propose a strategy how we might integrate the novel agents for CLL therapy into sequential treatment approaches in the near future.
Comprehensive analysis of PTEN status in Sézary syndrome
Authors: Cristofoletti Cristina , Picchio Maria Cristina , Lazzeri Cristina , Tocco Valeria , Pagani Elena , Bresin Antonella , Mancini Barbara , Passarelli Francesca , Facchiano Antonio , Scala Enrico , Lombardo Giuseppe Alfonso , Cantonetti Maria , Caprini Elisabetta , Russo Giandomenico , Narducci Maria Grazia 
Published: September 2013

Key Points
PTEN is downregulated in Sézary syndrome by different mechanisms, mostly by gene deletions and microRNAs. PTEN deficiency activates AKT in skin resident but not circulating Sezary cells.
Archetypal analysis of diverse Pseudomonas aeruginosatranscriptomes reveals adaptation in cystic fibrosis airways
Authors: Thøgersen Juliane Charlotte , Mørup Morten , Damkiær Søren , Molin Søren , Jelsbak Lars 
Published: September 2013

AbstractBackgroundAnalysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data.The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies ofPseudomonas aeruginosaisolated from the airways of cystic fibrosis patients.ResultsOur analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria.ConclusionsArchetypal analysis succeeded in identifying adaptive changes ofP. aeruginosa.The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data.
The sodium channel gene family is specifically expressed in hen uterus and associated with eggshell quality traits
Authors: Fan Yan-Feng , Hou Zhuo-Cheng , Yi Guo-Qiang , Xu Gui-Yun , Yang Ning 
Published: September 2013

Abstract

Background
Eggshell quality is important for the poultry industry. During eggshell formation a mass of inorganic minerals is deposited. The Sodium Channel (SCNN1) gene family plays an essential role in cation transportation. The objective of this study was to investigate the pattern of expression of members of the SCNN1 gene family, their variation and their effects on eggshell quality.

Result
The highest expression of SCNN1a, SCNN1b, and SCNN1g genes were in the active uterus during eggshell mineralization, while SCNN1d showed its highest expression level in the quiescent uterus (no egg present). Nineteen candidate SNPs from the four genes were genotyped in a population of 338 White Leghorn layers. Association analysis between SNPs (haplotypes/diplotypes) and eggshell traits was performed. Among seven significant SNPs, five SNPs were associated with eggshell strength, eggshell thickness, eggshell percentage or/and egg weight, while the other two SNPs within SCNN1d were only associated with eggshell percentage. These SNPs had a 0.25-6.99% contribution to phenotypic variance, depending on the trait. In haplotype analysis, SCNN1b and SCNN1d were associated with egg weight. The SCNN1b and SCNN1g were significantly associated with eggshell weight while only SCNN1g explained 2.04% of phenotypic variance. All the alleles of the members of SCNN1 gene family were associated with eggshell percentage and eggshell thickness, and others members had an association with eggshell strength except for SCNN1a. The contribution of different haplotypes of the SCNN1 gene family to eggshell phenotypic variance ranged from 0.09% to 5.74%.

Conclusions
Our study indicated that the SCNN1 gene family showed tissue expression specificity and was significantly associated with eggshell traits in chicken. This study provides evidence that genetic variation in members of the sodium channel can influence eggshell quality.
Genetic diversity in black South Africans from Soweto
Authors: May Andrew , Hazelhurst Scott , Li Yali , Norris Shane A , Govind Nimmisha , Tikly Mohammed , Hon Claudia , Johnson Keith J , Hartmann Nicole , Staedtler Frank , Ramsay Michèle 
Published: September 2013

Abstract

Background
Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg).

Results
Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture.

Conclusions
Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.
Genome-wide copy number variations in Oryza sativa L.
Authors: Yu Ping , Wang Cai-Hong , Xu Qun , Feng Yue , Yuan Xiao-Ping , Yu Han-Yong , Wang Yi-Ping , Tang Sheng-Xiang , Wei Xing-Hua 
Published: September 2013

Abstract

Background
Copy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organism with a well-annotated genome, but investigation of CNVs in rice lags behind its mammalian counterparts.

Results
We comprehensively assayed CNVs using high-density array comparative genomic hybridization in a panel of 20 Asian cultivated rice comprising six indica, three aus, two rayada, two aromatic, three tropical japonica, and four temperate japonica varieties. We used a stringent criterion to identify a total of 2886 high-confidence copy number variable regions (CNVRs), which span 10.28 Mb (or 2.69%) of the rice genome, overlapping 1321 genes. These genes were significantly enriched for specific biological functions involved in cell death, protein phosphorylation, and defense response. Transposable elements (TEs) and other repetitive sequences were identified in the majority of CNVRs. Chromosome 11 showed the greatest enrichment for CNVs. Of subspecies-specific CNVRs, 55.75% and 61.96% were observed in only one cultivar of ssp. indica and ssp. japonica, respectively. Some CNVs with high frequency differences among groups resided in genes underlying rice adaptation.

Conclusions
Higher recombination rates and the presence of homologous gene clusters are probably predispositions for generation of the higher number of CNVs on chromosome 11 by non-allelic homologous recombination events. The subspecies-specific variants are enriched for rare alleles, which suggests that CNVs are relatively recent events that have arisen within breeding populations. A number of the CNVs identified in this study are candidates for generation of group-specific phenotypes.
Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum
Authors: Jagadeesan Rajeswaran , Fotheringham Amelia , Ebert Paul R , Schlipalius David I 
Published: September 2013

Abstract

Background
Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically.

Results
Progeny from defined genetic crosses of Tribolium castaneum (F4 and F19) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations.

Conclusion
We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.