bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of phylogenetic data using a global sequence analysis method
Authors: Chapus Charles , Dufraigne Christine , Edwards Scott , Giron Alain , Fertil Bernard , Deschavanne Patrick 
Published: November 2005

AbstractBackgroundMolecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.ResultsHere we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.ConclusionThe signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.
Evolution of virulence: coinfection and propagule production in spore-producing parasites
Authors: Lively Curtis M 
Published: November 2005

AbstractBackgroundThe evolution of within-host growth rates by parasites is expected to depend on a trade-off between propagule production and virulence. The presence of coinfections, however, is thought to alter this trade-off, and hence alter the evolutionarily stable strategy (ESS) for the parasite. Here I consider a model wherein the number of coinfections that are identical by descent can depend on the parasite's reproductive strategy. Transmission success was treated as being either a negative-linear or a negative-exponential function of the total number of propagules produced by all coinfections.ResultsIncreasing the number of unrelated coinfections either selected for a decrease in reproductive output by the parasite (linear case), or had no effect on the ESS (exponential case). Nonetheless, the total number of propagules produced within each host increased in both cases. Increasing the relatedness among coinfections, however, selected for reductions in parasite reproduction in both cases.ConclusionUnrelated coinfection may increase overall parasite virulence, but the result stems from adding more infections rather than to more aggressive growth by the individual infections. However, all else being equal, if the coinfections are more related than expected by chance alone, then the total reproductive output by all coinfections would be expected to be reduced, resulting in reduced virulence.
Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test
Authors: Berlin Sofia , Smith Nick GC 
Published: November 2005

Abstract

Background
Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals.

Results
We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes.

Conclusion
We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.
Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes
Authors: Stefan Mihaela , Claiborn Kathryn C , Stasiek Edyta , Chai Jing-Hua , Ohta Tohru , Longnecker Richard , Greally John M , Nicholls Robert D 
Published: November 2005

Abstract

Background
Prader-Willi and Angelman syndrome (PWS and AS) patients typically have an ~5 Mb deletion of human chromosome 15q11-q13, of opposite parental origin. A mouse model of PWS and AS has a transgenic insertion-deletion (TgPWS/TgAS) of chromosome 7B/C subsequent to paternal or maternal inheritance, respectively. In this study, we define the deletion endpoints and examine the impact on expression of flanking genes.

Results
Using molecular and cytological methods we demonstrate that 13 imprinted and 11 non-imprinted genes are included in the TgPWS/TgAS deletion. Normal expression levels were found in TgPWS brain for genes extending 9.1- or 5.6-Mb centromeric or telomeric of the deletion, respectively. Our molecular cytological studies map the proximal deletion breakpoint between the Luzp2 and Siglec-H loci, and we show that overall mRNA levels of Luzp2 in TgPWS and TgAS brain are significantly reduced by 17%. Intriguingly, 5' Chrna7 shows 1.7-fold decreased levels in TgPWS and TgAS brain whereas there is a ≥15-fold increase in expression in neonatal liver and spleen of these mouse models. By isolating a Chrna7-Tg fusion transcript from TgAS mice, we mapped the telomeric deletion breakpoint in Chrna7 intron 4.

Conclusion
Based on the extent of the deletion, TgPWS/TgAS mice are models for PWS/AS class I deletions. Other than for the first gene promoters immediately outside the deletion, since genes extending 5.6–9.1 Mb away from each end of the deletion show normal expression levels in TgPWS brain, this indicates that the transgene array does not induce silencing and there are no additional linked rearrangements. Using gene expression, non-coding conserved sequence (NCCS) and synteny data, we have genetically mapped a putative Luzp2 neuronal enhancer responsible for ~33% of allelic transcriptional activity. The Chrna7 results are explained by hypothesizing loss of an essential neuronal transcriptional enhancer required for ~80% of allelic Chrna7 promoter activity, while the Chrna7 promoter is upregulated in B lymphocytes by the transgene immunoglobulin enhancer. The mapping of a putative Chrna7 neuronal enhancer inside the deletion has significant implications for understanding the transcriptional regulation of this schizophrenia-susceptibility candidate gene.
Preferential attachment in the evolution of metabolic networks
Authors: Light Sara , Kraulis Per , Elofsson Arne 
Published: November 2005

Abstract

Background
Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks.

Results
The connectivities of the enzymes in the metabolic network of Escherichia coli were determined and representatives for these enzymes were located in 11 eukaryotes, 17 archaea and 46 bacteria. E. coli enzymes which have representatives in eukaryotes have a higher average connectivity while enzymes which are represented only in the prokaryotes, and especially the enzymes only present in βγ-proteobacteria, have lower connectivities than expected by chance. Interestingly, the enzymes which have been proposed as candidates for horizontal gene transfer have a higher average connectivity than the other enzymes. Furthermore, It was found that new edges are added to the highly connected enzymes at a faster rate than to enzymes with low connectivities which is consistent with preferential attachment.

Conclusion
Here, we have found indications of preferential attachment in the metabolic network of E. coli. A possible biological explanation for preferential attachment growth of metabolic networks is that novel enzymes created through gene duplication maintain some of the compounds involved in the original reaction, throughout its future evolution. In addition, we found that enzymes which are candidates for horizontal gene transfer have a higher average connectivity than other enzymes. This indicates that while new enzymes are attached preferentially to highly connected enzymes, these highly connected enzymes have sometimes been introduced into the E. coli genome by horizontal gene transfer. We speculate that E. coli has adjusted its metabolic network to a changing environment by replacing the relatively central enzymes for better adapted orthologs from other prokaryotic species.
Specific and sensitive detection of the conifer pathogen Gremmeniella abietina by nested PCR
Authors: Zeng Qing-Yin , Hansson Per , Wang Xiao-Ru 
Published: November 2005

Abstract

Background

Gremmeniella abietina (Lagerb.) Morelet is an ascomycete fungus that causes stem canker and shoot dieback in many conifer species. The fungus is widespread and causes severe damage to forest plantations in Europe, North America and Asia. To facilitate early diagnosis and improve measures to control the spread of the disease, rapid, specific and sensitive detection methods for G. abietina in conifer hosts are needed.

Results
We designed two pairs of specific primers for G. abietina based on the 18S rDNA sequence variation pattern. These primers were validated against a wide range of fungi and 14 potential conifer hosts. Based on these specific primers, two nested PCR systems were developed. The first system employed universal fungal primers to enrich the fungal DNA targets in the first round, followed by a second round selective amplification of the pathogen. The other system employed G. abietina-specific primers in both PCR steps. Both approaches can detect the presence of G. abietina in composite samples with high sensitivity, as little as 7.5 fg G. abietina DNA in the host genomic background.

Conclusion
The methods described here are rapid and can be applied directly to a wide range of conifer species, without the need for fungal isolation and cultivation. Therefore, it represents a promising alternative to disease inspection in forest nurseries, plantations and quarantine control facilities.
Neurophysiological correlates of mismatch in lexical access
Authors: Friedrich Claudia K 
Published: November 2005

Abstract

Background
In the present study neurophysiological correlates related to mismatching information in lexical access were investigated with a fragment priming paradigm. Event-related brain potentials were recorded for written words following spoken word onsets that either matched (e.g., kan – Kante [Engl. edge]), partially mismatched (e.g., kan – Konto [Engl. account]), or were unrelated (e.g., kan – Zunge [Engl. tongue]). Previous psycholinguistic research postulated the activation of multiple words in the listeners' mental lexicon which compete for recognition. Accordingly, matching words were assumed to be strongly activated competitors, which inhibit less strongly activated partially mismatching words.

Results
ERPs for matching and unrelated control words differed between 300 and 400 ms. Difference waves (unrelated control words – matching words) replicate a left-hemispheric P350 effect in this time window. Although smaller than for matching words, a P350 effect and behavioural facilitation was also found for partially mismatching words. Minimum norm solutions point to a left hemispheric centro-temporal source of the P350 effect in both conditions. The P350 is interpreted as a neurophysiological index for the activation of matching words in the listeners' mental lexicon. In contrast to the P350 and the behavioural responses, a brain potential ranging between 350 and 500 ms (N400) was found to be equally reduced for matching and partially mismatching words as compared to unrelated control words. This latter effect might be related to strategic mechanisms in the priming situation.

Conclusion
A left-hemispheric neuronal network engaged in lexical access appears to be gradually activated by matching and partially mismatching words. Results suggest that neural processing of matching words does not inhibit processing of partially mismatching words during early stages of lexical identification. Furthermore, the present results indicate that neurophysiological correlates observed in fragment priming reflect different aspects of target processing that are cumulated in behavioural responses. Particularly the left-hemispheric P350 difference potential appears to be closely related to fine-grained activation differences of modality-independent representations in the listeners' mental lexicon. This neurophysiological index might guide future studies aimed at investigating neural aspects of lexical access.
Cardiovascular disease, risk factors and heart rate variability in the elderly general population: Design and objectives of the CARdiovascular disease, Living and Ageing in Halle (CARLA) Study
Authors: Greiser Karin H , Kluttig Alexander , Schumann Barbara , Kors Jan A , Swenne Cees A , Kuss Oliver , Werdan Karl , Haerting Johannes 
Published: November 2005

Abstract

Background
The increasing burden of cardiovascular diseases (CVD) in the ageing population of industrialized nations requires an intensive search for means of reducing this epidemic. In order to improve prevention, detection, therapy and prognosis of cardiovascular diseases on the population level in Eastern Germany, it is necessary to examine reasons for the East-West gradient of CVD morbidity and mortality, potential causal mechanisms and prognostic factors in the elderly.
Psychosocial and nutritional factors have previously been discussed as possible causes for the unexplained part of the East-West gradient. A reduced heart rate variability appears to be associated with cardiovascular disease as well as with psychosocial and other cardiovascular risk factors and decreases with age. Nevertheless, there is a lack of population-based data to examine the role of heart rate variability and its interaction with psychosocial and nutritional factors regarding the effect on cardiovascular disease in the ageing population. There also is a paucity of epidemiological data describing the health situation in Eastern Germany. Therefore, we conduct a population-based study to examine the distribution of CVD, heart rate variability and CVD risk factors and their associations in an elderly East German population. This paper describes the design and objectives of the CARLA Study.

Methods/design
For this study, a random sample of 45–80 year-old inhabitants of the city of Halle (Saale) in Eastern Germany was drawn from the population registry. By the end of the baseline examination (2002–2005), 1750 study participants will have been examined. A multi-step recruitment strategy aims at achieving a 70 % response rate.
Detailed information is collected on own and family medical history, socioeconomic, psychosocial, behavioural and biomedical factors. Medical examinations include anthropometric measures, blood pressure of arm and ankle, a 10-second and a 20-minute electrocardiogram, a general physical examination, an echocardiogram, and laboratory analyses of venous blood samples. On 200 participants, a 24-hour electrocardiogram is recorded. A detailed system of quality control ensures high data quality. A follow-up examination is planned.

Discussion
This study will help to elucidate pathways to CVD involving autonomic dysfunction and lifestyle factors which might be responsible for the CVD epidemic in some populations.
Measurement of the total antioxidant response using a novel automated method in subjects with nonalcoholic steatohepatitis
Authors: Horoz Mehmet , Bolukbas Cengiz , Bolukbas Fusun F , Sabuncu Tevfik , Aslan Mehmet , Sarifakiogullari Serpil , Gunaydin Necla , Erel Ozcan 
Published: November 2005

Abstract

Background
Oxidative stress, an increase in oxidants and/or a decrease in antioxidant capacity, is one of the potential biochemical mechanisms involved in the pathogenesis of nonalcoholic steatohepatitis. We aimed to investigate the total antioxidant response using a novel automated method in nonalcoholic steatohepatitis subjects. As a reciprocal measure, we also aimed to determine total peroxide level in the same plasma samples.

Methods
Twenty-two subjects with biopsy proven nonalcoholic steatohepatitis and 22 healthy controls were enrolled. Total antioxidant response and total peroxide level measurements were done in all participants. The ratio percentage of total peroxide level to total antioxidant response was regarded as oxidative stress index.

Results
Total antioxidant response of subjects with nonalcoholic steatohepatitis was significantly lower than controls (p < 0.05), while mean total peroxide level and mean oxidative stress index were higher (all p < 0.05).
In subjects with nonalcoholic steatohepatitis, fibrosis score was significantly correlated with total peroxide level, total antioxidant response and oxidative stress index (p < 0.05, r = 0.607; p < 0.05, r = -0.506; p < 0.05, r = 0.728, respectively). However, no correlation was observed between necroimflamatory grade and those oxidative status parameters (all p > 0.05).

Conclusion
Nonalcoholic steatohepatitis is associated with increased oxidant capacity, especially in the presence of liver fibrosis. The novel automated assay is a reliable and easily applicable method for total plasma antioxidant response measurement in nonalcoholic steatohepatitis.
Predicting the risk of falling – efficacy of a risk assessment tool compared to nurses' judgement: a cluster-randomised controlled trial [ISRCTN37794278]
Authors: Meyer Gabriele , Köpke Sascha , Bender Ralf , Mühlhauser Ingrid 
Published: November 2005

Abstract

Background
Older people living in nursing homes are at high risk of falling because of their general frailty and multiple pathologies. Prediction of falls might lead to an efficient allocation of preventive measures. Although several tools to assess the risk of falling have been developed, their impact on clinically relevant endpoints has never been investigated. The present study will evaluate the clinical efficacy and consequences of different fall risk assessment strategies.

Study design
Cluster-randomised controlled trial with nursing home clusters randomised either to the use of a standard fall risk assessment tool alongside nurses' clinical judgement or to nurses' clinical judgement alone. Standard care of all clusters will be optimised by structured education on best evidence strategies to prevent falls and fall related injuries. 54 nursing home clusters including 1,080 residents will be recruited. Residents must be ≥ 70 years, not bedridden, and living in the nursing home for more than three months. The primary endpoint is the number of participants with at least one fall at 12 months. Secondary outcome measures are the number of falls, clinical consequences including side effects of the two risk assessment strategies. Other measures are fall related injuries, hospital admissions and consultations with a physician, and costs.
Regional variation in hospitalization for stroke among Asians/Pacific Islanders in the United States: a nationwide retrospective cohort study
Authors: Nguyen-Huynh Mai N , Johnston S Claiborne 
Published: November 2005

Abstract

Background
In Asia, stroke incidence varies dramatically from country to country. Little is known about stroke incidence in Asians/Pacific Islanders in the US, where regional heterogeneity in Asian/Pacific Islander sub-populations is great. We sought to characterize both the national and regional incidences of first and recurrent hospitalized acute ischemic stroke, subarachnoid hemorrhage, and intracerebral hemorrhage in Asians/Pacific Islanders compared to non-Hispanic whites.

Methods
We used the National Inpatient Sample of the 1997 Healthcare Cost and Utilization Project. It is a 20% stratified sample of hospitalizations to nonfederal hospitals in the US. National and regional projections were made using sampling weights specific for patients and hospitals. We identified stroke subtypes using previously validated ICD-9 codes. Age-adjusted incidence rates were calculated using the direct method with the US population in 2000 as the standard.

Results
There were 169,386 stroke hospitalizations in the database. Nationally, compared to whites, Asians/Pacific Islanders were more likely to have subarachnoid hemorrhage (incidence rate ratio {RR} female: 1.53, 95% CI 1.41–1.65; male RR: 1.13, 95% CI 1.00–1.27) and intracerebral hemorrhage (female RR 1.29, 95% CI 1.22–1.36; male RR: 1.58, 95% CI 1.50–1.67). However, when examined by geographic regions, Asians/Pacific Islanders had higher incidence rates of subarachnoid hemorrhage and intracerebral hemorrhage predominantly in the West, and lower rates of stroke elsewhere.

Conclusion
Stroke incidence varies 3-fold among Asians/Pacific Islanders residing in different US regions. Geographic variation is less dramatic in whites. Whether genetic or cultural differences are responsible for dramatic heterogeneity among Asian/Pacific Islander populations is unclear and deserves further study.