bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mouse Limb Anatomy Atlas: An interactive 3D tool for studying embryonic limb patterning
Authors: DeLaurier April , Burton Nicholas , Bennett Michael , Baldock Richard , Davidson Duncan , Mohun Timothy J , Logan Malcolm PO 
Published: September 2008

Abstract

Background
The developing mouse limb is widely used as a model system for studying tissue patterning. Despite this, few references are available that can be used for the correct identification of developing limb structures, such as muscles and tendons. Existing textual references consist of two-dimensional (2D) illustrations of the adult rat or mouse limb that can be difficult to apply when attempting to describe the complex three-dimensional (3D) relationship between tissues.

Results
To improve the resources available in the mouse model, we have generated a free, web-based, interactive reference of limb muscle, tendon, and skeletal structures at embryonic day (E) 14.5 http://www.nimr.mrc.ac.uk/3dlimb/. The Atlas was generated using mouse forelimb and hindlimb specimens stained using immunohistochemistry to detect muscle and tendon. Limbs were scanned using Optical Projection Tomography (OPT), reconstructed to make 3D models and annotated using computer-assisted segmentation tools in Amira 3D Visualisation software. The annotated dataset is visualised using Java, JAtlasView software. Users click on the names of structures and view their shape, position and relationship with other structures within the 3D model and also in 2D virtual sections.

Conclusion
The Mouse Limb Anatomy Atlas provides a novel and valuable tool for researchers studying limb development and can be applied to a range of research areas, including the identification of abnormal limb patterning in transgenic lines and studies of models of congenital limb abnormalities. By using the Atlas for "virtual" dissection, this resource offers an alternative to animal dissection. The techniques we have developed and employed are also applicable to many other model systems and anatomical structures.
Phylogenetic reconstruction from transpositions
Authors: Yue Feng , Zhang Meng , Tang Jijun 
Published: September 2008

Abstract

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate methods for rearrangement phylogeny, both assuming inversion as the only event. However, due to the complexity of computing transposition distance, it is very difficult to analyze datasets when transpositions are dominant.

Results
We extend GRAPPA to handle transpositions. The new method is named GRAPPA-TP, with two major extensions: a heuristic method to estimate transposition distance, and a new transposition median solver for three genomes. Although GRAPPA-TP uses a greedy approach to compute the transposition distance, it is very accurate when genomes are relatively close. The new GRAPPA-TP is available from http://phylo.cse.sc.edu/.

Conclusion
Our extensive testing using simulated datasets shows that GRAPPA-TP is very accurate in terms of ancestor genome inference and phylogenetic reconstruction. Simulation results also suggest that model match is critical in genome rearrangement analysis: it is not accurate to simulate transpositions with other events including inversions.
MeDor: a metaserver for predicting protein disorder
Authors: Lieutaud Philippe , Canard Bruno , Longhi Sonia 
Published: September 2008

Abstract

Background
We have previously shown that using multiple prediction methods improves the accuracy of disorder predictions. It is, however, a time-consuming procedure, since individual outputs of multiple predictions have to be retrieved, compared to each other and a comprehensive view of the results can only be obtained through a manual, fastidious, non-automated procedure. We herein describe a new web metaserver, MeDor, which allows fast, simultaneous analysis of a query sequence by multiple predictors and provides a graphical interface with a unified view of the outputs.

Results
MeDor was developed in Java and is freely available and downloadable at: http://www.vazymolo.org/MeDor/index.html. Presently, MeDor provides a HCA plot and runs a secondary structure prediction, a prediction of signal peptides and transmembrane regions and a set of disorder predictions. MeDor also enables the user to customize the output and to retrieve the sequence of specific regions of interest.

Conclusion
As MeDor outputs can be printed, saved, commented and modified further on, this offers a dynamic support for the analysis of protein sequences that is instrumental for delineating domains amenable to structural and functional studies.
Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions
Authors: Ren Siyuan , Uversky Vladimir N , Chen Zhengjun , Dunker A Keith , Obradovic Zoran 
Published: September 2008

AbstractBackgroundProtein interactions are essential for most cellular functions. Interactions mediated by domains that appear in a large number of proteins are of particular interest since they are expected to have an impact on diversities of cellular processes such as signal transduction and immune response. Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs).ResultsIn this study, we systematically studied the evolutionary conservation of SLiMs recognized by SH2, SH3 and Ser/Thr Kinase domains in both ordered and disordered protein regions. Disordered protein regions are protein sequences that lack a fixed three-dimensional structure under putatively native conditions. We find that, in all these domains examined, SLiMs are more conserved in disordered regions. This trend is more evident in those protein functional groups that are frequently reported to interact with specific domains.ConclusionThe correlation between SLiM conservation with disorder prediction demonstrates that functional SLiMs recognized by each domain occur more often in disordered as compared to structured regions of proteins.
In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme
Authors: Yuan Jiazheng , Zhu Mengxia , Lightfoot David A , Iqbal M Javed , Yang Jack Y , Meksem Khalid 
Published: September 2008

Abstract

Background
Sudden death syndrome (SDS) of soybean (Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv). Due to the complexity and length of the soybean-Fusarium interaction, the molecular mechanisms underlying plant resistance and susceptibility to the pathogen are not fully understood. F. virguliforme has a very wide host range for the ability to cause root rot and a very narrow host range for the ability to cause a leaf scorch. Arabidopsis thaliana is a host for many types of phytopathogens including bacteria, fungi, viruses and nematodes. Deciphering the variations among transcript abundances (TAs) of functional orthologous genes of soybean and A. thaliana involved in the interaction will provide insights into plant resistance to F. viguliforme.

Results
In this study, we reported the analyses of microarrays measuring TA in whole plants after A. thaliana cv 'Columbia' was challenged with fungal pathogen F. virguliforme. Infection caused significant variations in TAs. The total number of increased transcripts was nearly four times more than that of decreased transcripts in abundance. A putative resistance pathway involved in responding to the pathogen infection in A. thaliana was identified and compared to that reported in soybean.

Conclusion
Microarray experiments allow the interrogation of tens of thousands of transcripts simultaneously and thus, the identification of plant pathways is likely to be involved in plant resistance to Fusarial pathogens. Dissection of the set functional orthologous genes between soybean and A. thaliana enabled a broad view of the functional relationships and molecular interactions among plant genes involved in F. virguliforme resistance.
Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
Authors: Yang Jack Y , Niemierko Andrzej , Yang Mary Qu , Deng Youping 
Published: September 2008

Abstract

Background
Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics have been used extensively to validate clinical data.

Results
We found that Poisson statistics on RT is actually derived from bacterial cells despite of many validations from clinical data. However cancerous cells do have abnormal cellular communications and use chemical messengers to signal both surrounding normal and cancerous cells to develop new blood vessels and to invade, to metastasis and to overcome intercellular spatial confinements in general. We therefore investigated the cell killing effects on adjuvant RT and found that radio-sensitivity is actually not a monotonic function of volume as it was believed before. We present detailed analysis and explanation to justify above statement. Based on EUD, we present an equivalent radio-sensitivity model.

Conclusion
We conclude that radio sensitivity is a sophisticated function over tumor volumes, since tumor responses upon radio therapy also depend on cellular communications.
Elevated CXCL12 expression in the bone marrow of NOD mice is associated with altered T cell and stem cell trafficking and diabetes development
Authors: Leng Qibin , Nie Yuchun , Zou Yongrui , Chen Jianzhu 
Published: September 2008

Abstract

Background
Type I diabetes (TID) is an autoimmune disease resulting from destruction of the insulin-producing β-cells by autoreactive T cells. Studies have shown that polymorphisms of chemokine CXCL12 gene are linked to TID in humans. In non-obese diabetic (NOD) mice, which are predisposed to develop the disease, reduction of CXCL12 level leads to significant delays in the onset of diabetes. Despite these initial observations, however, how CXCL12 affects development of TID has not been fully investigated.

Results
We found that the level of CXCL12 transcript is significantly elevated in the bone marrow of NOD mice as compared to Balb/c and C57BL/6 mice. Correspondingly, naïve T cells, regulatory T cells and hematopoietic stem cells (HSC) accumulate in the bone marrow of NOD mice. Treatment of NOD mice with AMD3100, an antagonist for CXCL12's receptor CXCR4, mobilizes T cells and HSC from the bone marrow to the periphery, concomitantly inhibits insulitis and delays the onset of diabetes.

Conclusion
These results suggest that the elevated CXCL12 expression promotes TID in NOD mice by altering T cell and hematopoietic stem cell trafficking. The findings highlight the potential usefulness of AMD3100 to treat or prevent TID in humans.
Predictive analysis of transmissible quinolone resistance indicates Stenotrophomonas maltophilia as a potential source of a novel family of Qnr determinants
Authors: Sánchez María B , Hernández Alvaro , Rodríguez-Martínez José M , Martínez-Martínez Luis , Martínez José L 
Published: September 2008

Abstract

Background
Predicting antibiotic resistance before it emerges at clinical settings constitutes a novel approach for preventing and fighting resistance of bacterial pathogens. To analyse the possibility that novel plasmid-encoded quinolone resistance determinants (Qnr) can emerge and disseminate among bacterial pathogens, we searched the presence of those elements in nearly 1000 bacterial genomes and metagenomes.

Results
We have found a number of novel potential qnr genes in the chromosomes of aquatic bacteria and in metagenomes from marine organisms. Functional studies of the Stenotrophomonas maltophilia Smqnr gene show that plasmid-encoded SmQnr confers quinolone resistance upon its expression in a heterologous host.

Conclusion
Altogether, the data presented in our work support the notion that predictive studies on antibiotic resistance are feasible, using currently available information on bacterial genomes and with the aid of bioinformatic and functional tools. Our results confirm that aquatic bacteria can be the origin of plasmid-encoded Qnr, and highlight the potential role of S. maltophilia as a source of novel Qnr determinants.
The HCV Synthesis Project: Scope, methodology, and preliminary results
Authors: Stern Rebecca K , Hagan Holly , Lelutiu-Weinberger Corina , Des Jarlais Don , Scheinmann Roberta , Strauss Shiela , Pouget Enrique R , Flom Peter 
Published: September 2008

Abstract

Background
The hepatitis C virus (HCV) is hyper-endemic in injecting drug users. There is also excess HCV among non-injection drug users who smoke, snort, or sniff heroin, cocaine, crack, or methamphetamine.

Methods
To summarize the research literature on HCV in drug users and identify gaps in knowledge, we conducted a synthesis of the relevant research carried out between 1989 and 2006. Using rigorous search methods, we identified and extracted data from published and unpublished reports of HCV among drug users. We designed a quality assurance system to ensure accuracy and consistency in all phases of the project. We also created a set of items to assess study design quality in each of the reports we included.

Results
We identified 629 reports containing HCV prevalence rates, incidence rates and/or genotype distribution among injecting or non-injecting drug user populations published between January 1989 and December 2006. The majority of reports were from Western Europe (41%), North America (26%), Asia (11%) and Australia/New Zealand (10%). We also identified reports from Eastern Europe, South America, the Middle East, and the Caribbean. The number of publications reporting HCV rates in drug users increased dramatically between 1989 and 2006 to 27–52 reports per year after 1998.

Conclusion
The data collection and quality assurance phases of the HCV Synthesis Project have been completed. Recommendations for future research on HCV in drug users have come out of our data collection phase. Future research reports can enhance their contributions to our understanding of HCV etiology by clearly defining their drug user participants with respect to type of drug and route of administration. Further, the use of standard reporting methods for risk factors would enable data to be combined across a larger set of studies; this is especially important for HCV seroconversion studies which suffer from small sample sizes and low power to examine risk factors.
Caregivers' active role in palliative home care – to encourage or to dissuade? A qualitative descriptive study
Authors: Weibull Anna , Olesen Frede , Neergaard Mette Asbjoern 
Published: September 2008

Abstract

Background
Spouses' involvement in palliative care is often a prerequisite for home death, but it is unclear whether active involvement of the spouse, e.g. administering and being in charge of oral or subcutaneous medication or taking care of the patient's personal hygiene, could be harmful or have negative effects on the spouse's experience of the palliative course of disease. The aim of this study was to explore the impact of bereaved spouses' active involvement in medical and physical care on their experience of the palliative course of disease.

Methods
The study was a qualitative, descriptive study based on semi-structured individual interviews with seven bereaved spouses.

Results
Four main categories were found: Degree of involvement, Positive and Negative impact and Prerequisites. The prerequisites found for a positive outcome were Safety (24-hour back-up), Confidence (Professionals' confidence in the spouses' abilities) and Dialog (Spouses' influence on decision-making and being asked).

Conclusion
The results from this study identified important issues whenever spouses take an active part in medical treatment and physical care of critically ill patients in palliative care. The results question the previous research that active involvement of family care givers could be harmful and add preconditions to a positive outcome. More research into these preconditions is needed.
Association of alleles carried at TNFA -850 and BAT1-22 with Alzheimer's disease
Authors: Gnjec Anastazija , D'Costa Katarzyna J , Laws Simon M , Hedley Ross , Balakrishnan Kelvin , Taddei Kevin , Martins Georgia , Paton Athena , Verdile Giuseppe , Gandy Samuel E , Broe G Anthony , Brooks William S , Bennett Hayley , Piguet Olivier , Price Patricia , Miklossy Judith , Hallmayer Joachim , McGeer Patrick L , Martins Ralph N 
Published: September 2008

AbstractBackgroundInflammatory changes are a prominent feature of brains affected by Alzheimer's disease (AD). Activated glial cells release inflammatory cytokines which modulate the neurodegenerative process. These cytokines are encoded by genes representing several interleukins andTNFA, which are associated with AD. The gene coding for HLA-B associated transcript 1 (BAT1) lies adjacent toTNFAin the central major histocompatibility complex (MHC). BAT1, a member of the DEAD-box family of RNA helicases, appears to regulate the production of inflammatory cytokines associated with AD pathology. In the current studyTNFAand BAT1 promoter polymorphisms were analysed in AD and control cases and BAT1 mRNA levels were investigated in brain tissue from AD and control cases.MethodsGenotyping was performed for polymorphisms at positions -850 and -308 in the proximal promoter ofTNFAand position -22 in the promoter ofBAT1. These were investigated singly or in haplotypic association in a cohort of Australian AD patients with AD stratified on the basis of theirAPOEε4 genotype. Semi-quantitative RT-PCR was also performed for BAT1 from RNA isolated from brain tissue from AD and control cases.ResultsAPOEε4 was associated with an independent increase in risk for AD in individuals withTNFA-850*2, while carriage ofBAT1-22*2 reduced the risk for AD, independent ofAPOEε4 genotype. Semi-quantitative mRNA analysis in human brain tissue showed elevated levels ofBAT1mRNA in frontal cortex of AD cases.ConclusionThese findings lend support to the application ofTNFAandBAT1polymorphisms in early diagnosis or risk assessment strategies for AD and suggest a potential role for BAT1 in the regulation of inflammatory reactions in AD pathology.
Unravelling the adaptation responses to osmotic and temperature stress in Chromohalobacter salexigens, a bacterium with broad salinity tolerance
Authors: Vargas Carmen , Argandoña Montserrat , Reina-Bueno Mercedes , Rodríguez-Moya Javier , Fernández-Aunión Cristina , Nieto Joaquín J 
Published: September 2008

AbstractChromohalobacter salexigens, a Gammaproteobacterium belonging to the familyHalomonadaceae, shows a broad salinity range for growth. Osmoprotection is achieved by the accumulation of compatible solutes either by transport (betaine, choline) or synthesis (mainly ectoine and hydroxyectoine). Ectoines can play additional roles as nutrients and, in the case of hydroxyectoine, in thermotolerance. A supplementary solute, trehalose, not present in cells grown at 37°C, is accumulated at higher temperatures, suggesting its involvement in the response to heat stress. Trehalose is also accumulated at 37°C in ectoine-deficient mutants, indicating that ectoines suppress trehalose synthesis in the wild-type strain. The genes for ectoine (ectABC) and hydroxyectoine (ectD,ectE) production are arranged in three different clusters within theC. salexigenschromosome. In order to cope with changing environment,C. salexigensregulates its cytoplasmic pool of ectoines by a number of mechanisms that we have started to elucidate. This is a highly complex process because (i) hydroxyectoine can be synthesized by other enzymes different to EctD (ii) ectoines can be catabolized to serve as nutrients, (iii) the involvement of several transcriptional regulators (σS, σ32, Fur, EctR) and hence different signal transduction pathways, and (iv) the existence of post-trancriptional control mechanisms. In this review we summarize our present knowledge on the physiology and genetics of the processes allowingC. salexigensto cope with osmotic stress and high temperature, with emphasis on the transcriptional regulation.
Infant feeding in Sweden: Socio-demographic determinants and associations with adiposity in childhood and adolescence
Authors: Grjibovski Andrej M , Ehrenblad Bettina , Yngve Agneta 
Published: September 2008

Abstract

Background
Recent reviews and meta-analyses conclude that breastfeeding constitutes a small but consistent protective effect against obesity or higher values of body mass index (BMI) in children, though in some studies this effect was weakened after adjustment for potential confounders. The aim of this study was to explore the socio-demographic determinants of the duration of breastfeeding in Sweden and the associations between breastfeeding duration and adiposity in childhood and adolescence.

Methods
This was a cross-sectional study of Swedish children. Height, weight and waist circumference were measured and the sum of five skin fold measurements were obtained in 1137 9- and 15-year old children. Breastfeeding data were retrospectively obtained from the medical records for 812 (71.4%) children. Multiple ordinal logistic regression was applied to study individual effects of the maternal characteristics on the duration of breastfeeding. The relationship between children's anthropometric characteristics and duration of breastfeeding was studied by multiple linear regression. Associations between the odds of being overweight or obese and the duration of breastfeeding were studied by multiple logistic regression. Both linear and logistic models were adjusted for children's age, gender, birth weight, maternal education and parental BMI in 1998 as well as maternal age and smoking status at childbirth.

Results
Maternal education was positively associated with the duration of breastfeeding in both 1983 and 1989. Non-smoking mothers were more likely to breastfeed longer than smokers in 1989 (OR = 1.9, 95%CI: 1.3, 3.0). Fifteen-year old children breastfed for shorter than 2 months had 1.2 kg/m2 (95%CI: 0.1, 2.4) higher BMI, 3.2 cm (95%CI: 0.2, 6.2) higher waist circumference and 10.6 mm (95%CI: 1.7, 19.6) higher sum of five skin fold measurements compared to those breastfed for 6 months or longer when adjusted for children's characteristics and maternal characteristics in 1998. Adjustment for maternal age and smoking status at childbirth weakened these associations to non-significant levels (0.9 kg/m2, 95%CI: -0.4, 2.1; 1.4 cm, 95%CI: -1.5, 4.4 and 5.1 mm, 95%CI: -4.0, 14.2, respectively). In the 9-year olds, the associations were less pronounced, but in the same direction. No trends between duration of breastfeeding and children's anthropometric characteristics were observed in any of the age groups.

Conclusion
Maternal education and smoking were significant predictors of breastfeeding duration in Sweden in the 1980s. Associations with measures of adiposity were observed only in 15-year old children between the children with shortest and longest breastfeeding duration, which were weakened after adjustment for maternal characteristics at childbirth.