bluuebunny/crossref_metadata_2025_split huggingface dataset:
A general approach to evaluating agreement between two observers or methods of measurement from quantitative data with replicated measurements
Authors: Haber Michael , Barnhart Huiman X 
Published: August 2007

We present a general approach to the definition and estimation of coefficients for evaluating agreement between two fixed methods of measurements or human observers. The measured variable is assumed to be continuous with a finite second moment. No other distributional assumptions are made. We introduce the term `disagreement function' for the function of the observations that is used to quantify the extent of disagreement between the two measurements made on the same subject. The proposed inter-methods agreement coefficients compare the disagreement between measurements made by different methods on the same subject to the corresponding disagreement between replicated measurements made by the same method. Therefore, the new coefficients require data with replications readings. We propose inter-methods agreement coefficients for two practical situations involving two methods that have a measurement error: 1) comparison of a new method to a gold standard (or a reference method), and 2) comparison of two methods where neither method is considered a gold standard. We consider three disagreement functions based on the differences between two measurements: 1 ) the mean squared difference, 2) the mean absolute difference and 3 ) the mean relative difference. We then derive non-parametric estimates for the various agreement coefficients. Our approach is illustrated using data from a study comparing systolic blood pressure measurements by a human observer and an automatic monitor. The performance of the new estimates is assessed via stochastic simulations.
Modeling influenza incidence for the purpose of on-line monitoring
Authors: Andersson Eva , Bock David , Frisén Marianne 
Published: August 2007

We describe and discuss statistical models of Swedish influenza data, with special focus on aspects which are important in on-line monitoring. Earlier suggested statistical models are reviewed and the possibility of using them to describe the variation in influenza-like illness (ILI) and laboratory diagnoses (LDI) is discussed. Exponential functions were found to work better than earlier suggested models for describing the influenza incidence. However, the parameters of the estimated functions varied considerably between years. For monitoring purposes we need models which focus on stable indicators of the change at the outbreak and at the peak. For outbreak detection we focus on ILI data. Instead of a parametric estimate of the baseline (which could be very uncertain), we suggest a model utilizing the monotonicity property of a rise in the incidence. For ILI data at the outbreak, Poisson distributions can be used as a first approximation. To confirm that the peak has occurred and the decline has started, we focus on LDI data. A Gaussian distribution is a reasonable approximation near the peak. In view of the variability of the shape of the peak, we suggest that a detection system use the monotonicity properties of a peak.
Microarray amplification bias: loss of 30% differentially expressed genes due to long probe – poly(A)-tail distances
Authors: Boelens Mirjam C , te Meerman Gerard J , Gibcus Johan H , Blokzijl Tjasso , Boezen H Marike , Timens Wim , Postma Dirkje S , Groen Harry JM , van den Berg Anke 
Published: August 2007

Abstract

Background
Laser microdissection microscopy has become a rising tool to assess gene expression profiles of pure cell populations. Given the low yield of RNA, a second round of amplification is usually mandatory to yield sufficient amplified-RNA for microarray approaches. Since amplification induces truncation of RNA molecules, we studied the impact of a second round of amplification on identification of differentially expressed genes in relation to the probe – poly(A)-tail distances.

Results
Disagreement was observed between gene expression profiles acquired after a second round of amplification compared to a single round. Thirty percent of the differentially expressed genes identified after one round of amplification were not detected after two rounds. These inconsistent genes have a significant longer probe – poly(A)-tail distance. qRT-PCR on unamplified RNA confirmed differential expression of genes with a probe – poly(A)-tail distance >500 nucleotides appearing only after one round of amplification.

Conclusion
Our data demonstrate a marked loss of 30% of truly differentially expressed genes after a second round of amplification. Therefore, we strongly recommend improvement of amplification procedures and importance of microarray probe design to allow detection of all differentially expressed genes in case of limited amounts of RNA.
Validation of rice genome sequence by optical mapping
Authors: Zhou Shiguo , Bechner Michael C , Place Michael , Churas Chris P , Pape Louise , Leong Sally A , Runnheim Rod , Forrest Dan K , Goldstein Steve , Livny Miron , Schwartz David C 
Published: August 2007

AbstractBackgroundRice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data.ResultsTo facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical andin silicorestriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies.ConclusionAnalysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences revealed by optical maps constructed from a broad range of rice subspecies and varieties.
Success of microvascular surgery; repair mesenteric injury and prevent short bowel syndrome: a case report
Authors: Aydin Unal , Unalp Omer V , Yazici Pinar , Guler Adem 
Published: August 2007

Abstract

Background
Superior mesenteric injury is a rare entity but when it occurs, short bowel syndrome is one of the uninvited results of the emergency surgical procedures.

Case presentation
We present a 19-year-old boy with blunt abdominal trauma which caused serious mesenteric injury. Because ultrasound revealed free intraabdominal fluid, he underwent emergency laparotomy. Adequate vascularization of approximately 20 cm of proximal jejunal segment and approximately 20 cm of terminal ileum was observed. Nevertheless, the mesentery of the rest of the small intestine segments was ruptured completely. We performed an end-to-end anastomosis between a distal branch of the superior mesenteric artery in the mesentery of the ileal segment and a branch of the superior mesenteric artery using separate sutures of 7.0 monofilament polypropylene. The patient's gastrointestinal passage returned to normal on the postoperative day 2. He recovered without any complication and was discharged from hospital on the postoperative day seven.

Discussion
In this case report, we emphasize the importance of preservation of injured mesenteric artery due to abdominal trauma which could have resulted in short bowel syndrome.
Analysis of the geographic distribution of HFRS in Liaoning Province between 2000 and 2005
Authors: Lin Hualiang , Liu Qiyong , Guo Junqiao , Zhang Jibo , Wang Jinfeng , Chen Huaxin 
Published: August 2007

Abstract

Background
Hemorrhagic fever with renal syndrome (HFRS) is endemic in Liaoning Province, China, and this province was the most serious area affected by HFRS during 2004 to 2005. In this study, we conducted a spatial analysis of HFRS cases with the objective to determine the distribution of HFRS cases and to identify key areas for future public health planning and resource allocation in Liaoning Province.

Methods
The annual average incidence at the county level was calculated using HFRS cases reported between 2000 and 2005 in Liaoning Province. GIS-based spatial analyses were conducted to detect spatial distribution and clustering of HFRS incidence at the county level, and the difference of relative humidity and forestation between the cluster areas and non-cluster areas was analyzed.

Results
Spatial distribution of HFRS cases in Liaoning Province from 2000 to 2005 was mapped at the county level to show crude incidence, excess hazard, and spatial smoothed incidence. Spatial cluster analysis suggested 16 and 41 counties were at increased risk for HFRS (p < 0.01) with the maximum spatial cluster sizes at ≤ 50% and ≤ 30% of the total population, respectively, and the analysis showed relative humidity and forestation in the cluster areas were significantly higher than in other areas.

Conclusion
Some clustering of HFRS cases in Liaoning Province may be etiologically linked. There was strong evidence some HFRS cases in Liaoning Province formed clusters, but the mechanism underlying it remains unknown. In this study we found the clustering was consistent with the relative humidity and amount of forestation, and showed data indicating there may be some significant relationships.
Microbial proteomics: a mass spectrometry primer for biologists
Authors: Graham Robert LJ , Graham Ciaren , McMullan Geoff 
Published: August 2007

AbstractIt is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level.In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS) and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.
An apricot story: view through a keyhole
Authors: Samdani Tushar , Singhal Tarun , Balakrishnan Santosh , Hussain Abdulzahra , Grandy-Smith Starlene , El-Hasani Shamsi 
Published: August 2007

Abstract

Background
Very few cases of small bowel obstruction due to ingested fruits have been described in literature, and most of these have managed by a laparotomy. Laparoscopic assisted surgery can effectively deal with such impacted foreign bodies, thereby avoiding a formal laparotomy.

Case presentation
A 75 years old lady was admitted via the Accident and Emergency to the surgical ward with a three-day history of abdominal pain and vomiting. Investigations were suggestive of acute small bowel obstruction. On laparoscopy, there was an area of sudden change in calibre of small bowel with dilated proximal and collapsed distal segment in distal jejunum. A foreign body, dried undigested apricot, was extracted by mini-laparotomy.

Discussion
Small bowel obstruction is a frequent cause of emergency surgery, and aetiology may include food bolus obstruction. Diagnosis is usually confirmed intra-operatively. Foreign body impacted in small bowel can be removed by open or laparoscopic methods.

Conclusion
Generally, laparotomy is performed for diagnosis and management in acute bowel obstruction, but with increasing expertise, laparoscopy can be equally effective with all the other advantages of minimal access approach.
DFsn collaborates with Highwire to down-regulate the Wallenda/DLK kinase and restrain synaptic terminal growth
Authors: Wu Chunlai , Daniels Richard W , DiAntonio Aaron 
Published: August 2007

Abstract
Background
The growth of new synapses shapes the initial formation and subsequent rearrangement of neural circuitry. Genetic studies have demonstrated that the ubiquitin ligase Highwire restrains synaptic terminal growth by down-regulating the MAP kinase kinase kinase Wallenda/dual leucine zipper kinase (DLK). To investigate the mechanism of Highwire action, we have identified DFsn as a binding partner of Highwire and characterized the roles of DFsn in synapse development, synaptic transmission, and the regulation of Wallenda/DLK kinase abundance.

Results
We identified DFsn as an F-box protein that binds to the RING-domain ubiquitin ligase Highwire and that can localize to the Drosophila neuromuscular junction. Loss-of-function mutants for DFsn have a phenotype that is very similar to highwire mutants – there is a dramatic overgrowth of synaptic termini, with a large increase in the number of synaptic boutons and branches. In addition, synaptic transmission is impaired in DFsn mutants. Genetic interactions between DFsn and highwire mutants indicate that DFsn and Highwire collaborate to restrain synaptic terminal growth. Finally, DFsn regulates the levels of the Wallenda/DLK kinase, and wallenda is necessary for DFsn-dependent synaptic terminal overgrowth.

Conclusion
The F-box protein DFsn binds the ubiquitin ligase Highwire and is required to down-regulate the levels of the Wallenda/DLK kinase and restrain synaptic terminal growth. We propose that DFsn and Highwire participate in an evolutionarily conserved ubiquitin ligase complex whose substrates regulate the structure and function of synapses.
Securinine, a GABAA receptor antagonist, enhances macrophage clearance of phase IIC. burnetii: comparison with TLR agonists
Authors: Lubick Kirk , Radke Miranda , Jutila Mark 
Published: August 2007

AbstractInnate immune cell stimulation represents a complementary approach to vaccines and antimicrobial drugs to counter infectious disease. We have used assays of macrophage activation and in vitro and in vivo phase II Coxiella burnetii infection models to compare and contrast the activity of a novel innate immune cell agonist, securinine, with known TLR agonists. As expected, TLR agonists, such as LPS (TLR4) and fibroblast-stimulating lipopeptide-1 (FSL-1; TLR2), induced macrophage activation and increased macrophage killing of phase II C. burnetii in vitro. FSL-1 also induced accelerated killing of C. burnetii in vivo. Securinine, a γ-aminobutyric acid type A receptor antagonist, was found to induce TLR-independent macrophage activation in vitro, leading to IL-8 secretion, L-selectin down-regulation, and CD11b and MHC Class II antigen up-regulation. As seen with the TLR agonists, securinine also induced accelerated macrophage killing of C. burnetii in vitro and in vivo. In summary, as predicted by the literature, TLR agonists enhance macrophage killing of phase II C. burnetii in vitro, and at least for TLR2 agonists, this activity occurs in vivo as well. Securinine represents a novel macrophage agonist, which has similar effects as TLR agonists in this model yet apparently, does not act through known TLRs. Securinine has minimal toxicity in vivo, suggesting it or structurally similar compounds may represent novel, therapeutic adjuvants, which increase resistance to intracellular pathogens.
Mycoplasmacontaminants present in exosome preparations induce polyclonal B cell responses
Authors: Quah Ben J C , O’Neill Helen C 
Published: August 2007

AbstractExosome fractions of dendritic cells (DC) produced in long-term cultures (LTC) were found to contain Mycoplasma contaminants. In this study, Mycoplasma-infected, -uninfected, and -reinfected cultures of DC and control cell lines have been compared for their capacity to activate lymphocytes. Using differential centrifugation, size fractionation, and inhibition assays, it has been possible to map Mycoplasma to the exosome or vesicle fraction purified from culture supernatant (CSN). Mycoplasma fractions were shown to induce proliferation of B and not T cells. The B cell response was sensitive to mitomycin C and primaquine, both known antibiotics, but resistant to protease and DNase, suggesting a role for lipoproteins. Mycoplasma-contaminated exosome fractions of LTC-DC were potent mitogens for naive B cells and promoted Ig secretion. In contrast to the polyclonal B cell mitogen LPS, they were unable to promote Ig isotype switching. They induced polyclonal activation of all B cell subsets, including naive B cells, the T1 and T2 subsets of transitional B cells, marginal zone (MZ), and follicular (FO) B cells. The B cell proliferative response was not antigen-specific and occurred independently of T cell help. Implications for autoimmune sequelae associated with Mycoplasma infection are discussed along with the possibility that primaquine could be an effective treatment for Mycoplasma infection in humans. This study highlights the close association between exosomes and infectious agents like Mycoplasma and cautions about purification procedures for preparation of exosomes for studies on immunity.
CCR7 mediates the migration of Foxp3+ regulatory T cells to the paracortical areas of peripheral lymph nodes through high endothelial venules
Authors: Ueha Satoshi , Yoneyama Hiroyuki , Hontsu Shigeto , Kurachi Makoto , Kitabatake Masahiro , Abe Jun , Yoshie Osamu , Shibayama Shiro , Sugiyama Tetsuya , Matsushima Kouji 
Published: August 2007

AbstractThymus-derived forkhead box p3+ naturally occurring regulatory T cells (nTreg) are thought to circulate throughout the body to maintain peripheral immunological self-tolerance through interactions with dendritic cells (DCs), resulting in regulation of conventional T cells. However, the chemokine receptors, which are putatively involved in the in vivo migration of nTreg, have not been fully established. Here, we demonstrated that lymph node nTreg preferentially migrated to the paracortical area of lymph nodes after adoptive transfer, where they were observed to make contact frequently with CD8α+ DCs and CD8α− CD11b− DCs. This migration of nTreg to the paracortical areas was impaired severely when cells were prepared from CCR7-deficient mice. However, to some extent, CCR7-independent migration of nTreg in such CCR7-deficient mice was also observed, but this occurred mainly in the medullary high endothelial venules. Taken together, these data provide the evidence that CCR7 mediates nTreg migration to the paracortical areas of lymph nodes under steady-state conditions; however, CCR7-independent migration also takes place in the medulla.
Childhood Metabolic Syndrome and Its Components in Premature Adrenarche
Authors: Utriainen Pauliina , Jääskeläinen Jarmo , Romppanen Jarkko , Voutilainen Raimo 
Published: August 2007

Abstract
Context: Premature pubarche (PP), the main clinical manifestation of premature adrenarche (PA), has been associated with insulin resistance and dyslipidemia in selected populations.
Objectives: Our aim was to determine the prevalence of childhood metabolic syndrome (cMBS) and to study its components in prepubertal Northern European girls with PA.
Design and Patients: We conducted a cross-sectional study on 63 prepubertal girls with PA (32 with PP = PP-PA, 31 without PP = nonPP-PA) and 80 healthy age-matched control girls. A standard 2-h oral glucose tolerance test with insulin sampling was performed. Plasma lipids and serum SHBG were analyzed, and blood pressure and weight-for-height were recorded. cMBS was defined by modified criteria of the U.S. National Cholesterol Education Project Adult Treatment Panel III and the World Health Organization.
Setting: The study was performed at University Hospital.
Results: The mean weight-for-height (P = 0.002) and the prevalence of cMBS by the modified Adult Treatment Panel III (24 vs. 10%) and World Health Organization definitions (16 vs. 5%) (P &lt; 0.05 for both) were higher in the PA than control girls. The weight-for-height adjusted serum insulin concentrations during the oral glucose tolerance test were elevated in the whole PA group, whereas the fasting insulin concentrations were increased and SHBG was decreased only in the PP-PA subgroup. The weight-for-height adjusted blood pressure, lipid, or glucose levels did not differ between the study groups.
Conclusions: Prepubertal Northern European PA girls have increased prevalence of cMBS mainly due to being overweight and their hyperinsulinism. Among the PA children, the nonPP-PA girls have milder metabolic changes than the PP-PA girls.