bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large scale genotype–phenotype correlation analysis based on phylogenetic trees
Authors: Habib Farhat , Johnson Andrew D. , Bundschuh Ralf , Janies Daniel 
Published: February 2007

AbstractWe provide two methods for identifying changes in genotype that are correlated with changes in a phenotype implied by phylogenetic trees. The first method, VENN, works when the number of branches over which the change occurred are modest. VENN looks for genetic changes that are completely penetrant with phenotype changes on a tree. The second method, CCTSWEEP, allows for a partial matching between changes in phenotypes and genotypes and provides a score for each change using Maddison's concentrated changes test. The mutations that are highly correlated with phenotypic change can be ranked by score. We use these methods to find SNPs correlated with resistance to Bacillus anthracis in inbred mouse strains. Our findings are consistent with the current biological literature, and also suggest potential novel candidate genes.Contact: farhat@pacific.mps.ohio-state.edu for software requests.
Robustness analysis of theE.colichemosensory system to perturbations in chemoattractant concentrations
Authors: Patnaik Pratap R. 
Published: February 2007

AbstractMotivation: Cells of Escherichia coli sense and move toward chemical attractants. This is done through an intricate sensory system that eventually directs the movements of flagellae which regulate the ‘runs’ and ‘tumbles’ of the cells. Under realistic conditions, chemical stimuli often fluctuate due to noise from the environment. The effect of noise on the chemosensory system has been investigated here through the sensitivity coefficients of the concentrations of four key proteins—the phosphorylated forms of CheA, CheB and CheY, and the FliM-CheY∼P complex—that govern chemotactic motility. The letter P denotes phosphorylation.Results: All sensitivities increased with time and then stabilized. However, the four sets of sensitivities differed in their magnitudes and the durations of their transient phases before stabilization. CheA∼P was the least sensitive and CheY∼P the most sensitive. Moreover, while the sensitivities of CheA∼P, CheB∼P and CheY∼P increased with chemoattractant concentration, that of the FliM complex decreased. These differences have been interpreted in terms of the mechanism of the chemosensory system and they have important implications for practical applications of chemotaxis.Contact: pratap@imtech.res.in
Repair of a Malleus‐Handle Fracture Using Calcium Phosphate Bone Cement
Authors: Hato Naohito , Okada Masahiro , Hakuba Nobuhiro , Hyodo Masamitsu , Gyo Kiyofumi 
Published: February 2007

AbstractWe report a case of a 60‐year‐old woman who reported a popping sound in her left ear, induced by changes in pressure, since she pulled her index finger out of her ear canal after accidentally inserting it while washing her hair. Otoscopic examination revealed a wrinkled tympanic membrane and irregular malleus handle. An isolated malleus‐handle fracture resulting from barotrauma was suspected. The fracture was repaired surgically using calcium phosphate bone cement. Postoperatively, the problem disappeared and her hearing recovered. This case is the first to demonstrate the efficacy of calcium phosphate bone cement for repairing a malleus‐handle fracture.
Natural Course of Retention Cysts of the Maxillary Sinus: Long‐Term Follow‐Up Results
Authors: Wang Jong Hwan , Jang Yong Ju , Lee Bong‐Jae 
Published: February 2007

AbstractObjectives: Retention cysts of the maxillary sinus are an incidental finding on radiographs. These cysts usually appear as rounded, dome‐shaped, soft tissue masses, most often on the floor of the maxillary sinus. The aim of this study was to investigate the long‐term natural course of retention cysts of the maxillary sinus.Methods: Between November 1997 and October 2002, 40 patients were incidentally found to have retention cysts of the maxillary sinus on Waters view films. Seventeen of these patients were followed for 38 to 102 (mean, 60) months. Medical records, endoscopic nasal examinations, and Waters view of all 40 patients were reviewed. The size of each retention cyst and the ratio of cyst size to antral size were measured.Results: Of the 40 patients, 21 (52.5%) had cysts in the left maxillary sinus, 17 (42.5%) had cysts in the right maxillary sinus, and 2 (5%) had cysts in both sinuses. Thirty of the 43 (69.7%) cysts appeared to arise from the floor of the sinus. Cyst size ranged from 108 mm2 to 1,001 mm2, and the ratio of cyst size to antral size ranged from 12.8% to 96.9%, as measured on Waters view. Follow‐up Waters view films in 17 patients showed that seven cysts disappeared completely, two decreased in size, four showed no significant change in size, and five increased in size.Conclusions: Most retention cysts of the maxillary sinus spontaneously regressed or showed no significant change in size over the long term. These findings suggest that, in the absence of associated complications, “wait and see” may be the appropriate management strategy for these retention cysts.
Pulmonary Recovery After Rigid Bronchoscopic Retrieval of Airway Foreign Body
Authors: Chung Man Ki , Jeong Han‐Sin , Ahn Kang Mo , Park Shin‐Hong , Cho Jae Keun , Son Young‐Ik , Baek Chung‐Hwan 
Published: February 2007

AbstractObjective: The aim of this study was to determine how long postoperative pulmonary care is needed in patients after rigid bronchoscopic retrieval of foreign body from the airway and to identify the factors affecting pulmonary recovery.Materials and Method: A retrospective review of 98 pediatric patients who had foreign body removed from the airway by rigid bronchoscopic procedure was conducted. After the removal of the foreign body, the time required for complete clinical and radiologic pulmonary recovery was reviewed for each subject. Factors examined included age, sex, preoperative symptoms, preoperative radiologic findings, duration between the aspiration event and treatment, the type of foreign body, the location of foreign body impaction, operation time, immediate postoperative radiologic changes, and treatment outcome.Results: More than 1 week for the complete pulmonary recovery was required in 25 (25.5%) cases, whereas 74.5% of subjects fully recovered within 1 week after the removal of foreign body. In the univariate analysis, preoperative inflammatory symptoms, and radiologic findings, an operation time of over 50 minutes and the aggravation of immediate postoperative radiologic findings predicted a delayed pulmonary recovery (more than 1 week). In the multivariate analysis, three of four variables previously noted, except preoperative inflammatory symptoms, showed significant predictability for a delayed pulmonary recovery.Conclusion: The recovery time of more than 1 week after rigid bronchoscopic retrieval of airway foreign body was associated with preoperative inflammatory findings by radiologic study, a prolonged procedure over 50 minutes, and aggravation of the immediate postoperative radiologic findings. Therefore, long‐term pulmonary care is required for this group of patients.
Endonasal Endoscopic Repair of Sternberg's Canal Cerebrospinal Fluid Leaks
Authors: Castelnuovo Paolo , Dallan Iacopo , Pistochini Andrea , Battaglia Paolo , Locatelli Davide , Bignami Maurizio 
Published: February 2007

AbstractObjectives: Management of cerebrospinal fluid leaks or encephaloceles of Sternberg's canal is challenging. Transnasal visualization of this area is difficult, especially when large pneumatization is present. External approaches to this region involve aggressive surgery and are often associated with significant morbidity. The aim of the study was to assess the real effectiveness of an endoscopic endonasal approach for treating cerebrospinal fluid leaks of the lateral recess of the sphenoid sinus.Study Design: The authors conducted a retrospective evaluation.Methods: Clinical charts of patients with cerebrospinal fluid leaks and/or encephaloceles of Sternberg's canal treated at our institution were retrospectively reviewed. All these patients were managed with an endonasal endoscopic procedure.Results: Fifteen patients (9 female and 6 male) were included in this study. Nine patients underwent a transethmoidal–pterygoidal–sphenoidal approach with a multilayer reconstructive technique. No cerebrospinal fluid leak recurrences were observed during follow up (mean follow up 37.6 ± 21.7 standard deviation months)Conclusions: The transethmoidal–pterygoidal–sphenoidal approach provides a wide, safe, and direct route to the lateral recess of the sphenoid sinus. Multilayered reconstruction of the skull base defects must be considered the first option for this kind of lesion.
Analysis of Salvage Operation in Head and Neck Microsurgical Reconstruction
Authors: Hyodo Ikuo , Nakayama Bin , Kato Hisakazu , Hasegawa Yasuhisa , Ogawa Tetsuya , Terada Akihiro , Torii Shuhei 
Published: February 2007

AbstractIn this study, we examined salvage operations after reexploration in head and neck reconstruction and analyzed ways to solve problems. Free flap reconstruction of the head and neck lesion was carried out for 513 cases in our hospital over the past 12 years. Twenty‐one cases of reexploration were caused by postoperative thrombosis (4.1%). We could only salvage seven cases (33.3%) of 21 cases from flap thrombosis. All seven cases were included in the category of venous thrombosis, and they were undertaken within 3 days postoperatively. Our results have shown that once thrombosis occurs, there is little possibility of flap salvage, particularly 3 days after operation and in infectious cases. When no flow phenomena are observed and no flap salvage is deemed possible, aggressive treatment such as a second free flap or next pedicle flap should be chosen as soon as possible to avoid any delay in postoperative treatment.
Reduction and S-Carboxymethylation of Proteins: Large-Scale Method
Authors: Simpson Richard J. 
Published: February 2007

INTRODUCTIONIntact interchain and/or intrachain disulfide linkage in a protein can present problems during proteolytic or chemical fragmentation procedures. Disulfide bonds are commonly cleaved by reducing cystine to yield cysteine residues. However, cysteine residues are highly reactive, which can complicate sequence work. In this protocol, the intact protein (>1 mg) is reduced and then S-alkylated with iodoacetic acid (or iodoacetamide). The resulting cysteine derivative S-carboxymethylcysteine (or S-carboximadomethylcysteine) is easily detectable during chemical sequencing.
In Situ SDS-PAGE Peptide-Mapping Procedure (Cleveland Method)
Authors: Simpson Richard J. 
Published: February 2007

INTRODUCTIONIn this protocol, sample proteins are first separated by either one- or two-dimensional gel electrophoresis. The gel is briefly stained and destained, and the proteins are excised for peptide mapping. Peptide fragmentation (either enzymatically or chemically) is performed in situ in the gel pieces, and the partial digest is separated in a second gel.
SDS-PAGE Peptide-Mapping Procedure (Cleveland Method)
Authors: Simpson Richard J. 
Published: February 2007

INTRODUCTIONThe Cleveland method for peptide mapping of proteins relies on partial hydrolysis of the protein yielding a considerable number of large peptides that can be readily identified by SDS-PAGE or tricine-SDS-PAGE. Small peptides obtained with a total digest are often poorly fixed within the gel and usually contribute nothing to the peptide map. In the method described here, the protein is partially digested in solution, and the resulting peptide fragments are separated by SDS-PAGE.
Analysis of the Topology of Protein Complexes Using Cross-Linking and Mass Spectrometry: Figure 1.
Authors: Rappsilber Juri , Mann Matthias 
Published: February 2007

INTRODUCTIONThis protocol is designed to allow identification of spatial relationships between proteins within a wide variety of multiprotein complexes. Details for optimizing cross-linking of proteins within multiprotein complexes are provided. Following the cross-linking reaction, the proteins are separated by one-dimensional PAGE, the cross-linked proteins are isolated from the gel, and the individual members of the cross-linked complexes are identified by mass spectrometry. The protocol can be used to analyze many protein complexes isolated by any purification technique, provided the protein complexes remain in their native configuration.
Transfecting Cultured Hippocampal Neurons with an Actin-GFP Plasmid
Authors: Matus Andrew , Biou Virginie , Brinkhaus Heike , Roelandse Martijn 
Published: February 2007

INTRODUCTIONThis protocol describes two transfection methods for expressing GFP-tagged actin in primary neurons. The lipid reagent DOTAP (Roche Diagnostics) method produces actin-GFP-expressing hippocampal neurons that survive well during long periods in culture. The calcium phosphate method can be used to transfect neurons that have already been growing on coverslips in vitro. Transfected cells suitable for imaging can be obtained in cultures up to 15 days in vitro. One to two percent transfected cells is a typical result. A disadvantage of the calcium phosphate method is that hippocampal neurons become “fragile” after treatment.
Studying Mitosis in Cultured Mammalian Cells
Authors: Wadsworth Patricia 
Published: February 2007

INTRODUCTIONA major challenge for those who study mitosis is the need to keep cells alive and mitotically active during observations. This protocol describes methods for maintaining healthy, dividing mammalian cells in culture and during imaging, when mitosis can be examined. Rose chambers are preferable for observation and microinjection of living mitotic cells, but slide/coverslip preparations are easy to make and do not require any special equipment. Another inexpensive and easy-to-use alternative is to grow cells in a culture dish with a glass bottom. Such dishes are suitable for microinjection experiments.
Gallery forests versus bosquets: conservation of natural fragments at Lopé National Park in central Gabon
Authors: Ukizintambara Tharcisse , White Lee , Abernethy Kate , Thébaud Christophe 
Published: February 2007

AbstractHuman‐induced forest fragmentation has been relatively well‐studied, however, we know very little about the role of natural fragmentation in sustaining rare or marginal species that could have been lost if the advancement of continuous forest had not been controlled. Between February 2001 and January 2003, we conducted a study on characteristics of natural forest fragments in the mosaic of forests and savannas in the north of Lopé National Park in Central Gabon.We surveyed 61 vegetation plots (0.08 ha each) and compared vegetation characteristics of isolated forest fragments (bosquets) with those of gallery forests. Both shared 39% of all 251 species inventoried. Gallery forests contained 45% plant species on their own, while 16% were encountered only in bosquets. Therefore, bosquets were found to be valuable component of the Lopé landscape worth protecting.In addition, the Shannon–Wienner diversity index (H′) was higher for bosquets neighbouring gallery forests or continuous forests regardless of their sizes because seeds of new plant species were easily dispersed in these bosquets. To protect these gallery forests and bosquets, one of the traditional conservation tools – a controlled savanna burning – should still be used to prevent forest fragments from being engulfed by the expanding continuous forest.
Differentiation of European cattle by AFLP fingerprinting
Authors: Negrini R. , Nijman I. J. , Milanesi E. , Moazami‐Goudarzi K. , Williams J. L. , Erhardt G. , Dunner S. , Rodellar C. , Valentini A. , Bradley D. G. , Olsaker I. , Kantanen J. , Ajmone‐Marsan P. , Lenstra J. A. ,   the European Cattle Genetic Diversity Consortium
Published: January 2007

SummaryThe Neolithic introduction of domestic cattle into Europe was followed by differential adaptation, selection, migration and genetic isolation, leading ultimately to the emergence of specialized breeds. We have studied the differentiation of European cattle by amplified fragment length polymorphism (AFLP) fingerprinting. Combining AFLP data sets from two laboratories yielded 81 biallelic polymorphic markers scored in 19–22 individual animals from 51 breeds. Model‐based clustering differentiated Podolian cattle as well as French and Alpine breeds from other European cattle. AFLP genetic distances correlated well with microsatellite‐based genetic distances calculated for the same breeds. However, the AFLP data emphasized the divergence of taurine and indicine cattle relative to the variation among European breeds and indicated an Eastern influence on Italian and Hungarian Podolian breeds. This probably reflects import from the East after the original introduction of domestic cattle into Europe. Our data suggest that Italian cattle breeds are relatively diverse at the DNA sequence level.
Teenage conceptions, abortions, and births in England, 1994–2003, and the national teenage pregnancy strategy
Authors: Reading Richard 
Published: February 2007

.

Wilkinson P.,
French R.,
Kane R.,
Lachowycz K.,
Stephenson J.,
Grundy C.,
Jacklin P.,
Kingori P.,
Stevens M. &
Wellings K.
(
2006
)

,
368
,
1879
–
1886
.
Background  The aim of this study was to quantify the change in the number of conceptions and abortions among women younger than 18 years in England in relation to the government's national teenage pregnancy strategy.Methods  We undertook geographical analysis of data for 148 top‐tier local authority areas. The main outcomes were changes in under‐18 conceptions, abortions and births between the 5‐year period before implementation of the strategy (1994–1998) and the period immediately after implementation (1999–2003).Findings  The number of teenage conceptions peaked in 1998, then declined after the implementation in 1999 of the teenage pregnancy strategy. Under‐18 conception rates fell by an average of 2.0% (95% CI 1.8–2.2) per year between 1998 and 2003, below the rate needed to achieve the target of 50% reduction by 2010. The net change between 1994–1998 and 1999–2003 was a fall in conceptions of 3.2% (2.6–3.9) or 1.4 per 1000 women aged 15–17 years, a rise in abortions of 7.5% (6.5–8.6) or 1.4 per 1000, and a fall in births of 10·6% (9.9–11.3) or 2.8 per 1000. The change in the number of conceptions was greater in deprived and more rural areas, and in those with lower educational attainment. The change was greater in areas where services and access to them were poorer, but greater where more strategy‐related resources had been targeted.Interpretation  The decline in under‐18 conception and birth rates since 1998 and evidence that the declines have been greatest in areas receiving higher amounts of strategy‐related funding provides limited evidence of the effect of England's national teenage pregnancy strategy. The full effect of local prevention will be clear only with longer observation, and substantial further progress is needed to remedy England's historically poor international position in teenage conceptions.
Socioeconomic inequalities in very preterm birth rates
Authors: Reading Richard 
Published: February 2007

.

Smith L.K.,
Draper E.S.,
Manktelow B.N.,
Dorling J.S. &
Field D.J.
(
2007
)

,
92
,
F11
–
F14
.
Aims  To investigate the extent of socio‐economic inequalities in the incidence of very preterm birth over the past decade.Methods  Ecological study of all 549 618 births in the former Trent health region, UK, from 1 January 1994 to 31 December 2003. All singleton births of 22+0−32+6 weeks gestation (7185 births) were identified from population surveys of neonatal services and stillbirths. Poisson regression was used to calculate incidence of very preterm birth (22–32 weeks) and extremely preterm birth (22–28 weeks) by year of birth and decile of deprivation (child poverty section of the Index of Multiple Deprivation).Results  Incidence of very preterm singleton birth rose from 11.9 per 1000 births in 1994 to 13.7 per 1000 births in 2003. Those from the most deprived decile were at nearly twice the risk of very preterm birth compared with those from the least deprived decile, with 16.4 per 1000 births in the most deprived decile compared with 8.5 per 1000 births in the least deprived decile (incidence rate ratio 1.94; 95% CI 1.73–2.17). This deprivation gap remained unchanged throughout the 10‐year period. The magnitude of socio‐economic inequalities was the same for extremely preterm births (22–28 weeks incidence rate ratio 1.94; 95% CI 1.62–2.32).Conclusions  This large, unique dataset of very preterm births shows wide socio‐economic inequalities that persist over time. These findings are likely to have consequences on the burden of long‐term morbidity. Our research can assist future healthcare planning, the monitoring of socio‐economic inequalities and the targeting of interventions in order to reduce this persistent deprivation gap.
Labile lead in polluted soils measured by stable isotope dilution
Authors: Degryse F. , Waegeneers N. , Smolders E. 
Published: February 2007

SummaryIt is well known that lead (Pb) is strongly immobilized in soil by adsorption or precipitation. However, the reversibility of these reactions is poorly documented. In this study, the isotopically exchangeable Pb concentration in soils (E‐value) was measured using a stable isotope (208Pb). Soils were collected at three industrialized sites where historical Pb emissions have resulted in elevated Pb concentrations in the surrounding soil. Lead concentrations ranged from background values, in the control soils collected far from the emission source, to highly elevated concentrations (5460–14440 mg Pb kg−1). The control soil of each site was amended in the laboratory with Pb(NO3)2 to the same total Pb concentrations as the field‐contaminated soils. The %E values (E‐value relative to total Pb content) were greater than 84% in the laboratory‐amended soils, and ranged from 45% to 78% (mean 58%) in the field‐contaminated soils. The relatively large labile fractions of Pb in the field‐contaminated soils show that the majority of Pb is reversibly bound despite the fact that the binding strength is large. The Pb concentrations in soil solution were up to 3500‐fold larger for the laboratory‐amended soils than for field‐contaminated soils at corresponding total Pb concentrations. These differences cannot be explained by differences in labile fractions of Pb but are attributed to the decrease in soil solution pH upon addition of Pb2+‐salt.