bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible organosedimentary structures on Mars
Authors: Rizzo Vincenzo , Cantasano Nicola 
Published: August 2009

AbstractThis study, using the Microscopic Imager (MI) of NASA Rover Exploration Mission's (REM) ‘Opportunity’, aims to explain the origin of laminated sediments lying at Meridiani Planum of Mars, and of the strange spherules, known as blueberries, about which several hypotheses have been formulated. To this purpose, images of the sedimentary textures of layers and fragments captured by REM have been analysed; sediments that NASA has already established as ‘pertinent to water presence’. Our study shows that such laminated sediments and the spherules they contain could be organosedimentary structures, probably produced by microorganisms. The laminated structures are characterized by a sequence of a thin pair of layers, which have the features of skeletal/agglutinated laminae and whose basic constituents are made by a partition of septa and vacuoles radially arranged around a central one. The growth of these supposed organosedimentary masses is based on the ‘built flexibility’ of such a basal element; it may be a coalescing microfossil formed by progressive film accretion (calcimicrobe), in a variety of geometrical gross forms, such as a repeated couplet sequence of laminae or domal mass and large composite polycentric spherule, both in elevation. The acquired structural and textural data seem to be consistent with the existence of life on Mars and could explain an origin of sediments at Meridiani Planum similar to that of terrestrial stromatolites. The Martian deposits, probably produced by cyanobacterial activity, and the embedded blueberries could represent a recurrent and multiform product of colonies with sheath forms, resembling in shape those of the fossil genus Archaeosphaeroides (stromatolites of Fig Tree, South Africa).
The rise of pragmatism in state/market debate
Authors: SALTMAN RICHARD B. 
Published: August 2009

Abstract:Discussion about the relative role of public and private in health care has evolved substantially across Europe since the 1980s. The previous, broadly ideological debate about state ‘versus’ market has been superceded by pragmatic considerations on how best to combine state ‘and’ market to achieve specific health sector outcomes. The London School of Economics debate about expanded patient choice demonstrated the extent to which pragmatism has gained the upper hand.
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Authors: Keller Andreas , Backes Christina , Gerasch Andreas , Kaufmann Michael , Kohlbacher Oliver , Meese Eckart , Lenhof Hans-Peter 
Published: August 2009

AbstractMotivation: Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for studying the activity of the signaling cascades and for understanding the information flow in the networks.Results: We present a novel dynamic programming algorithm for detecting deregulated signaling cascades. The so-called FiDePa (Finding Deregulated Paths) algorithm interprets differences in the expression profiles of tumor and normal tissues. It relies on the well-known gene set enrichment analysis (GSEA) and efficiently detects all paths in a given regulatory or signaling network that are significantly enriched with differentially expressed genes or proteins. Since our algorithm allows for comparing a single tumor expression profile with the control group, it facilitates the detection of specific regulatory features of a tumor that may help to optimize tumor therapy. To demonstrate the capabilities of our algorithm, we analyzed a glioma expression dataset with respect to a directed graph that combined the regulatory networks of the KEGG and TRANSPATH database. The resulting glioma consensus network that encompasses all detected deregulated paths contained many genes and pathways that are known to be key players in glioma or cancer-related pathogenic processes. Moreover, we were able to correlate clinically relevant features like necrosis or metastasis with the detected paths.Availability: C++ source code is freely available, BiNA can be downloaded from http://www.bnplusplus.org/.Contact: ack@bioinf.uni-sb.deSupplementary information: Supplementary data are available at Bioinformatics online.
UniMaP: finding unique mass and peptide signatures in the human proteome
Authors: Alexandridou Anastasia , Tsangaris George Th. , Vougas Konstantinos , Nikita Konstantina , Spyrou George 
Published: August 2009

AbstractSummary: The uniqueness of a measured molecular mass or peptide sequence plays a very important role in the fields of protein identification and peptide/protein-biomarker investigation. We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. These unique tags are remarkably important in research related to protein identification or biomarker discovery and measurements.Availability: UniMaP web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/Contact: gspyrou@bioacademy.grSupplementary information: Supplementary data are available at Bioinformatics online.
Concerns regarding the use of amphibians as metrics of critical biological thresholds: a comment on Welsh & Hodgson (2008)
Authors: KROLL ANDREW J. , HAYES MARC P. , MACCRACKEN JAMES G. 
Published: August 2009

Summary1. Welsh & Hodgson (2008)argued that stream‐associated amphibians (Ascaphus truei,Dicamptodon tenebrosusandRhyacotriton variegatus) are reliable indicators of ecosystem health in the Pacific Northwest (PNW), U.S.A. We demonstrate that their assertions rely on circular reasoning as well as logical and empirical assumptions that have not received rigorous evaluation.2. Welsh & Hodgson (2008)based their arguments on data collected in northwestern California, U.S.A. However, all three taxa occur across a wide range of environmental gradients in the PNW, and other research results suggest that the taxa respond differentially to environmental perturbations across their geographical distribution. Hence, differences in abundance are not always reliable indicators of the state of an ecosystem, as population numbers can be influenced by factors that may not be associated with habitat quality (e.g. predation and disease).3. Welsh & Hodgson (2008)present indices (rather than estimates) of abundance, which contain an unquantifiable amount of uncertainty not reliably attributable to either environmental or management factors. Evaluating parameters such as reproductive success and survival are more likely to provide strong inference about factors influencing population size than correlative studies that associate some measure of relative abundance with individual habitat features.4. We argue that direct measurement of physical features (water temperature, sediment and wood), for whichWelsh & Hodgson (2008)suggest using amphibians as surrogates, is more accurate, efficient and cost effective compared with monitoring cryptic species with methods that are unable to quantify spatial and temporal uncertainty in biological responses.5. Headwater streams are critical components of catchments in the PNW, and all three amphibian taxa show strong associations with low‐order streams. However, we think research and monitoring of headwater streams should be guided by hypotheses that evaluate causal mechanisms, rather than relying on descriptive patterns that are limited in geographical scope and which support only weak inference about ecosystem processes. Other studies provide direct links between physical features and responses of target populations (i.e. fish). Adding a second correlative link (i.e. amphibians) provides no added benefit, and increases uncertainty in the association between management actions and changes in population size.
Ecological and socio‐economic impacts of invasive water hyacinth (Eichhornia crassipes): a review
Authors: VILLAMAGNA A. M. , MURPHY B. R. 
Published: August 2009

Summary1. Water hyacinth (Eichhornia crassipes) is one of the world’s most invasive aquatic plants and is known to cause significant ecological and socio‐economic effects.2. Water hyacinth can alter water clarity and decrease phytoplankton production, dissolved oxygen, nitrogen, phosphorous, heavy metals and concentrations of other contaminants.3. The effects of water hyacinth on ecological communities appear to be largely nonlinear. Abundance and diversity of aquatic invertebrates generally increase in response to increased habitat heterogeneity and structural complexity provided by water hyacinth but decrease due to decreased phytoplankton (food) availability.4. Effects of water hyacinth on fish are largely dependent on original community composition and food‐web structure. A more diverse and abundant epiphytic invertebrate community may increase fish abundance and diversity, but a decrease in phytoplankton may decrease dissolved oxygen concentrations and planktivorous fish abundance, subsequently affecting higher trophic levels.5. Little is known about the effects of water hyacinth on waterbird communities; however, increases in macroinvertebrate and fish abundance and diversity suggest a potentially positive interaction with waterbirds when water hyacinth is at moderate density.6. The socio‐economic effects of water hyacinth are dependent on the extent of the invasion, the uses of the impacted waterbody, control methods and the response to control efforts. Ecosystem‐level research programmes that simultaneously monitor the effects of water hyacinth on multiple trophic‐levels are needed to further our understanding of invasive species.
Inversion of controlled‐source electromagnetic data using a model‐based approach
Authors: Li Maokun , Abubakar Aria , Habashy Tarek M. , Zhang Yan 
Published: August 2009

ABSTRACTA two‐and‐half dimensional model‐based inversion algorithm for the reconstruction of geometry and conductivity of unknown regions using marine controlled‐source electromagnetic (CSEM) data is presented. In the model‐based inversion, the inversion domain is described by the so‐called regional conductivity model and both geometry and material parameters associated with this model are reconstructed in the inversion process. This method has the advantage of using a priori information such as the background conductivity distribution, structural information extracted from seismic and/or gravity measurements, and/or inversion results a priori derived from a pixel‐based inversion method. By incorporating this a priori information, the number of unknown parameters to be retrieved becomes significantly reduced. The inversion method is the regularized Gauss‐Newton minimization scheme. The robustness of the inversion is enhanced by adopting nonlinear constraints and applying a quadratic line search algorithm to the optimization process. We also introduce the adjoint formulation to calculate the Jacobian matrix with respect to the geometrical parameters. The model‐based inversion method is validated by using several numerical examples including the inversion of the Troll field data. These results show that the model‐based inversion method can quantitatively reconstruct the shapes and conductivities of reservoirs.
Differences in genetic instability and cellular phenotype among Barrett’s, cardiac, and gastric intestinal metaplasia in a Japanese population with Helicobacter pylori
Authors: Watari Jiro , Moriichi Kentaro , Tanabe Hiroki , Sato Ryu , Fujiya Mikihiro , Miwa Hiroto , Das Kiron M , Kohgo Yutaka 
Published: August 2009

Aims:  Intestinal metaplasia is considered to be a precursor lesion in both Barrett’s and intestinal‐type gastric cancer. The aim was to clarify the differences in molecular pathology between specialized intestinal metaplasia (SIM) in Barrett’s oesophagus (BO), cardiac (CIM) and gastric intestinal metaplasia (GIM).Methods and results:  Eighty‐eight SIM cases with BO, 30 CIM cases and 52 GIM cases in patients with or without Helicobacter pylori infectionwere analysed for genetic instability and Das‐1. Microsatellite instability and a loss of heterozygosity were evaluated at five microsatellite loci. The incidence of genetic instability was 55.7% in SIM, 40.0% in CIM and 23.1% in GIM, revealing a significant difference between SIM and GIM (P < 0.0005). For each microsatellite marker analysed, there were obvious differences in frequency among the three conditions. Das‐1 reactivity was significantly higher in SIM than in CIM or GIM (P < 0.0001, both). Interestingly, both genetic instability and Das‐1 reactivity in SIM showed a significantly higher incidence in patients with H. pylori infection than in those without (P < 0.005 and P < 0.01, respectively).Conclusions:  SIM is distinct from CIM and GIM, and the pathogenesis of SIM, like that of GIM, is associated to some degree with H. pylori infection in a Japanese population.
Intraductal tubular adenoma (pyloric gland‐type) of the pancreas: a reappraisal and possible relationship with gastric‐type intraductal papillary mucinous neoplasm
Authors: Chetty Runjan , Serra Stefano 
Published: August 2009

Aims:  Intraductal tubular adenoma (ITA) is an uncommon intraluminal polypoid lesion that occurs in the main pancreatic duct and involves the main pancreatic duct in the region of head or body. Three cases of ITA are presented, the literature reviewed and their association with intraductal papillary mucinous neoplasm (IPMN) is postulated.Methods and results:  ITA is composed of tightly packed tubular structures with focal cystic dilation and papillary areas lined by gastric/pyloric epithelium showing minimal to mild cytological atypia. Pancreatic intraepithelial neoplasia (PanIN) 1A and B was present in smaller ducts of all cases. In addition, in the cases in this report and 50% of cases reported in the literature, an associated gastric‐type IPMN was present in the same duct as the ITA or in adjacent ducts. The coexistence of ITA and IPMN and the similarities of their epithelial lining (gastric/pyloric mucosa) suggest a possible pathogenic link.Conclusions:  ITA can occur without (type A) or with (type B) an associated gastric‐type IPMN. ITA could represent a localized, polypoid form of gastric‐type IPMN.It is a benign lesion with no evidence of invasion and no direct tumour‐related deaths. Its relationship to intraductal tubular carcinoma remains to be elucidated.
Evolutionary ecology of human birth sex ratio under the compound influence of climate change, famine, economic crises and wars
Authors: Helle Samuli , Helama Samuli , Lertola Kalle 
Published: August 2009

Summary 1.  Human sex ratio at birth at the population level has been suggested to vary according to exogenous stressors such as wars, ambient temperature, ecological disasters and economic crises, but their relative effects on birth sex ratio have not been investigated. It also remains unclear whether such associations represent environmental forcing or adaptive parental response, as parents may produce the sex that has better survival prospects and fitness in a given environmental challenge. 2.  We examined the simultaneous role of wars, famine, ambient temperature, economic development and total mortality rate on the annual variation of offspring birth sex ratio and whether this variation, in turn, was related to sex‐specific infant mortality rate in Finland during 1865–2003. 3.  Our findings show an increased excess of male births during the World War II and during warm years. Instead, economic development, famine, short‐lasting Finnish civil war and total mortality rate were not related to birth sex ratio. Moreover, we found no association between annual birth sex ratio and sex‐biased infant mortality rate among the concurrent cohort. 4.  Our results propose that some exogenous challenges like ambient temperature and war can skew human birth sex ratio and that these deviations likely represent environmental forcing rather than adaptive parental response to such challenges.
Blood surveillance and detection on platelet bacterial contamination associated with septic events
Authors: Hsueh J. C. , Ho C. F. , Chang S. H. , Pan F. Z. , Chen S. C. , Shi M. D. , Chien S. T. 
Published: August 2009

summary.The objective of this study was to evaluate the risk of transfusion‐associated septic events in Taiwan. In Taiwan, most blood components are provided from blood centres; so platelet (PLT) bacterial contaminations are rarely reported. The study's aim is to investigate the prevalence of PLT bacterial contamination in Kaoshiung Armed Forces General Hospital by using BacT/ALERT system for routine screening.A total of 82 apheresis and 2256 whole blood‐derived PLT units were tested. A measured quantity of 1 mL aliquots were taken as samplings from all blood bag tubing of PLT units, and then further incubated in a bacterial detection system (BacT/ALERT). The subcultures of true‐positive bottles underwent bacterial identification by using Vitek system, microscopic observation and culture‐based methods. Eight units (0·34%, 8 of 2338) were found to have bacterial contamination. The true‐positive rate of the whole blood‐derived and apheresis PLTs was 0·31% (7 of 2256) and 1·22% (1 of 82), respectively. Six microorganisms were identified with the most dominate being Staphylococcus epidermidis. One case of transfusion‐associated sepsis was confirmed; in addition, the holding period of PLTs (F = 4·522, P = 0·034) and positive detection of PLT bacterial contamination (F = 46·605,P < 0·001) were associated with post‐transfusion sepsis. Thus, in this study, although the transfusion‐associated septic event was rarely found and PLT units were provided from blood centres, bacterial screening was necessary to safely quarantine the transfusion. The holding period of PLT units should be no more than 4 days in order to avoid possible bacterial contamination.
Patient involvement in assessing consultation quality: a quantitative study of the Patient Enablement Instrument in Poland
Authors: Pawlikowska Teresa R.B. , Walker Jeremy J. , Nowak Pawel R. , Szumilo‐Grzesik Wieslawa 
Published: August 2009

AbstractBackground  Promoting a more patient‐responsive service has been the focus of policy initiatives in newer EU states. One measure of success should be the patient’s assessment of their consultation with their doctor.Objectives  To measure consultation quality in Polish primary care using patient enablement (a patient‐driven instrument developed in the UK) and to test its theoretical framework. To compare the patient enablement outcome of different types of doctor delivering primary care in Poland following reform.Design  Cross‐sectional quantitative questionnaire survey.Setting  Random sample of primary care doctors practising within a 60‐km radius of Gdansk, Poland.Subjects and outcome measures  Patient Enablement Instrument and correlates were measured in 7924 consecutive adult consultations of 48 doctors, stratified according to training: family medicine specialists (diploma holders), non‐diplomates and general medicine doctors (polyclinic internists).Results  Completion was high (78%). The mean patient enablement score in Poland was 4.0 (SD 3.3) and mean consultation length was 10.3 min (SD 5.4 min). Consultation length and knowing the doctor are independently related to patient enablement in the Polish context. Variation between doctors is significant, but earlier differences in enablement between alternative providers have largely been ameliorated in practice.Conclusion  It is feasible to use patient enablement on a large scale at routine consultation in primary care in Poland: acceptability was good in diverse environments. The internal consistency of enablement and its relationships broadly mirror those found in the UK. The effect of patient expectations shaped by social and cultural issues influencing enablement outcome requires further investigation.
The longitudinal course of cognition in older adults with bipolar disorder
Authors: Gildengers Ariel G , Mulsant Benoit H , Begley Amy , Mazumdar Sati , Hyams Adriana V , Reynolds III Charles F , Kupfer David J , Butters Meryl A 
Published: August 2009

Objectives:  Epidemiological studies suggest that elders with bipolar disorder (BD) may be at increased risk for dementia compared to the general population. We sought to investigate whether older adults with BD would present with more cognitive dysfunction than expected for their age and education, and whether they would experience a more rapid cognitive decline over three‐year prospective follow‐up.Methods:  Thirty‐three subjects age ≥ 50, mean (SD) age 69.7 (7.9) years, with BD I (n = 28) and II (n = 5) had neuropsychological examination at baseline and longitudinally over three years. All subjects were administered the Dementia Rating Scale (DRS) when euthymic. Thirty‐six mentally healthy comparators (‘controls’), equated on age and education, were selected from ongoing studies in our research center examining the longitudinal relationship between late‐life mood disorders and cognitive function.Results:  Compared to mentally healthy comparators, subjects with BD performed significantly worse on the DRS at baseline [mean (SD) 135.2 (4.7); n = 33 versus 139.5 (3.3); n = 36], and over follow‐up [131.9 (7.7); n = 14 versus 139.1 (3.4); n = 22]. There was a group‐by‐time interaction between the subjects with BD and the controls [group × time: F(1,64) = 5.07, p = 0.028].Conclusions:  In our study, older adults with BD had more cognitive dysfunction and more rapid cognitive decline than expected given their age and education. Cognitive dysfunction and accelerated cognitive decline may lead to decreased independence, with increased reliance on family and community supports, and potential placement in assisted‐living facilities.