bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic process analysis: when and how to use it
Authors: Hall Peter A 
Published: March 2006

AbstractChallenging the contention that statistical methods applied to large numbers of cases invariably provide better grounds for causal inference, this article explores the value of a method of systematic process analysis that can be applied in a small number of cases. It distinguishes among three modes of explanation — historically specific, multivariate, and theory‐oriented — and argues that systematic process analysis has special value for developing theory‐oriented explanations. It outlines the steps required to perform such analysis well and illustrates them with reference to Owen's investigation of the ‘democratic peace’. Comparing the results available from this kind of method with those from statistical analysis, it examines the conditions under which each method is warranted. Against conceptions of the ‘comparative method’ which imply that small‐ncase‐studies provide weak grounds for causal inference, it argues that the intensive examination of a small number of cases can be an appropriate research design for testing such inferences.
Can methods for analysing large numbers organize a productive dialogue with the actors they study?
Authors: Callon Michel 
Published: March 2006

AbstractThe creation of categories based on an analysis of large numbers of heterogeneous entities does not preclude the establishment of productive interactions with the entities studied. The nature of these interactions and the types of objectification they allow depend on the characteristics of the tools used. This article aims at characterizing the different methods in terms of the competencies they recognize in actors. Three types of methods are described: multidimensional analysis, social network analysis, and what is called ‘composition of egocentric heterogeneous networks’. The paper suggests that from one method to the next, the actors' competencies are enhanced. Consequently, the sociologist's ability to perceive the emergence of new categories increases; in endowing human and non‐human actors with larger and richer competencies, he upgrades his own competencies as an analyst. In addition, productive interactions between him and the actors he studies are made easier.
Reviving narratives in economics and management: towards an integrated perspective of modelling, statistical inference and narratives
Authors: Dumez Hervé , Jeunemaitre Alain 
Published: March 2006

AbstractMost articles in economics and management rely on modelling and/or statistical inference with a tendency to disregard narratives. By contrast, this paper argues in favour of reviving their role. It proposes an integrated perspective of modelling, quantification and narratives. The perspective is based on a set of principles (organon), use of the exploratory dimension, and colligation of rival hypotheses. The integrated narrative perspective is developed through an examination of the relationships between modelling and narratives, on one hand, and narratives and quantitative analysis, on the other. It is based upon an analysis of the exposed narratives in a few major economics publications.
A Computer‐Based Method for Determination of the Cell‐Free Layer Width in Microcirculation
Authors: KIM SANGHO , KONG ROBERT L. , POPEL ALEKSANDER S. , INTAGLIETTA MARCOS , JOHNSON PAUL C. 
Published: March 2006

ABSTRACTObjectives: The cell‐free layer between the erythrocyte column and the vessel wall is an important determinant of hydrodynamic resistance in microcirculatory vessels. The authors report a method for continuous measurement of the width of this layer.Methods: The light intensity of a linear array of pixels perpendicular to the vessel axis is continuously determined from a video image of a microcirculatory vessel. A threshold level based on Otsu's method is used to establish the interface between the cell‐free layer and the erythrocyte column. To test the method, video images at 750–4500 frames/s were obtained from venules and arterioles in rat spinotrapezius muscle at normal and reduced arterial pressures before and after induction of erythrocyte aggregation with Dextran 500. The current measurements were compared to manual measurements of the same images.Results: Values obtained by the manual and the new methods were in agreement within the 95% confidence limit by the Bland‐Altman analysis and within 90–95% range by the correlation coefficient (R2). The more frequent measurements reveal substantial, rapid variations in cell‐free layer width and changes in mean values with alteration of arterial pressure and red cell aggregability.Conclusions: A new, computer‐based technique has been developed that provides measurements of rapid, time‐dependent variations in the width of the cell‐free layer in the microcirculation.
Clot Fragments Formed from Original Thrombus Obstruct Downstream Arteries in the Ischemic Injured Brain
Authors: WANG CHEN XU , YANG TAO , SHUAIB ASHFAQ 
Published: March 2006

ABSTRACTObjective:Embolic occlusion of the middle cerebral artery (MCA) leads to distal perfusion deficits as the vessel is recanalized. However, the mechanism for the perfusion deficits is not fully understood. The authors examined whether distal movement of fragments formed from the original thrombus contributes to the perfusion deficits.Methods:In the first series, they studied whether the reduction in perfusion deficits is due to the dissolution of the original clots embolized or due to collateral perfusion. In the second series, they studied whether fragments formed from the original clots move to distal arterial system. In the third series, they studied whether plasmingen activator plays a role in the thrombolysis following ischemia.Results:Occlusion of MCA permanently resulted in large perfusion deficits in the ipsilateral hemisphere, and these perfusion deficits did not change significantly after the occlusion. In contrast, perfusion deficits reduced significantly in a model of transient MCA occlusion. The numbers of fragments formed from the original clots increased gradually after the MCA occlusion in the ischemic injured brain. In addition, expression of urokinase plasminogen activator was also upregulated.Conclusion:The present study thus reveals the mechanisms of the downstream arterial occlusion following the dissolution of original thrombus.
Evaluation of nitrogen balance on pig/crop farm systems in Jiulong River watershed, China
Authors: Zeng Yue , Hong Hua-Sheng , Cao Wen-Zhi , Chen Neng-Wang , Wang Wei-Ping , Zhang Luo-Ping 
Published: March 2006

Field surplus nitrogen and farm disposal nitrogen (N) are major sources of environmental pollution in farm systems. The purpose of this study was to use nitrogen balances at the field and farm level approaches to estimate the effects of pig production in the Jiulong River watershed, Fujian province, China, on nitrogen losses to the environment on 67 pig farms. The field surplus nitrogen ranged from 6.19 to 18.19 t nitrogen ha−1, which was caused by high pig density and excessive application of manure. Manure application rates of more than 450 to 510 kg nitrogen ha −1 would increase the potential nitrate concentration to more than 10 to 20 mg l −1. Therefore, 44 to 48 heads of pig ha −1 was suggested to as the environmental capacity for sustaining optimal nitrogen cycling in pig farms in the Jiulong River watershed.
The majority of farms have potential environmental risks because of high farm nitrogen imbalances. With more than a 2:1 ratio of N inputs to outputs, N inputs were 50 percent higher than outputs. Feed was the main input source, while pig production and manure exported were the major managed outputs. Based on the farm nitrogen balance calculation, the management options that would contribute to a more favorable nitrogen balance were also identified.
Size, frequency, and phylogenetic signal of multiple‐residue indels in sequence alignment of introns
Authors: Pons Joan , Vogler Alfried P. 
Published: March 2006

AbstractIndels in DNA sequences frequently affect more than a single nucleotide, creating problems for alignment, character coding and phylogenetic analysis. However, the size and frequency of multiple‐residue indels is not usually tested, and with popular alignment packages their reconstruction is indirectly acheived by reducing the affine (gap extension) cost. We explored the length distribution of indels in intron sequences of the gene Mp20 by modifying the gap opening and gap extension costs. Given a “known” tree for the study group, global homology levels were greatest under low gap cost, with gap extension costs of roughly 0.4‐fold the opening cost. Different approaches to gap coding and weighting suggested that taxonomic congruence was correlated with high frequencies of multiple‐position indels, with a maximum indel length of 2–5 bp and few indels above 15 bp, but also including a proportion of indels > 100 bp. Only a small minority of indels could be reconstructed as single‐position indels. Consequently, tree topologies improved when homologous multinucleotide indels were recoded as binary characters which are otherwise highly homoplastic and weighted characters in single‐position coding. In tree‐generating alignment procedures as implemented in POY, where gap penalty determines the character weight during tree search, the problem of assigning inappropriately high weight to multiple‐residue indels could partly be overcome by setting the extension costs to about 0.4‐fold lower than gap opening costs. We conclude that multiple consecutive gap positions are not independent characters and hence methods for parsimony reconstruction of long indels are required. Finally, we also observed a general lack of correlation between taxonomic and character congruence, demonstrating the difficulties of applying congruence criteria to decide among competing alignments. This highlights the value of recent model‐based alignment procedures which can implement the statistical distributions of indel size classes, and do not rely on potentially circular strategies for optimizing overall congruence.© The Willi Hennig Society 2006.
Phylogenetic relationships within Luzula DC. and Juncus L. (Juncaceae): A comparison of phylogenetic signals of trnL‐trnF intergenic spacer, trnL intron and rbcL plastome sequence data
Authors: Drábková Lenka , Kirschner Jan , Vlček Čestmír 
Published: March 2006

Abstract Juncus and Luzula are the largest, almost cosmopolitan, genera in the Juncaceae. Relationships within Juncus and Luzula and among other genera of Juncaceae (Distichia, Marsippospermum, Oxychloë, Patosia and Rostkovia) remain incompletely resolved. RbcL sequence data resolved a part of the supraspecific phylogeny, but many clades remain polytomic. For this reason, the non‐coding cpDNA regions, trnL intron and trnL‐trnF intergenic spacer, were sequenced. We intended to create hypotheses of relationships within Juncaceae and to test the classification of the sections, but a primary goal to this study was to assess the relationships within Juncus and Luzula and to test for monophyly of groups recognized from rbcL data (especially the monophyly of genus Luzula and the Southern Hemisphere Clade (SHC)). Furthermore, we tested the influence of different rooting and ingroup composition on the tree topology. The parsimony analyses revealed several well‐supported lineages. The traditionally distinguished genus Luzula is monophyletic and Juncus is non‐monophyletic. Two subgenera of Luzula (Pterodes and Luzula) are non‐monophyletic, while subg. Marlenia forms a sister group to the whole Luzula clade (trnL‐F data set). Within Juncus, both subgenus Juncus and subgenus Agathryon are non‐monophyletic. SHC is clustered not only with the South African J. lomatophylus and J. capensis, but also together with members of the section Juncus, Caespitosi and Graminifolii. These sections form a well‐separated sister group to the SHC. Within the genera Juncus and Luzula, monophyly is demonstrated for a number of groups (e.g., Juncus section Stygiopsis, Luzula section Luzula) but questioned for others (e.g., Juncus section Graminifolii). The unusual, separate positioning of Juncus trifidus and J. monanthos were clarified by trnL‐trnF sequence data, but vary within the tree topology depending on outgroup selection and also due to LBA phenomenon.© The Willi Hennig Society 2006.
The PhyloCode: a critical discussion of its theoretical foundation
Authors: Rieppel Olivier 
Published: March 2006

AbstractThe definition of taxon names as formalized by the PhyloCode is based on Kripke's thesis of “rigid designation” that applies to Millian proper names. Accepting the thesis of “rigid designation” into systematics in turn is based on the thesis that species, and taxa, are individuals. These largely semantic and metaphysical issues are here contrasted with an epistemological approach to taxonomy. It is shown that the thesis of “rigid designation” if deployed in taxonomy introduces a new essentialism into systematics, which is exactly what the PhyloCode was designed to avoid. Rigidly designating names are not supposed to change their meaning, but if the shifting constitution of a clade is thought to cause a shift of meaning of the taxon name, then the taxon name is not a “rigid designator”. Phylogenetic nomenclature either fails to preserve the stability of meaning of taxon names that it propagates, or it is rendered inconsistent with its own philosophical background. The alternative explored here is to conceptualize taxa as natural kinds, and to replace the analytic definition of taxon names by their explanatory definition. Such conceptualization of taxa allows taxon names to better track the results of ongoing empirical research. The semantic as well as epistemic gain is that if taxon names are associated with natural kind terms instead of being proper names, the composition of the taxon will naturally determine the meaning of its name.© The Willi Hennig Society 2006.
The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters
Authors: Simmons Mark P. , Zhang Li‐Bing , Webb Colleen T. , Reeves Aaron , Miller Jeremy A. 
Published: March 2006

AbstractWe tested whether it is beneficial for the accuracy of phylogenetic inference to sample characters that are evolving under different sets of parameters, using both Bayesian MCMC (Markov chain Monte Carlo) and parsimony approaches. We examined differential rates of evolution among characters, differential character‐state frequencies and character‐state space, and differential relative branch lengths among characters. We also compared the relative performance of parsimony and Bayesian analyses by progressively incorporating more of these heterogeneous parameters and progressively increasing the severity of this heterogeneity. Bayesian analyses performed better than parsimony when heterogeneous simulation parameters were incorporated into the substitution model. However, parsimony outperformed Bayesian MCMC when heterogeneous simulation parameters were not incorporated into the Bayesian substitution model. The higher the rate of evolution simulated, the better parsimony performed relative to Bayesian analyses. Bayesian and parsimony analyses converged in their performance as the number of simulated heterogeneous model parameters increased. Up to a point, rate heterogeneity among sites was generally advantageous for phylogenetic inference using both approaches. In contrast, branch‐length heterogeneity was generally disadvantageous for phylogenetic inference using both parsimony and Bayesian approaches. Parsimony was found to be more conservative than Bayesian analyses, in that it resolved fewer incorrect clades.© The Willi Hennig Society 2006.
Pathology of supraclavicular lymphadenopathy in Chandigarh, north India: an audit of 200 cases diagnosed by needle aspiration
Authors: Gupta N. , Rajwanshi A. , Srinivasan R. , Nijhawan R. 
Published: March 2006

Objective:  Fine needle aspiration cytology (FNAC) of lymph nodes can be used routinely as a first‐line diagnostic test. The majority of studies reveal a malignant cause for palpable supraclavicular lymph nodes. The present audit further emphasizes the use of FNAC as a first‐line investigation for the evaluation of enlarged supraclavicular lymph nodes.Methods:  A total of 200 cases of palpable supraclavicular lymph node(s) were included in the present study.Results:  Left supraclavicular lymph nodes were found to be more commonly involved (59.5% cases). Sixty‐four per cent cases showed metastatic deposits and 13.5% cases were diagnosed as tuberculosis. Ten per cent cases showed reactive lymphoid hyperplasia; 0.5% (one) case showed only necrosis and on autopsy, a microscopic focus of choriocarcinoma was found in the testis. In 7.5% cases, diagnostic material could not be aspirated despite repeated attempts. Common metastatic tumours were from lung (22% cases), breast (16.4% cases), cervix (11% cases) and oesophagus (8.6% cases). In 13.3% cases the primary site was unknown and the diagnosis of malignancy first came from FNAC.Conclusion:  The present study further highlights the importance of FNAC as a first‐line diagnostic modality in the evaluation of supraclavicular lymphadenopathy. A full history, radiological findings and immunochemistry in difficult cases can help to arrive at a definitive diagnosis.
Liquid‐based cytology can improve efficiency of cervical smear readers: evidence from timing surveys in two NHS cytology laboratories
Authors: Dowie R. , Stoykova B. , Crawford D. , Desai M. , Mather J. , Morgan K. , Shirt M. 
Published: March 2006

Objective:  Cervical screening programmes in England and Wales were advised by the National Institute for Clinical Excellence in 2003 to adopt liquid‐based cytology (LBC) in place of conventional Papanicolaou (Pap) cytology to facilitate laboratory efficiency. Pilot evaluations in England and Scotland monitored daily or weekly workloads of smear readers and concluded that LBC could increase hourly throughput rates. This study, instead, used timing surveys to determine screening rates.Methods:  Two National Health Service cytology laboratories in Manchester and Stockport were partially converted to the LBC ThinPrep® process for a cervical screening trial. Three 1‐week timing surveys were conducted over 7 months. The surveys covered all LBC‐trained staff. The first survey in Manchester also covered staff undertaking conventional Pap screening. The smear readers used timers to record time taken for examining and reporting each slide.Results:  In Manchester, in the first survey, nearly 1 minute per slide was saved by the LBC method during primary microscopy. In both laboratories, the mean microscopy time for primary screening of LBC slides was reduced by almost 1 minute between the first and second surveys. There was no difference between the second and third surveys. Microscopy by cytopathologists was also 1 minute per slide quicker with LBC than conventional Pap. The LBC inadequate rates for both laboratories were <2.0%. Organizational factors impacted on the hourly LBC primary screening rates in the laboratories, the rate for Stockport being higher than the rates in the pilot evaluations.Conclusions:  The timing surveys confirm that the LBC ThinPrep® technology can improve laboratory efficiency. However, decision‐makers should also consider the overall costs and benefits of introducing the technology in screening programmes, including the capital investment and workforce implications.
Liquid‐based cytology and conventional smears compared over two 12‐month periods
Authors: Williams A. R. W. 
Published: March 2006

Background and objective:  Liquid based cytology (LBC) was introduced across the Scottish Cervical Screening Programme in 2003–2004. The objective of this study was to compare in a large cytopathology laboratory the results of cervical samples over two twelve‐month periods, 2001–2002, when the great majority of smears were conventional, with 2003–2004, when all were LBC.Methods:  The results of smears in both periods were analysed to give overall reporting profiles, and correlated with results of cervical biopsies. The numbers of patients referred for colposcopy were compared.Results:  The percentage of unsatisfactory smears fell from 13.6% to 1.9%. Colposcopic referrals for repeated unsatisfactory smears fell from almost 25% to 0.5%. There was a decrease in overall smear numbers, but despite this there was an increase in the number of smears reported as showing dyskaryosis of any grade. There was an increase in positive predictive value for moderate dyskaryosis and above, from 79.5% to 86.1%. The outcome of biopsies from patients referred with mild dyskaryosis showed no decrease in accuracy of predicting a low grade histological lesion. Workload in the laboratory decreased, due to fewer smears received overall, more rapid primary screening times and fewer multi‐slide cases. Primary screening backlogs all but disappeared, and reporting times greatly improved.Conclusions:  Introduction of liquid based cytology led to improvements in unsatisfactory smear rates, with significant benefits to colposcopic referrals and laboratory turnaround times. Pick‐up rates of dyskaryosis were maintained, and the positive predictive value of a dyskaryotic smear report was improved.
Comparative study of the ThinPrep Pap test and conventional cytology results in a Canadian cohort
Authors: Duggan M. A. , Khalil M. , Brasher P. M. A. , Nation J. G. 
Published: March 2006

Objective:  To compare the frequency of Pap test results in a prospective series of direct to vial ThinPrep tests to a cohort of conventionally prepared tests. To follow‐up all test results for a minimum of 2 years and assess performance based on this outcome.Methods:  All women presenting for either routine screening or colposcopic examination in 2001 were enrolled in the ThinPrep cohort. A similar, population of conventionally prepared tests was extracted from the year 2000 laboratory data. Information on all concurrent and follow‐up cervical specimens over the ensuing 2 years was retrieved.Results:  The ThinPrep cohort comprised 2288 Pap tests and the conventional, 2211. The frequency of normal [within normal limits (WNL) and benign cellular changes (BCC)] results in the ThinPrep cohort was 6% lower and the frequency of abnormal [≥atypical squamous cells of undetermined significance (ASCUS)] results was 6.8% higher. Respective ThinPrep and conventional cohort results were 1156 (51%) and 1291 (58%) WNL, 625 (27%) and 561 (25%) BCC, 101 (4%) and 65 (3%) ASCUS, 21 (1%) and 2 (0.1%) atypical glandular cells of undetermined significance, 301 (13%) and 224 (10%) low‐grade squamous intraepithelial lesion (LSIL), and 74 (3%) and 40 (2%) high‐grade SIL (HSIL) (P < 0.0001). Follow‐up was available for nearly 80% of each cohort. LSIL or higher was confirmed in 57.5% (n = 266) of the abnormal ThinPrep and 60.9% (n = 190) of the abnormal conventional tests. The ThinPrep yield of confirmed tests however was almost 50% higher than the conventional test.Conclusion:  In this population, ThinPrep was superior to the conventional Pap test.