bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds
Authors: Suenaga Hikaru , Ohnuki Tsutomu , Miyazaki Kentaro 
Published: May 2007

SummaryA metagenomic approach was taken to retrieve catabolic operons for aromatic compounds from activated sludge used to treat coke plant wastewater. Metagenomic DNA extracted from the sludge was cloned into fosmids and the resulting Escherichia coli library was screened for extradiol dioxygenases (EDOs) using catechol as a substrate, yielding 91 EDO‐positive clones. Based on their substrate specificity for various catecholic compounds, 38 clones were subjected to sequence analysis. Each insert contained at least one EDO gene, and a total of 43 EDO genes were identified. More than half of these belonged to new EDO subfamilies: I.1.C (2 clones), I.2.G (20 clones), I.3.M (2 clones) and I.3.N (1 clone). The fact that novel I.2.G family genes were over‐represented in these clones suggested that these genes play a specific role in environmental aromatic degradation. The I.2.G clones were further classified into six groups based on single‐nucleotide polymorphisms (SNPs). Based on the combination of the SNPs, the evolutionary lineage of the genes was reconstructed; further, taking the activities of the clones into account, potential adaptive mutations were identified. The metagenomic approach was thus used to retrieve novel EDO genes as well as to gain insights into the gene evolution of EDOs.
Railing Rhymes Revisited: Libels, Scandals, and Early Stuart Politics
Authors: Bellany Alastair 
Published: May 2007

AbstractThis article surveys and assesses recent interdisciplinary scholarship on early Stuart verse libels – scandalous, defamatory poems surreptitiously circulating criticism of courtiers, councilors, and royal policies. It situates this scholarship within revisionist and post‐revisionist historians’ debates on the nature of early Stuart politics and the causes of the English Revolution, and within the cultural turn in early modern studies and in the discipline of history at large. The article then surveys what scholars have argued about the libel as a form of political media operating within an early modern literary underground and an emerging public sphere, and as a form of political expression which articulated serious critique through allegations of sexual and other forms of personal corruption. It concludes with suggestions for future research.
LRP16 is fused to RUNX1 in monocytic leukemia cell line with t(11;21)(q13;q22)
Authors: Imagama Shizuka , Abe Akihiro , Suzuki Momoko , Hayakawa Fumihiko , Katsumi Akira , Emi Nobuhiko , Kiyoi Hitoshi , Naoe Tomoki 
Published: May 2007

Abstract Objective: The RUNX1 (also known as AML1) gene is observed frequently as the target of chromosomal rearrangements in human acute leukemia. We describe here a previously unreported rearrangement, t(11;21)(q13;q22), that disrupts the RUNX1 gene in a patient with acute leukemia and the molecular analysis of the fusion gene.Methods: We have established a monocytic leukemia cell line, ELAM‐1, from a patient with acute leukemia evolving from myelodysplastic syndrome (MDS). Translocation (11;21) (q13;q22) was observed in both patient leukemia cells and ELAM‐1.Results: The split signal of RUNX1 was detected by fluorescence in situ hybridization and indicated the involvement of RUNX1 in ELAM‐1. Using 3′‐ Rapid amplification of cDNA ends and reverse transcription‐Polymerase chain reaction analysis, we detected both RUNX1 (exon 5)‐LRP16 and RUNX1 (exon 6)‐LRP16 transcripts, suggesting that the RUNX1 breakpoint lies in intron 6 and that alternative fusion splice variants are generated. Reciprocal LRP16‐RUNX1 fusion was also detected.Conclusions: We identified a novel RUNX1 fusion partner, LRP16 on 11q13 involving t(11;21)(q13;q22). Although it was reported that overexpression of LRP16 promotes human breast cancer cell proliferation, the function of LRP16 in leukemia remains to be studied. This fusion gene and cell line may provide a new research tool to investigate the mechanism of leukemogenesis generated by the RUNX1 fusion gene.
Hydrochemical Facies Evaluation in Umm Er Radhuma Limestone, Eastern Saudi Arabia
Authors: Sen Zeka̧i , Al‐Dakheel Abdulrahman 
Published: May 2007

ABSTRACTEvaluation of the local hydrochemical facies in the Umm Er Radhuma (UER) limestone aquifer in the eastern part of Saudi Arabia and the presentation of supplemental methods for the classical techniques in such an evaluation are presented. Equilibrium studies of ground‐water chemistry of the UER aquifer indicate that most waters arc of calcium sulfate or sodium chloride types. The ground water is saturated with respect to calcite but unsaturated for anhydrite in the northern part of the study area.Charts are developed to find, practically, the ionic activity of any major ion provided that TDS values are estimated. A detailed relationship is provided for estimating TDS values from field measurements of the electrical conductivity.
Laws of Biology, Laws of Nature: Problems and (Dis)Solutions
Authors: Hamilton Andrew 
Published: May 2007

AbstractThis article serves as an introduction to the laws‐of‐biology debate. After introducing the main issues in an introductory section, arguments for and against laws of biology are canvassed in Section 2. In Section 3, the debate is placed in wider epistemological context by engaging a group of scholars who have shifted the focus away from the question of whether there are laws of biology and toward offering good accounts of explanation(s) in the biological sciences. Section 4 introduces two relatively new pieces of science – metabolic scaling theory and ecological stoichiometry – that have not been topics of much discussion by philosophers but are relevant because they have at least some of the hallmarks of laws of nature. Section 5 concludes by pointing out that discovering laws of biology, if any there be, will not necessarily answer the questions raised by the debate in the first place: we will still want to know how biology compares to other sciences, how to characterize its systems and processes, and whether accounts in terms of laws always usually constitute adequate explanations in various sciences.
Existing theories do not explain sex ratio variation at birth in monomorphic roe deer (Capreolus capreolus)
Authors: VREUGDENHIL Stefan Jacob , VAN BREUKELEN Leo , VAN WIEREN Sipke Egbert 
Published: May 2007

AbstractThe phenomenon of skewed sex ratios at birth has been reported in many ungulate species. So far, no consistent trend has emerged for roe deer (Capreolus capreolus), because male‐biased, female‐biased and equal sex ratios at birth have all been found. Nevertheless, both the Trivers‐Willard hypothesis and the theory of local resource competition have gained support. Despite the great number of studies carried out regarding the ecology of roe deer, too many aspects remain unclear, and contradictory results have been produced with respect to several crucial elements. Without further research, the discussion on which theory applies will therefore remain inconclusive. We put forward the argument that eventually the theories of Trivers‐Willard and local resource competition can be considered as being not essentially different. After all, both theories explain the observed skewed sex ratios as being due to the effect of the progeny's sex on the mother's body condition and hence her reproductive success in subsequent years. Furthermore, neither theory is likely to prove to be suitable for roe deer, as several assumptions are unlikely to be met. In roe deer, skewed ratios probably only have a temporal character. As a matter of fact, several observations of skewed sex ratios in birds and mammals did not withstand the accumulation of further data, as sex ratios that were initially believed to be biased turned out to be equal in the long term. This is likely to be the case in roe deer as well. We hypothesize that roe deer, as r‐strategists, will produce as many offspring as possible, regardless of sex.
Does Freudian Theory Resolve “The Paradoxes of Irrationality”?*
Authors: GRÜNBAUM ADOLF 
Published: May 2007

This paper consists of two related parts:I. A detailed critique of Donald Davidson's thesis—in his “The Paradoxes of Irrationality”—that “…any satisfactory [explanatory] view [of irrationality] must embrace some of Freud's most important theses” (p. 290). I argue that this conclusion is doubly flawed: (i) Davidson's case for it is logically ill‐founded, and (ii) its Freudian plaidoyer is also factually false.II. Relatedly, in the second part, I confute the recent arguments given by Marcia Cavell, Thomas Nagel, et al. to establish that psychoanalytic causal explanations of irrationality are epistemically justified, because they are extensions of the desire‐cumbelief pattern of accounting for intentional actions. As a corollary, it becomes clear that these authors have failed to undermine my epistemological strictures on the foundations of psychoanalysis.
How Are We to Interpret Heidegger's Oeuvre? A Methodological Manifesto
Authors: PHILIPSE HERMAN 
Published: May 2007

One may have different objectives in interpreting texts. If a judge interprets a statute in order to obtain a satisfactory solution to a case, his aim may be called “applicative”. But if a historian of science wants to reconstruct the meaning of obscure passages of Ptolemy's “Hypotheses planetarum”, his objectives are purely historical and theoretical.The paper argues that these different aims, applicative and historical ones, require different methodologies of interpretation, and imply different criteria of success. In particular, the “principle of charity” according to which an interpretation is better to the extent that we agree more with what the text as interpreted says, is fitting for applicative interpretations, but not without further qualifications for historical ones.The paper argues further that we should apply the methodology of historical interpretation to the entire body of German texts now available, if we want to interpret Martin Heidegger's philosophical oeuvre, assess its philosophical value, and investigate its links to Nazism. These were the aims of Herman Philipse's book “Heidegger's Philosophy of Being. A Critical Interpretation” (Princeton University Press, 1998, 555 pp.). Criticisms of this book by Taylor Carman and others are often off target because they presuppose applicative interpretations that aim at making Heidegger say things the interpreter believes himself, instead of striving for historical adequacy, and that are based upon a small selection of translations instead of upon the entire corpus of extant German texts.
Contextualism and the Problem of the External World
Authors: NETA RAM 
Published: May 2007

A skeptic claims that I do not have knowledge of the external world. It has been thought that the skeptic reaches this conclusion because she employs unusually stringent standards for knowledge. But the skeptic does not employ unusually high standards for knowledge. Rather, she employs unusually restrictive standards of evidence. Thus, her claim that we lack knowledge of the external world is supported by considerations that would equally support the claim that we lack evidence for our beliefs about the external world. These considerations do not threaten the truth of our ordinary attributions of evidence, however, for such attributions are context‐sensitive in their semantics.It is argued that this solution to the problem of the external world enjoys all of the benefits. and suffers none of the problems, of other solutions to the problem of the external world.
Mechanism of saikosaponin-d in the regulation of rat mesangial cell proliferation and synthesis of extracellular matrix proteinsThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.
Authors: Zu Ning , Li Ping , Li Ning , Choy Patrick , Gong Yuewen 
Published: May 2007

Glomerulosclerosis is a common disorder in many types of chronic kidney diseases. Previous studies have shown that glomerular mesangial cells (MCs) play an important role in the pathogenesis of glomerulosclerosis. The ability of saikosaponin-d (SSd) to reduce the damage of kidney in progressive glomerulosclerosis has been demonstrated. In this study, the effects of saikosaponin-d on MC proliferation and synthesis of extracellular matrix proteins were investigated. Rat MCs were isolated from Wistar rats and cultured in Dulbecco's modified Eagle's medium. MCs were challenged with lipopolysacchorides and incubated with different concentrations of SSd. Cell proliferation and cytotoxicity were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, and lactate dehydrogenase assays. Type IV collagen, fibronectin, and TGF-β1 in the conditioned medium were measured. The expression of cyclin-dependent kinase 4, c-Jun, and c-Fos was determined by immunohistochemistry. At a concentration of 4 µg/mL or lower, SSd inhibited MC proliferation but did not cause cell death. SSd also inhibited lipopolysaccharide-induced secretion of type IV collagen, fibronectin, and TGF-β1 in MCs. Additionally, SSd reduced the expression of CDK4, c-Jun, and c-Fos in MCs. We conclude that SSd inhibited MC proliferation and synthesis of extracullular matrix proteins through the downregulation of the CDK4, c-Jun, and c-Fos genes.
The effect of delayed preconditioning on connexin 43 in ischemic myocardiumThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.
Authors: Lin Jijin , Li Yuguang , Lin Shuguang , Liang Qing , Tan Xuerui 
Published: May 2007

The objective of this study is to investigate the effects of preconditioning on the restoration and distribution of connexin 43 (Cx43) in ischemic myocardium in dogs. In this study, 40 dogs were randomly divided into 5 groups of 8 as follows: control, 0hI-R (ischemia followed by 0 h reperfusion), 6hI-R (ischemia followed by 6 h reperfusion), 24hI-R (ischemia followed by 24 h reperfusion), and 48hI-R (ischemia followed by 48 h reperfusion). Four dogs in each group were preconditioned with brief episodes of ischemia prior to the respective treatments and were referred as the PC groups, while the other 4 were not preconditioned and were referred as the nonPC groups. The myocardial ischemia was induced by ligation of the left anterior descending coronary artery. The expression and distribution of Cx43 within the ischemic myocardium were measured by Western blot analysis and studied using laser confocal microscopy using a double-label immunohistochemistry technique. Compared with the control group, there was a significant reduction in Cx43 content within ischemic myocardium of all test groups both with and without PC (P < 0.01, P < 0.05). Within the 0hI-R, 6hI-R, and 24hI-R groups, an insignificant difference was found in the expression and distribution of Cx43 within the ischemic region between the PC and the nonPC groups. However, in the 48hI-R group, the area and intensity of Cx43 staining within the ischemic region of the PC dogs were significantly larger and more intense than those of the nonPC dogs (P < 0.01), and the ratio of Cx43 pixel density in intercalated disk areas to that in side-to-side junction areas in the PC dogs was significantly greater than that in nonPC dogs (P < 0.01). Our results suggest that preconditioning has a significant effect on the restoration and distribution of Cx43 in the ischemic myocardium in dogs after 48 h. Hence, preconditioning may be a plausible cause for the observed reductions in cardiac arrhythmias.
False positive PCR detection of Tropheryma whipplei in the saliva of healthy people
Authors: Rolain Jean-Marc , Fenollar Florence , Raoult Didier 
Published: May 2007

Abstract

Background

Tropheryma whipplei, the agent of Whipple's disease (WD), has been recently isolated and the genomes of two isolates have been fully sequenced. Previous diagnosis tools for the diagnosis of the disease used sequence analysis of the 16S rRNA gene. Using this target gene, the high percentage of detection of the bacterium in saliva of healthy people was in contrast to the negative results obtained with specific target genes. The aim of our study was to compare previously published primers targeting the 16S rRNA gene to real-time PCR with Taqman* probes targeting specific repeat genes only found in the genome of T. whipplei in a series of 57 saliva from healthy people.

Results
Although the specific real-time PCR assays with both primers and probes were negative for all the samples, 13 out of 57 samples were positive with different primers previously reported targeting the 16S rRNA gene. Among the positive samples, 8 yielded a 231-bp sequence that was 99.1% identical to that of Actinomyces odontolyticus, 2 yielded a 226-bp that was 99.6% identical to that of A. turicensis, and 3 yielded a 160-bp sequence that was 98.5% identical to that of Capnocytophaga gingivalis. We found that the C. gingivalis and A. odontolyticus 16S rRNA sequences obtained in our study share more than 80% homology with the corresponding 16S rRNA sequences of the T. whipplei genomes especially at 5' and 3' end.

Conclusion
Asymptomatic carriers of T. whipplei in saliva may exist but their prevalence is much lower than those previously reported. Testing the specificity of designed primers is critical to avoid false positive detection of T. whipplei. In atypical case we recommend to test two different specific target genes before concluding.
Optimization and clinical validation of a pathogen detection microarray
Authors: Wong Christopher W , Heng Charlie Lee Wah , Wan Yee Leong , Soh Shirlena WL , Kartasasmita Cissy B , Simoes Eric AF , Hibberd Martin L , Sung Wing-Kin , Miller Lance D 
Published: May 2007

AbstractDNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.
Unexpected Events during the Intrahospital Transport of Critically Ill Patients
Authors: Papson Jonathan P.N. , Russell Kassandra L. , Taylor David McD. 
Published: May 2007

Objectives:To examine unexpected events (UEs) that occur during the intrahospital transport of critically ill emergency department patients. Methods:This was a prospective observational study of consecutive intrahospital transports between March 2003 and June 2004. The escorting emergency physician completed the data collection document either during or immediately after the transport. This document detailed equipment‐related UEs, patient instability and invasive line‐related UEs, whether the UEs required intervention, and whether the UEs were potentially life threatening (serious UEs). Results:Of 339 transports observed, 230 (67.9%; 95% confidence interval [CI] = 62.6% to 72.7%) were associated with 604 UEs. Overall, there was a median of 1.0 UE per transport (range, 0–16). There were 277 (45.9%; 95% CI = 41.8% to 49.9%) UEs related to equipment, 158 (26.2%; 95% CI = 22.7% to 29.9%) related to patient instability, 156 (25.8%; 95% CI = 22.4% to 29.6%) related to equipment lines, and 13 (2.2%, 95% CI = 1.2% to 3.8%) miscellaneous UEs. The most common UEs were oxygen saturation probe failures, lead and line tangles, hypotension, and the wearing off of sedation and/or paralysis. Most UEs (478 [79.1%]; 95% CI = 75.6% to 82.3%) required an intervention. Emergency physicians had a significantly lower UE rate than residents. Thirty serious UEs occurred; 5.0% (95% CI = 3.4% to 7.1%) of UEs and 8.9% (95% CI = 6.2% to 12.5%) of transports were associated with a serious UE. The most common were severe hypotension, decreasing consciousness requiring intubation, and increased intracranial pressure. Conclusions:Unexpected events during the intrahospital transport of critically ill patients from the emergency department are common and can be potentially life threatening. Transporting physician experience is associated with UE rate. Strict adherence to and review of existing transport guidelines is recommended.
Experimental verification of cross-angle for noise reduction in hydraulic piston pumps
Authors: Johansson A , Övander J , Palmberg J-O 
Published: May 2007

One of the most important drawbacks with hydraulic systems is noise and vibration, which mainly originate from the hydrostatic pump. A great number of noise-reducing design features have been developed, but they are all, to a greater or lesser extent, sensitive to variations in operational conditions. The present paper is concerned with optimal design and experimental verification of the cross-angle in an axial piston pump. The cross-angle is a small fixed incline of the swash plate in the direction that is perpendicular to the traditional displacement direction. It enables effective noise reduction throughout the whole range of displacement angles. Simulation-based optimization is used to design a pump with optimal cross-angle and a matching valve plate. The design is manufactured and experimentally evaluated. Source flow measurements using the two-microphone method show good agreement between simulation and experiments, which verifies the applicability of the simulation model used. The benefits from using the cross-angle are then verified by comparing it with a pump with a traditional swash plate design, i.e. without the cross-angle. Both source flow measurements and sound level measurements in an anechoic chamber show good improvements from using the cross-angle.