bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mine and the Furnace: Francis Bacon, Thomas Russell, and Early Stuart Mining Culture
Authors: Pastorino Cesare 
Published: September 2009

AbstractNotwithstanding Francis Bacon's praise for the philosophical role of the mechanical arts, historians have often downplayed Bacon's connections with actual artisans and entrepreneurs. Addressing the specific context of mining culture, this study proposes a rather different picture. The analysis of a famous mining metaphor in The Advancement of Learning shows us how Bacon's project of reform of knowledge could find an apt correspondence in civic and entrepreneurial values of his time. Also, Bacon had interesting and so far unexplored links with the early modern English mining enterprises, like the Company of Mineral and Battery Works, of which he was a shareholder. Moreover, Bacon's notes in a private notebook, Commentarius Solutus, and records of patents of invention, allow us to start grasping Bacon's connections with the metallurgist and entrepreneur Thomas Russell. Lastly, this paper argues that, to fully understand Bacon's links with the world of Stuart technicians and entrepreneurs, it is necessary to consider a different and insufficiently studied aspect of Bacon's interests, namely his work as patents referee while a Commissioner of Suits.
Multi-annual variation in female morph frequencies of the polymorphic damselfly, Nehalennia irene, at continental and regional scales
Authors: Iserbyt Arne , Bots Jessica , Ting Janice , Jvostov Felipe Pérez , Forbes Mark , Sherratt Thomas , Van Gossum Hans 
Published: September 2009

Abstract
Female-limited polymorphism occurs in different animal taxa but is particularly abundant among species of damselflies (Insecta: Odonata), most likely as a consequence of selection to avoid excessive male harassment. Recent work on the damselfly Nehalennia irene indicated that within year spatial variation in female morph frequencies was limited in nearby populations (i.e. intra-regional scale), but large at a continental scale. As anticipated, some of the observed variation in morph frequency was correlated with variation in the estimated degree of male harassment towards female morphs, measured by male density and operational sex ratio. Here, we extended earlier work by quantifying variation in morph frequency over two to three years, allowing us to elucidate how morph frequencies vary temporally at both intra-regional and continental scales (data for 8 populations over three years and for 33 populations over two years, respectively). Annual variation in morph frequencies was relatively high at the intra-regional scale, but was never large enough to obscure the underlying spatial pattern at the continental scale. At both geographic scales, male density and operational sex ratio were highly variable between years. The estimated degree of male harassment correlated with variation in morph frequency within some regions, but not all. Together, the observed natural variation in female morph frequencies may be partly explained by variation in male harassment, but it appears that a complete understanding will require considering the role of other environmental factors.
Prevalence of trypanosomes from Clarius batrachus (Linnaeus) of Purba Medinipur, West Bengal, India
Authors: Bag Sujoy , Bandyopadhyay Probir 
Published: September 2009

AbstractHaemoflagellates of the genus Trypanosoma Gruby, 1843 are prevalent in fresh water fishes and are transmitted by leech. A total of 133 Clairus batrachus were examined for haemoflagelates. The fishes were collected from ponds and water bodies of Purba Medinipur district, West Bengal, India, from January, 2006 to July, 2007. The slides were prepared taking blood from both males (97) and females (36). It was found that only 19 out of 36 (52.78%) females and 31 out of 97 (31.95%) males were infected. Thus females were recorded with a higher prevalence of trypanosome infection than males. There was a significant difference (P<0.05) in the infection rate with trypanosomes in males and females.
Non-visual sensory physiology and magnetic orientation in the Blind Cave Salamander, Proteus anguinus (and some other cave-dwelling urodele species). Review and new results on light-sensitivity and non-visual orientation in subterranean urodeles (Amphibia)
Authors: Schlegel Peter , Steinfartz Sebastian , Bulog Boris 
Published: September 2009

Abstract
A review is given on several sensory systems that enable troglophile and troglobian urodele species to orient non-visually in their extreme hypogean habitat. A new sense was discovered allowing the animals to orient according to the Earth's magnetic field, which could serve as a basic and always available reference for general spatial orientation. Moreover, working with permanent magnetic field stimuli offers a very sensitive experimental method to discover the urodeles' thresholds for other sensory modalities such as light, sounds, and other stimuli, perhaps in competition or combination with the magnetic one. Proteus' audition as underwater hearing and light sensitivity due to its partly remaining sensory cells and/or skin sensitivity were studied. Excellent underwater hearing abilities had been demonstrated for Proteus with an acoustic behavioural method. The ability of sound pressure registration in Proteus is supposed to be attained by the tight anatomical junction between the ceiling of the oral cavity and the oval window. More generally, all non-visual sensory capabilities may facilitate certain behavioral strategies, compensating for missing visual orientation. Troglobians are more likely than others to own and regularly use the sensorial opportunities of a magnetic sense for spatial orientation. Compared to their epigean relatives, cave animals may have retained phylogenetically older sensorial properties, transformed or improved them, or finally acquired new ones which enabled them to successfully survive in dark habitats. Neighbor populations living on surface did not necessarily take advantage of these highly evolved sensory systems and orientation strategies of the troglobian species and may have lost them. E.g. Desmognathus ochrophaeus is partly adapted to cave life and exhibits good magnetic sensitivity, whereas, D. monticula and D. quadrimaculatus are epigean and, although living in rather dark places, did not demonstrate magnetic sensitivity when tested with our method.
Acute effects of tobacco smoke on human airway dendritic cellsin vivo
Authors: Lommatzsch M. , Bratke K. , Knappe T. , Bier A. , Dreschler K. , Kuepper M. , Stoll P. , Julius P. , Virchow J. C. 
Published: September 2009

Airway dendritic cells (DCs) play a key role in smoke-related lung diseases; however, the acute effects of tobacco smoke on human airway DCsin vivoare unknown.A total of 16 smokers underwent bronchoalveolar lavage at two time-points: directly after a 4-h period of nonsmoking (no smoke exposure); and directly after a 4-h period during which eight cigarettes were smoked (acute smoke exposure). Using flow cytometry, myeloid DCs (mDCs) and plasmacytoid DCs (pDCs), as well as function-associated surface molecules on mDCs, were analysed in bronchoalveolar lavage fluid (BALF) and in blood.The numbers of macrophages, lymphocytes, neutrophils, eosinophils and pDCs were unchanged in BALF following acute smoke exposure, as compared to no smoke exposure. In contrast, there was a strong increase in mDC number in BALF and a concomitant decrease in mDC number in blood following acute smoke exposure. In addition, acute smoke exposure led to an increase in the expression of the surface molecules blood dendritic cell antigen 1 and 4 and a decrease in the expression of the lung homing receptor, CC chemokine receptor 5, on mDCs in BALF.Acute tobacco smoke inhalation results in an immediate and selective recruitment of mDCs into human airways, which might reflect the very early reaction of the adaptive immune system to smoke exposure.
The Borg dyspnoea score: a relevant clinical marker of inspiratory muscle weakness in amyotrophic lateral sclerosis
Authors: Just N. , Bautin N. , Danel-Brunaud V. , Debroucker V. , Matran R. , Perez T. 
Published: September 2009

The aim of the study was to determine whether the Borg dyspnoea scale could be a useful and simple marker to predict respiratory muscle weakness in amyotrophic lateral sclerosis (ALS).From April 1997 to 2001, respiratory function was perfomed in 72 patients together with the Borg score in both the upright (uBorg) and supine (sBorg) positions.Mean upright vital capacity (VC) was 81±24% predicted, sniff nasal inspiratory pressure (SNIP) was 55±26% pred, maximal inspiratory pressure (PI,max) was 57±26% pred and arterial carbon dioxide tension (Pa,CO2) was 41±6 mmHg. The mean Borg scores in the upright and supine positions were 1.7±1.5 and 2.2±2, respectively. A significant relationship between SNIP and uBorg (r = 0.4; p = 0.0007) and SNIP and sBorg (r = 0.58; p<0.0001) was observed. Upright VC, ΔVC (measured as the supine fall in VC as a percentage of seated VC),PI,maxandPa,CO2were significantly correlated with SNIP. A cut-off value of 3 on the sBorg scale provided the best sensitivity (80%) and specificity (78%) (area under the curve 0.8) to predict a SNIP ≤40 cmH2O, indicating severe inspiratory muscle weakness. Patients with a sBorg score ≥3 also exhibited significantly lower VC,PI,maxand twitch mouth pressure during cervical magnetic stimulation, and slightly higherPa,CO2(43.7±7versus39.2±5 mmHg; p = 0.05).The Borg dyspnoea scale is a valuable noninvasive test for the prediction of inspiratory muscle weakness in ALS patients.
CASSIOPE: An expert system for conserved regions searches
Authors: Rascol Virginie Lopez , Levasseur Anthony , Chabrol Olivier , Grusea Simona , Gouret Philippe , Danchin Etienne GJ , Pontarotti Pierre 
Published: September 2009

Abstract

Background
Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in genome evolution and their implications for the study of biological systems. Detection of conserved regions (descending from a common ancestor) not only helps clarify genome evolution but also makes it possible to identify quantitative trait loci (QTLs) and investigate gene function.
The identification and comparison of conserved regions on a genome scale is computationally intensive, making process automation essential. Three key requirements are necessary: consideration of phylogeny to identify orthologs between multiple species, frequent updating of the annotation and panel of compared genomes and computation of statistical tests to assess the significance of identified conserved gene clusters.

Results
We developed a modular system superimposed on a multi-agent framework, called CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution). CASSIOPE automatically identifies statistically significant conserved regions between multiple genomes based on automated phylogenies and statistical testing. Conserved regions were searched for in 19 species and 1,561 hits were found. To our knowledge, CASSIOPE is the first system to date that integrates evolutionary biology-based concepts and fulfills all three key requirements stated above. All results are available at http://194.57.197.245/cassiopeWeb/displayCluster?clusterId=1

Conclusion
CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions.

Source code is freely available, please contact: Pierre.pontarotti@univ-provence.fr
Evolutionary conservation and changes in insect TRP channels
Authors: Matsuura Hironori , Sokabe Takaaki , Kohno Keigo , Tominaga Makoto , Kadowaki Tatsuhiko 
Published: September 2009

Abstract

Background
TRP (Transient Receptor Potential) channels respond to diverse stimuli and thus function as the primary integrators of varied sensory information. They are also activated by various compounds and secondary messengers to mediate cell-cell interactions as well as to detect changes in the local environment. Their physiological roles have been primarily characterized only in mice and fruit flies, and evolutionary studies are limited. To understand the evolution of insect TRP channels and the mechanisms of integrating sensory inputs in insects, we have identified and compared TRP channel genes in Drosophila melanogaster, Bombyx mori, Tribolium castaneum, Apis mellifera, Nasonia vitripennis, and Pediculus humanus genomes as part of genome sequencing efforts.

Results
All the insects examined have 2 TRPV, 1 TRPN, 1 TRPM, 3 TRPC, and 1 TRPML subfamily members, demonstrating that these channels have the ancient origins in insects. The common pattern also suggests that the mechanisms for detecting mechanical and visual stimuli and maintaining lysosomal functions may be evolutionarily well conserved in insects. However, a TRPP channel, the most ancient TRP channel, is missing in B. mori, A. mellifera, and N. vitripennis. Although P. humanus and D. melanogaster contain 4 TRPA subfamily members, the other insects have 5 TRPA subfamily members. T. castaneum, A. mellifera, and N. vitripennis contain TRPA5 channels, which have been specifically retained or gained in Coleoptera and Hymenoptera. Furthermore, TRPA1, which functions for thermotaxis in Drosophila, is missing in A. mellifera and N. vitripennis; however, they have other Hymenoptera-specific TRPA channels (AmHsTRPA and NvHsTRPA). NvHsTRPA expressed in HEK293 cells is activated by temperature increase, demonstrating that HsTRPAs function as novel thermal sensors in Hymenoptera.

Conclusion
The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP family members. As shown for mammalian TRP channels, this may suggest that single TRP channels are responsible for integrating diverse sensory inputs to maintain the insect sensory systems. The above results demonstrate that there are both evolutionary conservation and changes in insect TRP channels. In particular, the evolutionary processes have been accelerated in the TRPA subfamily, indicating divergence in the mechanisms that insects use to detect environmental temperatures.
Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality
Authors: Vizoso Paula , Meisel Lee A , Tittarelli Andrés , Latorre Mariano , Saba Juan , Caroca Rodrigo , Maldonado Jonathan , Cambiazo Veronica , Campos-Vargas Reinaldo , Gonzalez Mauricio , Orellana Ariel , Silva Herman 
Published: September 2009

AbstractBackgroundCold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors.ResultsWe sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp(Prunus persicaO'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created.Statistically analyzing the EST population, we have identified genes that are differentially expressed during ripening, in response to cold storage or the combined effects of cold storage and ripening. Pair-wise comparisons revealed 197 contigs with at least one significant difference in transcript abundance between at least two conditions. Gene expression profile analyses revealed that the contigs may be classified into 13 different clusters of gene expression patterns. These clusters include groups of contigs that increase or decrease transcript abundance during ripening, in response to cold or ripening plus cold.ConclusionThese analyses have enabled us to statistically identify novel genes and gene clusters that are differentially expressed in response to post-harvest factors such as long-term cold storage, ripening or a combination of these two factors. These differentially expressed genes reveal the complex biological processes that are associated with these factors, as well as a large number of putative gene families that may participate differentially in these processes. In particular, these analyzes suggest that woolly fruits lack the increased boost of metabolic processes necessary for ripening. Additionally, these results suggest that the mitochondria and plastids play a major role in these processes. The EST sequences and full-length cDNA clones developed in this work, combined with the large population of differentially expressed genes may serve as useful tools and markers that will enable the scientific community to better define the molecular processes that affect fruit quality in response to post-harvest conditions and the organelles that participate in these processes.
Gene expression profiling of human alveolar macrophages infected by B. anthracisspores demonstrates TNF-α and NF-κb are key components of the innate immune response to the pathogen
Authors: Dozmorov Mikhail , Wu Wenxin , Chakrabarty Kaushik , Booth J Leland , Hurst Robert E , Coggeshall K Mark , Metcalf Jordan P 
Published: September 2009

Abstract

Background

Bacillus anthracis, the etiologic agent of anthrax, has recently been used as an agent of bioterrorism. The innate immune system initially appears to contain the pathogen at the site of entry. Because the human alveolar macrophage (HAM) plays a key role in lung innate immune responses, studying the HAM response to B. anthracis is important in understanding the pathogenesis of the pulmonary form of this disease.

Methods
In this paper, the transcriptional profile of B. anthracis spore-treated HAM was compared with that of mock-infected cells, and differentially expressed genes were identified by Affymetrix microarray analysis. A portion of the results were verified by Luminex protein analysis.

Results
The majority of genes modulated by spores were upregulated, and a lesser number were downregulated. The differentially expressed genes were subjected to Ingenuity Pathway analysis, the Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis, the Promoter Analysis and Interaction Network Toolset (PAINT) and Oncomine analysis. Among the upregulated genes, we identified a group of chemokine ligand, apoptosis, and, interestingly, keratin filament genes. Central hubs regulating the activated genes were TNF-α, NF-κB and their ligands/receptors. In addition to TNF-α, a broad range of cytokines was induced, and this was confirmed at the level of translation by Luminex multiplex protein analysis. PAINT analysis revealed that many of the genes affected by spores contain the binding site for c-Rel, a member of the NF-κB family of transcription factors. Other transcription regulatory elements contained in many of the upregulated genes were c-Myb, CP2, Barbie Box, E2F and CRE-BP1. However, many of the genes are poorly annotated, indicating that they represent novel functions. Four of the genes most highly regulated by spores have only previously been associated with head and neck and lung carcinomas.

Conclusion
The results demonstrate not only that TNF-α and NF-κb are key components of the innate immune response to the pathogen, but also that a large part of the mechanisms by which the alveolar macrophage responds to B. anthracis are still unknown as many of the genes involved are poorly annotated.
Pancreatic cancerrelated cachexia: influence on metabolism and correlation to weight loss and pulmonary function
Authors: Bachmann Jeannine , Ketterer Knut , Marsch Christiane , Fechtner Kerstin , Krakowski-Roosen Holger , Büchler Markus W , Friess Helmut , Martignoni Marc E 
Published: September 2009

Abstract

Background
Dramatic weight loss is an often underestimated symptom in pancreatic cancer patients. Cachexia- defined as an unintended loss of stable weight exceeding 10% – is present in up to 80% of patients with cancer of the upper gastrointestinal tract, and has a significant influence on survival. The aim of the study was to show the multiple systemic effects of cachexia in pancreatic cancer patients, in terms of resection rate, effects on pulmonary function, amount of fat and muscle tissue, as well as changes in laboratory parameters.

Methods
In patients with pancreatic cancer, clinical appearance was documented, including the amount of weight loss. Laboratory parameters and lung-function tests were evaluated, and the thickness of muscle and fat tissue was measured with computed tomography scans. Statistical analysis, including multivariate analysis, was performed using SPSS software. Survival curves were calculated using Kaplan-Meier analysis and the log-rank test. To test for significant differences between the examined groups we used Student's t-test and the Mann-Whitney U test. Significance was defined as p < 0.05.

Results
Of 198 patients with a ductal adenocarcinoma of the pancreas, 70% were suffering from weight loss when they presented for operation, and in 40% weight loss exceeded 10% of the stable weight. In patients with cachexia, metastases were diagnosed significantly more often (47% vs. 24%, P < 0.001), leading to a significantly reduced resection rate in these patients. Patients with cachexia had significantly reduced fat tissue amounts. Hence, dramatic weight loss in a patient with pancreatic cancer may be a hint of a more progressed or more aggressive tumour.

Conclusion
Pancreatic cancer patients with cachexia had a higher rate of more progressed tumour stages and a worse nutritional status. Furthermore, patients with cachexia had an impaired lung function and a reduction in fat tissue. Patients with pancreatic cancer and cachexia had significantly reduced survival. If weight loss exceeded 5% there was a significantly reduced resection rate to detect, but the changes were significantly more substantial if weight loss was 10% or more. We propose that a weight loss of 10% be defined as significant in pancreatic cancer.