bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network
Authors: Baudot Anaïs , Jacq Bernard , Brun Christine 
Published: September 2004

Abstract
Background
Studying the evolution of the function of duplicated genes usually implies an estimation of the extent of functional conservation/divergence between duplicates from comparison of actual sequences. This only reveals the possible molecular function of genes without taking into account their cellular function(s). We took into consideration this latter dimension of gene function to approach the functional evolution of duplicated genes by analyzing the protein-protein interaction network in which their products are involved. For this, we derived a functional classification of the proteins using PRODISTIN, a bioinformatics method allowing comparison of protein function. Our work focused on the duplicated yeast genes, remnants of an ancient whole-genome duplication.

Results
Starting from 4,143 interactions, we analyzed 41 duplicated protein pairs with the PRODISTIN method. We showed that duplicated pairs behaved differently in the classification with respect to their interactors. The different observed behaviors allowed us to propose a functional scale of conservation/divergence for the duplicated genes, based on interaction data. By comparing our results to the functional information carried by GO annotations and sequence comparisons, we showed that the interaction network analysis reveals functional subtleties, which are not discernible by other means. Finally, we interpreted our results in terms of evolutionary scenarios.

Conclusions
Our analysis might provide a new way to analyse the functional evolution of duplicated genes and constitutes the first attempt of protein function evolutionary comparisons based on protein-protein interactions.
Bioconductor: open software development for computational biology and bioinformatics
Authors: Gentleman Robert C , Carey Vincent J , Bates Douglas M , Bolstad Ben , Dettling Marcel , Dudoit Sandrine , Ellis Byron , Gautier Laurent , Ge Yongchao , Gentry Jeff , Hornik Kurt , Hothorn Torsten , Huber Wolfgang , Iacus Stefano , Irizarry Rafael , Leisch Friedrich , Li Cheng , Maechler Martin , Rossini Anthony J , Sawitzki Gunther , Smith Colin , Smyth Gordon , Tierney Luke , Yang Jean YH , Zhang Jianhua 
Published: September 2004

AbstractThe Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
The JAK3 inhibitor CP-690550 selectively reduces NK and CD8+ cell numbers in cynomolgus monkey blood following chronic oral dosing
Authors: Conklyn Maryrose , Andresen Catharine , Changelian Paul , Kudlacz Elizabeth 
Published: September 2004

AbstractJanus kinase 3 (JAK3) is a cytoplasmic tyrosine kinase associated with the common γ chain, an integral component of cytokine receptors of the interleukin (IL)-2 family, including IL-4, -7, -9, -15, and -21. CP-690550 is a JAK3 inhibitor with immunosuppressive properties under development for transplantation. We evaluated alterations in circulating lymphocyte subsets in cynomolgus monkey blood following chronic (3-week), oral CP-690550 administration. Natural killer (NK) and CD8+ T cell numbers were reduced in a dose- and time-dependent manner; the latter was a primary effect on memory subsets. CD4+ T and B cell numbers were unaffected or slightly increased, respectively. NK cell numbers were reduced ∼80% (vs. 35% in vehicle-treated animals) and returned to baseline levels within 3 weeks following treatment cessation. CD8+ T cells declined by a maximum 43% (vs. 25% for vehicle-treated animals) but rebounded significantly (300%) within 2 weeks after the last dose. Although CP-690550 did not result in reduction of CD4+ T cell number, these cells also increased (225%) within 2 weeks of treatment cessation. IL-15 is important for maintaining homeostasis of these cell types, and CP-690550 inhibited IL-15-induced CD69 expression in NK cells [inhibitory concentration 50% (IC50)=48.0±8.4 nM] and CD8+ T cells (IC50=16.2±1.5 nM).
Differential macrophage expression of IL-12 and IL-23 upon innate immune activation defines rat autoimmune susceptibility
Authors: Andersson Åsa , Kokkola Riikka , Wefer Judit , Erlandsson-Harris Helena , Harris Robert A 
Published: September 2004

AbstractRodents typically demonstrate strain-specific susceptibilities to induced autoimmune models such as experimental arthritis and encephalomyelitis. A common feature of the local pathology of these diseases is an extensive infiltration of activated macrophages (MΦ). Different functional activation states can be induced in MΦ during innate immune activation, and it is this differential activation that might be important in susceptibility/resistance to induction or perpetuation of autoimmunity. In this study, we present an extensive, comparative analysis of the activation phenotypes of MΦ derived from autoimmune-susceptible and autoimmune-resistant rat strains to describe a cellular phenotype that defines the disease phenotype. We included investigation of receptor function, intracellular signaling pathways, cytokines, and other soluble mediators released after activation of cells using a panel of stimuli embracing many activation routes. We report that activation of MΦ from the autoimmune-susceptible strain was associated with alternative activation indicated by induction of arginase activity, a lower production of classical proinflammatory mediators, and a high production of interleukin (IL)-23, and MΦ from the autoimmune-resistant strains were associated with a higher production of proinflammatory mediators, a classical activation phenotype, and preferential induction of IL-12. These MΦ phenotypes thus reflect disparate, genetic cellular programs that define autoimmune susceptibility.
A hepatitis C virus-encoded, nonstructural protein (NS3) triggers dysfunction and apoptosis in lymphocytes: role of NADPH oxidase-derived oxygen radicals
Authors: Thorén Fredrik , Romero Ana , Lindh Magnus , Dahlgren Claes , Hellstrand Kristoffer 
Published: September 2004

AbstractThe persistent infection caused by hepatitis C virus (HCV) is presumably explained by a deficient immune response to the infection, but the basis for the inefficiency of immune-mediated virus eradication is not known in detail. This study addresses mechanisms of relevance to dysfunction of cytotoxic lymphocytes in HCV infection, with a focus on the role of phagocyte-derived oxygen radicals. We show that NS3, a nonstructural, HCV-encoded protein, induces a prolonged release of oxygen radicals from mononuclear and polymorphnuclear phagocytes by activating a key enzyme in radical formation, the reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. The NS3-activated phagocytes, in turn, induced dysfunction and/or apoptosis in three major subsets of lymphocytes of relevance to defense against HCV infection: CD3+/56– T cells, CD3–/56+ natural killer (NK) cells, and CD3+/56+ NKT cells. Two inhibitors of the NADPH oxidase, histamine and diphenylene iodonium, suppressed the NS3-induced oxygen radical production and efficiently protected lymphocytes against NS3-induced apoptosis and dysfunction. In conclusion, we propose that NS3, by triggering oxygen radical formation in phagocytes, may contribute to the dysfunction of antiviral lymphocytes in HCV-infected liver tissue and that strategies to circumvent oxidative stress may be useful in preventing HCV-associated carcinogenesis and facilitating lymphocyte-mediated clearance of infected cells.
The Bremen Cog of 1380 – An electron microscopic study of its degraded wood before and after stabilization with PEG
Authors: Hoffmann P. , Singh A. , Kim Y.S. , Wi S.G. , Kim I.-J. , Schmitt U. 
Published: September 2004

Abstract
The Bremen Cog is a big ship built AD 1380 from oak
wood. After its recovery from the river Weser, the water-logged
ship's timbers were successfully stabilized using
a novel two-step polyethylene glycol (PEG) treatment. An
electron microscopic study of the patterns of degradation
and of the distribution of PEG within the Cog wood
is described. Descriptions like these do not exist for
many well known archaeological objects. SEM revealed
that in areas with extensive degradation, wood cell walls
are thinned and cells have a distorted appearance. TEM
provided evidence that the wood has been degraded primarily
by erosion bacteria. The stabilization treatment
involved impregnation first with PEG 200 and then with
PEG 3000. The SEM observations of PEG-impregnated
wood revealed that in degraded tissues all cell types are
well filled with PEG 3000. Non-degraded tissues are
impermeable to PEG 3000 and are impregnated only with
PEG 200. SEM confirmed earlier fluorescence microscopic
evidence, that PEG 200 is absorbed by the cell
walls.
Ultrastructure of iodine treated wood
Authors: Donaldson L. , Frankland A. 
Published: September 2004

AbstractIodine staining has been used to study the orientation of cellulose microfibrils in wood using light microscopy. The aim of this work was to understand the exact nature of the staining reaction with iodine and to provide insight into the properties and organisation of the wood cell wall. Based on transmission electron microscopy it is apparent that precipitation of the iodine following treatment with nitric acid results in the formation of crystal cavities within the cell wall, which follow the orientation of the cellulose microfibrils. There is no evidence that iodine precipitates within “drying checks” as previously speculated. High resolution confocal reflectance microscopy of crystal cavity orientation indicates that the microfibril arrangement within pit borders can be both spiral and circular. Crystal cavities are much more abundant within the S1 layer than elsewhere. All of the cells examined had crystal cavities in the S1 region, which may be related to the reduced lignification at the S1/S2 boundary resulting in greater porosity of the cell wall at this location. Within the S2 region, clusters of crystal cavities are randomly distributed and occur in widely varying numbers among adjacent cell walls, suggesting variations in the porosity of the S2 wall within and among adjacent tracheids. Cavities form preferentially within more electron lucent regions of the cell wall. The random nature of crystal cavity formation within S2 clusters probably reflects the underlying random nature of the cell wall nanostructure. We conclude that iodine staining can provide important clues to the nanostructural properties of tracheid cell walls.
Effects of refining on the fibre structure of kraft pulps as revealed by FE-SEM and TEM: Influence of alkaline degradation
Authors: Molin U. , Daniel G. 
Published: September 2004

Abstract
The aim of the study was to evaluate the effect of refining
on the ultrastructure of spruce pulp fibres. Pulps with different
molar masses of cellulose (estimated as intrinsic
viscosity) were studied after PFI-refining. The molar
masses of the polymers were decreased by increases in
alkali concentration during pulping. Fibre surface structures
were examined using Field Emission Scanning
Electron Microscopy (FE-SEM) and Transmission Electron
Microscopy (TEM) was used to observe changes in
the internal structure of the fibres. Pulps with lower (125
and 329 ml g−1) intrinsic viscosity showed more damaged
during refining than pulps with higher (620 and
1120 ml g−1) intrinsic viscosity. Observations showed
pulps with lower intrinsic viscosity to have large decreases
in fibre length after refining. Fibres with low intrinsic
viscosity (i.e., 125 ml g−1) had less primary wall and S1
layer remaining and the external fibrillation and damage
of the S2 layer had increased. The S2 wall of fibres with
high intrinsic viscosity showed characteristic delamination.
Similar delamination was not visible for fibres with
low intrinsic viscosity.
Changes in the fiber wall during refining of bleached pine kraft pulp
Authors: Laine C. , Wang X. , Tenkanen M. , Varhimo A. 
Published: September 2004

Abstract
The effect of refining on the fiber wall was studied for
bleached kraft pulp fractions from pine first thinnings and
pine sawmill chips. Hydrocyclone fractionation of both
pulps produced fractions enriched in earlywood and latewood
fibers. Some external fibrillation but no changes in
fiber wall thickness were observed for the thin-walled
earlywood fibers during refining. Refining the thick-walled
latewood fibers led to extensive external fibrillation and
a decrease in fiber wall thickness. The pore structure of
the fiber wall opened up during refining for all pulp fractions.
Earlywood fibers were more porous than latewood
fibers, and fibers from first thinnings more porous than
those from sawmill chips. The earlywood fibers from first
thinnings had more large pores than the other fiber fractions.
In the region of the smaller pores, the pore volume
did not change significantly with refining, whereas in the
region of the larger pores it increased markedly. In all the
fractions investigated, specific hydrolytic enzymes
hydrolyzed cellulose more easily after refining. This is an
indication of an increase in cellulose surface area and/or
disordering of cellulose as a result of refining, probably
due to local disorder of the cellulose in the fibril aggregates.
Bonding developed most strongly for the earlywood
fiber fraction from first thinnings. This is concluded
to be due to a combination of fiber dimensions and fiber
wall porosity.
An unusual formation of tension wood in a natural forest Acacia sp.
Authors: Hillis W.E. , Evans R. , Washusen R. 
Published: September 2004

Abstract
The determination of microfibril angle (MFA), cellulose
crystallite width and microdensity by SilviScan-2 at CSIRO
confirmed that several dark bands in the heartwood
of an Acacia species were associated with tension wood
(TW) fibres. The straight log was taken from a tree of
about 30 years of age that had been apparently growing
vertically as there were no signs of the usual stimuli for
TW formation. The continuous dark bands of about 5 mm
width extended radially from the inner heartwood in a
spiral pattern and were separated by continuous normal
wood bands of similar width. The TW bands continued
in the sapwood from the heartwood boundary to the
cambium but were not coloured. The dark colour of the
TW was probably caused by extractives being polymerised
at the heartwood boundary by enzymes in the TW
fibres in the sapwood. The MFA and cellulose crystallite
width indicated the TW in a band was of similar intensity
throughout its length, indicating similar microstructural
characteristics at different cambial ages. The initiation of
spiral grain formation occurs before that of tension wood
in the Acacia samples studied.
Changes in the surface properties of wood due to sanding
Authors: Sinn G. , Gindl M. , Reiterer A. , Stanzl-Tschegg S. 
Published: September 2004

Abstract
Spruce and beech wood specimens were sanded with
four different grain sizes. Surface morphological and
chemical changes were determined by roughness measurement,
surface free energy determination according to
acid-base theory and X-ray photoelectron spectroscopy.
An analysis model was proposed to describe chemical
changes due to sanding and the data were analysed
according to it. It could be shown that spruce and beech
behave similarly over a wide range and that chemical
changes are non-linear functions of grain size and thus
surface roughness. A maximum of surface free energy
and a maximum of carbon C1s sub-peak ratio (ratio of
carbon bonded to a single non-carbonyl oxygen to carbon
bonded only to hydrogen or other carbon atoms)
was found for middle grain size.
The creep of wood destabilized by change in moisture content. Part 1: The creep behaviors of wood during and immediately after drying
Authors: Takahashi C. , Ishimaru Y. , Iida I. , Furuta Y. 
Published: September 2004

Abstract
To better understand mechano-sorptive creep, creep
behaviors were compared in wood samples during the
drying process, immediately after drying, and after a long
conditioning under constant humidity and temperature.
Creep was greater in the sample tested immediately after
drying than in the sample conditioned for a long time
under relative humidity equal to that after drying, despite
the fact that these samples had almost the same moisture
content (MC). While the wood that has been moisture-conditioned for a long time is in a stable state, the
wood tested immediately after the drying is presumed to
be in an unstable state. Moreover, creep of the sample
tested during the drying process was greater than that
of the sample tested immediately after the drying. It has
also been found that the instability decreased with time,
indicating that stabilization and destabilization occur
simultaneously during the drying process. In recent studies,
a decrease in the elastic modulus and an increase in
the fluidity of wood immediately after a change in MC or
temperature have been reported. These findings are
attributed to the instability caused by changes in MC or
temperature. Based on the results of the present study
and recent studies, we consider the increase in the fluidity
of wood as the MC changes to be attributable to
instability.
Moisture adsorption thermodynamics of wood from fractal-geometry approach
Authors: Cao J. , Kamdem D.P. 
Published: September 2004

Abstract
The fractal-geometry approach was used to calculate the
thermodynamic properties of moisture sorption by wood
from the adsorption isotherms in this study. The results
were compared with those from an isosteric approach
and a calorimetric approach. The adsorption isotherms
of Southern yellow pine (Pinus spp.) were measured at
4, 15, 30, and 40°C to provide source data for the calculation
of both fractal-geometry and isosteric approaches.
The results show that the fractal dimensions of the
internal surfaces of wood vary between 2.4 and 2.5. The
curves of the differential heat of adsorption −∆H against
moisture content from the fractal-geometry approach are
similar to those from calorimetric measurements in previous
research. The −∆H values from the isosteric
approach increased with moisture content within a moisture
content range up to 3%. And, at moisture contents
higher than 3%, the −∆H values from this method are
much higher than those from the fractal-geometry
approach and calorimetric approach. As a result, the
fractal-geometry approach is applicable to calculate the
differential thermodynamic properties of moisture sorption
by wood in future research.
Ionic liquids in wood preservation
Authors: Pernak J. , Zabielska-Matejuk J. , Kropacz A. , Foksowicz-Flaczyk J. 
Published: September 2004

Abstract
In this study ionic liquids (3-alkoxymethyl-1-methylimidazolium
tetrafluoroborates and hexafluoro-phosphates)
are successfully used for wood preservation. These liquids
are new biocides as well as new solvents which
penetrate wood well. The prepared ionic liquids with an
alkoxymethyl substituent, which consisted of 7, 8 or 9
carbon atoms, exhibited fungicidal activity against Coniophora
puteana (Schum.: Fr.) Karst., Trametes versicolor
(L.: Fr.) Pilát and Sclerophoma pityophila (Corda) v.
Höhn. The effective and lethal doses were measured by
the agar-plate method. In their activity against wood
degrading fungi, ionic liquids such as 1-methyl-3-octyloxy-methylimidazolium
and 1-methyl-3-nonyloxymethylimidazolium
tetrafluoroborates were comparable with
commercially available benzalkonium chloride and didecyldimethylammonium
chloride. Ionic liquids both with
and without DDAC penetrated into Scots pine wood very
well.
New bis-quaternary ammonium and bis-imidazolium chloride wood preservatives
Authors: Zabielska-Matejuk J. , Urbanik E. , Pernak J. 
Published: September 2004

Abstract
Bis-quaternary ammonium and bis-imidazolium chlorides,
the compounds containing in their structure two
symmetrical quaternary nitrogen atoms, were prepared
and tested on wood destroying and sapstaining fungi.
The effect of the position of quaternary nitrogen atoms
upon fungicidal and surface properties was analysed.
The antifungal activity of new bis-quaternary ammonium
and bis-imidazolium chlorides against Coniophora
puteana (Schum.:Fr.)Kr., Trametes versicolor (L.:Fr.)Pilát
and Aspergillus niger van Tieghem was much more pronounced
than that of quaternary ammonium chlorides.
The results confirm the correlation between surface
activity and fungicidal activity. The adsorption of bisimidazolium
chloride onto pine wood was influenced by
pH of applied solutions and the initial solution concentration.
With increasing pH of ammonium solution, the
adsorption was much greater than in neutral or acidic
solutions. Cation structure of the quaternary ammonium
chloride exerted a strong influence on quantity of wood-adsorbed
chemicals and resistance to water leaching.
Fungal decay resistance of wood reacted with phosphorus pentoxide-amine system
Authors: Lee H.-L. , Chen G.C. , Rowell R.M. 
Published: September 2004

Abstract
Resistance of wood reacted in situ with phosphorus
pentoxide-amine to the brown-rot fungus Gloeophyllum
trabeum and white-rot fungus Trametes versicolor was
examined. Wood reacted with either octyl, tribromo, or
nitro derivatives were more resistant to both fungi.
Threshold retention values of phosphoramide-reacted
wood to white-rot fungus T. versicolor ranged from 2.9
to 13.3 mmol, while these for brown-rot fungus G. trabeum
ranged from 8.1 to 19.2 mmol. Wood reacted with
phosphoramide tested to be more resistant to white-rot
than brown-rot attack.
Bioactive phenolic substances in industrially important tree species. Part 1: Knots and stemwood of different spruce species
Authors: Willför S. , Nisula L. , Hemming J. , Reunanen M. , Holmbom B. 
Published: September 2004

Abstract
Knots (i.e., branch bases inside tree stems) in spruce
trees contained remarkably higher concentrations of lignans
and oligolignans than the adjacent stemwood. The
amount of lignans in some knots exceeded 10% (w w−1)
and some knots contained hundreds of times more lignans
than the heartwood in the same tree. However,
there were large variations between different species and
even between different knots in the same tree. 7-Hydroxymatairesinol was the predominant lignan in knots
of Picea abies, P. glauca, P. koraiensis, P. mariana, and
P. omorika, while liovil and secoisolariciresinol dominated
in P. sitchensis and P. pungens. The lignans occur in free
form in knots and are easily extracted with polar solvents.
In addition to the true lignans, especially the knots contained
large amounts of lignan-related oligomeric aromatic
substances, here called oligolignans, consisting of
three or four phenylpropane units.
7-Hydroxymatairesinol, but also other lignans, could
be extracted in large scale from spruce knots at pulp and
paper mills. Other potentially important lignans could be
produced from 7-hydroxymatairesinol by semisynthesis.
The ready availability of large amounts of lignans and oligolignans
now enables research to assess their bioactivity
and provide the basis for applications in medicine and
nutrition or as natural antioxidants and antimicrobial
agents in a variety of technical products.