bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated methods for improved protein identification by peptide mass fingerprinting
Authors: Levander Fredrik , Rögnvaldsson Thorsteinn , Samuelsson Jim , James Peter 
Published: June 2004

AbstractIn order to maximize protein identification by peptide mass fingerprinting noise peaks must be removed from spectra and recalibration is often required. The preprocessing of the spectra before database searching is essential but is time‐consuming. Nevertheless, the optimal database search parameters often vary over a batch of samples. For high‐throughput protein identification, these factors should be set automatically, with no or little human intervention. In the present work automated batch filtering and recalibration using a statistical filter is described. The filter is combined with multiple data searches that are performed automatically. We show that, using several hundred protein digests, protein identification rates could be more than doubled, compared to standard database searching. Furthermore, automated large‐scale in‐gel digestion of proteins with endoproteinase LysC, and matrix‐assisted laser desorption/ionization‐time of flight (MALDI‐TOF) analysis, followed by subsequent trypsin digestion and MALDI‐TOF analysis were performed. Several proteins could be identified only after digestion with one of the enzymes, and some less significant protein identifications were confirmed after digestion with the other enzyme. The results indicate that identification of especially small and low‐abundance proteins could be significantly improved after sequential digestions with two enzymes.
Phenol radical cations and phenoxyl radicals in electron transfer from the natural phenols sesamol, curcumin and trolox to the parent radical cations of 1‐chlorobutane
Authors: Joshi R. , Naumov S. , Kapoor S. , Mukherjee T. , Hermann R. , Brede O. 
Published: June 2004

AbstractThe free electron transfer from sesamol, curcumin and trolox to solvent (1‐chlorobutane) radical cations was studied. The solutes (ArOH) react with BuCl⋅+ at diffusion‐controlled rates (∼1010 dm3 mol−1 s−1) resulting, simultaneously, in phenol‐type radical cations (ArOH⋅+) and phenoxyl radicals (ArO⋅) with an ArOH⋅+/ArO⋅ ratio  > 1;1. It was found that the kinetics are markedly affected by the different substituents on the aromatic ring of ArOH⋅+. The various ArOH⋅+ react with triethylamine with rate constants of ∼109 dm3 mol−1 s−1, whereas ethanol and dioxane are ineffective as cation scavengers. The effect of substituents on the electron transfer and the ArOH⋅+/ArO⋅ ratio is discussed on the basis of experimental data and quantum chemical calculations. Copyright © 2004 John Wiley & Sons, Ltd.
Synthesis and characterization of secondary‐amine‐functional microparticles
Authors: Altintaş E. Banu , Kiliç Soner 
Published: June 2004

AbstractSecondary‐amine‐functional microparticles were prepared in the range of 50–250 μm through the suspension polymerization of styrene, divinylbenzene (DVB), and 2‐(tert‐butylamino)ethyl methacrylate (tBAEMA). This study focused on the effects of the DVB, tBAEMA, initiator, and stabilizer concentrations and shaking rate on the experimental amine content, swelling ratio, average particle size, and particle size distribution. The suspension polymerization experiments were carried out in two different systems. In the first system, an organic phase, including the monomers and initiator, was dispersed in an aqueous medium in the presence of Al2(SO4)3. Al2(SO4)3, in the presence of an amine monomer (pH ∼ 10), formed colloidal Al(OH)3, which built a nonsticky layer on the surface of the polymerizing droplets that prevented them from coalescing and aggregating. Individual and spherical particles within the range of 50–200 μm were obtained by this polymerization method. The second method was similar to the first polymerization protocol, except that a certain amount of sodium dodecyl sulfate was added as a costabilizer in the presence of Al2(SO4)3. In these experiments, individual and spherical particles were obtained within the range of 130–250 μm. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem: 3708–3719, 2004
Impacts of neuroimaging on psycho‐oncology
Authors: Tashiro Manabu 
Published: June 2004

AbstractNon‐invasive neuroimaging has become important in the field of psycho‐oncology. Positron emission tomography (PET) is a highly advanced form of scintigraphy and used for observation of regional tissue activities such as metabolism and perfusion. Nowadays, PET measurement of glucose consumption has been widely used not only for cancer diagnosis but also for evaluation of brain activity in various psychiatric and neurological disorders. Recently, it has been used for evaluation of relatively mild depression among cancer patients. In addition, magnetic resonance imaging (MRI) has been used for detection of brain metastasis in cancer patients, but also useful for evaluation of stressful events by measuring the sizes of tiny neural structures such as hippocampus and amygdala.In this report, recent findings of non‐invasive neuroimaging in cancer patients are overviewed, putting emphasis on the possible impacts of neuroimaging on psycho‐oncology. Copyright © 2004 John Wiley & Sons, Ltd.
Spatial heterogeneity and structure of bird populations: a case example with the eagle owl
Authors: Penteriani Vincenzo , Delgado María del Mar , Gallardo Max , Ferrer Miguel 
Published: June 2004

AbstractIf individuals of the same population inhabit territories different in landscape structure and composition, experiencing habitat‐specific demographic rates, then the landscape features become major determinants of the overall population characteristics. Few studies have tested how habitat‐specific demography interacts with landscape heterogeneity to affect populations of territorial species. Here we report a 29‐year study of an eagle owl (Bubo bubo) population in southern France. The aim of this study was to analyse how habitat heterogeneity could affect density and breeding performance. Mean productivity for the overall sample was 1.69±0.76 fledglings per breeding pair and, after controlling for year effect, significant differences between territories were detected for productivity. A positive correlation was found between the percentage of pairs producing 50% of the annual fledged young (an index of the distribution of fecundity among nesting territories) and the mean reproductive outputs, that is the heterogeneous structure of the population determined that most/all pairs contributed to the annual production of young during good years, but the opposite during poor years (i.e. fewer pairs produced the majority of fledglings). Mean reproductive output was positively affected by percentage of open country and diet richness. Although other factors different to territory quality could affect demography parameters (e.g. quality of breeders), our results clearly showed a significant correlation between landscape features and population productivity.
Chance and adaptation in the evolution of island bumblebee behaviour
Authors: Chittka Lars , Ings Thomas C. , Raine Nigel E. 
Published: June 2004

AbstractWe used a population biological approach to assist our understanding of the evolution of behaviour, with island bumblebees as our model system. The widespread European speciesBombus terrestrisoccurs on all major Mediterranean, and some Atlantic islands. Bees from different populations differ in a variety of behavioural traits, including floral colour preferences, flower detection, and learning behaviour. We attempted to correlate these behavioural differences with each population's environment, but could not find straightforward adaptive explanations. We also performed reciprocal transplant studies to compare nectar foraging performance of bees from three different populations, but found that non‐native bees consistently outcompeted native bees. Thus, we consider genetic drift, exaptation, and pleiotropy as possible alternative explanations to a strictly adaptive explanation for between population behavioural differences in bumblebees.
Community assembly along a species pool gradient: implications for multiple‐scale patterns of species diversity
Authors: Fukami Tadashi 
Published: June 2004

AbstractVarious ecological processes influence patterns of species diversity at multiple spatial scales. One process that is potentially important but rarely considered is community assembly. I assembled model communities using species pools of differing size to examine how the history of community assembly may affect multi‐scale diversity patterns. The model contained three scales at which diversity could be measured: local community, metacommunity, and species pool. Local species saturation occurred, as expected from the competition and predation built in the model. However, local communities did not become resistant to invasions except when the species pool was very small. Depending on dispersal rate and trophic level, the larger the species pool, the harder it was to predict which species invades which local community at a given time. Consequently, local‐community dissimilarity maintained by assembly history increased linearly with pool size, even though local diversity was decoupled from pool size. These results have two implications for multi‐scale diversity patterns. First, assembly history may provide an explanation for scale‐dependent relationships between local and regional diversity: assembly causes the relationship to be curvilinear at one scale (local community), while linear at another (metacommunity). Second, assembly history influences how γ‐diversity is partitioned into α‐ and β‐diversity: assembly causes the relative contribution of β to increase with pool size. Overall, this study suggests that community assembly history interacts with species pool size to regulate multi‐scale patterns of species diversity.
Modeling spatial dynamics of episodic and synchronous reproduction by plant populations: the effect of small‐scale pollen coupling and large‐scale climate
Authors: Satake Akiko 
Published: June 2004

AbstractMany plant species show masting, intermittent and synchronized reproduction at population level. In the present paper, we review the resource‐based model providing a theoretically plausible physiological mechanism underlying masting. In the model, a non‐linear allocation of energy reserves is considered: plants accumulate photosynthate every year, produce flowers when the energy reserve level exceeds a threshold, and set seeds at a rate limited by pollen availability. The model predicted that individual plants alter their reproductive dynamics from annual to intermittent depending on how heavily the plant invests resource in reproduction. When fruit production is limited by the availability of outcross pollen, a plant population showed diverse reproductive behavior such as completely synchronized or desynchronized reproduction. Spatial scale of reproductive synchrony tended to be a few times larger than the range of direct pollen exchange. Impact of climatic fluctuation correlated at a large spatial scale was also investigated as an alternative synchronizing factor. The variation in annual productivity and the reproductive threshold induced from climatic fluctuation was accounted for by incorporating an additional term in the model. When plants show a 2 year reproductive cycle, highly synchronized reproduction at a regional scale was induced due to correlated environmental forcing, but reproductive synchrony with long intermast periods was realized only when pollen coupling and environmental forcing were at work. These results suggest that distance‐dependent processes, such as pollen exchange between nearby trees, induce synchrony at a local scale and external environmental forcing correlated at geographically large scales works to strengthen and maintain such a synchrony.
Additive and non‐additive effects from a larger spatial scale determine small‐scale densities in a web spiderNeriene brongersmai
Authors: Takada Mayura , Miyashita Tadashi 
Published: June 2004

AbstractWe examined 15 populations ofNeriene brongersmai, a common sheet‐web spider inhabiting cedar forest floor, to find out how density at a small spatial scale (patch level) is determined by processes operating at this scale as well as those from a larger spatial scale (population level). Here we focus on two types of large‐scale effects that may influence small‐scale density: an additive effect that changes the density at patch level; and a non‐additive effect that changes the relationship between the density and its limiting factor at the patch level. ANCOVA showed that patch‐level density of this spider was positively correlated with web‐site availability at this level, but the density with a given amount of web‐site differed among populations (cedar forests), indicating the existence of an additive large‐scale effect. Multiple regression analysis showed that web‐site availability at a population level explained the additive large‐scale effect well, but prey availability and forest size did not. It seemed likely that increased web‐site availability may have reduced the mortality of spiders while moving to a new web‐site, and hence increased population density. A non‐additive large‐scale effect was also revealed: i.e. the relationship between density and web‐site availability at the patch level tended to be stronger in populations with a greater additive large‐scale effect. Higher intraspecific competition for web‐sites in these populations appeared to have strengthened this relationship.
A field assessment of reproductive seasonality in the threatened wild Namaqua dune mole‐rat (Bathyergus janetta)
Authors: Herbst M. , Jarvis J. U. M. , Bennett N. C. 
Published: June 2004

AbstractThe Namaqua dune mole‐rat Bathyergus janetta breeds seasonally, producing up to two litters during the early summer in the Cape. Females exhibit elevated urinary progesterone and oestradiol‐17β concentrations and males raised concentrations of testosterone, these correlate with the onset of the seasonal winter rainfall. The rains moisten the soil allowing excavation and provide the mole‐rats with the opportunity not only to extend burrow systems but also to search for mates. An increased incidence of hindfoot drumming and visitations to neighbouring burrow systems occurs during this period. Plural occupancy of burrows by adult mole‐rats was found during the onset of the winter, and pups, lactating and pregnant females were caught at the end of October and November (early Cape summer). Pups develop rapidly and their eyes open after c. 1 week. Pup body mass increases exponentially from birth to about 70 days. Inter‐sibling aggression increases progressively and after c. 60 days captive‐born pups had to be separated, suggesting that in the wild they would have dispersed.
Calcium availability affects bone growth in nestlings of free‐living great tits (Parus major), as detected by plasma alkaline phosphatase
Authors: Tilgar Vallo , Mänd Raivo , Ots Indrek , Mägi Marko , Kilgas Priit , Reynolds S. James 
Published: June 2004

AbstractRecent studies have revealed that calcium limitation of avian reproduction may be a widespread phenomenon, affecting both egg properties and chick development. The effect of calcium shortage on the final body size of fledglings is usually rather weak, possibly owing to compensatory growth. Achieving full skeletal size is not, however, a reliable indication of complete ossification and it is possible that chicks with similar tarsus lengths are in different stages of skeletal development. We hypothesized that measuring plasma activity of the bone alkaline phosphatase (ALP), a highly specific marker for bone calcification, may reveal subtle developmental differences in full‐grown fledglings, having experienced different levels of calcium availability during growth. In two seasons, a number of pairs of great tit Parus major were provided with calcium‐rich material during the nestling period, while others were not supplemented (controls). While no significant differences in size of fledglings were detected between groups, bone‐ALP activity at the pre‐fledging stage was lower in the calcium‐provided nestlings than in the control nestlings. This may indicate that supplemented chicks had completed the rapid phase of bone formation, but this process was delayed in controls. Measuring ALP as a marker of skeletal development expands our knowledge of how delayed skeletal development of chicks can result in protraction of the nestling period, thereby reducing the breeding success of adult birds.
Blockade of clearance of immune complexes by an anti-F(cγ) receptor monoclonal antibody
Authors: Clarkson SB , Kimberly RP , Valinsky JE , Witmer MD , Bussel JB , Nachman RL , Unkeless JC 
Published: June 2004

Clearance of immune complexes by the mononuclear phagocyte system is important for maintaining normal host defenses against bacterial and viral assault (1), but also contributes to the pathogenesis of a variety of immune- mediated diseases . For example, removal from the circulation of IgG-coated erythrocytes and platelets by the MPS is the sine qua non of immune-mediated cytopenias (2, 3). On the other hand, abnormally decreased removal by the MPS of smaller, soluble immune complexes may play a role in the pathogenesis of immune complex-mediated tissue damage found in such autoimmune diseases as SLE (4).
Although the physicochemical nature and the size of immune complexes can influence rates of clearance and sites of deposition (reviewed in 5), interactions between immune complexes and the MPS in vivo are poorly understood. The inability to directly measure binding or internalization of immune complexes by cells in the liver and spleen has made the analysis of the molecular basis of immune complex clearance very difficult . Receptors for the Fc portion of IgG (FcγR) and for complement (CR) undoubtedly play a role in the removal of immune complexes, but the relative importance of these receptors is not known.
An L-arginine-dependent mechanism mediates kupffer cell inhibition of hepatocyte protein synthesis in vitro
Authors: Billiar TR , Curran RD , Stuehr DJ , West MA , Bentz BG , Simmons RL 
Published: June 2004

The hepatic failure associated with severe sepsis is characterized by specific, progressive, and often irreversible defects in hepatocellular metabolism (1). Although the etiologic microbe can often be identified, the direct causes and mechanisms of the hepatocellular dysfunction are poorly understood. We have hypothesized that Kupffer cells (KC), which interact with ambient septic stimuli, respond by providing signals to adjacent hepatocytes (HC) in sepsis . Furthermore, we have provided evidence (2, 3) that KC activated by LPS from Gram-negative bacteria can induce profound changes in the function of neighboring HC in coculture. In our model, coculture of either KC (2) or peritoneal macrophages (Mφ)(3) with HC normally promotes HC protein synthesis ([(3)H]leucine incorporation). The addition of LPS or killed Escherichia colt' to such cocultures induces a profound decrease in HC protein synthesis, as well as qualitative changes ([(35)S]methionine, SDS-gel electrophoresis) in protein synthesis without inducing HC death (2, 3) . In this report we show that the inhibition in protein synthesis is mediated via an L-arginine-dependent mechanism.
The metabolism of L-arginine by activated Mφ to substances with cytostatic and even lethal effects on target cells is a relatively recent discovery. After the description by Stuehr and Marletta (4, 5) that LPS- triggered Mφ produced nitrite/nitrate (NO(2)(-)/NO(3)(-)), Hibbs et al. (6, 7) and Iyengar et al. (8) demonstrated that L-arginine was the substrate for the formation of both these nitrogen end products and citrulline. A role for the arginine-dependent mechanism in Mφ tumor cytotoxicity (6, 7) and microbiostatic activity (9) has been suggested. However, the in vivo functions of this novel Mφ mechanism have not yet been defined, but it is possible that there are both physiologic as well as pathologic roles. Our in vitro results raise the possibility that some metabolic responses to microbial invasion maybe partially mediated by the L-arginine-dependent mechanism. What other metabolic responses are affected and the possible pathologic consequences remain to be studied.
THE TOTAL NON-PROTEIN NITROGEN OF THE BLOOD IN NEPHRITIS AND ALLIED CONDITIONS
Authors: Farr Clifford B. , Austin J. Harold 
Published: June 2004

1. In a series of non-nephritic individuals the total non-protein nitrogen of the blood, determined by Folin's method, was found to lie between 15 and 43 milligrams per 100 cubic centimeters. From 50 to 60 per cent. of this was in the ammonia-urea fraction.
2. In cardiovascular disease with renal congestion, but without other renal lesion, there was no evidence of increase of non-protein nitrogen in the blood, nor of alteration of the ammonia-urea percentage.
3. In chronic nephritis with marked albuminuria and edema there was very little, if any, increase or alteration.
4. In chronic nephritis with hypertension the non-protein nitrogen was definitely increased, ranging from 40 to 180 milligrams per 100 cubic centimeters of blood. The percentage of the ammonia-urea fraction was usually higher than in non-nephritic cases.
5. Cases showing high non-protein nitrogen values were subject to rapid fluctuations in these values in the course of a few days. As a rule, clinical improvement was associated with a fall of the non-protein nitrogen figures to nearer the normal range.
6. Uremia was almost always accompanied by an increase of non-protein nitrogen in the blood, but no constant relation could be established between the degree of increase and the tendency to uremia.
7. Our cases have not yet been followed for a long enough period to admit of conclusions as to the possible relation between the degree of non-protein nitrogen retention and ultimate prognosis.
8. We believe this method to be a valuable aid in the clinical study of nephritis and that it can be readily carried out in any well equipped clinical laboratory.
ON IMMUNITY TO TRANSPLANTABLE CHICKEN TUMORS
Authors: Rous Peyton , Murphy James B. 
Published: June 2004

The phenomena of natural and acquired resistance to transplanted chicken tumors strikingly resemble those observed in the case of transplanted mammalian growths; and no more than those do they suggest that the tumors have an extrinsic cause.
That there may exist in fowls implanted with a chicken tumor a resistance directed against the tumor-causing agent distinct from the resistance manifested against the alien tumor cells has been shown in a previous article. Both sorts of resistance are present in a fowl in which a tumor has retrogressed, the resistance in such an instance being acquired. That directed against the agent is largely specific, giving little if any protection against the agents causing other tumors. There is some evidence that the conditions upon which a fowl's natural resistance depends are the same for the agents causing different chicken tumors.
It has proved impossible to protect chickens against the agent causing the simple sarcoma by injecting them with dried tumor material in which this agent has been attenuated by heat. The transfer of blood from resistant fowls to fowls with growing tumors is in our experience void of effect on the tumors.