bluuebunny/crossref_metadata_2025 huggingface dataset:
Tolerance of growing pigs to lupin alkaloids
Authors: Godfrey NW , Mercy AR , Emms Y , Payne HG
Published: March 2005

In two experiments with a total of 93 young pigs, we measured responses in growth rate and feed intake to dietary lupin alkaloid concentrations which ranged from 0.05 to 0.52 g/kg. In the first experiment increasing the alkaloid levels from 0.12 to 0.52 g/kg in increments of 0.08 g/kg produced a progressive decline in growth rate and feed intake. In the second experiment, pig productivity was unaffected by increasing dietary alkaloids from 0.05 to 0.20 g/kg, but was depressed when the alkaloid level reached 0.35 g/kg. It was concluded that, with ad libitum feeding, growing pigs could tolerate up to 0.20 g/kg of dietary lupin alkaloids.
Effects of stocking rate of goats and stage of crop growth when grazed on grain yield and goat production from pigeonpea (Cajanus cajan)
Authors: Wijnberg C , Whiteman PC
Published: March 2005

An early-maturing, photoperiod-insensitive cultivar of pigeonpea, Cajanus cajan (cv. QPL4), was grown in two experiments. In the first experiment, grazing began at different times by goats with a mean weight of 14 kg. On different plots grazing started 24 days (before flowering), 57 days (flowering), 98 days (50% pod fill) and 141 days (after harvest) after plant emergence. The crop was then allowed to grow unchecked to pod maturity at 139 or 154 days after emergence and was harvested on 5 April 1982 to compare the effects of time of grazing on phenology, growth and yield. Ratoons were harvested on 9 August 1982. Grain yields of main crop plus ratoons were: the ungrazed control 1920 plus 403 kg/ha, pre-flowering 8 15 plus 107 kg/ha; 50% flowering 1210 plus 3 kg/ha, pod fill 0 plus 428 kg/ha and post-harvest grazing 1250 plus 24 kg/ha. In the second experiment, young feral doe goats (mean weight 16 kg) grazed pigeonpea at 25, 50, 75 and 100 goats/ha. Grazing commenced when 50% of plants were in flower (11 January 1982). Mean daily liveweight gains per animal (over 42 days) were: 25 goats/ha, 68 g; 50 goats/ha, 49 g; 75 goats/ha, 58 g; 100 goats/ha, 35 g. Grain harvested on 14 May 1982 was 1085, 530,80, and 0 kg/ha for goat stocking rates of 25, 50,75, and 100 goats/ha. Compared with the ungrazed control, grazing in both experiments had marked effects on plant populations and dry matter yields and reduced grain yields. Pigeonpea does not seem to be a good forage, perhaps because of its low energy content; therefore, there seems little point in grazing the crop during growth because of the marked reduction in yield of grain.
A comparison of the growth of seedlings of Mediterranean and temperate tall fescues, phalaris and annual ryegrass
Authors: Hill MJ , Kay G , Yeates SJ
Published: March 2005

Seedlings of tall fescues (Festuca arundinacea), phalaris (Phalaris aquatica) and annual ryegrass (Lolium rigidum) were compared with those of other temperate grasses and cereals at 11 and 47 days after sowing at 18/13�C (12/12 h) to determine their relative seedling vigour. Also, the growth rates of two Mediterranean and two temperate cultivars of tall fescue were compared with those of phalaris and annual ryegrass at 14/6�C and 23/20�C (12/12 h) using growth analysis techniques. Shoot growth rates of seedlings were related to caryopsis weight (r = 0.99 at 11 days after sowing) when the range of weights was large, but there was no correlation among perennials with low caryopsis weights (<0.2 mg). Although they had heavier caryopses, seedlings of tall fescue grew more slowly than seedlings of phalaris. All seedlings grew faster at 23/20�C than at 14/6�C. Annual ryegrass had the highest dry matter yield, achieved through a rapid production of tillers, it grew relatively better with respect to ryegrass at 23/20�C than at 14/6�C. Phalaris depended on larger tillers for increased yield, and growth of these was favoured by the higher temperatures. Tall fescue seedlings were less vigorous than the other grasses, but temperate types grew much faster than Mediterranean types at 23/20�C. These trends occurred because of a high leaf area (equivalent to annual ryegrass) and leaf area ratio in phalaris at 23/20�C, and lower leaf extension rates and smaller leaves in Mediterranean fescues than in temperate fescues. The results indicate that: (1) because of better seedling growth, phalaris may be increasingly preferred to tall fescue for aerial seeding or direct drilling in regions where both are adapted; (2) at optimum temperatures, the Mediterranean fescues have poorer seedling vigour than the temperate types; and (3) at optimum temperatures, annual ryegrass may provide more serious competition to the fescues than to phalaris.
Infection studies with Cercospora zebrina on pasture legumes in Western Australia
Authors: Barbetti MJ
Published: March 2005

The effects of inoculum level, and temperature and humidity regimes on the development of Cercospora blackstem disease (caused by Cercospora zebrina) in subterranean clover (Trifolium subterraneum) were investigated. Mycelial fragments were an effective and reliable inoculum. The incidence, severity, and the rate of disease development increased with increasing period of high humidity after inoculation and with increasing concentrations of inoculum. Disease was greatest at 18/13� (12/12 h, day/ night), followed by 21/16�C, and then l5/10�C While all cultivars of T. subterraneum sprayed with hyphal fragments of C. zebrina became infected, Trikkala and Larisa showed some resistance. Of the alternative pasture legumes, lucerne (Medicago sativa), medic (M. littoralis, M. truncatula), drooping-flowered clover (T. cernuum), strawberry clover (T. fragiferum), rose clover (T. hirtum) and white clover (T. repens) were all susceptible; only serradella (Ornithopus compressus) was resistant.
Temporal variation in the results of soil phosphate analyses
Authors: Kemp DR , McDonald WJ , Murison RD
Published: March 2005

Soil phosphate (P) values were determined for 49 improved pasture sites on 11 occasions over a 3-year period. Each sample was taken from under an improved pasture on the Central Tablelands of New South Wales and analysed using the Bray No. 1 and Colwell (modified Olsen) tests. Variations in soil P values between samplings over time were significant (P<0.05). For individual sites, the 95% confidence limit, as a percentage of the mean, averaged � 19% for Bray P values and � 13% for Colwell P values. The pattern of variation in P values over time was not significantly (P<0.05) affected by soil P level, soil type or soil test. Variation in P values over time with both tests was significantly (P<0.05) correlated with a general estimate of soil moisture and thermal index for the sampling month. Both Colwell P and Bray P values showed negative correlations with increasing soil moisture or increasing thermal index. The correlation between Colwell P and Bray P values on any one soil type was not reliable enough to allow prediction of one soil-test P value from the other.
Effect of plant density on the sequential harvest yield of broccoli
Authors: Chung B
Published: March 2005

Field studies were conducted to determine the spear yield of three hybrid broccoli cultivars at each sequential harvest when the plants were grown at three plant populations - 2.8 (the common commercial density), 8.3 and 16.7 plants/m2. At 2.8 plants/m2, the terminal spears contribute about 60-70% of the total yield, with lateral spears contributing significantly. Almost 70% of the lateral spear yield was available at one pick 2-3 weeks after the first pick. A plant density of 8.3 plants/m2 gave a total yield of 23 t/ha, compared with 12 and 16 t/ha for 2.8 and 16- 7 plants/m2 respectively. This was due to higher yields of both terminal and lateral spears. The increase in yield at 16.7 compared with 2.8 plantdm2 was due mainly to a higher yield of terminal spears. Changing from the traditional low plant density to one of about 8 plants/m2 should increase yield significantly without causing cultural or marketing problems.
An assessment of old and new DNA sequence evidence for the paraphyly of Banksia with respect to Dryandra (Proteaceae)
Authors: Mast Austin R. , Jones Eric H. , Havery Shawn P.
Published: March 2005

Banksia (80 spp.; Proteaceae) has undergone extensive speciation and adaptive radiation on the island continent of Australia. Its members range from prostrate shrubs in the dry, infertile sandplains to 25 m tall trees in the loams of river margins, and they display striking variation in their fire survival strategies and floral and foliar morphologies. We examine the weight of both previously published (most trnL intron, trnL/F spacer, and rpl16 intron data) and new (matK, atpB, and waxy data, as well as most ITS data) DNA sequence evidence for the paraphyly of Banksia with respect to a monophyletic Dryandra (93 spp.). The nuclear waxy gene appears to be at two loci in the Proteaceae, and sequences presumably from the same locus resolve Banksia as paraphyletic with respect to Dryandra. The waxy and combined chloroplast DNA (cpDNA) data reject the monophyly of Banksia at a threshold of P = 0.05 using the winning sites and Kishino–Hasegawa tests. We consider this result and the repeated placement of Dryandra in the same clade (/Cryptostomata) of Banksia with each separate analysis of the DNA datasets (cpDNA, ITS, and waxy), to be strong molecular support for the paraphyly of Banksia with respect to Dryandra. The morphological synapomorphy of beaked follicles for /Cryptostomata (including Dryandra) reinforces this conclusion. We argue that realignment of taxa to produce one or more monophyletic genera is best attained by moving the taxa of Dryandra to Banksia. This would produce an easily recognised genus Banksia with four morphological synapomorphies. It would also probably confer some of the research attention garnered by the adaptive radiation of Banksia to the under-studied taxa of Dryandra, for Dryandra makes the radiation of Banksia even more remarkable.
Antigenic variation inPlasmodium falciparumis associated with movement ofvarloci between subnuclear locations
Authors: Ralph Stuart A. , Scheidig-Benatar Christine , Scherf Artur
Published: March 2005

Much of the success ofPlasmodium falciparumin establishing persistent infections is attributed to immune evasion through antigenic variation. This process involves periodically exchanging variants of the major surface antigen PfEMP1, a protein also responsible for parasite cytoadherence. PfEMP1 is encoded by genes of the 60-membervarfamily, located at subtelomeric and internal chromosome loci. The active or silenced state ofvargenes is heritable, and its control by nonsequence information remains puzzling. Using FISH analysis, we demonstrate that both internal and subtelomericvargenes are positioned at the nuclear periphery in their repressed state. Upon activation, the samevargenes are still found in the periphery, indicating that this zone can be transcriptionally competent, rather than uniformly silenced. However, activation of avargene is linked with altered positioning at the nuclear periphery, with subtelomericvarloci exiting chromosome end clusters and being relocated to distinct nuclear sites. Serial sectioning of parasite nuclei reveals areas of both condensed and noncondensed chromatin at the nuclear periphery. Our results demonstrate that regulation of antigenic variation is associated with subnuclear position effects and point to the existence of transcriptionally permissive perinuclear zones forvargenes.
Homology-dependent methylation in primate repetitive DNA
Authors: Meunier Julien , Khelifi Adel , Navratil Vincent , Duret Laurent
Published: March 2005

In mammals, several studies have suggested that levels of methylation are higher in repetitive DNA than in nonrepetitive DNA, possibly reflecting a genome-wide defense mechanism against deleterious effects associated with transposable elements (TEs). To analyze the determinants of methylation patterns in primate repetitive DNA, we took advantage of the fact that the methylation rate in the germ line is reflected by the transition rate at CpG sites. We assessed the variability of CpG substitution rates in nonrepetitive DNA and in various TE and retropseudogene families. We show that, unlike other substitution rates, the rate of transition at CpG sites is significantly (37%) higher in repetitive DNA than in nonrepetitive DNA. Moreover, this rate of CpG transition varies according to the number of repeats, their length, and their level of divergence from the ancestral sequence (up to 2.7 times higher in long, lowly divergent TEs compared with unique sequences). This observation strongly suggests the existence of a homology-dependent methylation (HDM) mechanism in mammalian genomes. We propose that HDM is a direct consequence of interfering RNA-induced transcriptional gene silencing.
Genomic characterization reveals a simple histone H4 acetylation code
Authors: Dion Michael F. , Altschuler Steven J. , Wu Lani F. , Rando Oliver J.
Published: March 2005

The histone code hypothesis holds that covalent posttranslational modifications of histone tails are interpreted by the cell to yield a rich combinatorial transcriptional output. This hypothesis has been the subject of active debate in the literature. Here, we investigated the combinatorial complexity of the acetylation code at the four lysine residues of the histone H4 tail in budding yeast. We constructed yeast strains carrying all 15 possible combinations of mutations among lysines 5, 8, 12, and 16 to arginine in the histone H4 tail, mimicking positively charged, unacetylated lysine states, and characterized the resulting genome-wide changes in gene expression by using DNA microarrays. Only the lysine 16 mutation had specific transcriptional consequences independent of the mutational state of the other lysines (affecting ≈100 genes). In contrast, for lysines 5, 8, and 12, expression changes were due to nonspecific, cumulative effects seen as increased transcription correlating with an increase in the total number of mutations (affecting ≈1,200 genes). Thus, acetylation of histone H4 is interpreted by two mechanisms: a specific mechanism for lysine 16 and a nonspecific, cumulative mechanism for lysines 5, 8, and 12.
Generalized Bienenstock–Cooper–Munro rule for spiking neurons that maximizes information transmission
Authors: Toyoizumi Taro , Pfister Jean-Pascal , Aihara Kazuyuki , Gerstner Wulfram
Published: March 2005

Maximization of information transmission by a spiking-neuron model predicts changes of synaptic connections that depend on timing of pre- and postsynaptic spikes and on the postsynaptic membrane potential. Under the assumption of Poisson firing statistics, the synaptic update rule exhibits all of the features of the Bienenstock–Cooper–Munro rule, in particular, regimes of synaptic potentiation and depression separated by a sliding threshold. Moreover, the learning rule is also applicable to the more realistic case of neuron models with refractoriness, and is sensitive to correlations between input spikes, even in the absence of presynaptic rate modulation. The learning rule is found by maximizing the mutual information between presynaptic and postsynaptic spike trains under the constraint that the postsynaptic firing rate stays close to some target firing rate. An interpretation of the synaptic update rule in terms of homeostatic synaptic processes and spike-timing-dependent plasticity is discussed.
Targeting of herpesvirus capsid transport in axons is coupled to association with specific sets of tegument proteins
Authors: Luxton G. W. Gant , Haverlock Sarah , Coller Kelly Elizabeth , Antinone Sarah Elizabeth , Pincetic Andrew , Smith Gregory Allan
Published: March 2005

The capsids of neurotropic herpesviruses have the remarkable ability to move in specific directions within axons. By modulating bidirectional capsid transport to favor either retrograde (minus-end) or anterograde (plus-end) motion, these viruses travel to sensory ganglia or peripheral tissue at specific stages of infection. By using correlative motion analysis to simultaneously monitor the trafficking of distinct viral proteins in living neurons, we demonstrate that viral “tegument” proteins are complexed to capsids moving in axons. The removal of a subset of tegument proteins from capsids invariably preceded retrograde transport to the cell body in sensory ganglia, whereas addition of these proteins was coupled to anterograde transport of progeny capsids to the distal axon. Although capsid transport never occurred without associated tegument proteins, anterograde-specific tegument proteins were competent to travel to the distal axon independent of capsids. These findings are compatible with a model of viral bidirectional transport in which tegument proteins direct capsid traffic to specific intracellular locations during the infectious cycle.
Hydrogen peroxide generated extracellularly by receptor–ligand interaction facilitates cell signaling
Authors: DeYulia Garrett J. , Cárcamo Juan M. , Bórquez-Ojeda Oriana , Shelton Christopher C. , Golde David W.
Published: March 2005

Reactive oxygen species (ROS) are key components of postreceptor intracellular signaling pathways; however, the role of ROS in signal initiation is uncertain. We discovered that receptor–ligand interaction caused the generation of hydrogen peroxide (H
2
O
2
). Using members of the hematopoietin receptor superfamily, as well as EGF receptor, we show that H
2
O
2
is generated by specific receptor–ligand interaction in cells and in cell-free systems. With cognate ligand, the extracellular domain of the receptor was sufficient for H
2
O
2
generation. We also found that production of H
2
O
2
was diminished in a granulocyte–macrophage colony-stimulating factor receptor mutant unable to bind ligand. Exogenously added H
2
O
2
induced signaling in the absence of ligand, whereas catalase and a membrane-bound peroxiredoxin inhibited ligand-dependent signaling. Our results suggest that H
2
O
2
produced by receptor–ligand interaction is involved as a chemical mediator that facilitates cell signaling.
23S rRNA base pair 2057–2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A→G
Authors: Pfister Peter , Corti Natascia , Hobbie Sven , Bruell Christian , Zarivach Raz , Yonath Ada , Böttger Erik C.
Published: March 2005

The 23S rRNA A2058G alteration mediates macrolide, lincosamide, and streptogramin B resistance in the bacterial domain and determines the selectivity of macrolide antibiotics for eubacterial ribosomes, as opposed to eukaryotic ribosomes. However, this mutation is associated with a disparate resistance phenotype: It confers high-level resistance to ketolides in mycobacteria but only marginally affects ketolide susceptibility in streptococci. We used site-directed mutagenesis of nucleotides within domain V of 23S rRNA to study the molecular basis for this disparity. We show that mutational alteration of the polymorphic 2057–2611 base pair from A-U to G-C in isogenic mutants of
Mycobacterium smegmatis
significantly affects susceptibility to ketolides but does not influence susceptibility to other macrolide antibiotics. In addition, we provide evidence that the 2057–2611 polymorphism determines the fitness cost of the 23S rRNA A2058G resistance mutation. Supported by structural analysis, our results indicate that polymorphic nucleotides mediate the disparate phenotype of genotypically identical resistance mutations and provide an explanation for the large species differences in the epidemiology of defined drug resistance mutations.
Relationship between follicle size at insemination and pregnancy success
Authors: Perry George A. , Smith Michael F. , Lucy Matthew C. , Green Jonathan A. , Parks Tina E. , MacNeil Michael D. , Roberts Andrew J. , Geary Thomas W.
Published: March 2005

Administration of gonadotropin-releasing hormone (GnRH) induces a surge of luteinizing hormone and ovulation in a variety of species, including human beings. Our objectives were to determine the effect of follicle size at the time of ovulation on corpus luteum function and establishment and maintenance of pregnancy in cows in which ovulation was either spontaneous or induced with GnRH. GnRH-induced ovulation of follicles ≲11 mm in diameter resulted in decreased pregnancy rates and increased late embryonic mortality. This decrease in fertility was associated with lower circulating concentrations of estradiol on the day of insemination, a decreased rate of increase in progesterone after insemination, and, ultimately, decreased circulating concentrations of progesterone. In contrast, ovulatory follicle size had no apparent effect on fertility when ovulation occurred spontaneously. Follicles undergoing spontaneous ovulation do so at a wide range of sizes when they are physiologically mature. Therefore, administration of GnRH to induce ovulation likely initiates a preovulatory gonadotropin surge before some dominant follicles attain physiological maturity. GnRH-induced ovulation of follicles that are physiologically immature has a negative impact on pregnancy rates and late embryonic/fetal survival. These observations in cattle may have implications for assisted reproductive procedures in human beings.
A role for CCR4 in development of mature circulating cutaneous T helper memory cell populations
Authors: Baekkevold Espen S. , Wurbel Marc-André , Kivisäkk Pia , Wain Clare M. , Power Christine A. , Haraldsen Guttorm , Campbell James J.
Published: March 2005

Expression of the chemokine receptor CCR4 is strongly associated with trafficking of specialized cutaneous memory T helper (Th) lymphocytes to the skin. However, it is unknown whether CCR4 itself participates in the development of cutaneous Th populations. We have addressed this issue via competitive bone marrow (BM) reconstitution assays; equal numbers of BM cells from CCR4+/+ and CCR4−/− donors were allowed to develop side-by-side within RAG-1−/− hosts. Cells from both donor types developed equally well into B cells, naive CD8 T cells, naive CD4 T cells, interferon-γ+ Th1 cells, and interleukin-4+ Th2 cells. In marked contrast, circulating cutaneous memory Th cells (i.e., E-selectin ligand+ [E-lig+]) were more than fourfold more likely to be derived from CCR4+/+ donors than from CCR4−/− donors. Most of this effect resides within the CD103+ subset of the E-lig+ Th population, in which donor CCR4+/+ cells can outnumber CCR4−/− cells by >12-fold. No similar effect was observed for α4β7+ intestinal memory Th cells or CD103+/E-lig− Th cells. We conclude that CCR4 expression provides a competitive advantage to cutaneous Th cells, either by participating in their development from naive Th cells, or by preferentially maintaining them within the memory population over time.
Protection from cytomegalovirus after transplantation is correlated with immediate early 1–specific CD8 T cells
Authors: Bunde Torsten , Kirchner Alexander , Hoffmeister Bodo , Habedank Dirk , Hetzer Roland , Cherepnev Georgy , Proesch Susanna , Reinke Petra , Volk Hans-Dieter , Lehmkuhl Hans , Kern Florian
Published: March 2005

T cells are crucial for the control of cytomegalovirus (CMV) in infected individuals. Although CMV-specific T cells can be quantified by various methods, clear correlates of protection from CMV disease have not been defined. However, responses to the pp65 protein are believed to play an important role. Here, the proportions of interferon γ–producing T cells following ex vivo activation with pools of overlapping peptides representing the pp65 and immediate early (IE)-1 proteins were determined at multiple time points and related to the development of CMV disease in 27 heart and lung transplant recipients. Frequencies of IE-1–specific CD8 T cells above 0.2 and 0.4% at day 0 and 2 wk, respectively, or 0.4% at any time during the first months discriminated patients who did not develop CMV disease from patients at risk, 50–60% of whom developed CMV disease. No similar distinction between risk groups was possible based on pp65-specific CD8 or CD4 T cell responses. Remarkably, CMV disease developed exclusively in patients with a dominant pp65-specific CD8 T cell response. In conclusion, high frequencies of IE-1 but not pp65-specific CD8 T cells correlate with protection from CMV disease. These results have important implications for monitoring T cell responses, adoptive cell therapy, and vaccine design.
The nuclear factor HMGB1 mediates hepatic injury after murine liver ischemia-reperfusion
Authors: Tsung Allan , Sahai Rohit , Tanaka Hiroyuki , Nakao Atsunori , Fink Mitchell P. , Lotze Michael T. , Yang Huan , Li Jianhua , Tracey Kevin J. , Geller David A. , Billiar Timothy R.
Published: March 2005

High-mobility group box 1 (HMGB1) is a nuclear factor that is released extracellularly as a late mediator of lethality in sepsis as well as after necrotic, but not apoptotic, death. Here we demonstrate that in contrast to the delayed role of HMGB1 in the systemic inflammation of sepsis, HMGB1 acts as an early mediator of inflammation and organ damage in hepatic ischemia reperfusion (I/R) injury. HMGB1 levels were increased during liver I/R as early as 1 h after reperfusion and then increased in a time-dependent manner up to 24 h. Inhibition of HMGB1 activity with neutralizing antibody significantly decreased liver damage after I/R, whereas administration of recombinant HMGB1 worsened I/R injury. Treatment with neutralizing antibody was associated with less phosphorylation of c-Jun NH2-terminal kinase and higher nuclear factor–κB DNA binding in the liver after I/R. Toll-like receptor 4 (TLR4)-defective (C3H/Hej) mice exhibited less damage in the hepatic I/R model than did wild-type (C3H/HeOuj) mice. Anti-HMGB1 antibody failed to provide protection in C3H/Hej mice, but successfully reduced damage in C3H/Ouj mice. Together, these results demonstrate that HMGB1 is an early mediator of injury and inflammation in liver I/R and implicates TLR4 as one of the receptors that is involved in the process.
More Telltale Signs: What Attention to Representation Reveals about Scientific Explanation
Authors: Woody Andrea I.
Published: March 2005

This essay explores the connection between representation and explanation in the sciences. I suggest that scientific representation schemes be viewed as pragmatic tools for acquiring the sort of articulated awareness that is the hallmark of nontrivial knowledge. Crystal field theory in chemistry illustrates this perspective. Certain representations achieve the status of being paradigmatically explanatory, thereby shaping models of intelligibility. In turn, these explanatory preferences serve largely to define and differentiate disciplinary communities by implicitly endorsing particular epistemic aims and values. In this way, the pragmatic nature of explanatory discourse effectively grants its intellectual utility.
Bridging the Gap between Human Kinds and Biological Kinds
Authors: Ereshefsky Marc
Published: March 2005

Many writers claim that human kinds are significantly different from biological and natural kinds. Some suggest that humans kinds are unique because social structures are essential for the etiology of human kinds. Others argue that human cultural evolution is decidedly different from other forms of evolution. In this paper I suggest that the gulf between humans and our biological relatives is not as wide as some argue. There is a taxonomic difference between human and nonhuman organisms, but such factors as social structure and cultural evolution do not distinguish us from many other organisms.
Causation and Misconnections
Authors: Dowe Phil
Published: March 2005

In this paper I show how the conserved quantity theory, or more generally the process theory of Wesley Salmon and myself, provides a sufficient condition in an analysis of causation. To do so I will show how it handles the problem of alleged ‘misconnections’. I show what the conserved quantity theory says about such cases, and why intuitions are not to be taken as sacrosanct.
Idealization and Formalism in Bohr's Approach to Quantum Theory
Authors: Tanona Scott
Published: March 2005

I reinterpret Bohr's attitude towards quantum mechanical formalism and its empirical content, based on his understanding of the correspondence principle and its approximate applicability. I suggest that Bohr understood complementarity as a limitation imposed by the commutation relations upon the applicability of the idealizations which had grounded the use of the correspondence principle. By discussing this interpretation against the contemporary background of discussions regarding “naïve realism” about operators (as observables), I suggest that a Bohrian view on the empirical content of quantum mechanical operators may provide a middle ground between complete contextualism and an untenable realism about quantum properties.
Laws and Statistical Mechanics
Authors: Winsberg Eric
Published: March 2005

This paper explores some connections between competing conceptions of scientific laws on the one hand, and a problem in the foundations of statistical mechanics on the other. I examine two proposals for understanding the time asymmetry of thermodynamic phenomenal: David Albert's recent proposal and a proposal that I outline based on Hans Reichenbach's “branch systems”. I sketch an argument against the former, and mount a defense of the latter by showing how to accommodate statistical mechanics to recent developments in the philosophy of scientific laws.
Manipulation and the Causal Markov Condition
Authors: Hausman Daniel , Woodward James
Published: March 2005

This paper explores the relationship between a manipulability conception of causation and the causal Markov condition (CM). We argue that violations of CM also violate widely shared expectations—implicit in the manipulability conception—having to do with the absence of spontaneous correlations. They also violate expectations concerning the connection between independence or dependence relationships in the presence and absence of interventions.
On Thought Experiments: Is There More to the Argument?
Authors: Norton John D.
Published: March 2005

Thought experiments in science are merely picturesque argumentation. I support this view in various ways, including the claim that it follows from the fact that thought experiments can err but can still be used reliably. The view is defended against alternatives proposed by my cosymposiasts.
Robert Boyle and the Masculine Methods of Science
Authors: Sargent Rose-Mary
Published: March 2005

In her recent case study, Elizabeth Potter attempts to show how Boyle's experimental method was biased by gender considerations. Part of her argument focuses on the combination of the “invisibility” of women in Boyle's published work together with his unpublished comments on female chastity, and part concerns Boyle's rejection of the animistic explanation of his air pump experiments by Francis Line. I argue that the historical and biographical elements of the case make Potter's arguments questionable. In addition, I address whether and how such historical cases can shed light on current debates about gender issues and argue that Boyle's methodological writings could be used to better advantage in the feminist cause.
Why Gender Is a Relevant Factor in the Social Epistemology of Scientific Inquiry
Authors: Rolin Kristina
Published: March 2005

In recent years, feminist philosophy of science has been subjected to criticism. The debate has focused on the implications of the underdetermination thesis for accounts of the role of social values in scientific reasoning. My aim here is to offer a different approach. I suggest that feminist philosophers of science contribute to our understanding of science by (1) producing gender-sensitive analyses of the social dimensions of scientific inquiry and (2) examining the relevance of these analyses for normative issues in philosophy of science.
Dissociable Realization and Kind Splitting
Authors: Craver Carl F.
Published: March 2005

It is a common assumption in contemporary cognitive neuroscience that discovering a putative realized kind to be dissociably realized (i.e., to be realized in each instance by two or more distinct realizers) mandates splitting that kind. Here I explore some limits on this inference using two deceptively similar examples: the dissociation of declarative and procedural memory and Ramachandran's argument that the self is an illusion.
Mechanism and Explanation in Cognitive Neuroscience
Authors: Eckardt Barbara Von , Poland Jeffrey S.
Published: March 2005

The aim of this paper is to examine the usefulness of the Machamer, Darden, and Craver (2000) mechanism approach to gaining an understanding of explanation in cognitive neuroscience. We argue that although the mechanism approach can capture many aspects of explanation in cognitive neuroscience, it cannot capture everything. In particular, it cannot completely capture all aspects of the content and significance of mental representations or the evaluative features constitutive of psychopathology.
Has Daltonian Atomism Provided Chemistry with Any Explanations?
Authors: Needham Paul
Published: March 2005

Philosophers frequently cite Dalton's chemical atomism, and its nineteenth century developments, as a prime example of inference to the best explanation. This was a controversial issue in its time. But the critics are dismissed as positivist-inspired antirealists with no interest in explanation. Is this a reasonable assessment?
The Physicists, the Chemists, and the Pragmatics of Explanation
Authors: Hendry Robin Findlay
Published: March 2005

In this paper I investigate two views of theoretical explanation in quantum chemistry, advocated by John Clarke Slater and Charles Coulson. Slater argued for quantum-mechanical rigor, and the primacy of fundamental principles in models of chemical bonding. Coulson emphasized systematic explanatory power within chemistry, and continuity with existing chemical explanations. I relate these views to the epistemic contexts of their disciplines.
Explanation, Unification, and What Chemistry Gets from Causation
Authors: Stemwedel Janet D.
Published: March 2005

I consider a way the concept of causation could be excised from chemical practice, suggested by Kitcher's view that causes are just a subset of unifying patterns which play a particular psychological role for us. Kitcherian chemistry is at first blush well equipped to handle explanatory tasks. However, it would force chemists to accept certain unifying patterns as explanatory, which they do not think are at all explanatory. This might head off some descriptive lines of enquiry and damage prospects for the identification of potentially larger-scale explanations. More important than this, to chemists, it could put them off from finding the explanatory patterns that are true—true because they get at the real structure of the chemical phenomena in the world.
David Lewis's Humean Theory of Objective Chance
Authors: Loewer Barry
Published: March 2005

The most important theories in fundamental physics, quantum mechanics and statistical mechanics, posit objective probabilities or chances. As important as chance is there is little agreement about what it is. The usual “interpretations of probability” give very different accounts of chance and there is disagreement concerning which, if any, is capable of accounting for its role in physics. David Lewis has contributed enormously to improving this situation. In his classic paper “A Subjectivist's Guide to Objective Chance” he described a framework for representing single case objective chances, showed how they are connected to subjective credences, and sketched a novel account what they are within his Humean account of scientific laws. Here I will describe these contributions and add a little to them.
Control of Ste6 Recycling by Ubiquitination in the Early Endocytic Pathway in Yeast
Authors: Krsmanović Tamara , Pawelec Agnes , Sydor Tobias , Kölling Ralf
Published: March 2005

We present evidence that ubiquitination controls sorting of the ABC-transporter Ste6 in the early endocytic pathway. The intracellular distribution of Ste6 variants with reduced ubiquitination was examined. In contrast to wild-type Ste6, which was mainly localized to internal structures, these variants accumulated at the cell surface in a polar manner. When endocytic recycling was blocked by Ypt6 inactivation, the ubiquitination deficient variants were trapped inside the cell. This indicates that the polar distribution is maintained dynamically through endocytic recycling and localized exocytosis (“kinetic polarization”). Ste6 does not appear to recycle through late endosomes, because recycling was not blocked in class E vps (vacuolar protein sorting) mutants (Δvps4, Δvps27), which are affected in late endosome function and in the retromer mutant Δvps35. Instead, recycling was partially affected in the sorting nexin mutant Δsnx4, which serves as an indication that Ste6 recycles through early endosomes. Enhanced recycling of wild-type Ste6 was observed in class D vps mutants (Δpep12, Δvps8, and Δvps21). The identification of putative recycling signals in Ste6 suggests that recycling is a signal-mediated process. Endocytic recycling and localized exocytosis could be important for Ste6 polarization during the mating process.
Parasite-mediated heterozygote advantage in an outbred songbird population
Authors: MacDougall-Shackleton Elizabeth A , Derryberry Elizabeth P , Foufopoulos Johannes , Dobson Andrew P , Hahn Thomas P
Published: March 2005

Coevolution with parasites is thought to maintain genetic diversity in host populations. However, while there are sound theoretical reasons to expect heterozygosity and parasite resistance to be related, this pattern has generally been shown only in inbred laboratory and island populations. This leaves doubt as to whether parasite-mediated selection for genetic diversity is in fact a general process. Here we show that haematozoan parasite load is linked to two complementary measures of microsatellite variability, in an outbred population of mountain white-crowned sparrows (Zonotrichia leucophrys oriantha) for which we know that parasites reduce fitness. Moreover, each of the genetic measures predicts a subtly different aspect of parasitism. Microsatellite heterozygosity is related to an individual's risk of parasitism, and meand2(a broader, more long-term measure of parental relatedness) to the severity of infection among parasitized individuals.
Severe inbreeding depression in a wild wolfCanis lupuspopulation
Authors: Liberg Olof , Andrén Henrik , Pedersen Hans-Christian , Sand Håkan , Sejberg Douglas , Wabakken Petter , Åkesson Mikael , Bensch Staffan
Published: March 2005

The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983–2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficientFvaried between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39,p<0.001). This inbreeding depression was recalculated to match standard estimates of lethal equivalents (2B), corresponding to 6.04 (2.58–9.48, 95% CI) litter-size-reducing equivalents in this wolf population.
Muscle directly meets the vast power demands in agile lizards
Authors: Curtin Nancy A , Woledge Roger C , Aerts Peter
Published: March 2005

Level locomotion in small, agile lizards is characterized by intermittent bursts of fast running. These require very large accelerations, often reaching several timesg. The power input required to increase kinetic energy is calculated to be as high as 214 W kg−1muscle (±20 W kg−1s.e.; averaged over the complete locomotor cycle) and 952 W kg−1muscle (±89 W kg−1s.e.; instantaneous peak power).In vitromuscle experiments prove that these exceptional power requirements can be met directly by the lizard's muscle fibres alone; there is no need for mechanical power amplifying mechanisms.
Cognitive Function in Preschool Children after Epilepsy Surgery: Rationale for Early Intervention
Authors: Freitag Hedwig , Tuxhorn Ingrid
Published: March 2005

Summary: Purpose:The detrimental effect of frequent early seizures on the cognitive potential of children is a significant clinical issue. Epilepsy surgery in childhood offers a good prognosis for seizure control and improved developmental outcome. We studied the postoperative outcome and the developmental velocity after surgery and analyzed risk factors for developmental delay in 50 consecutive preschool children treated surgically for severe epilepsy at ages 3 to 7 years.

Methods:Pre‐ and postoperative developmental quotients (DQs) were analyzed with analysis of variance; stepwise linear regressions were performed on preoperative DQs and on a difference score between post‐ and preoperative DQs to determine risk factors for preoperative development and factors influencing postoperative development.

Results:Of the 50 patients, 70% were retarded, with IQ < 70; 16% were of average intelligence, with IQ ranging from 85 to 115. Age at seizure onset and extent of lesion were predictive variables for preoperative cognitive development. Six to 12 months after surgery (early postoperative phase), 66% were seizure free (Engel outcome class I), 26% had substantial to worthwhile seizure reduction (classes II and III), and 8% were unchanged (class IV). Forty‐one (82%) children showed stable velocity of development; three children showed gains of ≥15 IQ points; three had developmental decline (loss of ≥10 IQ points), which was transient in two children; and three children moved from not assessable to assessable. At last follow‐up (6 months to 10 years after surgery), 11 children showed IQ/DQ gains of ≥15 IQ points. Gains in IQ were observed only in seizure‐free children and were stable over time. Shorter duration of epilepsy was significantly associated with a postoperative increase in DQ.

Conclusions:(a) Substantial global mental delay is common in young children treated for epilepsy with surgery; (b) In most patients, postoperative development proceeded at a stable velocity; (c) Catch‐up development may occur but only in seizure‐free patients; (d) Substantial cognitive losses were noted in only one child. and (e) Early seizure control stabilized developmental velocity in this patient cohort.
Correlation of Severity of FDG‐PET Hypometabolism and Interictal Regional Delta Slowing in Temporal Lobe Epilepsy
Authors: Altay Ebru Erbayat , Fessler A. James , Gallagher Martin , Attarian Hrayr P. , Dehdashti Farrokh , Vahle Victoria J. , Ojemann Jeffrey , Dowling Joshua L. , Gilliam Frank G.
Published: March 2005

Summary:  Purpose: We investigated the association of severity of hypometabolism detected by positron emission tomography (PET) with [18F]fluorodeoxyglucose (FDG) and persistence of interictal EEG focal slowing in patients with refractory temporal lobe epilepsy.

Methods: Eighty temporal lobes of 40 consecutive patients with intractable temporal lobe epilepsy (mean age, 43.5 years) were studied. All patients underwent video‐EEG monitoring, magnetic resonance imaging (MRI), and FDG‐PET. Patients with either normal MRI or with unilateral mesial temporal sclerosis, but no other structural abnormality, were included. Interictal EEG delta slowing was graded as none, infrequent (one episode or less/hour), intermediate (more than one episode/hour), or continuous. PET hypometabolism was graded as none, mild, moderate, or severe.

Results: The severity of temporal lobe hypometabolism with PET was significantly correlated with the amount of delta activity in the interictal EEG, independent of MRI findings (Spearman r = 0.46; p < 0.0005).

Conclusions: This observation suggests related underlying pathophysiologic mechanisms for metabolic and electrical dysfunction in temporal lobe epilepsy.
Limbic System Abnormalities Associated with Ammon's Horn Sclerosis Do Not Alter Seizure Outcome after Amygdalohippocampectomy
Authors: Urbach Horst , Siebenhaar Guido , Koenig Roy , Von Oertzen Joachim , Scorzin Jasmin , Kurthen Martin , Schild Hans H.
Published: March 2005

Summary: Purpose:To evaluate whether limbic system abnormalities associated with Ammon's horn sclerosis alter seizure outcome after selective amgydalohippocampectomy.

Methods:In 45 patients with unilateral mesial temporal lobe epilepsy, histologically proven Ammon's horn sclerosis, and uneventful postoperative course, volumes of the hippocampus, hemisphere, amygdala, entorhinal cortex, mamillary body, and fornix were measured by using a T1‐weighted 3‐D gradient‐echo sequence with roughly isotropic (1.17 × 1.17 × 1‐mm) voxels. In addition, signal intensity of the hippocampus and of the temporal lobe white matter was visually assessed and graded on a coronal T2‐weighted fast‐spin‐echo sequence with 2‐mm‐thick slices. Volumetric measurements and visual analysis were compared between seizure‐free and non–seizure‐free patients examined 12 months after surgery.

Results:Hippocampal, hemispheric, entorhinal cortex, mamillary body, and fornix volumes, but not amygdalar volumes, were significantly smaller on the operated‐on than on the non–operated‐on side and significantly smaller in patients compared with controls. No volume differences of the hippocampus, hemisphere, amygdala, entorhinal cortex, mamillary body, and fornix existed between seizure‐free (Engel class IA) and non–seizure‐free patients (Engel class IB‐IV). Increased temporal lobe white matter signal was observed in 15 patients but did not alter seizure outcome.

Conclusions:Limbic system abnormalities are not a surrogate marker to predict postsurgical seizure outcome in patients with unilateral Ammon's horn sclerosis.
Hippocampal Melatonin Receptors Modulate Seizure Threshold
Authors: Stewart Lee S. , Leung L. Stan
Published: March 2005

Summary:  Purpose: The pineal hormone melatonin has been shown to enhance hippocampal excitability. We therefore investigated whether inactivation of hippocampal melatonin receptors affects behavioral seizures.

Methods: Intrahippocampal infusions were performed in rats to study the effect of different melatonin receptor antagonists on behavioral activity, EEG, and seizure susceptibility. Experiments were conducted at 2 times of the day that coincided with the peak and trough of the daily melatonin rhythm.

Results: Local infusion of the Mel1b receptor antagonist 4‐phenyl‐2‐propionamidotetralin (4‐P‐PDOT) into the hippocampus, but not the overlying neocortex, significantly increased seizure latency and in some cases provided complete protection against seizure development. In addition, 4‐P‐PDOT suppressed open field activity and hippocampal EEG amplitude. The mixed Mel1a/Mel1b receptor antagonist luzindole also increased seizure latency but to a lesser degree than 4‐P‐PDOT. The behavioral effects of Mel1b receptor inhibition were comparable to those of the γ‐aminobutyric acid (GABA)A receptor agonist muscimol and were observed during the dark phase (2400–0200 h) but not the light phase (1200–1400 h) of the daily photocycle. The anticonvulsant effect of intrahippocampal infusion of 4P‐P‐DOT was blocked by coadministration of the GABAA antagonist bicuculline.

Conclusions: Our results suggest that nocturnal activation of hippocampal Mel1b receptors depresses GABAA receptor function in the hippocampus and enhances seizure susceptibility.