bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioluminescent response of individual dinoflagellate cells to hydrodynamic stress measured with millisecond resolution in a microfluidic device
Authors: Latz Michael I. , Bovard Michelle , VanDelinder Virginia , Segre Enrico , Rohr Jim , Groisman Alex 
Published: August 2008

SUMMARYDinoflagellate bioluminescence serves as a model system for examining mechanosensing by suspended motile unicellular organisms. The response latency, i.e. the delay time between the mechanical stimulus and luminescent response, provides information about the mechanotransduction and signaling process, and must be accurately known for dinoflagellate bioluminescence to be used as a flow visualization tool. This study used a novel microfluidic device to measure the response latency of a large number of individual dinoflagellates with a resolution of a few milliseconds. Suspended cells of several dinoflagellate species approximately 35 μm in diameter were directed through a 200 μm deep channel to a barrier with a 15 μm clearance impassable to the cells. Bioluminescence was stimulated when cells encountered the barrier and experienced an abrupt increase in hydrodynamic drag, and was imaged using high numerical aperture optics and a high-speed low-light video system. The average response latency for Lingulodinium polyedrum strain HJ was 15 ms (N&gt;300 cells) at the three highest flow rates tested, with a minimum latency of 12 ms. Cells produced multiple flashes with an interval as short as 5 ms between individual flashes,suggesting that repeat stimulation involved a subset of the entire intracellular signaling pathway. The mean response latency for the dinoflagellates Pyrodinium bahamense, Alexandrium monilatumand older and newer isolates of L. polyedrum ranged from 15 to 22 ms,similar to the latencies previously determined for larger dinoflagellates with different morphologies, possibly reflecting optimization of dinoflagellate bioluminescence as a rapid anti-predation behavior.
The movements of limb segments and joints during locomotion in African and Asian elephants
Authors: Ren Lei , Butler Melanie , Miller Charlotte , Paxton Heather , Schwerda Delf , Fischer Martin S. , Hutchinson John R. 
Published: August 2008

SUMMARYAs the largest extant terrestrial animals, elephants do not trot or gallop but can move smoothly to faster speeds without markedly changing their kinematics, yet with a shift from vaulting to bouncing kinetics. To understand this unusual mechanism, we quantified the forelimb and hindlimb motions of eight Asian elephants (Elephas maximus) and seven African elephants(Loxodonta africana). We used 240 Hz motion analysis (tracking 10 joint markers) to measure the flexion/extension angles and angular velocities of the limb segments and joints for 288 strides across an eightfold range of speeds (0.6–4.9 m s–1) and a sevenfold range of body mass (521–3684 kg). We show that the columnar limb orientation that elephants supposedly exemplify is an oversimplification – few segments or joints are extremely vertical during weight support (especially at faster speeds), and joint flexion during the swing phase is considerable. The`inflexible' ankle is shown to have potentially spring-like motion, unlike the highly flexible wrist, which ironically is more static during support. Elephants use approximately 31–77% of their maximal joint ranges of motion during rapid locomotion, with this fraction increasing distally in the limbs, a trend observed in some other running animals. All angular velocities decrease with increasing size, whereas smaller elephant limbs are not markedly more flexed than adults. We find no major quantitative differences between African and Asian elephant locomotion but show that elephant limb motions are more similar to those of smaller animals, including humans and horses, than commonly recognized. Such similarities have been obscured by the reliance on the term `columnar' to differentiate elephant limb posture from that of other animals. Our database will be helpful for identifying elephants with unusual limb movements, facilitating early recognition of musculoskeletal pathology.
Chemical and mechanical bioerosion of boring sponges from Mexican Pacific coral reefs
Authors: Nava Héctor , Carballo José Luis 
Published: August 2008

SUMMARYSpecies richness (S) and frequency of invasion (IF) by boring sponges on living colonies of Pocillopora spp. from National Park Isla Isabel(México, East Pacific Ocean) are presented. Twelve species belonging to the genera Aka, Cliona, Pione, Thoosa and Spheciospongia were found, and 56% of coral colonies were invaded by boring sponges, with Cliona vermifera Hancock 1867 being the most abundant species (30%). Carbonate dissolution rate and sediment production were quantified for C. vermifera and Cliona flavifodinaRützler 1974. Both species exhibited similar rates of calcium carbonate(CaCO3) dissolution (1.2±0.4 and 0.5±0.2 kg CaCO3 m–2 year–1, respectively,mean ± s.e.m.), and sediment production (3.3±0.6 and 4.6±0.5 kg CaCO3 m–2year–1), resulting in mean bioerosion rates of 4.5±0.9 and 5.1±0.5 kg CaCO3 m–2year–1, respectively. These bioerosion rates are close to previous records of coral calcification per unit of area, suggesting that sponge bioerosion alone can promote disequilibrium in the reef accretion/destruction ratio in localities that are heavily invaded by boring sponges. The proportion of dissolved material by C. vermifera and C. flavifodina (27 and 10.2%, respectively) confirms that chemical bioerosion plays an important role in sponge bioerosion and in the CaCO3 cycle in coral reefs.
Comparing memory-forming capabilities between laboratory-reared and wildLymnaea: learning in the wild, a heritable component of snail memory
Authors: Orr Michael V. , Hittel Karla , Lukowiak Ken 
Published: August 2008

SUMMARYWe set out to determine whether the ability to form long-term memory (LTM)is influenced by laboratory rearing. We investigated the ability of four populations of Lymnaea stagnalis to form LTM following operant conditioning both in the freely behaving animal and at the electrophysiological level in a neuron, RPeD1, which is a necessary site for LTM. We hypothesized that laboratory rearing results in a decreased ability to form LTM because rearing does not occur in an `enriched environment'. Of the four populations examined, two were collected in the wild and two were reared in the laboratory – specifically, (1) wild Dutch snails; (2) their laboratory-reared offspring; (3) wild Southern Alberta snails (Belly); and (4)their laboratory-reared offspring. We found that Belly snails had an enhanced capability of forming LTM compared with Dutch laboratory-reared snails. That is, the Belly snails, which are much darker in colour than laboratory-reared snails (i.e. blonds), were `smarter'. However, when we tested the offspring of Belly snails reared in the laboratory we found that these snails still had the enhanced ability to form LTM, even though they were now just as `blond' as their laboratory-reared Dutch cousins. Finally, we collected wild Dutch snails, which are also dark, and found that their ability to form LTM was not different to that of their laboratory-reared offspring. Thus, our hypothesis was not proved. Rather, we now hypothesize that there are strain differences between the Belly and Dutch snails, irrespective of whether they are reared in the wild or in the laboratory.
Quality Specifications for the Determination of Copper, Zinc, and Selenium in Human Serum or Plasma: Evaluation of an Approach Based on Biological and Analytical Variation
Authors: Arnaud Josiane , Weber Jean-Philippe , Weykamp Cas W , Parsons Patrick J , Angerer Jurgen , Mairiaux Eric , Mazarrasa Olav , Valkonen Sinikka , Menditto Antonio , Patriarca Marina , Taylor Andrew 
Published: August 2008

Abstract
Background: Trace element external quality assessment schemes monitor laboratory performance and provide a stimulus for improvement in accuracy. However, monitoring of participant performance varies according to the scheme and can lead to conflicting conclusions.
Methods: Quality specifications based on biological intra- and interindividual variability were calculated and compared to those currently used by various trace element external quality assessment schemes for plasma or serum copper, zinc, and selenium concentrations. For this purpose, we evaluated results reported by participating laboratories in different schemes, at key concentrations, using z scores.
Results: Minimal quality specifications developed from the biological intra- and interindividual variability were, for Cu, ±0.84 μmol/L or 12% of the assigned target concentration, whichever is greater; for Zn, ±1.20 μmol/L or 15% of the assigned target concentration, whichever is greater; and for Se, ±0.072 μmol/L or 12% of the assigned target concentration, whichever is greater. Reported performance of the participating laboratories depended on analyte, concentration, and the selected quality specification. In addition, the most commonly used methods for the determination of Cu, Zn, and Se may give different results.
Conclusions: The proposed minimal quality specifications based on biological variation are generally slightly less stringent than those currently in use, although they do not drastically change the performance evaluation in the different schemes. These specifications are a first step in the harmonization of practices among the schemes and remain to be evaluated.
Intraplatform Reproducibility and Technical Precision of Gene Expression Profiling in 4 Laboratories Investigating 160 Leukemia Samples: The DACH Study
Authors: Kohlmann Alexander , Haschke-Becher Elisabeth , Wimmer Barbara , Huber-Wechselberger Ariana , Meyer-Monard Sandrine , Huxol Heike , Siegler Uwe , Rossier Michel , Matthes Thomas , Rebsamen Michela , Chiappe Alberto , Diemand Adeline , Rauhut Sonja , Johnson Andrea , Liu Wei-min , Williams P Mickey , Wieczorek Lothar , Haferlach Torsten 
Published: August 2008

AbstractBackground: Gene expression profiling has the potential to offer consistent, objective diagnostic test results once a standardized protocol has been established. We investigated the robustness, precision, and reproducibility of microarray technology.Methods: One hundred sixty individual patient samples representing 11 subtypes of acute and chronic leukemias, myelodysplastic syndromes, and nonleukemia as a control group were centrally collected and diagnosed as part of the daily routine in the Munich Leukemia Laboratory. The custom AmpliChip Leukemia research microarray was used for technical analyses of quadruplicate mononuclear cell lysates in 4 different laboratories in Germany (D), Austria (A), and Switzerland (CH) (the DACH study).Results: Total-RNA preparations were successfully performed in 637 (99.5%) of 640 cases. Mean differences between pairs of laboratories in the total-RNA yield from the same sample ranged from 0.02 μg to 1.03 μg. Further processing produced 622 successful in vitro transcription reactions (97.6%); the mean differences between laboratories in the cRNA yield from the same sample ranged from 0.40 μg to 6.18 μg. After hybridization to microarrays, a mean of 47.6%, 46.5%, 46.2%, and 46.4% of probe sets were detected as present for the 4 laboratories, with mean signal-intensity scaling factors of 3.1, 3.7, 4.0, and 4.2, respectively. In unsupervised hierarchical cluster and principal component analyses, replicates from the same patient always clustered closely together, with no indications of any association between gene expression profiles due to different operators or laboratories.Conclusions: Microarray analysis can be performed with high interlaboratory reproducibility and with comparable quality and high technical precision across laboratories.
„Qualis artifex pereo” – Neros letzte Reise (“Qualis artifex pereo” – Nero's Last Journey)
Authors: Meier Mischa 
Published: August 2008

Zusammenfassung
Nero bleibt ein Rätsel. Der römische Kaiser (54–68 n. Chr.), der seine Mutter ermordete, der angeblich Rom in Brand gesteckt hat, der zum ersten Mal in größerem Stile Christen verfolgte, der als Wagenlenker, Dichter und Bühnenschauspieler öffentlich auftrat und sich schließlich einsam das Leben nehmen mußte, bereitet der Forschung noch immer erhebliche Probleme. In der vorliegenden Studie soll ein neuer Zugang zu diesem Princeps eröffnet werden: Ausgehend von seiner Griechenlandreise im Jahr 66/67 werden die Zeugnisse für das Wirken Neros mit den Rahmenbedingungen und Handlungsspielräumen eines Princeps der frühen römischen Kaiserzeit in Relation gesetzt. Dabei werden insbesondere die vielfach belächelten (allerdings durch archäologisches und numismatisches Material bestätigten) Hinweise in der antiken Historiographie auf Neros singuläres Selbstverständnis als Künstler konsequent ausgewertet und weitergedacht. Das Ergebnis zeigt einen Herrscher, der sich weniger als Princeps denn als Künstler definierte, der in dieser Rolle eine geradezu mythische Qualität erstrebt und die Umsetzung dieses Vorhabens letztlich nur deshalb nicht erreicht hat, weil er am Ende seiner Herrschaft nicht mehr imstande war, mit der zunehmenden Eigendynamik der Entwicklungen um ihn herum mitzuhalten.
Kleinstaaten in der Frühen Neuzeit: Konturen eines Forschungsfeldes (Small States in Early Modern Times: Contours of a Field of Research)
Authors: Schnettger Matthias 
Published: August 2008

Zusammenfassung
Der Beitrag regt zur Beschäftigung mit Kleinstaaten als einer Sonderform frühmoderner Staatlichkeit an, die bislang nicht im Fokus des wissenschaftlichen Interesses gestanden hat. Charakteristisch für frühneuzeitliche Kleinstaaten war neben einer geringen territorialen Ausdehnung und begrenzten Ressourcen eine reduzierte Souveränität: Die deutschen Reichsstände verfügten über die bloße Landeshoheit und waren Kaiser und Reich unterstellt, und auch die italienischen Kleinstaaten waren zumeist in das Reichs- oder das päpstliche Lehnssystem eingebunden. Ausgehend von diesen Grundüberlegungen fragt der Beitrag nach dem Verhältnis der Kleinen zu den Großen, nach Vernetzungen und Abgrenzungen der Kleinstaaten und beleuchtet die innenpolitische Perspektive. Damit erörtert er die Möglichkeit, unter Berücksichtigung der politik-, sozial- und kulturgeschichtlichen Dimension für einzelne Fallbeispiele zu einer Art „microhistoire totale” vorzustoßen, als ein neuer, intensivierter und europäisch vergleichender Zugang zur Geschichte frühmoderner Staatlichkeit.
Elevated free IGF2 levels in localized, early-stage breast cancer in women
Authors: Espelund Ulrick , Cold Søren , Frystyk Jan , Ørskov Hans , Flyvbjerg Allan 
Published: August 2008

ObjectiveEpidemiological studies imply an association between circulating IGF1 and breast cancer, whereas the role of IGF2, which also acts on the IGF1 receptor, is less settled. This study investigates the association between IGF2 and breast cancer in patients with localized disease.DesignThe participants were women with well-characterized, early stage, localized breast cancer (n=43) and matched healthy women (n=38), from whom fasting serum levels of IGF-related peptides were measured.ResultsIn patients, mean free IGF2 was increased (+57%, P<0.001), in spite of reduced total IGF2 levels (−12%, P=0.003) when compared with controls. Similar changes were seen in free IGF1 (+28%, P=0.004) and total IGF1 (−16% P=NS). Pro-IGF2 and IGF-binding protein 1 (IGFBP1) were unchanged. IGFBP2 was reduced by 22% in the patients (P=0.004). The patients showed reduced IGFBP3 protease activity and accordingly increased levels of intact IGFBP3, whereas total IGFBP3 was unchanged.ConclusionWomen with localized, early-stage breast cancer show elevated circulating free IGF1 and IGF2, reduced total IGF2 and alterations in IGFBPs. The changes observed despite minimal cancer disease suggest a role for the circulating IGF system in the progression of breast cancer in women.
Hitchhiking Both Ways: Effect of Two Interfering Selective Sweeps on Linked Neutral Variation
Authors: Chevin Luis-Miguel , Billiard Sylvain , Hospital Frédéric 
Published: August 2008

Abstract
The neutral polymorphism pattern in the vicinity of a selective sweep can be altered by both stochastic and deterministic factors. Here, we focus on the impact of another selective sweep in the region of influence of a first one. We study the signature left on neutral polymorphism by positive selection at two closely linked loci, when both beneficial mutations reach fixation. We show that, depending on the timing of selective sweeps and on their selection coefficients, the two hitchhiking effects can interfere with each other, leading to less reduction in heterozygosity than a single selective sweep of the same magnitude and more importantly to an excess of intermediate-frequency variants relative to neutrality under some parameter values. This pattern can be sustained and potentially alter the detection of positive selection, including by provoking spurious detection of balancing selection. In situations where positive selection is suspected a priori at several closely linked loci, the polymorphism pattern in the region may also be informative about their selective histories.
The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome
Authors: Jiang Zhihua , Wu Xiao-Lin , Zhang Ming , Michal Jennifer J , Wright Raymond W 
Published: August 2008

Abstract
Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C ↔ T and A ↔ G transitions have reverse complementary neighborhood patterns and so do A ↔ C and G ↔ T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C ↔ T/A ↔ G and A ↔ C/G ↔ T, the true neighborhood patterns for A ↔ T and C ↔ G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C ↔ G, but increased for C ↔ T/A ↔ G, further for A ↔ C/G ↔ T, and the most for A ↔ T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A ↔ G and C ↔ T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for ∼20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.
Sister Chromatid Cohesion Role for CDC28-CDK in Saccharomyces cerevisiae
Authors: Brands Alex , Skibbens Robert V 
Published: August 2008

Abstract
High-fidelity chromosome segregation requires that the sister chromatids produced during S phase also become paired during S phase. Ctf7p (Eco1p) is required to establish sister chromatid pairing specifically during DNA replication. However, Ctf7p also becomes active during G2/M in response to DNA damage. Ctf7p is a phosphoprotein and an in vitro target of Cdc28p cyclin-dependent kinase (CDK), suggesting one possible mechanism for regulating the essential function of Ctf7p. Here, we report a novel synthetic lethal interaction between ctf7 and cdc28. However, neither elevated CDC28 levels nor CDC28 Cak1p-bypass alleles rescue ctf7 cell phenotypes. Moreover, cells expressing Ctf7p mutated at all full- and partial-consensus CDK-phosphorylation sites exhibit robust cell growth. These and other results reveal that Ctf7p regulation is more complicated than previously envisioned and suggest that CDK acts in sister chromatid cohesion parallel to Ctf7p reactions.
Spermatogonial Stem Cell Self-Renewal Requires OCT4, a Factor Downregulated During Retinoic Acid-Induced Differentiation
Authors: Dann Christina Tenenhaus , Alvarado Alma L. , Molyneux Laura A. , Denard Bray S. , Garbers David L. , Porteus Matthew H. 
Published: August 2008

Abstract
The long-term production of billions of spermatozoa relies on the regulated proliferation and differentiation of spermatogonial stem cells (SSCs). To date only a few factors are known to function in SSCs to provide this regulation. Octamer-4 (OCT4) plays a critical role in pluripotency and cell survival of embryonic stem cells and primordial germ cells; however, it is not known whether it plays a similar function in SSCs. Here, we show that OCT4 is required for SSC maintenance in culture and for colonization activity following cell transplantation, using lentiviral-mediated short hairpin RNA expression to knock down OCT4 in an in vitro model for SSCs (“germline stem” [GS] cells). Expression of promyelocytic leukemia zinc-finger (PLZF), a factor known to be required for SSC self-renewal, was not affected by OCT4 knockdown, suggesting that OCT4 does not function upstream of PLZF. In addition to developing a method to test specific gene function in GS cells, we demonstrate that retinoic acid (RA) triggers GS cells to shift to a differentiated, premeiotic state lacking OCT4 and PLZF expression and colonization activity. Our data support a model in which OCT4 and PLZF maintain SSCs in an undifferentiated state and RA triggers spermatogonial differentiation through the direct or indirect downregulation of OCT4 and PLZF. The current study has important implications for the future use of GS cells as an in vitro model for spermatogonial stem cell biology or as a source of embryonic stem-like cells.
Disclosure of potential conflicts of interest is found at the end of this article.