bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-Based Study Evaluating and Predicting the Probability of Death Resulting From Thyroid Cancer and Other Causes Among Patients With Thyroid Cancer
Authors: Yang Limin , Shen Weidong , Sakamoto Naoko 
Published: December 2012

Purpose The purpose of this study was to evaluate the probability of death for patients with thyroid cancer and construct a comprehensive nomogram based on a competing risks model to predict cumulative incidence of death resulting from thyroid cancer, other cancers, and non–cancer-related causes. Patients and Methods Patients diagnosed with thyroid cancer between 1988 and 2003 were selected for the study from the Surveillance, Epidemiology, and End Results program. We estimated probabilities of death resulting from thyroid cancer, other cancers, and noncancer causes and analyzed associations of patient and tumor characteristics with probability of death. A nomogram for predicting probability of death was built using a proportional subdistribution hazard competing risks model. Results The entire cohort comprised 29,225 patients with malignant thyroid cancer. Median duration of follow-up until censoring or death was 85 months (range, 0 to 239 months). Five-year probabilities of death resulting from thyroid cancer, other cancer, and noncancer causes were 1.9%, 0.8%, and 1.7%, respectively. Increasing age and tumor size, male sex, poorly differentiated carcinoma, lymph node involvement, and regional and metastatic disease were associated with increased cumulative incidence of death resulting from thyroid cancer. Conclusion A nomogram based on a competing risks model was developed for predicting the probability of death for patients with thyroid cancer. Performance of the model was excellent. This nomogram may be useful for patients and clinicians when predictions are needed.
NODAL and SHH dose-dependent double inhibition promotes an HPE-like phenotype in chick embryos
Authors: Mercier Sandra , David Véronique , Ratié Leslie , Gicquel Isabelle , Odent Sylvie , Dupé Valerié 
Published: December 2012

SummaryHoloprosencephaly (HPE) is a common congenital defect that results from failed or incomplete forebrain cleavage. HPE is characterized by a wide clinical spectrum with inter- and intrafamilial variability. This heterogeneity is not well understood and it has been suggested that HPE involves a combination of multiple gene mutations. In this model, several mutated alleles or modifying factors are presumed to act in synergy to cause and determine the severity of HPE. This could explain the various clinical phenotypes. Screening for HPE-associated genes in humans suggests the involvement of NODAL or SHH signaling or both. To test this multigenic hypothesis, we investigated the effects of chemical inhibition of these two main HPE signaling pathways in a chick embryo model. SB-505124, a selective inhibitor of transforming Growth factor-B type I receptors was used to inhibit the NODAL pathway. Cyclopamine was used to inhibit SHH pathway. We report that both inhibitors caused HPE-like defects that were dependent on the drug concentration and the developmental stage at the time of treatment. We also investigated double inhibition of NODAL and SHH pathways from the onset of gastrulation using subthreshold inhibitor concentrations: the inhibitors of the NODAL and SHH pathways, even at low concentration, acted synergistically to promote an HPE-like phenotype. These findings support the view that genetic heterogeneity is important in the etiology of HPE and may contribute to the phenotypic variability.
A patient-derived stem cell model of hereditary spastic paraplegia with SPAST mutations
Authors: Abrahamsen Greger , Fan Yongjun , Matigian Nicholas , Wali Gautam , Bellette Bernadette , Sutharsan Ratneswary , Raju Jyothy , Wood Stephen A. , Veivers David , Sue Carolyn M. , Mackay-Sim Alan 
Published: December 2012

Summary
Hereditary spastic paraplegia (HSP) leads to progressive gait disturbances with lower limb muscle weakness and spasticity. Mutations in SPAST are a major cause of adult-onset, autosomal-dominant HSP. Spastin, the protein encoded by SPAST, is a microtubule-severing protein that is enriched in the distal axon of corticospinal motor neurons which degenerate in HSP patients. Animal and cell models have identified functions of spastin and mutated spastin but these models lack the gene dosage, mutation variability and genetic background that characterize patients with the disease. In this study, this genetic variability is encompassed by comparing neural progenitor cells derived from biopsies of the olfactory mucosa from healthy controls with similar cells from HSP patients with SPAST mutations, in order to identify cell functions altered in HSP. Patient-derived cells were similar to control-derived cells in proliferation and multiple metabolic functions but had major dysregulation of gene expression, with 57% of all mRNA transcripts affected, including many associated with microtubule dynamics. Compared to control cells, patient-derived cells had 50% spastin, 50% acetylated α-tubulin and 150% stathmin, a microtubule-destabilising enzyme. Patient-derived cells were smaller than control cells. They had altered intracellular distributions of peroxisomes and mitochondria and they had slower moving peroxisomes. These results suggest that patient-derived cells might compensate for reduced spastin, but their increased stathmin expression reduced stabilised microtubules and altered organelle trafficking. Sub-nanomolar concentrations of the microtubule-binding drugs, paclitaxel and vinblastine, increased acetylated α-tubulin levels in patient cells to control levels, indicating the utility of this cell model for screening other candidate compounds for drug therapies.
The repeatability of metabolic rate declines with time
Authors: White Craig R. , Schimpf Natalie G. , Cassey Phillip 
Published: December 2012

SummaryThe evolutionary causes of variation in metabolic rate within and among species are a topic of enduring interest. Since variation between individuals is the raw material on which natural selection acts, recent years have seen an increase in the number of studies that examine the consequences of inter-individual differences in metabolic rate for organismal performance. A minimum requirement for a trait to evolve is that it must differ consistently between individuals, and these differences must be heritable. The time constancy of a trait is assessed by estimating its repeatability, which represents the ratio of the between-individual component of phenotypic variance to total phenotypic variance. A previous meta-analysis of repeatability concluded that metabolic rate is, on average, repeatable. Here we expand on this earlier analysis by including extra data published in the intervening years and demonstrate that the repeatability of metabolic rate decreases as the interval between measurements increases.
The contribution of the lateral line to 'hearing' in fish
Authors: Higgs Dennis M. , Radford Craig A. 
Published: December 2012

Summary
In the underwater environment, sound propagates as both a pressure wave and as particle displacement, with particle displacement dominating close to the source (the nearfield). At the receptor level, both the fish ear and the neuromast hair cells act as displacement detectors and both are potentially stimulated by the particle motion component of sound sources, especially in the nearfield. A now common way to test 'hearing' in fish involves auditory evoked potentials (AEP), with recordings made from electrodes implanted near the auditory brainstem. These AEP recordings are typically conducted in enclosed acoustic environments with the fish well within the nearfield, especially for lower frequencies. We tested the contribution of neuromast hair cells to AEP by first testing intact goldfish (Carassius auratus), then ablating their neuromasts with streptomycin sulfate — disabling superficial and canal neuromasts — and retesting the same goldfish. We did a similar experiment where only the superficial neuromasts were physically ablated. At 100 and 200 Hz, there was a 10-15 dB increase in threshold after streptomycin treatment but no significant difference at higher frequencies. There was no difference in threshold in control fish or in fish that only had superficial neuromasts removed, indicating that the differential responses were driven by canal neuromasts. Taken together these results indicate that AEP results at lower frequencies should be interpreted as multimodal responses, rather than 'hearing'. The results also suggest that in natural situations both the ear and lateral line likely play an integrative role in detecting and localising many types of 'acoustic' stimuli.
Response of a free-flying songbird to an experimental shift of the light polarization pattern around sunset
Authors: Schmaljohann Heiko , Rautenberg Tobias , Muheim Rachel , Naef-Daenzer Beat , Bairlein Franz 
Published: December 2012

Summary
The magnetic field, the sun, the stars and the polarization pattern of visible light during twilight are important cues for orientation in nocturnally migrating songbirds. As these cues change with time and location on Earth, the polarization pattern was put forward as a likely key reference system calibrating the other compass systems. Whether this applies generally to migratory birds is, however, controversially discussed. We used an experimental approach in free-flying birds to study the role of polarization for their departure direction in autumn. Experimental birds experienced a 90° shift of the band of maximum polarization during sunset, whereas control-birds experienced the polarization pattern as under natural condition. Full view of the sunset cues near the horizon was provided during the cue conflict exposure. Here we show both the experimental and the control-birds being released after nautical twilight departed consistently towards south-southeast. Radio telemetry allowed tracking first 15 km of birds' way out, thus the intrinsic migration direction as chosen by the birds was measured. We found no recalibration of the magnetic compass after pre-exposure to a cue conflict between the natural magnetic field and the artificially shifted polarization pattern at sunset. The lacking difference in the departure direction of both groups may suggests that birds did not recalibrate any of the compass systems during the experiment. As free-flying migrants can use all available orientation cues after release, it remains unknown whether our birds might have used the magnetic and/or star compass to determine their departure direction.
A long life in the fast lane: positive association between peak metabolic rate and lifespan in a butterfly
Authors: Niitepõld Kristjan , Hanski Ilkka 
Published: December 2012

SummaryHigh peak metabolic may provide performance advantage, but it may also entail a physiological cost. A long-held assumption is that high mass-specific energy expenditure is associated with short lifespan. To examine the relationship between energy expenditure and lifespan we asked two questions. First, do individuals have a consistent rate of metabolism throughout their life? Second, is metabolic rate correlated with lifespan? We analysed the repeatability of measurements of resting (RMR) and peak flight metabolic rate (MRpeak) throughout the life of the Glanville fritillary butterfly (Melitaea cinxia). Measurements of MRpeak showed significant repeatability. Senescence occurred only shortly before death. RMR showed a U-shaped relationship with age and very low repeatability. Intraspecific association between metabolic rates and lifespan was tested under three conditions: in the laboratory, under field conditions, and in a laboratory experiment with repeated flight treatments. There was a significant correlation between MRpeak and lifespan in all three experiments, but the correlation was positive, not negative. RMR was not correlated with lifespan. Both MRpeak and lifespan may reflect physiological condition and be therefore positively correlated. Individuals with a large resource pool may be able to invest in mechanisms that slow down ageing. Individuals with high metabolic capacity may also possess adaptations against ageing. Molecular polymorphism in the gene phosphoglucose isomerase (Pgi) was significantly associated with both MRpeak and lifespan, and may have coevolved with defence mechanisms against senescence. Generalisations such as 'live fast, die young' may be too simple to explain the complex processes affecting ageing and lifespan.
Biodynamics of climbing: effects of substrate orientation on the locomotion of a highly arboreal lizard (Chamaeleo calyptratus)
Authors: Krause Cornelia , Fischer Martin 
Published: December 2012

SummaryArboreal substrates differ not only in diameter, but also continuity and orientation. To gain more insight into the dynamics of small-branch locomotion in tetrapods we studied the veiled chameleon walking on inclined and declined perches of up to 60° slope. Inclines and declines are characterized by fore- and hind limbs that equally contribute to body’s progression. The higher-positioned limb's vertical impulses decreased with slope. And while in the lower-positioned limb vertical impulses increased with substrate slope, peak vertical forces decreased. The decrease in peak vertical forces in the lower-positioned limb can be explained by a considerable increase of tensile forces in the higher-positioned limb the steeper the slope gets. In addition, limbs were more crouched on slopes while no changes in fore- and backward reach were observed. Mediolateral impulses were the smallest amongst the force components, and lateral impulses (medially-directed limb forces) exceeded medial impulses (laterally-directed limb forces). On inclines and declines limb placement was more variable than on level substrates. The tail never contacted the substrate during level locomotion. On inclines and declines the tail was held closer to the substrate, with short substrate contacts in one third of the analyzed trials. Regardless of substrate orientation the tail was always held straight above the branch, rotational moments induced by the tail were, therefore, minimized.
Divide-and-Conquer Electronic-Structure Study on the Mechanism of the West Nile Virus NS3 Protease Inhibitor
Authors: Saparpakorn Patchreenart , Kobayashi Masato , Nakai Hiromi 
Published: December 2012

Abstract
An effective tripeptide inhibitor, 2-naphthoyl–Lys–Lys–Arg–H (Naph-KKR-H), acts as an inhibitor against West Nile Virus (WNV) NS3 protease (NS3pro). Two conformations of Naph-KKR-H were found in the crystal structure of WNV NS2B cofactor and NS3pro. In this study, divide-and-conquer-based density functional theory and second-order Møller–Plesset perturbation theory calculations were applied in order to clarify the binding mechanism of both conformations. The solvent effect was also examined. In addition, bond energy density analysis (BEDA) was performed to investigate the binding interaction. Interestingly, even though conformations 1 and 2 revealed the difference of interaction energies, energy barriers, reaction energies, and type of reaction, the energy differences of tetrahedral intermediate forms as compared to their separated systems were close to each other with the energy difference of ca. 4 kcal mol−1. These results clearly indicated why both conformations existed in the crystal structure. The bond energy also showed the important interaction to the amino acids and role of water molecules in the active site. Furthermore, according to the high correlation between the changes of bond distance and bond energy, it was found that the BEDA technique is useful to study the binding mechanism.
Design and Synthesis of Gramicidin S Analogs with High Antibiotic Activity
Authors: Sato Kazuki , Yamaguchi Yoko , Nagai Ukon 
Published: December 2012

Abstract
Based on the β-turn preference of tetrapeptide sequences as analyzed by CD spectra of their chromophoric derivatives, 10 analogs of gramicidin S (GS) were designed and synthesized with general formula cyclo(–d-Leu1,1′–d-Lys2,2′–d-Leu3,3′–l-Pro4,4′–X5,5′–)2, where X is l-Asn, l-Ala, l-Leu, l-Phe, l-cyclohexylalanine, Gly, d-Ala, d-Leu, d-Phe, or d-cyclohexylalanine. Several analogs with high hydrophobicity showed antibiotic activity as strong as GS. CD spectra of the analogs with d-amino acid or Gly at the X position and their dinitrophenyl derivatives suggested that they have β-sheet conformation that is antipodal to that of GS.
Spectral Fitting of Action Spectra for Motions and Reactions of Single Molecules on Metal Surfaces
Authors: Motobayashi Kenta , Katano Satoshi , Kim Yousoo , Kawai Maki 
Published: December 2012

Abstract
We demonstrate the spectral fitting analysis of action spectroscopy with a scanning tunneling microscope (STM-AS) that enables us to determine the existence of two vibrational modes that overlap in energy and also the modes which exist in lower energy region than the actually observed spectral region. These hidden properties obtained only by spectral fitting are essential for the quantitative understanding of the action spectra. The assignment of vibrational signals in the analysis follows the approximate rule of which vibrational mode is active in STM-AS that was previously proposed based on the resonant tunneling model and supporting experimental results.
Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s)
Authors: Osakada Yasuko , Kawai Kiyohiko , Majima Tetsuro 
Published: December 2012

Abstract
Charge transfer (CT) in DNA has been studied extensively in the past decade. Several reasonable models, concerning delocalized charge over guanines (G’s) as well as localized charge on individual G’s, such as polaron and hopping mechanisms, are proposed based on theoretical and experimental research. It is likely that the dynamic nature of DNA such as electronic coupling and dynamic motion is important to promote this process. We previously reported the kinetic features of CT across the G and cytosine (C) repetitive sequence (GC repeats). Temperature-dependent experiments in GC repeats suggested the importance of the conformational flexibility and structure of DNA toward CT in DNA. In the present paper, we look further into the dynamic mechanisms of CT in DNA across GC repeats. Based on the nanosecond transient absorption measurement, we monitored the migration of a charge in DNA having GC repeats separated by A/T intervening base pair(s). Interestingly, the migration time of the charge varies depending on the position, where A/T base pair(s) are located among GC repeats. Thus, the data obtained here are not simply explained by G-hopping mechanisms, in which the charge localizes on individual G’s. These results possibly indicate that CT in DNA across GC repeats proceeds via delocalization of the charge over G’s to some extent, rather than localized G-hopping mechanisms.
Bioinspired Supramolecular Materials
Authors: Ikeda Masato 
Published: December 2012

Abstract
In biological systems, noncovalent interactions of molecular building blocks such as lipids, proteins, and nucleic acids play important roles in creating diverse complex structure and dynamic function. Inspired by such biological systems, we have designed a variety of functional supramolecular materials on the basis of self-assembly of covalently prefabricated small molecules. Among them, the following three topics are described in this account: (1) supramolecular self-assembled materials based on π-conjugated disk-shaped molecules, (2) supramolecular materials based on helical-shaped molecules, and (3) biofunctions of supramolecular materials based on amphiphilic molecules.
Plasmonic Photoelectrochemistry: Functional Materials Based on Photoinduced Reversible Redox Reactions of Metal Nanoparticles
Authors: Tatsuma Tetsu 
Published: December 2012

Abstract
Plasmonic metal nanoparticles absorb and scatter visible light due to localized surface plasmon resonance (LSPR). The optical properties including resonance wavelength and absorption intensity depend on particle size, shape, orientation, spacing, and dielectric environments. If silver nanoparticles are placed on TiO2, plasmonic excitation of the particles by visible or near-infrared light results in their oxidation due to plasmon-induced charge separation. Silver ions thus released are reduced back to silver nanoparticles by UV-excitation of TiO2. These pseudo-reversible processes induced by visible and UV light between silver nanoparticles and silver ions are applied to various photoelectrochemical devices and materials. Multicolor photochromism is a typical example, in which an ensemble of silver nanoparticles on TiO2 is colored by monochromated light to a color corresponding to the excitation wavelength. The use of silver nanorods allows infrared and polarization photochromism. The photoinduced oxidation is also applied to size, shape, and orientation control of silver nanoparticles. A photomorphing gel is an additional application of the reversible processes.
Indexical Color Predicates: Truth Conditional Semantics vs. Truth Conditional Pragmatics
Authors: Clapp Lenny 
Published: December 2012

Truth conditional semantics is the project of ‘determining a way of assigning truth conditions to sentences based on A) the extension of their constituents and B) their syntactic mode of combination’ (Rothschild and Segal, 2009). This research program has been subject to objections that take the form of underdetermination arguments, an influential instance of which is presented by Travis:
… consider the words ‘The leaf is green,’ speaking of a given leaf, and its condition at a given time, used so as to mean what they do mean in English. How many distinct things might be said in words with all that true of them? Many.… Suppose a Japanese maple leaf, turned brown, was painted green for a decoration. In sorting leaves by colour, one might truly call this one green. In describing leaves to help identify their species, it might, for all the paint, be false to call it that.