bluuebunny/crossref_metadata_2025 huggingface dataset:
Channel confinement of flexible and semiflexible macromolecules
Authors: Cifra Peter
Published: December 2009

We compare in detail the channel confinement of flexible and semiflexible chains over a broad range of confinements and chain lengths using molecular simulations. Flexible and semiflexible chains differ over the regimes involved under confinement. For the stiff chain we confirm a transition between strong and weak confinement at the tube diameter approximately equal to the chain persistence length. Deviations from the predicted behavior for confined semiflexible macromolecules in the tubelike channel under the weak confinement are explained by a tendency of chains toward ideal chain behavior. There are several indicators of this ideality based on the shape of chain extension R—confinement D curves, on the scaling of R with the chain length, on the structure factor of coil in the range of individual blobs in the channel, on ambiguity in introduction of excluded volume for confined stiff chains in theoretical treatments as well as on the reported experimental observation.
Intrinsic anisotropy of thermal conductance in graphene nanoribbons
Authors: Xu Yong , Chen Xiaobin , Gu Bing-Lin , Duan Wenhui
Published: December 2009

Thermal conductance of graphene nanoribbons (GNRs) with the width varying from 0.5 to 35 nm is systematically investigated using nonequilibrium Green’s function method. Anisotropic thermal conductance is observed with the room temperature thermal conductance of zigzag GNRs up to ∼30% larger than that of armchair GNRs. At room temperature, the anisotropy is found to disappear when the width is larger than 100 nm. This intrinsic anisotropy originate from different boundary condition at ribbon edges, and can be used to tune thermal conductance, which have important implications for the applications of GNRs in nanoelectronics and thermoelectricity.
Correlation of dynamic and quasistatic relaxations: The Cox–Merz rule for metallic glass
Authors: Kato Hidemi , Ichitsubo Tetsu , Igarashi Hitoshi , Inoue Akihisa
Published: December 2009

The correlation of quasistatic and dynamic relaxations was discussed in a typical strong Zr55Al10Ni5Cu30 metallic glass from room temperature to Tg. The quasistatic relaxation behavior, investigated by high temperature compressive testing at a constant strain rate, was compared with dynamic tensile relaxation behavior. A correlation equation of the dynamic frequency and quasistatic strain rate was successfully deduced, and then its validity was experimentally confirmed in a fragile metallic glass. Using this correlation, the Cox–Merz rule, derived for correlating the steady-state and dynamic viscosities of the polymers, is found to be applicable to metallic glasses.
Properties of vanadium and tantalum granular oxide-metal tunnel junctions fabricated by electrochemical anodization
Authors: Fan Wenbin , Kirkwood David , Lu Jiwei , Wolf Stuart A.
Published: December 2009

Localized electrochemical anodization has been used to prepare lateral vanadium (V) and tantalum (Ta) tunnel junctions. Electrical transport properties of these junctions were investigated at various temperatures ranging from 25 to 135 °C. A strong nonlinear current-voltage (I-V) curve indicates nonohmic transport which we believe is due to tunnel junction behavior. The metal-insulator transition was observed in the V junction at ∼80 °C. The microstructure of these junctions explored by transmission electron microscope is consistent with metallic grains embedded in an oxide matrix and we therefore expect tunneling between the metallic grains to be the dominant transport mechanism.
O
+
OH
→
O
2
+
H
: A key reaction for interstellar chemistry. New theoretical results and comparison with experiment
Authors: Lique F. , Jorfi M. , Honvault P. , Halvick P. , Lin S. Y. , Guo H. , Xie D. Q. , Dagdigian P. J. , Kłos J. , Alexander M. H.
Published: December 2009

We report extensive, fully quantum, time-independent (TID) calculations of cross sections at low collision energies and rate constants at low temperatures for the O+OH reaction, of key importance in the production of molecular oxygen in cold, dark, interstellar clouds and in the chemistry of the Earth’s atmosphere. Our calculations are compared with TID calculations within the J-shifting approximation, with wave-packet calculations, and with quasiclassical trajectory calculations. The fully quantum TID calculations yield rate constants higher than those from the more approximate methods and are qualitatively consistent with a low-temperature extrapolation of earlier experimental values but not with the most recent experiments at the lowest temperatures.
Synthesis and Structure of Novel RuII - N≡C - Me Complexes and their Activity Towards Nitrile Hydrolysis: An Examination of Ligand Effects
Authors: Mola Joaquim , Pujol David , Rodríguez Montserrat , Romero Isabel , Sala Xavier , Katz Néstor , Parella Teodor , Benet-Buchholz Jordi , Fontrodona Xavier , Llobet Antoni
Published: December 2009

The synthesis and isolation of new RuII–acetonitrile complexes, of general formula trans,fac-[Ru(bpea)(B)(MeCN)](BF4)2 (bpea = N,N-bis(2-pyridylmethyl)ethylamine; B = bpy, 2,2′-bipyridine, 4; B = dppe, 1,2-bis(diphenylphosphino)ethane, 5), together with a synthetic intermediate trans,fac-[Ru(NO3)(bpea)(dppe)](BF4), 6, are described. Ru(bpea)Cl3, 1, is used as the starting material for the synthesis of all complexes 2–6 presented in this paper, which are characterized by analytical, spectroscopic (IR, UV/Vis, 1D and 2D NMR), and electrochemical techniques (cyclic voltammetry). Furthermore, complexes 4, 5, and 6 have also been characterized in the solid state by single crystal X-ray diffraction analysis. Their structures show a distorted octahedral geometry where the bpea ligand binds in a facial mode, the bidentate ligands bpy and dppe bind in a chelate manner, and finally the MeCN or the NO3
– ligand occupy the sixth position of the octahedral Ru metal centre. The kinetics of the basic hydrolysis of the coordinated MeCN ligand for complexes 4 and 5 and for the related complex [Ru(phen)(MeCN)([9]aneS3)](BF4)2, 7, which contains the 1,4,7-trithiacyclonane ligand ([9]aneS3) and 1,10-phenanthroline (phen) is also described. Second-order rate constants for acetonitrile hydrolysis measured at 25°C of k = 1.01 × 10–3 M–1 s–1 for 4, 1.08 × 10–4 M–1 s–1 for 5, and 6.8 × 10–3 M–1 s–1 for 7, have been obtained through UV-vis spectroscopy. Activation parameters have also been determined over the temperature range 25.0–45.0°C and agree with a mechanism that involves an associative rate-determining step. Finally the electronic and steric influence of the auxiliary ligands on this reaction for the above and related complexes is discussed.
A Highly Selective Luminescent Sensor for Detecting Mercuric Ions in Water
Authors: Kanan Sofian M. , Abu-Yousef Imad A. , Hassouneh Nora , Malkawi Ahmed , Abdo Naser , Kanan Marsha C.
Published: December 2009

A chemoluminescent sensor utilizing the substrate 2,6-pyridinedicarboxaldehydebis(o-hydroxyphenylimine) (S1) was developed for low-concentration detection of mercuric ions in aqueous solutions. The sensor selectively detects mercury in the presence of sodium, calcium, magnesium, and iron ions. A strong binding was observed between the mercuric ions and the substrate at a pH range of 6.5–7.5, which makes the substrate a distinctive luminescence sensor for detecting mercury at ambient conditions. The sensor shows a linear response towards Hg2+ in the concentration range 5.0 × 10–5 to 2.5 × 10–8 M with a limit of detection of 5.0 × 10–8 M. The sensor can also detect zinc ions at a pH of 10 or higher. The results indicate that this sensor has a promising future for the detection of mercury in real environmental water samples.
Copper(I) Iodide-Catalyzed Cycloadditions of (1Z,4R*,5R*)-4-Benzamido-5-phenylpyrazolidin-3-on-1-azomethine Imines to Ethyl Propiolate
Authors: Pezdirc Lidija , Stanovnik Branko , Svete Jurij
Published: December 2009

Regioselective copper(i) iodide-catalyzed cycloadditions of chiral pyrazolidin-3-on-1-azomethine imines 3a–j to ethyl propiolate 4 gave cycloadducts 5a–h and 5′i and 5/5′j as single regioisomers. In terms of facial selectivity, cycloadducts 5a–h and 5′i were obtained as single diastereomers, whereas the reaction of dipole 3j was less selective and gave a mixture of 5j and 5′j in a ratio of 15:85. Stereoselectivity of copper(i) iodide-catalyzed cycloadditions of ethyl propiolate 4 to azomethine imines 3 was controlled by the stereodirecting phenyl group at position 5 and by the ortho-substituents at the 1′–Ar residue.
Synthesis, Characterization, DNA-Binding, and DNA-Photocleavage Properties of RuII Complexes
Authors: Tan Lifeng , Chen Xuejiao , Sheng Jianliang
Published: December 2009

A new polypyridyl ligand 2-benzo[b]thiophen-3-yl-1H-1,3,7,8-tetraazacyclopenta[l]phenanthrene (BTCP) and its RuII complexes [Ru(bpy)2(BTCP)]2+ (1) (bpy = 2,2′-bipyridine), [Ru(phen)2(BTCP)]2+ (2) (phen = 1,10-phenanthroline), and [Ru(dmb)2(BTCP)]2+ (3) (dmb = 4,4′-dimethyl-2,2′-bipyridine), have been synthesized and characterized. The DNA-binding properties of the three complexes were investigated by spectroscopic methods and viscosity measurements. The results indicate that complexes 1, 2, and 3 bind to DNA by an intercalative mode and the ancillary ligands have a significant effect on the binding strengths of RuII complexes to DNA. When irradiated at 365 nm, complex 2 was found to be a more effective DNA-cleaving agent than complexes 1 and 3.
Revising the recent evolutionary history of equids using ancient DNA
Authors: Orlando Ludovic , Metcalf Jessica L. , Alberdi Maria T. , Telles-Antunes Miguel , Bonjean Dominique , Otte Marcel , Martin Fabiana , Eisenmann Véra , Mashkour Marjan , Morello Flavia , Prado Jose L. , Salas-Gismondi Rodolfo , Shockey Bruce J. , Wrinn Patrick J. , Vasil'ev Sergei K. , Ovodov Nikolai D. , Cherry Michael I. , Hopwood Blair , Male Dean , Austin Jeremy J. , Hänni Catherine , Cooper Alan
Published: December 2009

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87–688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra,Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution ofEquus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle
Authors: Gérard Claude , Goldbeter Albert
Published: December 2009

We propose an integrated computational model for the network of cyclin-dependent kinases (Cdks) that controls the dynamics of the mammalian cell cycle. The model contains four Cdk modules regulated by reversible phosphorylation, Cdk inhibitors, and protein synthesis or degradation. Growth factors (GFs) trigger the transition from a quiescent, stable steady state to self-sustained oscillations in the Cdk network. These oscillations correspond to the repetitive, transient activation of cyclin D/Cdk4–6 in G
1
, cyclin E/Cdk2 at the G
1
/S transition, cyclin A/Cdk2 in S and at the S/G
2
transition, and cyclin B/Cdk1 at the G
2
/M transition. The model accounts for the following major properties of the mammalian cell cycle: (
i
) repetitive cell cycling in the presence of suprathreshold amounts of GF; (
ii
) control of cell-cycle progression by the balance between antagonistic effects of the tumor suppressor retinoblastoma protein (pRB) and the transcription factor E2F; and (
iii
) existence of a restriction point in G
1
, beyond which completion of the cell cycle becomes independent of GF. The model also accounts for endoreplication. Incorporating the DNA replication checkpoint mediated by kinases ATR and Chk1 slows down the dynamics of the cell cycle without altering its oscillatory nature and leads to better separation of the S and M phases. The model for the mammalian cell cycle shows how the regulatory structure of the Cdk network results in its temporal self-organization, leading to the repetitive, sequential activation of the four Cdk modules that brings about the orderly progression along cell-cycle phases.
Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3
Authors: Jura Natalia , Shan Yibing , Cao Xiaoxian , Shaw David E. , Kuriyan John
Published: December 2009

The kinase domain of human epidermal growth factor receptor (HER) 3/ErbB3, a member of the EGF receptor (EGFR) family, lacks several residues that are critical for catalysis. Because catalytic activity in EGFR family members is switched on by an allosteric interaction between kinase domains in an asymmetric kinase domain dimer, HER3 might be specialized to serve as an activator of other EGFR family members. We have determined the crystal structure of the HER3 kinase domain and show that it appears to be locked into an inactive conformation that resembles that of EGFR and HER4. Although the crystal structure shows that the HER3 kinase domain binds ATP, we confirm that it is catalytically inactive but can serve as an activator of the EGFR kinase domain. The HER3 kinase domain forms a dimer in the crystal, mediated by hydrophobic contacts between the N-terminal lobes of the kinase domains. This N-lobe dimer closely resembles a dimer formed by inactive HER4 kinase domains in crystal structures determined previously, and molecular dynamics simulations suggest that the HER3 and HER4 N-lobe dimers are stable. The kinase domains of HER3 and HER4 form similar chains in their respective crystal lattices, in which N-lobe dimers are linked together by reciprocal exchange of C-terminal tails. The conservation of this tiling pattern in HER3 and HER4, which is the closest evolutionary homolog of HER3, might represent a general mechanism by which this branch of the HER receptors restricts ligand-independent formation of active heterodimers with other members of the EGFR family.
The Typology of Tupi-Guarani as Reflected in the Grammars of Four Jesuit Missionaries
Authors: Bossong Georg
Published: December 2009

Some fundamental typological peculiarities of Guarani, namely the inclusive-exclusive distinction, transnumerality, the nominal tense, the (non)-distinction of subjects and objects, and duality (active-stative alignment) are presented and analyzed from both a modern and a historical perspective: first, to better understand the features of Guarani; second, to illuminate the difficulties missionaries faced when trying to cope with language structures that drastically differed from their training in Latin grammar. Using the missionaries’ grammars as first-hand testimony, the conclusion is reached that we have not significantly advanced beyond these works from the 17th and 18th centuries. Although none of the Jesuitpadresarrived at a clear understanding of all the peculiarities of Tupi- Guarani that are dealt with in this paper, they made substantial contributions to describing the unusual features of this language family adequately, and thus went deliberately beyond the framework of Latin school grammar.
Missionary Contributions to Bantu Languages in Tanzania
Authors: Legère Karsten
Published: December 2009

This paper deals with linguistic work by the lay missionary James Thomas Last (1850–1933), who was among the first Europeans to live up-country in what is now Tanzania. In the course of a seven-year stay he was exposed to African languages which have only partly been known outside Africa. Last collected linguistic data that culminated 1885 in the publication of the Polyglotta Africana Orientalis. This book is a collection of 210 lexical items and sentences elicited in or translated into 48 African languages, and supplemented by entries for some other languages. In order to demonstrate the relevance as well as the inconsistencies of this missionary’s contribution, special attention is paid to the book section on the Vidunda language currently spoken by approximately 10,000 people in Central Tanzania. It turns out that approximately 75 per cent of the Vidunda entries are still acceptable today. The data even provides insight into the grammatical set-up of Vidunda (e.g., the noun classes and constituents of the noun phrase). Less relevant are the verbal paradigms. In a nutshell, Last produced material which had for many years been the sole source of lexical and grammatical information about the Vidunda language.
Description and Qualitative Evaluation of Jigsaw, an Integrated Young Persons’ Mental Health Program
Authors: Callaly Thomas , Dodd Seetal , Ackerly Carmel , Hantz Paul , O'Shea Melissa , Berk Michael
Published: December 2009

Objective: The aim of this paper is to describe the establishment of an integrated young person's mental health service and the findings of a qualitative evaluation conducted 2 years after its establishment.

Method: A qualitative evaluation of the service was undertaken using a semi-structured interview, a service satisfaction survey and partnership analysis tool.

Results: The major problems encountered in establishing the service were insufficient recognition of the cultural challenges in working together, difficulty in recruiting general practitioners, establishing a youth friendly environment and maintaining the quality of the relationship between partners.

Conclusion: Despite almost 3 years of preparation, many important aspects of change management were underestimated or inadequately attended to.
Shyness 5: The Clinical Effectiveness of Internet-Based Clinician-Assisted Treatment of Social Phobia
Authors: Aydos Leticia , Titov Nickolai , Andrews Gavin
Published: December 2009

Objective: The present study explores the clinical effectiveness of an Internet-based cognitive behavioural treatment program for social phobia (the Shyness program) administered by a psychiatric registrar as part of standard clinical treatment at an outpatient mental health service (the Anxiety Disorders Clinic, St Vincent's Hospital, Sydney).

Method: Seventeen individuals with social phobia were assigned to this 8 week clinician-assisted program. All patients had access to online lessons, homework assignments, an online discussion forum with other patients, and regular emails from the clinician. Both completer and intention-to-treat models were used in data analyses.

Results: Fourteen (82%) patients completed all six lessons within the 8 weeks, and 11/17 (65%) completed post-treatment questionnaires. Mean within-group effect sizes (Cohen's d) for the two social phobia measures were 1.06 and 0.77, based on completer and intention-to-treat analyses, respectively. Data indicate that the procedure was acceptable to patients.

Conclusions: These results indicate that the procedure was clinically effective when operated as part of standard clinical treatment. These results provide further support for the potential clinical utility of the Shyness program.
The Prediction of Imminent Aggression in Patients with Mental Illness and/or Intellectual Disability Using the Dynamic Appraisal of Situational Aggression Instrument
Authors: Barry-Walsh Justin , Daffern Michael , Duncan Suzanne , Ogloff James
Published: December 2009

Objective: The aim of this paper was to determine whether imminent aggression in psychiatric inpatients can be accurately predicted using a structured risk assessment instrument, the Dynamic Appraisal of Situational Aggression (DASA).

Methods: This prospective validation study involved 10 013 DASA risk assessments of patients residing in a psychiatric hospital. Twenty-four hours after the risk assessment, psychiatric nurses documented whether patients had behaved aggressively towards others or whether they had deliberately damaged property. They also noted the target of aggression, whether towards staff, patients or property.

Results: The predictive validity of the DASA varied according to the type and target of aggression. The prediction of any aggressive behaviour, irrespective of type of aggression or target, was significantly greater than chance (AUC = 0.69). The strongest predictive accuracy (AUC = 0.80) was for physical aggression towards staff.

Conclusions: These results suggest that imminent aggression in psychiatric hospitals may be able to be accurately predicted by psychiatric nurses using a structured risk assessment instrument.
Time-delayed feedback control of stochastic resonance induced by a multiplicative signal in a bistable system driven by cross-correlated noises
Authors: Jia Zheng-Lin
Published: December 2009

A linear time-delayed feedback is introduced into the bistable system driven by cross-correlated noises to control the stochastic resonance (SR) induced by the multiplicative periodic signal. The expression for the signal-to-noise ratio (SNR) of the system is derived in the small delay approximation and the adiabatic limit. By numerical computations, the effects of the delay time and strength of its feedback on the SNR are analyzed. The results indicate that the SR phenomenon can be enhanced or suppressed by adjusting the delay time and feedback strength. The influence of the time-delayed feedback on the SR depends not only on the sign of feedback strength, but also on the initial condition of the system. Moreover, both the delay time and the feedback strength can induce the critical behavior on the SR under given conditions.
External field-controlled photovoltaic symbiotic spatial soliton pairs in two-photon photorefractive crystals
Authors: Konar S , Asif Noushin
Published: December 2009

We report the existence of incoherently coupled bright–bright steady state photovoltaic (PV) soliton pairs in biased two-photon photorefractive (TPPR) materials that arise due to the TPPR effect. A remarkable finding is that, with the application of electric field, it is possible to generate solitons and control them in such media, where soliton formation was actually prohibited hitherto. The present analysis indicates the existence of a plethora of bright–bright soliton pairs with dynamical properties controllable by the application of an external electric field of appropriate polarity and magnitude. We have identified two different power regimes in which the effect of external electric field is opposite. We have undertaken linear stability analysis which shows that these solitons are stable.
Goal‐Directed Acupuncture in Sports	Placebo or Doping?
Authors: Usichenko Taras I. , Gizhko Vasyl , Wendt Michael
Published: December 2009

The modern pentathlon (MP), sports discipline including fencing, swimming, steeplechase and a cross‐country run, requires a rapid change of central nervous and peripheral neuromuscular activity from one sport to another in order to achieve the best possible results. We describe the case where a top MP athlete was supported by a program of acupoint stimulation, which was directed to relieve the symptoms, preventing him from effective performance. Although the fact of acupoint stimulation was associated with improvement of his results, other factors like training effect, placebo and nonspecific physiological effects and their mechanisms in sports are discussed in a literature review. The popularity of complementary and alternative medicine methods among the athletes raises the question of their potential misuse as a doping in competitive sports.
Herbal Medicine Containing Licorice May Be Contraindicated for a Patient with an HSD11B2 Mutation
Authors: Harahap Indra Sari Kusuma , Sasaki Naoko , Gunadi  , Yusoff Surini , Lee Myeong Jin , Morikawa Satoru , Nishimura Noriyuki , Sasaki Tomohiro , Usuki Seiichiro , Hirai Midori , Ohta Mika , Takaoka Yutaka , Nishimoto Takashi , Nishio Hisahide
Published: December 2009

Licorice ingestion, as well as mutations in the HSD11B2 gene, inhibits 11β‐hydroxysteroid dehydrogenase type 2 (11βHSD2) enzyme activity, causing the syndrome of apparent mineral corticoid excess (AME). However, the combined effect of licorice ingestion and an HSD11B2 mutation has never been reported, until now. In this study, we demonstrated that licorice ingestion can produce overt hypertension in an individual without medical history of hypertension who is heterozygous for wild‐type and mutant HSD11B2 genes. Our patient was a 51‐year‐old female with serious hypertension who had been taking herbal medicine containing licorice for more than one year. She was clinically diagnosed as having licorice intoxication, because she did not present with hypertension after ceasing the herbal medicine. Molecular analysis showed that she carried a missense mutation, c.40C>T, in HSD11B2. In conclusion, licorice ingestion is an environmental risk factor for hypertension or AME state in patients with a mutation in HSD11B2. Carrying a mutation in HSD11B2 is, conversely, a genetic risk factor for licorice‐induced hypertension or AME state. Herbal medicine containing licorice may, therefore, be contraindicated in patients with an HSD11B2 mutation.
Reliability of size-selectivity estimates from paired-trawl and covered-codend experiments
Authors: Millar Russell B.
Published: December 2009

Millar, R. B. 2010. Reliability of size-selectivity estimates from paired-trawl and covered-codend experiments. – ICES Journal of Marine Science, 67: 530–536. To determine the size selectivity of a trawl codend from sea trials, the researcher must choose between using paired (experimental and control) and covered-codend gears. The paired-gear method has the advantage that the experimental codend can be deployed without modification, but has the disadvantage of a more complex statistical analysis. It has previously been claimed that this analysis is inherently biased regardless of sampling effort. This claim is shown to be erroneous, and it is seen that both methods produce estimators that have negligible bias under typical experimental conditions. However, paired-gear analyses were seen to produce estimators having greater statistical variability than the covered-codend analyses. Over the range of simulations employed herein, it was found that the paired-gear method generally had moderately higher (ratio of 1.3–1.9) statistical error for estimation of the length of 50% retention, when fished with equal sampling effort as the covered-codend gear. Paired-gear estimates of the selection range could have considerably higher standard error than covered-codend estimates (ratio of 1.6–4.2), with the highest ratio being for a scenario where the selection curve was asymmetric and sampling effort consisted of ten replicate deployments where the number of measured fish was restricted to 250.
Plausibility of inferred ancestral phenotypes and the evaluation of alternative models of limb evolution in scincid lizards
Authors: Skinner Adam , Lee Michael S. Y.
Published: December 2009

Phylogenetic approaches to inferring ancestral character states are becoming increasingly sophisticated; however, the potential remains for available methods to yield strongly supported but inaccurate ancestral state estimates. The consistency of ancestral states inferred for two or more characters affords a useful criterion for evaluating ancestral trait reconstructions. Ancestral state estimates for multiple characters that entail plausible phenotypes when considered together may reasonably be assumed to be reliable. However, the accuracy of inferred ancestral states for one or more characters may be questionable where combined reconstructions imply implausible phenotypes for a proportion of internal nodes. This criterion for assessing reconstructed ancestral states is applied here in evaluating inferences of ancestral limb morphology in the scincid lizard clade
Lerista
. Ancestral numbers of digits for the manus and pes inferred assuming the models that best fit the data entail ancestral digit configurations for many nodes that differ fundamentally from configurations observed among known species. However, when an alternative model is assumed for the pes, inferred ancestral digit configurations are invariably represented among observed phenotypes. This indicates that a suboptimal model for the pes (and not the model providing the best fit to the data) yields accurate ancestral state estimates.
Effects of disorder and motion in a radical pair magnetoreceptor
Authors: Lau Jason C. S. , Wagner-Rundell Nicola , Rodgers Christopher T. , Green Nicholas J. B. , Hore P. J.
Published: December 2009

A critical requirement in the proposed chemical model of the avian magnetic compass is that the molecules that play host to the magnetically sensitive radical pair intermediates must be immobilized and rotationally ordered within receptor cells. Rotational disorder would cause the anisotropic responses of differently oriented radical pairs within the same cell to interfere destructively, while rapid molecular rotation would tend to average the crucial anisotropic magnetic interactions and induce electron spin relaxation, reducing the sensitivity to the direction of the geomagnetic field. So far, experimental studies have been able to shed little light on the required degree of ordering and immobilization. To address this question, computer simulations have been performed on a collection of radical pairs undergoing restricted rigid-body rotation, coherent anisotropic spin evolution, electron spin relaxation and spin-selective recombination reactions. It is shown that the ordering and motional constraints necessary for efficient magnetoreception can be simultaneously satisfied if the radical pairs are uniaxially ordered with a moderate order parameter and if their motional correlation time is longer than about a quarter of their lifetime.
A novel sex determination system in a close relative of the house mouse
Authors: Veyrunes Frederic , Chevret Pascale , Catalan Josette , Castiglia Riccardo , Watson Johan , Dobigny Gauthier , Robinson Terence J. , Britton-Davidian Janice
Published: December 2009

Therian mammals have an extremely conserved XX/XY sex determination system. A limited number of mammal species have, however, evolved to escape convention and present aberrant sex chromosome complements. In this study, we identified a new case of atypical sex determination in the African pygmy mouseMus minutoides, a close evolutionary relative of the house mouse. The pygmy mouse is characterized by a very high proportion of XY females (74%,n= 27) from geographically widespread Southern and Eastern African populations. Sequencing of the high mobility group domain of the mammalian sex determining geneSry, and karyological analyses using fluorescencein situhybridization and G-banding data, suggest that the sex reversal is most probably not owing to a mutation ofSry, but rather to a chromosomal rearrangement on the X chromosome. In effect, two morphologically different X chromosomes were identified, one of which, designated X*, is invariably associated with sex-reversed females. The asterisk designates the still unknown mutation converting X*Y individuals into females. Although relatively still unexplored, such an atypical sex chromosome system offers a unique opportunity to unravel new genetic interactions involved in the initiation of sex determination in mammals.
Bayesian network analysis of targeting interactions in chromatin
Authors: van Steensel Bas , Braunschweig Ulrich , Filion Guillaume J. , Chen Menzies , van Bemmel Joke G. , Ideker Trey
Published: December 2009

In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7. Our network model provides a global view of the targeting interplay among dozens of chromatin components.
Chitinase-Like Protein CTL1 Plays a Role in Altering Root System Architecture in Response to Multiple Environmental Conditions
Authors: Hermans Christian , Porco Silvana , Verbruggen Nathalie , Bush Daniel R.
Published: December 2009

Plant root architecture is highly responsive to changes in nutrient availability. However, the molecular mechanisms governing the adaptability of root systems to changing environmental conditions is poorly understood. A screen for abnormal root architecture responses to high nitrate in the growth medium was carried out for a population of ethyl methanesulfonate-mutagenized Arabidopsis (Arabidopsis thaliana). The growth and root architecture of the arm (for anion altered root morphology) mutant described here was similar to wild-type plants when grown on low to moderate nitrate concentrations, but on high nitrate, arm exhibited reduced primary root elongation, radial swelling, increased numbers of lateral roots, and increased root hair density when compared to the wild-type control. High concentrations of chloride and sucrose induced the same phenotype. In contrast, hypocotyl elongation in the dark was decreased independently of nitrate availability. Positional cloning identified a point mutation in the AtCTL1 gene that encodes a chitinase-related protein, although molecular and biochemical analysis showed that this protein does not possess chitinase enzymatic activity. CTL1 appears to play two roles in plant growth and development based on the constitutive effect of the arm mutation on primary root growth and its conditional impact on root architecture. We hypothesize that CTL1 plays a role in determining cell wall rigidity and that the activity is differentially regulated by pathways that are triggered by environmental conditions. Moreover, we show that mutants of some subunits of the cellulose synthase complex phenocopy the conditional effect on root architecture under nonpermissive conditions, suggesting they are also differentially regulated in response to a changing environment.
A Raf-Like MAPKKK Gene DSM1 Mediates Drought Resistance through Reactive Oxygen Species Scavenging in Rice
Authors: Ning Jing , Li Xianghua , Hicks Leslie M. , Xiong Lizhong
Published: December 2009

Mitogen-activated protein kinase (MAPK) cascades have been identified in various signaling pathways involved in plant development and stress responses. We identified a drought-hypersensitive mutant (drought-hypersensitive mutant1 [dsm1]) of a putative MAPK kinase kinase (MAPKKK) gene in rice (Oryza sativa). Two allelic dsm1 mutants were more sensitive than wild-type plants to drought stress at both seedling and panicle development stages. The dsm1 mutants lost water more rapidly than wild-type plants under drought stress, which was in agreement with the increased drought-sensitivity phenotype of the mutant plants. DSM1-RNA interference lines were also hypersensitive to drought stress. The predicted DSM1 protein belongs to a B3 subgroup of plant Raf-like MAPKKKs and was localized in the nucleus. By real-time PCR analysis, the DSM1 gene was induced by salt, drought, and abscisic acid, but not by cold. Microarray analysis revealed that two peroxidase (POX) genes, POX22.3 and POX8.1, were sharply down-regulated compared to wild type, suggesting that DSM1 may be involved in reactive oxygen species (ROS) signaling. Peroxidase activity, electrolyte leakage, chlorophyll content, and 3,3′-diaminobenzidine staining revealed that the dsm1 mutant was more sensitive to oxidative stress due to an increase in ROS damage caused by the reduced POX activity. Overexpression of DSM1 in rice increased the tolerance to dehydration stress at the seedling stage. Together, these results suggest that DSM1 might be a novel MAPKKK functioning as an early signaling component in regulating responses to drought stress by regulating scavenging of ROS in rice.
Viral shedding after p53 adenoviral gene therapy in 10 cases of esophageal cancer
Authors: Kawahira Hiroshi , Matsushita Kazuyuki , Shiratori Tooru , Shimizu Takanori , Nabeya Yoshihiro , Hayashi Hideki , Ochiai Takenori , Matsubara Hisahiro , Shimada Hideaki
Published: December 2009

We detected adenoviral DNA fragments in excretions of 10 esophageal cancer patients by DNA‐PCR after tumor injection of Ad‐CMV‐vector. A total of 220 samples consisting of feces, gargling saliva, urine, and blood plasma were assessed. A total of 29.7% of feces samples and 13.2% of gargling saliva samples were positive for adenoviral DNA fragments, but 89.7% of the positive feces samples and all of the positive gargling saliva samples turned negative on day 12 after tumor injection. Although adenoviral DNA fragments may be pathogen‐free, patients’ feces and gargling saliva contain adenoviral DNA fragments for 12 days after injection. (Cancer Sci 2010; 101: 289–291)
Translational pharmacokinetic–pharmacodynamic modelling; application to cardiovascular safety data for PF‐00821385, a novel HIV agent
Authors: Langdon Grant , Davis John D. , McFadyen Lynn M. , Dewhurst Mark , Brunton Neil S. , Rawal Jaiessh K. , Van der Graaf Piet H. , Benson Neil
Published: December 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• While animal toxicology is routinely used for safety screening of compounds prior to their being tested in man, there is very little in the literature on the quantitative translation of cardiovascular drug effects from animal to man.

WHAT THIS STUDY ADDS

• This study compares pharmacokinetic–pharmacodynamic analysis of dog and human effects of PF‐00821385 on heart rate.

• This paper considers how quantitative translational knowledge of drug effects in dogs may be used to optimize future human studies.

AIMTo assess the translation of pharmacokinetic–pharmacodynamic (PK–PD) relationships for heart rate effects of PF‐00821385 in dog and man.

METHODSCardiovascular telemetric parameters and concentration data were available for animals receiving active doses (0.5–120 mg kg−1,n= 4) or vehicle. PF‐00821385 was administered to 24 volunteers and pharmacokinetic and vital signs data were collected. PK–PD models were fitted using nonlinear mixed effects.

RESULTSCompartmental models with linear absorption and clearance were used to describe pharmacokinetic disposition in animal and man. Diurnal variation in heart and pulse rate was best described with a single cosine function in both dog and man. Canine and human heart rate change were described by a linear model with free drug slope 1.76 bpm µM−1[95% confidence interval (CI) 1.17, 2.35] in the dog and 0.76 bpm µM−1(95% CI 0.54, 1.14) in man.

CONCLUSIONSThe preclinical translational of concentration–response has been described and the potential for further interspecies extrapolation and optimization of clinical trial design is addressed.
Habitat‐related differences in the frequency selectivity of auditory filters in songbirds
Authors: Henry Kenneth S. , Lucas Jeffrey R.
Published: December 2009

1. Environmental constraints in woodland habitats favour long‐range communication signals with slow modulations of frequency and amplitude, while constraints in open habitats favour faster modulations.

2. Spectral filtering by the peripheral auditory system results in a trade‐off between frequency resolution and temporal resolution of modulations. Greater frequency resolution requires integration of acoustic signals over a longer period of time, which in turn decreases responsiveness to temporal modulations.

3. Here, we test the hypothesis in songbirds that woodland habitats have selected for narrowly tuned auditory filters with high frequency resolution of tonal elements, while open habitats have selected for broader auditory filters with greater temporal resolution of rapid modulation.

4. Auditory filter shapes were measured at 2, 3 and 4 kHz in three woodland species, the dark‐eyed junco (Junco hyemalis), tufted titmouse (Baeolophus bicolor) and white‐breasted nuthatch (Sitta carolinensis), and two open‐habitat species, the house sparrow (Passer domesticus) and white‐crowned sparrow (Zonotrichia leucophrys). Auditory filter shapes were derived from auditory brainstem response thresholds in notched noise using Patterson’s rounded exponential (roex) auditory filter model.

5. Auditory filters increased in bandwidth with increasing frequency in all species except the dark‐eyed junco. Auditory filters were generally narrower in woodland species than open‐habitat species as predicted, although auditory filters of the junco were relatively narrow only at 4 kHz, and the difference between white‐crowned sparrows and tufted titmice was not significant. Finally, at 4 kHz, open‐habitat species had auditory filters with lower signal‐to‐noise response thresholds than woodland species (i.e. greater response efficiency).

6. The results suggest that environmental constraints on song structure have influenced the evolution of peripheral auditory filters in songbirds, although species using signals not optimized for long‐range transmission should be less affected. Differences in filter bandwidth between dark‐eyed juncos and white‐crowned sparrows are noteworthy because Junco and Zonotrichia share a recent common ancestor as sister genera within the Emberizidae. Finally, open‐habitat species may compensate for inherently lower sensitivity in noise of broad auditory filters with greater response efficiency.
High density of weak replication origins in a 75‐kb region of chromosome 2 of fission yeast
Authors: Dubey Dharani D , Srivastava Vinay K , Pratihar Aditya S , Yadava Mukesh P
Published: December 2009

Using a two‐dimensional gel electrophoresis origin mapping technique and cell synchronization, we have studied replication timing and mapped origins in a 75‐kb region of chromosome 2 of Schizosaccharomyces pombe. Three of the five mapped origins are moderately active and the other two are very weak. DNA fragments containing the three moderately active origins and one weak origin are ARS‐positive whereas that containing the other weak origin is ARS‐negative. Three ARS elements reported earlier from this region appear to be inactive as chromosomal origins. The centromere‐proximal 45 kb of this region replicates earlier than the telomere‐proximal 30 kb. A transition from early to late replication occurs within 10 kb of the chromosomally inactive ars727, suggesting a possible role of the previously reported late‐replication‐enforcing region in determining chromosomal replication timing of the region. These results in conjunction with those from some other studies suggest that, in S. pombe, the actual number of potential origins may be significantly higher than previously detected in many genome‐wide studies, and the relationship between ARS activity and chromosomal origin activity is not as simple as in Saccharomyces cerevisiae.
Regulatory mechanism for expression of GPX1 in response to glucose starvation and Ca2+ in Saccharomyces cerevisiae: involvement of Snf1 and Ras/cAMP pathway in Ca2+ signaling
Authors: Ohdate Takumi , Izawa Shingo , Kita Keiko , Inoue Yoshiharu
Published: December 2009

Saccharomyces cerevisiae has three homologues of the glutathione peroxidase gene, GPX1, GPX2, and GPX3. We have previously reported that the expression of GPX3 was constitutive, but that of GPX2 was induced by oxidative stress and CaCl2, and uncovered the regulatory mechanisms involved. Here, we show that the expression of GPX1 is induced by glucose starvation and treatment with CaCl2. The induction of GPX1 expression in response to glucose starvation and Ca2+ was dependent on the transcription factors Msn2 and Msn4 and cis‐acting elements [stress response element (STRE)] in the GPX1 promoter. The Ras/cAMP pathway is also involved in the expression of GPX1. We found that Snf1, a Ser/Thr protein kinase, is involved in the glucose starvation‐ and Ca2+‐induced expression of GPX1. The activation of Snf1 is accompanied by phosphorylation of Thr210. We found that the Ca2+‐treatment as well as glucose starvation causes the phosphorylation of Thr210 of Snf1 in a Tos3, Sak1, and Elm1 protein kinase‐dependent manner. As the timing of the initiation of Ca2+‐induced expression of GPX1 was retarded in an snf1Δ mutant, the activation of Snf1 seems pivotal to the early‐stage‐response of GPX1 to Ca2+.
A multi‐protein complex controls cAMP signalling and filamentation in the fungal pathogen Candida albicans
Authors: Hall Rebecca A. , Mühlschlegel Fritz A.
Published: December 2009

Candida albicans is an opportunistic fungal pathogen of humans. The ability of the fungus to grow as both yeast and filamentous forms is essential for its pathogenicity. Morphogenesis of C. albicans is largely regulated through the secondary messenger cAMP, produced by the soluble adenylyl cyclase, Cyr1p. Recent evidence suggests that Cyr1p can be directly stimulated by environmental cues to increase cytoplasmic cAMP levels and thus promote hyphal development. In this issue of Molecular Microbiology, Zou et al. demonstrate that, in response to some environmental cues, Cyr1p functions as part of a tripartite complex additionally involving Cap1p and G‐actin. All three proteins in the complex are required to raise cytosolic cAMP levels after stimulation with serum and bacterial peptidoglycan. The formation of such a complex highlights the importance of precise regulation of Cyr1p activity in response to host environmental cues.
Aquagenic acrokeratoderma
Authors: Luo Di‐Qing , Zhao Yu‐Kun , Zhang Wu‐Jun , Wu Liang‐Cai
Published: December 2009

Background  Aquagenic acrokeratoderma (AA) is a rare condition with female predilection that occurs after brief water exposure and disappears minutes to an hour after drying. The pathogenesis remains unclear.

Methods  Four Chinese patients with AA were reported and analyzed.

Results  There were 2 males and 2 females (age range: 14‐33 years) who presented with a 2‐week to more than 10‐year history of small white papules coalescing into edematous plaques on the hands; lesions appeared within 5‐10 minutes of water exposure, began to regress in 3–20 minutes and disappeared within 5 minutes to one hour after drying. Warm water provoked the lesions more rapidly than cold water. Lesions of a female patient could be triggered by detergent. In another female patient, lesions also involved the feet and were associated with palmoplantar erythema and hyperhidrosis. Biopsy from the lesion of one patient after water exposure revealed hyperkeratosis, mild hypergranulosis, and dilatated eccrine ducts. Biopsy from the lesion of another patient after drying showed normal epidermis and dermis. Two patients were treated with topical formalin 3% in alcohol, and two with 3% potassium aluminium sulfate solution with partial relief without any adverse effects.

Conclusion  AA may occur in both males and females and may involve the feet. Warm water triggers the lesions more rapidly than cold. Topical formalin 3% in alcohol and 3% potassium aluminium sulfate solution may be optional therapy.