bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comprehensive Expressed Sequence Tag Linkage Map for Tiger Salamander and Mexican Axolotl: Enabling Gene Mapping and Comparative Genomics in Ambystoma
Authors: Smith J J , Kump D K , Walker J A , Parichy D M , Voss S R 
Published: August 2005

Abstract
Expressed sequence tag (EST) markers were developed for Ambystoma tigrinum tigrinum (Eastern tiger salamander) and for A. mexicanum (Mexican axolotl) to generate the first comprehensive linkage map for these model amphibians. We identified 14 large linkage groups (125.5–836.7 cM) that presumably correspond to the 14 haploid chromosomes in the Ambystoma genome. The extent of genome coverage for these linkage groups is apparently high because the total map size (5251 cM) falls within the range of theoretical estimates and is consistent with independent empirical estimates. Unlike most vertebrate species, linkage map size in Ambystoma is not strongly correlated with chromosome arm number. Presumably, the large physical genome size (∼30 Gbp) is a major determinant of map size in Ambystoma. To demonstrate the utility of this resource, we mapped the position of two historically significant A. mexicanum mutants, white and melanoid, and also met, a quantitative trait locus (QTL) that contributes to variation in metamorphic timing. This new collection of EST-based PCR markers will better enable the Ambystoma system by facilitating development of new molecular probes, and the linkage map will allow comparative studies of this important vertebrate group.
Genetic and Genomic Analysis of the AT-Rich Centromere DNA Element II of Saccharomyces cerevisiae
Authors: Baker Richard E , Rogers Kelly 
Published: August 2005

Abstract
Centromere DNA element II (CDEII) of budding yeast centromeres is an AT-rich sequence essential for centromere (CEN) function. Sequence analysis of Saccharomyces cerevisiae CDEIIs revealed that A5–7/T5–7 tracts are statistically overrepresented at the expense of AA/TT and alternating AT. To test the hypothesis that this nonrandom sequence organization is functionally important, a CEN library in which the CDEII sequences were randomized was generated. The library was screened for functional and nonfunctional members following centromere replacement in vivo. Functional CENs contained CDEIIs with the highly biased An/Tn run distribution of native centromeres, while nonfunctional CDEIIs resembled those picked from the library at random. Run content, defined as the fraction of residues present in runs of four or more nucleotides, of the functional and nonfunctional CDEII populations differed significantly (P &lt; 0.001). Computer searches of the genome for regions with an A + T content comparable to CDEIIs revealed that such loci are not unique to centromeres, but for 14 of the 16 chromosomes the AT-rich locus with the highest An≥4 + Tn≥4 run content was the centromere. Thus, the distinctive and nonrandom sequence organization of CDEII is important for centromere function and possesses informational content that could contribute to the determination of centromere identity.
Mutations of a Drosophila NPC1 Gene Confer Sterol and Ecdysone Metabolic Defects
Authors: Fluegel Megan L , Parker Tracey J , Pallanck Leo J 
Published: August 2005

Abstract
The molecular mechanisms by which dietary cholesterol is trafficked within cells are poorly understood. Previous work indicates that the NPC1 family of proteins plays an important role in this process, although the precise functions performed by this protein family remain elusive. We have taken a genetic approach to further explore the NPC1 family in the fruit fly Drosophila melanogaster. The Drosophila genome encodes two NPC1 homologs, designated NPC1a and NPC1b, that exhibit 42% and 35% identity to the human NPC1 protein, respectively. Here we describe the results of mutational analysis of the NPC1a gene. The NPC1a gene is ubiquitously expressed, and a null allele of NPC1a confers early larval lethality. The recessive lethal phenotype of NPC1a mutants can be partially rescued on a diet of high cholesterol or one that includes the insect steroid hormone 20-hydroxyecdysone. We also find that expression of NPC1a in the ring gland is sufficient to rescue the lethality associated with the loss of NPC1a and that cholesterol levels in NPC1a mutant larvae are unchanged relative to controls. Our results suggest that NPC1a promotes efficient intracellular trafficking of sterols in many Drosophila tissues including the ring gland where sterols must be delivered to sites of ecdysone synthesis.
Multiple Bromodomain Genes Are Involved in Restricting the Spread of Heterochromatic Silencing at theSaccharomyces cerevisiae HMR-tRNA Boundary
Authors: Jambunathan Nithya , Martinez Adam W , Robert Elizabeth C , Agochukwu Nneamaka B , Ibos Megan E , Dugas Sandra L , Donze David 
Published: August 2005

AbstractThe transfer RNA gene downstream from the HMR locus in S. cerevisiae functions as part of a boundary (barrier) element that restricts the spread of heterochromatic gene silencing into the downstream region of chromosome III. A genetic screen for identifying additional genes that, when mutated, allow inappropriate spreading of silencing from HMR through the tRNA gene was performed. YTA7, a gene containing bromodomain and ATPase homologies, was identified multiple times. Previously, others had shown that the bromodomain protein Bdf1p functions to restrict silencing at yeast euchromatin-heterochromatin boundaries; therefore we deleted nonessential bromodomain-containing genes to test their effects on heterochromatin spreading. Deletion of RSC2, coding for a component of the RSC chromatin-remodeling complex, resulted in a significant spread of silencing at HMR. Since the bromodomain of YTA7 lacks a key tyrosine residue shown to be important for acetyllysine binding in other bromodomains, we confirmed that a GST-Yta7p bromodomain fusion was capable of binding to histones in vitro. Epistasis analysis suggests that YTA7 and the HMR-tRNA function independently to restrict the spread of silencing, while RSC2 may function through the tRNA element. Our results suggest that multiple bromodomain proteins are involved in restricting the propagation of heterochromatin at HMR.
Internal source monitoring and communication disturbance in patients with schizophrenia
Authors: NIENOW TASHA M. , DOCHERTY NANCY M. 
Published: August 2005

Background. This study examined the relationship between internal source monitoring and disordered speech in patients with schizophrenia or schizoaffective disorder. It was predicted that internal source monitoring would relate specifically to one type of communication disturbance, the missing information reference.Method. Immediate, working, and internal source memory were assessed in 47 out-patients diagnosed with schizophrenia or schizoaffective disorder. Speech samples were also collected from this sample and coded for six types of communication disturbance.Results. Of the six types of communication disturbance coded in this study, internal source monitoring indices were uniquely related to the frequency of the missing information reference. Furthermore, internal source monitoring was the only type of short-term memory process assessed in this study that was related to the missing information reference. Neither immediate nor working-memory capacity was related significantly to the frequency of this type of communication disturbance.Conclusions. This study adds to our knowledge of the neurocognitive processes that underlie communication disturbance in the speech of patients with schizophrenia.
Prevalence, service use, and demographic correlates of 12-month DSM-IV psychiatric disorders in Mexico: results from the Mexican National Comorbidity Survey
Authors: MEDINA-MORA M. ELENA , BORGES GUILHERME , LARA CARMEN , BENJET CORINA , BLANCO JERÓNIMO , FLEIZ CLARA , VILLATORO JORGE , ROJAS ESTELA , ZAMBRANO JOAQUÍN 
Published: August 2005

Background. This paper describes the 12-month prevalence, severity and demographic correlates of 16 DSM-IV psychiatric disorders and service utilization in the Mexican urban population aged 18–65 years of age. This is representative of 75% of the national adult population.Method. The sample design was a strict probability selection scheme. The response rate was 76·6%. The World Mental Health Survey version of the Composite International Diagnostic Interview was installed on laptops and administered by lay interviewers. An international WHO task force carried out its translation into Spanish.Results. The 12-month prevalence of any disorder was 12·1%. The most common disorders were specific phobia (4·0%), major depressive disorder (3·7%) and alcohol abuse or dependence (2·2%). The 12-month prevalence of very severe disorders was 3·7% of which only 24% used any services. Age was the only variable associated with any 12-month disorder, with the younger more likely to report any disorder. Income was associated with severity, with low and low–average incomes more likely to report a 12-month disorder. Females were more likely to report a mood and anxiety disorder, but less likely to report a substance disorder. The group of separated/widowed/divorced was more likely to report a mood and an impulse-control disorder.Conclusions. The results show that while psychiatric disorders are common in the Mexican population, very severe mental disorders are less common and there is extreme under-utilization of mental health services.
Age at onset and familial risk for major depression in a Swedish national twin sample
Authors: KENDLER KENNETH S. , GATZ MARGARET , GARDNER CHARLES O. , PEDERSEN NANCY L. 
Published: August 2005

Background. In many biomedical disorders, early age at onset (AAO) is an index of high liability to illness which is manifest by an increased risk of illness in relatives. Most but not all prior studies report such a pattern for major depression (MD).Method. Lifetime MD and AAO were assessed at personal interview using modified DSM-III-R criteria in 13864 twin pairs, including 4229 onsets of MD, from the Swedish National Twin Registry. Analyses were conducted using Cox proportional hazards models.Results. Controlling for year of birth, gender, zygosity, co-twin history of MD and the interaction of zygosity and co-twin history, the best-fit model showed a significant main effect and a quadratic effect of AAO of MD in the co-twin on the log hazard ratio for MD in the index twin. When examined together, these effects predicted that from the ages of 15 to ~35 years, AAO of MD is moderately negatively related to risk of illness in relatives. However, past age 35, the function flattens out, with little change of risk in relatives with further increases of AAO. Even when the co-twin had a late AAO, the risk in the index twin substantially exceeded that seen when the co-twin had no history of MD.Conclusion. In this large sample, AAO is a meaningful, albeit modest, index of familial liability to MD. The relationship is nonlinear and results largely from an increased liability in individuals with an early AAO. These results should be interpreted in the context of the limitations of long-term recall.
Effect of olvanil and anandamide on vagal C‐fiber subtypes in guinea pig lung
Authors: Lee Min‐Goo , Weinreich Daniel , Undem Bradley J 
Published: August 2005

Certain fatty acid amides such as anandamide (AEA) and olvanil are agonists for the transient receptor potential, vanilloid‐1 (TRPV1) receptor, but have been found to activate TRPV1‐containing C‐fibers in some tissues but not others. We used extracellular recording and whole‐cell patch clamp techniques to investigate the effect of olvanil and AEA on different types of vagal C‐fibers innervating the same tissue, namely jugular and nodose vagal C‐fibers in guinea pig lungs.
A 30 s exposure to AEA and olvanil caused action potential discharge in all nodose C‐fiber innervating lung but failed to activate jugular C‐fibers innervating lung and airways. The activation of nodose C‐fibers was blocked by the TRPV1 antagonist iodo‐resiniferatoxin.
In whole‐cell patch clamp recordings of dissociated nodose and jugular capsaicin‐sensitive neurons labeled from lungs and airways, olvanil induced large TRPV1‐dependent inward currents in cell bodies of both nodose and jugular ganglion neurons.
Prolonged exposure (up to 5 min) to olvanil caused action potential discharge in jugular C‐fiber innervating lung but the onset latency was four times longer in jugular than in nodose C‐fibers. The onsets of capsaicin response in nodose and jugular C‐fibers were not different.
Decreasing the tissue temperature to 25°C increased the onset latency of olvanil‐induced activation of nodose C‐fibers 2–3‐fold, but did not effect the latency of the capsaicin response.
Capsaicin, olvanil, and AEA stimulate jugular C‐fibers leading to tachykinergic contractions of isolated bronchi. The time to reach half‐maximum is more than four times longer for olvanil and AEA, as compared to capsaicin in evoking contractions.
We conclude that brief exposure to certain fatty acid amides, such as AEA and olvanil activate nodose but not jugular C‐fiber terminals in the lungs. We hypothesize that this is because the nodose C‐fiber terminals are equipped with a temperature‐dependent mechanism for effectively and rapidly transporting the TRPV1 agonists so that they gain access to the intracellular binding sites on TRPV1. This transport mechanism may be differently expressed in two distinct subtypes of pulmonary C‐fiber terminals innervating the same tissue.

British Journal of Pharmacology (2005) 146, 596–603. doi:10.1038/sj.bjp.0706339
Electrophysiological and functional effects of the KCNQ channel blocker XE991 on murine portal vein smooth muscle cells
Authors: Yeung Shuk Yin M , Greenwood Iain A 
Published: August 2005

The effect of the KCNQ channel blockers XE991, chromanol 293B and linopirdine, was studied on voltage‐dependent K+currents in smooth muscle cells dissociated freshly from mouse portal vein (mPV) and isometric tension recordings from whole mPV.Voltage clamp experiments showed XE991 inhibited an outward current in a concentration‐dependent manner with an IC50of 5.8 μM. Block was voltage independent. Chromanol 293B and linopirdine also blocked the voltage‐dependent K+current but were less potent than XE991.At least two components – a linear (Ilinear) and an outward relaxation (Iout) – contributed to the XE991‐sensitive conductance.XE991‐sensitive currents were sustained at all test potentials and XE991 inhibited the enhanced holding current at −60 mV produced by bathing cells in an external solution containing 36 mMKCl.Current clamp experiments in the perforated‐patch configuration showed XE991 and linopirdine depolarised the resting membrane potential and augmented the evoked response in a concentration‐dependent manner.In functional experiments the spontaneous contractile activity of the mPV was increased significantly by XE991 and linopirdine. The stimulatory effect of XE991 was not affected by the presence of 4‐AP, glibenclamide nor paxilline.These data provide evidence for an important role for KCNQ channels in governing cellular excitability in mPV smooth muscle cells.British Journal of Pharmacology(2005)146, 585–595. doi:10.1038/sj.bjp.0706342
Enhancement of trypsin‐induced contraction by in vivo treatment with 17β‐estradiol and progesterone in rat myometrium
Authors: Aman Murasaki , Hirano Katsuya , Nishimura Junji , Nakano Hitoo , Kanaide Hideo 
Published: August 2005

We have previously reported that the contractile response to thrombin and trypsin was enhanced in the pregnant rat myometrium. We herein determined whether or not sex hormones contribute to this enhancement and the expression of protease‐activated receptors (PARs).
The nonpregnant rats received daily injections of either 17β‐estradiol or progesterone, and then the contractile response of the myometrium was examined ex vivo. Treatment with either 17β‐estradiol or progesterone had almost no significant enhancing effect on the high K+‐ or oxytocin‐induced contraction. On the other hand, both 17β‐estradiol and progesterone dose‐dependently enhanced the contractile response to trypsin. A maximal enhancement was obtained at 25 and 40 mg kg weight−1 day−1 for 17β‐estradiol and progesterone, respectively. The extent of the enhancement of the trypsin‐induced contraction seen in the sex hormone‐treated rats in the present study was comparable to that reported in the pregnant rats.
However, the contractile response to thrombin and PAR1/PAR2‐AP, SFLLRNP was not enhanced either by progesterone or 17β‐estradiol. PAR2‐AP and PAR4‐AP failed to induce contraction under any conditions.
PAR1 mRNA was scarcely detected in the control myometrium by an RT–PCR analysis, while it slightly increased only in the progesterone‐treated rats. Neither PAR2 nor PAR4 mRNA was detected.
We thus conclude that the responsiveness to trypsin, but not thrombin, is controlled by sex hormones. A novel type of receptor, other than PAR1, PAR2 or PAR4, is suggested to mediate the trypsin‐induced contraction as in the case of the pregnant rat myometrium.

British Journal of Pharmacology (2005) 146, 425–434. doi:10.1038/sj.bjp.0706345
Use‐dependent inhibition of the skeletal muscle ryanodine receptor by the suramin analogue NF676
Authors: Wolner Ilse , Kassack Matthias U , Ullmann Heiko , Karel Anton , Hohenegger Martin 
Published: August 2005

The skeletal muscle Ca2+release channel, the ryanodine receptor, is activated by the trypanocidal drug suraminviathe calmodulin‐binding site. As calmodulin activates and inhibits the ryanodine receptor depending on whether Ca2+is absent or present, suramin analogues were screened for inhibition of the ryanodine receptor.Up to 300 μM, the novel suramin analogue, 4,4′‐(carbonyl‐bis(imino‐4,1‐phenylene‐(2,5‐benzimidazolylene)carbonylimino))‐bis‐benzenesulfonic acid disodium salt (NF676) was not able to significantly inhibit the basal [3H]ryanodine binding. However, kinetic analysis of the high affinity [3H]ryanodine binding elucidates a time‐dependent increment of inhibition by NF676, which is indicative for an open channel blocker.Moreover, the ryanodine receptor was much more sensitive towards inhibition by NF676 when preactivated with caffeine or the nonhydrolysable ATP analogue, adenylyl‐imidodiphosphate. Nonetheless, the suramin activated ryanodine receptor was not susceptible towards high‐affinity NF676 inhibition, indicating an allosteric hindrance between the binding sites of suramin and NF676.In the line of this finding, NF676per sewas not capable to elute the purified ryanodine receptor from a calmodulin‐Sepharose, but it prevented the elution by suramin.Other than suramin, NF676 did not inhibit the Ca2+ATPase of the sarcoplasmic reticulum. However, suramin‐induced Ca2+release from sarcoplasmic reticulum was completely abrogated by preincubation with NF676.Taken together, we conclude from these data that NF676 represents a novel lead compound as a potent use‐dependent blocker of the skeletal muscle ryanodine receptorviaan allosteric interaction with the suramin‐binding site.British Journal of Pharmacology(2005)146, 525–533. doi:10.1038/sj.bjp.0706359
FIRST PRINCIPLES CALCULATION OF THE ELECTRONIC AND STRUCTURAL PROPERTIES OF USn3 USING LDA+U METHOD
Authors: POURGHAZI A. , NOURBAKHSH Z. 
Published: August 2005

The actinide compounds exhibit a variety of unusual ground states. These states are dominated by the strong electron-electron correlations that are not included in normal density-functional electronic band-structure calculation with the local density approximation. These correlations are taken into account in the local density approximation +U (LDA+U) method. We have calculated the Coulomb repulsion term U for uranium in USn 3 compound, and investigated the total and partial DOS for USn 3 using LDA+U method. The LDA+U results for USn 3 have been compared with similar results from a ThSn 3 model calculation through which the number of 5f electrons outside the U muffin-tin sphere in USn 3 has been deduced. We have also calculated the electric field gradient (EFG), which may be regarded as a measure of the asymmetry in charge distribution, at the Sn site in USn 3 in LDA , LDA+SO and LDA+SO+U methods, and have shown that the Coulomb repulsion term does not introduce any considerable effect on the electric field gradient at the Sn site.
Using Clustered Climate Regimes to Analyze and Compare Predictions from Fully Coupled General Circulation Models
Authors: Hoffman Forrest M. , Hargrove William W. , Erickson David J. , Oglesby Robert J. 
Published: August 2005

Abstract
Changes in Earth’s climate in response to atmospheric greenhouse gas buildup impact the health of terrestrial ecosystems and the hydrologic cycle. The environmental conditions influential to plant and animal life are often mapped as ecoregions, which are land areas having similar combinations of environmental characteristics. This idea is extended to establish regions of similarity with respect to climatic characteristics that evolve through time using a quantitative statistical clustering technique called Multivariate Spatio-Temporal Clustering (MSTC). MSTC was applied to the monthly time series output from a fully coupled general circulation model (GCM) called the Parallel Climate Model (PCM). Results from an ensemble of five 99-yr Business-As-Usual (BAU) transient simulations from 2000 to 2098 were analyzed. MSTC establishes an exhaustive set of recurring climate regimes that form a “skeleton” through the “observations” (model output) throughout the occupied portion of the climate phase space formed by the characteristics being considered. MSTC facilitates direct comparison of ensemble members and ensemble and temporal averages since the derived climate regimes provide a basis for comparison. Moreover, by mapping all land cells to discrete climate states, the dynamic behavior of any part of the system can be studied by its time-varying sequence of climate state occupancy. MSTC is a powerful tool for model developers and environmental decision makers who wish to understand long, complex time series predictions of models. Strong predicted interannual trends were revealed in this analysis, including an increase in global desertification; a decrease in the cold, dry high-latitude conditions typical of North American and Asian winters; and significant warming in Antarctica and western Greenland.
Phase Transition and Electric Conductivity of ASnCl3 (A = Cs and CH3NH3)
Authors: Yamada Koji , Kuranaga Yasuhisa , Ueda Keita , Goto Shusaku , Okuda Tsutomu , Furukawa Yoshihiro 
Published: August 2005

Abstract
A first-order phase transition of CsSnCl3 to a cubic perovskite phase was observed at Ttr = 379 K. The electric conductivity increased from 10−6 S cm−1 to 10−3 S cm−1 at the phase transition. The temperature dependence of the electric conductivity and the X-ray diffraction data for CsSnCl3 suggested a reconstructive nature of the phase transition. On the other hand, CH3NH3SnCl3 showed successive phase transitions at 283, 307, 331, and 463 K with increasing temperature. The highest temperature phase belongs to a cubic perovskite structure, and pyramidal SnCl3− anion exists below 465 K having distorted perovskite structures. The 119Sn NMR spectra for CH3NH3SnCl3 supported the coordination change around the Sn atom, and also suggested the onset of chloride-ion diffusion just below the phase-transition temperature to the cubic phase. The activation energy for chloride-ion diffusion was found to be 54 kJ mol−1 by analyzing the temperature dependence of 119Sn NMR T1. The electric conductivity of Cs and CH3NH3 salts, however, is governed by the semiconducting property of these compounds.