bluuebunny/crossref_metadata_2025 huggingface dataset:
A Welch‐type test for homogeneity of contrasts under heteroscedasticity with application to meta‐analysis
Authors: Kulinskaya E. , Dollinger M. B. , Knight E. , Gao H.
Published: November 2004

A common problem that arises in the meta‐analysis of several studies, each with independent treatment and control groups, is to test for the homogeneity of effect sizes without the assumptions of equal variances of the treatment and the control groups and of equal variances among the separate studies. A commonly used test statistic, frequently denoted as Q, is the weighted sum of squares of the differences of the individual effect sizes from the mean effect size, with weights inversely proportional to the variances of the effect sizes. The primary contributions of this article are the presentation of improved and very accurate approximations to the distributions of the Q statistic when the effect size is a linear contrast such as the difference between the treatment and control means. Our improved approximation to the distribution of Q under the null hypothesis is based on a multiple of an F‐distribution; its use yields a substantial reduction in the type I error rate of the homogeneity test. Our improved approximation to the distribution of Q under an alternative hypothesis is based on a shift of a chi‐square distribution; its use allows for much greater accuracy in the computation of the power of the homogeneity test. These two improved approximate distributions are developed using the Welch methodology of approximating the moments of Q by the use of multivariate Taylor expansions. The quality of these approximations is studied by simulation.

A secondary contribution of this article is a study of how best to combine the variances of the treatment and control groups (needed for the calculation of weights in the Q statistic). Our conclusion, based on simulations, is that use of pooled variances can result in substantially erroneous conclusions. Copyright © 2004 John Wiley & Sons, Ltd.
Comparison of Bayesian model averaging and stepwise methods for model selection in logistic regression
Authors: Wang Duolao , Zhang Wenyang , Bakhai Ameet
Published: November 2004

Logistic regression is the standard method for assessing predictors of diseases. In logistic regression analyses, a stepwise strategy is often adopted to choose a subset of variables. Inference about the predictors is then made based on the chosen model constructed of only those variables retained in that model. This method subsequently ignores both the variables not selected by the procedure, and the uncertainty due to the variable selection procedure. This limitation may be addressed by adopting a Bayesian model averaging approach, which selects a number of all possible such models, and uses the posterior probabilities of these models to perform all inferences and predictions. This study compares the Bayesian model averaging approach with the stepwise procedures for selection of predictor variables in logistic regression using simulated data sets and the Framingham Heart Study data. The results show that in most cases Bayesian model averaging selects the correct model and out‐performs stepwise approaches at predicting an event of interest. Copyright © 2004 John Wiley & Sons, Ltd.
Physicochemical, Thermal, Morphological and Pasting Properties of Starches from some Indian Black Gram (Phaseolus mungo L.) Cultivars
Authors: Singh Narpinder , Kaur Maninder , Sandhu Kawaljit Singh , Guraya Harmeet Singh
Published: November 2004

The starches separated from thirteen different black gram cultivars were investigated for physicochemical, thermal, morphological and pasting properties. Amylose content, swelling power, solubility and water binding capacity of starches ranged between 30.2–34.6%, 16.0–22.3 g/g, 14.8–17.3% and 73.5–84.5%, respectively. The diameter of starch granules, measured using a laser‐light scattering particle‐size analyzer, varied from 12.8 to 14.3 μm in all black gram starches. The shape of starch granules varied from oval to elliptical. The transition temperatures (To, Tp and Tc) and enthalpy of gelatinization (ΔHgel) determined using differential scanning calorimetry, ranged between 66.1–71.3, 71.0–76.2, 75.9–80.4°C and 6.7–9.4 J/g, respectively. Pasting properties of starches measured using the Rapid Visco Analyser (RVA) also differed significantly. Pasting temperature, peak viscosity, trough, breakdown, final viscosity and setback were between 75.8–80.3°C, 422–514, 180–311, 134–212, 400–439 and 102–151 Rapid Visco Units (RVU), respectively. Turbidity values of gelatinized starch pastes increased during refrigerated storage. The relationships between different properties were also determined using Pearson correlation coefficients. Amylose content showed a positive correlation with swelling power, turbidity and granule diameter. Swelling power showed a negative correlation with solubility and setback. To, Tp and Tc showed positive correlation with turbidity, pasting temperature and were negatively correlated to peak and breakdown viscosity.
Unimolecular rectifiers and prospects for other unimolecular electronic devices
Authors: Metzger Robert M.
Published: November 2004

We briefly review the progress towards useful one‐molecule electronic devices, toward the ultimate reduction in integrated circuit sizes, and then describe five unimolecular rectifiers, or one‐way conductors of electrical current: γ‐hexadecylquinolinium tricyanoquinodimethanide, an acetyl sulfoxide derivative of this compound, 2,6‐di[dibutylamino‐phenylvinyl]‐1‐butylpyridinium iodide, dimethylanilino‐aza[C60]fullerene, and a new fullerene derivative. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 4: 291–304; 2004: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20015
Homochirality and life
Authors: Fujii Noriko , Saito Takeshi
Published: November 2004

Before the emergence of life, left‐handed amino acids (L‐enantiomers) were selected and right‐handed amino acids (D‐enantiomers) were eliminated on the primal earth. Nevertheless, with the progress of analytical methods, D‐amino acids have recently been found in higher order living organisms in the form of free amino acids, peptides, and proteins. Free D‐amino acids have numerous physiological functions. D‐amino acids containing animal peptides are well known as opioid peptides. D‐amino acids in protein are related to aging. In this review, we describe the D‐amino acids that are present and function as D‐amino acid biosystems in our bodies. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 4: 267–278; 2004: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20020
Butanol fermentation research: upstream and downstream manipulations
Authors: Ezeji Thaddeus C. , Qureshi Nasib , Blaschek Hans P.
Published: November 2004

An overview of advances in acetone–butanol fermentation research is presented with specific reference to the history of acetone–butanol fermentation, genetic manipulation of the butanol‐producing Clostridium beijerinckii NCIMB 8052, as well as upstream and downstream processing. Specific reference is made to the development of the hyperamylolytic, hyper‐“butanolagenic” C. beijerinckii BA101 strain. Amylolytic enzyme production by C. beijerinckii BA101 was 1.8‐ and 2.5‐fold greater than that of the C. beijerinckii NCIMB 8052 strain grown in starch and glucose, respectively. We confirmed the presence of a phosphoenolpyruvate (PEP)‐dependent phosphotransferase system (PTS) associated with cell extracts of C. beijerinckii BA101 by glucose phosphorylation by PEP and ATP‐dependent glucose phosphorylation. It was found that C. beijerinckii BA101 was defective in PTS activity and that it compensates for this defect with enhanced glucokinase activity, resulting in an ability to transport and utilize glucose during the solventogenic stage. The principal problem associated with acetone–butanol fermentation by C. beijerinckii or C. acetobutylicum is butanol toxicity/inhibition to the culture. To solve this problem, we have attempted various alternative in situ/online techniques of butanol removal including membrane‐based systems such as pervaporation, liquid–liquid extraction, and gas stripping. We found that gas stripping and pervaporation appear to be the most promising of the in situ acetone–butanol fermentation and recovery techniques but, in terms of cost‐effective industrial applications, gas stripping appears to be the most promising. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 4: 305–314; 2004: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20023
Professional development in inquiry‐based science for elementary teachers of diverse student groups
Authors: Lee Okhee , Hart Juliet E. , Cuevas Peggy , Enders Craig
Published: November 2004

As part of a larger project aimed at promoting science and literacy for culturally and linguistically diverse elementary students, this study has two objectives: (a) to describe teachers' initial beliefs and practices about inquiry‐based science and (b) to examine the impact of the professional development intervention (primarily through instructional units and teacher workshops) on teachers' beliefs and practices related to inquiry‐based science. The research involved 53 third‐ and fourth‐grade teachers at six elementary schools in a large urban school district. At the end of the school year, teachers reported enhanced knowledge of science content and stronger beliefs about the importance of science instruction with diverse student groups, although their actual practices did not change significantly. Based on the results of this first year of implementation as part of a 3‐year longitudinal design, implications for professional development and further research are discussed. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 1021–1043, 2004
Science literacy and academic identity formulation
Authors: Reveles John M. , Cordova Ralph , Kelly Gregory J.
Published: November 2004

The purpose of this article is to report findings from an ethnographic study that focused on the co‐development of science literacy and academic identity formulation within a third‐grade classroom. Our theoretical framework draws from sociocultural theory and studies of scientific literacy. Through analysis of classroom discourse, we identified opportunities afforded students to learn specific scientific knowledge and practices during a series of science investigations. The results of this study suggest that the collective practice of the scientific conversations and activities that took place within this classroom enabled students to engage in the construction of communal science knowledge through multiple textual forms. By examining the ways in which students contributed to the construction of scientific understanding, and then by examining their performances within and across events, we present evidence of the co‐development of students' academic identities and scientific literacy. Students' communication and participation in science during the investigations enabled them to learn the structure of the discipline by identifying and engaging in scientific activities. The intersection of academic identities with the development of scientific literacy provides a basis for considering specific ways to achieve scientific literacy for all students. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 1111–1144, 2004
Cell biology, chemogenomics and chemoproteomics
Authors: Gagna Claude E. , Winokur Dena , Lambert W. Clark
Published: November 2004

The scientific techniques used in molecular biological research and drug discovery have changed dramatically over the past 10 years due to the influence of genomics, proteomics and bioinformatics. Furthermore, genomics and functional genomics are now merging into a new scientific approach called chemogenomics.

Advancements in the study of molecular cell biology are dependent upon “omics” researchers realizing the importance of and using the experimental tools currently available to cell biologists. For example, novel microscopic techniques utilizing advanced computer imaging allow for the examination of live specimens in a fourth dimension, viz., time.

Yet, molecular biologists have not taken full advantage of these and other traditional and novel cell biology techniques for the further advancement of genomic and proteomic‐oriented research. The application of traditional and novel cellular biological techniques will enhance the science of genomics. The authors hypothesize that a stronger interdisciplinary approach must be taken between cell biology (and its closely related fields) and genomics, proteomics and bio‐chemoinformatics.

Since there is a lot of confusion regarding many of the “omics” definitions, this article also clarifies some of the basic terminology used in genomics, and related fields. It also reviews the current status and future potential of chemogenomics and its relationship to cell biology. The authors also discuss and expand upon the differences between chemogenomics and the relatively new term—chemoproteomics. We conclude that the advances in cell biology methods and approaches and their adoption by “omics” researchers will allow scientists to maximize our knowledge about life.
Women's Interpretation of their Coronary Heart Disease Symptoms
Authors: Lockyer Lesley
Published: November 2004

Background: Men and women are known to delay in seeking medical attention when experiencing acute cardiac symptoms. However, women are more likely to have had chronic undifferentiated symptoms prior to an acute episode and then when experiencing an acute episode delay longer than do men. Studies have shown once women do present they tend to be further along the disease trajectory than men.

Aims: The aim of this study was to explore women's own interpretation of the presenting symptoms they experienced.

Methods: Twenty-nine women consented to take part in semi-structured interviews that focussed on their experience of coronary heart disease (CHD). The women's narrative around the initial disruption of their illness was analysed focusing on routine and reconstructed forms of narration.

Results: The results showed that many failed to recognise and act on their symptoms. Most only sought medical attention after family or friends intervened. None of the women had seen themselves at risk of developing coronary heart disease despite many have a strong family history.

Conclusion: The women's early symptoms of coronary heart disease were often undifferentiated and difficult to interpret by the women themselves. There is a need for further research to understand and recognise early symptoms of coronary heart disease in women. This will allow women and health professionals to assess risk and identify women with coronary heart disease early on in their disease trajectory so therapy to prevent the morbidity associated with coronary heart disease and acute life threatening episodes will be reduced.
Restrictive filling pattern is associated with increased humoral activation and impaired exercise capacity in dilated cardiomyopathy
Authors: Patrianakos Alexander P. , Parthenakis Frangiskos I. , Papadimitriou Evangelos A. , Diakakis George F. , Tzerakis Panagiotis G. , Nikitovic Dragana , Vardas Panos E.
Published: November 2004

Objectives:

Although heart failure (HF) is characterized by increased proinflammatory cytokines, natriuretic peptide levels and impaired exercise capacity, the effect of concomitant diastolic dysfunction on those parameters has not been adequately studied.

Methods:

We analyzed circulating levels of IL‐1, IL‐6, TNF‐α and its soluble receptors, sTNFRI and sTNFRII, Nt‐ANP and Nt‐BNP natriuretic peptides in 81 patients, aged 56±12 years, with non‐ischemic dilated cardiomyopathy (NIDC), LVEF 29.7±7.75% and functional NYHA class II‐III. An echocardiographic study and cardiopulmonary exercise test (CPE) were performed in all patients.

Results:

Patients were divided into restrictive (24 patients, group I) and non‐restrictive (57 patients, group II) groups, according to their transmitral‐filling pattern. No differences in LV dimensions or LVEF were found between the two groups. Group I showed increased levels of IL‐6 (P=0.006), TNF‐α (P=0.05), sTNFRII (P=0.02), Nt‐ANP (P<0.001) and Nt‐BNP (P<0.001) and decreased exercise duration (P<0.001) and PVO2 (P<0.001) compared to group II. The strongest independent predictors for restrictive filling pattern were Nt‐ANP and IL‐6 levels, while Nt‐BNP levels were the strongest PVO2 predictor.

Conclusions:

Restrictive filling pattern implying greater diastolic dysfunction may contribute to increased cytokine production in the heart failure syndrome, as well as greater increases in natriuretic peptides and decreased exercise tolerance.
The diagnosis of heart failure in primary care: value of symptoms and signs
Authors: Fonseca Cândida , Morais Humberto , Mota Teresa , Matias Fernando , Costa Catarina , Gouveia‐Oliveira António , Ceia Fátima ,   on behalf of the EPICA Investigators
Published: November 2004

Background

The value of symptoms and signs in the diagnosis of CHF has rarely been tested in large numbers of patients in the community. The aim of this study was to evaluate the importance of symptoms, signs, and past medical history in the diagnosis of CHF in primary care.

Methods

Data on a sample of Portuguese men and women attending 365 primary care centres for any condition other than the treatment of acute infection, metabolic conditions or pregnancy were collected. All subjects who scored three or more points in the sum of categories one and two of the Boston questionnaire (history and physical examination) and those being treated for heart failure with loop or thiazide diuretics were considered to have possible heart failure and referred for further assessment including a resting echocardiogram. The sensitivity, specificity, positive predictive value, negative predictive value and likelihood ratio (LR) for the diagnosis of heart failure were calculated.

Results

A total of 5434 subjects were identified, of whom 1058 fulfilled the criteria for further assessment; 551 subjects had cardiac dysfunction at rest, of which 35.5% were in NYHA class I and 4.9% in class IV. Prior use of digoxin (LR 24.9) and/or diuretics (LR 10.6), a history of coronary artery disease (LR 7.1) or of pulmonary oedema (LR 54.2), were associated with a greater likelihood of having heart failure. Amongst current symptoms, a history of paroxysmal nocturnal dyspnoea (LR 35.5), orthopnea (LR 39.1) and breathlessness when walking on the flat (LR 25.8) were associated with a diagnosis of heart failure. However, these symptoms were not frequent amongst patients with heart failure within this population (sensitivity <36%). Jugular pressure > 6 cm with hepatic enlargement, and oedema of the lower limbs (LR 130.3), a ventricular gallop (LR 30.0), a heart rate above 110 bpm (LR 26.7), and rales at pulmonary auscultation (LR 23.3) were all associated with a diagnosis of heart failure, but were infrequent findings in patients with heart failure (sensitivity <10%).

Conclusions

Symptoms and signs, and clinical history had limited value in diagnosing heart failure when used alone. The signs and symptoms that best predicted a diagnosis of heart failure were those associated with more severe disease. If investigation is limited to patients with more definite symptoms and signs of heart failure, fewer than 50% of cases will be identified and a large number of patients with mild symptoms will be missed.
NMDA receptor‐mediated calcium influx plays an essential role in myoblast fusion
Authors: Lee Kun Ho , Park Jae-Yong , Kim Kyungjin
Published: November 2004

Ca2+ influx is known to be prerequisite for myoblast fusion during skeletal muscle differentiation. Here, we show that the N‐methyl‐D‐aspartate (NMDA) receptor is involved in the Ca2+ influx of C2C12 myoblasts. NMDA receptor (NR) 1 and NR2D were expressed in the myoblasts during muscle differentiation. Using Ca2+ imaging analysis, Ca2+ influx through NRs was directly measured at a single‐cell level. l‐Glutamate increased myoblast fusion as well as intracellular Ca2+ levels, and both effects were completely blocked by MK801, a selective antagonist of NRs. Furthermore, treatment with the Ca2+ ionophore A23187 recovered MK801‐mediated inhibition of myoblast fusion. These results suggest that the NRs may play an important role in myoblast fusion by mediating Ca2+ influx.
Specific association of annexin 1 with plasma membrane‐resident and internalized EGF receptors mediated through the protein core domain
Authors: Radke Susanne , Austermann Judith , Russo-Marie Francoise , Gerke Volker , Rescher Ursula
Published: November 2004

Phosphorylation of the Ca2+ and membrane‐binding protein annexin 1 by epidermal growth factor (EGF) receptor tyrosine kinase has been thought to be involved in regulation of the EGF receptor trafficking. To elucidate the interaction of annexin 1 during EGF receptor internalization, we followed the distribution of annexin 1‐GFP fusion proteins at sites of internalizing EGF receptors. The observed association of annexin 1 with EGF receptors was confirmed by immunoprecipitation. We found that this interaction was independent of a functional phosphorylation site in the annexin 1 N‐terminal domain but mediated through the Ca2+ binding core domain.
Hypoplastic Synpolydactyly as a New Clinical Subgroup of Synpolydactyly
Authors: KURU ILHAMI , SAMLI HALE , YUCEL AYLIN , BOZAN M. ERAY , TURKMEN SEVAL , SOLAK MUSTAFA
Published: November 2004

A large kindred which was first described in 1995 was investigated again. We present the clinical, radiological, genetic and surgical findings of the hand deformities found in homozygote individuals which we called “hypoplastic synpolydactyly”.

There were 125 affected (heterozygote or homozygote) people out of 245 subjects in the five last generations. We identified seven marriages of two affected people. Twelve offsprings, of these marriages had a homozygote genetic pattern and “hypoplastic synpolydactyly”. From both the clinical and surgical perspectives, their hand deformity was distinctive from that of their parents. We surgically treated both hands of three individuals with this deformity.

The hand deformity of these homozygotes was so complicated and distinctive that it can be evaluated as a new subgroup of synpolydactyly.
Late quaternary alluvial stratigraphy of a low-order tributary in central texas, USA and its response to climate and sediment supply
Authors: Nordt Lee
Published: November 2004

This paper presents the first comprehensive late Quaternary alluvial stratigraphic study of a low-order tributary in central Texas, using Cowhouse Creek as a case study. The late Pleistocene Jackson (JA) alluvium forms the elevated T2 terrace. The entrenched Holocene valley is filled with the buried Georgetown (GT) alluvium (approximately 11,000 to 8000 14C yr B.P.) and associated Royalty paleosol, and the surficially exposed Fort Hood (FH) alluvium (approximately 7000 to 5000 14C yr B.P.) and West Range (WR) alluvium (approximately 4200 to 600 14C yr B.P.) forming the broad T1 terrace. The Ford (FO) alluvium (<600 14C yr B.P.) forms the modern T0 floodplain entrenched into T1. Conditioned by cooler and wetter climates, Cowhouse Creek was characterized by relatively high base flow and low sediment supply during deposition of the JA and GT alluvium. Appreciable upland soil erosion ensued during the middle Holocene in response to warmer climate conditions, resulting in widespread valley filling by the FH alluvium. Deposition of the late Holocene WR and F0 alluvium was characterized by diminished sediment storage during relatively stable climate conditions. The temporal alluvial stratigraphic framework of the bedrock-confined Cowhouse Creek valley is out of phase with the alluvial sequence in the larger Brazos River valley.
Flow reversals during upwelling conditions on the New Jersey inner shelf
Authors: Chant Robert J. , Glenn Scott , Kohut Josh
Published: November 2004

The temporal evolution of a flow reversal during upwelling conditions along New Jersey's inner shelf is characterized with shipboard, moored, and remote observations. The flow reversal occurs nearshore in the form of a subsurface jet with maximum velocities exceeding 30 cm/s. The jet is most intense in the thermocline, commences during maximum alongshore wind stress, and has a spin‐up time approximately equal to the local inertial period. The jet also has a surface signature apparent in ocean current radar data that shows the jet veering offshore and feeding an upwelling center that drifts southward at 5 cm/s. Moored instrumentation within the upwelling center indicates that cross‐shelf transport in the warm surface layer is consistent with the predicted Ekman transport prior to the spin‐up of the jet, but exceeds Ekman transport thereafter. However, onshore transport in the lower layer never compensates for offshore flow in the surface layer, suggestive that the mass balance requires a three‐dimensional closure. Finally, we suggest that the flow reversal provides a significant fraction of cool water to the evolving upwelling center, and that the offshore veering is due to enhanced friction over a shoaling and rougher topography.
Exploring the multicollection approach for the40Ar/39Ar dating technique
Authors: Coulié E. , Quidelleur X. , Lefèvre J.‐C. , Gillot P.‐Y.
Published: November 2004

We present an original analytical system for40Ar/39Ar dating. It makes use of a 180° sector multicollection mass spectrometer equipped with five Faraday cups, which renders peak switching unnecessary during argon isotopic analyses. Compared to the single‐collector approach commonly used for argon isotopic analyses, our system presents greater stability during data acquisition. Faraday cup efficiencies, which can be a limiting factor for the multicollection mass spectrometer, were highly reproducible. The analytical validity of the40Ar/39Ar ages obtained using this new mass spectrometer has been preliminarily tested using geological standard minerals (MMhb‐1, FCT‐San, and HD‐B1) commonly used as neutron fluence monitors. Independent plateau age determinations of Ethiopian samples duplicated over a 1‐year interval demonstrated the reproducibility of the analyses. The results of these measurements highlight the good behavior of this new instrument for40Ar/39Ar step heating dating. The age reproducibility of successive steps leads to analytical errors lower than 0.1% for well‐behaved samples. This system, still in its initial stage of development, represents an alternative solution that is worth exploring in order to improve absolute dating by the40Ar/39Ar technique.
Modelling the exceptional Baltic Sea inflow events in 2002–2003
Authors: Lehmann Andreas , Lorenz Philip , Jacob Daniela
Published: November 2004

During 2002 and 2003 exceptional inflow events have been registered. In January 2003 a massive inflow of highly saline, cold and extremely oxygen‐rich water from the North Sea was recorded at Darss Sill. This event is considered to be the most important inflow since 1993. A coupled model system for the Baltic Sea region, called BALTIMOS, was developed in the frame of DEKLIM/BALTEX by linking existing model components for the atmosphere (model REMO), for the ocean including sea ice (model BSIOM), for the hydrology (model LARSIM) as well as for lakes. The model system consists of high resolution model components: 1/6° (∼18 km) with 20 vertical levels; ocean‐ice 5 km with 60 vertical levels, hydrology 1/6°. The model domain covers the whole drainage basin of the Baltic Sea as well as major parts of Europe. The exceptional inflow events have been simulated successfully with BALTIMOS. The simulation was initialized at 1st of February 2002 and the model has been run until October 2003. This period includes the exceptional warm water inflow in autumn 2002 and the major Baltic inflow in January 2003. Different inflow characteristics are presented and discussed. The simulated volume transport for the major inflow in January 2003 amounts to about 250 km3, half of which was of salinity 17 PSU which corresponds to a salt transport of 2.7 × 1012 kg.
Vulnerability of two European lakes in response to future climatic changes
Authors: Danis Pierre‐Alain , von Grafenstein Ulrich , Masson‐Delmotte Valérie , Planton S. , Gerdeaux D. , Moisselin J.‐M.
Published: November 2004

Temperate deep freshwater lakes are important resources of drinking water and fishing, and regional key recreation areas. Their deep water often hosts highly specialised fauna surviving since glacial times. Theoretical and observational studies suggest a vulnerability of these hydro‐ecosystems to reduced mixing and ventilation within the ongoing climatic change. Here we use a numerical thermal lake model, verified over the 20th century, to quantify the transient thermal behaviour of two European lakes in response to the observed 20th‐century and predicted 21th‐century climate changes. In contrast to Lac d'Annecy (France) which, after adaptation, maintains its modern mixing behaviour, Ammersee (Germany) is expected to undergo a dramatic and persistent lack of mixing starting from ∼2020, when European air temperatures should be ∼1°C warmer. The resulting lack of oxygenation will irreversibly destroy the deepwater fauna prevailing since 15 kyrs.
New paleomagnetic, rock magnetic, and petrographic results from the Valle Group, Baja California, Mexico: Exploring the causes of anomalously shallow paleomagnetic inclinations
Authors: Li Yong‐Xiang , Kodama Kenneth P. , Smith Douglas P.
Published: November 2004

A detailed paleomagnetic, rock magnetic, and sedimentologic study was conducted on Cenomanian‐age strata of the Valle Group at El Campito, Baja California, to examine the burial compaction effects on the paleomagnetic inclination of marine sedimentary rocks. Alternating field and thermal demagnetization isolated a characteristic remanence at 16 of 18 sites with a mean of Dec = 342.6°, Inc = 19.1°, and α95= 3.4°. The inclination is 38.7° shallower than that predicted by the reference paleopole for North America. Laboratory experiments indicate that compaction could account for only 7.5° of the inclination shallowing. Fold tests at different scales yield both positive and negative results, making a tight constraint on the remanence's age impossible. A primary postdepositional remanence is supported by bedding‐parallel foliations in the anisotropy of anhysteretic remanence fabric. Although primary anomalously shallow inclinations could indicate significant southerly, then northerly, paleolatitudinal offset, a more likely scenario is a late Cenozoic low‐temperature remagnetization, which is suggested by alteration along the edges of some detrital silicate grains and a bimodal magnetic grain size distribution revealed by isothermal remanence data. The synthesis of the data indicates that the Vizcaino terrane was contiguous with the Cordillera margin during remagnetization and underwent a subsequent 13.5 ± 5.4° clockwise rotation. We tentatively interpret that the remagnetization resulted from burial and/or Miocene volcanism, which caused an acquisition of thermochemical remanent magnetization (TCRM). This study reveals a complicated remanence that resists easy interpretation and suggests caution in studies of similar rocks.
ARF6‐dependent interaction of the TWIK1 K+ channel with EFA6, a GDP/GTP exchange factor for ARF6
Authors: Decressac Sonia , Franco Michel , Bendahhou Said , Warth Richard , Knauer Sebastian , Barhanin Jacques , Lazdunski Michel , Lesage Florian
Published: November 2004

TWIK1 belongs to a family of K+ channels involved in neuronal excitability and cell volume regulation. Its tissue distribution suggests a role in epithelial potassium transport. Here we show that TWIK1 is expressed in a subapical compartment in renal proximal tubules and in polarized MDCK cells. In nonpolarized cells, this compartment corresponds to pericentriolar recycling endosomes. We identified EFA6, an exchange factor for the small G protein ADP‐ribosylation factor 6 (ARF6), as a protein binding to TWIK1. EFA6 interacts with TWIK1 only when it is bound to ARF6. Because ARF6 modulates endocytosis at the apical surface of epithelial cells, the ARF6/EFA6/TWIK1 association is probably important for channel internalization and recycling.
An algebraic Birkhoff decomposition for the continuous renormalization group
Authors: Girelli Florian , Krajewski Thomas , Martinetti Pierre
Published: November 2004

This paper aims at presenting the first steps towards a formulation of the Exact Renormalization Group Equation in the Hopf algebra setting of Connes and Kreimer. It mostly deals with some algebraic preliminaries allowing us to formulate perturbative renormalization within the theory of differential equations. The relation between renormalization, formulated as a change of boundary condition for a differential equation, and an algebraic Birkhoff decomposition for rooted trees is explicited.
On spherically symmetric solutions with horizon in model with multicomponent anisotropic fluid
Authors: Dehnen H. , Ivashchuk V. D.
Published: November 2004

A family of spherically symmetric solutions in the model with m-component multicomponent anisotropic fluid is considered. The metric of the solution depends on parameters qs>0, s=1,…,m, relating radial pressures and the densities and contains (n−1)m parameters corresponding to Ricci-flat “internal space” metrics and obeying certain m(m−1)/2 (“orthogonality”) relations. For qs=1 (for all s) and certain equations of state (pis=±ρs) the metric coincides with the metric of intersecting black brane solution in the model with antisymmetric forms. A family of solutions with (regular) horizon corresponding to natural numbers qs=1,2,… is singled out. Certain examples of “generalized simulation” of intersecting M-branes in D=11 supergravity are considered. The post-Newtonian parameters β and γ corresponding to the four-dimensional section of the metric are calculated.
Relativistic electron beam acceleration by nonlinear Landau damping of electrostatic waves in a magnetized plasma
Authors: Sugaya R.
Published: November 2004

Acceleration and heating of a relativistic electron beam due to nonlinear electron Landau and cyclotron damping of electrostatic waves in a magnetized plasma are investigated theoretically and numerically on the basis of the relativistic kinetic wave and transport equations derived from the relativistic Vlasov–Maxwell equations. Two electrostatic waves interact nonlinearly with the relativistic electron beam satisfying the resonance condition for nonlinear electron Landau and cyclotron damping of ωk−ωk′−(k⊥−k⊥′)vd−(k∥−k∥′)vb≃mωce where vb and vd are the parallel and perpendicular velocities of the relativistic electron beam, respectively, and ωce is the relativistic electron cyclotron frequency. The beat waves produced by two electrostatic waves resonate with the relativistic electron beam. The relativistic transport equations using the relativistic drifted Maxwellian momentum distribution function of the relativistic electron beam were derived and analyzed. They show obviously its acceleration and heating (deceleration or cooling). Nonlinear electron Landau damping of the two lower-hybrid waves has been studied by the numerical analysis of relativistic nonlinear wave-particle coupling coefficients and it was clarified that the highly relativistic electron beam can be accelerated efficiently via the Compton scattering due to nonlinear electron Landau damping of the lower-hybrid waves.
Threshold-crossing counting technique for damping factor determination of resonator sensors
Authors: Zeng Kefeng , Grimes Craig A.
Published: November 2004

The behavior of resonator-type sensors at resonance is characterized by two fundamental parameters: resonance frequency and damping factor (or Q-factor). Practical applications require accurate and efficient measurements of these two parameters. Using magnetoelastic resonant sensors as a test case earlier work [K. Zeng, K. G. Ong, C. Mungle, and C. A. Grimes, Rev. Sci. Instrum. 73, 4375 (2002)] demonstrated the ability to determine resonance frequency by counting the number of cycles in the transient response of a pulsewise excited sensor. Presented in this paper is a novel technique for measuring the damping factor of a resonant magnetoelastic sensor, or any resonator type sensor, using threshold-crossing counting of the transient response. The damping factor determination technique eliminates the need for a lock-in amplifier or FFT analysis as in the conventional method of quality factor estimation from spectrum analysis, significantly simplifying the electronic implementation as well as improving measurement speed and accuracy.
Magnetic resonance-guided near-infrared tomography of the breast
Authors: Brooksby Ben , Jiang Shudong , Dehghani Hamid , Pogue Brian W. , Paulsen Keith D. , Kogel Christine , Doyley Marvin , Weaver John B. , Poplack Steven P.
Published: November 2004

The design and implementation of a multispectral, frequency-domain near infrared tomography system is outlined, which operates in a MRI magnet for utilization of MR-guided image reconstruction of tissue optical properties. Using long silica optical fiber bundles, measurements of light transmission through up to 12 cm of female breast tissue can be acquired simultaneously with MRI scans. The NIR system utilizes six optical wavelengths from 660 to 850 nm using intensity modulated diode lasers nominally working at 100 MHz. Photomultiplier tube detector gain levels are electronically controlled on a time scale of 200 ms, thereby allowing rapid switching of the source to locations around the tissue. There are no moving parts in the detection channels and for each source position, 15 PMTs operating in parallel allow sensitivity down to 0.5 pW/cm2 at the tissue surface. Images of breast tissue optical absorption and reduced scattering coefficients are obtained using a Newton-type reconstruction algorithm to solve for an optimal solution using the measurement data. In medical imaging, it is beneficial to compare the same tissue volume as seen by a variety of modalities, and perhaps more importantly, there is the hypothesis that one imaging system which has high spatial resolution can be used to enhance the reconstruction of another system which has good contrast resolution. In this study we explore the synergistic benefits of a combined NIR-MRI data set, specifically the ways in which MRI (i.e., high spatial resolution) enhances NIR (i.e., high contrast resolution) image reconstruction. The design, calibration, and performance of the imaging system are described in the context of preliminary phantom tests and initial in vivo patient imaging. Co-registered MRI validates and improves optical property estimation in 2D tomographic image reconstructions when specialized algorithms are used.
Bbs2
-null mice have neurosensory deficits, a defect in social dominance, and retinopathy associated with mislocalization of rhodopsin
Authors: Nishimura Darryl Y. , Fath Melissa , Mullins Robert F. , Searby Charles , Andrews Michael , Davis Roger , Andorf Jeaneen L. , Mykytyn Kirk , Swiderski Ruth E. , Yang Baoli , Carmi Rivka , Stone Edwin M. , Sheffield Val C.
Published: November 2004

Bardet–Biedl syndrome (BBS) is a heterogeneous, pleiotropic human disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, hypogenitalism, and an increased incidence of diabetes and hypertension. No information is available regarding the specific function of BBS2. We show that mice lacking
Bbs2
gene expression have major components of the human phenotype, including obesity and retinopathy. In addition, these mice have phenotypes associated with cilia dysfunction, including retinopathy, renal cysts, male infertility, and a deficit in olfaction. With the exception of male infertility, these phenotypes are not caused by a complete absence of cilia. We demonstrate that BBS2 retinopathy involves normal retina development followed by apoptotic death of photoreceptors, the primary ciliated cells of the retina. Photoreceptor cell death is preceded by mislocalization of rhodopsin, indicating a defect in transport. We also demonstrate that
Bbs2
–/–
mice and a second BBS mouse model,
Bbs4
–/–
, have a defect in social function. The evaluation of
Bbs2
–/–
mice indicates additional phenotypes that should be evaluated in human patients, including deficits in social interaction and infertility.
Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips
Authors: Huang Jing , Zhu Heng , Haggarty Stephen J. , Spring David R. , Hwang Heejun , Jin Fulai , Snyder Michael , Schreiber Stuart L.
Published: November 2004

The TOR (target of rapamycin) proteins play important roles in nutrient signaling in eukaryotic cells. Rapamycin treatment induces a state reminiscent of the nutrient starvation response, often resulting in growth inhibition. Using a chemical genetic modifier screen, we identified two classes of small molecules, small-molecule inhibitors of rapamycin (SMIRs) and small-molecule enhancers of rapamycin (SMERs), that suppress and augment, respectively, rapamycin's effect in the yeast
Saccharomyces cerevisiae
. Probing proteome chips with biotinylated SMIRs revealed putative intracellular target proteins, including Tep1p, a homolog of the mammalian PTEN (phosphatase and tensin homologue deleted on chromosome 10) tumor suppressor, and Ybr077cp (Nir1p), a protein of previously unknown function that we show to be a component of the TOR signaling network. Both SMIR target proteins are associated with PI(3,4)P
2
, suggesting a mechanism of regulation of the TOR pathway involving phosphatidylinositides. Our results illustrate the combined use of chemical genetics and proteomics in biological discovery and map a path for creating useful therapeutics for treating human diseases involving the TOR pathway, such as diabetes and cancer.
A simple tool for drawing proteolytic peptide maps
Authors: Beynon Robert J.
Published: November 2004

Summary: I describe a simple standalone program that assists in the preparation of peptide digestion maps. These are useful for comparative studies and for locating peptides within a primary sequence. The program creates an output file as scalable vector graphics that can then be viewed in a web browser or imported into a graphics-editing program.

Availability: The program, as a standalone executable, is available upon request from the author.

Contact:  r.beynon@liv.ac.uk
Predicting fold novelty based on ProtoNet hierarchical classification
Authors: Kifer Ilona , Sasson Ori , Linial Michal
Published: November 2004

Motivation: Structural genomics projects aim to solve a large number of protein structures with the ultimate objective of representing the entire protein space. The computational challenge is to identify and prioritize a small set of proteins with new, currently unknown, superfamilies or folds.

Results: We develop a method that assigns each protein a likelihood of it belonging to a new, yet undetermined, structural superfamily. The method relies on a variant of ProtoNet, an automatic hierarchical classification scheme of all protein sequences from SwissProt. Our results show that proteins that are remote from solved structures in the ProtoNet hierarchy are more likely to belong to new superfamilies. The results are validated against SCOP releases from recent years that account for about half of the solved structures known to date. We show that our new method and the representation of ProtoNet are superior in detecting new targets, compared to our previous method using ProtoMap classification. Furthermore, our method outperforms PSI-BLAST search in detecting potential new superfamilies.

Availability: An interactive tool implementing this method, named ProTarget, is available at http://www.protarget.cs.huji.ac.il. It can be used interactively to retrieve a list of candidate proteins for Structural genomics projects. Supplementary material is available at http://www.protarget.cs.huji.ac.il/supplement

Contact:  michall@cc.huji.ac.il
Plastid Regulation ofLhcb1Transcription in the Chlorophyte AlgaDunaliella tertiolecta
Authors: Chen Yi-Bu , Durnford Dion G. , Koblizek Michal , Falkowski Paul G.
Published: November 2004

We identify four novel DNA-binding complexes in the nuclear-encoded Lhcb1 promoter of the chlorophyte alga Dunaliella tertiolecta that are regulated by photosynthetic pathways in the plastid. The binding activities of three of the complexes were positively correlated with time-dependent changes in Lhcb1 transcript abundance, implicating their roles as transcriptional enhancers in a retrograde signal transduction pathway. Using a combination of inhibitors, uncouplers, and antimycin A, and by following the kinetic pattern of gene regulation, we infer two different sensors in the signal transduction pathway. On short time scales of 0.5 to about 4 h, the transthylakoid membrane potential appears to be a critical determinant of gene expression, whereas on time scales of 8 h or longer, the redox state of the plastoquinone pool becomes increasingly more important. The differentiation of these two types of signals was observed in parallel effects on gene transcription and on the patterns of DNA-binding activities in the Lhcb1 promoter. These signals appear to be transduced at the nuclear level via a coordinated ensemble of DNA-binding complexes located between −367 and −188 bp from the start codon of the gene. The regulation of these elements allows the cell to up- or down-regulate the expression on Lhcb1 in response to changes in irradiance.
Identification of Thlaspi caerulescens Genes That May Be Involved in Heavy Metal Hyperaccumulation and Tolerance. Characterization of a Novel Heavy Metal Transporting ATPase
Authors: Papoyan Ashot , Kochian Leon V.
Published: November 2004

Thlaspi caerulescens is a heavy metal hyperaccumulator plant species that is able to accumulate extremely high levels of zinc (Zn) and cadmium (Cd) in its shoots (30,000 μg g−1 Zn and 10,000 μg g−1 Cd), and has been the subject of intense research as a model plant to gain a better understanding of the mechanisms of heavy metal hyperaccumulation and tolerance and as a source of genes for developing plant species better suited for the phytoremediation of metal-contaminated soils. In this study, we report on the results of a yeast (Saccharomyces cerevisae) complementation screen aimed at identifying candidate heavy metal tolerance genes in T. caerulescens. A number of Thlaspi genes that conferred Cd tolerance to yeast were identified, including possible metal-binding ligands from the metallothionein gene family, and a P-type ATPase that is a member of the P1B subfamily of purported heavy metal-translocating ATPases. A detailed characterization of the Thlaspi heavy metal ATPase, TcHMA4, demonstrated that it mediates yeast metal tolerance via active efflux of a number of different heavy metals (Cd, Zn, lead [Pb], and copper [Cu]) out of the cell. However, in T. caerulescens, based on differences in tissue-specific and metal-responsive expression of this transporter compared with its homolog in Arabidopsis (Arabidopsis thaliana), we suggest that it may not be involved in metal tolerance. Instead, we hypothesize that it may play a role in xylem loading of metals and thus could be a key player in the hyperaccumulation phenotype expressed in T. caerulescens. Additionally, evidence is presented showing that the C terminus of the TcHMA4 protein, which contains numerous possible heavy metal-binding His and Cys repeats residues, participates in heavy metal binding. When partial peptides from this C-terminal domain were expressed in yeast, they conferred an extremely high level of Cd tolerance and Cd hyperaccumulation. The possibilities for enhancing the metal tolerance and phytoremediation potential of higher plants via expression of these metal-binding peptides are also discussed.