bluuebunny/crossref_metadata_2025 huggingface dataset:
Diethylstilbestrol induces fish oocyte maturation
Authors: Tokumoto Toshinobu , Tokumoto Mika , Horiguchi Ryo , Ishikawa Katsutoshi , Nagahama Yoshitaka
Published: March 2004

An endocrine-disrupting chemical, diethylstilbestrol (DES), a nonsteroidal estrogen, triggers oocyte maturation in fish. The morphology (the time course of the change in germinal vesicle breakdown) and an intracellular molecular event (the
de novo
synthesis of cyclin B) induced by DES were indistinguishable from those induced by a natural maturation-inducing hormone, 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-DHP). A synergistic action of DES on 17,20β-DHP-induced oocyte maturation was observed. Both 17,20β-DHP- and DES-induced oocyte maturation was inhibited by an antibody against the maturation-inducing hormone receptor. The structural requirement for the action of DES is discussed based on results obtained with DES analogs.
Siah-1b is a direct transcriptional target of p53: Identification of the functional p53 responsive element in the siah-1b promoter
Authors: Fiucci Giusy , Beaucourt Séverine , Duflaut Dominique , Lespagnol Alexandra , Stumptner-Cuvelette Pamela , Géant Anne , Buchwalter Gilles , Tuynder Marcel , Susini Laurent , Lassalle Jean-Michel , Wasylyk Christine , Wasylyk Bohdan , Oren Moshe , Amson Robert , Telerman Adam
Published: March 2004

Siah proteins are E3 ubiquitin ligases. They are homologues of the
Drosophila
seven in absentia (Sina), a protein required for the R7 photoreceptor development. We have previously found that the expression of human siah-1 and its mouse homologue siah-1b are induced by p53 during apoptosis and tumor reversion. So far, no evidence that the siah-1b gene is a direct transcriptional target of p53 has been provided. In the present study we investigate this issue. Northern blot analysis with a specific probe demonstrates an increase in siah-1b transcription on activation of endogenous and inducible exogenous p53. To explore whether this effect is directly mediated by p53 we analyzed 20 kb of chromosome X DNA, containing the siah-1b locus. A p53-binding site was identified in the siah-1b promoter, located at nucleotides -2155/-2103 relative to the translational start site. This site is composed of two half-sites, conforming to the p53-binding consensus sequence but separated by a nonclassical 33-bp spacer. In luciferase assays, p53 induces a substantial increase in siah-1b promoter activity. Gel shift and DNase-I-footprinting studies, combined with mutational analysis and chromatin immunoprecipitation, indicate that p53 effectively binds the siah-1b promoter
in vitro
and
in vivo
. Thus, the siah-1b gene is a direct transcriptional target of p53.
Site-specific Srb10-dependent phosphorylation of the yeast Mediator subunit Med2 regulates gene expression from the 2-μm plasmid
Authors: Hallberg Magnus , Polozkov Gennady V. , Hu Guo-Zhen , Beve Jenny , Gustafsson Claes M. , Ronne Hans , Björklund Stefan
Published: March 2004

The yeast Mediator complex is required for transcriptional regulation both
in vivo
and
in vitro
, and its function is conserved in all eukaryotes. Mediator interacts with both transcriptional activators and RNA polymerase II, but little is known about the mechanisms by which it operates at the molecular level. Here, we show that the cyclin-dependent kinase Srb10 interacts with, and phosphorylates, the Med2 subunit of Mediator both
in vivo
and
in vitro
. A point mutation of the single phosphorylation site in Med2 results in a strongly reduced expression of the
REP1
,
REP2
,
FLP1
, and
RAF1
genes, which are all located on the endogenous 2-μm plasmid. Combined with previous studies on the effects of
SRB10
/
SRB11
deletions, our data suggest that posttranslational modifications of Mediator subunits are important for regulation of gene expression.
Decreased expression of Cu–Zn superoxide dismutase 1 in ants with extreme lifespan
Authors: Parker Joel D. , Parker Karen M. , Sohal Barbara H. , Sohal Rajindar S. , Keller Laurent
Published: March 2004

Reactive oxygen species, the by-products of oxidative energy metabolism, are considered a main proximate cause of aging. Accordingly, overexpression of the enzyme Cu–Zn superoxide dismutase 1 (SOD1) can lengthen lifespan of
Drosophila melanogaster
in the laboratory. However, the role of SOD1 as a main determinant of lifespan has been challenged on the grounds that overexpression might be effective only in compromised genetic backgrounds. Moreover, interspecific comparisons show lower levels of antioxidant activities in longer-lived species, suggesting that life-span extension may evolve through less reactive oxygen species generation from the mitochondria rather than higher expression of SOD1. The tremendous variation in lifespan between ant castes, ranging over 2 orders of magnitude, coupled with the fact that all individuals share the same genome, provides a system to investigate the role of SOD1 in the wild. We used the ant
Lasius niger
as a model system, because queens can reach the extreme age of 28 years, whereas workers and males live only 1–2 years and a few weeks, respectively. We cloned SOD1 and found that long-lived queens have a lower level of expression than workers and males. Specific enzyme-activity assays also showed higher SOD1 activity levels in males and workers compared with queens, which had SOD1 activity levels similar to that of
D. melanogaster
. Altogether, these data show that increased expression of SOD1 is not required for the evolution of extreme lifespan, even in a system in which differential gene expression is the only way to express phenotypes with great lifespan differences.
Molecular mechanism of enantioselective proton transfer to carbon in catalytic antibody 14D9
Authors: Zheng Lei , Baumann Ulrich , Reymond Jean-Louis
Published: March 2004

Catalytic antibody 14D9 catalyzes the enantioselective protonation of prochiral enol ethers with high enantioselectivity (>99%
ee
) and a practical turnover (
k
cat
= 0.4 s
-1
), allowing for preparative scale applications. This antibody represents one of the rare examples of catalytic antibodies promoting acid-catalyzed processes. Antibody 14D9 was cloned and expressed as a chimeric Fab fragment in
Escherichia coli
. Crystal structures of Fab 14D9 as apo form and of its close analog 19C9 in complex with the transition state analog were determined at 2.8-Å resolution. A series of site-directed mutagenesis experiments was carried out to probe the role of individual active-site amino acids. Proton transfer to carbon is catalyzed by a hydrogen bond network formed by the side chains of Asp
H101
and Tyr
L36
with a water molecule serving as a relay. The intermediate oxocarbonium ion formed during the protonation step is trapped by the same water molecule, resulting in an overall
syn
-addition of water to the enol ether's double bond. The enantioselectivity is caused by steric crowding at the active site, mainly because of the side chain of Phe
H84
. The 20-fold lower activity of 19C9 compared with 14D9 was traced down to residue Thr
L46
, which forms a nonproductive hydrogen bond with the catalytic residue Asp
H101
, which competes with the critical Asp
H101
—Tyr
L36
hydrogen bond and therefore reduces catalytic efficiency. The catalytic activity of 19C9 was restored to that of 14D9 by using either site-directed mutagenesis (Thr
L46
Ala) or chain shuffling.
Basonuclin 2: An extremely conserved homolog of the zinc finger protein basonuclin
Authors: Vanhoutteghem Amandine , Djian Philippe
Published: March 2004

Basonuclin is a zinc finger protein specific to basal keratinocytes and germ cells. In keratinocytes, basonuclin behaves as a stem cell marker and is thought to be a transcription factor that maintains proliferative capacity and prevents terminal differentiation. The human gene is located on chromosome 15. We have discovered in the chicken the existence of basonuclin 2, a basonuclin homolog. We also report the entire sequence of mouse and human basonuclin 2; the corresponding genes are located on mouse chromosome 4 and human chromosome 9. Although the amino acid sequence of basonuclin 2 differs extensively from that of basonuclin 1, the two proteins share essential features. Both contain three paired zinc fingers, a nuclear localization signal, and a serine stripe. The basonuclin 2 mRNA has a wider tissue distribution than the basonuclin 1 mRNA: it is particularly abundant in testis, kidney, uterus, and intestine. The extreme conservation of the basonuclin 2 amino acid sequence across vertebrates suggests that basonuclin 2 serves an important function, presumably as a regulatory protein of DNA transcription.
The specificity of SNARE-dependent fusion is encoded in the SNARE motif
Authors: Paumet Fabienne , Rahimian Vahid , Rothman James E.
Published: March 2004

Soluble
N
-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins constitute the core of the fusion machinery, and isolated SNAREs fuse membranes with exquisite specificity by cognate pairing. Most SNAREs have a membrane-spanning region, an N-terminal domain, and a membrane proximal SNARE motif domain. Although the SNARE motif is critical for SNARE complex formation, is it the sole determinant of the specificity of SNARE-dependent fusion? To test this, we make use of a SNARE complex functioning in the late endosomal compartment in yeast. Studying this complex and the previously identified early endosomal SNARE complex, we find that the specificity of fusion resides in the SNARE motifs.
Decline in transcriptional activity of Nrf2 causes age-related loss of glutathione synthesis, which is reversible with lipoic acid
Authors: Suh Jung H. , Shenvi Swapna V. , Dixon Brian M. , Liu Honglei , Jaiswal Anil K. , Liu Rui-Ming , Hagen Tory M.
Published: March 2004

Glutathione (GSH) significantly declines in the aging rat liver. Because GSH levels are partly a reflection of its synthetic capacity, we measured the levels and activity of γ-glutamylcysteine ligase (GCL), the rate-controlling enzyme in GSH synthesis. With age, both the catalytic (GCLC) and modulatory (GCLM) subunits of GCL decreased by 47% and 52%, respectively (
P
< 0.005). Concomitant with lower subunit levels, GCL activity also declined by 53% (
P
< 0.05). Because nuclear factor erythroid2-related factor 2 (Nrf2) governs basal and inducible GCLC and GCLM expression by means of the antioxidant response element (ARE), we hypothesized that aging results in dysregulation of Nrf2-mediated GCL expression. We observed an ≈50% age-related loss in total (
P
< 0.001) and nuclear (
P
< 0.0001) Nrf2 levels, which suggests attenuation in Nrf2-dependent gene transcription. By using gel-shift and supershift assays, a marked reduction in Nrf2/ARE binding in old vs. young rats was noted. To determine whether the constitutive loss of Nrf2 transcriptional activity also affects the inducible nature of Nrf2 nuclear translocation, old rats were treated with (
R
)-α-lipoic acid (LA; 40 mg/kg i.p. up to 48 h), a disulfide compound shown to induce Nrf2 activation
in vitro
and improve GSH levels
in vivo
. LA administration increased nuclear Nrf2 levels in old rats after 12 h. LA also induced Nrf2 binding to the ARE, and, consequently, higher GCLC levels and GCL activity were observed 24 h after LA injection. Thus, the age-related loss in GSH synthesis may be caused by dysregulation of ARE-mediated gene expression, but chemoprotective agents, like LA, can attenuate this loss.
Dissecting virulence: Systematic and functional analyses of a pathogenicity island
Authors: Deng Wanyin , Puente José L. , Gruenheid Samantha , Li Yuling , Vallance Bruce A. , Vázquez Alejandra , Barba Jeannette , Ibarra J. Antonio , O'Donnell Paul , Metalnikov Pavel , Ashman Keith , Lee Sansan , Goode David , Pawson Tony , Finlay B. Brett
Published: March 2004

Bacterial pathogenicity islands (PAI) often encode both effector molecules responsible for disease and secretion systems that deliver these effectors to host cells. Human enterohemorrhagic
Escherichia coli
(EHEC), enteropathogenic
E. coli
, and the mouse pathogen
Citrobacter rodentium
(CR) possess the locus of enterocyte effacement (LEE) PAI. We systematically mutagenized all 41 CR LEE genes and functionally characterized these mutants
in vitro
and in a murine infection model. We identified 33 virulence factors, including two virulence regulators and a hierarchical switch for type III secretion. In addition, 7 potential type III effectors encoded outside the LEE were identified by using a proteomics approach. These non-LEE effectors are encoded by three uncharacterized PAIs in EHEC O157, suggesting that these PAIs act cooperatively with the LEE in pathogenesis. Our findings provide significant insights into bacterial virulence mechanisms and disease.
The herpes simplex virus 1

U
L
41

gene-dependent destabilization of cellular RNAs is selective and may be sequence-specific
Authors: Esclatine Audrey , Taddeo Brunella , Evans Linton , Roizman Bernard
Published: March 2004

In cells infected with herpes simplex virus 1, the RNA encoded by the stress-inducible immediate early response gene
IEX-1
was up-regulated immediately after infection. However, the accumulated RNA was degraded 3′-5′, and the protein was detectable only at very early times after infection. The degradation was dependent on the
U

L

41
gene encoding the virion host shutoff (vhs) protein and resulted in the accumulation of truncated RNA containing the 5′-end portion of the transcript.
IEX-1
contains an AU-rich element (ARE) in its 3′-untranslated domains known to regulate negatively the RNA lifespan. To examine the role of ARE in signaling the degradation, we compared the stability of several RNAs up-regulated during infection to WT virus. These were ARE-containing RNAs encoding IEX-1, c-fos, and IκBα and the non-ARE-containing RNAs GADD45β and tristetraprolin. We report that the ARE-containing RNAs exemplified by IEX-1 RNA are deadenylated and cleaved in the ARE within the 3′ UTR in a
U

L

41
-dependent manner. In contrast, Northern blot hybridizations and analyses of poly(A) tails revealed no evidence of degradation of GADD45β RNA. GADD45β protein was detected in WT virus-infected cells. These results indicate that the degradation of RNAs and the mechanism by which cellular RNAs are degraded are selective and may be sequence specific. The persistence of partially degraded ARE-containing RNAs may reflect specific targeting of the vhs proteins to the ARE and the modification of the RNA degradation machinery of the cell induced by the presence of the vhs protein.
RETRACTED: Annexin 2–caveolin 1 complex is a target of ezetimibe and regulates intestinal cholesterol transport
Authors: Smart Eric J. , De Rose Robert A. , Farber Steven A.
Published: March 2004

Modulation of cholesterol absorption in the intestine, the primary site of dietary cholesterol uptake in humans, can have profound clinical implications. We have undertaken a reverse genetic approach by disrupting putative cholesterol processing genes in zebrafish larvae by using morpholino (MO) antisense oligonucleotides. By using targeted MO injections and immunoprecipitation (IP) experiments coupled with mass spectrometry, we determined that annexin (ANX)2 complexes with caveolin (CAV)1 in the zebrafish and mouse intestine. The complex is heat stable and unaffected by SDS or reducing conditions. MO targeting of
anx2b
or
cav1
, which are both strongly expressed in the larval and adult zebrafish intestinal epithelium, prevents formation of the protein heterocomplex. Furthermore,
anx2b
MO injection prevents processing of a fluorescent cholesterol reporter and results in reduced sterol mass. Pharmacological treatment of mice with ezetimibe disrupts the heterocomplex in only hypercholesterolemic animals. These data suggest that ANX2 and CAV1 are components of an intestinal sterol transport complex.
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is required for induction of autophagy during lumen formation
in vitro
Authors: Mills Kenna R. , Reginato Mauricio , Debnath Jayanta , Queenan Bridget , Brugge Joan S.
Published: March 2004

The molecular events regulating the elimination of cells to create a hollow lumen during tissue development are poorly understood. By using an
in vitro
morphogenesis model in which MCF-10A human mammary epithelial cells form hollow acini-like structures, we have observed both caspase-mediated apoptosis and autophagy associated with cells that are lost during lumen formation. Here, we show that the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) mediates induction of autophagic processes associated with lumen formation. TRAIL is up-regulated during morphogenesis of MCF-10A mammary epithelial cells in 3D basement-membrane cultures and inhibition of TRAIL signaling during morphogenesis blocks the formation of autophagic vacuoles. In addition, treatment with exogenous TRAIL induces extensive autophagy in monolayer and 3D cultures. When combined with inhibition of caspase 3 activity (by Bcl-X
L
overexpression), inhibition of TRAIL-induced autophagy results in luminal filling. Thus, TRAIL regulates an autophagic program during acinar morphogenesis, which together with caspase-mediated apoptotic events, results in lumen formation during MCF-10A morphogenesis.
Toll-like receptors 9 and 3 as essential components of innate immune defense against mouse cytomegalovirus infection
Authors: Tabeta Koichi , Georgel Philippe , Janssen Edith , Du Xin , Hoebe Kasper , Crozat Karine , Mudd Suzanne , Shamel Louis , Sovath Sosathya , Goode Jason , Alexopoulou Lena , Flavell Richard A. , Beutler Bruce
Published: March 2004

Several subsets of dendritic cells have been shown to produce type I IFN in response to viral infections, thereby assisting the natural killer cell-dependent response that eliminates the pathogen. Type I IFN production can be induced both by unmethylated CpG-oligodeoxynucleotide and by double-stranded RNA. Here, we describe a codominant CpG-ODN unresponsive phenotype that results from anN-ethyl-N-nitrosourea-induced missense mutation in theTlr9gene (Tlr9CpG1). Mice homozygous for theTlr9CpG1allele are highly susceptible to mouse cytomegalovirus infection and show impaired infection-induced secretion of IFN-α/β and natural killer cell activation. We also demonstrate that both the Toll-like receptor (TLR) 9 → MyD88 and TLR3 → Trif signaling pathways are activatedin vivoon viral inoculation, and that each pathway contributes to innate defense against systemic viral infection. Whereas both pathways lead to type I IFN production, neither pathway offers full protection against mouse cytomegalovirus infection in the absence of the other. TheTlr9CpG1mutation alters a leucine-rich repeat motif and lies within a receptor domain that is conserved within the evolutionary cluster encompassing TLRs 7, 8, and 9. In other TLRs, including three mouse-specific TLRs described in this paper, the affected region is not represented. The phenotypic effect of theTlr9CpG1allele thus points to a critical role for TLR9 in viral sensing and identifies a vulnerable amino acid within the ectodomain of three TLR proteins, essential for a ligand response.
Synergistic activation of NF-κB by nontypeable
Haemophilus influenzae
and tumor necrosis factor α
Authors: Watanabe Takahiro , Jono Hirofumi , Han Jiahuai , Lim David J. , Li Jian-Dong
Published: March 2004

Nontypeable
Haemophilus influenzae
(NTHi) is an important human pathogen causing otitis media in children and exacerbation of chronic obstructive pulmonary disease in adults. Like most other bacterial infections, NTHi infections are also characterized by inflammation, which is mainly mediated by cytokines and chemokines such as tumor necrosis factor α (TNF-α). Among a variety of transcription regulators, NF-κB has been shown to play a critical role in regulating the expression of large numbers of genes encoding inflammatory mediators. In review of the current studies on NF-κB regulation, most of them have focused on investigating how NF-κB is activated by a single inducer at a time. However, in bacteria-induced inflammation
in vivo
, multiple inducers including both exogenous and endogenous mediators are present simultaneously. A key issue that has yet to be addressed is whether the exogenous inducers such as NTHi and the endogenous factors such as TNF-α activate NF-κB in a synergistic manner. We show that NTHi and TNF-α, when present together, synergistically induce NF-κB activation via two distinct signaling pathways: NF-κB translocation-dependent and -independent pathways. The NF-κB translocation-dependent pathway involves NF-κB-inducing kinase-IκB kinase β/γ-dependent phosphorylation and degradation of IκBα, whereas the NF-κB translocation-independent pathway involves mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase kinase kinase 1-dependent activation of MAPK kinase 3/6-p38 MAPK pathway. In addition, the same signaling pathways are also involved in synergistic induction of TNF-α, IL-1β, and IL-8. These studies should deepen our understanding of the molecular mechanisms underlying the combinatorial regulation of inflammation and lead to development of therapeutic strategies for NTHi-induced infections.
Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA
Authors: Johnson Neil P. , Baase Walter A. , von Hippel Peter H.
Published: March 2004

Circular dichroism is commonly used to investigate the conformations of nucleic acids. However, many biochemical processes implicate conformational changes of particular nucleotide residues within DNA or RNA that cannot be studied by this method, because the CD of these residues is buried in the total signal of the polynucleotide. Here, we report a method to study local conformations of DNA or RNA that is based on the use of the CD of 2-aminopurine (AP) residues as a probe. AP is readily incorporated into DNA in place of adenine and does not significantly alter DNA structure. Unlike adenine, AP is fluorescent and this property has been used for many years to investigate local nucleic acid structure. We show here that the CD spectrum of AP dinucleotide, (AP)
2
, exhibits a positive CD band at 326 nm, a spectral region in which nucleic acids (and proteins) do not absorb. Our results show that the bases of (AP)
2
are stacked in a right-handed helical conformation. A low-energy CD band is also observed when this nucleotide dimer is incorporated into double-stranded DNA. Control experiments show that this signal comes from the stacking of adjacent AP residues. We have used this CD signal to provide information about the conformation of the AP dinucleotide at a defined position within single- and double-stranded nucleic acids.
An investigation of H-atom positions in sulfuric acid crystal structures
Authors: Hirsch Tomas K. , Ojamäe Lars
Published: March 2004

Hydrogen conformations in crystalline H2SO4·8H2O and H2SO4·6.5H2O have been studied using a system developed by Hirsch [(2003), Z. Anorg. Allg. Chem.
629, 666–672]. New H-atom coordinates, as estimated from DFT calculations, are given for these structures.
Structure of incommensurate ammonium tetrafluoroberyllate studied by structure refinements and the maximum entropy method
Authors: Palatinus Lukás , Amami Mongi , van Smaalen Sander
Published: March 2004

Incommensurately modulated ammonium tetrafluoroberyllate (AFB) occurs in a narrow temperature interval between the paraelectric room-temperature phase with space group Pnma (Ti
= 178 K) and the ferroelectric low-temperature phase with space group Pna21 (Tc
= 173 K). The structure is determined from accurate single-crystal X-ray diffraction data collected with synchrotron radiation at 175 K. The superspace group of the structure is Pnma(α00)0ss with α = 0.4796 (4). Both structure refinements and the maximum entropy method lead to the same structure model, which involves only single harmonic modulations. The building units of the structure are BeF_4^{2-} and NH_4^+ complex ions with approximately tetrahedral point symmetry. They are relatively rigid and the modulations consist mainly of translations of the tetrahedra and their rotations around a fixed axis. The modulation is related to changes in the network of the hydrogen bonds. The low-temperature superstructure can be described as a commensurately modulated structure with the same superspace symmetry. The first harmonic modulations of the low-temperature and incommensurate phases are related by a scale factor with a value of approximately two. In addition, the low-temperature phase exhibits a second harmonic modulation that is responsible for shifts along c and the ferroelectricity in this phase. The experimental data of the incommensurate phase do not contain any evidence for the presence of a second harmonic in the modulation functions. This suggests that the development of the second harmonic, i.e. the development of the spontaneous polarization, is responsible for the lock-in transition.
Atomic volumes and charges in a system with a strong hydrogen bond: L-tryptophan formic acid
Authors: Scheins S. , Dittrich B. , Messerschmidt M. , Paulmann C. , Luger P.
Published: March 2004

A high-resolution X-ray diffraction data set was collected within 48 h at 100 K with synchrotron radiation and area detection. A full topological analysis was applied to the resulting electron-density model. This analysis was followed by a Bader partitioning making use of the zero-flux surfaces of the electron-density gradient vector field. The atomic and bonding properties obtained were compared with the results of previous experimental studies, and with theoretical calculations for the title complex and free tryptophan as reported in the literature. The agreement between experiment and theory is similar to the agreement between different theoretical calculations. There is no charge transfer via the strong hydrogen bond; however, its strength is indicated by the very small atomic volume of the H atom involved.
Calcium–lead fluoro-vanadinite apatites. II. Equilibrium structures
Authors: Dong ZhiLi , White T. J.
Published: March 2004

The synthetic vanadinites (Pb
x
Ca10−x
)(VO4)6(F1−2y
O
y
□
y
)2, 0.57 < x < 9 and 0.10 < y < 0.47, adopt the P63/m apatite structure with 9.7835 (3) ≤ a ≤ 10.0531 (1) Å and 7.0318 (2) ≤ c ≤ 7.3033 (1) Å. The calcium endmember is monoclinic, space group P21/m, with a = 9.7370 (3), b = 9.7358 (4), c = 7.00572 (9) Å, γ = 120.002 (5)°. For mixed metal compounds (x ≠ 0) the partitioning of calcium and lead over the A
I(4f) and A
II(6h) positions is nonstoichiometric, with lead preferentially favouring the larger A
II site at a partitioning coefficient k
Pb(A
I/A
II) ≃ 0.33 for all x < 7. A miscibility gap exists for 2 < x < 3. Trends in crystallographic parameters can be correlated through consideration of the A
IO6 metaprism twist angle (φ) that can be used to derive ideal cell parameters from triangular anion networks.
New bond-valence parameters for lanthanides
Authors: Trzesowska Agata , Kruszynski Rafal , Bartczak Tadeusz J.
Published: March 2004

The bond-valence method, especially the valence-sum rule, is very useful for checking if the structures formed by trivalent lanthanides are correct. In this work bond-valence parameters (R

ij
), which connect bond valences and bond lengths, have been computed for a large number of bonds taken from the Cambridge Structural Database, Version 5.24 (2002) [Allen (2002). Acta Cryst. B58, 380–388]. The calculated values of bond-valence parameters for metal-organic compounds decrease with an increase in lanthanide atomic number; the R

ij
values are also smaller than bond-valence parameters calculated for inorganic compounds. A summary of bond-valence sums calculated for R

ij
given in this work and reported in the literature, and a functional correlation between lanthanide–oxygen distances and coordination number are presented.
Structural studies of (N-phenylthioureidoalkyl- and -aryl)phosphonates
Authors: Chęcińska Lilianna , Fábián László , Kudzin Zbigniew H.
Published: March 2004

The crystal structures of three (N-phenylthioureidoalkyl- and -aryl)phosphonates, i.e. diphenyl [(3-phenylthioureido)phenylpropyl]phosphonate, diphenyl [1-(3-phenylthioureido)benzyl]phosphonate and diphenyl [2,2-dimethyl-1-(3-phenylthioureido)propyl]phosphonate, have been determined by X-ray diffraction. The conformations of the title molecules, the geometry of the thioureide fragments and molecular packing arrangements are analyzed and compared with literature data.
Model for the crystal packing and conformational changes of biphenyl in incommensurate phase transitions
Authors: Dzyabchenko Alexander , Scheraga Harold A.
Published: March 2004

Standard atom–atom potentials for hydrocarbons and a torsional potential to account for the π-electron conjugation energy were used to model the crystal structures and phase transitions of biphenyl. The model describes the high-temperature phase (I) with its planar molecule as a stationary point of the energy hypersurface. Phase I represents a low-energy barrier between the symmetry minima of the ground state (phase III), in which the molecule is twisted with torsion angles of opposite sign. Global-energy minimization was carried out by considering both regular structures, with one or two independent molecules, and quasi-one-dimensional superstructures built of N cells (N up to 16) of the high-temperature structure. The various energy-minimized biphenyl structures demonstrate remarkable similarity in their crystal packing; in particular, there are characteristic rows of cooperatively twisted molecules parallel to the superstructure dimension b. The structures built of centrosymmetric rows (P\bar 1, Z = 4 and 8) are almost as low in energy as the basic structure (an N = 2 superstructure, Pa, Z = 4); moreover, one of them is isostructural with the low-temperature p-quaterphenyl structure. With N > 8, structures of lower energy than that of the basic structure (N = 2) were found; their common feature is an M-fold modulation of the twist angle over the supercell period, with M smaller than N and generally not a simple fraction of it. The global minimum was found to conform to the ratio k = M/N = 6/14, which is close to the experimentally observed k = 6/13 in the incommensurate phase III. Enthalpy minimization showed an overall decrease in the magnitude of the twist angle down to τ ≃ 0°, as well as the evolution of the modulated structures towards the high-temperature structure with increasing pressure, in agreement with evidence for the high-pressure limit of the incommensurate biphenyl phases.
2-Biphenylol revisited
Authors: Parkin Sean , Hao Xiang , Brock Carolyn Pratt
Published: March 2004

The substantially disordered structure of 2-biphenylol [Perrin et al. (1987). Acta Cryst. C43, 980–982; Kapon & Reisner (1988). Acta Cryst. C44, 2039] has been reinvestigated as a function of temperature. The structure was determined at 305, 294, 145 and 90 K; crystals were taken to the lowest temperature both rapidly and slowly (0.1 K min−1). The results of the previous room-temperature study were confirmed and no important structural change was found down to 90 K. Comparisons with structures known for other simple 2- and 2,2′-substituted biphenyl derivatives suggest that the molecular stacks found for 2-biphenylol are probable for related molecules. The disorder in 2-biphenylol allows the formation of some O—H...O bonds, but packing efficiency is a more important factor in this structure than is hydrogen bonding.
Structure for perovskites with layered ordering of A-site cations
Authors: Howard Christopher J. , Zhang Zhaoming
Published: March 2004

The structure of La1/3NbO3 is that of a perovskite with La3+ cations ordered into alternate layers of perovskite A-sites. This is the description of a tetragonal structure and yet the room-temperature structure shows an orthorhombic distortion. The structure of La2/3TiO3 shows similar features. It has been recognized only very recently that the orthorhombic distortion in both these compounds is due to octahedral tilting. It seems clear from the literature that Ce2/3TiO3, Pr2/3TiO3, Nd2/3TiO3 and Ce1/3NbO3 adopt the same structure. Structures of other perovskites, such as Ln2/3TiO3, Ln1/3NbO3 and Ln1/3TaO3 (Ln = lanthanoid), when orthorhombically distorted, may be similar.
“Library as a Portal” – IFLA 69th Conference in Deutschland: A Rewarding Experience
Authors: Ghosh Maitrayee
Published: March 2004

Reports on some of the papers presented at the Interrnational Federation of Library Associations and Institutions] 2003 conference which had the theme of Library as a portal.
Humanizing Information Technology: The Annual Conference of the American Society for Information Science and Technology, Long Beach, California, 19‐22 October 2003
Authors: O’Connor Penny
Published: March 2004

Reports on papers presented at "Humanizing Information Technology", the Annual Conference of the American Society for Information Science and Technology, held in California in October 2003.
Ethics of Electronic Information in the 21st Century: 2003
Authors: Albright Kendra S.
Published: March 2004

Reports on the conference, "Ethics of Electronic Information in the 21st Century 20032, held in Tennessee, October 2003.
United Nations World Summit on the Information Society – Libraries @ the Heart of the Information Society
Authors: Gelfand Julia
Published: March 2004

Observations from the conference – from coverage and the vantage point of the IFLA Web site, press releases and other reports – held in Geneva in December 2003.
VITLE Experience: HKBU Library Supporting e‐Learning in a SARS Environment
Authors: Lee Paul T.P.
Published: March 2004

The outbreak of Severe Acute Respiratory Syndrome (SARS) in Hong Kong in 2003 caused massive disruptions in many sectors of the society. Many creative solutions were devised with the aim of continuing the teaching and learning process in educational areas. Among them, the initiative of VITLE classes was probably the only one involving the direct participation of an academic library. This article is to report such involvement of the Hong Kong Baptist University (HKBU) Library.
Around the World to the Institute of Agricultural Science of South Vietnam Library
Authors: Goh Jennifer
Published: March 2004

Describes a project undertaken at the library at the Institute of Agricultural Science of South Vietnam for 12 months. The main objectives were to train both two library staff members, neither of whom had formal library qualifications or training, to reclassify the library’s material using Dewey Decimal Classification and assist them to select and implement an electronic catalogue.
Multivariate Survival Trees: A Maximum Likelihood Approach Based on Frailty Models
Authors: Su Xiaogang , Fan Juanjuan
Published: March 2004

Summary. A method of constructing trees for correlated failure times is put forward. It adopts the backfitting idea of classification and regression trees (CART) (Breiman et al., 1984, inClassification and Regression Trees). The tree method is developed based on the maximized likelihoods associated with the gamma frailty model and standard likelihood‐related techniques are incorporated. The proposed method is assessed through simulations conducted under a variety of model configurations and illustrated using the chronic granulomatous disease (CGD) study data.
N‐Mixture Models for Estimating Population Size from Spatially Replicated Counts
Authors: Royle J. Andrew
Published: March 2004

Summary.  Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (N‐mixture models) which allow for estimation of population size from such data. The key idea is to view site‐specific population sizes, N, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for N. Carroll and Lombard (1985, Journal of American Statistical Association80, 423–426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on N that is exploited by the N‐mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the N‐mixture estimator compared to the Caroll and Lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.
Functional Form Diagnostics for Cox's Proportional Hazards Model
Authors: León Larry F. , Tsai Chih‐Ling
Published: March 2004

Summary. We propose a new type of residual and an easily computed functional form test for the Cox proportional hazards model. The proposed test is a modification of the omnibus test for testing the overall fit of a parametric regression model, developed byStute, González Manteiga, and Presedo Quindimil(1998,Journal of the American Statistical Association93,141–149), and is based on what we callcensoring consistent residuals. In addition, we develop residual plots that can be used to identify the correct functional forms of covariates. We compare our test with the functional form test ofLin, Wei, and Ying(1993,Biometrika80,557–572) in a simulation study. The practical application of the proposed residuals and functional form test is illustrated using both a simulated data set and a real data set.
Design and Analysis of Group Sequential Clinical Trials with Multiple Primary Endpoints
Authors: Kosorok Michael R. , Yuanjun Shi , DeMets David L.
Published: March 2004

Summary.  In many phase III clinical trials, it is desirable to separately assess the treatment effect on two or more primary endpoints. Consider the MERIT‐HF study, where two endpoints of primary interest were time to death and the earliest of time to first hospitalization or death (The International Steering Committee on Behalf of the MERIT‐HF Study Group, 1997, American Journal of Cardiology80[9B], 54J–58J). It is possible that treatment has no effect on death but a beneficial effect on first hospitalization time, or it has a detrimental effect on death but no effect on hospitalization. A good clinical trial design should permit early stopping as soon as the treatment effect on both endpoints becomes clear. Previous work in this area has not resolved how to stop the study early when one or more endpoints have no treatment effect or how to assess and control the many possible error rates for concluding wrong hypotheses. In this article, we develop a general methodology for group sequential clinical trials with multiple primary endpoints. This method uses a global alpha‐spending function to control the overall type I error and a multiple decision rule to control error rates for concluding wrong alternative hypotheses. The method is demonstrated with two simulated examples based on the MERIT‐HF study.
Bayesian Experimental Design for Nonlinear Mixed‐Effects Models with Application to HIV Dynamics
Authors: Han Cong , Chaloner Kathryn
Published: March 2004

Summary. Bayesian experimental design is investigated for Bayesian analysis of nonlinear mixed‐effects models. Existence of the posterior risk for parameter estimation is shown. When the same prior distribution is used for both design and inference, existence of the preposterior risk for design is also proven. If the prior distribution used in design is different from that used for inference, sufficient conditions are established for existence of the preposterior risk for design. A case study of design for an experiment in population HIV dynamics is provided.
Testing for Common Structures in a Panel of Threshold Models
Authors: Chan K. S. , Tong H. , Chr. Stenseth N.
Published: March 2004

Summary. We consider the problem of examining the extent of (partial) similarity in the dynamics of a panel of independent threshold autoregressive processes. We develop some tests for common structure via Wald's approach and by checking whether the parameter estimates of the unconstrained threshold models satisfy the constraints defining the common structure. One test concerns the equality of independent ratios of normal means, which is shown to have nonstandard asymptotic null distribution. These tests are illustrated with a modern panel of Canadian lynx data; our analysis suggests that the lynx data over Canada share similar dynamics in the decrease phase, but they appear to be different in the increase phase.
Exact Analysis of Dose Response for Multiple Correlated Binary Outcomes
Authors: Han Karen E. , Catalano Paul J. , Senchaudhuri Pralay , Mehta Cyrus
Published: March 2004

Summary.  The neurotoxicity of a substance is often tested using animal bioassays. In the functional observational battery, animals are exposed to a test agent and multiple outcomes are recorded to assess toxicity, using approximately 40 animals measured on up to 30 different items. This design gives rise to a challenging statistical problem: a large number of outcomes for a small sample of subjects. We propose an exact test for multiple binary outcomes, under the assumption that the correlation among these items is equal. This test is based upon an exponential model described by Molenberghs and Ryan (1999, Environmetrics10, 279–300) and extends the methods developed by Corcoran et al. (2001, Biometrics57, 941–948) who developed an exact test for exchangeably correlated binary data for groups (clusters) of correlated observations. We present a method that computes an exact p‐value testing for a joint dose–response relationship. An estimate of the parameter for dose response is also determined along with its 95% confidence bound. The method is illustrated using data from a neurotoxicity bioassay for the chemical perchlorethylene.
Hierarchical Bayesian Modeling in Dichotomous Processes in the Presence of Nonresponse
Authors: Oleson Jacob J. , He Chong Z.
Published: March 2004

Summary.  Sampling units that do not answer a survey may dramatically affect the estimation results of interest. The response may even be conditional on the outcome of interest in the survey. If estimates are found using only those who responded, the estimate may be biased, known as nonresponse bias. We are interested in finding estimates of success rates from a survey. We begin by looking at two current Bayesian approaches to treating nonresponse in a hierarchical model. However, these approaches do not consider possible spatial correlations between domains for either success rate or response rate. We build a Bayesian hierarchical spatial model to explicitly estimate the success rate, response rate given success, and response rate given failure. The success rates in the domains of the survey are allowed to be spatially correlated. We also allow spatial dependence between domains in both response rate given success and response rate given failure. Spatial dependence is induced by a common latent spatial structure between the two conditional response rates. We use the 1998 Missouri Turkey Hunting Survey to illustrate this methodology. We find significant spatial correlation in the success rates and incorporating nonrespondents has an impact on the success rate estimates.
Analyzing Excessive No Changes in Clinical Trials with Clustered Data
Authors: Lu Shou‐En , Lin Yong , Shih Wei‐Chung Joe
Published: March 2004

Summary. This article considers clinical trials in which the efficacy measure is taken from several sites within each patient, such as the alveolar bone height of the tooth sites, or bone mineral densities of the lumbar spine sites. Since usually only a small portion of these sites will exhibit changes, the conventional method using per patient average gives a diluted result due to excessive no changes in the data. Different methods have been proposed for this type of data in the case where the observations are mutually independent. This includes the popular “two‐part model” (Lachenbruch, 2001,Statistics in Medicine20,1215–1234; 2002,Statistical Methods in Medical Research11,297–302), which is related to the “composite approach” for discrete and continuous data inShih and Quan(1997,Statistics in Medicine16,1225–1239; 2001,Statistica Sinica11,53–62). In this article, we model the data with excessive zeros (no changes) in clustered data using a mixture of distributions, and taking into account possible measurement errors. This mixture model includes the two‐part model as a special case when one component of the mixture degenerates.
Partially Supervised Learning Using an EM‐Boosting Algorithm
Authors: Yasui Yutaka , Pepe Margaret , Hsu Li , Adam Bao‐Ling , Feng Ziding
Published: March 2004

Summary.  Training data in a supervised learning problem consist of the class label and its potential predictors for a set of observations. Constructing effective classifiers from training data is the goal of supervised learning. In biomedical sciences and other scientific applications, class labels may be subject to errors. We consider a setting where there are two classes but observations with labels corresponding to one of the classes may in fact be mislabeled. The application concerns the use of protein mass‐spectrometry data to discriminate between serum samples from cancer and noncancer patients. The patients in the training set are classified on the basis of tissue biopsy. Although biopsy is 100% specific in the sense that a tissue that shows itself to have malignant cells is certainly cancer, it is less than 100% sensitive. Reference gold standards that are subject to this special type of misclassification due to imperfect diagnosis certainty arise in many fields. We consider the development of a supervised learning algorithm under these conditions and refer to it as partially supervised learning. Boosting is a supervised learning algorithm geared toward high‐dimensional predictor data, such as those generated in protein mass‐spectrometry. We propose a modification of the boosting algorithm for partially supervised learning. The proposal is to view the true class membership of the samples that are labeled with the error‐prone class label as missing data, and apply an algorithm related to the EM algorithm for minimization of a loss function. To assess the usefulness of the proposed method, we artificially mislabeled a subset of samples and applied the original and EM‐modified boosting (EM‐Boost) algorithms for comparison. Notable improvements in misclassification rates are observed with EM‐Boost.
On the Construction of Bounds in Prospective Studies with Missing Ordinal Outcomes: Application to the Good Behavior Game Trial
Authors: Scharfstein Daniel O. , Manski Charles F. , Anthony James C.
Published: March 2004

Summary.  This article is concerned with drawing inference about aspects of the population distribution of ordinal outcome data measured on a cohort of individuals on two occasions, where some subjects are missing their second measurement. We present two complementary approaches for constructing bounds under assumptions on the missing data mechanism considered plausible by scientific experts. We develop our methodology within the context of a randomized trial of the “Good Behavior Game,” an intervention designed to reduce aggressive misbehavior among children.