bluuebunny/crossref_metadata_2025 huggingface dataset:
Zona pellucida solubility and cortical granule complements in human oocytes following assisted reproductive techniques
Authors: Manna C. , Rienzi L. , Greco E. , Sbracia M. , Rahman A. , Poverini R. , Siracusa G. , De Felici M.
Published: July 2002

In this study the solubility to α-chymotrypsin of the zona pellucida (ZP) of human oocytes and polyploid embryos obtained during various clinical procedures of assisted fertilisation (IVF, ICSI, cyropreservation) was evaluated. The aim of the study was to determine whether changes in ZP solubility occur during such procedures and whether abnormal solubility could be likened to fertilisation failure. Correlation between ZP solubility and cortical granule (CG) density was also studied. The results showed that ZP solubility varied considerably among germinal vesicle or metaphase oocytes obtained from different subjects, but was essentially identical for the oocyte cohort obtained from individual women. On the basis of ZP solubility metaphase oocytes were subdivided into two classes: class I, average ZP dissolution time ± SE = 24.1 ± 0.9 min, n = 28; and class II, 46.7 ± 2.0 min, n = 13. Prolonged ZP dissolution times of metaphase oocytes were significantly correlated with a low in vitro fertilisation rate in sibling oocytes. The zonae of fertilised eggs (polyploid embryos) showed long solubilisation times (IVF: 45.3 ± 3.4 min, n = 18; ICSI: 48.9 ± 2.7 min, n = 19). ZP solubility of oocytes that failed to fertilise was intermediate between that of class I metaphase oocytes and embryos (unfertilised IVF: 33.0 ± 2.7 min, n = 13; unfertilised ICSI: 43.0 ± 2.4 min, n = 9). A moderate spontaneous ZP hardening occurred when metaphase oocytes were cultured for 24 h. Finally, cryopreservation of unfertilised oocytes caused hardening of their ZP, with dissolution times that were comparable to those found in fertilised eggs (49.5 ± 2.3 min, n = 10). In most cases, an inverse correlation was found between ZP dissolution time and CG density (longer solubilisation times corresponding to lower CG density). ZP hardening caused by cryopreservation, however, was not associated with a significant reduction in CG density in most of the oocytes examined.
Double copulation of a female with sterile diploid and polyploid males recovers fertility in Bombyx mori
Authors: Sahara Ken , Kawamura Naoko
Published: July 2002

Silkworm males produce dimorphic sperm, nucleate eupyrene sperm and anucleate apyrene sperm. Apyrene sperm have been speculated to have an assisting role in fertilisation. However, the coexistence of eupyrene and apyrene sperm in the testis and female reproductive organs has made it difficult to define the role of apyrene sperm. Polyploid males are highly sterile. Microscopic observation revealed that the elimination of eupyrene nuclei by peristaltic squeezing caused the sterility of polyploids. Heat-shock applied to pupae of Daizo males (DH) also induced high sterility due to the lack of normal apyrene sperm. When eupyrene sperm of sterile DH males and apyrene sperm of sterile polyploid males were mixed by double copulation, a remarkable increase in fertility of the double-mated females was observed. This finding strongly suggests that the apyrene sperm are indispensable in fertilisation of the silkworm and that polyploid apyrene sperm function as a substitute for diploid sperm. We established an experimental system in which we can separate the two types of sperm for further studies on their functions without chemical and/or mechanical treatments.
Activation of ribosomal S6 kinase (RSK) during porcine oocyte maturation
Authors: Sugiura K. , Naito K. , Iwamori N. , Kagii H. , Goto S. , Ohashi S. , Naruoka H. , Yada E. , Yamanouchi K. , Tojo H.
Published: July 2002

The normal kinetics of ribosomal S6 kinase (RSK) during the meiotic maturation of porcine oocytes were examined. The phosphorylation states of RSK and extracellular signal-regulated kinase (ERK), major mitogen-activated protein (MAP) kinases in maturating porcine oocytes, were detected by Western blotting analysis. The S6 protein kinase activity was assayed using a specific substrate peptide which contained the major phosphorylation sites of S6 kinase. Full phosphorylation of RSK was correlated with ERK phosphorylation and was observed before germinal vesicle breakdown. S6 kinase activity was low in both freshly isolated and 20 h cultured oocytes. S6 kinase activity was significantly elevated in matured oocytes to a level about 6 times higher than that in freshly isolated oocytes. Furthermore, full phosphorylation of RSK was inhibited when oocytes were treated with U0126, a specific MAP kinase kinase inhibitor, in dose-dependent manner, indicating that RSK is one of the substrates of MAP kinase. These results suggest that the activation of RSK is involved in the regulation of meiotic maturation of porcine oocytes.
Living in both the real and virtual worlds
Authors: MAGNENAT-THALMANN NADIA
Published: July 2002

What is the cyberworld and what is it for? Until now, most virtual worlds have shown interplanetary worlds where aliens or exotic animals live. In the future, virtual worlds will be populated by virtual actors and these actors will act in different situations. For example, in medical simulation, where they will be used as models for surgery, or where such virtual actors will play our roles in telecommunications processes or in entertainment, where we could join a virtual ballet or concert and be, as a virtual self, part of the virtual world. We will also be able, as a virtual human, to interact with virtual actors and explain all kinds of situations. The virtual actors will embody intelligent agents and give a human touch to the interaction with the computer. It will be as if we could deal with kind, affordable and smart humans who will be at our disposal at any time, with a lot of knowledge, and who will help us to understand, to learn and to experience situations that would be impossible without them. The door is then open to an enormous amount of new experience coming from the virtual world.
Editorial: what about the human genome?
Authors: BURGEN ARNOLD
Published: July 2002

There are few weeks in which the news media do not announce some great breakthrough in medical or biological science, usually inferring some immediate benefit to mankind. Alas, the promise of these benefits is nearly always premature and leads to disappointment. However, the frequency of the reports does indeed reflect an astonishing rate of new discovery in a field of great complexity.
Acquisitions and applications of structure preference relations in Chinese
Authors: ZHOU QIANG , REN FUJI
Published: July 2002

In this paper, we propose a new ambiguity representation scheme; Structure Preference
Relation (SPR), which consists of useful quantitative distribution information for ambiguous
structures. Two automatic acquisition algorithms, the first acquired from a treebank, and
the second acquired from raw texts, are introduced, and some experimental results which
prove the availability of the algorithms are also given. Finally, we introduce some SPR
applications in linguistics and natural language processing, such as preference-based parsing
and the discovery of representative ambiguous structures, and propose some future research
directions.
A NARRATIVE EXPOSURE TREATMENT AS INTERVENTION IN A REFUGEE CAMP: A CASE REPORT
Authors: Neuner Frank , Schauer Margarete , Roth Walton T. , Elbert Thomas
Published: July 2002

We applied Narrative Exposure Treatment (NET) to a severely traumatized Kosovar refugee living in a Macedonian refugee camp during the Balkan War. NET is a pragmatic short-term approach that integrates effective therapeutic components deriving from Cognitive Behaviour Therapy and Testimony Therapy. Outcome was evaluated by clinical examination and the Posttraumatic Stress Diagnostic Scale (PDS). Three sessions of NET were enough to afford considerable relief, although some PTSD symptoms remained. Our experience indicates that Narrative Exposure is a promising and realistic approach for the treatment of even severely traumatized refugees living in camps. In addition, it can prove valid testimonies about human rights violations without humiliating the witness.
Rehabiliation after TBI
Authors: Kreutzer Jeffrey S.
Published: July 2002

Increasing survival rates after traumatic brain
injury have spawned a proliferation of rehabilitation facilities
and treatment programs during the past decade. The proliferation
has created a diversity of challenging opportunities for
neuropsychologists desiring to meet the full range of patients'
needs. For many years, neuropsychology focused on diagnosis
of neurological conditions, localization of impairment,
and describing performance levels on tests measuring abilities.
More recently neuropsychologists have been asked to participate
as full members of rehabilitation teams and serve as consultants
during the rehabilitation process. Now, on a more routine
basis, psychologists are asked to provide family support
and education, individual psychotherapy, social skills
training, cognitive rehabilitation therapy, and vocational
rehabilitation services.
Neuropsychiatry: The Second Edition of a Classic Text
Authors: Wasserstein Jeanette
Published: July 2002

Neuropsychological Assessment of Neuropsychiatric
Disorders was originally published in 1986, and in
1996 was selected one of the “essential books and
journals in North American Clinical Neuropsychology”
in a survey of ABPP Diplomats. The Second Edition promises
to maintain this position. As was the case in the original,
the editors aimed to (1) present leading approaches to
neuropsychological assessment in neuropsychiatric populations;
and (2) evaluate current understanding of the neuropsychology
of more important or problematic disorders. Organization
of this edition follows that of the First Edition. The
first section covers methods of neuropsychological assessment
and the second section covers targeted neuropsychiatric
disorders. This edition also adds a third section on psychosocial
consequences and moderating factors in neuropsychological
impairment, particularly as illustrated in people with
head injury and chronic pulmonary disease. Two-thirds of
the original authors, as well as 25 new authors, contributed.
More often than not these contributors are leading authorities
in their respective topic.
Natural resource sustainability and poverty reduction
Authors: HEADY CHRISTOPHER
Published: July 2002

This paper uses a model of an inland fishery in Bangladesh to investigate the relationship between poverty and resource sustainability in a specific case. It makes use of detailed fieldwork to build a numerical model of fishery decision making, which incorporates extensions to standard fisheries models. In particular, it includes fish migration between lease units and models the choice of fishing gear, as well as fishing effort, over the year. The modelling of fishing gear choice allows an analysis of the effect of management policies on employment in the fishery, a major factor that influences poverty in the locality. The numerical results show that while some simple policies to improve sustainability are likely to increase poverty, it is possible to design policies which affect gear choice and lead to reduced poverty without harming the sustainability of the resource.
Environmental impacts and mitigation costs associated with cloth and leather exports from Pakistan
Authors: Khan Shahrukh Rafi , Khwaja Mahmood A. , Khan Abdul Matin
Published: July 2002

We have drawn two propositions, critical from a developing country viewpoint, from the trade and environment literature and assessed them for cloth and leather production in Pakistan. The first is that trade liberalization will result in export by developing countries of their environmental capital. The second is that the costs of mitigating these damaging environmental effects in the South are very high. We find that, given the state of implementation of environmental laws in Pakistan, exports induced by trade liberalization can indeed have major negative environmental impacts. However, we do not find support for the proposition that the costs of mitigation are very high. We also find that the social benefits far exceed the costs of mitigation.
Music negotiation: routes in user-based description of music
Authors: Tanzi Dante
Published: July 2002

This paper will deal with the changes that have come about in the description of musical knowledge and with the ensuing needs in this field in the era of decentralisation. Throughout almost all the twentieth century, musical practices continued to be expressed by a system of cultural mediations that proved to be a practical impediment to the emergence of non-conventional cultures. Electronic music in particular and its corrosive tendencies, though spread and supported by remarkable composers, has ended up being devoured by academic immune systems. Now that the diffusion of Net computing has induced people to intervene in musical material, a poetics based on interference is spreading. By gaining ground on grammatical and self-referenced poetics, this trend has gradually become a palpable fact and music perceives itself as both individual writing and a production of social meaning. At present, a globe-net-transfer of sound material passes through different contexts and spaces, and seems to be adapting itself to different social speeds. Through the Net we can, on the one hand, replace, manipulate and recontextualise musical parameters until a different significance emerges; at the same time, randomising and hybridising musical objects can partially change our perception of the same musical events. On the other hand, music online databases, audio browsers and musical queries may open the way to overthrowing, reorganising and personalising music description. This could occur at different levels and to different degrees of complexity, both as a social event and as an active, user-based combination of musical structures.
A generic model for compositional approaches to audiovisual media
Authors: Hunt Andy , Kirk Ross , Orton Richard , Merrison Benji
Published: July 2002

The challenge of composing both sound and moving image within a coherent
computer-mediated framework is addressed, and some of the aesthetic issues
highlighted. A conceptual model for an audiovisual delivery system is
proposed, and this model acts as a guide for detailed discussion of some
illustrative examples of audiovisual composition. Options for types of score
generated as graphical output of the system are outlined. The need for
extensive algorithmic control of compositional decisions within an
interactive framework is proposed. The combination of Tabula Vigilans Audio
Interactive (TVAI), an algorithmic composition language for electroacoustic
music and realtime image generation, with MIDAS, a multiprocessor
audiovisual system platform, is shown to have the features desired for the
conceptual outline given earlier, and examples are
given of work achieved using these resources. It is shown that ultimately
delivery of new work may be efficiently distributed via the World Wide Web,
with composers' interactive scripts delivered remotely but rendered
locally by means of a user's ‘rendering black box’.
A computer environment for polymodal music
Authors: MAIA ADOLFO , DO VALLE PAUL , MANZOLLI JONATAS , PEREIRA LEONARDO N. S.
Published: July 2002

KYKLOS, an algorithmic composition program, is presented here. It
generalises musical scales for use in composition as well as in
performance. The sonic output of the system is referred to as
polymodal music since it consists of four independent voices
playing ‘synthetic modes’. KYKLOS is suitable for
computer-assisted composition because it generates MIDI files which can be
altered later by the composer. It can equally well be used in live
performance for dynamic modification of parameters enabling realtime
musical control.
Children and the Expanding Role of
the Criminal Law
Authors: Bandalli Sue
Published: July 2002

Looking back, the 1980s was a decade of enlightenment
and success in juvenile justice practice in this country;
diverting youngsters away from the criminal courts and
reducing the severity of response towards those who were
prosecuted did not result in crime waves or public demand
to stop this lenient treatment of the young. In the 1990s,
the whole criminal justice system took a significant turn
towards retribution and punishment. The movement may
have been aimed initially at certain groups of criminals,
particularly the persistent and serious, but swept all in its
wake, including children aged 10–14 who were neither.
There is little apparent appreciation of the damaging
consequences of this trend, not only for individual children
but also for the whole concept of childhood. There is now
a wide discrepancy between the approach taken by the
criminal and civil law towards children which current
criminal justice policies indicate is to continue into the
foreseeable future.
Thailand's Relations with Malaysia and Myanmar in Post-Cold War Southeast Asia
Authors: Ganesan N.
Published: July 2002

This article examines Thai policy towards Malaysia and Myanmar in the post-Cold War period and argues that bilateral relations between Thailand and these countries have deteriorated considerably. The immediate reason for the change is the collapse of structural arrangements associated with the Cold War, in particular the Indochina Security Complex and domestic political developments in Thailand and Myanmar. Whereas a number of issues like illegal migration, fishing and insurgency have contributed to the deteriorated relations, the situation has been reasonably well managed. Factors contributing to the stability of the situation include regular bilateral dialogue and exchanges as well as common membership in a number of multilateral fora like ASEAN, ARF, AFTA and APEC.
Messenger RNAs are recruited for nuclear export during transcription
Authors: Lei Elissa P. , Krebber Heike , Silver Pamela A.
Published: July 2002

Following transcription and processing, eukaryotic mRNAs are exported from the nucleus to the cytoplasm for translation. Here we present evidence that mRNAs are targeted for nuclear export cotranscriptionally. Combined mutations in the Saccharomyces cerevisiae hnRNP Npl3 and TATA-binding protein (TBP) block mRNA export, implying that cotranscriptional recruitment of Npl3 is required for efficient export of mRNA. Furthermore, Npl3 can be found in a complex with RNA Pol II, indicating that Npl3 associates with the transcription machinery. Finally, Npl3 is recruited to genes in a transcription dependent manner as determined by chromatin immunoprecipitation. Another mRNA export factor, Yra1, also associates with chromatin cotranscriptionally but appears to be recruited at a later step. Taken together, our results suggest that export factors are recruited to the sites of transcription to promote efficient mRNA export.
Genetic Linkage Mapping of Zebrafish Genes and ESTs
Authors: Kelly Peter D. , Chu Felicia , Woods Ian G. , Ngo-Hazelett Phuong , Cardozo Timothy , Huang Hui , Kimm Frankie , Liao Lingya , Yan Yi-Lin , Zhou Yingyao , Johnson Steven L. , Abagyan Ruben , Schier Alexander F. , Postlethwait John H. , Talbot William S.
Published: July 2002

Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes essential for vertebrate development, physiology, and behavior. We have constructed a genetic linkage map that will facilitate the identification of candidate genes for these mutations and allow comparisons among the genomes of zebrafish and other vertebrates. On this map, we have localized 771 zebrafish genes and expressed sequence tags (ESTs) by scoring single-stranded conformational polymorphisms (SSCPs) in a meiotic mapping panel. Of these sequences, 642 represent previously unmapped genes and ESTs. The mapping panel was comprised of 42 homozygous diploid individuals produced by heat shock treatment of haploid embryos at the one-cell stage (HS diploids). This “doubled haploid” strategy combines the advantages of mapping in haploid and standard diploid systems, because heat shock diploid individuals have only one allele at each locus and can survive to adulthood, enabling a relatively large quantity of genomic DNA to be prepared from each individual in the mapping panel. To integrate this map with others, we also scored 593 previously mapped simple-sequence length polymorphisms (SSLPs) in the mapping panel. This map will accelerate the molecular analysis of zebrafish mutations and facilitate comparative analysis of vertebrate genomes.

[A table of the mapped genes and ESTs is provided online at http://www.genome.org.]
A Behavioral and Genetic Dissection of Two Forms of Olfactory Plasticity in Caenorhabditis elegans: Adaptation and Habituation
Authors: Bernhard Nirit , van der Kooy Derek
Published: July 2002

Continuous presentation of an olfactory stimulus causes a decrement of the chemotaxis response in the nematode Caenorhabditis elegans. However, the differences between the learning process of habituation (a readily reversible decrease in behavioral response) and other types of olfactory plasticity such as adaptation (a decrement in response due to sensory fatigue, which cannot be dishabituated) have not been addressed. The volatile odorant diacetyl (DA) was used within a single paradigm to assess the distinct processes of olfactory adaptation and habituation. Preexposing and testing worms to 100% DA vapors caused a chemotaxis decrement that was not reversible despite the presentation of potentially dishabituating stimuli. This DA adaptation was abolished in worms with an odr-10 mutation (encoding a high-affinity DA receptor on the AWA neuron), even though naive chemotaxis remained unaffected. Conversely, DA adaptation remained intact in odr-1 mutants (defective in AWC neuron-mediated olfactory behavior), even though naive chemotaxis to DA decreased. Surprisingly, exposure to vapors of intermediate concentrations of DA (0.01% and 25%) did not cause worms to exhibit any response decrement. In contrast to preexposure to high DA concentrations, preexposure to low DA concentrations (0.001%) produced habituation of the chemotaxis response (a dishabituating stimulus could reverse the response decrement back to baseline levels). The distinct behavioral effects produced by DA preexposure highlight a concentration-dependent dissociation between two decremental olfactory processes: adaptation at high DA concentrations versus habituation at low DA concentrations.
Preexisting Systemic Acquired Resistance Suppresses Hypersensitive Response-Associated Cell Death in Arabidopsishrl1 Mutant
Authors: Devadas Sendil K. , Raina Ramesh
Published: July 2002

The hypersensitive response (HR) displayed by resistant plants against invading pathogens is a prominent feature of plant-pathogen interactions. The Arabidopsis hypersensitive response like lesions1 (hrl1) mutant is characterized by heightened defense responses that make it more resistant to virulent pathogens. However, hrl1 suppresses avirulent pathogen-induced HR cell death. Furthermore, the highPR-1 expression observed in hrl1 remains unaltered after avirulent and virulent pathogen infections. The suppressed HR phenotype in hrl1 is observed even when an elicitor is expressed endogenously from an inducible promoter, suggesting that an impaired transfer of avirulent factors is not the reason. Interestingly, the lack of HR phenotype in hrl1is reversed if the constitutive defense responses are compromised either by a mutation in NON EXPRESSOR OF PR-1(NPR1) or by depleting salicylic acid due to the expression of the nahG gene. The rescue of HR cell death in hrl1 npr1 and in hrl1 nahG depends on the extent to which the constitutive systemic acquired response (SAR) is compromised. Pretreating Arabidopsis wild-type plants with SAR-inducers, before pathogen infection resulted in a significant decrease in HR cell death. Together, these results demonstrate that the preexisting SAR may serve as one form of negative feedback loop to regulate HR-associated cell death in hrl1 mutant and in the wild-type plants.
Involvement of Protein Kinase and Extraplastidic Serine/Threonine Protein Phosphatases in Signaling Pathways Regulating Plastid Transcription and the psbD Blue Light- Responsive Promoter in Barley
Authors: Christopher D. A. , Xinli L. , Kim M. , Mullet J. E.
Published: July 2002

We investigated the signaling pathways that control changes in plastid transcription in response to development and light. Plastid gene expression was analyzed in dark-grown barley (Hordeum vulgare L.) seedlings treated in vivo with an inhibitor of protein phosphatases 1 and 2A, okadaic acid (OA), or an inhibitor of protein kinases (K252a), followed by exposure of the seedlings to either red, blue, or white light. OA prevented blue light from activating the plastid psbD blue-light-responsive promoter (BLRP) and prevented red and blue light from activating the expression of the plastid-encoded rbcL and psbA and the nuclear-encoded RbcS and Lhcb genes. OA reduced total plastid transcription activity in dark- and light-grown seedlings by 77 to 80%, indicating that OA prevented light-responsive transcription by reducing total plastid transcription. In contrast, K252a activated the accumulation of mRNAs arising from the BLRP. Blue light in combination with K252a increased psbD mRNA levels in an additive manner. The results indicate that protein phosphatases 1 and/or 2A, which reside external to the organelle, are required for proper function of plastid transcription and chloroplast development, whereas a protein kinase represses the BLRP in plants grown in the dark.
Association of Caffeoyl Coenzyme A 3-O-Methyltransferase Expression with Lignifying Tissues in Several Dicot Plants
Authors: Ye Z. H.
Published: July 2002

Caffeoyl coenzyme A 3-O-methyltransferase (CCoAOMT) was previously shown to be associated with lignification in both in vitro tracheary elements (TEs) and organs of zinnia (Zinnia elegans). However, it is not known whether this is a general pattern in dicot plants. To address this question, polyclonal antibodies against zinnia recombinant CCoAOMT fusion protein were raised and used for immunolocalization in several dicot plants. The antibodies predominantly recognized a protein band with a molecular mass of 28 kD on western analysis of tissue extracts from zinnia, forsythia (Forsythia suspensa), tobacco (Nicotiana tabacum), alfalfa (Medicago sativa), and soybean (Glycine max). Western analyses showed that the accumulation of CCoAOMT protein was closely correlated with lignification in in vitro TEs of zinnia. Immunolocalization results showed that CCoAOMT was localized in developing TEs of young zinnia stems and in TEs, xylem fibers, and phloem fibers of old stems. CCoAOMT was also found to be specifically associated with all lignifying tissues, including TEs, xylem fibers, and phloem fibers in stems of forsythia, tobacco, alfalfa, soybean, and tomato (Lycopersicon esculentum). The presence of CCoAOMT was evident in xylem ray parenchyma cells of forsythia, tobacco, and tomato. In forsythia and alfalfa, pith parenchyma cells next to the vascular cylinder were lignified. Accordingly, marked accumulation of CCoAOMT in these cells was observed. Taken together, these results showed a close association of CCoAOMT expression with lignification in dicot plants. This supports the hypothesis that the CCoAOMT-mediated methylation branch is a general one in lignin biosynthesis during normal growth and development in dicot plants.
A Determinant of Substrate Specificity Predicted from the Acyl-Acyl Carrier Protein Desaturase of Developing Cat's Claw Seed1
Authors: Cahoon Edgar B. , Shah Salehuzzaman , Shanklin John , Browse John
Published: July 2002

Cat's claw (Doxantha unguis-cati L.) vine accumulates nearly 80% palmitoleic acid (16:1Δ9) plus cis-vaccenic acid (18:1Δ11) in its seed oil. To characterize the biosynthetic origin of these unusual fatty acids, cDNAs for acyl-acyl carrier protein (acyl-ACP) desaturases were isolated from developing cat's claw seeds. The predominant acyl-ACP desaturase cDNA identified encoded a polypeptide that is closely related to the stearoyl (Δ9–18:0)-ACP desaturase from castor (Ricinis communisL.) and other species. Upon expression inEscherichia coli, the cat's claw polypeptide functioned as a Δ9 acyl-ACP desaturase but displayed a distinct substrate specificity for palmitate (16:0)-ACP rather than stearate (18:0)-ACP. Comparison of the predicted amino acid sequence of the cat's claw enzyme with that of the castor Δ9–18:0-ACP desaturase suggested that a single amino acid substitution (L118W) might account in large part for the differences in substrate specificity between the two desaturases. Consistent with this prediction, conversion of leucine-118 to tryptophan in the mature castor Δ9–18:0-ACP desaturase resulted in an 80-fold increase in the relative specificity of this enzyme for 16:0-ACP. The alteration in substrate specificity observed in the L118W mutant is in agreement with a crystallographic model of the proposed substrate-binding pocket of the castor Δ9–18:0-ACP desaturase.
Arabidopsis 22-Kilodalton Peroxisomal Membrane Protein. Nucleotide Sequence Analysis and Biochemical Characterization1
Authors: Tugal H. Bülent , Pool Martin , Baker Alison
Published: July 2002

We sequenced and characterized PMP22 (22-kDperoxisomal membrane protein) from Arabidopsis, which shares 28% to 30% amino acid identity and 55% to 57% similarity to two related mammalian peroxisomal membrane proteins, PMP22 and Mpv17. Subcellular fractionation studies confirmed that the Arabidopsis PMP22 is a genuine peroxisomal membrane protein. Biochemical analyses established that the Arabidopsis PMP22 is an integral membrane protein that is completely embedded in the lipid bilayer. In vitro import assays demonstrated that the protein is inserted into the membrane posttranslationally in the absence of ATP, but that ATP stimulates the assembly into the native state. Arabidopsis PMP22 is expressed in all organs of the mature plant and in tissue-cultured cells. Expression of PMP22 is not associated with a specific peroxisome type, as it is detected in seeds and throughout postgerminative growth as cotyledon peroxisomes undergo conversion from glyoxysomes to leaf-type peroxisomes. Although PMP22 shows increased accumulation during the growth of young seedlings, its expression is not stimulated by light.
Reporting and evaluating absolute-structure and absolute-configuration determinations
Authors: Flack H. D. , Bernardinelli G.
Published: July 2002

Detailed practical and numerical information is provided for undertaking and evaluating absolute-structure and absolute-configuration determinations. The interpretation of numerical values ofx, the Flack [Acta Cryst. (1983), A39, 876–881] parameter, and its standard uncertaintyuare explained in terms of the inversion-distinguishing power. Moreover, the conditions to obtain reliable values ofx(u) are detailed. Further explanatory material is provided on the use of right-handed axes, valid intensity data, the application to macromolecular structures, the dangers of polar-dispersion errors, Euclidean normalizers of space groups, the detection and reporting of molecular symmetry, enantiopurity and optical activity in solution. New CIF data names are introduced.
Microcrystallography with an X-ray waveguide
Authors: Müller M. , Burghammer M. , Flot D. , Riekel C. , Morawe C. , Murphy B. , Cedola A.
Published: July 2002

A waveguide microdiffraction setup is described for an undulator beamline at the European Synchrotron Radiation Facility. The composite optics consists of a waveguide, which confines the beam vertically, and a horizontally focusing multilayer mirror. A beam size of about 0.1 × 3 µm (vertical × horizontal) at λ = 0.095 nm has been obtained. The sample stage comprises a three-axis gantry with micrometre precision and a three-axis piezo-scanner with about 0.1 µm repeatability. Diffraction experiments are demonstrated for selected inorganic and polymeric samples. Possibilities for scanning diffractometry and small-angle scattering experiments are discussed.
Evaluation procedure for anisotropic SANS
Authors: Strunz P. , Wiedenmann A. , Gilles R. , Mukherji D. , Zrník J. , Schumacher G.
Published: July 2002

A brief description of an improvement of a special evaluation procedure for treatment of data from anisotropic Small-Angle Neutron Scattering (SANS) is presented. A spatial orientation distribution of particles, the improved calculation of a size distribution, the option to fit a data from a sample containing two types of particles as well as the raw-data treatment are the main extensions. The application of the procedure is demonstrated on data taken from investigation of precipitation in single-crystal nickel-base superalloys.
Refinement of proteins at subatomic resolution withMOPRO
Authors: Guillot Benoit , Viry Laurence , Guillot Regis , Lecomte Claude , Jelsch Christian
Published: July 2002

Crystallography at subatomic resolution permits the observation and measurement of the non-spherical character of the atomic electron density. Charge density studies are being performed on molecules of increasing size. TheMOPROleast-squares refinement software has thus been developed, by extensive modifications of the programMOLLY, for protein and supramolecular chemistry applications. The computation times are long because of the large number of reflections and the complexity of the multipolar model of the atomic electron density; the structure factor and derivative calculations have thus been parallelized. Stereochemical and dynamical restraints as well as the conjugate gradient algorithm have been implemented. A large number of the normal matrix off-diagonal terms turn out to be very small and the block diagonal approximation is thus particularly efficient in the case of large structures at very high resolution.
An X-ray interferometer with a large and variable path length difference
Authors: Fezzaa K. , Lee W.-K.
Published: July 2002

The first chromatic hard X-ray interferometer with a large and variable path length difference has been built and successfully tested. Interference fringe visibility was measured as a function of the path length difference. Based on the measurements, fringe visibility analysis was performed to give the transmitted beam coherence lengths. The results agree very well with expected coherence values based on the angular and spectral acceptances of the interferometer.
The resolution function for a time-of-flight diffractometer with curved slits chopper
Authors: Ionita I.
Published: July 2002

A procedure is presented for computing the resolution function for a time-of-flight diffractometer with curved slits chopper using the matrix computation technique. Some focusing conditions are deduced by compensating the major contributions to the variance of the scan variables; these conditions refer to the optimum sample and detector inclination angle and to the optimum chopper angular speed.
Simulation of electron density maps for two-dimensional crystal structures usingMathematica
Authors: Delatorre Plinio , de Azevedo Jr Walter Filgueira
Published: July 2002

The simulations presented here are based on the programMathematicaas a tool to present electron density maps of two-dimensional crystal structures. The models give further insights into the relationship between the thermal displacement parameters and the quality of the electron density maps. Furthermore, users can readily test the effects of several crystallographic parameters on the electron density maps, such as, the number of reflections, the thermal displacement parameters and the unit-cell dimensions.
Ultrafine nanostructure of partially crystallized bulk amorphous Zr54.5Ti7.5Al10Cu20Ni8
Authors: Hermann Helmut , Heinemann André , Bauer Hans-Dietrich , Mattern Norbert , Kühn Uta , Wiedenmann Albrecht
Published: July 2002

Bulk amorphous Zr54.5Ti7.5Al10Cu20Ni8was investigated by means of small-angle neutron scattering and high-resolution electron microscopy. Partially crystallized states were generated by annealing. The scattering data were analyzed in terms of a model taking into account both properties of the particles and interparticle interference. The mean radius of the particles is 1.3 nm. They are surrounded by a depletion zone with mean thickness of 2.6 nm. The volume fraction of the particles is estimated from the interparticle interference effect; its upper limit after annealing at 653 K for 4 h is 12%. Electron microscopy confirms the size determined from the scattering data and shows that the particles are crystalline.
The precision of diffraction peak location
Authors: Withers Philip J. , Daymond Mark R. , Johnson Michael W.
Published: July 2002

Much of crystallography is concerned with the accurate location of the centre of diffraction peak profiles. Simple analytical expressions are derived for estimating the precision of diffraction peak location that can be achieved for Gaussian diffraction peaks with a flat background, in terms of the standard deviation, integrated intensity and peak height (H) to background (B) ratio. Two formulations are derived using standard methods: one for the case of very low background, the other for significant backgrounds. It is found that in cases of significant background, peak position is less well determined by a factor of [1+2(21/2)B/H]1/2compared with the case of no background. The applicability of the expression has been demonstrated by Monte Carlo simulation of Gaussian profiles and by the analysis of real data collected at a large number of neutron and synchrotron sources, largely as part of the VAMAS TWA20 project. While the solution is presented for Gaussian peak shapes, it is believed to be approximately correct for a wide range of other common diffraction peak shapes (Lorentzian, Voigtianetc.). The method is applied to the assessment of the variation in optimal measuring time as a function of the depth of the gauge volume for residual strain scanning measurements.
Tracking: a method for structural characterization of grains in powders or polycrystals
Authors: Lauridsen E. M. , Schmidt S. , Suter R. M. , Poulsen H. F.
Published: July 2002

A method is presented for fast and non-destructive characterization of the individual grains inside bulk materials (powders or polycrystals). The positions, volumes and orientations of hundreds of grains are determined simultaneously. An extension of the rotation method is employed: a monochromatic beam of high-energy X-rays, focused in one dimension, impinges on the sample and the directions of the diffracted beams are traced by translation of two-dimensional detectors. Algorithms suitable for on-line analysis are described, including a novel indexing approach, where the crystal symmetry is used directly by scanning in Euler space. The method is verified with a simulation of 100 grains.
Three-dimensional maps of grain boundaries and the stress state of individual grains in polycrystals and powders
Authors: Poulsen H. F. , Nielsen S. F. , Lauridsen E. M. , Schmidt S. , Suter R. M. , Lienert U. , Margulies L. , Lorentzen T. , Juul Jensen D.
Published: July 2002

A fast and non-destructive method for generating three-dimensional maps of the grain boundaries in undeformed polycrystals is presented. The method relies on tracking of micro-focused high-energy X-rays. It is verified by comparing an electron microscopy map of the orientations on the 2.5 × 2.5 mm surface of an aluminium polycrystal with tracking data produced at the 3DXRD microscope at the European Synchrotron Radiation Facility. The average difference in grain boundary position between the two techniques is 26 µm, comparable with the spatial resolution of the 3DXRD microscope. As another extension of the tracking concept, algorithms for determining the stress state of the individual grains are derived. As a case study, 3DXRD results are presented for the tensile deformation of a copper specimen. The strain tensor for one embedded grain is determined as a function of load. The accuracy on the strain is Δ∊ ≃ 10−4.
The correction of reflection intensities for incomplete absorption of high-energy X-rays in the CCD phosphor
Authors: Wu G. , Rodrigues B. L. , Coppens P.
Published: July 2002

It is shown that incomplete absorption of the X-ray beam in the phosphor of an area detector causes an incident-angle dependence of the recorded X-ray intensities. An energy scan of a SMART-6000 CCD (charge-coupled device) phosphor using synchrotron radiation shows the correction to be of importance above about 17 keV. Intensities of single reflections, each collected several times at different angles of incidence on the phosphor surface, show a pronounced angle-dependence at shorter wavelengths. Both conventional structural refinement and multipole charge density studies confirm that an oblique-incidence correction leads to improved quality of the results. Atomic displacement parameters will be systematically biased when the correction is not applied. For a λ = 0.394 Å data set, neglecting the correction gives rise to artifacts in the deformation density maps that are likely to lead to misinterpretation of the experimental results.
Crystal data for the decavanadates of 2,4-, 3,4-, and 3,5- dimethylpyridine and 2,4,6-trimethylpyridine
Authors: Arrieta J. M. , Amigó J. M. , Gili P.
Published: July 2002

Indexed powder patterns of four monoclinic compounds of general formula (BH)3H3V10O28 .xH2O, where x = 1-2.5 and B = 2,4-dimethylpyridine (J8), (C7H10N)3H3V10O28.1.0H2O, 3,4-dimethylpyridine (J10), (C7H10N)3H3V10O28.1.0H2O, 3,5-dimethylpyridine (J11), (C7H10N)3H3V10O28.2.5H2O, and 2,4,6-trimethylpyridine (J12), (C8H12N)3H3V10O28.1.0H2O are given. The cell dimensions of the unit cells with two molecules are: J8 a = 18.360 (2), b = 10.438 (2), c = 13.503 (2) Å, β = 95.99 (1)°; J10 a = 12.538 (3), b = 13.634 (5), c = 16.662 (5) Å, β = 111.82 (2)°; J11 a = 19.483 (5), b = 10.711 (2), c = 13.020 (4) Å, β = 101.52 (2)°; J12 a = 12.776 (3), b = 22.470 (4), c = 11.790 (3) Å, β = 91.54 (1)°.
Macromolecular crystallography with synchrotron radiation. II. Results
Authors: Wilson K. S. , Stura E. A. , Wild D. L. , Todd R. J. , Stuart D. I. , Babu Y. S. , Jenkins J. A. , Standing T. S. , Johnson L. N. , Fourme R. , Kahn R. , Gadet A. , Bartels K. S. , Bartunik H. D.
Published: July 2002

Crystallographic data for three different protein crystals (glycogen phosphorylase b to 2 Å resolution, β-lactamase I to 2.5 Å resolution and troponin C to 6 Å resolution) have been recorded using the intense synchrotron radiation beam emitted by the DCI storage ring at LURE and the DORIS storage ring at DESY/EMBL. Reduction in exposure times of approximately 50-fold and an increase in crystal lifetime of at least fivefold are observed when data recorded at LURE are compared with those recorded with a conventional rotating-anode source. These factors have made possible data collection which otherwise would have been impossible. For large crystals of phosphorylase b a greater reduction in exposure time ( × 125) is made possible by the focusing geometry of the synchrotron-monochromator system which allowed irradiation of a larger volume of the crystal (collimator size increased from 0.3 to 1.0 mm) without significant increase in spot overlap on the film. The data processing statistics for phosphorylase b and β-lactamase compare favourably with those from data recorded on a conventional source (improvements in merging R values of between 1 and 4%). For phosphorylase b, but not for β-lactamase or troponin C, significant thermal diffuse scatter is observed on photographs recorded with synchrotron radiation. The possible origin of this phenomenon and its effect on data processing are discussed.
Some practical aspects of the Fourier deconvolution
Authors: Čerňanský M.
Published: July 2002

Simple rules for the Fourier deconvolution method are illustrated on experimental X-ray diffraction profiles. Comparison of various digital filters is given and criteria for a right solution are also discussed.
Replacement of monochromator and proportional gas counter by mercuric iodide detector in X-ray powder diffraction
Authors: Nissenbaum J. , Levi A. , Burger A. , Schieber M.
Published: July 2002

Low-resolution and therefore low-cost mercuric iodide detectors have successfully been applied to replace the combination of a graphite monochromator and a proportional gas radiation counter used in X-ray diffractometers. The mercuric iodide detector requires a lower DC bias of only 200 V rather than the 1500 V bias needed for the proportional gas counter. The much better stopping power of HgI2 allows higher counting efficiency and therefore a better signal-to-noise ratio. Results are shown for X-ray powder diffractions of polycrystalline cubic silicon and tetragonal HgI2.
Crystal data for antimony molybdenum oxide Sb2MoO6
Authors: Laarif A. , Hewat A. , Theobald F. , Vivier H.
Published: July 2002

The powder data for antimony molybdenum oxide Sb2MoO6 are reported. This compound is triclinic, P{\bar 1}, with a = 7.481(4), b = 7.504(3), c = 10.120(1) Å, α = 70.43(3), β = 70.91(4), γ = 83.34(7)°; U = 505.9(5) Å3; Z = 4; Dx
= 5.74 Mg m−3. The structure is of the fluorite type but it is distorted. Pseudo-monoclinic cells as reported by Parmentier, Courtois & Gleitzer [Bull. Soc. Chim. Ft. (1974), 1–2, 75–77] or that obtained with program TRACER [Lawton & Jacobson (1965). Mobil Oil Corporation Research Department; Lawton (1967). Mobil Oil Corporation Research Department] are also considered and discussed. Neutron diffraction gives further evidence of the triclinic lattice. The JCPDS Diffraction File No. for Sb2MoO6 is 33–1491.
The sampling theorem and small-angle scattering
Authors: Gerber T. , Schmidt P. W.
Published: July 2002

All information about the scattering sample obtainable from small-angle scattering data is shown to be contained in the discrete measured points of a scattering curve distorted by arbitrary collimation conditions, provided that the interval Δh between adjacent measured points fulfils the condition Δh ≤ π/L, where L is the largest correlation distance in the sample; h = 4πλ
−1sinθ; λ is the scattered wavelength; and 2θ is the scattering angle. A simple technique has been developed for separation of part of the noise. It is shown that if the total time for measuring a scattering curve is held constant, a scattering curve recorded with Δh equal to the sampling-point interval π/L gives results like those obtained for a scattering curve recorded with a measured point distance smaller than that sampling-point interval. Therefore, Δh should be chosen to be small enough to guarantee that Δh ≤ π/L. Furthermore, a technique has been developed to calculate missing data points from the measured intensities. The condition Δh ≤ π/L has been found to be important for this calculation.
Molecular surface Triangulation
Authors: Connolly M. L.
Published: July 2002

A method is presented for triangulating the surface of a molecule. A triangulated surface is a polyhedron, all of whose faces are triangles. The triangles are created by subdividing the curved faces of an analytical molecular surface that has been precalculated by an earlier algorithm. The triangulated surface has many applications. Molecular areas and volumes may be calculated from it. Packing defects in proteins may be identified. It may be used to determine whether a particular water molecule lies in the interior of the protein or on the surface. The triangulated surface may be drawn on pen plotters, vector graphics systems and raster graphics terminals. Mathematical functions defined on the surface may be contoured. Local maxima and minima of functions may be located. While the triangulated surface is less accurate than the analytical molecular surface it is derived from, it has the advantage of being much simpler and easier to deal with. It combines the simplicity of a dot surface with the continuity of an analytical surface.
Isomorphism of basic copper chromate, CuCrO42CuO.2H2O, and antlerite, Cu3(SO4)(OH)4
Authors: Pollack S. S.
Published: July 2002

The similarities of the observed and calculated powder X-ray diffraction patterns show that CuCrO4.2CuO.2H2O is isomorphous with Cu3(SO4)(OH)4. In an unusual replacement chromium substitutes for sulfur.