bluuebunny/crossref_metadata_2025 huggingface dataset:
The sociodemographic profile, risk categories and prevalence of HIV infection among people attending a London same-day testing clinic, 2000–2001
Authors: Sinclair M , Bor R , Evans A , Glass D , Levitt D , Johnson M A
Published: December 2003

The objectives were to determine the sociodemographic profile, risk category, and prevalence of HIV infection amongst people attending a confidential clinic providing counselling, medical advice and results of HIV antibody testing on the same day of consultation. Data were collected on all 1749 individuals attending the same-day HIV testing clinic at the Royal Free Hospital, London and proceeding to HIV testing between June 2000 and May 2001. One thousand, one hundred and forty-eight men and 601 women (mean age 33.3 years) were tested for HIV antibodies. The primary risk for HIV infection was heterosexual contact (69.9%; 1224/1749) and homosexual contact (27.7%; 485/1749). Fifty individuals tested HIV-positive (42 men and eight women). HIV seroprevalence was 2.8% (50/1749) and was highest among men who reported risk through homosexual contact (6.2%; 30/485). The rates for heterosexual men and women were 1.8% (12/648) and 1.4% (8/576), respectively, though they were highest among Black Caribbean (12%; 3/25) and Black African attendees from sub-Saharan African countries (11.2%; 18/160). Of the total number attending the clinic, more than half (56%; 981/1749) had previously been tested and received a negative test result. Of the fifty HIV antibody-positive individuals, 26%, (13) had previously received a negative result and had all reported risk through homosexual contact. Thirty of the HIV antibody-positive individuals were asymptomatic, 14 were symptomatic and three were diagnosed with an AIDS-defining condition. Half of all HIV-positive attendees (51.2%; 22/43) presented at the time of testing with CD4 cell counts below the normal range (>400×106/l). The high HIV seroprevalence among homosexual men, some of whom had previously tested negative, suggests that HIV prevention strategies used within this group may need to be reassessed. The continuing high HIV seroprevalence among individuals from African countries suggests that this population require specific targeting for HIV risk reduction and information on the advantages of early diagnosis and treatment.
Doubts about necessity and concerns about adverse effects: identifying the types of beliefs that are associated with non-adherence to HAART
Authors: Horne Robert , Buick Deanna , Fisher Martin , Leake Heather , Cooper Vanessa , Weinman John
Published: December 2003

This cross-sectional study assessed beliefs about highly active antiretroviral therapy (HAART) and their association with reported adherence to HAART among 109 HIV-positive patients receiving HAART while attending an ambulatory care clinic in Brighton, UK. Patients' beliefs about the necessity for and concerns about HAART and their adherence to it were assessed using validated questionnaires. There was considerable variation in beliefs and reported adherence. A quarter of participants reported low adherence to HAART and this was related to concerns about adverse effects as well as to the way in which each individual balanced concerns against perceptions of necessity. Patients were significantly more likely to report low adherence rates if their concerns were high relative to their perceptions of personal need for HAART. Patients with higher CD4 counts were significantly more likely to hold a view of HAART in which perceptions of necessity were higher relative to their concerns about adverse effects. CD4 was not related to reported adherence. A comparison of most recent viral load results between high and low adherence group identified differences in the predicted direction but these were not statistically significant. These preliminary findings suggest that patients' perceptions of HAART are important determinants of adherence with implications for future research and clinical practice.
The role of urethral samples in the diagnosis of gonorrhoea in women
Authors: Ghanem M , Radcliffe K , Allan P
Published: December 2003

We studied the value of carrying out urethral samples in women to diagnose gonorrhoea. All cases of genital gonorrhoea in women were identified (between 1 October 2000 and 30 September 2001) at the Whittall Street Clinic and the genitourinary medicine department at the Coventry and Warwickshire Hospital. Two hundred and twenty-four cases of female urethral gonorrhoea were identified. In 20 cases (6.3%) the urethra was the sole site of the infection. At the Whittall Street Clinic, we had to carry out 643 urethral samples in order to treat one additional case of gonorrhoea. On the other hand, 1204 urethral samples were requested to treat one additional case of female gonorrhoea at the Coventry and Warwickshire Hospital. In both units, use of the Gram-stained urethral smear permitted early treatment in only 1.8% of cases of genital gonorrhoea. Units with low prevalence of gonorrhoea should consider abandoning urethral samples for the diagnosis of gonorrhoea in women.
Aetiology of meningitis in HIV-infected patients in a referral hospital in Phnom Penh, Cambodia
Authors: Chhin S , Rozycki G , Pugatch D , Harwell J I
Published: December 2003

The HIV epidemic in Cambodia is one of the most extensive in Asia. Meningitis accounts for a substantial proportion of HIV-related morbidity and mortality in Cambodia. A retrospective chart review was performed to identify the clinical and spinal fluid characteristics of patients undergoing spinal tap at an AIDS referral hospital in Phnom Penh, Cambodia during a 16-month period. Of 932 charts reviewed, 89 met criteria for analysis. Overall mortality was 49.4%. Cryptococcus was the most commonly identified pathogen (83%), followed by mycobacteria (8%). No pathogen was identified in 9% of charts reviewed. In hospital mortality was similar in all groups.
Chlamydia trachomatis genital infection in apparently healthy adult population of Tamil Nadu, India: a population-based study
Authors: Joyee A G , Thyagarajan S P , Rajendran P , Hari R , Balakrishnan P , Jeyaseelan L , Kurien T ,   and the STD Study Group
Published: December 2003

Since the epidemiology of Chlamydia trachomatis infection in apparently healthy population has not been studied in India, a population-based study was conducted in the state of Tamil Nadu, India in order to analyse the prevalence of genital chlamydial infections in the community and to implement control programmes. A representative sample was taken from three randomly selected districts by using the 'probability proportional to size' cluster survey method. Households were the basic units of clusters. Adults aged 15-45 years, pre-identified from the selected households were enrolled during the medical camps conducted for a major study on community prevalence of sexually transmitted diseases in Tamil Nadu. Blood and urine samples collected from the study subjects were tested by enzyme-linked immunosorbent assay (ELISA) for anti-chlamydial IgM antibodies and by the commercial Amplicor polymerase chain reaction (PCR) test for chlamydial DNA. The prevalence of anti- C. trachomatis antibodies determined by IgM-ELISA was 2.4% (95% CI 1.6%-3.2%). The prevalence of genital chlamydial infection determined by PCR was 1.1% (95% CI 0.5%-1.7%). Majority of the detected infections (68.8%) were asymptomatic. This is the first Indian report on the prevalence of genital chlamydial infections in the general population. It is concluded that this study provides evidence for a substantial burden of approximately 10 million asymptomatic genital chlamydial infection cases in the sexually active age groups in the general population of India.
HIV/AIDS risk perception, attitudes and sexual behaviour in Portugal
Authors: Amaro Fausto , Frazão Carla , Pereira Maria Elizabete , da Cunha Teles Louise
Published: December 2003

One thousand individuals in the age group 18–69 were selected for a multistage nationwide random sample. Of the interviewees 68.3% were of the opinion that the risk of AIDS, in Portugal, is considerably high and 37.1% stated that they had feared being infected by the HIV; 28.0% established a connection between being afraid and the fact that AIDS is a serious/incurable disease; 31.5% believed that there are risks inherent to the health services; only 7.8% expressed fear of AIDS because of an infected partner. Only 42.6% regarded extra-marital sexual relations as either partially or totally acceptable. Sexual relations between youths were seen as totally acceptable by 11.9% and partially acceptable by 51.1%. Homosexual relations between men were seen as either totally or partially acceptable by 38%. Of the interviewees, 7.8% thought that recent treatments can definitely cure AIDS and 6.5% believed that with recent treatments HIV transmission would no longer be possible.
The 5′–3′ exoribonuclease xrn-1 is essential for ventral epithelial enclosure during C. elegans embryogenesis
Authors: NEWBURY SARAH , WOOLLARD ALISON
Published: December 2003

Ribonucleases have been studied in yeast and bacteria, but their biological significance to multicellular organisms is virtually unknown. However, there is increasing evidence that specific, timed transcript degradation is critical for regulation of many cellular processes, including early development and RNA interference. In this report we have investigated the effects of the 5′–3′ exoribonuclease xrn-1 on the development of the nematode worm Caenorhabditis elegans. Silencing of xrn-1 expression using RNA interference results in embryos that fail to complete ventral enclosure, where the outer layer of cells normally closes over the mesoderm in a purse-string movement. Our data suggest that xrn-1 is involved in a critical aspect of epithelial movement and reveal an unexpected link between RNA stability and morphogenesis. Because xrn-1 is highly conserved in all eukaryotes, it is possible that it plays a role in similar morphological processes such as dorsal or thorax closure in Drosophila and wound healing in humans. In contrast to work in human tissue culture cells, where the 3′–5′ pathway has been shown to be the most important for degradation of mRNAs, our work shows that the 5′–3′ degradation pathway is crucially important at a critical stage of development in C. elegans. We have also investigated whether xrn-1 can influence the response of C. elegans to RNA interference. Our data indicate that xrn-1 plays a facilitating, but not crucial role in this process.
The RNA binding domain within the nucleoporin Nup153 associates preferentially with single-stranded RNA
Authors: BALL JENNIFER R. , DIMAANO CHRISTIAN , ULLMAN KATHARINE S.
Published: December 2003

The nuclear pore protein Nup153 is important for the transport of protein and RNA between the nucleus and cytoplasm. Recently, a novel RNA binding domain (RBD) was mapped within the N-terminal region of Nup153; however, the determinants of RNA association were not characterized. Here we have tested a range of RNAs with different general features to better understand targets recognized by this domain. We have found that the RBD associates with single-stranded RNA with little sequence preference. These results provide new information about a novel RNA binding domain and suggest new models to consider for the contribution of Nup153 to nucleocytoplasmic transport.
Regulation of splicing: The importance of being translatable: FIGURE 1.
Authors: MIRIAMI ELANA , SPERLING RUTH , SPERLING JOSEPH , MOTRO UZI
Published: December 2003

RNA sequences that conform to the consensus sequence of 5′ splice sites but are not used for splicing occur frequently in protein coding genes. Mutational analyses have shown that suppression of splicing at such latent sites may be dictated by the necessity to maintain an open reading frame in the mRNA. Here we show that stop codon frequency in introns having latent 5′ splice sites is significantly greater than that of introns lacking such sites and significantly greater than the expected occurrence by chance alone. Both observations suggest the occurrence of a general mechanism that recognizes the mRNA reading frame in the context of pre-mRNA.
Analysis of a long-range interaction between conserved domains of human telomerase RNA
Authors: UEDA CHRISTINE T. , ROBERTS RICHARD W.
Published: December 2003

Telomerase is a ribonucleoprotein complex responsible for maintaining telomere length of eukaryotic chromosomes. Human telomerase has two main components, the human telomerase reverse transcriptase and the human telomerase RNA (hTR). Two domains of hTR essential for telomerase activity are the template domain, comprised of an 11-nt templating and alignment sequence, and the CR4/CR5 domain. Highly conserved residues in the CR4/CR5 domain form the stem–loop P6.1, which is important for assembly and activity of mammalian telomerase. Here, we have determined that stem–loop P6.1 can participate in a long-range RNA–RNA interaction with the template region of hTR. We characterized this interaction through mobility shift assays, mutation analysis, and UV cross-linking experiments. Mutation analysis revealed that the P6.1 loop nucleotides participate in the interaction with the template. The site of interaction at the template domain was determined via UV cross-linking experiments. These data show that an RNA–RNA interaction exists between two highly conserved regions of hTR that are critical for the higher order folding of telomerase RNA. This interaction argues for the proximity of the template and the CR4/CR5 domain, and provides the basis for a revised model of hTR, partitioning the RNA into a catalytic domain and a localization domain.
Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization
Authors: LINGER BENJAMIN R. , KUNOVSKA LYUDMYLA , KUHN RICHARD J. , GOLDEN BARBARA L.
Published: December 2003

In Sindbis virus, initiation of nucleocapsid core assembly begins with recognition of the encapsidation signal of the viral RNA genome by capsid protein. This nucleation event drives the recruitment of additional capsid proteins to fully encapsidate the genome, generating an icosahedral nucleocapsid core. The encapsidation signal of the Sindbis virus genomic RNA has previously been localized to a 132-nucleotide region of the genome within the coding region of the nsP1 protein, and the RNA-binding activity of the capsid was previously mapped to a central region of the capsid protein. It is unknown how capsid protein binding to encapsidation signal leads to ordered oligomerization of capsid protein and nucleocapsid core assembly. To address this question, we have developed a mobility shift assay to study this interaction. We have characterized a 32 amino acid peptide capable of recognizing the Sindbis virus encapsidation signal RNA. Using this peptide, we were able to observe a conformational change in the RNA induced by capsid protein binding. Binding is tight (Kdapp = 12 nM), and results in dimerization of the capsid peptide. Mutational analysis reveals that although almost every predicted secondary structure within the encapsidation signal is required for efficient protein binding, the identities of the bases within the helices and hairpin turns of the RNA do not need to be maintained. In contrast, two purine-rich loops are essential for binding. From these data, we have developed a model in which the encapsidation signal RNA adopts a highly folded structure and this folding process directs early events in nucleocapsid assembly.
Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations
Authors: HALL KATHLEEN B. , WILLIAMS D. JEREMY
Published: December 2003

The iron responsive element (IRE) RNA hairpin loop contains six phylogenetically conserved nucleotides, which constitute part of the sequence-specific binding site of the IRE-binding protein. The NMR structure of the loop has been solved, showing that 3 of the 6 nt are poorly constrained. Here, two purine nucleotides in the IRE loop are individually replaced with the fluorescent purine analog 2-aminopurine (2AP). Steady-state and time-resolved fluorescence methods are used to describe the structure and dynamics of 2AP in the IRE loop. The data indicate that 2AP at the position of the adenosine in the loop moves between stacked and unstacked positions, whereas 2AP at the adjacent guanosine is predominantly solvent exposed. Stochastic dynamics simulations are used to provide a physical description of how those nucleotides might move.
Crystal structure of the BstDEAD N-terminal domain: A novel DEAD protein from Bacillus stearothermophilus
Authors: CARMEL ANDREW B. , MATTHEWS BRIAN W.
Published: December 2003

Most cellular processes requiring RNA structure rearrangement necessitate the action of Asp-Glu-Ala-Asp (DEAD) proteins. Members of the family, named originally for the conserved DEAD amino acid sequence, are thought to disrupt RNA structure and facilitate its rearrangement by unwinding short stretches of duplex RNA. BstDEAD is a novel 436 amino acid representative of the DEAD protein family from Bacillus stearothermophilus that contains all eight conserved motifs found in DEAD proteins and is homologous with other members of the family. Here, we describe the 1.85 Å resolution structure of the N-terminal domain (residues 1–211) of BstDEAD (BstDEAD-NT). Similar to the corresponding domains of related helicases, BstDEAD-NT adopts a parallel α/β structure with RecA-like topology. In general, the conserved motifs superimpose on closely related DEAD proteins and on more distantly related helicases such as RecA. This affirms the current belief that the core helicase domains, responsible for mechanistic activity, are structurally similar in DEAD proteins. In contrast, however, the so-called Walker A P-loop, which binds the β- and γ-phosphates of ATP, adopts a rarely seen “closed” conformation that would sterically block ATP binding. The closed conformation may be indicative of a general regulatory feature among DEAD proteins (and RNA helicases) that differs from that used by DNA helicases. BstDEAD also contains a unique extension of ~60 residues at the C terminus that is highly basic, suggesting that it might bind nucleic acids and, in so doing, confer specificity to the helicase activity of the core region.
Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain
Authors: VAN NUES ROB W. , BROWN JEREMY D.
Published: December 2003

The contribution made by the RNA component of signal recognition particle (SRP) to its function in protein targeting is poorly understood. We have generated a complete secondary structure for Saccharomyces cerevisiae SRP RNA, scR1. The structure conforms to that of other eukaryotic SRP RNAs. It is rod-shaped with, at opposite ends, binding sites for proteins required for the SRP functions of signal sequence recognition (S-domain) and translational elongation arrest (Alu-domain). Micrococcal nuclease digestion of purified S. cerevisiae SRP separated the S-domain of the RNA from the Alu-domain as a discrete fragment. The Alu-domain resolved into several stable fragments indicating a compact structure. Comparison of scR1 with SRP RNAs of five yeast species related to S. cerevisiae revealed the S-domain to be the most conserved region of the RNA. Extending data from nuclease digestion with phylogenetic comparison, we built the secondary structure model for scR1. The Alu-domain contains large extensions, including a sequence with hallmarks of an expansion segment. Evolutionarily conserved bases are placed in the Alu- and S-domains as in other SRP RNAs, the exception being an unusual GU4A loop closing the helix onto which the signal sequence binding Srp54p assembles (domain IV). Surprisingly, several mutations within the predicted Srp54p binding site failed to disrupt SRP function in vivo. However, the strength of the Srp54p–scR1 and, to a lesser extent, Sec65p–scR1 interaction was decreased in these mutant particles. The availability of a secondary structure for scR1 will facilitate interpretation of data from genetic analysis of the RNA.
Purine bases at position 37 of tRNA stabilize codon–anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions
Authors: KONEVEGA ANDREY L. , SOBOLEVA NATALIA G. , MAKHNO VALENTIN I. , SEMENKOV YURI P. , WINTERMEYER WOLFGANG , RODNINA MARINA V. , KATUNIN VLADIMIR I.
Published: December 2003

The anticodon loop of tRNA contains a number of conserved or semiconserved nucleotides. In most tRNAs, a highly modified purine is found at position 37 immediately 3′ to the anticodon. Here, we examined the role of the base at position 37 for tRNAPhe binding to the A site of Escherichia coli ribosomes. Affinities and rate constants of A-site binding of native yeast peptidyl-tRNAPhe with hypermodified G (wybutine), or of unmodified peptidyl-tRNAPhe transcripts with G, A, C, or U, at position 37 were measured. The data indicate that purines stabilize binding due to stronger stacking and additional interactions with the ribosome mediated by Mg2+ ions. Paromomycin, an antibiotic that binds to 16S rRNA in the decoding center, greatly stabilized tRNAs in the A site and abolished the Mg2+-dependence of binding. Comparison of binding enthalpies and entropies suggests that hypermodification of the base at position 37 does not affect stacking in the codon–anticodon complex, but rather decreases the entropic penalty for A-site binding. Substitution of purines with pyrimidines at position 37 increases the rates of tRNA binding to and dissociation from the A site. The data suggest that initial binding of tRNA to the A site is followed by a rate-limiting rearrangement of the anticodon loop or the ribosome decoding center that is favored by purines at position 37 and involves stronger stacking, additional Mg2+ binding, and interactions with 16S rRNA.
EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding
Authors: SHARMA DIVYA , SOUTHWORTH DANIEL R. , GREEN RACHEL
Published: December 2003

Following peptide-bond formation, the mRNA:tRNA complex must be translocated within the ribosomal cavity before the next aminoacyl tRNA can be accommodated in the A site. Previous studies suggested that following peptide-bond formation and prior to EF-G recognition, the tRNAs occupy an intermediate (hybrid) state of binding where the acceptor ends of the tRNAs are shifted to their next sites of occupancy (the E and P sites) on the large ribosomal subunit, but where their anticodon ends (and associated mRNA) remain fixed in their prepeptidyl transferase binding states (the P and A sites) on the small subunit. Here we show that pre-translocation-state ribosomes carrying a dipeptidyl-tRNA substrate efficiently react with the minimal A-site substrate puromycin and that following this reaction, the pre-translocation-state bound deacylated tRNA:mRNA complex remains untranslocated. These data establish that pre-translocation-state ribosomes must sample or reside in an intermediate state of tRNA binding independent of the action of EF-G.
Spatial determinants of the alfalfa mosaic virus coat protein binding site
Authors: LAFOREST SIANA M. , GEHRKE LEE
Published: December 2003

The biological functions of RNA–protein complexes are, for the most part, poorly defined. Here, we describe experiments that are aimed at understanding the functional significance of alfalfa mosaic virus RNA–coat protein binding, an interaction that parallels the initiation of viral RNA replication. Peptides representing the RNA-binding domain of the viral coat protein are biologically active in initiating replication and bind to a 39-nt 3′-terminal RNA with a stoichiometry of two peptides: 1 RNA. To begin to understand how RNA–peptide interactions induce RNA conformational changes and initiate replication, the AMV RNA fragment was experimentally manipulated by increasing the interhelical spacing, by interrupting the apparent nucleotide symmetry, and by extending the binding site. In general, both asymmetric and symmetric insertions between two proposed hairpins diminished binding, whereas 5′ and 3′ extensions had minimal effects. Exchanging the positions of the binding site hairpins resulted in only a moderate decrease in peptide binding affinity without changing the hydroxyl radical footprint protection pattern. To assess biological relevance in viral RNA replication, the nucleotide changes were transferred into infectious genomic RNA clones. RNA mutations that disrupted coat protein binding also prevented viral RNA replication without diminishing coat protein mRNA (RNA 4) translation. These results, coupled with the highly conserved nature of the AUGC865–868 sequence, suggest that the distance separating the two proposed hairpins is a critical binding determinant. The data may indicate that the 5′ and 3′ hairpins interact with one of the bound peptides to nucleate the observed RNA conformational changes.
Aptamer redesigned tRNA is nonfunctional and degraded in cells
Authors: LEE DENNIS , MCCLAIN WILLIAM H.
Published: December 2003

An RNA aptamer derived from tRNAGln isolated in vitro and a rationally redesigned tRNAGln were used to address the relationship between structure and function of tRNAGln aminoacylation in Escherichia coli. Two mutant tRNAGln sequences were studied: an aptamer that binds 26-fold tighter to glutaminyl-tRNA synthetase than wild-type tRNAGln in vitro, redesigned in the variable loop, and a mutant with near-normal aminoacylation kinetics for glutamine, redesigned to contain a long variable arm. Both mutants were tested in a tRNAGln knockout strain of E. coli, but neither supported knockout cell growth. It was later found that both mutant tRNAs were present in very low amounts in the cell. These results reveal the difference between in vitro and in vivo studies, demonstrating the complexities of in vivo systems that have not been replicated in vitro.
Genetic evidence against the 16S ribosomal RNA helix 27 conformational switch model
Authors: RODRIGUEZ-CORREA DANIEL , DAHLBERG ALBERT E.
Published: December 2003

A mechanistic understanding of ribosome function demands knowledge of the conformational changes that occur during protein synthesis. One current model proposes a conformational switch in Helix 27 (H27) of 16S rRNA involved in the decoding of mRNA. This model was based on the behavior of mutations in the 912 region of H27 of Escherichia coli 16S rRNA, which were predicted to stabilize the helix in either of two alternative conformations. This interpretation was supported by evidence from both genetics and structural biochemistry. However, recently published X-ray crystallographic structures of the Thermus thermophilus 30S subunit at different stages of tRNA selection have raised doubts regarding the validity of this model. We have therefore revisited the model genetically by constructing a H27 quadruple mutation (C912G, C910G, G885C, and G887C), which would create multiple mismatches in the proposed alternative conformation without perturbing the native H27 conformation seen in the crystal structures. Inconsistent with the H27 switch model, cells containing pure populations of quadruple mutant ribosomes grow at essentially wild-type rates. The mutants used to construct the H27 switch model all carried A2058G in 23S rRNA and C1192U in 16S rRNA as selectable markers. The quadruple mutant carrying these additional marker mutations is deleterious, and we conclude that they have a synergistic effect when combined with other mutations and are not phenotypically silent. Their presence confounded the interpretation of the original mutant phenotypes and, in light of the viability of the quadruple mutant, we conclude that the genetic evidence no longer supports the model.
Latent splice sites and stop codons revisited: FIGURE 1.
Authors: ZHANG XIANG H-F. , CHASIN LAWRENCE A.
Published: December 2003

The accuracy of the data we reported in an RNA Letter to the Editor earlier this year on the possible relationship between stop codons and splicing is questioned by Miriami et al. (this issue). We reply here that we see no inaccuracy in our data presentation and offer a possible explanation for their interpretation.
In vitro selection of ribozymes dependent on peptides for activity
Authors: ROBERTSON MICHAEL P. , KNUDSEN SCOTT M. , ELLINGTON ANDREW D.
Published: December 2003

A peptide-dependent ribozyme ligase (aptazyme ligase) has been selected from a random sequence population based on the small L1 ligase. The aptazyme ligase is activated > 18,000-fold by its cognate peptide effector, the HIV-1 Rev arginine-rich motif (ARM), and specifically recognizes the Rev ARM relative to other peptides containing arginine-rich motifs. Moreover, the aptazyme ligase can preferentially recognize the Rev ARM in the context of the full-length HIV-1 Rev protein. The only cross-reactivity exhibited by the aptazyme is toward the Tat ARM. Reselection of peptide- and protein-dependent aptazymes from a partially randomized population yielded aptazymes that could readily discriminate against the Tat ARM. These results have important implications for the development of aptazymes that can be used in arrays for the detection and quantitation of multiple cellular proteins (proteome arrays).
Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs)
Authors: PERSENGIEV STEPHAN P. , ZHU XIAOCHUN , GREEN MICHAEL R.
Published: December 2003

RNA interference is an evolutionarily conserved process in which expression of a specific gene is post-transcriptionally inhibited by a small interfering RNA (siRNA), which recognizes a complementary mRNA and induces its degradation. Currently, RNA interference is being used extensively to inhibit expression of specific genes for experimental and therapeutic purposes. For applications in mammalian cells, siRNAs are designed to be <~30 base pairs to avoid nonspecific effects that arise from inducing the cellular double-stranded RNA (dsRNA)-dependent protein kinase (PKR) response. Here we perform expression profiling in mammalian tissue-culture cells treated under standard conditions with conventional 21-bp siRNAs and find, unexpectedly, that >1000 genes involved in diverse cellular functions are nonspecifically stimulated or repressed. The effects on gene expression are dependent upon siRNA concentration and are stable throughout the course of siRNA treatment. Our results can be explained by previous studies showing that dsRNAs can affect multiple signaling and transcription pathways in addition to PKR. The potential for this widespread, nonspecific effect on mammalian gene expression must be carefully considered in the design of siRNA experiments and therapeutic applications.
Development of a Questionnaire on Attitudes Towards Suicide (ATTS) and Its Application in a Swedish Population
Authors: Renberg Ellinor Salander , Jacobsson Lars
Published: December 2003

An instrument measuring attitudes toward suicide was developed through two postal questionnaire surveys, 1986 and 1996, approaching general population samples of 700 and 1,000 persons, respectively, and with response rates of 75% and 64%. A 10‐factor model was obtained and comparisons between waves revealed an overall more permissive and pro‐preventional attitude in 1996. The results implied complex relationships at the aggregated level between attitudes and suicidal behavior, depending on type of suicidal behavior, attitude factor, and subgroup. At the individual level, persons answering affirmative on own suicidal behavior, as compared to the nonsuicidal group, held a more permissive and understanding attitude toward suicide.
Homicide–Suicides in Fiji: Offense Patterns, Situational Factors, and Sociocultural Contexts
Authors: Adinkrah Mensah
Published: December 2003

Although there is growing literature on lethal violence in developing nations, homicide–suicides have rarely been studied. Addressing this issue, this paper analyzes all homicide–suicides that occurred in Fiji between 1982 and 1992. The study's results are consistent with prior research in Western developed nations, demonstrating that homicide–suicides constitute a minuscule proportion of all homicides, occur primarily between intimate relations, are precipitated by intrafamilial discord, and occur in the domestic setting. Contrary to prior research, however, perpetrators of homicide–suicide were equally divided between men and women and no firearms were utilized.
Sociocultural Determinants of Suicide Ideation: A Comparison Between American and Ghanaian College Samples
Authors: Eshun Sussie
Published: December 2003

This study investigated the role of gender, family cohesion, religiosity, and negative suicide attitudes as potential determinants of cultural differences in suicide ideation among 375 college students from Ghana and the United States. Significant cultural differences were found for suicide ideation, family closeness, religiosity, and negative suicide attitudes. Family cohesion and negative attitudes were significant predictors for both cultural groups. Gender was a significant determinant for suicide ideation among Ghanaians, but not Americans; religiosity was not a significant determinant for either group. More extensive research on sociocultural influences on suicide, especially among countries in which suicide is underreported or not documented, is encouraged.
The Werther Effect and Assisted Suicide
Authors: Frei Andreas , Schenker Tanja , Finzen Asmus , Dittmann Volker , Kraeuchi Kurt , Hoffmann‐Richter Ulrike
Published: December 2003

In the course of a large epidemiological study in the region of Basle, Switzerland, from 1992 to 1996, a considerable rise in suicides assisted by the right‐to‐die society EXIT was uncovered after wide press coverage of an assisted double suicide of a prominent couple in that region in March 1995. Further investigation revealed that the rise of assisted suicides for a period of 2 years after the critical event was statistically significant compared to the 2 years previous to the double suicide. This was especially true for women older than 65 years. Hence, the almost enthusiastic kind of reporting about this event was apt to induce imitation suicides or a “Werther‐effect.”
Prädiktive Regelung mit Dynamischer Programmierung für nichtlineare Systeme erster Ordnung (Predictive Control with Dynamic Programming for First Order Nonlinear Systems)
Authors: Back Michael , Terwen Stephan
Published: December 2003

Dieser Beitrag beschreibt die Einbindung der Dynamischen Programmierung nach Bellman in die Modellbasierte Prädiktive Regelung für nichtlineare Systeme erster Ordnung. Dabei wurden die Besonderheiten der Kombination dieser beiden Verfahren ausgenutzt, um eine Reduktion des Rechenaufwandes zu erzielen. Diese Reduktion wird anhand der Simulation einer prädiktiven Antriebsregelung eines Hybridfahrzeuges demonstriert.
Stabilitätseigenschaften nichtlinearer Abtastsysteme (Stability Properties of Nonlinear Sampled-data Systems)
Authors: Hohmann Sören
Published: December 2003

Dieser Beitrag gibt einen Überblick über die Stabilitätseigenschaften von nichtlinearen Abtastsystemen. Ausgegangen wird von einer Betrachtung des Abtastprozesses bei nichtlinearen Systemen. Bei der Analyse der Ruhelagen, der Stabilität, des relativen Grads und der Nulldynamik der Abtastsysteme wird herausgearbeitet, in welcher Weise diese Eigenschaften von denen des zugrunde liegenden zeitkontinuierlichen Systems und der Abtastzeit abhängen. Daraus lassen sich prinzipielle Anforderungen an die Erstellung eines Abtastmodells ableiten, wenn dieses bestimmte Eigenschaften aufweisen soll.
Aktive Beeinflussung des Eigenlenk- und Wankverhaltens eines Pkws (Influencing Vehicle Handling and Roll Dynamics)
Authors: Öttgen Oliver , Bertram Torsten
Published: December 2003

Die Sicherheit von Pkws wurde durch den Einsatz von aktiven und passiven Sicherheitssystemen erheblich gesteigert. Durch die Einführung eines aktiven Fahrwerks kann die Sicherheit von Pkws weiter erhöht sowie das Handling und der Komfort verbessert werden, da es die Größe und Verteilung der Normalkräfte an den vier Rädern beeinflusst. Somit ist eine Regelung der Vertikal-, Nick- sowie Wankbewegung und des Eigenlenkverhaltens möglich. Die Einflussnahme auf das Eigenlenkverhalten wird durch die Verteilung der Wanksteifigkeiten an der Vorder-beziehungsweise Hinterachse realisiert, wobei die Regelung auf aktiven Stabilisatoren basiert. Auf diese Weise wird das Querkraftpotenzial ausgeschöpft, die kritische Querbeschleunigung beim Übergang zum übersteuernden Verhalten heraufgesetzt und der Verlust an Lenkwilligkeit gegenüber einer neutralen Abstimmung kompensiert.
Texturanalyse von Bandgut- und Straßenoberflächen (Texture Analysis of Industrial and Road Surfaces)
Authors: Haus J. , Schaefer R.
Published: December 2003

Die Echtzeitanalyse bewegter Oberflächen wird heute bevorzugt mit CCD–Kameras, leistungsfähiger Hardware und ausgeklügelten Algorithmen vorgenommen, erfordert aber den Umgang mit riesigen Datenmengen in kürzester Zeit. In diesem Beitrag soll ein alternatives Verfahren vorgeschlagen werden, das das Kreuzkorrelationssignal zwischen der Oberfläche und einem optischen Gitter zur Inspektion heranzieht.
Ein neues beugungsbasiertes Laser-Messverfahren zur Teilchengrößenmessung (A New Diffraction-based Laser Measuring Principle for Particle Sizing)
Authors: Ruck B. , Pavlovski B.
Published: December 2003

Die vorliegende Arbeit beschreibt ein neues laseroptisches Messprinzip zur Messung des Durchmessers von in Fluiden suspendierten Kleinstteilchen bis hinunter in den Mikrometerbereich. Das neue Verfahren kann auf zwei Arten realisiert werden. Bei der ersten Version (sendeseitige Rotation) wird ein Laserstrahl in einem zuvor definierten Winkelbereich während der Messung um das zu analysierende Teilchen geführt, wobei das sich hinter dem Teilchen ergebende Beugungsmuster im Raum mitgedreht und über einen Punktdetektor geführt wird. Bei der zweiten Variante (empfangsseitige Rotation) erfolgt die Beleuchtung des zu analysierenden Teilchens feststehend und das für den Teilchendurchmesser charakteristische Beugungsmuster wird über einen Drehspiegel hinter dem Teilchen im Raum gedreht und über einen Punktdetektor geführt. In beiden Fällen detektiert ein einfacher Punktdetektor das über ihn hinwegstreichende Beugungsmuster des zu analysierenden Teilchens als zeitveränderliches Signal. Dieses Signal kann anschließend im Zeitbereich oder im Frequenzbereich ausgewertet werden. Aus der Information aus vielen Einzelteilchenmessungen kann die Teilchengrößenverteilung bestimmt werden.
Zur Identifizierung von Lochmustern (Identifying Plane Hole Patterns)
Authors: Späth H.
Published: December 2003

Es werden numerische Verfahren zur Identifizierung von Lochmustern bzw. Punktemengen entwickelt. Ziel ist es, zwei Punktemengen in der Ebene daraufhin zu untersuchen, ob sie durch eine Drehung und eine Translation näherungsweise zur Übereinstimmung gebracht werden können.
Anwendung einer segmentierten geoelektrischen Sonde zur Leckagendetektion in Abwasserkanälen (Applying a Multi-Segmented Geoelectrical Probe for Leak Detection in Sewer Systems)
Authors: Wolf Leif
Published: December 2003

Innerhalb des interdisziplinären Forschungsprojektes SAM (Schadensdetektion an Abwasserkanälen mit Multisensorsystemen) wurden auch geoelektrische Messmethoden bezüglich ihrer Eignung zur Integration in das zu entwickelnde Multisensorsystem untersucht. Das Prinzip ist hierbei das Messen des elektrischen Feldes in der Umgebung der durch den wassergefüllten Kanal gezogenen Sonde. Wassergefüllte Risse und sonstige Öffnungen sind zumeist durch niedrigere elektrische Widerstände als das intakte Rohr gekennzeichnet und erzeugen daher messbare Anomalien in der Feldverteilung. Während zu einzelnen Versuchen auch eine eigene Sondenkonstruktion verwendet wurde, bezieht sich die Mehrzahl der Versuche auf die neu konstruierte Multisegmentsonde AMS-4 S50 R der Firma Seba Dynatronic, Baunach. Die Messungen zeigten gute Korrelationen mit den bekannten Schäden an den Testanlagen. Das Signal der AMS4-Sonde wird deutlich von der Größe des Lecks beeinflusst und ist gut geeignet für die Fusion mit anderen Sensorsystemen
Hohlraumdetektion in der Umgebung erdverlegter Abwasserkanäle mit Hilfe einer γ-γ-Sonde
Authors: Heske Claus
Published: December 2003

Hohlräume in der Umgebung erdverlegter Kanäle können zu Rohrbrüchen, Oberflächenabsenkungen und Fahrbahneinbrüchen führen. Die Hohlräume entstehen dort, wo über Leckagen Bodenmaterial in den Kanal eingespült wird; sie sind mit den bisher angewendeten Verfahren der Kanalinspektion nicht zu orten. Mit Hilfe einer γ-γ-Sonde können Hohlräumen in der Umgebung der Kanäle aufgrund ihrer geringen Dichte im Vergleich zum umgebenden Erdreich detektiert werden.
Crystal structures of the double salt dihydrates K2Cd(SeO4)2·2H2O, K2Mn(SO4)2·2H2O, (NH4)2Cu(SeO4)2·2H2O and KFeH(SO4)2·2H2O
Authors: Fleck Michel , Kolitsch U. , Hertweck B. , Giester G. , Wildner M. , Prem M. , Wohlschläger A.
Published: December 2003

The crystal structures of the four synthetic double salt compounds K2Mn(SO4)2·2H2O (space group P1̅, no. 2, Z = 2, a = 6.574(1), b = 7.332(1), c = 10.700(1) Å, α = 72.89(1), β = 73.91(1), γ = 69.77(1)°, V = 453.6(1) Å3) and K2Cd(SeO4)2·2H2O(space group P1̅, no. 2, Z = 2, a = 6.625(1), b = 7.542(1), c = 11.349(1) Å, α = 72.17(1), β = 74.55(1), γ = 70.13(1)°, V = 499.3(1) Å3) as well as (NH4)2Cu(SeO4)2·2H2O (space group P1̅, no. 2, Z = 1, a = 5.784(1) Å, b = 7.107(1) Å, c = 7.371(1) Å, α = 104.21(2)°, β = 93.04(2)°, γ = 112.27(2)°, V = 268.19(7) Å3), and KFeH(SO4)2·2H2O(space group P1̅, no. 2, Z = 1, a = 4.626(1), b = 5.820(1), c = 8.265(1) Å, α = 103.86(1), β = 99.77(1), γ = 95.66(1)°, V = 210.64(2) Å3) have been determined from single-crystal X-ray diffraction data collected with a CCD area detector at 293 K, and were refined to R(F) = 0.0231, 0.0251, 0.0230 and 0.0194, respectively. The first two compounds are isostructural. The atomic arrangements are described, with a focus on the hydrogen bonding. All compounds contain kröhnkite [Na2Cu(SO4)2·2H2O]-type tetrahedral-octahedral chains but show different topological arrangements of these chains. A classification is proposed in an accompanying paper. A particular feature of KFeH(SO4)2·2H2O is a disordered H atom involved in a short hydrogen bond, which shows no ordering down to 110 K.
The crystal structure of Bi4O5I2 and its relation to the structure of Bi4O5Br2
Authors: Keller E. , Krämer V. , Schmidt M. , Oppermann H.
Published: December 2003

The crystal structure of Bi4O5I2 has been solved from a 3:1 twinned crystal; accurate lattice parameters have been determined by a Rietveld refinement. Bi4O5I2 crystallizes with space group P21 (no. 4), Z=4, a=14.944(1), b=5.6983(3), c=11.263(1) Å, β= 99.81(1)°. Its structure is isotypic to the structure of the homologous Bi4O5Br2 for which more reliable lattice parameters have been determined by a Rietveld refinement. The effects of replacement of Br by I on the structure are discussed and compared with corresponding effects in the BiOX family (X = Cl, Br, I). A structural reason for the deviation of the twin supercells of the two compounds from orthogonality is discussed.
Initial Processes of Laser Induced Diatomic Molecular Photodissociation in Matrices: Quantum Simulations for F2 in Ar in Reduced Dimensionality
Authors: Korolkov M. V. , Manz J.
Published: December 2003

Quantum dynamical simulations of ultrafast processes of F2 in an Ar matrix induced by a pump laser pulse show that photoexcitation (i) is followed by (ii) a stretch of the dissociative bond, (iii) collision with, vibrational excitations of, and possible exit through the nearest neighbour atoms of the surrounding cage, and (iv) finally, subsequent rescattering of the dissociated atoms causing vibrations of additional matrix atoms. If the laser pulse ended before the onset of process (iii), the initial steps (i) and (ii) are similar to photodissociations in the gas phase and are, therefore, well described in terms of the wavepacket dynamics of the diatomic molecule in reduced dimensionality. For specific symmetry constraints, the initial processes (i), (ii), and (iii) may be described in terms of just 1- and 2- or 3-dimensional wavepacket dynamics, respectively. At the end of the laser pulse, this low-dimensional wavepacket may serve to prepare the high-dimensional one for the subsequent laser-free dynamics of the total system.
Fine Theoretical Spectroscopy Using SAC-CI General-R Method: Outer- and Inner-Valence Ionization Spectra of N2O and HN3
Authors: Ehara M. , Yasuda S. , Nakatsuji H.
Published: December 2003

Fine theoretical spectroscopy for the outer- and inner-valence ionization spectra has been presented by using the SAC-CI (symmetry adapted cluster-configuration interaction) general-R method applied to N2O and HN3. The SAC-CI general-R method accurately simulated the experimental spectra and the detailed assignments of the satellite peaks were proposed. The continuous peaks I ∼ V of N2O observed by the dipole (e,2e) spectroscopy were finely reproduced. In particular, the low-lying satellites were calculated in good agreement with the experiment; two 2Π shake-up states at the foot of the C state, 2Σ and 2Π states for the peak I. For HN3, new interpretation was proposed for the outer-valence region, namely, peaks 3 ∼ 5 are composed of the mixture of the single-electron main peaks and the two-electron shake-up peaks. Inner-valence ionization spectrum of HN3 was theoretically predicted for which no experimental spectrum has been reported.