bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictors of unsafe injecting drug use
Authors: Crisp Beth R. , Barber James G. , Ross Michael W. , Wodak Alex , Gold Julian , Miller M. E. 
Published: July 2006

AbstractThis paper reports on the incidence of unsafe injecting and the factors which influence this practice in a sample of 1245 Sydney injecting drug users (IDUs). Using a needle and syringe after someone else at some time in the last six months was reported in 41.6% of the sample. Taking into account those who claimed always to clean used needles with virucidal methods, 32.9% had placed themselves at risk of HIV infection from shared needles in the six months prior to interview.Seven factors were predictive of unsafe behaviour. These were (a) the amount spent per week on drugs, (b) the number of times a single needle was used prior to disposal, (c) having shared with a person who is now HIV infected, (d) having a regular sexual partner, (e) the proportion of times high, stoned or drunk when injecting, (f) being part of a group that injects together and (g) having been in prison.
Structure of the MAST with an Australian sample of alcoholics
Authors: Crook Gabrielle M. , Oei Tian P. S. , Young Ross Mac 
Published: July 2006

AbstractThe dimensionality of the Michigan Alcoholism Screening Test (MAST) was examined utilizing an Australian sample (n = 196) of alcoholics. This study was specifically designed to overcome some of the problems with sampling and analytic techniques used in previous studies. Three moderately intercorrelated factors were revealed which covered (a) alcohol‐related disabilities; (b) help‐seeking behaviour and (c) recognition of a drinking problem. These factors were found to be internally consistent as shown by moderate to high alpha coefficients. Results indicate that the additive system of scoring all 24 items may result in an underestimation of the information afforded by the MAST.
Young offender drug use: knowledge and perceptions of Juvenile Justice Centre youth workers
Authors: Howard John , Zibert Ernie 
Published: July 2006

AbstractJuvenile Justice Centre youth workers in New South Wales (n = 106) were surveyed by questionnaire as to their knowledge and perceptions of alcohol and other drug issues of those in their care. Some background variables were also collected. About 30% of the sample reported having (had) a problem with alcohol and/or other drugs and approximately the same percentage came from families with such a problem. Over 50% had received some form of drug education. There was an overestimation of the level of use of narcotics, sedative/hypnotics, anti‐anxiety agents and hallucinogens of the youth workers and an underestimation of the level of use of analgesics, alcohol, cannabis and inhalants. Peer pressure was perceived as central in the initiation of use and “denial” in not gaining assistance; the style and belief systems of agencies were not seen as crucial in retaining young people in treatment. Youth workers, who are not required to have any specific education or training prior to employment, did not see themselves as well equipped to assist drug‐affected or detoxifying detainees and requested more training/education. It is recommended that this could be provided through tertiary courses and/or in‐service staff development.
Differences in assessment and treatment approaches for homosexual clients
Authors: MacEwan Ian 
Published: July 2006

AbstractThis study was undertaken to discover the similarities and the differences in assessment and treatment approaches for heterosexual and for homosexual clients. The purpose of the study was to investigate to what extent sexual orientation is incorporated into treatment plans and what effect this had for treatment outcomes. Responses to nine questions were obtained from 50 self‐reporting heterosexual and 50 self‐reporting homosexual clients of a range of treatment providers. Differences were found at each stage of the assessment and treatment process. There was evidence of sexual orientation not being utilized as a treatment factor. For both groups there was evidence of inadequate significant‐other involvement in treatment and post‐treatment planning.
The use of benzodiazepines among injecting drug users
Authors: Darke Shane 
Published: July 2006

AbstractBenzodiazepine use among injecting drug users (IDUs) presents a major clinical and public health problem that may increase in importance. The current paper examines the research on the extent of benzodiazepine use among IDUs and the harmful consequences associated with such use. Numerous studies have found benzodiazepine use to be widespread among IDUs, and to be associated with greater levels of risk‐taking and polydrug use, and poorer psychosocial functioning than other IDUs. The injection of benzodiazepines has also been reported, and presents problems in itself. The implications of existing research for both clinical practice and research are discussed.
Remote homology detection based on oligomer distances
Authors: Lingner Thomas , Meinicke Peter 
Published: July 2006

Abstract
Motivation: Remote homology detection is among the most intensively researched problems in bioinformatics. Currently discriminative approaches, especially kernel-based methods, provide the most accurate results. However, kernel methods also show several drawbacks: in many cases prediction of new sequences is computationally expensive, often kernels lack an interpretable model for analysis of characteristic sequence features, and finally most approaches make use of so-called hyperparameters which complicate the application of methods across different datasets.
Results: We introduce a feature vector representation for protein sequences based on distances between short oligomers. The corresponding feature space arises from distance histograms for any possible pair of K-mers. Our distance-based approach shows important advantages in terms of computational speed while on common test data the prediction performance is highly competitive with state-of-the-art methods for protein remote homology detection. Furthermore the learnt model can easily be analyzed in terms of discriminative features and in contrast to other methods our representation does not require any tuning of kernel hyperparameters.
Availability: Normalized kernel matrices for the experimental setup can be downloaded at . Matlab code for computing the kernel matrices is available upon request.
Contact: thomas@gobics.de, peter@gobics.de
Predicting methylation status of CpG islands in the human brain
Authors: Fang Fang , Fan Shicai , Zhang Xuegong , Zhang Michael Q. 
Published: July 2006

Abstract
Motivation: Over 50% of human genes contain CpG islands in their 5′-regions. Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulation. Mis-epigenetic silencing associated with aberrant CpG island methylation is one mechanism leading to the loss of tumor suppressor functions in cancer cells. Large-scale experimental detection of DNA methylation is still both labor-intensive and time-consuming. Therefore, it is necessary to develop in silico approaches for predicting methylation status of CpG islands.
Results: Based on a recent genome-scale dataset of DNA methylation in human brain tissues, we developed a classifier called MethCGI for predicting methylation status of CpG islands using a support vector machine (SVM). Nucleotide sequence contents as well as transcription factor binding sites (TFBSs) are used as features for the classification. The method achieves specificity of 84.65% and sensitivity of 84.32% on the brain data, and can also correctly predict about two-third of the data from other tissues reported in the MethDB database.
Availability: An online predictor based on MethCGI is available at
Contact: mzhang@cshl.edu
Supplementary Information: Supplementary data available at Bioinformatics online and
ADGO: analysis of differentially expressed gene sets using composite GO annotation
Authors: Nam Dougu , Kim Sang-Bae , Kim Seon-Kyu , Yang Sungjin , Kim Seon-Young , Chu In-Sun 
Published: July 2006

Abstract
Motivation: Genes are typically expressed in modular manners in biological processes. Recent studies reflect such features in analyzing gene expression patterns by directly scoring gene sets. Gene annotations have been used to define the gene sets, which have served to reveal specific biological themes from expression data. However, current annotations have limited analytical power, because they are classified by single categories providing only unary information for the gene sets.
Results: Here we propose a method for discovering composite biological themes from expression data. We intersected two annotated gene sets from different categories of Gene Ontology (GO). We then scored the expression changes of all the single and intersected sets. In this way, we were able to uncover, for example, a gene set with the molecular function F and the cellular component C that showed significant expression change, while the changes in individual gene sets were not significant. We provided an exemplary analysis for HIV-1 immune response. In addition, we tested the method on 20 public datasets where we found many ‘filtered’ composite terms the number of which reached ∼34% (a strong criterion, 5% significance) of the number of significant unary terms on average. By using composite annotation, we can derive new and improved information about disease and biological processes from expression data.
Availability: We provide a web application (ADGO: ) for the analysis of differentially expressed gene sets with composite GO annotations. The user can analyze Affymetrix and dual channel array (spotted cDNA and spotted oligo microarray) data for four species: human, mouse, rat and yeast.
Contact: chu@kribb.re.kr
Supplementary information:
Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome
c
oxidase
Authors: Moser Christopher C , Page Christopher C , Dutton P. Leslie 
Published: July 2006

Biological electron transfer is designed to connect catalytic clusters by chains of redox cofactors. A review of the characterized natural redox proteins with a critical eye for molecular scale measurement of variation and selection related to physiological function shows no statistically significant differences in the protein medium lying between cofactors engaged in physiologically beneficial or detrimental electron transfer. Instead, control of electron tunnelling over long distances relies overwhelmingly on less than 14 Å spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 Å) appear to be selected to generate tunnelling frequencies sufficiently high to scale the barriers of multi-electron, bond-forming/-breaking catalysis at physiological rates. We illustrate this behaviour in a tunnelling network analysis of cytochrome
c
oxidase. In order to surmount the large, thermally activated, adiabatic barriers in the 5–10 kcal mol
−1
range expected for H
+
motion and O
2
reduction at the binuclear centre of oxidase on the 10
3
–10
5
s
−1
time-scale of respiration, electron access with a tunnelling frequency of 10
9
or 10
10
s
−1
is required. This is provided by selecting closely placed redox centres, such as haem
a
(6.9 Å) or tyrosine (4.9 Å). A corollary is that more distantly placed redox centres, such as Cu
A
, cannot rapidly scale the catalytic site barrier, but must send their electrons through more closely placed centres, avoiding direct short circuits that might circumvent proton pumping coupled to haems
a
to
a
3
electron transfer. The selection of distances and energetic barriers directs electron transfer from Cu
A
to haem
a
rather than
a
3
, without any need for delicate engineering of the protein medium to ‘hard wire’ electron transfer. Indeed, an examination of a large number of oxidoreductases provides no evidence of such naturally selected wiring of electron tunnelling pathways.
Hexamer formation in tertiary butyl alcohol (2-methyl-2-propanol, C4H10O)
Authors: McGregor Pamela A. , Allan David R. , Parsons Simon , Clark Stewart J. 
Published: July 2006

The crystal structure of phase II of tertiary butyl alcohol (2-methyl-2-propanol, C4H10O) has been solved using a combination of single-crystal X-ray diffraction techniques and ab initio density functional calculations. This trigonal P\overline 3 phase, which is stable at both low temperature and high pressure, and the triclinic P\overline 1 phase (phase IV) have very similar enthalpies, the calculations revealing only a 3.859 kJ mol−1 enthalpy difference at ambient pressure, despite the substantial change of the intermolecular bonding motif from helical catemer to hexamer with an increase in pressure or reduction in temperature. The hexamers in the trigonal phase adopt a chair conformation. There are two unique hexamers: at low temperature these are centred at (0, 0, 1\over2) and (2\over3, 1\over3, 0.961 (13)), and at high pressure the centres are (0, 0, 1\over2) and (2\over3, 1\over3, 0.958 (14)). A slight flattening of the hexamers is observed at high pressure and the calculations confirm that phase II becomes more stable relative to phase IV on pressure increase.
Influence of the parathyroid glands on bone metabolism
Authors: Malluche H. H. , Koszewski N. , Monier‐Faugere M. C. , Williams J. P. , Mawad H. 
Published: July 2006

AbstractBone is a classic target tissue for parathyroid hormone (PTH), whose calciotropic effect is mediated largely via catabolic actions on this tissue. Paradoxically, PTH also exerts anabolic actions, with intermittent injections of PTH or its amino‐terminal fragments causing an increase in bone formation and bone mass, actions that form the basis for the use of PTH in the treatment of osteoporosis. Besides vitamin D, PTH is the only other known bone anabolic agent. High‐affinity PTH receptors (PTH‐1R) have been detected on osteoblasts and osteoclasts (albeit in lower numbers).Bone turnover, which includes activation of osteoclasts and osteoblasts, appears to be best reflected not by absolute concentrations of PTH (which can vary based on the assay and antibody used) but by a balance of circulating full‐length PTH‐(1–84) and amino‐terminally truncated C‐PTH fragments. When PTH‐(1–84) is predominant, bone turnover is promoted. Among PTH fragments, PTH‐(7–84) appears to be the most potent antagonist of PTH‐(1–84). The mechanisms involved in these effects are unclear although mediation via unique C‐terminal receptors has been suggested. We propose that, within the range of total PTH (100–1000 pg mL−1), the ratio of PTH‐(1–84)/C‐PTH fragment is a valuable tool for diagnosis of bone turnover. Data indicate that at PTH levels < 100–150 pg mL−1 and > 1000 pg mL−1, the ratio looses its predictive power. Assay type, patient characteristics (race, underlying renal disease) and treatment attributes (vitamin D, corticosteroids, phosphate binders) have an impact on the PTH ratio, and care should be used in interpreting assay results and making subsequent treatment decisions.
Characterization of the integrase of NBU1, a Bacteroides mobilizable transposon
Authors: Rajeev Lara , Salyers Abigail A. , Gardner Jeffrey F. 
Published: July 2006

SummaryNBU1 is a Bacteroides mobilizable transposon (MTn) that is integrated within the host chromosome and requires CTnDOT functions for its excision and transfer into a new host. The NBU1 integrase IntN1 has been classified as a tyrosine recombinase based on the presence of conserved residues. We created alanine mutants of the residues R291, K314, H393, R396, H419 and the conserved substitution Y429F and tested them for integration efficiency. The results suggest that these residues in IntN1 are important for integration, and Y429 could be the catalytic nucleophile. We employed suicide substrates and partially purified IntN1 to determine the positions of IntN1 cleavage within the 14 bp common core region that is identical in both NBU1 att sites. We show that IntN1 makes 7 bp staggered cuts on the top and bottom strands. From previous mutational analysis of the att sites, we show that two specific mutations near the site of bottom strand cleavage within this 7 bp region increased integration, and mutations of the two bases near top strand cleavage site had no effect on integration. These results indicate that IntN1 lacks the strict requirement for homology between the recombining sites seen with other tyrosine recombinases. We also show that phosphorothioate substitutions at the cleavage site and 1 bp downstream inhibited cleavage by IntN1. This differs from other studied tyrosine recombinases where inhibition occurs by substitutions at the cleavage site only.
Follow up of 12 patients with trachyonychia
Authors: Sakata Shinichiro , Howard Anne , Tosti Antonella , Sinclair Rodney 
Published: July 2006

SUMMARYA follow‐up study was performed to determine the outcomes of all patients (five males and seven females, mean age 18.4 years) who were referred to a specialist nail clinic with trachyonychia. The average number of affected nails per patient was 8.8 fingernails and 6.2 toenails. None of our patients tested positive for onychomycosis. Nail biopsies were performed in two patients, revealing non‐specific changes. Eight patients did not present with or develop accompanying skin or mucosal disease. Two patients presented with alopecia areata and two others with psoriasis. Of our patients, 50% showed total resolution or marked improvement in their nail disease within the first 6 years regardless of treatment.
Treatment of palmoplantar warts with a diphencyprone and salicylic acid ointment
Authors: Armour Katherine , Orchard David 
Published: July 2006

SUMMARYWe report on 50 consecutive suitable patients with one or more palmoplantar warts who were treated with a patient‐applied ointment comprising 0.1% diphencyprone and 15% salicylic acid in white soft paraffin. All patients sensitized to diphencyprone were followed up clinically and assessed by patient questionnaire. The intention to treat success rate in this series was 88%. The time to wart clearance ranged from less than 4 weeks to 4 months. In our patient group, 90% rated their treatment as ‘excellent’ or ‘good’, whereas 10% stated that the reaction induced by diphencyprone was ‘too severe’. Our results are compared with those previously published using diphencyprone in the treatment of palmoplantar warts.
Primary cutaneous mucinous carcinoma: Report of two cases treated with Mohs’ micrographic surgery
Authors: Cecchi Roberto , Rapicano Valentina 
Published: July 2006

SUMMARYWe present a 72‐year‐old woman who presented with a slowly enlarging, asymptomatic, cystic nodule on the right eyebrow, and a 66‐year‐old woman who had a reddish, nodular lesion on the left lower eyelid. Incisional biopsy from the two neoplasms showed dermal epithelial cell islands embedded in mucin pools. Tumour cells stained positive for cytokeratin 7, oestrogen and progesterone receptors, and negative for vimentin and S‐100 protein. These findings were consistent with a diagnosis of mucinous carcinoma. Extensive work‐ups excluded cutaneous metastases from primary visceral mucinous carcinomas. To ensure complete tumour removal, both patients underwent Mohs’ micrographic surgery (standard fresh‐frozen technique). They remain disease‐free 42 and 26 months after surgical excision, respectively. Mohs’ micrographic surgery appears to be a rational and effective treatment for this uncommon malignancy.
Allergic contact dermatitis to basic red 46 occurring in an HIV‐positive patient
Authors: Curr Nathan , Nixon Rosemary 
Published: July 2006

SUMMARYA 41‐year‐old HIV‐positive man presented with a 2‐month history of a generalized pruritic rash, which had started on his feet. Patch testing made a diagnosis of allergic contact dermatitis to the textile dye basic red 46, likely to have been present in his dark‐blue‐coloured socks. Complete resolution of his symptoms occurred with avoidance of these socks. The patient had developed allergic contact dermatitis with a low CD4 T lymphocyte count of 361 cells/µl (normal range 410–1545 cells/µl). This raised the question of the level of CD4 count necessary for an individual to develop allergic contact dermatitis to an allergen, given its role in delayed hypersensitivity. It was concluded that a low CD4 count as a result of HIV infection does not decrease the ability of an individual to develop allergic contact dermatitis. Whereas the effector role in delayed type 4 hypersensitivity reactions is mediated by CD4 T lymphocytes, in allergic contact dermatitis it appears that CD4 T lymphocytes have the suppressor role, with CD8 T lymphocytes having the effector role.
Allergic contact dermatitis to sodium benzoate chloroacetamide in a sorbolene lotion
Authors: Sutton Tina , Nixon Rosemary 
Published: July 2006

SUMMARYSodium benzoate chloroacetamide is sometimes used as a combination preservative in cosmetics to prevent the growth of bacteria, mould, fungi and yeasts. A case of occupational allergic contact dermatitis to this preservative is described in a 32‐year‐old female personal care assistant, who was found to have allergic contact dermatitis involving the hands, caused by the sorbolene lotion supplied in her workplace. Patch testing to chloroacetamide, sodium benzoate chloroacetamide and the sorbolene lotion was positive. Patch testing to sodium benzoate alone was negative. She had been found to react to chloroacetamide 12 months earlier, but the relevance of the reaction had not been ascertained.
A framework for systematically improving occupational therapy expert opinions on work capacity
Authors: Allen Shelley , Carlson Glenys , Ownsworth Tamara , Strong Jenny 
Published: July 2006

Aim: To present an evidence‐based framework to improve the quality of occupational therapy expert opinions on work capacity for litigation, compensation and insurance purposes.Methods: Grounded theory methodology was used to collect and analyse data from a sample of 31 participants, comprising 19 occupational therapists, 6 medical specialists and 6 lawyers. A focused semistructured interview was completed with each participant. In addition, 20 participants verified the key findings.Results: The framework is contextualised within a medicolegal system requiring increasing expertise. The framework consists of (i) broad professional development strategies and principles, and (ii) specific strategies and principles for improving opinions through reporting and assessment practices.Conclusions: The synthesis of the participants’ recommendations provides systematic guidelines for improving occupational therapy expert opinion on work capacity.
Pretend play and parents’ view of social competence: The construct validity of the Child‐Initiated Pretend Play Assessment
Authors: Swindells Dianne , Stagnitti Karen 
Published: July 2006

Background and Aims:  Play is the primary means through which children develop skills and socially interact with other children. The aim of this study was to investigate the relationship between pretend play and social competence in 4–5‐year‐old typically developing children, thereby adding further knowledge to the construct validity of the Child‐Initiated Pretend Play Assessment (ChIPPA). Procedure:  The pretend play ability of 35 preschool children aged 4–5 years was assessed using the ChIPPA. Parent/guardians of the children were interviewed regarding their child's social competence using the Vineland Social–Emotional Early Childhood Scales (Vineland SEEC Scales). Main Findings:  No significant correlations were found between the children's play scores and their Vineland SEEC Scales scores. A significant and negative relationship was found between cooperation and sharing and elaborate play scores, suggesting that children who scored poorly on the play assessment were rated as cooperative by parents. Principal Conclusions:  Parent report of social competence cannot be inferred from play scores. Reasons for the negative and significant finding are put forward and clinical implications of the findings are discussed. Additional investigations are necessary to further explore the construct validity of inferring social competence using the ChIPPA.