bluuebunny/crossref_metadata_2025_split huggingface dataset:
AIDS and injecting drug use: very risky behaviour in a Perth sample of injecting drug users
Authors: Loxley Wendy M. , Hawks David V. 
Published: July 2006

AbstractThis research was carried out in 1990 to examine high‐risk injecting and sexual behaviour in a sample of injecting drug users (IDUs) in Perth. The study was a cross‐sectional survey with a convenience sample drawn from drug treatment (54%) and non‐treatment (46%) populations. In the sample of 150 IDUs, there were 11 very risky drug behaviour (VRDB) and 63 very risky sex behaviour (VRSB) respondents. Four respondents fell into both categories. Independent comparisons were made between each risk group and the rest of the sample. The VRDB respondents were heterosexual men, most of whom were in long‐term monogamous relationships, with heavier levels of drug use than the rest of the sample. The VRSB respondents were largely single and mainly heterosexual, with more sexual partners than the rest of the sample. It was concluded that there was little evidence that very risky behaviour was related to a general risk‐taking dimension, to inadequate knowledge about AIDS or to a low assessment of personal vulnerability to AIDS. However, situational influences in association with heavy drug use appeared to be a major component of high‐risk injecting behaviour, while high‐risk sexual behaviour appeared more to be a reflection of community norms about heterosexual sexual behaviour. The study should be replicated with larger samples, particularly as the VRDB group was so small, but if the findings are reproduced in other studies, it suggests that serious attention should be paid to the promotion of safer sex among injecting drug users.
Imagery and craving in alcohol dependent persons
Authors: Felstead Boyce , Love Anthony W. , Pead John , Taylor Stephen 
Published: July 2006

AbstractThere is limited evidence supporting the effectiveness of imagery techniques in exposure‐based treatments for alcohol dependence. Changes in craving for alcohol following imagery instruction, measured by cognitive and physiological indices, have not been demonstrated. Furthermore, the influence of different imagery script content has not been investigated. This study compared levels of craving elicited, measured by self‐report and salivation, under control and imagery conditions, in subjects receiving treatment for alcohol dependence. Imagery script content was varied across three levels. Participants generally reported forming good quality images with strong affective components. Significant effects of imagery treatment were found for changes in self‐reported craving levels, but not for the salivation measure. Significant decay in levels of self‐reported craving was also observed. No differences in effectiveness between the three script types were discovered. Implications of the results for therapy approaches such as cue exposure are considered.
Allocation of research funds in the drug and alcohol field: report of the Consensus Workshop
Authors: Walsh Raoul A. , Sanson‐Fisher Rob 
Published: July 2006

AbstractIssues concerning the allocation of research funds in the drug and alcohol field have been widely debated. A consensus workshop involving senior researchers and policy makers was convened to examine the appropriateness of current drug and alcohol research activities in Australia. The workshop identified several major barriers restricting research developments including lack of monitoring of research efforts, limited community support, inappropriate allocations of research funds which contributed to a low level of intervention studies, the lack of application of research findings by practitioners and ethical constraints in studies involving Aboriginal populations and in multi‐centre trials. Agreement was reached on 16 recommendations which could increase the amount of high quality research in Australia directed at reducing the harm associated with alcohol, tobacco and other drug use. Strategies which funding bodies could use to encourage intervention studies were identified. A proposal for the Australian Medical and Professional Society on Alcohol and other Drugs to establish a Researchers' Group to encourage implementation of the recommendations was also endorsed by workshop participants.
Minimizing drug‐related harm in Australia—Australia's National Drug Strategy
Authors: Wares Malcolm C. 
Published: July 2006

AbstractThe article describes the nature, origins and development of Australia's recently announced National Drug Strategy (NDS). The NDS aims to minimize the harmful effects of drugs and drug use in Australian society and covers the period 1993‐97. The National Drug Strategic Plan is discussed, and the means by which the NDS will be monitored. The National Campaign Against Drug Abuse (NCADA), the forerunner to the NDS, is reviewed in terms of its major achievements. The Campaign was particularly successful in raising the policy profile of alcohol and tobacco, the drugs causing the most harm in Australian society. The relationship between the latest evaluation of NCADA and the NDS is also described.
Dysarthria and Friedreich's ataxia: what can intelligibility assessment tell us?
Authors: Blaney Bronagh , Hewlett Nigel 
Published: July 2006

AbstractBackground: Friedreich's ataxia is one of the most common hereditary disorders of the nervous system. Dysarthria is a pervasive symptom of Friedreich's ataxia, yet the clinical presentation of speech symptoms remains poorly understood, leaving clinicians without the evidence required to develop therapy interventions.Aims: The research reported herein had three aims: the first was to document the severity of the intelligibility deficit associated with Friedreich's ataxia dysarthria; the second was to document the phonetic profile of the intelligibility deficit; and the third was to use the results of the phonetic profile to estimate the motor control mechanisms and neurological substrates implicated in Friedreich's ataxia dysarthria.Methods & Procedures: Eleven adult males with Friedreich's ataxia were recruited. Intelligibility was assessed using a single‐word multiple‐choice task completed by ten listeners.Outcomes & Results: Intelligibility severity ratings ranged from mild to severe. The majority of subjects fell into the mild category. The phonetic errors revealed a distinctive profile, with word‐final plosive voicing contrast representing the highest source of error. Involvement of cerebro‐cerebellar loops was considered to be compatible with the profile results.Conclusions: Friedreich's ataxia dysarthria has a distinctive phonetic profile and contains subgroups of different severity. High sources of error identified in the phonetic profile should be considered when developing targets for therapy intervention. Neurological substrates are considered to vary across individuals and to include involvement of cerebro‐cerebellar loops. Further research involving acoustic analysis of final plosive voicing contrasts would provide further insights into the neurological substrates involved.
Substring selection for biomedical document classification
Authors: Han Bo , Obradovic Zoran , Hu Zhang-Zhi , Wu Cathy H. , Vucetic Slobodan 
Published: July 2006

Abstract
Motivation: Attribute selection is a critical step in development of document classification systems. As a standard practice, words are stemmed and the most informative ones are used as attributes in classification. Owing to high complexity of biomedical terminology, general-purpose stemming algorithms are often conservative and could also remove informative stems. This can lead to accuracy reduction, especially when the number of labeled documents is small. To address this issue, we propose an algorithm that omits stemming and, instead, uses the most discriminative substrings as attributes.
Results: The approach was tested on five annotated sets of abstracts from iProLINK that report on the experimental evidence about five types of protein post-translational modifications. The experiments showed that Naive Bayes and support vector machine classifiers perform consistently better [with area under the ROC curve (AUC) accuracy in range 0.92–0.97] when using the proposed attribute selection than when using attributes obtained by the Porter stemmer algorithm (AUC in 0.86–0.93 range). The proposed approach is particularly useful when labeled datasets are small.
Contact: vucetic@ist.temple.edu
Supplementary Information: The supplementary data are available from
Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine
Authors: Zheng Mingyue , Liu Zhiguo , Xue Chunxia , Zhu Weiliang , Chen Kaixian , Luo Xiaomin , Jiang Hualiang 
Published: July 2006

AbstractMotivation: Mutagenicity is among the toxicological end points that pose the highest concern. The accelerated pace of drug discovery has heightened the need for efficient prediction methods. Currently, most available tools fall short of the desired degree of accuracy, and can only provide a binary classification. It is of significance to develop a discriminative and informative model for the mutagenicity prediction.Results: Here we developed a mutagenic probability prediction model addressing the problem, based on datasets covering a large chemical space. A novel molecular electrophilicity vector (MEV) is first devised to represent the structure profile of chemical compounds. An extended support vector machine (SVM) method is then used to derive the posterior probabilistic estimation of mutagenicity from the MEVs of the training set. The results show that our model gives a better performance than TOPKAT () and other previously published methods. In addition, a confidence level related to the prediction can be provided, which may help people make more flexible decisions on chemical ordering or synthesis.Availability: The binary program (ZGTOX_1.1) based on our model and samples of input datasets on Windows PC are available at upon request from the authors.Contact: hljiang@mail.shcnc.ac.cn; xmluo@mail.shcnc.ac.cn
VISTAL—a new 2D visualization tool of protein 3D structural alignments
Authors: Kolodny Rachel , Honig Barry 
Published: July 2006

Abstract
Summary: We offer a tool, denoted VISTAL, for two-dimensional visualization of protein structural alignments. VISTAL describes aligned structures as a series of matched secondary structure elements, colored according to the three-dimensional distance of their Cα atoms.
Availability: VISTAL can be downloaded from
Contact: bh6@columbia.edu
An initial strategy for comparing proteins at the domain architecture level
Authors: Lin Kui , Zhu Lei , Zhang Da-Yong 
Published: July 2006

Abstract
Motivation: Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal γ function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures.
Results: Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database.
Conclusion: The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins.
Availability:
Contact: linkui@bnu.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
RBR: library-less repeat detection for ESTs
Authors: Malde Ketil , Schneeberger Korbinian , Coward Eivind , Jonassen Inge 
Published: July 2006

Abstract
Motivation: Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are available for the widely studied organisms, but for most other organisms the lack of such libraries is likely to compromise the quality of EST analysis.
Results: We present a fast, flexible and library-less method for masking repeats in EST sequences, based on match statistics within the EST collection. The method is not linked to a particular clustering algorithm. Extensive testing on datasets using different clustering methods and a genomic mapping as reference shows that this method gives results that are better than or as good as those obtained using RepeatMasker with a repeat library.
Availability: The implementation of RBR is available under the terms of the GPL from
Contact: ketil.malde@bccs.uib.no
Supplementary Information: Supplementary data are available at Bioinformatics online.
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
Authors: Vernikos Georgios S. , Parkhill Julian 
Published: July 2006

Abstract
Motivation: There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.
Results: We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared with fixed-order methods. For optimal localization of the boundaries of each predicted region, a second order, two-state hidden Markov model (HMM) is implemented in a change-point detection framework. We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events.
Availability: The software is available under a GPL license as a standalone application at
Contact: gsv@sanger.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Detecting functional modules in the yeast protein–protein interaction network
Authors: Chen Jingchun , Yuan Bo 
Published: July 2006

Abstract
Motivation: Identification of functional modules in protein interaction networks is a first step in understanding the organization and dynamics of cell functions. To ensure that the identified modules are biologically meaningful, network-partitioning algorithms should take into account not only topological features but also functional relationships, and identified modules should be rigorously validated.
Results: In this study we first integrate proteomics and microarray datasets and represent the yeast protein–protein interaction network as a weighted graph. We then extend a betweenness-based partition algorithm, and use it to identify 266 functional modules in the yeast proteome network. For validation we show that the functional modules are indeed densely connected subgraphs. In addition, genes in the same functional module confer a similar phenotype. Furthermore, known protein complexes are largely contained in the functional modules in their entirety. We also analyze an example of a functional module and show that functional modules can be useful for gene annotation.
Contact: yuan.33@osu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online
Immunopathogenesis of psoriasis
Authors: Lee Michael R , Cooper Alan J 
Published: July 2006

SUMMARYThis paper reviews the pathogenesis of psoriasis, in particular, the immunological cascade in psoriasis. Psoriasis is an immune‐mediated skin disease where the T cell plays a pivotal role in the pathogenesis of the disease. The critical steps involved in the pathogenesis include Langerhans cell activation and maturation by antigens in the skin, activation of the T cell by mature Langerhans cells, differentiation and expansion of T cells within the lymph nodes, trafficking of activated T cells from the lymph node to the skin and the subsequent release of cytokines. These cytokines are responsible for epidermal and vascular hyperproliferation and pro‐inflammatory effects. Each of these steps provides an opportunity for biological agents designed to block the psoriatic immunological cascade. This paper reviews the immunopathogenesis of psoriasis. Biologic agents in psoriasis, to be published separately, reviews the new biologic therapies that aim to selectively block the immunological steps implicated in the pathogenesis of psoriasis outlined in this paper.
Merkel cell carcinoma (primary cutaneous neuroendocrine carcinoma): An overview on management
Authors: Veness Michael J 
Published: July 2006

SUMMARYMerkel cell carcinoma is an uncommon but aggressive primary cutaneous neuroendocrine (small cell) carcinoma. There is ongoing debate regarding the optimal treatment of this disease. The early literature comprised small institutional studies with inherent weaknesses. Recent data have emerged from larger studies, including those from Australian institutions, that adds support to a multimodality approach as best practice. Despite this, the outcome for patients with unfavourable disease remains poor and in most series 25–30% of patients die as a direct result of Merkel cell carcinoma. The head and neck is the commonest site for presentation (50–60%) and wide excision (2–3 cm) of the primary lesion is usually recommended, although achieving this is often difficult within functional and cosmetic constraints. All clinically node‐negative patients should be considered candidates for elective nodal treatment and those with clinical nodal disease should undergo nodal dissection and adjuvant radiotherapy. Recent evidence suggests that patients treated with surgery and adjuvant locoregional radiotherapy experience a better disease‐free survival compared with those undergoing surgery alone. The role of platinum‐based chemotherapy is evolving. The aim of this article is to discuss relevant issues in the management of a patient with Merkel cell carcinoma.
Use of 5% imiquimod cream in the treatment of facial basal cell carcinoma: A 3‐year retrospective follow‐up study
Authors: Vun Yin , Siller Greg 
Published: July 2006

SUMMARYThere has been considerable research into the safety and efficacy of topical 5% imiquimod cream for the treatment of skin cancers in recent years, in particular superficial and nodular basal cell carcinomas. However, there are limited long‐term follow‐up studies. This retrospective study aims to determine the efficacy of 5% imiquimod cream in the treatment of facial basal cell carcinomas over 3 years. Medical records of 12 patients treated with 5% imiquimod cream at a private dermatology practice during 2001 and 2002 were retrospectively reviewed. Target tumours included superficial and nodular basal cell carcinomas, giving a total lesion number of 19. Patients were commenced on a once daily treatment regimen for up to 9 weeks, and given rest periods as required according to the severity of application site reactions. We found that 5% imiquimod cream is an effective treatment option for superficial and nodular basal cell carcinomas, giving a clearance rate of 89.5% at an average of 39 months of follow up.
Prevalence of atopy in a population of hairdressing students and practising hairdressers in Melbourne, Australia
Authors: Roberts Hugh , Frowen Kathryn , Sim Malcolm , Nixon Rosemary 
Published: July 2006

SUMMARYHairdressers are one of the largest groups affected by occupational contact dermatitis. In this population‐based study, 193 trainee hairdressers and 184 practising hairdressers each completed a questionnaire and had their hands examined. Participants were asked about past or present atopy including eczema, asthma or hayfever, which occurred in 59.2%, and were individually correlated with a history of occupational skin problems. Almost 60% of hairdressers and trainees had experienced changes on their hands since commencing hairdressing, while 29% had evidence of abnormal skin on examination on the day of participation. Atopic individuals, who plan to work in a career such as hairdressing with known high rates of occupational contact dermatitis, should be advised to care for and protect their skin from the outset to prevent the development of this condition. There has been little awareness of this issue in Australia, despite longstanding knowledge of the association of hairdressing and contact dermatitis.
Invasive squamous cell carcinoma after treatment of carcinoma in situ with 5% imiquimod cream
Authors: Goh Michelle SY 
Published: July 2006

SUMMARYSquamous cell carcinoma in situ has the potential to progress to invasive squamous cell carcinoma. This report presents two cases of punch biopsy‐proven squamous cell carcinoma in situ, treated with once‐daily application of 5% imiquimod cream for 6 weeks. Both patients developed moderate local inflammatory reactions during treatment. The first patient demonstrated clinical clearance of the scalp lesion after treatment. Two months later, he re‐presented with a subcutaneous nodule at the same site. Histology was consistent with recurrent squamous cell carcinoma. Five months following excision of the recurrent tumour, he presented with metastatic squamous cell carcinoma to a cervical lymph node. The second patient had low‐grade chronic lymphocytic leukaemia and presented with squamous cell carcinoma in situ of the leg that failed to clear clinically after treatment with imiquimod. He presented 4 months later with a focus of invasive squamous cell carcinoma within the lesion.
Wolf’s isotopic response: Rosacea appearing at the site of healed herpes zoster
Authors: Sezer Engin , Koseoglu Resit D , Filiz Nurper 
Published: July 2006

SUMMARYA 40‐year‐old man developed an erythematous rash on the right side of his face 3 weeks after a herpes zoster infection at the same location. Examination revealed an erythematous papular eruption and telangiectasias along the ophthalmic and maxillary divisions of the right trigeminal nerve, exactly at the site of the consistent with previous herpes zoster infection, Wolf’s isotopic response. Histological examination showed vascular ectatic dilatation and perivascular and perifollicular infiltration of lymphocytes and histiocytes consistent with rosacea. The rash was resistant to oral doxycycline and topical metronidazole 1% cream and resolved with oral isotretinoin therapy.
Juxta‐clavicular beaded lines
Authors: Franco Gennaro , Donati Pietro , Muscardin Luca , Maini Antonio , Morrone Aldo 
Published: July 2006

SUMMARYWe present a case series of 63 patients diagnosed with juxta‐clavicular beaded lines. This condition is more frequent in dark‐skinned people and corresponds to an anatomical variant of simple sebaceous hyperplasia. In view of the strong reactivity of the melanocytes in dark‐skinned people, and of the possible hypochromic results, no treatment is advised.