bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
Authors: Kiryu Hisanori , Kin Taishin , Asai Kiyoshi 
Published: December 2006

AbstractMotivation: Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures.Results: We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs.Availability: The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available atContact: kiryu-h@aist.go.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Bax and the Ballet
Authors: Foreman Lewis 
Published: January 2007

On 27 July 1913 Colin Taylor, a music master at Eton and confidant of the young Philip Heseltine, wrote to his protégé:
By the way I was introduced to Bax at the Russian Ballet the other night – do you know him? I have always pictured him as a slow speaking dreamy man – dreamy he may be, but in his speech he is short, dry and quite unpoetical. He told me he has a splendid ‘Book’ for a ballet and he is longing to get to work on it. At present however he is finishing a work for (I think he said) the Norwich Triennial Festival. A ballet should suit him.
Repetition and Variation in the Thirteenth-Century Refrain
Authors: Butterfield Ardis 
Published: January 2007

Is there an answer to the question ‘what is a refrain?’ Traditionally, scholars of thirteenth-century French song begin their reply by noting that a refrain is the characteristic formal feature of a rondeau, that is, an element which is repeated, usually with a separate half-repetition, in alternation with a strophic ‘respond’:Aaliz main se leva,bon jor ait qui mon cuer a!Biau se vesti et para,desoz l'aunoi.Bon jor ait qui mon cuer an'est pas o mot.Moreover, most modern attempts to define refrains have explicitly begun by collecting rondeaux. But since only a small proportion of refrains occurs in rondeaux (in van den Boogaard's bibliography approximately one tenth), it is clearly not a comprehensive definition.
Knowledge, Strategy, and Momentum in Presidential Primaries
Authors: Brady Henry E. 
Published: January 2007

Two dynamic rational choice models of primaries are analyzed that demonstrate both reformers and their critics are right about primaries. Primaries can provide public instruction and a better informed electorate, and they can be poorly designed lotteries: A “recognition” and learning model describes how changing media coverage affects voters' knowledge about candidates and their subsequent voting behavior. A “strategic” voting model describes the dynamic implications of strategic voting and “horse-race” coverage by the media. We find that the recognition model has the normatively appealing dynamic of information leading to broadly self-interested outcomes while the strategy model has the unappealing behavior of a lottery the odds of which are fixed by the media's harsh judgments of who's winning and who's losing.In coming to these conclusions, this paper illustrates a number of methodological points such as the usefulness of macromodels based upon assumptions about individual behavior, the analysis of macromodels using methods from electrical engineering, the strengths and limitations of analytical results versus simulations for understanding dynamic models, and the use of “ideal type” recognition and strategic voting models to clarify the systemic consequences of individual risk aversion and strategic voting. More generally, the paper shows how models can be used as narratives or parables for organizing disparate observations, refining our intuitions, and directing our research efforts.
Prediction of metastases in melanoma patients with positive sentinel node: Histological and molecular approach
Authors: TSUTSUMIDA Arata , FURUKAWA Hiroshi , HATA Shinya , SAITO Akira , YAMAMOTO Yuhei 
Published: December 2006

ABSTRACTIt is now established that sentinel node (SN) biopsy is a minimally‐invasive procedure that accurately indicates the regional nodal status. In our institute, 14 consecutive patients had only one node micrometastases after elective lymph node dissection or positive SN for primary cutaneous melanoma. These 14 patients could be clearly divided into two groups: (i) patients who developed distant metastases or in‐transit metastases (metastasized group); and (ii) and patients who remains free from metastases (non‐metastasized group). The purpose of this study was to identify the histological and molecular factors that might predict the further dissemination beyond the SN. We assessed the maximum depth from the capsule to the deepest melanoma cells and the maximum diameter of melanoma nests in the lymph nodes as histological parameters and also evaluated the quantitative expression of tyrosinase mRNA as a molecular approach. The mean maximum depth and the maximum diameter were significantly smaller in the metastasized group than those in the non‐metastasized group. Tyrosinase mRNA expression was strongly correlated with the histological tumor burden. Tyrosinase mRNA expression was higher in the former group than that in the latter group but there were no significant differences between them. Melanoma patients with small micrometastases (<0.5 mm deep, <1 mm in diameter) and a low level of tyrosinase mRNA had less chances for hematogenous metastases via lymph nodes.
Topical 5‐aminolaevulinic acid photodynamic therapy for intractable palmoplantar psoriasis
Authors: KIM Ji Yeon , KANG Hee Young , LEE Eun‐So , KIM You Chan 
Published: December 2006

ABSTRACTPhotodynamic therapy (PDT) has been reported to be useful in treating non‐melanoma skin cancers and a variety of benign skin conditions including psoriasis. However, only two reports of palmoplantar pustular psoriasis (PPP) treated with PDT have been reported. We treated three intractable cases of PPP with PDT, using 20% 5‐aminolaevulinic acid and a 630 ± 50 nm light‐emitting diode device. The power density was 30 mW/cm2 and the fluence was 15 J/cm2. After treatment, all cases showed mild to marked improvement. Topical PDT may be an alternative therapy in the treatment of PPP, but further study is necessary to confirm the effectiveness of topical PDT in PPP.
Case of metastatic melanoma in an epitrochlear lymph node arising in a pregnant woman
Authors: YOSHIDA Yuichi , TAKAHASHI Akira , KOGA Monji , KOGA Kaori , KUBOTA Yumiko , NAKAYAMA Juichiro 
Published: December 2006

ABSTRACTWe describe a rare case of metastatic melanoma in an epitrochlear lymph node in a 29‐year‐old female patient. The patient had been aware of a brown macule on her right posterior forearm at puberty. Because the lesion had enlarged rapidly, she was referred to our hospital. Histological examination revealed a malignant melanoma. She underwent wide local excision with 3‐cm margins and split thickness skin graft closure, but we were not able to perform sentinel node biopsy. She also received three cycles of systemic chemotherapy with dacarbazine, nimustine, vincristine and interferon‐β. However, an epitrochlear node (interval node) metastasis occurred during pregnancy (seventh week) 2 years after the operation. We emphasize that it is important for clinicians to pay attention to the possibility of epitrochlear node metastasis in patients with malignant melanoma in the upper extremity and that it is necessary to perform sentinel node biopsy to identify uncommon lymph node metastasis.
Melanocytic nevi clinically simulating melanoma
Authors: MAKINO Eiichi , UCHIDA Takafumi , MATSUSHITA Yoshiko , INAOKI Makoto , FUJIMOTO Wataru 
Published: December 2006

ABSTRACTMelanoma and other benign or malignant pigmented skin tumors can significantly overlap in their clinical and dermoscopical presentations. Thus, pigmented skin lesions may be misdiagnosed in a large number of cases. An extensive review of the published work provides numerous examples of benign lesions mimicking melanoma. Although a number of melanocytic nevi may have been identified as melanomas, information about their clinical appearance is limited. In this report, we present the clinical appearances of two melanocytic nevi on the vulva and the upper extremity that were difficult to diagnose clinically. Detecting melanoma at an early stage is of the utmost importance. However, more attention should be given to the diagnostic accuracy of benign pigmented skin lesions, which otherwise may be diagnosed and treated as melanoma.
Atypical melanosis of the foot showing a dermoscopic feature of the parallel ridge pattern
Authors: KILINC KARAARSLAN Isil , AKALIN Taner , UNAL Idil , OZDEMIR Fezal 
Published: December 2006

ABSTRACTA 62‐year‐old male Turkish patient had a pigmented lesion on the sole with a 10‐year history. It was an asymmetrical macular lesion with an irregular border and irregular brown pigmentation and had a diameter of 1.2 cm × 1.7 cm.Dermoscopy revealed a parallel ridge pattern and an abrupt cut‐off of pigmentation on the upper edge. Histologically lentiginous hyperplasia decorated by innocent melanocytes and scattered melanocytic proliferation with slight to moderate cytological atypia were seen. Atypical melanocytes were very scattered and it was insufficient to call it a melanoma in situ. A second finding was a microvascular proliferation located in the papillary dermis. There was no sign of regression such as fibrous tissue or host reaction. Atypical melanosis of the foot has rarely been reported in the published work, which are from Japan and Korea. This case is presented to emphasize the significance of this rare entity which has recently been reported to be a very early phase of acral melanoma.
Does subtle screening for substance abuse work? A review of the Substance Abuse Subtle Screening Inventory (SASSI)
Authors: Feldstein Sarah W. , Miller William R. 
Published: December 2006

ABSTRACTAim  Through a complex combination of direct (face‐valid) and indirect (subtle) subscales, the Substance Abuse Subtle Screening Inventory (SASSI) is purported to detect substance use disorders with a high degree of validity regardless of respondent honesty or motivation. This review evaluates empirical evidence regarding the reliability and validity of this widely used screening instrument.Methods  Source documents were 36 peer‐reviewed reports yielding data regarding the SASSI's internal consistency, test–retest reliability, psychometric structure, convergent and divergent validity and criterion (predictive) validity.Results  The total N of the studies reviewed equaled 22 110. Internal consistency is high for the overall SASSI and for its direct but not its indirect (subtle) subscales, suggesting that the instrument taps a single face‐valid construct. SASSI classifications converged with those from other direct screening instruments, and were also correlated with ethnicity, general distress and social deviance. Studies found test–retest reliability lower than that reported in the test manuals. Sensitivity was found to be similar to that for public domain screening instruments, but on specificity the SASSI appears to yield a high rate of false positives.Conclusion  No empirical evidence was found for the SASSI's claimed unique advantage in detecting substance use disorders through its indirect (subtle) scales to circumvent respondent denial or dishonesty. Recommendations for screening and for future research with the SASSI are offered.
The role of sensory perception in the development and targeting of tobacco products
Authors: Carpenter Carrie M. , Wayne Geoffrey Ferris , Connolly Gregory N. 
Published: December 2006

ABSTRACTAims  To examine tobacco industry research on smoking‐related sensory effects, including differences in sensory perception across smoker groups, and to determine whether this research informed targeted product development and impacted the development of commercial tobacco products.Design  We searched previously secret internal tobacco industry documents available online through document databases housed at Tobacco Documents Online, the British American Tobacco Document Archive and the Legacy Tobacco Documents Library. We identified relevant documents using a snowball sampling method to first search the databases using an initial set of key words and to then establish further search terms.Findings  Sensory research is a priority within the tobacco industry directly impacting commercial markets both in the United States and internationally. Sensory factors contribute to smoker satisfaction and product acceptance, and play an important role in controlling puffing behavior. Cigarette manufacturers have capitalized on distinct sensory preferences across gender, age and ethnic groups by tailoring products for specific populations.Conclusions  Regulation of tobacco products is needed to address product changes that are used to reinforce or contribute to tobacco dependence; for instance, the incorporation of additives that target attributes such as smoothness, harshness and aftertaste. Greater understanding of the role of sensory effects on smoking behavior may also help to inform the development of tobacco treatment options that support long‐term tobacco abstinence.
Abundance and distribution of fish in the lower Mnembo River, Malawi‐Mozambique
Authors: Delaney Leanda M. , Jamu Daniel M. , Campbell Christine E. 
Published: December 2006

AbstractEndorheic Lake Chilwa is one of the most productive lakes for fisheries in Africa. High human population densities and agricultural practices in the Chilwa catchment have been linked to observed declines of the annual fish catch in the lake. The Mnembo River is a major inflow into Lake Chilwa which has received little scientific study to date. In 2003/2004, fish diversity, abundance and distribution were monitored monthly at three sites in the Mnembo River. Twelve fish species were collected, a subset of the fourteen fish species present in Lake Chilwa. Although Barbus spp. were the most abundant species sampled in the Mnembo, total biomass was higher for Labeo cylindricus (6709 and 10,434 g, respectively). Total biomass of Pareutropius longifilis (1741 g) and Brycinus imberi (1174 g) were also high in the river. Catches of Barbus and Labeo were highly correlated (r = 0.763). Compared with other inflows into Lake Chilwa (Likangala and Domasi), the Mnembo River appears to be less adversely influenced by human populations, with high abundance of Barbus and strong presence of the riverine species Labeo, Pareutropius and Brycinus.
Genome‐wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection
Authors: Zenger K. R. , Khatkar M. S. , Cavanagh J. A. L. , Hawken R. J. , Raadsma H. W. 
Published: December 2006

SummaryPast breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome‐wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [Ho] and allelic richness [A]) were observed over the 25‐year time period (1975–1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub‐sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome‐wide level.
Phase II trial of denileukin diftitox for relapsed/refractory T‐cell non‐Hodgkin lymphoma
Authors: Dang Nam H. , Pro Barbara , Hagemeister Fredrick B. , Samaniego Felipe , Jones Dan , Samuels Barry I. , Rodriguez Maria A. , Goy Andre , Romaguera Jorge E. , McLaughlin Peter , Tong Ann T. , Turturro Francesco , Walker Pamela L. , Fayad Luis 
Published: December 2006

SummaryThis phase II study evaluated the safety and efficacy of denileukin diftitox, an interleukin‐2–diphtheria toxin fusion protein, in relapsed/refractory T‐cell non‐Hodgkin lymphoma (T‐NHL), excluding cutaneous T‐cell lymphoma. Eligible patients received denileukin diftitox 18 μg/kg/d × 5 d every 3 weeks for up to eight cycles. Tumour staging was performed every two cycles and the primary endpoint was the objective response rate [complete response (CR) + partial response (PR)]. For 27 patients enrolled, median age: 55 years (range 26–80 years), 70·4% male, and mean prior therapies: 2·5 (range 1–6). Objective responses (six CRs, seven PRs) were achieved in 13 patients (48·1%), stable disease in eight (29·6%) and six (22·2%) had progressive disease. An objective response was achieved in eight of 13 patients (61·5%) with CD25+ tumours (four CR/four PR) and five of 11 patients (45·5%) with CD25− tumours (two CR/three PR). Median progression‐free survival was 6 months (range, 1–38+ months). Most adverse reactions were grade 1/2 and transient. No grade 4–5 toxicities were reported. Denileukin diftitox had significant activity and was well tolerated in relapsed/refractory T‐NHL, with responses observed in both CD25+ and CD25− tumours. Further studies of denileukin diftitox in combination with other agents are warranted in previously untreated and relapsed/refractory T‐NHL.
Detection of an allergen in dog dander that cross‐reacts with the major cat allergen, Fel d 1
Authors: Reininger R. , Varga E. M. , Zach M. , Balic N. , Lindemeier A. D. , Swoboda I. , Grönlund H. , Van Hage M. , Rumpold H. , Valenta R. , Spitzauer S. 
Published: December 2006

SummaryBackground
A considerable proportion of animal‐allergic patients are sensitized to both cat and dog allergens but knowledge about cross‐reactive allergens in cat and dog dander is limited.Objective
To investigate whether dog dander contains an allergen that cross‐reacts with the major cat allergen, Fel d 1.Methods
Recombinant Fel d 1 with the same immunological properties as natural Fel d 1 was used for quantitative (CAP) IgE competition experiments performed with sera obtained from cat‐allergic patients (n=36). A Fel d 1 cross‐reactive dog allergen was characterized by one‐ and two‐dimensional immunoblotting using rFel d 1 for IgE inhibition experiments and with monospecific, polyclonal rabbit anti‐recombinant Fel d 1 antibodies.Results
In 25% of Fel d 1‐reactive cat‐allergic patients, more than 50% inhibition of IgE reactivity to dog allergens was achieved with recombinant Fel d 1. An Fel d 1 cross‐reactive 20 kDa allergen with a pI of approximately 3.4 was detected in dander extracts of several different dog breeds.Conclusion
This is the first report demonstrating the presence of an Fel d 1‐like allergen in dog dander extracts, which may be responsible for double positivity to cat and dog in serology. However, the clinical relevance of this cross‐sensitization needs to be confirmed. These results are important for the diagnostic and therapeutic use of dog dander allergen extracts.
Hypoallergenic mutants of Ole e 1, the major olive pollen allergen, as candidates for allergy vaccines
Authors: Marazuela E. G. , Rodríguez R. , Barber D. , Villalba M. , Batanero E. 
Published: December 2006

SummaryBackground
The C‐terminal region of Ole e 1, a major allergen from olive pollen, is a dominant IgE‐reactive site and offers a target for site‐directed mutagenesis to produce variants with reduced IgE‐binding capability.Objective
To evaluate in vitro and in vivo the immunogenic properties of three engineered derivatives of Ole e 1.Methods
One point (Y141A) and two deletion (135Δ10 and 140Δ5) mutants were generated by site‐directed mutagenesis of Ole e 1‐specific cDNA and produced in Pichia pastoris. Ole e 1 mutants were analysed for IgE reactivity by ELISA using sera from olive pollen‐allergic patients. Their allergenicity was also investigated in both a mouse model of allergic sensitization and in basophil activation assays. IgG1 response was assayed by immunoblotting and competitive ELISA. T cell reactivity was evaluated by proliferation assays and cytokine production in splenocyte cultures.Results
The 135Δ10 mutant showed the strongest reduction in the IgE‐binding capability of sera from olive pollen‐allergic patients. Rat basophil leukaemia assays identified the deletion mutant 135Δ10 as the variant with the lowest β‐hexosaminidase‐releasing capacity. Furthermore, the same 135Δ10 mutant induced the lowest IgE levels in a BALB/c mouse model of sensitization. All Ole e 1 mutants retained their allergen‐specific T cell reactivity. Immunization of mice with the mutants induced IgG1 antibodies, which cross‐reacted with Ole e 1 and Ole e 1‐like allergens from ash, lilac and privet pollens. The ability of the human IgE to block the binding of anti‐Ole e 1 mutant‐specific mouse IgG1 antibodies to natural Ole e 1 demonstrated that Ole e 1 mutants are able to induce in vivo antibodies reactive to the natural allergen.Conclusion
The 135Δ10 mutant with reduced allergenicity, intact T cell reactivity and capacity to induce blocking antibodies could provide a suitable candidate vaccine for efficient and safer therapy of olive pollen allergy.