Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Postharvest quality of strawberry fruits produced in organic and conventional systems Qualidade pós-colheita de frutos de morangueiro produzidos em sistemas orgânico e convencional

The aim of this study was to determine some physicochemical characteristics of fruits of eight strawberry cultivars (Aromas, Camino Real, Campinas, Dover, Oso Grande, Toyonoka, Tudla-Milsei and Ventana) cultivated in organic and conventional systems. The evaluated characteristics were soluble solids (SS), titratable acidity (TA), SS/AT ratio and anthocyanins. Evaluated sensory characteristics were flavor and appearance. The cultivars had a differential performance between themselves and among the systems for the evaluated characteristics. Generally, the conventional system produced fruit with higher levels of soluble solids and, organic system produced higher concentrations of anthocyanins. The fruits of the cultivar Toyonoka had the best soluble solids content in both systems and the anthocyanins content of 'Tudla-Milsei' and 'Camino Real' were proeminent in comparison to the other cultivars. The fruits from the organic system of production were preferred by judges on the sensorial attributes. The highest notes were given to the appearance of the cultivar Ventana in the conventional system and 'Tudla-Milsei' in the organic system.<br>O presente trabalho teve como objetivo determinar as características químicas e sensoriais de frutos de oito cultivares de morangueiro (Aromas, Camino Real, Campinas, Dover, Oso Grande, Toyonoka, Tudla-Milsei e Ventana) provenientes de sistemas orgânico e convencional de cultivo. As características químicas avaliadas foram sólidos solúveis (SS), acidez titulável (AT), relação SS/AT e teor de antocianinas. As características sensoriais avaliadas foram sabor e aparência. As cultivares apresentaram um comportamento diferenciado entre si e frente aos sistemas de produção para as características avaliadas. De modo geral, o sistema convencional produziu frutos com maiores teores de sólidos solúveis e o sistema orgânico, maiores valores de acidez titulável e maiores concentrações de antocianinas. Os frutos da cultivar Toyonoka apresentaram o maior teor de sólidos solúveis nos dois sistemas de cultivo avaliados. Destaque para o teor de antocianinas das cultivares Tudla-Milsei e Camino Real. Quanto às características sensoriais, os frutos provenientes do sistema orgânico de produção foram preferidos pelos julgadores para os atributos avaliados. As maiores notas foram atribuídas para a aparência dos frutos da cultivar Ventana no sistema convencional e de 'Tudla-Milsei' no orgânico

Pflanzenentwicklung und bioaktive Substanzen bei der kernlosen Tafeltraubensorte ‘Recel Uzümü’ (V. vinifera L.) in Abhängigkeit von Dosierung und Zeitpunkt der Applikation von Thidiazuron

The purpose of this research was to appreciate the impact of the synthetic cytokinin, well known as thidiazuron (TDZ) on seedless berry quality of cv. 'Recel Uzumu'. Three concentration levels including 0, 5 and 10 mg/L were applied on the grapevines during different phenological stages of grapevine such as Time 1: beginning of berry stetting, Time 2: berries pepper corn size and Time 3: berries pea size. While TDZ application times had no impacts on cultivar characteristics, it was determined that the application doses of TDZ had major impacts on yield and quality components of cv. 'Recel Uzumu'. Consequently, ascending TDZ doses increased berry and cluster size and led to decreases in total soluble solids content, total phenolic compound content, total anthocyanin content and p-value of grape juice regardless of TDZ application time. The most effective TDZ dose was 10 ppm for improving berry and cluster size in cv. 'Recel Uzumu'

Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials

Background Quinquennial overviews (1985-2000) of the randomised trials in early breast cancer have assessed the 5-year and 10-year effects of various systemic adjuvant therapies on breast cancer recurrence and survival. Here, we report the 10-year and 15-year effects. Methods Collaborative meta-analyses were undertaken of 194 unconfounded randomised trials of adjuvant chemotherapy or hormonal therapy that began by 1995. Many trials involved CMF (cyclophosphamide, methotrexate, fluorouracil), anthracycline-based combinations such as FAC (fluorouracil, doxombicin, cyclophosphamide) or FEC (fluorouracil, epirubicin, cyclophosphamide), tamoxifen, or ovarian suppression: none involved taxanes, trastuzumab, raloxifene, or modem aromatase inhibitors. Findings Allocation to about 6 months of anthracycline-based polychemotherapy (eg, with FAC or FEC) reduces the annual breast cancer death rate by about 38% (SE 5) for women younger than 50 years of age when diagnosed and by about 20% (SE 4) for those of age 50-69 years when diagnosed, largely irrespective of the use of tamoxifen and of oestrogen receptor (ER) status, nodal status, or other tumour characteristics. Such regimens are significantly (2p=0 . 0001 for recurrence, 2p<0 . 00001 for breast cancer mortality) more effective than CMF chemotherapy. Few women of age 70 years or older entered these chemotherapy trials. For ER-positive disease only, allocation to about 5 years of adjuvant tamoxifen reduces the annual breast cancer death rate by 31% (SE 3), largely irrespective of the use of chemotherapy and of age (<50, 50-69, &GE; 70 years), progesterone receptor status, or other tumour characteristics. 5 years is significantly (2p<0 . 00001 for recurrence, 2p=0 . 01 for breast cancer mortality) more effective than just 1-2 years of tamoxifen. For ER-positive tumours, the annual breast cancer mortality rates are similar during years 0-4 and 5-14, as are the proportional reductions in them by 5 years of tamoxifen, so the cumulative reduction in mortality is more than twice as big at 15 years as at 5 years after diagnosis. These results combine six meta-analyses: anthracycline-based versus no chemotherapy (8000 women); CMF-based versus no chemotherapy (14 000); anthracycline-based versus CMF-based chemotherapy (14 000); about 5 years of tamoxifen versus none (15 000); about 1-2 years of tamoxifen versus none (33 000); and about 5 years versus 1-2 years of tamoxifen (18 000). Finally, allocation to ovarian ablation or suppression (8000 women) also significantly reduces breast cancer mortality, but appears to do so only in the absence of other systemic treatments. For middle-aged women with ER-positive disease (the commonest type of breast cancer), the breast cancer mortality rate throughout the next 15 years would be approximately halved by 6 months of anthracycline-based chemotherapy (with a combination such as FAC or FEC) followed by 5 years of adjuvant tamoxifen. For, if mortality reductions of 38% (age <50 years) and 20% (age 50-69 years) from such chemotherapy were followed by a further reduction of 31% from tamoxifen in the risks that remain, the final mortality reductions would be 57% and 45%, respectively (and, the trial results could well have been somewhat stronger if there had been full compliance with the allocated treatments). Overall survival would be comparably improved, since these treatments have relatively small effects on mortality from the aggregate of all other causes. Interpretation Some of the widely practicable adjuvant drug treatments that were being tested in the 1980s, which substantially reduced 5-year recurrence rates (but had somewhat less effect on 5-year mortality rates), also substantially reduce 15-year mortality rates. Further improvements in long-term survival could well be available from newer drugs, or better use of older drugs

Overview of the randomized trials of radiotherapy in ductal carcinoma in situ of the breast.

Individual patient data were available for all four of the randomized trials that began before 1995, and that compared adjuvant radiotherapy vs no radiotherapy following breast-conserving surgery for ductal carcinoma in situ (DCIS). A total of 3729 women were eligible for analysis. Radiotherapy reduced the absolute 10-year risk of any ipsilateral breast event (ie, either recurrent DCIS or invasive cancer) by 15.2% (SE 1.6%, 12.9% vs 28.1% 2 P <.00001), and it was effective regardless of the age at diagnosis, extent of breast-conserving surgery, use of tamoxifen, method of DCIS detection, margin status, focality, grade, comedonecrosis, architecture, or tumor size. The proportional reduction in ipsilateral breast events was greater in older than in younger women (2P < .0004 for difference between proportional reductions; 10-year absolute risks: 18.5% vs 29.1% at ages <50 years, 10.8% vs 27.8% at ages ≥ 50 years) but did not differ significantly according to any other available factor. Even for women with negative margins and small low-grade tumors, the absolute reduction in the 10-year risk of ipsilateral breast events was 18.0% (SE 5.5, 12.1% vs 30.1%, 2P = .002). After 10 years of follow-up, there was, however, no significant effect on breast cancer mortality, mortality from causes other than breast cancer, or all-cause mortality.Journal ArticleResearch Support, Non-U.S. Gov'tReviewinfo:eu-repo/semantics/publishe