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

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

Чи завжди слід використовувати антибактеріальні засоби після уродинамічних досліджень у пацієнток з групи високого ризику?

Aim. The aim of this observational study was to evaluate the effectiveness of a phytotherapic drug (Canephron N) in preventing urinary tract infection (UTI) in high-risk women undergoing urodynamic studies (UDS).Methods. The study protocol was approved by the local institutional ethical committee. Adult women with at least one risk factor for acquiring UTI (defined as: age over 70, elevated postvoid residual urine>100 ml, recurrent UTI, pelvic organ prolapse (POP) ≥II in POP-Q scale, and neurogenic bladder) had received after UDS either a single oral dose of fosfomycin trometamol (FT) (3 grams) or a phytodrug containing centaury herb, lovage root, and rosemary leaves (5 ml taken orally three times daily for one week). All patients included in the study had no pyuria according to urine dipstick (nitrite and/or blood and/or leukocyte esterase) and negative urine culture (CFU < 103/ml) before UDS. Urine samples were also tested 7 days after UDS.Results. Seventy-two high-risk participants completed the study. Seven days after urodynamic studies UTI symptoms, pyuria (nitrite and/or blood and/or leukocyte esterase) and bacteriuria with E. coli occurred in two patients (one (2.8 %) in the FT and one (2.7 %) in the phytodrug group, respectively). No statistical differences in UTI incidence were found between both treatment groups.We did not observe any additional adverse events in both groups. The major disadvantage of prophylaxis with the phytodrug as compared to FT was the necessity of continuing therapy for 7 days.Conclusion. Prophylaxis of UTI with a phytodrug (Canephron N) may be considered a good alternative to antibiotic prophylaxis use after UDS in high-risk female patients.Цель исследования: оценить эффективность фитотерапевтического препарата (Канефрон® Н) в предотвращении инфекции мочевыводящих путей (ИМП) у женщин из группы высокого риска, принимавших участие в уродинамических исследованиях (УДИ).Материалы и методы. Протокол исследования был утвержден местным комитетом по этике медицинского учреждения. Взрослые женщины с хотя бы одним фактором риска развития ИМП (возраст старше 70 лет, увеличен остаточный объем мочи после мочеиспускания >100 мл, рецидивирующие ИМП, опущение тазовых органов (POP) ≥ІІ по шкале POP-Q и нейрогенный мочевой пузырь), после УДИ получали или одноразовую пероральную дозу фосфомицина трометамола (ФТ) (3 г), или фитопрепарат, содержащий траву золототысячника, корень любистка и листья розмарина (5 мл принимают перорально три раза в сутки в течение одной недели). У пациенток, которые были включены в исследование, до начала УДИ не фиксировали пиурию по результатам пробы мочи (нитрита и/или крови и/или лейкоцитарной эстеразы) и отмечали отрицательный результат бактериального посева мочи (КОЕ<103/мл). Образцы мочи также проверяли через 7 дней после УДИ.Результаты. Исследование завершили семьдесят две участницы с высоким риском развития ИМП. Через семь дней после проведения уродинамических исследований симптомы ИМП, пиурии (нитрит и/или кровь и/или лейкоцитарная эстераза), а также бактериурия с E. coli наблюдали у двух пациенток (у одной (2,8 %) в группе применения ФТ и одной (2,7 %) в группе применения фитопрепарата соответственно). Между обеими группами лечения не выявлено статистических различий по заболеваемости ИМП. Дополнительных побочных реакций в обеих группах не наблюдалось. Основным недостатком профилактики фитопрепаратами по сравнению с ФТ была необходимость продолжения терапии в течение 7 дней.Заключение. Профилактика ИМП с помощью фитопрепаратов (Канефрон® Н) может считаться хорошей альтернативой профилактике антибактериальными средствами после проведения УДИ у пациенток из группы высокого риска.Мета дослідження: оцінити ефективність фітотерапевтичного препарату (Канефрон® Н) у запобіганні інфекції сечовивідних шляхів (ІСШ) у жінок з групи високого ризику, які брали участь в уродинамічних дослідженнях (УДД).Матеріали та методи. Протокол дослідження був затверджений місцевим комітетом з етики медичного закладу. Дорослі жінки, що мають хоча б один фактор ризику розвитку ІСШ (вік старше 70 років, збільшений залишковий об’єм сечі після сечовипускання >100 мл, рецидивуючі ІСШ, опущення тазових органів (POP) ≥ІІ за шкалою POP-Q та нейрогенний сечовий міхур), після УДД отримували або одноразову пероральну дозу фосфоміцину трометамолу (ФТ) (3 г), або фітопрепарат, що містить траву золототисячника, корінь любистку та листя розмарину (5 мл приймають перорально три рази на добу протягом одного тижня). У пацієнток, що були включені в дослідження, до початку УДД не фіксували піурії за результатами проби сечі (нітриту та/або крові та/або лейкоцитарної естерази) та відзначали негативний результат бактеріального посіву сечі (КУО<103/мл). Зразки сечі також перевіряли через 7 днів після УДД.Результати. Дослідження завершили сімдесят дві учасниці з високим ризиком розвитку ІСШ. Через сім днів після проведення уродинамічних досліджень симптоми ІСШ, піурії (нітрит та/або кров та/або лейкоцитарна естераза), а також бактеріурія з E. coli спостерігалися у двох пацієнток (в однієї (2,8 %) в групі застосування ФТ та однієї (2,7 %) у групі застосування фітопрепарату відповідно). Між обома групами лікування не виявлено статистичних відмінностей щодо захворюваності на ІСШ. Додаткові побічні реакції в обох групах не спостерігалися. Основним недоліком профілактики фітопрепаратами порівняно з ФТ була необхідність продовження терапії протягом 7 днів.Заключення. Профілактика ІСШ за допомогою фітопрепаратів (Канефрон® Н) може вважатися хорошою альтернативою профілактиці антибактеріальними засобами після проведення УДД у пацієнток з групи високого ризику

Effectiveness of botulinum toxin injection in the treatment of de novo OAB symptoms following midurethral sling surgery

Introduction and hypothesis Intravesical onabotulinumtoxinA (Botox®) is effective for idiopathic overactive bladder (OAB) symptoms. Our primary objective was to compare the efficacy of onabotulinumtoxinA for women with de novo OAB after midurethral sling (MUS) surgery and women with idiopathic OAB. Methods Women enrolled in this prospective study had idiopathic (n=53) or de novo (n=49) OAB symptoms after MUS, with at least one episode of urgency urine incontinence per day. OnabotulinumtoxinA (100 U) was administered in 20 intradetrusor injections. Postvoid residual volumes were checked at 2, 4 and 12 weeks. Participants completed a 3- day bladder diary and the King’s Health Questionnaire (KHQ) before and 12 weeks after treatment. Results After 12 weeks, 22 patients (41.5 %) in the idiopathic OAB and 19 patients (38.8 %) in the de novo OAB groups were completely dry. OnabotulinumtoxinA injections had a significant benefit within both groups (p 90 ml in both groups. Urinary retention was observed in four patients. Conclusions We observed similar improvement in OAB symptoms after intravesical onabotulinumtoxinA injections within both groups. The rates of retention and requirement for catheterization even for women with a prior MUS were acceptable. These observational data provide evidence that onabotulinumtoxinA can effectively treat patients with OAB following stress urinary incontinence surger

VEGF release is associated with reduced oxygen tensions in experimental inflammatory arthritis.

OBJECTIVE: The contribution of local VEGF production and subsequent angiogenesis within the synovial membrane to the propagation of arthritis is unclear. The relationship between synovial oxygenation and blood flow in the development of arthritic disease is unknown. We have therefore measured oxygen levels and perfusion rates in the synovial space in a murine model of arthritis. METHODS: Arthritis was induced in DBA/1 mice by immunisation with type II collagen. Oxygen and perfusion levels were measured polarographically using silver needle microelectrodes within the knee joints prior to and 10 days after the onset of arthritis. In addition, synovial cells were isolated from knee joints of naive, pre-arthritic and arthritic mice. RESULTS: Onset of arthritis was associated with a marked reduction in synovial oxygen tensions (pO2). The perfusion rates in naive and arthritic animals were not significantly different: in naive mice, the rate was 0.58 +/- 0.11 ml/min/g and in arthritic joints, 0.64 +/- 0.17 ml/min/g. Furthermore, synovial cells isolated from the knee joints of naive animals did not express mRNA for VEGF, but significant levels were detected in cells from non-arthritic mice immunised with collagen. The onset of arthritis was associated with expression of VEGF mRNA and protein, and correlated negatively with pO2 levels. CONCLUSION: These data demonstrate that decreases in intra-articular pO2 occur in established arthritic conditions and may be the stimulus for local VEGF production. However, perfusion was not increased in arthritic animals and vascular density was unaltered, suggesting that the neovascularisation associated with inflammatory arthritis, is insufficient to restore oxygen homeostasis in the joint

Future prospects for anti-cytokine treatment.

The era of anti-cytokine treatment in rheumatology has just begun. The first generation therapeutic agents, biological agents that block tumour necrosis factor alpha such as monoclonal antibodies or receptor Ig fusion proteins are safe and effective, and so this has generated much interest in how to increase the benefit or deliver it more cost effectively. This article provides a personal view of the coming trends in anti-cytokine treatment. Which of these will be realised in the future will be of interest