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

Multisensory coding of angular head velocity in the cortex

To successfully navigate the environment, animals depend on their ability to continuously track their heading direction and speed. Neurons that encode angular head velocity (AHV) are fundamental to this process, yet the contribution of various motion signals to AHV coding in the cortex remains elusive. By performing chronic single-unit recordings in the retrosplenial cortex (RSP) of the mouse and tracking the activity of individual AHV cells between freely moving and head-restrained conditions, we find that vestibular inputs dominate AHV signaling. Moreover, the addition of visual inputs onto these neurons increases the gain and signalto-noise ratio of their tuning during active exploration. Psychophysical experiments and neural decoding further reveal that vestibular-visual integration increases the perceptual accuracy of angular self-motion and the fidelity of its representation by RSP ensembles. We conclude that while cortical AHV coding requires vestibular input, where possible, it also uses vision to optimize heading estimation during navigation

Mass reconstruction techniques and cross section measurement for Z→ττ→eμ+4υ with the ATLAS experiment

Die Suche nach dem Higgs Boson ist ein zentraler Forschungsschwerpunkt der modernen Teilchenphysik. Zum einen ist das Higgs Boson das einzige bislang unentdeckte Teilchen des Standard Modells. Zum anderen gibt seine mögliche Entdeckung eine bessere Einsicht in die Natur neuer Physik. Mit der Inbetriebnahme des Large Hadron Colliders, LHC, am europäischen Kernforschungszentrum CERN bei Genf konnten Proton-Proton Kollisionen mit bislang unerreichten Schwerpunktsenergien von √s = 7 TeV beziehungsweise √s = 8 TeV erzielt werden. In der vorliegenden Arbeit wird die Messung des Wechselwirkungsquerschnitts pp→Z/γ→τ⁺τ⁻ im gemischten leptonischen Endzustand mit Daten des ATLAS Detektors durchgeführt. Der Zerfall der kohärenten Summe aus Photon, γ, und Z Boson in zwei τ -Leptonen ist ein irreduzibler Untergrund von Higgs Boson Zerfällen in zwei τ -Leptonen. Eine genaue Kenntniss des Massenspektrums sowie dessen Normierung ist deswegen für die Higgs Boson Suche essentiell. Die verwendeten Daten entsprechen einer integrierten Luminosität von L = 35,51 pb⁻¹ bei einer Schwerpunktsenergie von √s = 7 TeV. Die Messung erzielt einen Wechselwirkungsquerschnitt von σ×BR(Z→ττ ) = (1041 ± 143 ± 74 ± 35) pb. Die angegebenen Unsicherheiten entsprechen den statistischen, den systematischen und den Unsicherheiten aus Luminositätsmessungen. Das Ergebnis stimmt mit dem theoretisch bestimmten Wert sowie dem Ergebnis anderer Experimente innerhalb seiner Unsicherheiten überein. Im zweiten Teil der Arbeit werden verschiedene Massenrekonstruktionsmethoden von Zerfällen in zwei τ-Leptonen untersucht. Die Analyse konzentriert sich dabei auf Higgs Bosonen, der minimalen supersymmetrischen Erweiterung des Standard Modells; insbesondere auf deren Zerfall in zwei τ-Leptonen und weiter in den gemischten leptonischen Endzustand, Φ→τ⁺τ⁻→eμ+4υ. Die untersuchten Massenrekonstruktionsmethoden sind die sichtbare Masse, die effektive Masse, sowie die früh- und spät-projizierte transversale Masse. Weiterhin werden Abhängigkeiten der Massenverteilungen vom transversalen Impuls der Leptonen des Endzustandes, sowie der fehlenden transversalen Energie festgestellt. Eine Abhängigkeit vom transversalen Impuls des energiereichsten Jets hingegen konnte nicht nachgewiesen werden. Eine mögliche Eliminierung der Variablenabhängigkeiten wird untersucht, zeigt jedoch dass sie zu einer schlechteren Trennung zwischen Signal und Untergrundprozessen sowie einer schlechteren Auflösung unterschiedlicher Higgs Boson Massen führt. Mit der Kalibrierung der berechneten Massen der verschiedenen Rekonstruktionstechniken wird die Arbeit abgeschlossen

Determinação quantitativa de grupos de bactérias em sucos de laranja ao natural Quantitative determination of bacteria groups in fresh, natural orange juice

Foi realizada investigação com a finalidade de se conhecer a microbiota aeróbia do suco de laranja ao natural oferecido ao consumo público, através das contagens de bactérias mesófilas e ácido-produtoras, e da determinação do número mais provável (NMP) de bactérias coliformes totais e fecais e de estreptococos fecais.<br>This investigation was carried out to discover the aerobic microbiota in natural orange juice served the public. Counts were made of mesophilic bacteria and acid producers, and the most probable number of totally coliform bacteria, fecal bacteria, and fecal streptocci was determined