Automatic detection of anchor points for multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Determining beforehand specific positions to align (<it>anchor points</it>) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. <it>Multiple </it>local similarities are be expected to be more adequate, as more biologically relevant. However, even good multiple local similarities can prove incompatible with the ordering of an alignment.</p> <p>Results</p> <p>We use a recently developed algorithm to detect multiple local similarities, which returns subsets of positions in the sequences sharing similar contexts of appearence. In this paper, we describe first how to get, with the help of this method, subsets of positions that could form partial columns in an alignment. We introduce next a graph-theoretic algorithm to detect (and remove) positions in the partial columns that are inconsistent with a multiple alignment. Partial columns can be used, for the time being, as guide only by a few MSA programs: ClustalW 2.0, DIALIGN 2 and T-Coffee. We perform tests on the effect of introducing these columns on the popular benchmark BAliBASE 3.</p> <p>Conclusions</p> <p>We show that the inclusion of our partial alignment columns, as anchor points, improve on the whole the accuracy of the aligner ClustalW on the benchmark BAliBASE 3.</p

Stable Flags and the Riemann-Hilbert Problem

We tackle the Riemann-Hilbert problem on the Riemann sphere as stalk-wise logarithmic modifications of the classical R\"ohrl-Deligne vector bundle. We show that the solutions of the Riemann-Hilbert problem are in bijection with some families of local filtrations which are stable under the prescribed monodromy maps. We introduce the notion of Birkhoff-Grothendieck trivialisation, and show that its computation corresponds to geodesic paths in some local affine Bruhat-Tits building. We use this to compute how the type of a bundle changes under stalk modifications, and give several corresponding algorithmic procedures.Comment: 39 page

ANALISIS KESANTUNAN BERBAHASA DALAM TINDAK TUTUR PEMBAWA ACARA SHABEKURI 007

Penelitian ini bertujuan untuk mendeskripsikan kesantunan berbahasa yang dilakukan oleh pembawa acara dalam acara talkshow Shabekuri 007 berdasarkan teori-teori yang dikemukakan oleh Brown dan Levinson (1987), Ide (1982), serta Mizutani dan Mizutani (1987). Alasan dari pemilihan topik tersebut adalah karena kesantunan berbahasa menjadi suatu hal yang banyak diperbincangkan, terutama ketika memasuki era globalisasi. Kemajuan teknologi komunikasi yang semakin tidak ada batasnya, serta penggunaan bahasa yang semakin beragam membuat kesantunan berbahasa ini menjadi penanda bahwa seseorang memiliki adab atau tatakrama dalam berbahasa. Dalam tuturan, terdapat kemungkinan terjadinya suatu tindakan pengancaman muka yang dilakukan oleh masing-masing pihak yang dapat mengganggu kelancaran proses komunikasi, sehingga terdapat aturan-aturan yang membatasi tindakan penutur dan mitra tutur serta strategi-strategi yang dilakukan agar terjalin komunikasi yang baik. Metode pengumpulan data yang digunakan adalah metode simak bebas libat cakap dan dianalisis menggunakan metode padan pragmatik. Hasil penelitian kemudian dijabarkan secara deskriptif. Hasil penelitian ini adalah dari 106 tuturan yang ditemukan dalam acara Shabekuri 007 terdapat enam penanda kesantunan berbahasa Mizutani dan Mizutani (1987), yaitu perubahan intonasi, penggunaan partikel pada akhir kalimat, penggunaan kalimat yang terkesan ragu-ragu, aizuchi, pemakaian bahasa Jepang yang santun dan halus, dan penyampaian maksud keinginan secara tidak langsung. Kemudian berdasarkan aturan kesantunan berbahasa Ide (1982) terdapat 71 tuturan yang mengabaikan aturan tersebut dan 35 tuturan yang memenuhi aturan tersebut. Aturan tersebut terdiri dari berlaku santun terhadap orang yang memiliki kedudukan yang tinggi, memiliki kekuasaan yang lebih besar, dan terhadap orang yang lebih tua. Kemudian strategi kesantunan Brown dan Levinson (1987) yang digunakan dalam acara Shabekuri 007 terdiri dari strategi kesantunan negatif, strategi on-record, strategi kesantunan positif, dan strategi off-record. Tujuan dilakukannya strategi-strategi tersebut adalah untuk menghindari ketidaknyamanan mitra tutur terhadap tuturan yang dilakukan oleh penutur. This study aims to describe the language politeness which used by presenters in the talk show Shabekuri 007 based on the theories proposed by Brown and Levinson (1987), Ide (1982), and Mizutani and Mizutani (1987). The reason for choosing this topic is because politeness in language is widely discussed, especially when entering the globalization era. The advances of communication technology that are increasingly limitless, as well as the usage of increasingly diverse languages make this language politeness is a sign that someone has etiquette or manners in language. In speech, there is the possibility of a face-threatening act carried out by each party that can interfere the communication process, so that there are rules that limit the actions of speakers and speech partners as well as strategies used to establish a good communication. This study’s data was collected using the free-to-talk method and analyzed using the pragmatic equivalent method. The results of the study were then described descriptively. The results of this study are from the 106 utterances found in the Shabekuri 007 program, there are six signs of politeness in Mizutani and Mizutani (1987), namely changes in intonation, use of particles at the end of sentences, use of sentences that seem hesitant, aizuchi, use of polite Japanese, and conveying the intention of the desire indirectly. Then, based on the Ide language politeness rules (1982) there are 71 utterances that ignore these rules and 35 utterances that fulfill these rules. The rules consist of being polite to people who have a high position, have more power, and to people who are older. Then, Brown and Levinson's (1987) politeness strategies used in the Shabekuri 007 program consist of negative politeness strategies, on-record strategies, positive politeness strategies, and off-record strategies. The purpose of doing these strategies is to avoid the inconvenience of the speech partner to the speech made by the speaker

Determinación del ángulo de incidencia de un proyectil disparado por arma de fuego a partir de los signos generados en el orificio de un blanco de acrílico

El presente trabajo se planteó como objetivo establecer el ángulo de incidencia con el que un proyectil penetra un blanco construido en acrílico a partir de los signos generados en el orificio. En la experiencia, se utilizó un arma de fuego de tipo pistola semiautomática calibre 9 mm, marca FM Hi–Power, con munición Luger proyectil punta ojival, de la fábrica Magtech. Luego de efectuar cada disparo, se inspeccionó físicamente mediante observación directa la superficie de acrílico impactada. Se describieron las características de las distintas muestras, las cuales se separaron en tres categorías: orificio, bisel y fracturas radiales. El análisis de la experiencia concluyó que a partir de las características encontradas en las tres categorías anteriormente mencionadas, no se puede establecer el ángulo de incidencia mediante el análisis de un solo signo. En algunos casos la combinación de ellos permite acotar a un rango de ángulos la trayectoria incidente. Este trabajo de investigación tuvo un fin criminalístico, el cual fue el reconocimiento de los signos que se generan en los ángulos de incidencia de la experiencia para luego poder acotar la posición del tirador.The present work was raised as objective to establish the incidence angle with which a projectile penetrates a built in white acrylic from the signs generated in the hole. In the experience, a firearm was used to type semi-automatic pistol caliber 9 mm, mark FM Hi-Power, with ammunition ogival Luger bullet tip, of the factory Magtech. After each shot, inspected physically through direct observation of the acrylic surface impacted. They described the characteristics of the different samples, which were separated into three categories: hole, bevel, and radial fractures. The analysis concluded that the experience from the features found in the three categories above can not be set the angle of incidence by analyzing a single sign. In some cases a combination of these allows to delimit a range of angles incident path. This research work had a criminalistic, which was the recognition of the signs that are generated in the angles of incidence of the experience and then to refine the position of the shooter.Fil: Peñaranda, Corel Yasmí

Characterizing emergency departments to improve understanding of emergency care systems

International emergency medicine aims to understand different systems of emergency care across the globe. To date, however, international emergency medicine lacks common descriptors that can encompass the wide variety of emergency care systems in different countries. The frequent use of general, system-wide indicators (e.g. the status of emergency medicine as a medical specialty or the presence of emergency medicine training programs) does not account for the diverse methods that contribute to the delivery of emergency care both within and between countries. Such indicators suggest that a uniform approach to the development and structure of emergency care is both feasible and desirable. One solution to this complex problem is to shift the focus of international studies away from system-wide characteristics of emergency care. We propose such an alternative methodology, in which studies would examine emergency department-specific characteristics to inventory the various methods by which emergency care is delivered. Such characteristics include: emergency department location, layout, time period open to patients, and patient type served. There are many more ways to describe emergency departments, but these characteristics are particularly suited to describe with common terms a wide range of sites. When combined, these four characteristics give a concise but detailed picture of how emergency care is delivered at a specific emergency department. This approach embraces the diversity of emergency care as well as the variety of individual emergency departments that deliver it, while still allowing for the aggregation of broad similarities that might help characterize a system of emergency care

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences

International audienc

MOTEMO-OUTDOOR: ensuring learning and health security during the COVID-19 pandemic through outdoor and online environments in higher education

The restriction measures put in place during the COVID-19 pandemic posed notable challenges for formal teaching-learning processes because they had to be adapted to ensure health security. An active learning programme applied to three environments (indoors, outdoors, and online) was tested with 273 undergraduate university students in a within-subjects experimental study. Each student was assigned to two indoor and two outdoor seminars, with a subsample (n = 30) also participating in online seminars implemented in response to the university's lockdown protocols. The learning experience and learning conditions were evaluated through six dimensions: learning, evaluative impact, hedonic experience, technical conditions, environmental conditions, and health security. Outdoor seminars were more effective than indoor seminars in terms of the learning experience, with greater differences in hedonic experience, while the indoor seminars were rated more highly than the outdoor seminars in terms of learning conditions, with a larger difference in the environmental conditions. No differences were found between online and face-to-face environments in terms of the learning experience, even though the online environment yielded better scores in the learning conditions. Apparently, this adaptation to both outdoor and online contexts through active methodologies allows overcoming of technical, environmental, and teaching limitations and improves health security, while ensuring a good learning experience and added flexibility to teaching-learning processes