Rule extraction in gene–disease relationship discovery

Background

Biomedical data available to researchers and clinicians have increased dramatically over the past years because of the exponential growth of knowledge in medical biology. It is difficult for curators to go through all of the unstructured documents so as to curate the information to the database. Associating genes with diseases is important because it is a fundamental challenge in human health with applications to understanding disease properties and developing new techniques for prevention, diagnosis and therapy.

Methods

Our study uses the automatic rule-learning approach to gene–disease relationship extraction. We first prepare the experimental corpus from MEDLINE and OMIM. A parser is applied to produce some grammatical information. We then learn all possible rules that discriminate relevant from irrelevant sentences. After that, we compute the scores of the learned rules in order to select rules of interest. As a result, a set of rules is generated.

Results

We produce the learned rules automatically from the 1000 positive and 1000 negative sentences. The test set includes 400 sentences composed of 200 positives and 200 negatives. Precision, recall and F-score served as our evaluation metrics. The results reveal that the maximal precision rate is 77.8% and the maximal recall rate is 63.5%. The maximal F-score is 66.9% where the precision rate is 70.6% and the recall rate is 63.5%.

Conclusions

We employ the rule-learning approach to extract gene–disease relationships. Our main contributions are to build rules automatically and to support a more complete set of rules than a manually generated one. The experiments show exhilarating results and some improving efforts will be made in the future.     

The Upper Palaeolithic site of Kalavan 1 (Armenia): An Epigravettian settlement in the Lesser Caucasus

The open-air site of Kalavan 1 is located in the Aregunyats mountain chain (at 1640 m above sea level) on the northern bank of Lake Sevan. It is the first Upper Palaeolithic site excavated in Armenia. Led by an Armenian-French team, several excavations (2005–2009) have revealed a well preserved palaeosoil, dated to around 14,000 BP (years before present), containing fauna, lithic artefacts, as well as several hearths and activity areas that structure the settlement. The initial studies enable placement of the site in its environment and justify palaeoethnological analysis of the Epigravettian human groups of the Lesser Caucasus.     

Dating the Lower to Middle Paleolithic transition in the Levant: A view from Misliya Cave,Mount Carmel,Israel

The transition from the Lower to the Middle Paleolithic in the Levant is a crucial event in human evolution, since it may involve the arrival of a new human population. In the current study, we present thermoluminescence (TL) dates obtained from 32 burnt flints retrieved from the late Lower Paleolithic (Acheulo-Yabrudian) and Early Middle Paleolithic (Mousterian) layers of Misliya Cave, Mount Carmel, Israel. Early Middle Paleolithic industries rich in Levallois and laminar products were assigned mean ages ranging from ∼250 to ∼160 ka (thousands of years ago), suggesting a production of this industry during MIS 7 and the early part of MIS 6. The mean ages obtained for the samples associated with the Acheulo-Yabrudian (strengthened by an isochron analysis) indicate a production of this cultural complex ∼250 ka ago, at the end of MIS 8. According to the Misliya TL dates, the transition from the Lower to the Middle Paleolithic in the site took place at the limit MIS 8/7 or during the early part of MIS 7. The dates, together with the pronounced differences in lithic technology strongly suggest the arrival of a new population during this period.     

Psychiatric disturbance as a consequence of abnormal periodic cardiac variation

Abstract

The relationship between cardiac rate variation, resting sinus rhythm heart rate in beats per minute, and mental state is reviewed. A small series of 12 psychiatric patients in whom these variables were studied both before and after appropriate psychiatric treatment is reported. Comparison with the periodicity of cardiac rate variation in a normal group of subjects showed that the setting of the biological clock governing cardiac rate variation in psychiatric patients is abnormal, and in these cases running at a slower frequency than that of mental health. Appropriate psychiatric therapy re‐sets this clock in patients responding to treatment, but fails to do so in those patients who remain unimproved. Resting mean sinus rhythm heart rate in beats per minute does not show this relationship.     

Time and space in the middle paleolithic: Spatial structure and occupation dynamics of seven open‐air sites

The spatial structure of archeological sites can help reconstruct the settlement dynamics of hunter‐gatherers by providing information on the number and length of occupations. This study seeks to access this information through a comparison of seven sites. These sites are open‐air and were all excavated over large spatial areas, up to 2,000 m², and are therefore ideal for spatial analysis, which was done using two complementary methods, lithic refitting and density zones. Both methods were assessed statistically using confidence intervals. The statistically significant results from each site were then compiled to evaluate trends that occur across the seven sites. These results were used to assess the “spatial consistency” of each assemblage and, through that, the number and duration of occupations. This study demonstrates that spatial analysis can be a powerful tool in research on occupation dynamics and can help disentangle the many occupations that often make up an archeological assemblage.     

Hunter‐gatherer mobility and embedded raw‐material procurement strategies in the mediterranean upper paleolithic

Since the early 1980s, the sourcing of lithic raw materials has become central to studies of the territorial range and mobility strategies of Pleistocene foraging societies. Results have been fruitful but somehow repetitive. We will discuss the embedded procurement strategy, which presumes that raw material acquisition was part of other subsistence activities rather than an autonomous technological task. We argue that this theoretical assumption, when taken as dogma, restricts the role of technology in human history and also underestimates the way some lithic resources may have affected the organization of past hunter‐gatherers. We base our discussion on the Upper Paleolithic (UP) from the Liguro‐Provençal arc, with examples from the Proto‐Aurignacian and the Epigravettian. Our regional record shows that in this context the movement of rocks over distances greater than 100 km was the norm rather than the exception. We argue that these long‐distance procurements mirror technical needs that were oriented toward the selection of high‐quality flints. We support the hypothesis that indirect procurement was an important component of regional socio‐economic networks.     

怀来盆地西沟湾1号旧石器地点试掘简报

西沟湾1号旧石器地点位于河北省张家口市怀来县官厅镇珠窝园村,埋藏于永定河右岸第二级阶地后缘。2015年8-9月对该地点进行试掘,揭露面积约27m2,出土232件石制品和19件动物化石。石制品原料以粗面岩为主,应为就地取材;类型包括石核、石片、断块等,标本大小总体以小型为主;石核剥片均采用硬锤锤击法。石制品的类型和技术特征显示其总体属于石片石器技术体系。结合遗物和堆积状况,推测西沟湾1号地点为一处原地埋藏类型的临时性石制品剥片场所。依碳十四年代测定,初步推断该地点的时代为旧石器时代晚期。     

数据科学在旧石器考古学中的应用

从考古学诞生之初,对抽象数据的解读与分析就一直伴随。对于旧石器考古学而言,“人工制品”成为了传达史前物质文化信息的主要载体,对人工制品中所提取的数据进行科学解读,成为了复原古代人类历史的关键步骤。数据科学在旧石器考古学中的应用具有三个主要因素,分别是数理统计学、计算机应用,以及旧石器考古学的基础数据与核心科学问题以及理论知识,即采用某种或多种逻辑将旧石器考古学领域的数据进行基于计算机平台的数理统计,并借助计算机语言对庞大的数据进行快速计算,从而帮助我们解释和重建史前人类社会。在目前的旧石器考古学领域,研究者们已经不再满足于对标本所进行的基础的描述性信息统计,对数据进行科学的处理并系统解读的诉求前所未有的强烈,这种诉求不断推动着学科的发展,深化了我们原本对史前社会的认识,甚至开拓出了新的研究领域,极大地推动了旧石器考古学的发展。本文就数据科学的概念、技术路线,以及在旧石器考古学中的应用历史与发展前景做详细介绍,希望通过系统性的梳理,使更多读者熟悉相关的研究手段与具体技术,使更多考古学者对数据科学的应用产生兴趣,从而应用于相关的项目研究中。     

Signification des technologies bifaciales au Paléolithique moyen des montagnes de l’Altaï

Previously the single bifacial tools found in different industrial variants of the Altai Middle Paleolithic (Sibiryachikha and Kara-bom) were not considered to be cultural markers that could be used to differentiate the technological/cultural variants, but rather a bright, but situational manifestation of the typological variability, especially in the case of the Sibiryachika assemblages. As a result of recent studies of Chagyrskaya Cave, the key-site of Sibiryachikha, it was found that all the bifaces are made using plano-convex technology. In the Chagyrskaya Cave assemblage all stages of bifacial production have been found: pre-forms, bifacial tools and tools made on the bifacial thinning flakes, accompanied by numerous bifacial thinning flakes and bifacial thinning chips. A preliminary study of the bifaces from the second Sibiryachikha site, Okladnikov Cave evidenced the use of the same plano-convex technology. On the other hand, in the Kara-bom complexes (Kara-Bom, Ust-Karakol-1, Anuy-3), all bifacial tools are made using bi-convex bifacial technology. Thus, the criteria for the technological distinction of bifacial production assume special importance as a cultural marker that allows the differentiation the Altai Middle Paleolithic technological variants. Taking into account the fact that Chagyrskaya Cave and Okladnikov Cave are associated only with Neanderthal remains, it can be assumed that bifacial plano-convexe technology in the Middle Paleolithic of Altai is linked to the appearance and existence of their population in the region.     

Le site Paléolithique supérieur de Yudinovo : résultats des recherches archéologiques des années 2004–2016

The Upper Palaeolithic site of Yudinovo is one of the reference sites, located in the Desna River Basin. Multidisciplinary field studies, organized by the Desna mission (MAE RAS) and conducted between 2004 and 2016, have changed the vision existed so far on the structure and character of the Yudinovo site as well as on the duration of its occupations. The researchers found an ancient ford used by mammoths and other big mammals to cross the river, and a water source was one of the main factors in explaining the location of the Yudinovo site. The site has been occupied in a cyclical way for stays of varied duration. It was frequented by Prehistoric Men during the different seasons, and periods of occupation were apparently of different duration. The stratigraphy of the Yudinovo site reveals two major episodes in the evolution of the site. The dating of the lower archaeological layer dates back to 15,000–13,500 BC. J.C., while the upper layer is attributed to the period of 12,500–12,000 BC. The lower layer, which was formed during the major episode of occupation of the site, is rather thin and shows the complex stratigraphic structure. Various areas of activities, evacuation structures, storage areas with mammoth bones are discovered. Some elements of the lower archaeological layer are perfectly correlated with different episodes of sporadic occupation.