Exploring supervised and unsupervised methods to detect topics in biomedical text

Background  

Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language processing tasks including information retrieval, text summarization and question answering; and is a necessary step towards the building of an information system that provides an efficient way for biologists to seek information from an ocean of literature.     

谈细胞生物学启发讨论式教学中的问题设置

启发讨论式教学是素质教育对各科教学的新要求。问题设置是启发讨论式教学中的关键环节。探讨了细胞生物学启发讨论式教学中问题设置的基本方式及其应注意的几个方面。     

Protein translation, 2007

Translation of RNA to protein is essential for life. It should perhaps not be surprising, therefore, that appropriate regulation of translation plays a key role in determining longevity. This Hot Topic article discusses papers published in the last year related to the importance of translation and its regulation by signaling through the target of rapamycin kinase, in modulating aging and age-associated diseases.     

Does the basement membrane control the mitotic activity of the inner dental epithelium of the embryonic mouse first lower molar

In cultured first lower mouse molars, the mitotic index (MI) of the inner dental epithelium was significantly higher than that of the outer dental epithelium (ODE). Trypsin treatment of tooth germs had no effects on the MI. In heterotopic associations between ODE and trypsin-isolated dental papilla, the MI increased in comparison with the MI of ODE in isotopic associations between IDE and dental papilla. In heterotopic associations between ODE and EDTA-isolated dental papilla which remained covered by a continuous, intact basement membrane, the MI and the labeling index of ODE were significantly higher than those in heterotopic associations of ODE with trypsin-isolated dental papilla. The possible role of the dental papilla in the control of the cell kinetics of the dental epithelium via mesenchyme-dependent modifications of the BM is discussed.     

Finding academic concerns of the Three Gorges Project based on a topic modeling approach

The Three Gorges Project (TGP) has gone into the overall completion acceptance stage in 2014. As the world's largest hydropower project, the TGP has attracted worldwide attention over the past few decades. Previous studies mainly focused on a single aspect, such as engineering technologies, social impacts and environmental impacts, of the TGP. However, a large-scale review gathering systematic data to find academic concerns about the TGP is missing. Topic model is a text mining approach for discovering latent topics in a collection of documents. In this article, an emerging topic modeling approach, Latent Dirichlet Allocation (LDA), was introduced to uncover the intellectual structure of the academic literature focusing on the TGP. A collection of 8280 Chinese research articles highly related to the TGP was established with a time frame ranging from 2001 to 2013, and an 18-topic model was used to describe the intellectual structure. Two novel bibliometric indicators, including topic proportion and topic trend, were constructed to describe the academic concerns of the TGP. Topic proportion analysis shows that post-construction issues, including the social and environmental impacts brought by the TGP, have attracted more attention than the construction issues. “Ecology”, “Reservoir Operation”, “Land Administration”, and “Water Pollution”, have become the dominant research topics regarding the TGP during these years. Meanwhile, “Construction Technology” and “Design”, have gradually lost scholars’ interest. The results show that the approach reported in this study can provide sound and credible conclusions of the major academic concerns for a hydropower project. The topic modeling approach is expected to be widely applied as a methodological strategy in future hydropower and other infrastructure project assessment.     

Fate map of the dental mesenchyme: dynamic development of the dental papilla and follicle

At the bud stage of tooth development the neural crest derived mesenchyme condenses around the dental epithelium. As the tooth germ develops and proceeds to the cap stage, the epithelial cervical loops grow and appear to wrap around the condensed mesenchyme, enclosing the cells of the forming dental papilla. We have fate mapped the dental mesenchyme, using in vitro tissue culture combined with vital cell labelling and tissue grafting, and show that the dental mesenchyme is a much more dynamic population then previously suggested. At the bud stage the mesenchymal cells adjacent to the tip of the bud form both the dental papilla and dental follicle. At the early cap stage a small population of highly proliferative mesenchymal cells in close proximity to the inner dental epithelium and primary enamel knot provide the major contribution to the dental papilla. These cells are located between the cervical loops, within a region we have called the body of the enamel organ, and proliferate in concert with the epithelium to create the dental papilla. The condensed dental mesenchymal cells that are not located between the body of the enamel organ, and therefore are at a distance from the primary enamel knot, contribute to the dental follicle, and also the apical part of the papilla, where the roots will ultimately develop. Some cells in the presumptive dental papilla at the cap stage contribute to the follicle at the bell stage, indicating that the dental papilla and dental follicle are still not defined populations at this stage. These lineage-tracing experiments highlight the difficulty of targeting the papilla and presumptive odontoblasts at early stages of tooth development. We show that at the cap stage, cells destined to form the follicle are still competent to form dental papilla specific cell types, such as odontoblasts, and produce dentin, if placed in contact with the inner dental epithelium. Cell fate of the dental mesenchyme at this stage is therefore determined by the epithelium.     

Study on the relationship between Helicobacter pylori in the dental plaque and the occurrence of dental caries or oral hygiene index

Background: The aims of our study were to determine the presence of Helicobacter pylori DNA in the dental plaque of Chinese children aged 3–6 years by nested polymerase chain reaction (PCR) and to investigate the relationship between this infection and the occurrence of dental caries or oral hygiene index.
Methods: Two hundred and fourteen children from a kindergarten in Guangzhou City of China were evaluated. The children's plaques were assessed by plaque indices of Quigley–Hein. Dental plaque was analyzed using nested PCR for two sets of primers directed to the 860-bp fragment of H. pylori genomic DNA, which have been reported to be highly sensitive and specific by other researchers.
Results: H. pylori was detected in dental plaque samples from 126 children, and 70 children with dental caries carried H. pylori in dental plaque. Of these children without infection, only 36 of 88 suffered dental caries. Besides, the average dental plaque index of 126 H. pylori -positive children was higher than that of 88 children without infection. In the present study, there was a significant correlation between H. pylori infection and dental caries or dental hygiene.
Conclusion: The oral cavity may be a reservoir for H. pylori infection in children. H. pylori in dental plaque may play a role in the occurrence of dental caries, and poor oral hygiene may represent a risk factor for H. pylori in the oral cavity.     

Dental Care for the Elderly

The geriatric population in many parts of the United States is underserved by dentistry. Socioeconomic problems, difficult access to dental facilities, and confusion about the need for dental care often prevent the elderly from seeking dental service. Because dental diseases are not life threatening or outwardly disabling, administrators of institutions for the elderly and health legislators place a low priority on dental care for the elderly. These factors working in concert with the insidious, progressive, and cummulative nature of denture diseases contribute to the poor dental health experienced by some segments of the geriatric population. Dentistry has the manpower and the technology to improve the oral health of the elderly, but society must be made aware of the importance of dental health in the total health of elderly persons in order that dentistry be given a chance to achieve that goal.     

Temporospatial tissue interactions regulating the regeneration of the enamel knot in the developing mouse tooth

The enamel knot (EK), which is a transient signaling center in the tooth germ, regulates both the differential growth of the dental epithelium and the tooth shape. In this study, the regeneration of the EK was evaluated. The EK regions were removed from the E14 and E16 dental epithelia, and the remaining epithelia were recombined with their original dental mesenchymes. All these tooth germs could develop into calcified teeth after being transplanted into the kidney capsule for 3 weeks. One primary EK was regenerated earlier, and two or three secondary EKs were regenerated later in culture. When simply recombined without removing the EK, the tooth germ, which had four secondary EKs and four cuspal areas of the dental papilla, generated one primary EK first and subsequent secondary EKs. These results indicate that the patterning of the EK in all tooth germs always starts from a primary EK independent of the direct epithelial or mesenchymal control. This suggests that neither the dental epithelium nor the dental mesenchyme can dictate the pattern or number of the EK formation, but the interaction between the dental epithelium and the dental mesenchyme is essential for the regeneration and patterning of the EKs.     

秦岭野生大熊猫牙齿的形态机能

大熊猫(Ailuropoda melanoleuca)是国家一级保护动物,被誉为国宝.牙齿作为大熊猫消化器官之一,相对于其他动物而言,大熊猫牙齿有其自身的构造特点.以往学者和专家对大熊猫牙齿形态的研究侧重于为大熊猫的种群分类寻找根据(Dvadi,1869; Milne-Edwards,1870;王将克,1974),更多关注牙齿在大熊猫进化、演变过程中的意义(王令红等,1982;黄万波,1993).研究的齿位大多局限于臼齿(张鹤宇和刘理,1959),所得结果或数据并不详细和全面.此外,还有一些学者对大熊猫牙齿釉质的超微组织结构进行研究(赵资奎等,1984 ).     

济南大辛庄遗址商代居民的牙齿疾病

大辛庄遗址位于济南市历城区大辛庄村,是山东省内已知面积最大的一处商代遗址,甲骨文及其他丰富遗存的出土对于鲁北及整个山东地区商文化研究具有重要意义。本文主要从人骨的牙齿健康状况入手,对济南大辛庄商代遗址2003、2010年出土的45例人骨标本的牙病情况,尤其是龋病、牙周病、牙结石以及牙齿磨耗情况进行统计与分析,得知大辛遗址商代人群牙齿疾病的基本情况:1)牙结石的出现率男女之间存在明显的性别差异,除此之外其他牙病在罹患率的性别分组上的差异不显著,但均为女性的罹患率要高于男性;2)牙病的罹患率在年龄分组上存在显著差异,随年龄的增长罹患牙病的风险增高;3)龋病、牙周病及牙结石多好发于臼齿;4)重度磨耗牙齿患牙病的风险增加,牙周病表现尤为明显;5)牙病的罹患率不仅受到性别、年龄、牙位以及齿冠磨耗程度的影响,而且与大辛庄商代人群农业经济发展的食物结构有关。     

Role of dental pulp in the histogenesis of the enamel organ]

The histological study of in vitro cultured associations between dental pulps and outer dental epithelium showed that the predontoblasts initiated the histogenesis of the enamel organ and particularly the differentiation of the inner dental epithelium.     

Inhibition of enzymes of insecticide detoxication in insects by an alkylating analog of a cytochrome P-450 substrate

It was shown that the alkylating analog of cytochrome P-450 substrate - 4-bromomethyl-2,2,5,5-tetramethyl-3-imidazoline-3-oxide-1-oxyl effectively inhibits in vitro the activities of monooxygenases, glutathione-S-transferases and esterases from the abdomen of the house fly Musca domestica L. The non-alkylating analog (RH) appeared to be a very weak inhibitor of these enzymes. It was demonstrated that the inhibitory action of the alkylating analog consists in its covalent binding to the enzyme protein. Topical application of the cytochrome P-450 alkylating analog on insects led to a decrease of the enzyme activity by approximately 20%.     

The distribution and ultrastructure of the forming blood capillaries and the effect of apoptosis on vascularization in mouse embryonic molar mesenchyme

Vascularization is essential for organ and tissue development. Teeth develop through interactions between epithelium and mesenchyme. The developing capillaries in the enamel organ, the dental epithelial structure, occur simultaneously by mechanisms of vasculogenesis and angiogenesis at the onset of dentinogenesis. The vascular neoformation in the dental mesenchyme has been reported to start from the cap stage. However, the mechanisms of vascularization in the dental mesenchyme remain unknown. In the hope of understanding the mechanisms of the formation of dental mesenchymal vasculature, mouse lower molar germs from embryonic day (E) 13.5 to E16.5 were processed for immunostaining of CD31 and CD34, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) and transmission electron microscopy (TEM). In addition, the role of apoptosis for the vascularization in dental mesenchyme was examined by in vitro culture of E14.0 lower molars in the presence of the apoptosis inhibitor (z-VAD-fmk) and a subsequent subrenal culture. Our results showed that CD31- and CD34-positive cells progressively entered the central part of the dental papilla from the peridental mesenchyme. For TEM, angioblasts, young capillaries with thick endothelium and endothelial cells containing vacuoles were observed in peripheral dental mesenchyme, suggesting vasculogenesis was taking place. The presence of lateral sprouting, cytoplasmic filopodia and transluminal bridges in the dental papilla suggested angiogenesis was also occurring. Inhibition of apoptosis delayed the angiogenic vascularization of the dental papilla. Therefore, these data demonstrated that molar mesenchyme is progressively vascularized by mechanisms of both vasculogenesis and angiogenesis and apoptosis partially contributes to the vascularization of the dental papilla.     

Changing trends in the outpatient dental visits during the COVID – 19 pandemic in a tertiary care hospital

The coronavirus pandemic has caused a global public health crisis with an unprecedented shutdown of major establishments and non-emergency services. Disruptions across the country in dental hospitals led to challenges in addressing patient’s dental complaints. The present study aimed to analyse the difference in the pattern of the Outpatient dental visits during the pandemic period in comparison to that of the pre-pandemic period in a tertiary care hospital. This retrospective study was carried out by retrieving the patient data from the diagnostic register of the Department of Oral Medicine and Radiology for a period of one year. The data that was retrieved from 24th September 2019 to 23rd March 2020 was categorized under the pre-pandemic period and the data from 24th March 2020 to 24th September 2020 was grouped under the pandemic period. Patient data regarding the age, gender and clinical diagnosis was recorded and categorized under three main categories: “Emergency”, “urgent” and “elective”. 7550 patients during pre-pandemic period and 4035 patients during the pandemic period visited the dental hospital during the study period. Under the “emergency dental care” category, during the pre-pandemic period, majority of the cases reported of acute dental pain (71.0%) followed by cellulitis and space infection (20.1%) and maxillofacial trauma (8.7%). During the pandemic period, acute dental pain consisted of all emergency visits (n = 307). The proportion of emergency dental visits during the pandemic were significantly higher than the pre-pandemic period. Elective dental visits were significantly higher during pre-pandemic period in comparison to the pandemic period. (P < 0.001). There was a notable change in the outpatient trend of the dental visits during the COVID-19 pandemic in comparison to the pre-pandemic period. Emergency dental services were utilized at a higher rate during the pandemic period in comparison to the pre-pandemic counterpart.     

Negritos, Australian aborigines, and the "proto-sundadont" dental pattern: the basic populations in east Asia, V.

Five evolutionarily significant dental traits were identified from a B-square distance analysis of nine crown characters recorded for several populations of East Asia and Oceania. Intergroup variation in these traits distinguishes three major divisions of the Mongoloid dental complex: sundadonty, sinodonty, and the dental pattern of Australian Aborigines. The Australian crown features may be characterized as having high frequencies of evolutionarily conservative characters. Negritos, one of the probable representatives of indigenous inhabitants of Southeast Asia who may have shared a common ancestor with Australians, possess the more derived sundadont dental pattern. As far as the five crown traits treated here are concerned, Australian dental features may be described as conforming to a "proto-sundadont" dental pattern, applying Turner's terminology. This pattern may represent a microevolutionary step prior to the emergence of the sundadont and sinodont patterns.     

Self-Assessed General Health and Dental Status Among the Elderly in a Swedish County

A random sample of non-institutionalized elderly people in Örebro County, Sweden, has been examined. The present paper reports on the general health conditions obtained from interviews in this population and on the relation between general health and dental status. Eighty-one percent of the clinically examined subjects considered that they were healthy or fairly healthy. A higher percentage of women as compared to men regarded themselves to be moderately or very ill. Women also used more drugs than men did. Only 6% did not feel strong enough for extensive dental treatment. Physically handicapped people used dental services less than the rest of the population did. Otherwise, general health seemed to have limited influence on the use of dental services. Subjects with better dental status reported less frequent illness, chronic diseases, and medication as compared to subjects with poorer dental status. The self-assessed general health, also in the presence of age, sex, and residence variables, showed significant correlation with the dental status but not if socio-economic variables were also included in a regression model.     

Relationship between vestibular lamina, dental lamina, and the developing oral vestibule in the upper jaw of the field vole (Microtus agrestis, Rodentia)

Formation of the oral vestibule is ignored in most studies on tooth development, although dental and vestibular lamina are closely related to each other. Knowledge about morphogenetic processes shaping the oral vestibule is missing almost completely. The aim of this study was to assess the developmental relationship between dental and vestibular lamina as well as formation of the oral vestibule in the upper jaw of the field vole (Microtus agrestis), a small rodent representing an attractive model species for comparative dental studies. Three-dimensional reconstruction revealed that the upper vestibular lamina of the vole joins the antemolar part of the diastemal dental lamina, similar to mouse. Later, this lamina complex regresses and the vestibular lamina is separated from the molar epithelium. Participation of the vestibular lamina in dental lamina formation, as hypothesized for mouse, therefore remains unclear. Except for increased apoptosis in the regressing diastemal dental lamina, spatial segregation of mitoses or apoptoses could be detected neither in the jaw arch epithelium nor in the adjacent mesenchyme. Therefore, in contrast to tooth primordia, apoptosis and mitosis seem to play a minor role in shaping of the upper oral vestibule. The buccal vestibule develops secondarily, probably in consequence of general growth of the head and localized differentiation of cells.     

The effect of colchicine on protein secretion by differentiating odontoblasts and ameloblasts in the hamster tooth in vitro as shown by radioautography with 3H-proline

Summary We have examined radioautographically the protein synthetic and secretory activity of differentiating odontoblasts and ameloblasts, exposed for 9 h in vitro to various concentrations of colchicine in the presence of ³H-proline. Colchicine impairs the cytodifferentiation of the dental epithelium into ameloblasts and of the dental mesenchyme into odontoblasts; the effects depend on the dose. However, denial epithelial cells are more sensitive to the drug than dental mesenchymal cells. In stages prior to odontoblast differentiation, colchicine enhances the number of radioautographic grains over the dental epithelium without changing the grain counts over the dental basement membrane area: This suggests that in vitro the dental epithelium synthesizes and secretes proline-containing components that are not constituents of the dental basement membrane. Also, during the subsequent stages of ameloblast differentiation colchicine increases the number of radioautographic grains over the preameloblasts. The present data suggest that the primary in vitro target of colchicine is not the dental mesenchyme, but the dental epithelium. The data also indicate that differentiating ameloblasts synthesize and secrete significant amounts of proteins in vitro prior to the first deposition of enamel.