Utility and features of a customized PC Windows-based relational database for managing microbial strain data

In addition to storing microbes, culture collections in industry, government or universities manage a vast and continuously expanding library of information on strain history and properties. An efficient and cost-effective computer database system is required for entering, analyzing and searching these data. This report describes the utility and features of a comprehensive database which consists of a commercially available relational database system combined with customized screens for data entry, viewing and report generation. The application was developed using Microsoft Access and Visual Basic to operate in the Windows environment on a local area network. Received 18 June 1997/ Accepted in revised form 21 November 1997     

Fish-AMAZBOL: a database on freshwater fishes of the Bolivian Amazon

The Bolivian part of the Amazon Basin contains a mega diverse and well-preserved fish fauna. Since the last decade, this fish fauna has received an increasing attention from scientists and the national authorities as fishes represent one of the most important sources of proteins for local human communities. However, this fish fauna still remains poorly documented. Here, we present a database for fishes from the Bolivian Amazon. To build the database, we conducted an extensive literature survey of native and non-native (exotic) fishes inhabiting all major sub-drainages of the Bolivian Amazon. The database, named Fish-AMAZBOL, contains species lists for 13 Amazonian hydrological units, covering 100% of the Bolivian Amazon and approximately 65% (722,137 km²) of the all territory. Fish-AMAZBOL includes 802 valid species, 12 of them being non-native, that have been checked for systematic reliability and consistency. To put this number in perspective, this represents around 14% of the all Neotropical ichthyofauna and around 6% of all strictly freshwater fishes inhabiting the planet. This database is currently the most comprehensive database of native and non-native fish species richness available so far for the Bolivian Amazon.     

Converse Bergmann cline in a Eucalyptus herbivore,Paropsis atomaria Olivier (Coleoptera: Chrysomelidae): phenotypic plasticity or local adaptation?

Aim  To measure latitude-related body size variation in field-collected Paropsis atomaria Olivier (Coleoptera: Chrysomelidae) individuals and to conduct common-garden experiments to determine whether such variation is due to phenotypic plasticity or local adaptation.
Location  Four collection sites from the east coast of Australia were selected for our present field collections: Canberra (latitude 35°19' S), Bangalow (latitude 28°43' S), Beerburrum (latitude 26°58' S) and Lowmead (latitude 24°29' S). Museum specimens collected over the past 100 years and covering the same geographical area as the present field collections came from one state, one national and one private collection.
Methods  Body size (pronotum width) was measured for 118 field-collected beetles and 302 specimens from collections. We then reared larvae from the latitudinal extremes (Canberra and Lowmead) to determine whether the size cline was the result of phenotypic plasticity or evolved differences (= local adaptation) between sites.
Results  Beetles decreased in size with increasing latitude, representing a converse Bergmann cline. A decrease in developmental temperature produced larger adults for both Lowmead (low latitude) and Canberra (high latitude) individuals, and those from Lowmead were larger than those from Canberra when reared under identical conditions.
Main conclusions  The converse Bergmann cline in P. atomaria is likely to be the result of local adaptation to season length.     

An image analysis protocol for the quantification of interglobular dentine in anthropological tooth sections

The histological identification of interglobular dentine (IGD) in archeological human remains with macroscopic evidence of rickets has opened a promising new avenue for the investigation of metabolic disease in the past. Recent paleopathological studies have shown that histological analysis of archeological human teeth may allow the identification of periods of vitamin D deficiency occurring within very narrow developmental windows, yielding new information on the seasonality or even maternal‐fetal transmission of this disease. However, currently available techniques for recording IGD rely on subjective scoring systems or visual estimations, potentially leaving them open to inter and intra‐observer error and rendering comparisons of datasets difficult. Here we describe a new imaging protocol that utilizes open access software and may yield more objective and quantitative data on the amount of IGD present within a dentinal region of interest. We demonstrate that grayscale histograms in FIJI®/ImageJ® might be used to provide less subjective estimates of the percentage of a region of interest affected by IGD. Application of this technique may enable more accurate comparison of datasets between researchers.     

全球健康史项目亚洲模块——亚洲古代人群健康、疾病和生活方式的大数据

“全球健康史项目”探导新石器时期以来人类的疾病史,以前所未有的大数据研究方式回顾近代人类的历史,来衡量人类的生活质量和人类在充满挑战的生活条件下的适应能力。我们于2018年5月启动了全球健康史项目亚洲模块,将这个起源于美洲和欧洲的宏伟的项目扩展到亚洲。在全球健康史项目中纳入亚洲数据,不仅可以从进化的角度丰富近代人类演化历史上的第一手骨骼和口腔健康状况,还可以为健康政策制定的视野提供历史性的深度。     

Cell-culture Database: Literature-based reference tool for human and mammalian experimentallybased cell culture applications

Cultivation of primary cells is essential for biotechnological research and viral vaccine production. Significant advances in cell and tissue culture, more specifically, advances in the transfection and transduction of human and mammalian cells, has directly led to giant leaps forward in fields such as cancer research, genetics, and public health. At the same time, a corresponding increase has been seen in available cell culture related literature. Often times, due to the sheer number and degree of variability of available literature, it is a challenge to find specific, yet practical cell culture related information.To respond to this rising tide of information, a practical, user-friendly database containing cell-lines, plasmids, vectors, selection agents, concentrations and media was created. The database currently consists of over 3,900 cell lines (Human and Mammalian) and 1,900 plasmids/vectors collected from 2,700 pieces of published literature. The database is continually being expanded and it is hoped that through the continual addition of unique data, the database can further serve and enrich the work of cell and molecular biologists, life-science professionals, and the worldwide scientific community at large. AVAILABILITY: The database is available for free at http://cell-lines.toku-e.com/     

Conservation Genetic Resources for Effective Species Survival (ConGRESS): Bridging the divide between conservation research and practice

Policy makers and managers are increasingly called upon to assess the state of biodiversity, and make decisions regarding potential interventions. Genetic tools are well-recognised in the research community as a powerful approach to evaluate species and population status, reveal ecological and demographic processes, and inform nature conservation decisions. The wealth of genetic data and power of genetic methods are rapidly growing, but the consideration of genetic information and concerns in policy and management is limited by the currently low capacity of decision-makers to access and apply genetic resources. Here we describe a freely available, user-friendly online resource for decision-makers at local and national levels (http://congressgenetics.eu), which increases access to current knowledge, facilitates implementation of studies and interpretation of available data, and fosters collaboration between researchers and practitioners. This resource was created in partnership with conservation practitioners across the European Union, and includes a spectrum of taxa, ecosystems and conservation issues. Our goals here are to (1) introduce the rationale and context, (2) describe the specific tools (knowledge summaries, publications database, decision making tool, project planning tool, forum, community directory), and the challenges they help solve, and (3) summarise lessons learned. This article provides an outlook and model for similar efforts to build policy and management capacity.     

Reintroduced Eurasian beavers (<Emphasis Type="Italic">Castor fiber</Emphasis>): colonization and range expansion across human-dominated landscapes

The protected Eurasian beaver Castor fiber is recolonizing its former range hereby entering human-dominated landscapes. This ecosystem engineer can cause considerable damage to human infrastructures and agriculture, by feeding, digging and damming. To prevent human–wildlife conflict and ensure continued support from the local residents, a better understanding of habitat selection is required. By using species distribution models (SDMs) to quantify habitat requirements in our study area in Flanders, Belgium, based on 1792 occurrence data from 71 territories, and a fine-scale land use and vegetation map, we explored the potential for future beaver settlements. The results indicate that even in a highly human-dominated landscape, there is sufficient habitat available to support beaver populations. We highlight the importance of distance to water, willow stands, wetland vegetation and poplar trees. We show that there is currently sufficient habitat to support 924 territories (619–1515, 90% confidence interval) in Flanders (but this does not imply these locations are conflict-free). Our findings indicate that 12 year after the reintroduction, there continues to be a large expansion potential, both in range and in densities within the currently recolonized area. Our results can be used as a management tool in order to evaluate possible risks linked with the return of beavers in a human dominated landscape. At these critical locations, increased monitoring or structural measures can prevent conflicts. By preventing or quickly resolving human wildlife conflicts, long-term coexistence between humans and beavers can be achieved.     

Database and software for the analysis of mutations at the human hprt gene.

A computerized database containing DNA sequence information regarding human HPRT mutants has been created. The database itself is in the dBASE format and contains information on about 1500 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet.     

Database and software for the analysis of mutations at the human p53 gene.

A computerized database containing DNA sequence information regarding human p53 mutants has been created. The database itself is in the dBASE format and contains information on nearly 3000 mutants. In addition, an IBM PC compatible software package to analyze the information in the database has been developed. Both the database and software are freely available via the Internet.     

The Italian Twin Project: from the personal identification number to a national twin registry.

The unique opportunity given by the "fiscal code", an alphanumeric identification with demographic information on any single person residing in Italy, introduced in 1976 by the Ministry of Finance, allowed a database of all potential Italian twins to be created. This database contains up to now name, surname, date and place of birth and home address of about 1,300,000 "possible twins". Even though we estimated an excess of 40% of pseudo-twins, this still is the world's largest twin population ever collected. The database of possible twins is currently used in population-based studies on multiple sclerosis, Alzheimer's disease, celiac disease, and type 1 diabetes. A system is currently being developed for linking the database with data from mortality and cancer registries. In 2001, the Italian Government, through the Ministry of Health, financed a broad national research program on twin studies, including the establishment of a national twin registry. Among all the possible twins, a sample of 500,000 individuals are going to be contacted and we expect to enrol around 120,000 real twin pairs in a formal Twin Registry. According to available financial resources, a sub sample of the enrolled population will be asked to donate DNA. A biological bank from twins will be then implemented, guaranteeing information on future etiological questions regarding genetic and modifiable factors for physical impairment and disability, cancers, cardiovascular diseases and other age related chronic illnesses.     

Water consumption in Iron Age,Roman, and Early Medieval Croatia

Patterns of water consumption by past human populations are rarely considered, yet drinking behavior is socially mediated and access to water sources is often socially controlled. Oxygen isotope analysis of archeological human remains is commonly used to identify migrants in the archeological record, but it can also be used to consider water itself, as this technique documents water consumption rather than migration directly. Here, we report an oxygen isotope study of humans and animals from coastal regions of Croatia in the Iron Age, Roman, and Early Medieval periods. The results show that while faunal values have little diachronic variation, the human data vary through time, and there are wide ranges of values within each period. Our interpretation is that this is not solely a result of mobility, but that human behavior can and did lead to human oxygen isotope ratios that are different from that expected from consumption of local precipitation. Am J Phys Anthropol 154:535–543, 2014. © 2014 Wiley Periodicals, Inc.     

An integrated database on ticks and tick-borne zoonoses in the tropics and subtropics with special reference to developing and emerging countries

Tick-borne zoonoses (TBZ) are emerging diseases worldwide. A large amount of information (e.g. case reports, results of epidemiological surveillance, etc.) is dispersed through various reference sources (ISI and non-ISI journals, conference proceedings, technical reports, etc.). An integrated database-derived from the ICTTD-3 project ( http://www.icttd.nl )-was developed in order to gather TBZ records in the (sub-)tropics, collected both by the authors and collaborators worldwide. A dedicated website ( http://www.tickbornezoonoses.org ) was created to promote collaboration and circulate information. Data collected are made freely available to researchers for analysis by spatial methods, integrating mapped ecological factors for predicting TBZ risk. The authors present the assembly process of the TBZ database: the compilation of an updated list of TBZ relevant for (sub-)tropics, the database design and its structure, the method of bibliographic search, the assessment of spatial precision of geo-referenced records. At the time of writing, 725 records extracted from 337 publications related to 59 countries in the (sub-)tropics, have been entered in the database. TBZ distribution maps were also produced. Imported cases have been also accounted for. The most important datasets with geo-referenced records were those on Spotted Fever Group rickettsiosis in Latin-America and Crimean-Congo Haemorrhagic Fever in Africa. The authors stress the need for international collaboration in data collection to update and improve the database. Supervision of data entered remains always necessary. Means to foster collaboration are discussed. The paper is also intended to describe the challenges encountered to assemble spatial data from various sources and to help develop similar data collections.     

What does it mean to be wild? Assessing human influence on the environments of nonhuman primate specimens in museum collections

ObjectivesNatural history collections are often thought to represent environments in a pristine natural state—free from human intervention—the so‐called “wild.” In this study, we aim to assess the level of human influence represented by natural history collections of wild‐collected primates over 120 years at the Smithsonian Institution''s National Museum of Natural History (NMNH).Materials and MethodsOur sample consisted of 875 catarrhine primate specimens in NMNH collections, representing 13 genera collected in 39 countries from 1882 to 2004. Using archival and accession information we determined the approximate locations from which specimens were collected. We then plotted location coordinates onto publicly available anthrome maps created by Ellis et al. (Global Ecology and Biogeography, 2010, 19, 589), which delineate terrestrial biomes of human population density and land use worldwide since the 1700s.ResultsWe found that among primates collected from their native ranges, 92% were from an environment that had some level of human impact, suggesting that the majority of presumed wild‐collected primate specimens lived in an environment influenced by humans during their lifetimes.DiscussionThe degree to which human‐modified environments may have impacted the lives of primates currently held in museum collections has been historically ignored, implicating unforeseen consequences for collection‐based research. While unique effects related to commensalism with humans remain understudied, effects currently attributed to natural phenomena may, in fact, be related to anthropogenic pressures on unmanaged populations of primates.     

Rethinking the links between systematic studies and ex situ living collections as a contribution to the Global Strategy for Plant Conservation

The Muséum national d’histoire naturelle (MNHN) in Paris holds ca. 70 million specimens. The collections were in need of a strategy to ensure their long-term conservation. We discuss how the Department of Botanical and Zoological Gardens (DJBZ; tropical living collections), and the Department of Systematics and Evolution (DSE; herbarium) contribute to achieving GSPC’s Target 1 (‘a widely accessible working list of known plant species as a step towards a complete world flora’). The DJBZ started encouraging better management of the collections, evolving towards focused reference collections, where all specimens have well-documented collection data. The objective is to link all collections to a scientific referee. This has already been achieved for a number of taxa. The herbarium of the DSE (acronym P) is among the world’s largest (11 million specimens, including 400,000 types). The collection’s heterogeneity impedes access to its data, since P is a mix of recent well-documented collections and historical collections at various curational levels. P is currently under renovation, which started by mounting all ca. 2 million unmounted specimens. The project also includes databasing and imaging of every specimen. The database now holds around 1,000,000 records. For taxonomic studies, living collections are crucial, especially for plants that are not easily preserved as herbarium specimens. Living collections also enable studies impossible to forecast at the time of collecting. Herbaria and living collections should therefore be conceived as interoperable entities requiring common scientific curation. Through a combination of its assets and the expertise of its researchers, the MNHN is well prepared to tackle the new objectives of the GSPC beyond 2010.     

Current LCA database development in Japan -results of the LCA project

In 1998, the Japan’s Ministry of Economy, Trade, and Industry (METI) launched a five-year national project entitled ‘Development of Life Cycle Impact Assessment for Products’ (commonly known as ‘the LCA Project’). The purpose of the project is to develop common LCA methodology as well as a highly reliable database that can be shared in Japan. Activities over these five years have resulted in the supply of LCI data on some 250 products. Industrial associations voluntarily provided data. The results of these activities are currently being made available on the Internet on a trial basis in the form of an LCA database. In addition, a method entitled ‘Life-cycle Impact assessment Method based on Endpoint modeling (LIME)’ was developed. It is expected that these results will be widely used in Japan in the future. This paper presents an outline of the results of the research and development that has been conducted in the LCA Project in Japan.     

李济先生与周口店研究：纪念李济先生诞辰100周年

李济先生是中国考古学的奠基人,中国第一位人类学家。他毕生从事考古学研究,著作等身,桃李满天下。他的功绩主要体现在安阳殷墟的发掘与研究上,考古学的其他方面亦建树甚丰。本文仅就李先生在中国旧石器考古草创时期,特别是在周口店本世纪３０年代初发掘方法改革中的贡献等方面作简要的介绍。以此纪念济先生诞辰１００周年。为使读者了解他取得巨大成就的历史背景,对其生平亦作点录。     

Getting the Data Flowing: Lessons Learned from Existing Reporting Systems in the Forestry Sector in Indonesia for REDD+ MRV

In the context of REDD+, Measurement, Reporting and Verification (MRV) is one way to manage forest change information. A national carbon and non-carbon database will be used in REDD+ to negotiate compensation schemes with the international community. Much of this data will be collected at the local level, thus a reporting system that can integrate these locally collected data into the national database is crucial. In this paper we compare and draw lessons from three existing local to national reporting systems that include the participation of local communities: 1) the government extension services, 2) the government owned forestry company, and 3) a private logging company in Indonesia, and provide recommendations for REDD+ reporting systems. The results suggest that the main desired conditions for effective data flow are: benefits to motivate local participation, based on contributions to reporting activities; simple data format and reporting procedures to allow local participation in the reporting process, and to support data aggregation at the national level; a facilitator to mediate data aggregation at the village level to ensure data consistency, completeness and accuracy; and a transparent and clear data flow. Under these conditions, continuous, accountable and consistent data flow from the local level will reach the national level where it can be fully utilized.