Building bio-assays with magnetic particles on a digital microfluidic platform

Digital microfluidics (DMF) has emerged as a promising liquid handling technology for a variety of applications, demonstrating great potential both in terms of miniaturization and automation. DMF is based on the manipulation of discrete, independently controllable liquid droplets, which makes it highly reconfigurable and reprogrammable. One of its most exclusive advantages, compared to microchannel-based microfluidics, is its ability to precisely handle solid nano- and microsized objects, such as magnetic particles. Magnetic particles have become very popular in the last decade, since their high surface-to-volume ratio and the possibility to magnetically separate them from the matrix make them perfect suitable as a solid support for bio-assay development. The potential of magnetic particles in DMF-based bio-assays has been demonstrated for various applications. In this review we discuss the latest developments of magnetic particle-based DMF bio-assays with the aim to present, identify and analyze the trends in the field. We also discuss the state-of-the art of device integration, current status of commercialization and issues that still need to be addressed. With this paper we intend to stimulate researchers to exploit and unveil the potential of these exciting tools, which will shape the future of modern biochemistry, microbiology and biomedical diagnostics.     

Variability of human blood pressure with reference mostly to the non-chronobiologic literature

The voluminous literature on the variability encountered in 24-h recordings of human blood pressure in health is here presented by reference to selected clinical articles. Most references are cited by number for the sake of brevity, with a few cited by author when this appears to be of particular interest. Reports of work on laboratory animals are included when the findings are directly pertinent as background to studies on human beings. Results from semiautomatic and automatic direct and indirect measurements are briefly reviewed and aligned with results from work in which blood pressure was self-measured or measured conventionally by staff. The considerable and not generally recognized range of human blood pressure variability is thus extracted from the literature. An apparently limited extent of variation is shown to result mostly from the averaging of data from individuals constituting the groups investigated. Once variation is overwhelmingly documented and recognized as a fact, the different ways in which variations are presented and utilized by different author-investigators gain in importance. In a number of studies, methods of time series analysis are used. Thus, major attention can be paid to the extent to which predictable changes, so-called rhythms, characterize the data. Circadian rhythms are found to be quite prominent. By the assessment of these rhythms and about-yearly (circannual) ones, one quantifies health and individualized risk as well as disease. Otherwise 'unmanageable' variability, reviewed herein, can be resolved by relatively simple inferential statistical procedures as a set of new endpoints. A formidable foe thus becomes a powerful friend: the rhythm characteristics can be used in cardiovascular physiology and epidemiology, and preventive and curative medicine. Long-term blood pressure monitoring is no longer a mere research tool and a curiosity for the practitioner of medicine. Results from such monitoring should immediately be used in the clinic, in the school and at home. Automatic blood pressure monitoring, cost-effectively used in combination with self-measurement, as needed, may become a routine procedure if data collection can be wedded to appropriate analyses yielding new endpoints as sensitive gauges of health.     

Investigations of protein structure and function using the scientific literature: an assignment for an undergraduate cell physiology course

Undergraduate biology curricula are being modified to model and teach the activities of scientists better. The assignment described here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College. Students work in small groups to read and present in poster format on the content of a single research article reporting on the structure and/or function of a protein. Goals of the assignment include highlighting the interdependence of protein structure and function; asking students to review, integrate, and apply previously acquired knowledge; and helping students see protein structure/function in a context larger than cell physiology. The assignment also is designed to build skills in reading scientific literature, oral and written communication, and collaboration among peers. Assessment of student perceptions of the assignment in two separate offerings indicates that the project successfully achieves these goals. Data specifically show that students relied heavily on their peers to understand their article. The assignment was also shown to require students to read articles more carefully than previously. In addition, the data suggest that the assignment could be modified and used successfully in other courses and at other institutions.     

序言：打造精品学术期刊 服务科研创新

正《生物化学与生物物理进展》(以下简称《进展》)创刊于1974年,作为记录科学成果的载体和促进科学交流的平台,它经历了中国科学研究从艰难起步到蓬勃发展的重要时期,是我国科学事业发展的见证者,也是其中重要的参与者.经过40年的艰苦努力,《进展》得到了很大的发展:已初步被国际学术界认知,被SCI、CA、俄罗斯文摘等国际检索系统收录;2009年起全部论文注册DOI,每年均收到海外学者的直接投稿;同时,《进展》被国内生物     

An international proficiency study with the tumor marker CA 125

A strict and adequate quality assurance program is the only real guarantee of the reliability of laboratory test results. Such proficiency testing was carried out for the CA 125 test system in five university laboratories over a period of three years (1984-1987) using five different reference materials (BIOREF, FRG). A concentration-dependent performance profile could thus be established evaluating a total of 301 assays. Intra-assay precision of the test ranged between 4.8 and 11.5%, and interassay precision between 13.6 and 19.1%. Laboratory specific average values of the individual reference materials ranged between 26 and 32 U/ml for reference 1, 51 and 59 U/ml for reference 2, 109 and 121 U/ml and 193 to 240 U/ml for references 3 and 4, respectively. Mean values for reference 5 ranged between 401 and 458 U/ml. There was no significant difference between mean values for the laboratories. Considerable batch-dependent variations of values became evident during the study but these were not indicated by the kit control supplied by the manufacturer. During the whole investigation period no systematic drift in values could be observed using trend analysis, indicating excellent stability of the reference material if stored frozen (-20 degrees C).     

A protocol for the update of references to scientific literature in biological databases

Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.     

Racializing teenage pregnancy: 'culture' and 'tradition' in the South African scientific literature

The signifiers, 'race', 'culture' or 'ethnicity' are utilized in the teenage pregnancy literature (1) to highlight 'differences' in adolescent sexual and reproductive behaviour and (2) as explanatory tools. When 'white' teenagers are the focus of research, psychological explanations are usually invoked, whereas for 'black' teenagers, explanations are socio-cultural in nature. In this article, we explore how, through a process of racialization, the psychomedical literature on teenage pregnancy in South Africa contributes to the entrenchment of 'race', 'culture' and 'ethnicity' as fixed, 'natural' signifiers. We utilize Derrida's notion of différance , together with Phoenix and Woollett's adaptation - 'normalized absence/pathologized presence' - to indicate how 'black' people are cast as the Other, the pathologized presence which relies on the normalized absent trace, 'whiteness', for definition. We analyse how the notions of 'tradition' and 'culture' are deployed to sanitize or disguise the underlying racializing project. 'Black' is exoticized and rendered strange and thus open to scrutiny, monitoring and intervention. 'Culture' and 'tradition' appeal to the myth of origin, thus providing pseudohistorical explanations which essentialize and naturalize racialized collectivities.     

The value of protein structure classification information—Surveying the scientific literature

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.