Methods for facilitating web-based participatory research informatics

Scientific datasets are often generated and used by “communities”, or groups of users and creators. These communities, today often virtual, can include researchers, decision-makers, and the general public; participants in these communities may contribute different components during various iterations in the data generation process, and have different needs for resulting data products. As this “participatory research informatics” model, which includes elements of collaborative research, public participation, and digital data libraries, becomes the norm, new approaches to dynamic data management will be important. Researchers commonly use the web as a medium for research collaboration among colleagues, as well as to disseminate results to decision-makers and the public. In addition, the web can be used to facilitate dynamic collaboration by allowing research-in-progress to be accessed and edited by multiple participants. Indeed, one key benefit of using the web to facilitate research projects is that data can undergo revisions and corrections while being displayed in some form over the web. However, it can be a challenge to keep track of multiple edits to files while maintaining the integrity of a web-interface. Here we describe a system for promoting collaboration in the creation, maintenance, and use of dynamic data over the web. Using simple Microsoft Excel spreadsheets combined with traditional relational databases to facilitate dynamic data generation and updates and maintain a data schema, we are able to facilitate efficient collaboration within and among participant communities. This approach allows for the separation of web display and content, which in turn allows participants to be responsible for their own content. This separation simplifies the interaction between those responsible for the content (researchers and other participants), those responsible for the data display (web designers), and those responsible for data management, storage, and retrieval (web programmers). The approach described here is particularly well suited to large, spatially-specific ecological datasets because it can be used to facilitate the “real-time” editing and display of visual data such as web-maps, as well as to encourage multiple participants to both contribute to and interact with “beta” data and content.     

Acute Alcohol Consumption Impairs Controlled but Not Automatic Processes in a Psychophysical Pointing Paradigm

Numerous studies have investigated the effects of alcohol consumption on controlled and automatic cognitive processes. Such studies have shown that alcohol impairs performance on tasks requiring conscious, intentional control, while leaving automatic performance relatively intact. Here, we sought to extend these findings to aspects of visuomotor control by investigating the effects of alcohol in a visuomotor pointing paradigm that allowed us to separate the influence of controlled and automatic processes. Six male participants were assigned to an experimental “correction” condition in which they were instructed to point at a visual target as quickly and accurately as possible. On a small percentage of trials, the target “jumped” to a new location. On these trials, the participants’ task was to amend their movement such that they pointed to the new target location. A second group of 6 participants were assigned to a “countermanding” condition, in which they were instructed to terminate their movements upon detection of target “jumps”. In both the correction and countermanding conditions, participants served as their own controls, taking part in alcohol and no-alcohol conditions on separate days. Alcohol had no effect on participants’ ability to correct movements “in flight”, but impaired the ability to withhold such automatic corrections. Our data support the notion that alcohol selectively impairs controlled processes in the visuomotor domain.     

A comparison of eating habits between retired or semi-retired aged subjects and younger subjects in full-time work

An analysis of eating habits in older retired subjects (“No Work group”) and younger subjects employed in full-time work (“Work group”) has been carried out. It used a questionnaire that assessed why individuals chose to eat or not to eat meals during the course of the day, and subjective responses to the meals. The questionnaire was answered every three hours over a “typical week” which, for the Work group, entailed working during the weekdays and resting at the weekend. For the “No Work” group, breakfast was the most frequently taken meal of the day whereas, for the “Work” group, this meal was often missed. Patterns of meal intake were not significantly different between the weekdays and weekend for the “No Work” group, but the “Work” group ate more hot food at the weekend. The reasons cited for eating/not eating a meal and for choosing the type of meal eaten were dominated by hunger/lack of hunger in both groups. In addition, whereas habits were also important for the “No Work” group, it was time availability or the lack of it that was of major importance to the Work group, though this was significantly less important at the weekend. Meals which required more time for preparation and cooking were appreciated significantly more (appetite before the meal, enjoyment during it, and satiety afterwards) than meals such as snacks and cold food, which could be prepared more quickly. Some implications of these results, with regard to regular meals acting as a social zeitgeber in older subjects and the additional constraints imposed upon night workers, are considered.     

The Role of Ions and Second Messengers in Circadian Clock Function

The fact that single cells can exhibit circadian rhythmicity simultaneously in quite different processes, such as those of photosynthesis, bioluminescence, and cell division, suggests that membrane-bound compartmentalization is important for temporal organization. Since these rhythms, as well as others, are known to be affected by changes in the ionic environment and are probably membrane-bound systems, it is not surprising that transmembrane ion transport or flux has been proposed to be a key feature of the underlying circadian oscillator(s). Likewise, signal transduction along the entrainment pathway leading to the clock, among the elements, or “gears,” of the timing loop itself, and within the output pathway between the oscillator and its “hands” likely is mediated by ions and second messengers. In this overview, we examine the theoretical and experimental evidence supporting the possible roles of intracellular free calcium and cyclic AMP in these capacities, particularly in view of the fact that oscillations in the concentrations of both species have been proposed to form the basis of pacemaker activity and other biological rhythms.     

The co-evolution of culturally inherited altruistic helping and cultural transmission under random group formation

Limited migration results in kin selective pressure on helping behaviors under a wide range of ecological, demographic and life-history situations. However, such genetically determined altruistic helping can evolve only when migration is not too strong and group size is not too large. Cultural inheritance of helping behaviors may allow altruistic helping to evolve in groups of larger size because cultural transmission has the potential to markedly decrease the variance within groups and augment the variance between groups. Here, we study the co-evolution of culturally inherited altruistic helping behaviors and two alternative cultural transmission rules for such behaviors. We find that conformist transmission, where individuals within groups tend to copy prevalent cultural variants (e.g., beliefs or values), has a strong adverse effect on the evolution of culturally inherited helping traits. This finding is at variance with the commonly held view that conformist transmission is a crucial factor favoring the evolution of altruistic helping in humans. By contrast, we find that under one-to-many transmission, where individuals within groups tend to copy a “leader” (or teacher), altruistic helping can evolve in groups of any size, although the cultural transmission rule itself hitchhikes rather weakly with a selected helping trait. Our results suggest that culturally determined helping behaviors are more likely to be driven by “leaders” than by popularity, but the emergence and stability of the cultural transmission rules themselves should be driven by some extrinsic factors.     

The Phylogenetics of Mycotoxin and Sclerotium Production in Aspergillus flavus and Aspergillus oryzae

Aspergillus flavus is a common filamentous fungus that produces aflatoxins and presents a major threat to agriculture and human health. Previous phylogenetic studies of A. flavus have shown that it consists of two subgroups, called groups I and II, and morphological studies indicated that it consists of two morphological groups based on sclerotium size, called “S” and “L.” The industrially important non-aflatoxin-producing fungus A. oryzae is nested within group I. Three different gene regions, including part of a gene involved in aflatoxin biosynthesis (omt12), were sequenced in 33 S and L strains of A. flavus collected from various regions around the world, along with three isolates of A. oryzae and two isolates of A. parasiticus that were used as outgroups. The production of B and G aflatoxins and cyclopiazonic acid was analyzed in the A. flavus isolates, and each isolate was identified as “S” or “L” based on sclerotium size. Phylogenetic analysis of all three genes confirmed the inference that group I and group II represent a deep divergence within A. flavus. Most group I strains produced B aflatoxins to some degree, and none produced G aflatoxins. Four of six group II strains produced both B and G aflatoxins. All group II isolates were of the “S” sclerotium phenotype, whereas group I strains consisted of both “S” and “L” isolates. Based on the omt12 gene region, phylogenetic structure in sclerotium phenotype and aflatoxin production was evident within group I. Some non-aflatoxin-producing isolates of group I had an omt12 allele that was identical to that found in isolates of A. oryzae.     

Improving achievement through problem-based learning

In this study, the effect of problem-based learning on students' academic achievement and performance skills in a unit on he human excretory system was investigated. Sixty-one 10th grade students, from two full classes instructed by the same iology teacher, were involved in the study. Classes were randomly assigned as either the experimental or the control group and were pre- and post-tested to determine their academic achievement and performance skills before and after the treatment. The experimental group was taught with problem-based learning while the control group received traditionally-designed biology instruction. Results showed that although there was no pre-existing difference between two groups, students instructed with problem-based learning earned significantly higher scores than those instructed with traditionally-designed biology instruction — in terms of academic achievement and performance skills. Students in the experimental group appeared to be more proficient in the use and organisation of relevant information, in constructing knowledge and moving toward better conclusions.     

The Upper Cave at Zhoukoudian and the origins of the Mongoloids

The best evidence for identifying the inhabitants of northeast Asia in the terminal Pleistocene or early Holocene periods is provided by the human burials from the Upper Cave at Zhoukoudian, and in particular the “Old Man”. Apart from the Minatogawa finds on Okinawa, all Late Pleistocene human remains from East Asia that are reasonably well published are poorly preserved and often have equivocal dates. Since the time the Upper Cave was excavated it has been supposed that the human remains were the link between “Peking Man” and the modern Mongoloid complex. We have carried out multivariate analyses of the “Old Man” cranium employing new measurements of Weidenreich's cast of the skull and comparative data from Howells' survey of modern human groups. Despite our expectations the analyses have not shown the “Old Man” to be closely linked with the Mongoloids. Considering all the evidence available we conclude that the common belief of a close biological relationship between the people buried in the Upper Cave and the modern Mongoloids is not yet adequately demonstrated. Of crucial importance in interpreting the Upper Cave burials is their antiquity, which is still commonly thought to be in the order of at least 18 000 years. We believe that recent C-14 dates of about 11 000 years, determined from animal bones, indicate the earliest possible date for the burials. The time span between the Upper Cave burials and the earliest known modern Mongoloids in north China is in the order of about 4–5000 years. It is possible that a major population shift has occurred in north China between the terminal Pleistocene and the mid Holocene, when farming first appears. If this is so, the Upper Cave people may not have been closely allied to the Mongoloid groups that now inhabit East Asia and the Americas.     

Self-awareness of impairment and the decision to drive after an extended period of wakefulness

Fatigue is an increasingly noted factor in road accidents. The ability to predict and be aware of impairment in terms of driving capability is important for potential legal liability and road safety. However, to date, there have been few studies that have investigated the accuracy of individuals in predicting how safely they could drive during conditions of sleep loss. Research has demonstrated that individuals rate themselves as better than the population average in a number of domains, including driving-related skills. Therefore, this study also aimed to investigate self-ratings of predicted driving ability during extended wakefulness and compare them to ratings made of a hypothetical other person under the same conditions. Thirty-two participants remained awake for a period of 40 h. Every 2 h, they completed the Psychomotor Vigilance Task (PVT) and rated on a seven-point scale how well they thought they could drive safely, react quickly in an emergency, and stay in their own lane. They were also asked to assess how they thought someone else in their own position could drive. The participants rated their driving ability as becoming significantly poorer at the same time that their PVT performance became significantly slower. Self-ratings indicating a qualitative assessment of poorer than neutral driving occurred at 03:00 h for both the “drive safely” and “react quickly” questions, after 19 h of continuous wakefulness (starting at 08:00 h). This occurred at 05:00 h for the “keep in my lane” question. Previous studies with a similar protocol demonstrated that under these conditions, individuals exhibit a performance decrements equivalent to someone with a blood alcohol concentration of 0.05% (the legal driving limit in Australia). Participants consistently rated the ability of others to drive as poorer than their own. The main implication from this study for road safety and legal liability is that it is reasonable to focus on a person's perception of the situation, as it does align with objective reality to a certain extent. A concern in terms of road safety is potential overconfidence, indicated by rating others consistently poorer than themselves.     

Phosphorus-containing purines and pyrimidines: A new class of transition state analogs

Synthetic routes to the [1,5,2]-diazaphosphorine (“4-phosphapyrimidine”), imidazo[4,5-e][1,5,2]-diazaphosphorine (“6-phosphapurine”), and imidazo[4,5-d][1,3,2]-diazaphosphorine (“2-phosphapurine”) ring systems have been developed. Appropriately functionalized derivatives of these heterocycles are desired as possible transition state analogs of the nucleoside deaminases.     

Inbreeding depression for various traits in two cultured populations of the American bay scallop, Argopecten irradians irradians Lamarck (1819) introduced into China

This paper examines the effect of inbreeding level of population on the magnitude of inbreeding depression expressed by comparing them between two cultured populations (A and B) in the hermaphroditic animal of the bay scallop Argopecten irradians irradians. Population A is expected to have less genetic variations and higher inbreeding level due to longer cultured history (20 generations) and less “ancestral” individuals (26 individuals) than population B due to shorter cultured history (4 generations) and more “ancestral” individuals (406 individuals). Two groups within each population were produced, one using self-fertilization and one using mass-mating within the same population. Selfed offspring (AS and BS) from two populations both had lower fitness components than their mass-mated counterparts (AM and BM) and exhibited inbreeding depression for all examined traits, e.g. lower hatching, less viability and slower growth, indicating that inbreeding depression is a common feature in this animal. Fitness components in all traits of offspring from population A significantly differed those from population B and the magnitude of inbreeding depression for all traits in population A with higher inbreeding level was significantly smaller than that in population B with lower inbreeding level, indicating that both fitness components and magnitude of inbreeding depression were significantly affected by inbreeding level of populations and genetic load harbored in population A may be partially purged through inbreeding. Moreover, the magnitude of inbreeding depression in the two populations both varied among traits and life history stages. The present results support the partial-dominance hypothesis of inbreeding depression.     

Renewable enzyme reactors based on beds of artificial gel antibodies

A novel approach is described for the synthesis of beds for enzyme reactors. The method is based on the use of artificial antibodies in the form of polyacrylamide gel particles with diameters around 0.1–0.3 mm. These gel particles mimic protein antibodies, raised in experimental animals, in the sense that they selectively recognize and adsorb only the protein present during the preparation of the “antibodies”. The gel antibodies have several advantages over conventional protein antibodies, which can be taken advantage of in the design of enzyme reactors; for instance, if upon prolonged use the immobilized enzyme loses its activity it can easily be replaced by an active enzyme, which is not possible when the enzyme is immobilized via a conventional protein antibody (a new bed with immobilized protein antibodies must be prepared); and equally or more remarkable: the enzyme can be applied in the form of a non-purified extract since the selectivity of the artificial gel antibodies is so high that they will “fish-out” the enzyme, but no other proteins in the extract. In addition, no preconcentration of the enzyme solution is required prior to the immobilization, since the enzyme is enriched at the top of the column upon the application. These unique properties make enzyme reactors based on artificial gel antibodies very attractive, also in process chromatography. The potential application range of the artificial gel antibodies is enormous since the same method for their synthesis can be used independent of the structure and the size of the “antigen”; for instance, renewable biosensors based on gel antibodies for the selective detection of protein biomarkers, as well as pathogenic viruses, bacteria, and spores (for instance Anthrax) should not be difficult to design.     

Categories and gatherings: Group selection and the mythology of cultural anthropology

If the term “group selection” is to have any meaning beyond mere semantics, it must refer to situations where individuals live in groups. Although the terminology of cultural anthropology suggests that humans live in bounded and enduring gatherings that might serve as group “vehicles” of selection, we argue that none of the terms asserted to be such an entity (i.e., clans, lineages, villages, bands, tribes, populations, societies, and cultures) fulfill this requirement. This is because these terms refer to: (1) reified abstractions, (2) groups only in the sense of categories of people instead of groups in the sense of people gathered together, or (3) gatherings that are much too fluid and fuzzy in their membership to be “vehicles.” Following Murdock (1972), we refer to this obsession with groups as “anthropology's mythology,” and we suggest that it is the result of our evolved capacity for categorical perception. Although classifying phenomena into categories is useful in many situations, it has hindered our understanding of human social organization and human evolution.     

"Live memory" of the cell, the other hereditary memory of living systems

We propose to designate by the term “live memory” of the cell, the cytoplasmic memory. This phenomenon consists of non-genetic memory, but nevertheless includes transmission function, which may be “hereditary” via the ovum, from mother cell to daughter cell, or simply within the same cell from instant t to instant t + 1. To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.     

Tainted Blood and Vengeful Spirits: The Legacy of Japan’s Yakugai Eizu (AIDS) Trial

Medical anthropologists often point to the importance of “illness narratives” as emergent or incipient forms in which patients attempt to make sense of the moral dimensions of illness and suffering (Kleinman 1988; Mattingly 1998). In this article I draw upon published accounts, newspapers, and legal documents, supplemented by ethnographic interviews carried out from 1999 to 2001, to show how plaintiffs in the yakugai AIDS trials brought by HIV-infected hemophiliacs against the Japanese government and the pharmaceutical industries that sold them tainted blood products appropriated powerful cultural themes in producing narrative accounts of their suffering. These narratives resonate with themes of lost trust, filial piety, and the desire for a “good death.” In contrast, I show how the neat and tidy narrative that emerged in the course of the yakugai AIDS trial served to impose meaning upon the plaintiffs’ unruly experiences such that, when it was over, the Japanese public was convinced that the “AIDS problem” had been “solved.”     

Regulation of estrogen receptor protein and messenger ribonucleic acid by estradiol and progesterone in rat uterus

The objective of this study was to examine the mechanisms of estrogen receptor (ER) processing and replenishment in the uterus of ovariectomized rats after estradiol and progesterone treatment. Uterine ER binding activity, ER protein and ER mRNA were measured by receptor binding exchange assay, Western blot and slot blot, respectively. The regulation of ER levels in rat uterus by estradiol and progesterone was very dramatic. Changes in ER protein were faithfully reflected by changes in binding activity. Estradiol caused receptor “processing” within 4 h of administration followed by recovery or “replenishment” of ER levels to the initial level by 20 h. The term “processing” has previously been used to describe the loss of ER binding activity in the early phase of estradiol-action, but it was never clear whether the ligand binding site was inactivated by processing or if the receptor molecule actually disappeared. This study shows that receptor “processing” constitutes disappearance of receptor protein and the later “replenishment” phase represents new ER protein rather than recycling of “processed” receptor. Progesterone-action, on the other hand, influenced only the “replenishment” phase by blocking recovery of ER protein. ER mRNA was suppressed by estradiol at 8 h, after the receptor was “processed” and “replenishment” already initiated. Progesterone, on the other hand, did not alter the steady state level of the message. Other mechanisms, such as regulation of translation rate of existing mRNA and changes in the rate of degradation of ER proteins are more likely involved in acute regulation of ER by these ovarian steroid hormones.     

“Carrier” theory and thermodynamics of irreversible processes

A theory of transport via a “carrier” based on Wyman's theory on multiple equilibria is presented. By taking into account the detailed balance principle, it is possible to simplify the flux expressions and their coupling coefficients. In this way, Onsager's rules are derived. An experimental approach to the model is proposed.