Investigating heterogeneous protein annotations toward cross-corpora utilization

Background  

The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity recognition (NER) systems have been developed based on these corpora. However, in the biomedical community, there is yet no general consensus regarding named entity annotation; thus, the resources are largely incompatible, and it is difficult to compare the performance of systems developed on resources that were divergently annotated. On the other hand, from a practical application perspective, it is desirable to utilize as many existing annotated resources as possible, because annotation is costly. Thus, it becomes a task of interest to integrate the heterogeneous annotations in these resources.     

Resource quantity, not resource heterogeneity, maintains plant diversity

Resource heterogeneity has often been proposed to explain the maintenance of plant species diversity and patterns of species diversity along productivity gradients. Resource heterogeneity should maintain biodiversity by preventing competitive exclusion because different species are superior competitors in different parts of a heterogeneous environment. In natural systems, however, resource heterogeneity covaries with average resource supply rate, making the effect of heterogeneity difficult to isolate. Using a novel experimental approach, we tested the independent effects of resource heterogeneity and average supply rate on plant species diversity. We show that the average supply rate of the most limiting resource controlled species diversity, whereas heterogeneity of this resource had virtually no effect. These findings also suggest that biodiversity declines with increasing productivity because at high enough levels of productivity one resource may always be driven to sufficiently short supply to exclude many species.     

Learning to extract relations for protein annotation

MOTIVATION: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real-world scenarios such as in the biomedical domain. In this article, we describe an IE system that requires only sentences labelled according to their relevance or not to a given topic by domain experts. RESULTS: We applied our system to meet the annotation needs of a well-known protein family database; the results show that our IE system can annotate proteins with a set of extracted relations by learning relations and IE rules for disease, function and structure from only relevant and irrelevant sentences.     

The ovaries and reproduction in Pontoporia blainvillei (Cetacea: Platanistidae)

The ovaries of 113 Pontoporia blainvillei (Franciscana dolphin) were examined and their characteristics related to season, body length of the animals and, in some individuals, foetal length. The following conclusions were drawn from the results: most females attain sexual maturity when they reach 136–146 cm body length; most conceptions occur in the period December to February, with a peak in the first half of January; usually only one ovulation occurs, and no animal ovulated more than twice, in a season; postpartum ovulation may occur, and evidence is presented that this is probably followed by conception and that animals may breed once a year but most females breed every other year; body length at birth is greater than 70 cm and less than 85 cm, and probably nearer the smaller figure; the gestation period is 10.5–12 months (depending on what is the actual figure for length at birth, but probably less than 11 months); lactation lasts at least nine months; the corpus luteum contains two morphologically distinct, but apparently functional cell types; there is no apparent morphological difference between corpora lutea which are not associated with pregnancy, and corpora lutea of pregnancy; corpora albicantia may persist for a maximum of four years before being reabsorbed completely.     

Power Struggles, Dominance Testing, and Reproductive Skew

Models of reproductive skew are concerned with the partitioning of reproduction between dominant and subordinate members of a group. In an interesting extension of these models, Reeve and Ratnieks briefly considered whether it might benefit subordinates to engage in aggressive behavior to test the fighting ability of a dominant. Their analysis suggested that such testing should be more probable in groups that feature high skew and, hence, perhaps among closer relatives (because high relatedness favors high skew). Here we explore in more detail the possibility of dominance testing. Three models that differ in the outcome of fights over dominance are presented: in the first model, the loser of the challenge is killed; in the second model, the loser is evicted from the nest; and, in the third model, the loser becomes (or remains) subordinate. In each case we consider the independent effects of the parameters that determine skew (namely, relatedness, group productivity, and ecological constraints) on the predicted level of dominance testing. We then construct an amalgamated model to examine situations where fights may lead to any one of the three outcomes. Our analysis reveals that, in the majority of cases, higher relatedness will in fact lead to lower levels of aggression. Moreover, dominance testing need not be associated with high skew. Rather, the relationship between skew and dominance testing will depend on which factor (relatedness, group productivity, or level of ecological constraints) is principally responsible for variation in the distribution of reproduction.     

Modularity and the units of evolution

Summary While many developmental processes (e. g., gene networks or signaling pathways) are astonishingly conserved during evolution, they may be employed differently in different metazoan taxa or may be used multiply in different contexts of development. This suggests that these processes belong to building blocks or modules, viz., highly integrated parts of the organism, which develop and/or function relatively independent from other parts. Such modules may be relatively easy to dissociate from other modules and, therefore, could also serve as units of evolution. However, in order to further explore the implications of modularity for evolution, the vague notion of “modularity” as well as its relation to concepts like “unit of evolution” need to be more precisely specified. Here, a module is characterized as a certain type of dynamic pattern of couplings among the constituents of a process. It may or may not form a spatially contiguous unit. A unit of selection is defined as a unit of those constituents of a reproducing process/system, which exists in different variants and acts as a non-decomposable unit of fitness and variant reproduction during a particular selection process. The more general notion of a unit of evolution is characterized as a nondecomposable unit of constituents with reciprocal fitness dependence, be it due to fitness epistasis or due to the lack of independent variability. Because such fitness dependence may only be observed for some combinations of variants, several constituents may act as a unit of evolution only with a certain probability (coevolution probability). It is argued, that under certain conditions modules are likely to act as units of evolution with high coevolution probabilities, because there is likely to be a close tie between the pattern of couplings of the constituents of a reproducing system and their interdependent fitness contributions. Moreover and contrary to the traditional dichotomy of genes versus organisms as units of selection, modules tend to be more important in delimiting actual units of selection than either organisms or genes, because they are less easily disrupted by recombination than organisms, while having less contextsensitive fitness values than genes. Finally, it is suggested that the evolution of modularity is self-reinforcing, because the flexibility of intermodular connections facilitates the recombination among modules and their multiple employment in new contexts.     

Relationships between phenotype, mating behavior, and fitness of queens in the ant Lasius niger

Considerable attention has focused on why females of many species mate with several males. For social hymenopteran insects, efforts have primarily concentrated on determining whether multiple mating increases colony performance due to the increased genetic diversity. Most of these studies are correlative because it is difficult or impossible to experimentally mate queens in most species. Thus, the positive associations found between multiple paternity and colony fitness in some cases may not be due to direct effects of genetic diversity but could, in theory, arise from high-quality queens having more mates. Here we show that in the ant Lasius niger variation in the number of matings covaries with queen phenotype. Young queens that were heavier at the time of the mating flight were significantly more likely to mate with several males. As a result, heavier queens stored more sperm. The initial weight of queens was significantly associated with the probability of surviving mating flights during the two years of the study, with queens of intermediate weight having the highest across-year survival. Queen initial weight was also significantly and positively associated with the quantity of brood at the time of the first worker eclosion as well as colony productivity at the time of hibernation. By contrast, there was little evidence for a positive effect of the number of matings on colony performance when the effect of mate number and queen initial weight were considered simultaneously.     

A system for de-identifying medical message board text

There are millions of public posts to medical message boards by users seeking support and information on a wide range of medical conditions. It has been shown that these posts can be used to gain a greater understanding of patients' experiences and concerns. As investigators continue to explore large corpora of medical discussion board data for research purposes, protecting the privacy of the members of these online communities becomes an important challenge that needs to be met. Extant entity recognition methods used for more structured text are not sufficient because message posts present additional challenges: the posts contain many typographical errors, larger variety of possible names, terms and abbreviations specific to Internet posts or a particular message board, and mentions of the authors' personal lives. The main contribution of this paper is a system to de-identify the authors of message board posts automatically, taking into account the aforementioned challenges. We demonstrate our system on two different message board corpora, one on breast cancer and another on arthritis. We show that our approach significantly outperforms other publicly available named entity recognition and de-identification systems, which have been tuned for more structured text like operative reports, pathology reports, discharge summaries, or newswire.     

Suffix combinations in Bulgarian: parsability and hierarchy-based ordering

This article extends the empirical scope of the most recent approach to affix ordering, the Parsability Hypothesis (Hay 2001, 2002, 2003) or Complexity-Based Ordering (CBO) (Plag 2002; Hay and Plag 2004; Plag and Baayen 2009), to the inflecting-fusional morphological type, as represented by the South Slavic language Bulgarian. In order to account properly for the structure of the Bulgarian word, I distinguish between suffixes that are in the derivational word slot and suffixes that are in the inflectional word slot and show that inflectional suffix combinations are more easily parsable than derivational suffix combinations. Derivational suffixes participate in mirror-image combinations of AB–BA type and can be also attached recursively. The order of 12 out of the 22 derivational suffixes under scrutiny in this article is thus incompatible with CBO. With respect to recursiveness and productivity, the Bulgarian word exhibits three domains of suffixation (in order of increasing productivity): (1) a non-diminutive derivational domain, where a suffix may attach recursively on non-adjacent cycles; (2) a diminutive domain, where a suffix may attach recursively on adjacent cycles; and (3) an inflectional domain, where a suffix never attaches recursively. Overall, the results of this study conform to the last revision of the Parsability Hypothesis (Baayen et al. 2009); and if we see the derivational suffix slot and the inflectional suffix slot of the Bulgarian word as parallel to the non-native stratum and the Germanic stratum respectively in English word-formation, we can conclude that suffixes that are closer to the root tend to exhibit idiosyncrasies and appear less parsable in both languages.     

Effects of parasites on fish populations: practical considerations

Fish populations are subject to numerous natural and anthropogenic factors which reduce abundance. In wild populations it is difficult to isolate and quantify the effects of any single factor, such as prédation, or starvation, or disease, on fish stock size. Evidence is accumulating, however, which supports the notion that some of the animal parasites, and particularly the Protozoa, can act as severe pathogens, causing direct mortality or rendering the hosts more vulnerable to other environmental or biotic Stressors. Lethal effects of parasites can be determined statistically or by experiment, but actual observation of mortalities is rare—especially in the sea—principally because of prédation or scavenging. Sublethal effects (a partial misnomer since many such effects lead indirectly to mortality) include muscle degeneration, liver dysfunction, interference with nutrition, cardiac disruption, nervous system involvement, castration or mechanical interference with spawning, weight loss, and gross distortion of the body.Study of fish in captivity or under culture conditions has provided much information about the effects of animal parasites on survival. Epizootics occur, mortalities ensue, immunity may or may not develop, and parasites considered inocuous may prove to be not so under added Stressors such as crowding and poor water quality found in the culture environment.     

Why more productive sites have more species: an experimental test of theory using tree-hole communities

One of the most common explanations for an increase in species richness with productivity is what we have dubbed the "More Individuals Hypothesis." According to this hypothesis, more productive sites can support higher total abundances and, since species richness is an increasing function of total abundance, so will it be of productivity. This hypothesis assumes that communities are limited by productivity. We tested the More Individuals Hypothesis using the detritivorous aquatic insect communities of tree holes. When tree holes with varying levels of productivity (debris amount) were allowed to be colonized (through oviposition), more productive tree holes did have more species but not more individuals. Neither was total energy use strictly proportional to productivity. Only in communities forced to disassemble through productivity reductions were the predictions of the More Individuals Hypothesis satisfied. Ovipositing adults may prefer productive tree holes not because they contain more resources but because they are anticipated to be less likely to dry out. In tree holes, and more generally, the More Individuals Hypothesis is an insufficient explanation for increases in species richness with productivity because it neither accounts for the different processes of local colonization and extinction nor allows body size to correlate with extinction risk.     

Ecological benefits assessment: A policy‐oriented alternative to regional ecological risk assessment

As the focus of many environmental and resource management decisions shifts to larger ecological units such as watersheds and ecoregions, the respective roles of ecological risk and ecological benefits must be reassessed. At larger ecological scales, risk becomes much more difficult to characterize because of the focus on the system rather than individual species. However, quantifying the monetary value of many ecological benefits is also difficult because no direct measures of their value exist, and the indirect techniques used by economists are not fully accepted in some policy‐making settings. This dilemma may be resolved by considering ecological resource/service flows, which are ecological benefits in physical rather than monetary units. By assessing the whole range of resource/service flows and the changes to each that would result from different management/control alternatives, scientists would be able to provide policy‐makers a much better basis for their decisions, and the resulting assessment would characterize changes in ecological features that are more familiar to both policy‐makers and the public.     

Population size and age determination in the Antarctic Fur seal Arctocephalus gazella

The population of Antarctic Fur seals Arctocephalus gazella at South Georgia is increasing rapidly and is therefore of great interest. Investigations of the population depend on two main techniques.
(1) Population assessment, because the population size is now too large for direct counts to be completely reliable, and serious underestimates are appearing in areas of high density. Aerial photography was used but needs further refinement before it becomes a consistently useful technique. Marking all pups on sample beaches was largely unsuccessful because pups moved from beach to beach before they could all be marked. A mark–recapture method was finally adopted and indicated that the numbers of pups present may be up to 54% higher than the numbers actually counted.
(2) The process of age determination from tooth characters, which is more difficult for Fur seals than other pinnipeds. The preparation and interpretation of the teeth of breeding cows is described, based on eleven specimens of known age. The most accurate results are obtained from whole teeth up to the age of 6, but thereafter interpretation of cement and dentine layers in thin sections must be used. It is concluded that while young animals are aged quite accurately, there is probably a tendency to underestimate the age of seals of more than 9 years.     

Effects of pesticides and related organic compounds in the sea

The majority of organic chemicals identified so far in the sea are pesticides and products of technical use; most contain chlorine. Only a limited amount of the actual pollutant load is detectable because few data for “unconventional ” pollutants are available. In view of the considerable structural variety of the large number of chemicals produced, there is a need for prediction measurements of bioconcentration and toxic effects. Physico-chemical data may be used for predicting bioconcentration and life-cycle toxicity tests for the estimation of safe levels. The degree of biomagnification via food chains increases with half lives of the pollutants. When comparing pollutant concentrations with toxicological data it becomes apparent that estuaries and coastal areas deserve special concern, whereas pollutant levels of open ocean waters are unlikely to endanger marine life at present.     

Prenatal bias in sex ratios in a marsupial,Antechinus agilis.

Biased sex ratios of young of birds and mammals clearly occur and may have an adaptive significance, but we rarely know the stage at which a bias is generated, or the mechanism. If a bias is generated prior to birth, studies of marsupials may be insightful because gestation is short and neonates are relatively undifferentiated. This study investigated whether biased sex ratios in Antechinus agilis are generated in the brief period between birth and the attachment of young to the mother''s teats. When all young born, or just pouch young, or supernumerary young were considered, litters were strongly biased towards females (0.32 males), and there was no significant difference across the groups, so a bias is generated before birth in this species. Evidence from counts of corpora lutea suggests that embryo loss during gestation cannot account fully for the level of bias observed. Therefore, prefertilization mechanisms must contribute to the generation of sex-biased litters in this marsupial.     

Breed of cow and herd productivity affect milk nutrient recovery in curd,and cheese yield,efficiency and daily production

Little is known about cheese-making efficiency at the individual cow level, so our objective was to study the effects of herd productivity, individual herd within productivity class and breed of cow within herd by producing, then analyzing, 508 model cheeses from the milk of 508 cows of six different breeds reared in 41 multi-breed herds classified into two productivity classes (high v. low). For each cow we obtained six milk composition traits; four milk nutrient (fat, protein, solids and energy) recovery traits (REC) in curd; three actual % cheese yield traits (%CY); two theoretical %CYs (fresh cheese and cheese solids) calculated from milk composition; two overall cheese-making efficiencies (% ratio of actual to theoretical %CYs); daily milk yield (dMY); and three actual daily cheese yield traits (dCY). The aforementioned phenotypes were analyzed using a mixed model which included the fixed effects of herd productivity, parity, days in milk (DIM) and breed; the random effects were the water bath, vat, herd and residual. Cows reared in high-productivity herds yielded more milk with higher nutrient contents and more cheese per day, had greater theoretical %CY, and lower cheese-making efficiency than low-productivity herds, but there were no differences between them in terms of REC traits. Individual herd within productivity class was an intermediate source of total variation in REC, %CY and efficiency traits (10.0% to 17.2%), and a major source of variation in milk yield and dCY traits (43.1% to 46.3%). Parity of cows was an important source of variation for productivity traits, whereas DIM affected almost all traits. Breed within herd greatly affected all traits. Holsteins produced more milk, but Brown Swiss cows produced milk with higher actual and theoretical %CYs and cheese-making efficiency, so that the two large-framed breeds had the same dCY. Compared with the two large-framed breeds, the small Jersey cows produced much less milk, but with greater actual and theoretical %CYs, similar efficiencies and a slightly lower dCY. Compared with the average of the specialized dairy breeds, the three dual-purpose breeds (Simmental and the local Rendena and Alpine Grey) had, on average, similar dMY, lower actual and theoretical %CY, similar fat and protein REC, and slightly greater cheese-making efficiency.     

Programming,induction, or prevention of the breakdown of the prothoracic gland in the cockroach, Nauphoeta cinerea

Changes of the prothoracic gland (PGL) diameter and of the corpora allata (CA) volume during the second last and last larval instar, and transplantation experiments as well as juvenile hormone (JH) analogue applications, demonstrate that only an activated PGL seems to be competent to degenerate and that the breakdown of the activated PGL is programmed by the absence of JH for a few days. Then, some days later, at the time of apolysis induction which occurs 7 to 6 days before an ecdysis the breakdown of a programmed PGL is induced by factors present in the haemolymph and it is suggested that β-ecdysone in apolysis-inducing amounts could be responsible for the induction of degeneration. However, PGL-protecting factors released probably from the corpora cardiaca (CC) are capable of partially preventing the breakdown of PGLs that have already been induced to degenerate, and it seems that the actual degeneration process is initiated by the absence of PGL-protecting factors only.     

Ovarian growth and folliculogenesis in breeding and nonbreeding females of a social rodent,the Zambian common mole-rat,Cryptomys sp.

Zambian common mole-rats are subterranean rodents that live in families with only one female breeding. Her offspring remain in the parental nest and do not reproduce. Behavioral experiments (Burda, '95) demonstrated that their apparent “sterility” is based on incest avoidance and individual recognition of family members. To elucidate whether some kind of morphologically apparent ovarian suppression still takes place in daughters, ovaries of females of known age, weight, and reproductive histories were examined histologically and morphometrically. The body mass of old females (more than 3 years of age) begins to decrease, and the ovaries seem to begin to atrophy at the age of about 3–6 years. Ovaries in neonates exhibited primordial and primary follicles, sometimes clustered in nests. Ovaries of adult nonbreeding females expressed all stages of the follicular development up to tertiary follicles. Many unruptured luteinized follicles were present, but true corpora lutea as a morphological sign of ovulation were missing. Unruptured luteinized follicles also could be found (additionally to true corpora lutea) in ovaries of breeding females. The number of primordial follicles dropped rapidly during the first 2 years of age; the number of primary, secondary, and tertiary follicles was subject to individual variation; and there was no clear correlation with age or reproductive status. While a tendency to form accessory unruptured luteinized follicles may just reflect taxonomic affinities of bathyergids to hystricomorphs, the otherwise complete folliculogenesis in “sterile” daughters and the presence of unruptured luteinized follicles even in breeding females are further evidence that there is no hormonal suppression of the ovarial cycle. We suggest that ovulation in nonbreeding females is not actively suppressed by the breeding female, but instead that it is not released because the triggering mechanisms, most probably repeated copulation, are missing. J. Morphol. 237:33–41, 1998. © 1998 Wiley-Liss, Inc.     

The fine structure of the lutein cells in the mink (Mustela vison) with special reference to the secretory activity during pregnancy

Summary The ultrastructure of the lutein cells in the mink throughout pregnancy and the regression periodpost partum is described. To correlate the fine structure with the changes in the peripheral plasma progesterone levels, the concentrations of progesterone were measured by a rapid competitive protein-binding assay.Even during the delay period (e.g. as long the plasma progesterone levels remain at the basal level, <8ng/ml), the lutein cells in the mink exhibit structural criteria of functional activity. However, the increase in progesterone secretion is accompanied by some morphological transformations, characterized by the presence of more and more small dense homogenous bodies in the cytoplasm, which become irregular and scalloped during the stage with maximum release of progesterone. At this stage the agranular endoplasmic reticulum is often cisternal or vesicular.During the decline of the progesterone levels, typical and moderate electron-dense lipid droplets are found increasingly more within the lutein cells. The expanded agranular ER is now more sparse, while the granular ER becomes more pronounced, often forming parallel arrays. During this phase the mitochondria become elongated, dumb-bell, or cup shaped. After parturition the corpora lutea consist of cells in various stages of degeneration. At day 14post partum only a few lutein cells are still identifiable.Evidently the observed morphological changes take place in the lutein cells during the life span of corpora lutea. This feature lends further support to the concept that the mink lutein cells are steroid-producing cells and furthermore, that the corpora lutea may be the main sites of gestagen production during pregnancy.     

Dreamwork as Etymology

This essay proposes that etymology, the study of word roots, presents analogies with dreamwork, although parallels between them must be carefully framed. Quoting Freud and the seventh century encyclopedist Isidore of Seville, weaknesses in their use of etymological arguments are identified. Theories forged from word origins should not blur distinctions between word and thing or force linguistic process into support of a preconceived theoretical project. To explore Freud's notion of contraries in words and dreams, examples are offered of single Indo-European word roots capable of engendering divergent or contradictory modern meanings, as well as examples of divergent or contradictory modern meanings for words that have two or more derivations, e.g., the English word dream and French rêve. Tracing a place-name (Campidoglio) in an actual dream demonstrates that etymology and dreamwork are both reconstructive processes that should avoid determinism, accept uncertainty, and respect complexity.